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The effect of exposure to neighborhood violence on GR signaling in lung tumors [CUT&Run]

ABSTRACT: The effect of exposure to neighborhood violence on GR signaling in lung tumors [CUT&Run]

PROVIDER: PRJNA1114098 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29111700_1.fastq.gz	Fastqsanger.gz
	SRR29111700_2.fastq.gz	Fastqsanger.gz
	SRR29111701_1.fastq.gz	Fastqsanger.gz
	SRR29111701_2.fastq.gz	Fastqsanger.gz
	SRR29111702_1.fastq.gz	Fastqsanger.gz

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The effect of exposure to neighborhood violence on GR signaling in lung tumors [CUT&Run]

Project description:Despite lower rates and intensity of smoking, Black men experience a higher incidence of lung cancer compared to White men. The racial disparity in lung cancer is particularly pronounced in Chicago, a highly segregated urban city. Neighborhood conditions, particularly social stress, may play a role in lung tumorigenesis. Preliminary studies indicate that Black men residing in neighborhoods with higher rates of violent crime have significantly higher levels of hair cortisol, an indicator of stress response. To examine the relationship between social stress exposure and gene expression in lung tumors, we investigated glucocorticoid receptor (GR) binding in lung tumor samples in relation to GR target gene expression levels and zip code level residential neighborhood violence. Spatial transcriptomics and a version of ChIP-sequencing known as CUT & RUN were used. GR recruitment to chromatin was correlated with neighborhood violent crime rate and overall GR binding increased with increasing neighborhood violent crime rates. Among patients residing in high-violence neighborhoods, tumor samples, compared to normal neighboring lung tissue, had fewer GR binding sites. The opposite was seen in patients residing in low-violence neighborhoods, with tumor samples having more GR binding sites when compared to normal lung tissue. Tumor samples from patients living in high-violence neighborhoods exhibited increased GR recruitment to genes associated with greater tumor aggressiveness. Our findings suggest that exposure to neighborhood violence may influence tumor biology via reprogramming GR recruitment. Prioritizing lung cancer screening in neighborhoods with increased social stress, such as high violence, may reduce racial disparities in lung cancer.

2024-07-10 | GSE268048 | GEO

The effect of exposure to neighborhood violence on GR signaling in lung tumors [Spatial Transcriptomics]

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The effect of exposure to neighborhood violence on GR signaling in lung tumors [Spatial Transcriptomics]

Project description:The effect of exposure to neighborhood violence on GR signaling in lung tumors [Spatial Transcriptomics]

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Epigenetic signatures of intergenerational exposure to violence during pregnancy

Project description:There is substantial evidence for intergenerational health effects of trauma. The biological mechanisms linking traumatic exposures with intergenerational health effects remain unclear, but epigenetics represent a candidate mechanism. We measured DNA methyation to test for intergenerational epigenetic signatures of exposure to violence during pregnancy. Participating families were recruited based on generational exposure to violence trauma. There were four groups: unexposed controls, directly exposed to violence, prenatally exposed to violence, and germline exposed to violence. Three separate epigenome-wide association studies compared direct, prenatal, and germline exposure to unexposed controls to test for differentially methylated positions.

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Bulk Cut&run and Cut&tag

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EMT-Cut&Run

Project description:HOXA10 and CUT &amp RUN

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CUT&RUN HUDEP1 OE SOX6-Flag

Project description:SOX6 CUT&RUN on HUDEP1 over expressing SOX6-Flag. The experiment is done using and anti Flag Ab to assist the genome wide binding profile of SOX6 in HUDEP1 (Human Umbilical cord blood-Derived Erythroid Progenitor-1).

2023-04-07 | E-MTAB-12800 | biostudies-arrayexpress

Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag

Project description:Here we describe successful implementation of CUT&RUN for profiling protein-DNA interactions in zebrafish embryos. We apply modified a CUT&RUN method to generate high resolution maps of enrichment for H3K4me3, H3K27me3, H3K9me3, and RNA polymerase II during zebrafish gastrulation. Using this data, we identify a conserved subset of developmental genes that are enriched in both H3K4me3 and H3K27me3 during gastrulation, and we demonstrate the increased effectiveness of CUT&RUN for detecting protein enrichment at repetitive sequences with reduced mappability. Our work demonstrates the power of combining CUT&RUN with the strengths of the zebrafish system to better understand the changing embryonic chromatin landscape and its roles in shaping development.

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CUT&RUN-seq of DPPA2 in Esg1-tdTomato reporter mESC line

Project description:Enrichment of DPPA2 was assessed by CUT&RUN-sequencing in wildtype Esg1-tdTomato reporter mESC line.

2021-11-23 | E-MTAB-11182 | biostudies-arrayexpress

CUT&RUN LoV-U for SMAD4 in human melanoma cells

Project description:CUT&RUN LoV-U was performed against SMAD4 using two different antibodies in M170117 human melanoma cells under 4 conditions: Control (DMSO), TGFb, MEKi and TGFb + MEKi (Both).

2024-04-22 | E-MTAB-13951 | biostudies-arrayexpress

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