Differential expression analysis of genes from the mantle tissue of pearl oyster: Pinctada maxima. Series GSE14303
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The mantle is a thin tissue from which proteins are secreted dictating the mollusk shell construction. As a conserved organ involved in shell formation throughout mollusks, the mantle is an excellent foundation from which to study biomineralization. A P. maxima mantle tissue specific complementary DNA (cDNA) microarray, termed PmaxArray 1.0, has been developed comprising 5000 cDNA transcripts derived from the mantle tissue of P. maxima. This tool has been used to investigate the spatial functional dynamics of the mantle tissue identifying over 2000 PmaxArray 1.0 spots as differentially expressed spatially within this organ. Gene expression profiles observed for these transcripts indicated 5 major spatial functions for the mantle, 3 of which have been putatively attributed to shell formation roles associated with nacre microstructure, calcite prismatic microstructure and periostracum. These transcripts are further examined with in situ expression localization and comparative sequence analyses in reference to potential shell formation roles. This spatial investigation has expedited the elucidation of functions within the dynamic mantle organ, paying particular attention to of shell biomineralization.
The mantle tissue from 9 animals was dissected into 5 separate sections: outer fold (OF), middle fold (MF), inner fold (IF), ventral mantle tissue (VM) and dorsal mantle tissue (DM). Total RNA was extracted from these tissues and pooled across subjects in order to reduce the effect of biological variation; such that 3 individuals were pooled together totaling 3 pooled replicate samples for each tissue. All the biologically pooled tissue types were compared against a common reference in which total RNA from all tissues types and all nine animals was equally pooled. A total of 30 dual channel microarrays hybridizations were performed and analyzed.
Access rights
This data has been published in the Gene Expression Omnibus (GEO) a public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted. Tools are provided to help users query and download experiments and curated gene expression profiles.
Geographical area of data collection
kmlPolyCoords
153.552920,-26.777500 152.452799,-26.777500 152.452799,-28.037280 153.552920,-28.037280 153.552920,-26.777500
Research areas
Gene
Expression
(incl.
Microarray
and
other
genome-wide
approaches)
Biomineralization
complementary DNA
Cite this collection
Gardner LD, Elizur A. (2010) Differential expression analysis of genes from the mantle tissue of pearl oyster: Pinctada maxima. Series 14303. [ National Center for Biotechnology Information (NCBI)]
Gardner ,Luke; Elizur,A. (2014): Differential expression analysis of genes from the mantle tissue of pearl oyster: Pinctada maxima. Series GSE14303. [Queensland University of Technology]. https://doi.org/10.4225/09/5858cb1577a1a
Related information
Gardner LD, Mills D, Wiegand A, Leavesley D et al. Spatial analysis of biomineralization associated gene expression from the mantle organ of the pearl oyster Pinctada maxima. BMC Genomics 2011 Sep 21;12:455. PMID: 21936921
http://www.ncbi.nlm.nih.gov/pubmed/21936921
Gene Expression Omnibus Metadata Record
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14303
Related to BioProject PRJNA114555
http://www.ncbi.nlm.nih.gov/bioproject/PRJNA114555
Access the data
Data file types
.soft .xml .text .tar
Copyright
©
Dates of data collection
From 2008-01-01 to 2008-12-31
Connections
Contacts
Name: Luke Gardner
Email: lgardner@stanford.edu
Other
Date record created:
2014-07-18T08:40:04
Date record modified:
2019-08-22T11:14:23
Record status:
Published - Open Access