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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptome response of maize (B73) shoot-borne root stele to local high nitrate stimulation

ABSTRACT: In this study RNA-sequencing was used to monitor gene expression changes in stele tissue of maize (Zea mays L.) shoot-borne roots in response to local high nitrate stimulation to gain a better understanding of the mechanisms underlying nitrate signal and lateral root development.M

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Zea mays

SUBMITTER: Chunjian Li

PROVIDER: E-MTAB-4253 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Cell Type-Specific Gene Expression Analyses by RNA Sequencing Reveal Local High Nitrate-Triggered Lateral Root Initiation in Shoot-Borne Roots of Maize by Modulating Auxin-Related Cell Cycle Regulation.

Yu Peng P Eggert Kai K von Wirén Nicolaus N Li Chunjian C Hochholdinger Frank F

Plant physiology 20150721 1

Plants have evolved a unique plasticity of their root system architecture to flexibly exploit heterogeneously distributed mineral elements from soil. Local high concentrations of nitrate trigger lateral root initiation in adult shoot-borne roots of maize (Zea mays) by increasing the frequency of early divisions of phloem pole pericycle cells. Gene expression profiling revealed that, within 12 h of local high nitrate induction, cell cycle activators (cyclin-dependent kinases and cyclin B) were up ...[more]

PMID: 26198256

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Zea mays Transcriptome or Gene expression

Project description:In this study RNA-sequencing was used to monitor gene expression changes in four tissues (meristematic zone, elongation zone, and cortex and stele of the mature zone) of maize (Zea mays L.) primary roots in response to water deficit to gain a better understanding of the mechanisms underlying drought tolerance.

2015-10-08 | E-MTAB-4297 | biostudies-arrayexpress

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Project description:The definition of cell identity is a central problem in biology. Single-cell RNA-seq provides a wealth of information regarding the developmental state of individual cells. However, better methods are needed to map the identity of single cells, especially during identity transitions. We have developed a quantitative classification method that is robust to expression noise and can detect primary and chimeric identities from single-cell RNA sequencing profiles. The method uses existing transcriptome repositories of grouped cell-types to define a set of optimal cell-identity markers, which are then used to define a cell identity metric. This metric accurately classified diverse cell identities in Arabidopsis root tips and human glioblastoma cells. We demonstrate the strength of the approach to resolve a dynamic developmental process by analyzing the identity of single cells captured from regenerating Arabidopsis roots following removal of their stem-cell-niche. We discover that, apart from new niche formation at the vicinity of the cut site, cells that are distant from the injury site also undergo a transient, partial collapse of identity during the regeneration and reorganization of the root, demonstrating the usefulness of a quantitative cell identity metric. Overall design: 4 Technical replicates (pooled-and-split single QC cells), 23 cells from the QC, 3 cells from the Stele, and 4 cells from the stele, 16h following root tip decapitation

2015-03-12 | E-MTAB-4125 | biostudies-arrayexpress

TTV018 RORC IBD associated genotype effects on RORgT expression and function in ex vivo T cells

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2016-07-11 | E-ERAD-443 | biostudies-arrayexpress

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Transcriptome and Metabolite Profiling of the Infection Cycle of Zymoseptoria tritici on Wheat Reveals a Biphasic Interaction with Plant Immunity Involving Differential Pathogen Chromosomal Contributions and a Variation on the Hemibiotrophic Lifestyle Definition.

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2015-03-12 | E-MTAB-4116 | biostudies-arrayexpress

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Project description: Not available

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2013-11-20 | E-MTAB-4126 | biostudies-arrayexpress

Genome-wide transcript analysis of early maize leaf development reveals gene cohorts associated with the differentiation of C4 Kranz anatomy

Project description:Photosynthesis underpins the viability of most ecosystems, with C4 plants that exhibit âKranzâ anatomy being the most efficient primary producers. Kranz anatomy is characterized by closely spaced veins that are encircled by two morphologically distinct photosynthetic cell types. Although Kranz anatomy evolved multiple times, the underlying genetic mechanisms remain largely elusive, with only the maize scarecrow gene so far implicated in Kranz patterning. To provide a broader insight into the regulation of Kranz differentiation, we performed a genome-wide comparative analysis of developmental trajectories in Kranz (foliar leaf blade) and non-Kranz (husk leaf sheath) leaves of the C4 plant maize. Using profile classification of gene expression in early leaf primordia, we identified cohorts of genes associated with procambium initiation and vascular patterning. In addition, we used supervised classification criteria inferred from anatomical and developmental analyses of five developmental stages to identify candidate regulators of cell-type specification. Our analysis supports the suggestion that Kranz anatomy is patterned, at least in part, by a SCARECROW/SHORTROOT regulatory network, and suggests likely components of that network. Furthermore, the data imply a role for additional pathways in the development of Kranz leaves.

2013-07-29 | E-MTAB-4134 | biostudies-arrayexpress

Zea mays Transcriptome or Gene expression

Project description:The classical maize mutant lazy1 (la1), displayed prostrate growth with reduced shoot gravitropism. We compared the transcriptome profile of the third node in la1-ref mutants with those in wild-type plants using RNA-SEQ to examine the genome-wide effect of the ZmLA1 gene. We generated 14.6 and 36.5 million paired-end reads from two biological samples of wild-type and la1-ref mutant plants, respectively.

2013-11-20 | E-MTAB-4196 | biostudies-arrayexpress

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