|
| Status |
Public on Jan 02, 2021 |
| Title |
AT1 cells pH 7.4 adapted #3 |
| Sample type |
SRA |
| |
|
| Source name |
prostate cancer
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell line: R3327-AT1 carcinoma
organ: prostate
treatment: pH 7.4; 5 weeks
|
| Treatment protocol |
After growing solid tumors tumors were either sham-treated or inspiratory hypoxia (10% O2)+metaiodobenzylguanidine (itensifying glycolytic acidosis=metabolic acidosis)
|
| Growth protocol |
For cell culture cells were either incubated at pH 7.4 (HEPES buffered) or pH 6.6 (MES buffered) (-) medium for 24 h. For chronic adaptation cells were kept at pH 7.4 or 6.6 for 11 passages (= 5 weeks)
|
| 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 HiSeq2000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
OT03AA_1
AT1_cells_long-term_acidosis.csv
|
| Data processing |
Adaptor removal (Cutadapt - v1.8.1)
Alignment (tophat - 2.0.14)
Counting (featureCounts - 2.0.1)
Annotation with ensembl 98
Genome_build: Rnor6
Supplementary_files_format_and_content: .csv files containing raw counts obtained after Counting with featureCounts
|
| |
|
| Submission date |
Dec 04, 2020 |
| Last update date |
Jan 02, 2021 |
| Contact name |
Oliver Thews |
| E-mail(s) |
oliver.thews@medizin.uni-halle.de
|
| Phone |
+49-345-5574048
|
| Organization name |
University of Halle
|
| Department |
Institute of Physiology
|
| Street address |
Magdeburger Str. 6
|
| City |
Halle/S. |
| ZIP/Postal code |
06112 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17116 |
| Series (1) |
| GSE162705 |
Impact of short- and long-term extracellular acidosis on gene expression of tumors in vitro and in vivo |
|
| Relations |
| BioSample |
SAMN17004616 |
| SRA |
SRX9633917 |
