Geisha: A Gallus (chicken) EST and in situ hybridization approach for identifying genes expressed during early embryogenesis

Persistent Link:
http://hdl.handle.net/10150/298791
Title:
Geisha: A Gallus (chicken) EST and in situ hybridization approach for identifying genes expressed during early embryogenesis
Author:
Bell, George W.
Issue Date:
2003
Publisher:
The University of Arizona.
Rights:
Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author.
Abstract:
With ever-increased quality and quantity of vertebrate genomic sequences, gene finding remains problematic, and predicting gene function from sequence remains a tremendous challenge. Nevertheless, similarity of sequence and patterns of gene expression are rapid methods for providing insight into potential functional roles of novel genes. For developmental studies, microarrays offer a means for screening a large number of sequences for expression within defined tissues and/or organs, but each experiment profiles expression level for only one anatomical region at one specific developmental stage. Whole mount in situ hybridization (ISH) offers an alternative approach that gives precise spatial and temporal resolution of gene expression throughout an embryo. I predicted that combined high throughput analysis of expressed sequence tags (ESTs) and whole mount ISH analysis of novel clones would effectively identify novel developmentally regulated avian genes. 5' ESTs were generated from randomly chosen cDNA clones of a chick late gastrula endoderm-mesoderm library. Following screening to remove ubiquitously expressed clones, internal clustering, and comparison to GenBank sequences, remaining cDNAs (both similar and dissimilar to known genes) were screened for expression in HH stage 4-12 embryos by automated high throughput whole mount ISH. Comparison to GenBank sequences by blastn and blastx (e < 0.05) revealed that one quarter of all 955 ESTs represented novel genes. Of these novel clones, ISH showed that about one quarter (60 clones) exhibited patterned expression during embryogenesis. EST sequences, ISH images and corresponding blast reports were assembled into a freely accessible Web database at http://geisha.biosci.arizona.edu.
Type:
text; Dissertation-Reproduction (electronic)
Keywords:
Biology, Molecular.; Biology, Animal Physiology.
Degree Name:
Ph.D.
Degree Level:
doctoral
Degree Program:
Graduate College; Physiological Sciences
Degree Grantor:
University of Arizona
Advisor:
Antin, Parker B.

Full metadata record

DC FieldValue Language
dc.language.isoen_USen_US
dc.titleGeisha: A Gallus (chicken) EST and in situ hybridization approach for identifying genes expressed during early embryogenesisen_US
dc.creatorBell, George W.en_US
dc.contributor.authorBell, George W.en_US
dc.date.issued2003en_US
dc.publisherThe University of Arizona.en_US
dc.rightsCopyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author.en_US
dc.description.abstractWith ever-increased quality and quantity of vertebrate genomic sequences, gene finding remains problematic, and predicting gene function from sequence remains a tremendous challenge. Nevertheless, similarity of sequence and patterns of gene expression are rapid methods for providing insight into potential functional roles of novel genes. For developmental studies, microarrays offer a means for screening a large number of sequences for expression within defined tissues and/or organs, but each experiment profiles expression level for only one anatomical region at one specific developmental stage. Whole mount in situ hybridization (ISH) offers an alternative approach that gives precise spatial and temporal resolution of gene expression throughout an embryo. I predicted that combined high throughput analysis of expressed sequence tags (ESTs) and whole mount ISH analysis of novel clones would effectively identify novel developmentally regulated avian genes. 5' ESTs were generated from randomly chosen cDNA clones of a chick late gastrula endoderm-mesoderm library. Following screening to remove ubiquitously expressed clones, internal clustering, and comparison to GenBank sequences, remaining cDNAs (both similar and dissimilar to known genes) were screened for expression in HH stage 4-12 embryos by automated high throughput whole mount ISH. Comparison to GenBank sequences by blastn and blastx (e < 0.05) revealed that one quarter of all 955 ESTs represented novel genes. Of these novel clones, ISH showed that about one quarter (60 clones) exhibited patterned expression during embryogenesis. EST sequences, ISH images and corresponding blast reports were assembled into a freely accessible Web database at http://geisha.biosci.arizona.edu.en_US
dc.typetexten_US
dc.typeDissertation-Reproduction (electronic)en_US
dc.subjectBiology, Molecular.en_US
dc.subjectBiology, Animal Physiology.en_US
thesis.degree.namePh.D.en_US
thesis.degree.leveldoctoralen_US
thesis.degree.disciplineGraduate Collegeen_US
thesis.degree.disciplinePhysiological Sciencesen_US
thesis.degree.grantorUniversity of Arizonaen_US
dc.contributor.advisorAntin, Parker B.en_US
dc.identifier.proquest3089909en_US
dc.identifier.bibrecord.b44417755en_US
All Items in UA Campus Repository are protected by copyright, with all rights reserved, unless otherwise indicated.