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Series GSE48020 Query DataSets for GSE48020
Status Public on Jun 17, 2013
Title Genome-wide ChIP-Seq reveals a dramatic shift in the binding of the transcription factor erythroid Kruppel-like factor during erythrocyte differentiation
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Erythropoiesis is dependent on the activity of transcription factors, including the erythroid-specific erythroid Kruppel-like factor (EKLF). ChIP followed by massively parallel sequencing (ChIP-Seq) is a powerful, unbiased method to map transfactor occupancy. We used ChIP-Seq to study the interactome of EKLF in mouse erythroid progenitor cells and more differentiated erythroblasts. We correlated these results with the nuclear distribution of EKLF, RNA-Seq analysis of the transcriptome, and the occupancy of other erythroid transcription factors. In progenitor cells, EKLF is found predominantly at the periphery of the nucleus, where EKLF primarily occupies the promoter regions of genes and acts as a transcriptional activator. In erythroblasts, EKLF is distributed throughout the nucleus, and erythroblast-specific EKLF occupancy is predominantly in intragenic regions. In progenitor cells, EKLF modulates general cell growth and cell cycle regulatory pathways, whereas in erythroblasts EKLF is associated with repression of these pathways. The EKLF interactome shows very little overlap with the interactomes of GATA1, GATA2, or TAL1, leading to a model in which EKLF directs programs that are independent of those regulated by the GATA factors or TAL1. (Blood.2011;118(17):e139-e148)
Overall design We used ChIP-Seq to study the interactome of EKLF in mouse erythroid progenitor cells and more differentiated erythroblasts and RNA-Seq analysis of the transcriptome.
Contributor(s) Pilon AM, Ajay SS, Kumar SA, Steiner LA, Cherukuri PF, Wincovitch S, Anderson SM, Mullikin JC, Gallagher PG, Hardison RC, Margulies EH, Bodine DM
Citation(s) 21900194
Submission date Jun 17, 2013
Last update date May 15, 2019
Contact name Ross Hardison
Organization name Pennsylvania State University
Street address 303 Wartik Lab
City University Park
State/province PA
ZIP/Postal code 16802
Country USA
Platforms (1)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (7)
GSM1165492 Erythroid_Progenitor_EKLF
GSM1165493 Erythroblast_EKLF
GSM1165494 Erythroid_Progenitor_RNA
BioProject PRJNA208710
SRA SRP026111

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE48020_KLF1_RPKM.txt.gz 648.6 Kb (ftp)(http) TXT
GSE48020_RAW.tar 5.6 Gb (http)(custom) TAR (of BED, BW)
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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