Ontology highlight
ABSTRACT:
PROVIDER: PRJNA965809 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Bumblebees (Hymenoptera: Apidae) are important pollinating insects that play pivotal roles in crop production and natural ecosystem services. To achieve a comprehensive profile of accessible chromatin regions and provide clues for all possible regulatory elements in the bumblebee genome, we did ATAC-seq for Bombus terrestris samples derived from its four developmental stages: egg, larva, pupa, and adult, respectively. The sequencing reads of ATAC-seq were mapped to B. terrestris reference genome, and its accessible chromatin regions were identified and characterized using bioinformatic methods. Our study will provide important resources not only for uncovering regulatory elements in the bumblebee genome, but also for expanding our understanding of bumblebee biology.
2020-10-02 | GSE151858 | GEO
Project description:Reforestation is effective in restoring ecosystem functions and enhancing ecosystem services of degraded land. The three most commonly employed reforestation methods of natural reforestation, artificial reforestation with native Masson pine (Pinus massoniana Lamb.), and introduced slash pine (Pinus elliottii Engelm.) plantations were equally successful in biomass yield in southern China. However, it is not known if soil ecosystem functions, such as nitrogen (N) cycling, are also successfully restored. Here, we employed a functional microarray to illustrate soil N cycling. The composition and interactions of N-cycling genes in soils varied significantly with reforestation method. Natural reforestation had more superior organization of N-cycling genes, and higher functional potential (abundance of ammonification, denitrification, assimilatory, and dissimilatory nitrate reduction to ammonium genes) in soils, providing molecular insight into the effects of reforestation.
2019-11-04 | GSE100379 | GEO
Project description:Soil fungi are key players in biomass recycling. Predation influences fungal communities and modulates ecosystem services provided by fungi. Fungal chemical defense against predation comprises toxic proteins and secondary metabolites. The intent of this experiment was to generate transcriptomic information when a fungus, in this case Fusarium graminearum, was in the presence of a predator (Folsomia candida). We assumed that defense metabolites are synthesized on demand and transcriptome analysis can be used to pinpoint genes of defense pathways. To carry out the experiment, cultures of F. graminearum were subjected to grazing by springtail F. candida. After 48 hours at 15°C in dark, springtails were removed, and RNA was extracted from mycelium. Controls were incubated under the same conditions without animals. Each group consisted of four replicates. Strand-specific cDNA libraries were prepared using Illumina’s TruSeq stranded mRNA kit (75 bp paired-end) and sequenced on Illumina NextSeq 500V2.
2018-07-01 | E-MTAB-6939 | biostudies-arrayexpress
Project description:Groundwater-derived microorganisms are known to play an important role in biogeochemical C, S and N cycling. Thereby, the presence and majorly the activity of microorganisms in aquifers affect enormously the nutrient cycling. However, the diversity and their functional capability in natural aquifers are still rare and therefore a better knowledge of the core microbial communities is urgently needed. Metaproteome analysis was applied to characterize the repertoire of microbes in the depth and to identify the key drivers of major biogeochemical processes. Therefore, 1000 L water from the aquifer was sampled by filtration on 0.3 µm glass filters. After protein extraction, proteolytic cleavage and mass spectrometric analysis (Ultimate 3000 nanoRSLC coupled to Q Exactive HF instrument), 3808 protein groups (2371 proteins with ≥2 peptides) were identified from 13,204 peptides. The findings of our study have broad implications for the understanding of aquifer cycling’s which finally leads to a greatly improved understanding of the ecosystem services provided by the microbial communities present in aquifers. In the future, functional results would allow to monitor and to assess pollution effects which would beneficially assist groundwater resource management.
2016-12-23 | PXD004351 | Pride
Project description:As the only truly flying mammals, bats use their unique wing formed from elongated digits connected by membranes to power their flight. The forelimb of bats consists of four elongated digits (digits II-V) and one shorter digit (digit I) that is morphologically similar to the hindlimb digits. Elongation of bat forelimb digits is thought to results from changes in the temporal and spatial expression of a number of developmental genes. As a result, comparing gene expression profiles between short and elongated digit morphologies of the fore- and hindlimbs may elucidate the molecular mechanisms underlying digit elongation in bats. Here, we performed a large-scale analysis of gene expression of forelimb digit I, forelimb digits II-V, and all five hindlimb digits in Myotis ricketti using digital gene expression tag profiling approach. Results of this study not only implicate several developmental genes as robust candidates underlying digit elongation in bats, but also provide a better understanding of the genes involved in autopodial development in general. A large-scale analysis of gene expression of 3 different parts of autopods in Myotis ricketti using digital gene expression tag profiling approach.
2010-12-06 | E-GEOD-20038 | biostudies-arrayexpress