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 periderm, forming during secondary growth in the Arabidopsis root, serves as a protective outer barrier in many seed plant species. This multi-layered tissue is comprised of three distinct cell types: the phellogen, phellem and phelloderm. Periderm development has become a trait of interest to increase plant resilience and plant-mediated CO2 sequestration in soils. However, the genes underlying periderm development remain largely unknown. Employing single-nuclei sequencing, we have generated an expression atlas capturing the transcriptional landscape of the Arabidopsis root periderm. Using transcriptional reporter lines, we show that these data can be used to accurately track the progression of the three distinct periderm cell layers across multiple, transcriptionally unique, developmental stages. Making use of these data, we identify MYB67 as a novel regulator of periderm development and show that this gene serves as a developmental switch for the onset of phellem cell maturation. Our periderm expression atlas represents a rich resource that can be used to fuel novel discoveries and engineering efforts in this fascinating and important tissue.
2024-12-05 | GSE261441 | GEO
Project description:The periderm, forming during secondary growth in the Arabidopsis root, serves as a protective outer barrier in many seed plant species. This multi-layered tissue is comprised of three distinct cell types: the phellogen, phellem and phelloderm. Periderm development has become a trait of interest to increase plant resilience and plant-mediated CO2 sequestration in soils. However, the genes underlying periderm development remain largely unknown. Employing single-nuclei sequencing, we have generated an expression atlas capturing the transcriptional landscape of the Arabidopsis root periderm. Using transcriptional reporter lines, we show that these data can be used to accurately track the progression of the three distinct periderm cell layers across multiple, transcriptionally unique, developmental stages. Making use of these data, we identify MYB67 as a novel regulator of periderm development and show that this gene serves as a developmental switch for the onset of phellem cell maturation. Our periderm expression atlas represents a rich resource that can be used to fuel novel discoveries and engineering efforts in this fascinating and important tissue.
2024-12-05 | GSE261431 | GEO
Project description:Here we explore the feasibility of single-cell proteomics on plant samples. We focus on Arabidopsis thaliana, examining isolated single cells from the cortex and endodermis, which are two adjacent root cell-types derived from a common stem cell.
2024-04-17 | MSV000094558 | MassIVE
Project description:The periderm, forming during secondary growth in the Arabidopsis root, serves as a protective outer barrier in many seed plant species. This multi-layered tissue is comprised of three distinct cell types: the phellogen, phellem and phelloderm. Periderm development has become a trait of interest to increase plant resilience and plant-mediated CO2 sequestration in soils. However, the genes underlying periderm development remain largely unknown. Employing single-nuclei sequencing, we have generated an expression atlas capturing the transcriptional landscape of the Arabidopsis root periderm. Using transcriptional reporter lines, we show that these data can be used to accurately track the progression of the three distinct periderm cell layers across multiple, transcriptionally unique, developmental stages. Making use of these data, we identify MYB67 as a novel regulator of periderm development and show that this gene serves as a developmental switch for the onset of phellem cell maturation. Our periderm expression atlas represents a rich resource that can be used to fuel novel discoveries and engineering efforts in this fascinating and important tissue.
2024-12-05 | GSE261437 | GEO