https://bionmr.unl.edu/mediawiki/mediawiki/api.php?action=feedcontributions&feedformat=atom&user=Acrook 2026-05-02T21:28:34Z User contributions MediaWiki 1.38.2 https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=PCA_Classify_Example_Script&diff=761 2021-01-07T17:13:17Z

<p>Acrook: Created page with &quot;== PCA Classify Function == Project new samples into PCA model using appropriate scaling. Xtest = test/second dataset;clsRtest = test/second class. result = PCA mode...&quot;</p> <hr /> <div>== PCA Classify Function == <br /> <br /> Project new samples into PCA model using appropriate scaling. <br /> <br /> Xtest = test/second dataset;clsRtest = test/second class.<br /> result = PCA model (MVApack) <br /> mn = result.mean.X;sd = result.scale.X;<br /> X_g1a = Xtest;%X_g2a = Xtrain;<br /> X_g2new = (X_g1a-(repmat(mn,[size(X_g1a,1),1])))./(repmat(sd,[size(X_g1a,1),1]));%size(X_g2new)<br /> T_g2new = X_g2new*result.P;<br /> scores = T_g2new;<br /> S = boxplot(X_g2new');</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=Category:Protocols&diff=760 2021-01-07T17:10:39Z

<p>Acrook: </p> <hr /> <div>''General Maintenance''<br /> *[[Changing the high pressure dewar]]<br /> *[[Filling a Magnet with Nitrogen]]<br /> *[[Autoclaving Laboratory Glassware and Media]]<br /> *[[Chemical Disinfection of Glassware]]<br /> *[[Requesting Balance Calibration]]<br /> *[[Requesting Pipette Calibration]]<br /> *[[Using the UV-Vis]]<br /> *[[Using and Maintaining pH Meter]]<br /> *[[-80 Freezer Storage and Maintenance]]<br /> *[[Freeze Dryer Maintenance]]<br /> *[[Lab Notebook Guidelines]]<br /> *[[Sample Barcoding]]<br /> <br /> ''Protein Preparation''<br /> *[[Buffer Exchange and Solution Concentration]]<br /> *[[Finding a Protein Target on the NESG website]]<br /> *[[Choosing a Plasmid]]<br /> *[[Plasmid Purification and Transformation Protocol]]<br /> *[[Creating Stock Cultures of Bacteria]]<br /> *[[Luria-Bertani Media]]<br /> *[[M9 Minimal Media]]<br /> *[[Protein Overexpression and Extraction]]<br /> *[[SDS-PAGE Protocol]]<br /> *[[Running a Cobalt Affinity Column]]<br /> *[[Dialysis]]<br /> *[[Centrifugal Protein Concentration and Buffer Exchange]]<br /> *[[Using the Stirred Cell Concentrator]]<br /> <br /> ''Data Collection''<br /> *[[Gap Sampling]]<br /> *[[Water Suppression with presaturation pulses (zgpr/zgcppr]]<br /> *[[Non-uniform Sampling]]<br /> *[[Collecting a 15N Edited HSQC]]<br /> *[[Collecting CEST Data]]<br /> <br /> ''Data Processing and Analysis''<br /> *[[Analysis of 1D Line-Broadening Screen]]<br /> *[[FastModelFree]]<br /> *[[2D NMR Analysis (CCPNMR)]]<br /> *[[1H NMR Analysis (SIMCA)]]<br /> *[[1H NMR Analysis (ACDLab)]]<br /> *[[Processing CEST Data]]<br /> *[[Titration Data Analysis in nmrPipe]]<br /> *[[Non-Uniform Sampling]]<br /> *[[NMRFAM-SPARKY Guide]]<br /> *[[NMRFAM-SPARKY: Automated Peak Assignment]]<br /> *[[2D NMR Processing in Linux and Windows]]<br /> *[[2D Metabolomics NMRPipe Processing]]<br /> *[[1D NMR Processing in Linux and Windows Example Script]]<br /> *[[NMR Batch Correction Example Script]]<br /> *[[PCA Classify Example Script]]<br /> *[[Sample Collection and Processing for Protein Backbone Assignments]]<br /> *[[Example Scripts for NMRPipe Processing]]<br /> <br /> <br /> ''Miscellaneous''<br /> *[[Agarose Gel]]<br /> *[[700 MHz NMR checklist]]<br /> *[[500 MHz NMR checklist]]<br /> *[[1D Macro]]<br /> *[[Setting Up a Virtual Screen with AutoDock]]<br /> *[[Simple Protein Crosslinking]]<br /> *[[1D NMR Titrations]]<br /> *[[Setting Up &amp; Running MD Simulations]]<br /> <br /> Cell Culturing<br /> *[[Cell Culturing Dr. Franco Lab]]<br /> <br /> ''Metabolomics''<br /> *[[Metabolite Extraction]]<br /> *[[MetPa for metabolomics]]<br /> *[[Making Heatmaps]]<br /> *[[One way ANOVA in R]]<br /> *[[P-Value adjustment for multiple comparisons]]<br /> *[[PCA-Utils]]<br /> *[[NMR Tube Deep Cleaning]]<br /> *[[Noise Removal for PCA]]<br /> *[[Weighted Linear Least Squares]]<br /> *[[Serum Preparation for 1D NMR]]<br /> *[[Whole Blood Preparation for 1D NMR]]<br /> *[[Urine Preparation for 1D NMR]]<br /> *[[Cell Culture Preparation for 1D NMR]]<br /> *[[LC-MS metabolomics guide-CIBC collaborations]]<br /> <br /> ''Safety and Inspections''<br /> *[[Lab Responsibilities]]<br /> *[[Inspection Checklist]]<br /> *[[Safety Contacts, Resources]]<br /> <br /> ''Demos''<br /> *[[Peroxide Clock]]<br /> *[[Traffic Light Reaction]]<br /> *[[Orange Juice Clock]]<br /> *[[Gummy Bear Freeze]]<br /> *[[Lava Lamps]]<br /> *[[Batteries]]<br /> *[[Rocket Launcher]]<br /> *[[Women in Science: Checklist]]<br /> *[[Maxey Day: Checklist]]</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=NMR_Batch_Correction_Example_Script&diff=759 2021-01-07T17:09:22Z

<p>Acrook: Created page with &quot;== PLS Fit Model == X = whole dataset (first &amp; second);clsD = class info (dummy matrix). result = pls(X, clsD, @suv, [7,1], 1); mn = result.mean.X;sd = result.scale....&quot;</p> <hr /> <div>== PLS Fit Model == <br /> X = whole dataset (first &amp; second);clsD = class info (dummy matrix).<br /> result = pls(X, clsD, @suv, [7,1], 1);<br /> mn = result.mean.X;sd = result.scale.X;<br /> Xscaled = (X-(repmat(mn,[size(X,1),1])))./(repmat(sd,[size(X,1),1]));%size(Xscaled)<br /> XPLSfit = result.T*result.P';<br /> XscaledNew = Xscaled - XPLSfit;<br /> XNew = (XscaledNew.*(repmat(sd,[size(XscaledNew,1),1]))) + (repmat(mn,[size(XscaledNew,1),1]));<br /> <br /> == Mean of Mean Model == <br /> <br /> Xall = [Xtrain;Xtest];<br /> refX = median(median(Xall));<br /> mnXtrain = mean(mean(Xtrain));<br /> newXtrain = Xtrain/repmat(mnXtrain, [size(Xtrain, 1), size(Xtrain, 2)]);<br /> newXtrain = newXtrain*repmat(refX, [size(Xtrain, 1), size(Xtrain, 2)]);<br /> mnXtest = mean(mean(Xtest));<br /> newXtest = Xtest/repmat(mnXtest, [size(Xtest, 1), size(Xtest, 2)]);<br /> newXtest = newXtest*repmat(refX, [size(Xtest, 1), size(Xtest, 2)]);<br /> <br /> Note: mean can be replaced with median in a median of median model.</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=Category:Protocols&diff=758 2021-01-07T17:05:09Z

<p>Acrook: </p> <hr /> <div>''General Maintenance''<br /> *[[Changing the high pressure dewar]]<br /> *[[Filling a Magnet with Nitrogen]]<br /> *[[Autoclaving Laboratory Glassware and Media]]<br /> *[[Chemical Disinfection of Glassware]]<br /> *[[Requesting Balance Calibration]]<br /> *[[Requesting Pipette Calibration]]<br /> *[[Using the UV-Vis]]<br /> *[[Using and Maintaining pH Meter]]<br /> *[[-80 Freezer Storage and Maintenance]]<br /> *[[Freeze Dryer Maintenance]]<br /> *[[Lab Notebook Guidelines]]<br /> *[[Sample Barcoding]]<br /> <br /> ''Protein Preparation''<br /> *[[Buffer Exchange and Solution Concentration]]<br /> *[[Finding a Protein Target on the NESG website]]<br /> *[[Choosing a Plasmid]]<br /> *[[Plasmid Purification and Transformation Protocol]]<br /> *[[Creating Stock Cultures of Bacteria]]<br /> *[[Luria-Bertani Media]]<br /> *[[M9 Minimal Media]]<br /> *[[Protein Overexpression and Extraction]]<br /> *[[SDS-PAGE Protocol]]<br /> *[[Running a Cobalt Affinity Column]]<br /> *[[Dialysis]]<br /> *[[Centrifugal Protein Concentration and Buffer Exchange]]<br /> *[[Using the Stirred Cell Concentrator]]<br /> <br /> ''Data Collection''<br /> *[[Gap Sampling]]<br /> *[[Water Suppression with presaturation pulses (zgpr/zgcppr]]<br /> *[[Non-uniform Sampling]]<br /> *[[Collecting a 15N Edited HSQC]]<br /> *[[Collecting CEST Data]]<br /> <br /> ''Data Processing and Analysis''<br /> *[[Analysis of 1D Line-Broadening Screen]]<br /> *[[FastModelFree]]<br /> *[[2D NMR Analysis (CCPNMR)]]<br /> *[[1H NMR Analysis (SIMCA)]]<br /> *[[1H NMR Analysis (ACDLab)]]<br /> *[[Processing CEST Data]]<br /> *[[Titration Data Analysis in nmrPipe]]<br /> *[[Non-Uniform Sampling]]<br /> *[[NMRFAM-SPARKY Guide]]<br /> *[[NMRFAM-SPARKY: Automated Peak Assignment]]<br /> *[[2D NMR Processing in Linux and Windows]]<br /> *[[2D Metabolomics NMRPipe Processing]]<br /> *[[1D NMR Processing in Linux and Windows Example Script]]<br /> *[[NMR Batch Correction Example Script]]<br /> *[[Sample Collection and Processing for Protein Backbone Assignments]]<br /> *[[Example Scripts for NMRPipe Processing]]<br /> <br /> <br /> ''Miscellaneous''<br /> *[[Agarose Gel]]<br /> *[[700 MHz NMR checklist]]<br /> *[[500 MHz NMR checklist]]<br /> *[[1D Macro]]<br /> *[[Setting Up a Virtual Screen with AutoDock]]<br /> *[[Simple Protein Crosslinking]]<br /> *[[1D NMR Titrations]]<br /> *[[Setting Up &amp; Running MD Simulations]]<br /> <br /> Cell Culturing<br /> *[[Cell Culturing Dr. Franco Lab]]<br /> <br /> ''Metabolomics''<br /> *[[Metabolite Extraction]]<br /> *[[MetPa for metabolomics]]<br /> *[[Making Heatmaps]]<br /> *[[One way ANOVA in R]]<br /> *[[P-Value adjustment for multiple comparisons]]<br /> *[[PCA-Utils]]<br /> *[[NMR Tube Deep Cleaning]]<br /> *[[Noise Removal for PCA]]<br /> *[[Weighted Linear Least Squares]]<br /> *[[Serum Preparation for 1D NMR]]<br /> *[[Whole Blood Preparation for 1D NMR]]<br /> *[[Urine Preparation for 1D NMR]]<br /> *[[Cell Culture Preparation for 1D NMR]]<br /> *[[LC-MS metabolomics guide-CIBC collaborations]]<br /> <br /> ''Safety and Inspections''<br /> *[[Lab Responsibilities]]<br /> *[[Inspection Checklist]]<br /> *[[Safety Contacts, Resources]]<br /> <br /> ''Demos''<br /> *[[Peroxide Clock]]<br /> *[[Traffic Light Reaction]]<br /> *[[Orange Juice Clock]]<br /> *[[Gummy Bear Freeze]]<br /> *[[Lava Lamps]]<br /> *[[Batteries]]<br /> *[[Rocket Launcher]]<br /> *[[Women in Science: Checklist]]<br /> *[[Maxey Day: Checklist]]</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=Category:Protocols&diff=747 2021-01-06T20:28:41Z

<p>Acrook: </p> <hr /> <div>''General Maintenance''<br /> *[[Changing the high pressure dewar]]<br /> *[[Filling a Magnet with Nitrogen]]<br /> *[[Autoclaving Laboratory Glassware and Media]]<br /> *[[Chemical Disinfection of Glassware]]<br /> *[[Requesting Balance Calibration]]<br /> *[[Requesting Pipette Calibration]]<br /> *[[Using the UV-Vis]]<br /> *[[Using and Maintaining pH Meter]]<br /> *[[-80 Freezer Storage and Maintenance]]<br /> *[[Freeze Dryer Maintenance]]<br /> *[[Lab Notebook Guidelines]]<br /> *[[Sample Barcoding]]<br /> <br /> ''Protein Preparation''<br /> *[[Buffer Exchange and Solution Concentration]]<br /> *[[Finding a Protein Target on the NESG website]]<br /> *[[Choosing a Plasmid]]<br /> *[[Plasmid Purification and Transformation Protocol]]<br /> *[[Creating Stock Cultures of Bacteria]]<br /> *[[Luria-Bertani Media]]<br /> *[[M9 Minimal Media]]<br /> *[[Protein Overexpression and Extraction]]<br /> *[[SDS-PAGE Protocol]]<br /> *[[Running a Cobalt Affinity Column]]<br /> *[[Dialysis]]<br /> *[[Centrifugal Protein Concentration and Buffer Exchange]]<br /> *[[Using the Stirred Cell Concentrator]]<br /> <br /> ''Data Collection''<br /> *[[Gap Sampling]]<br /> *[[Water Suppression with presaturation pulses (zgpr/zgcppr]]<br /> *[[Non-uniform Sampling]]<br /> *[[Collecting a 15N Edited HSQC]]<br /> *[[Collecting CEST Data]]<br /> <br /> ''Data Processing and Analysis''<br /> *[[Analysis of 1D Line-Broadening Screen]]<br /> *[[FastModelFree]]<br /> *[[2D NMR Analysis (CCPNMR)]]<br /> *[[1H NMR Analysis (SIMCA)]]<br /> *[[1H NMR Analysis (ACDLab)]]<br /> *[[Processing CEST Data]]<br /> *[[Titration Data Analysis in nmrPipe]]<br /> *[[Non-Uniform Sampling]]<br /> *[[NMRFAM-SPARKY Guide]]<br /> *[[NMRFAM-SPARKY: Automated Peak Assignment]]<br /> *[[2D NMR Processing in Linux and Windows]]<br /> *[[1D NMR Processing in Linux and Windows Example Script]]<br /> *[[Sample Collection and Processing for Protein Backbone Assignments]]<br /> *[[Example Scripts for NMRPipe Processing]]<br /> <br /> <br /> ''Miscellaneous''<br /> *[[Agarose Gel]]<br /> *[[700 MHz NMR checklist]]<br /> *[[500 MHz NMR checklist]]<br /> *[[1D Macro]]<br /> *[[Setting Up a Virtual Screen with AutoDock]]<br /> *[[Simple Protein Crosslinking]]<br /> *[[1D NMR Titrations]]<br /> <br /> Cell Culturing<br /> *[[Cell Culturing Dr. Franco Lab]]<br /> <br /> ''Metabolomics''<br /> *[[MetPa for metabolomics]]<br /> *[[Making Heatmaps]]<br /> *[[One way ANOVA in R]]<br /> *[[P-Value adjustment for multiple comparisons]]<br /> *[[PCA-Utils]]<br /> *[[NMR Tube Deep Cleaning]]<br /> *[[Noise Removal for PCA]]<br /> *[[Weighted Linear Least Squares]]<br /> *[[Serum Preparation for 1D NMR]]<br /> *[[Whole Blood Preparation for 1D NMR]]<br /> *[[Urine Preparation for 1D NMR]]<br /> *[[Cell Culture Preparation for 1D NMR]]<br /> *[[LC-MS metabolomics guide-CIBC collaborations]]<br /> <br /> ''Safety and Inspections''<br /> *[[Lab Responsibilities]]<br /> *[[Inspection Checklist]]<br /> *[[Safety Contacts, Resources]]<br /> <br /> ''Demos''<br /> *[[Peroxide Clock]]<br /> *[[Traffic Light Reaction]]<br /> *[[Orange Juice Clock]]<br /> *[[Gummy Bear Freeze]]<br /> *[[Lava Lamps]]<br /> *[[Batteries]]<br /> *[[Rocket Launcher]]<br /> *[[Women in Science: Checklist]]<br /> *[[Maxey Day: Checklist]]</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=Category:Protocols&diff=746 2021-01-06T20:27:24Z

