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Sample GSM2720032 Query DataSets for GSM2720032
Status Public on Feb 26, 2019
Title 19NS-control
Sample type SRA
 
Source name 19NS glioblastoma cell line, control
Organism Homo sapiens
Characteristics cell line: 19NS
cell type: Glioblastoma cells
transfection: pLL CMV puro
Growth protocol 19NS cell line was cultured in Dulbecco’s Modified Eagle’s Medium/F12 (DMEM/F12) supplemented with B27 (0.2%), epidermal growth factor (EGF; 20 ng/mL), basic fibroblast growth factor (bFGF; 20 ng/mL), penicillin/streptomycin (1%), L-glutamine (2 mmol/L), and gentamicin (50 μg/mL).
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from 19NS cells using Qiazol reagent (Qiagen) according to the manufacturer's instructions.
Libraries were prepared for RNA-seq by using CG RNA-seq platform. All procedures were proceeded by Beijing Genomics Institute (BGI) corporation.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Complete Genomics
 
Description Processed data file: 19NS-control_vs_19NS-TP53-R248L_Processed data.txt
Data processing Data were processed using Complete Genomics sequencing instrument.
Briefly, raw reads were filtered through several steps; removing reads with adaptors, removing reads when unknown bases are more than 10%, and have low quality. After filtering, the remaining reads are stored as FASTQ format.
Reads mapping were processed by using Bowtie2 and BWA softwares.
Gene expression was calculated by FPKM method to eliminate the influence of different gene length and sequencing discrepancy.
Finally, a probability value (PA) was calculated to screen differentially expressed genes.
Genome_build: GRCh38.p4
Supplementary_files_format_and_content: 19NS-control_vs_19NS-TP53-R248L_Processed data.txt: Tab-delimited text file includes contents: [1] NCBI gene accession ID, [2] Gene length, [3] Means of FPKM values for each experimental sets, [4] Log2 ratio of gene expression, [5] Probability value (PA), [6] Gene symbol, [7] Gene description, [8] KEGG orthology, [9] GO component, [10] GO function, [11] GO process, [12] Blast nr.
 
Submission date Jul 27, 2017
Last update date May 15, 2019
Contact name Seok Won Ham
Organization name Korea University
Department College of Life Sciences & Biotechnology
Street address Anam-ro 145
City Seoul
ZIP/Postal code 02841
Country South Korea
 
Platform ID GPL23525
Series (1)
GSE101980 Transcriptome analysis of TP53-R248L overexpressed 19NS patient-derived glioblastoma cells
Relations
BioSample SAMN07419983
SRA SRX3044542

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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