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
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
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
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
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
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
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
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
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]
