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Identifying the role of FOXM1 in human primary renal tubular epithelials using bulk RNA-seq and Cut&Run to understand its role in acute kidney injury and repair

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE234444 | GEO | 2024/07/10

REPOSITORIES: GEO

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Identifying the role of FOXM1 in human primary renal tubular epithelials using bulk RNA-seq and Cut&Run to understand its role in acute kidney injury and repair [CUT&RUN]

Project description:In this dataset, we study the role of FOXM1 in human primary renal tubular epithelial cells (hRPTECs) by first performing Foxm1 knockdown with an siRNA approach and then performing bulk RNA sequencing. We also sought to identify FOXM1 binding sites on hRPTECs using Cut&Run. These studies will help better understand the role of Foxm1 in acute kidney injury and repair.

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Identifying the role of FOXM1 in human primary renal tubular epithelials using bulk RNA-seq and Cut&Run to understand its role in acute kidney injury and repair [RNA-seq]

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Identifying the role of FOXM1 in human primary renal tubular epithelials using bulk RNA-seq and Cut&Run to understand its role in acute kidney injury and repair [CUT&RUN]

Project description:Identifying the role of FOXM1 in human primary renal tubular epithelials using bulk RNA-seq and Cut&Run to understand its role in acute kidney injury and repair [CUT&RUN]

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Identifying the role of FOXM1 in human primary renal tubular epithelials using bulk RNA-seq and Cut&Run to understand its role in acute kidney injury and repair

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Identifying the role of FOXM1 in human primary renal tubular epithelials using bulk RNA-seq and Cut&Run to understand its role in acute kidney injury and repair [RNA-seq]

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CUT&RUNTools 2.0: a pipeline for single-cell and bulk-level CUT&RUN and CUT&Tag data analysis.

Project description:MotivationGenome-wide profiling of transcription factor binding and chromatin states is a widely-used approach for mechanistic understanding of gene regulation. Recent technology development has enabled such profiling at single-cell resolution. However, an end-to-end computational pipeline for analyzing such data is still lacking.ResultsHere, we have developed a flexible pipeline for analysis and visualization of single-cell CUT&Tag and CUT&RUN data, which provides functions for sequence alignment, quality control, dimensionality reduction, cell clustering, data aggregation and visualization. Furthermore, it is also seamlessly integrated with the functions in original CUT&RUNTools for population-level analyses. As such, this provides a valuable toolbox for the community.Availability and implementationhttps://github.com/fl-yu/CUT-RUNTools-2.0.Supplementary informationSupplementary data are available at Bioinformatics online.

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A tissue-specific role for Nlrp3 in tubular epithelial repair after renal ischemia/reperfusion.

Project description:Ischemia/reperfusion injury is a major cause of acute kidney injury. Improving renal repair would represent a therapeutic strategy to prevent renal dysfunction. The innate immune receptor Nlrp3 is involved in tissue injury, inflammation, and fibrosis; however, its role in repair after ischemia/reperfusion is unknown. We address the role of Nlrp3 in the repair phase of renal ischemia/reperfusion and investigate the relative contribution of leukocyte- versus renal-associated Nlrp3 by studying bone marrow chimeric mice. We found that Nlrp3 expression was most profound during the repair phase. Although Nlrp3 expression was primarily expressed by leukocytes, both leukocyte- and renal-associated Nlrp3 was detrimental to renal function after ischemia/reperfusion. The Nlrp3-dependent cytokine IL-1? remained unchanged in kidneys of all mice. Leukocyte-associated Nlrp3 negatively affected tubular apoptosis in mice that lacked Nlrp3 expression on leukocytes, which correlated with reduced macrophage influx. Nlrp3-deficient (Nlrp3KO) mice with wild-type bone marrow showed an improved repair response, as seen by a profound increase in proliferating tubular epithelium, which coincided with increased hepatocyte growth factor expression. In addition, Nlrp3KO tubular epithelial cells had an increased repair response in vitro, as seen by an increased ability of an epithelial monolayer to restore its structural integrity. In conclusion, Nlrp3 shows a tissue-specific role in which leukocyte-associated Nlrp3 is associated with tubular apoptosis, whereas renal-associated Nlrp3 impaired wound healing.

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High-Resolution Chromatin Profiling Using CUT&RUN.

Project description:Determining the genomic location of DNA-binding proteins is essential to understanding their function. Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is a powerful method for mapping protein-DNA interactions at high resolution. In CUT&RUN, a recombinant protein A-microccocal nuclease (pA-MN) fusion is recruited by an antibody targeting the chromatin protein of interest; this can be done with either uncrosslinked or formaldehyde-crosslinked cells. DNA fragments near sites of antibody binding are released from the insoluble bulk chromatin through endonucleolytic cleavage and used to build barcoded DNA-sequencing libraries that can be sequenced in pools of at least 30. Therefore, CUT&RUN provides an alternative to ChIP-seq approaches for mapping chromatin proteins, which typically have relatively high signal-to-noise ratios, while using fewer cells and at a lower cost. Here, we describe the methods for performing CUT&RUN, generating DNA-sequencing libraries, and analyzing the resulting datasets. © 2019 by John Wiley & Sons, Inc.

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