Ontology highlight
ABSTRACT:
PROVIDER: PRJNA870295 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR21199600_1.fastq.gz | Fastqsanger.gz | |||
| SRR21199600_2.fastq.gz | Fastqsanger.gz | |||
| SRR21199601_1.fastq.gz | Fastqsanger.gz | |||
| SRR21199601_2.fastq.gz | Fastqsanger.gz |
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Project description:RPTEC cells were cultured and irradiated to induce cellular senescence. Bulk RNA-seq was performed to observe the transcriptional response.
2025-03-25 | GSE252584 | GEO
Project description:Renal Tubular Epithelial Cells (RPTEC) from two donors were cultivated in vitro until irreversible growth arrest was observed. Total RNA from young (replicating) as well as growth arrested cells was harvested and hybridized to LNA based microRNA microarrays using a looped design. After data processing, differential expression of miRNAs in senescent vs. young RPTEC cells was calculated.
2010-04-19 | E-MEXP-2393 | biostudies-arrayexpress
Project description:Purpose: Next-generation sequencing (NGS) is emmerged as a highthrough-put technique to analyze cellular pathways. The goals of this study are to profile NGS-derived renal proximal tubule epithelial cells (RPTEC) transcriptome (RNA-seq), to identify transcription signature in RPTEC upon Plasmodium Chabaudi Chabaudi (Pcc) infection and steady state (NI). We also would like to understand how iron export affect the transcriptome in this cell compartment. Therefore, we will compare the transcriptome between Pcc infected (or steady state) Egfp.l10Pepck and Egfp.l10PepckSlc40a1Pepckdelta/delta mice. Methods: TRAP (Translating Ribosome Affinity Purification) were performed in the kidneys of Pcc infected (or steady state) 10-16 weeks Egfp.l10Pepck and Egfp.l10PepckSlc40a1Pepckdelta/delta mice. RPTEC TRAP mRNA profiles were generated by next generation sequencing, in triplicate, using Illumina High output kit v2.5 and NextSeq500 sequencer. Results: Using an optimized data analysis workflow, we mapped an average 32.54 million sequence reads per sample to the mouse genome (build mm39) and identified 19,052 transcripts in the TRAP mRNA of in the kidneys of Pcc infected or steady state 10-16 week old Egfp.l10Pepck and Egfp.l10PepckSlc40a1Pepckdelta/delta mice. Differential gene expression was performed using the DESeq2 R package (v.1.32) and gene expression was modeled by genotype and condition. Differentially expressed genes were considered for genes with an adjusted p-value<0.05 and an absolute log2 fold change>0. Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
2022-11-25 | GSE189579 | GEO
Project description:The first GSSM of V. vinifera was reconstructed (MODEL2408120001). Tissue-specific models for stem, leaf, and berry of the Cabernet Sauvignon cultivar were generated from the original model, through the integration of RNA-Seq data. These models have been merged into diel multi-tissue models to study the interactions between tissues at light and dark phases.
2024-09-02 | MODEL2408160001 | BioModels
Project description:The kidneys are essential for eliminating drugs and chemicals from the human body, with renal epithelial cells being particularly vulnerable to damage caused by xenobiotics and their metabolites. Predicting renal toxicity before clinical trials remains a pressing challenge, necessitating more predictive in vitro models. However, the abundance of commercially available renal proximal tubule epithelial cell (RPTEC) sources complicates the selection of the most predictive cell types. This study compared RPTEC sources, including primary cells (Lonza) and various RPTEC lines, such as ciPTECs (Cell4Pharma), TERT1/RPTECs (ATCC), and HEK293 (GenoMembrane), alongside HepG2 cells for specificity comparison. We tested these cells' responses to 12 drugs to evaluate their predictive capabilities. Cells were cultured in 96-well or 384-well plates and exposed to drugs for 72 hours at concentrations ranging from 0.3 to 300 µM. The CellTiterGlo® assay measured cell viability, and transcriptome data from unexposed cells analyzed gene expression profiles using the TempO-seq® S1500+ panel. Cell viability data determined points of departure (PODs), compared to human serum Cmax,free values to assess safety margins. Gene expression showed primary kidney cells closely matched the human kidney medulla, followed by TERT1 and ciPTEC lines, with HEK lines showing the least correlation. This study highlights differences among RPTEC sources and their utility in drug safety studies for the renal proximal tubule, emphasizing unique gene expression patterns related to metabolism, ion transport, and cell development, which are vital for improving predictive models in renal toxicity assessment.
