Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Integrative Transcriptomic and Proteomic Analysis Reveals Mechanisms of Silica-induced Pulmonary Fibrosis in Rats

ABSTRACT: To explore proteomic and transcriptomic changes in rat model of silicosis, transcriptomic analysis by microarray and tandem mass tags (TMT)-based proteomic analysis were performed to reveal the expression of mRNAs and proteins in lung tissues. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were applied to analyze the alterated genes and proteins. The integrated analysis was performed between transcriptome and proteome. Furthermore, the data were further verified by RT-qPCR and parallel reaction monitoring (PRM). In total, 244 differentially expressed proteins (DEPs) showed the same trend as that of the corresponding differentially expressed genes (DEGs) (named DEPs/DEGs). GM2a, CHI3L1, LCN2 and GNAI1, which were validated consistently by RT-qPCR and PRM, are involved in the extracellular matrix (ECM) and inflammation contributed to fibrosis in silicosis.

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE188520 | GEO | 2022/01/12

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Proteogenomic analysis of psoriasis reveals discordant and concordant changes in mRNA and protein abundance

Project description:Background: Psoriasis is a chronic disease characterized by the development of scaly red skin lesions and possible co-morbid conditions. The psoriasis lesional skin transcriptome has been extensively investigated, but mRNA levels do not necessarily reflect protein abundance. Methods: Lesional (PP) and uninvolved (PN) skin samples from 14 patients were analyzed using high-throughput complementary DNA sequencing (RNA-seq) and liquid chromatography-tandem mass spectrometry (LC-MS/MS). Results: We identified 4122 differentially expressed genes (DEGs) along with 748 differentially expressed proteins (DEPs). Global shifts in mRNA were modestly correlated with changes in protein abundance (r = 0.40). We identified similar numbers of increased and decreased DEGs, but 4-fold more increased than decreased DEPs. Ribosomal subunit and translation proteins were elevated within lesions, without a corresponding shift in mRNA expression (RPL3, RPS8, RPL11). We identified 209 differentially expressed genes/proteins (DEGPs) with corresponding trends at the transcriptome and proteomic levels. Most DEGPs were similarly altered in at least one other skin disease. Psoriasis-specific and non-specific DEGPs had distinct cytokine-response patterns, with only the former showing disproportionate induction by IL-17A in cultured keratinocytes. Conclusions: Our findings reveal global imbalance between the number of increased and decreased proteins in psoriasis lesions, consistent with heightened translation. This effect could not have been discerned from mRNA profiling data alone. We have also identified high-confidence DEGPs and shown that only those most specific to psoriasis are enriched with IL-17A targets. RNA-seq-based comparison between gene expression in psoriasis lesions and uninvolved skin from 14 patients

2015-08-23 | E-GEOD-67785 | biostudies-arrayexpress

Integrative analyses of transcriptome and proteome provides new insights into energy metabolism and light utilzation in cigar tobacco during different light intensities

Project description:In this study, we have used the comparative transcriptomic and proteomic approaches to decipher the changes in genes and protein abundances in cigar tobacco leaves under LL. In this study, DEGs and DEPs related to glycolysis, starch and sucrose metabolism, tyrosine metabolism, photosynthesis-antenna proteins, and photosynthesis pathways are significantly enriched. This study offers novel insights into both transcriptome and proteome levels response mechanisms under different light intensities.

2022-08-26 | GSE211923 | GEO

Heat-induced alternations in proteomic and transcriptomic profiles of spinach (Spinacia oleracea)

Project description:Spinach (Spinacia oleracea L.) is an economically important and globally consumed popular leafy vegetable that is heat-sensitive. Heat stress caused by global climate change is one of the primary deleterious elements limiting spinach production worldwide. Little work has been done to explore the heat-responsive mechanisms of spinach under high temperature-induced stress. In the present study, we used iTRAQ-based proteomic and transcriptomic approaches to investigate physiological, metabolic, and proteomic responses of spinach in response to day / night temperature of 35°C / 25°C compared to 20°C / 15°C for 4 days. A total of 3,543 differentially expressed genes (DEGs) were detected using transcriptome sequencing, of which 2,086 DEGs were downregulated and 1,457 were upregulated. The DEGs were mainly involved in superoxide dismutase activity, catalase, and peroxidase activity. A total of 3,246 differentially abundant proteins were detected using iTAQ-based quantitative proteomic approach, from which 567 differentially expressed proteins (DEPs) (277 upregulated and 290 downregulated) were identified. DEPs were mainly assigned to pathways related to metabolism, signal transduction, protein degradation, defense, and antioxidant. Four genes - superoxide dismutase (SOD, LOC110788339), catalase (CAT, LOC110790286), peroxidase (POD, LOC110775253), and heat shock protein (HSP, LOC110799288) - were validated using quantitative real-time PCR (qRT-PCR) to verify the proteomic and transcriptomic analyses, showing different transcriptional and translational expression levels. The findings of this study provide a fundamental understanding of the metabolic pathways and biological processes that control adaptation to heat stress in spinach, and provide novel insight into the development of heat-tolerant spinach.

