Lamina joint initiation in rice
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ABSTRACT:
PROVIDER: PRJEB40431 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Oryza sativa LIGULELESS 2s determine lamina joint positioning and differentiation by inhibiting auxin signaling
| PRJEB40447 | ENA
Project description:Identification of factors regulating leaf inclination reveal a complex regulatory network of lamina joint development, however, the dynamic transcriptional programming of it remain to be elucidated. We used microarrays to detail the global gene expression profiles at different developmental stages of lamina joint and identified distinct classes of differentially expressed genes during this process, characterized the regulating factors of rice lamina joint development.
2017-08-29 | GSE92895 | GEO
Project description:The leaf lamina joint joins the rice leaf blade and sheath, contributing significantly to the leaf angle trait. A more erect leaf facilitates the penetration of sunlight, enhancing photosynthetic efficiency and occupying less space in dense planting. Genetic screening found a mutant increased leaf angle1, ila1 from rice T-DNA insertional mutants library. We used microarrays to detail the transcriptional profile changes in the mutant ila1 lamina joint. Two biological replicate sample of leaf lamina joints from the ila1 and wild-type plants at tillering stage were collected for RNA extraction. Total RNAs were isolated from each replicate via the TRIzol method (Invitrogen) and used in target synthesis for the Rice Genome Array from Affymetrix. The microarray analyses were performed through following standard protocols (Affymetrix).
2012-04-30 | E-GEOD-33361 | biostudies-arrayexpress
Project description:We compared transcripts using microarray hybridization between lamina joint samples of WT and OsBUL1 KO.
2017-09-05 | GSE93714 | GEO
Project description:The leaf lamina joint joins the rice leaf blade and sheath, contributing significantly to the leaf angle trait. A more erect leaf facilitates the penetration of sunlight, enhancing photosynthetic efficiency and occupying less space in dense planting. Genetic screening found a mutant increased leaf angle1, ila1 from rice T-DNA insertional mutants library. We used microarrays to detail the transcriptional profile changes in the mutant ila1 lamina joint.
2012-05-01 | GSE33361 | GEO
Project description:We compared transcripts using microarray hybridization between lamina joint samples of WT and pOsBUL1:OsBDG1 plants.
2017-09-05 | GSE93816 | GEO
Project description:A large fraction of the mammalian genome is organized into inactive chromosomal domains associated with the nuclear lamina. Using genomic repositioning assays we show that Lamina associated domains (LADs), spanning the developmentally regulated IgH and Cyp3a loci, contain transportable DNA regions that associate chromatin with the nuclear lamina and repress gene activity in fibroblasts. We characterized DNA regions within LADs that are functionally capable of positioning chromatin domains at the inner nuclear membrane (INM) lamina. We mapped and characterized the IgH and other LADs in murine fibroblasts. We show that these murine LADs have a unique chromatin structure with discrete boundaries. We demonstrate DNA regions within LADs that are capable of directing the association of chromatin domains with the INM-lamina as well as the silencing of a co-integrated reporter gene.
2012-02-24 | E-GEOD-36048 | biostudies-arrayexpress
Project description:The angle of rice leaf inclination is an important agronomic trait and closely related to the yield and architecture of crops. Through genetic screening, a rice gain-of-function mutant leaf inclination1, lc1, was identified . Phenotypic analysis confirmed the exaggerated leaf angels of lc1 due to the stimulated cell elongation at the collar.In this series, we compare the transcriptome of zhonghua11 and lc1 collar. The lamina joint (1-cm long) of the flag leaves of lc1 and WT plants were collected and frozen in liquid nitrogen, which were then used for RNAs extraction. The obtained RNA samples were processed as recommended by Affymetrix, including RNA extraction, converting to double-stranded cDNA, and synthesis of biotin-labeled copy RNA. Fifteen micrograms of biotin-labeled copy RNA was purified and fragmented into 35- to 300-nucleotide fragments and then hybridized with a Rice genome array (Affymetrix). The hybridization was performed with two biological replicates for each sample. After hybridization, arrays were scanned using an Agilent GeneArray scanner (Affymetrix G2500A). Microarray data were normalized using the Affymetrix Microarray Suit program (version 5.0). The algorithm absolute call flag was set to indicate the reliability of the data points according to P (present), M (marginal), and A (absent). Significant differences for each gene between the WT and lc1 mutant plants were examined using the Wilcoxon rank test of the Affymetrix Microarray Suit program (P<0.01) and analysis of variance by fitting a mixed model in the MAANOVA package under R 1.8.0 for multiple testing (false discovery rate-corrected P<0.05). Genes with the consensus significant difference in two independent samples were selected and listed. Annotations for the selected probe set identification were rechecked at the Affymetrix website.
2011-06-16 | E-GEOD-16640 | biostudies-arrayexpress
Project description:The nuclear lamina (NL) interacts with hundreds of large genomic regions termed lamina-associated domains (LADs). The dynamics of these interactions and the relation to epigenetic modifications are poorly understood. We visualized the fate of LADs in single cells using a novel 'molecular contact memory' approach. In each interphase nucleus, only ~30% of LADs are positioned at the periphery; these LADs are in intermittent molecular contact with the NL but remain constrained to the periphery. Upon mitosis, LAD positioning is not detectably inherited but instead is stochastically reshuffled. Contact of individual LADs with the NL correlates with their degree of H3K9 dimethylation in single cells, and inactivation of the H3K9 methyltransferase G9a reduces the NL contact frequencies. These results indicate that nuclear positioning and histone modification of LADs are both stochastic yet linked in single cells. Collectively, these results highlight principles of the dynamic spatial architecture of chromosomes. LaminB1-chromatin interactions were assayed in human HT1080 cells by induction of Dam_LMNB1 expression in a stable cell line with shield1.
2013-01-31 | E-GEOD-40094 | biostudies-arrayexpress
Project description:Genome wide gene expression was determined in paired samples of OA affected and preserved cartilage of the same joint using microarray analysis for 33 patients of the RAAK-study. Among the 1717 genes that were significantly different expressed between OA affected and preserved cartilage we found significant enrichment for genes involved in skeletal development (e.g. TNFRSF11B and FRZB). Also several inflammatory genes such as CD55, PTGES and TNFAIP6, previously identified in within-joint analyses as well as in analyses comparing preserved cartilage from OA affected joints versus healthy cartilage were among the top genes. A notable new gene was NGF, highly up-regulated in OA cartilage. To identify gene expression profiles associated with OA processes in articular cartilage and determine pathways responsive to the disease process gene expression profiles of paired preserved and OA affected cartilage samples of the same joint were determined.
2014-07-28 | E-GEOD-57218 | biostudies-arrayexpress