Seawater metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA777059 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16700200_1.fastq.gz | Fastqsanger.gz | |||
| SRR16700200_2.fastq.gz | Fastqsanger.gz | |||
| SRR16700201_1.fastq.gz | Fastqsanger.gz | |||
| SRR16700201_2.fastq.gz | Fastqsanger.gz | |||
| SRR16700202_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 184 |
Similar Datasets
Project description:TGF-beta1 is the major cytokine driver of fibrotic scarring observed in diabetic nephropathy and other fibrosis-related diseases. RNA-sequencing offers the potential for more sensitive assessment of the TGF-M-CM-^_1-driven transcriptome. There were two treatment groups: vehicle, 48 hr TGFb1. Each treatment was carried out in triplicate. Upon quality control assessment, one TGFM-CM-^_1 treated sample was excluded from further analyses, leaving 3 unstimulated and 2 TGFM-CM-^_1 samples.
2012-03-31 | E-GEOD-29660 | biostudies-arrayexpress
Project description:D-galactose orally intake ameliorate DNCB-induced atopic dermatitis by modulating microbiota composition and quorum sensing. The increased abundance of bacteroidetes and decreased abundance of firmicutes was confirmed. By D-galactose treatment, Bacteroides population was increased and prevotella, ruminococcus was decreased which is related to atopic dermatitis.
2022-04-29 | E-MTAB-11632 | biostudies-arrayexpress
Project description:Analysis of nucleosides (dC, dG, 5mdC and 5hmdC) using mass spectrometry and digested DNA samples.
Experimental data description:
- 12 h restoration (corresponding to EDFig2 b, EDFig5 b,c,h), E14 mESCs, labelled samples and followed for 12h, total DNA and stranded, 4 biological replicates (rep1, rep2, rep3 and rep4) and 2 technical replicates (_1, _2).
- KST061-62-63 (corresponding to Fig1 e-f, Fig2 b-g, Fig5 b-e, EDFig5 a,f), E14 mESCs, labelled samples and followed for 8h, total DNA and stranded, 3 biological replicates (KST061, KST062 and KST063) and 2 technical replicates (_1, _2).
- KST73-74-75 (corresponding to EDFig5 d,e,g), NIH3T3 cell line, labelled samples and followed for 8h, total DNA and stranded, 3 biological replicates (KST073, KST074 and KST075) and 2 technical replicates (_1, _2).
- KST76-77-78 (corresponding to Fig6 b-e, EDFig6 b-c), E14 mESCs, ChIP mass spectrometry samples for several histone modifications antibodies, total DNA and ChIP DNA, 3 biological replicates (KST076, KST077 and KST078) and 2 technical replicates (_1, _2).
- KST035 (corresponding to Fig1 c-d), E14 mESCs, DNA abundance and methylation levels, 2 technical replicates (_1, _2)
- KST045-46-47 (corresponding to Fig3 b, EDFig3 a), E14 mESCs, labelled early S phase samples and followed for 8h, total DNA and EdU+ pull down, 3 biological replicates (KST045, KST046 and KST047) and 2 technical replicates (_1, _2).
- KST050-51-52 (corresponding to Fig3 c, EDFig3 b), E14 mESCs, labelled late S phase samples and followed for 8h, total DNA and EdU+ pull down, 3 biological replicates (KST050, KST051 and KST052) and 2 technical replicates (_1, _2).
- KST056-57-60 (corresponding to EDFig4 a), E14 mESCs, cell cycle phases sorted using EdU labelling, 3 biological replicates (KST056, KST057 and KST060) and 2 technical replicates (_1, _2).
Standard curve data used for quantification are named as MM1-MM10, 2 technical replicates (_1, _2).
