Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Arabidopsis thaliana strain:Col-0 Transcriptome or Gene expression

ABSTRACT: Arabidopsis thaliana infiltrated with different strains of DC3000 were used to elicit PTI, ETI, or a disease response compared to a mock control. This experiment was carried out in both Col-0 wild-type plants as well as mutants deficient in non-sense mediated decay via disruption of the promoter of upf1 (genotype background upf1-5). To identify differentially expressed and alternatively spliced transcripts elicited by bacterial infection, the NMD-impaired and wild-type host transcriptomes were profiled using RNA-seq. Wild-type and upf1-5 mutant plants were independently challenged with pathogenic (DC3000 COR-) or non-pathogenic P. syringae strains (DC3000 COR- ÎhrpS and DC3000 COR- avrPphB).

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Sergei Filichkin

PROVIDER: E-MTAB-4416 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Environmental stresses modulate abundance and timing of alternatively spliced circadian transcripts in Arabidopsis.

Filichkin Sergei A SA Cumbie Jason S JS Dharmawardhana Palitha P Jaiswal Pankaj P Chang Jeff H JH Palusa Saiprasad G SG Reddy A S N AS Megraw Molly M Mockler Todd C TC

Molecular plant 20150108 2

Environmental stresses profoundly altered accumulation of nonsense mRNAs including intron-retaining (IR) transcripts in Arabidopsis. Temporal patterns of stress-induced IR mRNAs were dissected using both oscillating and non-oscillating transcripts. Broad-range thermal cycles triggered a sharp increase in the long IR CCA1 isoforms and altered their phasing to different times of day. Both abiotic and biotic stresses such as drought or Pseudomonas syringae infection induced a similar increase. Ther ...[more]

PMID: 25680774

Similar Datasets

Transcriptome sequencing of tomato leaves treated with different Pst DC3000 mutant strains

Project description:We designed an experiment to assess ETI and PTI in RG-PtoR using a series of Pst DC3000 strains which have different mutations that allow dissection of the plant immune response. We collected samples at 6 hai and monitored the development of disease in these plants. Plants infiltrated with DC3000 ΔfliC had no disease symptoms due to the recognition of AvrPto and AvrPtoB effectors by Pto. In contrast, when these two effectors were absent, the plants developed speck disease (DC3000 ΔavrPto ΔavrPtoB and DC3000 ΔavrPto ΔavrPtoB ΔfliC strains). Plants infiltrated with the triple mutant showed the greatest disease severity due to the absence of ETI and flagellin-activated PTI induction. This experimental design allowed us to identify gene expression changes associated with flagellin-activated PTI (DC3000 ΔavrPto ΔavrPtoB versus DC3000 ΔavrPto ΔavrPtoB ΔfliC) and Pto/Prf-mediated ETI (DC3000 ΔfliC versus DC3000 ΔavrPto ΔavrPtoB ΔfliC). NOTE: Samples in SRA were assigned the same sample accession. This is incorrect as there are different samples, hence 'Source Name' was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.

2014-11-04 | E-MTAB-4797 | biostudies-arrayexpress

Solanum lycopersicum Transcriptome or Gene expression

Project description:To characterize the PTI response of tomato and the effect of the delivery of a subset of effectors, we performed an RNA-seq analysis of tomato Rio Grande prf3 leaves challenged with either the flgII-28 peptide or the following bacterial strains: Agrobacterium tumefaciens GV2260, Pseudomonas fluorescens 55, Pseudomonas putida KT2440, Pseudomonas syringae pv. tomato (Pst) DC3000, Pst DC3000 deltahrcQ-U deltafliC and Pst DC3000 deltaavrPto deltaavrPtoB. NOTE: Samples in SRA were assigned the same sample accession. This is incorrect as there are different samples, hence âSource Nameâ was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.

2013-08-21 | E-MTAB-4789 | biostudies-arrayexpress

Transcriptome sequencing of leaves of resistant (RG-PtoR) and susceptible (RG-prf3 and RG-prf19) tomato plants treated with Pst DC3000

Project description:In order to study the transcriptome changes in tomato during Pto/Prf-mediated ETI, we infiltrated tomato Rio Grande (RG)-PtoR resistant plants (plants that have a functional Pto/Prf signaling pathway, Pto/Pto, Prf/Prf) and two different susceptible plants: RG-prf3 and RG-prf19 (Pto/Pto, prf/prf), with Pseudomonas syringae pv. tomato DC3000 (DC3000). The susceptible lines have a non-functional Prf gene due to a 1.1 kb deletion or a G-insertion at position 2,584 (which causes a frameshift), respectively. We collected leaf tissue at 4 and 6 h after inoculation (hai) to assess early changes in host gene expression after translocation of DC3000 effectors AvrPto and AvrPtoB, which occur at about 3 hai. The plants were then maintained in the same conditions to observe signs of disease. As expected, RG-PtoR plants did not develop speck disease whereas the RG-prf plants did. NOTE: Samples in SRA were assigned the same sample accession. This is incorrect as there are different samples, hence Ã¢ÂÂSource NameÃ¢ÂÂ was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.

