snm3C-seq and spatial transcriptomic profiling of developing human basal ganglia and inhibitory neurons

Paper: A Single-Cell and Spatial 3D Multi-omic Atlas of Developing Human Basal Ganglia and Inhibitory Neurons. (2026) bioRxiv

Data: GSE322468 NeMO Archive: dat-n5emc24 WashU Epigenome Browser

snmCT-seq profiling of Autism Spectrum Disorder brains

Paper: A Single-Cell Atlas of DNA Methylation in Autism Spectrum Disorder Reveals Distinct Regulatory and Aging Signatures. (2025) bioRxiv

Data: GSE298243 NeMO Archive: dat-htywcnb

snm3C-seq profiling of developing human brains

Paper: Temporally distinct 3D multi-omic dynamics in the developing human brain. (2024) Nature

Data: GSE213950 NeMO Archive: dat-obec38w UCSC Single-Cell browser UCSC Track browser

Single-nucleus joint profiling of RNA, methylation and chromatin accessibility

Paper: Single nucleus multi-omics identifies human cortical cell regulatory genome diversity. (2022) Cell Genomics.

Data: GSE140493 AnnoJ browser

Human frontal cortex cell-type specific chromatin conformation

Paper: Simultaneous profiling of 3D genome structure and DNA methylation in single human cells. (2019) Nature Methods.

Data: GSE124391 GSE130711 AnnoJ browser HiGlass browser
Cell-type Annotation

Mouse induced neuron (iN) methylomes

Paper: Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons. (2019) Elife.

Data: GSE111283 AnnoJ browser

Single cell methylomes of human and mouse frontal cortex

Paper: Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex. (2017) Science.

Data: GSE97179 Mouse and human brain snmC-seq data

Human cerebral organoids methylomes

Paper: Cerebral Organoids Recapitulate Epigenomic Signatures of the Human Fetal Brain. (2016) Cell Reports.

Data: GSE82022 AnnoJ browser