scanarray microarray scanner (Lumonics Inc)

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Lumonics Inc scanarray microarray scanner

Schematic representation of TraSH procedure. (A) Chromosomal region encompassing genes A–C from six different mutant strains (rectangles) is shown. Each mutant carries a single transposon insertion (triangles) that disrupts the function of a gene. Pools of mutants are grown under two different selective conditions. Genes A and C are nonessential for growth. Gene B is essential only under growth condition 2, and mutants harboring insertions in this gene are lost from this pool (represented by light shading). TraSH target that is complementary to the chromosomal DNA flanking each transposon insertion is generated from the two pools, labeled with different fluorophores, and hybridized to a <t>microarray.</t> The DNA probes representing genes A and C on the microarray will hybridize to the target generated from both pools. However, the target representing gene B will only be present in the pool from growth condition 1. By measuring the ratio of the two fluorophores for each probe, differential gene requirements are detected. (B) Method for generating TraSH target. The chromosomal DNA containing a transposon insertion (green) is digested with frequent cutting restriction enzymes, and adapters (blue) are ligated to the ends of the resulting DNA. PCR is then performed with primers (red) that hybridize to transposon and adapter sequences. To avoid the amplification of fragments that do not contain transposon sequence, the adapter contains the adapter–primer sequence but not the complementary strand, which serves as a binding site for this primer. Thus, the binding site must be generated by extension from the transposon-specific primer. To allow for the linear extension of these products, the transposon primer was designed with a higher melting temperature than the adapter primer, and higher annealing temperatures were used in the initial cycles of PCR (see Materials and Methods). Extension of the adapter itself, which would generate a binding site for the adapter primer, is prevented by a 3′-amino modification. The resulting PCR product is used as a template for the in vitro transcription of RNA target. This RNA is labeled and used for microarray hybridization.

Scanarray Microarray Scanner, supplied by Lumonics 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/scanarray+4000+microarray+scanner/pmc00060119-122-5-9?v=Lumonics+Inc
Average 90 stars, based on 1 article reviews

scanarray microarray scanner - by Bioz Stars, 2026-06

90/100 stars

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1) Product Images from "Comprehensive identification of conditionally essential genes in mycobacteria"

Article Title: Comprehensive identification of conditionally essential genes in mycobacteria

Journal:

doi: 10.1073/pnas.231275498

Figure Legend Snippet: Schematic representation of TraSH procedure. (A) Chromosomal region encompassing genes A–C from six different mutant strains (rectangles) is shown. Each mutant carries a single transposon insertion (triangles) that disrupts the function of a gene. Pools of mutants are grown under two different selective conditions. Genes A and C are nonessential for growth. Gene B is essential only under growth condition 2, and mutants harboring insertions in this gene are lost from this pool (represented by light shading). TraSH target that is complementary to the chromosomal DNA flanking each transposon insertion is generated from the two pools, labeled with different fluorophores, and hybridized to a microarray. The DNA probes representing genes A and C on the microarray will hybridize to the target generated from both pools. However, the target representing gene B will only be present in the pool from growth condition 1. By measuring the ratio of the two fluorophores for each probe, differential gene requirements are detected. (B) Method for generating TraSH target. The chromosomal DNA containing a transposon insertion (green) is digested with frequent cutting restriction enzymes, and adapters (blue) are ligated to the ends of the resulting DNA. PCR is then performed with primers (red) that hybridize to transposon and adapter sequences. To avoid the amplification of fragments that do not contain transposon sequence, the adapter contains the adapter–primer sequence but not the complementary strand, which serves as a binding site for this primer. Thus, the binding site must be generated by extension from the transposon-specific primer. To allow for the linear extension of these products, the transposon primer was designed with a higher melting temperature than the adapter primer, and higher annealing temperatures were used in the initial cycles of PCR (see Materials and Methods). Extension of the adapter itself, which would generate a binding site for the adapter primer, is prevented by a 3′-amino modification. The resulting PCR product is used as a template for the in vitro transcription of RNA target. This RNA is labeled and used for microarray hybridization.

Techniques Used: Mutagenesis, Generated, Labeling, Microarray, Amplification, Sequencing, Binding Assay, Modification, In Vitro, Hybridization

Auxotrophic mutations identified by TraSH. Intensities are the average of duplicate features from two independent microarray TraSH hybridizations.

Figure Legend Snippet: Auxotrophic mutations identified by TraSH. Intensities are the average of duplicate features from two independent microarray TraSH hybridizations.

Techniques Used: Microarray

TraSH identifies mutations that result in auxotrophy. The bar graphs display the fluorescence intensity observed for each gene across the genomic region surrounding auxotrophic mutations (in bold). Gray bars and white bars represent fluorescence observed from pools grown on minimal or rich medium, respectively. Data are the average of duplicate measurements from a single microarray and are represented on a log scale. Error bars representing standard deviations are shown for all features. The absence of error bars indicates that the value was too small to be plotted. Genes for which the intensity from the rich medium pool did not exceed two-times the background were omitted.

Figure Legend Snippet: TraSH identifies mutations that result in auxotrophy. The bar graphs display the fluorescence intensity observed for each gene across the genomic region surrounding auxotrophic mutations (in bold). Gray bars and white bars represent fluorescence observed from pools grown on minimal or rich medium, respectively. Data are the average of duplicate measurements from a single microarray and are represented on a log scale. Error bars representing standard deviations are shown for all features. The absence of error bars indicates that the value was too small to be plotted. Genes for which the intensity from the rich medium pool did not exceed two-times the background were omitted.

Techniques Used: Fluorescence, Microarray

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scanarray microarray scanner (Lumonics Inc)

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1) Product Images from "Comprehensive identification of conditionally essential genes in mycobacteria"

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