2022-10-21 | MSV000090568 | MassIVE
Project description:The characterization of microbial communities based on sequencing and analysis of their genetic information has become a popular approach also referred to as metagenomics; in particular, the recent advances in sequencing technologies have enabled researchers to study even the most complex communities. Metagenome analysis, the assignment of sequences to taxonomic and functional entities, however, remains a tedious task: large amounts of data need to be processed. There are a number of approaches addressing particular aspects, but scientific questions are often too specific to be answered by a general-purpose method.We present MGX, a flexible and extensible client/server-framework for the management and analysis of metagenomic datasets; MGX features a comprehensive set of adaptable workflows required for taxonomic and functional metagenome analysis, combined with an intuitive and easy-to-use graphical user interface offering customizable result visualizations. At the same time, MGX allows to include own data sources and devise custom analysis pipelines, thus enabling researchers to perform basic as well as highly specific analyses within a single application.With MGX, we provide a novel metagenome analysis platform giving researchers access to the most recent analysis tools. MGX covers taxonomic and functional metagenome analysis, statistical evaluation, and a wide range of visualizations easing data interpretation. Its default taxonomic classification pipeline provides equivalent or superior results in comparison to existing tools.
| S-EPMC5937802 | biostudies-other
Project description:In the collective genomes (the metagenome) of the microorganisms inhabiting the Earth's diverse environments is written the history of life on this planet. New molecular tools developed and used for the past 15 years by microbial ecologists are facilitating the extraction, cloning, screening, and sequencing of these genomes. This approach allows microbial ecologists to access and study the full range of microbial diversity, regardless of our ability to culture organisms, and provides an unprecedented access to the breadth of natural products that these genomes encode. However, there is no way that the mere collection of sequences, no matter how expansive, can provide full coverage of the complex world of microbial metagenomes within the foreseeable future. Furthermore, although it is possible to fish out highly informative and useful genes from the sea of gene diversity in the environment, this can be a highly tedious and inefficient procedure. Microbial ecologists must be clever in their pursuit of ecologically relevant, valuable, and niche-defining genomic information within the vast haystack of microbial diversity. In this report, we seek to describe advances and prospects that will help microbial ecologists glean more knowledge from investigations into metagenomes. These include technological advances in sequencing and cloning methodologies, as well as improvements in annotation and comparative sequence analysis. More significant, however, will be ways to focus in on various subsets of the metagenome that may be of particular relevance, either by limiting the target community under study or improving the focus or speed of screening procedures. Lastly, given the cost and infrastructure necessary for large metagenome projects, and the almost inexhaustible amount of data they can produce, trends toward broader use of metagenome data across the research community coupled with the needed investment in bioinformatics infrastructure devoted to metagenomics will no doubt further increase the value of metagenomic studies in various environments.
| S-EPMC1915608 | biostudies-other
Project description:Microbes are increasingly being implicated in autoimmune disease. This calls for a re-evaluation of how these chronic inflammatory illnesses are routinely treated. The standard of care for autoimmune disease remains the use of medications that slow the immune response, while treatments aimed at eradicating microbes seek the exact opposite-stimulation of the innate immune response. Immunostimulation is complicated by a cascade of sequelae, including exacerbated inflammation, which occurs in response to microbial death. Over the past 8 years, we have collaborated with American and international clinical professionals to research a model-based treatment for inflammatory disease. This intervention, designed to stimulate the innate immune response, has required a reevaluation of disease progression and amelioration. Paramount is the inherent conflict between palliation and microbicidal efficacy. Increased microbicidal activity was experienced as immunopathology-a temporary worsening of symptoms. Further studies are needed, but they will require careful planning to manage this immunopathology.
| S-EPMC4076734 | biostudies-other
Project description:Chlamydiales bacterium BSEPT1 genome assembly, xbBatSept2.Chlamydiales_sp._1
| PRJEB76743 | ENA
Project description:Nitrospina gracilis Nb-211 transcriptome - 211N-1 _1
| PRJNA1095939 | ENA
Project description:RBSR1-CTAP expressing cells were transfected with RNAi targeting RBSR1. 3 independent clones were used and RNAi was induced for 24 hours with 100ng/ml tetracycline. PolyA enriched samples are paired-end reads, file names ending _1 are one strand and _2 are the other strand. rRNA depleted sample are single end reads.
2022-04-29 | E-MTAB-11627 | biostudies-arrayexpress