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atgenexpress data sets  (Schmid GmbH)

 
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    Schmid GmbH atgenexpress data sets
    Atgenexpress Data Sets, supplied by Schmid GmbH, 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/ath1+microarray+chip/atgenexpress+database/pmc02048726-305-14-18
    Average 90 stars, based on 1 article reviews
    atgenexpress data sets - by Bioz Stars, 2026-10
    90/100 stars

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    Related Articles

    Expressing:

    Article Title: Selection is no more efficient in haploid than in diploid life stages of an angiosperm and a moss.
    Article Snippet: .. The first data set combines the AtGenExpress expression data (Schmid et al. 2005) and a data set published by Wuest at al. (2010). ..

    Article Title: A plant-specific HUA2-LIKE ( HULK ) gene family in Arabidopsis thaliana is essential for development
    Article Snippet: .. For the analysis of HULK gene expression patterns across tissues and developmental stages, we used the expression microarray AtGenExpress dataset (Schmid et al ., ), RNA-Seq read data and in situ localization (see Methods S2). .. For nuclear localization studies, HULK cDNAs were amplified using Phusion polymerase (NEB, http://www.neb.com ) with the primer pairs listed in Table S7.

    Article Title: Detailed characterization of the UMAMIT proteins provides insight into their evolution, amino acid transport properties, and role in the plant.
    Article Snippet: .. To get a glimpse of the diversity of the expression patterns of the UMAMITs, we focused on the Arabidopsis family, for which a profusion of public data is available, notably the AtGenExpress dataset (Schmid et al., 2005) (Table 1). .. Unfortunately, the ATH1 Affymetrix chip used for these analyses lacked probes for six members (from Clade J), namely AtUMAMIT35, 36, 38, 40, 45, and 46, and no information on the expression of these genes could thus be gathered.

    Article Title: New BAR tools for mining expression data and exploring Cis-elements in Arabidopsis thaliana.
    Article Snippet: This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record.. Please cite this article as doi: 10.1111/tpj.13261 This article is protected by copyright.. All rights reserved.

    Article Title: Genome-wide analyses for dissecting gene regulatory networks in the shoot apical meristem.
    Article Snippet: .. In particular, there were over 1000 genes for which expression was detected in the cell-type specific SAM datasets, but not in the entire AtGenExpress developmental series of wildtype plants (Schmid et al., 2005): rare transcripts and genes that might be expressed in only a few cells or cell-types of the meristem, as further shown by in situ hybridization experiments for selected genes (Yadav et al., 2009). ..

    Gene Expression:

    Article Title: A plant-specific HUA2-LIKE ( HULK ) gene family in Arabidopsis thaliana is essential for development
    Article Snippet: .. For the analysis of HULK gene expression patterns across tissues and developmental stages, we used the expression microarray AtGenExpress dataset (Schmid et al ., ), RNA-Seq read data and in situ localization (see Methods S2). .. For nuclear localization studies, HULK cDNAs were amplified using Phusion polymerase (NEB, http://www.neb.com ) with the primer pairs listed in Table S7.

    Article Title: Boron-bridged RG-II and calcium are required to maintain the pectin network of the Arabidopsis seed mucilage ultrastructure.
    Article Snippet: of seed mucilage covering the seed surface, which consists of a water-soluble outer layer and an adherent inner layer.. Our study of mur1 seed mucilage has revealed that the pectin in the outer layer of mucilage was relocated to the inner layer.. Nevertheless, the mur1 inner mucilage was more vulnerable to rough shaking or ethylene diamine tetraacetic acid (EDTA) extraction than that of the wild type.

    Microarray:

    Article Title: A plant-specific HUA2-LIKE ( HULK ) gene family in Arabidopsis thaliana is essential for development
    Article Snippet: .. For the analysis of HULK gene expression patterns across tissues and developmental stages, we used the expression microarray AtGenExpress dataset (Schmid et al ., ), RNA-Seq read data and in situ localization (see Methods S2). .. For nuclear localization studies, HULK cDNAs were amplified using Phusion polymerase (NEB, http://www.neb.com ) with the primer pairs listed in Table S7.

    RNA sequencing:

    Article Title: A plant-specific HUA2-LIKE ( HULK ) gene family in Arabidopsis thaliana is essential for development
    Article Snippet: .. For the analysis of HULK gene expression patterns across tissues and developmental stages, we used the expression microarray AtGenExpress dataset (Schmid et al ., ), RNA-Seq read data and in situ localization (see Methods S2). .. For nuclear localization studies, HULK cDNAs were amplified using Phusion polymerase (NEB, http://www.neb.com ) with the primer pairs listed in Table S7.

