|
| Status |
Public on Sep 27, 2023 |
| Title |
COS-7, siLONP2, biol rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
kidney
|
| Organism |
Chlorocebus aethiops |
| Characteristics |
tissue: kidney
cell line: COS-7
cell type: fibroblast-like cell
genotype: LONP2 knockdown
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from each cell using RNeasy Plus (QIAGEN) after 168 h siRNA transfection.
RNA libraries for RNA-seq were prepared using KAPA stranded RNA‐seq LibraryPrep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
STAR version 2.7.1a
Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35.
Trimmed sequence reads were aligned to the reference Chlorocebus sabaeus genome version ChlSab1.1 (gene annotation from Ensembl 104) or Homo sapiens genome version GRCh38 (gene annotation from Gencode version 37) using STAR version 2.7.1a.
Raw gene expression counts were obtained directly from STAR, and normalization and differential expression analysis were performed using DESeq2 version 1.30.1.
For comparison analyses between COS-7 and U2OS, gene identifiers were converted from C. sabaeus to H. sapiens using the R/Bioconductor package biomaRt (version 2.48.3).
Assembly: ChlSab1.1 and GRCh38
Supplementary files format and content: tab-delimited excel file includes normilised read counts for genes and differential expression analysis for each samples
|
| |
|
| Submission date |
Feb 09, 2023 |
| Last update date |
Sep 27, 2023 |
| Contact name |
Akihiro Yamashita |
| E-mail(s) |
akihiro.yamashita@mail.mcgill.ca
|
| Organization name |
McGill University
|
| Street address |
3801 University Ave
|
| City |
Montreal |
| ZIP/Postal code |
H3A 2B4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL22096 |
| Series (1) |
| GSE224992 |
Effect of peroxisomal proteotoxic stress on gene expression in mammalian cells |
|
| Relations |
| BioSample |
SAMN33230426 |
| SRA |
SRX19325503 |
