Ontology highlight
ABSTRACT:
PROVIDER: PRJNA769738 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16264815.fastq.gz | Fastqsanger.gz | |||
| SRR16264816.fastq.gz | Fastqsanger.gz | |||
| SRR16264817.fastq.gz | Fastqsanger.gz | |||
| SRR16264818.fastq.gz | Fastqsanger.gz | |||
| SRR16264819.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 13 |
Similar Datasets
Project description:This is a genome-wide association study performed in Sjogrens syndrome in which gene expression data was used in conjunction with genotype data to perform expression quantitative trait loci (eQTL) analysis.
2013-10-06 | GSE51092 | GEO
Project description:This is a genome-wide association study performed in Sjogrens syndrome in which gene expression data was used in conjunction with genotype data to perform expression quantitative trait loci (eQTL) analysis. This is a case/control study.
2013-10-06 | E-GEOD-51092 | biostudies-arrayexpress
Project description:Tear fluid is emerging as a valuable resource for biomarker discovery, but its low sample volume and dynamic composition pose significant challenges for analytical testing. Most tear proteomics studies have focused on samples collected with Schirmer strips, while capillary tube collection has received less attention. To address these challenges, we developed a novel in-capillary trypsin digestion workflow that requires as little as 0.5 μL of tear fluid for bottom-up shotgun proteomics. This method uses liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify a higher number of proteins with enhanced efficiency compared to previously reported methods, which typically required 5-10 μL of pooled tear fluid. Using the same microcentrifuge tube for both tear collection and sample processing, this streamlined workflow simplifies sample handling and minimizes both sample loss and experimental errors associated with sample transfer. This method also efficiently reduced sample processing time to under 2 hours prior to overnight trypsin di-gestion, compared to the 5-8 hours required by other methods. With this workflow, we identified 500-800 proteins per 0.5 μL sample without the need for fractionation, allowing for at least three technical replicates. This optimized workflow greatly enhances the efficiency of tear proteomics for biomarker discovery.
2025-05-07 | PXD056978 | Pride
Project description:Tear fluid, a complex biofluid that contains thousands of proteins and can be collected non-invasively, has emerged as a promising source of biomarkers for ocular and systemic health. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is currently the primary method for discovering novel biomarkers in tear fluid. However, the method of tear collection can sig-nificantly impact LC-MS/MS analysis outcomes. Tear fluid is commonly collected using either Schirmer strips or capillary tubes. While capillary tubes offer distinct advantages, such as reduced extracellular contamination and reflex tearing, most LC-MS/MS protocol development has focused on optimizing protocols for Schirmer strips. This study addresses this gap by evaluating digestion protocols for tear fluid collected with capillary tubes, focusing on biomarker discovery using small-volume samples. In this study, we evaluated multiple digestion protocols for the shotgun quantitative LC-MS/MS analysis of small-volume tear fluid samples collected using glass capillary tubes. Protocol optimization was performed using pooled samples and then compared with the analysis of individual samples. Using the optimized protocol, 0.5μL were processed using a timsTOF Pro 2 mass spectrometer (Bruker) coupled online with an Evosep One liquid chroma-tography system (Evosep), leading to the identification of an average of 368 ± 87 proteins in pooled samples and 502 ± 127 proteins in individual small-volume tear fluid samples. This protocol highlights the practicality of using glass capillary tubes for comprehensive LC-MS/MS-based tear proteomics analysis, paving the way for detailed proteomics characterization of individual tear fluid samples rather than pooled samples. By shifting from pooled to individual samples, this approach greatly accelerates tear biomarker discovery, advancing precision and personalized medicine.
2025-05-07 | PXD060101 | Pride
Project description:Glycosylation of proteins is one of the most common post-translational modification (PTM) and plays important regulatory functions in diverse biological processes such as protein stability or cell signaling. Accordingly, glycoproteins are also a consistent part of the human tear film proteome maintaining the proper function of the ocular surface and forming the first defense barrier of the ocular immune system. Irregularities in the glycoproteomic composition of the tear film might promote development of chronic eye diseases indicating glycoproteins as valuable source for biomarker discovery or drug target identification. The present study aimed to develop a lectin-based affinity method for the enrichment and concentration of tear glycoproteins/glycopeptides and the characterization of their specific N-glycosylation sites by high-resolution mass spectrometry (MS). For method development and evaluation, we accumulated first native glycoproteins from human tear sample pools and assessed the enrichment efficiency of different lectin column systems by 1D gel electrophoresis and specific protein stainings (Coomassie and glycoproteins). The best-performing multi-lectin column system (comprising the four lectins ConA, JAC, WGA and UEA I, termed as 4L) was applied for glycopeptide enrichment from human tear sample digests followed by MS-based detection and localization of their specific N-glycosylation sites. As main result, the present study identified in total 26 N glycosylation sites of 11 N-glycoproteins in tear sample pools of healthy individuals (n=3 biological sample pools). Amongst others, we identified tear film proteins lactotransferrin (N497 and N642, LTF), Ig heavy chain constant α-1 (N144 and 340, IGHA1), prolactin-inducible protein (N105, PIP) as well as extracellular lacritin (N105, LACRT) as highly reliable and significant N glycoproteins, which were already associated with the pathogenesis of various chronic eye diseases such as the dry eye syndrome (DES). In conclusion, the results of the present study will serve as important tear film N-glycoprotein catalogue for future studies focusing the human tear film and ocular surface-related inflammatory diseases.
2023-01-25 | PXD038280 | Pride
Project description:The IFN type I signature is present in over half of primary Sjögren’s syndrome (pSS) patients and associated with higher disease-activity and autoantibody presence. Plasmacytoid dendritic cells (pDCs) are considered to be the source of enhanced IFN type I expression. The objective of this study was to unravel the molecular pathways underlying IFN type I bioactivity in pDCs of pSS patients. We used microarray gene expression analysis to detail the programme of gene expression underlying IFN type I bioactivity in pDCs of primary Sjogrens' Syndrome patients.
2016-09-28 | GSE83558 | GEO