    In Situ:

    Article Title: A plant-specific HUA2-LIKE ( HULK ) gene family in Arabidopsis thaliana is essential for development
    Article Snippet: .. For the analysis of HULK gene expression patterns across tissues and developmental stages, we used the expression microarray AtGenExpress dataset (Schmid et al ., ), RNA-Seq read data and in situ localization (see Methods S2). .. For nuclear localization studies, HULK cDNAs were amplified using Phusion polymerase (NEB, http://www.neb.com ) with the primer pairs listed in Table S7.

    other:

    Article Title: Proteome Analysis of Peroxisomes from Etiolated Arabidopsis Seedlings Identifies a Peroxisomal Protease Involved in ?-Oxidation and Development
    Article Snippet: To determine whether genes encoding peroxisomal proteins of etiolated seedlings identified from this study confer any tissue-specific expression pattern, we queried the Botany Array Resource expression browser with all 77 genes (technically 76, as GOX1 and GOX2 shared the same probe), downloaded log 2 -normalized data for the relative expression of these genes from the AtGenExpress developmental time-line data set ( Schmid et al., 2005 ; Toufighi et al., 2005 ; Supplemental Tables S12 and S13), and generated heat maps that clustered the peroxisomal genes based on their level of coexpression.

    Article Title: Enrichment of Triticum aestivum gene annotations using ortholog cliques and gene ontologies in other plants
    Article Snippet: Expression datasets available in GEO for 4 plant species were used, such as: A. thaliana (AtGenExpress data series of Schmid et al., 2005 [ ]), O. sativa (GEO accession numbers GSE7951 and GSE6893), H. vulgare (GEO accession number GSE16754) and Z. mays (PlexDB experiment number ZM37).

    Generated:

    Article Title: Boron-bridged RG-II and calcium are required to maintain the pectin network of the Arabidopsis seed mucilage ultrastructure.
    Article Snippet: of seed mucilage covering the seed surface, which consists of a water-soluble outer layer and an adherent inner layer.. Our study of mur1 seed mucilage has revealed that the pectin in the outer layer of mucilage was relocated to the inner layer.. Nevertheless, the mur1 inner mucilage was more vulnerable to rough shaking or ethylene diamine tetraacetic acid (EDTA) extraction than that of the wild type.

    In Situ Hybridization:

    Article Title: Genome-wide analyses for dissecting gene regulatory networks in the shoot apical meristem.
    Article Snippet: .. In particular, there were over 1000 genes for which expression was detected in the cell-type specific SAM datasets, but not in the entire AtGenExpress developmental series of wildtype plants (Schmid et al., 2005): rare transcripts and genes that might be expressed in only a few cells or cell-types of the meristem, as further shown by in situ hybridization experiments for selected genes (Yadav et al., 2009). ..



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    A pie graph of GO categorization of genes differentially expressed in the ams mutant . (A-B) GO categorization of genes up- and down-regulated in ams , with enriched categories circled compared with all genes on <t>ATH1.</t> (C) GO categorization of all genes on the ATH1 chip.
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    Expression level of nuclear genes encoding components of the chloroplast transcription machinery in selected mitochondrial mutants and plants growing under hypoxic conditions. (a) Colour scale represents up (red) or down (blue) fold change values relative to the wild-type. Publicly available dataset GSE 14420 [45] representing three-week-old wild-type plant exposed to 4 h of hypoxia was analysed. (b) Common differentially expressed nuclear genes encoding chloroplast transcription machinery components (ppde. p > 0.95, FC (fold change) 1.5) in representative <t>microarray</t> datasets. (Online version in colour.)
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    Image Search Results


    A pie graph of GO categorization of genes differentially expressed in the ams mutant . (A-B) GO categorization of genes up- and down-regulated in ams , with enriched categories circled compared with all genes on ATH1. (C) GO categorization of all genes on the ATH1 chip.

    Journal: BMC Plant Biology

    Article Title: AMS-dependent and independent regulation of anther transcriptome and comparison with those affected by other Arabidopsis anther genes

    doi: 10.1186/1471-2229-12-23

    Figure Lengend Snippet: A pie graph of GO categorization of genes differentially expressed in the ams mutant . (A-B) GO categorization of genes up- and down-regulated in ams , with enriched categories circled compared with all genes on ATH1. (C) GO categorization of all genes on the ATH1 chip.

