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Sample GSM2253676 Query DataSets for GSM2253676
Status Public on Apr 28, 2017
Title MKN7_EB#3_RNAseq
Sample type SRA
 
Source name Gastric cancer cell line
Organism Homo sapiens
Characteristics cell line: MKN7
genotype/variation: EBV infected
tissue: stomach
Treatment protocol To transfect TET2 overexpressiong vector and Mock vector, cells were cultured from 16 hours before transfection in RPMI 1640 medium with 10% FBS without Penicillin-Streptomycin, and 2 ug of each vector were transfected with lipofectamine 2000 (Invitrogen, Carlsbad, CA). The transfectants were selected with 2 ug/mL puromycin (Sigma-Aldrich) and cultured for 30 days.
Growth protocol These cells were cultured in RPMI 1640 (Wako, Tokyo, Japan) with 10% fetal bovine serum (FBS) (HyClone SH30910.03, GE Healthcare, Chicago, IL) and Penicillin-Streptomycin (Sigma-Aldrich, St. Louis, MO) at 37 °C in 5% CO2 incubator.
Extracted molecule total RNA
Extraction protocol DNA was extracted using QIAamp DNA Mini Kit (QIAGEN, Hilden, Germany) and RNA was extracted using RNeasy Mini Kit (QIAGEN) following included protocol and treated with DNaseI (QIAGEN).
Libraries were prepared using NEBNext ChIP-Seq Library Preparation Set for Illumina (New England Biolabs) for hMeDIP-seq and MeDIP-seq and TruSeq Stranded mRNA Sample Prep Kit (Illumina) for RNA-seq following the manufacturer’s protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Reads were aligned with BWA (version 0.5.9) for hMeDIP-seq and MeDIP-Seq.
Number of reads were counted for 10 slidings of 300 bp window size and size of each slidings was 100 bp, and the read count within a 300 bp window was divided by total read count with coustom script for hMeDIP-seq.
Aligned reads were converted to BedGraph format with bedtools v2.20.1 for MeDIP-Seq.
Read were aligned with TopHat v1.3.2 and Bowtie (version 0.12.9). Command line options for Tophat were '-r 100' for RNA-Seq.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.0.2. Command line options for cufflinks were '--max-bundle-flags 4000000' for RNA-seq
Genome_build: hg19
Supplementary_files_format_and_content: csv files containing number of reads for each regions of genes divided by total read count were generated from coustom script and converted to xls files. Bedgraph files are generated from bedtools and converted to bigwig file. gtf files include FPKM values were generated using Cufflinks v2.0.2.
 
Submission date Jul 27, 2016
Last update date May 15, 2019
Contact name Masaki Fukuyo
E-mail(s) fukuyo@chiba-u.jp
Organization name Chiba University
Department Department of Molecular Oncology
Street address 1-8-1 Inohana, Chuo-ku
City Chiba
ZIP/Postal code 260-8670
Country Japan
 
Platform ID GPL18573
Series (1)
GSE84897 Genome-wide analysis of DNA hydroxymethylation and methylation during epstein-barr virus infection.
Relations
BioSample SAMN05449696
SRA SRX1981316

Supplementary file Size Download File type/resource
GSM2253676_MKN7_EB3_transcripts.gtf.gz 5.5 Mb (ftp)(http) GTF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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