Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

A novel aCGH method for non-model organisms for assessing genomes and de-novo transcriptome sequencing reads

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Danio rerio

SUBMITTER: Paul Wackers

PROVIDER: E-GEOD-52122 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Absence/presence calling in microarray-based CGH experiments with non-model organisms.

Jonker Martijs J MJ de Leeuw Wim C WC Marinković Marino M Wittink Floyd R A FR Rauwerda Han H Bruning Oskar O Ensink Wim A WA Fluit Ad C AC Boel C H CH Jong Mark de Md Breit Timo M TM

Nucleic acids research 20140425 11

Structural variations in genomes are commonly studied by (micro)array-based comparative genomic hybridization. The data analysis methods to infer copy number variation in model organisms (human, mouse) are established. In principle, the procedures are based on signal ratios between test and reference samples and the order of the probe targets in the genome. These procedures are less applicable to experiments with non-model organisms, which frequently comprise non-sequenced genomes with an unknow ...[more]

PMID: 24771343

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Project description:The proper transition between the skotomorphogenic and photomorphogenic developmental programs is key for seedling survival and it is therefore tightly regulated. Besides light, which is the major cue that triggers this transition, several hormone pathways participate in this control, mainly antagonizing the light effect. Two of these hormones are gibberellins (GA) and brassinosteroids (BR). Both hormones promote the skotomorphogenesis and prevent photomorphogenesis, as evidenced by the partially de-etiolated phenotype caused by GA or BR deficiency, or by a blockage in the respective signaling pathways. We have previously shown that BR mediate GA activity in the control of this transition. For instance, treatment of dark-grown, GA-deficient seedlings with BRs was able to partially restore morphological phenotypes such as hypocotyl growth, and importantly to restore completely the molecular phenotype of CAB2 and RbcS gene expression. On the contrary, GA-treatment did not alter the same phenotypes in the BR deficient det2 mutant. Thus, the aim of this study was to investigate to what extent BRs mediate GA activity in dark-grown seedlings, and for that purpose we have the examined global changes in gene expression caused by treatment with GA and BRs in BR- and GA-deficient seedlings, respectively. We performed two sets of experiments, each one including three different samples. The first experiment included dark-grown, WT Col-0 mock-treated seedlings, or seedlings treated with either the GA biosynthesis inhibitor paclobutrazol (PAC) or with PAC+epibrassinolide (EBR). In this experiment, PAC samples were labelled with Cy3 and compared to WT and PAC+EBR samples, which were labelled with Cy5. Two biological repeast were performed. The second experiment included dark-grown, WT Col-0 seedlings and the det2-1 mutant, which was either mock-treated or treated with GA3. Two biological replicates were performed, in the first one the WT and det2-1+GA3 were labelled with Cy3 and the det2-1 sample with Cy5. The reverse labelling was used in the second replicate.

Dataset Information

A novel aCGH method for non-model organisms for assessing genomes and de-novo transcriptome sequencing reads

Publications

Absence/presence calling in microarray-based CGH experiments with non-model organisms.

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