|
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.
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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
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|
|
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 |