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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
...it is only a few hundred gigabases at most for PacBio. A common solution is the parallel use of both short-read and long-read sequencing, where the same single-cell barcodes are used on both platforms. Clustering is performed on the short-read data, allowing the long reads to be categorized without...
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Perspective: Tagmentation-based single-cell genomics
- Andrew C. Adey
Genome Res. October 2021 31: 1693-1705; doi:10.1101/gr.275223.121
...of mitochondrial reads was considered a problem, but their inclusion in single-cell ATAC-seq data presented the opportunity to track clonal lineages based on mitochondrial DNA variants, as well as heteroplasmy within individual cells. This strategy to capture mtDNA in parallel was also leveraged in a novel...
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Resource: A temporal in vivo catalog of chromatin accessibility and expression profiles in pineoblastoma reveals a prevalent role for repressor elements
- Salam Idriss,
- Mohammad Hallal,
- Abdullah El-Kurdi,
- Hasan Zalzali,
- Inaam El-Rassi,
- Erik A. Ehli,
- Christel M. Davis,
- Philip E.D. Chung,
- Deena M.A. Gendoo,
- Eldad Zacksenhaus,
- Raya Saab,
- and Pierre Khoueiry
Genome Res. February 2023 33: 269-282; Published in Advance January 17, 2023, doi:10.1101/gr.277037.122
...of CCND1-driven PB. We identified PB-specific enhancers and super-enhancers, and found that in some cases, the accessible dynamics precede transcriptomic changes, a characteristic that is underexplored in tumor progression. During progression of PB, newly acquired open chromatin regions lacking H3K27ac...
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Research: Single-cell sequencing of primate preimplantation embryos reveals chromosome elimination via cellular fragmentation and blastomere exclusion
- Brittany L. Daughtry,
- Jimi L. Rosenkrantz,
- Nathan H. Lazar,
- Suzanne S. Fei,
- Nash Redmayne,
- Kristof A. Torkenczy,
- Andrew Adey,
- Melissa Yan,
- Lina Gao,
- Byung Park,
- Kimberly A. Nevonen,
- Lucia Carbone,
- and Shawn L. Chavez
Genome Res. March 2019 29: 367-382; Published in Advance January 25, 2019, doi:10.1101/gr.239830.118
...indicated by the extensive γH2A.X signals in CCFs and excluded blastomeres is selectively eliminated from the embryo to prevent further propagation of highly unstable chromosomes (Fig. 7B). Given the parallels between embryonic and somatic cell micronuclei as well as recent evidence that polyploid giant...
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Research: Cell type–specific analysis by single-cell profiling identifies a stable mammalian tRNA–mRNA interface and increased translation efficiency in neurons
- William Gao,
- Carlos J. Gallardo-Dodd,
- and Claudia Kutter
Genome Res. January 2022 32: 97-110; Published in Advance December 2, 2021, doi:10.1101/gr.275944.121
...RNA abundances, with a recent study showing that the tRNA levels obtained from different methods are lowly correlated (ρ ∼ 0.22–0.62) (Pinkard et al. 2020). Alternatively, chromatin immunoprecipitation with massively parallel DNA sequencing (ChIP-seq) can be performed in bulk with an antibody targeting an active...
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Resource: Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans
- Aaron C. Daugherty,
- Robin W. Yeo,
- Jason D. Buenrostro,
- William J. Greenleaf,
- Anshul Kundaje,
- and Anne Brunet
Genome Res. December 2017 27: 2096-2107; Published in Advance November 15, 2017, doi:10.1101/gr.226233.117
..., Wu B, Litzenburger UM, Ruff D, Gonzales ML, Snyder MP, Chang HY, Greenleaf WJ. 2015. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523: 486–490. ↵Byerly L, Cassada RC, Russell RL. 1976. The life cycle of the nematode Caenorhabditis elegans. I. Wild-type growth...
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Method: Theoretical framework for the difference of two negative binomial distributions and its application in comparative analysis of sequencing data
- Alicia Petrany,
- Ruoyu Chen,
- Shaoqiang Zhang,
- and Yong Chen
Genome Res. October 2024 34: 1636-1650; Published in Advance October 15, 2024, doi:10.1101/gr.278843.123
...University, Tianjin 300387, China Corresponding authors: chenyong@rowan.edu, zhangshaoqiang@tjnu.edu.cnAbstractHigh-throughput sequencing (HTS) technologies have been instrumental in investigating biological questions at the bulk and single-cell levels. Comparative analysis of two HTS data sets often relies...
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Research: Single-cell gene expression analysis reveals regulators of distinct cell subpopulations among developing human neurons
- Jiaxu Wang,
- Piroon Jenjaroenpun,
- Akshay Bhinge,
- Vladimir Espinosa Angarica,
- Antonio Del Sol,
- Intawat Nookaew,
- Vladimir A. Kuznetsov,
- and Lawrence W. Stanton
Genome Res. November 2017 27: 1783-1794; Published in Advance October 13, 2017, doi:10.1101/gr.223313.117
...72205, USA The stochastic dynamics and regulatory mechanisms that govern differentiation of individual human neural precursor cells (NPC) into mature neurons are currently not fully understood. Here, we used single-cell RNA-sequencing (scRNA-seq) of developing neurons to dissect/identify NPC subtypes...
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Research: De novo transcriptome assembly of mouse male germ cells reveals novel genes, stage-specific bidirectional promoter activity, and noncoding RNA expression
- Mark E. Gill,
- Alexia Rohmer,
- Serap Erkek-Ozhan,
- Ching-Yeu Liang,
- Sunwoo Chun,
- Evgeniy A. Ozonov,
- and Antoine H.F.M. Peters
Genome Res. December 2023 33: 2060-2078; Published in Advance December 21, 2023, doi:10.1101/gr.278060.123
...of the validity of our transcriptome annotation, we performed chromatin immunoprecipitation (ChIP) sequencing for trimethylation of lysine 4 of histone H3 (H3K4me3) in cells isolated from adult testes. H3K4me3 is a well-known histone modification found around the transcription start sites of expressed genes...
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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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