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| Status |
Public on Jun 21, 2022 |
| Title |
PBMC, 10 nM 1,25(OH)2D3, 24 h, rep3 |
| Sample type |
SRA |
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| Source name |
PBMC
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| Organism |
Homo sapiens |
| Characteristics |
cell type: peripheral blood mononuclear cells
Sex: male
treatment: 1alpha,25-dihydroxyvitamin D3 (10 nM)
time point: 24 h
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| 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).
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| 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.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction of total RNA using High Pure RNA Isolation kit (Roche).
rRNA-deplete cDNA library following NEB protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
10 nM 1,25(OH)2D3 for 24 h
125D3_10nM_24h_R3
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| 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).
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| Submission date |
Mar 23, 2022 |
| Last update date |
Jun 21, 2022 |
| Contact name |
Andrea Hanel |
| E-mail(s) |
[email protected], [email protected]
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| Organization name |
University of Eastern Finland
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| Department |
Institute of Biomedicine
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| Lab |
Prof. Carsten Carlberg Lab
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| Street address |
Yliopistonranta 1E, POB 1627
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| City |
Kuopio |
| ZIP/Postal code |
70211 |
| Country |
Finland |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE199273 |
Gene-regulatory potential of 25-hydroxyvitamin D3 and D2 |
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| Relations |
| BioSample |
SAMN26898796 |
| SRA |
SRX14589470 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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