November 2022 Data Release

We are pleased to release following datasets:

• MPRA of MIN6
• MPRA to prioritize disease-associated variants for five autoimmune diseases

• The three-dimensional chromatin structure of the major human pancreatic cell types reveals lineage-specific regulatory architecture of T2D risk

• ChIP-seq binding sites from 161 TFs across 91 cell types from the ENCODE project

• cis-caQTL Fine-mapping, trans-ancestral and genomic analyses identify causal variants, cells, genes and drug targets for type 1 diabetes

• Chromatin site QTLs of skeletal muscle

• Bulk & single atac-seq data from following studies:

1. ATAC-Seq analysis reveals a widespread decrease of chromatin accessibility in age-related macular degeneration
2. Cis-regulatory architecture of human ESC-derived hypothalamic neuron differentiation aids in variant-to-gene mapping of relevant complex traits
3. Common schizophrenia risk variants are enriched in open chromatin regions of human glutamatergic neurons
4.  Joint disease-specificity at the regulatory base-pair level
5. Chromatin accessibility and gene expression during adipocyte differentiation identify context-dependent effects at cardiometabolic GWAS loci
6. Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk

New tool to visuliaze single cell assays: ShinyCell

ShinyCell is a R package that allows users to create interactive Shiny-based web applications to visualise single-cell data via (i) visualising cell information and/or gene expression on reduced dimensions e.g. UMAP, (ii) visualising the coexpression of two genes on reduced dimensions, (iii) visualising the distribution of continuous cell information e.g. nUMI / module scores using violin plots / box plots, (iv) visualising the composition of different clusters / groups of cells using proportion plots and (v) visualising the expression of multiple genes using bubbleplots / heatmap.

All the single cell datasets in CMDGA can now be visualized on ShinyCell. Find on homepage, linkout to each data set on embedding page or under the Tools menu.

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 contact us.