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Sample GSM7979670 Query DataSets for GSM7979670
Status Public on Dec 20, 2023
Title HGC27, wt, H3K27ac HiChIP, rep1
Sample type SRA
 
Source name HGC27
Organism Homo sapiens
Characteristics cell line: HGC27
cell type: wildtype
chip antibody: H3K27ac
Growth protocol MEM, 10% fetal bovine serum, 1x penicillin/streptmycin. Cells were cultured at 37C at 5% CO2.
Extracted molecule genomic DNA
Extraction protocol Cells were fixed with 1% formaldehyde for 10 minutes.
Cross-linked cells were lysed and digested with a restriction enzyme, MboI. Digested chromatin was labeled with biotin–14-dATP and blunt-end ligated. Ligated chromatin samples were fragmented using Covaris S220 and immunoprecipitated using anti-H3K27ac antibody, followed by reversal of the crosslinking and DNA purification. Biotinylated DNA fragments were pulled down with streptavidin beads and performed tagmentation with Tn5 transposase (Illumina, Cat. No. 20034198). Bead-conjugated DNA was amplified by PCR and libraries were sequenced using Illumina Hiseq1500 or Novaseq6000.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing *library strategy: HiChIP
Basecalls were performed using bcl2fastq.
H3K27ac HiChIP reads were processed using HiC-Pro v2.11.4.
HiChIP matrix file (hic file) was generated using the Juicer-tools v1.9.862.
Assembly: hg19
Supplementary files format and content: hic
 
Submission date Dec 18, 2023
Last update date Dec 20, 2023
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 GPL24676
Series (2)
GSE250480 Aberrant upregulation of RUNX3 activates developmental genes to drive metastasis in gastric cancer (HiChIP)
GSE250481 Aberrant upregulation of RUNX3 activates developmental genes to drive metastasis in gastric cancer.
Relations
BioSample SAMN38914971
SRA SRX22955529

Supplementary file Size Download File type/resource
GSM7979670_HGC27_wt_H3K27ac_HiChIP_rep1.hic 1.7 Gb (ftp)(http) HIC
SRA Run SelectorHelp
Raw data are available in SRA

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