Microarray using WT (TNG67) and pOsBUL1:OsBDG1 Lamina joint samples (TNG67 vs. #13 vs. #20)
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa
PROVIDER: GSE93816 | GEO | 2017/09/05
SECONDARY ACCESSION(S): PRJNA362477
REPOSITORIES: GEO
Similar Datasets
Project description:We compared transcripts using microarray hybridization between lamina joint samples of WT and OsBUL1 KO.
2017-09-05 | GSE93714 | GEO
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: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:Oryza sativa LIGULELESS 2s determine lamina joint positioning and differentiation by inhibiting auxin signaling
| PRJEB40431 | ENA
Project description:Oryza sativa LIGULELESS 2s determine lamina joint positioning and differentiation by inhibiting auxin signaling
| PRJEB40447 | ENA
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:we performed single cell RNA-Seq analysis of 2,267 cells from E17.5 murine knee joint. Using computational analytics and in situ hybridization, we identified five sub-populations contributing to joint constituents, and the underlying transcriptional networks, signaling, and core regulators involving in potential lineage transition during late joint developmental stage.
2022-03-30 | GSE179701 | GEO
Project description:Synovial joint development begins with the formation of the interzone, a region of condensed mesenchymal cells at the site of the prospective joint. Recently, lineage tracing strategies have revealed that Gdf5-lineage cells native to and from outside the interzone contribute to most, if not all, of the major joint components. However, there is limited knowledge of the specific transcriptional and signaling programs that regulate interzone formation and fate diversification of synovial joint constituents. To address this, we have performed single cell RNA-Seq analysis of 7,329 synovial joint progenitor cells from the developing murine knee joint from E12.5 to E15.5. By using a combination of computational analytics, in situ hybridization, and in vitro characterization of prospectively isolated populations, we have identified the transcriptional profiles of the major developmental paths for joint progenitors. Our freely available single cell transcriptional atlas will serve as a resource for the community to uncover transcriptional programs and cell interactions that regulate synovial joint development.
2020-06-23 | GSE151985 | GEO
Project description:Mouse intestinal innate immune cells have been identified as inducing Th17 cell differentiation. However, few studies have investigated innate immune cells that are involved in CD (Crohn's disiease) pathogenesis in humans. The present study aimed to identify a human intestinal lamina propria cell subset that induces Th17 cells, and to clarify its role in CD pathogenesis. Intestinal mucosa samples were obtained from patients who underwent resection of colorectal cancer or CD. Lamina propria cells (LPCs) were obtained by enzymatic digestion, and were analyzed for expression of HLA-DR, lineage markers (Lin), CD14, and CD163 using flow cytometry. Among HLA-DRhigh Lin- cells, we identified a CD14+ CD163low cell subset that was selectively present in intestinal LPCs. We identified CD14+ CD163low cells as having a potent capacity to induce Th17 cell differentiation in human intestinal lamina propria. The Th17-inducing activity of these cells was enhanced in CD patients.
2013-08-24 | GSE49066 | GEO