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Series GSE22111 Query DataSets for GSE22111
Status Public on Feb 08, 2011
Title The Atoh1 targetome in murine postnatal cerebellum
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary A relatively small number of proneural transcription factors specify a multitude of neural progenitor populations in the developing mammalian brain. Despite their importance, little is known about their targets, cellular processes they regulate, or what genomic sites they occupy in vivo. We used an integrated experimental and computational approach, combining RNA-seq, Histone-seq, and Atoh1 ChIP-seq in cerebellar tissue, to identify over 600 targets of Atoh1, an important developmental transcription factor. We validated 10% of these targets and found that Atoh1 directly regulates genes involved not only in early proliferation but also later differentiation, migration, cell adhesion, metabolism, and cytoskeletal organization by recognizing a novel 10 nucleotide Atoh1 E-Box associated motif (AtEAM). This Atoh1 “targetome” is not only a resource for studies aimed at understanding the molecular mechanisms involved in cerebellar development, but our integrated approach provides a framework for future in vivo studies of transcription factors and their targetomes.
Overall design Examination of RNA-seq WT and null expression data (2 reps each), 2 different histone modifications (2 rep each) and IgG control, and Atoh1 DNA-binding (2 reps each) and control in the developing cerebellum
Contributor(s) Klisch TJ, Xi Y
Citation(s) 21300888
Submission date Jun 03, 2010
Last update date May 15, 2019
Contact name Yuanxin Xi
Phone 530-220-2067
Organization name The University of Texas MD Anderson Cancer Center
Department Bioinformatics and Computational Biology
Street address 1400 Pressler St
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
Platforms (1)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
Samples (12)
GSM549935 Atoh1.rep1
GSM549936 Atoh1.rep2
GSM549937 Atoh1.control
BioProject PRJNA128899
SRA SRP002802

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Supplementary file Size Download File type/resource
GSE22111_RAW.tar 7.8 Gb (http)(custom) TAR (of TXT)
GSE22111_readme.txt.gz 1.9 Kb (ftp)(http) TXT
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Processed data provided as supplementary file
Raw data are available in SRA

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