GEO DataSets

(Submitter supplied) Digestive Gland Samples: A manila clam oligo microarray platform (GPL10900) was used to profile gene expression in digestive gland of R. philippinarum. Total RNA was extracted from three (3) independent biological replicates of digestive gland for each sampling site, each consisting of tissue pools of five (5) animals. Statistical analysis with SAM (Significance Analysis of Microarray) identified1,127 probes differentially expressed. more...

Organism:

Ruditapes philippinarum

Type:

Expression profiling by array

Platform:

GPL10900

12 Samples

Download data: TXT

(Submitter supplied) A manila clam oligo microarray platform (GPL10900) was used to profile gene expression in digestive gland of R. philippinarum sampled in four seasons in 4 different areas of Venice Lagoon. For each tissue, total RNA was extracted from four (4) independent biological replicates of digestive gland, each consisting of tissue pools of five (5) animals.

Organism:

Ruditapes philippinarum

Type:

Expression profiling by array

Platform:

GPL10900

64 Samples

Download data: TXT

(Submitter supplied) A manila clam oligo microarray platform (GPL10900) was used to profile gene expression in gills and digestive gland of R. philippinarum. For each tissue, total RNA was extracted from three (3) independent biological replicates of digestive gland and gills, each consisting of tissue pools of five (5) animals. Statistical analysis with SAM (Significance Analysis of Microarray) identified 8,257 probes differentially expressed between the two different tissues.

Organism:

Ruditapes philippinarum

Type:

Expression profiling by array

Platform:

GPL10900

6 Samples

Download data: TXT

(Submitter supplied) Four pools of digestive glands were treated as biological replicates in order to evaluate the repeatability of Ruditapes philippinarum oligo microarray platform.

Organism:

Ruditapes philippinarum

Type:

Expression profiling by array

Platform:

GPL10900

4 Samples

Download data: TXT

(Submitter supplied) An R.decussatus microarray platform was developed to to profile gene expression in R. decussatus heavy infected by Perkinsus olseni

Organism:

Ruditapes decussatus

Type:

Expression profiling by array

Platform:

GPL15303

8 Samples

Download data: TXT

(Submitter supplied) The Manila clam (Ruditapes philippinarum) is a cultured bivalve species with high worldwide commercial importance. Nevertheless, diseases can cause high economical losses. For this reason, the study of immune genes in bivalve mollusks has increased in the last years. The present work describes the construction of the first R. philippinarum microarray containing immune-related hemocyte sequences and its application for the study of the gene transcription profiles of hemocytes from clams challenged with Vibrio alginolyticus through a time course.

Organism:

Ruditapes philippinarum

Type:

Expression profiling by array

Platform:

GPL16450

36 Samples

Download data: TXT

(Submitter supplied) A sea bass oligo microarray platform was used to profile gene expression in whole heads of 38 days-old sea bass affected by prognathism, a skeletal malformation that strongly affects sea bass production. Two different conditions: i) prognathous individuals, and ii) normal individuals were analyzed. For each condition, total RNA was extracted from three (3) independent biological replicates, each consisting of pools of five (5) heads. more...

Organism:

Dicentrarchus labrax

Type:

Expression profiling by array

Platform:

GPL9663

6 Samples

Download data: TXT

(Submitter supplied) A sea bass oligo microarray platform was used to profile gene expression in mandibles of 58 days-old sea bass affected by prognathism, a skeletal malformation that strongly affects sea bass production. Two different conditions: i) protruding jaws, and ii) normal jaws were used for gene expression analysis. For each condition, total RNA was extracted from four (4) independent biological replicates, each consisting of pools of five (5) jaws. more...

Organism:

Dicentrarchus labrax

Type:

Expression profiling by array

Platform:

GPL9663

8 Samples

Download data: TXT

(Submitter supplied) The Manila clam (Ruditapes philippinarum) is the bivalve species with the highest world production from both fisheries and aquaculture, but its production is seriously threatened by perkinsosis, a disease caused by the protozoan parasite Perkinsus olseni. To understand the molecular mechanisms underlying R. philippinarum–P. olseni interaction, we analyzed the gene expression profiles of in vitro challenged clam hemocytes and P. more...

