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Sample GSM8403761 Query DataSets for GSM8403761
Status Public on Jan 19, 2025
Title 60-M-Pt-K4
Sample type SRA
 
Source name eye
Organism Homo sapiens
Characteristics tissue: eye
cell type: pterygium
developmental stage: stage 3
Extracted molecule genomic DNA
Extraction protocol Tissues were fixed with 1% formaldehyde for 15min. After quenching and cell lysis, chromatin sheared via sonication and incubated with protein A agarose beads conjugated with anti-H3K4me3 and anti-H3K9me3. The DNA was extracted with QIAquick PCR purification kits.
ChIP-seq libraries were constructed using TruSeq DNA Sample prep kits and sequenced on an Illumina Novaseq 6000.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Data processing Basecalls were performed for Illumina NovaSeq 6000 output.
ChIP-seq reads were trimmed using Trimmomatic v0.38.
ChIP-seq reads were aligned to the Homo sapiens reference genome GRCh38 using BowTie v1.1.2.
Peaks were called using MACS2 v2.1.1.20160309 and duplicate reads were processed using Picard v0.118.
Peaks annotated using ChIPseeker 1.16.1.
Normalized bedGraph files were generated using MACS2 and converted to bigwig files using bedGraphToBigWig program.
Assembly: hg38
Supplementary files format and content: bigwig
 
Submission date Jul 18, 2024
Last update date Jan 19, 2025
Contact name Hong-Yeoul Ryu
E-mail(s) lme75514757@gmail.com
Organization name Kyungpook National University
Department Biotechnology
Lab Lab of Molecular Epigenetics
Street address Daehak-ro 80
City Daegu
State/province Buk-Gu
ZIP/Postal code 41566
Country South Korea
 
Platform ID GPL24676
Series (1)
GSE272511 Histone H3 lysine 9 tri-methylation is associated with pterygium
Relations
BioSample SAMN42569668
SRA SRX25371031

Supplementary file Size Download File type/resource
GSM8403761_60-M-Pt-K4.bw 174.1 Mb (ftp)(http) BW
GSM8403761_60-M-Pt-K4_tmm.bw 123.7 Mb (ftp)(http) BW
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Raw data are available in SRA

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