GEISHA, a Whole-Mount in Situ Hybridization Gene Expression Screen in Chicken Embryos

George W. Bell, Tatiana A. Yatskievych, Parker B Antin

Research output: Contribution to journalArticle

60 Citations (Scopus)

Abstract

Despite the increasing quality and quantity of genomic sequence that is available to researchers, predicting gene function from sequence information remains a challenge. One method for obtaining rapid insight into potential functional roles of novel genes is through gene expression mapping. We have performed a high throughput whole-mount in situ hybridization (ISH) screen with chick embryos to identify novel, differentially expressed genes. Approximately 1,200 5′ expressed sequence tags (ESTs) were generated from cDNA clones of a Hamburger and Hamilton (HH) stage 4-7 (late gastrula) chick embryo endoderm-mesoderm library. After screening to remove ubiquitously expressed cDNAs and internal clustering and after comparison to GenBank sequences, remaining cDNAs (representing both characterized and uncharacterized genes) were screened for expression in HH stage 3-14 embryos by automated high throughput ISH. Of 786 cDNAs for which ISH was successfully performed, approximately 30% showed ubiquitous expression, 40% were negative, and approximately 30% showed a restricted expression pattern. cDNAs were identified that showed restricted expression in every embryonic region, including the primitive streak, somites, developing cardiovascular system and neural tube/neural crest. A relational database was developed to hold all EST sequences, ISH images, and corresponding BLAST report information, and to enable browsing and querying of data. A user interface is freely accessible at http://geisha.biosci.arizona.edu. Results show that high throughput whole-mount ISH provides an effective approach for identifying novel genes that are differentially expressed in the developing chicken embryo.

Original languageEnglish (US)
Pages (from-to)677-687
Number of pages11
JournalDevelopmental Dynamics
Volume229
Issue number3
DOIs
StatePublished - Mar 2004

Fingerprint

In Situ Hybridization
Chickens
Embryonic Structures
Complementary DNA
Gene Expression
Genes
Expressed Sequence Tags
Chick Embryo
Primitive Streak
Gastrula
Somites
Endoderm
Neural Tube
Neural Crest
Chromosome Mapping
Nucleic Acid Databases
Mesoderm
Cardiovascular System
Cluster Analysis
Clone Cells

Keywords

  • Chicken
  • Database
  • Embryo
  • Gallus
  • Gene expression
  • In situ hybridization

ASJC Scopus subject areas

  • Developmental Biology
  • Cell Biology

Cite this

GEISHA, a Whole-Mount in Situ Hybridization Gene Expression Screen in Chicken Embryos. / Bell, George W.; Yatskievych, Tatiana A.; Antin, Parker B.

In: Developmental Dynamics, Vol. 229, No. 3, 03.2004, p. 677-687.

Research output: Contribution to journalArticle

Bell, George W. ; Yatskievych, Tatiana A. ; Antin, Parker B. / GEISHA, a Whole-Mount in Situ Hybridization Gene Expression Screen in Chicken Embryos. In: Developmental Dynamics. 2004 ; Vol. 229, No. 3. pp. 677-687.
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