Time course microarray analysis during xylem cell differentiation in leaf-disk culture system
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE61941 | GEO | 2014/12/31
SECONDARY ACCESSION(S): PRJNA262720
REPOSITORIES: GEO
Similar Datasets
Project description:Expression of defense response-related transcripts could be affected upon leaf wounding such as after excision of leaf disks. In this experiment, transcripts were isolated from whole leaves and 5-cm2 excised leaf disks samples from interaction assays between leaves of the 'Beaupré' poplar cultivar (Poplus trichocarpa x Poplus deltoides) and virulent (98AG31, compatible interaction) and avirulent (93ID6, incompatible interaction) urediniospores of Melampsora larici-populina, the fungus responsible for the foliar rust disease in poplar. For each type of interaction, three samples were collected in a time-course series (18, 21 and 24 hpi for strain 93ID6, and 18, 24 and 48 hpi for strain 98AG31). Both leaf disks and whole leaves were inoculated in strictly similar conditions, so differential transcript expression is likely attributable to the wounding effect in leaf disks. The aim of this study is to identify genes that are induced by wounding in leaf disks compared with whole leaves. For this purpose, cDNA templates were used for hybridization on poplar oligoarrays.
2015-10-01 | GSE39727 | GEO
Project description:Expression profiling of the affect of eggs of the Pieris brassicae butterfly on Arabidopsis thaliana local leaf vs. the distal leaf using leaf disks the size of the egg batch.
2007-04-04 | E-CAGE-190 | biostudies-arrayexpress
Project description:In order to pinpoint the most differentially expressed genes between Eucalyptus grandis leaf blades and vascular (xylem) tissues as well as between E. grandis and Eucalyptus globulus xylem tissues, a total number of nine 50mer-oligoprobes covering the length of each one of 21,432 unique sequences derived from the Genolyptus EST dataset were synthesized “on-chip” in duplicate, randomly distributed in two blocks of each slide. Probes were also synthesized from ten cDNA sequences encoding known human proteins as negative controls, totaling 21,442 sequences. Leaves and xylem samples were taken from two E. grandis clonal trees, i.e., both derived from the same matrix tree and harboring the same genotype. Two additional xylem samples were collected from two other E. grandis clonal trees of a different genotype, as well as from two E. globulus clonal trees. Therefore, ten cDNA samples and ten identical chips were produced at Roche NimbleGen for the microarray assays, with a total number of 385,956 features per slide. Besides the discovery of differentially expressed genes between leaf and xylem, we wanted to test the validity of the assumed “technical” and “biological duplicates” since all trees were field-grown and four years-old in age.
2011-12-31 | GSE31696 | GEO
Project description:The leaf vasculature plays a key role in solute translocation. Veins consist of at least seven distinct cell types, with specific roles in transport, metabolism, and signaling. Little is known about the vascular cells in leaves, in particular the phloem parenchyma (PP). PP effluxes sucrose into the apoplasm as a basis for phloem loading; yet PP has only been characterized microscopically. Here, we enriched vascular cells from Arabidopsis leaves to generate a single-cell transcriptome atlas of leaf vasculature. We identified ?19 cell clusters, encompassing epidermis, guard cells, hydathodes, mesophyll, and all vascular cell types, and used metabolic pathway analysis to define their roles. Clusters comprising PP cells were enriched for transporters, including SWEET11 and SWEET12 sucrose and UmamiT amino acid efflux carriers. PP development occurs independently from APL, a transcription factor required for phloem differentiation. PP cells have a unique pattern of amino acid metabolism activity distinct from companion cells (CC), explaining differential distribution/metabolism of amino acids in veins. The kinship relation of the vascular clusters is strikingly similar to the vein morphology, except for a clear separation of CC from the other vascular cells including PP. In summary, our scRNA-seq analysis provides a wide range of information into the leaf vasculature and the role and relationship of the leaf cell types.
2020-12-31 | GSE161411 | GEO
Project description:We established a novel in vitro tissue culture system (named VISUAL), in which xylem and phloem differentiation can be induced with Arabidopsis thaliana cotyledons To compare gene expression profiles between WT and apl during vascular development, we performed GeneChip analysis using VISUAL.
2016-05-25 | GSE80026 | GEO
Project description:We have previously established an in vitro tissue culture system (named VISUAL; Kondo et al., 2016), in which xylem and phloem differentiation can be induced with Arabidopsis thaliana cotyledons To compare gene expression profiles between WT and bes1 during vascular development, we performed GeneChip analysis using VISUAL.
