|
| Status |
Public on Feb 27, 2023 |
| Title |
N8 NRK-52E cells, pH6 |
| Sample type |
SRA |
| |
|
| Source name |
NRK-52E
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell line: NRK-52E
cell type: Epithelial
treatment: pH6
|
| Treatment protocol |
Cells were synchronized for 24h with medium without FCS. The incubation with pH 7.4 or 6.0 was then started and was maintained for 48h
|
| Growth protocol |
NRK-52E and NRK-49F were cultivated with DMEM medium (5% FCS, 1.5g/L NaHCO3), at 37°C, 5% CO2. For co-culture conditions, NRK-49F were directly sed in wells of 6-well plates, while NRK-52E were grown on permeable filter inserts that were embed onto the 6-well plates with the NRK-49F.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with BluZol Reagent, following the manufacturer's instructions. Eventual gDNA contaminations were removed using Turbo DNAse (ambion, Life Technologies).
polyA enrichment (performed by Novogene Europe)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Read alignment (HISAT2 2.1.0)
Read counting (featureCounts - 2.0.0)
Annotation with biomaRt and Ensembl 99
Assembly: rn6
Supplementary files format and content: .csv file including annotation raw counts (output of featureCounts) for each sample
|
| |
|
| Submission date |
Nov 23, 2022 |
| Last update date |
Feb 27, 2023 |
| Contact name |
Virginie Dubourg |
| Organization name |
Martin Luther University - Halle-Wittenberg
|
| Department |
Julius Bernstein Institute for Physiology
|
| Street address |
Magdeburger Str. 6
|
| City |
Halle (Saale) |
| ZIP/Postal code |
06112 |
| Country |
Germany |
| |
|
| Platform ID |
GPL25947 |
| Series (1) |
| GSE218626 |
Acidosis activates the Nrf2-pathway in renal proximal tubule-derived cells through a crosstalk with renal fibroblasts |
|
| Relations |
| BioSample |
SAMN31851373 |
| SRA |
SRX18360544 |
