Human metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA48477 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Human Microbiome Project (HMP) Metagenomic WGS Projects, deeper sequencing of the human microbiome samples: Mock Pilot
| PRJNA48475 | ENA
Project description:Human Microbiome Project (HMP) Metagenomic WGS Projects, deeper sequencing of the human microbiome samples: Production Phase
| PRJNA48479 | ENA
Project description:EMG produced TPA metagenomics assembly of the Human Microbiome Project (HMP) Metagenomic WGS Projects, deeper sequencing of the human microbiome samples: Production Phase (human metagenome) data set
| PRJEB22283 | ENA
Project description:Deeper shotgun sequencing of human microbiome samples for the Human Microbiome Project (HMP)
| PRJNA43017 | ENA
Project description:Evaluation of short-read-only, long-read-only, and hybrid assembly approaches on metagenomic samples demonstrating how they affect gene and protein prediction which is relevant for downstream functional analyses. For a human gut microbiome sample, we use complementary metatranscriptomic, and metaproteomic data to evaluate the metagenomic-based protein predictions.
2022-02-17 | PXD025505 | Pride
Project description:Sub-Saharan Africa represents 69% of the total number of individuals living with HIV infection worldwide and 72% of AIDS deaths globally. Pulmonary infection is a common and frequently fatal complication, though little is known regarding the lower airway microbiome composition of this population. Our objectives were to characterize the lower airway microbiome of Ugandan HIV-infected patients with pneumonia, to determine relationships with demographic, clinical, immunological, and microbiological variables and to compare the composition and predicted metagenome of these communities to a comparable cohort of patients in the US (San Francisco). Bronchoalveolar lavage samples from a cohort of 60 Ugandan HIV-infected patients with acute pneumonia were collected. Amplified 16S ribosomal RNA was profiled and aforementioned relationships examined. Ugandan airway microbiome composition and predicted metagenomic function were compared to US HIV-infected pneumonia patients. Among the most common bacterial pulmonary pathogens, Pseudomonas aeruginosa was most prevalent in the Ugandan cohort. Patients with a richer and more diverse airway microbiome exhibited lower bacterial burden, enrichment of members of the Lachnospiraceae and sulfur-reducing bacteria and reduced expression of TNF-alpha and matrix metalloproteinase-9. Compared to San Franciscan patients, Ugandan airway microbiome were significantly richer, and compositionally distinct with predicted metagenomes that encoded a multitude of distinct pathogenic pathways e.g secretion systems. Ugandan pneumonia-associated airway microbiome is compositionally and functionally distinct from those detected in comparable patients in developed countries, a feature which may contribute to adverse outcomes in this population. Please note that the data from the comparable cohort of patients in the USUS data was published as supplemental material of PMID: 22760045 but not submitted to GEO The 'patient_info.txt' contains 12 clinical, 7 immunological and 3 microbiological variables for each patient. The G2 PhyloChip microarray platform (commercially available from Second Genome, Inc.) was used to profile bacteria in lower airway samples from 60 subjects
2014-02-20 | E-GEOD-52791 | biostudies-arrayexpress
Project description:Pilot projects for the human ENCODE project.
| PRJNA13681 | ENA
Project description:Metagenomic sequencing data of human gut microbiome
| EGAD00001007735 | EGA
Project description:Despite the uniform mortality in pancreatic adenocarcinoma (PDAC), clinical disease heterogeneity exists with limited genomic differences. A highly aggressive tumor subtype termed basal-like was identified to show worse outcomes and higher inflammatory responses. Here, we focus on the microbial effect in PDAC progression and present a comprehensive analysis of the tumor microbiome in different PDAC subtypes. Tumors from 62 resectable PDAC patients were subjected to metagenomic sequencing and RNA-seq.
2021-08-30 | GSE172356 | GEO
Project description:This project reanalzyes data from 4 other projects. Information about the samples can be found in the following four publications. The four samples used in this study include a ocean metaproteome sample, a human sample, a E. coli sample, and a Plamodium falciparum sample. B. N. Pease, E. L. Huttlin, M. P. Jedrychowski, E. Talevich, J. Harmon, T. Dillman, N. Kannan, C. Doerig, R. Chakrabarti, S. P. Gygi, and D. Chakrabarti. Global analysis of protein expression and phosphorylation of three stages of Plasmodium falciparum intraerythrocytic development. Journal of Proteome Research, 12:4028–4045, 2013. Damon H. May, Emma Timmins-Schiffman, Molly P. Mikan, H. Rodger Harvey, Elhanan Borenstein, Brook L. Nunn, and William S. Noble. An alignment-free metapeptide strategy for metaproteomic characterization of microbiome samples using shotgun metagenomic sequencing. Journal of Proteome Research, 15(8):2697–2705, 2016. PMID: 27396978. M. Kim, S. M. Pinto, D. Getnet, R. S. Nirujogi, S. S. Manda, R. Chaerkady, A. K. Madugundu, D. S. Kelkar, R. Isserlin, S. Jain, et al. A draft map of the human proteome. Nature, 509(7502):575–581, 2014. Hansjrg G ̋tzke, Claudio Muheim, A.F. Maarten Altelaar, Albert J.R. Heck, Gianluca Maddalo, and Daniel O. Daley. Identification of putative substrates for the periplasmic chaperone yfgm in Escherichia coli using quantitative proteomics. Molecular & Cellular Proteomics, 14(1):216–226, 2015.
2018-09-19 | PXD009265 | Pride