Rice Lateral Root Inducible System timeseries
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB63327 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR11580820.fastq.gz | Fastqsanger.gz | |||
| ERR11580821.fastq.gz | Fastqsanger.gz | |||
| ERR11580822.fastq.gz | Fastqsanger.gz | |||
| ERR11580823.fastq.gz | Fastqsanger.gz | |||
| ERR11580824.fastq.gz | Fastqsanger.gz |
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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:We sorted for GFP+ cells using the enhancer trap line J2632 with the UAS promoter driving the expression of an inducible (by dexamethasone - Dex) constitutive active version of the ARR1 gene (ARR1ΔDDK). We obtained the transcriptional profile of lateral root cap cells
2019-03-19 | GSE117424 | 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
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:The goal of this experiment was to identify the downstream targets of the GOLVEN6 peptide signaling pathway in Arabidopsis thaliana, specifically during lateral root initiation. Using an estradiol inducible GLV6 overexpression construct in wildtype and rgi1rgi5 double mutant (mutant in receptors for the GLV6 peptide) backgrounds, in combination with gravistimulation induced lateral root formation, the RGI receptor dependent transcriptional effects of GLV6 overexpression were characterized. An estradiol inducible GLV6 overexpression line in a wildtype (iGLV6) and in an rgi1rgi5 double receptor mutant background (rgi1rgi5/iGLV6) were used. 4-day old seedlings of both lines were gravistimulated (vertically grown seedlings were turned counterclockwise by 90°) to induce lateral root initiation in the resulting root bends. 8h after gravistimulation, seedlings of both lines were treated with 2µM of estradiol to induce GLV6 overexpression, or DMSO as a mock treatment. 3h and 6h after treatment, root bends were dissected and collected for RNA-sequencing. This yielded a total of 8 samples per replicate; 3h mock treated iGLV6 (IM3), 3h estradiol treated iGLV6 (IE3), 3h mock treated rgi1rgi5/iGLV6 (RM3), 3h estradiol treated rgi1rgi5/iGLV6 (RE3), 6h mock treated iGLV6 (IM6), 6h estradiol treated iGLV6 (IE6), 6h mock treated rgi1rgi5/iGLV6 (RM6), 6h estradiol treated rgi1rgi5/iGLV6 (RE6). For each sample, 4 replicates were obtained. This setup enabled the comparison of the GLV6 induced transcriptional effects between wildtype and rgi1rgi5 mutants at 2 time points after treatment, in samples that are strongly enriched for lateral root initiation events.
2022-02-13 | E-MTAB-10891 | biostudies-arrayexpress
Project description:In the lateral root repression system described by Babé et al. (2012), the first asymetric divisions of pericycle cells preceding lateral root formation are repressed during water deficit treatments. During an 8-hr long treatment, an 8-mm long root segment is formed where LR formation has been repressed. The experiment was designed to monitor changes in gene expression during early events of LR formation in barley using this LR repression system.
2016-12-31 | GSE67367 | GEO
Project description:To get a genome wide picture of the effects of TOR knockdown during the early phase of lateral root formation, we compared by RNA-seq the transcriptomes of roots 6h after the synchronous induction of lateral formation by auxin treatment (Himanen et al, 2002 - http://dx.doi.org/10.1105/tpc.004960) in the inducible UB10pro>>amiR-TOR background.
2022-03-23 | GSE199202 | 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: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:Protein phosphorylation is instrumental to early signaling events. Studying system-wide phosphorylation in relation to processes under investigation requires a quantitative proteomics approach. In Arabidopsis, auxin application can induce pericycle cell divisions and lateral root formation. Initiation of lateral root formation requires transcriptional reprogramming following auxin-mediated degradation of transcriptional repressors. The immediate early signaling events prior this derepression are virtually uncharacterized. To identify the signal molecules responding to auxin application we used the Lateral Root Inducible System which was previously developed to trigger synchronous division of pericycle cells. To identify and quantify the early signaling events following this induction we combined 15N based metabolic labeling and phospho-enrichment and applied a mass spectrometry based approach. In total, 3068 phosphopeptides were identified from auxin treated root tissue. This experiment represents one of the largest quantitative phosphoprotein dataset on Arabidopsis to date. Key proteins responding to auxin treatment included the MDR and PIN2 auxin carriers, auxin response factor2, suppressor of auxin resistance3 and sorting nexin1 (SNX1). Mutational analysis of Serine16 of SNX1 showed that overexpression of the mutated forms of SNX1led to retarded growth and reduction of lateral root formation due to the reduced outgrowth of the primodium, showing proof of principle for our approach. Data Processing: All MS/MS spectra were centroided and merged to a single peak list file using MaxQuant (version 1.0.13.13), which was searched using the Mascot search engine (version 2.2.0, Matrix Science) containing a total 67344 entries (which includes contaminants and an equivalent number of decoy sequences) generated from the publicly available Arabidopsis database (The Arabidopsis Information Resource (TAIR9); June 2009; file name, TAIR9_pep_20090619) with carbamidomethylcysteine as a fixed modification. Oxidized methionine and phosphorylation (serine, threonine, and tyrosine) were searched as variable modifications. Searches were done with tryptic specificity allowing two miscleavages and an initial tolerance on mass measurement of 50 ppm in MS mode and 0.6 Da for MS/MS ions and score cutoff of 20. The resulting .dat files were exported and filtered for a <1% false discovery rate (FDR) at the peptide level using in-house developed software Rockerbox (Version1.1.0) (35). Relative quantification ratios of the identified phosphopeptides and protein were derived by MSQuant (MSQ2.0b4, 2010-02-25) (36). Proteins were quantified with at least two unique non phosphopeptides or single peptide with a score no less than 60. The phospho peptide ratio was normalized by dividing the ratio of its protein of origin. To determine whether phosphorylation ratios for normalized peptides were significantly different a p-value was generated using significance B which is part of the MaxQuant package. The changes were considered significant at a p-value of 0.05 or less. For comparison at the phosphopeptide level the most recent the full dataset with experimental sites was downloaded from PhosPhAt 4.0. Phosphopeptides with ambiguous residues denoted as (s), (t), etc., were converted to S and T, respectively. In addition we used Supplementary Table S1 from Lan et al., (2012) for phosphopeptide comparison. Modifications other than nonambiguous phosphorylation were ignored resulting in a reduction from the original 879 phosphopeptides to 556 peptides. We used pep2pro 'TAIR10 wos' dataset for comparison at the protein level.
2014-02-25 | PXD000177 | Pride