Similar Datasets
Project description:A single cell RNA sequencing atlas of the Arabidopsis root distinguishes cells both by developmental fate and time, revealing defining expression features that depict a complex cascade of developmental progressions from stem cell through differentiation supported by mirroring waves of transcription factor expression. Methods: mRNA profiles of 6-day-old wild-type (WT) and shortroot-knockout Arabidopsis thaliana roots were generated by deep sequencing of single cell (all) and bulk RNA libraries (wild type only), in duplicate (bulk & wild-type single cell) and singlicate (shr-3), using Illumina NextSeq. The sequence reads that passed quality filters were analyzed at the transcript level. Single Cell libraries were processed and analysed using Cell Ranger, STAR, Seurat. Bulk libraries were processed using Trimmomatic, STAR, HTSeq and DEseq2. Results: For Single Cell - Using an optimized data analysis workflow, we mapped ~87k sequence reads per wild-type cell to the Arabidopsis genome (TAIR10) and identified a median of 4,276 genes and 14,758 transcripts per cell. In total, transcripts for 16,975 genes were detected (RPM ≥1) from wild-type cells. After correction for read depth, this represents ~90% of genes detected by bulk RNA-seq of protoplasted root tissue. Bulk RNA-seq data identified genes induced by protplasting of the Arabidopsis root which could be discounted from single cell analysis. The global gene expression profiles of pooled scRNA-seq and bulk RNA-seq are highly correlated (r = 0.9) indicating that plant scRNA-seq is highly sensitive. Conclusions: Our high-resolution single cell RNA sequencing atlas of the Arabidopsis root captures precise temporal information for all major cell types, revealing new regulators and defining features foreach. Developmental trajectories derived from pseudotime analysis depict a finely resolved cascade of developmental progressions between stem cell and final differentiation supported by mirroring waves of transcription factor expression.
2019-03-25 | GSE123818 | GEO
Project description:We report both raw and processed scRNA-seq data profiling brassinosteroid response and related mutants in Arabidopsis roots
2022-09-14 | GSE212230 | GEO
Project description:We report both raw and processed scRNA-seq profiling reveals how root tissues adapt to soil conditions and compaction stress
2024-02-01 | GSE251706 | GEO
Project description:We provide an atlas of gene and protein expression in Arabidopsis root hair cells, generated by paired-end RNA-seq and LC/MS-MS analysis from protoplasts that carry the root hair-specific pEXP7-GFP reporter construct. In total, transcripts from 23,234 genes were detected in root hairs; those related to cell wall biosynthesis and translation differed most dramatically in abundance when compared to non-GFP root protoplasts.
2012-12-04 | E-MTAB-4375 | biostudies-arrayexpress
Project description:Waters Raw data can be downloaded for shoot- and root parts of Arabidopsis thaliana accessions.
2018-11-14 | ST001096 | MetabolomicsWorkbench
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.
2019-02-05 | GSE123013 | GEO
Project description:The root epidermis of Arabidopsis provides a simple and experimentally useful model for studying the molecular basis of cell fate and differentiation. The goal of this study was to define the larger gene regulatory network that governs the differentiation of the root hair and non-hair cell types of the Arabidopsis root epidermis. Transcript levels in the root epidermis of wild-type and mutant lines were assessed by purifying populations of root epidermal cells using fluorescence-based cell-sorting. Further, the role of the plant hormones auxin and ethylene on root epidermis development was assessed by defining transcript levels in the root epidermis of plants grown on media containing IAA or ACC. These microarray results were used to construct a comprehensive gene regulatory network that depicts the transcriptional control of root epidermal cell fate and differentiation in Arabidopsis.
2011-12-01 | GSE30547 | GEO
Project description:In order to identify the possible protein targets of cyanide in the regulation of root hair, we have carried out a single cell proteomic approach to characterize the protein atlas in wild type root hair cells compared to the cas-c1 mutant cells. Root hair specific cells were obtained from isolated protoplast from root tissues of Arabidopsis wt-pCOBL9:GFP and cas-c1-pCOBL9:GFP lines. To analyze the effect of the CAS-C1 mutation, we isolated 1 x 106 root hair cells by Fluorescence-activated cell sorting (FACS) from three independent replicate of wt-pCOBL9:GFP and cas-c1-pCOBL9:GFP roots. The extracted proteins from each sample were trypsin-digested and the digested peptides were analyzed by liquid chromatography-high resolution mass spectrometry (LC-MS/MS) for protein identification. In wild type samples, we have identified 3829 unique proteins at a false discovery rate below 1% (FDR<1%), that represent almost 10% of the total Arabidopsis proteome. In protein extract of the cas-c1-pCOBL9:GFP roots samples, we have identified 3972 proteins of which 3515 were commons in both cell types, 310 were only identified y wild type and 457 only in cas-c1 mutant (Fig. 5).
2024-01-26 | PXD028991 | Pride
Project description:The nuclei of Arabidopsis root seedlings were isolated then use to establish a single cell level resolution transcriptome (sNucRNA-seq) and profile of chromatin accessibility (sNucATAC-seq) applying 10X Genomics technologies.
2021-01-11 | GSE155304 | GEO
Project description:The root epidermis of Arabidopsis provides a simple and experimentally useful model for studying the molecular basis of cell fate and differentiation. The goal of this study was to define the transcript changes in the root epidermis of mutants associated with root epidermis cell specification, including mutants that lack a visible phenotypic alteration (try, egl3, myb23, and ttg2). Transcript levels were assessed by purifying populations of root epidermal cells using fluorescence-based cell-sorting with the WER::GFP transgene. These microarray results were used to compare the effects of single and double mutants on the gene regulatory network that controls root epidermal cell fate and differentiation in Arabidopsis.
2013-11-21 | GSE47632 | GEO