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GeoMx Cancer Transcriptome Atlas (CTA) mRNA assay on 191 ROIs from a NSCLC tumor.

ABSTRACT: Dense spatial gene expression profiling of a NSCLC tumor. This study was part of Danaher & Kim et al., "Advances in mixed cell deconvolution enable quantification of cell types in spatially resolved gene expression data"

ORGANISM(S): Homo sapiens

PROVIDER: GSE174743 | GEO | 2021/06/10

REPOSITORIES: GEO

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GeoMx Cancer Transcriptome Atlas (CTA) mRNA assay on 191 ROIs from a NSCLC tumor. [NSCLC_191_grid]

Project description:Dense spatial gene expression profiling of a NSCLC tumor. This study was part of Danaher & Kim et al., "Advances in mixed cell deconvolution enable quantification of cell types in spatially resolved gene expression data"

2021-06-10 | GSE174749 | GEO

GeoMx Cancer Transcriptome Atlas (CTA) mRNA assay on an FFPE cell pellet array of mixed HEK293T and CCRF-CEM cell lines.

Project description:Gene expression profiling of mixed cell lines, used to evaluate the performance of deconvolution methods. This study was part of Danaher & Kim et al., "Advances in mixed cell deconvolution enable quantification of cell types in spatially resolved gene expression data"

2021-06-10 | GSE174746 | GEO

GeoMx Cancer Transcriptome Atlas (CTA) mRNA assay on 191 ROIs from a NSCLC tumor.

Project description:GeoMx Cancer Transcriptome Atlas (CTA) mRNA assay on 191 ROIs from a NSCLC tumor.

| PRJNA731400 | ENA

GeoMx Cancer Transcriptome Atlas (CTA) mRNA assay on 191 ROIs from a NSCLC tumor. [NSCLC_191_grid]

Project description:GeoMx Cancer Transcriptome Atlas (CTA) mRNA assay on 191 ROIs from a NSCLC tumor. [NSCLC_191_grid]

| PRJNA731460 | ENA

GeoMx Cancer Transcriptome Atlas (CTA) mRNA assay

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

2021-06-10 | GSE175927 | GEO

GeoMx Cancer Transcriptome Atlas (CTA) mRNA assay

Project description:GeoMx Cancer Transcriptome Atlas (CTA) mRNA assay

| PRJNA734310 | ENA

Reprogramming of Tumor-infiltrating Immune Cells in Early Stage of NSCLC

Project description:Comparing the relative proportions of immune cells in tumor and adjacent normal tissue from NSCLC patients demonstrates the early changes of tumor immunity and provides insights to guide immunotherapy design. We mapped the immune ecosystem using computational deconvolution of bulk transcriptome data from the Cancer Genome Atlas (TCGA) and single cell RNA sequencing (scRNA-seq) data of dissociated tumors from early-stage non-small cell lung cancer (NSCLC) to investigate early immune landscape changes occurring during tumorigenesis. Computational deconvolution of immune infiltrates in 44 NSCLC and matching adjacent normal samples from TCGA showed heterogeneous patterns of alterations in immune cells. The scRNA-seq analyses of 11,485 cells from 4 treatment-naïve NSCLC patients comparing tumor to adjacent normal tissues showed diverse changes of immune cell compositions. Notably, CD8+ T cells and NK cells are present at low levels in adjacent normal tissues, and are further decreased within tumors. Myeloid cells exhibited marked dynamic reprogramming activities, which were delineated with differentiation paths through trajectory analysis. A common differentiation path from CD14+ monocytes to M2 macrophages was identified among the 4 cases, accompanied by up-regulated genes (e.g. ALCAM/CD166, CD59, IL13RA1, IL7R) with enriched functions (adipogenesis, lysosome), and down-regulated genes (e.g. CXCL2, IL1B, IL6R) with enriched functions (TNFa signaling via NF-kB, inflammatory response). Computational deconvolution and single cell sequencing analyses have revealed a highly dynamic immune reprogramming that occurs in early stage NSCLC development, suggesting that normalizing both immune compartments may represent a viable strategy for treatment of early stage cancer and prevention of progression.

2019-04-30 | GSE117570 | GEO

GeoMX spatial transcriptomic on biphasic Malignant Pleural Mesothelioma

Project description:We applied a spatially resolved, high-dimensional transcriptomic approach to study MPM morpho-logical evolution. 139 regions across 8 biphasic MPMs (B-MPMs) were profiled using the GeoMx™Digital Spatial Profiler and Cancer Transcriptome Atlas to compare epithelioid and sarcomatoid components transcriptional profile and reconstruct the positional context of transcriptional activities and the spatial topology of MPM cells interactions.

2023-12-07 | E-MTAB-13043 | biostudies-arrayexpress

Baseline NSCLC cell lines compared to a reference mix consisting of 45 NSCLC cell lines

Project description:34 NSCLC cell lines were transcriptionally profiled against a reference mix of 45 NSCLC cell lines to look subtype specific differential gene expression 34 individual cell lines were compared to a reference mix consiting of 45 NSCLC cell lines

2013-01-18 | E-GEOD-43567 | biostudies-arrayexpress

Dicer knockout NSCLC RNAseq and miRseq

Project description:Dicer knockout NSCLC mRNAseq profiles the transcriptome, Dicer knockout NSCLC miRseq profiles the miRnome DicerHet and DicerKO NSCLC, 2 biological reps each genotype for mRNAseq, 1 biological rep each for miRseq

2014-04-25 | E-GEOD-57043 | biostudies-arrayexpress

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