<p>Acrook: </p> <hr /> <div>''General Maintenance''<br /> *[[Changing the high pressure dewar]]<br /> *[[Filling a Magnet with Nitrogen]]<br /> *[[Autoclaving Laboratory Glassware and Media]]<br /> *[[Chemical Disinfection of Glassware]]<br /> *[[Requesting Balance Calibration]]<br /> *[[Requesting Pipette Calibration]]<br /> *[[Using the UV-Vis]]<br /> *[[Using and Maintaining pH Meter]]<br /> *[[-80 Freezer Storage and Maintenance]]<br /> *[[Freeze Dryer Maintenance]]<br /> *[[Lab Notebook Guidelines]]<br /> *[[Sample Barcoding]]<br /> <br /> ''Protein Preparation''<br /> *[[Buffer Exchange and Solution Concentration]]<br /> *[[Finding a Protein Target on the NESG website]]<br /> *[[Choosing a Plasmid]]<br /> *[[Plasmid Purification and Transformation Protocol]]<br /> *[[Creating Stock Cultures of Bacteria]]<br /> *[[Luria-Bertani Media]]<br /> *[[M9 Minimal Media]]<br /> *[[Protein Overexpression and Extraction]]<br /> *[[SDS-PAGE Protocol]]<br /> *[[Running a Cobalt Affinity Column]]<br /> *[[Dialysis]]<br /> *[[Centrifugal Protein Concentration and Buffer Exchange]]<br /> *[[Using the Stirred Cell Concentrator]]<br /> <br /> ''Data Collection''<br /> *[[Gap Sampling]]<br /> *[[Water Suppression with presaturation pulses (zgpr/zgcppr]]<br /> *[[Non-uniform Sampling]]<br /> *[[Collecting a 15N Edited HSQC]]<br /> *[[Collecting CEST Data]]<br /> <br /> ''Data Processing and Analysis''<br /> *[[Analysis of 1D Line-Broadening Screen]]<br /> *[[FastModelFree]]<br /> *[[2D NMR Analysis (CCPNMR)]]<br /> *[[1H NMR Analysis (SIMCA)]]<br /> *[[1H NMR Analysis (ACDLab)]]<br /> *[[Processing CEST Data]]<br /> *[[Titration Data Analysis in nmrPipe]]<br /> *[[Non-Uniform Sampling]]<br /> *[[NMRFAM-SPARKY Guide]]<br /> *[[NMRFAM-SPARKY: Automated Peak Assignment]]<br /> *[[NMR Processing in Linux and Windows]]<br /> *[[1D NMR Processing in Linux and Windows Example Script]]<br /> *[[Sample Collection and Processing for Protein Backbone Assignments]]<br /> *[[Example Scripts for NMRPipe Processing]]<br /> <br /> <br /> ''Miscellaneous''<br /> *[[Agarose Gel]]<br /> *[[700 MHz NMR checklist]]<br /> *[[500 MHz NMR checklist]]<br /> *[[1D Macro]]<br /> *[[Setting Up a Virtual Screen with AutoDock]]<br /> *[[Simple Protein Crosslinking]]<br /> *[[1D NMR Titrations]]<br /> <br /> Cell Culturing<br /> *[[Cell Culturing Dr. Franco Lab]]<br /> <br /> ''Metabolomics''<br /> *[[MetPa for metabolomics]]<br /> *[[Making Heatmaps]]<br /> *[[One way ANOVA in R]]<br /> *[[P-Value adjustment for multiple comparisons]]<br /> *[[PCA-Utils]]<br /> *[[NMR Tube Deep Cleaning]]<br /> *[[Noise Removal for PCA]]<br /> *[[Weighted Linear Least Squares]]<br /> *[[Serum Preparation for 1D NMR]]<br /> *[[Whole Blood Preparation for 1D NMR]]<br /> *[[Urine Preparation for 1D NMR]]<br /> *[[Cell Culture Preparation for 1D NMR]]<br /> *[[LC-MS metabolomics guide-CIBC collaborations]]<br /> <br /> ''Safety and Inspections''<br /> *[[Lab Responsibilities]]<br /> *[[Inspection Checklist]]<br /> *[[Safety Contacts, Resources]]<br /> <br /> ''Demos''<br /> *[[Peroxide Clock]]<br /> *[[Traffic Light Reaction]]<br /> *[[Orange Juice Clock]]<br /> *[[Gummy Bear Freeze]]<br /> *[[Lava Lamps]]<br /> *[[Batteries]]<br /> *[[Rocket Launcher]]<br /> *[[Women in Science: Checklist]]<br /> *[[Maxey Day: Checklist]]</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=1D_NMR_Processing_in_Linux_and_Windows_Example_Script&diff=744 2021-01-06T20:03:49Z

<p>Acrook: Created page with &quot;&#039;&#039;&#039;Load MVAPACK&#039;&#039;&#039; addpath(&#039;/opt/mvapack/&#039;); &#039;&#039;&#039;Load Data&#039;&#039;&#039; F.dirs = glob(&#039;???&#039;); [F.data, F.parms, F.t] = loadnmr(F.dirs); &#039;&#039;&#039;Add Classes and Labels&#039;&#039;&#039; c...&quot;</p> <hr /> <div>'''Load MVAPACK''' <br /> addpath('/opt/mvapack/');<br /> <br /> '''Load Data''' <br /> F.dirs = glob('???');<br /> [F.data, F.parms, F.t] = loadnmr(F.dirs);<br /> <br /> '''Add Classes and Labels''' <br /> <br /> cls.Y = classes([7,8,6,8,8,8,7,8,7,8,8,8,8,8,8]);<br /> cls.labels = {'1','2','3','4','5','6','7','8','9','10','11','12','13','14','15'};<br /> <br /> '''Zerofills'''<br /> <br /> F.data = zerofill(F.data, F.parms, 2); #number of zerofills can be adjusted<br /> <br /> '''Build the Spectra/FT'''<br /> <br /> [S.data, S.ppm] = nmrft(F.data, F.parms);<br /> <br /> Note: Check out the Quality (spit out a couple plots)<br /> <br /> #plot(S.ppm,S.data(1,:)) - Change 1 to a different number to inspect that spectrum.<br /> <br /> '''Autophase the Spectra'''<br /> <br /> #Note, some users run this ~2-3 times for convergence<br /> <br /> [S.data, S.phc0, S.phc1] = autophase(S.data, F.parms); <br /> [S.data, S.phc0, S.phc1] = autophase(S.data, F.parms); <br /> [S.data, S.phc0, S.phc1] = autophase(S.data, F.parms); <br /> <br /> '''Extract the Real Spectral Components'''<br /> <br /> XF.data = realnmr(S.data, F.parms);<br /> XF.ppm = S.ppm;<br /> <br /> '''Check Plot to Find Reference Standard'''<br /> <br /> plot(XF.ppm, XF.data)<br /> <br /> '''Reference Adjustment'''<br /> <br /> XF.ppm = refadj(XF.ppm, -0.160, 0.0);<br /> <br /> '''Icoshift'''<br /> <br /> XF.data = icoshift(XF.data, XF.ppm);<br /> <br /> '''Remove Undesired Regions'''<br /> <br /> r0= findnearest(XF.ppm, min(XF.ppm));<br /> r1=findnearest(XF.ppm, 0.4);<br /> r2=findnearest(XF.ppm, 0.97);<br /> r3=findnearest(XF.ppm, 1.33); <br /> r4=findnearest(XF.ppm, 4.5);<br /> r5=findnearest(XF.ppm, 5.2);<br /> r6=findnearest(XF.ppm, 8.5);<br /> r7=findnearest(XF.ppm, max(XF.ppm));<br /> X.rm.var = [r7:r6,r5:r4,r3:r2,r1:r0];<br /> [XF.data, XF.ppm] = rmvar(XF.data, XF.ppm, X.rm.var);<br /> <br /> '''Normalize Data'''<br /> <br /> X1.data= pqnorm(XF.data);<br /> X1.ppm=XF.ppm<br /> <br /> '''Binning'''<br /> <br /> [B.data, B.ppm, B.widths]=binadapt(XF.data,XF.ppm,F.parms);<br /> <br /> == Build Models ==<br /> <br /> ''' ''Principle Component Analysis'' '''<br /> <br /> mdlpca= pca(X1.data); <br /> mdlpca = addclasses(mdlpca, cls.Z); <br /> scoresplot(mdlpca, 2, [], true);<br /> print -deps -color 'FB-2-mdlPCA.eps'<br /> print -dpdf -color 'Fb-2-mdlPCA.pdf'<br /> <br /> '''RQ Plot'''<br /> rqplot(mdlpca)<br /> print -deps -color 'FB-2-rqmdlPCA.eps'<br /> print -dpdf -color 'Fb-2-rqmdlPCA.pdf'<br /> <br /> '''Save Scores'''<br /> savescores (mdlpca,FB-2-scoresPCA,3,cls.Y,cls.labels)<br /> <br /> ''' ''Orthogonal Projection to Latent Squares (OPLS)'' '''<br /> <br /> Note: no seperation with binned data<br /> <br /> mdlopls = opls(X1.data, cls.Y);<br /> mdlopls = addlabels(mdlopls, cls.labels);<br /> print -deps -color 'FB-2-mdlOPLS.eps'<br /> print -dpdf -color 'Fb-2-mdlOPLS.pdf'<br /> <br /> '''Validation Stages for OPLS Models'''<br /> <br /> ''RQ Plot''<br /> rqplot(mdlopls);<br /> <br /> ''Permutation Test''<br /> mdl.cv.perm = permtest(mdlopls);<br /> permscatter(mdl.cv.perm) <br /> <br /> ''CV Anova''<br /> mdl.cv.anova = cvanova(mdlopls);<br /> mdl.cv.anova</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=Category:Protocols&diff=741 2021-01-06T19:32:11Z

<p>Acrook: </p> <hr /> <div>''General Maintenance''<br /> *[[Changing the high pressure dewar]]<br /> *[[Filling a Magnet with Nitrogen]]<br /> *[[Autoclaving Laboratory Glassware and Media]]<br /> *[[Chemical Disinfection of Glassware]]<br /> *[[Requesting Balance Calibration]]<br /> *[[Requesting Pipette Calibration]]<br /> *[[Using the UV-Vis]]<br /> *[[Using and Maintaining pH Meter]]<br /> *[[-80 Freezer Storage and Maintenance]]<br /> *[[Freeze Dryer Maintenance]]<br /> *[[Lab Notebook Guidelines]]<br /> *[[Sample Barcoding]]<br /> <br /> ''Protein Preparation''<br /> *[[Buffer Exchange and Solution Concentration]]<br /> *[[Finding a Protein Target on the NESG website]]<br /> *[[Choosing a Plasmid]]<br /> *[[Plasmid Purification and Transformation Protocol]]<br /> *[[Creating Stock Cultures of Bacteria]]<br /> *[[Luria-Bertani Media]]<br /> *[[M9 Minimal Media]]<br /> *[[Protein Overexpression and Extraction]]<br /> *[[SDS-PAGE Protocol]]<br /> *[[Running a Cobalt Affinity Column]]<br /> *[[Dialysis]]<br /> *[[Centrifugal Protein Concentration and Buffer Exchange]]<br /> *[[Using the Stirred Cell Concentrator]]<br /> <br /> ''Data Collection''<br /> *[[Gap Sampling]]<br /> *[[Water Suppression with presaturation pulses (zgpr/zgcppr]]<br /> *[[Non-uniform Sampling]]<br /> *[[Collecting a 15N Edited HSQC]]<br /> *[[Collecting CEST Data]]<br /> <br /> ''Data Processing and Analysis''<br /> *[[Analysis of 1D Line-Broadening Screen]]<br /> *[[FastModelFree]]<br /> *[[2D NMR Analysis (CCPNMR)]]<br /> *[[1H NMR Analysis (SIMCA)]]<br /> *[[1H NMR Analysis (ACDLab)]]<br /> *[[Processing CEST Data]]<br /> *[[Titration Data Analysis in nmrPipe]]<br /> *[[Non-Uniform Sampling]]<br /> *[[NMRFAM-SPARKY Guide]]<br /> *[[NMRFAM-SPARKY: Automated Peak Assignment]]<br /> *[[NMR Processing in Linux and Windows]]<br /> *[[1D NMR Processing in Linux and Windows Example Script]]<br /> *[[Sample Collection and Processing for Protein Backbone Assignments]]<br /> *[[Example Scripts for NMRPipe Processing]]<br /> *[[2D Metabolomics NMRPipe Processing]]<br /> <br /> ''Miscellaneous''<br /> *[[Agarose Gel]]<br /> *[[700 MHz NMR checklist]]<br /> *[[500 MHz NMR checklist]]<br /> *[[1D Macro]]<br /> *[[Setting Up a Virtual Screen with AutoDock]]<br /> *[[Simple Protein Crosslinking]]<br /> *[[1D NMR Titrations]]<br /> <br /> Cell Culturing<br /> *[[Cell Culturing Dr. Franco Lab]]<br /> <br /> ''Metabolomics''<br /> *[[MetPa for metabolomics]]<br /> *[[Making Heatmaps]]<br /> *[[One way ANOVA in R]]<br /> *[[P-Value adjustment for multiple comparisons]]<br /> *[[PCA-Utils]]<br /> *[[NMR Tube Deep Cleaning]]<br /> *[[Noise Removal for PCA]]<br /> *[[Weighted Linear Least Squares]]<br /> *[[Serum Preparation for 1D NMR]]<br /> *[[Whole Blood Preparation for 1D NMR]]<br /> *[[Urine Preparation for 1D NMR]]<br /> *[[Cell Culture Preparation for 1D NMR]]<br /> *[[LC-MS metabolomics guide-CIBC collaborations]]<br /> <br /> ''Safety and Inspections''<br /> *[[Lab Responsibilities]]<br /> *[[Inspection Checklist]]<br /> *[[Safety Contacts, Resources]]<br /> <br /> ''Demos''<br /> *[[Peroxide Clock]]<br /> *[[Traffic Light Reaction]]<br /> *[[Orange Juice Clock]]<br /> *[[Gummy Bear Freeze]]<br /> *[[Lava Lamps]]<br /> *[[Batteries]]<br /> *[[Rocket Launcher]]<br /> *[[Women in Science: Checklist]]<br /> *[[Maxey Day: Checklist]]</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=2D_Metabolomics_NMRPipe_Processing&diff=740 2021-01-06T19:22:01Z

<p>Acrook: </p> <hr /> <div>== NMRPipe Processing to obtain .ft2 and .nv files ==<br /> 1. The data files from ICONNMR can be used directly by NMRPipe to process the 2D 1H–13C-HSQC spectra.<br /> <br /> 2. On a Linux workstation, open a terminal and go to the directory that contains the NMR data. Type bruker to start the NMRpipe software.<br /> <br /> 3. Read in the experimental parameters file by clicking Read Parameters and verify that all the parameters have been correctly updated. Confirm that the mode of data collection has been set to echo-antiecho if the NMR spectrum was collected with the hsqcetgpsisp2 pulse program.<br /> <br /> 4. Click Update Script to save an NMRPipe processing script fid.com file in the working directory.<br /> <br /> 5. Type ./fid.com to start the NMRPipe processing script.<br /> <br /> 6. When the NMRPipe processing has finished, type nmrDraw to view the processed NMR spectrum. <br /> <br /> 7. Phase the NMR spectrum in NMRpipe and note the p0 and p1 values for both the 1H and 13C dimensions.<br /> <br /> 8. Edit the NMRPipe processing script hsqcproc.com and replace the parameters associated with the NMRPipe phase correction command, ps, with the p0 and p1 values obtained from step 7.<br /> <br /> 9. Type ./hsqcproc.com to start the NMRPipe processing script.<br /> <br /> 10. Repeat steps 3–9 for each 2D 1H–13C-HSQC NMR spectrum in the dataset. This produces a set .ft2 files. One .ft2 file is created for each 2D 1H–13C-HSQC NMR spectrum collected for each replicate from each group.<br /> <br /> 11. Copy all of the .ft2 files into a new folder and use the NMRPipe script addnmr.com to generate NMRviewJ files from the .ft2 files. A .nv file will be generated for each individual spectrum (.ft2 file) with a numerically incremented root name of Final_. In addition, the script will combine all of the NMR spectra together into a single file called results.nv. The script will also generate the text file, rate.txt, which lists all of the individual. nv files (Final_).<br /> <br /> ----<br /> <br /> <br /> == Peak Picking and Peak Integration of 2D 1H–13C-HSQC Spectra in NMRviewJ ==<br /> <br /> 1. Type nmrviewj to start NMRviewJ. <br /> <br /> 2. From the Dataset toolbar in the main window, use the Open and Draw Datasets function to select the result.nv file.<br /> <br /> 3. Right click and select attributes to open the attributes window.<br /> <br /> 4. In the attributes window, select the PeakPick tab.<br /> <br /> 5. In the blank Lists field in the attribute window, type a filename (i.e., lists) for the new peak pick list. Click the Pick button. The software will automatically peak pick the displayed spectrum and populate lists with the peak ID number, chemical shifts, and intensity.<br /> <br /> 6. Choose Show Peak Table from the Peak toolbar on the main window. A peak table window will open that lists the peak ID, peak intensity, and the peak chemical shifts.<br /> <br /> 7. Manually edit the peak list and remove solvent peaks, noise peaks, or other spectral artifacts. Peaks are deleted from the peak table by using the delete function in the PeakPick tab in the attributes window along with the spectrum display window. In the spectrum display window, use the mouse to position the two cursors around any peak or spectral region to form a box. Then, click the Delete button under the PeakPick tab in the attributes window to remove the peak(s).<br /> <br /> 8. After the peak table has been completely edited, on the peak table window, choose the Edit tab and select Compress and Degap. Answer yes to the pop-up question. This will finalize changes to the peak list and prevent any further edits.<br /> <br /> 9. On the peak table window, choose the Edit tab and then select Save Table. A file browser window will open in order to choose a name and location to save the new peak list file. The saved peak pick file can be viewed and edited in Excel.<br /> <br /> 10. In order to obtain peak intensities across the entire set of NMR spectra in the dataset, click on the Analysis tab on the main window and select Rate Analysis. A setup window for the Rate Analysis will open.<br /> <br /> 11. In the Rate Analysis setup window:<br /> <br /> (a) Set the Prefix for matrix numbers field to Final_.<br /> <br /> (b) Set the Peaklist field to lists (defined in step 5).<br /> <br /> (c) Make sure Auto fit is checked.<br /> <br /> (d) Use all other default settings.<br /> <br /> (e) Click Load time file.<br /> <br /> (f) In the file browser window, select rate.txt (created in NMRPipe Processing, step 11).<br /> <br /> (g) Click Measure All. The software automatically populates the table in the Rate Analysis setup window with all of the peak intensities across the entire NMR dataset.<br /> <br /> (h) Click Save Table. In the file browser window, save the peak intensities table to a new filename (i.e., intensities).<br /> <br /> 12. The peak list (i.e., list) and the peak intensities (i.e., intensities) files are merged in Microsoft Excel using the common peak ID column. The ppm1 (1H ppm) and ppm2 (13C ppm) columns are added to the peak intensities columns to generate a complete matrix of NMR peaks and intensities across the entire dataset.<br /> <br /> 13. The merged Excel file is saved to a new filename.<br /> <br /> ----<br /> <br /> <br /> == Metabolite Assignments from 2D 1H–13C-HSQC Peak Lists ==<br /> <br /> 1. The complete list of peaks obtained from the NMRviewJ analyses is searched using NMR metabolomics databases such as HMDB, BMRB, or other databases.<br /> <br /> 2. On the HMDB homepage, choose the Search tab and select 2D NMR Search.<br /> <br /> 3. From the Spectra Library pull-down menu, choose 13C HSQC.<br /> <br /> 4. Cut and paste the 2D 1H–13C-HSQC peak lists into the Peak List field. One set of 1H and 13C chemical shifts, respectively,per line. Chemical shift values should only be separated by white space.<br /> <br /> 5. Set the 1H chemical shift error tolerance to 0.05 ppm (X-axis Peak Tolerance +/- field) and the 13C chemical shift error tolerance to 0.10 ppm (Y-axis Peak Tolerance +/- field).<br /> <br /> 6. Click the Search button. Depending on the size of the peak list,the software will return a ranked-order list of possible metabolites based on the number of chemical shift matches to reference spectrum.<br /> <br /> 7. Manually curate the list of potential metabolite assignments based on the number of chemical shift assignments, the quality of the spectral overlap (i.e., chemical shift match), the number of other metabolites in the same metabolic pathway, and the biological system (i.e., is it a reasonable or possible metabolitefor the organism).<br /> <br /> 8. Obtain additional NMR (e.g., HMBC, HSQC-TOCSY) and/or MS spectral data to confirm or refute the assignment.<br /> <br /> 9. An assigned 2D 1H–13C-HSQC spectrum</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=2D_Metabolomics_NMRPipe_Processing&diff=739 2021-01-06T19:18:38Z

