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Status |
Public on Aug 03, 2017 |
Title |
U87MG-control |
Sample type |
SRA |
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Source name |
U87MG_control
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Organism |
Homo sapiens |
Characteristics |
cell line: U87MG cell type: Glioblastoma cells cell line source gender: male cell line source age: 44 years cell line source tissue: Brain transfected with: pCDH-CMV-MCS-EF1-Puro (U87MG-control)
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Growth protocol |
U87MG cells were grown in DMEM medium supplemented with 10% FBS, 1% penicillin-streptomycin, 1% L-glutamine, and gentamicin sulfate (50 μg/ml).
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was isolated from U87MG cells using TRIzol reagent (3 prime) 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) coporation.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Complete Genomics |
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Data processing |
Data were processed using Complete Genomics RNA-seq program. 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: Excel spreadsheet format which 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 |
May 29, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Seon Yong Lee |
E-mail(s) |
sylee2793@gmail.com
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Phone |
010-2699-6715
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Organization name |
Korea University
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Lab |
Cell Growth Regulation Lab.
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Street address |
145 Anam-ro, Seungbuk-gu
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City |
Seoul |
ZIP/Postal code |
02841 |
Country |
South Korea |
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Platform ID |
GPL23525 |
Series (1) |
GSE99385 |
Transcriptome analysis of CD133 overexpressed U87MG glioblastoma cells |
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Relations |
BioSample |
SAMN07175253 |
SRA |
SRX2873456 |
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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