Transcriptomics

Dataset Information

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Estimates of total imprint number withstand transcriptome test


ABSTRACT: The number of transcripts where allelic bias is dependent parent-of-origin was predicted at 100-200 until two recent studies applied RNA-Seq to brain regions from reciprocally crossed inbred mouse strains and identified over a thousand novel imprinted loci, including hundreds present in only males or females. Reanalysis revealed that the vast majority of these novel loci are explained by technical and biological variation of the approach, and are not genuine cases of general or sex-specific parent-of-origin allelic expression. Independent replication projects that, at most, a few dozen novel imprinted transcripts are present in the dataset, in line with previous projections of 100-200 total imprinted transcripts. Whole brain transcriptome analysis of E17.5 F1 embryos from reciprocally crossed C57BL/6J and CastEi/J parents

ORGANISM(S): Mus musculus  

SUBMITTER: Brian DeVeale   Tomas Babak 

PROVIDER: E-GEOD-27016 | ArrayExpress | 2011-12-01

SECONDARY ACCESSION(S): GSE27016SRP006212PRJNA137705

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Critical evaluation of imprinted gene expression by RNA-Seq: a new perspective.

DeVeale Brian B   van der Kooy Derek D   Babak Tomas T  

PLoS genetics 20120329 3


In contrast to existing estimates of approximately 200 murine imprinted genes, recent work based on transcriptome sequencing uncovered parent-of-origin allelic effects at more than 1,300 loci in the developing brain and two adult brain regions, including hundreds present in only males or females. Our independent replication of the embryonic brain stage, where the majority of novel imprinted genes were discovered and the majority of previously known imprinted genes confirmed, resulted in only 12.  ...[more]

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