|
| Status |
Public on Feb 12, 2021 |
| Title |
ER-RAS Induced D5plusT |
| Sample type |
SRA |
| |
|
| Source name |
ER-RAS Induced D5plus
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: IMR90 ER:RAS
passage: p13
days after 4oht induction: 5
|
| Treatment protocol |
To induce RAS expression, cells were treated with 4OHT [100nM]
|
| Growth protocol |
IRM90 ER:RAS were grown in DMEM 10% FBS for 7 days. Media was changed at Day 4
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Qiagen RNAeasy kit, following the instructions.
Libraries were prepared according to Illumina's kit instructions (mRNA stranded library prep kit)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
D5plusT_GCCAAT
|
| Data processing |
Illumina Casava version 1.8.4 was used for basecalling.
RNA-seq reads were aligned to human genome hg19 (GRCh37) using TopHat2 version 2.0.11
Gene annotation information from Ensembl GRCh37 were employed
Rsubread featureCounts version 1.18.0 was used to generate gene-based read counts matrix
Genome_build: hg19
Supplementary_files_format_and_content: CSV file containing gene-based read counts matrix
|
| |
|
| Submission date |
Jul 07, 2020 |
| Last update date |
Feb 12, 2021 |
| Contact name |
LMS Bioinformatics Core |
| E-mail(s) |
bioinformatics@lms.mrc.ac.uk
|
| Organization name |
MRC London Institute of Medical Sciences
|
| Department |
Bioinformatics Core
|
| Street address |
Hammersmith Hospital Campus, Du Cane Road
|
| City |
London |
| ZIP/Postal code |
W12 0NN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE153921 |
Analysis of senescence transcriptome upon knockdown of XPO7 [RNA-seq] |
|
| Relations |
| BioSample |
SAMN15463297 |
| SRA |
SRX8678445 |
