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| Status |
Public on Apr 07, 2020 |
| Title |
ChIP_HL60_SMC1_WT_rep1 |
| Sample type |
SRA |
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| Source name |
HL-60
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HL-60
genotype: WT
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq experiments were performed using c-Kit+ HSPCs or HL-60 cell lines.
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), total Pol II (CST, D8L4Y), Ser5-P Pol II (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 or NovaSeq 6000 (Illumina).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
The sequencing reads were aligned to the reference genome (hg19 or 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: hg19, 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 |
Mar 04, 2020 |
| Last update date |
Apr 08, 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 |
GPL24676 |
| 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 |
SAMN14290361 |
| SRA |
SRX7847347 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4378623_ChIP_HL60_SMC1_rep1_peaks.bed.gz |
27.6 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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