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Bioarray Inc software environment database base 1.2.12
Software Environment Database Base 1.2.12, supplied by Bioarray Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/software+environment+(base)+database/software+environment+database+base+1+2+12/pm21741888-102-2-2
Average 90 stars, based on 1 article reviews
software environment database base 1.2.12 - by Bioz Stars, 2026-10
90/100 stars

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Microarray:

Article Title: Nickel response in function of temperature differences: effects at different levels of biological organization in Daphnia magna.
Article Snippet: a Laboratory for Ecophysiology, Biochemistry and Toxicology, Department of Biology, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium b Plantijn Hogeschool, Kronenburgstraat 47, B-2000 Antwerp, Belgium c CESAM & Department of Biology, University of Aveiro, Campus Universitario de Santioago, 3810-193 Aveiro, Portugal d Apeiron-Team NV, Pluyseghemstraat 69, B-2550 Antwerp, Belgium

Article Title: Histone H3 lysine 4 trimethylation marks meiotic recombination initiation sites
Article Snippet: For transcriptome analyses, these ratios, representing the transcript abundance relative to the reference mix, were normalized using the Lowess algorithm implemented in BASE (BioArray Software Environment) 1.0.7 program ( Saal et al , 2002 ; Yang et al , 2002 ).

Article Title: Nickel and binary metal mixture responses in Daphnia magna: molecular fingerprints and (sub)organismal effects.
Article Snippet: The recent development of a custom cDNA microarray platform for one of thé standard organisms in aquatic toxicology, Daphnia magna, opened up new ways to mechanistic insights of toxicological responses.. In this study, the mRNA expression of several genes and (sub)organismal responses (Cellular Energy Allocation, growth) were assayed after short-term waterborne metal exposure.. Microarray analysis of Ni-exposed daphnids revealed several affected functional gene classes, of which the largest ones were involved in different metabolic processes (mainly protein and chitin related processes), cuticula turnover, transport and signal transduction.

Article Title: Mechanistic profiling of the cAMP-dependent steroidogenic pathway in the H295R endocrine disrupter screening system: new endpoints for toxicity testing.
Article Snippet: The need for implementation of effects on steroid synthesis and hormone processing in screening batteries of endocrine disruptive compounds is widely acknowledged.. In this perspective, hormone profiling in the H295R adrenocortical cell system is extensively examined and recently OECD validated (TG 456) as a replacement of the minced testis assay.. To further elucidate the complete mechanisms and endocrine responsiveness of this cell system, microarray-based gene expression profiling of the cAMP response pathway, one of the major pathways in steroidogenesis regulation, was examined in H295R cells.

Article Title: Development of a microarray for Enchytraeus albidus (Oligochaeta): preliminary tool with diverse applications.
Article Snippet: Standard bioassays allow hazard assessment at the population level, but much remains to be learned about the molecular level response of organisms to stressors.. The main aim of this study was the development of a DNA microarray for Enchytraeus albidus, a common soil worm species.. Further, this microarray was tested using worms exposed to Cu, phenmedipham, and different soil types.

Article Title: Gene transcription profiles, global DNA methylation and potential transgenerational epigenetic effects related to Zn exposure history in Daphnia magna.
Article Snippet: Subsequently, datawere evaluated with the MIAME platform based Bioarray Software Environment (BASE 1.2.17, http://www.islab.ua.ac. be/base/), using local background subtraction, variance stabilization normalization (Huber et al., 2002) and Limma (linear models for microarray data) (Smyth, 2004; Smyth et al., 2005).

Article Title: Identification of fibroblast growth factor-8b target genes associated with early and late cell cycle events in breast cancer cells.
Article Snippet: Primary hybridization data was collected using GenePix Pro 4.0 software (Axon Instruments, Foster City, CA) and raw data files were uploaded into BioArray Software Environment (BASE) version 1.2.17 (Saal et al., 2002).

