|
| Status |
Public on May 13, 2024 |
| Title |
DMSO 3 16h |
| Sample type |
SRA |
| |
|
| Source name |
fibroblast cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: hTERT-immortalized fibroblasts
skin: foreskin
agent: DMSO
time point: 16h
|
| Treatment protocol |
Cells fully confluent were seeded at 20 % confluence in 150 mm dishes, and grown overnight. Cells were synchronized in the G0/G1 phase in serum starvation medium (DMEM supplemented with 0.2 % FBS, 2mM L-glutamine and penicillin/streptomycin) in 5 % CO2 at 37°C for 26 h, and released into S-phase with regular DMEM for the indicated timepoints. 15h or 21h after release cells were treated for 1h with DMSO, DRB (100 microM) or alpha-amanitin (a-Am, 3 microg/ml), followed by RNA extraction.
|
| Growth protocol |
Human immortalized fibroblasts (BJ-hTERT cells) were cultured in DMEM (Sigma-Aldrich) supplemented with 10 % FBS, 2 mM L-glutamine and penicillin/streptomycin in 5 % CO2 at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extracted with RNeasy MiniKit (QIAGEN)
RNA libraries were prepared according to NEBNext Ultra II mRNA Kit (NEB)
single end on 4 Lanes (L1-L4)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
expression analysis at the specific timepoint
DRB_ctr_16_only, aam_ctr_16_only
|
| Data processing |
Single-end RNA-seq data were aligned to the hg38 genome assembly using STAR v.020201
Reads were trimmed to remove RNA contamination via BBDuk
BAM files were sorted and indexed using SAMtools
Counts for each transcribed gene were computed by featureCounts using the annotation of the GENCODE genes
Differential expression analysis in RNA-seq data was conducted by using the package DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: .txt, containing the quantifications over each gene as above described
|
| |
|
| Submission date |
Mar 25, 2021 |
| Last update date |
May 13, 2024 |
| Contact name |
Marco Saponaro |
| E-mail(s) |
m.saponaro@bham.ac.uk
|
| Organization name |
University of Birmingham
|
| Department |
Institute of Cancer and Genomic Sciences
|
| Street address |
Vincent Drive
|
| City |
Birmingham |
| ZIP/Postal code |
B15 2TT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE169596 |
Genome wide identification of replication fork stalling/pausing sites and the interplay between RNA Pol II transcription and DNA replication progression |
| GSE169620 |
Genome wide identification of replication fork stalling/pausing sites and the interplay between RNA Pol II transcription and DNA replication progression |
|
| Relations |
| BioSample |
SAMN18479103 |
| SRA |
SRX10441587 |
