|
| Status |
Public on Jan 26, 2021 |
| Title |
SFN_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
WT 9-12 cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell line background: WT 9-12
cell type: immortalized epithelial cell line obtained from patients with ADPKD
genotype/variation: control
treatment: Nrf2 activator sulforaphane (SFN)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA isolation was performed using TRIzol (Invitrogen). Total RNAs from whole kidney were subjected to Oligo dT selection and adaptor ligation.
Construction of RNA-seq library was completed by Novogene company (Beijing, China).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
HISAT2 (version 2.1.0) was used to align paired-end reads to human (hg38) genome. Only unique mapped reads were used in further analysis.
FeatureCounts (version 1.6.0) was used to count reads number for each sample.
R package DESeq2 was used to identify differentially expressed genes, cut-offs were set at foldchange = 1.5 and FDR at 0.05.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.
|
| |
|
| Submission date |
Dec 10, 2019 |
| Last update date |
Jan 29, 2021 |
| Contact name |
Zhiheng Liu |
| E-mail(s) |
[email protected]
|
| Organization name |
Tianjin Medical University
|
| Department |
Tianjin Research Center for Basic Medical Science
|
| Lab |
Gene Expression Laboratory
|
| Street address |
No.22 Qixiangtai Road
|
| City |
Tianjin |
| State/province |
Tianjin |
| ZIP/Postal code |
300070 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE141740 |
Nrf2-mediated enhancer activation ameliorates oxidative stress and cystogenesis in autosomal dominant polycystic kidney disease [RNA-seq] |
| GSE141741 |
Nrf2-mediated enhancer activation ameliorates oxidative stress and cystogenesis in autosomal dominant polycystic kidney disease |
|
| Relations |
| BioSample |
SAMN13521334 |
| SRA |
SRX7299262 |