<p>Acrook: /* NMRPipe Processing to obtain .ft2 and .nv files */</p> <hr /> <div>== NMRPipe Processing to obtain .ft2 and .nv files ==<br /> 1. The data files from ICONNMR can be used directly by NMRPipe to process the 2D 1H–13C-HSQC spectra.<br /> <br /> 2. On a Linux workstation, open a terminal and go to the directory that contains the NMR data. Type bruker to start the NMRpipe software.<br /> <br /> 3. Read in the experimental parameters file by clicking Read Parameters and verify that all the parameters have been correctly updated. Confirm that the mode of data collection has been set to echo-antiecho if the NMR spectrum was collected with the hsqcetgpsisp2 pulse program.<br /> <br /> 4. Click Update Script to save an NMRPipe processing script fid.com file in the working directory.<br /> <br /> 5. Type ./fid.com to start the NMRPipe processing script.<br /> <br /> 6. When the NMRPipe processing has finished, type nmrDraw to view the processed NMR spectrum. Please see the NMRPipe and nmrDraw tutorials at [spin.niddk.nih.gov/NMRPipe/doc1/] for detailed instructions.</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=2D_Metabolomics_NMRPipe_Processing&diff=738 2021-01-06T19:14:49Z

<p>Acrook: /* NMRPipe Processing to obtain .ft2 and .nv files */</p> <hr /> <div>== NMRPipe Processing to obtain .ft2 and .nv files ==<br /> 1. The data files from ICONNMR can be used directly by NMRPipe to process the 2D 1H–13C-HSQC spectra.<br /> <br /> 2. On a Linux workstation, open a terminal and go to the directory that contains the NMR data. Type bruker to start the NMRpipe software.<br /> <br /> 3. Read in the experimental parameters file by clicking Read Parameters and verify that all the parameters have been correctly updated. Confirm that the mode of data collection has been set to echo-antiecho if the NMR spectrum was collected with the hsqcetgpsisp2 pulse program.<br /> <br /> 4. Click Update Script to save an NMRPipe processing script fid.com file in the working directory.<br /> <br /> 5. Type ./fid.com to start the NMRPipe processing script.</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=2D_Metabolomics_NMRPipe_Processing&diff=737 2021-01-06T19:14:30Z

<p>Acrook: /* NMRPipe Processing to obtain .ft2 and .nv files */</p> <hr /> <div>== NMRPipe Processing to obtain .ft2 and .nv files ==<br /> 1. The data files from ICONNMR can be used directly by NMRPipe to process the 2D 1H–13C-HSQC spectra.<br /> <br /> 2. On a Linux workstation, open a terminal and go to the directory that contains the NMR data. Type bruker to start the NMRpipe software.</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=2D_Metabolomics_NMRPipe_Processing&diff=736 2021-01-06T19:14:04Z

<p>Acrook: Created page with &quot;== NMRPipe Processing to obtain .ft2 and .nv files ==&quot;</p> <hr /> <div>== NMRPipe Processing to obtain .ft2 and .nv files ==</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=Women_in_Science:_Checklist&diff=735 2021-01-06T19:09:48Z

<p>Acrook: Created page with &quot;- Two table (provided by hotel) 1 for demostrations and 1 for recruiting material - Recruiting material Powerpoint slide/video (from Robert), extension cords, power stri...&quot;</p> <hr /> <div>- Two table (provided by hotel)<br /> 1 for demostrations and 1 for recruiting material<br /> - Recruiting material<br /> Powerpoint slide/video (from Robert), extension cords, power strip, projector (Cluster Room)<br /> - Demonstration (request material from undergrad stock room two weeks before event)<br /> <br /> <br /> == Demonstrations ==<br /> <br /> Oscillating clock<br /> Stop light reaction (can put more NaOH in)<br /> Orange Juice Clock <br /> Liquid Nitrogen Gummy Bear<br /> Lava lamps<br /> <br /> == Miscellaneous Items ==<br /> A big empty used chemical container with cap<br /> A big beaker (1L)<br /> Nitrile glove (small)</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=Lava_Lamps&diff=734 2021-01-06T19:02:17Z

<p>Acrook: </p> <hr /> <div><br /> == Supplies ==<br /> <br /> Oil (veg oil)(1/3)<br /> <br /> Water(2/3)<br /> <br /> Alka saltzer tablets<br /> <br /> Food coloring<br /> <br /> Several empty soda bottles (20/16 OZ plastic)<br /> <br /> Flashlight or search light under the bottle<br /> <br /> <br /> == Procedure ==<br /> <br /> Mix all ingredients in the empy soad bottles.</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=Lava_Lamps&diff=733 2021-01-06T19:01:59Z

<p>Acrook: Created page with &quot; == Supplies == Oil (veg oil)(1/3) Water(2/3) Alka saltzer tablets Food coloring Several empty soda bottles (20/16 OZ plastic) Flashlight or search light under the bottle...&quot;</p> <hr /> <div><br /> == Supplies ==<br /> <br /> Oil (veg oil)(1/3)<br /> Water(2/3)<br /> Alka saltzer tablets<br /> Food coloring<br /> Several empty soda bottles (20/16 OZ plastic)<br /> Flashlight or search light under the bottle<br /> <br /> <br /> == Procedure ==<br /> <br /> Mix all ingredients in the empy soad bottles.</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=Category:Protocols&diff=732 2021-01-06T19:00:51Z

<p>Acrook: </p> <hr /> <div>''General Maintenance''<br /> *[[Changing the high pressure dewar]]<br /> *[[Filling a Magnet with Nitrogen]]<br /> *[[Autoclaving Laboratory Glassware and Media]]<br /> *[[Chemical Disinfection of Glassware]]<br /> *[[Requesting Balance Calibration]]<br /> *[[Requesting Pipette Calibration]]<br /> *[[Using the UV-Vis]]<br /> *[[Using and Maintaining pH Meter]]<br /> *[[-80 Freezer Storage and Maintenance]]<br /> *[[Freeze Dryer Maintenance]]<br /> *[[Lab Notebook Guidelines]]<br /> *[[Sample Barcoding]]<br /> <br /> ''Protein Preparation''<br /> *[[Buffer Exchange and Solution Concentration]]<br /> *[[Finding a Protein Target on the NESG website]]<br /> *[[Choosing a Plasmid]]<br /> *[[Plasmid Purification and Transformation Protocol]]<br /> *[[Creating Stock Cultures of Bacteria]]<br /> *[[Luria-Bertani Media]]<br /> *[[M9 Minimal Media]]<br /> *[[Protein Overexpression and Extraction]]<br /> *[[SDS-PAGE Protocol]]<br /> *[[Running a Cobalt Affinity Column]]<br /> *[[Dialysis]]<br /> *[[Centrifugal Protein Concentration and Buffer Exchange]]<br /> *[[Using the Stirred Cell Concentrator]]<br /> <br /> ''Data Collection''<br /> *[[Gap Sampling]]<br /> *[[Water Suppression with presaturation pulses (zgpr/zgcppr]]<br /> *[[Non-uniform Sampling]]<br /> *[[Collecting a 15N Edited HSQC]]<br /> *[[Collecting CEST Data]]<br /> <br /> ''Data Processing and Analysis''<br /> *[[Analysis of 1D Line-Broadening Screen]]<br /> *[[FastModelFree]]<br /> *[[2D NMR Analysis (CCPNMR)]]<br /> *[[1H NMR Analysis (SIMCA)]]<br /> *[[1H NMR Analysis (ACDLab)]]<br /> *[[Processing CEST Data]]<br /> *[[Titration Data Analysis in nmrPipe]]<br /> *[[Non-Uniform Sampling]]<br /> *[[NMRFAM-SPARKY Guide]]<br /> *[[NMRFAM-SPARKY: Automated Peak Assignment]]<br /> *[[NMR Processing in Linux and Windows]]<br /> *[[Sample Collection and Processing for Protein Backbone Assignments]]<br /> *[[Example Scripts for NMRPipe Processing]]<br /> *[[2D Metabolomics NMRPipe Processing]]<br /> <br /> ''Miscellaneous''<br /> *[[Agarose Gel]]<br /> *[[700 MHz NMR checklist]]<br /> *[[500 MHz NMR checklist]]<br /> *[[1D Macro]]<br /> *[[Setting Up a Virtual Screen with AutoDock]]<br /> *[[Simple Protein Crosslinking]]<br /> *[[1D NMR Titrations]]<br /> <br /> Cell Culturing<br /> *[[Cell Culturing Dr. Franco Lab]]<br /> <br /> ''Metabolomics''<br /> *[[MetPa for metabolomics]]<br /> *[[Making Heatmaps]]<br /> *[[One way ANOVA in R]]<br /> *[[P-Value adjustment for multiple comparisons]]<br /> *[[PCA-Utils]]<br /> *[[NMR Tube Deep Cleaning]]<br /> *[[Noise Removal for PCA]]<br /> *[[Weighted Linear Least Squares]]<br /> *[[Serum Preparation for 1D NMR]]<br /> *[[Whole Blood Preparation for 1D NMR]]<br /> *[[Urine Preparation for 1D NMR]]<br /> *[[Cell Culture Preparation for 1D NMR]]<br /> *[[LC-MS metabolomics guide-CIBC collaborations]]<br /> <br /> ''Safety and Inspections''<br /> *[[Lab Responsibilities]]<br /> *[[Inspection Checklist]]<br /> *[[Safety Contacts, Resources]]<br /> <br /> ''Demos''<br /> *[[Peroxide Clock]]<br /> *[[Traffic Light Reaction]]<br /> *[[Orange Juice Clock]]<br /> *[[Gummy Bear Freeze]]<br /> *[[Lava Lamps]]<br /> *[[Batteries]]<br /> *[[Rocket Launcher]]<br /> *[[Women in Science: Checklist]]<br /> *[[Maxey Day: Checklist]]</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=Gummy_Bear_Freeze&diff=731 2021-01-06T18:59:40Z

<p>Acrook: Created page with &quot; == Supplies == - Liquid nitrogen - Gummy bears - Hammer - A folded box as supporter of smashing - Tong to hold gummy bear - Safety glasses, thermal gloves - Bucket (hold l...&quot;</p> <hr /> <div><br /> == Supplies ==<br /> <br /> - Liquid nitrogen<br /> - Gummy bears<br /> - Hammer<br /> - A folded box as supporter of smashing<br /> - Tong to hold gummy bear <br /> - Safety glasses, thermal gloves<br /> - Bucket (hold liquid N2), <br /> - Tape<br /> <br /> <br /> == Procedure==<br /> <br /> Bring all supplies to demo and set up for gummy bear smashing. Make sure to clean up bummy bears immediately after demo is finished - much harder to clean after gummy bears have thawed.</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=Orange_Juice_Clock&diff=730 2021-01-06T18:57:28Z

<p>Acrook: Created page with &quot; == Supplies == -Clock connected with two alligator clips - Electrodes:Mg (negative end) and Cu (positive end) - Ring stand+clampe - Two beakers (250ml) - Orange juice bottle...&quot;</p> <hr /> <div><br /> == Supplies ==<br /> <br /> -Clock connected with two alligator clips<br /> - Electrodes:Mg (negative end) and Cu (positive end)<br /> - Ring stand+clampe<br /> - Two beakers (250ml)<br /> - Orange juice bottle<br /> <br /> == Procedure ==<br /> <br /> Put the two electrodes into a beaker with orange juice.</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=Traffic_Light_Reaction&diff=729 2021-01-06T18:55:48Z

<p>Acrook: Created page with &quot; == Supplies == - Glucose:0.1M,250ml (take Glucose bottle) - NaOH:3M,10ml (take NaOH bottle) - Indicator: Indigo carmine - 500ml Flask with a stopper (good stopper!) and g...&quot;</p> <hr /> <div><br /> == Supplies ==<br /> <br /> - Glucose:0.1M,250ml (take Glucose bottle)<br /> <br /> - NaOH:3M,10ml (take NaOH bottle)<br /> <br /> - Indicator: Indigo carmine<br /> <br /> - 500ml Flask with a stopper (good stopper!) and glass rod for stiring<br /> <br /> <br /> == Procedure ==<br /> <br /> In a beaker containing 250 ml of distilled water, add 3 g of dextrose and stir until it dissolves. Next, add 5 g of sodium hydroxide pellets into the same beaker, and use a stirring rod to break apart the pellets so that they will dissolve quickly. Once this is done, pour the contents of the beaker into the glass flask, and add between 5-10 ml of the indigo carmine indicator. Enough should be added to the solution so that it turns a yellow color. Put the stopper in the flask, and let it sit for ten minutes. After ten minutes, the solution should be ready for the demonstration. Shake the flask once or twice, and it should turn a red color. Shake once or twice again, and it should turn green. Then, if it sits, it should turn back to the yellow color.</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=Peroxide_Clock&diff=728 2021-01-06T18:53:52Z

<p>Acrook: Created page with &quot;1. Solution A: Prepare 100 mL of 9% H2O2 by diluting 30 mL of 30% H2O2 with 70 mL of deionized H2O. 2. Solution B: Prepare an acidified 0.2 M KIO3 solution by adding 10 mL of...&quot;</p> <hr /> <div>1. Solution A: Prepare 100 mL of 9% H2O2 by diluting 30 mL of 30% H2O2 with 70 mL of deionized H2O.<br /> <br /> 2. Solution B: Prepare an acidified 0.2 M KIO3 solution by adding 10 mL of 1.0 M H2SO4 to 80 mL of deionized water. Dissolve 4.3 g KIO3 in this solution and dilute to 100 mL.<br /> <br /> 3. Solution C: Prepare starch solution by dissolving 0.1 g of soluble starch in 90 mL of boiling deionized water. When cool, add 1.5 g malonic acid, 0.4 g MnSO4·H2O, stir and dilute to 100 mL.<br /> <br /> 4. Add 50 mL of Solution A to a clean beaker fitted with a stir bar. Next add 50 mL of Solution B and let solutions mix thoroughly. Once complete, add 50 mL of Solution C and let reaction stir. Upon addition of the final solution, bubbles should appear. The solution will turn yellow then blue, then colorless. This reaction will oscillate for 5-10 minutes.</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=Maxey_Day:_Checklist&diff=727 2021-01-06T18:45:18Z