2020-06-24 | GSE153070 | GEO

Integrated analysis of transcriptome and proteome of the human cornea and aqueous humor reveal novel biomarkers for corneal endothelial cell dysfunction

Project description:Previous studies have reported that elevated protein levels in the aqueous humor (AH) are associated with corneal endothelial cell dysfunction (CECD), but the detailed underlying mechanism as well as specific biomarkers for CECD remain elusive. In the present study, we aimed to identify protein markers in AH directly associated with changes in Corneal endothelial cells (CECs), as AH can be easily obtained for analysis. We carried out an in-depth proteomic analysis of patient-derived AH as well as transcriptomic analysis of CECs from the same patients with bullous keratopathy (BK) resulting from CECD. We first determined differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) from CECs and AH in CECD, respectively. By combining transcriptomic and proteomic analyses, 13 shared upregulated markers were observed between DEGs and DEPs. Through data integration with individual analysis via data-independent acquisition, three upregulated transcripts and proteins were identified, namely metallopeptidase inhibitor 1 (TIMP1), Fc fragment of IgG binding protein (FCGBP), and angiopoietin-related protein 7 (ANGPTL7). Furthermore, we confirmed AH biomarkers for CECD using individual proteome verification and immunoassay validation. Conclusively, our findings may provide valuable insights into the disease process and identify biofluid markers for the assessment of CEC function during BK development.

2021-06-10 | GSE176481 | GEO

Comparative transcriptomic and proteomic analysis reveals common molecular factors responsive to heat and drought stress in sweetpotato (Ipomoea batatas)

Project description:In the process of field production, crops are often affected by a variety of abiotic stresses, among which heat (HT) and drought (DR) stress are the most common co-stresses in summer. Although a large number of studies have been carried out on HT and DR stress respectively, little is known about how their combination (DH) affects plants. In this study, we investigated the responses of sweetpotato to HT, DR or DH stress by RNA-seq and DIA technologies, and set up a controlled experiment and quantified gene expression and protein concentrations from paired samples. A total of 12 cDNA libraries were constructed under HT, DR, DH and control condition. We identified 536, 389 and 907 DEGs in response to HT, DR or DH stress, of which 147 were shared and 447 were specifically identified under DH stress. Proteomic analysis identified 1609, 1168 and 1535 DEPs under HT, DR and DH treatments compared to the control, of which 656 were shared and 358 were exclusively identified under DH stress. Further analysis revealed that some DEGs/DEPs associated with heat shock protein, carbon metabolism, phenylalanine metabolism, starch and cellulose metabolism, plant defense and so on. Correlation analysis identified a number of co-expressed genes and proteins under HT, DR or DH stress. Meanwhile, a cross-comparison of transcriptomics and proteomics data identified 59, 35 and 86 significant co DEGs and DEPs genes under HT, DR and DH stress respectively. This is the first time that studies the differential genes and proteins of sweet potato under DH stress, and hopes that the results of this study will help us to understand the molecular mechanism of sweet potato resistance to heat and drought stress.

2022-10-23 | GSE216152 | GEO

Proteogenomic analysis of psoriasis reveals discordant and concordant changes in mRNA and protein abundance

2015-08-23 | GSE67785 | GEO

Tuber-omics in potato with the T and D types of cytoplasm showed differentially expressed genes and proteins in response to cold storage

Project description:For the first time, we report differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) in potato (Solanum tuberosum L.) tubers characterized by light and dark chip color after cold storage. Two potato diploid progenies derived from reciprocal crosses of parental clones possessing the T- and D-type cytoplasm were used. We recognized 48 and 15 DEGs as compared to RNA-seq data of contrasting segregants. We identified DEPs in potato tuber amyloplast and mitochondrial fractions. Seven and five DEPs were identified in the amyloplast fractions of the T – and D – type cytoplasm, respectively. Higher number of DEPs were selected from the mitochondrial fraction. The corresponding values were 97 and 105, including 39 common DEPs in the T – and D – type cytoplasm. These findings suggest that mitochondria may play a more important role than amyloplasts in response of potato tubers to cold treatment and that this influence can be different for the T – and D – type cytoplasm. However, we showed that the mt/nucDNA and pt/nucDNA ratios tend to increase for tubers characterized by dark chip color when compared with light chip color samples. Therefore, a protective effect of reducing sugars on both amyloplasts and mitochondria during low temperature treatment should be considered.

2021-09-17 | GSE184141 | GEO

Downregulation of miR-19a as a Biomarker for Early Detection of Silicosis

Project description:To explore the early diagnostic value for silicosis we have employed the Human microRNA OneArray® v5 as a discovery platform to identify microRNAs as biomarkers of silicosis use.To be followed,a microRNA-gene network in silicosis wasestablished by the differential expression profiles so that candidate markers of silicosis could be spotted and validated. Then, the relative expression levels of potential biomarkers were measured by Quantitative Real-time PCR (qPCR) and the sensitivity and specificity were assessed by ROC curves.

2016-04-22 | GSE80555 | GEO

Project description:RT-qPCR of mice brains

| PRJNA869346 | ENA

Project description:RT-qPCR of mice brain

| PRJNA864033 | ENA