PXD014591

PXD014591 is an original dataset announced via ProteomeXchange.

Title	Comparison of sample preservation methods for field collection of animal-microbe symbioses for metaproteomic analyses
Description	When studying gene expression in microbe-animals symbioses collected in the field it is essential to quickly and efficiently preserve in situ symbiont and host gene expression patterns. One of the most commonly used sample preservation methods for samples targeted for proteomic analyses is flash freezing, however, liquid nitrogen or dry ice needed for flash freezing are often not available at remote field sites. We tested if RNAlater allows to preserve proteins in animal-microbe symbioses as efficiently as flash freezing and without introducing issues with downstream processing. We used the marine gutless oligochaete Olavius algarvensis as a model for testing. Olavius algarvensis lives in shallow water sediments off the coast of Elba, Italy. It has no digestive and excretory system and harbors five bacterial symbionts that fulfill its nutritional and waste recycling needs (Kleiner et al., 2012, PNAS 109(19):1173-82). We compared five RNAlater preserved and five flash frozen samples in terms of the number of identified proteins, abundances of individual proteins and potential biases against specific protein or taxonomic groups. Five worms were incubated in RNAlater for 24 hours. After incubation, RNAlater was removed and samples were stored at -80°C. The remaining five worms were preserved with liquid nitrogen and stored at -80 °C immediately after preservation.
HostingRepository	PRIDE
AnnounceDate	2023-09-28
AnnouncementXML	Submission_2023-09-28_03:42:18.068.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	MarleneJensen
SpeciesList	scientific name: Olavius algarvensis spirochete endosymbiont; NCBI TaxID: 260710; scientific name: Olavius algarvensis Gamma 1 endosymbiont; NCBI TaxID: 260705; scientific name: Olavius algarvensis sulfate-reducing endosymbiont; NCBI TaxID: 146479; scientific name: Chromatiales bacterium OalgGamma1; NCBI TaxID: 1123869; scientific name: Olavius algarvensis Gamma 3 endosymbiont; NCBI TaxID: 260704; scientific name: Spirochaeta sp. ELBA; NCBI TaxID: 1117957; scientific name: Olavius algarvensis; NCBI TaxID: 188229; scientific name: Olavius algarvensis Delta 1 endosymbiont; NCBI TaxID: 334747; scientific name: Olavius algarvensis Delta 4 endosymbiont; NCBI TaxID: 260707;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-07-12 06:23:01	ID requested
1	2021-11-03 04:53:41	announced
⏵ 2	2023-09-28 03:42:18	announced	2023-09-28: Updated project metadata.

Jensen M, Wippler J, Kleiner M, as a Field-Compatible Preservation Method for Metaproteomic Analyses of Bacterium-Animal Symbioses. Microbiol Spectr, 9(2):e0142921(2021) [pubmed]

submitter keyword: 1D-LC, Olavius algarvensis, metaproteome, gutless oligochaetes, microbiome, RNAlater, chemosynthetic symbiosis, field samples, proteobacteria, sample preservation, thiotrophic endosymbionts, metaproteomics

Dr. ManuelKleiner
contact affiliation	North Carolina State University
contact email	manuel_kleiner@ncsu.edu
lab head
MarleneJensen
contact affiliation	North Carolina State University
contact email	mjensen2@ncsu.edu
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/2021/11/PXD014591

PRIDE project URI

• PRIDE
  1. PXD014591
     1. Label: PRIDE project
     2. Name: Comparison of sample preservation methods for field collection of animal-microbe symbioses for metaproteomic analyses