Single-cell sequencing of full-length transcripts and T-cell receptors with automated high-throughput Smart-seq3
Abstract We developed an automated high-throughput Smart-seq3 (HT Smart-seq3) workflow that integrates best practices and an optimized protocol to enhance efficiency, scalability, and method reproducibility. This workflow consistently produces high-quality data with high cell capture efficiency and...
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BMC
2024-11-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-024-11036-0 |
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| author | Hsiu-Chun Chuang Ruidong Li Huang Huang Szu-Wen Liu Christine Wan Subhra Chaudhuri Lili Yue Terence Wong Venina Dominical Randy Yen Olivia Ngo Nam Bui Hubert Stoppler Tangsheng Yi Silpa Suthram Li Li Kai-Hui Sun |
| author_facet | Hsiu-Chun Chuang Ruidong Li Huang Huang Szu-Wen Liu Christine Wan Subhra Chaudhuri Lili Yue Terence Wong Venina Dominical Randy Yen Olivia Ngo Nam Bui Hubert Stoppler Tangsheng Yi Silpa Suthram Li Li Kai-Hui Sun |
| author_sort | Hsiu-Chun Chuang |
| collection | DOAJ |
| description | Abstract We developed an automated high-throughput Smart-seq3 (HT Smart-seq3) workflow that integrates best practices and an optimized protocol to enhance efficiency, scalability, and method reproducibility. This workflow consistently produces high-quality data with high cell capture efficiency and gene detection sensitivity. In a rigorous comparison with the 10X platform using human primary CD4 + T-cells, HT Smart-seq3 demonstrated higher cell capture efficiency, greater gene detection sensitivity, and lower dropout rates. Additionally, when sufficiently scaled, HT Smart-seq3 achieved a comparable resolution of cellular heterogeneity to 10X. Notably, through T-cell receptor (TCR) reconstruction, HT Smart-seq3 identified a greater number of productive alpha and beta chain pairs without the need for additional primer design to amplify full-length V(D)J segments, enabling more comprehensive TCR profiling across a broader range of species. Taken together, HT Smart-seq3 overcomes key technical challenges, offering distinct advantages that position it as a promising solution for the characterization of single-cell transcriptomes and immune repertoires, particularly well-suited for low-input, low-RNA content samples. |
| format | Article |
| id | doaj-art-2b56699385fd48abb9748547bae2c25e |
| institution | OA Journals |
| issn | 1471-2164 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj-art-2b56699385fd48abb9748547bae2c25e2025-08-20T02:22:33ZengBMCBMC Genomics1471-21642024-11-0125111810.1186/s12864-024-11036-0Single-cell sequencing of full-length transcripts and T-cell receptors with automated high-throughput Smart-seq3Hsiu-Chun Chuang0Ruidong Li1Huang Huang2Szu-Wen Liu3Christine Wan4Subhra Chaudhuri5Lili Yue6Terence Wong7Venina Dominical8Randy Yen9Olivia Ngo10Nam Bui11Hubert Stoppler12Tangsheng Yi13Silpa Suthram14Li Li15Kai-Hui Sun16Gilead Sciences, Inc.Gilead Sciences, Inc.Gilead Sciences, Inc.Gilead Sciences, Inc.Gilead Sciences, Inc.Gilead Sciences, Inc.Gilead Sciences, Inc.Gilead Sciences, Inc.Gilead Sciences, Inc.Gilead Sciences, Inc.Gilead Sciences, Inc.Gilead Sciences, Inc.Gilead Sciences, Inc.Gilead Sciences, Inc.Gilead Sciences, Inc.Gilead Sciences, Inc.Gilead Sciences, Inc.Abstract We developed an automated high-throughput Smart-seq3 (HT Smart-seq3) workflow that integrates best practices and an optimized protocol to enhance efficiency, scalability, and method reproducibility. This workflow consistently produces high-quality data with high cell capture efficiency and gene detection sensitivity. In a rigorous comparison with the 10X platform using human primary CD4 + T-cells, HT Smart-seq3 demonstrated higher cell capture efficiency, greater gene detection sensitivity, and lower dropout rates. Additionally, when sufficiently scaled, HT Smart-seq3 achieved a comparable resolution of cellular heterogeneity to 10X. Notably, through T-cell receptor (TCR) reconstruction, HT Smart-seq3 identified a greater number of productive alpha and beta chain pairs without the need for additional primer design to amplify full-length V(D)J segments, enabling more comprehensive TCR profiling across a broader range of species. Taken together, HT Smart-seq3 overcomes key technical challenges, offering distinct advantages that position it as a promising solution for the characterization of single-cell transcriptomes and immune repertoires, particularly well-suited for low-input, low-RNA content samples.https://doi.org/10.1186/s12864-024-11036-0High-throughput Smart-seq310XSingle-cell RNA sequencingSingle-cell TCR sequencing |
| spellingShingle | Hsiu-Chun Chuang Ruidong Li Huang Huang Szu-Wen Liu Christine Wan Subhra Chaudhuri Lili Yue Terence Wong Venina Dominical Randy Yen Olivia Ngo Nam Bui Hubert Stoppler Tangsheng Yi Silpa Suthram Li Li Kai-Hui Sun Single-cell sequencing of full-length transcripts and T-cell receptors with automated high-throughput Smart-seq3 BMC Genomics High-throughput Smart-seq3 10X Single-cell RNA sequencing Single-cell TCR sequencing |
| title | Single-cell sequencing of full-length transcripts and T-cell receptors with automated high-throughput Smart-seq3 |
| title_full | Single-cell sequencing of full-length transcripts and T-cell receptors with automated high-throughput Smart-seq3 |
| title_fullStr | Single-cell sequencing of full-length transcripts and T-cell receptors with automated high-throughput Smart-seq3 |
| title_full_unstemmed | Single-cell sequencing of full-length transcripts and T-cell receptors with automated high-throughput Smart-seq3 |
| title_short | Single-cell sequencing of full-length transcripts and T-cell receptors with automated high-throughput Smart-seq3 |
| title_sort | single cell sequencing of full length transcripts and t cell receptors with automated high throughput smart seq3 |
| topic | High-throughput Smart-seq3 10X Single-cell RNA sequencing Single-cell TCR sequencing |
| url | https://doi.org/10.1186/s12864-024-11036-0 |
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