Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1832810.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 1 of 1 |
Similar Datasets
Project description:Metagenome data from soil samples were collected at 0 to 10cm deep from 2 avocado orchards in Channybearup, Western Australia, in 2024. Amplicon sequence variant (ASV) tables were constructed based on the DADA2 pipeline with default parameters.
2025-06-15 | GSE298403 | GEO
Project description:Meckel Syndrome, Nephronophthisis, Joubert Syndrome, and Bardet-Biedl Syndrome have mutations in proteins that localize to the ciliary transition zone (TZ). The phenotypically distinct syndromes suggest these TZ proteins have differing functions. However, mutations in a single TZ gene can result in multiple syndromes suggesting the phenotype is influenced by modifier genes. We performed a comprehensive analysis of ten zebrafish TZ mutants including mks1, tmem216, tmem67, rpgrip1l, cc2d2a, b9d2, cep290, tctn1, nphp1, and nphp4, as well as mutants in ift88 and ift172. Our data indicate variations in phenotypes exists between different TZ mutants, supporting different tissue specific functions of these TZ genes. Further we observed phenotypic variations within progeny of a single TZ mutant, reminiscent of multiple disease syndromes being associated with mutations in one gene. In some mutants the dynamics of the phenotype became complex with transitory phenotypes that are corrected over time. We have also demonstrated that multiple-guide derived CRISPR/Cas9 F0 “Crispant” embryos recapitulate zygotic null phenotypes, and rapidly identified ciliary phenotypes in 11 cilia-associated gene candidates (ankfn1, ccdc65, cfap57, fhad1, nme7, pacrg, saxo2, c1orf194, ttc26, zmynd12, and cfap52).
2022-11-30 | GSE217001 | GEO
Project description:Here, we report 17 metagenome-assembled genomes (MAGs) recovered from microbial consortia of forest and pasture soils in the Brazilian Eastern Amazon. The bacterial MAGs have the potential to act in important ecological processes, including carbohydrate degradation and sulfur and nitrogen cycling.
| S-EPMC9670897 | biostudies-literature
Project description:The metagenomes of complex microbial communities are rich sources of novel biocatalysts. We exploited the metagenome of a mixed microbial population for isolation of more than 15 different genes encoding novel biocatalysts by using a combined cultivation and direct cloning strategy. A 16S rRNA sequence analysis revealed the presence of hitherto uncultured microbes closely related to the genera Pseudomonas, Agrobacterium, Xanthomonas, Microbulbifer, and Janthinobacterium. Total genomic DNA from this bacterial community was used to construct cosmid DNA libraries, which were functionally searched for novel enzymes of biotechnological value. Our searches in combination with cosmid sequencing resulted in identification of four clones encoding 12 putative agarase genes, most of which were organized in clusters consisting of two or three genes. Interestingly, nine of these agarase genes probably originated from gene duplications. Furthermore, we identified by DNA sequencing several other biocatalyst-encoding genes, including genes encoding a putative stereoselective amidase (amiA), two cellulases (gnuB and uvs080), an alpha-amylase (amyA), a 1,4-alpha-glucan branching enzyme (amyB), and two pectate lyases (pelA and uvs119). Also, a conserved cluster of two lipase genes was identified, which was linked to genes encoding a type I secretion system. The novel gene aguB was overexpressed in Escherichia coli, and the enzyme activities were determined. Finally, we describe more than 162 kb of DNA sequence that provides a strong platform for further characterization of this microbial consortium.
| S-EPMC201203 | biostudies-literature
Project description:Soil microbial communities contain the highest level of prokaryotic diversity of any environment, and metagenomic approaches involving the extraction of DNA from soil can improve our access to these communities. Most analyses of soil biodiversity and function assume that the DNA extracted represents the microbial community in the soil, but subsequent interpretations are limited by the DNA recovered from the soil. Unfortunately, extraction methods do not provide a uniform and unbiased subsample of metagenomic DNA, and as a consequence, accurate species distributions cannot be determined. Moreover, any bias will propagate errors in estimations of overall microbial diversity and may exclude some microbial classes from study and exploitation. To improve metagenomic approaches, investigate DNA extraction biases, and provide tools for assessing the relative abundances of different groups, we explored the biodiversity of the accessible community DNA by fractioning the metagenomic DNA as a function of (i) vertical soil sampling, (ii) density gradients (cell separation), (iii) cell lysis stringency, and (iv) DNA fragment size distribution. Each fraction had a unique genetic diversity, with different predominant and rare species (based on ribosomal intergenic spacer analysis [RISA] fingerprinting and phylochips). All fractions contributed to the number of bacterial groups uncovered in the metagenome, thus increasing the DNA pool for further applications. Indeed, we were able to access a more genetically diverse proportion of the metagenome (a gain of more than 80% compared to the best single extraction method), limit the predominance of a few genomes, and increase the species richness per sequencing effort. This work stresses the difference between extracted DNA pools and the currently inaccessible complete soil metagenome.