<p>Acrook: /* Demos for Dr. Powers */</p> <hr /> <div><br /> == Demos for Dr. Powers ==<br /> <br /> '''1. OJ clock''' <br /> <br /> - Clock set up, 500ML beaker, (x3) and electrodes (x2) <br /> <br /> '''2. Elephants toothpaste''' <br /> <br /> -Hydrogen peroxide(500mL 30%) , dish soap and KI (500 mL), Long cyclinder (x2), and a Nalgene tray to catch the foam <br /> <br /> '''3. Red Cabbage and solid CO2''' <br /> <br /> - Gallon of juice, a cooler of dry ice (night before), Large cyclinder with wooden base, and giant stir bar<br /> <br /> '''4. Peroxide clock''' <br /> <br /> - Hydrogen peroxide KIO3 and starch solutions with beakers (100mLx3), beakers (50mLx3), stir plate, and stir bar <br /> '''<br /> 5. Glowing pickles''' <br /> <br /> - Power supply and pickle <br /> '''<br /> 6. Slides''' <br /> <br /> - Projector, screen, extension cord, and power strips (Dr. Powers’ laptop)<br /> <br /> '''7. Cryogens with banana and gummy bears''' <br /> <br /> - Liq Nitrogen in 4L carrier, two foam buckets, a hammer, and cardboard set up to catch fly-away (Dr. J Powers brings the gummy bears and banana) <br /> <br /> '''8. Stop light''' (We make these solutions)<br /> <br /> - Glucose, Indigo Carmine, and NaOH. Get three 500mL Erlenmeyer flasks with good rubber stoppers from stock room. <br /> <br /> ----<br /> <br /> == Outdoor Demos for Dr. Powers ==<br /> <br /> '''1. Mentos and Coke''' (Dr. J Powers brings these supplies)<br /> <br /> '''2. Potato Launcher''' <br /> <br /> '''3. Isopropanol Rocket''' <br /> <br /> -Demo room for 109/110 has this set up. Bring the Ignition <br /> <br /> -Handwashing Station Demo for Dr. Joan Powers <br /> <br /> '''1. Non-Newtonian fluids''' <br /> <br /> -Corn Starch and water with drops of food color (make on site)<br /> <br /> ----<br /> <br /> <br /> == Hands-on Stations ==<br /> <br /> '''1. Nylon Experiment''' <br /> <br /> -hexamethylenediamine and sebacic acid; (from Bob) <br /> <br /> -10ml measuring cylinders (x50) atleast and 10mL beakers or paper cups (x100) <br /> <br /> -Hooks to draw out the nylon polymer<br /> <br /> '''2. Vitamin C in Juice''' <br /> <br /> -Fruit Juices (Dr. J Powers brings these) <br /> <br /> -Starch solution (1 gallon) (make the night before)<br /> <br /> -Iodine solution ++ (1-2 L) <br /> <br /> -10mL beakers (x50) and 50mL beakers (x20) plastic droppers (x1 box) <br /> <br /> '''3. Batteries''' <br /> <br /> -Pennies <br /> <br /> -Meters (as many as working) <br /> '''<br /> 4. Blue Dye UV-Vis <br /> '''<br /> -Spec 20s (from 109 Labs ask Lab manager for these) <br /> <br /> -Plastic cuvettes <br /> <br /> -Blue dye and their dilutions (1L) each <br /> <br /> -Beakers (10mL x 20) <br /> <br /> '''5. Computer Stations''' <br /> <br /> - Printer <br /> <br /> - Paper <br /> <br /> - Laptops (x5) <br /> <br /> - Cords and extension cables <br /> <br /> '''6. Slime making''' <br /> <br /> - Glue (2 gallons 50%) <br /> <br /> - Borax saturated (1 gallon)<br /> <br /> - Paper cups <br /> <br /> - Wipes <br /> <br /> - Zip lock bags to take along <br /> <br /> - Food colors</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=Maxey_Day:_Checklist&diff=726 2021-01-06T18:44:45Z

<p>Acrook: </p> <hr /> <div><br /> == Demos for Dr. Powers ==<br /> <br /> '''1. OJ clock''' <br /> <br /> - Clock set up, 500ML beaker, (x3) and electrodes (x2) <br /> <br /> '''2. Elephants toothpaste''' <br /> <br /> -Hydrogen peroxide(500mL 30%) , dish soap and KI (500 mL), Long cyclinder (x2), and a Nalgene tray to catch the foam <br /> <br /> '''3. Red Cabbage and solid CO2''' <br /> <br /> - Gallon of juice, a cooler of dry ice (night before), Large cyclinder with wooden base, and giant stir bar<br /> '''<br /> 4. Peroxide clock''' <br /> <br /> - Hydrogen peroxide KIO3 and starch solutions with beakers (100mLx3), beakers (50mLx3), stir plate, and stir bar <br /> '''<br /> 5. Glowing pickles''' <br /> <br /> - Power supply and pickle <br /> '''<br /> 6. Slides''' <br /> <br /> - Projector, screen, extension cord, and power strips (Dr. Powers’ laptop)<br /> <br /> '''7. Cryogens with banana and gummy bears''' <br /> <br /> - Liq Nitrogen in 4L carrier, two foam buckets, a hammer, and cardboard set up to catch fly-away (Dr. J Powers brings the gummy bears and banana) <br /> <br /> '''8. Stop light''' (We make these solutions)<br /> <br /> - Glucose, Indigo Carmine, and NaOH. Get three 500mL Erlenmeyer flasks with good rubber stoppers from stock room. <br /> <br /> ----<br /> <br /> == Outdoor Demos for Dr. Powers ==<br /> <br /> '''1. Mentos and Coke''' (Dr. J Powers brings these supplies)<br /> <br /> '''2. Potato Launcher''' <br /> <br /> '''3. Isopropanol Rocket''' <br /> <br /> -Demo room for 109/110 has this set up. Bring the Ignition <br /> <br /> -Handwashing Station Demo for Dr. Joan Powers <br /> <br /> '''1. Non-Newtonian fluids''' <br /> <br /> -Corn Starch and water with drops of food color (make on site)<br /> <br /> ----<br /> <br /> <br /> == Hands-on Stations ==<br /> <br /> '''1. Nylon Experiment''' <br /> <br /> -hexamethylenediamine and sebacic acid; (from Bob) <br /> <br /> -10ml measuring cylinders (x50) atleast and 10mL beakers or paper cups (x100) <br /> <br /> -Hooks to draw out the nylon polymer<br /> <br /> '''2. Vitamin C in Juice''' <br /> <br /> -Fruit Juices (Dr. J Powers brings these) <br /> <br /> -Starch solution (1 gallon) (make the night before)<br /> <br /> -Iodine solution ++ (1-2 L) <br /> <br /> -10mL beakers (x50) and 50mL beakers (x20) plastic droppers (x1 box) <br /> <br /> '''3. Batteries''' <br /> <br /> -Pennies <br /> <br /> -Meters (as many as working) <br /> '''<br /> 4. Blue Dye UV-Vis <br /> '''<br /> -Spec 20s (from 109 Labs ask Lab manager for these) <br /> <br /> -Plastic cuvettes <br /> <br /> -Blue dye and their dilutions (1L) each <br /> <br /> -Beakers (10mL x 20) <br /> <br /> '''5. Computer Stations''' <br /> <br /> - Printer <br /> <br /> - Paper <br /> <br /> - Laptops (x5) <br /> <br /> - Cords and extension cables <br /> <br /> '''6. Slime making''' <br /> <br /> - Glue (2 gallons 50%) <br /> <br /> - Borax saturated (1 gallon)<br /> <br /> - Paper cups <br /> <br /> - Wipes <br /> <br /> - Zip lock bags to take along <br /> <br /> - Food colors</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=Maxey_Day:_Checklist&diff=725 2021-01-06T18:43:11Z

<p>Acrook: /* Demos for Dr. Powers */</p> <hr /> <div><br /> == Demos for Dr. Powers ==<br /> <br /> 1. OJ clock <br /> <br /> - Clock set up, 500ML beaker, (x3) and electrodes (x2) <br /> <br /> 2. Elephants toothpaste <br /> <br /> -Hydrogen peroxide(500mL 30%) , dish soap and KI (500 mL), Long cyclinder (x2), and a Nalgene tray to catch the foam <br /> <br /> 3. Red Cabbage and solid CO2 <br /> <br /> - Gallon of juice, a cooler of dry ice (night before), Large cyclinder with wooden base, and giant stir bar<br /> <br /> 4. Peroxide clock <br /> <br /> - Hydrogen peroxide KIO3 and starch solutions with beakers (100mLx3), beakers (50mLx3), stir plate, and stir bar <br /> <br /> 5. Glowing pickles <br /> <br /> - Power supply and pickle <br /> <br /> 6. Slides <br /> <br /> - Projector, screen, extension cord, and power strips (Dr. Powers’ laptop)<br /> <br /> 7. Cryogens with banana and gummy bears <br /> <br /> - Liq Nitrogen in 4L carrier, two foam buckets, a hammer, and cardboard set up to catch fly-away (Dr. J Powers brings the gummy bears and banana) <br /> <br /> 8. Stop light (We make these solutions)<br /> <br /> - Glucose, Indigo Carmine, and NaOH. Get three 500mL Erlenmeyer flasks with good rubber stoppers from stock room. <br /> <br /> ----<br /> <br /> == Outdoor Demos for Dr. Powers ==<br /> <br /> 1. Mentos and Coke (Dr. J Powers brings these supplies)<br /> <br /> 2. Potato Launcher <br /> <br /> 3. Isopropanol Rocket <br /> <br /> -Demo room for 109/110 has this set up. Bring the Ignition <br /> <br /> -Handwashing Station Demo for Dr. Joan Powers <br /> <br /> 1. Non-Newtonian fluids <br /> <br /> -Corn Starch and water with drops of food color (make on site)<br /> <br /> ----<br /> <br /> <br /> == Hands-on Stations ==<br /> <br /> 1. Nylon Experiment <br /> <br /> -hexamethylenediamine and sebacic acid; (from Bob) <br /> <br /> -10ml measuring cylinders (x50) atleast and 10mL beakers or paper cups (x100) <br /> <br /> -Hooks to draw out the nylon polymer<br /> <br /> 2. Vitamin C in Juice <br /> <br /> -Fruit Juices (Dr. J Powers brings these) <br /> <br /> -Starch solution (1 gallon) (make the night before)<br /> <br /> -Iodine solution ++ (1-2 L) <br /> <br /> -10mL beakers (x50) and 50mL beakers (x20) plastic droppers (x1 box) <br /> <br /> 3. Batteries <br /> <br /> -Pennies <br /> <br /> -Meters (as many as working) <br /> <br /> 4. Blue Dye UV-Vis <br /> <br /> -Spec 20s (from 109 Labs ask Lab manager for these) <br /> <br /> -Plastic cuvettes <br /> <br /> -Blue dye and their dilutions (1L) each <br /> <br /> -Beakers (10mL x 20) <br /> <br /> 5. Computer Stations <br /> <br /> - Printer <br /> <br /> - Paper <br /> <br /> - Laptops (x5) <br /> <br /> - Cords and extension cables <br /> <br /> 6. Slime making <br /> <br /> - Glue (2 gallons 50%) <br /> <br /> - Borax saturated (1 gallon)<br /> <br /> - Paper cups <br /> <br /> - Wipes <br /> <br /> - Zip lock bags to take along <br /> <br /> Food colors</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=Maxey_Day:_Checklist&diff=724 2021-01-06T18:42:36Z

<p>Acrook: Created page with &quot; == Demos for Dr. Powers == 1. OJ clock - Clock set up, 500ML beaker, (x3) and electrodes (x2) 2. Elephants toothpaste -Hydrogen peroxide(500mL 30%) , dish soap and KI...&quot;</p> <hr /> <div><br /> == Demos for Dr. Powers ==<br /> <br /> 1. OJ clock <br /> <br /> - Clock set up, 500ML beaker, (x3) and electrodes (x2) <br /> <br /> 2. Elephants toothpaste <br /> <br /> -Hydrogen peroxide(500mL 30%) , dish soap and KI (500 mL), Long cyclinder (x2), and a Nalgene tray to catch the foam <br /> <br /> 3. Red Cabbage and solid CO2 <br /> <br /> - Gallon of juice, a cooler of dry ice (night before), Large cyclinder with wooden base, and giant stir bar<br /> <br /> 4. Peroxide clock <br /> <br /> - Hydrogen peroxide KIO3 and starch solutions with beakers (100mLx3), beakers (50mLx3), stir plate, and stir bar <br /> <br /> 5. Glowing pickles <br /> <br /> - Power supply and pickle <br /> <br /> 6. Slides <br /> <br /> - Projector, screen, extension cord, and power strips (Dr. Powers’ laptop)<br /> <br /> 7. Cryogens with banana and gummy bears <br /> <br /> - Liq Nitrogen in 4L carrier, two foam buckets, a hammer, and cardboard set up to catch fly-away (Dr. J Powers brings the gummy bears and banana) <br /> <br /> 8. Stop light (We make these solutions)<br /> <br /> - Glucose, Indigo Carmine, and NaOH. Get three 500mL Erlenmeyer flasks with good rubber stoppers from stock room. <br /> <br /> ----<br /> <br /> <br /> == Outdoor Demos for Dr. Powers ==<br /> <br /> 1. Mentos and Coke (Dr. J Powers brings these supplies)<br /> <br /> 2. Potato Launcher <br /> <br /> 3. Isopropanol Rocket <br /> <br /> -Demo room for 109/110 has this set up. Bring the Ignition <br /> <br /> -Handwashing Station Demo for Dr. Joan Powers <br /> <br /> 1. Non-Newtonian fluids <br /> <br /> -Corn Starch and water with drops of food color (make on site)<br /> <br /> ----<br /> <br /> <br /> == Hands-on Stations ==<br /> <br /> 1. Nylon Experiment <br /> <br /> -hexamethylenediamine and sebacic acid; (from Bob) <br /> <br /> -10ml measuring cylinders (x50) atleast and 10mL beakers or paper cups (x100) <br /> <br /> -Hooks to draw out the nylon polymer<br /> <br /> 2. Vitamin C in Juice <br /> <br /> -Fruit Juices (Dr. J Powers brings these) <br /> <br /> -Starch solution (1 gallon) (make the night before)<br /> <br /> -Iodine solution ++ (1-2 L) <br /> <br /> -10mL beakers (x50) and 50mL beakers (x20) plastic droppers (x1 box) <br /> <br /> 3. Batteries <br /> <br /> -Pennies <br /> <br /> -Meters (as many as working) <br /> <br /> 4. Blue Dye UV-Vis <br /> <br /> -Spec 20s (from 109 Labs ask Lab manager for these) <br /> <br /> -Plastic cuvettes <br /> <br /> -Blue dye and their dilutions (1L) each <br /> <br /> -Beakers (10mL x 20) <br /> <br /> 5. Computer Stations <br /> <br /> - Printer <br /> <br /> - Paper <br /> <br /> - Laptops (x5) <br /> <br /> - Cords and extension cables <br /> <br /> 6. Slime making <br /> <br /> - Glue (2 gallons 50%) <br /> <br /> - Borax saturated (1 gallon)<br /> <br /> - Paper cups <br /> <br /> - Wipes <br /> <br /> - Zip lock bags to take along <br /> <br /> Food colors</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=Category:Protocols&diff=723 2021-01-06T18:15:20Z

<p>Acrook: </p> <hr /> <div>''General Maintenance''<br /> *[[Changing the high pressure dewar]]<br /> *[[Filling a Magnet with Nitrogen]]<br /> *[[Autoclaving Laboratory Glassware and Media]]<br /> *[[Chemical Disinfection of Glassware]]<br /> *[[Requesting Balance Calibration]]<br /> *[[Requesting Pipette Calibration]]<br /> *[[Using the UV-Vis]]<br /> *[[Using and Maintaining pH Meter]]<br /> *[[-80 Freezer Storage and Maintenance]]<br /> *[[Freeze Dryer Maintenance]]<br /> *[[Lab Notebook Guidelines]]<br /> *[[Sample Barcoding]]<br /> <br /> ''Protein Preparation''<br /> *[[Buffer Exchange and Solution Concentration]]<br /> *[[Finding a Protein Target on the NESG website]]<br /> *[[Choosing a Plasmid]]<br /> *[[Plasmid Purification and Transformation Protocol]]<br /> *[[Creating Stock Cultures of Bacteria]]<br /> *[[Luria-Bertani Media]]<br /> *[[M9 Minimal Media]]<br /> *[[Protein Overexpression and Extraction]]<br /> *[[SDS-PAGE Protocol]]<br /> *[[Running a Cobalt Affinity Column]]<br /> *[[Dialysis]]<br /> *[[Centrifugal Protein Concentration and Buffer Exchange]]<br /> *[[Using the Stirred Cell Concentrator]]<br /> <br /> ''Data Collection''<br /> *[[Gap Sampling]]<br /> *[[Water Suppression with presaturation pulses (zgpr/zgcppr]]<br /> *[[Non-uniform Sampling]]<br /> *[[Collecting a 15N Edited HSQC]]<br /> *[[Collecting CEST Data]]<br /> <br /> ''Data Processing and Analysis''<br /> *[[Analysis of 1D Line-Broadening Screen]]<br /> *[[FastModelFree]]<br /> *[[2D NMR Analysis (CCPNMR)]]<br /> *[[1H NMR Analysis (SIMCA)]]<br /> *[[1H NMR Analysis (ACDLab)]]<br /> *[[Processing CEST Data]]<br /> *[[Titration Data Analysis in nmrPipe]]<br /> *[[Non-Uniform Sampling]]<br /> *[[NMRFAM-SPARKY Guide]]<br /> *[[NMRFAM-SPARKY: Automated Peak Assignment]]<br /> *[[NMR Processing in Linux and Windows]]<br /> *[[Sample Collection and Processing for Protein Backbone Assignments]]<br /> *[[Example Scripts for NMRPipe Processing]]<br /> *[[2D Metabolomics NMRPipe Processing]]<br /> <br /> ''Miscellaneous''<br /> *[[Agarose Gel]]<br /> *[[700 MHz NMR checklist]]<br /> *[[500 MHz NMR checklist]]<br /> *[[1D Macro]]<br /> *[[Setting Up a Virtual Screen with AutoDock]]<br /> *[[Simple Protein Crosslinking]]<br /> *[[1D NMR Titrations]]<br /> <br /> Cell Culturing<br /> *[[Cell Culturing Dr. Franco Lab]]<br /> <br /> ''Metabolomics''<br /> *[[MetPa for metabolomics]]<br /> *[[Making Heatmaps]]<br /> *[[One way ANOVA in R]]<br /> *[[P-Value adjustment for multiple comparisons]]<br /> *[[PCA-Utils]]<br /> *[[NMR Tube Deep Cleaning]]<br /> *[[Noise Removal for PCA]]<br /> *[[Weighted Linear Least Squares]]<br /> *[[Serum Preparation for 1D NMR]]<br /> *[[Whole Blood Preparation for 1D NMR]]<br /> *[[Urine Preparation for 1D NMR]]<br /> *[[Cell Culture Preparation for 1D NMR]]<br /> *[[LC-MS metabolomics guide-CIBC collaborations]]<br /> <br /> ''Safety and Inspections''<br /> *[[Lab Responsibilities]]<br /> *[[Inspection Checklist]]<br /> *[[Safety Contacts, Resources]]<br /> <br /> ''Demos''<br /> *[[Peroxide Clock]]<br /> *[[Traffic Light Reaction]]<br /> *[[Orange Juice Clock]]<br /> *[[Gummy Bear Freeze]]<br /> *[[Batteries]]<br /> *[[Rocket Launcher]]<br /> *[[Women in Science: Checklist]]<br /> *[[Maxey Day: Checklist]]</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=Category:Protocols&diff=722 2021-01-06T17:49:55Z

