About this project

As a part of the International Human Epigenome Consortium (IHEC) project, we collected ChIP-seq data of histone modifications as well as RNA-seq and DNA methylation data from various vascular cell types from multiple donors. To catalogue and characterize the transcriptomic and epigenomic landscape in the vascular system, we implemented comprehensive analysis for genome-wide data of active histone modifications and gene expression for nine types of human endothelial cells show below.

• Human aortic endothelial cells (HAoECs)
• Human coronary artery endothelial cells (HCoAECs)
• Human endocardial cells (HENDCs)
• Human pulmonary artery endothelial cells (HPAECs)
• Human umbilical vein endothelial cells (HUVECs)
• Human umbilical artery endothelial cells (HUAECs)
• Human common carotid artery endothelial cells (HCCaECs)
• Human renal artery endothelial cells (HRAECs)
• Human great saphenous vein endothelial cells (HGSVECs)

Data

• Raw read file (Fastq)
  • ChIP-seq: GEO GSE131953
  • RNA-seq: GEO GSE131681
• Mapped read file (BAM)
  • Due to the restriction of my Dropbox account, the folders are locked by the password. The password is humanEC.
  • ChIP-seq
    • Build hg19 and hg38, mapped by BWA
    • B: H3K4me3, C: H3K27ac, INP: Input. For example, “IHEC13_B3.hg19.sort.bam” is a sorted BAM file (build hg19) of H3K4me3 ChIP-seq for IHEC13 (EC13).
  • RNA-seq
    • Build hg19 and hg38, mapped by STAR
• Quality check (QC) results
  • Due to the restriction of my Dropbox account, the folders are locked by the password. The password is humanEC.
  • ChIP-seq
    • B: H3K4me3, C: H3K27ac, INP: Input
  • RNA-seq
• Peak files
  • The reference promoter sites
  • The reference enhancer sites
  • The peak list of each sample is also available at GEO GSE131953.
• Read distribution of histone modifications (PDF)
  • Due to the restriction of my Dropbox account, the folders are locked by the password. The password is humanEC.
  • Build hg19, generated by DROMPA3
  • 1Mbp-width is recommended for a general purpose. 100kbp-width is higher resolution but the file size is large.
  • In H3K4me3andH3K27ac, H3K4me3 and H3K27ac are colored in green and orange, respectively.
• Gene expression data
  • Build GRCh37, generated by kallisto, RSEM and edgeR
  • IMR90 cells from the SRA SRR2952390.
• ChIA-PET for RNA Polymerase II (HUVEC cells)
  • Fastq data is from GEO GSE41553
  • Generated by Mango with default parameter settings.

Program

• DROMPA3
• SSP

Reference

• Nakato R, Wada Y, et al., Comprehensive epigenome characterization reveals diverse transcriptional regulation across human vascular endothelial cells, Epigenetics & Chromatin, vol. 12, issue 1, 77, 2019.
• (In Japanese) 中戸隆一郎,　和田洋一郎, 白髭克彦, エピゲノムのダイナミズムを解き明かす大規模比較解析　―血管内皮細胞を例に, 羊土社「実験医学」増刊号 2016年6月, P1562-1568.

Contact

This site is maintained by Ryuichiro Nakato (rnakato AT iqb.u-tokyo.ac.jp)