2025-04-02 | GSE268877 | GEO
Project description:Plasmacytoid dendritic cells (pDCs) play a key role in the activation of the autoimmune response in LN. Recently we demonstrated that these cells infiltrate the kidney of patients with LN at tubulointerstitial level. The pDCs are the main producers of IFN-alpha, whose effects on the renal tubule are poorly understood. The aim of the study was to investigate the effects of INF-alpha in renal epithelial cells (RPTEC). We investigated the effect of IFN-alpha on the whole-genome gene expression profile in RPTEC cells,. Genomic analysis showed that after stimulation, 108 genes are up-regulated and only 7 are down-regulated, with a fold-change> 2. The Gene Set Enrichment analysis confirmed that IFN-alpha induced the pathway of antigen presentation and the inflammatory signaling in RPTEC. Among the up-regulated genes involved in these pathways, there were HLA-I, the ubiquitins (FBXO6 and DTX3L) and the immunoproteasome subunits LMP7. We performed the validation of these genes by real time PCR and citometry experiments on RPTEC stimulated with IFN-alpha. Immunohistochemical analysis of LMP7 and MXA protein, specific marker of IFN-alpha, showed a significant upregulatation of both proteins in renal biopsies of patients with LN class IV compared to class I. Confocal microscopy showed the colocalization of LMP7-MXA in tubular epithelium of patients with LN class IV and activation of inflammatory signaling via NF-kB in the MXA+ tubules. Our data suggested that inhibition of INF-alpha pathways could represent a novel therapeutic strategy to reduce renal tubular damage in patients with LN. To identify genes specifically modulated by INF-alpha in RPTEC, we stimulated 3 different cell clones with 100U/ml INF-alpha for 48 hours and compared their whole-genome gene expression profiles with that from 3 RPTEC clones cultured without stimuli.
2015-12-15 | E-GEOD-48551 | biostudies-arrayexpress
Project description:Aim of the study was to characterize the transcriptional response of human primary renal proximal tubule epithelial cells (RPTEC) to low oxygen stress.
2008-09-17 | GSE12792 | GEO
Project description:The advent of micro-physiological systems (MPS) in biomedical research has enabled the introduction of more complex and relevant physiological into in vitro models. The recreation of complex morphological features in three-dimensional environments can recapitulate otherwise absent dynamic interactions in conventional models. In this study we developed an advanced in vitro Renal Cell Carcinoma (RCC) that mimics the interplay between healthy and malignant renal tissue. Based on the TissUse Humimic platform our model combines healthy renal proximal tubule epithelial cells (RPTEC) and RCC. Co-culturing reconstructed RPTEC tubules with RCC spheroids in a closed micro-perfused circuit resulted in significant phenotypical changes to the tubules. Expression of immune factors revealed that interleukin-8 (IL-8) and tumor necrosis factor-alfa (TNF-α) were upregulated in the non-malignant cells while neutrophil gelatinase-associated lipocalin (NGAL) was downregulated in both RCC and RPTEC. Metabolic analysis revealed that RCC prompted a shift in the energy production of RPTEC tubules, inducing glycolysis, in a metabolic adaptation that likely supports RCC growth and immunogenicity. In contrast, RCC maintained stable metabolic activity, emphasizing their resilience to external factors. RNA-seq and biological process analysis of primary RTPTEC tubules demonstrated that the 3D tubular architecture and MPS conditions reverted cells to a predominant oxidative phosphorylate state, a departure from the glycolytic metabolism observed in 2D culture. This dynamic RCC co-culture model, approximates the physiology of healthy renal tubules to that of RCC, providing new insights into tumor-host interactions. Our approach can show that an RCC-MPS can expand the complexity and scope of pathophysiology and biomarker studies in kidney cancer research.
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