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Molecular biology protocols

  • PCR cloning [download] Updated 09/2018
  • shRNA cloning into pLKO.1 vectors [download] Updated 04/2015
  • Gateway LR recombination [download]
  • Production and purification of GST fusion proteins [download] Updated 12/2012
  • In vitro transcription of haptenylated riboprobes for RNA FISH [download] Updated 12/2012
  • RNA purification and first-strand cDNA synthesis [download] Updated 12/28/2016
  • Real-time quantitative PCR [download] Updated 06/21/2017
  • Microplate BCA protein assay [download] Updated 11/2011
  • Western blotting for Chemiluminescence [download]
  • Western blotting on the Licor Odyssey [download] Updated 12/2014
  • Receptome profiling [download] NEW 08/2013
  • Transformation of chemically competent bacteria [download] NEW 03/2017
  • Preparation of electrocompetent bacteria [download] NEW 09/2018

Cell biology protocols

  • Preparation of amphotropic retroviruses and lentiviruses [download] Updated 10/2011
  • Viral transduction and selection of mammalian cells [download] Updated 10/2011
  • Preparation and titering of coxsackievirus B3 [download] NEW 12/2014
  • Differentiation of AC16 cells [download] NEW 9/2018
  • Immunofluorescence on coverslips [download] Updated 10/2011
  • Immunofluorescence on cells in suspension [download] Updated 8/2015
  • Immunofluorescence on FFPE sections [download] Updated 08/2014
  • Multicolor RNA fluorescence in situ hybridization [download] Updated 10/2011
  • Flow cytometry [download] Updated 08/2014

Three-dimensional breast epithelial culture protocols

  • Imaging 3D cultures by brightfield microscopy [download] NEW 08/2013
  • Live-cell imaging 3D cultures by laser-scanning confocal microscopy [download] 1/16/2016
  • Embedding of fixed frozen 3D structures [download] Updated 10/2011
  • Sectioning of fixed frozen of 3D structures [download] Updated 10/2011
  • Immunofluorescence on cryofixed sections [download] Updated 08/2014
  • Whole-mount immunofluorescence of 3D structures [download] Updated 10/2011
  • Chromatin immunoprecipitation under 3D-mimetic conditions [download]

Specialized protocols

  • Embedding of fresh frozen 3D structures for LCM [download] Updated 10/2011
  • Embedding of fresh brain samples for LCM [download] NEW 9/2018
  • Sectioning of fresh frozen 3D structures for LCM [download] Updated 10/2011
  • Sectioning of fresh brain samples for LCM [download] NEW 9/2018
  • Laser-capture microdissection of 3D structures [download] Updated 10/2011
  • Fluorescence-guided laser-capture microdissection [download] NEW 9/2018
  • Small-sample cDNA amplification [download] Updated 10/2011
  • Small-sample cDNA reamplification and labeling [download]
  • Small-sample cDNA reamplification for RNA-seq [download] NEW 9/2018
  • MAPK phosphatase activity assay [download] NEW 04/2013
  • Subcellular phosphatase activity assay [download] NEW 04/2017

Lab-specific protocols

  • Calibration and maintenance of the lab pH meter [download]
  • Cell counting with the Coulter Z1 Particle Counter [download] Updated 04/2014
  • Cryosectioning on the CryoStar NX50 [download] NEW 9/2018
  • Protocol template for the Janes Lab website [download] NEW 6/2019
  • Plasmid deposition in lab repository [download] Updated 07/19/2018
  • Plasmid register data entry template [download] Updated 08/2013
  • Plasmid requests from the human ORFeome and plasmid database [download] NEW 09/2018

Molecular biology recipes

Video tutorials

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