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 […]
The Ups and Downs of miRNA and MeCP2 in Fetal BrainsFebruary 26, 2013What goes up must come down. And in the developing human brain, when miR-483-5p levels go up, it makes MeCP2 levels go down, according to researchers in a recent report. Problems with MeCP2 cause Rett Syndrome and other neurological disorders. MeCP2 levels are low in fetal stages of development, but high after birth in the […]
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 […]
High Def DNA Methylome Maps Point Out Male and Female Germ Cell DifferencesFebruary 20, 2013What sets males and females apart? Actually, let’s not head there, but how about at the methylome level? Quite a bit it appears. In a recent paper, researchers from Japan report that male and female primordial germ cells (PGCs) have different methylomes during development—at least in mice. While these germ cells divide and move to […]