Organism:

Ruditapes philippinarum; Perkinsus olseni

Type:

Expression profiling by array

Platforms:

GPL23501 GPL27953

48 Samples

Download data: TXT

(Submitter supplied) The Manila clam (Ruditapes philippinarum) is the bivalve species with the highest world production from both fisheries and aquaculture, but its production is seriously threatened by perkinsosis, a disease caused by the protozoan parasite Perkinsus olseni. To understand the molecular mechanisms underlying R. philippinarum–P. olseni interaction, we analyzed the gene expression profiles of in vitro challenged clam hemocytes and P. more...

Organism:

Perkinsus olseni

Type:

Expression profiling by array

Platform:

GPL27953

16 Samples

Download data: TXT

(Submitter supplied) The Manila clam (Ruditapes philippinarum) is the bivalve species with the highest world production from both fisheries and aquaculture, but its production is seriously threatened by perkinsosis, a disease caused by the protozoan parasite Perkinsus olseni. To understand the molecular mechanisms underlying R. philippinarum–P. olseni interaction, we analyzed the gene expression profiles of in vitro challenged clam hemocytes and P. more...

Organism:

Ruditapes philippinarum

Type:

Expression profiling by array

Platform:

GPL23501

32 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Ruditapes philippinarum

Type:

Expression profiling by array

Platform:

GPL18750

36 Samples

Download data: GPR

(Submitter supplied) The production of Manila clam (Ruditapes philippinarum) is seriously threatened by the protistan parasite Perkinsus olseni. We characterized and compared gene expression of Manila clam haemocytes in response to P. olseni in a time-course (10 h, 24 h, 8 d) controlled laboratory challenge (LC), representing the first steps of infection, and in a more complex infection in the wild (WI) using a validated oligo-microarray containing 11,232 mostly annotated transcripts. more...

Organism:

Ruditapes philippinarum

Type:

Expression profiling by array

Platform:

GPL23501

16 Samples

Download data: TXT

(Submitter supplied) A microarray platform for Solea solea was developed to study gene expression profiles of common sole developmental stages.

Organism:

Solea solea

Type:

Expression profiling by array

Platform:

GPL16124

31 Samples

Download data: TXT

(Submitter supplied) 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.

Organism:

Ruditapes philippinarum

Type:

Expression profiling by array

Platform:

GPL16450

24 Samples

Download data: TXT

(Submitter supplied) A Ruditapes philippinarum microarray platform was developed to assess variations on transcritpomic response to copper exposures in Manila clam colelctted in Venice lagoon areas subjected to different anthropogenic impact

Organism:

Ruditapes philippinarum

Type:

Expression profiling by array

Platform:

GPL20320

68 Samples

Download data: TXT

(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis. Methods: Retinal mRNA profiles of 21-day-old wild-type (WT) and neural retina leucine zipper knockout (Nrl−/−) mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11002

6 Samples

Download data: BAM, TXT, XLS

(Submitter supplied) A Ruditapes philippinarum microarray platform was developed to identify digestive gland gene expression profiles in response to 100 µg /l and 1000 µg/l ibuprofen exposure.

Organism:

Ruditapes philippinarum

Type:

Expression profiling by array

Platform:

GPL15723

60 Samples

Download data: TXT

(Submitter supplied) This is a song bird (Junco hyemalis) whole-genome expression array in HD2 12x135K format manufactured by Roche NimbleGen. DESIGN_ID : 537583 native array description file : 100702_Jhye_JL_exp.ndf native array description file : 100702_Jhye_JL_exp.txt Peterson MP, Whittaker DJ, Ambreth S, Sureshchandra S, Buechlein A, Podicheti R, Choi JH, Lai Z, Mockatis K, Colbourne J, Tang H, Ketterson ED. De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis): genomic tools for an ecological model system. more...

Organism:

Junco hyemalis

1 Series

48 Samples

Download data: NDF, TXT

(Submitter supplied) Technical replicates, consisting of four independent hybridizations of the same labelled cRNA, were performed to determine array-to-array reproducibility. After normalization, correlation index between all replicates exceeded 98%.

Organism:

Sparus aurata

Type:

Expression profiling by array

Platform:

GPL6467

4 Samples

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