|
| Status |
Public on Aug 22, 2022 |
| Title |
PolII_ChIP_DMSO_R2 |
| Sample type |
SRA |
| |
|
| Source name |
PolII_DMSO
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
spiked-in mouse cell line: BV2a
treatment: DMSO
antibody: RNA pol II antibody (mAb), 39097, Active Motif
|
| Treatment protocol |
Cells were treated with DMSO, DRB, CA, or DRB & CA for the amount of time indicated in the sample's name.
|
| Growth protocol |
HeLa and BV2a cells were maintained in DMEM with 10% fetal bovine serum.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was purified following standard ChIP-seq protocol.
Libraries were prepared according to the protocol of NEBNext(R) Ultra(TM) II DNA Library Prep Kit for Illumina(R) (NEB).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Adapters were trimmed with Cutadapt v1.18.
Mapping to the hg38 and mm10 genomes was performed with STAR v2.7.3a.
Extraction of properly paired and properly mapped reads and Bam files sorting and indexing were done with SAMtools v1.9.
SAMtools was used to PCR deduplicate and subsampling.
Bigwig files were generated with the Deeptools2 v3.4.2 bamCoverage tool.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: bigwig files: Genome-coverage files for all samples.
|
| |
|
| Submission date |
Dec 16, 2021 |
| Last update date |
Aug 22, 2022 |
| Contact name |
Michael Tellier |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Leicester
|
| Department |
Department of Molecular and Cell Biology
|
| Lab |
Tellier Lab
|
| Street address |
Lancaster Road
|
| City |
Leicester |
| State/province |
Select State |
| ZIP/Postal code |
LE1 7HB |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE176541 |
CDK9 and PP2A regulate RNA polymerase II transcription termination and coupled RNA maturation |
|
| Relations |
| BioSample |
SAMN24144945 |
| SRA |
SRX13440549 |
