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Series GSE62965 Query DataSets for GSE62965
Status Public on Jan 22, 2015
Title Identification of SNPs using genomic DNA and allele specific expression using nascent RNA on snp6 array
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary Disappearance of the Barr body has long been considered a hallmark of cancer, although whether this corresponds to epigenetic instability and transcriptional reactivation, or to genetic loss, has remained unclear. Here we show that in breast cancer cell lines as well as primary breast tumors, the inactive X chromosome frequently displays a highly abnormal 3D nuclear organization, with global perturbations in its characteristic heterochromatic state, including apparent gain of euchromatic marks and lessening of repressive marks such as H3K27me3 and promoter DNA methylation. Genome-wide profiling of chromatin and transcription reveal modified epigenomic landscapes in cancer cells accompanied by a significant degree of X-linked gene reactivation, affecting genes previously implicated in cancer, including the histone deacetylase, HDAC8 and transducin (Beta)-Like 1X-Linked, TBL1X. We provide proof of principle that epigenetic deregulation can indeed perturb the dosage of some X-linked factors and demonstrate that many of these genes are reactivated in primary breast tumors. Our study establishes that the inactive X is subject to epigenetic erosion in a cancer context and sets the stage for the use of chromatin marks and X- chromosome genes as potential biomarkers to assess epigenetic changes in cancer.
Overall design Examination of allele specific expression of genes using nascent RNA on snp6 array by comparing it with snp6 results from genomic DNA.
Contributor(s) Chaligne R, Popova T, Mendoza-Parra M, Saleem MM, Gentien D, Ban K, Piolot T, Leroy O, Mariani O, Gronemeyer H, Vincent-Salomon A, Stern M, Heard E
Citation(s) 25653311
Submission date Nov 04, 2014
Last update date Nov 27, 2018
Contact name Ronan Chaligné
Organization name Institut Curie
Lab Edith Heard's lab
Street address 26, Rue d'Ulm
City Paris
ZIP/Postal code 75248
Country France
Platforms (1)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (10)
GSM1537273 ZR-75-1_nascentRNA_SNP6
GSM1537274 SKBR3_nascentRNA_SNP6
GSM1537275 MDAMB436_nascentRNA_SNP6
This SubSeries is part of SuperSeries:
GSE62907 The inactive X chromosome is epigenetically unstable and transcriptionally labile in breast cancer
BioProject PRJNA266313

Download family Format
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Supplementary file Size Download File type/resource
GSE62965_RAW.tar 604.2 Mb (http)(custom) TAR (of CEL, TXT)
Processed data provided as supplementary file

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