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Title: Characterization of the Imprinting Signature of Mouse Embryo Fibroblasts by RNA Deep Sequencing      
dateReleased:
11-18-2013
description:
Mouse embryo fibroblasts (MEFs) closely resemble mouse embryos and are convenient sources for biochemical studies when cell number may be limiting from mouse embryos. To derive the imprinting signature of MEFs and potentially detect novel imprinted genes we characterized them using strand- and allele-specific RNA deep sequencing. We used Sequenom allelotyping in embryo and adult organs to verify parental allele-specific expression patterns. We found correct parental allele-specific transcription of 32 known ubiquitously imprinted genes in MEFs. Our analysis did not reveal any novel imprinted genes in MEFs, but detected extended parental allele-specific transcription in several known imprinted domains: maternal allele-specific transcription downstream of Grb10 and downstream of Meg3, Rtl1as and Rian in the Dlk1-Dio3 cluster, an imprinted domain implicated in development. We detected paternal allele-specific transcription downstream of Nespas, Peg3, Peg12 and Snurf/Snrpn. These imprinted transcript extensions were not unique to MEFs, but were also present in other somatic cells. Their 5’ end points did not carry opposing chromatin marks or parental allele-specific DNA methylation, suggesting that their parental allele-specific transcription is under the control of the extended genes. Based on the imprinting signature of MEFs, they provide valid models for understanding the biochemical aspects of genomic imprinting. Strand-specific and parental allele-specific RNA-seq was done in female mouse embryo fibroblasts.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-49538
refinement:
raw
alternateIdentifiers:
49538
keywords:
functional genomics
dateModified:
05-03-2014
availability:
available
types:
gene expression
name:
Mus musculus
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-49538/E-GEOD-49538.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-49538/E-GEOD-49538.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE49538
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

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