|
| Status |
Public on Mar 06, 2019 |
| Title |
Nuclear RNA-seq EXOSC10-AID Plus auxin rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
HCT116 Nuclear RNA-seq EXOSC10-AID Sleeping Beauty(TIR1) plus auxin
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
genotype/variation: EXOSC10-AID_P2A_[HygromycinR/NeomycinR]_SV40-pA; sleeping_beauty(TIR1; BlasticidinR)
treatment: auxin treated Nuclear RNA
molecule subtype: Nucleoplasmic RNA
|
| Treatment protocol |
Auxin was added to cell media at a final concentration of 500 µM 1 h prior to collection.
|
| 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.
Nuclear RNA was depleted of ribosomal RNA using Illumina Ribo-Zero Gold (Illumina #MRZE706). Library was constructed using Illumina TruSeq® Stranded Total RNA (Illumina #20020596)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
bigwig coverage file were generated for total read or for separate stranded reads
|
| Data processing |
[RNA-seq] Adapters removed from sequencing nuclear RNA-seq reads using Trim Galore v0.4.4 (wrapper tool for Cutadapt v1.9.1).
[RNA-seq] Alignment of nuclear RNA-Seq reads with Hisat2 v2.1.0 to ensembl GRCh38.
[RNA-seq] Properly mapped single end reads were extracted using samtools v1.4.1.
[RNA-seq] For stranded coverge analysis, sense and antisense reads were seperated using samtools v1.4.1.
[RNA-seq] Bigwig files of nuclear RNA-seq reads were generated from BAM files using the bamCoverage of Deeptools v3.0.2
Genome_build: GRCh38
Supplementary_files_format_and_content: Bigwig files of nuclear RNA-seq reads represent normalised read coverage (RPKM) over single bp windows across the genome.
|
| |
|
| Submission date |
Sep 27, 2018 |
| Last update date |
Mar 06, 2019 |
| 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 |
GPL16791 |
| Series (1) |
| GSE120574 |
The immediate impact of exoribonucleolysis on nuclear RNA processing, turnover and transcriptional control revealed by rapid depletion of DIS3, EXOSC10 or XRN2 from human cells |
|
| Relations |
| BioSample |
SAMN10138461 |
| SRA |
SRX4745213 |
