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Sample GSM4975611 Query DataSets for GSM4975611
Status Public on Dec 02, 2021
Title BT_549_SAHA(Vorinostat)_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-HDACi (SAHA/Vorinostat)
Treatment protocol Total RNA was isolated from BT-549 cells treated with vehicle (DMSO), EC359 (100nM), HDACi(Vorinostat-10┬ÁM), 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 HDACi(SAHA/Vorinostat)
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 Dec 02, 2021
Contact name YI ZOU
E-mail(s) zou@uthscsa.edu
Organization name UTHSA-GCCRI
Street address 8403 Floyd Curl Drive
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 SAMN17084590
SRA SRX9686900

Supplementary file Size Download File type/resource
GSM4975611_BT_549_SAHA_1_Genes_ReadCount.txt.gz 93.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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