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Sample GSM3991500 Query DataSets for GSM3991500
Status Public on May 23, 2020
Title 4Cseq_Bait1_SNU719_Rep1
Sample type SRA
 
Source name Gastric cancer cell line
Organism Homo sapiens
Characteristics cell type: EBV(+) Gastric cancer cell line
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 Chromosome conformation capture (3C) template was prepared from fixed chromatin following Splinter et al., 2012 (PMID: 22609568). The template was amplified with Expand Long Template Polymerase (Roche #11759060001) using a 4C library construction primers which designed at each bait region.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 1500
 
Description 4Cseq_Bait1_SNU719.bigwig
Data processing BCL2FASTQ version1.8.4 software was used for basecalling.
4C-seq reads were processed using w4Cseq.
fastq files for each sample were extracted from pooled fastq files by w4Cseq using bait region sequence.
bigwig files were generated by w4Cseq.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig
 
Submission date Jul 31, 2019
Last update date May 23, 2020
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 GPL18460
Series (2)
GSE135174 Genome-wide analysis of histone modification alteration in EBV(+) GC cell lines (4C-Seq).
GSE135176 Genome-wide analysis of histone modification alteration in EBV(+) GC cell lines
Relations
BioSample SAMN12400597
SRA SRX6622601

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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