2018-02-07 | GSE110199 | GEO
Project description:In order to pinpoint the most differentially expressed genes between Eucalyptus grandis leaf blades and vascular (xylem) tissues as well as between E. grandis and Eucalyptus globulus xylem tissues, a total number of nine 50mer-oligoprobes covering the length of each one of 21,432 unique sequences derived from the Genolyptus EST dataset were synthesized “on-chip” in duplicate, randomly distributed in two blocks of each slide. Probes were also synthesized from ten cDNA sequences encoding known human proteins as negative controls, totaling 21,442 sequences. Leaves and xylem samples were taken from two E. grandis clonal trees, i.e., both derived from the same matrix tree and harboring the same genotype. Two additional xylem samples were collected from two other E. grandis clonal trees of a different genotype, as well as from two E. globulus clonal trees. Therefore, ten cDNA samples and ten identical chips were produced at Roche NimbleGen for the microarray assays, with a total number of 385,956 features per slide. Besides the discovery of differentially expressed genes between leaf and xylem, we wanted to test the validity of the assumed “technical” and “biological duplicates” since all trees were field-grown and four years-old in age. A ten chip study using total RNA recovered from mature leaf and vascular (xylem) tissues of Eucalyptus grandis and xylem from Eucalyptus globulus trees. Two clonal trees of E. grandis (E.grandis_Clone A_Ramet 1 and E.grandis_Clone A_Ramet 2), derived from a single matrix tree and therefore genomically identical, were the source of two samples of leaf RNA and two samples of xylem RNA, individually hybridized to four chips after cDNA synthesis/Cy3 labeling. Two other clonal trees of E. grandis (E.grandis_Clone B_Ramet 1 and E.grandis_Clone B_Ramet 2), derived from a different matrix tree, were the source of two additional samples of xylem RNA individually hybridized to four chips after cDNA synthesis/Cy3 labeling. Likewise, two pairs of clonal trees of E. globulus (E.globulus_Clone A_Ramet 1 and E.globulus_Clone A_Ramet 2/ E.globulus_Clone B_Ramet 1 and E.globulus_Clone B_Ramet 2), derived from two distinct matrix trees, were the source of four additional samples of xylem RNA, individually hybridized to four chips after cDNA synthesis/Cy3 labeling. Each chip measures the expression level of 21,432 genes from Eucalyptus sp. and ten human genes (negative controls) with nine 50-mer probe pairs (PM/MM) per gene in two separate blocks per chip (technical duplicate), totalizing 18 hybridization signal values per gene per chip.
2011-12-31 | E-GEOD-31696 | biostudies-arrayexpress
Project description:The veins of leaves are a highly evolved vascular network that allows plants to grow large and complex. The patterning process leading to their formation involves the integration of several internal and external signals, such as plant hormone auxin. Here, we show that an evolutionarily conserved transcription factor controlling leaf vein growth in flowering plants VDOF1 is dependent on autophagy for its activity in Arabidopsis thaliana leaf, suggesting that this pathway might be required for proper vascular system development in leaf. Taken together, our data forms that during leaf vein patterning there is presents a network in which a module that links VDOF1-ATG8-ANT1-SCR-SHR factors integrates Space-time dimension to provide more vein density, which establish a precondition for C4 photosynthesis transition.
2023-07-01 | GSE216739 | GEO
Project description:We established a micro-patterned respiratory epithelial cell culture system in vitro. In this culture system, various types of lung epithelial cells were identified.
2024-02-29 | GSE249762 | GEO
Project description:The leaf vasculature plays a key role in solute translocation. Veins consist of at least seven distinct cell types, with specific roles in transport, metabolism, and signaling. Little is known about the vascular cells in leaves, in particular the phloem parenchyma (PP). PP effluxes sucrose into the apoplasm as a basis for phloem loading; yet PP has only been characterized microscopically. Here, we enriched vascular cells from Arabidopsis leaves to generate a single-cell transcriptome atlas of leaf vasculature. We identified ?19 cell clusters, encompassing epidermis, guard cells, hydathodes, mesophyll, and all vascular cell types, and used metabolic pathway analysis to define their roles. Clusters comprising PP cells were enriched for transporters, including SWEET11 and SWEET12 sucrose and UmamiT amino acid efflux carriers. PP development occurs independently from APL, a transcription factor required for phloem differentiation. PP cells have a unique pattern of amino acid metabolism activity distinct from companion cells (CC), explaining differential distribution/metabolism of amino acids in veins. The kinship relation of the vascular clusters is strikingly similar to the vein morphology, except for a clear separation of CC from the other vascular cells including PP. In summary, our scRNA-seq analysis provides a wide range of information into the leaf vasculature and the role and relationship of the leaf cell types.
2020-12-31 | GSE161332 | GEO