Ontology highlight
ABSTRACT:
PROVIDER: PRJNA736417 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14767800_1.fastq.gz | Fastqsanger.gz | |||
| SRR14767800_2.fastq.gz | Fastqsanger.gz | |||
| SRR14767900_1.fastq.gz | Fastqsanger.gz | |||
| SRR14767900_2.fastq.gz | Fastqsanger.gz | |||
| SRR14768000_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 578 |
Similar Datasets
Project description:Seagrass Halophila ovalis samples Raw sequence reads
| PRJNA1062533 | ENA
Project description:The Malaysian Node of the Human Variome Project Database (MyHVPDb) is a country specific database of human variant and gene mutation that was established in 2011. This ethnic specific mutation and variation databases are being continuously updated, recording extensive information over the genetic heterogeneity of the Malaysian ethnic groups. The database comprises of SNP Database and Mutation Database. The SNP database has stored 291718 SNPs that was obtained by genotyping the SNPs of 101 healthy individuals from six Malay sub-ethnic groups which consist of Malay Kelantan, Malay Banjar, Malay Kedah, Malay Jawa, Malay Bugis and Malay Champa.
2015-02-11 | GSE65760 | GEO
Project description:Identification of chromosomal deletion and duplications in childhood acute lymphoblastic leukemia with t(12;21). This study was performed to correlate clinical parameters with chromosomal aberrations by array-CGH and to identify other potential novel cancer genes involved in leukaemia. In brief, PALL-6 was a Malay male diagnosed with B-ALL, had undergone a remission but late relapse and passed away. He was assessed under medium risk. PALL-7 is a Malay male and has a medium risk assessment, and is currently in remission. PALL-8 is a Malay female and has a medium risk assessment, and is currently in remission. PALL-9 is a Chinese male and has a high risk assessment, and is currently in remission. PALL-10 is a Malay male and has a standard risk assessment, had a relapse but is currently in remission. PALL-11 was a Malay male and had a medium risk assessment, but died during transplant.
2012-06-20 | GSE32897 | GEO
Project description:The Malaysian Node of the Human Variome Project Database (MyHVPDb) is a country specific database of human variant and gene mutation that was established in 2011. This ethnic specific mutation and variation databases are being continuously updated, recording extensive information over the genetic heterogeneity of the Malaysian ethnic groups. The database comprises of SNP Database and Mutation Database. The SNP database has stored 291718 SNPs that was obtained by genotyping the SNPs of 101 healthy individuals from six Malay sub-ethnic groups which consist of Malay Kelantan, Malay Banjar, Malay Kedah, Malay Jawa, Malay Bugis and Malay Champa. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from blood samples.
2015-02-11 | E-GEOD-65760 | biostudies-arrayexpress
Project description:Because of severe abiotic limitations, Antarctic soils represent simplified ecosystems, where microorganisms are the principle drivers of nutrient cycling. This relative simplicity makes these ecosystems particularly vulnerable to perturbations, like global warming, and the Antarctic Peninsula is among the most rapidly warming regions on the planet. However, the consequences of the ongoing warming of Antarctica on microorganisms and the processes they mediate are unknown. Here, using 16S rRNA gene pyrosequencing and qPCR, we report a number of highly consistent changes in microbial community structure and abundance across very disparate sub-Antarctic and Antarctic environments following three years of experimental field warming (+ 0.5-2°C). Specifically, we found significant increases in the abundance of fungi and bacteria and in the Alphaproteobacteria-to-Acidobacteria ratio. These alterations were linked to a significant increase in soil respiration. Furthermore, the shifts toward generalist or opportunistic bacterial communities following warming weakened the linkage between bacterial diversity and functional diversity. Warming also increased the abundance of some organisms related to the N-cycle, detected as an increase in the relative abundance of nitrogenase genes via GeoChip microarray analyses. Our results demonstrate that soil microorganisms across a range of sub-Antarctic and Antarctic environments can respond consistently and rapidly to increasing temperatures, thereby potentially disrupting soil functioning. We conducted in situ warming experiments for three years using open-top chambers (OTCs) at one sub-Antarctic (Falkland Islands, 52ºS) and two Antarctic locations (Signy and Anchorage Islands, 60ºS and 67ºS respectively) (see Supplementary Fig. 1 for a map). OTCs increased annual soil temperature by an average of 0.8°C (at a depth of 5 cm), resulting in 8-43% increase in positive-degree days annually and a decrease in freeze-thaw cycle frequency by an average of 15 cycles per year (8). At each location, we included densely vegetated and bare fell-field soils in the experimental design for a total of six environments. Densely vegetated and bare environments represent two contrasting environments for Antarctic soil microorganisms, with large differences in terms of C and N inputs to soils. Massively parallel pyrosequencing (Roche 454 GS FLX Titanium) of 16S rRNA gene amplicons was used to follow bacterial diversity and community composition [GenBank Accession Numbers: HM641909-HM744649], and functional gene microarrays (GeoChip 2.0)(11) were used to assess changes in functional gene distribution. Bacterial and fungal communities were also quantified using real-time PCR.
2010-12-30 | E-GEOD-22825 | biostudies-arrayexpress
Project description:The rate, timing, and mode of species dispersal is recognized as a key driver of the structure and function of communities of macroorganisms, and may be one ecological process that determines the diversity of microbiomes. Many previous studies have quantified the modes and mechanisms of bacterial motility using monocultures of a few model bacterial species. But most microbes live in multispecies microbial communities, where direct interactions between microbes may inhibit or facilitate dispersal through a number of physical (e.g., hydrodynamic) and biological (e.g., chemotaxis) mechanisms, which remain largely unexplored. Using cheese rinds as a model microbiome, we demonstrate that physical networks created by filamentous fungi can impact the extent of small-scale bacterial dispersal and can shape the composition of microbiomes. From the cheese rind of Saint Nectaire, we serendipitously observed the bacterium Serratia proteamaculans actively spreads on networks formed by the fungus Mucor. By experimentally recreating these pairwise interactions in the lab, we show that Serratia spreads on actively growing and previously established fungal networks. The extent of symbiotic dispersal is dependent on the fungal network: diffuse and fast-growing Mucor networks provide the greatest dispersal facilitation of the Serratia species, while dense and slow-growing Penicillium networks provide limited dispersal facilitation. Fungal-mediated dispersal occurs in closely related Serratia species isolated from other environments, suggesting that this bacterial-fungal interaction is widespread in nature. Both RNA-seq and transposon mutagenesis point to specific molecular mechanisms that play key roles in this bacterial-fungal interaction, including chitin utilization and flagellin biosynthesis. By manipulating the presence and type of fungal networks in multispecies communities, we provide the first evidence that fungal networks shape the composition of bacterial communities, with Mucor networks shifting experimental bacterial communities to complete dominance by motile Proteobacteria. Collectively, our work demonstrates that these strong biophysical interactions between bacterial and fungi can have community-level consequences and may be operating in many other microbiomes.
2017-08-02 | GSE85095 | GEO