SaDA: From Sampling to Data Analysis—An Extensible Open Source Infrastructure for Rapid, Robust and Automated Management and Analysis of Modern Ecological  High-Throughput Microarray Data

Singh, Kumar Saurabh; Thual, Dominique; Spurio, Roberto; Cannata, Nicola

doi:10.3390/ijerph120606352

Cited by 7 publications

(3 citation statements)

References 23 publications

(20 reference statements)

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“…Preliminary assays based on the use of spiked diatom cell mixtures and field-testing are currently ongoing in our laboratory. As the outcomes of these studies become available, they will provide a solid background to test SaDA, a software developed in a parallel study for rapid and automated management and analysis of ecological high-throughput data [ 58 ].…”

Section: Discussionmentioning

confidence: 99%

Molecular Tools for the Selective Detection of Nine Diatom Species Biomarkers of Various Water Quality Levels

Cimarelli

Singh

Nhu

et al. 2015

IJERPH

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Our understanding of the composition of diatom communities and their response to environmental changes is currently limited by laborious taxonomic identification procedures. Advances in molecular technologies are expected to contribute more efficient, robust and sensitive tools for the detection of these ecologically relevant microorganisms. There is a need to explore and test phylogenetic markers as an alternative to the use of rRNA genes, whose limited sequence divergence does not allow the accurate discrimination of diatoms at the species level. In this work, nine diatom species belonging to eight genera, isolated from epylithic environmental samples collected in central Italy, were chosen to implement a panel of diatoms covering the full range of ecological status of freshwaters. The procedure described in this work relies on the PCR amplification of specific regions in two conserved diatom genes, elongation factor 1-a (eEF1-a) and silicic acid transporter (SIT), as a first step to narrow down the complexity of the targets, followed by microarray hybridization experiments. Oligonucleotide probes with the potential to discriminate closely related species were designed taking into account the genetic polymorphisms found in target genes. These probes were tested, refined and validated on a small-scale prototype DNA chip. Overall, we obtained 17 highly specific probes targeting eEF1-a and SIT, along with 19 probes having lower discriminatory power recognizing at the same time two or three species. This basic array was validated in a laboratory setting and is ready for tests with crude environmental samples eventually to be scaled-up to include a larger panel of diatoms. Its possible use for the simultaneous detection of diatoms selected from the classes of water quality identified by the European Water Framework Directive is discussed.

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Section: Discussionmentioning

confidence: 99%

Molecular Tools for the Selective Detection of Nine Diatom Species Biomarkers of Various Water Quality Levels

Cimarelli

Singh

Nhu

et al. 2015

IJERPH

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“…The paper by Singh et al [ 35 ] describes the development of a bioinformatics tool for the management of the vast amount of data deriving from microarray experiments involving environmental samples. SaDA, the software described in this paper, is composed of two layers, layer 1 for data upload processing and retrieval and layer 2 for data storage.…”

Section: Rapid and Efficient Methods To Monitor The Presence Of Emmentioning

confidence: 99%

Scientific Symposium “Small Solution for Big Water-Related Problems: Innovative Microarrays and Small Sensors to Cope with Water Quality and Food Security”

Marcheggiani

Spurio

Cimarelli

et al. 2015

IJERPH

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This issue presents the conclusive results of two European Commission funded Projects, namely Universal Microarrays for the Evaluation of Fresh-water Quality Based on Detection of Pathogens and their Toxins (MicroAQUA) and Rationally Designed Aquatic Receptors (RADAR). These projects focused their activities on the quality of drinking water as an extremely important factor for public health of humans and animals. The MicroAQUA Project aimed at developing a universal microarray chip for the detection of various pathogens (cyanobacteria, bacteria, viruses and parasitic protozoa) and their toxins in waters. In addition, the project included the detection of select species of diatoms, which represent reliable bio-indicators to assess overall water quality. Large numbers of compounds are released into the environment; some of these are toxins such as endocrine disrupting compounds (EDCs) and can affect the endocrine, immune and nervous systems of a wide range of animals causing alterations such as reproductive disorders and cancer. Detection of these contaminants in water systems is important to protect sensitive environmental sites and reduce the risk of toxins entering the food chain. A modular platform for monitoring toxins in water and food production facilities, using biosensors derived from aquatic organisms, was the main goal of RADAR Project.

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“…Next to analysis tools, solutions are developed for storage and management of microarray datasets. While the National Center for Biology Information ( NCBI ) solution Gene Expression Omnibus ( GEO ) is widely used, alternative infrastructures such as SaDA emerge .…”

Section: Introductionmentioning

confidence: 99%

Array Analysis Manager—An automated DNA microarray analysis tool simplifying microarray data filtering, bias recognition, normalization, and expression analysis

Haar

Lindner

Scheper

et al. 2017

Engineering in Life Sciences

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Desoxyribonucleic acid (DNA) microarray experiments generate big datasets. To successfully harness the potential information within, multiple filtering, normalization, and analysis methods need to be applied. An in-depth knowledge of underlying physical, chemical, and statistical processes is crucial to the success of this analysis. However, due to the interdisciplinarity of DNA microarray applications and experimenter backgrounds, the published analyses differ greatly, for example, in methodology. This severely limits the comprehensibility and comparability among studies and research fields. In this work, we present a novel end-user software, developed to automatically filter, normalize, and analyze two-channel microarray experiment data. It enables the user to analyze single chip, dye-swap, and loop experiments with an extended dynamic intensity range using a multiscan approach. Furthermore, to our knowledge, this is the first analysis software solution, that can account for photobleaching, automatically detected by an artificial neural network. The user gets feedback on the effectiveness of each applied normalization regarding bias minimization. Standardized methods for expression analysis are included as well as the possibility to export the results in the Gene Expression Omnibus (GEO) format. This software was designed to simplify the microarray analysis process and help the experimenter to make educated decisions about the analysis process to contribute to reproducibility and comparability.

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SaDA: From Sampling to Data Analysis—An Extensible Open Source Infrastructure for Rapid, Robust and Automated Management and Analysis of Modern Ecological High-Throughput Microarray Data

Cited by 7 publications

References 23 publications

Molecular Tools for the Selective Detection of Nine Diatom Species Biomarkers of Various Water Quality Levels

Molecular Tools for the Selective Detection of Nine Diatom Species Biomarkers of Various Water Quality Levels

Scientific Symposium “Small Solution for Big Water-Related Problems: Innovative Microarrays and Small Sensors to Cope with Water Quality and Food Security”

Array Analysis Manager—An automated DNA microarray analysis tool simplifying microarray data filtering, bias recognition, normalization, and expression analysis

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