|
| Status |
Public on Jul 09, 2019 |
| Title |
SUM159_DMSO_72hr |
| Sample type |
SRA |
| |
|
| Source name |
SUM159 breast carcinoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SUM159
treatment: DMSO 72hr
culture media: DMEM/F12 1:1 supplemented with 5% FBS, 5 µg/ml insulin, 1 µg/ml hydrocortisone
library preparation kit: Illumina TruSeq RNA library kit v2
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated using Qiagen RNeasy Plus kit.
4 µg total RNA and 10 cycles of amplification were used for libraries constructed with KAPA Stranded mRNAseq kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were aligned to the human reference genome (hg38) using STAR 2.4..2a
reads were translated to transcriptome coordinates using Salmon 0.60
Isoform data were collated to single gene IDs using the R package biomaRt, and abundance estimates were upper quartile normalized using R
Genome_build: hg38
Supplementary_files_format_and_content: Processed files (.xlsx) contain normalized transcript abundance estimates, organized by official gene symbol.
|
| |
|
| Submission date |
Jul 10, 2018 |
| Last update date |
Jul 09, 2019 |
| Contact name |
Gary L Johnson |
| E-mail(s) |
glj@med.unc.edu
|
| Phone |
919-843-3107
|
| Organization name |
UNC Chapel Hill SOM
|
| Department |
Pharmacology
|
| Lab |
Gary L. Johnson
|
| Street address |
120 Mason Farm Road Genetic Medicine Building CB#7365
|
| City |
Chapel Hill |
| State/province |
North Carolina |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE116907 |
Response of triple negative breast cancer to BAZ2A/B inhibition and BET bromodomain inhibition alone and in combination (RNAseq) |
| GSE116919 |
Response of triple negative breast cancer to BAZ2A/B inhibition and BET bromodomain inhibition alone and in combination |
|
| Relations |
| BioSample |
SAMN09642229 |
| SRA |
SRX4378998 |