<p>Acrook: </p> <hr /> <div>''General Maintenance''<br /> *[[Changing the high pressure dewar]]<br /> *[[Filling a Magnet with Nitrogen]]<br /> *[[Autoclaving Laboratory Glassware and Media]]<br /> *[[Chemical Disinfection of Glassware]]<br /> *[[Requesting Balance Calibration]]<br /> *[[Requesting Pipette Calibration]]<br /> *[[Using the UV-Vis]]<br /> *[[Using and Maintaining pH Meter]]<br /> *[[-80 Freezer Storage and Maintenance]]<br /> *[[Freeze Dryer Maintenance]]<br /> *[[Lab Notebook Guidelines]]<br /> *[[Sample Barcoding]]<br /> <br /> ''Protein Preparation''<br /> *[[Buffer Exchange and Solution Concentration]]<br /> *[[Finding a Protein Target on the NESG website]]<br /> *[[Choosing a Plasmid]]<br /> *[[Plasmid Purification and Transformation Protocol]]<br /> *[[Creating Stock Cultures of Bacteria]]<br /> *[[Luria-Bertani Media]]<br /> *[[M9 Minimal Media]]<br /> *[[Protein Overexpression and Extraction]]<br /> *[[SDS-PAGE Protocol]]<br /> *[[Running a Cobalt Affinity Column]]<br /> *[[Dialysis]]<br /> *[[Centrifugal Protein Concentration and Buffer Exchange]]<br /> *[[Using the Stirred Cell Concentrator]]<br /> <br /> ''Data Collection''<br /> *[[Gap Sampling]]<br /> *[[Water Suppression with presaturation pulses (zgpr/zgcppr]]<br /> *[[Non-uniform Sampling]]<br /> *[[Collecting a 15N Edited HSQC]]<br /> *[[Collecting CEST Data]]<br /> <br /> ''Data Processing and Analysis''<br /> *[[Analysis of 1D Line-Broadening Screen]]<br /> *[[FastModelFree]]<br /> *[[2D NMR Analysis (CCPNMR)]]<br /> *[[1H NMR Analysis (SIMCA)]]<br /> *[[1H NMR Analysis (ACDLab)]]<br /> *[[Processing CEST Data]]<br /> *[[Titration Data Analysis in nmrPipe]]<br /> *[[Non-Uniform Sampling]]<br /> *[[NMRFAM-SPARKY Guide]]<br /> *[[NMRFAM-SPARKY: Automated Peak Assignment]]<br /> *[[NMR Processing in Linux and Windows]]<br /> *[[Sample Collection and Processing for Protein Backbone Assignments]]<br /> *[[Example Scripts for NMRPipe Processing]]<br /> <br /> ''Miscellaneous''<br /> *[[Agarose Gel]]<br /> *[[700 MHz NMR checklist]]<br /> *[[500 MHz NMR checklist]]<br /> *[[1D Macro]]<br /> *[[Setting Up a Virtual Screen with AutoDock]]<br /> *[[Simple Protein Crosslinking]]<br /> *[[1D NMR Titrations]]<br /> <br /> Cell Culturing<br /> *[[Cell Culturing Dr. Franco Lab]]<br /> <br /> ''Metabolomics''<br /> *[[MetPa for metabolomics]]<br /> *[[Making Heatmaps]]<br /> *[[One way ANOVA in R]]<br /> *[[P-Value adjustment for multiple comparisons]]<br /> *[[PCA-Utils]]<br /> *[[NMR Tube Deep Cleaning]]<br /> *[[Noise Removal for PCA]]<br /> *[[Weighted Linear Least Squares]]<br /> *[[Serum Preparation for 1D NMR]]<br /> *[[Whole Blood Preparation for 1D NMR]]<br /> *[[Urine Preparation for 1D NMR]]<br /> *[[Cell Culture Preparation for 1D NMR]]<br /> *[[LC-MS metabolomics guide-CIBC collaborations]]<br /> <br /> ''Safety and Inspections''<br /> *[[Lab Responsibilities]]<br /> *[[Inspection Checklist]]<br /> *[[Safety Contacts, Resources]]<br /> <br /> ''Demos''<br /> *[[Peroxide Clock]]<br /> *[[Traffic Light Reaction]]<br /> *[[Orange Juice Clock]]<br /> *[[Gummy Bear Freeze]]<br /> *[[Batteries]]<br /> *[[Rocket Launcher]]<br /> *[[Women in Science: Checklist]]<br /> *[[Maxey Day: Checklist]]</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=Cell_Culture_Preparation_for_1D_NMR&diff=721 2021-01-06T17:48:27Z

<p>Acrook: Created page with &quot;All samples should be kept on ice or at 4 oC during sample preparation or handling. Samples should be stored at -80 oC, but, ideally, samples should be immediately analyzed. I...&quot;</p> <hr /> <div>All samples should be kept on ice or at 4 oC during sample preparation or handling. Samples should be stored at -80 oC, but, ideally, samples should be immediately analyzed. In addition to keeping samples cold, there are four other issues that are critical to the successful preparation of metabolomics samples: (1) speed, (2) consistency, (3) random processing of samples, and (4) the efficient removal of all biomolecules and cell debris [8]. The processing of all metabolomics samples should proceed as quickly as possible while minimizing any loss in quality. Metabolites can chemically degrade or transform within milliseconds due to enzymatic activity, oxidation, chemical instability, or any number of other chemical processes [35]. Accordingly, rapidly inactivating and removing all biomolecules and cell debris (usually through methanol/ethanol precipitation) that may transform or bind a metabolite is a necessary step of the protocol (see Notes 9). <br /> Note: Keep methanol and water on ice throughout procedure!! Keep samples on ice as much as possible. <br /> ----<br /> 1. All media is collected. Media is spun at 300g for 5 min to pellet any derby or cells and transfered to new tube(s). 500uL of the media is reserved for metabolomic analysis. Save 1mL media separately for reserve analysis. <br /> <br /> 2. Cells are washed twice with 5 mL of PBS to remove debris. Discard the wash.<br /> <br /> 3. Lyse and quench cells with 1 mL of pre-chilled methanol at -20 oC. Incubate cells at -80 °C for 15 min.<br /> <br /> 4. Using a cell scraper, cell debris and methanol is detached and collected in a 2 mL microcentrifuge tube. Confirm cell detachment using a microscope and repeat lyse and quenching if necessary.<br /> <br /> 5. 2 mL microcentrifuge tube is centrifuged for 5 min at 15,000 g and 4 °C to pellet the cell debris.<br /> <br /> 6. Supernatant collected and transfered to a new 2 mL microcentrifuge tube.<br /> <br /> 7. Metabolome extraction is repeated by adding 0.5 mL of an 80%/20% mixture of methanol/water kept at -20°C to the cell pellet. <br /> <br /> 8. Centrifuge the cell pellet with the extraction solvent for 5 min at 15,000 g at 4 °C to pellet the cell debris.<br /> <br /> 9. Supernatant collected and transfered it to the 2 mL microcentrifuge tube containing the original methanol extract. Combine the two extraction supernatants into a single tube. <br /> <br /> 10. Metabolome extraction is repeated a third time by adding 0.5 mL of ice cold water to the cell pellet.<br /> <br /> 11. Cell pellet is centrifuged with the extraction solvent for 5 min at 15,000 g at 4 °C to pellet the cell debris.<br /> <br /> 12. Supernatant collected and transfered it to the 2 mL microcentrifuge tube containing the two previous extraction supernatants. Combine the three extraction supernatants into a single tube.<br /> <br /> Note: If supernatant exceeds 1.5mL keep samples split and concentrate sample down in liophilizer and combining before either is fully dry (partially lyophile) <br /> <br /> 13. Sample split into two 2 mL Eppendorf tube. Aliquot 100 uL for MS analysis and the remainder of the sample is used for NMR analysis.<br /> <br /> 14. Pellet stored. <br /> <br /> 15. Samples are snap frozen in Liquid Nitrogen and freeze dried to remove methanol by speed vacuum centrifugation (SpeedVac R Plus, Savant) and water by lyophilization using FreeZone™ (Labconco, Kansas City, MO) for 24 hours and stored at -20°C until NMR analysis.</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=Category:Protocols&diff=720 2021-01-06T17:40:59Z

<p>Acrook: </p> <hr /> <div>''General Maintenance''<br /> *[[Changing the high pressure dewar]]<br /> *[[Filling a Magnet with Nitrogen]]<br /> *[[Autoclaving Laboratory Glassware and Media]]<br /> *[[Chemical Disinfection of Glassware]]<br /> *[[Requesting Balance Calibration]]<br /> *[[Requesting Pipette Calibration]]<br /> *[[Using the UV-Vis]]<br /> *[[Using and Maintaining pH Meter]]<br /> *[[-80 Freezer Storage and Maintenance]]<br /> *[[Freeze Dryer Maintenance]]<br /> *[[Lab Notebook Guidelines]]<br /> *[[Sample Barcoding]]<br /> <br /> ''Protein Preparation''<br /> *[[Buffer Exchange and Solution Concentration]]<br /> *[[Finding a Protein Target on the NESG website]]<br /> *[[Choosing a Plasmid]]<br /> *[[Plasmid Purification and Transformation Protocol]]<br /> *[[Creating Stock Cultures of Bacteria]]<br /> *[[Luria-Bertani Media]]<br /> *[[M9 Minimal Media]]<br /> *[[Protein Overexpression and Extraction]]<br /> *[[SDS-PAGE Protocol]]<br /> *[[Running a Cobalt Affinity Column]]<br /> *[[Dialysis]]<br /> *[[Centrifugal Protein Concentration and Buffer Exchange]]<br /> *[[Using the Stirred Cell Concentrator]]<br /> <br /> ''Data Collection''<br /> *[[Gap Sampling]]<br /> *[[Water Suppression with presaturation pulses (zgpr/zgcppr]]<br /> *[[Non-uniform Sampling]]<br /> *[[Collecting a 15N Edited HSQC]]<br /> *[[Collecting CEST Data]]<br /> <br /> ''Data Processing and Analysis''<br /> *[[Analysis of 1D Line-Broadening Screen]]<br /> *[[FastModelFree]]<br /> *[[2D NMR Analysis (CCPNMR)]]<br /> *[[1H NMR Analysis (SIMCA)]]<br /> *[[1H NMR Analysis (ACDLab)]]<br /> *[[Processing CEST Data]]<br /> *[[Titration Data Analysis in nmrPipe]]<br /> *[[Non-Uniform Sampling]]<br /> *[[NMRFAM-SPARKY Guide]]<br /> *[[NMRFAM-SPARKY: Automated Peak Assignment]]<br /> *[[NMR Processing in Linux and Windows]]<br /> *[[Sample Collection and Processing for Protein Backbone Assignments]]<br /> *[[Example Scripts for NMRPipe Processing]]<br /> <br /> ''Miscellaneous''<br /> *[[Agarose Gel]]<br /> *[[700 MHz NMR checklist]]<br /> *[[500 MHz NMR checklist]]<br /> *[[1D Macro]]<br /> *[[Setting Up a Virtual Screen with AutoDock]]<br /> *[[Simple Protein Crosslinking]]<br /> *[[1D NMR Titrations]]<br /> <br /> Cell Culturing<br /> *[[Cell Culturing Dr. Franco Lab]]<br /> <br /> ''Metabolomics''<br /> *[[MetPa for metabolomics]]<br /> *[[Making Heatmaps]]<br /> *[[Metabolite Extraction]]<br /> *[[One way ANOVA in R]]<br /> *[[P-Value adjustment for multiple comparisons]]<br /> *[[PCA-Utils]]<br /> *[[NMR Tube Deep Cleaning]]<br /> *[[Noise Removal for PCA]]<br /> *[[Weighted Linear Least Squares]]<br /> *[[Serum Preparation for 1D NMR]]<br /> *[[Whole Blood Preparation for 1D NMR]]<br /> *[[Urine Preparation for 1D NMR]]<br /> *[[Cell Culture Preparation for 1D NMR]]<br /> *[[LC-MS metabolomics guide-CIBC collaborations]]<br /> <br /> ''Safety and Inspections''<br /> *[[Lab Responsibilities]]<br /> *[[Inspection Checklist]]<br /> *[[Safety Contacts, Resources]]<br /> <br /> ''Demos''<br /> *[[Peroxide Clock]]<br /> *[[Traffic Light Reaction]]<br /> *[[Orange Juice Clock]]<br /> *[[Gummy Bear Freeze]]<br /> *[[Batteries]]<br /> *[[Rocket Launcher]]<br /> *[[Women in Science: Checklist]]<br /> *[[Maxey Day: Checklist]]</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=Whole_Blood_Preparation_for_1D_NMR&diff=719 2021-01-06T17:39:08Z

<p>Acrook: Created page with &quot;1. Blood samples are first aliquoted 2. Proteins are precipitated by the addition of twice the amount of cold methanol purged of oxygen for 30 minutes by nitrogen gas. 3. A...&quot;</p> <hr /> <div>1. Blood samples are first aliquoted<br /> <br /> 2. Proteins are precipitated by the addition of twice the amount of cold methanol purged of oxygen for 30 minutes by nitrogen gas. <br /> <br /> 3. Antibacterial NaN3 is added 2.0% by volume to avoid any bacterial growth<br /> <br /> 4. The 1:2 mixture of serum: solvent is then vortexed for 10 seconds<br /> <br /> 5. Samples are then sonicated in a water bath for 10 min at 4°C, followed by incubation at -20°C for 20 minutes<br /> <br /> 6. Samples are diluted with 600 μL H2O and thoroughly mixed by pipette followed by centrifugation at 14,000 rpm for 30 min at 4°C to pellet cell debris<br /> <br /> 7. Supernatant is collected and divided for NMR and MS analysis, 80/20% respectively. Samples are snap frozen in Liquid Nitrogen and freeze dried to remove methanol by speed vacuum centrifugation (SpeedVac R Plus, Savant) and water by lyophilization using FreeZone™ (Labconco, Kansas City, MO) for 24 hours and stored at -20°C until NMR analysis.</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=Category:Protocols&diff=718 2021-01-06T17:37:27Z

<p>Acrook: </p> <hr /> <div>''General Maintenance''<br /> *[[Changing the high pressure dewar]]<br /> *[[Filling a Magnet with Nitrogen]]<br /> *[[Autoclaving Laboratory Glassware and Media]]<br /> *[[Chemical Disinfection of Glassware]]<br /> *[[Requesting Balance Calibration]]<br /> *[[Requesting Pipette Calibration]]<br /> *[[Using the UV-Vis]]<br /> *[[Using and Maintaining pH Meter]]<br /> *[[-80 Freezer Storage and Maintenance]]<br /> *[[Freeze Dryer Maintenance]]<br /> *[[Lab Notebook Guidelines]]<br /> *[[Sample Barcoding]]<br /> <br /> ''Protein Preparation''<br /> *[[Buffer Exchange and Solution Concentration]]<br /> *[[Finding a Protein Target on the NESG website]]<br /> *[[Choosing a Plasmid]]<br /> *[[Plasmid Purification and Transformation Protocol]]<br /> *[[Creating Stock Cultures of Bacteria]]<br /> *[[Luria-Bertani Media]]<br /> *[[M9 Minimal Media]]<br /> *[[Protein Overexpression and Extraction]]<br /> *[[SDS-PAGE Protocol]]<br /> *[[Running a Cobalt Affinity Column]]<br /> *[[Dialysis]]<br /> *[[Centrifugal Protein Concentration and Buffer Exchange]]<br /> *[[Using the Stirred Cell Concentrator]]<br /> <br /> ''Data Collection''<br /> *[[Gap Sampling]]<br /> *[[Water Suppression with presaturation pulses (zgpr/zgcppr]]<br /> *[[Non-uniform Sampling]]<br /> *[[Collecting a 15N Edited HSQC]]<br /> *[[Collecting CEST Data]]<br /> <br /> ''Data Processing and Analysis''<br /> *[[Analysis of 1D Line-Broadening Screen]]<br /> *[[FastModelFree]]<br /> *[[2D NMR Analysis (CCPNMR)]]<br /> *[[1H NMR Analysis (SIMCA)]]<br /> *[[1H NMR Analysis (ACDLab)]]<br /> *[[Processing CEST Data]]<br /> *[[Titration Data Analysis in nmrPipe]]<br /> *[[Non-Uniform Sampling]]<br /> *[[NMRFAM-SPARKY Guide]]<br /> *[[NMRFAM-SPARKY: Automated Peak Assignment]]<br /> *[[NMR Processing in Linux and Windows]]<br /> *[[Sample Collection and Processing for Protein Backbone Assignments]]<br /> *[[Example Scripts for NMRPipe Processing]]<br /> <br /> ''Miscellaneous''<br /> *[[Agarose Gel]]<br /> *[[700 MHz NMR checklist]]<br /> *[[500 MHz NMR checklist]]<br /> *[[1D Macro]]<br /> *[[Setting Up a Virtual Screen with AutoDock]]<br /> *[[Simple Protein Crosslinking]]<br /> *[[1D NMR Titrations]]<br /> <br /> Cell Culturing<br /> *[[Cell Culturing Dr. Franco Lab]]<br /> <br /> ''Metabolomics''<br /> *[[MetPa for metabolomics]]<br /> *[[Making Heatmaps]]<br /> *[[Metabolite Extraction]]<br /> *[[One way ANOVA in R]]<br /> *[[P-Value adjustment for multiple comparisons]]<br /> *[[PCA-Utils]]<br /> *[[NMR Tube Deep Cleaning]]<br /> *[[Noise Removal for PCA]]<br /> *[[Weighted Linear Least Squares]]<br /> *[[Serum Preparation for 1D NMR]]<br /> *[[Whole Blood Preparation for 1D NMR]]<br /> *[[Urine Preparation for 1D NMR]]<br /> *[[LC-MS metabolomics guide-CIBC collaborations]]<br /> <br /> ''Safety and Inspections''<br /> *[[Lab Responsibilities]]<br /> *[[Inspection Checklist]]<br /> *[[Safety Contacts, Resources]]<br /> <br /> ''Demos''<br /> *[[Peroxide Clock]]<br /> *[[Traffic Light Reaction]]<br /> *[[Orange Juice Clock]]<br /> *[[Gummy Bear Freeze]]<br /> *[[Batteries]]<br /> *[[Rocket Launcher]]<br /> *[[Women in Science: Checklist]]<br /> *[[Maxey Day: Checklist]]</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=Urine_Preparation_for_1D_NMR&diff=717 2021-01-06T17:36:42Z

