|
| Status |
Public on Apr 24, 2024 |
| Title |
young-rep1-Ribo-seq |
| Sample type |
SRA |
| |
|
| Source name |
IMR90
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: IMR90
cell type: human lung fibroblast
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
IMR90s grown to near-confluence in a 15cm plate were directly lysed using Trizol (Invitrogen), total RNA was isolated using the DirectZol kit (Zymo).
Ribomaps Ltd according to Ivanov et al, 2018
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads pairs were aligned to the human reference genome (GRCh37) and transcriptome (Gencode.v29) using STAR (v2.6.0c).
Quantification of unique quants was done with featureCounts. RUVs function of RUVseq was used to further normalize the counts, prior to differential gene expression estimation using DESeq2
Read coverage tracks (BigWig) were generated and normalized by scale factor using the bamCoverage function of deepTools2 (v3.5.1).
Assembly: GRCh37
Library strategy: Ribo-seq
|
| |
|
| Submission date |
Jul 25, 2023 |
| Last update date |
Apr 24, 2024 |
| Contact name |
Argyris Papantonis |
| E-mail(s) |
argyris.papantonis@med.uni-goettingen.de
|
| Organization name |
University Medical Center Göttingen
|
| Department |
Institute of Pathology
|
| Street address |
Robert-Koch-Str. 40
|
| City |
Göttingen |
| State/province |
Goettingen |
| ZIP/Postal code |
37075 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE238251 |
Rapid and synchronous chemical induction of replicative-like senescence via a small molecule inhibitor [Ribo-seq] |
| GSE238256 |
Rapid and synchronous chemical induction of replicative-like senescence via a small molecule inhibitor |
|
| Relations |
| BioSample |
SAMN36705663 |
| SRA |
SRX21156683 |
