Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomic profiling of rabbit eyes

ABSTRACT: Rabbits have been widely used for studying ocular physiology and pathology due to their relatively large eye size and similar structures with human eyes. Various rabbit ocular disease models, such as dry eye, age-related macular degeneration, and glaucoma, have been established. Despite the growing application of proteomics in vision research using rabbit ocular models, there is no spectral assay library for rabbit eye proteome publicly available. Here, we generated spectral assay libraries for rabbit eye compartments, including conjunctiva, cornea, iris, retina, sclera, vitreous humor, and tears using fractionated samples and ion mobility separation enabling deep proteome coverage. The rabbit eye spectral assay library includes 9,153 protein groups, and 107,898 peptides. We present the data as a freely available community resource for proteomic studies in the vision field.

INSTRUMENT(S): timsTOF Pro

ORGANISM(S): Oryctolagus Cuniculus (rabbit)

TISSUE(S): Eye, Iris, Cornea, Tear, Vitreous Humor, Retina, Conjunctiva, Sclera

SUBMITTER: Guoting Qin

LAB HEAD: Guoting Qin

PROVIDER: PXD029818 | Pride | 2021-11-24

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	RabbitConjunctiva-Fraction10_Slot1-37_01_3008.d.zip	Other
	RabbitConjunctiva-Fraction11_Slot1-38_01_3009.d.zip	Other
	RabbitConjunctiva-Fraction12_Slot1-39_01_3010.d.zip	Other
	RabbitConjunctiva-Fraction13_Slot1-40_01_3011.d.zip	Other
	RabbitConjunctiva-Fraction14_Slot1-41_01_3012.d.zip	Other

Items per page:

1 - 5 of 132

Similar Datasets

Proteomic profiling of various rabbit eye tissues

Project description:Rabbits have been widely used for studying ocular physiology and pathology due to their relatively large eye size and similar structures with human eyes. Various rabbit ocular disease models, such as dry eye, age-related macular degeneration, and glaucoma, have been established. Despite the growing application of proteomics in vision research using rabbit ocular models, there is no spectral assay library for rabbit eye proteome publicly available. Here, we generated spectral assay libraries for rabbit eye compartments, including conjunctiva, cornea, iris, retina, sclera, vitreous humor, and tears using fractionated samples and ion mobility separation enabling deep proteome coverage. The rabbit eye spectral assay library includes 9,830 protein groups and 113,593 peptides. We present the data as a freely available community resource for proteomic studies in the vision field.

2022-02-21 | PXD031194 | Pride

Eye proteome of Drosophila melanogaster

Project description:We report the proteome composition of the Drosophila eye – a compound organ that is highly enriched in membrane proteins. The fly eye is a popular model to study the physiology of vision by means of genetic, pharmacological, and dietary interference.While the eye transcriptome and development-related changes of gene expression profiles have been extensively studied, little is known about the eye proteome.we employed GeLC-MS/MS to identify and rank the abundances of 3516 eye proteins. Moreover, we applied our MS Western method to determine the absolute (molar) abundances of a related set of proteins that are important for photoreceptor structure (including maintenance) and function (phototransduction). Altogether, we provide a comprehensive and expandable proteomics resource that will be valuable for a variety of studies of ocular biochemistry, physiology, and development.

2024-08-09 | PXD044845 | Pride

RNA-Seq of eye tissues from A/J, BALB/c, and C57BL/6 background mice

Project description:We report RNA-Seq experiments of whole eye tissues from A/J, BALB/c, and C57BL/6 background mice. Examine ocular tissue from 3 different background mice that display varying rates of retinal degeneration.

2012-06-07 | E-GEOD-38359 | biostudies-arrayexpress

RNA-Seq of eye tissues from C57BL/6J background mice at 1.5 h and 9.0 h after light onset

Project description:We report RNA-Seq experiments of whole eye tissues from C57BL/6J background mice at 1.5 h and 9.0 h after light onset to better understand photoreceptor phagocytosis Examine ocular tissue from mice at different time points

2013-08-07 | E-GEOD-48974 | biostudies-arrayexpress

Alanine scan of 11 amino acid long novel linear epitope from C. jejuni cj0669 protein

Project description:A short sequence of 11 amino acids belonging to the cj0669 protein from Campylobacter jejuni NCTC 11168, which was previously identified as potentially immunogenic, was analyzed via alanine scanning to narrow down the significant amino acid residues within the sequence. Twelve peptides, one representing the original sequence and eleven peptides with each residue replaced by alanine in turn, were synthesized on microarrays by JPTs Pepstar Technology. For each microarray, nine replicates for each peptide were spotted. The microarray was separated into three incubation chambers by the ProPlate 3-well module (Grace Biolabs) to allow for incubation with different antibodies in parallel. For specific interactions, rabbit polyclonal IgG to C. jejuni was used, while unspecific binding to the epitope sequence was checked using rabbit polyclonal IgG to Salmonella enterica.

