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MiRNA and mRNA Signatures in Human Acute Kidney Injury Tissue [mRNA, minimal change disease]

ABSTRACT: miRNA and mRNA Signatures in Human Acute Kidney Injury Tissue [mRNA, minimal change disease]

PROVIDER: PRJNA1032050 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26516400_1.fastq.gz	Fastqsanger.gz
	SRR26516400_2.fastq.gz	Fastqsanger.gz
	SRR26516401_1.fastq.gz	Fastqsanger.gz
	SRR26516401_2.fastq.gz	Fastqsanger.gz
	SRR26516402_1.fastq.gz	Fastqsanger.gz

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miRNA and mRNA Signatures in Human Acute Kidney Injury Tissue [mRNA, minimal change disease]

Project description:Acute kidney injury (AKI) is an important contributor to the development of chronic kidney disease (CKD). We performed miRNA and mRNA sequencing on biobanked human kidney tissues obtained in the routine clinical care of patients with the diagnoses of AKI and minimal change disease (MCD), in addition to nephrectomized (Ref) tissue from individuals without known kidney disease. From all renal biopsy samples, 2 cryosections (10 μM) including the entire cross-section of the tissue were placed directly into PicoPure RNA extraction buffer. RNA was isolated using the PicoPure isolation kit. Total RNA was evaluated for quantity and quality using an Agilent Bioanalyzer. Approximately 10 ng of total RNA were used for each sample’s library preparation. Ribosomal RNA was removed using RiboGone – Mammalian Kit protocol. After rRNA depletion, double-stranded cDNA was synthesized and amplified using the SMARTer Universal Low Input RNA Kit protocol. The cDNA was sheared by Covaris, and the library was prepared and barcoded following the Ion Plus Fragment Library Kit protocol. Each resulting barcoded library was quantified and quality assessed by Agilent Bioanalyzer. Multiple libraries were pooled in equal molarity. Finally, 8 μL of 100 pM pooled libraries were loaded into lanes of an Illumina HiSeq 4000. At least 30M reads per library were generated.

2024-07-11 | GSE246204 | GEO

miRNA and mRNA Signatures in Human Acute Kidney Injury Tissue [miRNA]

Project description:Acute kidney injury (AKI) is an important contributor to the development of chronic kidney disease (CKD). We performed miRNA and mRNA sequencing on biobanked human kidney tissues obtained in the routine clinical care of patients with the diagnoses of AKI and minimal change disease (MCD), in addition to nephrectomized (Ref) tissue from individuals without known kidney disease. From all renal biopsy samples, 2 cryosections (10 μM) including the entire cross-section of the tissue were placed directly into PicoPure RNA extraction buffer. RNA was isolated using the PicoPure isolation kit. Total RNA was evaluated for quantity and quality using an Agilent Bioanalyzer. Approximately 100 ng of total RNA was used for library construction with QIASeq miRNA Library Kit. Each resulting indexed library was quantified and its quality assessed by Qubit and Agilent Bioanalyzer. The libraries were then loaded onto an Illumina NextSeq 500 for 75 bp single-read sequencing to a depth of 15-20M reads per library. Sequence reads were uploaded to the Qiagen GeneGlobe Data Analysis Center (https://www.qiagen.com/us/resources/geneglobe) for quality control, alignment and expression quantification. Reads were mapped to different databases for mature, hairpin, noncoding RNA, mRNA and other RNA using bowtie v1.2. Read counts and UMI counts for each RNA category (mature, hairpin, piRNA, tRNA, rRNA, mRNA and otherRNA) were calculated for each sample, using miRbase V21 for miRNA, and piRNABank for piRNA.

2024-07-11 | GSE246205 | GEO

Digital Spatial Profiling of Human Kidney Biopsies from Patients with Minimal Change Disease

Project description:Digital Spatial Profiling of Human Kidney Biopsies from Patients with Minimal Change Disease

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miRNA and mRNA Signatures in Human Acute Kidney Injury Tissue

Project description:miRNA and mRNA Signatures in Human Acute Kidney Injury Tissue

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miRNA and mRNA Signatures in Human Acute Kidney Injury Tissue [miRNA]

Project description:miRNA and mRNA Signatures in Human Acute Kidney Injury Tissue [miRNA]

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Idiopathic membranous nephropathy and minimal change disease (MCD) transcriptome

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Pathogenesis of focal segmental glomerulosclerosis and minimal change disease

Project description:Podocyte injury is the hallmark of both focal segmental glomerulosclerosis (FSGS) and minimal change disease (MCD) and is ultimately reflected in foot process effacement proteinuria. Triggers and pathogenic pathways leading to podocyte cytoskeleton rearrangements are however incompletely explained. Here, we aimed to contribute to the understanding of these pathways using tissue bottom-up proteomic profiling of laser capture micro dissected glomeruli from MCD and FSGS.

2025-03-12 | MSV000097297 | MassIVE

Co-expression Analysis Reveals Dysregulated miRNAs and miRNA-mRNA Interactions in the Development of Contrast-induced Acute Kidney Injury [mRNA]

Project description:Purpose:The pathogenesis of contrast-induced acute kidney injury (CI-AKI) has not yet been clearly understood. miRNAs are important mediators which normally work by post-transcriptional degradation of target mRNAs. Emerging evidence indicated a number of differentially expressed miRNAs in CI-AKI following intravenous contrast medium injection. However, there exist differences in the pathological mechanisms and incidences of CI-AKI between intravenous and intra-arterial contrast administration. We aimed to investigate the critical roles of dysregulated miRNAs and the correlated mRNAs in the kidney injury following intra-arterial contrast exposure. Methods:Based on a reliable CI-AKI rat model, we sought to investigate the roles of miRNA-mRNA interactions in the kidney injury following intra-arterial contrast exposure using the Illumina Genome Analyzer IIx. Results:In the study, 36 differentially expressed mature miRNAs were identified ( fold change > 1.5 and p value < 0.05) in the kidney of CI-AKI rats (n = 3) compared with controls (n = 3), consisting of 23 up-regulated and 13 down-regulated ones. Bioinformatics analysis revealed that Wnt, TGF-β, and AMPK signaling pathways were most likely to be modulated by these dysregulated miRNAs. Around 453 dysregulated genes ( fold change > 2.0 and p value < 0.05) were identified. Integrated analysis revealed 2037 putative miRNA-mRNA pairs with negative correlations. Of which, 6 differential miRNAs and 13 genes were selected for further quantitative real-time polymerase chain reaction validation (n = 6 for each group), and a well correspondence between the 2 techniques was observed. Conclusions:In conclusion, our present study contributes to the first evidence of miRNA-mRNA regulations in the development of kidney injury following an intra-arterial contrast injection route. These novel findings provide insights into the underlying mechanisms of CI-AKI.

2020-04-10 | GSE130795 | GEO

Comparison of Glomerular Transcriptome Profiles of Adult-Onset Steroid Sensitive Focal Segmental Glomerulosclerosis and Minimal Change Disease

Project description:To search for biomarkers to differentiate Adult-Onset Steroid Sensitive focal segmental glomerulosclerosis (FSGS) and minimal change disease (MCD).

2017-01-04 | GSE69814 | GEO