{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,25]],"date-time":"2026-02-25T11:19:42Z","timestamp":1772018382440,"version":"3.50.1"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2022,11,1]],"date-time":"2022-11-01T00:00:00Z","timestamp":1667260800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32222026"],"award-info":[{"award-number":["32222026"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32170660"],"award-info":[{"award-number":["32170660"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81972551"],"award-info":[{"award-number":["81972551"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shanghai Rising Star Program","award":["21QA1408200"],"award-info":[{"award-number":["21QA1408200"]}]},{"DOI":"10.13039\/100007219","name":"Natural Science Foundation of Shanghai","doi-asserted-by":"publisher","award":["21ZR1467600"],"award-info":[{"award-number":["21ZR1467600"]}],"id":[{"id":"10.13039\/100007219","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100018542","name":"Natural Science Foundation of Sichuan Province","doi-asserted-by":"publisher","award":["2022NSFSC0054"],"award-info":[{"award-number":["2022NSFSC0054"]}],"id":[{"id":"10.13039\/501100018542","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010097","name":"CAST","doi-asserted-by":"publisher","award":["2021QNRC001"],"award-info":[{"award-number":["2021QNRC001"]}],"id":[{"id":"10.13039\/100010097","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Understanding gene expression patterns across different human cell types is crucial for investigating mechanisms of cell type differentiation, disease occurrence\u00a0and progression. The recent development of single-cell RNA-seq (scRNA-seq) technologies significantly boosted the characterization of cell type heterogeneities in different human tissues. However, the huge number of datasets in the public domain also posed challenges in data integration and reuse. We present Human Universal Single Cell Hub (HUSCH, http:\/\/husch.comp-genomics.org), an atlas-scale curated database that integrates single-cell transcriptomic profiles of nearly 3 million cells from 185 high-quality human scRNA-seq datasets from 45 different tissues. All the data in HUSCH were uniformly processed and annotated with a standard workflow. In the single dataset module, HUSCH provides interactive gene expression visualization, differentially expressed genes, functional analyses, transcription regulators\u00a0and cell\u2013cell interaction analyses for each cell type cluster. Besides, HUSCH integrated different datasets in the single tissue module and performs data integration, batch correction, and cell type harmonization. This allows a comprehensive visualization and analysis of gene expression within each tissue based on single-cell datasets from multiple sources and platforms. HUSCH is a flexible and comprehensive data portal that enables searching, visualizing, analyzing, and downloading single-cell gene expression for the human tissue atlas.<\/jats:p>","DOI":"10.1093\/nar\/gkac1001","type":"journal-article","created":{"date-parts":[[2022,11,1]],"date-time":"2022-11-01T15:44:45Z","timestamp":1667317485000},"page":"D1029-D1037","source":"Crossref","is-referenced-by-count":18,"title":["HUSCH: an integrated single-cell transcriptome atlas for human tissue gene expression visualization and analyses"],"prefix":"10.1093","volume":"51","author":[{"given":"Xiaoying","family":"Shi","sequence":"first","affiliation":[{"name":"Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital, School of Life Science and Technology, Tongji University,\u00a0Tongji ,\u00a0 200092 ,\u00a0 China"},{"name":"Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University , Shanghai \u00a0200092,\u00a0 China"}]},{"given":"Zhiguang","family":"Yu","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University , Guangxi \u00a0530004,\u00a0 China"}]},{"given":"Pengfei","family":"Ren","sequence":"additional","affiliation":[{"name":"Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital, School of Life Science and Technology, Tongji University,\u00a0Tongji ,\u00a0 200092 ,\u00a0 China"},{"name":"Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University , Shanghai \u00a0200092,\u00a0 China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7112-0224","authenticated-orcid":false,"given":"Xin","family":"Dong","sequence":"additional","affiliation":[{"name":"Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital, School of Life Science and Technology, Tongji University,\u00a0Tongji ,\u00a0 200092 ,\u00a0 China"},{"name":"Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University , Shanghai \u00a0200092,\u00a0 China"}]},{"given":"Xuanxin","family":"Ding","sequence":"additional","affiliation":[{"name":"Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital, School of Life Science and Technology, Tongji University,\u00a0Tongji ,\u00a0 200092 ,\u00a0 China"},{"name":"Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University , Shanghai \u00a0200092,\u00a0 China"}]},{"given":"Jiaming","family":"Song","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University , Guangxi \u00a0530004,\u00a0 China"}]},{"given":"Jing","family":"Zhang","sequence":"additional","affiliation":[{"name":"Research Center for Translational Medicine, Shanghai East Hospital, School of Life Science and Technology, Tongji University ,\u00a0 Shanghai ,\u00a0 China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7940-8196","authenticated-orcid":false,"given":"Taiwen","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University , Chengdu \u00a0610041,\u00a0 China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7573-3768","authenticated-orcid":false,"given":"Chenfei","family":"Wang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital, School of Life Science and Technology, Tongji University,\u00a0Tongji ,\u00a0 200092 ,\u00a0 China"},{"name":"Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University , Shanghai \u00a0200092,\u00a0 China"}]}],"member":"286","published-online":{"date-parts":[[2022,11,1]]},"reference":[{"key":"2023010804200585300_B1","doi-asserted-by":"crossref","first-page":"1145","DOI":"10.1038\/nbt.3711","article-title":"Revealing the vectors of cellular identity with single-cell genomics","volume":"34","author":"Wagner","year":"2016","journal-title":"Nat. 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