Searching journal content for articles similar to Pleasance et al. 13 (6a): 1203.

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Method: Mapping and quantifying nascent transcript start sites using TT-TSS-seq
- Eleanor Elgood Hunt,
- Claudia Vivori,
- Richard Mitter,
- Vedis Agnadottir,
- and Folkert J. van Werven
Genome Res. March 2026 36: 600-610; Published in Advance February 17, 2026, doi:10.1101/gr.280726.125
...and in vivo labeling of unperturbed cells (TT-seq or TTchem-seq) (Schwalb et al. 2016; Gregersen et al. 2020). TT-seq methods have been widely used to study transcription dynamics.To balance RNA yield without compromising transcription dynamics, we assessed the degree of 4sU incorporation following different...
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Method: Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq
- Robert A. Policastro,
- R. Taylor Raborn,
- Volker P. Brendel,
- and Gabriel E. Zentner
Genome Res. June 2020 30: 910-923; Published in Advance July 6, 2020, doi:10.1101/gr.261545.120
...expression. In conjunction with our ready-to-use computational workflows, STRIPE-seq is a straightforward, efficient means by which to probe the landscape of transcriptional initiation.Understanding the spatiotemporal control of transcriptional initiation hinges on accurate identification of transcription...
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Research: Roles for transcript leaders in translation and mRNA decay revealed by transcript leader sequencing
- Joshua A. Arribere and
- Wendy V. Gilbert
Genome Res. June 2013 23: 977-987; Published in Advance April 11, 2013, doi:10.1101/gr.150342.112
...-length cDNA sequencing (Miura et al. 2006), 5′ serial analysis of gene expression (5′SAGE) (Zhang and Dietrich 2005), and computational identification of transcript boundaries from measurements using tiling microarrays (Xu et al. 2009) or RNA-seq (Nagalakshmi et al. 2008). Importantly, the latter two...
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Method: Gene expression profiling of human breast tissue samples using SAGE-Seq
- Zhenhua Jeremy Wu,
- Clifford A. Meyer,
- Sibgat Choudhury,
- Michail Shipitsin,
- Reo Maruyama,
- Marina Bessarabova,
- Tatiana Nikolskaya,
- Saraswati Sukumar,
- Armin Schwartzman,
- Jun S. Liu,
- Kornelia Polyak,
- and X. Shirley Liu
Genome Res. December 2010 20: 1730-1739; Published in Advance November 2, 2010, doi:10.1101/gr.108217.110
...-throughput sequencing, SAGE-Seq, for the accurate quantification of normal and neoplastic mammary epithelial cell transcriptomes. We develop data analysis pipelines that allow the mapping of sense and antisense strands of mitochondrial and RefSeq genes, the normalization between libraries, and the identification...
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METHODS: A Quantitative Evaluation of SAGE
- Jes Stollberg,
- Johann Urschitz,
- Zsolt Urban,
- and Charles D. Boyd
Genome Res. August 1, 2000 10: 1241-1248; doi:10.1101/gr.10.8.1241
...by the given species). Following this notation, the probability that a transcript will be detected in copy numbers between r1 and r2 (inclusive) is: The binomial distribution of tag sampling provides a simple assessment of the significance of the difference detected in SAGE experiments directed at differential...
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Research: Transcription and potential functions of a novel XIST isoform in male peripheral glia
- Kevin S. O'Leary,
- Meng-Yen Li,
- Kevyn Jackson,
- Lijie Shi,
- Elena Ezhkova,
- Bernice E. Morrow,
- and Deyou Zheng
Genome Res. February 2026 36: 257-274; Published in Advance December 12, 2025, doi:10.1101/gr.280832.125
...integrated analyses of single-cell RNA-seq data from multiple human tissues and organs. Single-cell epigenomic data further indicate that the expression is likely driven by an alternative promoter at the end of the first exon, resulting in at least one shorter transcript (referred to as sXIST) that is active...
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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
.... , Bourque, G. , George, J. , Leong, B. , Liu, J. , et al. ( 2006 ) The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells . Nat. Genet. 38 : 431 – 440 . ↵ Margulies, E.H. , Kardia, S.L. , Innis, J.W. ( 2001 ) Identification and prevention of a GC content bias in SAGE...
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Methods: Analysis of mRNA With Microsomal Fractionation Using a SAGE-Based DNA Microarray System Facilitates Identification of the Genes Encoding Secretory Proteins
- Nobuaki Toyoda ,
- Shigenori Nagai,
- Yuya Terashima,
- Kazushi Motomura,
- Makoto Haino,
- Shin-ichi Hashimoto,
- Hajime Takizawa,
- and Kouji Matsushima
Genome Res. July 2003 13: 1728-1736; Published in Advance June 12, 2003, doi:10.1101/gr.709603
...Analysis of mRNA With Microsomal Fractionation Using a SAGE-Based DNA Microarray System Facilitates Identification of the Genes Encoding Secretory Proteins Nobuaki Toyoda 1 , 2 , Shigenori Nagai 1 , Yuya Terashima 1 , Kazushi Motomura 1...
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LETTER: A Comparative Molecular Analysis of Developing Mouse Forelimbs and Hindlimbs Using Serial Analysis of Gene Expression (SAGE)
- Elliott H. Margulies,
- Sharon L.R. Kardia,
- and Jeffrey W. Innis
Genome Res. October 1, 2001 11: 1686-1698; Published in Advance September 20, 2001, doi:10.1101/gr.192601
...,544 vs. 97,948), representing an increase in the number of unique transcripts by 20.1% (34,525 vs. 28,738). Ninety-five percent of the additional unique transcripts were represented by SAGE tags observed once. Therefore, using phred in combination with eSAGE allowed us to define the minimum acceptable...
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Method: Genome-wide identification of conserved regulatory function in diverged sequences
- Leila Taher,
- David M. McGaughey,
- Samantha Maragh,
- Ivy Aneas,
- Seneca L. Bessling,
- Webb Miller,
- Marcelo A. Nobrega,
- Andrew S. McCallion,
- and Ivan Ovcharenko
Genome Res. July 2011 21: 1139-1149; Published in Advance May 31, 2011, doi:10.1101/gr.119016.110
...Genome-wide identification of conserved regulatory function in diverged sequences Leila Taher 1 , David M. McGaughey 2 , Samantha Maragh 2 , 3 , Ivy Aneas 4 , Seneca L. Bessling 2 , Webb Miller 5 , Marcelo A. Nobrega 4...
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