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Title: Transcriptional changes in Manila clam (Ruditapes philippinarum) in response to brown ring disease      
dateReleased:
01-01-2015
description:
Transcriptional profiling of different clam tissues (hemolymph, extrapallial fluid and mantle) in response to brown ring disease; Brown ring disease (BRD) is a bacterial infection affecting the economically-important clam Ruditapes philippinarum. The disease is caused by a bacterium, Vibrio tapetis, that colonizes the edge of the mantle, altering the biomineralization process and normal shell growth. Altered organic shell matrices accumulate on the inner face of the shell leading to the formation of the typical brown ring in the extrapallial space (between the mantle and the shell). Even though structural and functional changes have been described in solid (mantle) and fluid (hemolymph and extrapallial fluids) tissues from infected clams, the underlying molecular alterations and responses remain largely unknown. This study was designed to gather information on clam molecular responses to the disease and to compare focal responses at the site of the infection (mantle and extrapallial fluid) with systemic (hemolymph) responses. To do so, we designed and produced a Manila clam expression oligoarray (15K Agilent) using transcriptomic data available in public databases and used this platform to comparatively assess transcriptomic changes in mantle, hemolymph and extrapallial fluid of infected clams. Results showed significant regulation in diseased clams of molecules involved in pathogen recognition (e.g. lectins, C1q domain-containing proteins) and killing (defensin), apoptosis regulation (death-associated protein, bcl-2) and in biomineralization (shell matrix proteins, perlucin, galaxin, chitin- and calcium-binding proteins). While most changes in response to the disease were tissue-specific, systemic alterations included co-regulation in all 3 tested tissues of molecules involved in microbe recognition and killing (complement-related factors, defensin). These results provide a first glance at molecular alterations and responses caused by BRD and identify targets for future functional investigations. Two-condition experiment (healthy/diseased), 3 tissues, 6 biological replicates/tissue/condition Please note that mantle tissues from this study were labelled with Cy3 and hybridized against a set of reference samples that are not part of this study. Thus, the Cy5 data from the associated raw data files were excluded in the analysis. Please note that hemocytes are collected from hemolymph or extrapallial fluid and hybridized on the same array (i.e. technically as dual channel) but the results were processed as though they are single channel (Cy3 and Cy5 signals are calculated). The hemocytes from extrapallial fluid were labelled with Cy3, while hemocytes from hemolymph were labelled with Cy5. The raw data files that are associated with two sample records are linked as series supplementary files and are indicated in the sample description field.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-58198
refinement:
raw
alternateIdentifiers:
58198
keywords:
functional genomics
dateModified:
02-11-2015
availability:
available
types:
gene expression
name:
Ruditapes philippinarum
ID:
A-GEOD-18750
name:
Agilent-034518 Ruditapes philippinarum 15K v2
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-58198/E-GEOD-58198.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-58198/E-GEOD-58198.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58198
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

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