GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE31331 Query DataSets for GSE31331
Status Public on Mar 05, 2012
Title Genome-wide transcription factor binding and chromatin methylation marks in the G1ME megakaryocytic progenitor model cell line
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary There are many examples of transcription factor families whose members control gene expression profiles of diverse cell types. However, the mechanism by which closely related factors occupy distinct regulatory elements and impart lineage specificity is largely undefined. Here we demonstrate on a genome wide scale that the hematopoietic GATA factors GATA-1 and GATA-2 bind overlapping sets of genes, often at distinct sites, as a means to differentially regulate target gene expression and to regulate the balance between proliferation and differentiation. We also reveal that the GATA switch, which entails a chromatin occupancy exchange between GATA2 and GATA1 in the course of differentiation, operates on more than a third of GATA1 bound genes. The switch is equally likely to lead to transcriptional activation or repression and, in general, GATA1 and GATA2 act oppositely on switch target genes. In addition, we reveal that genomic regions co-occupied by GATA2 and the ETS factor ETS1 are strongly enriched for regions marked by H3K4me3 and occupied by Pol II. Finally, by comparing GATA1 occupancy in erythroid cells and megakaryocytes, we find that the presence of ETS factor motifs is a major discriminator of megakaryocyte versus red cell specification.
Overall design We used Illumina ChIP-Seq to examine binding of GATA1, GATA2, and ETS1 transcription factors as well as the genomic locations of two histone methylation marks, H3K4me3 and H3K27me3. Except H3K4me3 (1 sample), all data were generated from at least 2 biological replicates of immunoprecipitations from megakaryocyte progenitor cells, G1ME. Input DNA was prepared and sequenced along with each immunoprecipitation and used as a control dataset for binding site identification.
Contributor(s) Dore LC, Chlon TM, Brown CD, White KP, Crispino JD
Citation(s) 22383799, 22771118
Submission date Aug 11, 2011
Last update date May 15, 2019
Contact name Louis C Dore
Organization name Northwestern University
Department Feinberg School of Medicine
Lab Division of Hematology/Oncology
Street address 303 E Superior St., Lurie Bldg 5-250D
City Chicago
State/province IL
ZIP/Postal code 60611
Country USA
Platforms (2)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (7)
GSM777091 G1ME_GATA2
GSM777092 G1ME_GATA1
GSM777093 G1ME_ETS1
SRA SRP007897
BioProject PRJNA146001

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
GSE31331_INPUT.bed.gz 785.1 Mb (ftp)(http) BED
GSE31331_RAW.tar 2.1 Gb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap