Lab Tools (old)
Pulling Out Proteins
Kelly Rae Chi | Apr 1, 2009
Troubleshooting discovery and validation of protein biomarkers for cancer.
Mass Spectacle
Jeffrey M. Perkel | Mar 1, 2009
Making the most of mass spectrometry imaging.
Freeze Frame
Jeffrey M. Perkel | Feb 1, 2009
How to troubleshoot sample preparation for cryo-electron microscopy, an up-and-coming structural biology technique.
Let's Get Physical
Kelly Rae Chi | Jan 1, 2009
How to modify your tools to prevent pain at the bench.
Pluripotency for the Masses
Kelly Rae Chi | Dec 1, 2008
What beginners need to know as they dive into studies on pluripotent cells.
Lab Tools: Fret-free FRET
Kelly Rae Chi | Nov 1, 2008
How to put FRET biosensors to work for you when tracking cell signaling.
Lab Tools: Close Encounters
Jeffrey M. Perkel | Oct 1, 2008
Protein-protein interaction assays for all occasions.
Middling Measures
Kelly Rae Chi | Sep 1, 2008
Avoiding the pitfalls of medium-throughput SNP detection.
Modifications Abound
Jeffrey M. Perkel | Aug 1, 2008
How to conduct your next large-scale epigenetic analysis
ChIP-on-chip
Jeffrey M. Perkel | Aug 1, 2008
Researcher: Richard Young, member, Whitehead Institute for Biomedical Research, Cambridge, Mass. Project: Mapping transcription factor binding across the yeast genome. Problem: Chromatin immunoprecipita
ChIP-Sequence
Jeffrey M. Perkel | Aug 1, 2008
Credit: © 2008 Illumina Inc. All Rights Reserved." /> Credit: © 2008 Illumina Inc. All Rights Reserved. Researcher: Steven Jones, head, Bioinformatics, Genome Sciences Center, British Columbia Cancer Research Center, Vancouver, BC, Canada Project: Mapping transcription-factor binding in interferon-gamma-stimulated and unstimu
Enrichment HELP
Jeffrey M. Perkel | Aug 1, 2008
Credit: Courtesy of John Greally, Albert Einstein College of Medicine, and PLoS ONE" /> Credit: Courtesy of John Greally, Albert Einstein College of Medicine, and PLoS ONE Researcher: John Greally, associate professor of Molecular Genetics, Albert Einstein College of Medicine, NY Project: Comparing ep
Single-base detection
Jeffrey M. Perkel | Aug 1, 2008
Credit: Courtesy of Matteo Pellegrini, University of California, Los Angeles" /> Credit: Courtesy of Matteo Pellegrini, University of California, Los Angeles Researcher: Matteo Pellegrini, assistant professor of Molecular, Cell and Developmental Biology, University of California, Los Angeles Project:
Recognizing RNA
Jeffrey M. Perkel | Aug 1, 2008
Credit: Courtesy of Phillip Zamore, University of Massachusetts Medical School, and Science." /> Credit: Courtesy of Phillip Zamore, University of Massachusetts Medical School, and Science. Researcher: Phillip Zamore, Gretchen Stone Cook Professor of Biomedical Sciences, University of Massachusetts Medical School, Worcester Project:
Tips for wide-scale epigenetic detection
Jeffrey M. Perkel | Aug 1, 2008
1. Try orthagonal approaches Every assay has strengths and weaknesses, so it's a good idea to try more than one, if possible. ChIP-on-chip is significantly cheaper than ChIP-Seq, but unless you tile the entire genome, you will miss any region not represented on your chip. HELP probes only a fraction of the genome, but a genome's worth of testable HpaII fragments will fit on a single array, making analysis relatively inexpensive. (Greally now uses a 1.32-million element Nimblegen array.)
In the Live Light
Richard Gaughan | Jul 1, 2008
How to troubleshoot your in-vivo fluorescence imaging studies
Source lighting
Richard Gaughan | Jul 1, 2008
C6 glioma cells label with self-illuminating quantum dots conjugated with cell penetrating peptides. Credit: Jianghong Rao, Stanford School of Medicine" />C6 glioma cells label with self-illuminating quantum dots conjugated with cell penetrating peptides. Credit: Jianghong Rao, Stanford School of Medicine User: Jianghong Rao, Assistant Professor in Radiology, Stanford University
Mixed gel
Josh P. Roberts | Jun 1, 2008
Mammary FSK-3 cells plated onto matrix pads consisting of rat mammary ECM isolated from a nulliparous mouse, treated with 24hr pulse of BrdU and processed for immunohistochemical detection. Credit: Pepper Schedin / University of Colorado Health Sciences Center" />Mammary FSK-3 cells plated onto matrix pads consisting of rat mammary ECM isolated from a nulliparous mouse, treated with 24hr
Planar imaging
Josh P. Roberts | Jun 1, 2008
3D cultures of pancreatic tumor cells are embedded in agarose for imaging with light sheet-based fluorescence microscopy. Credit: Francesco Pampaloni / EMBL" />3D cultures of pancreatic tumor cells are embedded in agarose for imaging with light sheet-based fluorescence microscopy. Credit: Francesco Pampaloni / EMBL User: Ernst Stelzer, European Molecular Biology Laboratory, Heid
Commercial 3D matrices
Josh P. Roberts | Jun 1, 2008
Credit: Trevigen" /> Credit: Trevigen Reconstituted basement membrane extract (BME) Who: BD (Matrigel), Trevigen (Cultrex). Uses and Perks: Supports the growth and differentiation of cells and tissues. Recapitulates the morphology and viscoelasticity of the ECM. Can be remodeled by cells Drawbacks: Expensive, composition is variable.