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Method: De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotype-resolved germline assemblies
- John Beaulaurier,
- Lynn Ly,
- J. Andrew Duty,
- Carly Tyer,
- Christian Stevens,
- Chuan-Tien Hung,
- Akash Sookdeo,
- Alex W. Drong,
- Shreyas Kowdle,
- Axel Guzman-Solis,
- Domenico Tortorella,
- Daniel J. Turner,
- Sissel Juul,
- Scott Hickey,
- and Benhur Lee
Genome Res. April 2025 35: 929-941; Published in Advance March 21, 2025, doi:10.1101/gr.279392.124
...Sorted B cells in the ASC and MBC gates were separately processed for single-cell RNA-seq using the Chromium Next GEM Single-Cell 3′ Reagent kits v3.1 (10x Genomics) according to the manufacturer instructions with modifications: After the GEM-RT cleanup and full-length cDNA amplification step, 50% of the cDNA...
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Resource: Full-length RNA transcript sequencing traces brain isoform diversity in house mouse natural populations
- Wenyu Zhang,
- Anja Guenther,
- Yuanxiao Gao,
- Kristian Ullrich,
- Bruno Huettel,
- Aftab Ahmad,
- Lei Duan,
- Kaizong Wei,
- and Diethard Tautz
Genome Res. November 2024 34: 2118-2132; Published in Advance September 17, 2024, doi:10.1101/gr.279166.124
...with hallmarks of both, a 5′ CAP and a poly(A) tail. It has been reported that the TeloPrime Full-Length cDNA Amplification Kit could selectively synthesize cDNA molecules from mRNAs carrying a 5′ CAP, in complement to the standard PacBio cDNA library preparation protocol that could only selectively synthesize cDNA...
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Method: Long-read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation
- Alexander J. Ritter,
- Jolene M. Draper,
- Christopher Vollmers,
- and Jeremy R. Sanford
Genome Res. November 2024 34: 2000-2011; Published in Advance June 5, 2024, doi:10.1101/gr.279170.124
...using HiSeq 4000 PE150 (50 million to 100 million reads per library).Long-read Frac-seqFrom the same fractionated mRNA used prior for Illumina sequencing, full-length cDNA was prepared using the rolling circle amplification to concatemeric consensus (R2C2) method (Volden et al. 2018). Libraries were...
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Method: Quantifying full-length circular RNAs in cancer
- Ken Hung-On Yu,
- Christina Huan Shi,
- Bo Wang,
- Savio Ho-Chit Chow,
- Grace Tin-Yun Chung,
- Raymond Wai-Ming Lung,
- Ke-En Tan,
- Yat-Yuen Lim,
- Anna Chi-Man Tsang,
- Kwok-Wai Lo,
- and Kevin Y. Yip
Genome Res. December 2021 31: 2340-2353; Published in Advance October 18, 2021, doi:10.1101/gr.275348.121
...transcriptases for an NTRK2 BSJ and a full-length transcript isoform of it (Supplemental Fig. S8A).To get a more quantitative evaluation of the deduced expression levels, we further performed RT-qPCR on two short full-length isoforms, selected according to the detection limit of RT-qPCR. The results (Fig. 7E...
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Method: Marker-free characterization of full-length transcriptomes of single live circulating tumor cells
- Sarita Poonia,
- Anurag Goel,
- Smriti Chawla,
- Namrata Bhattacharya,
- Priyadarshini Rai,
- Yi Fang Lee,
- Yoon Sim Yap,
- Jay West,
- Ali Asgar Bhagat,
- Juhi Tayal,
- Anurag Mehta,
- Gaurav Ahuja,
- Angshul Majumdar,
- Naveen Ramalingam,
- and Debarka Sengupta
Genome Res. January 2023 33: 80-95; Published in Advance November 22, 2022, doi:10.1101/gr.276600.122
...) on the Polaris IFC and single CTO+ & Calcein AM+ & PTPRC− & CD31− cells were selected to capture sites. Finally, single-cell processing was achieved through template-switching mRNA-seq chemistry for full-length cDNA generation and preamplification on IFC. Supplemental Note 5 elaborates the steps involved in m...
