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Sentinel p16INK4a+ cells in the basement membrane form a reparative niche in the lung [RNA-Seq]

ABSTRACT: Sentinel p16INK4a+ cells in the basement membrane form a reparative niche in the lung [RNA-Seq]

PROVIDER: PRJNA590468 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10493700_1.fastq.gz	Fastqsanger.gz
	SRR10493700_2.fastq.gz	Fastqsanger.gz
	SRR10493701_1.fastq.gz	Fastqsanger.gz
	SRR10493701_2.fastq.gz	Fastqsanger.gz
	SRR10493702_1.fastq.gz	Fastqsanger.gz

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Sentinel p16INK4a+ cells in the basement membrane form a reparative niche in the lung

Project description:Sentinel p16INK4a+ cells in the basement membrane form a reparative niche in the lung

| PRJNA590466 | ENA

Sentinel p16INK4a+ cells in the basement membrane form a reparative niche in the lung [scRNA-Seq]

Project description:Sentinel p16INK4a+ cells in the basement membrane form a reparative niche in the lung [scRNA-Seq]

| PRJNA590469 | ENA

Sentinel p16INK4a+ cells in the basement membrane form a reparative niche in the lung [RNA-Seq]

Project description:We collected freshly sorted mesenchyme (live CD45-Epcam-CD31-PDGFRa+GFP- or GFP+) from dissociated lung tissue of INKBRITE animals to characterize the transcriptome difference between p16INK4a+ vs p16INK4a- cells at homeostasis and during injury. We used fluorescence activated cell sorting (FACS) to exclude immune (CD45+), epithelial (Epcam+), and endothelial (CD31+) cells and positively select for PDGFRa+ mesenchyme. Cells were sequenced at a depth of average of 45 million reads/sample. The results revealed an increase of senescence associated secretory phenotype (SASP) signature in p16INK4+ cells that becomes refined after injury. We found the expression of an epithelial growth factor epiregulin (ereg) increased in p16INK4a+ cells after injury suggesting a possible role of p16INK4a+ senescence during regeneration of lung epithelium.

2022-11-02 | GSE140654 | GEO

Sentinel p16INK4a+ cells in the basement membrane form a reparative niche in the lung [scRNA-Seq]

Project description:A single-cell transcriptional analysis was performed on p16INK4a+ cells from the adult murine lung. Whole adult murine lung tissue was dissociated to single cells and subjected to fluorescence activated cell sorting (FACS) to select all live p16INK4a + cells. The single cell RNA-sequencing library was then subsequently generated. Cells were sequenced at a depth of ~30,506 mean reads/cell. We captured approximately 8752 cells with a mean of 2457 genes detected per cell utilizing a droplet-based barcoding approach to capture single cells for RNA sequencing. The results demonstrate that the p16INK4a + population are predominantly in the immune CD45+ populations and PDGFRa+ mesenchyme.

2022-11-16 | GSE140656 | GEO

Sentinel p16INK4a+ cells in the basement membrane form a reparative niche in the lung

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-11-02 | GSE140657 | GEO

Gene expression profile of a C. elegans Anchor cell invading through Basement Membrane

Project description:Cell invasion through basement membrane is crucial for development and immune cell trafficking, and is misregulated in many human diseases, such as cancer. Understanding the gene expression profile of invading cells is challening, because cell invasion events are often stochastic and rare. Thus, it has been difficult to isolate cells during the act of basement membrane invasion. Here, we have taken advantage of the stereotyped timing of anchor cell invasion in C. elegans, along with synchronized animal culturing, Fluorescence activated cell sorting (FACS), and RNA-Seq and identified the gene expression profile of an invasive cell at the time of basement membrane breaching.

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Effects of a Tricaprylin Emulsion on Anti-glomerular Basement Membrane Glomerulonephritis in Rats

2015-07-14 | GSE46295 | GEO

Effects of a Tricaprylin Emulsion on Anti-glomerular Basement Membrane Glomerulonephritis in Rats

Project description:Expression data from rat with anti-glomerular basement membrane nephritis (anti-GBM). We used microarrays to analyze the transcriptome of kidney from anti-GBM model rat with or without drug treatment RNA from whole kidneys was extracted and processed for hybridization on Affymetrix microarrays.

2015-07-14 | E-GEOD-46295 | biostudies-arrayexpress

Cysteine oxidation triggers amyloid fibril formation of the tumor suppressor p16INK4A

Project description:p16INK4A inhibits the CDK4/6 kinases and is therefore an important cell cycle regulator. Accumulation of p16INK4A in response to oncogenic transformation leads to cellular senescence and it is therefore frequently lost in cancer. p16INK4A is also known to accumulate under conditions of cellular oxidative stress and therefore could potentially be regulated by redox signaling, which is a form of signal transduction that is mediated by the reversible oxidation of cysteine-thiol side chains in proteins. We found that oxidation of the single cysteine residue in p16INK4A in human cells occurs under relatively mild oxidizing conditions and that this leads to disulfide dependent dimerization. p16INK4A is a well-characterized all alpha-helical protein, but we find that upon cysteine-dependent dimerization, p16INK4A undergoes a dramatic structural rearrangement and forms aggregates that have the typical features of amyloid fibrils, including binding of diagnostic dyes, presence of cross-β sheet structure, and typical dimensions found in electron microscopy. We find that p16INK4A amyloid formation abolishes its function as a CDK4/6 inhibitor in human cells. Taken together, these observations mechanistically link the cellular redox state to the inactivation of p16INK4A through the formation of amyloid fibrils.

2019-09-04 | PXD012353 | Pride

The kidney microenvironment influences macrophage response and basement membrane homeostasis

Project description:The kidney microenvironment influences macrophage response and basement membrane homeostasis

| PRJEB51479 | ENA