Oplopanax elatus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1009977 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25775188_1.fastq.gz | Fastqsanger.gz | |||
| SRR25775188_2.fastq.gz | Fastqsanger.gz | |||
| SRR25775189_1.fastq.gz | Fastqsanger.gz | |||
| SRR25775189_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 4 of 4 |
Similar Datasets
Project description:Transcriptome analysis of root development related genes in terrestrial and hydroponic ramie. Ramie seedlings were cultivated in soil, and in hydroponic with the shoot-cutting propagation method. The root samples from hydrophonic ramie were collected from the early stage (5-day-old seedling) and the late stage (30-day-old seedling) of acquatic roots induction. The roots of ramie seedling cultivated in soil were also collected for comparative analysis. Our study represents the detailed analysis of ramie root transcriptomes with biologic replicates.
2017-09-15 | GSE98903 | GEO
Project description:Purpose: The goals of this study are to identify the downstream regulated genes of ARR1. Methods: RNA was extracted from wild-type, arr1 single mutant, and AOE root explants at the nascent SAM formation stage. Library construction and RNA-Seq were performed by Biomarker Co. (www.biomarker.com.cn, Beijing, China). DESeq and the Q value were used to identify differentially transcribed genes (DTGs). Differential transcription was inferred by applying a false discovery rate threshold of 0.001 and the |log2 Ratio| ≥ 1. Functional categorization was inferred from a BLAST search of the non-redundant GenBank (http://www.ncbi.nlm.nih.gov/genbank/), KEGG Pathway (http://www.genome.jp/kegg/pathway.html), and UniProt protein databases (http://www.uniprot.org/), and was further analyzed by the Gene Ontology (http://geneontology.org/) method. Results: In the transcriptomes of arr1 vs. wild-type explants, we detected 177 up- and 260 downregulated DTGs, and in the AOE vs. wild-type transcriptomes, we detected 129 and 6 DTGs, respectively. The pathways involved in hormone signal transduction and indole alkaloid synthesis were well represented among the DTGs in arr1 vs. wild type. These DTGs also included genes involved in auxin transport and signaling, as well as IAA17, an Aux/IAA repressor gene, which was downregulated in arr1 root explants. Conclusions: Our study showed that IAA17 was downstream gene of ARR1 in root explants.
2020-03-10 | GSE146690 | GEO
Project description:We study the effect of nitrogen limitation on the growth and development of poplar roots. We used microarrays to detail the global program of gene expression underlying morphological and developmental changes driven by low nitrogen in the growth media. We report the effect of nitrogen limitation on the growth and development of poplar roots. Low nitrogen concentration led to increased root elongation followed by lateral root proliferation and finally increased root biomass. These morphological responses correlated with high and specific activation of genes encoding regulators of cell cycle and enzymes involved in cell wall biogenesis, growth and remodeling. Comparative analysis of poplar and Arabidopsis root transcriptomes under nitrogen deficiency indicated many similarities and diversification in the response in the two species. A reconstruction of genetic regulatory network (GRN) analysis revealed a sub-network centered on a PtaNAC1-like transcription factor. Consistent with the GRN predictions, root-specific upregulation of PtaNAC1 in transgenic poplar plants increased root biomass and led to significant changes in the expression of the connected genes specifically under low nitrogen. PtaNAC1 and its regulatory miR164 showed inverse expression profiles during response to LN, suggesting of a micro RNA mediated attenuation of PtaNAC1 transcript abundance in response to nitrogen deprivation. Poplar roots from low nitrogen treated and untreated from in vitro condition was selected for RNA extraction and hybridization on Affymetrix microarrays. Roots were sampled at 6, 12, 24, 48, 96 and 504h after transfer to control and low nitrogen media and RNA was extacted.
2013-07-17 | E-GEOD-43162 | biostudies-arrayexpress
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:De novo shoot organogenesis (DNSO) is a commonly used pathway for plant biotechnology, and is a hormonally regulated process, where auxin and cytokinin coordinates suites of genes encoding transcription factors, general transcription factors, and RNA metabolism machinery genes. Here we report that silencing Arabidopsis thaliana CTD phosphatase-like 4 (CPL4RNAi), which increases phosphorylation level of RNA polymerase II (pol II) CTD, altered lateral root development and DNSO efficiency of the host plants, suggesting an importance of precise control of pol II activities during DNSO. Under standard condition, roots of CPL4RNAi lines produced no or few lateral roots. When induced by high concentration of auxin, CPL4RNAi lines failed to produce focused auxin maxima at the meristem of lateral root primordia, and produced fasciated lateral roots. By contrast, root explants of CPL4RNAi lines were highly competent for DNSO. Efficient DNSO of CPL4RNAi lines were observed even under 10 times less cytokinin required for wild type explants. Transcriptome analysis showed CPL4RNAi but not wild type explants expressed high levels of shoot meristem related genes during priming by high auxin/cytokinin ratio, and subsequent shoot induction with cytokinin. These results indicate that CPL4 functions as a repressor of the early stage of DNSO, during acquisition of competency by high auxin/cytokinin ratio, perhaps via regulation of pol II activities.
