MBD-Sequencing: The Latest Methylation Analysis Cocktail DeliversNovember 17, 2009Add 1 part enriched methylated DNA to 2 parts sequencing lanes, and you have a cocktail that delivers key insights without a data hangover. Last week, a team of Ohio scientists added the latest research recipe that is destined to become a lab fav in Nucleic Acids Research. The crew took the benefits of methylation […]
The Dark-side of Being a Regulatory Star: miRNA Labeling and ManipulationNovember 11, 2009It wasn’t that long ago when cellular miRNAs lived under the radar. They went to work on their targets each day and hung out with other members of the extended RISC family. Their small size and lack of poly-A tails may have kept them out of the spotlight for decades, but the last few years […]
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, […]
miRNA Target Prediction Program Round-upOctober 21, 2009As miRNA discovery continues to skyrocket, the obvious question is: What are these miRNAs targeting? Lately, that topic seems to be as hot as any “Jon & Kate Plus 8” gossip. Several programs have been created to get at that question, and predict targets for miRNAs, but it’s hard to know which ones are really […]
Dr. Adrian Bird: Interview With A Pioneer in Methylated DNAOctober 21, 2009One of the things we enjoy most at EpiGenie is chatting with the researchers who are driving epigenetics forward. So, naturally we were stoked to come across an interview with Dr. Adrian Bird in PLoS Genetics. Adrian Bird is the Buchanan Chair of Genetics at the University of Edinburgh and is also Director of the […]
Non-Coding (RNA) Doesn’t Have to Mean Non-SenseOctober 14, 2009Our understanding of non-coding RNAs has ramped up like a quarter pipe at the X Games over the last several years and, if recent publications are any indication, we’ve only scratched the surface. The realization that just a sliver of our vast transcriptomes is protein-coding, much of it is churned out in both directions, and […]
The First Completed DNA Methylomes Cover All the BasesOctober 14, 2009Halfway into October, we’re deep into post-season baseball. Although, the Padres haven’t given us local San Diegans much to boast about this year (or last), local standouts at the Salk Institute and UCSD knocked one out of the park this week in Nature. Here’s a team that really knows how to cover the bases, all […]
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 […]