Computational Protocols
Cell Biology
Immunofluorescence on cells in suspension
Immunofluorescence on coverslips
Immunofluorescence on FFPE sections
RNA fluorescence in situ hybridization on cryosections
Flow cytometry
Differentiation of AC16 cells
Preparation of amphotropic retroviruses and lentiviruses
Viral transduction and selection of mammalian cells
Preparation and titering of coxsackievirus B3
Immunofluorescence on coverslips
Immunofluorescence on FFPE sections
RNA fluorescence in situ hybridization on cryosections
Flow cytometry
Differentiation of AC16 cells
Preparation of amphotropic retroviruses and lentiviruses
Viral transduction and selection of mammalian cells
Preparation and titering of coxsackievirus B3
Lab-specific protocols
Molecular Biology
Western Blotting for Chemiluminescence
Western Blotting for Chemiluminescence
Real-time quantitative PCR
In vitro transcription of haptenylated riboprobes for RNA FISH
Gateway LR recombination
Microplate BCA protein assay
PCR cloning
Preparation of electrocompetent bacteria
Production and purification of GST fusion proteins
Receptome profiling
shRNA cloning into pLKO.1 vectors
Western blotting for Chemiluminescence
Western blotting on the Licor Odyssey
Transformation of chemically competent bacteria
RNA purification and first-strand cDNA synthesis
Western Blotting for Chemiluminescence
Real-time quantitative PCR
In vitro transcription of haptenylated riboprobes for RNA FISH
Gateway LR recombination
Microplate BCA protein assay
PCR cloning
Preparation of electrocompetent bacteria
Production and purification of GST fusion proteins
Receptome profiling
shRNA cloning into pLKO.1 vectors
Western blotting for Chemiluminescence
Western blotting on the Licor Odyssey
Transformation of chemically competent bacteria
RNA purification and first-strand cDNA synthesis
Molecular Biology Recipes
Specialized Protocols
Small-sample cDNA amplification from microdissected cells
Embedding of fresh brain samples for LCM
Embedding of fresh frozen 3D structures for LCM
Fluorescence-guided laser-capture microdissection
Laser-capture microdissection of 3D structures
Sectioning of fresh brain samples for LCM
Sectioning of fresh frozen 3D structures for LCM
Small-sample cDNA amplification
Small-sample cDNA reamplification and labeling
Small-sample cDNA reamplification for RNA-seq
Subcellular phosphatase activity assay
Embedding of fresh brain samples for LCM
Embedding of fresh frozen 3D structures for LCM
Fluorescence-guided laser-capture microdissection
Laser-capture microdissection of 3D structures
Sectioning of fresh brain samples for LCM
Sectioning of fresh frozen 3D structures for LCM
Small-sample cDNA amplification
Small-sample cDNA reamplification and labeling
Small-sample cDNA reamplification for RNA-seq
Subcellular phosphatase activity assay
Three-dimensional breast epithelial culture
Matrigel handling
Whole-mount immunofluoresence of MCF10A 3D structures
Chromatin immunoprecipitation under 3D-mimetic conditions
Embedding of fixed frozen 3D structures
Sectioning of fixed frozen of 3D structures
Live-cell imaging 3D cultures by laser-scanning confocal microscopy
Imaging 3D cultures by brightfield microscopy
Whole-mount immunofluoresence of MCF10A 3D structures
Chromatin immunoprecipitation under 3D-mimetic conditions
Embedding of fixed frozen 3D structures
Sectioning of fixed frozen of 3D structures
Live-cell imaging 3D cultures by laser-scanning confocal microscopy
Imaging 3D cultures by brightfield microscopy
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]
