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Series GSE22162 Query DataSets for GSE22162
Status Public on Nov 02, 2010
Title A SNF2 protein targets variable copy number repeats and thereby influences allele-specific expression
Organisms Homo sapiens; Mus musculus
Experiment type Genome binding/occupancy profiling by array
Genome binding/occupancy profiling by high throughput sequencing
Summary ATRX is an X-linked gene of the SWI/SNF family whose role in vivo is currently unknown. Mutations in ATRX cause syndromal mental retardation. ATRX binds to tandem repeat (TR) sequences both in heterochromatin (e.g. telomeres) and euchromatin. Genes associated with these TRs can be dysregulated when ATRX is mutated and the degree to which their expression changes is determined by the size of the TR, producing skewed allelic expression. This explains the nature of the affected genes, the variable phenotypes seen with identical ATRX mutations and also illustrates a new mechanism underlying variable penetrance. Many of the TRs in ATRX targets are G-rich and predicted to form non-B DNA structures (including G quadruplex) in vivo. We have shown that ATRX binds G quadruplex structures in vitro suggesting a mechanism by which ATRX may play a role in various nuclear processes and how this is perturbed when ATRX is mutated.
Overall design 4 Human Erythroblast, 1 HEP3B and 1 Fibroblast ChIP-ChIP Sample
For ChIP-Seq: one human erythroblasts, one mouse ES, one human erythroblast reference Sample, and one mouse ES input reference Sample.
Contributor(s) Law MJ, Lower KM, Voon HP, Garrick D, Viprakasit V, Mitson M, Zhao Y, Hughes JR, Morris A, Abbott A, Wilder SP, Taylor S, Santos GM, Cross J, Ayyub H, Jones S, Ragoussis J, Rhodes D, Dunham I, Higgs DR, Gibbons RJ
Citation(s) 21029860
Submission date Jun 04, 2010
Last update date May 15, 2019
Contact name Richard J Gibbons
Phone +441865222632
Fax +441865222500
Organization name Weatherall Institute of Molecular Medicine
Department MRC Molecular Haematology Unit
Lab Gibbons
Street address John Radcliffe Hospital,
City Oxford
State/province Oxon
ZIP/Postal code OX3 9DU
Country United Kingdom
Platforms (3)
GPL9052 Illumina Genome Analyzer (Homo sapiens)
GPL9185 Illumina Genome Analyzer (Mus musculus)
GPL10485 Dunham lab Human 16p Array H300A
Samples (10)
GSM551130 FigS4_H300b
GSM551131 ATRX_29-1-7_rep1
GSM551132 FigS4-H300d
SRA SRP002608
BioProject PRJNA127699

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
GSE22162_RAW.tar 4.7 Gb (http)(custom) TAR (of BED, SAM, TXT)
SRA Run SelectorHelp
Processed data provided as supplementary file
Processed data included within Sample table
Raw data are available in SRA

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