|
| Status |
Public on Mar 11, 2024 |
| Title |
vitamin D bolus, day 1, Individual 21 |
| Sample type |
SRA |
| |
|
| Source name |
peripheral blood mononuclear cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: peripheral blood mononuclear cells
disease state: Healthy Individuals
cell type: PBMC
treatment: 80000 IU vitamin D3
time: day 1
|
| Treatment protocol |
Before and after intake of 80000 IU of vitamin D3
|
| Growth protocol |
no in vitro culture
|
| 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 |
After 1 day of vitamin D bolus intake
d1_Ind21
|
| Data processing |
Read alignment using STAR v2.7.2a using defualt parameters
Quantification using FastQC v0.11.9 and Featurecounts v2.0.1 using default parameters
Filtering for protein coding genes and read counts normalization via EdgeR v4.0.14 (TMM-normalized CPM)
Assembly: hg38, Aligned to Ensembl annotation version 111, final annotation (via Biomart) to Ensembl version 111.38
Supplementary files format and content: Excel table of TMM-normalized read counts (CPM; EdgeR pipeline)
|
| |
|
| Submission date |
Mar 06, 2024 |
| Last update date |
Mar 11, 2024 |
| Contact name |
Carsten Carlberg |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute of Animal Reproduction and Food Research, Polish Academy of Sciences
|
| Department |
Food Technology
|
| Lab |
Nutrigenomics
|
| Street address |
Tuwima 10
|
| City |
Olsztyn |
| State/province |
Warmia-Mazury |
| ZIP/Postal code |
10-748 |
| Country |
Poland |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE260981 |
Transcriptome of vitamin D3 bolus supplementation in a cohort of 25 individuals |
|
| Relations |
| BioSample |
SAMN40281476 |
| SRA |
SRX23853775 |
