Description

The Human Methylation Atlas tracks display genome-wide DNA methylation profiles from deep whole-genome bisulfite sequencing (WGBS) of 39 primary human cell types sorted from 205 healthy tissue samples. This comprehensive resource enables fragment-level analysis across thousands of unique markers, providing a detailed reference for cell-type-specific methylation patterns.

Human Methylation Atlas Summary consists of the following subtracks:

• All unmethylated regions track displays a comprehensive catalogue of unmethylated genomic regions identified independently for each of the 39 cell types in the atlas using a fragment-level analysis, retaining regions where at least 85% of sequenced DNA fragments covering four or more CpGs are unmethylated.


• Putative enhancers from unmethylated regions track displays a genome-wide catalogue of putative transcriptional enhancers derived from regions where at least 85% of sequenced DNA fragments are unmethylated, and that overlap H3K27ac but not H3K4me3 ChIP-seq peaks, distinguishing distal enhancer elements from active promoters. This track covers 32 of the 39 cell types, as H3K27ac ChIP-seq data were unavailable for Adipocytes, Bone Osteoblasts, Erythrocyte Progenitors, Fallopian Epithelium, Gallbladder, Ovary Epithelium, and Smooth Muscle.


• Top 250 unmethylated regions specific to each cell type track displays the top 250 genomic regions most specifically unmethylated in each of the 39 cell types, identified using a one-versus-all comparison approach. Some regions are shared across closely related cell types (for example, Neuron:Oligodend or Colon-Ep:Gastric-Ep:Small-Int-Ep), indicating they are unmethylated across those cell types but methylated in all others in the atlas.

Unsupervised clustering of these methylomes recapitulates key elements of tissue ontogeny and developmental lineage relationships.

Display Conventions and Configuration

Track Colors

Tracks are colored by tissue/cell type category as follows:

Color	Cell Type(s)
	Neurons
	Oligodendrocytes
	Thyroid Epithelium
	Prostate Epithelium
	Bladder Epithelium
	Heart Cardiomyocytes
	Smooth Muscle
	Heart Fibroblasts
	Skeletal Muscle
	Erythrocyte Progenitors
	Blood Granulocytes
	Blood Monocytes/Macrophages
	Blood T Cells
	Blood B Cells
	Blood NK Cells
	Pancreas Beta Cells
	Pancreas Alpha Cells
	Pancreas Delta Cells
	Pancreas Duct Cells
	Pancreas Acinar Cells
	Colon Epithelium
	Colon Fibroblasts
	Small Intestine Epithelium
	Gastric Epithelium
	Gallbladder
	Liver Hepatocytes
	Lung Bronchus Epithelium
	Lung Alveolar Epithelium
	Kidney Epithelium
	Endothelial
	Breast Basal Epithelium
	Breast Luminal Epithelium
	Fallopian Epithelium
	Ovary Epithelium
	Adipocytes
	Epidermal Keratinocytes
	Dermal Fibroblasts
	Bone Osteoblasts
	Head Neck Epithelium

Items in these tracks can be filtered by:

• Cell/Tissue Type - The cell or tissue type associated with each region. Filter values include the 39 cell types for the All Unmethylated Regions track, 32 cell types for the Putative Enhancers track, and 39 cell types plus combined cell type groups for the Top 250 Unmethylated Regions track. The default is no filtering.

Methods

Sample Collection and Sequencing

Primary human cells were isolated from freshly dissociated adult healthy tissues using fluorescence-activated cell sorting (FACS), yielding high-purity preparations across major cell lineages. A total of 205 samples representing 77 primary cell types were collected from 137 consenting donors and merged into 39 cell type groups based on methylation similarity. Average sample purity exceeded 90% as determined by flow cytometry, gene expression, and DNA methylation analysis. Some cell types showed lower purity, including colon fibroblasts (78%), smooth muscle cells (82%), endothelial cells (86%), and adipocytes (87%).

Several cell types are absent from the atlas, typically due to limited availability of primary material. These include osteoblasts, cholangiocytes, cells of the adrenal gland, urethral epithelium, and haematopoietic stem cells. Subpopulations of interest, such as distinct neuronal or lymphocyte subtypes, were also not resolved separately.

Whole-genome bisulfite sequencing was performed using 150 bp paired-end reads at an average sequencing depth of 30× (minimum 6.62×). Libraries were prepared using the Accel-NGS Methyl-Seq DNA library preparation kit and sequenced on the Illumina NovaSeq 6000 platform.

Processing and Analysis

Reads were mapped to the human genome (hg38) using bwa-meth, deduplicated with Sambamba, and processed into per-CpG methylation calls. The genome was segmented into 7.1 million non-overlapping methylation blocks using a multi-channel dynamic programming algorithm that identifies regions of homogeneous methylation across samples.

Cell-type-specific differentially methylated regions were identified using a one-versus-all comparison approach. Regions uniquely unmethylated in specific cell types were found to be enriched for transcriptional enhancers and tissue-specific transcription factor binding motifs.

Data processing was performed using wgbstools, an open-source computational suite for DNA methylation sequencing data representation, visualization, and analysis.

Data Access

The raw data for these tracks can be explored interactively using the Table Browser or the Data Integrator. For automated analysis, the data may also be queried from our REST API.

The complete dataset, including all WGBS data files and processed methylation calls, is available from GEO accession GSE186458.

For questions regarding the data, please contact Prof. Tommy Kaplan at the Hebrew University of Jerusalem.

Credits

Data generation and analysis were performed at the Hebrew University of Jerusalem by the Dor, Kaplan, and Glaser laboratories and collaborators. Sample collection involved collaboration with Hadassah Medical Center, Oregon Health & Science University, Karolinska Institute, and University of Alberta.

References

Loyfer N, Magenheim J, Peretz A, Cann G, Bredno J, Klochendler A, Fox-Fisher I, Shabi-Porat S, Hecht M, Pelet T et al. A DNA methylation atlas of normal human cell types. Nature. 2023 Jan;613(7943):355-364. PMID: 36599988

Loyfer N, Rosenski J, Kaplan T. wgbstools: a computational suite for DNA methylation sequencing data analysis. Life Sci Alliance. 2026 Apr;9(4):e202503514. PMID: 41611450