Project description:To demonstrate our method of controlling for technical noise in single-cell RNA-seq experiments we manually collected single A. thaliana cells marked by the expression of green fluorescent protein (GFP) driven by either the GL2 or WOX5 promoters. Seven and six cells were collected from each cell type, respectively. The GL2 promoter marks the non-hair cells in the root epidermis whereas the WOX5 promoter specifies the quiescent center (QC) of the root. Each cell selected was processed together with 50 pg of total HeLa RNA spike-in to prepare RNA-seq libraries using the Tang protocol. For comparison, we again added the commercially available ERCC spike-ins. We also performed RNA-seq on a set of technical replicates of total A. thaliana RNA using starting amounts ranging from 5000pg down to 10pg, a range that covers the RNA content obtainable from single cells of various sizes.
Project description:WOX5 maintains columella stem cells in the Arabidopsis root and prevents their differentiation. In order to understand the molecular mode of WOX5 action the genes differentially expressed by WOX5 inducible over-expression were determined by analysis of microarray hybridizations. Seedlings transformed with a dexamethasone inducible WOX5 construct were induced for one or four hours with dexamethasone or a mock solution. Other seedlings were treated one hour with cycloheximide ( a protein synthesis inhibitor to reduce secondary transcriptional effects after WOX5 activation) and either dexamethasone or a mock solution. Root tips were harvested, RNA extracted, and the RNA samples prepared for hybridization to Affymetrix microarrays. Potential target genes of WOX5 were further analyzed by transcriptional markers, qPCR and EMSA (electrophoretic mobility shift assay).
Project description:The Arabidopsis quiescent center (QC) is a small group of cells with low mitotic activity located at the center of the root stem cell niche. Its transcriptional profile was previously analyzed using two repeats of cells FACS isolated using the WOX5 marker. To get more power in analyzing QC transcriptional profile, we generated three additional samples of the QC, using the QC-specific marker WOX5.
Project description:The Arabidopsis quiescent center (QC) is a small group of cells with low mitotic activity located at the center of the root stem cell niche. Its transcriptional profile was previously analyzed using two repeats of cells FACS isolated using the AGL42 marker. To get more power in analyzing QC transcriptional profile, we generated three additional samples of the QC, using the QC-specific marker WOX5. Three replicates of FACS-sorted GFP-positive cells from WOX5:GFP roots.
Project description:This study evaluates the effects of exogenous auxin on the Arabidopsis thaliana root proteome at 8, 12, and 24 hours post-treatment.
Project description:Plant roots located in the upper soil layers are prone to experience high temperatures. To gain insight into the effect of high temperature on root development and functioning, we exposed five-day-old Arabidopsis thaliana seedlings grown on agar plates to 30 °C for 48 hours, and compared the gene expression profile in the root tip with that from seedlings that remained at 22 °C.