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Status |
Public on Sep 19, 2022 |
Title |
100 pSer2 Pol II ChIP_input |
Sample type |
SRA |
|
|
Source name |
CAL-62_100 nM THZ531
|
Organism |
Homo sapiens |
Characteristics |
cell line: CAL-62 cell type: representative anaplastic thyroid carcinoma cell line treatment: treated with 100 nM THZ531 for 6h chip antibody: none (input)
|
Treatment protocol |
CAL-62 cells were treated with either DMSO or THZ531 for 6 h.
|
Growth protocol |
CAL-62 cells were cultured in Dulbecco's Modified Eagle Medium supplemented with 10% fetal bovine serum (FBS).
|
Extracted molecule |
genomic DNA |
Extraction protocol |
CAL-62 cells were fixed with 1% formaldehyde for 10 minutes at room temperature (RT). Cross-linking was stopped with 150 mM glycine. Cells were harvested and sonicated to obtain chromatin fragments (100–500 bp) with SONICS Vibra-cellTM. Library construction were performed using VAHTS Universal DNA Library Prep Kit (Vazyme, ND607-02) and VATHS DNA Adapters set2 for Illumina (Vazyme Biotech, Cat.N802-01)
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|
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
HiSeq X Ten |
|
|
Data processing |
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. ChIP-Seq data were mapped to reference genome by bowtie2. ChIP-Seq peaks were generated using peak finding algorithm MACS2. Genome_build: hg19 Supplementary_files_format_and_content: bw files were generated by MACS2.
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|
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Submission date |
Sep 19, 2019 |
Last update date |
Sep 19, 2022 |
Contact name |
Meijuan Geng |
E-mail(s) |
gengmeijuan@tmu.edu.cn
|
Organization name |
Tianjin Medical Universuty
|
Street address |
No.22 Qixiangtai Road
|
City |
Tianjin |
ZIP/Postal code |
300070 |
Country |
China |
|
|
Platform ID |
GPL20795 |
Series (2) |
GSE137696 |
Targeting CDK12-mediated transcription regulation in anaplastic thyroid carcinoma [ChIP-seq] |
GSE137698 |
Targeting CDK12-mediated transcription regulation in anaplastic thyroid carcinoma |
|
Relations |
BioSample |
SAMN12786819 |
SRA |
SRX6871367 |