|
| Status |
Public on Jul 08, 2022 |
| Title |
R362N_ctrl_S4 |
| Sample type |
SRA |
| |
|
| Source name |
Kidney
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Kidney
cell type: Primary tubular epithelial cells
genotype: WT
treatment: Control
|
| Treatment protocol |
Cells were transfected with 50 nM siRNA for SOX9 (siSOX9), negative control (siSCR) or control medium (ctrl) for 24 h before harvest.
|
| Growth protocol |
Cells were maintained in DMEM low glucose supplemented with 10% FBS and 1% PEST in humidified atmosphere with 5% CO2 at 37C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Trizol and Qiagen RNeasy kit. 500 ng of total RNA was used for library construction.
Illumina TruSeq Stranded mRNA Library Prep was used for library construction following the manufacturer's protocol with a modification of 15 to 13 PCR cycles in the "Enrich DNA Fragment" step.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Quality of the data was assessed using FastQC (version 0.11.3)
Data was mapped to the human reference genome from Ensembl database (hg19/GRCh37) using STAR (version 2.5.2b)
Mapped reads for each gene were counted using FeatureCount (version 1.6.4)
Differentially expressed genes analysis was performed using DESeq2 (version 1.28.1) in R (version 3.6.1)
Assembly: hg19/GRCh37
Supplementary files format and content: matrix_fixed.txt is a text file containing counts for each sample (columns) and gene (rows)
|
| |
|
| Submission date |
Jul 06, 2022 |
| Last update date |
Jul 08, 2022 |
| Contact name |
Martin E Johansson |
| Organization name |
University of Gothenburg
|
| Street address |
Medicinaregatan 1G
|
| City |
Gothenburg |
| ZIP/Postal code |
41390 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE207594 |
The injury-induced transcription factor SOX9 alters the expression of LBR, HMGA2, and HIPK3 in human kidney |
|
| Relations |
| BioSample |
SAMN29542855 |
| SRA |
SRX16043617 |
