Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1002317 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR22875413_1.fastq.gz | Fastqsanger.gz | |||
| SRR22875413_2.fastq.gz | Fastqsanger.gz | |||
| SRR22875414_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR24725191_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 7 |
Similar Datasets
Project description:Cyrtodaria siliqua (northern propeller clam) genome assembly, xbCyrSili1
| PRJNA1027850 | ENA
Project description:Cyrtodaria siliqua (northern propeller clam) genome sequencing and assembly, xbCyrSili1
| PRJNA862933 | ENA
Project description:Cyrtodaria siliqua (northern propeller clam) genome assembly, xbCyrSili1, alternate haplotype
| PRJNA1027851 | ENA
Project description:Transcriptional profiling of different clam tissues (hemolymph and mantle) in response to QPX disease and temperautre Quahog Parasite Unknown (QPX) is a fatal protistan parasite that causes severe losses in the hard clam (Mercenaria mercenaria) fisheries along the northeastern coast of the US. Field and laboratory studies of QPX disease have demonstrated a major role for water temperature and M. mercenaria genetic origin in disease development. Infections are more likely to occur at cold temperatures, with clam stocks originating from southern states being more susceptible than clams from northern origin where disease is enzootic. Even though the influence of temperature on QPX infection have been examined in susceptible and resistant M. mercenaria at physiological and cellular scales, the underlying molecular mechanisms associated with host-pathogen interactions remain largely unknown. This study was carried out to explore the molecular changes in M. mercenaria in response to temperature and QPX infection on the transcriptomic level, and also to compare molecular responses between susceptible and resistant clam stocks. A M. mercenaria oligoarray (15K Agilent) platform was produced based on our previously generated transcriptomic data and was used to compare gene expression profiles in naive and QPX-infected susceptible (Florida stock) and resistant (Massachusetts) clams maintained at temperatures favoring disease development (13 °C) or clam healing (21 °C). In addition, transcriptomic changes reflecting focal (the site of infection, mantle) and systemic (circulating hemocytes) responses were also assessed using the oligoarray platform. Results revealed significant regulation of multiple biological pathways by temperature and QPX infection, mainly associated with immune recognition, microbial killing, protein synthesis, oxidative protection and metabolism. Alterations were widely systemic with most changes in gene expression revealed in hemocytes, highlighting the role of circulating hemocytes as the first line of defense against pathogenic stress. A large number of complement-related recognition molecules with fibrinogen or C1q domains were shown to be specially induced following QPX challenge, and the expression of these molecules was significantly higher in resistant clams as compared to susceptible ones. These highly variable immune proteins may be potent candidate molecular markers for future study of M. mercenaria resistance against QPX. Beyond the specific case of clam response to QPX, this study also provides insights into the primitive complement-like system in the hard clam. Three-condition interaction experiment (Temperature x clam/infection type x tissue type), 2 temperatures, 3 clam/infection types, 2 tissues, 3 biological replicates for each condition
2015-12-20 | E-GEOD-76182 | biostudies-arrayexpress
Project description:Transcriptional profiling of different clam tissues (hemolymph and mantle) in response to QPX disease and temperautre Quahog Parasite Unknown (QPX) is a fatal protistan parasite that causes severe losses in the hard clam (Mercenaria mercenaria) fisheries along the northeastern coast of the US. Field and laboratory studies of QPX disease have demonstrated a major role for water temperature and M. mercenaria genetic origin in disease development. Infections are more likely to occur at cold temperatures, with clam stocks originating from southern states being more susceptible than clams from northern origin where disease is enzootic. Even though the influence of temperature on QPX infection have been examined in susceptible and resistant M. mercenaria at physiological and cellular scales, the underlying molecular mechanisms associated with host-pathogen interactions remain largely unknown. This study was carried out to explore the molecular changes in M. mercenaria in response to temperature and QPX infection on the transcriptomic level, and also to compare molecular responses between susceptible and resistant clam stocks. A M. mercenaria oligoarray (15K Agilent) platform was produced based on our previously generated transcriptomic data and was used to compare gene expression profiles in naive and QPX-infected susceptible (Florida stock) and resistant (Massachusetts) clams maintained at temperatures favoring disease development (13 °C) or clam healing (21 °C). In addition, transcriptomic changes reflecting focal (the site of infection, mantle) and systemic (circulating hemocytes) responses were also assessed using the oligoarray platform. Results revealed significant regulation of multiple biological pathways by temperature and QPX infection, mainly associated with immune recognition, microbial killing, protein synthesis, oxidative protection and metabolism. Alterations were widely systemic with most changes in gene expression revealed in hemocytes, highlighting the role of circulating hemocytes as the first line of defense against pathogenic stress. A large number of complement-related recognition molecules with fibrinogen or C1q domains were shown to be specially induced following QPX challenge, and the expression of these molecules was significantly higher in resistant clams as compared to susceptible ones. These highly variable immune proteins may be potent candidate molecular markers for future study of M. mercenaria resistance against QPX. Beyond the specific case of clam response to QPX, this study also provides insights into the primitive complement-like system in the hard clam.
2015-12-20 | GSE76182 | GEO
Project description:This study aimed to establish a genome-wide association for heat tolerance using the newly developed 66K SNP array for Mercenaria mercenaria. Northern quahogs from three local farms were combined for a heat challenge by increasing temperature at 1°C per day from 24°C to 35°C (Phase I), maintaining at 35°C for two days before decreasing to 27°C within the next 24 hr, then to 24°C within 24 hr. Survival-time analysis showed different survivals among quahogs from these three farms during the heat challenge. Mortality during the temperature increase period (Phase I) was 38, 46, and 55%, and after the temperature decrease was 36, 30, and 29%. For the survivors, no changes were found in body weight before and after the heat shock challenges (p < 0.265). The PCA analyses of SNP frequencies indicated significant genetic differences associated with clam survival under heat stress across the different farms. The fastStructure analysis also revealed the proportions of different ancestral components within the clams, highlighting the genetic factors that may contribute to their varying survival rates under heat stress. The heritability of the heat tolerance traits was 0.680 ± 0.063. GWAS analysis indicated that one SNP exhibited a significant association with the time-to-death trait of northern quahogs and was in chromosome 7. More significant SNPs (p < 10-3.5) were inside genes that have been reported to function in heat tolerance such as serine/threonine-protein kinase 31 and carbohydrate sulfotransferase 11, and some genes found within 50K bp far from SNP sites have a relationship with heat tolerance such as toll-like receptors 4 and 6 (TLRs 4 and TLRs 6), uracil-DNA glycosylase, and a disintegrin and metalloproteinase with thrombospondin motifs gon-1 (ADAMTs). Overall, these findings highlight the power of high-throughput approaches for the identification of superior clam genotypes for further breeding.
2025-02-26 | GSE290453 | GEO
Project description: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.
2015-07-31 | GSE59399 | GEO