|
| Status |
Public on Nov 27, 2024 |
| Title |
S-001656716 |
| Sample type |
SRA |
| |
|
| Source name |
TH2 cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: TH2 cells
genotype: WT
treatment: control
|
| Treatment protocol |
To assess the effects of vitamin D, calcitriol stimulation was applied to TH2 cells at a final concentration of 100 nM during the last 24 hours of culture. The vehicle control group was treated with 2% ethanol as a solvent control for calcitriol.
|
| Growth protocol |
Mice were maintained in a virus- and parasite-free animal facility under a 12-hour light/dark cycle with unrestricted access to food and water. Male and female Balb/c mice (aged 6–8 weeks) were obtained from Charles River Laboratories. The mice were bred on diets with varying vitamin D3 concentrations (400 IU, 1000 IU, or 4000 IU per kg of diet) for two generations to establish vitamin D equilibrium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At day 5 of polarization, cells were harvested and total RNA was isolated using the microRNeasy kit (Qiagen) according to the manufacturer's instructions. RNA quality and concentration were evaluated using a Nanodrop 8000 spectrophotometer.
RNA-seq libraries were prepared using the TruSeq® Stranded Total RNA Library Prep Globin Kit (Illumina) following the manufacturer’s protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Library name: S-001656716
Column name in mouse_calcitriol_th2_matrix.csv: S-001656716
|
| Data processing |
Trimmed reads were aligned to the mouse reference genome (GRCm38) using the STAR aligner (v2.7.10a). Gene expression read counts were quantified using HTSeq (v0.13.5).
Assembly: GRCm38
Supplementary files format and content: The processed data files are tab-delimited text files, containing normalized expression values (log-CPM) for each gene across all samples. Gene identifiers are based on Ensembl (GRCm38).
|
| |
|
| Submission date |
Nov 26, 2024 |
| Last update date |
Nov 27, 2024 |
| Contact name |
Vrushali Dipak Fangal |
| E-mail(s) |
[email protected]
|
| Organization name |
Harvard Medical School
|
| Department |
Brigham and Women's Hospital
|
| Lab |
Channing Division of Network Medicine
|
| Street address |
181 Longwood Avenue
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE282941 |
Effect of Vitamin D Modulation on the TH2 Cell Transcriptomic Landscape |
|
| Relations |
| BioSample |
SAMN45068434 |
| SRA |
SRX26888652 |
