|
| Status |
Public on Aug 21, 2020 |
| Title |
MDA_MB_231 RNA-seq [SH4-54_1] |
| Sample type |
SRA |
| |
|
| Source name |
Human Breast Cancer
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
cell type: Breast cancer cell line
treatment: SH5-54
|
| Treatment protocol |
Samples were treated for 24 hours with 1µM of Dexamethasone (DEX), 8µM SH4-54, no treatment, or a combination of DEX and SH4-54.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The cells were lysed using 350µL of Qiagen RLT buffer and 1% BME. RNA was extracted using Norgen Animal Tissue RNA Purification Kit according to manufacturer instructions.
RNA-seq libraries were prepared using Illumina TruSeq Stranded RNA Kit with Ribo-Zero Gold and sequenced on the Illumina HiSeq 2500 as 50 cycle single-end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
SH4-54_1
mRNA
processed data file: MB231_DEXwSH454TreamtentsFeatureCountsedited_SH454wDEX.counts.txt
|
| Data processing |
Reads were mapped using HISAT2 version 2.1.0 with parameters --dta -p 28 -t -q -U and sorted with samtools.
A counts file was generated from the bam files using featureCounts version 1.5.1.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: MB231_DEXwSH454TreamtentsFeatureCountsedited_SH454wDEX.counts.txt: Counts file of gene counts for each treatment created with featureCounts version 1.5.1.
|
| |
|
| Submission date |
Sep 16, 2019 |
| Last update date |
Aug 21, 2020 |
| Contact name |
Katherine E Varley |
| Organization name |
University of Utah
|
| Department |
Oncological Sciences
|
| Street address |
2000 Cir of Hope Dr.
|
| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84112 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE137535 |
Gene expression profiling of MDA_MB_231 cell line in response to treatment with Dexamethasone and SH4-54 |
|
| Relations |
| BioSample |
SAMN12768496 |
| SRA |
SRX6855068 |
