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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
..., various human cell lines, and authentic tissue samples, consistently demonstrate the model's superior versatility and accuracy across different biological systems. Furthermore, in silico simulations of the sequencing process closely align with actual sequencing data, strongly reinforcing the critical role...
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Method: Long-read RNA sequencing reveals allele-specific N⁶-methyladenosine modifications
- Dayea Park and
- Can Cenik
Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124
....Read processing of RNA-seq and ribosome profilingFor mESC, RNA-seq and Ribo-seq data were processed using RiboFlow v0.0.1 (Ozadam et al. 2020). For the Ribo-seq library, Unique Molecular Identifier (UMI) sequences were isolated employing the following parameters: “umi_tools extract -p ‘∧(?P<umi_1>.{12})(?P...
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Method: 3′-end ligation sequencing is a sensitive method to detect DNA nicks at potential sites of off-target activity induced by prime editors
- Jacob Stewart-Ornstein,
- Matthew J. Irby,
- Marina K. Lilieholm,
- Dylan Laprise,
- Maria D. Collier,
- Thomas Aunins,
- Dewi Harjanto,
- Aaron N. Chang,
- Deepak Reyon,
- and Jeremy S. Duffield
Genome Res. September 2025 35: 2064-2075; Published in Advance August 5, 2025, doi:10.1101/gr.280164.124
...sequence, a unique molecular identifier (UMI), i5 index sequence, and a P5 sequence. It is annealed to a short oligo that is complementary to part of the read 1 sequence. This short oligo has a randomized 3′ end for capture, a 3′ amino group for blocking, and a 5′ biotin. Bulk stocks of P5 capture adapter...
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Research: Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders
- Susan M. Hiatt,
- James M.J. Lawlor,
- Lori H. Handley,
- Donald R. Latner,
- Zachary T. Bonnstetter,
- Candice R. Finnila,
- Michelle L. Thompson,
- Lori Beth Boston,
- Melissa Williams,
- Ivan Rodriguez Nunez,
- Jerry Jenkins,
- Whitley V. Kelley,
- E. Martina Bebin,
- Michael A. Lopez,
- Anna C.E. Hurst,
- Bruce R. Korf,
- Jeremy Schmutz,
- Jane Grimwood,
- and Gregory M. Cooper
Genome Res. November 2024 34: 1747-1762; Published in Advance September 19, 2024, doi:10.1101/gr.279227.124
...yield (7/96, 7.3%) beyond srGS. We anticipate that as lrGS analysis improves, and as lrGS data sets grow allowing for better variant-frequency annotation, the additional lrGS-only rare disease yield will grow over time.Although and exome sequencing (GS/ES) are increasingly used to identify molecular...
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Research: Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations
- Alicja Pacholewska,
- Matthias Lienhard,
- Mirko Brüggemann,
- Heike Hänel,
- Lorina Bilalli,
- Anja Königs,
- Felix Heß,
- Kerstin Becker,
- Karl Köhrer,
- Jesko Kaiser,
- Holger Gohlke,
- Norbert Gattermann,
- Michael Hallek,
- Carmen D. Herling,
- Julian König,
- Christina Grimm,
- Ralf Herwig,
- Kathi Zarnack,
- and Michal R. Schweiger
Genome Res. November 2024 34: 1832-1848; Published in Advance September 13, 2024, doi:10.1101/gr.279327.124
..., and SNRPN) identified in CLL based on Nanopore sequencing (Tang et al. 2020), a 3′AS in SEPTIN6 reported in MDS-SF3B1mut/wt patients (Supplemental Fig. S16; Dolatshad et al. 2016), and 13 3′AS events (BCL2L1, COASY, DPH5, DYNLL1, EI24, ERGIC3, MED6, METTL5, SERBP1, SKIV2L, TMEM14C, ZBED5, and ZDHHC16...
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Method: Mapping and quantifying nascent transcript start sites using TT-TSS-seq
- Eleanor Elgood Hunt,
- Claudia Vivori,
- Richard Mitter,
- Vedis Agnadottir,
- and Folkert J. van Werven
Genome Res. March 2026 36: 600-610; Published in Advance February 17, 2026, doi:10.1101/gr.280726.125
...optimize the TSS-seq protocol to enhance sensitivity and accuracy. Specifically, we refine enzymatic reactions for decapping and RNA ligation and incorporate 5′ oligonucleotides containing unique molecular identifiers (UMIs) and barcodes to enable accurate quantification and sample multiplexing. The TT...
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Method: Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates
- Haiyue Liu and
- Lea H. Gregersen
Genome Res. November 2025 35: 2550-2562; Published in Advance October 22, 2025, doi:10.1101/gr.280852.125
...to 5 min, with 4sU added during the last 5 min of the experiments. Library preparation remains similar to DRB/TTchem-seq but incorporates Unique Molecular Identifier (UMI) as part of the sequencing adapter for PCR duplicates identification. Following sequencing, RNAPII elongation progression...
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Method: Dissecting and improving gene regulatory network inference using single-cell transcriptome data
- Lingfeng Xue,
- Yan Wu,
- and Yihan Lin
Genome Res. September 2023 33: 1609-1621; Published in Advance August 14, 2023, doi:10.1101/gr.277488.122
...the accuracy of regulatory inference is limited. Here, we systematically characterized factors limiting the accuracy of inferred GRNs and demonstrated that using pre-mRNA information can help improve regulatory inference compared to the typically used information (i.e., mature mRNA). Using kinetic modeling...
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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
...sequencing (scRNA-seq and snRNA-seq) technologies have been widely used to explore gene expression profiles at the single-cell resolution and offer a unique opportunity to trace dynamic 3′ UTR patterns across cell lineages. Several pioneering studies have systematically examined cell type–specific APA events...
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Research: Historical RNA expression profiles from the extinct Tasmanian tiger
- Emilio Mármol-Sánchez,
- Bastian Fromm,
- Nikolay Oskolkov,
- Zoé Pochon,
- Panagiotis Kalogeropoulos,
- Eli Eriksson,
- Inna Biryukova,
- Vaishnovi Sekar,
- Erik Ersmark,
- Björn Andersson,
- Love Dalén,
- and Marc R. Friedländer
Genome Res. August 2023 33: 1299-1316; Published in Advance July 18, 2023, doi:10.1101/gr.277663.123
...originating from the same RNA molecules were identified and deduplicated based on identical sequences and unique molecular identifiers (UMIs). This procedure reduced the number of sequences to 2.6 million to 12 million per sample, indicating a PCR duplication rate of approximately 21.3 and 11 for skeletal...
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