NDLI: GPR-Analyzer: a simple tool for quantitative analysis of hierarchical multispecies microarrays

Content Provider	Springer Nature Link
Author	Dittami, Simon M. Edvardsen, Bente
Copyright Year	2012
Abstract	Monitoring of marine microalgae is important to predict and manage harmful algae blooms. It currently relies mainly on light-microscopic identification and enumeration of algal cells, yet several molecular tools are currently being developed to complement traditional methods. MIcroarray Detection of Toxic ALgae (MIDTAL) is an FP7-funded EU project aiming to establish a hierarchical multispecies microarray as one of these tools. Prototype arrays are currently being tested with field samples, yet the analysis of the large quantities of data generated by these arrays presents a challenge as suitable analysis tools or protocols are scarce. This paper proposes a two-part protocol for the analysis of the MIDTAL and other hierarchical multispecies arrays: Signal-to-noise ratios can be used to determine the presence or absence of signals and to identify potential false-positives considering parallel and hierarchical probes. In addition, normalized total signal intensities are recommended for comparisons between microarrays and in order to relate signals for specific probes to cell concentrations using external calibration curves. Hybridization- and probe-specific detection limits can be calculated to help evaluate negative results. The suggested analyses were implemented in “GPR-Analyzer”, a platform-independent and graphical user interface-based application, enabling non-specialist users to quickly and quantitatively analyze hierarchical multispecies microarrays. It is available online at http://folk.uio.no/edvardse/gpranalyzer .
Starting Page	6808
Ending Page	6815
Page Count	8
File Format	PDF
ISSN	09441344
Journal	Environmental Science and Pollution Research
Volume Number	20
Issue Number	10
e-ISSN	16147499
Language	English
Publisher	Springer Berlin Heidelberg
Publisher Date	2012-07-06
Publisher Place	Berlin, Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Multispecies DNA microarrays Hierarchical probes Phylochips Cell concentrations Analysis software Environment Environmental Chemistry Ecotoxicology Environmental Health Atmospheric Protection/Air Quality Control/Air Pollution Waste Water Technology Water Pollution Control Water Management Aquatic Pollution
Content Type	Text
Resource Type	Article
Subject	Environmental Chemistry Health, Toxicology and Mutagenesis Pollution Medicine

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

An evaluation of the applicability of microarrays for monitoring toxic algae in Irish coastal waters

Molecular probes and microarrays for the detection of toxic algae in the genera Dinophysis and Phalacroma (Dinophyta)

Introduction to project MIDTAL: its methods and samples from Arcachon Bay, France

Microarray testing for the presence of toxic algae monitoring programme in Galicia (NW Spain)

A bioluminescent arsenite biosensor designed for inline water analyzer

Recent sediments: environmental chemistry, ecotoxicology and engineering

Erratum to: Modeling of air pollutant concentrations in an industrial region of Turkey

Advanced oxidation processes for environmental protection

Process engineering for pollution control and waste minimization

GPR-Analyzer: a simple tool for quantitative analysis of hierarchical multispecies microarrays

Similar Documents

An evaluation of the applicability of microarrays for monitoring toxic algae in Irish coastal waters

Molecular probes and microarrays for the detection of toxic algae in the genera Dinophysis and Phalacroma (Dinophyta)

Introduction to project MIDTAL: its methods and samples from Arcachon Bay, France

Microarray testing for the presence of toxic algae monitoring programme in Galicia (NW Spain)

A bioluminescent arsenite biosensor designed for inline water analyzer

Recent sediments: environmental chemistry, ecotoxicology and engineering

Erratum to: Modeling of air pollutant concentrations in an industrial region of Turkey

Advanced oxidation processes for environmental protection

Process engineering for pollution control and waste minimization

GPR-Analyzer: a simple tool for quantitative analysis of hierarchical multispecies microarrays