Zea nicaraguensis
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA267167 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1665103_1.fastq.gz | Fastqsanger.gz | |||
| SRR1665103_2.fastq.gz | Fastqsanger.gz | |||
| SRR1665104_1.fastq.gz | Fastqsanger.gz | |||
| SRR1665104_2.fastq.gz | Fastqsanger.gz | |||
| SRR1665105_1.fastq.gz | Fastqsanger.gz |
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Project description:Zea mays subsp. mays Transcriptome or Gene expression Atlas.
2012-09-13 | E-MTAB-4342 | biostudies-arrayexpress
Project description:RNA-directed DNA methylation (RdDM) in plants is a well-characterized example of RNA interference-related transcriptional gene silencing. To determine the relationships between RdDM and heterochromatin in the repeat-rich maize (Zea mays) genome, we performed whole-genome analyses of several heterochromatic features: dimethylation of lysine 9 and lysine 27 (H3K9me2 and H3K27me2), chromatin accessibility, DNA methylation, and small RNAs; we also analyzed two mutants that affect these processes, mediator of paramutation1 and zea methyltransferase2.
2014-12-05 | E-MTAB-4191 | biostudies-arrayexpress
Project description:The Helicoverpa armigera single-capsid nucleopolyhedrovirus (HaSNPV) can be propagated using H. zea insect cell cultures, for use as a biopesticide against Heliothine agricultural pests.This study sequenced, assembled and functionally annotated 29,586 transcript sequences from cultured H. zea cells using Illumina 100 bps and paired-end transcriptome sequencing (RNA-seq). From these sequences, a genome-scale microarray platform was constructed and validated for effective expression analysis of H. zea genes. This array also included probes for all HaSNPV genes, thereby allowing virus and host gene changes to be monitored simultaneously.
2012-03-01 | GSE34418 | GEO
Project description:Transcriptome of 3 developmental stages of Colletotrichum graminicola during infection of Zea mays leaf sheaths
2012-06-04 | GSE34632 | GEO
Project description:Papain-like cysteine proteases (PLCPs) play important roles in plant defense mechanisms. Previous work identified a set of five apoplastic PLCPs (CP1A, CP1B, CP2, XCP2 and CatB) which are crucial for the orchestration of SA-dependent defense signaling and vice versa in maize (Zea mays). One central question from these findings is which mechanism is triggered by apoplastic PLCPs to induce SA-dependent defenses. By a mass spectrometry approach we discovered a novel peptide (Zip1 = Zea mays immune signaling peptide) to be enriched in apoplastic fluid upon SA treatment. Zip1 induces PR-gene expression when applied to naїve maize leaves. Moreover, it activates apoplastic PLCPs similar as SA does, suggesting Zip1 to play an important role in SA-mediated defense signaling. In vitro studies using recombinant protein showed that CP1A and CP2, but not XCP2 and CatB, release Zip1 from its pro-peptide (PROZIP1) in vitro. Strikingly, metabolite analysis showed direct induction of SA de novo synthesis by Zip1 in maize leaves. In line with this, RNA sequencing revealed that Zip1-mediated changes in maize gene expression largely resemble SA-induced responses. Consequently, Zip1 increases maize susceptibility to the necrotrophic fungal pathogen Botrytis cinerea. In summary, this study identifies the PLCP-released peptide signal Zip1, which triggers SA signaling in maize.
2019-02-15 | PXD006751 | Pride
Project description:This is a cell culture based study to asses the impact of ZEA (Zearalenone) and E. coli co-contamination on IPEC cells, these is a normal epithelial cell line isolated from a new born piglet. ZEA is a mycotoxin with a negative impact in human health. The microarray is a custom Agilent Technology array slide with the AMAID: 05685.
2016-11-15 | E-MTAB-3885 | biostudies-arrayexpress
Project description:Purpose: The goals of this study are studies the response of annual Zea mays ssp. mexicana L. under cold and drought stress Methods: The seedlings of zea may ssp. mexicana L. were generated by Illumina HiSeq2500 deep-sequencing. In order to generate a global overview of Zea mexicana transcriptome data, 3 of complement DNA (cDNA) libraries were prepared from RNA isolated from root, stem, and leave mixed tissues of Zea Mexicana from Control (24℃), Cold (4℃) and Drought (PEG2000, 20%) treatments and each teatment has two repetitions. The sequence reads that passed quality filters were merged and de novo to generate all transcripts set by Trinity with default parameter, which will be treated as reference genome. The number of paired-reads of each sample were mapped to reference genome by Bowtie software v1.1.1 and the number of mapped reads were calculated by RSEM. qRT-PCR validation was performed using BIO-RAD CFX96 sequence detection system and SYBR Green assays. Results: Using RNA-Seq technology with the Trinity assembled method, we generated a seedling plant transcriptome at a sequencing size of 51.78Gb of Zea mays ssp. mexicana L. from pooled RNA samples which included control (CK), cold (4℃) and drought (PEG2000, 20%) stressed plant samples. A total of 414,232,462 high quality clean reads were used to conduct de novo assembly and annotation of genes without reference genome information. All of these reads were assembled into 251,145 transcripts (N50 = 1,269 bp) and 184,280 unigenes (N50 = 923 bp). A total of 3,504 up-regulated and 1,220 down-regulated genes were detected under cold stress and 532 up-regulated and 82 down-regulated genes were detected under drought stress. A Venn diagram indicated that 208 genes were affected by both cold and drought stresses. 3 cold stress pathways and 5 drought related pathways showed significant KEGG pathways. Functional enrichment analyses identified many common or specific biological processes and gene sets in response to drought and cold stresses. The ABA dependent pathway, trehalose synthetic pathway and CBF6 gene of ICE1-CBF pathway may play important roles in the DEGs co-up-regulated by both stresses of Zea mays ssp. mexicana L. Conclusions: We analyzed transcriptome data and gene expression profile information from seedlings of Zea mays ssp. mexicana L. under cold and drought stresses. Together these data provides the most comprehensive sequence study available for Zea mays ssp. mexicana L. and provides some important functional genes and molecular mechanism information for improving the quality characteristic of maize in the future.
2016-01-19 | GSE76939 | GEO
Project description:We report the application of whole transcriptome sequencing technology for high-throughput profiling of coding and non-coding RNAs associated with Spodoptera frugiperda feeding in Zea mays. 4,366 mRNAs and 233 lncRNAs were differentially expressed during Spodoptera frugiperda feeding in Zea mays. Our data contribute to the understanding of the function of coding and non-coding RNAs in the regulation of plant-insect interactions.
2023-11-21 | GSE247976 | GEO