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Sample GSM2794665 Query DataSets for GSM2794665
Status Public on Apr 10, 2018
Title U87-ERβ-KO-1
Sample type SRA
Source name U87 MG glioblastoma cell line
Organism Homo sapiens
Characteristics cell line: U87 MG glioblastoma
genotype/treatment: ERbeta was knocked out in U87 cells using CRISPR/Cas9 system
Treatment protocol Total RNA was isolated from U87 control, U87-ERβ-KO, U87-ERβ1 and U87-ERβ5 cells and subjected to RNAseq analysis
Growth protocol U87 cells were cultured in DMEM supplemented with 10% FBS
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from U87, U87 ERβ-KO, U87 ERβ-KO cells expressing ERβ1 and ERβ5 isoforms using RNeEasy mini kit using manufacturer’s protocol (Qiagen, Valencia, CA).
Total RNA samples about 1-2 µg 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
Data processing Illumina bcl2fastq 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 Sep 26, 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)
GSE104296 Differential effects of estrogen receptor beta isoforms on glioblastoma progression
BioSample SAMN07703377
SRA SRX3218116

Supplementary file Size Download File type/resource
GSM2794665_U87_KO_3_Genes_ReadCount.txt.gz 96.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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