|
| Status |
Public on Jan 15, 2020 |
| Title |
HK2_5_OTA100 |
| Sample type |
SRA |
| |
|
| Source name |
HK-2_100 nM OTA
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HK-2
tissue source: Kidney
cell type: Proximal tubule epithelial cell line
treatment: 100 nM OTA
|
| Treatment protocol |
Cells were incubated for 48h with 0, 10 or 100nM OTA in serum-free media.
|
| Growth protocol |
HK-2 and HEK293-T were cultivated in DMEM/F12 media with 5% FCS. Prior to incubation with OTA, cells were incubated for 24h with serum-free media.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with TriZol Reagent, following the manufacturer's instructions. Eventual gDNA contaminations were removed using Turbo DNAse (ambion, Life Technologies).
rRNA were removed using RiboMinus (Life Technologies) according to the manufacturer's instructions. RNA was fragmented (w/ Tris-acetate, Potassium acetate and Magnesium acetate) and precipitated (w/ 100% Ethanol, Ammonium acetate and glycogen).
Resulting RNAs were used to generate cDNA libraries using Illumina index adapters. 10nM of pools of up to 10 libraries were used for cluster generation (Illumina cBot). Paired end sequencing (2x100bp) was performed on Illumina HiScanHQ and HiSeq 2000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file: HK2_rawCounts.txt
|
| Data processing |
Adaptor removal (Cutadapt - v1.8.1)
Alignment (tophat - 2.0.14)
Counting (featureCounts - 1.4.6)
Genome_build: hg38
Supplementary_files_format_and_content: txt files containing raw counts obtained after Counting with featureCounts
|
| |
|
| Submission date |
Jul 04, 2019 |
| Last update date |
Jan 15, 2020 |
| 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 |
GPL11154 |
| Series (1) |
| GSE133831 |
Whole transcriptome analysis of human kidney cells after exposure to Ochratoxin A |
|
| Relations |
| BioSample |
SAMN12216451 |
| SRA |
SRX6406129 |
