<<< Full experiment listing

PXD014591-1

PXD014591 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleComparison of sample preservation methods for field collection of animal-microbe symbioses for metaproteomic analyses
DescriptionWhen 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.
HostingRepositoryPRIDE
AnnounceDate2021-11-03
AnnouncementXMLSubmission_2021-11-03_04:53:41.102.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterMarlene Jensen
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: Olavius algarvensis; NCBI TaxID: 188229; scientific name: Spirochaeta sp. ELBA; NCBI TaxID: 1117957; scientific name: Olavius algarvensis Delta 1 endosymbiont; NCBI TaxID: 334747; scientific name: Olavius algarvensis Delta 4 endosymbiont; NCBI TaxID: 260707;
ModificationListmonohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02019-07-12 06:23:01ID requested
12021-11-03 04:53:41announced
22023-09-28 03:42:18announced2023-09-28: Updated project metadata.
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: 1D-LC, metaproteomics, metaproteome, chemosynthetic symbiosis, gutless oligochaetes, Olavius algarvensis, proteobacteria, thiotrophic endosymbionts, RNAlater, sample preservation, field samples, microbiome
Contact List
Dr. Manuel Kleiner
contact affiliationNorth Carolina State University
contact emailmanuel_kleiner@ncsu.edu
lab head
Marlene Jensen
contact affiliationNorth Carolina State University
contact emailmjensen2@ncsu.edu
dataset submitter
Full Dataset Link List
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
Repository Record List
[ + ]