Category:Protocols: Difference between revisions

Latest revision as of 04:31, 11 September 2021

Subcategories

This category has the following 22 subcategories, out of 22 total.

A

AutoDock‎ (2 P)

F

FAST-NMR‎ (6 P)

G

Gel‎ (2 P)
General Maintenance‎ (14 P)

L

Lab Safety‎ (14 P)

M

Metabolomics‎ (1 C, 4 P)
Molecular Docking‎ (1 P)
MVAPACK‎ (4 P)

N

Needs Updating‎ (25 P)
NMR Usage‎ (1 C, 10 P)

P

Protein Work‎ (3 C, 2 P)
Proteomics‎ (empty)

S

Sample Preparation‎ (9 P)

T

Troubleshooting‎ (2 P)

U

Update Wiki‎ (3 P)

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-Creating a E.Coli Stock Culture
+<!--''General Maintenance''
+*[[Changing the high pressure dewar]]
+*[[Filling a Magnet with Nitrogen]]
+*[[Autoclaving Laboratory Glassware and Media]]
+*[[Chemical Disinfection of Glassware]]
+*[[Requesting Balance Calibration]]
+*[[Requesting Pipette Calibration]]
+*[[Using the UV-Vis]]
+*[[Using and Maintaining pH Meter]]
+*[[-80 Freezer Storage and Maintenance]]
+*[[Freeze Dryer Maintenance]]
+*[[Lab Notebook Guidelines]]
+*[[Sample Barcoding]]
-. Make LB media as per the protocol titled Media Preparation
+''Protein Preparation''
+*[[Buffer Exchange and Solution Concentration]]
+*[[Finding a Protein Target on the NESG website]]
+*[[Choosing a Plasmid]]
+*[[Plasmid Purification and Transformation Protocol]]
+*[[Creating Stock Cultures of Bacteria]]
+*[[Luria-Bertani Media]]
+*[[M9 Minimal Media]]
+*[[Protein Overexpression and Extraction]]
+*[[SDS-PAGE Protocol]]
+*[[Running a Cobalt Affinity Column]]
+*[[Dialysis]]
+*[[Centrifugal Protein Concentration and Buffer Exchange]]
+*[[Using the Stirred Cell Concentrator]]
-. Transfer 25mL of LB media in to a sterile (autoclave) 250 mL  erlenmeyer flask using a sterile Falcon Transfer Pipet
+''Data Collection''
+*[[Gap Sampling]]
+*[[Water Suppression with presaturation pulses (zgpr/zgcppr]]
+*[[Non-uniform Sampling]]
+*[[Collecting a 15N Edited HSQC]]
+*[[Collecting CEST Data]]
-. Inoculate the flask with enough stock culture(Glycerol stock obtained from a lab mate/purchased) to create a final OD600 of 0.025
+''Data Processing and Analysis''
+*[[Analysis of 1D Line-Broadening Screen]]
+*[[FastModelFree]]
+*[[2D NMR Analysis (CCPNMR)]]
+*[[1H NMR Analysis (SIMCA)]]
+*[[1H NMR Analysis (ACDLab)]]
+*[[Processing CEST Data]]
+*[[Titration Data Analysis in nmrPipe]]
+*[[Non-Uniform Sampling]]
+*[[Chara]]
+*[[2D NMR Processing in Linux and Windows]]
+*[[2D Metabolomics NMRPipe Processing]]
+*[[1D NMR Processing in Linux and Windows Example Script]]
+*[[NMR Batch Correction Example Script]]
+*[[PCA Classify Example Script]]
+*[[Sample Collection and Processing for Protein Backbone Assignments]]
+*[[Example Scripts for NMRPipe Processing]]
-. Make note to have 1:10 ratio of liquid to air in your inoculated flask for aerobic growth of E.coli
-. Incubate the flask at 37C and a shaker speed of 100-150 rpm
+''Miscellaneous''
+*[[Agarose Gel]]
+*[[700 MHz NMR checklist]]
+*[[500 MHz NMR checklist]]
+*[[1D Macro]]
+*[[Setting Up a Virtual Screen with AutoDock]]
+*[[Simple Protein Crosslinking]]
+*[[1D NMR Titrations]]
+*[[Setting Up & Running MD Simulations]]
+*[[Analyzing MD Simulations]]
+*[[iRed Analysis of MD Simulations]]
-. Over every 30 min take an OD600 reading to track the growth of the E.coli cells in your flask
+Cell Culturing
+*[[Cell Culturing Dr. Franco Lab]]
-. When the cells hit Stationary phase (OD600 greater than or equal to 10 in 1ml of culture) the culture is ready to make stock tubes for storage
+''Metabolomics''
+*[[Metabolite Extraction]]
+*[[MetPa for metabolomics]]
+*[[Making Heatmaps]]
+*[[One way ANOVA in R]]
+*[[P-Value adjustment for multiple comparisons]]
+*[[PCA-Utils]]
+*[[NMR Tube Deep Cleaning]]
+*[[Noise Removal for PCA]]
+*[[Weighted Linear Least Squares]]
+*[[Serum Preparation for 1D NMR]]
+*[[Whole Blood Preparation for 1D NMR]]
+*[[Urine Preparation for 1D NMR]]
+*[[Cell Culture Preparation for 1D NMR]]
+*[[LC-MS metabolomics guide-CIBC collaborations]]
-. At this point, take 1ml of culture and add 0.5ml of glycerol in a 2ml sterile tube, create 10-15 of these 2ml glycerol stock tubes
-. Store the tubes with appropriate labeling in the -80C freezer for until you need to use them again.
+''Demos''
+*[[Peroxide Clock]]
+*[[Traffic Light Reaction]]
+*[[Orange Juice Clock]]
+*[[Gummy Bear Freeze]]
+*[[Lava Lamps]]
+*[[Women in Science: Checklist]]
+*[[Maxey Day: Checklist]]
+-->