Computational Protocols

Computational Protocols   Pubmed

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   Pubmed
Plasmid deposition   Pubmed
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

Proximity Ligation   PDF
Western blotting for chemiluminescence   PDF
Real-time quantitative PCR   Pubmed
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

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

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: