GEO DataSets

(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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(Submitter supplied) Two different early developmental stages of gilthead sea bream: i) larvae at 24 hours post-hatching ( Stage 1), and ii) larvae at 96 hours post-hatching (Stage 4), were used for gene expression analysis. For each stage, total RNA was extracted from five (5) independent biological replicates, each consisting of pools of approximately 40-50 larvae. Based on SAM analysis, 1518 genes were differentially expressed between the two stages with a FDR (False Discovery Rate) of 0.0.

Organism:

Sparus aurata

Type:

Expression profiling by array

Platform:

GPL6467

10 Samples

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(Submitter supplied) GE 4x44k oligo microarray that covers 19,715 unique transcripts of the gilthead sea bream (Sparus aurata). Oligonucleotides, 60-mer plus a “linker”, are synthesized directly on glass slide using the Agilent’s SurePrint Tecnology; oligo design was carried out by Agilent and two non overlapping probes were designed for each ESTs cluster. The number of transcripts represented by two probes is 19,664 while 51 targets have only one probe; the total number of target probes in the platform is 39379. more...

Organism:

Sparus aurata

6 Series

1 Related Platform

66 Samples

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(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) Juvenile gilthead sea bream of 10-15 g initial body weight were randomly distributed in eight 500-L tanks in a seawater re-circulatory system equipped with physical and biological filters, and a heat-unit system that maintained water temperature above 18-19 ºC. Fish grew from July to December at a density of 8-10 kg/m3 with an overall daily growth index of 1.9 ± 0.01. Extruded pellets (47 % protein, 21% lipid; Proaqua, Palencia, Spain) were offered to visual satiety. more...

Organism:

Sparus aurata

Type:

Expression profiling by array

Platform:

GPL8467

72 Samples

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(Submitter supplied) Hybridization of one kidney of cortisol treated fish vs. one kidney of control fish. Kidneys were collected from untreated juvenile sea bream (n=4) and from fish, which received for 72h a coconut-oil implant containing 10mg/Kg (fish wet weight) (n=4) cortisol. Experiments were carried out at the University of the Algarve, Portugal in accordance with National legislation for the welfare of animals. Experiments were conducted in two 125 l cylindriconical tanks supplied with a continuous through-flow of oxygenated seawater at 20+1 °C using juvenile sea bream (25 g + 3 g) adapted for 1 week to the experimental conditions. One tank contained 8 untreated fish (control) and the other tank 8 cortisol treated fish and the end of experiments fish were removed form tanks, decapitated and the kidneys rapidly removed and place in RNAlater (Qiagen) at –20 °C. No mortality occurred in the control tank but 2 fish died in the cortisol treated tank. Keywords: other

Organism:

Sparus aurata

Type:

Expression profiling by array

Platform:

GPL1516

2 Samples

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(Submitter supplied) Five different developmental stages, neurula (1), hatching (48 h post-fertilization) (2), pectoral fin budding (96 h post-fertilization) (4), mouth opening (144 h post-fertilization) (6), and eye pigmentation (168 h post-fertilization) (7) were compared directly to each other in all possible combinations (Loop design).All experiments were perfomed by dye swap hybridizations. Keywords: time-course

Organism:

Sparus aurata

Type:

Expression profiling by array

Platform:

GPL1516

20 Samples

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(Submitter supplied) For the microarray production a cDNA library of mixed embryos/larvae of gilthead sea bream, Sparus aurata (Sarropoulou et al., in press) was used. A total of 10,176 clones were arrayed into 384 square well plates. In order to amplify the inserts culture PCR was performed as followed. The total volume of one PCR reaction was 50 µl, containing 43.5 µl reaction mix (2 µl 10x PCR Puffer, 0.04 µl 100 mM of each dATP, dCTP, dGTP and dTTP, 12.12 µl dH20), 1.5 µl of T7 and 1.5 µl of T3 primer (20 µM), 1 µl Taq polymerase (5U/µl) and 2.5 µl of culture. more...

Organism:

Sparus aurata

2 Series

22 Samples

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(Submitter supplied) Euryhaline teleosts can live in a wide range of environmental salinities. Transcriptomic analysis in important osmoregulatory and non-osmoregulatory tissues (liver, gills and hypothalamus) by means of a specific oligo-microarray revealed new aspects related to the osmoregulatory processes mediated by different canonical pathways after hypo- or hyper-omotic challenges in gilthead sea bream (Sparus aurata) juveniles. more...

