Lab Protocols

Autoclaving
Changing CO2 tanks on incubators

Thawing mammalian cells
Freezing mammalian cells
Heat inactivation of FBS

Lysis buffer recipe
Lysing adherent mammalian cells
IP lysis buffer recipe
Immunoprecipitation protocol

MicroBCA Protein Assay
NuPage Western Blot Protocol
Trans-Blot Turbo Semidry Blotting
Wet tank transfer protocol

Lentivirus preparation
    Lentivirus transfection worksheet, 3rd generation packaging
    Lentivirus transfection worksheet, 2nd generation packaging
Retrovirus preparation using Phoenix cells
    Retrovirus transfection worksheet

Coverslip immunofluorescence
Growing cell spheroids in collagen
Soft agar colony formation assay
Wound healing assay

Ethanol fixation for cell cycle analysis

Media recipe for mouse PDAC cell lines

Transforming competent bacterial cells
Growing bacterial cultures
Concentrating DNA by precipitation in ethanol
Reconstituting DNA from filter paper

Creating a heatmap in MeV
R Studio code for PCA, Pearson correlations, & heatmaps

Protocol-relevant links

Typical concentrations of antibiotic selection agents

Lab equipment manuals & links to tutorials

Thermo TSU -80 freezer
Thermo Locator 6 Plus Cryogenic Bank
Thermo Forma i160 SteriCycle CO2 incubators
Eppendorf 5430/5430R Centrifuges
Heraeus Megaufuge 16
    TX-400 Rotor
Mettler Toledo ML54T Balance
Millipore Synergy

BioRad Trans-Blot Turbo Blotting System
LI-COR Odyssey CLx Operator's Manual
    Odyssey CLx Application Protocols Manual   
    Tech Note -- Near-Infrared (NIR) Western Blot Detection
    Good Westerns Gone Bad for NIR -- Tips to Make Your NIR Western Blot Great
    Good Normalization Gone Bad
    Image Studio Online Tutorial   
    Image Studio Lite Online Tutorial

Basic Concepts in Microscopy (Zeiss)
Chroma optical filter sets (Axiovert 40 CFL)
    DAPI/Hoechst; AF488/FITC; TRITC/Rhodamine
Zeiss optical filter sets (AxioObserver Z1)
    Available filter sets & objectives
    DAPI; CFP; AF488; YFP; AF546; AF594; AF647


Databases

cBioPortal for Cancer Genomics
PROGeneV2 Prognostic Database
PRECOG - Prediction of Clinical Outcomes from Genomic Profiles
CellMiner (NCI)
COSMIC Catalogue of somatic mutations in cancer
Genomics of Drug Sensitivity in Cancer Project


Other links

UVA MolMart
UVA Environmental Health & Safety