|
| Status |
Public on Sep 01, 2022 |
| Title |
RD.R1 |
| Sample type |
SRA |
| |
|
| Source name |
RPE-1 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: RPE-1
treatment: DMSO
|
| Treatment protocol |
Cells were treated with 0.4micromolar aphidicolin or similar volume vehicle (DMSO) as control, for 24hrs, before RNA was extracted.
|
| Growth protocol |
RPE-1 and BJ cells were cultured in media (DMEM-F12 or DMEM, respectively) supplemented with 10% FBS and 100U penicillin/streptomycin, in flasks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Qiagen RNEasy kit
Library construction was performed using Lexogen 3’ tagSeq kit and RNAseq was carried out at Bart's and the London Genome Centre.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RPE-1 cells in DMSO replicate 1
bcc34_Log2CPM.txt
|
| Data processing |
RNA-Seq reads were mapped to the human genome (hg38, Genome Reference Consortium GRCh38) using using HISAT2 version 2.1.0
Number of reads aligned to the exonic region of each gene were counted using htseq-count based on the Ensembl annotation.
Genes that achieved at least one read count per million reads (CPM) in at least 25% of the samples were kept.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes log2 cpm values for each sample
|
| |
|
| Submission date |
Mar 10, 2021 |
| Last update date |
Sep 01, 2022 |
| Contact name |
Eleni Maniati |
| E-mail(s) |
e.maniati@qmul.ac.uk
|
| Organization name |
Queen Mary University of London
|
| Department |
Barts Cancer Institute
|
| Lab |
Cancer and Inflammation
|
| Street address |
John Vane Science Centre, Charterhouse Square
|
| City |
London |
| ZIP/Postal code |
EC1M 6BQ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE168689 |
DNA Replication Stress Generates Distinctive landscapes of DNA copy number alterations and chromosome scale losses |
|
| Relations |
| BioSample |
SAMN18250509 |
| SRA |
SRX10310881 |
