|
| Status |
Public on Dec 02, 2021 |
| Title |
BT_549_EC359_1 |
| Sample type |
SRA |
| |
|
| Source name |
BT-549, triple negative breast cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BT-549
cell type: triple negative breast cancer
treatment: Treatment-EC359
|
| Treatment protocol |
Total RNA was isolated from BT-549 cells treated with vehicle (DMSO), EC359 (100nM), HDACi(Vorinostat-10µM), EC359+HDACi for 24 h and subjected to RNA-seq analysis
|
| Growth protocol |
BT-549 cells were cultured in RPMI media supplemented with 10% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from BT-549 cells treated with vehicle, EC359, HDACi, and EC359+HDACi was isolated using RNeasy mini kit (Qiagen, Valencia, CA). Illumina TruSeq RNA Sample preparation and sequencing was done using UT Health San Antonio sequencing core protocol.
Total RNA samples about 1-2 micro grams were used for sequencing library preparation according to Illumina TruSeq Total RNA Sample Preparation Guide (Illumina Cat. #: RS-122-2201). Each library was bar-coded and then pooled for cluster generation and sequencing run with 50bp single-end (SE) sequencing protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
BT-549 cells treated with EC359
|
| Data processing |
Illumina bcl2fastq software used for base-calling
Sequenced reads were mapped to Homo_sapiens genome UCSC hg19 using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count with RefSeq annotation
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in tabular format. The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count
|
| |
|
| Submission date |
Dec 15, 2020 |
| Last update date |
May 05, 2025 |
| Contact name |
Zhao Lai |
| E-mail(s) |
laiz@uthscsa.edu
|
| Organization name |
university of texas health science center at san antonio
|
| Department |
GCCRI
|
| Lab |
Genome Sequencing Facility
|
| Street address |
8403 Floyd Curl, MC 7784
|
| City |
San Antonio |
| State/province |
TX |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE163249 |
Targeted inhibition of LIFR enhances therapeutic efficacy of HDAC inhibitors in triple negative breast cancer |
|
| Relations |
| BioSample |
SAMN17084593 |
| SRA |
SRX9686898 |
