Mite metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA320913 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Morus alba L. Raw protein sequence reads and sequence
2024-02-08 | PXD049451 |
Project description:Purpose: Identify whole lung gene expression patterns in a house dust mite model of severe asthma Methods: Lung gene expression profiles of 10 week old BALB/c female mice were generated by ribosome-depleted, 100 nt, paired-end, stranded RNA-seq with Illumina HiSeq v4. Sequence reads were analyzed with Sailfish-cir to identify linear RNA transcripts and circular RNAs. Differential expression of linear RNAs was assessed with Deseq2 . QRT–PCR validation was performed using TaqMan and SYBR Green methods. Results: 100 million sequence reads per sample were mapped to the mouse genome (build mm10) using Sailfish-cir to identify linear and circular RNA transcripts. Pathway analysis of differentially expressed genes identified upregulation of gene sets for human Th17 high, Th2 low asthma. An LNA/DNA miR-155 antagonist upregulated interferon signaling pathways suggesting a general antiinflammatory effect of LNA/DNA oligos in the lung. Dexamethasone did not consistently reduce expression of Th2 or Th17 biomarker genes. Conclusions: Cyclic di-GMP plus house dust mite allergens elicited a Th2 low, Th17 high gene expression profile that was not consistently modified by treatment with dexamethasone.
2019-06-08 | GSE132377 | GEO
Project description:Purpose: Identify whole lung gene expression patterns in a house dust mite model of mild/moderate asthma Methods: Lung gene expression profiles of 10 week old BALB/c female mice were generated by ribosome-depleted, 150 nt, paired-end, stranded RNA-seq with Illumina HiSeq v4. Sequence reads that passed quality filters after trimming were analyzed with Sailfish-cir to identify linear RNAs and circular RNAs. Differential expression of linear RNAs was assessed with Deseq2 . QRT–PCR validation was performed using TaqMan and SYBR Green methods. Results: 100 million sequence reads per sample were mapped to the mouse genome (build mm10) using Sailfish-cir to identify linear and circular RNA transcripts. Pathway analysis of differentially expressed genes identified upregulation of gene sets for human asthma, mouse lung allergic inflammation, Muc5ac regulated genes and smooth muscle genes after allergic sensitization. Gene level exppression in each asthma-related pathway was reduced by the miR-145 antagonist. The miR-145 antagonist and several nontargeting oligos also upregulated interferon signaling pathways suggesting a general antiinflammatory effect of LNA/DNA oligos in the lung. Conclusions: Lung-directed delivery of LNA/DNA oligonucleotides with cationic lipid nanoparticles is an efffective means to prevent inflammatory gene expression in a house dust mite model of mild/moderate asthma.
2019-06-06 | GSE132263 | GEO
Project description:Purpose: Identify whole lung gene expression patterns modified by nanoparticle delivery of an antisense LNA/DNA oligonucleotide targeting mmu-miR145a-5p and nontargeting oligonucleotides Methods: Lung gene expression profiles of 10 week old BALB/c female mice were generated by polyA RNA-seq with Illumina HiSeq v4. Sequence reads that passed quality filters after timming were analyzed at the gene level with RNA STAR, featureCounts and Deseq2 . qRT–PCR validation was performed using TaqMan and SYBR Green methods. Results: 10-15 million sequence reads per sample were mapped to the mouse genome (build mm10). Pathway analysis of differentially expressed genes identified upregulation of gene sets for human asthma, mouse lung allergic inflammation, Muc5ac regulated genes and smooth muscle genes after allergic sensitization. Gene level exppression in each asthma-related pathway was reduced by the miR-145 antagonist. The miR-145 antagonist and several nontargeting oligos also upregulated interferon signaling pathways suggesting a general antiinflammatory effect of LNA/DNA oligos in the lung. Conclusions: Lung-directed delivery of LNA/DNA oligonucleotides with cationic lipid nanoparticles is an efffective means to prevent inflammatory gene expression in a house dust mite model of asthma
2019-02-16 | GSE126610 | GEO
Project description:We generated 38-bp Illumina reads from single messenger RNA libraries from three diverse developmental stages of the two-spotted spider mite to capture small RNA diversity across development. Adult, nymphal+larvae and embryonic stages were separated using sieves of various pore sizes, and mites of various developmental stages were carefully selected for small RNA library preparation. Samples were a mix of males and females to capture male and female patterns of small RNA composition and were reared on beans (Phaseolus vulgaris cv California Red Kidney). Small RNA reads were used for miRNA prediction, piRNA discovery, and for quantitation of small RNA-generating loci (i.e. expression across development).
2011-11-23 | GSE32005 | GEO
Project description:The goal of our microarray experiments was to compare the gene expression profile of two spirodiclofen resistant spider mite strains (SR-VP and SR-TK) with that of a susceptible spider mite strain (LS-VL)
2013-06-26 | GSE43538 | GEO
Project description:The goal of our microarray experiments was to compare the gene expression profile of two spirodiclofen resistant spider mite strains (SR-VP and SR-TK) with that of a susceptible spider mite strain (LS-VL) 5 samples were analyzed: 3 biological replicates for SR-VP, 2 biological replicates for SR-TK
2013-06-26 | E-GEOD-43538 | biostudies-arrayexpress
Project description:We generated 38-bp Illumina reads from single messenger RNA libraries from three diverse developmental stages of the two-spotted spider mite to capture small RNA diversity across development. Adult, nymphal+larvae and embryonic stages were separated using sieves of various pore sizes, and mites of various developmental stages were carefully selected for small RNA library preparation. Samples were a mix of males and females to capture male and female patterns of small RNA composition and were reared on beans (Phaseolus vulgaris cv California Red Kidney). Small RNA reads were used for miRNA prediction, piRNA discovery, and for quantitation of small RNA-generating loci (i.e. expression across development). Examination of small RNA from spider mites of adult, embryonic and pooled larval/nymphal developmental stages.
2011-11-23 | E-GEOD-32005 | biostudies-arrayexpress
Project description:Nitrate-reducing iron(II)-oxidizing bacteria are widespread in the environment contribute to nitrate removal and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing iron(II)-oxidizing bacteria is rarely investigated and poorly understood. The most prominent model system for this type of studies is enrichment culture KS, which originates from a freshwater sediment in Bremen, Germany. To gain insights in the metabolism of nitrate reduction coupled to iron(II) oxidation under in the absence of organic carbon and oxygen limited conditions, we performed metagenomic, metatranscriptomic and metaproteomic analyses of culture KS. Raw sequencing data of 16S rRNA amplicon sequencing, shotgun metagenomics (short reads: Illumina; long reads: Oxford Nanopore Technologies), metagenome assembly, raw sequencing data of shotgun metatranscriptomes (2 conditions, triplicates) can be found at SRA in https://www.ncbi.nlm.nih.gov/bioproject/PRJNA682552. This dataset contains proteomics data for 2 conditions (heterotrophic and autotrophic growth conditions) in triplicates.
2021-05-17 | PXD023186 | Pride