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Sample GSM2579149 Query DataSets for GSM2579149
Status Public on Aug 21, 2017
Title MKN7_wt_H3K27me3
Sample type SRA
Source name MKN7_wt
Organism Homo sapiens
Characteristics cell line: MKN7
cell type: Gastric cancer cell line
infected with: none (control)
chip antibody: H3K27me3 (Millipore, 07–449,lot 2686928)
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 For ChIP-seq, sonicated nuclear fraction was incubated with each antibody and histone-DNA complexes were isolated.
ChIP-seq libraries were prepared according to Illumina's instructions.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 1500
Data processing For ChIP-seq (K4me3, K27ac), Illumina CASAVA1.8.2 software was used for basecalling and demultiplexing.
For ChIP-seq (K4me3, K27ac), ChIP-seq reads were aligned to hg19 reference human genome, using ELAND (Illumina mapping program)
For H3K27me3 ChIP-seq, BCL2FASTQ version1.8.4 software was used for basecalling.
For H3K27me3 ChIP-seq, ChIP-seq reads were aligned to hg19 reference human genome, using bowtie.
The mapped sequence reads were extended to 500 bp and converted to the continuous signal data in wig format. Wig files were converted to bigwig files using UCSC wigToBigWig program.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig
Submission date Apr 14, 2017
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)
GSE97837 Histone modification (H3K4me3, H3K27ac, and H3K27me3) change during EBV infection in gastric epithelial cells
BioSample SAMN06758388
SRA SRX2737856

Supplementary file Size Download File type/resource
GSM2579149_MKN7_wt_H3K27me3.bigwig 23.6 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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