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Method: Tn5 tagments and transposes oligos to single-stranded DNA for strand-specific RNA sequencing
- Yanjun Zhang,
- Yin Tang,
- Zhongxing Sun,
- Junqi Jia,
- Yuan Fang,
- Xinyi Wan,
- and Dong Fang
Genome Res. March 2023 33: 412-426; Published in Advance March 23, 2023, doi:10.1101/gr.277213.122
...-stranded DNA longer than 140 nucleotides. Based on this property of Tn5, we developed a tagmentation-based and ligation-enabled single-stranded DNA sequencing method called TABLE-seq. Through a series of reaction temperature, time, and enzyme concentration tests, we applied TABLE-seq to strand-specific RNA...
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Method: Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data
- Song Li,
- Louisa M. Liberman,
- Neelanjan Mukherjee,
- Philip N. Benfey,
- and Uwe Ohler
Genome Res. October 2013 23: 1730-1739; Published in Advance July 1, 2013, doi:10.1101/gr.149310.112
...framework to incorporate protocol error rate (PE) in the analysis of deep sequencing data sets. Results Strand-specific RNA-seq of Arabidopsis roots We generated replicate ssRNA-seq data from total RNA isolated from Arabidopsis whole roots (sample names: unWR1, unWR2, unWR3; generated from unsorted cells...
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Method: Using long-read CAGE sequencing to profile cryptic-promoter-derived transcripts and their contribution to the immunopeptidome
- Ju Heon Maeng,
- H. Josh Jang,
- Alan Y. Du,
- Shin-Cheng Tzeng,
- and Ting Wang
Genome Res. December 2023 33: 2143-2155; Published in Advance December 8, 2023, doi:10.1101/gr.277061.122
...to improve cancer immunotherapy approaches; however, current genomics and computational tools are not optimized for their detection. Here we combined CAGE technology with full-length long-read transcriptome sequencing (long-read CAGE, or LRCAGE) and developed a suite of computational tools to significantly...
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Research: Acute depletion of METTL3 implicates N⁶-methyladenosine in alternative intron/exon inclusion in the nascent transcriptome
- Guifeng Wei,
- Mafalda Almeida,
- Greta Pintacuda,
- Heather Coker,
- Joseph S. Bowness,
- Jernej Ule,
- and Neil Brockdorff
Genome Res. August 2021 31: 1395-1408; Published in Advance June 15, 2021, doi:10.1101/gr.271635.120
...-binding motifs occurring at RBM15 CITS and CIMS. (D) The RBM15 binding (CITS) metaprofile and heat map for intronic m6A peaks of three different confidence groups (red, blue, and gray for Cfg1, Cfg2, and Cfg3, respectively). The color key is shown on the right; 0.5-kb strand-specific flanking regions on each...
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Resource: Native RNA sequencing in fission yeast reveals frequent alternative splicing isoforms
- José Carlos Montañés,
- Marta Huertas,
- Simone G. Moro,
- William R. Blevins,
- Mercè Carmona,
- José Ayté,
- Elena Hidalgo,
- and M. Mar Albà
Genome Res. June 2022 32: 1215-1227; Published in Advance May 26, 2022, doi:10.1101/gr.276516.121
...; Brar and Weissman 2015), to uncover the complete transcriptome and translatome of S. pombe. Oxford Nanopore Technologies (ONT) direct RNA (dRNA) sequencing (dRNA-seq) offers several important advantages over previous RNA-seq approaches: (1) It provides an unbiased snapshot of the native polyadenylated...
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Resource: Long-read RNA sequencing reveals widespread sex-specific alternative splicing in threespine stickleback fish
- Alice S. Naftaly,
- Shana Pau,
- and Michael A. White
Genome Res. August 2021 31: 1486-1497; Published in Advance June 15, 2021, doi:10.1101/gr.274282.120
...concentration. Illumina strand-specific RNA library preparation and sequencing was completed by GENEWIZ. Strand-specific libraries were sequenced on an Illumina HiSeq (2 × 150 bp).Nuclei isolation and ATAC-seq library preparationLiver samples were collected from two juvenile males (∼4.4 cm in standard length...
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Research: Single worm transcriptomics identifies a developmental core network of oscillating genes with deep conservation across nematodes
- Shuai Sun,
- Christian Rödelsperger,
- and Ralf J. Sommer
Genome Res. September 2021 31: 1590-1601; Published in Advance July 22, 2021, doi:10.1101/gr.275303.121
...organism Pristionchus pacificus to provide a high-resolution map of the developmental transcriptome. We selected 38 time points from hatching of the J2 larvae to young adults to perform transcriptome analysis over 60 h of postembryonic development. A mean sequencing depth of 4.5 million read pairs allowed...
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Method: Whole-genome bisulfite sequencing with improved accuracy and cost
- Masako Suzuki,
- Will Liao,
- Frank Wos,
- Andrew D. Johnston,
- Justin DeGrazia,
- Jennifer Ishii,
- Toby Bloom,
- Michael C. Zody,
- Soren Germer,
- and John M. Greally
Genome Res. September 2018 28: 1364-1371; Published in Advance August 9, 2018, doi:10.1101/gr.232587.117
...affect our conclusions.The resulting alignments were marked for duplicates using Picard v2.4.1 (default parameters). To calculate strand-specific duplicates, alignments were separated based on their orientation to the reference , then MarkDuplicates was run on the two alignment sets separately. Our use...
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Resource: Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution
- Flavia Angela Maria Maggiolini,
- Ashley D. Sanders,
- Colin James Shew,
- Arvis Sulovari,
- Yafei Mao,
- Marta Puig,
- Claudia Rita Catacchio,
- Maria Dellino,
- Donato Palmisano,
- Ludovica Mercuri,
- Miriana Bitonto,
- David Porubský,
- Mario Cáceres,
- Evan E. Eichler,
- Mario Ventura,
- Megan Y. Dennis,
- Jan O. Korbel,
- and Francesca Antonacci
Genome Res. November 2020 30: 1680-1693; Published in Advance October 22, 2020, doi:10.1101/gr.265322.120
...), these approaches often lead to false positives or fail to detect inversions flanked by highly identical sequences.Recently, strand-specific sequencing technologies have been developed and successfully applied to detect inversions in human s (Sanders et al. 2016; Chaisson et al. 2019). Single-cell template strand...
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Research: Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human embryonic stem cells
- Gabriel Kolle,
- Jill L. Shepherd,
- Brooke Gardiner,
- Karin S. Kassahn,
- Nicole Cloonan,
- David L.A. Wood,
- Ehsan Nourbakhsh,
- Darrin F. Taylor,
- Shivangi Wani,
- Hun S. Chy,
- Qi Zhou,
- Kevin McKernan,
- Scott Kuersten,
- Andrew L. Laslett,
- and Sean M. Grimmond
Genome Res. December 2011 21: 2014-2025; Published in Advance October 31, 2011, doi:10.1101/gr.119321.110
...transcriptome A thorough survey of the human ESC transcriptome (HES-2 cell line) was generated using strand-specific shotgun sequencing (Tuch et al. 2010) of the following ribosomal RNA-depleted RNA populations: (1) cytoplasmic, poly-adenylated RNA (known hereafter as the ‘‘mRNA’’ fraction); (2) cytoplasmic...
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