|
| Status |
Public on Mar 19, 2024 |
| Title |
dTAG-RBBP6_minus_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
HCT116
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
cell type: colorectal carcinoma
genotype: BlasticidinR_P2A_2xHA-dTAG-RBBP6
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
Bigwig files were generated from split strand BAM files using the bamCoverage of Deeptools v3.5.0
Log2FC bigwigs files were generated using bamCompare of split strand BAM files
Assembly: GRCh38
Supplementary files format and content: Single nucleotide resolution RPKM bigwig coverage was generated from split strand merged replicates
Supplementary files format and content: Log2FC split strand bigwig RPKM coverage of merged replicates at single nucleotide resolution
|
| |
|
| 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) |
| GSE243265 |
Human promoter directionality is determined by transcriptional initiation and the opposing activities of INTS11 and CDK9 (RBBP6_POINT-Seq) |
| GSE243266 |
Human promoter directionality is determined by transcriptional initiation and the opposing activities of INTS11 and CDK9 |
|
| Relations |
| BioSample |
SAMN37397842 |
| SRA |
SRX21778802 |