Organism:

Sparus aurata

Type:

Expression profiling by array

Platform:

GPL17218

36 Samples

Download data: TXT

(Submitter supplied) We developped a new oligo microarray platform to analyse flax transcriptome. Here, we validated this microarray on several tissues of flax, at different developmental stages.

Organism:

Linum usitatissimum

Type:

Expression profiling by array

Platform:

GPL10419

30 Samples

Download data: CALLS, PAIR

(Submitter supplied) Analysis of the gene expression profiles of Sparus aurata head kidney after infection with Photobaterium damselae piscicida. The expression levels of 21,497 sea bream transcripts, on both directions, 24 and 48 hours post-infection, were compared with the levels detected in uninfected individuals.

Organism:

Sparus aurata

Type:

Expression profiling by array

Platform:

GPL11489

16 Samples

Download data: TXT

(Submitter supplied) In Sparus aurata, seasonal temperature variations outside the normal thermal range, may trigger physiological responses leading to pathologies and death. In the present study two groups of wild sea bream were exposed for 21 days to two temperature regimes: 16 ± 0.3 °C (control group) and 6.8 ± 0.3 °C (cold-exposed group). Samples were collected during the acute phase (0, 6 and 24 hours after temperature drop) and upon chronic exposure (21 days).

Organism:

Sparus aurata

Type:

Expression profiling by array

Platform:

GPL6467

24 Samples

Download data: TXT

(Submitter supplied) Gilthead sea bream fed plant-protein based diets with either fish oil or vegetable oil as the most iportant source of dietary lipids were experimentally exposed to the intestinal parasite Enteromyxum leei by water effluent. A specific gilthead sea bream oligo-microarray was used to determine the intestine transcriptomic response.

Organism:

Sparus aurata

Type:

Expression profiling by array

Platform:

GPL15203

41 Samples

Download data: TXT

(Submitter supplied) Fish were fed from May to August (11 weeks) with a commercial diet (D-2 Excel 1P, Skretting, Stavanger, Norway) twice per day at two different feeding levels: full ration until visual satiety (MAX group), and maintenance ration (30% of the satiation level) (MANT group). The effect of ration size on aerobic (red skeletal muscle, heart) and anaerobic (white skeletal muscle) muscle tissue transcriptome was addressed by means of microarray analysis.

Organism:

Sparus aurata

Type:

Expression profiling by array

Platform:

GPL17218

34 Samples

Download data: TXT

(Submitter supplied) Agilent custom-made 8x60k 60-mer oligonucleotide microarray slides were used, covering unique sequences (21,093 annotated sequences and 4,299 unannotated sequences) of Sparus aurata transcriptomic data obtained from assembling of reads deposited in the NCBI SRA database corresponding to BioProject ID PRJNA391557, together with controls (8 transcripts of Sparus aurata plus Agilent controls). Two probes per sequence were used (in sense orientation for annotated sequences).

Organism:

Sparus aurata

Type:

Expression profiling by array

Platform:

GPL23648

16 Samples

Download data: TXT

(Submitter supplied) Gilthead sea bream larvae were sampled at 30 dph during a 24 h cycle taking 10 individuals every 3 hours (00:00, 03:00, 06:00, 09:00, 12:00, 15:00, 18:00, 21:00 and 24:00 h Zeitgeber time) and their expression profile was analyzed by means of a specific oligo-microarray. One-way ANOVA showed that 2,229 genes present in the microarray were differentially expressed among the nine temporal groups. Principal component analysis of these differentially expressed genes clearly showed a cyclic distribution of the groups along the two components that accounted for most of the total variation (48.3% and 32.8%, respectively). more...

Organism:

Sparus aurata

Type:

Expression profiling by array

Platform:

GPL19579

53 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) High density oligonucleotide microarrays have been used on Plasmodium vivax field isolates to estimate whole genome expression. However, no microarray platform has been experimentally optimized for studying the transcriptome of field isolates. In the present study, we adopted both bioinformatics and experimental testing approaches to select best optimized probes suitable for detecting parasite transcripts from field samples and included them in designing a custom 15K P. more...

Organism:

Plasmodium vivax

Type:

Expression profiling by array

Platform:

GPL18382

14 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