PXD001796

PXD001796 is an original dataset announced via ProteomeXchange.

Title	Integration of transcriptome and proteome annotation in the naive Ixodes ricinus midgut with genome sequencing
Description	In Europe, ticks are the most important vectors of diseases threatening humans, livestock, wildlife and companion animals. Nevertheless, genomic sequence information and functional annotation of proteins of the most important European tick, Ixodes ricinus, is limited. Here we present the first analysis of the I. ricinus genome and of the transcriptome of the unfed I. ricinus midgut. We combined and integrated data from genome, transcriptome and proteome. The de novo assembly of 1 billion paired-end sequences identified 6,415 putative genes providing an unprecedented insight into the I. ricinus genome. Mapping of our midgut mRNA reads to the assembled contigs let us estimate to cover around two third of the unique genomic sequences. In addition, more than 10,000 transcripts from naïve midgut were annotated functionally and/or locally. By combining the alignment-based with a motif-search based annotation approach, we could double the number of annotations throughout all groups without shifting the dataset. Moreover, 1,175 proteins expressed in the naïve midgut were identified by mass spectrometry confirming the high completeness of our transcriptome database, and 608 were significantly annotated for function and/or localization. This multiple-omics study vastly extends the publicly available DNA, RNA and protein databases for I. ricinus and ticks in general.
HostingRepository	PRIDE
AnnounceDate	2017-08-08
AnnouncementXML	Submission_2017-08-08_06:13:56.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD001796
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Wibke Cramaro
SpeciesList	scientific name: Ixodes ricinus (Common tick); NCBI TaxID: 34613;
ModificationList	dihydroxylated residue; (18)O label at both C-terminal oxygens; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	AB SCIEX TOF/TOF T2D file

Revision	Datetime	Status	ChangeLog Entry
0	2015-02-09 04:57:02	ID requested
1	2015-11-04 05:57:18	announced
⏵ 2	2017-08-08 06:13:58	announced	Updated project metadata.

Cramaro WJ, Revets D, Hunewald OE, Sinner R, Reye AL, Muller CP, ve midgut. BMC Genomics, 16():871(2015) [pubmed]

curator keyword: Biological, Biomedical

submitter keyword: Ixodes ricinus, midgut, naive, unfed

Claude P Muller
contact affiliation	Department of Immunology Luxembourg Institute of Health Luxembourg
contact email	claude.muller@lih.lu
lab head
Wibke Cramaro
contact affiliation	Department of Immunology, Luxembourg Institute of Health
contact email	wibke.jochum@lih.lu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD001796
     1. Label: PRIDE project
     2. Name: Integration of transcriptome and proteome annotation in the naive Ixodes ricinus midgut with genome sequencing