MRNA expression analysis in primary renal tubular cells.
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ABSTRACT:
PROVIDER: PRJNA930009 | ENA |
REPOSITORIES: ENA
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Project description:Activation of hypoxia-inducible transcription factors (HIF) leading to expression of hundred of target genes is a fundamental mechanism in acute and chronic kidney disease mediating protective but also possibly harmful effects. Furthermore, dysregulation of the HIF pathway in chronic kidney disease causes renal anemia through insufficient induction of erythropoietin (EPO) in interstitial cells. Hence, pharmacological compounds to treat renal anemia by stabilizing HIF have recently been introduced to the clinical practice. RNA-seq analysis was performed in primary renal tubular cells to analyse the effect of HIF stabilization on the expression of pathogenic Mucin1 (MUC1) variants. This study links the regulation of the kidney-disease gene MUC1 with the HIF-pathway in renal tubular cells.
2023-06-07 | GSE224177 | GEO
Project description:Multiomics analysis of HIF-stabilization in primary renal tubular cells
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Project description:The activation of hypoxia-inducible transcription factors (HIF) leading to the expression of hundreds of target genes is a fundamental mechanism in acute and chronic kidney disease, mediating protective but possibly harmful effects. Furthermore, dysregulation of the HIF pathway in chronic kidney disease causes renal anemia through insufficient erythropoietin (EPO) induction in interstitial cells. RNA-seq analysis was performed in human primary renal tubular cells to analyse the effect of HIF stabilization on the expression of genes in tubular cells. ATAC-seq and HIF-CHIP-seq complement the data to analyse transcription factor binding and chromatin configuration changes.
2023-05-05 | GSE227848 | GEO
Project description:The activation of hypoxia-inducible transcription factors (HIF) leading to the expression of hundreds of target genes is a fundamental mechanism in acute and chronic kidney disease, mediating protective but possibly harmful effects. Furthermore, dysregulation of the HIF pathway in chronic kidney disease causes renal anemia through insufficient erythropoietin (EPO) induction in interstitial cells. RNA-seq analysis was performed in human primary renal tubular cells to analyse the effect of HIF stabilization on the expression of genes in tubular cells. ATAC-seq and HIF-CHIP-seq complement the data to analyse transcription factor binding and chromatin configuration changes.
2023-05-05 | GSE227823 | GEO
Project description:The activation of hypoxia-inducible transcription factors (HIF) leading to the expression of hundreds of target genes is a fundamental mechanism in acute and chronic kidney disease, mediating protective but possibly harmful effects. Furthermore, dysregulation of the HIF pathway in chronic kidney disease causes renal anemia through insufficient erythropoietin (EPO) induction in interstitial cells. RNA-seq analysis was performed in human primary renal tubular cells to analyse the effect of HIF stabilization on the expression of genes in tubular cells. ATAC-seq and HIF-CHIP-seq complement the data to analyse transcription factor binding and chromatin configuration changes.
2023-05-05 | GSE227821 | GEO
Project description:The Role of SOX9 in hypoxia/reoxygenation (H/R) injuried mice primary renal tubular epithelial cells Purpose: we performed comparative RNA-seq analyses to identify differentially expressed genes between Knockdown of Sox9 and negtive control in hypoxia/reoxygenation (H/R) injuried mice primary renal tubular epithelial cells. Methods:we grew mouse primary renal tubular epithelial cells to approximately 50% confluence, transfected using EndoFectin™ Max (GeneCopoeia, China) 12h before suffering to H/R injury. H/R was used to mimic IRI in vitro. Briefly, cells were incubated in glucose-free medium in a tri-gas incubator (94% N2, 5% CO2 and 1.0% O2) at 37 °C for 6 hours. Subsequently, cells were incubated in complete medium under normal conditions for 18 hours for reoxygenation. Cells were then collected by 1ml TRIzol (Invitrogen, Carlsbad), and sent to Annoroad Corporation (Beijing, China) for high throughout Illumina NovaSeq 6000 sequencing (GPL24247) (Illumina, San Diego, CA, USA). Results: To determine the possible pathways of Sox9 in protecting mice primary renal tubular epithelial cells from injury, we conduct the transcriptomotic sequencing. After sequence, the clean reads rate of all samples were ≥98%.The quality of the assembled transcriptome is good enough for functional annotation and further analysis. Conclusions: We performed RNA-sequencing (RNA-Seq) on isolated mouse renal tubular epithelial cells of two groups, treated with H/R and transfected with siNC (H/R+siNC group) or siSox9 (H/R+siSox9 group). SOX9-responsive genes showed significant enrichment of the WNT signaling pathway in primary tubular epithelial cells.
2022-12-19 | GSE174811 | GEO
Project description:The Role of EGR1 in hypoxia/reoxygenation (H/R) injuried mice primary renal tubular epithelial cells Purpose: we performed comparative RNA-seq analyses to identify differentially expressed genes between Knockdown of Egr1 and negtive control in hypoxia/reoxygenation (H/R) injuried mice primary renal tubular epithelial cells. Methods:we grew mouse primary renal tubular epithelial cells to approximately 50% confluence, transfected using EndoFectin™ Max (GeneCopoeia, China). H/R was used to mimic IRI in vitro. Briefly, cells were incubated in glucose-free medium in a tri-gas incubator (94% N2, 5% CO2 and 1.0% O2) at 37 °C for 6 hours. Subsequently, cells were incubated in complete medium under normal conditions for 18 hours for reoxygenation. Cells were then collected by 1ml TRIzol (Invitrogen, Carlsbad), and sent to Annoroad Corporation (Beijing, China) for high throughout Illumina NovaSeq 6000 sequencing (GPL24247) (Illumina, San Diego, CA, USA). Results: To determine the possible pathways and downregulated genes of Egr1 in protecting mice primary renal tubular epithelial cells from injury, we conduct the transcriptomotic sequencing. After sequence, the clean reads rate of all samples were ≥98%.The quality of the assembled transcriptome is good enough for functional annotation and further analysis. Conclusions: We performed RNA-sequencing (RNA-Seq) on isolated mouse renal tubular epithelial cells of 3 groups, negtive control(Sham group) treated with H/R (H/R group) or Egr1 overexpression plasmid (Egr1OV group). Egr1-responsive genes showed significant enrichment in proliferation pathway.
2022-12-19 | GSE174808 | GEO
Project description:Multiomics analysis of HIF-stabilization in primary renal tubular cells [ChIP-Seq]
| PRJNA947177 | ENA
Project description:Multiomics analysis of HIF-stabilization in primary renal tubular cells [RNA-Seq]
| PRJNA947180 | ENA
Project description:Multiomics analysis of HIF-stabilization in primary renal tubular cells [ATAC-Seq]
| PRJNA947178 | ENA