Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Phenotyping tumor-immune microenvironment in vivo in skin cancer patients

ABSTRACT: Phenotyping tumor-immune microenvironment in vivo in skin cancer patients

PROVIDER: PRJNA750449 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR15279818_1.fastq.gz	Fastqsanger.gz
	SRR15279818_2.fastq.gz	Fastqsanger.gz
	SRR15279819_1.fastq.gz	Fastqsanger.gz
	SRR15279819_2.fastq.gz	Fastqsanger.gz
	SRR15279820_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 28

Similar Datasets

Phenotyping tumor-immune microenvironment in vivo in skin cancer patients

Project description:Phenotyping of tumors into hot, altered, or cold based on assessment of only T-cell infiltration in static tumor biopsies provides suboptimal prediction of immunotherapy response. In vivo dynamic mechanisms within the tumor microenvironment such as tumor angiogenesis and leukocyte trafficking also play a central role in modulating anti-tumor immunity and therefore immunotherapy response. Here, we report novel tumor immune microenvironment (TiME) phenotyping in vivo in patients with non-invasive spatially-resolved cellular-level imaging based on endogenous contrast. Investigating skin cancers as a model, with reflectance confocal microscopy (RCM) imaging, we determined four major phenotypes with variable prevalence of vasculature (Vasc) and inflammation (Inf) features: VaschiInfhi, VaschiInflo, VascloInfhi and Vascmed/hiInflo. The VaschiInfhi phenotype correlates with high immune activation, exhaustion, and vascular signatures while VaschiInflo with endothelial anergy and immune exclusion. Automated quantification of TiME features demonstrates moderate-high accuracy and correlation with corresponding gene expression. Prospectively analyzed response to topical immunotherapy show highest response in VascloInfhi, and reveals the added value of vascular features in predicting treatment response.

2022-07-03 | GSE181037 | GEO

Transcriptional profiling of in vivo immune responses to mycobacteria using the tuberculin skin test

Project description:Transcriptional profiling of biopsies from tuberculin skin test sites was performed to investigate the interaction of complex cellular and molecular networks at the interface between innate and adaptive immunity which coordinate anti-mycobacterial responses in vivo.

2012-05-13 | E-TABM-1157 | biostudies-arrayexpress

CAF variants control the tumor-immune microenvironment and predict skin cancer malignancy

Project description:CAF variants control the tumor-immune microenvironment and predict skin cancer malignancy

| PRJNA1072630 | ENA

Skin response to urban pollution in an ex vivo model

Project description:A vast range of pollutants (polycyclic aromatic hydrocarbons, heavy metals, particulate matters) are generated by increasing urbanization. The skin epidermis, as the outermost line of defense of the body, is continuously exposed to external aggressions, including environmental pollution. To study the effects of air pollutant exposure on skin physiology, the first challenge was to define a model that mimics as close as possible the in vivo skin exposure to atmospheric pollution. In the present study, the pollutant mixture was designed on the basis of the French non-profit organization ‘Air Parif’ database and nebulized on human skin explants using the Pollubox® device. Cellular and molecular modifications in skin explants were investigated from several donors exposed to a pollutant mix (P) or an organic solvent (OS). Transcriptomic analyses coupled to immunolabelling showed that P exposure induced the expression of detoxifying enzymes notably in the stratum granulosum. Interestingly, transmission electron microscopy observations demonstrated that, in our model, diesel particles smaller than 300 nm could penetrate the skin up to the granular layer. This may cause local alterations of the microenvironment which alter the skin physiology. Therefore, the response of the epidermis to pollutant exposure is likely to be layer-specific.

2021-01-31 | GSE126440 | GEO

Functional stem cell aging dictated by skin tissue microenvironment

Project description:Functional stem cell aging dictated by skin tissue microenvironment

| PRJNA514242 | ENA

Malassezia sympodialis host response studied with an ex-vivo human skin model

Project description:An ex-vivo human skin model was used to investigate the host skin response to M. sympodialis on oily (supplemented with oleic acid) and non-oily skin. Host-pathogen interactions were analysed by different molecular techniques including proteomics.

2021-09-09 | PXD018404 | Pride

ENCODE H1_ES cell phenotyping study

Project description:These samples are part of the ENCODE consortium’s proposed time-limited Pilot Study for confirmation of the utility of RNA abundance measurements as a standard reference phenotyping tool. Keywords: cell type comparison For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Each batch of H1-ES cells cultured by Cellular Dynamics International for use by the ENCODE labs was processed on Affymetrix Exon 1.0 ST arrays to obtain phenotyping data.

2009-02-16 | E-GEOD-14863 | biostudies-arrayexpress

ENCODE Tier2 cell phenotyping study

Project description:These samples are part of the ENCODE consortium’s proposed time-limited Pilot Study for confirmation of the utility of RNA abundance measurements as a standard reference phenotyping tool. Keywords: cell type comparison For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Each of the 7 ENCODE laboratories submitted biological triplicates for at least one of the four Tier2 cell lines. These were processed on Affymetrix Exon 1.0 ST arrays to obtain phenotyping data for each cell ine.

2009-08-24 | E-GEOD-17778 | biostudies-arrayexpress

Comparison of metastasis-inclined microenvironment (MIM) and metastasis-averse microenvironment (MAM) HCC patients

Project description:To determine the role of the hepatic microenvironment in HCC metastasis, we compared the gene expression profiles of 20 noncancerous surrounding hepatic tissues from two HCC patient groups, those with primary HCC together with venous metastasis which we termed a metastasis-inclined microenvironment (MIM) and those with HCC without detectable metastasis, which we termed a metastasis-averse microenvironment (MAM). There were a total of 20 cDNA microarrays performed, comparing 9 MIM or 11 MAM HCC patient samples to a common reference pool of 8 normal liver tissues.

2010-07-01 | E-GEOD-5093 | biostudies-arrayexpress

In vivo gene expression profile between vermilion and skin

Project description:In vivo gene expression profile between vermilion and skin

| PRJNA922871 | ENA