18S rRNA sequencing Dark Earth
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB10851 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1016680.fastq.gz | Fastqsanger.gz | |||
| ERR1016690.fastq.gz | Fastqsanger.gz | |||
| ERR1016681.fastq.gz | Fastqsanger.gz | |||
| ERR1016691.fastq.gz | Fastqsanger.gz | |||
| ERR1016682.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 24 |
Similar Datasets
Project description:Differential abundance affect fungal communities structure and composition in Amazonian Dark Earth and black carbon particles
| PRJEB12675 | ENA
Project description:The goal of this study is to compare the transcriptome (RNA-seq) modulations in the roots and shoots of Arabidopsis thaliana, as a plant model, exposed to two toxic concentrations of rare earth elements. Lanthanum and ytterbium were used as representative of light and heavy rare earth elements, respectively.
2023-07-23 | GSE237657 | GEO
Project description:Quantification of fungal dark matter using qPCR
| PRJEB69215 | ENA
Project description:Purpose: The goals of this study is to compare the transcriptome (RNA-seq) modulations in Saccharomyces cerevisiae exposed to two rare earth elements. Lanthanum and ytterbium were used as representative of light and heavy rare earth elements, respectively. Methods: mRNA were sequenced from Saccharomyces cerevisiae exposed to two different rare earth elements. Lanthanum and ytterbium were used as representative of light and heavy rare earth elements respectively. The transcriptome of S. cerevisiae was analysed after being exposed for one hour to the EC10 (Effective concentration 10 %) and the EC50 (Effective concentration 50 %) of lanthanum (50 and 160 µM) and ytterbium (6 and 8 µM). The sequence reads were trimmed using Trimmomativ v0.36.1 and FastQC v0.67 used for quality check. Reads passing the quality check were mapped on the reference genome (S288C R64-2-1 of 2015-01-31 from https://www.yeastgenome.org/) of S. cerevisiae using TopHat v2.1.1. Reads that were mapped on the reference genome were quantified using HTSeq-count v0.6.1p1. Finally, differential gene expression analysis between treatments was carried out using DESeq2 v1.14.1. Differentially expressed genes between conditions were obtained and expressed as log2-fold change with adjusted p-values calculated via a Benjamini-Hochberg test. A cut-off adjusted p-value of < 0.01 was applied. Results: The transcription of genes related to several crucial pathways was modulated in response to both REEs, such as oxidative-reduction processes, DNA replication, and carbohydrate metabolism. REE-specific responses involving the cell wall and the pheromone signalling pathways were highlighted, while these were not reported for other metals. REE exposure also modified the expression and abundance of several ion transport systems, for which strong discrepancies were observed between the two contrasted REEs. Conclusions: Our results demonstrate the discrepancies in yeast response to different rare earth elements (light vs heavy rare earth elements). This results are valuable to prioritize key genes and proteins involved in REE detoxification mechanisms that would deserve further characterisation to better understand the REE toxicity on the environment and human health.
2021-06-01 | GSE175826 | GEO
Project description:Because of their ubiquity and resistance to spacecraft decontamination, bacterial spores are considered likely potential forward contaminants on robotic missions to Mars. Thus it is important to understand their global responses to long-term exposure to space or Mars environments. As part of the PROTECT experiment, spores of B. subtilis 168 were exposed to real space conditions and to simulated martian conditions for 559 days in low Earth orbit mounted on the EXPOSE-E exposure platform outside the European Columbus module on the International Space Station. Upon return, spores were germinated, total RNA extracted and fluorescently labeled, and used to probe a custom Bacillus subtilis microarray to identify genes preferentially activated or repressed relative to ground control spores. Increased transcript levels were detected for a number of stress-related regulons responding to DNA damage (SOS response, SPβ prophage induction), protein damage (CtsR/Clp system), oxidative stress (PerR regulon) and cell envelope stress (SigV regulon). Spores exposed to space demonstrated a much broader and more severe stress response than spores exposed to simulated Mars conditions. The results are discussed in the context of planetary protection for a hypothetical journey of potential forward contaminant spores from Earth to Mars and their subsequent residence on Mars. Two-color microarrays were performed comparing germination of Space-exposed or Mars-exposed vs. ground-control (Earth) spores.
2012-05-31 | E-GEOD-37124 | biostudies-arrayexpress
Project description:Coral disease is one of the major causes of reef degradation and therefore of concern to management and conservation efforts. Dark Spot Syndrome (DSS) was described in the early 1990’s as brown or purple amorphous areas of tissue on a coral and has since become one of the most prevalent diseases reported on Caribbean reefs. It has been identified in a number of coral species, but there is debate as to whether it is in fact the same disease in different corals. Further, it is questioned whether these macroscopic signs are in fact diagnostic of an infectious disease, since they can also be caused by physical injury in some species. The most commonly affected species in the Caribbean is the massive starlet coral Siderastrea siderea. We sampled this species in two geographic locations, Dry Tortugas National Park and Virgin Islands National Park. Tissue biopsies were collected from both healthy colonies with normal pigmentation and those with dark spot lesions. Microbial-community DNA was extracted from coral samples (mucus, tissue, and skeleton), amplified using bacterial-specific primers, and applied to PhyloChip™ G3 microarrays to examine the bacterial diversity associated with this coral. Samples were also screened for the presence of a fungal ribotype that has recently been implicated as a causative agent of DSS in another coral species, however the amplicon pools were overwhelmed by coral 18S rRNA genes from S. siderea. Unlike a similar study on a white-plague-like disease, S. siderea samples did not cluster consistently based on health state (i.e., normal versus dark spot). Various bacteria, including Cyanobacteria and Vibrios, were observed to have increased relative abundance in the discolored tissue, but the patterns were not consistent across all DSS samples. Overall, our findings do not support the hypothesis that DSS in S. siderea is linked to a bacterial pathogen or pathogens. This dataset provides the most comprehensive overview to date of the bacterial community associated with the healthy scleractinian coral S. siderea.
2014-09-30 | GSE60622 | GEO
Project description:fapesp-bra-inra-10-01_bioen_hypocotyl - dark hypocotyls tor rnai - Transcriptional comparison between 2 TOR RNAi mutants versus GUS control. - Sowing after 24h imbibition at 4°C in the dark, on MS1/5, no sucrose, 10 mM ethanol, 8 g/l agar, vertical growth with 3h light, 6 days growth in the dark (20°C), hypocotyls were harvested under green light ; cotyledons and root were removed.
2012-10-10 | GSE41404 | GEO
Project description:Compared with the well-studied soil prokaryotic communities, little is known about soil eukaryotic communities. Here, we investigated the eukaryotic community structures in 43 arable soils using amplicon sequencing of 18S rRNA genes. Major taxonomic groups, such as Fungi, Holozoa, and Stramenopiles, were detected in all samples.
| S-EPMC7272547 | biostudies-literature