| S-EPMC3067229 | biostudies-literature
Project description:The Arecibo Observatory (AO) located in Arecibo, Puerto Rico, is the most sensitive, powerful and active planetary radar system in the world [1]. One of its principal components is the 305 m-diameter spherical reflector dish (AORD), which is exposed to high frequency electromagnetic waves. To unravel the microbial communities that inhabit this environment, soil samples from underneath the AORD were collected, DNA extracted, and sequenced using Illumina MiSeq. Taxonomic and functional profiles were generated using the MG-RAST server. The most abundant domain was Bacteria (91%), followed by Virus (8%), Archaea (0.9%) and Eukaryota (0.9%). The most abundant phylum was Proteobacteria (54%), followed by Actinobacteria (8%), Bacteroidetes (5%) and Firmicutes (4%). In terms of functions, the most abundant among the metagenome corresponded to phages, transposable elements and plasmids (16%), followed by clustering-based subsystems (11%), carbohydrates (10%), and amino acids and derivatives (9%). This is the first soil metagenomic dataset from dish antennas and radar systems, specifically, underneath the AORD. Data can be used to explore the effect of high frequency electromagnetic waves in soil microbial composition, as well as the possibility of finding bioprospects with potential biomedical and biotechnological applications.
| S-EPMC6920479 | biostudies-literature
Project description:Bacteriophages are abundant in soils. However, the majority are uncharacterized, and their hosts are unknown. Here, we apply high-throughput chromosome conformation capture (Hi-C) to directly capture phage-host relationships. Some hosts have high centralities in bacterial community co-occurrence networks, suggesting phage infections have an important impact on the soil bacterial community interactions. We observe increased average viral copies per host (VPH) and decreased viral transcriptional activity following a two-week soil-drying incubation, indicating an increase in lysogenic infections. Soil drying also alters the observed phage host range. A significant negative correlation between VPH and host abundance prior to drying indicates more lytic infections result in more host death and inversely influence host abundance. This study provides empirical evidence of phage-mediated bacterial population dynamics in soil by directly capturing specific phage-host interactions.
| S-EPMC10667309 | biostudies-literature
Project description:The identification of cellular and functional heterogeneity within the prostate and between the transitional zone (TZ) and peripheral zone (PZ) is critical for understanding the spatial distribution of prostate diseases. Three paired human prostate PZ and TZ tissue samples were used for scRNA-seq.
2024-02-13 | GSE166782 | GEO
Project description:We established a tumor model in which Notch overexpression can induce tumor formation in a transition-zone (TZ) region in the Drosophila salivary gland imagnal ring (ImR). TZ cells are polyploid cells and do not devide during normal development, however, polyploid TZ cells reenter to mitosis and form tumor after Notch induction. Growth and progression of the TZ tumor are fueled by a combination of polyploid mitosis, endoreplication, and depolyploidization. To determine the molecular mechanisms underlying tumor formation in the NICD-induced TZ tumors, we did RNA-seq and compared the transcriptomes between tumor and control. We found the mitosis of the salivary gland ImR tumor was due to the Drosophila Cdc25 homolog String (Stg), a M-phase inducer phosphatase, was significantly upregulated in the tumor sample. Besides, we found DNA damage response genes, also active during meiosis, are upregulated in these tumors and are required for the ploidy reduction division. This study suggests that polyploidy and associated cell-cycle variants are critical for increased tumor cell heterogeneity and genome instability during cancer progression.
2022-05-20 | GSE175415 | GEO
Project description:ERBB2 overexpression is associated with aggressive breast cancer (BCa) disease. The introduction in the clinic of Trastuzumab (Tz) targeting this receptor has considerably improved patient outcomes. However, de novo or acquired resistance to Tz occurs and negatively impacts prognosis. Many molecular mechanisms have been reported in the development of Tz resistance. This study aimed to establish whether common mechanisms could be identified in in vitro models of acquired BCa Tz resistance. In particular, we used widely available ERBB2+ Breast cancer cell lines BT474, MDA-MB-361, and SKBR-3, adapted in vitro to grow in Tz concentration ten times higher than the saturation one. Wt and TZ-R cells were studied to address changes in phenotype, proliferation, apoptosis, and ERBB2 membrane expression that did not highlight alterations common to the three cell lines. We used high-resolution mass spectrometry analysis to gain insight into the mechanisms associated to the adaptation of continuous growth in very high Tz concentration. This analysis identified a common set of differentially expressed proteins (DEPs) in Tz-R vs. wt cells. Bioinformatic tools available in the public domain revealed that all three Tz-R cell models shared modulation of proteins involved in the metabolism of lipids, organophosphate biosynthetic process, and macromolecule methylation. This data was partially supported by evidence of a higher number of lipid droplets in TZ-R SKBR-3 with respect to wt. In conclusion, our data strongly support previous evidence that complex metabolic adaptation, including lipid metabolism, protein phosphorylation, and possibly chromatin remodeling, may fuel Tz resistance. At the same time, identifying a common set of 10 DEPs in all three TZ-resistant cell lines may provide possible novel targets for therapeutic intervention.
2023-05-23 | PXD037657 | Pride