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Sample GSM4085075 Query DataSets for GSM4085075
Status Public on Sep 19, 2022
Title DMSO pSer2 Pol II ChIP_input
Sample type SRA
 
Source name CAL-62_DMSO
Organism Homo sapiens
Characteristics cell line: CAL-62
cell type: representative anaplastic thyroid carcinoma cell line
treatment: treated with DMSO 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)
 
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.
 
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 SAMN12786822
SRA SRX6871365

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not provided for this record

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