|
| Status |
Public on Sep 06, 2021 |
| Title |
VDR ko THP-1, 24 h 1,25(OH)2D3, replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
human monocytic cell line THP-1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: monocytic cell line THP-1
crispr/cas9-editing: VDR knockout
treatment: 100 nM 1,25(OH)2D3
treatment time: 24 h
|
| Treatment protocol |
VDR knockout or control cells were either treated with 100 nM of the natural VDR ligand 1,25-dihydroxyvitamin D3 (Sigma-Aldrich) or with vehicle (EtOH).
|
| Growth protocol |
THP-1 human monocytic leukemia cells were grown in RPMI 1640 supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin and the cells were kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with the Quick-RNA Miniprep Kit (Zymo Research).
with VAHTS Stranded mRNA-seq Library Prep Kit for Illumina V2 (Vazyme NR612, poly(A) enrichment)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
V24_KO_N3
|
| Data processing |
FastQC: assessed for quality, adapter content and duplication rates
STAR: alignment to reference genome with the parameter –quantMode GeneCounts for gene-level quantification and otherwise default parameters
DESeq2: computation of differential gene expression with standard parameters and an adjusted p-value cutoff of 0.05
Genome_build: hg19
Supplementary_files_format_and_content: VDR.KO.RNAseq.ResultsTables.4N_l.xlsx
|
| |
|
| Submission date |
Sep 04, 2020 |
| Last update date |
Sep 06, 2021 |
| Contact name |
Timothy Warwick |
| E-mail(s) |
[email protected]
|
| Organization name |
Goethe Universität Frankfurt am Main
|
| Department |
Institute for Cardiovascular Physiology
|
| Street address |
Theodor-Stern-Kai 7
|
| City |
Frankfurt am Main |
| State/province |
Hesse |
| ZIP/Postal code |
60590 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE157514 |
mRNA-seq in VDR knockout and control THP-1 cells |
|
| Relations |
| BioSample |
SAMN16062927 |
| SRA |
SRX9078131 |
