|
| Status |
Public on Sep 18, 2023 |
| Title |
GSC-040815-C3 |
| Sample type |
SRA |
| |
|
| Source name |
Patient derived Glioma stem cells (GSC)- 040815
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: GSC-040815
treatment: Control
|
| Treatment protocol |
GSC-040815 were treated with vehicle (0.1% DMSO v/v) or ERβ agonist (CIDD-0149897-20 µM) syntesized by Center for Innovative Drug Discovery-UTSA. GSCs 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) for 48 hrs. After 48 hrs of treatment cell pellet were collected and used for RNA isolation.
|
| Growth protocol |
GSC-040815 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 |
Total RNA from vehicle (0.1% DMSO v/v) and CIDD-0149897 treated cells were isolated using RNeasy mini kit (Qiagen). Illumina TruSeq RNA Sample preparation and sequencing was done using UT Health San Antonio sequencing core protocol.
RNA-seq library preparation by following the Illumina TruSeq stranded mRNA sample preparation guide
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
GSCs cultures in neurobasal medium
|
| Data processing |
Illumina bcl2fastq v2.20.0.422 used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC hg19) using HiSAT2 default settings. The aligned BAM files sorted (SAMTools) and then processed using FatureCounts to obtain the counts per gene
gene count measurements were obtained using FeatureCounts
Assembly: hg19
Supplementary files format and content: The processed data files are in tabular format generated by FeatureCounts. Seven (7) columns are: Geneid; Chr; Start; End; Strand; Length; bamFileName
|
| |
|
| Submission date |
Mar 06, 2023 |
| Last update date |
Sep 18, 2023 |
| Contact name |
Yidong Chen |
| E-mail(s) |
cheny8@uthscsa.edu
|
| 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 |
GPL24676 |
| Series (1) |
| GSE226765 |
Preclinical development of brain permeable ERβ agonist for the treatment of glioblastoma |
|
| Relations |
| BioSample |
SAMN33604223 |
| SRA |
SRX19578453 |