<p>Acrook: Created page with &quot;1. Urine samples are aliquoted and centrifuged at 14,000 × rpm for 10 min to pellet debris 2. Supernatant samples are collected and snap frozen in Liquid Nitrogen and freeze...&quot;</p> <hr /> <div>1. Urine samples are aliquoted and centrifuged at 14,000 × rpm for 10 min to pellet debris<br /> <br /> 2. Supernatant samples are collected and snap frozen in Liquid Nitrogen and freeze dried to remove methanol by speed vacuum centrifugation (SpeedVac R Plus, Savant) and water by lyophilization using FreeZone™ (Labconco, Kansas City, MO) for 24 hours and stored at -20°C until NMR and MS analysis. <br /> <br /> Note: Methanol extration used in serum preperation can be used to minimize protein content and urea peak in NMR analysis.</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=Serum_Preparation_for_1D_NMR&diff=716 2021-01-06T17:34:36Z

<p>Acrook: Created page with &quot;1. Serum sample are first aliquoted 2. Proteins are precipitated by the addition of twice the amount of methanol as sample 3. Antibacterial NaN3 is added 2.0% by volume to a...&quot;</p> <hr /> <div>1. Serum sample are first aliquoted<br /> <br /> 2. Proteins are precipitated by the addition of twice the amount of methanol as sample<br /> <br /> 3. Antibacterial NaN3 is added 2.0% by volume to avoid any bacterial growth<br /> <br /> 4. The 1:2 mixture of serum: solvent is then vortexed for 10 seconds<br /> <br /> 5. Samples are incubated at 4°C for 10 minutes<br /> <br /> 6. Next, the samples are centrifuged at 14,000 rpm for 20 mins at 4°C to pellet the proteins<br /> <br /> 7. The supernatant is collected and centrifuged at 14,000 rpm for 5 min a 4°C to pellet any leftover protein<br /> <br /> 8. At this point, the supernatant samples are collected and snap frozen in Liquid Nitrogen and freeze dried to remove methanol by speed vacuum centrifugation (SpeedVac R Plus, Savant) and water by lyophilization using FreeZone™ (Labconco, Kansas City, MO) for at least 24 hours and stored at -20°C until NMR analysis.</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=Cell_Culturing_Dr._Franco_Lab&diff=715 2021-01-06T17:13:51Z

<p>Acrook: Created page with &quot; Important notes: 1. Always wear gloves and lab coat while working with cells 2. Spray ethanol on the gloves before you will contact culture wares 3. After warming up and b...&quot;</p> <hr /> <div><br /> Important notes:<br /> <br /> 1. Always wear gloves and lab coat while working with cells<br /> <br /> 2. Spray ethanol on the gloves before you will contact culture wares<br /> <br /> 3. After warming up and before opening up, the bottles for medium, PBS, antibiotics etc. should be sprayed with ethanol<br /> <br /> 4. Before and after using the biosafety hood, spray ethanol, and especially spray disinfectant after working with virus<br /> <br /> 5. Always use filtered pipet tips for cells <br /> <br /> 6. Avoid creating aerosols, especially while transferring the cells<br /> <br /> 7. Try to use long serological pipets or glass transfer pipets while aspirating medium from culture flasks or 15/50ml centrifuge tubes, or adding medium into, or resuspensing the cells<br /> <br /> 8. Your own clothes sleeve should be shorter than lab coat <br /> <br /> 9. Cells/virus/medium contaminated pipet tips or pipets or culture wares go to the biohazard waste bags, and non-contaminated waste go to general trash can<br /> <br /> 10. Tape the culture wares bag after using it<br /> <br /> 11. Do not warm trypsin, leave it at room temperature for 20min; warm medium no more than 20min <br /> <br /> ----<br /> Medium: <br /> <br /> Base medium DMEM : F12 medium supplement with 10% fetal bovine serum and 1% antibiotics (penicillin-streptomycin (10,000units/ml) and 1% glutamine 2mM final concentration (200mM stock in -20oC, Invitrogen, cat#25030)<br /> 5% CO2 and 37oC incubator<br /> <br /> Initial growth from frozen vial:<br /> <br /> 1. Take one vial of frozen cells from liquid nitrogen tank, thaw it in 37oC and transfer the cells into 10ml pre-warmed medium in a 15ml centrifuge tube before totally thawed. DO NOT ALLOW VIAL TO REMAIN THWAWED FOR LONG PERIODS OF TIME<br /> <br /> 2. Spin at 1300rpm x 5min, room temperature<br /> <br /> 3. Discard the supernatant and resuspend cells in 1ml medium with gently pipet up and down for 4-6 times<br /> <br /> 4. Then transfer cells to a T25 flask with 10ml complete medium <br /> <br /> 5. Change medium every 2 to 3 days<br /> <br /> 6. Wait and see until 80% confluence, then trypsinize and split<br /> <br /> ----<br /> Splitting<br /> <br /> 7. Wash cells twice with PBS, then remove<br /> <br /> 8. Add 1x trypsin-EDTA (0.25% trypsin-0.53mM EDTA) diluted 1:1 with PBS and incubate at 37oC for 3-5min until detach. DO NOT LEAVE CELLS WITH TRYPSIN AFTER THEY HAVE BEEN DETACHED OR OVER 5 MIN<br /> <br /> 9. Add two times the amount of trypsin in fresh medium to neutralize trypsin and gently pipet up and down cells several times<br /> <br /> 10. Transfer cells to a centrifuge tube, and spin down at 1300rpm x 5min<br /> <br /> 11. Discard medium, add 1ml fresh medium and resuspend cells using p1000 pipette. Determine cell density and seed according to the table below.<br /> <br /> 12. Incubate at 37oC culture<br /> <br /> ----<br /> Freezing cells<br /> <br /> 13. Trypsinize cells as above and determine cell density<br /> <br /> 14. Resuspend cells in 10% DMSO 90% fresh medium to adensity of 2 x 106 cells/ml.<br /> <br /> 15. Aliquot 1ml to each cryogenic vial, put in the freeze box (with isopropanol), -80oC for 24hours, then transfer to liquid nitrogen tank for long storage<br /> Counting cells (with trypan blue exclusion)<br /> <br /> 16. After resuspending cells take 20ul cells and transfer them to a clean 0.5ml tube, mix with 20ul trypan blue (dilution factor)<br /> <br /> 17. Take 10-20ul mixture, and add from the gap between cover glass and hemocytometer chamber, until the cells fill the counting area. AVOID BUBBLES<br /> <br /> 18. Count 4 big 16-well squares, get a total number A, then cell density will be:<br /> (A/4) x dilution factor =***x104 cells/ml</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=Lab_Notebook_Guidelines&diff=700 2019-09-30T22:45:52Z

<p>Acrook: </p> <hr /> <div>== General Rules and Regulations ==<br /> <br /> A lab notebook is a legal document! <br /> * All work must be thoroughly and accurately recorded<br /> * Keep the notebook current and up to date<br /> * Lab notebook should be a complete record of ALL of your research efforts<br /> ** Include both successful and unsuccessful experiments or data analysis<br /> ** Even seemingly trivial work done in the lab must be properly recorded<br /> ** Detailed experimental methods only need to be entered ONCE into the lab notebook<br /> *** When repeating the experiment, just refer to the lab notebook page containing the original methods and simply note all modifications to the original protocol.<br /> ** Lab notebooks are not a personal diary<br /> * Lab notebooks should not leave the office or lab <br /> * Lab notebooks do not belong to you. They are the property of the university.<br /> Everything must be neatly written in ink and legible to all readers <br /> * Experiments and analysis should be easily reproducible from only the notebook <br /> Maintain a Table of Contents in the front of each lab notebook <br /> <br /> All documents and figures must be secured on a lab notebook page and within the defined page’s boarders<br /> <br /> All reports, notes, raw data, software, and received samples should be documented and date stamped in the notebook or appendix<br /> * All large results should be included in an appendix (software output or source code, detailed reports, processing scripts, etc.)<br /> *A three-ring binder is an acceptable appendix. <br /> **The binder should be labeled with Name, lab notebook number and appendix number. <br /> **The binder should include paper inserts to provide page numbers, project titles and dates for each appendix entry.<br /> *Location of large results in appendix should be documented in the lab notebook (i.e., page and appendix number should be cross-listed in both lab notebook and appendix)<br /> *A reference to the location (i.e., directory path, instrument, specific computer name) of ALL raw data and digital documentation should be included in the lab notebook <br /> *Physical description and location of ALL samples should be referenced in the lab notebook (including location (i.e, room number, freezer name, dates, name, and abbreviations). <br /> All digital data should be backed up and archived<br /> * Location of archived data should be noted in the lab notebook<br /> As appropriate, a separate notebook may be used for each individual projects<br /> <br /> Every completed lab notebook page must include a signature by the inventor, recorder, and witness<br /> *Inventor and recorder is the person who did the work and recorded the work<br /> *Witness is the person who read, understood, and reviewed the work<br /> Significant unused space should be crossed out with X, initialed and dated<br /> <br /> No pages should be left blank<br /> *All entries should be recorded in chronological order <br /> Outcomes, conclusions, and results of any project good or bad need to be recorded! <br /> *Your documented and dated insights, interpretations or hypothesis are critical to supporting any patents or intellectual property.<br /> *Also critical to establishing your ownership of your thesis work <br /> <br /> == Lab Notebook Violations == <br /> <br /> *Do not tear out pages <br /> *Do not leave blank pages between entries <br /> *Everything should be recorded in chorological order <br /> *Do not use white out or anything erasable <br /> *Strike through all mistakes, do not make the mistake illegible<br /> *Do not write sloppily, or use vague terms<br /> **What is written in the notebook should be legible and understandable to anyone reading the notebook; and the experiments easily reproduced by reading the lab notebook <br /> *Do not make changes to a lab notebook after it has been signed and witnessed.<br /> **If a mistake needs to be corrected, then the change should be dated and initialed <br /> *Do not keep loose paper consisting of notes, data or figures shoved between notebook pages<br /> *Do not make entries into your lab notebook weeks or months after you actually completed the experiments or data analysis<br /> **Record your experiments and data analysis as you are doing the work and obtaining the results <br /> *Avoid spills, ripping or tearing pages, or anything that makes the lab notebook page unreadable<br /> *Do not write long rambling entries, be succinct and precise. <br /> **A series of numbered steps or bullet points is preferable<br /> *Do not include confusing or uninterpretable figures or tables<br /> **Make sure all tables and figures are properly, labeled, annotated and explained<br /> ***Axis labels with units<br /> ***All sample symbols/colors identified<br /> ***Quality factors are included (R2, Q2, p-values, etc.)<br /> ***Explain how the data was fit or modeled, the validity of the fit/model <br /> <br /> == Completed lab notebook page should contain == <br /> <br /> All sections should be labeled, separated and easily distinguishable <br /> <br /> *Title <br /> *Purpose or Objective <br /> *Description of Experiment (i.e., methods and materials)<br /> **Note the name and versions of any software or instrumentation used<br /> *Sample preparation <br /> *Instrument description and set up<br /> *Results<br /> **Appendix may be added for extended results including ligand libraries, metabolite lists, software code, software output, processing scripts, peak lists, chemical shift assignments, PDB files reports, or published work<br /> **Essentially, any result or outcome that needs to be recorded, but cannot easily fit on a single lab notebook page. <br /> *Figures and figure legends <br /> *Preliminary conclusions and comments<br /> **Record any insights, thoughts or hypothesis<br /> **Include any relevant literature citations <br /> *Author Signature and date <br /> *Witness Signature and date</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=Lab_Notebook_Guidelines&diff=699 2019-09-30T22:34:30Z

<p>Acrook: /* Completed Lab notebook page should contain */</p> <hr /> <div>A lab notebook is a legal document! <br /> * All work must be thoroughly and accurately recorded<br /> * Keep the notebook current and up to date<br /> * Lab notebook should be a complete record of ALL of your research efforts<br /> ** Include both successful and unsuccessful experiments or data analysis<br /> ** Even seemingly trivial work done in the lab must be properly recorded<br /> ** Detailed experimental methods only need to be entered ONCE into the lab notebook<br /> *** When repeating the experiment, just refer to the lab notebook page containing the original methods and simply note all modifications to the original protocol.<br /> ** Lab notebooks are not a personal diary<br /> * Lab notebooks should not leave the office or lab <br /> * Lab notebooks do not belong to you. They are the property of the university.<br /> Everything must be neatly written in ink and legible to all readers <br /> * Experiments and analysis should be easily reproducible from only the notebook <br /> Maintain a Table of Contents in the front of each lab notebook <br /> <br /> All documents and figures must be secured on a lab notebook page and within the defined page’s boarders<br /> <br /> All reports, notes, raw data, software, and received samples should be documented and date stamped in the notebook or appendix<br /> * All large results should be included in an appendix (software output or source code, detailed reports, processing scripts, etc.)<br /> *A three-ring binder is an acceptable appendix. <br /> **The binder should be labeled with Name, lab notebook number and appendix number. <br /> **The binder should include paper inserts to provide page numbers, project titles and dates for each appendix entry.<br /> *Location of large results in appendix should be documented in the lab notebook (i.e., page and appendix number should be cross-listed in both lab notebook and appendix)<br /> *A reference to the location (i.e., directory path, instrument, specific computer name) of ALL raw data and digital documentation should be included in the lab notebook <br /> *Physical description and location of ALL samples should be referenced in the lab notebook (including location (i.e, room number, freezer name, dates, name, and abbreviations). <br /> All digital data should be backed up and archived<br /> * Location of archived data should be noted in the lab notebook<br /> As appropriate, a separate notebook may be used for each individual projects<br /> <br /> Every completed lab notebook page must include a signature by the inventor, recorder, and witness<br /> *Inventor and recorder is the person who did the work and recorded the work<br /> *Witness is the person who read, understood, and reviewed the work<br /> Significant unused space should be crossed out with X, initialed and dated<br /> <br /> No pages should be left blank<br /> *All entries should be recorded in chronological order <br /> Outcomes, conclusions, and results of any project good or bad need to be recorded! <br /> *Your documented and dated insights, interpretations or hypothesis are critical to supporting any patents or intellectual property.<br /> *Also critical to establishing your ownership of your thesis work <br /> <br /> == Lab Notebook Violations == <br /> *Do not tear out pages <br /> *Do not leave blank pages between entries <br /> *Everything should be recorded in chorological order <br /> *Do not use white out or anything erasable <br /> *Strike through all mistakes, do not make the mistake illegible<br /> *Do not write sloppily, or use vague terms<br /> **What is written in the notebook should be legible and understandable to anyone reading the notebook; and the experiments easily reproduced by reading the lab notebook <br /> *Do not make changes to a lab notebook after it has been signed and witnessed.<br /> **If a mistake needs to be corrected, then the change should be dated and initialed <br /> *Do not keep loose paper consisting of notes, data or figures shoved between notebook pages<br /> *Do not make entries into your lab notebook weeks or months after you actually completed the experiments or data analysis<br /> **Record your experiments and data analysis as you are doing the work and obtaining the results <br /> *Avoid spills, ripping or tearing pages, or anything that makes the lab notebook page unreadable<br /> *Do not write long rambling entries, be succinct and precise. <br /> **A series of numbered steps or bullet points is preferable<br /> *Do not include confusing or uninterpretable figures or tables<br /> **Make sure all tables and figures are properly, labeled, annotated and explained<br /> ***Axis labels with units<br /> ***All sample symbols/colors identified<br /> ***Quality factors are included (R2, Q2, p-values, etc.)<br /> ***Explain how the data was fit or modeled, the validity of the fit/model <br /> <br /> == Completed lab notebook page should contain == <br /> All sections should be labeled, separated and easily distinguishable <br /> <br /> *Title <br /> *Purpose or Objective <br /> *Description of Experiment (i.e., methods and materials)<br /> **Note the name and versions of any software or instrumentation used<br /> *Sample preparation <br /> *Instrument description and set up<br /> *Results<br /> **Appendix may be added for extended results including ligand libraries, metabolite lists, software code, software output, processing scripts, peak lists, chemical shift assignments, PDB files reports, or published work<br /> **Essentially, any result or outcome that needs to be recorded, but cannot easily fit on a single lab notebook page. <br /> *Figures and figure legends <br /> *Preliminary conclusions and comments<br /> **Record any insights, thoughts or hypothesis<br /> **Include any relevant literature citations <br /> *Author Signature and date <br /> *Witness Signature and date</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=Lab_Notebook_Guidelines&diff=698 2019-09-30T22:34:08Z

