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ultragapstm γ-amino-propyl-silane-coated microarray slides  (Corning Life Sciences)

 
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    Corning Life Sciences ultragapstm γ-amino-propyl-silane-coated microarray slides
    (A) Hierarchical clustering analysis of 887 light-inducible transcripts. Included are transcripts from the NSF45K light vs. dark <t>microarray</t> data with >3.1-fold induction in light and FDR≤10 −4 and which are reported on by all three whole genome rice microarrays. Roman numerals delineate eighteen transcript clusters with similar expression patterns. For hierarchical clustering analysis, we used average log 2 ratios. In the case of the Affymetrix array data, we downloaded raw data from NCBI GEO and normalized the intensities of all array data (See ). The resulting values were transformed to ratios by comparing with a reference data set followed by log 2 transformation of the resulting ratios. For BGI/Yale array data, we downloaded from NCBI GEO data in the form of log 2 ratios of target samples relative to reference samples. We used the average log 2 ratio for multiple replicates for each condition. (B) Hierarchical clustering analysis of a refined list of 485 consistently light-inducible transcripts. Roman numerals delineate eight clusters with similar expression patterns. Yellow boxed regions indicate the data from light vs. dark experiments, and blue boxed regions indicate Affymetrix data for expression patterns relative to young seedling tissue.
    Ultragapstm γ Amino Propyl Silane Coated Microarray Slides, supplied by Corning Life Sciences, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Refinement of Light-Responsive Transcript Lists Using Rice Oligonucleotide Arrays: Evaluation of Gene-Redundancy"

    Article Title: Refinement of Light-Responsive Transcript Lists Using Rice Oligonucleotide Arrays: Evaluation of Gene-Redundancy

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0003337

    (A) Hierarchical clustering analysis of 887 light-inducible transcripts. Included are transcripts from the NSF45K light vs. dark microarray data with >3.1-fold induction in light and FDR≤10 −4 and which are reported on by all three whole genome rice microarrays. Roman numerals delineate eighteen transcript clusters with similar expression patterns. For hierarchical clustering analysis, we used average log 2 ratios. In the case of the Affymetrix array data, we downloaded raw data from NCBI GEO and normalized the intensities of all array data (See ). The resulting values were transformed to ratios by comparing with a reference data set followed by log 2 transformation of the resulting ratios. For BGI/Yale array data, we downloaded from NCBI GEO data in the form of log 2 ratios of target samples relative to reference samples. We used the average log 2 ratio for multiple replicates for each condition. (B) Hierarchical clustering analysis of a refined list of 485 consistently light-inducible transcripts. Roman numerals delineate eight clusters with similar expression patterns. Yellow boxed regions indicate the data from light vs. dark experiments, and blue boxed regions indicate Affymetrix data for expression patterns relative to young seedling tissue.
    Figure Legend Snippet: (A) Hierarchical clustering analysis of 887 light-inducible transcripts. Included are transcripts from the NSF45K light vs. dark microarray data with >3.1-fold induction in light and FDR≤10 −4 and which are reported on by all three whole genome rice microarrays. Roman numerals delineate eighteen transcript clusters with similar expression patterns. For hierarchical clustering analysis, we used average log 2 ratios. In the case of the Affymetrix array data, we downloaded raw data from NCBI GEO and normalized the intensities of all array data (See ). The resulting values were transformed to ratios by comparing with a reference data set followed by log 2 transformation of the resulting ratios. For BGI/Yale array data, we downloaded from NCBI GEO data in the form of log 2 ratios of target samples relative to reference samples. We used the average log 2 ratio for multiple replicates for each condition. (B) Hierarchical clustering analysis of a refined list of 485 consistently light-inducible transcripts. Roman numerals delineate eight clusters with similar expression patterns. Yellow boxed regions indicate the data from light vs. dark experiments, and blue boxed regions indicate Affymetrix data for expression patterns relative to young seedling tissue.

