|
| Status |
Public on Oct 16, 2019 |
| Title |
TS603_2 |
| Sample type |
SRA |
| |
|
| Source name |
grade III oligodendroglioma
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: TS603
cell type: Glioma stem cells
idh1 status: IDH1 mutant
|
| Treatment protocol |
Untreated
|
| Growth protocol |
Cells were seeded in DMEM F12 media supplemented with N2, EGF, FGF and Heparan sulphate for 3 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using PureLink RNA Mini kit (Thermo Fisher Scientific) and RNA quality was measured on an Agilent 2100 Bioanalyzer using the RNA 6000 Pico kit (Agilent Technologies).
The transcriptome library was prepared using Illumina TruSeq Stranded mRNA Library Prep kit following the manufacturer’s instructions.
The library was sequenced on Illumina HiSeq 3000 using 150 bp paired-end reads targeting an average coverage of 25 million reads per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Strand-specific RNA-seq reads were analyzed using CCBR Pipeliner
Sequencing reads that passed QC thresholds were trimmed of adaptor sequences and aligned to the human genome (hg19) and STAR was then used for genomic alignment
The transcripts were quantified using salmon and rsem, and differentially-expressed genes were determined using edgeR, DESeq2 and limma/voom.
Derived differentially-expressed genes using thresholds of FDR ≤ 0.05 and fold changes ≥ 1.5 or ≤ -1.5 across all three methods (for some contrasts p ≤ 0.05 and fold change 1.3 or ≤ -1.3).
The functional annotation was carried out using Ingenuity Pathway Analysis (IPA, www.qiagenbioinformatics.com) software.
|
| |
|
| Submission date |
Oct 15, 2019 |
| Last update date |
Oct 16, 2019 |
| Contact name |
Mioara Larion |
| E-mail(s) |
mioara.larion@nih.gov
|
| Phone |
2407606825
|
| Organization name |
National Institutes of Health
|
| Department |
NCI, CCR
|
| Lab |
Neuro-Oncology Branch
|
| Street address |
37 Convent Drive, Building 37
|
| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20893 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE138858 |
RNA sequencing of BT142 and TS603 cell lines |
| GSE138873 |
Metabolic Reprogramming Associated with Aggressiveness Occurs in the G-CIMP-High Molecular Subtypes of IDH1mut Lower Grade Gliomas |
|
| Relations |
| BioSample |
SAMN13031473 |
| SRA |
SRX6991965 |
