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Series GSE62966 Query DataSets for GSE62966
Status Public on Jan 22, 2015
Title Analysis of allele specific expression and its chromatin state to identify genes that are escaping X chromosome inactivation
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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 in chrX using histone marks, transcriptome, exome and SNP data on two normal cell-line and three cancer cell-line.
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 May 15, 2019
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 (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (29)
GSM1537283 H3K4me3-HMEC_ChIP-seq
GSM1537284 H3K4me3-WI38_ChIP-seq
GSM1537285 H3K4me3-SKBR3_ChIP-seq
This SubSeries is part of SuperSeries:
GSE62907 The inactive X chromosome is epigenetically unstable and transcriptionally labile in breast cancer
BioProject PRJNA266312
SRA SRP049507

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

Supplementary file Size Download File type/resource
GSE62966_HMEC-table-simple_1KbFlankingRegion_Absolute.xls.gz 98.3 Kb (ftp)(http) XLS
GSE62966_HMEC_ChIP-Exome-mRNA_combined.snps.txt.gz 3.6 Kb (ftp)(http) TXT
GSE62966_MDAMB436-table-simple_1KbFlankingRegion_Absolute.xls.gz 114.0 Kb (ftp)(http) XLS
GSE62966_MDAMB436_ChIP-Exome-mRNA_combined.snps.txt.gz 213.4 Kb (ftp)(http) TXT
GSE62966_RAW.tar 391.5 Mb (http)(custom) TAR (of BEDGRAPH, FPKM_TRACKING)
GSE62966_SKBR3-table-simple_1KbFlankingRegion_Absolute.xls.gz 105.2 Kb (ftp)(http) XLS
GSE62966_SKBR3_ChIP-Exome-mRNA_combined.snps.txt.gz 205.7 Kb (ftp)(http) TXT
GSE62966_WI38-table-simple_1KbFlankingRegion_Absolute.xls.gz 110.2 Kb (ftp)(http) XLS
GSE62966_WI38_ChIP-Exome-mRNA_combined.snps.txt.gz 211.3 Kb (ftp)(http) TXT
GSE62966_ZR751-table-simple_1KbFlankingRegion_Absolute.xls.gz 100.5 Kb (ftp)(http) XLS
GSE62966_ZR751_ChIP-Exome-mRNA_combined.snps.txt.gz 202.1 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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