{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T02:02:55Z","timestamp":1789524175400,"version":"build-2803163510"},"reference-count":42,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2025,4,21]],"date-time":"2025-04-21T00:00:00Z","timestamp":1745193600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Chinese Academy of Sciences (Strategic Priority Research Program)","award":["XDA26050102"],"award-info":[{"award-number":["XDA26050102"]}]},{"name":"Chinese Academy of Sciences (Strategic Priority Research Program)","award":["2022JJ10054"],"award-info":[{"award-number":["2022JJ10054"]}]},{"name":"Chinese Academy of Sciences (Strategic Priority Research Program)","award":["32072760"],"award-info":[{"award-number":["32072760"]}]},{"name":"Natural Science Foundation of Hunan Province of China","award":["XDA26050102"],"award-info":[{"award-number":["XDA26050102"]}]},{"name":"Natural Science Foundation of Hunan Province of China","award":["2022JJ10054"],"award-info":[{"award-number":["2022JJ10054"]}]},{"name":"Natural Science Foundation of Hunan Province of China","award":["32072760"],"award-info":[{"award-number":["32072760"]}]},{"name":"National Natural Science Foundation of China","award":["XDA26050102"],"award-info":[{"award-number":["XDA26050102"]}]},{"name":"National Natural Science Foundation of China","award":["2022JJ10054"],"award-info":[{"award-number":["2022JJ10054"]}]},{"name":"National Natural Science Foundation of China","award":["32072760"],"award-info":[{"award-number":["32072760"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>The objective of this study was to determine whether single-cell RNA sequencing (scRNA-seq) or single-nucleus RNA sequencing (snRNA-seq) was more effective for studying the goat pancreas. Pancreas tissues from three healthy 10-day-old female Xiangdong black goats were processed into single-cell and single-nucleus suspensions. These suspensions were then used to compare cellular composition and gene expression levels following library construction and sequencing. Both scRNA-seq and snRNA-seq were eligible for primary analysis but produced different cell identification profiles in pancreatic tissue. Both methods successfully annotated pancreatic acinar cells, ductal cells, alpha cells, beta cells, and endothelial cells. However, pancreatic stellate cells, immune cells, and delta cells were uniquely annotated by scRNA-seq, while pancreatic stem cells were uniquely identified by snRNA-seq. Furthermore, the genes related to digestive enzymes showed a higher expression in scRNA-seq than in snRNA-seq. In the present study, scRNA-seq detected a great diversity of pancreatic cell types and was more effective in profiling key genes than snRNA-seq, demonstrating that scRNA-seq was better suited for studying the goat pancreas. However, the choice between scRNA-seq and snRNA-seq should consider the sample compatibility, technical differences, and experimental objectives.<\/jats:p>","DOI":"10.3390\/ijms26083916","type":"journal-article","created":{"date-parts":[[2025,4,21]],"date-time":"2025-04-21T20:42:00Z","timestamp":1745268120000},"page":"3916","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Single-Cell RNA Sequencing Outperforms Single-Nucleus RNA Sequencing in Analyzing Pancreatic Cell Diversity and Gene Expression in Goats"],"prefix":"10.3390","volume":"26","author":[{"given":"Jie","family":"Cheng","sequence":"first","affiliation":[{"name":"National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China"},{"name":"College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tianxi","family":"Zhang","sequence":"additional","affiliation":[{"name":"National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China"},{"name":"College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5089-5592","authenticated-orcid":false,"given":"Yan","family":"Cheng","sequence":"additional","affiliation":[{"name":"National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China"},{"name":"College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9286-955X","authenticated-orcid":false,"given":"Kefyalew","family":"Gebeyew","sequence":"additional","affiliation":[{"name":"National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China"},{"name":"College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhiliang","family":"Tan","sequence":"additional","affiliation":[{"name":"National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China"},{"name":"College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China"},{"name":"Yuelushan Laboratory, Changsha 410125, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4802-3506","authenticated-orcid":false,"given":"Zhixiong","family":"He","sequence":"additional","affiliation":[{"name":"National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China"},{"name":"College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China"},{"name":"Yuelushan Laboratory, Changsha 410125, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,4,21]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1071\/BI9850059","article-title":"Insulin, glucagon, pancreatic polypeptide hormone and somatostatin in the goat pancreas: Demonstration by immunocytochemistry","volume":"38","author":"Reddy","year":"1985","journal-title":"Aust. 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