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Series GSE59399 Query DataSets for GSE59399
Status Public on Jul 31, 2015
Title Gene expression profile of hemocytes from Manila clam (Venerupis philippinarum) after a Perkinsus olseni challenge using an immune-enriched oligo-microarray
Organism Ruditapes philippinarum
Experiment type Expression profiling by array
Summary Parasites of the genus Perkinsus spp. cause high mortalities and economic losses to the most noticeable bivalves produced in the worldwide aquaculture. In this study, we analyze how P. olseni influences the gene expression profiles of hemocytes from Manila clam (Venerupis philippinarum) using experimental infections along a temporal series and a Manila clam immune-enriched DNA microarray.
 
Overall design Healthy and Perkinsus-infected clams (V. philippinarum) were obtained from Carril and Pontevedra shellfish farms, respectively (Galicia, NW Spain). The presence-absence of P. olseni was confirmed using the Ray`s fluid thioglycollate medium assay (RFTM) (Ray, 1966). Healthy clams were maintained in an open circuit filtered sea water tanks at 15°C with aeration. Natural infected animals were maintained in the same conditions using closed circuit sea water. All animals were fed daily with a mixture of microalgae containing Phaeodactylum tricornutum, Isochrysis galbana and Rhodomonas lens. Clams were acclimatized to the aquarium conditions for one week before the experiments were conducted. Perkinsus trophozoites were isolated from naturally infected animals following the protocol established by Ford et al., (2002). The concentration was adjusted to 5x104 trophozoites /ml in filtered sea water (FSW). Healthy clams (P. olseni free animals) (n=100) with a weight of 2.25 ± 0.64 g soft tissue, were notched in the shell and intramuscularly injected with 100 µl of the trophozoites suspension. Control animals (n=100) were injected with 100 µl of FSW. After infection, clams were maintained in 50 l tanks with aeration.Twenty animals from each experimental group and time point were sampled at 5, 10, 14, and 31 days post infection (pi).Hemolymph were extracted to perform microarrays experiments. In each condition hemolymph from three five individuals was pooled. Total RNA isolation was conducted following the manufacturer’s specifications. Isolated RNAs were treated with DNase I and purified again using the RNeasy Mini kit (Qiagen). A 8x15K Agilent 60-mer oligo-microarray (GPL16450) was used to compare gene expression profiles of clams after P. olseni infection with uninfected animals. The Agilent Feature Extraction Software (version 9.5.1) was used for the data extraction and background subtraction following standard procedures. The GeneSpring software (Agilent) was used to normalize and analyze the microarray fluorescence data.
 
Contributor(s) Milan M, Bargelloni L, Moreira R, Alejandro R, Figueras A, Novoa B
Citation(s) 25555813
Submission date Jul 14, 2014
Last update date Aug 14, 2015
Contact name Massimo Milan
E-mail(s) massimo.milan@unipd.it
Phone +39 0498272941
Organization name University of Padova
Department Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene
Street address Viale dell'Università 16
City Legnaro
State/province PD
ZIP/Postal code 35020
Country Italy
 
Platforms (1)
GPL16450 Agilent-035923 UniversityPadova_Ruditapes philippinarum_8x15K_v2.0
Samples (24)
GSM1436287 Hemocytes after 5 days challenge with filtered sea water (FSW)
GSM1436288 Hemocytes after 5 days challenge with trophozoites suspension_1
GSM1436289 Hemocytes after 5 days challenge with trophozoites suspension_2
Relations
BioProject PRJNA255239

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE59399_RAW.tar 47.9 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table
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