Project description:We used single cell RNA sequencing (scRNA-seq) to analyze the response to jasmonate treatment in root tips at the single cell level.
Project description:The transcriptional response of Arabidopsis thaliana cell suspensions following treatment with the stress hormone methyl jasmonate (MeJA) was monitored over time 16 hours after subcultivation. Three time points were included: 30 minutes, 2 hours and 6 hours after elicitation with 50µm MeJA or DMSO as a control.
Project description:To study genes specially expressed in root tip, leaf tip, shoot tip, root (without root tip) and leaf (without leaf tip) of Ceratopteris richardii, we carried out an RNA-seq to analyze gene expression levels from these five tissues.
Project description:As part of the CAGE consortium, Col-4 plants (1.04, 1.08, 1.12 or 5.10 stage) were exposed to a methyl jasmonate stimulus (or to the ethanol as a control) and leaves 1 and 2 were harvested. Hybridizations were performed using the oligo reference labeled with Cy3. The stress samples can be analyzed together with the basal/normal genomic expression patterns for Col-4 wildtype plants collectively produced by CAGE members.
Project description:The transcriptomic changes induced in the human liver cell line HepG2 by 100µM menadione, 200µM TBH or 50µM H2O2 after treatment for 0.5, 1, 2, 4, 6, 8 and 24h.
Project description:Arabidopsis plants transfer information from the leaf tip to the petiole base to induce adaptive upward leaf movement upon neighbour detection through Far-Red light enrichment in the leaf tip. To determine how a distally derived signal can specifically regulate growth in the abaxial petiole we analysed the transcriptome in the leaf tip and abaxial-adaxially split petiole sections during the first hours of far-red enrichment.
Project description:In Arabidopsis, jasmonate is required for stamen and pollen maturation. Mutants deficient in jasmonate synthesis, such as opr3, are male-sterile but become fertile when jasmonate is applied to developing flower buds. We have used ATH1 oligonucleotide arrays to follow gene expression in opr3 stamens for 22 hours following jasmonate treatment. In these experiments, a total of 821 genes were specifically induced by jasmonate and 480 repressed. Comparisons with data from previous studies indicate that these genes constitute a stamen-specific jasmonate transcriptome, with a large proportion (70%) of the genes expressed in the sporophytic tissue but not in the pollen. Bioinformatics tools allowed us to associate many of the induced genes with metabolic pathways that are likely up-regulated during jasmonate-induced maturation. Our pathway analysis led to the identification of specific genes within larger families of homologues that apparently encode stamen-specific isozymes. Extensive additional analysis of our dataset identified 13 transcription factors that may be key regulators of the stamen maturation processes triggered by jasmonate. Two of these transcription factors, MYB21 and MYB24, are the only members of subgroup 19 of the R2R3 family of MYB proteins. A myb21 mutant obtained by reverse genetics exhibited shorter anther filaments, delayed anther dehiscence and greatly reduced male fertility. A myb24 mutant was phenotypically wild type, but production of a myb21Â myb24 double mutant indicated that introduction of the myb24 mutation exacerbated all three aspects of the myb21 phenotype. Exogenous jasmonate could not restore fertility to myb21 or myb21Â myb24 mutant plants. Together with the data from transcriptional profiling, these results indicate that MYB21 and MYB24 are induced by jasmonate and mediate important aspects of the jasmonate response during stamen development. Experiment Overall Design: Three replicates for opr3 at each time point of 0 hour, 30 minutes, 2 hours, 8 hours and 22 hourss of either JA or OPDA treatment. One replicate of wild-type stamens. <br><br>Note that data files GSM106833.txt and GSM106907.txt as downloaded from GEO are identical.
Project description:Jasmonate and ethylene are two important plant hormones contributing plant resistance to biotic stresses synergistically. Our experimental results showed that two ethylene activated transcription factors (EIN3/EIL1) integrated both jasmonate and ethylene signaling in multiple developmental and defense events. To understand the importance of EIN3/EIL1 in jasmonate signaling, we utilized microarray analysis to identify how much the jasmonate regulated genes are governed by EIN3/EIL1. Our results indicated that EIN3/EIL1 act sequentially in a cascade of transcriptional regulation initiated by jasmonate.
Project description:The development of the vertebrate vascular system is mediated by both genetic patterning of vessels and by angiogenic sprouting in response to hypoxia. Both of these processes depend on the detection of environmental guidance cues by endothelial cells. A specialized subtype of endothelial cell known as the tip cell is believed to be involved in the detection and response to these cues, but the molecular signaling pathways utilized by tip cells to mediate tissue vascularization remain largely uncharacterized. To identify genes critical to tip cell function, we have developed a method to isolate them using laser capture microdissection, permitting comparison of RNA extracted from endothelial tip cells to that of endothelial stalk cells using microarray analysis. Genes enriched in tip cells include ESM-1, Angiopoietin-2, and SLP-76. CXCR4, a receptor for the chemokine SDF-1, was also identified as a tip cell-enriched gene, and we provide evidence for a novel role for this receptor in mediating tip cell morphology and vascular patterning in the neonatal retina.