Ontology highlight
ABSTRACT:
PROVIDER: PRJNA706766 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR20729075_1.fastq.gz | Fastqsanger.gz | |||
| SRR20729075_2.fastq.gz | Fastqsanger.gz | |||
| SRR20729076_1.fastq.gz | Fastqsanger.gz | |||
| SRR20729076_2.fastq.gz | Fastqsanger.gz |
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Project description:we performed a comparative proteomics analysis of Korla fragrant pear after inoculation with Alternaria sp., at 0h, 24h, 72h, 120 h using iTRAQ-based quantitative proteomic technique. This study aimed to investigate the protein species expression profiles in response to Alternaria sp., infection, explore the potential molecular mechanisms of Korla fragrant pear response against Alternaria sp., and further obtain a comprehensive understanding of Korla fragrant pear-Alternaria sp interactions. The finding may provide novel clues to Korla fragrant pear resistance to Alternaria sp., and may lay the foundation for an in-depth understanding of the interaction between Korla fragrant pear and Alternaria sp., at the proteome level.
2020-06-04 | PXD019558 |
Project description:Background: Alternaria exposure is associated with severe asthma in humans. Alternaria exposure in mice potently activates group 2 innate lymphoid cells (ILC2s) via the IL-33/ST2 axis and causes ILC2s to robustly secrete type 2 cytokines. Objective: Our aim was to determine whether conventionally used ILC2 markers, ST2 (IL-33R) and CD127 (IL-7Ra), were sufficient to identify all Th2-cytokine producing ILCs after Alternaria exposure. Methods: Mice received intranasal Alternaria for three days prior to analysis. Lung ILCs were identified by flow cytometry as CD45+Lineage−Thy1.2+ lymphocyte-sized cells, divided into four subsets based on ST2 and CD127 expression, and stained for intracellular cytokines and transcription factors. Sort-purified ILC subpopulations were also analyzed by RNA sequencing and qPCR. Results: Alternaria exposure led to accumulation of all ILC populations regardless of ST2 or CD127 expression. Nearly half of the GATA-3+, IL-5+, and IL-13+ ILCs were “unconventional” as they were either single or double negative for ST2/CD127. Further, these populations upregulated CD25, KLRG1, and ICOS after Alternaria challenge. Some activated unconventional IL-5+ ILC2s also produced IFNγ and IL-17A. In addition to shared ILC2 transcripts (Gata3, Il5, Il13) in all populations, RNA-seq further identified novel transcripts enriched in each subset. Finally, transcripts from all populations that correlated best with IL-5 and IL-13 production included Tnfrsf18, Ffar2, and Pde4b. Conclusions: Unconventional ST2- and CD127-negative mouse lung ILC2 populations are induced by Alternaria. Thus, commonly used lung ILC2 identification methods based on ST2 and CD127 do not accurately account for the total ILC2 burden and may exclude nearly half of these cells.
2019-08-22 | GSE136156 | GEO
Project description:Two component sensor-response regulator systems (TCSs) are very common in the genomes of the Streptomyces species that have been fully sequenced to date. It has been suggested that this large number is an evolutionary response to the variable environment that Streptomyces encounter in soil. Notwithstanding this, TCSs are also more common in the sequenced genomes of other Actinomycetales when these are compared to the genomes of most other eubacteria. In this study, we have used DNA/DNA genome microarray analysis to compare fourteen Streptomyces species and one closely related genus to Streptomyces coelicolor in order to identify a core group of such systems. This core group is compared to the syntenous and non-syntenous TCSs present in the genome sequences of other Actinomycetales in order to separate the systems into those present in Actinomycetales in general, the Streptomyces specific systems and the species specific systems. Horizontal transfer does not seem to play a very important role in the evolution of the TCS complement analyzed in this study. However, cognate pairs do not necessarily seem to evolve at the same pace, which may indicate the evolutionary responses to environmental variation may be reflected differently in sequence changes within the two components of the TCSs. The overall analysis allowed subclassification of the orphan TCSs and the TCS cognate pairs and identification of possible targets for further study using gene knockouts, gene overexpression, reporter genes and yeast two hybrid analysis.
2009-01-31 | GSE13621 | GEO
Project description:Cross-species spectral networks analysis of species with no sequenced genomes
2016-03-01 | MSV000079552 | MassIVE
Project description:5-Hydroxymethyluracil (5hmU) is a thymine modification existing in the genomes of a number of living organisms. The post-replicative formation of 5hmU occurs via hydroxylation of thymine, which can be mediated by the ten-eleven translocation (TET) dioxygenases in mammalian and J-binding proteins (JBPs) in protozoan genomes, respectively. In addition, 5hmU also can be generated through oxidation of thymine by reactive oxygen species or from deamination of 5hmC by activation-induced cytidine deaminase (AID) or APOBEC family enzymes. While the biological roles of 5hmU have not been fully explored, identifying its genomic location will assist in elucidating its functions. Herein, we report a method of enzyme-mediated bioorthogonal labeling to selectively enrich genomic regions containing 5hmU. 5hmU DNA kinase (5hmUDK) was utilized to selectively install an azide group or alkynyl group into the hydroxyl group of 5hmU followed by incorporation of the biotin linker through click chemistry and capture of 5hmU-containing DNA fragments via streptavidin pull-down. The enriched fragments were applied to deep sequencing to map the location of 5hmU. With this established enzyme-mediated bioorthogonal labeling strategy, we achieved the genome-wide mapping of 5hmU in Trypanosoma brucei (T. brucei) genomes. The method described here will allow for a better understanding of the functional roles and dynamics of 5hmU in genomes
2021-07-11 | GSE179809 | GEO
Project description:Aspergillus flavus and A. oryzae represent two unique species predicted to have spent centuries in vastly different environments. A. flavus is an important opportunistic plant pathogen known for contaminating crops with the carcinogenic mycotoxin, aflatoxin and A. oryzae is a domesticated fungus used in food fermentations. Remarkably, the genomes of these two species are still nearly identical. We have used the recently sequenced genomes of A. oryzae RIB40 and A. flavus NRRL3357 along with array based comparative genome hybridization (CGH) as a tool to compare genomes across several strains of these two species. A comparison of three strains from each species by CGH revealed only 42 and 129 genes unique to A. flavus and A. oryzae, respectively. Further, only 709 genes were identified as being polymorphic between the species. Despite the high degree of similarity between these two species, correlation analysis among all data from the CGH arrays for all strains used in this study reveals a species split. However, this view of species demarcation becomes muddled when focused on only those genes for secondary metabolism.
2010-04-10 | GSE15650 | GEO
Project description:Whole genome sequencing of Alternaria species (Illumina)
| PRJNA612050 | ENA
Project description:Whole genome sequencing of Alternaria species (Nanopore)
| PRJNA702449 | ENA