    Techniques Used: Microarray, Expressing, Transformation Assay

    (A) Depiction of the rice photorespiration pathway as provided in the RiceCyc pathways in Gramene ( http://www.gramene.org/pathway/ ). Step 1 is catalyzed by ribulose-1,5 bisphosphate carboxylase, which is regulated by rubisco activase (RCA) 1 , , for which there are two gene family members (1-1 and 1-2). Rubisco oxygenase activity results in the two-carbon molecule, 2-phosphoglycolate. 2-phosphoglycolate is converted to glycine by phosphoglycolate phosphatase (Step 2), glycolate oxidase (Step 3) and glycine aminotransferase (Step 4). There are 23 gene family members for phosphoglycolate phosphatase (PGP; 2-1 to 2-23). Glycolate oxidase (GLO) has seven gene family members (3-1 to 3-7). Serine-glyoxylate aminotransferase (SGAT) is a unique gene (4). The decarboxylation of two glycines by the glycine cleavage system (GCS; Step 6) generates serine, CO 2 and NH 3 . Serine is further converted to 3-phosphoglycerate by serine hydroxymethyltransferase (SHMT; Step 5), hydroxyacid dehydrogenase (HPDH; Step 7), and glycerate kinase (GLK; Step 8). There are five genes for SHMT (5-1 to 5-5). There are three GCS gene family members (6-1 to 6-3); Ten d-isomer specific 2-HDPHs (7-1 to 7-10). GLK is a unique gene (8). The three-carbon molecule, 3-phosphoglycerate generated from photorespiration re-enters the CO 2 fixation Calvin cycle . The SHMT (Step 5) gene identified in this study for which a mutant gives a defect is in the red box. (B) Average expression levels of the 52 candidate photorespiration pathway genes in the NSF45K light vs. dark data set. Open bars show the average absolute signal intensity in the light of four replicates; black bars show the average absolute signal intensity in the dark of four replicates. Underlining indicates genes that are unique or predominantly expressed compared to other gene family members. Asterisks indicate genes that have high expression, but with levels that do not clearly predominate over other gene family members. (C) Hierarchical clustering analysis of the differential expression patterns of the 52 candidate photorespiration pathway genes carried out using 40 microarray data sets. The yellow box delimits data from light vs. dark experiments; the blue box indicates Affymetrix developmental data compared to young seedling tissue. Clusters VI and VII (red-filled brackets) have more significant gene expression patterns in NSF 45K and BGI/Yale microarray data in response to light. Underlined gene labels indicate unique or predominantly expressed genes in the photorespiration pathway, based on the consistency of light induction and preferential expression patterns in young seedling tissue. Asterisks indicate gene family members that fall within the same cluster and are expected to have functional redundancy. Genes in step 5 are marked with red open boxes. The microarray data corresponding to the putative photorespiration genes are provided in .
    Figure Legend Snippet: (A) Depiction of the rice photorespiration pathway as provided in the RiceCyc pathways in Gramene ( http://www.gramene.org/pathway/ ). Step 1 is catalyzed by ribulose-1,5 bisphosphate carboxylase, which is regulated by rubisco activase (RCA) 1 , , for which there are two gene family members (1-1 and 1-2). Rubisco oxygenase activity results in the two-carbon molecule, 2-phosphoglycolate. 2-phosphoglycolate is converted to glycine by phosphoglycolate phosphatase (Step 2), glycolate oxidase (Step 3) and glycine aminotransferase (Step 4). There are 23 gene family members for phosphoglycolate phosphatase (PGP; 2-1 to 2-23). Glycolate oxidase (GLO) has seven gene family members (3-1 to 3-7). Serine-glyoxylate aminotransferase (SGAT) is a unique gene (4). The decarboxylation of two glycines by the glycine cleavage system (GCS; Step 6) generates serine, CO 2 and NH 3 . Serine is further converted to 3-phosphoglycerate by serine hydroxymethyltransferase (SHMT; Step 5), hydroxyacid dehydrogenase (HPDH; Step 7), and glycerate kinase (GLK; Step 8). There are five genes for SHMT (5-1 to 5-5). There are three GCS gene family members (6-1 to 6-3); Ten d-isomer specific 2-HDPHs (7-1 to 7-10). GLK is a unique gene (8). The three-carbon molecule, 3-phosphoglycerate generated from photorespiration re-enters the CO 2 fixation Calvin cycle . The SHMT (Step 5) gene identified in this study for which a mutant gives a defect is in the red box. (B) Average expression levels of the 52 candidate photorespiration pathway genes in the NSF45K light vs. dark data set. Open bars show the average absolute signal intensity in the light of four replicates; black bars show the average absolute signal intensity in the dark of four replicates. Underlining indicates genes that are unique or predominantly expressed compared to other gene family members. Asterisks indicate genes that have high expression, but with levels that do not clearly predominate over other gene family members. (C) Hierarchical clustering analysis of the differential expression patterns of the 52 candidate photorespiration pathway genes carried out using 40 microarray data sets. The yellow box delimits data from light vs. dark experiments; the blue box indicates Affymetrix developmental data compared to young seedling tissue. Clusters VI and VII (red-filled brackets) have more significant gene expression patterns in NSF 45K and BGI/Yale microarray data in response to light. Underlined gene labels indicate unique or predominantly expressed genes in the photorespiration pathway, based on the consistency of light induction and preferential expression patterns in young seedling tissue. Asterisks indicate gene family members that fall within the same cluster and are expected to have functional redundancy. Genes in step 5 are marked with red open boxes. The microarray data corresponding to the putative photorespiration genes are provided in .

