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| 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.
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| 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.
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| |
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| Contributor(s) |
Nishi Y, McMahon AP |
| Citation(s) |
23249739 |
| |
| Submission date |
Nov 07, 2012 |
| Last update date |
May 16, 2019 |
| Contact name |
Kevin Peterson |
| E-mail(s) |
kevin.peterson@med.usc.edu
|
| 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 |
| |
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| Platforms (3) |
| GPL9185 |
Illumina Genome Analyzer (Mus musculus) |
| GPL9250 |
Illumina Genome Analyzer II (Mus musculus) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (10)
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| This SubSeries is part of SuperSeries: |
| GSE42594 |
cis-Regulation of Shh-directed neural pattering |
|
| Relations |
| BioProject |
PRJNA179206 |
| SRA |
SRP017126 |
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