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Resource: Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs
- Qiuhan Wen,
- Zhen Wang,
- Qi Bao,
- Tianli Ding,
- Haihan Zhang,
- Jianbo Li,
- Zhuang Liu,
- Jieping Huang,
- and Guoqiang Yi
Genome Res. September 2025 35: 2116-2129; Published in Advance June 16, 2025, doi:10.1101/gr.280095.124
...Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs Qiuhan Wen1,2, Zhen Wang1, Qi Bao1, Tianli Ding1, Haihan Zhang3, Jianbo Li4, Zhuang Liu5, Jieping Huang2 and Guoqiang Yi1,6,7 1Shenzhen Branch, Guangdong Laboratory of Lingnan...
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Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
- Kangli Wang,
- Weikun Xia,
- Yingli Gu,
- Songpeng Zu,
- Qian Yang,
- Maria Luisa Amaral,
- Yaozhi Wang,
- Allen Wang,
- Xiang-Dong Fu,
- William C. Mobley,
- and Bing Ren
Genome Res. April 2026 36: 849-864; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...months (old) using 10x Genomics Chromium Multiome (Fig. 1A). We conducted two biological replicates for each stage, resulting in a total of eight samples for both single-nucleus ATAC-seq (snATAC-seq) and single-nucleus RNA-seq (snRNA-seq).View larger version: In this window In a new window Figure 1...
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Research: Differences in molecular sampling and data processing explain variation among single-cell and single-nucleus RNA-seq experiments
- John T. Chamberlin,
- Younghee Lee,
- Gabor T. Marth,
- and Aaron R. Quinlan
Genome Res. February 2024 34: 179-188; Published in Advance February 14, 2024, doi:10.1101/gr.278253.123
...-H, Streets A. 2022. Characterization of transcript enrichment and detection bias in single-nucleus RNA-seq for mapping of distinct human adipocyte lineages. Genome Res 32: 242–257. doi:10.1101/gr.275509.121 ↵Habib N, Avraham-Davidi I, Basu A, Burks T, Shekhar K, Hofree M, Choudhury SR, Aguet F, Gelfand E...
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Method: Tree-based differential testing using inferential uncertainty for RNA-seq
- Noor Pratap Singh,
- Euphy Y. Wu,
- Jason Fan,
- Michael I. Love,
- and Rob Patro
Genome Res. October 2025 35: 2326-2338; Published in Advance August 21, 2025, doi:10.1101/gr.279981.124
...-aware differential transcript/gene expression methods. Our method detects inner nodes that show a strong signal for differential expression, which would have been overlooked when analyzing the transcripts alone.RNA-seq has become the de facto technology for measuring the expression profiles of different genomic...
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Method: Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks
- Prashanthi Ravichandran,
- Princy Parsana,
- Rebecca Keener,
- Kasper D. Hansen,
- and Alexis Battle
Genome Res. September 2025 35: 2087-2103; Published in Advance July 17, 2025, doi:10.1101/gr.280808.125
...and AI Institute, Johns Hopkins University, Baltimore, Maryland 21218, USA Corresponding author: ajbattle@jhu.eduAbstractGene coexpression networks (GCNs) describe relationships among genes that maintain cellular identity and homeostasis. However, typical RNA-seq experiments often lack sufficient sample...
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Resource: Single-nucleus transcriptomic mapping uncovers targets for traumatic brain injury
- Qiuyun Yang,
- Lingxuan Zhang,
- Manrui Li,
- Yang Xu,
- Xiaogang Chen,
- Ruixuan Yuan,
- Xiaofeng Ou,
- Min He,
- Miao Liao,
- Lin Zhang,
- Hao Dai,
- Meili Lv,
- Xiaoqi Xie,
- Weibo Liang,
- and Xiameng Chen
Genome Res. October 2023 33: 1818-1832; Published in Advance September 20, 2023, doi:10.1101/gr.277881.123
...: In this window In a new window Figure 1. Major cell types in adult SVZ and cell type–specific markers based on single-cell profiling. (A) Workflow of sample preparation, single-nucleus RNA-seq, and the downstream analysis. (B) Neurological severity score (NSS) of the control group and mTBI group. Three mice...
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Method: Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression
- Howard J. Womersley,
- Daniel Muliaditan,
- Ramanuj DasGupta,
- and Lih Feng Cheow
Genome Res. January 2025 35: 162-177; Published in Advance December 2, 2024, doi:10.1101/gr.279105.124
...Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression Howard J. Womersley1,4, Daniel Muliaditan2,3,4, Ramanuj DasGupta3 and Lih Feng Cheow1,2 1Institute for Health Innovation and Technology, National University...
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Research: Epigenetic characterization of pseudogenes across human tissues
- Yunzhe Jiang,
- Beatrice Borsari,
- and Mark Gerstein
Genome Res. April 15, 2026 gr.280768.125; Published in Advance April 15, 2026, doi:10.1101/gr.280768.125
...level of ≥ 1 transcripts per million (TPM) across all available donors and their technical replicates (Fig. 1C; Supplemental Figs. S1 and S2). We also used long-read RNA-seq data available from EN-TEx for the heart left ventricle to corroborate expression calls obtained from short-read RNA-seq...
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Method: A gene regulatory network–aware graph learning method for cell identity annotation in single-cell RNA-seq data
- Mengyuan Zhao,
- Jiawei Li,
- Xiaoyi Liu,
- Ke Ma,
- Jijun Tang,
- and Fei Guo
Genome Res. July 2024 34: 1036-1051; Published in Advance August 12, 2024, doi:10.1101/gr.278439.123
.... Accordingly, the average F1-score of scHGR is higher than those of other methods, proving the effectiveness of HGNN across technologies. The scRNA-seq data generated from different technologies, platforms, and operators exhibit intrinsic differences owing to measurement bias, technical settings, and other...
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Method: Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq
- Alejandro Paniagua,
- Cristina Agustín-García,
- Francisco J. Pardo-Palacios,
- Thomas Brown,
- Maite De Maria,
- Nancy D. Denslow,
- Camila J. Mazzoni,
- and Ana Conesa
Genome Res. April 2025 35: 1053-1064; Published in Advance December 23, 2024, doi:10.1101/gr.279864.124
...(Scalzitti et al. 2020). Recently, long-read RNA sequencing (lrRNA-seq) has started to be used for this purpose (Peng et al. 2022; Zhang et al. 2022). lrRNA-seq has the potential to capture full-length transcripts and reveal the complexity of the transcriptomes. However, lrRNA-seq data also contain...
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