Project description:We report the use of high-throughput single-cell RNA sequencing (scRNA-seq) to analyze gene expression in wild-type and mutant Arabidopsis root cells. We demonstrate that using a commercially available platform for droplet-based scRNA-seq (10X Genomics Chromium) enables transcriptional profiling of individual protoplasts representing all of the major cell/tissue types of the root. Furthermore, rare cell types and subtypes have been identified. These single-cell transcriptomes were also used to generate a pseudotime series for the root hair and non-hair cell differentiation pathways. In addition, scRNA-seq was used to define and compare transcriptomes from root epidermis mutants, which enabled a detailed molecular analysis of the mutant phenotype. This study demonstrates the feasibility and usefulness of scRNA-seq in plants and provides a gene expression map at single-cell resolution for the Arabidopsis root.
Project description:We report the application of Illumina sequencing for high-throughput profiling of miRNA in citrus root responded to long-term boron toxicity. We find miR319 is involved in citrus adapation to long-term boron toxicity via targeting a MYB gene, Ciclev10000756m.g.v1.0, which is homologus with several MYBs that modulate lateral root development in Arabidopsis.
Project description:Purpose: The goal of this study is to compare NGS-derived Arabidopsis thaliana transcriptome profiling (RNA-Seq) obtained from tissues infected with a variety of Pseudomonas syryingae effector mutants to better understand their impact on their host's transcriptional program. We report the application of RNA-sequencing technology (Illumina Hi-Seq) for high-throughput profiling Arabidopsis thaliana transcriptomes upon infection with the model pathogen Pseudomonas syringae (wild-type and mutants).
Project description:Cytosine methylation is an important mechanism for dynamical regulation of gene expression and transposon mobility during plant developmental processes. Recently, the variation of DNA methylation has been described between wild type and DNA methylation-related mutants in Arabidopsis thaliana. However, the elaborate representation of soybean DNA methylomes remains lacking. Here, we described the epigenome maps of soybean root, stem, leaf, and cotyledon of developing seed at a single-base resolution. We confirmed the transcription start sites of genes using high-throughput sequencing and reported the DNA methylation patterns in gene and transposon regions. The correlation between gene expression and DNA methylation was revealed through transcriptome sequencing. We found CHH methylation may function in promotion of gene expression and ten cotyledon-preferred genes were identified CHH hypermethylated in cotyledon. Small RNA library sequencing showed that DNA methylation was enhanced by small RNAs not by strand-specific way, and the variation of DNA methylation between the organs was highly related with expression of small RNAs. small RNA profiling of roots, stems, leaves, and cotyledons of developing seeds
Project description:Comparison of the endogenous small RNA content of Arabidopsis flower bud tissue: wild type vs. mutants in polIV pathways Keywords: High throughput 454 small RNA sequencing.
Project description:Part of a set of highly integrated epigenome maps for Arabidopsis thaliana. Keywords: Illumina high-throughput transcriptome sequencing Transcriptome sequencing of wildtype Arabidopsis plants (Columbia-0), and met1, drm1 drm2 cmt3, and ros1 dml2 dml3 null mutants using the Illumina Genetic Analyzer.
Project description:Part of a set of highly integrated epigenome maps for Arabidopsis thaliana. Keywords: Illumina high-throughput bisulfite sequencing Whole genome shotgun bisulfite sequencing of wildtype Arabidopsis plants (Columbia-0), and met1, drm1 drm2 cmt3, and ros1 dml2 dml3 null mutants using the Illumina Genetic Analyzer.
Project description:Part of a set of highly integrated epigenome maps for Arabidopsis thaliana. Keywords: Illumina high-throughput small RNA sequencing Small RNA sequencing of wildtype Arabidopsis plants (Columbia-0), and met1, drm1 drm2 cmt3, and ros1 dml2 dml3 null mutants using the Illumina Genetic Analyzer.
Project description:Comparison of the endogenous small RNA content of Arabidopsis flower bud tissue: wild type vs. mutants in polIV pathways Keywords: High throughput 454 small RNA sequencing. Size fractionated small RNA from total RNA extracts was ligated to adapters, purified again and reverse transcribed. After PCR amplification the sample was subjected to 454 high throughput pyrosequencing. Please see www.454.com for details of the sequencing technology.
Project description:We used a two-component transgene system to study the RNA-dependent DNA methylation (RdDM) and transcriptional gene silencing (TGS) in Arabidopsis. By profiling the small RNA population in mutants defected in RdDM or RNA polymerase II-transcribed trigger for generating silencing siRNA, we investigated how repetitive loci such as tandem repeats were regulated transcriptionally through the action of RNA polymerase IV. Genome-wide small RNA profiling was done by Illumina TruSeq sample preparation followed by high-throughput sequencing with the Illumina HiSeq 2000 platform. The six samples represent mutants and their corresponding control lines.