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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: SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification
- Manuel Tardaguila,
- Lorena de la Fuente,
- Cristina Marti,
- Cécile Pereira,
- Francisco Jose Pardo-Palacios,
- Hector del Risco,
- Marc Ferrell,
- Maravillas Mellado,
- Marissa Macchietto,
- Kenneth Verheggen,
- Mariola Edelmann,
- Iakes Ezkurdia,
- Jesus Vazquez,
- Michael Tress,
- Ali Mortazavi,
- Lennart Martens,
- Susana Rodriguez-Navarro,
- Victoria Moreno-Manzano,
- and Ana Conesa
Genome Res. March 2018 28: 396-411; Published in Advance February 9, 2018, doi:10.1101/gr.222976.117
...the Clontech SMARTer kit followed by building single-molecule SMRTbell libraries with specific PacBio linkers that are subsequently sequenced. PacBio reads are typically longer than the full-length cDNA sequence, which means that each molecule can go through several passes of sequencing. The consensus...
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Resource: The C. elegans embryonic transcriptome with tissue, time, and alternative splicing resolution
- Adam D. Warner,
- Louis Gevirtzman,
- LaDeana W. Hillier,
- Brent Ewing,
- and Robert H. Waterston
Genome Res. June 2019 29: 1036-1045; Published in Advance May 23, 2019, doi:10.1101/gr.243394.118
...-cell RNA-seq methods also rely on the end sequencing of cDNA molecules and thus largely fail to capture alternative splicing events.To address the need for a more comprehensive mRNA data set that captures the transcripts in specific tissues during embryonic development, we have used fluorescence...
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ARTICLE: Targeting a Complex Transcriptome: The Construction of the Mouse Full-Length cDNA Encyclopedia
- Piero Carninci,
- Kazunori Waki,
- Toshiyuki Shiraki,
- Hideaki Konno,
- Kazuhiro Shibata,
- Masayoshi Itoh,
- Katsunori Aizawa,
- Takahiro Arakawa,
- Yoshiyuki Ishii,
- Daisuke Sasaki,
- Hidemasa Bono,
- Shinji Kondo,
- Yuichi Sugahara,
- Rintaro Saito,
- Naoki Osato,
- Shiro Fukuda,
- Kenjiro Sato,
- Akira Watahiki,
- Tomoko Hirozane-Kishikawa,
- Mari Nakamura,
- Yuko Shibata,
- Ayako Yasunishi,
- Noriko Kikuchi,
- Atsushi Yoshiki,
- Moriaki Kusakabe,
- Stefano Gustincich,
- Kirk Beisel,
- William Pavan,
- Vassilis Aidinis,
- Akira Nakagawara,
- William A. Held,
- Hiroo Iwata,
- Tomohiro Kono,
- Hiromitsu Nakauchi,
- Paul Lyons,
- Christine Wells,
- David A. Hume,
- Michela Fagiolini,
- Takao K. Hensch,
- Michelle Brinkmeier,
- Sally Camper,
- Junji Hirota,
- Peter Mombaerts,
- Masami Muramatsu,
- Yasushi Okazaki,
- Jun Kawai,
- and Yoshihide Hayashizaki
Genome Res. June 2003 13: 1273-1289; doi:10.1101/gr.1119703
...Developmental Biology and Neurogenetics, The Rockefeller University, New York, New York 10021, USA Abstract We report the construction of the mouse full-length cDNA encyclopedia,the most extensive view of a complex transcriptome,on the basis of preparing and sequencing 246 libraries. Before cloning,cDNAs were...
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Methods: X chromosome cDNA microarray screening identifies a functional PLP2 promoter polymorphism enriched in patients with X-linked mental retardation
- Lilei Zhang,
- Chunfa Jie,
- Cassandra Obie,
- Fatima Abidi,
- Charles E. Schwartz,
- Roger E. Stevenson,
- David Valle,
- and Tao Wang
Genome Res. May 2007 17: 641-648; Published in Advance April 6, 2007, doi:10.1101/gr.5336307
...al. ( 2004 ) Complete sequencing and characterization of 21,243 full-length human cDNAs . Nat. Genet. 36 : 40 – 45 . ↵ Read, A. , Mountford, R. , Forrest, S. , Kenwrick, S. , Davies, K. , Harris, R. ( 1988 ) Patterns of exon deletions in Duchenne and Becker muscular dystrophy . Hum. Genet. 80 : 152...
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Resource: Extensive alternative polyadenylation during zebrafish development
- Igor Ulitsky,
- Alena Shkumatava,
- Calvin H. Jan,
- Alexander O. Subtelny,
- David Koppstein,
- George W. Bell,
- Hazel Sive,
- and David P. Bartel
Genome Res. October 2012 22: 2054-2066; Published in Advance June 21, 2012, doi:10.1101/gr.139733.112
...stages, papolg is up-regulated in the ovary and the early embryo, whereas papolb is repressed (Fig. 3D). In mouse, PAP is alternatively spliced and polyadenylated, which generates at least five isoforms, the shorter of which (PAP III, IV, and V) contain only about half of the exons of the full-length m...
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PERSPECTIVE: Genome-wide analyses of alternative splicing in plants: Opportunities and challenges
- W. Brad Barbazuk,
- Yan Fu,
- and Karen M. McGinnis
Genome Res. September 2008 18: 1381-1392; Published in Advance July 30, 2008, doi:10.1101/gr.053678.106
...splice isoform with cDNAs representing intron retention as a minor splice form. In general, intron retention is associated with weaker splice sites, short intron lengths and higher expression levels, and a reduction in ESS signature sequences. However, this study did not permit the discovery of novel...
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Methods: ECgene: Genome-based EST clustering and gene modeling for alternative splicing
- Namshin Kim,
- Seokmin Shin,
- and Sanghyuk Lee
Genome Res. April 2005 15: 566-576; doi:10.1101/gr.3030405
...and Lee found many tissue-specific ( Xu et al. 2002 ) and cancer-specific ( Xu and Lee 2003 ) alternative splicing events by classifying cDNA libraries according to tissue and cancer types of origin. However, SAGE tags provide more direct and quantitative description of gene expression patterns, even...
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Method: Quantitative evaluation of all hexamers as exonic splicing elements
- Shengdong Ke,
- Shulian Shang,
- Sergey M. Kalachikov,
- Irina Morozova,
- Lin Yu,
- James J. Russo,
- Jingyue Ju,
- and Lawrence A. Chasin
Genome Res. August 2011 21: 1360-1374; Published in Advance June 9, 2011, doi:10.1101/gr.119628.110
...evaluation of all 6-mers in splicing central exon (termed hereafter as ‘‘spliced’’) were isolated by size selection. After conversion to cDNA, the substituted regions of these output molecules were similarly sequenced. For each 6-mer an enrichment of output proportion over input proportion (enrichment index...
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Research: RNA sequencing reveals the role of splicing polymorphisms in regulating human gene expression
- Emilie Lalonde,
- Kevin C.H. Ha,
- Zibo Wang,
- Amandine Bemmo,
- Claudia L. Kleinman,
- Tony Kwan,
- Tomi Pastinen,
- and Jacek Majewski
Genome Res. April 2011 21: 545-554; Published in Advance December 20, 2010, doi:10.1101/gr.111211.110
.... This level of correlation is remarkable since it has been obtained using independent biological replicates, distinct cDNA library preparation protocols, and compares hybridization-based (microarray) and direct sequencing approaches. It should be noted that a high level of correlation between microarray...

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