PXD023710

PXD023710 is an original dataset announced via ProteomeXchange.

Title	LC-MS/MS of autotrophic culture BP, that performs nitrate reduction coupled to iron(II) oxidation (NDFO)
Description	Nitrate-reducing iron(II)-oxidizing (NDFO) bacteria are widespread in the environment contribute to nitrate removal and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing iron(II)-oxidizing bacteria is rarely investigated and poorly understood. The most prominent model system for this type of studies is enrichment culture KS, which originates from a freshwater sediment in Bremen, Germany. A second NDFO culture, culture BP, was obtained with a sample taken in 2015 at the same pond and cultured in a similar way. To gain insights in the metabolism of nitrate reduction coupled to iron(II) oxidation under in the absence of organic carbon and oxygen limited conditions, we performed metagenomic, metatranscriptomic and metaproteomic analyses of culture BP. Raw sequencing data of 16S rRNA amplicon sequencing (V4 region with Illumina and near full-length with PacBio), shotgun metagenomics, metagenome assembly, raw sequencing data of shotgun metatranscriptomes (2 conditions, triplicates) can be found at SRA in https://www.ncbi.nlm.nih.gov/bioproject/PRJNA693457. This dataset contains proteomics data for 2 conditions in triplicates. Samples R23, R24, and R25 are grown in autotrophic conditions, samples R26, R27, and R28 in heterotrophic conditions.
HostingRepository	PRIDE
AnnounceDate	2021-05-17
AnnouncementXML	Submission_2021-05-17_12:22:04.281.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Daniel Straub
SpeciesList	scientific name: freshwater sediment metagenome; NCBI TaxID: 556182;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2021-01-20 08:18:13	ID requested
⏵ 1	2021-05-17 12:22:04	announced

Dataset with its publication pending

submitter keyword: metagenome, LC-MS/MS, nitrate reduction, iron oxidation

Sara Kleindienst
contact affiliation	Department of Geosciences Eberhard-Karls-University Tübingen Schnarrenbergstrasse 94-96 72076 Tübingen Germany
contact email	sara.kleindienst@uni-tuebingen.de
lab head
Daniel Straub
contact affiliation	University of Tübingen
contact email	daniel.straub@uni-tuebingen.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/05/PXD023710

PRIDE project URI

• PRIDE
  1. PXD023710
     1. Label: PRIDE project
     2. Name: LC-MS/MS of autotrophic culture BP, that performs nitrate reduction coupled to iron(II) oxidation (NDFO)