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RESOURCE: An Oligonucleotide Fingerprint Normalized and Expressed Sequence Tag Characterized Zebrafish cDNA Library
- Matthew D. Clark,
- Steffen Hennig,
- Ralf Herwig,
- Sandy W. Clifton,
- Marco A. Marra,
- Hans Lehrach,
- Stephen L. Johnson,
- and the WU-GSC EST Group
Genome Res. September 1, 2001 11: 1594-1602; Published in Advance August 16, 2001, doi:10.1101/gr.186901
...An Oligonucleotide Fingerprint Normalized and Expressed Sequence Tag Characterized Zebrafish cDNA Library Matthew D. Clark 1 , 5 , Steffen Hennig 1 , Ralf Herwig 1 , Sandy W. Clifton 3 , Marco A. Marra 3 , Hans Lehrach 1...
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RESOURCE: The Status, Quality, and Expansion of the NIH Full-Length cDNA Project: The Mammalian Gene Collection (MGC) Genome Res. October 15, 2004 14: 2121-2127; doi:10.1101/gr.2596504

...of experimental artifact, such as PCR, cloning, or reverse transcriptase errors. Recently, a rat cDNA component was added to the project, and ongoing frog ( Xenopus ) and zebrafish ( Danio ) cDNA projects were expanded to take advantage of the high-throughput MGC pipeline. Footnotes [Supplemental...
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ARTICLE: A Gene Expression Screen in Zebrafish Embryogenesis
- Tetsuhiro Kudoh,
- Michael Tsang,
- Neil A. Hukriede,
- Xiongfong Chen,
- Michael Dedekian,
- Christopher J. Clarke,
- Anne Kiang,
- Stephanie Schultz,
- Jonathan A. Epstein,
- Reiko Toyama,
- and Igor B. Dawid
Genome Res. December 1, 2001 11: 1979-1987; Published in Advance November 12, 2001, doi:10.1101/gr.209601
...-throughput in situ hybridization with clones derived from a normalized embryonic cDNA library. The zebrafish embryo is an important system for the study of vertebrate embryogenesis, offering advantages that have been expounded in many recent publications. In brief, the high fecundity and small size of this animal...
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LETTER: Characterizing Embryonic Gene Expression Patterns in the Mouse Using Nonredundant Sequence-Based Selection
- Rita Sousa-Nunes,
- Amer Ahmed Rana,
- Ross Kettleborough,
- Joshua M. Brickman,
- Melanie Clements,
- Alistair Forrest,
- Sean Grimmond,
- Philip Avner,
- James C. Smith,
- Sally L. Dunwoodie,
- and Rosa S.P. Beddington
Genome Res. December 2003 13: 2609-2620; Published in Advance January 1, 2003, doi:10.1101/gr.1362303
...Plasmodium yoelii yoelii. Nature 419 : 512 -519. ↵ Christiansen, J.H., Coles, E.G., Robinson, V., Pasini, A., and Wilkinson, D.G. 2001 . Screening from a subtracted embryonic chick hindbrain cDNA library: Identification of genes expressed during hindbrain, midbrain and cranial neural crest development. Mech...
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ARTICLE: Functional Divergence of Two Zebrafish Midkine Growth Factors Following Fish-Specific Gene Duplication
- Christoph Winkler,
- Matthias Schäfer,
- Jutta Duschl,
- Manfred Schartl,
- and Jean-Nicolas Volff
Genome Res. June 2003 13: 1067-1081; Published in Advance May 12, 2003, doi:10.1101/gr.1097503
...a conceptual translation product now called Mdka, presenting 68% amino acid identity(72% similarity) with Mdkb ( Fig. 1A ). Both zebrafish mdka and mdkb cDNAs encode secreted proteins as analyzed by expression of MYC epitope-tagged Mdka and Mdkb in cell culture ( Fig. 1B ). Phylogenetic analysis showed...
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Research: Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers
- Valer Gotea,
- Axel Visel,
- John M. Westlund,
- Marcelo A. Nobrega,
- Len A. Pennacchio,
- and Ivan Ovcharenko
Genome Res. May 2010 20: 565-577; Published in Advance April 2, 2010, doi:10.1101/gr.104471.109
...is additionally supported by a strong correlation between HCTs and the binding of the enhancer-associated coactivator protein Ep300 (also known as p300). Experimental validation of HCT-containing elements in both zebrafish and mouse suggest that HCTs could be used to predict both the presence of enhancers...
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Methods: Targeted discovery of novel human exons by comparative genomics
- Adam Siepel,
- Mark Diekhans,
- Broňa Brejová,
- Laura Langton,
- Michael Stevens,
- Charles L.G. Comstock,
- Colleen Davis,
- Brent Ewing,
- Shelly Oommen,
- Christopher Lau,
- Hung-Chun Yu,
- Jianfeng Li,
- Bruce A. Roe,
- Phil Green,
- Daniela S. Gerhard,
- Gary Temple,
- David Haussler,
- and Michael R. Brent
Genome Res. December 2007 17: 1763-1773; Published in Advance November 7, 2007, doi:10.1101/gr.7128207
...hybridizations to zebrafish embryos To test the possibility that some NGFs might be specifically expressed in embryonic development, we identified 23 that had little or no other cDNA support and that could be mapped, via whole- syntenic alignments, to the zebrafish . We then synthesized probes for the zebrafish...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...were widely used to quantify transcript levels across the by hybridizing fluorescently labeled cDNA to thousands of predefined DNA probes immobilized on a solid surface. Each probe was designed to be complementary to a specific transcript, allowing its abundance in a sample to be inferred from...
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Research: Antisense RNAs during early vertebrate development are divided in groups with distinct features
- Sanjana Pillay,
- Hazuki Takahashi,
- Piero Carninci,
- and Aditi Kanhere
Genome Res. June 2021 31: 995-1010; Published in Advance April 1, 2021, doi:10.1101/gr.262964.120
...indicate that NATs play a role in embryonic development in vertebrates. Previous transcriptomics studies have identified large number of lncRNAs during embryonic development in vertebrates such as zebrafish (Ulitsky et al. 2011; Pauli et al. 2012; Haque et al. 2014). Up to 50% of maternally deposited RNAs...
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Resource: Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci
- Jonathan M. Mudge,
- Irwin Jungreis,
- Toby Hunt,
- Jose Manuel Gonzalez,
- James C. Wright,
- Mike Kay,
- Claire Davidson,
- Stephen Fitzgerald,
- Ruth Seal,
- Susan Tweedie,
- Liang He,
- Robert M. Waterhouse,
- Yue Li,
- Elspeth Bruford,
- Jyoti S. Choudhary,
- Adam Frankish,
- and Manolis Kellis
Genome Res. December 2019 29: 2073-2087; Published in Advance September 19, 2019, doi:10.1101/gr.246462.118
...GENCODE annotation is based on cDNA and EST libraries, our new workflow integrated multiple modern transcriptomic data sets. In 20 instances, the CDS was discovered after an existing “noncoding” GENCODE model was extended to incorporate the entire reading frame. In 15 other cases, CDS annotation required...
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