Lab Protocols

      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

      Sequencing (Eurofins)

      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

      Z2 Coulter Counter

      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)
      Zeiss optical filter sets (AxioObserver Z1)
          Available filter sets & objectives in Lazzara lab
          Zeiss Filter Assistant: DAPICFPAF488YFPAF546AF594AF647
          ThermoFisher: Fluorescence SpectraViewer

      Cytation Quick Reference Guide (BioTek)
      Gen5 Getting Started Guide
      Lazzara Lab Cytation5 Objectives, Filters, LEDs


      cBioPortal for Cancer Genomics
      Cancer Cell Line Encyclopedia
      MD Anderson Cell Lines Project
      Cancer Dependency Map Portal (DepMap)
      UCSC Xena Functional Genomics Explorer
      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


      UVA MolMart

      Laboratory safety

      UVA SDS Database
      UVA Environmental Health & Safety