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Single-cell genome-wide analysis of macula densa cell gene expression in control and physiological stimulatory conditions

ABSTRACT: Single-cell genome-wide analysis of macula densa cell gene expression in control and physiological stimulatory conditions

PROVIDER: PRJNA785265 | ENA |

REPOSITORIES: ENA

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			Action	DRS
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	SRR17085169_1.fastq.gz	Fastqsanger.gz
	SRR17085169_2.fastq.gz	Fastqsanger.gz
	SRR17085170_1.fastq.gz	Fastqsanger.gz
	SRR17085170_2.fastq.gz	Fastqsanger.gz

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Single-cell genome-wide analysis of macula densa cell gene expression in control and physiological stimulatory conditions

Project description:Single cell based gene expression analysis of the rare kidney cell type, the macula densa in control and physiological stimulatory conditions. The hypothesis tested in the study was that macula densa cells utilize unique and cell-specific molecular networks that play important roles in sensory, regulatory, and secretory functions, and in the physiological stimulation of these cells by environmental clues such as low salt condition. Results provide important information of the identity, biological and physiological functions of macula densa cells consistent with their chief role in the regulation of kidney functions.

2021-12-21 | GSE189954 | GEO

Genome-wide analysis of macula densa cell gene expression in control and physiological stimulatory conditions

Project description:Analysis of the function and physiological regulation of the rare kidney cell type of the macula densa at gene expression level. The hypothesis tested in the study was that macula densa cells utilize unique and cell-specific molecular networks that play important roles in sensory, regulatory, and secretory functions, and in the physiological stimulation of these cells by environmental clues such as low salt condition. Results provide important information of the identity, biological and physiological functions of macula densa cells consistent with their chief role in the regulation of kidney functions.

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Genome-wide analysis of macula densa cell gene expression in control and physiological stimulatory conditions

Project description:Genome-wide analysis of macula densa cell gene expression in control and physiological stimulatory conditions

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The effect of pre-analytical and physiological variables on cell-free DNA fragmentation

Project description:Background: assays that account for the biological properties and fragmentation of cell-free DNA (cfDNA) can improve the performance of liquid biopsy. However, pre-analytic and physiological differences between individuals on fragmentomic analysis are poorly defined. Methods: we analyzed the impact of collection tube, plasma processing time and physiology on the size distribution of cfDNA, their genome-wide representation and sequence diversity at the cfDNA fragment-ends using shallow Whole Genome Sequencing. Results: we observed that using different stabilizing collection tubes, or processing times does not affect the cfDNA fragment sizes, but can impact the genome-wide fragmentation patterns and fragment-end sequences of cfDNA. In addition, beyond differences depending on the gender, the physiological conditions tested between 63 individuals (age, body mass index, use of medication and chronic conditions) minimally influenced the outcome of fragmentomic methods. Conclusions: our results highlight that fragmentomic approaches have potential for implementation in the clinic, pending clear traceability of analytical and physiological factors.

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Effect of HIV infection on co-stimulatory capacity of dendritic cells

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Effect of HIV infection on co-stimulatory capacity of dendritic cells

Project description:HIV uses dendritic cells as a carrier to infect its target CD4+ T cells. At the same time, it also hampers DCs function in terms of their T cell stimulatory capacity and cytokine secretion. We have shown that HIV causes reduction in the expression of co-stimulatory molecules, CD80 and CD86 by DCs at the mRNA level irrespective of the viral subtype or the mode in DC-HIV interaction. The microarray experiments were performed to understand the changes in the transcription factor profile of HIV infected DCs which may in turn lead to reduced CD80/CD86 expression as well as the effect of HIV infection on other co-stimulatory molecules on DCs. The data suggests that TFs NFKB1, NFKB2, REL and MYB may be responsible for the observed decrease in CD80 and CD86 expression and that HIV infection also hampers the expression of other co-stimulatory molecules like CD70, CD30, 4-1BB, OX40L etc. The total RNA was isolated from LPS matured DCs (positive control) and HIV infected DCs using Qiagen RNeasy Minikit. Agilent Quick-Amp Labelling kit (p/n 5190-0444) was used to synthesize the labeled cDNA from 3 ug of total RNA and further process the hybridized cDNA on the array. All the steps were carried out according to manufacturerM-bM-^@M-^Ys instructions (www.agilent.com/chem/dnamauals-protocol). The array slides were scanned immediately using high throughput Agilent scanner with SureScan technology. Agilent feature extraction software was used for normalization and statistical analysis,. Pathway and gene ontology analysis was done using Genespring GX v 10.0 and biointerpreter software. The experiments were performed on DCs cultured from two independent donors. The differential expression was considered if the Log 2 mean of at least -1 for the down regulated genes and +1 for the upregulated genes. We considered only the genes that were differentially regulated genes in both the donors.

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Project description:Molecular characterization of the individual cell types in human kidney as well as model organisms are critical in defining organ function and understanding translational aspects of biomedical research. Previous studies have uncovered gene expression profiles of several kidney glomerular cell types, however, important cells, including mesangial (MCs) and glomerular parietal epithelial cells (PECs), were missing or incompletely described, and a systematic comparison between mouse and human kidney is lacking. To this end, we used Smart-seq2 to profile 4332 individual glomerulus-associated cells isolated from human living donor renal biopsies and mouse kidney. The analysis revealed genetic programs for all four glomerular cell types (podocytes, glomerular endothelial cells, MCs and PECs) as well as rare glomerulus-associated macula densa cells (MDCs). Importantly, we detected heterogeneity in glomerulus-associated Pdgfrb-expressing cells, including bona fide intraglomerular MCs with the functionally active phagocytic molecular machinery, as well as a unique mural cell type located in the central stalk region of the glomerulus tuft. Furthermore, we observed remarkable species differences in the individual gene expression profiles of defined glomerular cell types that highlight translational challenges in the field and provide a guide to design translational studies.

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Single cell of human retina

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