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Sample GSM2991147 Query DataSets for GSM2991147
Status Public on Aug 22, 2018
Title U87_shPRMT2_1_RNAseq
Sample type SRA
 
Source name U87_shPRMT2_RNAseq
Organism Homo sapiens
Characteristics cell line: U87
cell type: glioblastoma cells
transfected with: shPRMT2 lentivirus
Treatment protocol U87 cells were infected with shPRMT2 lentivirus
Growth protocol The glioblastoma cell lines U87 was cultured in DMEM containing 10% fetal bovine serum (FBS). TPC1115 was obtained from fresh surgical specimens of human primary GBMs and cultured as either monolayer or tumorspheres in DMEM/F12 medium supplemented with N2, B27 (Gibco), 20 ng/ml human Fibroblast Growth Factor-basic (bFGF, Sino Biological, Beijing, China), 20 ng/ml Epidermal Growth Factor-basic (EGF, Sino Biological, Beijing, China).
Extracted molecule total RNA
Extraction protocol Total RNA isolated using Trizol reagent (Ambion)
Construction of RNA-seq library was completed by BGI company (Shenzhen,China).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model BGISEQ-500
 
Data processing RNA-seq analysis was completed by BGI company(Shenzhen,China). For ChIP-seq, Clean reads were obtained from sequencing company.
Clean reads were aligned to human reference genome (hg19) using Bowtie2 version 2.2.9. Only unique mapped reads were used in further analysis.
Peak calling and annotation were performed using MACS version 1.4.2. and ChIPseeker package respectively.
Heatmaps and average profiles were generated by deepTools V2.4.0.
Genome_build: hg19
Supplementary_files_format_and_content: For RNA-seq, tab-delimited text files include FPKM values for each sample. For ChIP-seq, bigwig files were generated using deepTools V2.4.0, score represents the normalized coverage of DNA fragments at a given genomic coordinate.
 
Submission date Feb 09, 2018
Last update date Aug 22, 2018
Contact name xudong Wu
Organization name Tianjin medical university
Street address Qixiangtai Road
City Tianjin
ZIP/Postal code 300070
Country China
 
Platform ID GPL23227
Series (1)
GSE110424 PRMT2 links histone H3R8 asymmetric dimethylation to oncogenic activation and tumorigenesis of glioblastoma
Relations
BioSample SAMN08513919
SRA SRX3678216

Supplementary file Size Download File type/resource
GSM2991147_U87_KD_1_FPKM.txt.gz 123.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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