2013-04-06 | E-GEOD-45556 | biostudies-arrayexpress

Human Corneal Epithelial Cells (hTCEpi) 6h Treatment with 100nM Vitamin D (1,25D3) vs. Vehicle Control

Project description:Inflammatory signals must be regulated and kept in check in order to prevent tissue damage. This is especially true in the cornea, where damage can induce loss of transparency, essential for vision. Toll-like receptors (TLRs) are present at the ocular surface and, in addition to being protective against infection, have also been implicated in the pathogenesis of dry eye syndrome, an inflammatory condition that affects millions of individuals in the United States each year. Therefore, an important area of research is the development of new anti-inflammatory therapeutics that limit aberrant ocular surface inflammation. Vitamin D has been studied for its role in suppressing inflammation in other tissues. In previous studies, we have demonstrated that vitamin D is able to decrease proinflammatory mediators induced by TLRs in human corneal epithelial cells (HCEC). Therefore, the goal of the current study was to examine this mechanism further through an evaluation of vitamin Dâs influence on gene expression in two different HCEC cell lines. Microarray comparing hTCEpi, human corneal epithelial cells, treated for 6 hours with Vitamin D (1,25D3) and control (0.1% ethanol) Two-condition arrays: hTCEpi cells were treated with either 100nM 1,25D3 or 0.1% Ethanol for 6h. Two biological replicates, one per array, with a dye swap (technical replicate).

2016-09-01 | E-GEOD-72662 | biostudies-arrayexpress

Lacripep promotes corneal regeneration in autoimmune mediated dry eye disease

Project description:Corneal architecture is essential for vision and is greatly perturbed by the absence of tears due to the highly prevalent disorder dry eye. With no regenerative therapies available, pathological alterations of the ocular surface in response to dryness, including persistent epithelial defects and poor wound healing, result in lifelong morbidity. Here, using a mouse model of aqueous-deficient dry eye, we reveal that topical application of the synthetic tear protein lacripep reverses the pathological outcomes of dry eye through restoring the extensive network of corneal nerves that are essential for tear secretion, barrier function, epithelial homeostasis and wound healing. Intriguingly, the restorative effects of lacripep occur despite extensive immune cell infiltration, suggesting tissue reinnervation and regeneration can be achieved under chronic inflammatory conditions. In summary, our data highlight lacripep as a first-in-class regenerative therapy for returning the cornea to a near homeostatic state in individuals who suffer from dry eye.

2022-07-18 | GSE208297 | GEO

The transcriptome of rabbit conjunctiva in dry eye disease: Large-scale changes and similarity to the human dry eye

Project description:Rabbit Dry Eye Diesease model induced with 3 weekly injections of Concanavalin A into the periorbital lacrimal glands Male Dutch-Belted rabbits. The pathophysiology of dry eye disease (DED) remains largely unknown, accounting in part for the lack of successful treatments. The transcriptome of full-thickness’s conjunctival tissue from rabbits with DED and from normal controls was determined using microarrays. DED induced large-scale changes in gene transcription involving 5,184 genes (22% of the total). Differentially expressed genes could be segregated into: functional modules and clusters; altered pathways; functionally linked genes; and groups of individual genes of known or suspected pathophysiological relevance to DED. A common feature of these subgroups is the breadth and magnitude of the changes that encompass ocular immunology and essentially all aspects of cell biology. Prominent changes concerned innate and adaptive immune responses; ocular surface inflammation; at least 25 significantly altered signaling pathways; a large number of chemokines; cell cycle; and apoptosis. Comparison of our findings to the limited extant transcriptomic data from DED patients associated with either Sjogren’s syndrome or non-Sjogren’s etiologies revealed a significant correlation between human and rabbit DED transcriptomes. Our data, establishing the large-scale transcriptomic changes of DED and their potential similarity to the human, underscore the enormous complexity of DED; establish a robust animal model of DED; will help expand our understanding of its pathophysiology; and could guide the development of successful therapeutic strategies.

2021-03-30 | GSE171043 | GEO

Alanine scan of 11 amino acid long novel linear epitope from C.jejuni cj0669 protein [2]

Project description:A short sequence of 11 amino acids belonging to the cj0669 protein from Campylobacter jejuni NCTC 11168 which was previously identified as potentially immunogenig was analyzed via alanine scanning to narrow down the significant amino acid residues within the sequence. Twelve peptides, one representing the original sequence and eleven peptides with each residue replaced by alanine in turn, were synthesized on microarrays by JPTs Pepstar Technology. For each microarray, nine replicates for each peptide were spotted. The microarray was seperated into three incubation chambers by the ProPlate 3-well module (Grace Biolabs) to allow for incubation with different antibodies in parallel. For specific interaction rabbit polyclonal IgG to C.jejuni was used, while non-specific binding to the epitope sequence was checked using rabbit polyclonal IgG to H. pylori (Abcam ab20459).

2013-05-06 | E-GEOD-46651 | biostudies-arrayexpress

A DNA methylation atlas of the human eye and its diseases

Project description:Genome-scale DNA methylation profiling using the Infinium DNA methylation BeadChip platform and samples from normal human eye and five ocular- related diseases DNA methylation analysis of eye samples from patient suffering ocular diseases (retinal detachment, diabetic retinopathy, glaucoma, uveal melanoma and retinoblastoma) using the Infinium DNA methylation BeadChip platform .

2017-05-02 | E-GEOD-57362 | biostudies-arrayexpress