PXD004931

PXD004931 is an original dataset announced via ProteomeXchange.

Title	Two distinct extracellular protein signatures released by a single cell type identified by LC-MS/MS
Description	Cells secrete extracellular RNA (exRNA) to their surrounding environment and exRNA has been found in many body fluids such as blood, breast milk and cerebrospinal fluid. However, there are conflicting results regarding the nature of exRNA. Here, we have separated two distinct exRNA profiles released by mast cells, here termed high-density (HD) and low-density (LD) exRNA. The exRNA in both fractions was characterized by microarray and next-generation sequencing. Both exRNA fractions contained mRNA and miRNA, and the mRNAs in the LD exRNA correlated closely with the cellular mRNA, whereas the HD mRNA did not. Furthermore, the HD exRNA was enriched in lincRNA, antisense RNA, vault RNA, snoRNA, and snRNA with little or no evidence of full-length 18S and 28S rRNA. The LD exRNA was enriched in mitochondrial rRNA, mitochondrial tRNA, tRNA, piRNA, Y RNA, and full-length 18S and 28S rRNA. The proteomes of the HD and LD exRNA-containing fractions were determined with LC-MS/MS and analysed with Gene Ontology term finder, which showed that both proteomes were associated with extracellular vesicles. Additionally, the proteins in the HD fractions tended to be associated with the nucleus and ribosomes, whereas the LD fraction proteome tended to be associated with the mitochondrion. We show that the two exRNA signatures released by a single cell type can be separated by floatation on a density gradient. These results show that cells can release multiple types of exRNA with substantial differences in RNA species content. This is important for any future studies determining the nature and function of exRNA released from different cells under different conditions.
HostingRepository	PRIDE
AnnounceDate	2018-10-26
AnnouncementXML	Submission_2018-10-26_13:58:33.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Dae-Kyum Kim
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2016-09-12 02:22:10	ID requested
⏵ 1	2018-10-26 13:58:34	announced

L, ä, sser C, Shelke GV, Yeri A, Kim DK, Crescitelli R, Raimondo S, Sj, ö, strand M, Gho YS, Van Keuren Jensen K, L, ö, tvall J, Two distinct extracellular RNA signatures released by a single cell type identified by microarray and next-generation sequencing. RNA Biol, 14(1):58-72(2017) [pubmed]

curator keyword: Biological

submitter keyword: Exosome

Jan Lötvall
contact affiliation	Krefting Research Centre, Department of Internal Medicine and Clinical Nutrition, University of Gothenburg, Gothenburg, Sweden
contact email	jan.lotvall@gu.se
lab head
Dae-Kyum Kim
contact affiliation	Department of Life Science
contact email	sses162@postech.ac.kr
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/2018/10/PXD004931

PRIDE project URI

• PRIDE
  1. PXD004931
     1. Label: PRIDE project
     2. Name: Two distinct extracellular protein signatures released by a single cell type identified by LC-MS/MS