    Techniques Used: Activity Assay, Generated, Mutagenesis, Expressing, Microarray, Functional Assay

    Strategy employed for validating the data from the rice NSF45K array.
    Figure Legend Snippet: Strategy employed for validating the data from the rice NSF45K array.

    Techniques Used: Expressing, Binding Assay, Activity Assay, Northern Blot, Microarray

    Related Articles

    Polymerase Chain Reaction:

    Article Title: Transcription profiling of fertilization and early seed development events in a solanaceous species using a 7.7 K cDNA microarray from Solanum chacoense ovules
    Article Snippet: .. PCR products were resuspended in 10 μl of 50% DMSO and arrayed from 384 well microtiter plates onto UltraGAPSTM slides (Corning incorporated, Corning, NY, USA). ..

    Article Title: Regulatory RNAs and the HptB/RetS signalling pathways fine-tune Pseudomonas aeruginosa pathogenesis
    Article Snippet: Microarrays were printed at the DNA microarray production platform at Sophia-Antipolis (IPMC-CNRS) using a ChipWriter Proarrayer (Bio-Rad). .. Each PCR product was spotted 4 times on commercial UltraGAPSTM slides of 24 × 60 mm (Corning Incorporated, MA, USA). ..

    Gene Expression:

    Article Title: Protist-Type Lysozymes of the Nematode Caenorhabditis elegans Contribute to Resistance against Pathogenic Bacillus thuringiensis
    Article Snippet: Thereafter, nematodes were washed off, pelleted by centrifugation, washed in 10 ml sterile Millipore H 2 O to remove external bacteria, pelleted, snap-frozen in liquid nitrogen, followed by addition of 1.5 ml Trizol (Invitrogen) on ice (4°C), RNA extraction according to manufacturer's instructions (Trizol, Invitrogen), and storage of RNA isolates at −20°C. .. Gene expression patterns were compared between pathogenic and non-pathogenic treatments for the three C. elegans strains separately (MY15, MY18, N2) using whole genome microarrays containing oligonucleotide sequences of 20,334 genes, designed at the Genome Sequencing Center (St. Louis, USA) and spotted on UltraGAPSTM slides (Corning) at the Plateforme Transcriptome (Marseille-Nice génopole/CNRS/INRA; Sophia Antipolis, France). .. 10 μg total RNA was employed for cDNA synthesis with SuperScript II Reverse Transcriptase (SSII, Invitrogen) using oligo dT 24 -V primer (Sigma-Aldrich) and aminoallyl-dUTP (Sigma-Aldrich) nucleotide analogs. cDNA was purified with the Qiagen PCR purification kit and labelled either with Cy 3 or Cy 5 mono-reactive dye packs (Amersham).

