Guide: Peak Calling for ChIP-SeqFebruary 27, 2013Chromatin-immunoprecipitation sequencing (ChIP-seq) is the most widely used technique for analyzing Protein:DNA interactions. Very briefly, cells are cross-linked, fragmented and immunoprecipitated with an antibody specific to the target protein; the resulting ChIP DNA fragments are used as the template in a next-generation sequencing library preparation and many millions of short sequence reads are generated for […]
Guide: Getting Started with ChIP-SeqFebruary 27, 2013Chromatin-immunoprecipitation (ChIP) followed by sequencing of the immuno-precipitated DNA is a powerful tool for the investigation of Protein:DNA interactions. To perform ChIP-seq, chromatin is isolated from cells or tissues and fragmented. Antibodies against chromatin associated proteins are used to enrich for specific chromatin fragments. The DNA is recovered, sequenced and aligned to a reference genome […]
EpiGenie Reviews: Genomic Imprinting – Methods and ProtocolsFebruary 24, 2013Genomic imprinting, or examining instances where paternal and maternal genomes aren’t represented equally, has kept many brilliant minds busy for decades. It has also established the foundations for emerging field of epigenetics. In the 2012 update of Genomic Imprinting: Methods and Protocols, edited by Nora Engel, experts in the field cover the most up to […]
Tackling Heterogeneity with DNA MethylationFebruary 12, 2013Heterogeneity adds value to our culture in numerous ways, but when it comes to analyzing large-scale case/control studies with blood, heterogeneity can be more frustrating than a Rubik’s Cube. Since blood is an easy-to-get, relatively noninvasive specimen, it’s ideal for disease diagnosis and for monitoring the effectiveness of treatments. Scientists have reported that DNA methylation […]
EpiGenie Guide: ChIP Antibody ValidationFebruary 11, 2013If you can find a ChIP Grade or ChIP Validated antibody, then you’ve got a head start. But there’s no reason to stress if you can’t. Leave that for the data analysis part of your experiments (only kidding). A quick check of the spec sheet of any antibody can reveal lots of useful info. Here […]
EpiGenie Reviews: RNA Interference and Viruses – Current Innovations and Future TrendsFebruary 11, 2013RNA interference (RNAi) was first discovered in 1998 and has sparked new innovations and novel research tools for biological research ever since. RNAi has the scientific community buzzing because of it’s huge potential to tackle some of our most dreaded viral infectious diseases, like hepatitis C virus (HCV) and human immunodeficiency virus (HIV). But there […]
The Epigenetics of Organ TransplantationJanuary 31, 2013Dr. Daniel Salomon discusses the state of organ transplants, what obstacles exist, and how epigenetics might be central to improving long-term health in patients. The Challenges in Transplantation My background is in transplantation medicine, transplantation immunology. And my interests are to change the way we manage patients. There’s a huge series of challenges right […]
Top Epigenetics and Non-Coding RNA Conferences for MarchJanuary 23, 2013Although it’s warm and sunny at EpiGenie’s headquarters, we know that most of the northern hemisphere is counting the days to spring. Researchers hungry for great epigenetics and ncRNA conferences also have a lot to look forward to with an impressive line up of conference options kicking off in March. We’ve been paralyzed trying to […]
Making Sense of the Grade: ChIP Validation TerminologyJanuary 17, 2013Antibody vendors have been hard at work to offer antibodies that are suitable for applications like ChIP. Usually these antibodies have been used successfully in peer-reviewed publications. In many cases they’ve been validated internally by an R&D team, and in some cases, each lot may be validated to work in ChIP applications. The tricky part […]
5hmC Analysis TimelineDecember 10, 2012EpiGenie has probably covered developments in 5hmC more than any topic the last couple of years, so we’ve compiled this timeline for you. Scroll along to see what you may have missed if you’ve been out of the loop or lab for a sabbatical.