2020-09-19 | GSE104083 | GEO
Project description:The Medicago truncatula line 2HA has a 500-fold greater capacity to regenerate plants in culture by somatic embryogenesis than wild-type Jemalong. We have compared transcriptomes of tissue cultures from leaf explants of these two lines. We have used the Affymetrix Medicago Genome Array GeneChip to compare leaf explants of Medicago truncatula Jemalong and the superembryogenic line 2HA after two weeks of tissue culture on 10 µM 1-naphthaleneacetic acid (NAA) and 4 µM 6-benzylaminopurine (BAP) (P4 10:4) Experiment Overall Design: Leaf explants from the two genotypes were treated with 10:4 for two weeks; total RNA was extracted and used for hybridization to Affymetrix arrays
2008-06-16 | E-GEOD-8131 | biostudies-arrayexpress
Project description:The Medicago truncatula line 2HA has a 500-fold greater capacity to regenerate plants in culture by somatic embryogenesis than wild-type Jemalong. We have compared transcriptomes of tissue cultures from leaf explants of these two lines. We have used the Affymetrix Medicago Genome Array GeneChip to compare leaf explants of Medicago truncatula Jemalong and the superembryogenic line 2HA after two weeks of tissue culture on 10 µM 1-naphthaleneacetic acid (NAA) and 4 µM 6-benzylaminopurine (BAP) (P4 10:4) Keywords: Genotype comparison
2007-09-01 | GSE8131 | GEO
Project description:We define genome-wide temporal expression patterns of root development genes in seven vascular plants, enabling a detailed comparative analysis of the molecular development of a single organ across diverse species.
2015-08-24 | GSE64665 | GEO
Project description:We study the effect of nitrogen limitation on the growth and development of poplar roots. We used microarrays to detail the global program of gene expression underlying morphological and developmental changes driven by low nitrogen in the growth media. We report the effect of nitrogen limitation on the growth and development of poplar roots. Low nitrogen concentration led to increased root elongation followed by lateral root proliferation and finally increased root biomass. These morphological responses correlated with high and specific activation of genes encoding regulators of cell cycle and enzymes involved in cell wall biogenesis, growth and remodeling. Comparative analysis of poplar and Arabidopsis root transcriptomes under nitrogen deficiency indicated many similarities and diversification in the response in the two species. A reconstruction of genetic regulatory network (GRN) analysis revealed a sub-network centered on a PtaNAC1-like transcription factor. Consistent with the GRN predictions, root-specific upregulation of PtaNAC1 in transgenic poplar plants increased root biomass and led to significant changes in the expression of the connected genes specifically under low nitrogen. PtaNAC1 and its regulatory miR164 showed inverse expression profiles during response to LN, suggesting of a micro RNA mediated attenuation of PtaNAC1 transcript abundance in response to nitrogen deprivation.
2013-07-17 | GSE43162 | GEO
Project description:Unlike most animal cells, plant cells can easily regenerate new tissues from a wide variety of organs when properly cultured. The common elements that provide varied plant cells with their remarkable regeneration ability are still largely unknown. Here we describe the initial process of Arabidopsis in vitro regeneration, where a pluripotent cell mass termed callus is induced. We demonstrate that callus resembles the tip of a root meristem, even if it is derived from aerial organs such as petals, which clearly shows that callus formation is not a simple reprogramming process backwards to an undifferentiated state as widely believed. Furthermore, callus formation in roots, cotyledons and petals is blocked in mutant plants incapable of lateral root initiation. It thus appears that the ectopic activation of a lateral root development program is a common mechanism in callus formation from multiple organs. Four sets of biologically independent tissue samples were collect for root, cotyledon and petal explants just after being excised from plants (d0) or after ten days on callus-inducing medium (CIM, d10). Samples derived from the same organ were co-hybridized in the array experiments. Dyes used for labeling the RNA populations derived from the individual samples were switched in the replicate experiments to reduce dye-related artefacts.
2010-01-31 | E-GEOD-19863 | biostudies-arrayexpress