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Series GSE76922 Query DataSets for GSE76922
Status Public on Sep 05, 2017
Title Comprehensive molecular phenotypic effects of the large deletion on chromosome 22q11.2
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
Summary Purpose: 22q11 Deletion Syndrome (22q11DS) is a disorder caused by a heterozygous deletion of 3 million base pairs containing approximately 50 known genes on chromosome 22q. It occurs in around 1 in 4,000 live births. The common phenotypes of 22q11DS include a large spectrum of congenital anomalies, most notably of the cardiovascular system as well as several developmental neuropsychiatric disorders, in particular schizophrenia and autism spectrum disorders.Here we are testing the hypothesis that, in addition to changing the gene dosage of genes located within the CNV boundaries, large CNVs may have an effect on long-range chromosome interactions and epigenetic profiles.
Methods: We generated Hi-C contact maps for 11 human lymphoblastoid cell lines and performed RNA-Seq on 14 cell lines and ChIP-seq of H3K27ac, H3K27me3 and CTCF for some of the cell lines.
Results: We found dosage effects of 22q11del on chromosome contacts, epigenetic profiles and gene expressions. Extensive changes on these levels caused by 22q11del are global instead of confined to the deletion region only.
Conclusions: Our results shed light on the comprehensive effects of 22q11del on different molecular levels in lymphoblastoid cell lines.
 
Overall design Hi-C data of 6 control and 5 22q11DS cell lines were generated. RNA-seq were performed for 9 control and 5 22q11DS cell lines. ChIP-seq of H3K27ac, H3K27me3 and CTCF were performed for 2 or 3 controls and 3 22q11DS cell lines. All the sequencing was performed using Illumina HiSeq.
 
Contributor(s) Zhang Y, Zhang X, Zhu X, Purmann C, Ward T, Haney M, Weissman S, Urban A
Citation(s) 30559385
Submission date Jan 15, 2016
Last update date May 15, 2019
Contact name Alexander Eckehart Urban
Organization name Stanford University
Department PSYCHIATRY AND BEHAVIORAL SCIENCES
Street address 3165 Porter Drive
City Palo Alto
State/province CA
ZIP/Postal code 94304
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (59)
GSM2040719 ID00014 Hi-C
GSM2040720 ID00015 Hi-C
GSM2040721 ID00016 Hi-C
Relations
BioProject PRJNA308940
SRA SRP068513

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
GSE76922_500000.cbins.txt.gz 39.6 Kb (ftp)(http) TXT
GSE76922_RAW.tar 2.3 Gb (http)(custom) TAR (of BROADPEAK, FPKM_TRACKING, NARROWPEAK, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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