|
| Status |
Public on Mar 19, 2024 |
| Title |
Rep2 POINT-Seq NVP2 INTS11 minus dTAGv-1 |
| 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
|
| Growth protocol |
HCT116 cell lines were maintained in DMEM with 10% fetal bovine serum, pen/strep at 37 °C and 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA for POINT-Seq was extracted using a protocol designed by Sousa-Luis et al., 2021.
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Processed using usegalaxy.org
Adapters removed from sequencing reads using Trim Galore
Alignment with Hisat2 to ensembl GRCh38 (default settings)
Removal of unmapped, multimapped and discordant mapped reads (MAPQ <30) using SAMTools
Merge biological replicates using BamTools
Split reads by strand using SAMTools
Normalised to Drosophila spike-in
Bigwig files generated from split strand BAM files using the bamCoverage of Deeptools
Assembly: GRCh38
Supplementary files format and content: Single nucleotide resolution RPKM bigwig coverage was generated from split strand merged, Drosophila spike-in normalised, replicates
|
| |
|
| 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) |
| GSE243260 |
Human promoter directionality is determined by transcriptional initiation and the opposing activities of INTS11 and CDK9 (TS11dTAG_NVP2_POINT-seq) |
| GSE243266 |
Human promoter directionality is determined by transcriptional initiation and the opposing activities of INTS11 and CDK9 |
|
| Relations |
| BioSample |
SAMN37397717 |
| SRA |
SRX21778639 |
