Comprehensive atlas for regulatory elements and functional annotations

Dataset Available

Mouse Brain

Species: Mus musculus
Sample: 45 brain sub-regions
Method: snATAC-seq
Nuclei count: > 800,000

Last updated May,2020

Human Tissues

Species: Homo Sapiens
Samples: 30 adult tissues
Method: snATAC-Seq
Cell counts: >1.3 million

Human Heart

Species: Homo Sapiens
Samples: Left/right Atria and ventricules from 4 donors
Method: snATAC-Seq and snRNA-Seq
Cell counts: 80K snATAC cells and 36K snRNA cells


Mouse Cortex

Species: Mus musculus
Samples: Frontal cortex & hippocampus
Method: Paired-Tag
Cell counts: 64,849

Human Brain

Species: Homo Sapiens
Samples: 42 brain regions
Method: snATAC-seq
Cell counts: >1.1 million

Mouse Aging

Species: Mus musculus
Samples: brains, hearts, skeletal muscles, and bone marrows from young, middle-aged, and old mice
Method: snATAC-seq
Cell counts: 227,529


Whole Mouse Brain

Species: Mus musculus
Sample: 117 brain sub-regions
Method: snATAC-seq
Nuclei count: > 2.3 million

Last updated March,2023

Coming soon


We hope you find this data resource useful. Please write us with experiences and suggestions. We would love stories about how people are using it in their work.


We provide comprehensive reference maps of cis-regulatory elements identified from single-cell epigenetic datasets. You can explore cell clusters from different tissues and organisms, detailed annotations for every cell types, and genomic signal tracks and functional predictions.



A comparative atlas of single-cell chromatin accessibility in the human brain

Yang Eric Li, Sebastian Preissl, Michael Miller, Nicholas D Johnson, Zihan Wang, Henry Jiao, Chenxu Zhu, Zhaoning Wang, Yang Xie, Olivier Poirin, Colin Kern, Antonio Pinto-Duarte, Wei Tian, Kimberly Siletti, Nora Emerson, Julia Osteen, Jacinta Lucero, Lin Lin, Qian Yang, Sarah Espinoza, Quan Zhu, Nathan Zemke, Anna Marie Yanny, Julie Nyhus, Nick Dee, Tamara Casper, Nadiya Shapovalova, Daniel Hirschstein, Rebecca D Hodge, Sten Linnarsson, Trygve E Bakken, Boaz Levi, C Dirk Keene, Jingbo Shang, Ed S Lein, Allen Wang, M Margarita Behrens, Joseph R Ecker, Bing Ren.
bioRxiv, 2022. doi: https://doi.org/10.1101/2022.11.09.515833

Single-cell Epigenome Analysis Reveals Age-associated Decay of Heterochromatin Domains in Excitatory Neurons in the Mouse Brain

Yanxiao Zhang*,#, Maria Luisa Amaral*, Chenxu Zhu, Steven F. Grieco, Xiaomeng Hou, Lin Lin, Justin Buchanan, Liqi Tong, Sebastian Preissl, Xiangmin Xu#, Bing Ren#.
Cell Research, 2022. doi:10.1038/s41422-022-00719-6


A single-cell atlas of chromatin accessibility in the human genome

Kai Zhang*, James D. Hocker*, Michael Miller, Xiaomeng Hou, Joshua Chiou, Olivier B. Poirion, Yunjiang Qiu, Yang E. Li, Kyle J. Gaulton, Allen Wang, Sebastian Preissl, Bing Ren.
Cell, 2021. doi:https://doi.org/10.1016/j.cell.2021.10.024

An Atlas of Gene Regulatory Elements in Adult Mouse Cerebrum

Yang Eric Li*, Sebastian Preissl*, Xiaomeng Hou, Ziyang Zhang, Kai Zhang, Yunjiang Qiu, Olivier Poirion, Bin Li, Joshua Chiou, Hanqing Liu, Antonio Pinto-Duarte, Naoki Kubo, Xiaoyu Yang, Rongxin Fang, Xinxin Wang, Jee Yun Han, Jacinta Lucero, Yiming Yan, Michael Miller, Samantha Kuan, David Gorkin, Kyle Gaulton, Yin Shen, Michael Nunn, Eran A. Mukame, M. Margarita Behrens, Joseph Ecker and Bing Ren.
Nature, 2021. doi:https://doi.org/10.1038/s41586-021-03604-1

Cardiac Cell Type-Specific Gene Regulatory Programs and Disease Risk Association

James D Hocker, Olivier B Poirion, Fugui Zhu, Justin Buchanan, Kai Zhang, Joshua Chiou, Tsui-Min Wang, Qingquan Zhang, Xiaomeng Hou, Yang Eric Li, Yanxiao Zhang, Elie Farah, Allen Wang, Andrew D McCulloch, Kyle J Gaulton, Bing Ren#, Neil C Chi#, Sebastian Preissl#
Science Advances, 2021. doi:10.1126/sciadv.abf1444

Joint profiling of histone modifications and transcriptome in single cells from mouse brain

Chenxu Zhu, Yanxiao Zhang, Yang Eric Li, Jacinta Lucero, M. Margarita Behrens & Bing Ren.
Nature Methods, 2021. doi:10.1038/s41592-021-01060-3


Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation

Sebastian Preissl*, Rongxin Fang*, Hui Huang, Yuan Zhao, Ramya Raviram, David U. Gorkin, Yanxiao Zhang, Brandon C. Sos, Veena Afzal, Diane E. Dickel, Samantha Kuan, Axel Visel, Len A. Pennacchio, Kun Zhang, Bing Ren.
Nature Neuroscience, 2018. doi:10.1038/s41593-018-0079-3



  • RENlab
    Laboratory of Gene Regulation
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    • Lab location: 9500 Gilman Dr, CMME #2071, La Jolla, CA-92093, USA (Ludwig Institute for Cancer Research, San Diego)
      Lab phone: +1-858-822-5767
      Fax: +1-858-534-7750

      Web Maintenance:
      Yang (Eric) Li < yal054 AT health.ucsd.edu >
      Bin Li < bil022 AT ucsd.edu >