Single Cell Atlas: a single-cell multi-omics human cell encyclopedia

Lu Pan; Paolo Parini; Roman Tremmel; Joseph Loscalzo; Volker M Lauschke; Bradley A Maron; Paola Paci; Ingemar Ernberg; Nguan Soon Tan; Zehuan Liao; Weiyao Yin; Sundararaman Rengarajan; Xuexin Li; SCA Consortium

doi:10.1186/s13059-024-03246-2

Single Cell Atlas: a single-cell multi-omics human cell encyclopedia

Genome Biol. 2024 Apr 19;25(1):104. doi: 10.1186/s13059-024-03246-2.

Authors

Lu Pan¹, Paolo Parini^{2

3}, Roman Tremmel^{4

5}, Joseph Loscalzo⁶, Volker M Lauschke^{4

5

7}, Bradley A Maron⁶, Paola Paci⁸, Ingemar Ernberg⁹, Nguan Soon Tan^{10

11}, Zehuan Liao^{9

10}, Weiyao Yin¹, Sundararaman Rengarajan¹², Xuexin Li^{13

14}; SCA Consortium

Affiliations

¹ Institute of Environmental Medicine, Karolinska Institutet, 171 65, Solna, Sweden.
² Cardio Metabolic Unit, Department of Medicine, and, Department of Laboratory Medicine , Karolinska Institutet, 141 86, Stockholm, Sweden.
³ Theme Inflammation and Ageing, Medicine Unit, Karolinska University Hospital, 141 86, Stockholm, Sweden.
⁴ Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376, Stuttgart, Germany.
⁵ University of Tuebingen, 72076, Tuebingen, Germany.
⁶ Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
⁷ Department of Physiology and Pharmacology, Karolinska Institutet, 171 65, Solna, Sweden.
⁸ Department of Computer, Control and Management Engineering, Sapienza University of Rome, 00185, Rome, Italy.
⁹ Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65, Solna, Sweden.
¹⁰ School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
¹¹ Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, 308232, Singapore.
¹² Department of Physical Therapy, Movement & Rehabilitation Sciences, Northeastern University, Boston, MA, 02115, USA.
¹³ Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China. xuexin.li@ki.se.
¹⁴ Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 65, Solna, Sweden. xuexin.li@ki.se.

Abstract

Single-cell sequencing datasets are key in biology and medicine for unraveling insights into heterogeneous cell populations with unprecedented resolution. Here, we construct a single-cell multi-omics map of human tissues through in-depth characterizations of datasets from five single-cell omics, spatial transcriptomics, and two bulk omics across 125 healthy adult and fetal tissues. We construct its complement web-based platform, the Single Cell Atlas (SCA, www.singlecellatlas.org ), to enable vast interactive data exploration of deep multi-omics signatures across human fetal and adult tissues. The atlas resources and database queries aspire to serve as a one-stop, comprehensive, and time-effective resource for various omics studies.

Keywords: Flow cytometry; Human database; Mass cytometry; Multi-omics; Single Cell Atlas; Single-cell ATAC-sequencing; Single-cell RNA-sequencing; Single-cell immune profiling; Single-cell omics; Spatial transcriptomics.

MeSH terms

Adult
Ascomycota*
Databases, Factual
Fetus
Gene Expression Profiling
Humans
Multiomics*

Abstract

MeSH terms

Grants and funding