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Series GSE22341 Query DataSets for GSE22341
Status Public on Jun 16, 2010
Title CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression.
Organism Mus musculus
Experiment type Expression profiling by array
Genome binding/occupancy profiling by high throughput sequencing
Summary Gene expression changes were measured between mouse ES cells of three genotypes: WT Chd7, Heterzygous Chd7 Null, Homozygous Chd7 Null. The hypothesis being tested was that CHD7, a chromatin remodeling protein, functions as a transcriptional regulator. This experiment was performed to detect gene targets of CHD7-mediated regulation.

We report the genome-wide binding profile of CHD7, the protein implicated in CHARGE syndrome, in mouse ES cells using ChIP-Seq technology. Combining these data with other genomic datasets, we discover CHD7 to colocalize with other transcription factors including Oct4, Nanog, Sox2, and p300 at gene enhancer elements to regulate ES cell specific gene expression.
Overall design Chd7 wildtype, heterozygous, and homozygous ES cells derived from preimplantation embryos were grown on feeder cells and total RNA was isolated using Trizol. The ratio of ES to feeder cells was estimated at 5:1.

ChIP sequencing of CHD7 and p300 in mouse ES cells
Contributor(s) Schnetz MP, Handoko L, Wei C, Scacheri PC
Citation(s) 20657823
Submission date Jun 14, 2010
Last update date May 15, 2019
Contact name Mike Paul Schnetz
Phone 216.368.1256
Organization name Case Western Reserve University
Department Genetics
Lab Scacheri
Street address 10900 Eulid Ave
City Cleveland
State/province OH
ZIP/Postal code 44106
Country USA
Platforms (2)
GPL6885 Illumina MouseRef-8 v2.0 expression beadchip
GPL9250 Illumina Genome Analyzer II (Mus musculus)
Samples (8)
GSM556139 WT Chd7 replicate 1
GSM556140 Heterozygous Chd7 Null replicate 1
GSM556141 Heterozygous Chd7 Null replicate 2
SRA SRP002695
BioProject PRJNA127519

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Supplementary file Size Download File type/resource
GSE22341_RAW.tar 190.4 Mb (http)(custom) TAR (of SGR, TXT)
GSE22341_matrix_non-normalized.txt.gz 660.9 Kb (ftp)(http) TXT
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Raw data are available on Series record
Processed data included within Sample table
Raw data are available in SRA

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