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Method: Statistically robust methylation calling for whole-transcriptome bisulfite sequencing reveals distinct methylation patterns for mouse RNAs
- Carine Legrand,
- Francesca Tuorto,
- Mark Hartmann,
- Reinhard Liebers,
- Dominik Jacob,
- Mark Helm,
- and Frank Lyko
Genome Res. September 2017 27: 1589-1596; Published in Advance July 6, 2017, doi:10.1101/gr.210666.116
...at single-base resolution. More recently, next-generation sequencing has provided opportunities to establish transcriptome-wide maps of this modification. Here, we present a computational approach that integrates tailored filtering and data-driven statistical modeling to eliminate many of the artifacts...
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Method: Strand-specific deep sequencing of the transcriptome
- Ana P. Vivancos,
- Marc Güell,
- Juliane C. Dohm,
- Luis Serrano,
- and Heinz Himmelbauer
Genome Res. July 2010 20: 989-999; Published in Advance June 2, 2010, doi:10.1101/gr.094318.109
.... Discussion We have tested DSSS in two species, in a simple prokaryotic organism, and in a mammal. We have observed a high degree of strand specificity, single base resolution, and highly covered transcripts. Recent studies have reported exhaustive transcriptomic maps (Cloonan et al. 2008; He et al. 2008...
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Research: Parallel evolution of transcriptome architecture during genome reorganization
- Sung Ho Yoon,
- David J. Reiss,
- J. Christopher Bare,
- Dan Tenenbaum,
- Min Pan,
- Joseph Slagel,
- Robert L. Moritz,
- Sujung Lim,
- Murray Hackett,
- Angeli Lal Menon,
- Michael W.W. Adams,
- Adam Barnebey,
- Steven M. Yannone,
- John A. Leigh,
- and Nitin S. Baliga
Genome Res. November 2011 21: 1892-1904; Published in Advance July 12, 2011, doi:10.1101/gr.122218.111
...have further characterized how microbes deal with operon instability by mapping and comparing transcriptome architectures of four phylogenetically diverse extremophiles that span the range of operon stabilities observed across archaeal lineages: a photoheterotrophic halophile ( Halobacterium salinarum...
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Resource: The Drosophila melanogaster transcriptome by paired-end RNA sequencing
- Bryce Daines,
- Hui Wang,
- Liguo Wang,
- Yumei Li,
- Yi Han,
- David Emmert,
- William Gelbart,
- Xia Wang,
- Wei Li,
- Richard Gibbs,
- and Rui Chen
Genome Res. February 2011 21: 315-324; Published in Advance December 22, 2010, doi:10.1101/gr.107854.110
...Biology, Baylor College of Medicine, Houston, Texas 77030, USA ↵ 6 These authors contributed equally to this work. Abstract RNA-seq was used to generate an extensive map of the Drosophila melanogaster transcriptome by broad sampling of 10 developmental stages. In total, 142...
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Research: The chromatin landscape of the histone-possessing Bacteriovorax bacteria
- Georgi K. Marinov,
- Benjamin Doughty,
- Anshul Kundaje,
- and William J. Greenleaf
Genome Res. January 2025 35: 109-123; Published in Advance November 21, 2024, doi:10.1101/gr.279418.124
...to improve resolution in its very small and compact (for details, see Methods).Hi-C has been previously applied to study the physical organization of several bacterial and archaeal strains such as, originally, C. crescentus (Le et al. 2013; Yildirim and Feig 2018) and, later, multiple others (Marbouty et al...
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Method: Transposase mediated construction of RNA-seq libraries
- Jason Gertz,
- Katherine E. Varley,
- Nicholas S. Davis,
- Bradley J. Baas,
- Igor Y. Goryshin,
- Ramesh Vaidyanathan,
- Scott Kuersten,
- and Richard M. Myers
Genome Res. January 2012 22: 134-141; Published in Advance November 29, 2011, doi:10.1101/gr.127373.111
..., Gnirke A, Regev A. 2010. Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods 7: 709–715. Lister R, O’Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR. 2008. Highly integrated single-base resolution maps of the epi in Arabidopsis. Cell 133: 523...
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Method: Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes
- Alexandre Lomsadze,
- Karl Gemayel,
- Shiyuyun Tang,
- and Mark Borodovsky
Genome Res. July 2018 28: 1079-1089; Published in Advance May 17, 2018, doi:10.1101/gr.230615.117
...JH, Kang SG, Cho BK. 2017. Genome-wide primary transcriptome analysis of H2-producing archaeon Thermococcus onnurineus NA1. Sci Rep 7: 43044. ↵Cortes T, Schubert OT, Rose G, Arnvig KB, Comas I, Aebersold R, Young DB. 2013. Genome-wide mapping of transcriptional start sites defines an extensive...
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Resource: Structural and operational complexity of the Geobacter sulfurreducens genome
- Yu Qiu,
- Byung-Kwan Cho,
- Young Seoub Park,
- Derek Lovley,
- Bernhard Ø. Palsson,
- and Karsten Zengler
Genome Res. September 2010 20: 1304-1311; Published in Advance June 30, 2010, doi:10.1101/gr.107540.110
...35: 4809–4819. Wurtzel O, Sapra R, Chen F, Zhu Y, Simmons BA, Sorek R. 2010. A single-base resolution map of an archaeal transcriptome. Genome Res 20: 133–141. Zhang Y, Zhang Z, Ling L, Shi B, Chen R. 2004. Conservation analysis of small RNA genes in Escherichia coli. Bioinformatics 20: 599...
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Research: Core promoter sequence in yeast is a major determinant of expression level
- Shai Lubliner,
- Ifat Regev,
- Maya Lotan-Pompan,
- Sarit Edelheit,
- Adina Weinberger,
- and Eran Segal
Genome Res. July 2015 25: 1008-1017; Published in Advance May 12, 2015, doi:10.1101/gr.188193.114
...were performed by fluorescence activated sorting (FACS) of the yeast cells into 16 bins of YFP/mCherry levels, next-generation sequencing of the variable core promoter region, mapping the non-YFP-barcoded sequencing reads (while discarding YFPbarcoded reads to avoid the effect of the barcode mutations...

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