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Sample GSM2746653 Query DataSets for GSM2746653
Status Public on Feb 12, 2019
Title MIG whole cell lysate
Sample type SRA
Source name hepatopoietic stem cells
Organism Mus musculus
Characteristics cell type: hepatopoietic stem cells
condition: retrovirally transduced with GFP alone (MIG)
chip antibody: none
Treatment protocol EML cells were retrovirally transduced with GFP alone (MIG) or BCR-ABL and GFP (BCR-ABL), then GFP positive cells were purified using FACSAria cell sorter.
Growth protocol EML cells were maintained in Iscove Modified Dulbecco’s Medium (IMDM) (Gibco) supplemented with 20 % heat-inactivated horse serum (Gibco) and 10% BHK-MKL conditioned medium as a source of SCF.
Extracted molecule genomic DNA
Extraction protocol EML cells were fixed with fixation buffer (11.1% formaldehyde in culture medium) followed by adding 1.5 M Glycine for neutralization. Fixed cells were lysed with buffer containing sodium dodecyl sulfate and sonicated using Bioruptor (Cosmo Bio, Tokyo, Japan). The sheared chromatin samples were subjected to immunoprecipitation using protein G magnet beads (Dynabeads Protein G, Thermo Fisher Scientific) Antibodies used for ChIP were as follows; normal rabbit IgG (sc-2027X, Santa Cruz Biotechnology), anti-STAT5 (sc-835X, Santa Cruz Biotechnology), anti-STAT5a antibody (sc-1081X, Santa Cruz Biotechnology), normal mouse IgG (sc-2025, Santa Cruz Biotechnology), anti-STAT1 antibody (sc-592X, Santa Cruz Biotechnology), anti-H3K27Ac antibody (308-34843, Wako). Immunoprecipitated chromatins were purified using PCR Purification Kit (Qiagen).
Purified immunoprecipitated chromatins were subjected to a library preparation for next-generation sequencing using TruSeq ChIP Sample Prep Kit (illumina, San Diego, CA, USA), according to the manufacturer’s instruction.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiScanSQ
Data processing Base calls were performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 (ver2.1.0).
Peak call was performed using MACS2 ( ver2.1.0), and the significant enriched regions were determined using whole cell lysate as input (FDR = 0.05).
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files represent the peak calls generated using MACS2
Submission date Aug 18, 2017
Last update date May 15, 2019
Contact name Hideyo Hirai
Phone 81-75-751-3630
Organization name Kyoto University Hospital
Street address 54 Kawahara-cho, Sakyo-ku
City Kyoto
State/province Kyoto
ZIP/Postal code 606-8507
Country Japan
Platform ID GPL16173
Series (1)
GSE102809 BCR-ABL-mediated recruitment of STAT5 revealed by ChIPseq
BioSample SAMN07518940
SRA SRX3102754

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not provided for this record

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