Creosote bush (Larrea tridentata), Juniper (Juniperus osteosperma), alfalfa based rabbit chow, cactus (Opuntia spp.)
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ABSTRACT:
PROVIDER: PRJNA766427 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We present the de novo transcriptome sequencing, analysis and microarray development for a vertebrate herbivore, the woodrat (Neotoma spp.). This genus is of ecological and evolutionary interest, especially with respect to ingestion and hepatic metabolism of potentially toxic plant secondary compounds. We generated a liver transcriptome of the desert woodrat (Neotoma lepida) with the Roche 454 platform. The assembled contigs were well annotated using rodent references (99.7% annotation), and biotransformation function was reflected in the gene ontology. The transcriptome was used to develop a custom microarray (eArray, Agilent). To compare the effect of native diet/habitat and phylogenetic similarity, we performed 3 experiments with the Neotoma probes only: one across species with similar habitat niches (N. lepida versus N. bryanti, Palm Springs), one across species with different habitat niches (N. lepida versus N. bryanti, Caspers Wilderness), and one across populations within a species (N. bryant Palm Springs versus Caspers Wilderness). The resulting one-color arrays had high technical and biological quality. Probes designed from the woodrat transcriptome performed significantly better than functionally similar probes from the Norway rat (Rattus norvegicus). Biotransformation processes and functions were highly represented in the results. Comparisons between ecologically similar woodrat species revealed fewer gene expression differences than ecologically different woodrat species. The conspecific comparison had overall fewest differences. Gene expression was compared across 3 groups of woodrats: Neotoma lepida (n=4), N. bryanti Palm Springs (n=4), and N. bryanti Caspers Wilderness (n=4). Animals were fed a rabbit chow diet, called control; intake was monitored over 10 days, after which RNA was extracted from hepatic tissue. One-color arrays were performed.
2013-07-30 | E-GEOD-43941 | biostudies-arrayexpress
Project description:We present the de novo transcriptome sequencing, analysis and microarray development for a vertebrate herbivore, the woodrat (Neotoma spp.). This genus is of ecological and evolutionary interest, especially with respect to ingestion and hepatic metabolism of potentially toxic plant secondary compounds. We generated a liver transcriptome of the desert woodrat (Neotoma lepida) with the Roche 454 platform. The assembled contigs were well annotated using rodent references (99.7% annotation), and biotransformation function was reflected in the gene ontology. The transcriptome was used to develop a custom microarray (eArray, Agilent). To compare the effect of native diet/habitat and phylogenetic similarity, we performed 3 experiments with the Neotoma probes only: one across species with similar habitat niches (N. lepida versus N. bryanti, Palm Springs), one across species with different habitat niches (N. lepida versus N. bryanti, Caspers Wilderness), and one across populations within a species (N. bryant Palm Springs versus Caspers Wilderness). The resulting one-color arrays had high technical and biological quality. Probes designed from the woodrat transcriptome performed significantly better than functionally similar probes from the Norway rat (Rattus norvegicus). Biotransformation processes and functions were highly represented in the results. Comparisons between ecologically similar woodrat species revealed fewer gene expression differences than ecologically different woodrat species. The conspecific comparison had overall fewest differences.
2013-07-30 | GSE43941 | GEO
Project description:Neotoma lepida Transcriptome or Gene expression
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Project description:Neotoma lepida fecal inventories Targeted Locus (Loci)
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Project description:This study aimed to assess the capability of supercritical fluid extraction (SFE) as an alternative and green technique compared to Soxhlet extraction for the production of oils from Opuntia ficus-indica (OFI) seeds originating from Yemen and Italy and Opuntia dillenii (OD) seeds from Yemen. The following parameters were used for SFE extraction: a pressure of 300 bar, a CO2 flow rate of 1 L/h, and temperatures of 40 and 60 °C. The chemical composition, including the fatty acids and tocopherols (vitamin E) of the oils, was determined using chromatographic methods. The highest yield was achieved with Soxhlet extraction. The oils obtained with the different extraction procedures were all characterized by a high level of unsaturated fatty acids. Linoleic acid (≤62% in all samples) was the most abundant one, followed by oleic and vaccenic acid. Thirty triacylglycerols (TAGs) were identified in both OFI and OD seed oils, with trilinolein being the most abundant (29-35%). Vanillin, 4-hydroxybenzaldehyde, vanillic acid, and hydroxytyrosol were phenols detected in both OFI and OD oils. The highest γ-tocopherol content (177 ± 0.23 mg/100 g) was obtained through the SFE of OFI seeds from Yemen. Overall, the results highlighted the potential of SFE as green technology to obtain oils suitable for functional food and nutraceutical products.
| S-EPMC9914625 | biostudies-literature
Project description:Neotoma lepida isolate:417 Genome sequencing and assembly
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