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Series GSE39757 Query DataSets for GSE39757
Status Public on Dec 21, 2012
Title Transcriptomic analysis of XIST+ and XIST- hES cells
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: Compare the transcriptome of homogeneous XIST+ and XIST- hES cell populations.
Methods: We isolated homogeneous XIST+ and XIST- cell populations. The XIST+ cells correspond to cells with a XIST cloud and one ATRX pinpoint. The XIST- cells correspond to cells with no XIST cloud and one ATRX pinpoint.
Results: We took advantage of the clonal pattern of X-chromosome inactivation in H9 cells and analyzed the data in an allelic manner. By comparing the RNA-Seq data with known H9 SNPs, we identified genomic positions which were relaxed from XCI in XIST- cells compared to XIST+ cells.
Conclusions: Genic as well as unannotated transcripts are massively relaxed from XCI in H9 cells when XIST expression is lost, however, this reactivation is only partial and a large region around the centromere is protected from relaxation of silencing.
Overall design Total RNA (rRNA depleted) profiles of XIST+ and XIST- human embryonic stem cells
Contributor(s) Vallot C, Rougeulle C
Citation(s) 23334669
Submission date Jul 30, 2012
Last update date May 15, 2019
Contact name Céline Vallot
Organization name CNRS/UMR7216
Street address 35 rue Hélène Brion
City Paris
ZIP/Postal code 75013
Country France
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (2)
GSM978784 H9 XIST+
GSM978785 H9 XIST-
BioProject PRJNA171584
SRA SRP014626

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Supplementary file Size Download File type/resource
GSE39757_RAW.tar 417.5 Mb (http)(custom) TAR (of BW)
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Raw data are available in SRA
Processed data provided as supplementary file

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