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Sample GSM2462754 Query DataSets for GSM2462754
Status Public on Sep 18, 2017
Title ES2-Liquiritigenin-2
Sample type SRA
Source name ES2 ovarian cancer cell line
Organism Homo sapiens
Characteristics treatment: Treatment
Treatment protocol Total RNA was isolated from ES2 cells that are trated with vehicle or liquiritigenin for 24 h were subjected to RNA-seq analysis
Growth protocol ES2 were cultured in phenol red–free RPMI-1640 medium containing 5% dextran-charcoal treated FBS
Extracted molecule total RNA
Extraction protocol ES2 cells were treated with either vehicle or liquiritigenin for 24 h, and total RNA was isolated using RNAesy mini kit (Qiagen) according to the manufacturer’s instructions. The purity of isolated RNA was determined using Agilent 2100 BioAnalyzer. Illumina TruSeq RNA Sample preparation was performed following manufacturer's protocol, and the samples were run on an Illumina HiSeq 2000 in duplicates.
Total RNA samples about 1-2 micrograms 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 100bp single-end (SE) sequencing protocol.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
Description ES2 cells trated with liquiritigenin
Data processing Illumina bcl2fastq v2.17.1.14 software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
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 Jan 18, 2017
Last update date May 15, 2019
Contact name Yidong Chen
Phone 2105629163
Organization name UT Health Science Center at San Antonio
Department Population Health Sciences
Street address 8403 Floyd Curl Drive, MSC 7784
City San Antonio
State/province Texas
ZIP/Postal code 78229
Country USA
Platform ID GPL21290
Series (1)
GSE93807 Therapeutic utility of natural estrogen receptor beta agonists on ovarian cancer
BioSample SAMN06239801
SRA SRX2501922

Supplementary file Size Download File type/resource
GSM2462754_Sample_ES2_Liq4_Genes_ReadCount.txt.gz 96.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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