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Method: Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR
- Artem Mikelov,
- George Nefediev,
- Alexander Tashkeev,
- Oscar L. Rodriguez,
- Diego Aguilar Ortmans,
- Valeriia Skatova,
- Mark Izraelson,
- Alexey N. Davydov,
- Stanislav Poslavsky,
- Souad Rahmouni,
- Corey T. Watson,
- Dmitriy Chudakov,
- Scott D. Boyd,
- and Dmitry Bolotin
Genome Res. December 2024 34: 2293-2303; Published in Advance October 21, 2024, doi:10.1101/gr.278775.123
...a/b Profiling Kit v2 (Takara Bio). Briefly, a rapid amplification of cDNA ends (RACE) approach with a template-switch effect was used to introduce 5′ adaptors during cDNA synthesis. cDNA corresponding to TRA and TRB transcripts was further amplified and prepared for sequencing, which was performed...
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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
...the transcriptome profile to isoform usage, mutations, and translocations in full-length transcripts at a single-cell level (Wu and Schmitz 2023).In recent years, several high-throughput methods have been developed to enable single-cell long-read sequencing. These approaches typically involve barcoding of cDNA...
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Review: Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics
- Natan Belchikov,
- Justine Hsu,
- Xiang Jennie Li,
- Julien Jarroux,
- Wen Hu,
- Anoushka Joglekar,
- and Hagen U. Tilgner
Genome Res. November 2024 34: 1735-1746; doi:10.1101/gr.279640.124
...solely on the ONT data. All three tools allow the user to derive a more accurate set of cell barcodes (and UMIs in the case of ScNaUmi-seq and BLAZE) from ONT sequencing output. Finally, MAS-ISO-seq avoids short reads by relying on the concatenation of cDNA molecules to improve the efficiency...
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Research: Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications
- Matthias H. Weissensteiner,
- Andy W.C. Pang,
- Ignas Bunikis,
- Ida Höijer,
- Olga Vinnere-Petterson,
- Alexander Suh,
- and Jochen B.W. Wolf
Genome Res. May 2017 27: 697-708; Published in Advance March 30, 2017, doi:10.1101/gr.215095.116
...M Tris-Buffer and stored at 4°C. DNA concentration was measured with a Nanodrop spectrophotometer (ThermoFisherScientific) and visualized on a 0.5% agarose gel (run time >8 h with 25 V) to confirm high molecular weight. Three DNA libraries were produced using the SMRTbell Template Prep Kit 1.0 (Pacific...
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Method: Application of microdroplet PCR for large-scale targeted bisulfite sequencing
- H. Kiyomi Komori,
- Sarah A. LaMere,
- Ali Torkamani,
- G. Traver Hart,
- Steve Kotsopoulos,
- Jason Warner,
- Michael L. Samuels,
- Jeff Olson,
- Steven R. Head,
- Phillip Ordoukhanian,
- Pauline L. Lee,
- Darren R. Link,
- and Daniel R. Salomon
Genome Res. October 2011 21: 1738-1745; Published in Advance July 14, 2011, doi:10.1101/gr.116863.110
.... Amplified cDNA was prepared from 100 ng total RNA using theOvation RNA-seq System (Nugen).Onehundred ng cDNA Komori et al. 1744 Genome Research www..org was treated with S1 Nuclease (Promega), and sequencing libraries were prepared as described above. Data access The sequencing data from this study have...
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Method: Sequencing Illumina libraries at high accuracy on the ONT MinION using R2C2
- Alexander Zee,
- Dori Z.Q. Deng,
- Matthew Adams,
- Kayla D. Schimke,
- Russell Corbett-Detig,
- Shelbi L. Russell,
- Xuan Zhang,
- Robert J. Schmitz,
- and Christopher Vollmers
Genome Res. November/December 2022 32: 2092-2106; Published in Advance November 9, 2022, doi:10.1101/gr.277031.122
...repeats of the original molecule's sequence. These long molecules can then be sequenced on ONT instruments to generate long raw reads, which are then computationally processed into accurate consensus reads. In previous studies focused on full-length cDNA molecules, we have achieved median read accuracies...
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Research: Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis
- Weisheng Wu,
- Christapher S. Morrissey,
- Cheryl A. Keller,
- Tejaswini Mishra,
- Maxim Pimkin,
- Gerd A. Blobel,
- Mitchell J. Weiss,
- and Ross C. Hardison
Genome Res. December 2014 24: 1945-1962; Published in Advance October 15, 2014, doi:10.1101/gr.164830.113
...Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis Weisheng Wu 1 , 4 , Christapher S. Morrissey 1 , Cheryl A. Keller 1 , Tejaswini Mishra 1 , Maxim...
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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
...wild isolate VSL2202 and ZF1220 compared with C. briggsae strains. (E) Heatmap showing cDNA sequence identity of Cni-shls-1 (top), Cni-otub-3 (middle), and Cni-neib-1 (bottom) across all C. nigoni strains. Note that Cni-neib-1 sequences are 100% identical across all strains. (F) Gene models flanking...
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Research: Degrees of convergent evolution in rodent adaptations to arid environments
- Domitille Chalopin,
- Carine Rey,
- Jeremy Ganofsky,
- Juliana Blin,
- Pascale Chevret,
- Marion Mouginot,
- Laurent Guéguen,
- Bastien Boussau,
- Sophie Pantalacci,
- and Marie Sémon
Genome Res. March 2026 36: 472-486; Published in Advance January 21, 2026, doi:10.1101/gr.280089.124
...for the kidney. We combined publicly available data (cDNA from published s and kidney RNA-seq data) with newly generated RNA-seq data to obtain coding sequence and expression data in a variety of rodents, ensuring a reasonable overlap between the two types of data (12 families, 48 species out of which 33 species...
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Methods: Large-scale production of SAGE libraries from microdissected tissues, flow-sorted cells, and cell lines
- Jaswinder Khattra,
- Allen D. Delaney,
- Yongjun Zhao,
- Asim Siddiqui,
- Jennifer Asano,
- Helen McDonald,
- Pawan Pandoh,
- Noreen Dhalla,
- Anna-liisa Prabhu,
- Kevin Ma,
- Stephanie Lee,
- Adrian Ally,
- Angela Tam,
- Danne Sa,
- Sean Rogers,
- David Charest,
- Jeff Stott,
- Scott Zuyderduyn,
- Richard Varhol,
- Connie Eaves,
- Steven Jones,
- Robert Holt,
- Martin Hirst,
- Pamela A. Hoodless,
- and Marco A. Marra
Genome Res. January 2007 17: 108-116; Published in Advance November 29, 2006, doi:10.1101/gr.5488207
...concatenation. Construction of SAGE-Lite libraries Until the development described above, samples yielding &lt;100 ng of total RNA were subjected to a cDNA amplification step according to the SAGE-Lite method ( Peters et al. 1999 ). SAGE-Lite biochemistry is based upon the SMART ( S witching M echanism A t...

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