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Lab Tools (old)

Pulling Out Proteins
Kelly Rae Chi | Apr 1, 2009 | 8 min read
Troubleshooting discovery and validation of protein biomarkers for cancer.
Mass Spectacle
Jeffrey M. Perkel | Mar 1, 2009 | 8 min read
Making the most of mass spectrometry imaging.
Freeze Frame
Jeffrey M. Perkel | Feb 1, 2009 | 10 min read
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 | 6 min read
How to modify your tools to prevent pain at the bench.
Pluripotency for the Masses
Kelly Rae Chi | Dec 1, 2008 | 7 min read
What beginners need to know as they dive into studies on pluripotent cells.
Lab Tools: Fret-free FRET
Kelly Rae Chi | Nov 1, 2008 | 7 min read
How to put FRET biosensors to work for you when tracking cell signaling.
Lab Tools: Close Encounters
Jeffrey M. Perkel | Oct 1, 2008 | 7 min read
Protein-protein interaction assays for all occasions.
Middling Measures
Kelly Rae Chi | Sep 1, 2008 | 1 min read
Avoiding the pitfalls of medium-throughput SNP detection.
Modifications Abound
Jeffrey M. Perkel | Aug 1, 2008 | 2 min read
How to conduct your next large-scale epigenetic analysis
ChIP-on-chip
Jeffrey M. Perkel | Aug 1, 2008 | 2 min read
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 | 2 min read
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 | 2 min read
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 | 2 min read
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 | 2 min read
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 | 2 min read
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 | 1 min read
How to troubleshoot your in-vivo fluorescence imaging studies
Source lighting
Richard Gaughan | Jul 1, 2008 | 2 min read
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
Planar imaging
Josh P. Roberts | Jun 1, 2008 | 2 min read
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 | 2 min read
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.
Tips for setting up 3-D cell cultures
Josh P. Roberts | Jun 1, 2008 | 2 min read
Choose your substrate. Basement membrane extract (BME) is fine for studying tissue-specific differentiation, because it can approximate the morphology and viscoelasticity of the tissues in extracellular matrices in vivo, explains Valerie Weaver of the University of California, San Francisco. If you're working on invasive tumors, however, try collagen or a similar substra
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