|
| Status |
Public on Nov 28, 2024 |
| Title |
3' QUANT-Seq XRN2-dTAG plus dTAGv-1 minus EPAP rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
HCT116
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
cell type: colorectal carcinoma
genotype: XRN2-dTAG_2xHA_P2A_PuromycinR
treatment: 4sU labelled, plus dTAGv-1, minus EPAP
|
| Growth protocol |
HCT116 cell lines were maintained in DMEM with 10% fetal bovine serum, pen/strep at 37 °C and 5% CO2.
|
| Extracted molecule |
nuclear RNA |
| Extraction protocol |
Nuclear RNA was extracted from isolated nuclei using Trizol reagent
DNA-free & rRNA-free nuclear RNA libraries were constructed using QUANT-Seq mRNA 3′ end library preparation kit (Lexogen)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
XRN2_antisense.bw
XRN2_sense.bw
|
| Data processing |
Adapters removed from sequencing reads using Trim Galore
Alignment with Hisat2 v2.0.0-beta to ensembl GRCh38 (default settings)
Removal of unmapped and multimapped reads (MAPQ <30) using SAMTools
Merge biological replicates using BamTools
Split reads by strand using SAMTools
Aligned read lengths were reduced to the 3'-most aligned nucleotide
Bigwig files were generated from split strand BAM files of the 3'-most aligned nucleotide using the bamCoverage of Deeptools, scaling samples based on aligned Drosophila S2 spike-in reads
Assembly: GRCh38
Supplementary files format and content: Single nucleotide resolution S2 spike-in scaled RPKM bigwig coverage was generated from split strand merged replicates
|
| |
|
| Submission date |
Apr 21, 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 |
GPL24676 |
| Series (1) |
| GSE264499 |
Widespread termination of mammalian RNA polymerase II at T-rich DNA sequences (RNA-Seq) |
|
| Relations |
| BioSample |
SAMN41030856 |
| SRA |
SRX24323185 |
