SingleQ: a comprehensive database of single-cell expression quantitative trait loci (sc-eQTLs) cross human tissues

Zhiwei Zhou; Jingyi Du; Jianhua Wang; Liangyi Liu; M Gracie Gordon; Chun Jimmie Ye; Joseph E Powell; Mulin Jun Li; Shuquan Rao

doi:10.1093/database/baae010

SingleQ: a comprehensive database of single-cell expression quantitative trait loci (sc-eQTLs) cross human tissues

Database (Oxford). 2024 Mar 9:2024:baae010. doi: 10.1093/database/baae010.

Authors

Zhiwei Zhou^{1

2}, Jingyi Du^{1

2}, Jianhua Wang³, Liangyi Liu¹, M Gracie Gordon^{4

5

6

7}, Chun Jimmie Ye^{5

6

8

9

10

11

12}, Joseph E Powell^{13

14}, Mulin Jun Li³, Shuquan Rao^{1

2}

Affiliations

¹ State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin 300020, China.
² Tianjin Institutes of Health Science, 28 Tuanbo Avenue, Tianjin 301600, China.
³ Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, 22 Qixiangtai Road, Tianjin 300070, China.
⁴ Biological and Medical Informatics Graduate Program, University of California, 500 Parnassus Avenue, San Francisco, CA 94143, USA.
⁵ Division of Rheumatology, Department of Medicine, University of California, 500 Parnassus Avenue, San Francisco, CA 94143, USA.
⁶ Institute for Human Genetics, University of California, 500 Parnassus Avenue, San Francisco, CA 94143, USA.
⁷ Department of Bioengineering and Therapeutic Sciences, University of California, 500 Parnassus Avenue, San Francisco, CA 94143, USA.
⁸ Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, University of California, 500 Parnassus Avenue, San Francisco, CA 94143, USA.
⁹ Department of Epidemiology and Biostatistics, University of California, 500 Parnassus Avenue, San Francisco, CA 94143, USA.
¹⁰ Parker Institute for Cancer Immunotherapy, University of California, 500 Parnassus Avenue, San Francisco, CA 94143, USA.
¹¹ Chan Zuckerberg Biohub, 499 Illinois Street, San Francisco, CA 94158, USA.
¹² Bakar Computational Health Sciences Institute, University of California, 500 Parnassus Avenue, San Francisco, CA 94143, USA.
¹³ Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW 2010, Australia.
¹⁴ UNSW Cellular Genomics Futures Institute, University of New South Wales, UNSW Sydney, Sydney, NSW 2052, Australia.

Abstract

Mapping of expression quantitative trait loci (eQTLs) and other molecular QTLs can help characterize the modes of action of disease-associated genetic variants. However, current eQTL databases present data from bulk RNA-seq approaches, which cannot shed light on the cell type- and environment-specific regulation of disease-associated genetic variants. Here, we introduce our Single-cell eQTL Interactive Database which collects single-cell eQTL (sc-eQTL) datasets and provides online visualization of sc-eQTLs across different cell types in a user-friendly manner. Although sc-eQTL mapping is still in its early stage, our database curates the most comprehensive summary statistics of sc-eQTLs published to date. sc-eQTL studies have revolutionized our understanding of gene regulation in specific cellular contexts, and we anticipate that our database will further accelerate the research of functional genomics. Database URL: http://www.sqraolab.com/scqtl.

MeSH terms

Gene Expression Regulation*
Genome-Wide Association Study
Genomics
Humans
Polymorphism, Single Nucleotide
Quantitative Trait Loci* / genetics
RNA-Seq

Abstract

MeSH terms

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