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| Status |
Public on Oct 09, 2020 |
| Title |
ChIP-seq WS-sgNTC-H3K23ac-rep2 |
| Sample type |
SRA |
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| Source name |
CRISPR Screening
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| Organism |
Homo sapiens |
| Characteristics |
genotype: Wild type
cell type: WS hMSCs
antibody: Millipore: anti-H3K23ac (07-355)
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| Growth protocol |
MSCs were maintained in MEM-α medium (invitrogen) with 10% fetal bovine serum (FBS, Gemcell), 1% penicillin/streptomycin (Gibco), 10 ng/ml bFGF (JPC). Media was added and the cultured cells were expanded onto additional plates to keep cells at an appropriate culture density.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
One million cells per sample were cross-linked by 1% vol/vol formaldehyde for 8 or 12 minutes at room temperature, if for acetylated ChIP, add additional 20 mM sodium butyrate. Samples were then re-suspended in lysis buffer (50 mM Tris-HCl, 10 mM EDTA, 1% SDS, pH8.0) for 5 min on ice. Subsequently, lysates were sonicated using a Covaris S2 instrument.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Illumina CASAVA version 1.8 were used to the basecalling.
Sequencing adapters, low quality sequences and amplification primers were trimmed from the raw sequencing reads.
Raw ChIP-seq sequencing data were firstly removed adaptors with custom scripts, and then the clean reads were mapped to the reference genome (UCSC human hg19 or the custom combined reference) using bowtie2 (version: 2.2.3) with default parameters. For H3K14ac and H3K23ac, we mapped clean reads into the custom combined reference which was concatenated with human (hg19) and drosophila (dm6) genome, as previously reported. To build the combined reference, we labelled the drosophila reference genome chromosome names with ‘_dm6’ suffix so that we can easily separate the reads mapped into the human or drosophila furtherly. A custom alignment library was built for the combined reference with bowtie2. After mapping process, uniquely mapped reads were retained and then only reads mapped against human genome were removed duplicated reads with macs2 (version: 2.1.1.20160309). For H3K4me3 and H3K9me3, we directly mapped these ChIP-seq data into human genome hg19, and normalized ChIP-seq signal with the number of reads uniquely mapped into the human reference genome.
Genome_build: UCSC human reference genome hg19 and UCSC drosophila reference genome dm6
Supplementary_files_format_and_content: bigwig files include ChIP-seq signal value
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| Submission date |
Dec 20, 2018 |
| Last update date |
Oct 11, 2020 |
| Contact name |
Yuxuan Zheng |
| Organization name |
Fudan University
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| Street address |
825 Zhangheng Rd.
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| City |
Shanghai |
| ZIP/Postal code |
201203 |
| Country |
China |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE124197 |
A Genome-wide CRISPR-Based Screen Identifies KAT7 as a Senescence Driver |
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| Relations |
| BioSample |
SAMN10620700 |
| SRA |
SRX5170681 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3523733_WS-sgNTC-H3K23ac-rep2_norm.bigwig |
268.8 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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