Agave americana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA998363 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Agave americana Genome sequencing and assembly
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Project description:Agave americana strain:marginata Transcriptome or Gene expression
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Project description:We studied transcriptional responses comparing an Agave strain ITD00185 with a wine strain T73 in a synthetic agave must
2017-03-01 | GSE95507 | GEO
Project description:Agave americana 3 year-old clones were allowed to grow for one month under greenhouse 12h/12h light/dark conditions with regular irrigation. Three biological replicates of mature leaf were flash-frozen and ground under liquid nitrogen. Each cell pellet was resuspended in SDS buffer and sonicated. Proteins were extracted via TCA precipitation. Samples were denatured and reduced followed by enzymatic digestion using trypsin. Samples were analyzed via 2D (SCX-RP) nano-LC-MS/MS on an Orbitrap-Velos-Pro. MS/MS spectra were searched and filtered with MyriMatch and IDPicker.
Note, the Peak List and Result files do not have the same sample description as found in the published manuscript. Please use the key provided in the Supplemental Files.
2016-05-27 | MSV000079780 | MassIVE
Project description:(Agave angustifolia x Agave amaniensis) x Agave amaniensis overview
| PRJNA629034 | ENA
Project description:Background: Germ-free or axenic organisms are valuable tools for studying immunity, digestion, and development in different hosts. Although most of these studies have been conducted on mice, recently, germ-free invertebrate models (e.g. Drosophila and Apis) are used due to their easy husbandry, low cost for production, maintenance and the high number of individuals per generation they produce. However, a limitation of using these insects is the simple bacterial community present in their guts. The gut of the American cockroach Periplaneta americana displays a complex gut bacterial community composed of hundreds of species. Using P. americana, we developed a germ-free omnivorous invertebrate model to investigate how gut bacteria stimulate and shape normal gut development and metabolism. To determine if the insect host is directly affected by the presence of specific members of their bacterial community, gnotobiotic cockroaches were generated by inoculating a set of various P. americana gut-endemic Gram-negative (Bacteroidetes; n=11) and Gram-positive (Firmicutes; n=2) bacterial strains into germ-free insects. Additionally, we were able to recover the ‘normal’ bacterial-induced gut phenotype by co-housing germ-free cockroaches with wildtype P. americana to produce gut-bacteria conventionalized insects. Changes in gene expression profiles from two distinct regions (midgut and hindgut) of P. americana guts were quantified by RNA-Seq analysis of the germfree, gnotobiotic and conventionalized insects. Basic transcriptomics description: High-resolution transcriptome profiling of germ-free, gnotobiotic, and conventionalized treated P. americana midgut and hindguts. Ca. 43 million reads were obtained for each treatment. A de-novo assembly of all sequence reads was performed by Trinity assembler. Transcriptome assembly yielded 369,082 gene models and 554,155 isoforms. After running Trinotate pipeline, 65,047 (12 %) these transcripts matched an annotated product in at least one of the reference databases used (Uniprot, pfam, KEGG, COG). Additionally, 1,008 putative bacterial genes were annotated in the P. americana genome and ultimately excluded from these analyses. After bacteria decontamination, 553,147 assembled isoforms were used for transcript quantification and differential expression analysis using the DESeq2 pipeline. DESeq2 analysis detected 6,730 and 3,958 differentially expressed transcripts among the germ-free, gnotobiotic and conventionalized treatments in P. americana hindgut and midgut, respectively.
2021-07-30 | GSE159954 | GEO
Project description:(Agave angustifolia x Agave amaniensis) x Agave amaniensis Raw sequence reads
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Project description:(Agave angustifolia x Agave amaniensis) x Agave amaniensis Raw sequence reads
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Project description:(Agave angustifolia x Agave amaniensis) x Agave amaniensis Raw sequence reads
| PRJNA527342 | ENA