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Series GSE39849 Query DataSets for GSE39849
Status Public on Jan 27, 2013
Title Chromatin dynamics and genome-wide profiling of repetitive elements during early mammalian embryogenesis.
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary We have used repetitive elements, including retrotransposons, as model loci to address how and when heterochromatin forms during development. High throughput RNA-sequencing using a Nano-CAGE protocol throughout early embryogenesis revealed that the expression of repetitive elements is abundant in embryonic cells, highly dynamic and stage-specific, with most repetitive elements becoming repressed before implantation. Furthermore, we show that Line L1 elements and IAP retrotransposons become reactivated from both parental genomes in mouse embryos after fertilisation, indicating an open chromatin configuration at the beginning of development. Our data show that the reprogramming process that follows fertilisation is accompanied by a robust transcriptional activation of retrotransposons and suggests that expression of repetitive elements is initially regulated through an RNA-dependent mechanism in mammals.
Overall design Genome Wide profiling of CAGE transcripts using Nano-CAGE and RNAseq in oocytes and 3 different stages of mouse pre-implantation development
Contributor(s) Fadloun A, Torres Padilla M
Citation(s) 23353788
Submission date Aug 02, 2012
Last update date May 15, 2019
Contact name Stephanie Le Gras
Organization name IGBMC
Street address 1, rue Laurent Fries
ZIP/Postal code 67404
Country France
Platforms (1)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (4)
GSM980385 2cells_nanoCage
GSM980386 8cells_nanoCage
GSM980387 blastocyste_nanoCage
BioProject PRJNA171857
SRA SRP014655

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE39849_RAW.tar 37.6 Mb (http)(custom) TAR (of BED)
GSE39849_ReadCountPerRepeat.txt.gz 1.3 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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