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Sample GSM860153 Query DataSets for GSM860153
Status Public on Jan 12, 2012
Sample type SRA
Source name MEF_STAT5-OE-IgG
Organism Mus musculus
Characteristics background strain: C57BL/6
genotype/variation: STAT5 overexpression; STAT5A-Stat5-/-
tissue origin: 12.5-13.5-day fetuses
cell type: mouse embryonic fibroblasts (MEFs)
passages: 9-10
chip antibody: IgG control
chip antibody vendor: R&D System
chip antibody cat. #: AB-105C
Treatment protocol After 5 hours starvation in serum free medium with 0.1% of BSA, MEFs were treated with growth hormone for indicated time period.
Growth protocol Stat5+/- mice were bred into the C57BL/6 background. Stat5+/- mice were intercrossed and mouse embryonic fibroblasts (MEFs) were isolated from 12.5-13.5-day fetuses. MEFs were expanded in DMEM with high glucose supplements and 15% fetal bovine serum (FBS). MEFs of passage 9-10 were used for experiments.
Extracted molecule genomic DNA
Extraction protocol After 5-hour starvation, WT, Stat5-/-, or STAT5A-Stat5-/- MEFs were stimulated with or without 1 ug/ml GH for 45 min. MEFs were then cross-linked with 1% formaldehyde for 10 min. Chromatin from 5 × 10^6 cells was used for each ChIP experiment. Antibodies against STAT5 (sc-835, Santa Cruz, California) and IgG (AB-105C, R&D System) were used. The ChIP DNA fragments were blunt-ended, ligated to the Solexa paired-end adaptors, and sequenced with the Illumina Hi-seq 2000 genome analyzer.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Description processed data files: mm9_OE_STAT5_Peaks.bedgraph (available as Series supplementary files)
Data processing Experimental data sets came from wild type (WT-GH), Stat5-/- (KO-GH) and Stat5-/-overexpressing STAT5A (OE-GH) MEFs upon GH stimulation. The mapped tags of STAT5 antibodies and IgG samples were analyzed using the MACS program ( with the following parameters; -mfold = 10,20 -g mm -p 1.0e-4 (p-value cutoff). The identified peaks were further split by using PeakSplitter ( ChIP-seq data obtained from GH-treated Stat5-/- MEFs (Transfected with an empty vector, KO-empty-GH) served as negative controls and were independently processed with the same parameters. We utilized the GAS motif information to accurately identify bona fide STAT5 binding sites. The FIMO DNA motif identification tool ( was used to scan the peak regions with a STAT5 position-specific scoring matrix (p-value threshold: 1e-3). The peaks including at least one GAS motif within their peak regions were regarded as bona fide STAT5 binding and used in this study.
Submission date Jan 11, 2012
Last update date May 15, 2019
Contact name Keunsoo Kang
Phone 82-41-550-3456
Organization name Dankook University
Department Microbiology
Lab Computational Biology Lab
Street address Dandae-ro 119
City Cheonan
State/province Chungnam
ZIP/Postal code 31116
Country South Korea
Platform ID GPL13112
Series (1)
GSE34986 Genome-wide analyses reveal the extent of opportunistic STAT5 binding that does not yield transcriptional activation of neighboring genes.
SRA SRX115361
BioSample SAMN00771529

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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