Single cell RNA sequencing of maize root
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA759548 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The root system is fundamental for maize growth and yield. The primary root system is the most important structure of maize seedlings and is the first organ that emerges at germination, providing water and nutrients for the growing seedlings. However, it is difficult to characterize them at single cell level, due to their complex and heterogeneous cell types. In this study, we profiled the transcriptomes of more than 7000 cells derived from maize root tips of seedlings grown on media with (nitrate+) or without nitrate (nitrate-).
2021-09-03 | GSE183171 | GEO
Project description:We investigated root hair-specific transcriptome using RNA-seq in maize. ZmLRL5 was further identified as a key regulator of maize root hair elongation.
2019-02-02 | GSE123164 | GEO
Project description:We report the use of high-throughput single-cell RNA sequencing (scRNA-seq) to analyze gene expression in Mesophyll cells from Maize. We using the 10x genomics platform to generate several millions of RNA-seq reads and enable transcriptional profiling of all genes of maize in a single-cell resolution. Tsne methods was used to perform dimension reduction analysis to visualize cells in a two-dimension axis.
2021-10-07 | GSE138526 | GEO
Project description:Root exudates play an important role in plant-microbe interaction. The transcriptional profilings of plant growth-promoting rhizobacteria Bacillus amyloliquefaciens SQR9 in response to maize root exudates under static condition, were investigated by an Illumina RNA-seq for understanding the regulatory roles of the root exudates.
2014-11-01 | GSE54987 | GEO
Project description:Low phosphate concentrations are frequently a constraint for maize growth and development, and therefore, enormous quantities of phosphate fertilizer are expended in maize cultivation, which increases the cost of planting. Low phosphate stress not only increases root biomass but can also cause significant changes in root morphology. Low phosphate availability has been found to favor lateral root growth over primary root growth by dramatically reducing primary root length and increasing lateral root elongation and lateral root density in Arabdopsis. While in our assay when inbred line Q319 subjected to phosphate starvation, The numbers of lateral roots and lateral root primordia were decreased after 6 days of culture in a low phosphate solution (LP) compared to plants grown under normal conditions (sufficient phosphate, SP), and these differences were increased associated with the stress caused by phosphate starvation. However, the growth of primary roots appeared not to be sensitive to low phosphate levels. This is very different to Arabidopsis. To elucidate how low phosphate levels regulate root modifications, especially lateral root development, a transcriptomic analysis of the 1.0-1.5 cm lateral root primordium zone (LRZ) of maize Q319 treated after 2 and 8 days by low phosphate was completed respectively. The present work utilized an Arizona Maize Oligonucleotide array 46K version slides, which contained 46,000 maize 70-mer oligonucleotides designated by TIGR ID, and the sequence information is available at the website of the Maize Oligonucleotide Array Project as the search item representing the >30,000 identifiable unique maize genes (details at http://www.maizearray.org). Keywords: low phosphate, Lateral Root Primordium Zone, maize
2012-03-09 | GSE36368 | GEO
Project description:Root exudates contain specialised metabolites that affect the plant’s root microbiome. How host-specific microbes cope with these bioactive compounds, and how this ability shapes root microbiomes, remains largely unknown. We investigated how maize root bacteria metabolise benzoxazinoids, the main specialised metabolites of maize. Diverse and abundant bacteria metabolised the major compound in the maize rhizosphere MBOA and formed AMPO. AMPO forming bacteria are enriched in the rhizosphere of benzoxazinoid-producing maize and can use MBOA as carbon source. We identified a novel gene cluster associated with AMPO formation in microbacteria. The first gene in this cluster, bxdA encodes a lactonase that converts MBOA to AMPO in vitro. A deletion mutant of the homologous bxdA genes in the genus Sphingobium, does not form AMPO nor is it able to use MBOA as a carbon source. BxdA was identified in different genera of maize root bacteria. Here we show that plant-specialised metabolites select for metabolisation-competent root bacteria. BxdA represents a novel benzoxazinoid metabolisation gene whose carriers successfully colonize the maize rhizosphere and thereby shape the plant’s chemical environmental footprint
2024-04-05 | GSE263275 | GEO
Project description:Dark-grown maize seedlings with primary roots 12-20 mm in length were transplanted to high (-0.03 MPa) water potential vermiculite. About 1,000 roots were collected. Each root was divided into 4 segments (distances are from the junction of the root apex and root cap): segment 1, 0-3 mm plus the root cap; segment 2, 3-7 mm; segment 3, 7-12 mm; segment 4, 12-20 mm. Details of the conditions and nutrient modifications have been described before (Sharp et al., 1988; Spollen et al, 2000). From each segment, 250 mg of material was used and RNA was isolated form the combined sample containing all four segments. RNA was isolated using the RNeasy Maxi Kit (Qiagen). RNA integrity was verified by denaturing agarose gel electorphoresis and spectrophotometry.
2010-12-01 | GSE25761 | GEO
Project description:Root exudates play an important role in plant-microbe interaction. The transcriptional profilings of plant growth-promoting rhizobacteria Bacillus amyloliquefaciens SQR9 in response to maize root exudates under static condition, were investigated by an Illumina RNA-seq for understanding the regulatory roles of the root exudates. 4 treatments, including 2 blank control (24 h and 48 h-post inoculation, named as 5 and 15, respectively), and 2 treatments with maize root exudates (24 h and 48 h-post inoculation, named as 7 and 17, respectively)
2014-11-01 | E-GEOD-54987 | biostudies-arrayexpress
Project description:We report raw bulk RNA sequencing data of rice root sections from Meristem, Elongation and Maturation zones. For each section, we include 6 biological replicates. We also include the whole-root samples that include all developmental zones. The genes with enriched expression in certain developmental zones were used as developmental stage markers for our following single-cell RNA sequencing annotation.
2024-07-01 | E-MTAB-13889 | biostudies-arrayexpress
Project description:Low phosphate concentrations are frequently a constraint for maize growth and development, and therefore, enormous quantities of phosphate fertilizer are expended in maize cultivation, which increases the cost of planting. Low phosphate stress not only increases root biomass but can also cause significant changes in root morphology. Low phosphate availability has been found to favor lateral root growth over primary root growth by dramatically reducing primary root length and increasing lateral root elongation and lateral root density in Arabdopsis. While in our assay when inbred line Q319 subjected to phosphate starvation, The numbers of lateral roots and lateral root primordia were decreased after 6 days of culture in a low phosphate solution (LP) compared to plants grown under normal conditions (sufficient phosphate, SP), and these differences were increased associated with the stress caused by phosphate starvation. However, the growth of primary roots appeared not to be sensitive to low phosphate levels. This is very different to Arabidopsis. To elucidate how low phosphate levels regulate root modifications, especially lateral root development, a transcriptomic analysis of the 1.0-1.5 cm lateral root primordium zone (LRZ) of maize Q319 treated after 2 and 8 days by low phosphate was completed respectively. The present work utilized an Arizona Maize Oligonucleotide array 46K version slides, which contained 46,000 maize 70-mer oligonucleotides designated by TIGR ID, and the sequence information is available at the website of the Maize Oligonucleotide Array Project as the search item representing the >30,000 identifiable unique maize genes (details at http://www.maizearray.org). Keywords: low phosphate, Lateral Root Primordium Zone, maize Two-condition experiment, low phosphate treated lateral root primordium zone of maize root vs. normal cultrued lateral root primordium zone. Biological replicates: 9 control, 9 treated, independently grown and harvested. One replicate per array.
2012-03-09 | E-GEOD-36368 | biostudies-arrayexpress