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Status |
Public on Feb 26, 2019 |
Title |
19NS-control |
Sample type |
SRA |
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Source name |
19NS glioblastoma cell line, control
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Organism |
Homo sapiens |
Characteristics |
cell line: 19NS cell type: Glioblastoma cells transfection: pLL CMV puro
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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).
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Complete Genomics |
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Description |
Processed data file: 19NS-control_vs_19NS-TP53-R248L_Processed data.txt
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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.
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Submission date |
Jul 27, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Seok Won Ham |
Organization name |
Korea University
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Department |
College of Life Sciences & Biotechnology
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Street address |
Anam-ro 145
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City |
Seoul |
ZIP/Postal code |
02841 |
Country |
South Korea |
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Platform ID |
GPL23525 |
Series (1) |
GSE101980 |
Transcriptome analysis of TP53-R248L overexpressed 19NS patient-derived glioblastoma cells |
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Relations |
BioSample |
SAMN07419983 |
SRA |
SRX3044542 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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