|
| Status |
Public on Nov 27, 2021 |
| Title |
Individual #05, 10000 nM 25D, rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Individual #05_10000 nM 25D_PBMC
|
| Organism |
Homo sapiens |
| Characteristics |
subject id: Individual #05
tissue: peripheral blood mononuclear cells (PBMC)
treatment: 10000 nM 25(OH)D3 for 24 h
|
| Treatment protocol |
treatment for 24 h with either 100 nM, 250 nM, 1000 nM, 10.000 nM 25(OH)D3 (Sigma-Aldrich), 250 nM D3 (Sigma-Aldrich) 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 |
Doseresponse_Individual05_Vit25D3_24h_10000nM_Jan-Feb2019
HKWT5BGXG_Pool1_20s003468-1-1_Carlberg_lane125OH15
|
| Data processing |
Read alignment and quantification via nf-core/rnaseq STAR-Salmon pipeline 3.0 (http://doi.org/10.5281/zenodo.4323183)
Read counts normalization via EdgeR 3.21.1 (TMM)
Differential gene expression analysis via EdgeR 3.21.1
Genome_build: hg38, Ensembl annotation version 103
Supplementary_files_format_and_content: Excel tables of normalized read counts and statistical metrics
|
| |
|
| Submission date |
Jun 30, 2021 |
| Last update date |
Nov 27, 2021 |
| 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) |
| GSE179225 |
Transcriptome-wide profile of 25-hydroxyvitamin D3 in primary immune cells from human peripheral blood |
|
| Relations |
| BioSample |
SAMN19976648 |
| SRA |
SRX11322172 |
