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Sample GSM3790124 Query DataSets for GSM3790124
Status Public on Apr 07, 2020
Title ChIP_HSPC_H3K4me3_WT_rep2
Sample type SRA
 
Source name bone marrow cells
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: bone marrow
cell type: HSPC
genotype: WT
Extracted molecule genomic DNA
Extraction protocol ChIP-seq experiments were performed using c-Kit+ HSPCs.
Cells were fixed in PBS with 1% formaldehyde (Thermo Fisher Scientific) for 10 min at room temperature with gentle mixing. The reaction was stopped by adding glycine solution (10x) (Cell Signaling Technology) and incubating for 5 minutes at room temperature, and the cells were washed in cold PBS twice. The cells were then processed with SimpleChIP Plus Sonication Chromatin IP Kit (Cell Signaling Technology) and Covaris E220 (Covaris) according to the manufacturer’s protocol. The antibodies used for ChIP are as follows: STAG1 (Protein Tech, 14015-1-AP), STAG2 (Novus, NBP1-30472), SMC1 (Abcam, ab9262), CTCF (Cell Signaling Technology, D31H2), RUNX1 (Abcam, 23980), Pol2 (Abcam, ab5408), H3K27ac (Cell Signaling Technology, D5E4), H3K27me3 (Cell Signaling Technology, C36B11), H3K4me1 (Cell Signaling Technology, D1A9), or H3K4me3 (Cell Signaling Technology, C42D8). ChIP-seq libraries were constructed using ThruPLEX DNA-seq kit (Takara) according to the manufacturer’s protocol, and then subjected to sequencing using HiSeq 2500 (Illumina).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Data processing The sequencing reads were aligned to the mouse reference genome (mm9) using bowtie (v1.2.2) following trimming of adapters and read tails to a total length of 50 base pairs using cutadapt.
Duplicates and reads on blacklisted regions (ENCODE) were removed by Picard and bedtools, respectively.
Peaks were called using MACS (v2.1.1) for each replicate individually with a p value threshold of 1 x 10–3.
Genome_build: mm9
Supplementary_files_format_and_content: Peaks were called using MACS (v2.1.1) for each replicate individually with a p value threshold of 1 x 10–3.
 
Submission date May 21, 2019
Last update date Apr 08, 2020
Contact name Yotaro Ochi
Organization name Kyoto Univiersity
Department Department of Pathology and Tumor Biology
Street address Yoshida-Konoe-cho
City Kyoto
ZIP/Postal code 606-8501
Country Japan
 
Platform ID GPL17021
Series (2)
GSE131577 Combined Cohesin-Runx1 Deficiency Synergistically Perturbs Chromatin Looping and Causes Myelodysplastic Syndromes [ChIP-seq]
GSE131583 Combined Cohesin-Runx1 Deficiency Synergistically Perturbs Chromatin Looping and Causes Myelodysplastic Syndromes
Relations
BioSample SAMN11807836
SRA SRX5877806

Supplementary file Size Download File type/resource
GSM3790124_ChIP_HSPC_H3K4me3_WT_rep2_peaks2.bed.gz 631.4 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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