    Article Snippet: For the identification of the functions of the differentially expressed genes, the annotations of genes on ATH1 microarray chip were downloaded from Affymetrix website and we used the GO categorization function on TAIR website [ ].

    Techniques: Mutagenesis

    Venn diagrams of microarray results and previous related study . (A) A comparison of anther preferential genes identified in our study with previously known pollen genes and stamen genes. (B-D) Comparisons between genes differentially expressed in the ams anther and those preferentially expressed in certain organ: anther preferential, stamen and pollen respectively.

    Journal: BMC Plant Biology

    Article Title: AMS-dependent and independent regulation of anther transcriptome and comparison with those affected by other Arabidopsis anther genes

    doi: 10.1186/1471-2229-12-23

    Figure Lengend Snippet: Venn diagrams of microarray results and previous related study . (A) A comparison of anther preferential genes identified in our study with previously known pollen genes and stamen genes. (B-D) Comparisons between genes differentially expressed in the ams anther and those preferentially expressed in certain organ: anther preferential, stamen and pollen respectively.

    Article Snippet: For the identification of the functions of the differentially expressed genes, the annotations of genes on ATH1 microarray chip were downloaded from Affymetrix website and we used the GO categorization function on TAIR website [ ].

    Techniques: Microarray

    Gene regulatory network of anther development during early stages . Gene regulation is represented by T-bars (negatively) and arrows (positively). The direct regulation confirmed by experiment is represented in bold line. Genes encoding proteins with interaction is represented by double arrows. Gene expression patterns in different tissues are shown by colors (blue for anther specific; red for anther-preferential; green for reproductive-preferential and yellow for genes not included in ATH1 chip). Gene function in tapetum formation is marked by an apostrophe; in pollen wall formation by an asterisk; in callose dissolution by double asterisks; in stamen and petal formation by the letter b; in stamen and carpel formation by the letter c.

    Journal: BMC Plant Biology

    Article Title: AMS-dependent and independent regulation of anther transcriptome and comparison with those affected by other Arabidopsis anther genes

    doi: 10.1186/1471-2229-12-23

    Figure Lengend Snippet: Gene regulatory network of anther development during early stages . Gene regulation is represented by T-bars (negatively) and arrows (positively). The direct regulation confirmed by experiment is represented in bold line. Genes encoding proteins with interaction is represented by double arrows. Gene expression patterns in different tissues are shown by colors (blue for anther specific; red for anther-preferential; green for reproductive-preferential and yellow for genes not included in ATH1 chip). Gene function in tapetum formation is marked by an apostrophe; in pollen wall formation by an asterisk; in callose dissolution by double asterisks; in stamen and petal formation by the letter b; in stamen and carpel formation by the letter c.

    Article Snippet: For the identification of the functions of the differentially expressed genes, the annotations of genes on ATH1 microarray chip were downloaded from Affymetrix website and we used the GO categorization function on TAIR website [ ].

    Techniques: Expressing

    Expression level of nuclear genes encoding components of the chloroplast transcription machinery in selected mitochondrial mutants and plants growing under hypoxic conditions. (a) Colour scale represents up (red) or down (blue) fold change values relative to the wild-type. Publicly available dataset GSE 14420 [45] representing three-week-old wild-type plant exposed to 4 h of hypoxia was analysed. (b) Common differentially expressed nuclear genes encoding chloroplast transcription machinery components (ppde. p > 0.95, FC (fold change) 1.5) in representative microarray datasets. (Online version in colour.)

    Journal: Philosophical Transactions of the Royal Society B: Biological Sciences

    Article Title: Joint inhibition of mitochondrial complex IV and alternative oxidase by genetic or chemical means represses chloroplast transcription in Arabidopsis

    doi: 10.1098/rstb.2019.0409

    Figure Lengend Snippet: Expression level of nuclear genes encoding components of the chloroplast transcription machinery in selected mitochondrial mutants and plants growing under hypoxic conditions. (a) Colour scale represents up (red) or down (blue) fold change values relative to the wild-type. Publicly available dataset GSE 14420 [45] representing three-week-old wild-type plant exposed to 4 h of hypoxia was analysed. (b) Common differentially expressed nuclear genes encoding chloroplast transcription machinery components (ppde. p > 0.95, FC (fold change) 1.5) in representative microarray datasets. (Online version in colour.)

    Article Snippet: Analysis of the global changes in transcript abundance in rps10 mutant was performed using Affymetrix ATH1 microarray gene chips.

    Techniques: Expressing, Microarray