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Sample GSM7979661 Query DataSets for GSM7979661
Status Public on Dec 20, 2023
Title HGC27, RUNX3KO, H3K4me1, ChIP, rep1
Sample type SRA
 
Source name HGC27
Organism Homo sapiens
Characteristics cell line: HGC27
cell type: RUNX3 knock-out
chip antibody: H3K4me1
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. After quenching and cell lysis, chromatin was sonicated using Picoruptor (Diagenode).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit. 10 ng of DNA was used as starting material for Input and ChIP samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450 bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using Tapestation.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 1500
 
Data processing Basecalls were performed using bcl2fastq.
ChIP-seq experiment were aligned to UCSC human genome (hg19) using bowtie 1.0.1.
Duplicated reads were removed with Picard tools 2.3.0.
bigWig files were generated using HOMER 4.11.1.
Peaks were called using HOMER 4.11.1 findPeaks.
Assembly: hg19
Supplementary files format and content: bigWig
 
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 GPL18460
Series (2)
GSE250479 Aberrant upregulation of RUNX3 activates developmental genes to drive metastasis in gastric cancer (ChIP-seq)
GSE250481 Aberrant upregulation of RUNX3 activates developmental genes to drive metastasis in gastric cancer.
Relations
BioSample SAMN38914980
SRA SRX22955453

Supplementary file Size Download File type/resource
GSM7979661_HGC27_RUNX3KO_H3K4me1_rep1.bw 134.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA

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