|
| Status |
Public on Mar 01, 2019 |
| Title |
CAL_62_H3K27ac |
| Sample type |
SRA |
| |
|
| Source name |
Anaplastic thyroid carcinoma cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Thyroid
tissue type: Anaplastic thyroid carcinoma
chip antibody: H3K27ac (Abcam cat# ab4728)
cell line: CAL-62
|
| Growth protocol |
BCPAP cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin. CAL-62 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) medium supplemented with 20% fetal bovine serum (FBS). All cells were maintained at 37°C in a humidified atmosphere with 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
BCPAP and CAL-62 cells were cross-linked with 1% formaldehyde for 10 min at RT. The crosslink was stopped by adding 1/20 volume of 2.5 M glycine. Cells were washed with PBS and harvested using ChIP lysis buffer. Cells were then sonicated to obtain fragments (100-500 bp) with Bioruptor Sonicator. Immunoprecipitation was performed with H3K27ac antibody (Abcam cat# ab4729). After elution and reversal cross-linking, DNA was purified and sequenced on BGISEQ-500.
Construction of ChIP-seq library was completed by BGI company (Shenzhen,China).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
ChIP-seq data were mapped to human reference genome (GRCh37/hg19) by SOAPaligner/SOAP2
ChIP-Seq peaks were generated using peak finding algorithm MACS (Model-based Analysis for ChIP -Seq, version: MACS-1.4.2)
Reads mapped only once at locus were allowed for peak calling.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files were generated by MACS-1.4.2.
|
| |
|
| Submission date |
Sep 19, 2018 |
| Last update date |
Mar 01, 2019 |
| Contact name |
Xinyi Cao |
| E-mail(s) |
cxyldd@tmu.edu.cn
|
| Phone |
86-22-83336728
|
| Organization name |
Collaborative Innovation Center of Tianjin for Medical Epigenetics
|
| Street address |
Tianjin Medical University No.22 Qixiangtai Road
|
| City |
Tianjin |
| State/province |
Tianjin |
| ZIP/Postal code |
300070 |
| Country |
China |
| |
|
| Platform ID |
GPL23227 |
| Series (2) |
| GSE120175 |
Targeting super-enhancer-driven oncogenic transcription by CDK7 inhibition in anaplastic thyroid cancer [ChIP-Seq] |
| GSE120177 |
Targeting super-enhancer-driven oncogenic transcription by CDK7 inhibition in anaplastic thyroid cancer |
|
| Relations |
| BioSample |
SAMN10092213 |
| SRA |
SRX4715700 |