    Sequencing:

    Article Title: Protist-Type Lysozymes of the Nematode Caenorhabditis elegans Contribute to Resistance against Pathogenic Bacillus thuringiensis
    Article Snippet: Thereafter, nematodes were washed off, pelleted by centrifugation, washed in 10 ml sterile Millipore H 2 O to remove external bacteria, pelleted, snap-frozen in liquid nitrogen, followed by addition of 1.5 ml Trizol (Invitrogen) on ice (4°C), RNA extraction according to manufacturer's instructions (Trizol, Invitrogen), and storage of RNA isolates at −20°C. .. Gene expression patterns were compared between pathogenic and non-pathogenic treatments for the three C. elegans strains separately (MY15, MY18, N2) using whole genome microarrays containing oligonucleotide sequences of 20,334 genes, designed at the Genome Sequencing Center (St. Louis, USA) and spotted on UltraGAPSTM slides (Corning) at the Plateforme Transcriptome (Marseille-Nice génopole/CNRS/INRA; Sophia Antipolis, France). .. 10 μg total RNA was employed for cDNA synthesis with SuperScript II Reverse Transcriptase (SSII, Invitrogen) using oligo dT 24 -V primer (Sigma-Aldrich) and aminoallyl-dUTP (Sigma-Aldrich) nucleotide analogs. cDNA was purified with the Qiagen PCR purification kit and labelled either with Cy 3 or Cy 5 mono-reactive dye packs (Amersham).

    Concentration Assay:

    Article Title: Linking toxicant physiological mode of action with induced gene expression changes in Caenorhabditis elegans
    Article Snippet: .. The oligonucleotides were printed onto UltraGAPSTM (Corning, Barry, UK) slides at a concentration of 15 μM. .. Appropriate landmarks of 8 replicates of the Lucida Scorecard (Amersham) were across slides sub-array.

    Article Title: Application of physiologically based modelling and transcriptomics to probe the systems toxicology of aldicarb for Caenorhabditis elegans (Maupas 1900)
    Article Snippet: .. These were printed in 3× SSC buffer using a Perkin Elmer SpotArray 72 onto UltraGAPSTM slides (Corning, Barry, UK) at a concentration of 15 μM. .. Landmarks were printed in the top left hand corner of each sub-array for orientation and the Lucidea universal scorecard (Amersham, Buckinghamshire, UK) also printed at a concentration of 25 μM.



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    Image Search Results


    (A) Hierarchical clustering analysis of 887 light-inducible transcripts. Included are transcripts from the NSF45K light vs. dark microarray data with >3.1-fold induction in light and FDR≤10 −4 and which are reported on by all three whole genome rice microarrays. Roman numerals delineate eighteen transcript clusters with similar expression patterns. For hierarchical clustering analysis, we used average log 2 ratios. In the case of the Affymetrix array data, we downloaded raw data from NCBI GEO and normalized the intensities of all array data (See ). The resulting values were transformed to ratios by comparing with a reference data set followed by log 2 transformation of the resulting ratios. For BGI/Yale array data, we downloaded from NCBI GEO data in the form of log 2 ratios of target samples relative to reference samples. We used the average log 2 ratio for multiple replicates for each condition. (B) Hierarchical clustering analysis of a refined list of 485 consistently light-inducible transcripts. Roman numerals delineate eight clusters with similar expression patterns. Yellow boxed regions indicate the data from light vs. dark experiments, and blue boxed regions indicate Affymetrix data for expression patterns relative to young seedling tissue.

    Journal: PLoS ONE

    Article Title: Refinement of Light-Responsive Transcript Lists Using Rice Oligonucleotide Arrays: Evaluation of Gene-Redundancy

