Dataset Information

Bering Strait surface water and Chukchi Sea bottom water microbiome metaproteomics

ABSTRACT: Analysis of bacterial fraction collected on GF/F filters post pre-filtration on 1um filter. 15L were filtered from Bering Strait (BSt) surface water and Chukchi Sea (station 2) bottom waters.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Marine Metagenome

TISSUE(S): Cell Suspension Culture

SUBMITTER: Brook Nunn

LAB HEAD: Brook L. Nunn

PROVIDER: PXD006472 | Pride | 2019-01-25

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

Items per page:

1 - 5 of 7

Publications

An Alignment-Free "Metapeptide" Strategy for Metaproteomic Characterization of Microbiome Samples Using Shotgun Metagenomic Sequencing.

May Damon H DH Timmins-Schiffman Emma E Mikan Molly P MP Harvey H Rodger HR Borenstein Elhanan E Nunn Brook L BL Noble William S WS

Journal of proteome research 20160719 8

In principle, tandem mass spectrometry can be used to detect and quantify the peptides present in a microbiome sample, enabling functional and taxonomic insight into microbiome metabolic activity. However, the phylogenetic diversity constituting a particular microbiome is often unknown, and many of the organisms present may not have assembled genomes. In ocean microbiome samples, with particularly diverse and uncultured bacterial communities, it is difficult to construct protein databases that c ...[more]

PMID: 27396978

Similar Datasets

Project description:Cross species comparison of genomes and transcriptomes is a powerful tool for understanding underlying biological processes, accurate functional classification of genes, and discovery of novel elements. The shift to next-generation sequencing platforms has tremendously accelerated the analysis of genomes and transcriptomes. The use of this technology for transcriptome analysis has many advantages over hybridization based technologies, including higher sensitivity and specificity, and eliminates the need for probe design. Using Illumina sequencing of mRNAs, we have captured the global transcriptional profiles of the developmental cycles of D. discoideum and D. purpureum. The morphology and transcriptional profiles in these two species have been largely conserved even after greater than 300 million years of divergence. We also captured the transcriptional profiles of prespore and prestalk cells from both species. The RNA-seq results correlate well with previously known markers and reveal many new transcripts with unique developmental regulation and cell type enrichment. Our analysis provides the first complete picture of the transcriptional landscape in both D. discoideum and D. purpureum. Transcriptional abundance of over 13,900 genome elements from seven time points of development, and prespore/prestalk cell types will be available through a graphical, highly-interactive, explorative web interface at: http://www.ailab.si/dictyexpress , which currently displays all of our published microarray data. Sequence coverage at a single nucleotide resolution will also be available through an interactive genome browser. These data, from morphology to genome to transcriptome, provide a global picture of the developmental cycles of D. discoideum and D. purpureum and will facilitate the functional classification of genes, as well as discovery of novel genes, splice variants, regulatory elements and non-coding RNAs. Keywords: Transcriptome Analysis Examination of 7 developmental time points in two cell types with 2 biological replicates for each sample.

			Action	DRS
	2016_Jan_12_QE2_45.raw	Raw
	2016_Jan_12_QE2_46.raw	Raw
	2016_Jan_12_QE2_47.raw	Raw
	2016_Jan_12_QE2_51.raw	Raw
	2016_Jan_12_QE2_52.raw	Raw