Article Title: High expression of cholesterol biosynthesis genes is associated with resistance to statin treatment and inferior survival in breast cancer
Article Snippet: Microarray data were pre-processed and quantile-normalized using the GenomeStudio Software V2011.1 and BioArray Software Environment (BASE) V3.4.1 respectively.

Software:

Article Title: Nickel response in function of temperature differences: effects at different levels of biological organization in Daphnia magna.
Article Snippet: a Laboratory for Ecophysiology, Biochemistry and Toxicology, Department of Biology, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium b Plantijn Hogeschool, Kronenburgstraat 47, B-2000 Antwerp, Belgium c CESAM & Department of Biology, University of Aveiro, Campus Universitario de Santioago, 3810-193 Aveiro, Portugal d Apeiron-Team NV, Pluyseghemstraat 69, B-2550 Antwerp, Belgium

Article Title: Histone H3 lysine 4 trimethylation marks meiotic recombination initiation sites
Article Snippet: For transcriptome analyses, these ratios, representing the transcript abundance relative to the reference mix, were normalized using the Lowess algorithm implemented in BASE (BioArray Software Environment) 1.0.7 program ( Saal et al , 2002 ; Yang et al , 2002 ).

Article Title: Nickel and binary metal mixture responses in Daphnia magna: molecular fingerprints and (sub)organismal effects.
Article Snippet: The recent development of a custom cDNA microarray platform for one of thé standard organisms in aquatic toxicology, Daphnia magna, opened up new ways to mechanistic insights of toxicological responses.. In this study, the mRNA expression of several genes and (sub)organismal responses (Cellular Energy Allocation, growth) were assayed after short-term waterborne metal exposure.. Microarray analysis of Ni-exposed daphnids revealed several affected functional gene classes, of which the largest ones were involved in different metabolic processes (mainly protein and chitin related processes), cuticula turnover, transport and signal transduction.

Article Title: Mechanistic profiling of the cAMP-dependent steroidogenic pathway in the H295R endocrine disrupter screening system: new endpoints for toxicity testing.
Article Snippet: The need for implementation of effects on steroid synthesis and hormone processing in screening batteries of endocrine disruptive compounds is widely acknowledged.. In this perspective, hormone profiling in the H295R adrenocortical cell system is extensively examined and recently OECD validated (TG 456) as a replacement of the minced testis assay.. To further elucidate the complete mechanisms and endocrine responsiveness of this cell system, microarray-based gene expression profiling of the cAMP response pathway, one of the major pathways in steroidogenesis regulation, was examined in H295R cells.

Article Title: Development of a microarray for Enchytraeus albidus (Oligochaeta): preliminary tool with diverse applications.
Article Snippet: Standard bioassays allow hazard assessment at the population level, but much remains to be learned about the molecular level response of organisms to stressors.. The main aim of this study was the development of a DNA microarray for Enchytraeus albidus, a common soil worm species.. Further, this microarray was tested using worms exposed to Cu, phenmedipham, and different soil types.

Article Title: Gene transcription profiles, global DNA methylation and potential transgenerational epigenetic effects related to Zn exposure history in Daphnia magna.
Article Snippet: Subsequently, datawere evaluated with the MIAME platform based Bioarray Software Environment (BASE 1.2.17, http://www.islab.ua.ac. be/base/), using local background subtraction, variance stabilization normalization (Huber et al., 2002) and Limma (linear models for microarray data) (Smyth, 2004; Smyth et al., 2005).

Article Title: Identification of fibroblast growth factor-8b target genes associated with early and late cell cycle events in breast cancer cells.
Article Snippet: Primary hybridization data was collected using GenePix Pro 4.0 software (Axon Instruments, Foster City, CA) and raw data files were uploaded into BioArray Software Environment (BASE) version 1.2.17 (Saal et al., 2002).

Article Title: High expression of cholesterol biosynthesis genes is associated with resistance to statin treatment and inferior survival in breast cancer
Article Snippet: Microarray data were pre-processed and quantile-normalized using the GenomeStudio Software V2011.1 and BioArray Software Environment (BASE) V3.4.1 respectively.