    doi: 10.1371/journal.pone.0003337

    Figure Lengend Snippet: (A) Hierarchical clustering analysis of 887 light-inducible transcripts. Included are transcripts from the NSF45K light vs. dark microarray data with >3.1-fold induction in light and FDR≤10 −4 and which are reported on by all three whole genome rice microarrays. Roman numerals delineate eighteen transcript clusters with similar expression patterns. For hierarchical clustering analysis, we used average log 2 ratios. In the case of the Affymetrix array data, we downloaded raw data from NCBI GEO and normalized the intensities of all array data (See ). The resulting values were transformed to ratios by comparing with a reference data set followed by log 2 transformation of the resulting ratios. For BGI/Yale array data, we downloaded from NCBI GEO data in the form of log 2 ratios of target samples relative to reference samples. We used the average log 2 ratio for multiple replicates for each condition. (B) Hierarchical clustering analysis of a refined list of 485 consistently light-inducible transcripts. Roman numerals delineate eight clusters with similar expression patterns. Yellow boxed regions indicate the data from light vs. dark experiments, and blue boxed regions indicate Affymetrix data for expression patterns relative to young seedling tissue.

    Article Snippet: The oligos were combined with 1× Pronto!™ Universal Spotting Solution (Corning, Inc., Corning, NY) to a final concentration of 25 µM in 0.5× spotting solution and spotted onto bar-coded Corning UltraGAPS™ γ-amino-propyl-silane-coated microarray slides (Corning, Inc., Corning, NY).

    Techniques: Microarray, Expressing, Transformation Assay

    (A) Depiction of the rice photorespiration pathway as provided in the RiceCyc pathways in Gramene ( http://www.gramene.org/pathway/ ). Step 1 is catalyzed by ribulose-1,5 bisphosphate carboxylase, which is regulated by rubisco activase (RCA) 1 , , for which there are two gene family members (1-1 and 1-2). Rubisco oxygenase activity results in the two-carbon molecule, 2-phosphoglycolate. 2-phosphoglycolate is converted to glycine by phosphoglycolate phosphatase (Step 2), glycolate oxidase (Step 3) and glycine aminotransferase (Step 4). There are 23 gene family members for phosphoglycolate phosphatase (PGP; 2-1 to 2-23). Glycolate oxidase (GLO) has seven gene family members (3-1 to 3-7). Serine-glyoxylate aminotransferase (SGAT) is a unique gene (4). The decarboxylation of two glycines by the glycine cleavage system (GCS; Step 6) generates serine, CO 2 and NH 3 . Serine is further converted to 3-phosphoglycerate by serine hydroxymethyltransferase (SHMT; Step 5), hydroxyacid dehydrogenase (HPDH; Step 7), and glycerate kinase (GLK; Step 8). There are five genes for SHMT (5-1 to 5-5). There are three GCS gene family members (6-1 to 6-3); Ten d-isomer specific 2-HDPHs (7-1 to 7-10). GLK is a unique gene (8). The three-carbon molecule, 3-phosphoglycerate generated from photorespiration re-enters the CO 2 fixation Calvin cycle . The SHMT (Step 5) gene identified in this study for which a mutant gives a defect is in the red box. (B) Average expression levels of the 52 candidate photorespiration pathway genes in the NSF45K light vs. dark data set. Open bars show the average absolute signal intensity in the light of four replicates; black bars show the average absolute signal intensity in the dark of four replicates. Underlining indicates genes that are unique or predominantly expressed compared to other gene family members. Asterisks indicate genes that have high expression, but with levels that do not clearly predominate over other gene family members. (C) Hierarchical clustering analysis of the differential expression patterns of the 52 candidate photorespiration pathway genes carried out using 40 microarray data sets. The yellow box delimits data from light vs. dark experiments; the blue box indicates Affymetrix developmental data compared to young seedling tissue. Clusters VI and VII (red-filled brackets) have more significant gene expression patterns in NSF 45K and BGI/Yale microarray data in response to light. Underlined gene labels indicate unique or predominantly expressed genes in the photorespiration pathway, based on the consistency of light induction and preferential expression patterns in young seedling tissue. Asterisks indicate gene family members that fall within the same cluster and are expected to have functional redundancy. Genes in step 5 are marked with red open boxes. The microarray data corresponding to the putative photorespiration genes are provided in .

