http://www.cell.com/cell-reports/fulltext/S2211-1247(13)00788-2
Posts Tagged ‘rnaseq’
The Earliest Transcribed Zygotic Genes Are Short, Newly Evolved, and Different across Species
January 26, 2014Allele-specific expression at single cell resolution
January 19, 2014QT:{{”
We discovered abundant (12 to 24%) monoallelic expression of autosomal genes and that expression of the two alleles occurs independently. The monoallelic expression appeared random and dynamic because there was considerable variation among closely related embryonic cells. Similar patterns of monoallelic expression were observed in mature cells. Our allelic expression analysis also demonstrates the de novo inactivation of the paternal X chromosome.
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Use of ontologies in RNAseq data analysis
December 16, 2013came across this paper: http://genomebiology.com/content/11/2/R14, which uses GO for RNA-seq data analysis
looks interesting – GoSeq !
RGASP papers online
November 11, 2013The RGASP papers are now out, back-to-back:
http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.2722.html http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.2714.html A tour de force.
.@markgerstein Both #rnaseq #RGASP papers list the “RGASP Consortium” as an author. But this comprises different people in the 2 papers!
Some notes from a senior author:
* Due to space constraints unfortunately most of the results are in the supplemental data.
* If it is helpful for testing updates to programs, or to compare the results against future methods not yet considered, the analysis code from each study is on GitHub: https://github.com/RGASP-Consortium.
* The papers are not open access, unfortunately.
RNA editing in Drosophila
October 2, 2013http://www.nature.com/nsmb/journal/vaop/ncurrent/full/nsmb.2675.html
They say most editing sites identified by modENCODE are technical artifacts !
Reliable Identification of Genomic Variants from RNA-Seq Data
October 2, 2013Accounting for technical noise in single-cell RNA-seq experiments : Nature Methods : Nature Publishing Group
October 2, 2013Systematic identification of trans eQTLs as putative drivers of known disease associations
September 15, 2013http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.2756.html
“They found SNPs that regulate one gene (Ikaros) in different cell types, meaning they found different cis-regulatory regions for a single gene, that map to different pathways…. they used the cell-type specific information from ENCODE data.”
PLOS Collections: A Primer on Regression Methods for Decoding cis-Regulatory Logic
August 4, 2013#Regression Methods for Decoding cis-Regulatory Logic, incl. interaction terms & non-linear sigmoidal relationships
http://www.ploscollections.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000269
Global Epigenomic Reconfiguration During Mammalian Brain Development
July 27, 2013Lister… Ecker
MT @BiomedRevon: Global #epigenomic reconfiguration during mammalian #brain development http://bit.ly/16lbboa cortex methylation over time
A “map showing how methylation changes in the frontal cortex over time. During the first two years of life… a wave of methylation alters the DNA in genes ”
http://www.sciencemag.org/content/early/2013/07/05/science.1237905
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