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Method: Single-cell Rapid Capture Hybridization sequencing reliably detects isoform usage and coding mutations in targeted genes
- Hongke Peng,
- Jafar S. Jabbari,
- Luyi Tian,
- Changqing Wang,
- Yupei You,
- Chong Chyn Chua,
- Natasha S. Anstee,
- Noorul Amin,
- Andrew H. Wei,
- Nadia M. Davidson,
- Andrew W. Roberts,
- David C.S. Huang,
- Matthew E. Ritchie,
- and Rachel Thijssen
Genome Res. April 2025 35: 942-955; Published in Advance January 10, 2025, doi:10.1101/gr.279322.124
...-read single-cell RNA sequencing (scRNA-seq) data reveals significant gene expression differences in SF3B1-mutated CLL cells, although it does not impact the sensitivity of the anticancer drug venetoclax. scRaCH-seq's capability to study long-read transcripts of multiple genes makes it a powerful tool...
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Method: Deep structural clustering reveals hidden systematic biases in RNA sequencing data
- Qiang Su,
- Yi Long,
- Deming Gou,
- Junmin Quan,
- Xiaoming Zhou,
- and Qizhou Lian
Genome Res. November 2025 35: 2563-2577; Published in Advance September 19, 2025, doi:10.1101/gr.280713.125
...visualization of GMM clustering on one-hot encoded sequences. Spike-in RNAs are clustered using GMM based on one-hot encoded nucleotide sequences into ten clusters. The UMAP plot visualizes the distribution of RNAs across these clusters, with silhouette scores assessing the quality of cluster separation. (H...
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Method: Iterative epigenomic analyses in the same single cell
- Hidetaka Ohnuki,
- David J. Venzon,
- Alexei Lobanov,
- and Giovanna Tosato
Genome Res. October 2021 31: 1819-1830; Published in Advance February 24, 2021, doi:10.1101/gr.269068.120
...transcriptome alkylation-dependent single-cell RNA sequencing (NASC-seq); results of this analysis are shown in Supplemental Figure S14E. On average, 612 genes/K562 cell were transcribed over 60 min, suggesting that Pol II is present on the body of these genes. We found that a portion of Pol II+ genes detected...
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Method: A transcriptome-based single-cell biological age model and resource for tissue-specific aging measures
- Shulin Mao,
- Jiayu Su,
- Longteng Wang,
- Xiaochen Bo,
- Cheng Li,
- and Hebing Chen
Genome Res. August 2023 33: 1381-1394; Published in Advance July 31, 2023, doi:10.1101/gr.277491.122
...the features learned from single-cell omics data can capture other dimensions of biological aging.Here, we developed single-cell aging-level estimator (SCALE), a tissue-specific measure that quantifies aging in individual cells using single-cell RNA-sequencing (scRNA-seq) data (Fig. 1). Unlike other clocks...
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Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
- Carolina Monzó,
- Adam Frankish,
- and Ana Conesa
Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
...provided by synthetic spike-in RNA variants (SIRVs) or Sequins spike-in controls (Hardwick et al. 2016), to those in a real sample. For example, we used the SQANTI3 framework to analyze the reads associated with Lexogen's E0 mix SIRV transcripts spiked into the aforementioned mouse brain samples, sequenced...
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Research: Single-cell RNA-sequencing reveals the existence of naive and primed pluripotency in pre-implantation rhesus monkey embryos
- Denghui Liu,
- Xinyi Wang,
- Dajian He,
- Chunli Sun,
- Xiechao He,
- Lanzhen Yan,
- Yizhou Li,
- Jing-Dong J. Han,
- and Ping Zheng
Genome Res. October 2018 28: 1481-1493; Published in Advance August 28, 2018, doi:10.1101/gr.233437.117
...the lineage specification of human pre-implantation embryos by large-scale single-cell RNA-sequencing analysis and reported the overall similarities as well as differences of lineage regulation between human and mouse (Xue et al. 2013; Nakamura et al. 2016; Petropoulos et al. 2016). Despite these advances...
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Perspective: Defining cell types and states with single-cell genomics
- Cole Trapnell
Genome Res. October 2015 25: 1491-1498; doi:10.1101/gr.190595.115
...analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells. Nat Biotechnol 33: 155–160. Buganim Y, Faddah DA, Cheng AW, Itskovich E, Markoulaki S, Ganz K, Klemm SL, van Oudenaarden A, Jaenisch R. 2012. Single-cell expression analyses during cellular...
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Method: SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells
- Kyung Yeon Han,
- Kyu-Tae Kim,
- Je-Gun Joung,
- Dae-Soon Son,
- Yeon Jeong Kim,
- Areum Jo,
- Hyo-Jeong Jeon,
- Hui-Sung Moon,
- Chang Eun Yoo,
- Woosung Chung,
- Hye Hyeon Eum,
- Sangmin Kim,
- Hong Kwan Kim,
- Jeong Eon Lee,
- Myung-Ju Ahn,
- Hae-Ock Lee,
- Donghyun Park,
- and Woong-Yang Park
Genome Res. January 2018 28: 75-87; Published in Advance December 5, 2017, doi:10.1101/gr.223263.117
...the performance of this method using real-time PCR demonstrated that it efficiently recovered genomic DNA and total RNA. Thorough data quality assessments showed that DNA and RNA simultaneously fractionated by the SIDR method were suitable for and transcriptome sequencing analysis at the single-cell level...
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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
...play important roles in this process. To address these issues, we performed deep transcriptome sequencing to reveal the extent and character of PGE within distinct TEC subpopulations and within single mature TEC. The digital nature and increased dynamic range of RNA-seq permit a more precise assessment...
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Resource: Small RNA expression and miRNA modification dynamics in human oocytes and early embryos
- Pauliina Paloviita,
- Christel Hydén-Granskog,
- Dawit A. Yohannes,
- Priit Paluoja,
- Juha Kere,
- Juha S. Tapanainen,
- Kaarel Krjutškov,
- Timo Tuuri,
- Urmo Võsa,
- and Sanna Vuoristo
Genome Res. August 2021 31: 1474-1485; doi:10.1101/gr.268193.120
...of the study include suboptimal read data quantification owing to absence of UMIs or ERCC spike-ins in the sequencing libraries and small sample size. Improved sRNA-seq library preparation methods coupled with increased sequencing depth would enable better coverage and detection of lowly expressed sRNA classes...

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