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Sample GSM8075533 Query DataSets for GSM8075533
Status Public on Feb 13, 2024
Title T86 GBM cells after TMZ treatment
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: 50 μM TMZ
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_TMZ
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

Supplementary data files not provided
Raw data not provided for this record

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