|
| Status |
Public on Dec 03, 2021 |
| Title |
M2VD1 |
| Sample type |
SRA |
| |
|
| Source name |
PBMC
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: peripheral blood mononuclear cells
agent: VD
|
| Treatment protocol |
In Model 1 (M1) treatment with 10 ng/ml lipopolysaccharide (L), 5 µg/ml beta-glucan (B) or 0.1% DMSO (D) for 24 h, then for another 24 h with 10 nM 1,25(OH)2D3 (V) or 0.1% ethanol (E). In Model 2 (M2) treatment order was reversed and in Model 3 (M3) treatment was with both type of stimuli in parallel for 24 h.
|
| 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 |
| |
|
| Data processing |
Read alignment via STAR version 2.6.0c (no trimming step performed)
Read quantification via STAR version 2.6.0c (--quantMode GeneCounts)
Read counts normalization via EdgeR (TMM)
Differential gene expression analysis via EdgeR
Genome_build: hg38, Ensembl annotation version 93
Supplementary_files_format_and_content: Excel tables of normalized read counts and statistical metrics
|
| |
|
| Submission date |
Apr 14, 2021 |
| Last update date |
Dec 03, 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) |
| GSE172052 |
Vitamin D treatment timing is critical for transcriptome modulation of immune challenged primary human cells |
|
| Relations |
| BioSample |
SAMN18740628 |
| SRA |
SRX10600265 |
