|
| Status |
Public on Feb 13, 2024 |
| Title |
T86 control cells |
| Sample type |
SRA |
| |
|
| Source name |
Primary GBM
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Primary GBM
cell line: T86 (patient derived)
cell type: Primary GBM tumor cells
treatment: DMSO
|
| Treatment protocol |
4 million T78, T86 and T111 cells were treated with 50 μM of temozolomide (Sigma-Aldrich) or a DMSO (Sigma-Aldrich) control for 48 hours, after which the media was removed, and the cells were grown in NB + all media for a week
|
| Growth protocol |
Cells were grown in Neurobasal media supplemented with FGF; EGF; N2 and B27 and maintained at 37˚C in a humidified atmosphere of 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Treated and untreated cells in suspension were harvested, and RNA extraction was performed using the RNeasy Mini Kit (Qiagen).
RNA was converted to ds cDNA using the TrueSeq Stranded Total RNA Gold Kit (Illumina), and the ds cDNA pools were sequenced using the HiSeq 1500 System (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
T86
|
| Data processing |
Bowtie2 version 2.1.0 and Tophat2 version 2.0.10 with default parameters were used to align the RNA-seq reads against the human transcriptome and genome. The output files were indexed using Samtools version 0.1.19, and Cufflinks version 2.1.1 was used for sample transcriptome assembly, transcript isoform identification and abundance estimation. Differential gene expression analysis on known UCSC genes was done using the edgeR R-package (version 3.4.2), from the R version 3.0.2 open source-environment.
Assembly: UCSC hg19
Supplementary files format and content: Excel matrix showing cpms
Supplementary files format and content: Text file showing cpms
|
| |
|
| Submission date |
Feb 12, 2024 |
| Last update date |
Feb 13, 2024 |
| Contact name |
Inès CN Avenel |
| E-mail(s) |
ines.clemence.nati.avenel@regionh.dk
|
| Organization name |
BRIC
|
| Street address |
Ole Maaløes Vej 5
|
| City |
København Nv |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL18460 |
| Series (1) |
| GSE255581 |
GDNF/GFRA1 signaling contributes to chemo- and radioresistance in glioblastoma |
|
