|
| Status |
Public on Sep 12, 2023 |
| Title |
WT-GR Veh 2 |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MB-231 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
genotype: wt-GR
treatment: Veh
|
| Treatment protocol |
Cells were treated with vehicle treatment or either 1 uM of Dex for 6 hrs.
|
| Growth protocol |
MDA-MB-231 expressing either wt-GR or S134A-GR were serum starved in IMEM containing 1% DCC for 18 hrs.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Qiagen RNAeasy kit. RNA quality and concentration were assessed by nanodrop.
A TruSeq RNA kit was utilized to prepare and generate the mRNA libraries that were sequenced on the Illumina HiSeq2500 in a 75-base paired-end mode. Forty million reads were sequenced on average per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Total RNA was extracted using the Qiagen RNAeasy kit. RNA quality and concentration were assessed by nanodrop. A TruSeq RNA kit was utilized to prepare and generate the mRNA libraries that were sequenced on the Illumina HiSeq2500 in a 75-base paired-end mode. Forty million reads were sequenced on average per sample.
Quality of raw RNA-seq sequences for each sample was assessed with FastQC. Trimmommatic(v0.33) was used to remove low quality bases and trim adapters. FastQC(v0.11.7) was used again on each filtered FASTQ files to generate a sequence quality plot.
Abundance of transcript was estimated with the featureCounts program in the SubRead package. DESeq2 (Version 1.22.2) was used to evaluate differential expression across groups and generate Principal Component Analysis (PCA) plots
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each sample
|
| |
|
| Submission date |
Dec 19, 2022 |
| Last update date |
Sep 12, 2023 |
| Contact name |
Carol Lange |
| E-mail(s) |
langelab@umn.edu
|
| Organization name |
University of Minnesota
|
| Department |
Masonic Cancer Center
|
| Street address |
2231 6th ST SE
|
| City |
Minneapolis |
| State/province |
MN |
| ZIP/Postal code |
55455 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE221355 |
Glucocorticoid receptors drive breast cancer cell migration and metabolic reprograming via pSer134-GR-induced expression of PDK4 |
|
| Relations |
| BioSample |
SAMN32314604 |
| SRA |
SRX18774970 |
