RIP-Chip Tears Into miRNP Complex AnalysisJanuary 6, 2010Solving the mysteries of miRNA:mRNA interactions has been a tough case to crack. Correlation studies, and miRNA target prediction algorithms point us in the right direction, but their indirect nature is a little like going to trial with only circumstantial evidence. Researchers from University of Kentucky published a new paper demonstrating how RIP-Chip techniques can […]
Developing Technologies for Improved In Vivo Epigenetic Imaging/AnalysisDecember 15, 2009The NIH is opening up its wallet again for epigenetic technology development. $3.5M will be allocated in 2010 for developing in vivo epigenetic imaging and analysis technologies. According to the grant description, the NIH has recognized that “… the technologies available to determine the epigenetic state of tissues in vivo are extremely limited. The specific […]
ChIPing Away at Small Samples with Direct SequencingDecember 1, 2009One rarely hears mention of deep sequencing without “more” being dropped into the sentence. More coverage, more depth,…more sample? That’s right. As valuable as next generation sequencing platforms have become, those library construction protocols demand a fair amount of sample. Often more than can be coaxed out of a biopsy, or other small cell population. […]
Got miR-2861? Novel miRNA Is Linked to OsteoporosisNovember 18, 2009What can you do to keep your bones healthy and strong? In addition to sporting the ever-trendy milk mustache, you might want to avoid mutations in miR-2861, a newly discovered miRNA involved in osteoblast differentiation. A team of Chinese researchers identified miR-2861 by cloning miRNAs from primary mouse osteoblasts (the cells responsible for bone formation). […]
Epigenetic Drugs: More Than Hype in the PipelineNovember 5, 2009It’s 10 p.m. on a Friday night, and you’re still stuck in the lab doing ChIP assays. As the piercing whine of the sonicator frays your last nerve, you ask yourself again, “Why did I go into epigenetics research…why couldn’t I have chosen something simpler and more straightforward (like rocket science)?” At times like these, […]
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 […]
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 […]
A Tangled Web We Weave When We Practice to RegulateSeptember 10, 2009We’ve all seen them hanging on the freezers and filling otherwise empty wall space in labs–signal transduction maps that look like abstract artwork. They’re enough to make even the most dedicated researcher wonder if there’s light at the end of the tunnel. As difficult as it is to make sense of complex transcriptional cascades, generating […]
