Transcriptional dissection of lateral root primordium cells
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ABSTRACT:
PROVIDER: PRJNA680241 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13108500.fastq.gz | Fastqsanger.gz | |||
| SRR13108600.fastq.gz | Fastqsanger.gz | |||
| SRR13108700.fastq.gz | Fastqsanger.gz | |||
| SRR13108800.fastq.gz | Fastqsanger.gz | |||
| SRR13108900.fastq.gz | Fastqsanger.gz |
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Project description:To specifically profile early stages of lateral root formation we used the marker pHB53:NLS-3xmCherry, which is only expressed in lateral root primordium cells. We isolated ~2,000 lateral root primordium cells from stages I to IV through Fluorescent Activated Cell Sorting, and profiled the transcriptome of 573 of these cells. As a LR primordium has ~6-10 cells at stage I and ~30-40 cells at stage IV, the number of sequenced cells would approximately cover 5-6 fold the total number of cells in the stages profiled.
2021-08-05 | GSE161970 | 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 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
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:We report the comparison of transcriptomic profiles in specific lateral root tissues for Col-0 wild type and puchi-1 mutant seedlings. Lateral root organogenesis is a key process in plant root system development and adaptation to the environment. To dissect the molecular events occurring during the early phase, we generated time-series transcriptomic datasets profiling lateral root development in puchi-1 and wild type backgrounds. Consistent with a mutually inhibitory mechanism, transcriptomic and reporter analysis revealed meristem-related genes were ectopically expressed during early stages of lateral root primordium formation in puchi-1. We conclude that PUCHI participates to the coordination of lateral root patterning and represses ectopic establishment of meristematic cell identities during early stages of organ development.
2022-03-25 | GSE199142 | GEO
Project description:In Arabidopsis, lateral roots (LRs) originate from pericycle cells located adjacent to vascular tissues, deep within the primary root. Consequently, new LR organs have to emerge through several overlying tissues. Eight stages of LR primordium development have been defined, with stage I representing a single layer of primordium cells generated by the first round of asymmetric divisions and stage VIII defining primordia that have fully emerged through the outer cell layers. To identify novel genes involved in LR development, we generated a transcriptomic time course dataset encompassing each LR developmental stage from pre-initiation to post-emergence.
2015-02-01 | E-MTAB-2565 | biostudies-arrayexpress
Project description:To transcriptionally characterize lateral root development in rice, we subjected the rice LRIS to genome-wide transcript profiling via RNA-sequencing. Taking into account the appearance of the first (stage I primordium) cell divisions starting from 6 hours after NAA treatment, we sampled at 2 hours and at 5 hours after NAA treatment to capture the primary auxin response and the gene expression related to initiation, respectively. Additionally, we sampled at 8 hours, 14 hours and 20 hours, in which the root was highly enriched for stage I, II and III primordia, respectively. As the spatiotemporal assessment of the primordia in the LRIS showed a highly synchronous induction and development of lateral roots in particular in the region just above the root meristem, root sections between 750 µm and 2000 µm from the root tip were microdissected and used for RNA-extraction. To assess possible artefacts induced by the replacement of the medium, we sampled a control before and 2 hours after replacement with NPA containing medium.
2023-08-24 | E-MTAB-13094 | biostudies-arrayexpress
Project description:Previous transcript profiling of the Arabidopsis LRIS only occurred after 2 and 6 hours of NAA treatment (Himanen et al., 2004, Vanneste et al., 2005, De Smet et al., 2008). Here, we extended the time-course of the Arabidopsis LRIS to capture the expression during primordium formation. Therefore, we first characterized lateral root primordium development in the Arabidopsis LRIS, and performed staging in different regions of the root. We observed a slight loss of the synchronization in higher parts of the root. Nevertheless at 1 to 2 mm distance from the root tip, different stages of primordia were highly synchronously induced, and stage I, II and III primordia could be observed at 12, 18 and 24 hours after NAA treatment, respectively. We therefore sampled the 1 to 2 mm region from the root tip at 0, 12, 18 and 24 hours in the Arabidopsis LRIS, to sample stage I, II and III primordia, respectively.
2023-08-24 | E-MTAB-13112 | biostudies-arrayexpress
Project description:The chemical modifications of histones between others process are important to modify the chromatin structure and permit the access to DNA. The ARABIDOPSIS HOMOLOG OF TRITHORAX1 (ATX1/SDG27) is a known regulator of floral development which encodes a histone methyltransferase (H3K4me). ATX1 is directly involved in the H3K4 trimethylation which is associated with maintenance of transcriptionally active chromatin state. To study the ATX1 role in lateral root development, we performed a root phenotypic analysis of atx1setm mutant, and the transcriptome profiling (using RNA-seq approach). The atx1setm mutant express the catalytically inactive form of the ATX1 protein (that maintains its structural integrity) in the atx1-1 (null mutant) background. Here, we showed that the primary root and lateral root (LR) primordium (LRP) development in the atx1setm mutant are abnormal, and the phenotype is stronger compared to the atx1-1 mutant. We identified ATX1-activated genes involved in the LR development like PEROXIDASE35 (PER35), AGAMOUS LIKE14 (AGL14), HOMEOBOX PROTEIN 21 (ATHB21), KIDARI (KDR) and USUALLY MULTIPLE ACIDS MOVE IN AND OUT TRANSPORTERS 20 (UMAMIT20). Here, we studied PEROXIDASE 35 gene whose expression is promoted by ATX1 activity. Interestingly, in the per35 mutant the primary root growth was greater compared to Wt and the LRP morphogenesis was abnormal with a phenotype like that found in atx1setm mutant. The data suggest that PER35 gene is a new player related to lateral root primordium morphogenesis in Arabidopsis thaliana.
2025-06-25 | GSE252067 | GEO
Project description:To identify the mechanism of how the microbiota induces lateral root development independently of auxin signalling, we performed a transcriptional analysis using roots of wild type plants and lateral root mutants arf7 arf19, nph4-1, lbd16-1, and gnom184, in mono-association with a selection of 16 bacteria able to restore the lateral root formation in the mutants used.
2022-10-31 | GSE210742 | GEO
Project description:Lateral root initiation was used as a model system to study the mechanisms behind auxin-induced cell division. Genome-wide transcriptional changes were monitored during the early steps of lateral root initiation. Inclusion of the dominant auxin signaling mutant solitary root1 (slr1) identified genes involved in lateral root initiation that act downstream of the AUX/IAA signaling pathway. Interestingly, key components of the cell cycle machinery were strongly defective in slr1, suggesting a direct link between AUX/IAA signaling and core cell cycle regulation. However, induction of the cell cycle in the mutant background by overexpression of the D-type cyclin (CYCD3;1) was able to trigger complete rounds of cell division in the pericycle that did not result in lateral root formation. Therefore, lateral root initiation can only take place when cell cycle activation is accompanied by cell fate respecification of pericycle cells. The microarray data also yielded evidence for the existence of both negative and positive feedback mechanisms that regulate auxin homeostasis and signal transduction in the pericycle, thereby fine-tuning the process of lateral root initiation. Keywords: time-course wild type vs mutant comparison
2005-11-01 | GSE3350 | GEO