Protocols
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
Cell fractionation-isolation of nuclei
MicroBCA Protein Assay
Mini gel casting
Midi gel casting, electrophoresis, blotting
SDS-PAGE recipe
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
Retrovirus preparation, VSVG pseudotyping
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
Subculturing glioma stem cells
Transforming competent bacterial cells
Making LB agar plates
Growing bacterial cultures
Concentrating DNA by precipitation in ethanol
Reconstituting DNA from filter paper
DNA gel electrophoresis
qRT-PCR using SYBR green
Qiagen RNeasy Mini Kit Handbook
Creating a heatmap in MeV
R Studio code for PCA, Pearson correlations, & heatmaps
PLSR using SIMCA-P
PLSR using R
PLSR using MATLAB
PTM-SEA using R
Puncta quantification in ImageJ
Protocol for Spheroid Analysis
Protocol for Quantifying Protein Expression with Correlation Plots
Protocol for Puncta, Edge Intensity, Area and Shape Analysis
Protocol-relevant links
Typical concentrations of antibiotic selection agents
Lab equipment manuals & links to tutorials
Thermo TSU series -80 freezer
Thermo TSX series -80 freezer
Thermo Locator 6 Plus Cryogenic Bank
Thermo Forma i160 SteriCycle CO2 incubators
Thermo MaxQ Mini 4450 Shaker
Eppendorf 5430/5430R Centrifuges
Eppendorf 5424R Centrifuge
Heraeus Megaufuge 16
TX-400 Rotor
Mettler Toledo ML54T Balance
Ohaus top-loading balance
Mettler Toledo pH Meter
Millipore Synergy
Applied Biosystems QuantStudio3 Real-Time PCR System
BioRad GelDoc Go Imaging System
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 in Lazzara lab
Zeiss Filter Assistant: DAPI; CFP; AF488; YFP; AF546; AF594; AF647
ThermoFisher: Fluorescence SpectraViewer
Cytation Quick Reference Guide (BioTek)
Gen5 Getting Started Guide
Lazzara Lab Cytation5 Objectives, Filters, LEDs
Databases
cBioPortal for Cancer Genomics
Cancer Cell Line Encyclopedia
MD Anderson Cell Lines Project
Cancer Dependency Map Portal (DepMap)
UCSC Xena Functional Genomics Explorer
ChIP-Atlas
CellMiner (NCI)
COSMIC Catalogue of somatic mutations in cancer
Genomics of Drug Sensitivity in Cancer Project
PROGeneV2 Prognostic Database
PRECOG - Prediction of Clinical Outcomes from Genomic Profiles
Kaplan Meier Plotter