Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Deep sequencing of the Caenorhabditis elegans transcriptome using RNA isolated from various developmental stages under various experimental conditions RW0001 - uninfected worms

ABSTRACT: The goal of this study, started as a part of the modENCODE project, is to detect and characterize previously unannotated transcripts of the C. elegans genome. This dataset has been imported from the Sequence Read Archive and curated by the WormBase and ArrayExpress teams. It is a subset of study E-MTAB-2683 (SRP00401) and only contains assays on worms not infected by pathogens.

INSTRUMENT(S): Illumina Genome Analyzer II, Illumina MiSeq, Illumina Genome Analyzer, Illumina HiSeq 2000

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: ArrayExpress ArrayExpress

PROVIDER: E-MTAB-2812 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Validation of predicted gene expression of human mesangial cells after 24h Tacrolimus stimulus Objective: To evaluate tacrolimus as therapeutic option for diabetic nephropathy (DN) based on molecular profile and network-based molecular model comparisons. Materials and Methods: We generated molecular models representing pathophysiological mechanisms of DN and tacrolimus mechanism of action (MoA) based on literature derived data and transcriptomics datasets. Shared enriched molecular pathways were identified based on both model datasets. A newly generated transcriptomics dataset studying the effect of tacrolimus on mesangial cells in vitro was added to identify mechanisms in DN pathophysiology. We searched for features in interference between the DN molecular model and the tacrolimus MoA molecular model already holding annotation evidence as diagnostic or prognostic biomarker in the context of DN. Results: Thirty nine molecular features were shared between the DN molecular model, holding 252 molecular features and the tacrolimus MoA molecular model, holding 209 molecular features, with six additional molecular features affected by tacrolimus in mesangial cells. Significantly affected molecular pathways by both molecular model sets included cytokine-cytokine receptor interactions, adherens junctions, TGF-beta signaling, MAPK signaling, and calcium signaling. Molecular features involved in inflammation and immune response contributing to DN progression were significantly downregulated by tacrolimus (e.g. the tumor necrosis factor alpha (TNF), interleukin 4, or interleukin 10). On the other hand, pro-fibrotic stimuli being detrimental to renal function were induced by tacrolimus like the transforming growth factor beta 1 (TGFB1), endothelin 1 (EDN1), or type IV collagen alpha 1 (COL4A1). Conclusion: Patients with DN and elevated TNF levels might benefit from tacrolimus treatment regarding maintaining GFR and reducing inflammation. TGFB1 and EDN1 are proposed as monitoring markers to assess degree of renal damage. Next to this stratification approach, the use of drug combinations consisting of tacrolimus in addition to ACE inhibitors, angiotensin receptor blockers, TGFB1- or EDN1-receptor antagonists might warrant further studies. comparison of gene expression of human mesangial cells after 24h Tacrolimus vs. Ctrl; 4 independent experiments were conducted (4xTacrolimus 24h and 4x ctrl. 24h with Drug solvent (DMSO))

Dataset Information

Deep sequencing of the Caenorhabditis elegans transcriptome using RNA isolated from various developmental stages under various experimental conditions RW0001 - uninfected worms

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