<p>Acrook: Created page with &quot;A lab notebook is a legal document! * All work must be thoroughly and accurately recorded * Keep the notebook current and up to date * Lab notebook should be a complete recor...&quot;</p> <hr /> <div>A lab notebook is a legal document! <br /> * All work must be thoroughly and accurately recorded<br /> * Keep the notebook current and up to date<br /> * Lab notebook should be a complete record of ALL of your research efforts<br /> ** Include both successful and unsuccessful experiments or data analysis<br /> ** Even seemingly trivial work done in the lab must be properly recorded<br /> ** Detailed experimental methods only need to be entered ONCE into the lab notebook<br /> *** When repeating the experiment, just refer to the lab notebook page containing the original methods and simply note all modifications to the original protocol.<br /> ** Lab notebooks are not a personal diary<br /> * Lab notebooks should not leave the office or lab <br /> * Lab notebooks do not belong to you. They are the property of the university.<br /> Everything must be neatly written in ink and legible to all readers <br /> * Experiments and analysis should be easily reproducible from only the notebook <br /> Maintain a Table of Contents in the front of each lab notebook <br /> <br /> All documents and figures must be secured on a lab notebook page and within the defined page’s boarders<br /> <br /> All reports, notes, raw data, software, and received samples should be documented and date stamped in the notebook or appendix<br /> * All large results should be included in an appendix (software output or source code, detailed reports, processing scripts, etc.)<br /> *A three-ring binder is an acceptable appendix. <br /> **The binder should be labeled with Name, lab notebook number and appendix number. <br /> **The binder should include paper inserts to provide page numbers, project titles and dates for each appendix entry.<br /> *Location of large results in appendix should be documented in the lab notebook (i.e., page and appendix number should be cross-listed in both lab notebook and appendix)<br /> *A reference to the location (i.e., directory path, instrument, specific computer name) of ALL raw data and digital documentation should be included in the lab notebook <br /> *Physical description and location of ALL samples should be referenced in the lab notebook (including location (i.e, room number, freezer name, dates, name, and abbreviations). <br /> All digital data should be backed up and archived<br /> * Location of archived data should be noted in the lab notebook<br /> As appropriate, a separate notebook may be used for each individual projects<br /> <br /> Every completed lab notebook page must include a signature by the inventor, recorder, and witness<br /> *Inventor and recorder is the person who did the work and recorded the work<br /> *Witness is the person who read, understood, and reviewed the work<br /> Significant unused space should be crossed out with X, initialed and dated<br /> <br /> No pages should be left blank<br /> *All entries should be recorded in chronological order <br /> Outcomes, conclusions, and results of any project good or bad need to be recorded! <br /> *Your documented and dated insights, interpretations or hypothesis are critical to supporting any patents or intellectual property.<br /> *Also critical to establishing your ownership of your thesis work <br /> <br /> == Lab Notebook Violations == <br /> *Do not tear out pages <br /> *Do not leave blank pages between entries <br /> *Everything should be recorded in chorological order <br /> *Do not use white out or anything erasable <br /> *Strike through all mistakes, do not make the mistake illegible<br /> *Do not write sloppily, or use vague terms<br /> **What is written in the notebook should be legible and understandable to anyone reading the notebook; and the experiments easily reproduced by reading the lab notebook <br /> *Do not make changes to a lab notebook after it has been signed and witnessed.<br /> **If a mistake needs to be corrected, then the change should be dated and initialed <br /> *Do not keep loose paper consisting of notes, data or figures shoved between notebook pages<br /> *Do not make entries into your lab notebook weeks or months after you actually completed the experiments or data analysis<br /> **Record your experiments and data analysis as you are doing the work and obtaining the results <br /> *Avoid spills, ripping or tearing pages, or anything that makes the lab notebook page unreadable<br /> *Do not write long rambling entries, be succinct and precise. <br /> **A series of numbered steps or bullet points is preferable<br /> *Do not include confusing or uninterpretable figures or tables<br /> **Make sure all tables and figures are properly, labeled, annotated and explained<br /> ***Axis labels with units<br /> ***All sample symbols/colors identified<br /> ***Quality factors are included (R2, Q2, p-values, etc.)<br /> ***Explain how the data was fit or modeled, the validity of the fit/model <br /> <br /> == Completed Lab notebook page should contain == <br /> All sections should be labeled, separated and easily distinguishable <br /> <br /> *Title <br /> *Purpose or Objective <br /> *Description of Experiment (i.e., methods and materials)<br /> **Note the name and versions of any software or instrumentation used<br /> *Sample preparation <br /> *Instrument description and set up<br /> *Results<br /> **Appendix may be added for extended results including ligand libraries, metabolite lists, software code, software output, processing scripts, peak lists, chemical shift assignments, PDB files reports, or published work<br /> **Essentially, any result or outcome that needs to be recorded, but cannot easily fit on a single lab notebook page. <br /> *Figures and figure legends <br /> *Preliminary conclusions and comments<br /> **Record any insights, thoughts or hypothesis<br /> **Include any relevant literature citations <br /> *Author Signature and date <br /> *Witness Signature and date</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=Category:Protocols&diff=697 2019-09-30T22:17:31Z

<p>Acrook: </p> <hr /> <div>''General Maintenance''<br /> *[[Changing the high pressure dewar]]<br /> *[[Filling a Magnet with Nitrogen]]<br /> *[[Autoclaving Laboratory Glassware and Media]]<br /> *[[Chemical Disinfection of Glassware]]<br /> *[[Requesting Balance Calibration]]<br /> *[[Requesting Pipette Calibration]]<br /> *[[Using the UV-Vis]]<br /> *[[Using and Maintaining pH Meter]]<br /> *[[-80 Freezer Storage and Maintenance]]<br /> *[[Freeze Dryer Maintenance]]<br /> *[[Lab Notebook Guidelines]]<br /> <br /> ''Protein Preparation''<br /> *[[Buffer Exchange and Solution Concentration]]<br /> *[[Finding a Protein Target on the NESG website]]<br /> *[[Choosing a Plasmid]]<br /> *[[Plasmid Purification and Transformation Protocol]]<br /> *[[Creating Stock Cultures of Bacteria]]<br /> *[[Luria-Bertani Media]]<br /> *[[M9 Minimal Media]]<br /> *[[Protein Overexpression and Extraction]]<br /> *[[SDS-PAGE Protocol]]<br /> *[[Running a Cobalt Affinity Column]]<br /> *[[Dialysis]]<br /> *[[Centrifugal Protein Concentration and Buffer Exchange]]<br /> *[[Using the Stirred Cell Concentrator]]<br /> <br /> ''Data Collection''<br /> *[[Gap Sampling]]<br /> *[[Water Suppression with presaturation pulses (zgpr/zgcppr]]<br /> *[[Non-uniform Sampling]]<br /> *[[Collecting a 15N Edited HSQC]]<br /> *[[Collecting CEST Data]]<br /> <br /> ''Data Processing and Analysis''<br /> *[[Analysis of 1D Line-Broadening Screen]]<br /> *[[FastModelFree]]<br /> *[[2D NMR Analysis (CCPNMR)]]<br /> *[[1H NMR Analysis (SIMCA)]]<br /> *[[1H NMR Analysis (ACDLab)]]<br /> *[[Processing CEST Data]]<br /> *[[Titration Data Analysis in nmrPipe]]<br /> *[[Non-Uniform Sampling]]<br /> *[[NMRFAM-SPARKY Guide]]<br /> *[[NMRFAM-SPARKY: Automated Peak Assignment]]<br /> *[[NMR Processing in Linux and Windows]]<br /> *[[Sample Collection and Processing for Protein Backbone Assignments]]<br /> *[[Example Scripts for NMRPipe Processing]]<br /> <br /> ''Miscellaneous''<br /> *[[Agarose Gel]]<br /> *[[700 MHz NMR checklist]]<br /> *[[500 MHz NMR checklist]]<br /> *[[1D Macro]]<br /> *[[Setting Up a Virtual Screen with AutoDock]]<br /> *[[Simple Protein Crosslinking]]<br /> *[[1D NMR Titrations]]<br /> <br /> Cell Culturing<br /> *[[Cell Culturing Dr. Franco Lab]]<br /> <br /> ''Metabolomics''<br /> *[[MetPa for metabolomics]]<br /> *[[Making Heatmaps]]<br /> *[[Metabolite Extraction]]<br /> *[[One way ANOVA in R]]<br /> *[[P-Value adjustment for multiple comparisons]]<br /> *[[PCA-Utils]]<br /> *[[NMR Tube Deep Cleaning]]<br /> *[[Noise Removal for PCA]]<br /> *[[Weighted Linear Least Squares]]<br /> *[[Serum Preparation for 1D NMR]]<br /> *[[Urine Preparation for 1D NMR]]<br /> <br /> ''Safety and Inspections''<br /> *[[Lab Responsibilities]]<br /> *[[Inspection Checklist]]<br /> *[[Safety Contacts, Resources]]<br /> <br /> ''Demos''<br /> *[[Peroxide Clock]]<br /> *[[Traffic Light Reaction]]<br /> *[[Orange Juice Clock]]<br /> *[[Gummy Bear Freeze]]<br /> *[[Batteries]]<br /> *[[Rocket Launcher]]<br /> *[[Women in Science: Checklist]]<br /> *[[Maxey Day: Checklist]]</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=-80_Freezer_Storage_and_Maintenance&diff=696 2019-09-13T12:23:22Z

<p>Acrook: </p> <hr /> <div><br /> == Freezer Storage ==<br /> <br /> <br /> Every lab member is assigned a section of 10x10 freezer boxes on shelves 1 and 4. In addition, every member has an assigned overflow box for all samples on shelves 2 or 3. All samples and the sample container should be labeled with the owner’s initials, date, and sample contents. Be cautious and quick when opening the freezer door, best practice for retrieving samples is to keep the freezer door open less then 2 min at a time. This helps to keep a consistent temperature in the freezer and keep the frost levels to a minimum. <br /> <br /> == -80 Freezer Logbook ==<br /> <br /> All boxes stored in the -80 Freezer should be identified in the “-80 Freezer Logbook”. When a box is added to either of the freezer racks 1 or 4, mark the corresponding spot with the appropriate color assigned to that lab member. All empty boxes can be left blank. The link for the “-80 Freezer Logbook” can be found here [https://docs.google.com/spreadsheets/d/1fgMQraoWun8AAsPiXyh6hMHEwWZ25V5aJiSUR2LW17k/edit#gid=0]. <br /> <br /> == General Rules of the -80 Freezer == <br /> <br /> • Close the freezer door immediately when the alarm go off. <br /> <br /> • Do not relocate boxes or samples of other lab members without their consent.<br /> <br /> • Do not leave loose samples or boxes in open spaces of the fridge or freezer (they will get lost)<br /> <br /> • Do not store bulk chemicals in the -80 freezer. All chemicals should be stored in the chemical fridge and freezer only.<br /> <br /> == Freezer Maintenance == <br /> <br /> The -80 Freezer in lab will be emptied and defrosted once a year for routine maintenance. All samples not located in the proper locations specified above with be discarded. Please check the maintenance log located on the door of the freezer for date of the next defrost. If there are any issues or concerns occur while using the freezer contact the freezer manager immediately.</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=Main_Page&diff=694 2019-08-26T13:54:30Z

<p>Acrook: </p> <hr /> <div>'''Welcome to the BioNMR Wiki Page.'''<br /> <br /> This wiki exists to provide better access to lab protocols for the Powers lab. It is not a replacement for lab notebooks. Feel free to begin documenting new lab protocols or procedures here, or even moving old protocols onto this wiki.<br /> <br /> [[Special:Categories|View All Categories]]<br /> <br /> Commonly used categories:<br /> <br /> * [[:Category:Protocols|Protocols]]<br /> * [[:Category:Bioscreen|Bioscreen]]<br /> * [[:Category:FAST-NMR|FAST-NMR]]<br /> * [[:Category:Molecular Docking|Molecular Docking]]<br /> * [[:Category:Metabolomics|Metabolomics]]<br /> * [[:Category:Maxey Demos|Maxey Demos]]<br /> * [[:Category:Protein expression|Protein expression]]<br /> * [[:Category:SMACMS|SMACMS]]<br /> * [[:Category:Lab Safety | Lab Safety]]<br /> * [[:Category:Cell culture | culture and passage cells]]<br /> * [[:Protein Software]]<br /> <br /> <br /> And, very likely, an unpopular category:<br /> * [[:Category:Sysadmin | System Administration]]</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=Freeze_Dryer_Maintenance&diff=693 2019-08-26T13:35:37Z

<p>Acrook: Created page with &quot; == Maintenance for Freeze Dryer System == When the Freeze Dryer has accumulated 1000 operating hours, an alarm will flash on the display menu. Press and hold SELECT for 5 s...&quot;</p> <hr /> <div><br /> == Maintenance for Freeze Dryer System ==<br /> <br /> <br /> When the Freeze Dryer has accumulated 1000 operating hours, an alarm will flash on the display menu. Press and hold SELECT for 5 seconds until the error has cleared. Check the oil at this point, if the oil is clean and clean then the system is fine to operate as usual. If the oil is cloudy and/or contains particles replace the pump oil. <br /> <br /> == Replacing Pump Oil ==<br /> <br /> Use Edwards Ultra Grad Pump Oil (Catalog Number H11025015) to ensure an efficient system. Open the exit valve located on the lower right-hand side of the pump and allow the used pump oil to drain into a sealable receptacle. This receptacle will need to be stored and disposed of through EHS. Once the pump is empty of used oil flush the system will new oil and run the pump for 5 to 10 minutes to allow the oil in the pump to warm up. Empty the oil again into the used oil container and seal up the exit value. Fill the pump with clean oil past the safety line and seal up the pump. Ensure that the filter is clean of dried oil and working properly. Filter is located on the upper left-hand corner of the pump.</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=Category:Protocols&diff=692 2019-08-26T13:34:30Z

<p>Acrook: </p> <hr /> <div>''General Maintenance''<br /> *[[Changing the high pressure dewar]]<br /> *[[Filling a Magnet with Nitrogen]]<br /> *[[Autoclaving Laboratory Glassware and Media]]<br /> *[[Chemical Disinfection of Glassware]]<br /> *[[Requesting Balance Calibration]]<br /> *[[Requesting Pipette Calibration]]<br /> *[[Using the UV-Vis]]<br /> *[[Using and Maintaining pH Meter]]<br /> *[[-80 Freezer Storage and Maintenance]]<br /> *[[Freeze Dryer Maintenance]]<br /> <br /> ''Protein Preparation''<br /> *[[Buffer Exchange and Solution Concentration]]<br /> *[[Finding a Protein Target on the NESG website]]<br /> *[[Choosing a Plasmid]]<br /> *[[Plasmid Purification and Transformation Protocol]]<br /> *[[Creating Stock Cultures of Bacteria]]<br /> *[[Luria-Bertani Media]]<br /> *[[M9 Minimal Media]]<br /> *[[Protein Overexpression and Extraction]]<br /> *[[SDS-PAGE Protocol]]<br /> *[[Running a Cobalt Affinity Column]]<br /> *[[Dialysis]]<br /> *[[Centrifugal Protein Concentration and Buffer Exchange]]<br /> *[[Using the Stirred Cell Concentrator]]<br /> <br /> ''Data Collection''<br /> *[[Gap Sampling]]<br /> *[[Water Suppression with presaturation pulses (zgpr/zgcppr]]<br /> *[[Non-uniform Sampling]]<br /> *[[Collecting a 15N Edited HSQC]]<br /> *[[Collecting CEST Data]]<br /> <br /> ''Data Processing and Analysis''<br /> *[[Analysis of 1D Line-Broadening Screen]]<br /> *[[FastModelFree]]<br /> *[[2D NMR Analysis (CCPNMR)]]<br /> *[[1H NMR Analysis (SIMCA)]]<br /> *[[1H NMR Analysis (ACDLab)]]<br /> *[[Processing CEST Data]]<br /> *[[Titration Data Analysis in nmrPipe]]<br /> *[[Non-Uniform Sampling]]<br /> *[[NMRFAM-SPARKY Guide]]<br /> *[[NMRFAM-SPARKY: Automated Peak Assignment]]<br /> *[[NMR Processing in Linux and Windows]]<br /> <br /> ''Miscellaneous''<br /> *[[Agarose Gel]]<br /> *[[700 MHz NMR checklist]]<br /> *[[500 MHz NMR checklist]]<br /> *[[1D Macro]]<br /> *[[Setting Up a Virtual Screen with AutoDock]]<br /> *[[Simple Protein Crosslinking]]<br /> *[[1D NMR Titrations]]<br /> <br /> Cell Culturing<br /> *[[Cell Culturing Dr. Franco Lab]]<br /> <br /> ''Metabolomics''<br /> *[[MetPa for metabolomics]]<br /> *[[Making Heatmaps]]<br /> *[[Metabolite Extraction]]<br /> *[[One way ANOVA in R]]<br /> *[[P-Value adjustment for multiple comparisons]]<br /> *[[PCA-Utils]]<br /> *[[NMR Tube Deep Cleaning]]<br /> *[[Noise Removal for PCA]]<br /> *[[Weighted Linear Least Squares]]<br /> *[[Serum Preparation for 1D NMR]]<br /> *[[Urine Preparation for 1D NMR]]<br /> <br /> ''Safety and Inspections''<br /> *[[Lab Responsibilities]]<br /> *[[Inspection Checklist]]<br /> *[[Safety Contacts, Resources]]<br /> <br /> ''Demos''<br /> *[[Peroxide Clock]]<br /> *[[Traffic Light Reaction]]<br /> *[[Orange Juice Clock]]<br /> *[[Gummy Bear Freeze]]<br /> *[[Batteries]]<br /> *[[Rocket Launcher]]<br /> *[[Women in Science: Checklist]]<br /> *[[Maxey Day: Checklist]]</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=-80_Freezer_Storage_and_Maintenance&diff=689 2019-07-31T16:45:24Z

<p>Acrook: </p> <hr /> <div><br /> == Freezer Storage ==<br /> <br /> <br /> Every lab member is assigned a section of 10x10 freezer boxes on shelves 1 and 4. In addition, every member has an assigned overflow box for all samples on shelves 2 or 3. All samples and the sample container should be labeled with the owner’s initials, date, and sample contents. Be cautious and quick when opening the freezer door, best practice for retrieving samples is to keep the freezer door open less then 2 min at a time. This helps to keep a consistent temperature in the freezer and keep the frost levels to a minimum. <br /> <br /> == -80 Freezer User Logbook ==<br /> <br /> All boxes stored in the -80 Freezer should be identified in the “-80 Freezer Logbook”. When a box is added to either of the freezer racks 1 or 4, mark the corresponding spot with the appropriate color assigned to that lab member. All empty boxes can be left blank. The link for the “-80 Freezer Logbook” can be found here [https://docs.google.com/spreadsheets/d/1fgMQraoWun8AAsPiXyh6hMHEwWZ25V5aJiSUR2LW17k/edit#gid=0]. <br /> <br /> == General Rules of the -80 Freezer == <br /> <br /> • Close the freezer door immediately when the alarm go off. <br /> <br /> • Do not relocate boxes or samples of other lab members without their consent.<br /> <br /> • Do not leave loose samples or boxes in open spaces of the fridge or freezer (they will get lost)<br /> <br /> • Do not store bulk chemicals in the -80 freezer. All chemicals should be stored in the chemical fridge and freezer only.<br /> <br /> == Freezer Maintenance == <br /> <br /> The -80 Freezer in lab will be emptied and defrosted once a year for routine maintenance. All samples not located in the proper locations specified above with be discarded. Please check the maintenance log located on the door of the freezer for date of the next defrost. If there are any issues or concerns occur while using the freezer contact the freezer manager immediately.</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=-80_Freezer_Storage_and_Maintenance&diff=688 2019-07-31T16:44:22Z

