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

Oryza sativa Transcriptome or Gene expression

ABSTRACT: The transcriptomes of resistant BPH15 introgression line and the susceptible recipient line were analyzed using high-throughput RNA sequencing. In total, 2,914 differentially expressed genes (DEGs) were identified. BPH-responsive transcript profiles were distinct between resistant and susceptible plants and between the early stage (6 h after infestation, HAI) and late stage (48 HAI). The key defense mechanism was related to jasmonate signaling, ethylene signaling, receptor kinase, MAPK cascades, Ca2+ signaling, PR genes, transcription factors, and protein post-translational modifications. Note: All samples in SRA were assigned the same sample accession (SRS565690 and SRS565691). 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.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Oryza sativa

SUBMITTER: Wentang Lv

PROVIDER: E-MTAB-4293 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

BAC and RNA sequencing reveal the brown planthopper resistance gene BPH15 in a recombination cold spot that mediates a unique defense mechanism.

Lv Wentang W Du Ba B Shangguan Xinxin X Zhao Yan Y Pan Yufang Y Zhu Lili L He Yuqing Y He Guangcun G

BMC genomics 20140811

<h4>Background</h4>Brown planthopper (BPH, Nilaparvata lugens Stål), is the most destructive phloem-feeding insect pest of rice (Oryza sativa). The BPH-resistance gene BPH15 has been proved to be effective in controlling the pest and widely applied in rice breeding programs. Nevertheless, molecular mechanism of the resistance remain unclear. In this study, we narrowed down the position of BPH15 on chromosome 4 and investigated the transcriptome of BPH15 rice after BPH attacked.<h4>Results</h4>We ...[more]

PMID: 25109872

Similar Datasets

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

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

Oryza sativa strain:CL 161, CL 151 Transcriptome or Gene expression

Project description:Bacterial panicle blight caused by the bacterium Burkholderia glumae is an emerging disease of rice in the United States. Not much is known about this disease, the disease cycle or any source of disease resistance. To understand the interaction between rice and Burkholderia glumae, we used transcriptomics via next-generation sequencing (RNA-Seq) and bioinformatics to identify differentially expressed transcripts between resistant and susceptible interactions and formulate a model for rice resistance to the disease. There was a total of 36 tissue samples that included 2 rice genotypes (CL 151 and CL 161) Ã 2 treatment groups (water control and bacterium inoculated) Ã 3 time points Ã 3 biological replicates. 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.

2012-09-18 | E-MTAB-4406 | biostudies-arrayexpress

Triticum aestivum strain:Wangshuibai Transcriptome or Gene expression

Project description:To get an overview of transcriptome characteristics of Wangshuibai during infection by Fg, a high-throughput RNA sequencing based on next generation sequencing (NGS) technology (Illumina) were performed. Each spike of 4 central spikelets was injected with 10 Î¼l of conidial inoculant (105 macro conidia per milliliter) and covered with a plastic bag to maintain humidity until sampling. Both non-inoculated spikes and inoculated spikes at 12, 24, 48, 72 and 96 hours after inoculation (hai) were sampled. Inoculations and sampling were conducted at 7 a.m. except for the sample at 12 hai at 7 p.m. A total of 12 samples (one treatment, two genotypes and six time points) were prepared for RNA extraction. The samples for transcriptome analysis were the mixture of equal amount of RNA from non-inoculated spikes and spikes at 12, 24 and 48 hai of Wangshuibai. Transcriptome library with fragments between 200 to 700 bp was prepared following the Illuminaâs kits provided by manufacturer and sequenced on Illumina HiSeqâ¢ 2000 using paired-end technology in a single run.

2013-04-25 | E-MTAB-4384 | biostudies-arrayexpress

transcriptome sequencing of tomato

Project description:Gene expression of all tomato genes was determined by replicated (two biological replicates of each tissue) strand-specific Illumina RNA-Seq of root, leaf, flower (2 stages) and fruit (6 stages). 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.

2012-02-15 | E-MTAB-4812 | biostudies-arrayexpress

Populus tricho Raw sequence reads

Project description:We performed RNA-Seq of P. trichocarpa calluses that were firstly induced from roots. Then the total RNAs were isolated from the control and salt-stressed calluses (200 mM NaCl for 6, 12, 24, and 48 h) using a CTAB procedure. Note: All samples in SRA were assigned the same sample accession (SRS938530). 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.

2015-06-01 | E-MTAB-4364 | biostudies-arrayexpress

Solanum lycopersicum strain:M82 Transcriptome or Gene expression

Project description:We sequenced mRNA from immature green (15 days after anthesis) and red (Breaker+10 days) tomato (Solanum lycopersicum) fruit tissues from plants over-expressing SlGLK1 and SlGLK2 and from control plants 'M82' to compare gene expression levels between transgenic fruit and the control. 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.

2013-06-01 | E-MTAB-4819 | biostudies-arrayexpress

Transcript profiling of the biotrophic interaction between Theobroma cacao and the fungal pathogen Moniliophthora perniciosa

Project description:RNA-seq to simultaneously inspect the transcriptomes of cacao and M. perniciosa during their biotrophic interaction. Five biological replicates of each condition (healthy seedlings and seedlings at 30 d after infection) were harvested for transcriptome sequencing using RNA-seq. For this experiment, the entire green broom structure was collected, including cacao leaves and shoots. Samples in SRA were assigned the same sample accession (SRS396688, SRS396689). 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.

2014-02-12 | E-MTAB-5134 | biostudies-arrayexpress

Oryza sativa Japonica strain:EFR-XA21 | cultivar:Kitaake Transcriptome or Gene expression

Project description:We analyzed the transcriptomic profile of EFR:XA21:GFP rice lines treated with elf18 to identify genes differentially regulated during this response. We sequenced cDNA from EFR:XA21:GFP leaves treated with 500 nM elf18 for 0.5, 1, 3, 6, and 12 h. We also included untreated EFR:XA21:GFP and Kitaake as controls. Note: All samples in SRA were assigned the same sample accession (SRS843490). 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.

2015-02-12 | E-MTAB-5170 | 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

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