Computational Protocols

Computational Protocols   [Github]

Cell Biology

Immunofluorescence on cells in suspension   [PDF]
Immunofluorescence on coverslips   [PDF]
Immunofluorescence on FFPE sections   [PDF]
RNA fluorescence in situ hybridization on cryosections   [PDF]
Flow cytometry   [PDF]
Differentiation of AC16 cells   [PDF]
Preparation of amphotropic retroviruses and lentiviruses   [PDF]
Viral transduction and selection of mammalian cells   [PDF]
Preparation and titering of coxsackievirus B3   [PDF]

Lab-specific protocols

Using glass culture tubes   [PDF]
Plasmid deposition   [PDF]
Calibration and maintenance of the lab pH meter   [PDF]
Cell counting with the Coulter Z1 Particle Counter   [PDF]
Cryosectioning on the CryoStar NX50   [PDF]
Plasmid requests from the human ORFeome and plasmid database   [PDF]

Molecular Biology

Microplate microBCA protein assay   [PDF]
Proximity Ligation   [PDF]
Western blotting for chemiluminescence   [PDF]
Real-time quantitative PCR   [PDF]
In vitro transcription of haptenylated riboprobes for RNA FISH   [PDF]
Gateway LR recombination   [PDF]
Microplate BCA protein assay   [PDF]
PCR cloning   [PDF]
Preparation of electrocompetent bacteria   [PDF]
Production and purification of GST fusion proteins   [PDF]
Receptome profiling   [PDF]
shRNA cloning into pLKO.1 vectors   [PDF]
Western blotting on the Licor Odyssey   [PDF]
Transformation of chemically competent bacteria   [PDF]
RNA purification and first-strand cDNA synthesis   [PDF]

Molecular Biology Recipes

Agarose gel loading buffer   [PDF]
Homemade ECL reagent   [PDF]
LB/Amp plates   [PDF]
Common cell lysis buffers   [PDF]

Specialized Protocols

FISH riboprobes   [PDF]
Matrigel Handling   [PDF]
Small-sample cDNA amplification from microdissected cells   [PDF]
Embedding of fresh brain samples for LCM   [PDF]
Embedding of fresh frozen 3D structures for LCM   [PDF]
Fluorescence-guided laser-capture microdissection   [PDF]
Laser-capture microdissection of 3D structures   [PDF]
Sectioning of fresh brain samples for LCM   [PDF]
Sectioning of fresh frozen 3D structures for LCM   [PDF]
Small-sample cDNA amplification   [PDF]
Small-sample cDNA reamplification and labeling   [PDF]
Small-sample cDNA reamplification for RNA-seq   [PDF]
Subcellular phosphatase activity assay   [PDF]

Three-dimensional breast epithelial culture

Matrigel handling   [PDF]
Whole-mount immunofluoresence of MCF10A 3D structures   [PDF]
Chromatin immunoprecipitation under 3D-mimetic conditions   [PDF]
Embedding of fixed frozen 3D structures   [PDF]
Sectioning of fixed frozen of 3D structures   [PDF]
Live-cell imaging 3D cultures by laser-scanning confocal microscopy   [PDF]
Imaging 3D cultures by brightfield microscopy   [PDF]

Video tutorials

Using the aligner tool in ApE   [Video]
DNA recombinations using ApE   [Video]
Figure polishing and small-multiple replication   [Video]
Image processing of immunoblot data   [Video]
Image processing of multicolor fluorescence data   [Video]
Immunoblot densitometry   [Video]
Intraductal injections of human breast cancer cells into SCID-beige mice   [Video]
Nonlinear least-squares curve fitting in Excel   [Video]
Putting molecular-weight markers on Licor immunoblots   [Video]
Use of Igor   [Video]

Stochastic Profiling Hands-on Workshop

    • Introductory Lecture [PDF] [Video]
    • Sample Preparation [PDF] [Video]
    • Laser-capture Microdissection and Poly(A) Amplification [PDF] [Video]
    • Quantitative PCR with Stochastic Profiling Samples [PDF] [Video]
      • Troubleshooting [PDF]
    • Reamplification and Purification for RNA-seq [PDF] [Video]
    • Monte Carlo Simulation [PDF] [Video]
    • Array Processing [PDF] [Video]
    • Maximum Likelihood Inference [PDF] [Video]
    • Applications [PDF Part 1] [PDF Part 2] [Video]
    • Hands-on Research Update [Video]
      • Amelia Helms [PDF]
      • Alan Zwart [PDF]
      • Bryan Cardiac [PDF]
      • Meyer Waters [PDF]
      • Joseph Shin [PDF]
      • Will Matern [ PDF]
      • Amanda Pellowe [PDF]
      • Yuan Stoch [PDF]

This workshop was supported by the following sponsors: