PXD014881-2

PXD014881 is an original dataset announced via ProteomeXchange.

Title	Testing long-term (up to 4 weeks) RNAlater preservation of field collected animal-microbe symbioses at room temperature 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 first tested if RNAlater allows to preserve proteins in animal-microbe symbioses as efficiently as flash freezing and without introducing issues with downstream processing (see PXD014591). Second, for the data in this PRIDE submission we tested if RNAlater preserves protein expression patterns over time at room temperature. We used the marine gutless oligochaete Olavius algarvensis as a test case. 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). For this dataset, we fixed a total of 33 worms and incubated them in RNAlater for up to 4 weeks. We then evaluated proteome preservation quality in terms of the number of identified proteins, abundances of individual proteins and potential biases against specific protein or taxonomic groups. Out of this 33 samples, eleven worms were incubated for 24 hours in RNAlater at 4°C (t0), while the other worms were incubated in RNAlater at room temperature (21-23°C) for additional 24 hours (t1, 6 worms), one week (t2, 8 worms), and four weeks (t3, 8 worms). We removed RNAlater from the worms after incubation and froze the samples at -80°C.
HostingRepository	PRIDE
AnnounceDate	2023-09-28
AnnouncementXML	Submission_2023-09-28_03:42:07.306.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 4 endosymbiont; NCBI TaxID: 260707; scientific name: Olavius algarvensis Delta 1 endosymbiont; NCBI TaxID: 334747;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-08-01 09:01:27	ID requested
1	2021-11-03 05:15:33	announced
⏵ 2	2023-09-28 03:42:08	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/PXD014881

PRIDE project URI

• PRIDE
  1. PXD014881
     1. Label: PRIDE project
     2. Name: Testing long-term (up to 4 weeks) RNAlater preservation of field collected animal-microbe symbioses at room temperature for metaproteomic analyses