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Sample GSM4955399 Query DataSets for GSM4955399
Status Public on Dec 01, 2023
Title GSC11_LY500307_2
Sample type SRA
 
Source name glioma stem cells
Organism Homo sapiens
Characteristics treatment: ER[beta] agonist LY500307
tissue: Glioma stem cells
Treatment protocol Total RNA was isolated from GSC11 after treatmet with either vehicle or LY500307 for 24 hours.
Growth protocol Primary GBM cells (GSC-111010) were subjected to CD133 sorting, and isolated CD133+ GSCs (GSC11) were treated with either vehicle or LY500307 (5 µM) for 24 h. Cells were cultured as neurospheres in neurobasal medium supplemented with B27 serum-free supplement, EGF (20 ng/mL), bFGF (20 ng/mL), LIF (10 ng/mL) and heparin (5 µg/mL).
Extracted molecule total RNA
Extraction protocol Cells were subjected to CD133 sorting and isolated CD133+ GSCs were treated with either vehicle or LY500307 (5 µM) for 24 h. Total RNA was isolated using RNeasy mini kit according to the manufacturer’s instructions (Qiagen, Valencia, CA).
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 2000
 
Description Glioma stem cells treated with ERβ agonist LY500307
Data processing Illumina Casava v1.8.2 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 contains the read counts of the genes using htseq-count
 
Submission date Dec 03, 2020
Last update date Dec 01, 2023
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 GPL11154
Series (1)
GSE162614 Activation of estrogen receptor beta signaling reduces stemness of glioma stem cells
Relations
BioSample SAMN16988598
SRA SRX9627069

Supplementary file Size Download File type/resource
GSM4955399_LY_2_Genes_ReadCount.txt.gz 95.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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