Defining a large set of full-length clones from a Xenopus tropicalis EST project

Developmental Biology
Michael J GilchristEnrique Amaya

Abstract

Amphibian embryos from the genus Xenopus are among the best species for understanding early vertebrate development and for studying basic cell biological processes. Xenopus, and in particular the diploid Xenopus tropicalis, is also ideal for functional genomics. Understanding the behavior of genes in this accessible model system will have a significant and beneficial impact on the understanding of similar genes in other vertebrate systems. Here we describe the analysis of 219,270 X. tropicalis expressed sequence tags (ESTs) from four early developmental stages. From these, we have deduced a set of unique expressed sequences comprising approximately 20,000 clusters and 16,000 singletons. Furthermore, we developed a computational method to identify clones that contain the complete coding sequence and describe the creation for the first time of a set of approximately 7000 such clones, the full-length (FL) clone set. The entire EST set is cloned in a eukaryotic expression vector and is flanked by bacteriophage promoters for in vitro transcription, allowing functional experiments to be carried out without further subcloning. We have created a publicly available database containing the FL clone set and related clustering data (http:/...Continue Reading

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Jul 24, 1998·Trends in Genetics : TIG·E AmayaR M Grainger
Apr 27, 1999·The International Journal of Biochemistry & Cell Biology·A W van der Velden, A A Thomas
Aug 14, 1999·Mechanisms of Development·F StennardJ B Gurdon
Mar 23, 2000·Mechanisms of Development·L S Gammill, H Sive
Jul 19, 2000·Genome Research·E BeaudoingD Gautheret
Jul 18, 2001·Developmental Biology·C R AltmannA H Brivanlou
Jul 31, 2001·Genesis : the Journal of Genetics and Development·S L NuttE Amaya
Mar 9, 2002·Developmental Biology·Janet Heasman
Nov 28, 2002·Developmental Dynamics : an Official Publication of the American Association of Anatomists·Steven L KleinPaul Richardson
Nov 28, 2002·Developmental Dynamics : an Official Publication of the American Association of Anatomists·Nicolas HirschRobert M Grainger
Nov 28, 2002·Developmental Dynamics : an Official Publication of the American Association of Anatomists·Mustafa K KhokhaTimothy C Grammer
Dec 13, 2002·Proceedings of the National Academy of Sciences of the United States of America·Robert L StrausbergUNKNOWN Mammalian Gene Collection Program Team
Feb 5, 2003·Genome Research·Marco M KesslerGuillaume Cottarel
Jun 24, 2003·Genome Research·Piero CarninciYoshihide Hayashizaki
Jan 28, 2004·Developmental Dynamics : an Official Publication of the American Association of Anatomists·Sue KenwrickNancy Papalopulu

❮ Previous
Next ❯

Citations

Apr 24, 2014·Development·Clara CollartMichael J Gilchrist
May 17, 2014·Longevity & Healthspan·Ankita BansalHeidi A Tissenbaum
Sep 12, 2007·BMC Genomics·Stefan E SeemannJan Gorodkin
Nov 7, 2007·Nucleic Acids Research·Jeff B BowesPeter D Vize
Oct 22, 2008·BMC Bioinformatics·Michael J GilchristNancy Papalopulu
May 7, 2010·BMC Research Notes·Ann-Britt NygardMerete Fredholm
May 14, 2010·Molecular Biology and Evolution·Xinjiang Cai, Sandip Patel
Nov 17, 2011·BMC Developmental Biology·Nick R LoveEnrique Amaya
Apr 5, 2007·Nature Protocols·Stuart J SmithTimothy J Mohun
Jan 21, 2009·Computational Biology and Chemistry·K Scheibye-AlsingJ Gorodkin
Sep 24, 2015·Developmental Biology·Ian M GrantMichael J Gilchrist
Dec 30, 2006·Seminars in Cell & Developmental Biology·Andrew S Warkman, Paul A Krieg
Oct 12, 2005·Developmental Dynamics : an Official Publication of the American Association of Anatomists·Quincy A Quick, Elba E Serrano
Mar 1, 2005·Developmental Dynamics : an Official Publication of the American Association of Anatomists·Stuart J SmithTimothy J Mohun
Apr 23, 2009·Developmental Dynamics : an Official Publication of the American Association of Anatomists·Jered V McGivernMichael D Sheets
Apr 23, 2009·Development, Growth & Differentiation·Hajime Ogino, Haruki Ochi
Mar 27, 2009·Developmental Dynamics : an Official Publication of the American Association of Anatomists·Robert LeaKarel Dorey
May 24, 2008·Developmental Dynamics : an Official Publication of the American Association of Anatomists·Lisa M SevillaJames C Smith
Feb 23, 2007·Biological Reviews of the Cambridge Philosophical Society·Gregory R Handrigan, Richard J Wassersug
Feb 12, 2008·Animal Genetics·K Scheibye-AlsingJ Gorodkin
Feb 22, 2012·Genesis : the Journal of Genetics and Development·Michael J Gilchrist
Feb 8, 2006·Gene Expression Patterns : GEP·Vivian M ChoiMustafa K Khokha
Jan 24, 2006·Seminars in Cell & Developmental Biology·Samantha Carruthers, Derek L Stemple
Sep 6, 2005·Ecotoxicology and Environmental Safety·Naoko MitsuiTaisen Iguchi

❮ Previous
Next ❯

Related Concepts

Related Feeds

Antisense Oligonucleotides: ND

This feed focuses on antisense oligonucleotide therapies such as Inotersen, Nusinursen, and Patisiran, in neurodegenerative diseases including amyotrophic lateral sclerosis.

Bacteriophage: Phage Therapy

Phage therapy uses bacterial viruses (bacteriophages) to treat bacterial infections and is widely being recognized as an alternative to antibiotics. Here is the latest research.

Alternative splicing

Alternative splicing a regulated gene expression process that allows a single genetic sequence to code for multiple proteins. Here is that latest research.

Related Papers

Developmental Dynamics : an Official Publication of the American Association of Anatomists
Mustafa K KhokhaTimothy Grammer
Trends in Genetics : TIG
Enrique AmayaRobert Grainger
Developmental Dynamics : an Official Publication of the American Association of Anatomists
Steven L KleinPaul Richardson
© 2022 Meta ULC. All rights reserved