2014-11-04 | E-MTAB-4796 | biostudies-arrayexpress

Fine kinetic transcriptome analysis during jasmonate signaling

Project description:To study the role of the plant hormone jasmonate in regulating stress-induced allocation of photosynthetic products between growth- and defense-related processes, we used RNA-sequencing to query the Arabidopsis transcriptome at high temporal resolution over 24 h after treatment with the bacterial toxin coronatine (COR, 5 micromolar), a high-affinity agonist of the JA receptor, or with a mock solution to account for diurnal changes in gene expression. These data establish a fine-scale view of the kinetics of jasmonate signaling, as well as of the diurnal patterns of gene expression.

2015-06-01 | E-MTAB-4218 | biostudies-arrayexpress

S mansoni male and female adult worm reproductive organs pre and post pairing

Project description:Study description:This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Schistosomes are blood dwelling digenean trematodes that mature as adults in the intestinal or urinary veins, predominantly of mammals. Adult female Schistosomes produce eggs of which approximately 40% fail to pass into faeces or urine (species-dependent) but are dispersed by the blood stream into different organs where they provoke severe inflammation. This parasitic infection is known as schistosomiasis and considered by the WHO as the second most socioeconomically devastating parasitic disease, next only to malaria, with hundreds of millions infected worldwide. As the eggs represent the causative pathogenic agents, the understanding of egg forming processes, and therefore of the schistosomal reproductive biology in general, is of fundamental interest. Additionally the differences between immature (pre-mating) and mature (post-mating) adult worms are of significant interest; adults only reach maturity upon mating. Trasncriptomic sequencing of gonad-specific cellular material will help to unravel signal transduction cascades involved in e.g. gametogenesis and/or vitellogenesis. This project aims to characterize the transcriptome profiles of immature and mature adult ovaries and adult testes.

2016-07-05 | E-ERAD-516 | biostudies-arrayexpress

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.

Project description:The hemibiotrophic fungus Zymoseptoria tritici causes Septoria tritici blotch disease of wheat (Triticum aestivum). Pathogen reproduction on wheat occurs without cell penetration, suggesting that dynamic and intimate intercellular communication occurs between fungus and plant throughout the disease cycle. We used deep RNA sequencing and metabolomics to investigate the physiology of plant and pathogen throughout an asexual reproductive cycle of Z. tritici on wheat leaves. Over 3,000 pathogen genes, more than 7,000 wheat genes, and more than 300 metabolites were differentially regulated. Intriguingly, individual fungal chromosomes contributed unequally to the overall gene expression changes. Early transcriptional down-regulation of putative host defense genes was detected in inoculated leaves. There was little evidence for fungal nutrient acquisition from the plant throughout symptomless colonization by Z. tritici, which may instead be utilizing lipid and fatty acid stores for growth. However, the fungus then subsequently manipulated specific plant carbohydrates, including fructan metabolites, during the switch to necrotrophic growth and reproduction. This switch coincided with increased expression of jasmonic acid biosynthesis genes and large-scale activation of other plant defense responses. Fungal genes encoding putative secondary metabolite clusters and secreted effector proteins were identified with distinct infection phase-specific expression patterns, although functional analysis suggested that many have overlapping/redundant functions in virulence. The pathogenic lifestyle of Z. tritici on wheat revealed through this study, involving initial defense suppression by a slow-growing extracellular and nutritionally limited pathogen followed by defense (hyper) activation during reproduction, reveals a subtle modification of the conceptual definition of hemibiotrophic plant infection.

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

Oryza sativa strain:Nipponbare Transcriptome or Gene expression

Project description: Not available

2014-11-04 | E-MTAB-4123 | biostudies-arrayexpress

Populus trichocarpa Transcriptome or Gene expression

Project description:Our analysis provides a comprehensive picture of how P. trichocarpa responds to drought stress at physiological and transcriptome levels which may help to understand molecular mechanisms associated with drought response and could be useful for genetic engineering of woody plants. Drought stress treatment was performed dividing P. trichocarpa plants into the well-watered (WW) group (soil volumetric water content of 40â45 %) and the water-limited group (soil volumetric water content of 10â15 %). Two cDNA libraries constructed separately from the WW and WL groups were subjected to high-throughput Illumina sequencing.

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

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data