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Series GSE102405 Query DataSets for GSE102405
Status Public on Jul 27, 2018
Title Differential gene expression between long-term affected and naïve flat oyster (Ostrea edulis) stocks in response to Bonamia ostreae
Organism Ostrea edulis
Experiment type Expression profiling by array
Summary The European flat oyster (Ostrea edulis) production has suffered a severe decline in the last decades mostly due to bonamiosis disease. The responsible parasite, Bonamia ostreae, enters the oyster immune-effector cells, the haemocytes, causing their breakage and an acute inflammatory response frequently leading to oyster death. Here, we used an oyster immune-enriched oligo-microarray to understand the haemocyte response to B. ostreae using two different oyster stocks, naïve (NS) and long-term affected (AS), evaluated at three time points, 1 day post-challenge (dpc), 30 dpc and 90 dpc, using five biological replicates per condition. A total of 213 (134 up-, 79 down-regulated) and 538 (330 up-, 208 down-regulated) regulated genes (RGs) were detected in NS and AS stocks, respectively. AS oysters showed a remarkably higher response at 1 dpc when compared to NS (507 vs 86 RGs), while more RGs were found in NS at 90 dpc (127 vs 31 RGs in AS). No RGs were detected at 30 dpc, which suggests some kind of parasite latency during infection. Further, a total of 837 genes resulted differentially expressed (DE) when comparing NS and AS profiles. The stronger response of the AS stock at the early stage might be indicative of the process of selection for resistance. Genes related to extracellular matrix and proteases inhibitors, up-regulated in the AS oysters, and those related to histones, broadly down-regulated in NS, might have an important role during the infection process. A set of 24 candidate genes potentially related to B. ostreae resistance/susceptibility were identified and they should be further validated for selection programmes aimed to control this parasitosis.
 
Overall design Oysters from two strain ( Limfjord and Ortigueira) were experimentally challenged with B. ostreae, along with the corresponding non-challenged controls. The Limfjord oyster population was still naïve regarding bonamiosis in 2010 (NS: naïve stock onwards). Conversely, bonamiosis affects oysters in Ortigueira since early 1980's (AS: long-term affected stock onwards) and oysters from this bed are more resistant to B. ostreae than oysters from other geographic originsAfter challenge, haemolymph samples were taken at 3 different times after the challenge (1, 30 and 90 days). A number of 5 biological replicated for each condition (control and challenged), strain (naïve and tolerant) and sample times (1, 30 and 90 days) was taken. Samples were centrifuged (800g, 10 min, 4C) and the cell fractions (pellets) were resuspended in RNA later and stored at -20ºC after one night at 4ºC until further processing. RNA was individually extracted using RNeasy Mini Kit (Qiagen, Germany) following manufacturer's instructions with slight modifications, including two additional RPE washes and DNase digestion. For each experimental condition, the control group was pooled by combining equimolar RNA quantities of the five biological replicates, while the RNA of each challenged oyster was processed individually (five replicates). Next, 50 ng of total RNA were labeled using the Low Input Quick Amp Labeling Kit, One-Color (Cy3; Agilent Technologies). A total of 36 microarrays were used for hybridizations of 6 control (RNA pools from 2 stocks x 3 sample times) and 30 challenged oysters (5 biological replicates x 2 stocks x 3 sample times). Copy RNA (cRNA) was hybridized overnight during 17 h at 65ºC and washed with the corresponding buffers on the following day. Hybridized slides were scanned using an Agilent G2565B microarray scanner (Agilent Technologies).
 
Contributor(s) Ronza P, Cao A, Robledo D, Gómez-Tato A, Álvarez-Dios JA, Hasanuzzaman AF, Quiroga MI, Villalba A, Pardo BG, Martínez P
Citation(s) 29678683
Submission date Aug 09, 2017
Last update date Jul 25, 2021
Contact name Belen G Pardo
E-mail(s) belen.gomez@usc.es
Phone +34 982822428
Organization name University of Santiago de Compostela
Department Zoology, Genetics and Physical Anthropology
Lab Acuigen
Street address Avda. Carballo Calero s/n
City LUGO
State/province LUGO
ZIP/Postal code 27002
Country Spain
 
Platforms (1)
GPL23881 USC/ACUIGEN-Agilent-038418 Ostrea edulis 8X15 array
Samples (36)
GSM2736097 Limfjord, haemocytes, 1 day, control
GSM2736098 Limfjord, haemocytes, 1 day, Bonamia, sample 3
GSM2736099 Limfjord, haemocytes, 1 day, Bonamia, sample 9
Relations
BioProject PRJNA397711

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
GSE102405_RAW.tar 71.4 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table
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