March 2021 Data Release

Our latest data release has 2679 annotations and 802 assays from tissues and cell types related to diabetes, diabetic complications,              cardiovascular disease, musculoskeletal disease and many other common diseases.

        Annotations

•  718 Binding Site Annotations from ChIP Atlas
• 840 Histone Modification Annotations from ChIP Atlas
• T1D tissue relevant accessible chromatin and target gene predictions
• Annotations from publications

Publication	Annotation Type
Genetic Regulatory Mechanisms of Smooth Muscle Cells Map to Coronary Artery Disease Risk Loci	accessible chromatin & gene expression
Evolutionary Selection and Constraint on Human Knee Chondrocyte Regulation Impacts Osteoarthritis Risk	accessible chromatin
Genome-scale Capture C promoter interactions implicate effector genes at GWAS loci for bone mineral density	accessible chromatin
Expanded encyclopaedias of DNA elements in the human and mouse genomes	candidate regulatory regions
Index and biological spectrum of human DNase I hypersensitive sites	representative DNase hypersensitivity sites
Adipose Tissue Gene Expression Associations Reveal Hundreds of Candidate Genes for Cardiometabolic Traits	eQTL
Genetic variant effects on gene expression in human pancreatic islets and their implications for T2D	eQTL
Integrative analysis of gene expression, DNA methylation, physiological traits, and genetic variation in human skeletal muscle	eQTL
Effects of Age and Estrogen on Skeletal Gene Expression in Humans as Assessed by RNA Sequencing	gene expression
Adipose Tissue Gene Expression Associations Reveal Hundreds of Candidate Genes for Cardiometabolic Traits	gene expression
Single Cell RNA Sequencing of Human Liver Reveals Distinct Intrahepatic Macrophage Populations	gene expression
Differential open chromatin profile and transcriptomic signature define depot-specific human subcutaneous preadipocytes: primary outcomes	gene expression
Methylome and transcriptome maps of human visceral and subcutaneous adipocytes reveal key epigenetic differences at developmental genes	gene expression
Defining human cardiac transcription factor hierarchies using integrated single-cell heterogeneity analysis	gene expression
An integrated multi-omics approach identifies the landscape of interferon-α-mediated responses of human pancreatic beta cells	gene expression
Cardiomyocyte Gene Programs Encoding Morphological and Functional Signatures in Cardiac Hypertrophy and Failure	gene expression
A Single-nucleus RNA-sequencing Pipeline to Decipher the Molecular Anatomy and Pathophysiology of Human Kidneys	gene expression
A temporal transcriptome and methylome in human embryonic stem cell-derived cardiomyocytes identifies novel regulators of early cardiac development	gene expression
Single-cell Transcriptomics Reveals Gene Expression Dynamics of Human Fetal Kidney Development	gene expression
Genetic-Variation-Driven Gene-Expression Changes Highlight Genes with Important Functions for Kidney Disease	gene expression
Protein quantitative trait locus study in obesity during weight-loss identifies a leptin regulator	gene expression
Genome-scale Capture C promoter interactions implicate effector genes at GWAS loci for bone mineral density	gene expression

 

Experiments

• 27 snATAC-seq, 14 WGBS, 34 total RNA-seq, 4 ATAC-seq and 52 single cell RNA-seq from HPAP project
• Experiments from publications

Publication title	Assay Nickname
Genetic Regulatory Mechanisms of Smooth Muscle Cells Map to Coronary Artery Disease Risk Loci	ATAC-seq
Evolutionary Selection and Constraint on Human Knee Chondrocyte Regulation Impacts Osteoarthritis Risk	ATAC-seq
Differential open chromatin profile and transcriptomic signature define depot-specific human subcutaneous preadipocytes: primary outcomes	ATAC-seq
Genome-scale Capture C promoter interactions implicate effector genes at GWAS loci for bone mineral density	ATAC-seq
Characterization of TCF21 Downstream Target Regions Identifies a Transcriptional Network Linking Multiple Independent Coronary Artery Disease Loci	ChIP-seq
HNF4A Regulates the Formation of Hepatic Progenitor Cells from Human iPSC-Derived Endoderm by Facilitating Efficient Recruitment of RNA Pol II	ChIP-seq
Effects of Age and Estrogen on Skeletal Gene Expression in Humans as Assessed by RNA Sequencing	total RNA-seq
Genetic Regulatory Mechanisms of Smooth Muscle Cells Map to Coronary Artery Disease Risk Loci	total RNA-seq
Single Cell RNA Sequencing of Human Liver Reveals Distinct Intrahepatic Macrophage Populations	single cell RNA-seq
Differential open chromatin profile and transcriptomic signature define depot-specific human subcutaneous preadipocytes: primary outcomes	total RNA-seq
Methylome and transcriptome maps of human visceral and subcutaneous adipocytes reveal key epigenetic differences at developmental genes	total RNA-seq
An integrated multi-omics approach identifies the landscape of interferon-α-mediated responses of human pancreatic beta cells	total RNA-seq
A temporal transcriptome and methylome in human embryonic stem cell-derived cardiomyocytes identifies novel regulators of early cardiac development	total RNA-seq
Single-cell Transcriptomics Reveals Gene Expression Dynamics of Human Fetal Kidney Development	single cell RNA-seq
Mapping Human Pluripotent-to-Cardiomyocyte Differentiation: Methylomes, Transcriptomes, and Exon DNA Methylation "Memories"	total RNA-seq
Protein quantitative trait locus study in obesity during weight-loss identifies a leptin regulator	total RNA-seq
Genome-scale Capture C promoter interactions implicate effector genes at GWAS loci for bone mineral density	total RNA-seq
	pCHi-C

All data are free and accessible for use. Please refer to our Data Use Policy for any questions. For questions    about Diabetes Epienome Atlas data, please email t2depigenome.help@gmail.com.