|
| Status |
Public on Nov 23, 2023 |
| Title |
Acute Vehicle #2 |
| Sample type |
SRA |
| |
|
| Source name |
GBM PDX tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: GBM PDX tumor
cell type: GBM PDX-derived
group: Acute
treatment: Vehicle
|
| Treatment protocol |
For acute samples, mice were treated with vehicle, radiation (2 gy x 3; MWF), quisinostat (10mg/kg; MWF) or combination of IR + quisinostat for one week. For survival studies, similar treatments and treatment groupsw were included except quisinostat treatment was continued until animals were moribund.
|
| Growth protocol |
GB126TdT cells were grown in serum-free neural stem cell media supplemented with EGF and bFGF and puromycin. GB126TdT cells were injected intracranially to induce tumors
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was harvested using the Qiagen Rneasy kit
Library were constructed using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human (Illumina) following the manufacturer's protocol.
RNA-seq (stranded)
|
| |
|
| Library strategy |
ssRNA-seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
700-015
|
| Data processing |
Base calling was done using Bcl2fastq by Illumina
Alignment using Tophat2.1.1, default settings except for --library-type fr-firststrand; used hg19 gtf as reference
RPKM calculated using Cufflinks2.2.1, default setting except -u, --library-type fr-firststrand; used hg19 gtf as reference
Custom pipeline to convert the RPKM to attomoles using ERCC spike-in mix as reference
Average of replicates using custom pipeline
Calculation of relative RNA levels in quisinostat, radiation or quisinostat + radiation treated as compared to vehicle treated samples
Assembly: hg19; PR8 sequences downloaded from FluDB
|
| |
|
| Submission date |
Aug 18, 2023 |
| Last update date |
Nov 23, 2023 |
| Contact name |
Shwetal Mehta |
| Organization name |
Barrow Neurological Institute
|
| Department |
Ivy Brain Tumor Center
|
| Street address |
350 W Thomas Rd
|
| City |
Phoenix |
| State/province |
AZ |
| ZIP/Postal code |
85013 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE241227 |
Quisinostat is a brain-penetrant radiosensitizer in glioblastoma |
|
| Relations |
| BioSample |
SAMN37052220 |
| SRA |
SRX21419514 |
