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Sample GSM4120504 Query DataSets for GSM4120504
Status Public on Oct 16, 2019
Title BT142_3
Sample type SRA
 
Source name grade III oligoastrocytoma
Organism Homo sapiens
Characteristics cell line: BT142
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 SAMN13031475
SRA SRX6991963

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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