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Research: Integrating short-read and long-read single-cell RNA sequencing for comprehensive transcriptome profiling in mouse retina
- Meng Wang,
- Yumei Li,
- Jun Wang,
- Soo Hwan Oh,
- Yexuan Cao,
- and Rui Chen
Genome Res. April 2025 35: 740-754; Published in Advance March 6, 2025, doi:10.1101/gr.279167.124
...@bcm.eduAbstractThe vast majority of protein-coding genes in the human produce multiple mRNA isoforms through alternative splicing, significantly enhancing the complexity of the transcriptome and proteome. To establish an efficient method for characterizing transcript isoforms within tissue samples, we conducted...
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Review: Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics
- Natan Belchikov,
- Justine Hsu,
- Xiang Jennie Li,
- Julien Jarroux,
- Wen Hu,
- Anoushka Joglekar,
- and Hagen U. Tilgner
Genome Res. November 2024 34: 1735-1746; doi:10.1101/gr.279640.124
..., the abundance of noncoding transcripts of protein-coding genes visible in the long-read data would have resulted in an ∼20% overestimation of protein expression based on short-read data (Dondi et al. 2023). Associations between genotype and splicing changes using ONT single-cell RNA-seq were likewise observed...
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Method: Single-cell RNA-seq of human induced pluripotent stem cells reveals cellular heterogeneity and cell state transitions between subpopulations
- Quan H. Nguyen,
- Samuel W. Lukowski,
- Han Sheng Chiu,
- Anne Senabouth,
- Timothy J.C. Bruxner,
- Angelika N. Christ,
- Nathan J. Palpant,
- and Joseph E. Powell
Genome Res. July 2018 28: 1053-1066; Published in Advance May 11, 2018, doi:10.1101/gr.223925.117
...has a unique expression state comprising a collection of regulatory factors and target gene behavior, single-cell RNA sequencing (scRNA-seq) can provide a transcriptome-level understanding of how individual cells function in pluripotency (Wen and Tang 2016). These data can also reveal insights...
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Method: Identifying cell state–associated alternative splicing events and their coregulation
- Carlos F. Buen Abad Najar,
- Prakruthi Burra,
- Nir Yosef,
- and Liana F. Lareau
Genome Res. July 2022 32: 1385-1397; Published in Advance July 20, 2022, doi:10.1101/gr.276109.121
...@berkeley.eduAbstractAlternative splicing shapes the transcriptome and contributes to each cell's unique identity, but single-cell RNA sequencing (scRNA-seq) has struggled to capture the impact of alternative splicing. We previously showed that low recovery of mRNAs from single cells led to erroneous conclusions about the cell...
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Research: RBFOX splicing factors contribute to a broad but selective recapitulation of peripheral tissue splicing patterns in the thymus
- Kathrin Jansen,
- Noriko Shikama-Dorn,
- Moustafa Attar,
- Stefano Maio,
- Maria Lopopolo,
- David Buck,
- Georg A. Holländer,
- and Stephen N. Sansom
Genome Res. November 2021 31: 2022-2034; Published in Advance October 14, 2021, doi:10.1101/gr.275245.121
.... Comprehensiveness of self-representation by TEC cannot, however, be measured by gene number alone because self-peptidome diversity is elaborated by alternative mRNA splicing (Anderson et al. 2000; Klein et al. 2000; Wang and Burge 2008), expression of “untranslated” regions (Starck and Shastri 2016), RNA...
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Research: Population and single-cell genomics reveal the Aire dependency, relief from Polycomb silencing, and distribution of self-antigen expression in thymic epithelia
- Stephen N. Sansom,
- Noriko Shikama-Dorn,
- Saule Zhanybekova,
- Gretel Nusspaumer,
- Iain C. Macaulay,
- Mary E. Deadman,
- Andreas Heger,
- Chris P. Ponting,
- and Georg A. Holländer
Genome Res. December 2014 24: 1918-1931; Published in Advance September 15, 2014, doi:10.1101/gr.171645.113
...mechanisms that underlie this process. Presently, these remain largely unknown with the notable exception of the involvement of AIRE which interacts with proteins involved in chromatin structure, DNA damage response, gene transcription, and RNA processing (Abramson et al. 2010; Gaetani et al. 2012...
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Method: Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ
- Joseph W. Foley,
- Chunfang Zhu,
- Philippe Jolivet,
- Shirley X. Zhu,
- Peipei Lu,
- Michael J. Meaney,
- and Robert B. West
Genome Res. November 2019 29: 1816-1825; Published in Advance September 13, 2019, doi:10.1101/gr.234807.118
...-quality RNA samples.Demonstration with microdissected cellsTo take advantage of Smart-3SEQ's compatibility with small amounts of degraded RNA, we used the method to study single-cell gene expression in the context of the tumor microenvironment, which is a mix of benign and malignant cells. We compared...
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Research: LTR-mediated retroposition as a mechanism of RNA-based duplication in metazoans
- Shengjun Tan,
- Margarida Cardoso-Moreira,
- Wenwen Shi,
- Dan Zhang,
- Jiawei Huang,
- Yanan Mao,
- Hangxing Jia,
- Yaqiong Zhang,
- Chunyan Chen,
- Yi Shao,
- Liang Leng,
- Zhonghua Liu,
- Xun Huang,
- Manyuan Long,
- and Yong E. Zhang
Genome Res. December 2016 26: 1663-1675; Published in Advance October 20, 2016, doi:10.1101/gr.204925.116
...be an underestimation given that genes without high transcriptional levels (Fragments Per Kilobase of exon per Million fragments mapped, FPKM> 100) like LTR-mediated retrocopies (Supplemental Table 11) tend to be neglected in single-cell RNA-seq data (Marinov et al. 2014). Overall, these lines of evidence in mouse...
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Method: FFPEcap-seq: a method for sequencing capped RNAs in formalin-fixed paraffin-embedded samples
- Jeffery M. Vahrenkamp,
- Kathryn Szczotka,
- Mark K. Dodson,
- Elke A. Jarboe,
- Andrew P. Soisson,
- and Jason Gertz
Genome Res. November 2019 29: 1826-1835; Published in Advance October 24, 2019, doi:10.1101/gr.249656.119
...↵Love MI, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15: 550. doi:10.1186/s13059-014-0550-8 ↵Marinov GK, Williams BA, McCue K, Schroth GP, Gertz J, Myers RM, Wold BJ. 2014. From single-cell to cell-pool transcriptomes...
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