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| Status |
Public on Jan 01, 2020 |
| Title |
U87_Con_2 |
| Sample type |
SRA |
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| Source name |
U87MG cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Glioblastoma cells
tissue: Brain
gender: Male
age: 44 y
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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 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.p12
Supplementary_files_format_and_content: Tab-delimited text file 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 |
Sep 28, 2018 |
| Last update date |
Jan 01, 2020 |
| Contact name |
Jung Yun Kim |
| E-mail(s) |
jyk00300@gmail.com
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| Organization name |
Korea University
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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) |
| GSE120627 |
Transcriptome analysis of ABCB7 overexpressed U87MG glioblastoma cells |
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| Relations |
| BioSample |
SAMN10142644 |
| SRA |
SRX4775274 |
| 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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