Hybridization:

Article Title: Nickel response in function of temperature differences: effects at different levels of biological organization in Daphnia magna.
Article Snippet: a Laboratory for Ecophysiology, Biochemistry and Toxicology, Department of Biology, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium b Plantijn Hogeschool, Kronenburgstraat 47, B-2000 Antwerp, Belgium c CESAM & Department of Biology, University of Aveiro, Campus Universitario de Santioago, 3810-193 Aveiro, Portugal d Apeiron-Team NV, Pluyseghemstraat 69, B-2550 Antwerp, Belgium

Article Title: Histone H3 lysine 4 trimethylation marks meiotic recombination initiation sites
Article Snippet: For transcriptome analyses, these ratios, representing the transcript abundance relative to the reference mix, were normalized using the Lowess algorithm implemented in BASE (BioArray Software Environment) 1.0.7 program ( Saal et al , 2002 ; Yang et al , 2002 ).

Article Title: Nickel and binary metal mixture responses in Daphnia magna: molecular fingerprints and (sub)organismal effects.
Article Snippet: The recent development of a custom cDNA microarray platform for one of thé standard organisms in aquatic toxicology, Daphnia magna, opened up new ways to mechanistic insights of toxicological responses.. In this study, the mRNA expression of several genes and (sub)organismal responses (Cellular Energy Allocation, growth) were assayed after short-term waterborne metal exposure.. Microarray analysis of Ni-exposed daphnids revealed several affected functional gene classes, of which the largest ones were involved in different metabolic processes (mainly protein and chitin related processes), cuticula turnover, transport and signal transduction.

Article Title: Mechanistic profiling of the cAMP-dependent steroidogenic pathway in the H295R endocrine disrupter screening system: new endpoints for toxicity testing.
Article Snippet: The need for implementation of effects on steroid synthesis and hormone processing in screening batteries of endocrine disruptive compounds is widely acknowledged.. In this perspective, hormone profiling in the H295R adrenocortical cell system is extensively examined and recently OECD validated (TG 456) as a replacement of the minced testis assay.. To further elucidate the complete mechanisms and endocrine responsiveness of this cell system, microarray-based gene expression profiling of the cAMP response pathway, one of the major pathways in steroidogenesis regulation, was examined in H295R cells.

Article Title: Development of a microarray for Enchytraeus albidus (Oligochaeta): preliminary tool with diverse applications.
Article Snippet: Standard bioassays allow hazard assessment at the population level, but much remains to be learned about the molecular level response of organisms to stressors.. The main aim of this study was the development of a DNA microarray for Enchytraeus albidus, a common soil worm species.. Further, this microarray was tested using worms exposed to Cu, phenmedipham, and different soil types.

Article Title: Gene transcription profiles, global DNA methylation and potential transgenerational epigenetic effects related to Zn exposure history in Daphnia magna.
Article Snippet: Subsequently, datawere evaluated with the MIAME platform based Bioarray Software Environment (BASE 1.2.17, http://www.islab.ua.ac. be/base/), using local background subtraction, variance stabilization normalization (Huber et al., 2002) and Limma (linear models for microarray data) (Smyth, 2004; Smyth et al., 2005).

Article Title: Identification of fibroblast growth factor-8b target genes associated with early and late cell cycle events in breast cancer cells.
Article Snippet: Primary hybridization data was collected using GenePix Pro 4.0 software (Axon Instruments, Foster City, CA) and raw data files were uploaded into BioArray Software Environment (BASE) version 1.2.17 (Saal et al., 2002).

Article Title: High expression of cholesterol biosynthesis genes is associated with resistance to statin treatment and inferior survival in breast cancer
Article Snippet: Microarray data were pre-processed and quantile-normalized using the GenomeStudio Software V2011.1 and BioArray Software Environment (BASE) V3.4.1 respectively.



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