Ontology highlight
ABSTRACT:
PROVIDER: PRJNA907318 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22485982_1.fastq.gz | Fastqsanger.gz | |||
| SRR22485982_2.fastq.gz | Fastqsanger.gz |
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Project description:Gene expression cascade in a plant is altered in times of stress. Reprogramming of the expression profiles of genes is required for a robust and specific response. Until now, tomato transcriptomic alteration in response to Alternaria fungal stress were not known. This study presents the profile of genes that are differentially expressed during Alternaria stress in local tomato cultivar (Pusa Ruby). At least 2944 genes expression was varied and pathways that are altered during this compatible interaction have been identified. Supported by DBT, Govt. of India.
2016-05-20 | GSE75923 | GEO
Project description:MicroRNAs are crucial regulator of reprogramming of gene expression cascade during plant-pathogen interaction. We have used tomato (Pusa Ruby) plant and early blight pathogen, Alternaria for the analysis of tomato miRNA expression profiles in a compatible interaction. Illumina next generation sequencing (NGS) technique based whole transcriptome analysis revealed that, (i) about 188 known miRNAs, ranging from 18nt to 24nt expressed in tomato, which belonged to 124 miRNA families and (ii) both conserved and Solanaceae specific miRNAs were differentially expressed. Most of the miRNAs were down-regulated, and around 7 miRNAs were highly differentially regulated (log2FC ≥ ±3). Furthermore, using stringent selection criteria we could detect approximately 74 putative novel miRNAs. GO terms enrichment and KEGG pathway analyses of predicted targets of differentially expressed miRNAs have been performed to identify the pathways that were perturbed during the infection. Supported by DBT, Govt. of India.
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Project description:Purpose: To understand the molecular mechanisms involved in disease development during plant-nematode interactions. Methods: We have taken a comprehensive transcriptomic approach to investigate the expression of both tomato and RKN genes in tomato roots at five infection time points from susceptible plants (PR: Pusa Ruby) and two infection time points from resistant plants (M36: Transgenic MM line), grown under soil conditions. Results: Differentially expressed genes during susceptible (1827 tomato, 462 RKN) and resistance (25 tomato, 160 RKN) interactions were identified and a set of genes were validated by qRT-PCR. Conclusion: Our findings, for the first time, provide insights into the transcriptome dynamics of both tomato and RKN during susceptible and resistance interactions and reveal involvement of a complex network of biosynthetic pathways during disease development.
2017-08-21 | GSE88763 | GEO
Project description:The aim of this study was to identify candidate genes responsible for grain number per panicle between a pair of rice varieties (Pusa 1266 and Pusa Basmati 1) by combining QTL analysis with expression analysis. Microarray analysis of RNA extracted from the panicle primordia showed 2741 differentially expressed genes. The differentially expressed genes were shortened to 18 on the basis of their occurance in the QTL region (responsible for grain number regulation) detected in RIL population derived from Pusa 1266 and Pusa Basmati 1. RNA from the stage '0' panicle primordia of Pusa 1266 and Pusa Basmati 1 were analysed in two different biological replications (A and B) making total four samples
2010-04-28 | E-GEOD-15912 | biostudies-arrayexpress
Project description:miR6024 overexpression may lead to changes in the transcriptome profile of tomato plants. Further changes may be noticed on infecting these plants with the necrotrophic pathogen Alternaria solani. These changes can only be gauged by carrying out a comparative transcriptome analysis with the wild type plants under similar conditions. We have used tomato (Pusa Ruby) for generation of miR6024 overexpressing transgenics. Disease study on these plants were carried out with the necrotrophic fungus A. solani. We carried an RNA-seq analysis using Illumina hiseq sequencing of 5 RNA libraries created from leaf tissues of wild type, OVX6024 transgenics and A. solani infected wild type and OVX6024 plants. The analysis revealed that 334 and 781 genes were significantly regulated in the transgenic plants and the infected transgenic plants respectively, with respect to their suitable wild type controls. GO enrichment analysis and pathway analysis have been carried out as well. This work is supported by grants from DBT and SERB, GoI.
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Project description:H. volcanii Cdc48a, RecJ3/4 and RNase J associate with Ubl-coated beads. A) Strategy to isolate H. volcanii proteins that bind agarose beads charged with monomeric Ubl (vs. BSA) as bait. Cell lysate was from triplicate cultures of H. volcanii NH02-pJAM957. B) Left, Non-reducing SDS-PAGE of H. volcanii proteins that bound BSA- (control, lane 1) vs. Ubl- (lane 2) decorated beads in the presence of ATP. Gels were stained with SYPRO Ruby. Red bar, HMW(250kDa) and LMW(50kDa) (high and low molecular weight) regions of gel excised from lanes 1 and 2 for LC- MS/MS analysis. Right, Proteins identified at > 99.9% probability and < 0.1 % false discovery rate (FDR) in the Ubl (not BSA) samples. Similar trend was observed in independent experiment. ATP was required for this association. Theor. Mr, theoretical molecular mass based on genome sequence. Normalized total spectra of sample minus control is indicated.
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