|
| Status |
Public on Mar 19, 2024 |
| Title |
RNA Pol II ChIP-Seq INTS11-dTAG minus rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
HCT116
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
cell type: colorectal carcinoma
genotype: INTS11-dTAGv-1_2xHA_P2A_[HygromycinR/NeomycinR]
treatment: minus dTAGv-1
chip antibody: total RNA Pol II
|
| Growth protocol |
HCT116 cell lines were maintained in DMEM with 10% fetal bovine serum, pen/strep at 37 °C and 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling Technologies) using the above mentioned antibody
NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Adapters removed from sequencing reads using Trim Galore 0.6.5dev (Cutadapt v2.9)
Alignment with Hisat2 v2.0.0-beta to ensembl GRCh38 (default settings) with splice awareness disabled
Removal of unmapped, multimapped, discordant mapped and PCR duplicate reads (MAPQ <30) using SAMTools v.1.13
Convert BAM to BEDPE using bedtools v2.30.0 and perform MACS2 v2.2.7.1 peak calling
MACS2 output -log10 qvalue coverage was scaled to Drosophila S2 spike-in reads and converted from bedgraph to bigwig. Scaled biological replicates were merged
Assembly: GRCh38
Supplementary files format and content: Single nucleotide resolution S2 spike-in scaled merged replicate bigwig coverage was generated from MACS2 called peak coverage (-log10 qvalue)
|
| |
|
| Submission date |
Sep 14, 2023 |
| Last update date |
Mar 19, 2024 |
| Contact name |
Steven West |
| E-mail(s) |
s.west@exeter.ac.uk
|
| Phone |
0044(0)1392727458
|
| Organization name |
University of Exeter
|
| Department |
Living Systems Institute
|
| Street address |
Stocker Rd
|
| City |
Exeter |
| State/province |
Devon |
| ZIP/Postal code |
EX4 4QD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE243259 |
Human promoter directionality is determined by transcriptional initiation and the opposing activities of INTS11 and CDK9 (INTS11-dTAG_ChIP-seq) |
| GSE243266 |
Human promoter directionality is determined by transcriptional initiation and the opposing activities of INTS11 and CDK9 |
|
| Relations |
| BioSample |
SAMN37398083 |
| SRA |
SRX21779537 |
