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Sample GSM2253670 Query DataSets for GSM2253670
Status Public on Apr 28, 2017
Title GES1_Mock_hMeDIPseq
Sample type SRA
Source name Fetal gastric mucosal cell line
Organism Homo sapiens
Characteristics cell line: GES1
genotype/variation: Mock vector
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 genomic DNA
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 MeDIP-Seq
Library source genomic
Library selection 5-methylcytidine antibody
Instrument model Illumina HiSeq 1500
Description 5-hmC antibody (#39769, Active Motif lot#10310001)
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
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 GPL18460
Series (1)
GSE84897 Genome-wide analysis of DNA hydroxymethylation and methylation during epstein-barr virus infection.
BioSample SAMN05449694
SRA SRX1981310

Supplementary file Size Download File type/resource
GSM2253670_20150908_10_hMe_GES1mock_countread.xlsx 3.7 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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