Dataset Information

The Comprehensive Mouse Retina PhosphoProteome

ABSTRACT: Diverse groups of proteins play integral roles in both the physiology and pathophysiology of the mouse retina. A comprehensive mouse retina phosphoproteome has been developed using a discovery-based proteomic approach in conjunction with an enrichment procedure for phosphopeptides.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Retina

SUBMITTER: Jessie Guidry

LAB HEAD: Jessie Guidry

PROVIDER: PXD009981 | Pride | 2019-02-16

REPOSITORIES: Pride

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Publications

Comprehensive characterization of the adult ND4 Swiss Webster mouse retina: Using discovery-based mass spectrometry to decipher the total proteome and phosphoproteome.

Harman Jarrod C JC Guidry Jessie J JJ Gidday Jeffrey M JM

Molecular vision 20181231

<h4>Purpose</h4>Diverse groups of proteins play integral roles in both the physiology and pathophysiology of the retina. However, thorough proteomic analyses of retinas of experimental species are currently unavailable. The purpose of the present paper is providing the field with a comprehensive proteomic characterization of the retina of a commonly used laboratory mouse using a discovery-based mass spectrometry (MS) approach.<h4>Methods</h4>Retinas from eight male and eight female 30-week-old o ...[more]

PMID: 30713425

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Project description:Background: MycobacteriumM-BM- bovis, the causative agent of bovine tuberculosis, is an intracellular pathogen that can persist inside host macrophages during infection via a diverse range of mechanisms that subvert the host immune response. In the current study, we have analysed and compared the transcriptomes of M.M-BM- bovis-infected monocyte-derived macrophages (MDM) purified from six Holstein-Friesian females with the transcriptomes of non-infected control MDM from the same animals over a 24 h period using strand-specific RNA sequencing (RNA-seq). In addition, we compare gene expression profiles generated using RNA-seq with those previously generated by us using the high-density AffymetrixM-BM-. GeneChipM-BM-. Bovine Genome Array platform from the same MDM-extracted RNA. Results: A mean of 7.2 million reads from each MDM sample mapped uniquely and unambiguously to single BosM-BM- taurus reference genome locations. Analysis of these mapped reads showed 2,584 genes (1,392 upregulated; 1,192 downregulated) and 757 putative natural antisense transcripts (558 upregulated; 119 downregulated) that were differentially expressed based on sense and antisense strand data, respectively (adjusted P-value M-bM-^IM-$ 0.05). Of the differentially expressed genes, 694 were common to both the sense and antisense data sets, with the direction of expression (i.e. up- or downregulation) positively correlated for 693 genes and negatively correlated for the remaining gene. Gene ontology analysis of the differentially expressed genes revealed an enrichment of immune, apoptotic and cell signalling genes. Notably, the number of differentially expressed genes identified from RNA-seq sense strand analysis was greater than the number of differentially expressed genes detected from microarray analysis (2,584 genes versus 2,015 genes). Furthermore, our data reveal a greater dynamic range in the detection and quantification of gene transcripts for RNA-seq compared to microarray technology.M-BM- Conclusions: This study highlights the value of RNA-seq in identifying novel immunomodulatory mechanisms that underlie host-mycobacterial pathogen interactions during infection, including possible complex post-transcriptional regulation of host gene expression involving antisense RNA. Description of the transcriptomic host response after infection of bovine monocyte-derived macrophages with Mycobacterium bovis

Dataset Information

The Comprehensive Mouse Retina PhosphoProteome

Publications

Comprehensive characterization of the adult ND4 Swiss Webster mouse retina: Using discovery-based mass spectrometry to decipher the total proteome and phosphoproteome.

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