|
| Status |
Public on Nov 28, 2024 |
| Title |
POINT5-Seq INTS1 plus IAA rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
HCT116
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
cell type: colorectal carcinoma
genotype: INTS1-AID_P2A_[HygromycinR/NeomycinR]_AAVS1(TIR1; PuromycinR)
treatment: plus IAA
|
| 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 HiSeq 4000 |
| |
|
| Data processing |
Adapters removed from sequencing reads using Trim Galore (paired-end mode), discarding read with length <10 bases and quality below Phred score <20.
Alignment with STAR to reference human genome GRCh38 (default settings)
Extract uniquely mapped concordant reads (MAPQ <30) using SAMTools
The 5’ end of each read in POINT-5 was extracted alongside their directionality using an adaptation of the script created for mNET-seq (Nojima et al., 2015)
Merge biological replicates using and separate into forward and reverse strands using SAMTools bitwise flags.
Generate BPM normalised coverage using genomeCoveragebed from Bedtools.
Assembly: GRCh38
Supplementary files format and content: Single nucleotide resolution bins per million (BPM) bigwig coverage was generated from split strand merged replicates
|
| |
|
| Submission date |
Apr 23, 2024 |
| Last update date |
Nov 28, 2024 |
| Contact name |
Steven West |
| E-mail(s) |
[email protected]
|
| 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 |
GPL20301 |
| Series (1) |
| GSE264716 |
Widespread termination of mammalian RNA polymerase II at T-rich DNA sequences (POINT5-Seq) |
|
| Relations |
| BioSample |
SAMN41064284 |
| SRA |
SRX24349673 |
