|
| Status |
Public on Jul 07, 2022 |
| Title |
Y1 Dexamethasone 1H rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Y1 Dexamethasone 1H rep3
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Y-1 adrenocortical cells
agent: dexamethasone
treatment: 1h
|
| Treatment protocol |
Cells were subcultured separately onto three groups. Cells were subcultured separately onto three groups. The control group treated with vehicle. One group treated with 100nM dexamethasone with 1h. One group treated with 100nM dexamethasone with 24h.
|
| Growth protocol |
Y-1 cells were cultured in DMEM/F12 media supplemented with 10% fetal bovine serum and 1% streptomycin/penicillin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from cell cultures was extracted using TRIzol.
Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Pre Kit for Illumina.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
YD6
|
| Data processing |
Raw data was transformed by Casava version1.8 base calling
Reads were removed with adaptor contamination. The trimmed reads were then aligned to the mouse genome (mm10, GRCm38.95) using STAR (v. 2.5). Reads were mapped to each gene and counted using HTSeq (v.0.6.1).
Fragments Per Kilobase of transcript sequence per Millions (FPKM) were calculated using sequencing depth and gene length on counting of fragments (Mortazavi et al. 2008).
Genome_build: mm10
Supplementary_files_format_and_content: Microsoft excel open XML spreadsheet include read counts
|
| |
|
| Submission date |
Nov 22, 2021 |
| Last update date |
Jul 07, 2022 |
| Contact name |
Sophia Zheng |
| E-mail(s) |
sophia.zheng@auburn.edu
|
| Organization name |
Auburn University
|
| Department |
Anatomy, Physiology 7 Pharmacology
|
| Lab |
Huang Lab
|
| Street address |
1130 Wire Road
|
| City |
Auburn |
| State/province |
AL |
| ZIP/Postal code |
36832 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE189305 |
Next generation sequencing analysis in Y-1 mouse adrenocortical cells after dexamethasone treatment |
|
| Relations |
| BioSample |
SAMN23382832 |
| SRA |
SRX13190083 |
