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Series GSE42132 Query DataSets for GSE42132
Status Public on Dec 15, 2012
Title ChIP-seq analysis of Gli1 and Sox2 input to neural progenitor program and integration with actve histone marks
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary In the vertebrate neural tube, regional Sonic hedgehog (Shh) signaling invokes a time- and concentration-dependent induction of six different cell populations mediated through Gli transcriptional regulators. Elsewhere in the embryo, Shh/Gli responses invoke different tissue appropriate regulatory programs. To elucidate Shh/Gli regulation of neural fate sepcification, we performed Gli1 ChIP-Seq analysis. We further analyzed two transcription factors whose motifs were enriched in Gli1 ChIP data (Sox2 and Foxa2). Two active histone marks (H3K4me2 and H3K27ac) were additionally analyzed to study activity status of Shh-responsive cis-elements.
Overall design Active enhancer histone marks and transcription factor binding patterns were obtained from neuralized emrbyoid bodies. Biological replicates were performed for Gli1 and mock FLAG chips. Histone profiling for enhancer marks were taken from time course experiment performed in parallel.
Contributor(s) Nishi Y, McMahon AP
Citation(s) 23249739
Submission date Nov 07, 2012
Last update date May 16, 2019
Contact name Kevin Peterson
Phone 323-442-8077
Organization name Eli and Edythe Broad-CIRM Center for Regenerative Medicine, University of Southern California Keck School of Medicine
Department Department of Stem Cell Biology and Regenerative Medicine
Lab Andrew McMahon
Street address 1425 San Pablo St.
City Los Angeles
State/province CA
ZIP/Postal code 90033
Country USA
Platforms (3)
GPL9185 Illumina Genome Analyzer (Mus musculus)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (10)
GSM1033095 Gli1FLAG
GSM1033096 Sox2-72h-SAG
GSM1033097 YFP- (mock)
This SubSeries is part of SuperSeries:
GSE42594 cis-Regulation of Shh-directed neural pattering
BioProject PRJNA179206
SRA SRP017126

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Supplementary file Size Download File type/resource
GSE42132_RAW.tar 833.7 Mb (http)(custom) TAR (of BED, TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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