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| Status |
Public on Aug 21, 2017 |
| Title |
MKN7_wt_H3K27me3 |
| Sample type |
SRA |
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| Source name |
MKN7_wt
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| 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)
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| 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.
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| 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1500 |
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| 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
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| Submission date |
Apr 14, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Masaki Fukuyo |
| E-mail(s) |
fukuyo@chiba-u.jp
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| Organization name |
Chiba University
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| Department |
Department of Molecular Oncology
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| Street address |
1-8-1 Inohana, Chuo-ku
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| City |
Chiba |
| ZIP/Postal code |
260-8670 |
| Country |
Japan |
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| Platform ID |
GPL18460 |
| Series (1) |
| GSE97837 |
Histone modification (H3K4me3, H3K27ac, and H3K27me3) change during EBV infection in gastric epithelial cells |
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| Relations |
| BioSample |
SAMN06758388 |
| SRA |
SRX2737856 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2579149_MKN7_wt_H3K27me3.bigwig |
23.6 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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