ChIP-Seq Analysis: May All Sequences Be Treated EqualOctober 14, 2009“All men are created equal” is one of the most famous phrases in U.S. politics, but it took a while for this concept to be adopted by researchers dealing with repetitive sequences during ChIP-Seq analysis. The short length of individual deep sequencing reads creates some sequence runs that don’t map to a unique loci on […]
Putting Epigenetics on the MapOctober 12, 2009Between the mapping centers, generating enormous quantities of data for the NIH Roadmap Epigenomics Initiative, and the NCBI that is archiving and distributing it, lies the Epigenomics Data Analysis and Coordination Center. Aleksandar Milosavljevic and co-PI Arthur Beaudet won the 5-year, $7+ million U01 grant last year to set up and run the EDACC informatics […]
Raising the Bar on ChIP Antibody QCOctober 1, 2009Nowadays, we still find antibodies at the core of many key lab techniques, but there’s a big difference in what’s going on downstream of the IP today. A few years ago researchers were looking at varying shades of grey on a gel; a gel that didn’t eat up too much grant money. Now, the downstream […]
Small RNA Sequencing Adds Color(Space) to miRNA Dynamics in Stem Cell RegulationOctober 1, 2009For the last few years, stem cell researchers have been intrigued by miRNAs’ Houdini-esqe disappearing act as stem cells embrace their fate. Add in evidence showing how knocking out endogenous miRNA machinery like Ago2 can really add a few kinks to proper neural development and you get a stem cell community that’s fired up to […]
BayesPeak Analysis Ups Your ChIP-Seq GameOctober 1, 2009Proteins have been binding DNA for some time now, but only recently has ChIP-Seqencing (ChiP-Seq) pointed exactly where. As the technique becomes more popular, more researchers are wondering; what’s the best way to analyze the mounds of data they’ve just created with their ChIP-seq experiments? To tackle this problem, a group of bioinformaticians from the […]