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Resource: Recent, full-length gene retrocopies are common in canids
- Kevin Batcher,
- Scarlett Varney,
- Daniel York,
- Matthew Blacksmith,
- Jeffrey M. Kidd,
- Robert Rebhun,
- Peter Dickinson,
- and Danika Bannasch
Genome Res. August 2022 32: 1602-1611; Published in Advance August 12, 2022, doi:10.1101/gr.276828.122
...), as described at http://creativecommons.org/licenses/by-nc/4.0/.References ↵The 1000 Genomes Project Consortium. 2015. A global reference for human genetic variation. Nature 526: 68–74. doi:10.1038/nature15393 ↵Abyzov A, Gerstein M. 2011. AGE: defining breakpoints of genomic structural variants at single...
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Method: Complete characterization of the human immune cell transcriptome using accurate full-length cDNA sequencing
- Charles Cole,
- Ashley Byrne,
- Matthew Adams,
- Roger Volden,
- and Christopher Vollmers
Genome Res. April 2020 30: 589-601; Published in Advance April 20, 2020, doi:10.1101/gr.257188.119
...resolve this because the variants are outside the protein-coding region, where they affect 8-digit but not 6-digit HLA resolution (Fig. 3E).Overall, these findings show that accurate full-length cDNA sequencing at high depth allows the determination of highly accurate sequences of HLA alleles, which can...
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Method: A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry
- Meilin Zhang,
- Heng Du,
- Yu Zhang,
- Yue Zhuo,
- Zhen Liu,
- Yahui Xue,
- Lei Zhou,
- Sixuan Zhou,
- Wanying Li,
- and Jian-Feng Liu
Genome Res. August 2025 35: 1875-1886; Published in Advance July 15, 2025, doi:10.1101/gr.280176.124
...data in population stratification analysis, ancestry prediction, and breed diversity assessments leads to overfitting issues in computational models and creates computational bottlenecks. Therefore, selecting genetic variants that express high amounts of information for use in population diversity...
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Method: The SeqSplice multiplexed minigene splicing assay for characterization and quantitation of variant-induced BRCA1 and BRCA2 splice isoforms
- Daffodil M. Canson,
- Michael T. Parsons,
- Gemma Moir-Meyer,
- Troy Dumenil,
- Gemma Montalban,
- Erica Lin,
- Terri P. McVeigh,
- Aimee L. Davidson,
- Shaun M. Bouckaert,
- Matt Trau,
- Darren Korbie,
- and Amanda B. Spurdle
Genome Res. September 2025 35: 2104-2115; Published in Advance August 6, 2025, doi:10.1101/gr.279557.124
...Splice exhibits excellent reproducibility across cDNA input and PCR cycle differences and is able to identify and quantitate transcripts that differed by a single base. Of the 193 BRCA1 and 72 BRCA2 variants profiled, 89% (237/265) had no publicly available RNA splicing data. Complete or near complete impact...
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Resource: Direct full-length RNA sequencing reveals unexpected transcriptome complexity during Caenorhabditis elegans development
- Runsheng Li,
- Xiaoliang Ren,
- Qiutao Ding,
- Yu Bi,
- Dongying Xie,
- and Zhongying Zhao
Genome Res. February 2020 30: 287-298; Published in Advance February 5, 2020, doi:10.1101/gr.251512.119
..., full-length cDNAs, and RNA sequencing (RNA-seq) of cDNA fragments using massively parallel sequencing (Reboul et al. 2003; Ramani et al. 2011; Uyar et al. 2012; Grün et al. 2014; Boeck et al. 2016; Tourasse et al. 2017). Short RNA-seq reads, typically shorter than 200 nt, have played a leading role...

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