|
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 |