<p>Acrook: </p> <hr /> <div><br /> == Freezer Storage ==<br /> <br /> <br /> Every lab member is assigned a section of 10x10 freezer boxes on shelves 1 and 4. In addition, every member has an assigned overflow box for all samples on shelves 2 or 3. All samples and the sample container should be labeled with the owner’s initials, date, and sample contents. Be cautious and quick when opening the freezer door, best practice for retrieving samples is to keep the freezer door open less then 2 min at a time. This helps to keep a consistent temperature in the freezer and keep the frost levels to a minimum. <br /> <br /> '''-80 Freezer User Logbook'''<br /> <br /> All boxes stored in the -80 Freezer should be identified in the “-80 Freezer Logbook”. When a box is added to either of the freezer racks 1 or 4, mark the corresponding spot with the appropriate color assigned to that lab member. All empty boxes can be left blank. The link for the “-80 Freezer Logbook” can be found here [https://docs.google.com/spreadsheets/d/1fgMQraoWun8AAsPiXyh6hMHEwWZ25V5aJiSUR2LW17k/edit#gid=0]. <br /> <br /> '''General Rules of the -80 Freezer''' <br /> <br /> • Close the freezer door immediately when the alarm go off. <br /> <br /> • Do not relocate boxes or samples of other lab members without their consent.<br /> <br /> • Do not leave loose samples or boxes in open spaces of the fridge or freezer (they will get lost)<br /> <br /> • Do not store bulk chemicals in the -80 freezer. All chemicals should be stored in the chemical fridge and freezer only.<br /> <br /> '''Freezer Maintenance''' <br /> <br /> The -80 Freezer in lab will be emptied and defrosted once a year for routine maintenance. All samples not located in the proper locations specified above with be discarded. Please check the maintenance log located on the door of the freezer for date of the next defrost. If there are any issues or concerns occur while using the freezer contact the freezer manager immediately.</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=-80_Freezer_Storage_and_Maintenance&diff=687 2019-07-31T16:43:53Z

<p>Acrook: </p> <hr /> <div><br /> == Freezer Storage ==<br /> <br /> <br /> Every lab member is assigned a section of 10x10 freezer boxes on shelves 1 and 4. In addition, every member has an assigned overflow box for all samples on shelves 2 or 3. All samples and the sample container should be labeled with the owner’s initials, date, and sample contents. Be cautious and quick when opening the freezer door, best practice for retrieving samples is to keep the freezer door open less then 2 min at a time. This helps to keep a consistent temperature in the freezer and keep the frost levels to a minimum. <br /> <br /> '''-80 Freezer User Logbook'''<br /> <br /> All boxes stored in the -80 Freezer should be identified in the “-80 Freezer Logbook”. When a box is added to either of the freezer racks 1 or 4, mark the corresponding spot with the appropriate color assigned to that lab member. All empty boxes can be left blank. The link for the “-80 Freezer Logbook” can be found here [https://docs.google.com/spreadsheets/d/1fgMQraoWun8AAsPiXyh6hMHEwWZ25V5aJiSUR2LW17k/edit#gid=0]. <br /> <br /> '''General Rules of the -80 Freezer''' <br /> <br /> • Close the freezer door immediately when the alarm go off. <br /> • Do not relocate boxes or samples of other lab members without their consent <br /> • Do not leave loose samples or boxes in open spaces of the fridge or freezer (they will get lost)<br /> • Do not store bulk chemicals in the -80 freezer. All chemicals should be stored in the chemical fridge and freezer only.<br /> <br /> '''Freezer Maintenance''' <br /> <br /> The -80 Freezer in lab will be emptied and defrosted once a year for routine maintenance. All samples not located in the proper locations specified above with be discarded. Please check the maintenance log located on the door of the freezer for date of the next defrost. If there are any issues or concerns occur while using the freezer contact the freezer manager immediately.</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=-80_Freezer_Storage_and_Maintenance&diff=686 2019-07-31T16:43:36Z

<p>Acrook: </p> <hr /> <div><br /> == Freezer Storage ==<br /> <br /> <br /> Every lab member is assigned a section of 10x10 freezer boxes on shelves 1 and 4. In addition, every member has an assigned overflow box for all samples on shelves 2 or 3. All samples and the sample container should be labeled with the owner’s initials, date, and sample contents. Be cautious and quick when opening the freezer door, best practice for retrieving samples is to keep the freezer door open less then 2 min at a time. This helps to keep a consistent temperature in the freezer and keep the frost levels to a minimum. <br /> <br /> '''-80 Freezer User Logbook'''<br /> All boxes stored in the -80 Freezer should be identified in the “-80 Freezer Logbook”. When a box is added to either of the freezer racks 1 or 4, mark the corresponding spot with the appropriate color assigned to that lab member. All empty boxes can be left blank. The link for the “-80 Freezer Logbook” can be found here [https://docs.google.com/spreadsheets/d/1fgMQraoWun8AAsPiXyh6hMHEwWZ25V5aJiSUR2LW17k/edit#gid=0]. <br /> <br /> '''General Rules of the -80 Freezer''' <br /> • Close the freezer door immediately when the alarm go off. <br /> • Do not relocate boxes or samples of other lab members without their consent <br /> • Do not leave loose samples or boxes in open spaces of the fridge or freezer (they will get lost)<br /> • Do not store bulk chemicals in the -80 freezer. All chemicals should be stored in the chemical fridge and freezer only.<br /> <br /> '''Freezer Maintenance''' <br /> The -80 Freezer in lab will be emptied and defrosted once a year for routine maintenance. All samples not located in the proper locations specified above with be discarded. Please check the maintenance log located on the door of the freezer for date of the next defrost. If there are any issues or concerns occur while using the freezer contact the freezer manager immediately.</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=-80_Freezer_Storage_and_Maintenance&diff=685 2019-07-31T16:43:10Z

<p>Acrook: </p> <hr /> <div><br /> == Freezer Storage ==<br /> <br /> <br /> Every lab member is assigned a section of 10x10 freezer boxes on shelves 1 and 4. In addition, every member has an assigned overflow box for all samples on shelves 2 or 3. All samples and the sample container should be labeled with the owner’s initials, date, and sample contents. Be cautious and quick when opening the freezer door, best practice for retrieving samples is to keep the freezer door open less then 2 min at a time. This helps to keep a consistent temperature in the freezer and keep the frost levels to a minimum. <br /> <br /> '''-80 Freezer User Logbook'''<br /> All boxes stored in the -80 Freezer should be identified in the “-80 Freezer Logbook”. When a box is added to either of the freezer racks 1 or 4, mark the corresponding spot with the appropriate color assigned to that lab member. All empty boxes can be left blank. The link for the “-80 Freezer Logbook” can be found [here: https://docs.google.com/spreadsheets/d/1fgMQraoWun8AAsPiXyh6hMHEwWZ25V5aJiSUR2LW17k/edit#gid=0]. <br /> <br /> '''General Rules of the -80 Freezer''' <br /> • Close the freezer door immediately when the alarm go off. <br /> • Do not relocate boxes or samples of other lab members without their consent <br /> • Do not leave loose samples or boxes in open spaces of the fridge or freezer (they will get lost)<br /> • Do not store bulk chemicals in the -80 freezer. All chemicals should be stored in the chemical fridge and freezer only.<br /> <br /> '''Freezer Maintenance''' <br /> The -80 Freezer in lab will be emptied and defrosted once a year for routine maintenance. All samples not located in the proper locations specified above with be discarded. Please check the maintenance log located on the door of the freezer for date of the next defrost. If there are any issues or concerns occur while using the freezer contact the freezer manager immediately.</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=-80_Freezer_Storage_and_Maintenance&diff=684 2019-07-31T16:41:22Z

<p>Acrook: Created page with &quot;Freezer Storage Every lab member is assigned a section of 10x10 freezer boxes on shelves 1 and 4. In addition, every member has an assigned overflow box for all samples on s...&quot;</p> <hr /> <div>Freezer Storage <br /> <br /> Every lab member is assigned a section of 10x10 freezer boxes on shelves 1 and 4. In addition, every member has an assigned overflow box for all samples on shelves 2 or 3. All samples and the sample container should be labeled with the owner’s initials, date, and sample contents. Be cautious and quick when opening the freezer door, best practice for retrieving samples is to keep the freezer door open less then 2 min at a time. This helps to keep a consistent temperature in the freezer and keep the frost levels to a minimum. <br /> <br /> -80 Freezer User Logbook<br /> All boxes stored in the -80 Freezer should be identified in the “-80 Freezer Logbook”. When a box is added to either of the freezer racks 1 or 4, mark the corresponding spot with the appropriate color assigned to that lab member. All empty boxes can be left blank. The link for the “-80 Freezer Logbook” can be found [https://docs.google.com/spreadsheets/d/1fgMQraoWun8AAsPiXyh6hMHEwWZ25V5aJiSUR2LW17k/edit#gid=0]. <br /> <br /> General Rules of the -80 Freezer <br /> • Close the freezer door immediately when the alarm go off. <br /> • Do not relocate boxes or samples of other lab members without their consent <br /> • Do not leave loose samples or boxes in open spaces of the fridge or freezer (they will get lost)<br /> • Do not store bulk chemicals in the -80 freezer. All chemicals should be stored in the chemical fridge and freezer only. <br /> Freezer Maintenance <br /> The -80 Freezer in lab will be emptied and defrosted once a year for routine maintenance. All samples not located in the proper locations specified above with be discarded. Please check the maintenance log located on the door of the freezer for date of the next defrost. If there are any issues or concerns occur while using the freezer contact the freezer manager immediately.</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=Category:Protocols&diff=683 2019-07-31T16:39:19Z

<p>Acrook: </p> <hr /> <div>''General Maintenance''<br /> *[[Changing the high pressure dewar]]<br /> *[[Filling a Magnet with Nitrogen]]<br /> *[[Autoclaving Laboratory Glassware and Media]]<br /> *[[Chemical Disinfection of Glassware]]<br /> *[[Requesting Balance Calibration]]<br /> *[[Requesting Pipette Calibration]]<br /> *[[Using the UV-Vis]]<br /> *[[Using and Maintaining pH Meter]]<br /> *[[-80 Freezer Storage and Maintenance]]<br /> <br /> ''Protein Preparation''<br /> *[[Buffer Exchange and Solution Concentration]]<br /> *[[Finding a Protein Target on the NESG website]]<br /> *[[Choosing a Plasmid]]<br /> *[[Plasmid Purification and Transformation Protocol]]<br /> *[[Creating Stock Cultures of Bacteria]]<br /> *[[Luria-Bertani Media]]<br /> *[[M9 Minimal Media]]<br /> *[[Protein Overexpression and Extraction]]<br /> *[[SDS-PAGE Protocol]]<br /> *[[Running a Cobalt Affinity Column]]<br /> *[[Dialysis]]<br /> *[[Centrifugal Protein Concentration and Buffer Exchange]]<br /> *[[Using the Stirred Cell Concentrator]]<br /> <br /> ''Data Collection''<br /> *[[Gap Sampling]]<br /> *[[Water Suppression with presaturation pulses (zgpr/zgcppr]]<br /> *[[Non-uniform Sampling]]<br /> *[[Collecting a 15N Edited HSQC]]<br /> *[[Collecting CEST Data]]<br /> <br /> ''Data Processing and Analysis''<br /> *[[Analysis of 1D Line-Broadening Screen]]<br /> *[[FastModelFree]]<br /> *[[2D NMR Analysis (CCPNMR)]]<br /> *[[1H NMR Analysis (SIMCA)]]<br /> *[[1H NMR Analysis (ACDLab)]]<br /> *[[Processing CEST Data]]<br /> *[[Titration Data Analysis in nmrPipe]]<br /> *[[Non-Uniform Sampling]]<br /> *[[NMRFAM-SPARKY Guide]]<br /> *[[NMRFAM-SPARKY: Automated Peak Assignment]]<br /> *[[NMR Processing in Linux and Windows]]<br /> <br /> ''Miscellaneous''<br /> *[[Agarose Gel]]<br /> *[[700 MHz NMR checklist]]<br /> *[[500 MHz NMR checklist]]<br /> *[[1D Macro]]<br /> *[[Setting Up a Virtual Screen with AutoDock]]<br /> *[[Simple Protein Crosslinking]]<br /> *[[1D NMR Titrations]]<br /> <br /> Cell Culturing<br /> *[[Cell Culturing Dr. Franco Lab]]<br /> <br /> ''Metabolomics''<br /> *[[MetPa for metabolomics]]<br /> *[[Making Heatmaps]]<br /> *[[Metabolite Extraction]]<br /> *[[One way ANOVA in R]]<br /> *[[P-Value adjustment for multiple comparisons]]<br /> *[[PCA-Utils]]<br /> *[[NMR Tube Deep Cleaning]]<br /> *[[Noise Removal for PCA]]<br /> *[[Weighted Linear Least Squares]]<br /> *[[Serum Preparation for 1D NMR]]<br /> *[[Urine Preparation for 1D NMR]]<br /> <br /> ''Safety and Inspections''<br /> *[[Lab Responsibilities]]<br /> *[[Inspection Checklist]]<br /> *[[Safety Contacts, Resources]]<br /> <br /> ''Demos''<br /> *[[Peroxide Clock]]<br /> *[[Traffic Light Reaction]]<br /> *[[Orange Juice Clock]]<br /> *[[Gummy Bear Freeze]]<br /> *[[Batteries]]<br /> *[[Rocket Launcher]]<br /> *[[Women in Science: Checklist]]<br /> *[[Maxey Day: Checklist]]</div>

Acrook https://bionmr.unl.edu/mediawiki/mediawiki/index.php?title=Category:Protocols&diff=682 2019-07-31T16:38:53Z

<p>Acrook: </p> <hr /> <div>''General Maintenance''<br /> *[[Changing the high pressure dewar]]<br /> *[[Filling a Magnet with Nitrogen]]<br /> *[[Autoclaving Laboratory Glassware and Media]]<br /> *[[Chemical Disinfection of Glassware]]<br /> *[[Requesting Balance Calibration]]<br /> *[[Requesting Pipette Calibration]]<br /> *[[Using the UV-Vis]]<br /> *[[Using/Maintaining pH Meter]]<br /> *[[Using/-80 Freezer Storage and Maintenance]]<br /> <br /> ''Protein Preparation''<br /> *[[Buffer Exchange and Solution Concentration]]<br /> *[[Finding a Protein Target on the NESG website]]<br /> *[[Choosing a Plasmid]]<br /> *[[Plasmid Purification and Transformation Protocol]]<br /> *[[Creating Stock Cultures of Bacteria]]<br /> *[[Luria-Bertani Media]]<br /> *[[M9 Minimal Media]]<br /> *[[Protein Overexpression and Extraction]]<br /> *[[SDS-PAGE Protocol]]<br /> *[[Running a Cobalt Affinity Column]]<br /> *[[Dialysis]]<br /> *[[Centrifugal Protein Concentration and Buffer Exchange]]<br /> *[[Using the Stirred Cell Concentrator]]<br /> <br /> ''Data Collection''<br /> *[[Gap Sampling]]<br /> *[[Water Suppression with presaturation pulses (zgpr/zgcppr]]<br /> *[[Non-uniform Sampling]]<br /> *[[Collecting a 15N Edited HSQC]]<br /> *[[Collecting CEST Data]]<br /> <br /> ''Data Processing and Analysis''<br /> *[[Analysis of 1D Line-Broadening Screen]]<br /> *[[FastModelFree]]<br /> *[[2D NMR Analysis (CCPNMR)]]<br /> *[[1H NMR Analysis (SIMCA)]]<br /> *[[1H NMR Analysis (ACDLab)]]<br /> *[[Processing CEST Data]]<br /> *[[Titration Data Analysis in nmrPipe]]<br /> *[[Non-Uniform Sampling]]<br /> *[[NMRFAM-SPARKY Guide]]<br /> *[[NMRFAM-SPARKY: Automated Peak Assignment]]<br /> *[[NMR Processing in Linux and Windows]]<br /> <br /> ''Miscellaneous''<br /> *[[Agarose Gel]]<br /> *[[700 MHz NMR checklist]]<br /> *[[500 MHz NMR checklist]]<br /> *[[1D Macro]]<br /> *[[Setting Up a Virtual Screen with AutoDock]]<br /> *[[Simple Protein Crosslinking]]<br /> *[[1D NMR Titrations]]<br /> <br /> Cell Culturing<br /> *[[Cell Culturing Dr. Franco Lab]]<br /> <br /> ''Metabolomics''<br /> *[[MetPa for metabolomics]]<br /> *[[Making Heatmaps]]<br /> *[[Metabolite Extraction]]<br /> *[[One way ANOVA in R]]<br /> *[[P-Value adjustment for multiple comparisons]]<br /> *[[PCA-Utils]]<br /> *[[NMR Tube Deep Cleaning]]<br /> *[[Noise Removal for PCA]]<br /> *[[Weighted Linear Least Squares]]<br /> *[[Serum Preparation for 1D NMR]]<br /> *[[Urine Preparation for 1D NMR]]<br /> <br /> ''Safety and Inspections''<br /> *[[Lab Responsibilities]]<br /> *[[Inspection Checklist]]<br /> *[[Safety Contacts, Resources]]<br /> <br /> ''Demos''<br /> *[[Peroxide Clock]]<br /> *[[Traffic Light Reaction]]<br /> *[[Orange Juice Clock]]<br /> *[[Gummy Bear Freeze]]<br /> *[[Batteries]]<br /> *[[Rocket Launcher]]<br /> *[[Women in Science: Checklist]]<br /> *[[Maxey Day: Checklist]]</div>

Acrook