    Journal: PLoS ONE

    Article Title: Refinement of Light-Responsive Transcript Lists Using Rice Oligonucleotide Arrays: Evaluation of Gene-Redundancy

    doi: 10.1371/journal.pone.0003337

    Figure Lengend Snippet: (A) Depiction of the rice photorespiration pathway as provided in the RiceCyc pathways in Gramene ( http://www.gramene.org/pathway/ ). Step 1 is catalyzed by ribulose-1,5 bisphosphate carboxylase, which is regulated by rubisco activase (RCA) 1 , , for which there are two gene family members (1-1 and 1-2). Rubisco oxygenase activity results in the two-carbon molecule, 2-phosphoglycolate. 2-phosphoglycolate is converted to glycine by phosphoglycolate phosphatase (Step 2), glycolate oxidase (Step 3) and glycine aminotransferase (Step 4). There are 23 gene family members for phosphoglycolate phosphatase (PGP; 2-1 to 2-23). Glycolate oxidase (GLO) has seven gene family members (3-1 to 3-7). Serine-glyoxylate aminotransferase (SGAT) is a unique gene (4). The decarboxylation of two glycines by the glycine cleavage system (GCS; Step 6) generates serine, CO 2 and NH 3 . Serine is further converted to 3-phosphoglycerate by serine hydroxymethyltransferase (SHMT; Step 5), hydroxyacid dehydrogenase (HPDH; Step 7), and glycerate kinase (GLK; Step 8). There are five genes for SHMT (5-1 to 5-5). There are three GCS gene family members (6-1 to 6-3); Ten d-isomer specific 2-HDPHs (7-1 to 7-10). GLK is a unique gene (8). The three-carbon molecule, 3-phosphoglycerate generated from photorespiration re-enters the CO 2 fixation Calvin cycle . The SHMT (Step 5) gene identified in this study for which a mutant gives a defect is in the red box. (B) Average expression levels of the 52 candidate photorespiration pathway genes in the NSF45K light vs. dark data set. Open bars show the average absolute signal intensity in the light of four replicates; black bars show the average absolute signal intensity in the dark of four replicates. Underlining indicates genes that are unique or predominantly expressed compared to other gene family members. Asterisks indicate genes that have high expression, but with levels that do not clearly predominate over other gene family members. (C) Hierarchical clustering analysis of the differential expression patterns of the 52 candidate photorespiration pathway genes carried out using 40 microarray data sets. The yellow box delimits data from light vs. dark experiments; the blue box indicates Affymetrix developmental data compared to young seedling tissue. Clusters VI and VII (red-filled brackets) have more significant gene expression patterns in NSF 45K and BGI/Yale microarray data in response to light. Underlined gene labels indicate unique or predominantly expressed genes in the photorespiration pathway, based on the consistency of light induction and preferential expression patterns in young seedling tissue. Asterisks indicate gene family members that fall within the same cluster and are expected to have functional redundancy. Genes in step 5 are marked with red open boxes. The microarray data corresponding to the putative photorespiration genes are provided in .

    Article Snippet: The oligos were combined with 1× Pronto!™ Universal Spotting Solution (Corning, Inc., Corning, NY) to a final concentration of 25 µM in 0.5× spotting solution and spotted onto bar-coded Corning UltraGAPS™ γ-amino-propyl-silane-coated microarray slides (Corning, Inc., Corning, NY).

    Techniques: Activity Assay, Generated, Mutagenesis, Expressing, Microarray, Functional Assay

    Strategy employed for validating the data from the rice NSF45K array.

    Journal: PLoS ONE

    Article Title: Refinement of Light-Responsive Transcript Lists Using Rice Oligonucleotide Arrays: Evaluation of Gene-Redundancy

    doi: 10.1371/journal.pone.0003337

    Figure Lengend Snippet: Strategy employed for validating the data from the rice NSF45K array.

    Article Snippet: The oligos were combined with 1× Pronto!™ Universal Spotting Solution (Corning, Inc., Corning, NY) to a final concentration of 25 µM in 0.5× spotting solution and spotted onto bar-coded Corning UltraGAPS™ γ-amino-propyl-silane-coated microarray slides (Corning, Inc., Corning, NY).

    Techniques: Expressing, Binding Assay, Activity Assay, Northern Blot, Microarray