Exploring the utility of snRNA-seq in profiling human bladder tissue: A comprehensive comparison with scRNA-seq
Summary: Single cell sequencing technologies have revolutionized our understanding of biology by mapping cell diversity and gene expression in healthy and diseased tissues. While single-cell RNA sequencing (scRNA-seq) has been widely used, interest in single-nucleus RNA sequencing (snRNA-seq) is gro...
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Elsevier
2025-01-01
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| Series: | iScience |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2589004224028554 |
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| author | Briana Santo Emily E. Fink Alexandra E. Krylova Yi-Chia Lin Mohamed Eltemamy Alvin Wee Oliver Wessely Byron H. Lee Angela H. Ting |
| author_facet | Briana Santo Emily E. Fink Alexandra E. Krylova Yi-Chia Lin Mohamed Eltemamy Alvin Wee Oliver Wessely Byron H. Lee Angela H. Ting |
| author_sort | Briana Santo |
| collection | DOAJ |
| description | Summary: Single cell sequencing technologies have revolutionized our understanding of biology by mapping cell diversity and gene expression in healthy and diseased tissues. While single-cell RNA sequencing (scRNA-seq) has been widely used, interest in single-nucleus RNA sequencing (snRNA-seq) is growing due to its benefits, including the ability to analyze archival tissues and capture rare cell types that are challenging to dissociate. However, comparative studies across tissues have yielded mixed results, with some reporting enhanced cell type retention using snRNA-seq while others finding cell type identification to be challenging in snRNA-seq data. The GUDMAP consortium aims to construct a molecular atlas of the lower urinary tract (LUT); thus, we set out to determine the strengths and limitations of each approach in characterizing LUT cell types. Using the human bladder, we determined that scRNA-seq offered more discriminative gene sets for identification while snRNA-seq could facilitate capture of previously underrepresented cell types. |
| format | Article |
| id | doaj-art-ce17c1dcad564489962db9d469070fcf |
| institution | Kabale University |
| issn | 2589-0042 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | iScience |
| spelling | doaj-art-ce17c1dcad564489962db9d469070fcf2025-01-04T04:56:48ZengElsevieriScience2589-00422025-01-01281111628Exploring the utility of snRNA-seq in profiling human bladder tissue: A comprehensive comparison with scRNA-seqBriana Santo0Emily E. Fink1Alexandra E. Krylova2Yi-Chia Lin3Mohamed Eltemamy4Alvin Wee5Oliver Wessely6Byron H. Lee7Angela H. Ting8Epigenetics & Molecular Carcinogenesis, M.D. Anderson Cancer Center, Houston, TX 77054, USAGenomic Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Charles River Laboratories, Garfield Heights, OH 44128, USAEpigenetics & Molecular Carcinogenesis, M.D. Anderson Cancer Center, Houston, TX 77054, USADepartment of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH 44195, USADepartment of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH 44195, USADepartment of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH 44195, USADepartment of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USADepartment of Urology, M.D. Anderson Cancer Center, Houston, TX 77054, USAEpigenetics & Molecular Carcinogenesis, M.D. Anderson Cancer Center, Houston, TX 77054, USA; Corresponding authorSummary: Single cell sequencing technologies have revolutionized our understanding of biology by mapping cell diversity and gene expression in healthy and diseased tissues. While single-cell RNA sequencing (scRNA-seq) has been widely used, interest in single-nucleus RNA sequencing (snRNA-seq) is growing due to its benefits, including the ability to analyze archival tissues and capture rare cell types that are challenging to dissociate. However, comparative studies across tissues have yielded mixed results, with some reporting enhanced cell type retention using snRNA-seq while others finding cell type identification to be challenging in snRNA-seq data. The GUDMAP consortium aims to construct a molecular atlas of the lower urinary tract (LUT); thus, we set out to determine the strengths and limitations of each approach in characterizing LUT cell types. Using the human bladder, we determined that scRNA-seq offered more discriminative gene sets for identification while snRNA-seq could facilitate capture of previously underrepresented cell types.http://www.sciencedirect.com/science/article/pii/S2589004224028554Biological sciencesCell biologyTranscriptomics |
| spellingShingle | Briana Santo Emily E. Fink Alexandra E. Krylova Yi-Chia Lin Mohamed Eltemamy Alvin Wee Oliver Wessely Byron H. Lee Angela H. Ting Exploring the utility of snRNA-seq in profiling human bladder tissue: A comprehensive comparison with scRNA-seq iScience Biological sciences Cell biology Transcriptomics |
| title | Exploring the utility of snRNA-seq in profiling human bladder tissue: A comprehensive comparison with scRNA-seq |
| title_full | Exploring the utility of snRNA-seq in profiling human bladder tissue: A comprehensive comparison with scRNA-seq |
| title_fullStr | Exploring the utility of snRNA-seq in profiling human bladder tissue: A comprehensive comparison with scRNA-seq |
| title_full_unstemmed | Exploring the utility of snRNA-seq in profiling human bladder tissue: A comprehensive comparison with scRNA-seq |
| title_short | Exploring the utility of snRNA-seq in profiling human bladder tissue: A comprehensive comparison with scRNA-seq |
| title_sort | exploring the utility of snrna seq in profiling human bladder tissue a comprehensive comparison with scrna seq |
| topic | Biological sciences Cell biology Transcriptomics |
| url | http://www.sciencedirect.com/science/article/pii/S2589004224028554 |
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