|
| Status |
Public on Jun 21, 2022 |
| Title |
PBMC, 1000 nM 25(OH)D3, 08 h, rep3 |
| Sample type |
SRA |
| |
|
| Source name |
PBMC
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: peripheral blood mononuclear cells
Sex: male
treatment: 25-hydroxyvitamin D3 (1000 nM)
time point: 8 h
|
| Treatment protocol |
Treatment for 4, 8 or 24 h either with 1,25(OH)2D3 (0.1, 1 and 10 nM), 25(OH)2D3 (100, 250, 500, 750 and 1000 nM), 25(OH)D2 (100, 250, 500, 750 and 1000 nM) or solvent (0.1% EtOH).
|
| Growth protocol |
RPMI 1640 medium supplemented with 10% charcoal-depleted fetal calf serum, 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin and were at 37 °C in a humidified 95% air/5% CO2 incubator.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction of total RNA using High Pure RNA Isolation kit (Roche).
rRNA-deplete cDNA library following NEB protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
1000 nM 25(OH)D3 for 8 h
25D3_1000nM_08h_R3
|
| Data processing |
Read alignment and quantification via nf-core/rnaseq STAR-Salmon pipeline 3.0 (http://doi.org/10.5281/zenodo.4323183).
Filtering for protein coding genes, read counts normalization via EdgeR 3.36.0 (TMM-normalized CPM).
Assembly: hg38, Aligned to Ensembl annotation version 103, final annotation (via Biomart) to Ensembl version 104.
Supplementary files format and content: normalized_counts.xlsx: Excel table of TMM-normalized read counts (CPM; EdgeR pipeline).
|
| |
|
| Submission date |
Mar 23, 2022 |
| Last update date |
Jun 21, 2022 |
| Contact name |
Andrea Hanel |
| E-mail(s) |
[email protected], [email protected]
|
| Organization name |
University of Eastern Finland
|
| Department |
Institute of Biomedicine
|
| Lab |
Prof. Carsten Carlberg Lab
|
| Street address |
Yliopistonranta 1E, POB 1627
|
| City |
Kuopio |
| ZIP/Postal code |
70211 |
| Country |
Finland |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE199273 |
Gene-regulatory potential of 25-hydroxyvitamin D3 and D2 |
|
| Relations |
| BioSample |
SAMN26898811 |
| SRA |
SRX14589455 |
