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| Status |
Public on Apr 07, 2020 |
| Title |
ChIP_HSPC_Ser5-P_PolII_input_DKO_rep2 |
| Sample type |
SRA |
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| Source name |
bone marrow cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: bone marrow
cell type: HSPC
genotype: DKO
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| 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).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| 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.
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| Submission date |
May 21, 2019 |
| Last update date |
Apr 07, 2020 |
| Contact name |
Yotaro Ochi |
| Organization name |
Kyoto Univiersity
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| Department |
Department of Pathology and Tumor Biology
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| Street address |
Yoshida-Konoe-cho
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| City |
Kyoto |
| ZIP/Postal code |
606-8501 |
| Country |
Japan |
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| 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 |
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| Relations |
| BioSample |
SAMN11807922 |
| SRA |
SRX5877836 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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