Searching journal content for articles similar to Furuno et al. 13 (6b): 1478.

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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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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
...assemblies (Supplemental Table S7). We also identified the insertion site for six retroCNVs that had not been resolved through discordant read mapping (Supplemental Table S7). Most of the retroCNVs were full length with respect to the parent genes, with 153/179 (85.5%) containing the entire parental gene...
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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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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
...are therefore ultimately arbitrary and do not carry biological significance. Together, this indicated that isoform features identified by Mandalorion were indeed present within our cDNA pool even if they did not match the GENCODE annotation (Fig. 2D).To showcase the usefulness of deep full-length isoform data...
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Resource: Generation and analysis of a mouse multitissue genome annotation atlas
- Matthew Adams and
- Christopher Vollmers
Genome Res. November 2024 34: 2108-2117; Published in Advance October 23, 2024, doi:10.1101/gr.279217.124
...annotation should contain information on what tissues express what transcript isoforms at what level. This tissue-level isoform information can then inform a wide range of research questions as well as experiment designs. Long-read sequencing technology combined with advanced full-length cDNA library...
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Resource: The full-length transcriptome of C. elegans using direct RNA sequencing
- Nathan P. Roach,
- Norah Sadowski,
- Amelia F. Alessi,
- Winston Timp,
- James Taylor,
- and John K. Kim
Genome Res. February 2020 30: 299-312; Published in Advance February 5, 2020, doi:10.1101/gr.251314.119
...used high-throughput cDNA sequencing technologies. For example, in the annotation of the Caenorhabditis elegans transcriptome, more than half of the transcript isoforms lack full-length support and instead rely on inference from short reads that do not span the full length of the isoform. We applied...
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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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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
...sequence tags (ESTs) and cDNAs, with fewer than 0.5 M cDNAs and ∼8.5 M ESTs ever captured. In an era of relative data sparsity, annotating every transcript detected was a plausible goal notwithstanding the immaturity of much of the software and computational tooling supporting the annotation effort...
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