|
| Status |
Public on Jul 29, 2024 |
| Title |
SKOV3 cells,shSAT1, detached condition, bio rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
SKOV3
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SKOV3
cell type: Ovarian cancer cell line
genotype: SAT1 knockdown
treatment: cell cultured in detached condition
|
| Treatment protocol |
SKOV3 cells were cultured in the attached or detached conditions for 12 hours
|
| Growth protocol |
SKOV3 cells were cultured in complete McCoy’s 5a medium with fetal bovine serum (10%) and penicillin/streptomycin (1%)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated using RNeasy Mini Kit (Qiagen), 1 μg of total RNA was used for the construction of library
RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation (San Diego, CA) using 1μg of total RNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
ds1_quant
raw counts&fold change--shSAT1 vs pLKO--detached_condition.csv
|
| Data processing |
Fastp (version 0.19.7) (Chen et al 2018) was used to perform basic statistics on the quality of the raw reads and obtain clean data.
Salmon (version 1.10.2) was used for transcript quantification from RNA-seq data.
The tximport R package (version 1.32.0) was used to import salmon’s results into DESeq2.
DESeq2 package (version 1.44.0) was used for the detection and analysis of differentially expressed genes
GSEA software and clusterProfiler were used for downstream enriched pathway analysis.
Assembly: hg19
Supplementary files format and content: csv file include fold change, p value and raw counts of genes
|
| |
|
| Submission date |
May 15, 2024 |
| Last update date |
Jul 29, 2024 |
| Contact name |
Chaoyun Pan |
| E-mail(s) |
chaoyun.pan@outlook.com
|
| Organization name |
Sun Yat-sen University
|
| Street address |
74 Zhongshan Er Rd.
|
| City |
Guangzhou |
| ZIP/Postal code |
510080 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE267614 |
Effect of detachment culture condition and depletion of SAT1 on gene expression in SKOV3 ovarian cancer cell line |
|
| Relations |
| BioSample |
SAMN41411348 |
| SRA |
SRX24569515 |
