 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 12, 2019 |
| Title |
BCR-ABL STAT5 rep2 |
| Sample type |
SRA |
| |
|
| Source name |
hepatopoietic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: hepatopoietic stem cells
condition: retrovirally transduced with BCR-ABL and GFP (BCR-ABL)
chip antibody: anti-STAT5 (sc-835X, Santa Cruz Biotechnology, lot# A0915)
|
| 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 |
| E-mail(s) |
hhirai@kuhp.kyoto-u.ac.jp
|
| 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 |
|
| Relations |
| BioSample |
SAMN07518935 |
| SRA |
SRX3102759 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2746658_AR012_treat_pileup.bdg.bedgraph.gz |
1.1 Gb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
