GEO DataSets

(Submitter supplied) Tumors comprise a complex microenvironment of interacting malignant and stromal cell types. Much of our understanding of the tumor microenvironment comes from in vitro studies isolating the interactions between malignant cells and a single stromal cell type, often along a single pathway. To develop a deeper understanding of the interactions between cells within human lung tumors we performed RNA-seq profiling of flow-sorted malignant cells, endothelial cells, immune cells, fibroblasts, and bulk cells from freshly resected human primary non-small-cell lung tumors. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

185 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL19807 GPL9257 GPL6696

60 Samples

Download data

(Submitter supplied) Using single-cell RNA sequencing (scRNA-seq) profiles gene expression pattern of each individual cell to characterize of the entire tumor ecosystem

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

42 Samples

Download data: TXT

(Submitter supplied) Mice bearing a G12D activating mutation in Kras consistently develop lung adenocarcinomas in a manner analogous to humans. By performing small and large RNA sequencing on KrasG12D tumors from F1 hybrid mice we were able to identify genes and microRNAs differentially expressed in these tumor samples. Quantification of reads that cover single nucleotide polymorphisms that distinguish between the parental mouse strains enabled an analysis of allele specific expression and imprinting status in these tumors.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL13112 GPL9250

12 Samples

Download data: TXT

(Submitter supplied) In order to find the difference between human lung tissue-derived fibroblasts and human vascular adventitial fibroblasts for enhancing tumor formation ablity of human lung adenocarcinoma cell line A549, we found that human vascular adventitial fibroblasts enhance A549 tumor formation in vivo compared to human lung tissue-derived fibroblasts. To find the responsible genes for this phenomena, we used microarray analysis to find the expression difference between lung tissue-derived fibroblasts and vascular adventitial fibroblas

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

4 Samples

Download data: CEL

(Submitter supplied) Tumor tissue of lung carcinoid tumors (pulmonary neuroendocrine tumors) and adjacent normal lung tissue was profiled using scRNA-seq

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

13 Samples

Download data: H5, TSV

(Submitter supplied) We established co-cultures of invasive or non-invasive NSCLC cell lines and various types of fibroblasts (FBs) to more precisely characterize the molecular mechanism of tumor-stroma crosstalk in lung cancer Differential expression analysis of the respective mono- and co-cultures revealed an upregulation of NFκB-related genes exclusively in co-cultures with Calu-1. Cytokine Array- and ELISA-based characterization of the “cytokine fingerprints” identified CSF2 (GM-CSF), CXCL1, CXCL6, VEGF, IL6, RANTES and IL8 as being specifically upregulated in various co-cultures

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL19859

66 Samples

Download data: CEL

(Submitter supplied) The delicate interaction between cancer cells and the surrounding stroma plays an essential role in all stages of tumourigenesis. Despite the significance of this interplay, alterations in protein composition underlying tumour-stroma interactions are largely unknown. The aim of this study was to identify stromal proteins with clinical relevance in non-small cell lung cancer. A list encompassing 203 stromal candidate genes was compiled based on gene expression array data and available literature. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

10 Samples

Download data: CEL

(Submitter supplied) The tumor microenvironment strongly influences cancer development, progression and metastasis. The role of carcinoma-associated fibroblasts (CAFs) in these processes and their clinical impact has not been studied systematically in non-small cell lung carcinoma (NSCLC). We established primary cultures of CAFs and matched normal fibroblasts (NFs) from 15 resected NSCLC. We demonstrate that CAFs have greater ability than NFs to enhance the tumorigenicity of lung cancer cell lines. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platform:

GPL13135

8 Samples

Download data: TXT

(Submitter supplied) The tumor microenvironment strongly influences cancer development, progression and metastasis. The role of carcinoma-associated fibroblasts (CAFs) in these processes and their clinical impact has not been studied systematically in non-small cell lung carcinoma (NSCLC). We established primary cultures of CAFs and matched normal fibroblasts (NFs) from 15 resected NSCLC. We demonstrate that CAFs have greater ability than NFs to enhance the tumorigenicity of lung cancer cell lines. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

10 Samples

Download data: TXT

(Submitter supplied) The tumor microenvironment strongly influences cancer development, progression and metastasis. The role of carcinoma-associated fibroblasts (CAFs) in these processes and their clinical impact has not been studied systematically in non-small cell lung carcinoma (NSCLC). We established primary cultures of CAFs and matched normal fibroblasts (NFs) from 15 resected NSCLC. We demonstrate that CAFs have greater ability than NFs to enhance the tumorigenicity of lung cancer cell lines. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by array; Genome variation profiling by SNP array; SNP genotyping by SNP array

Platforms:

GPL13135 GPL8490 GPL5175

78 Samples

Download data: CEL

(Submitter supplied) The tumor microenvironment strongly influences cancer development, progression and metastasis. The role of carcinoma-associated fibroblasts (CAFs) in these processes and their clinical impact has not been studied systematically in non-small cell lung carcinoma (NSCLC). We established primary cultures of CAFs and matched normal fibroblasts (NFs) from 15 resected NSCLC. We demonstrate that CAFs have greater ability than NFs to enhance the tumorigenicity of lung cancer cell lines. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5175

30 Samples

Download data: CEL

(Submitter supplied) The tumor microenvironment strongly influences cancer development, progression and metastasis. The role of carcinoma-associated fibroblasts (CAFs) in these processes and their clinical impact has not been studied systematically in non-small cell lung carcinoma (NSCLC). We established primary cultures of CAFs and matched normal fibroblasts (NFs) from 15 resected NSCLC. We demonstrate that CAFs have greater ability than NFs to enhance the tumorigenicity of lung cancer cell lines. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5175

30 Samples

Download data: CEL

(Submitter supplied) We demonstrate that miR-708 is one of the most highly overexpressed miRNAs in non-small cell lung cancer. High level of miR-708 in tumor is also associated with a reduced overall survival in lung adenocarcinomas from never smokers. Functionally, miR-708 overexpression increases the proliferation, migration, and invasion in cultured cells and down regulates TMEM88, a negative regulator of Wnt signaling. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL8179

206 Samples

Download data: TXT

(Submitter supplied) We sequenced mRNA from individual stormal cells (Macrophages, Monocytes, and Neutrophils) and tumor epithelial cells from KrasG12dD; p53-/- murine lung cancer model and WT control mouse to compare gene expressio profiles of lung cancer stroma and tumor cells to their counterparts of WT lugns. The tumor was generated by injecting HKP1 lung cancer cell line, which was driven by KrasG12D activation and loss of p53, via tail vein. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

27 Samples

Download data: TXT

(Submitter supplied) Lung cancer has been the leading cause of cancer death seriously threatening human health. The lung cancers display high heterogeneity in terms of pathology and molecular biomarkers. However, previous studies are mainly based on population of cancer cells due to technical limitations, which would conceal important information from rare single cells. Hence, using a modified STRT-seq technique, we profiled transcriptomes of over 9,000 single cells from 20 primary non-small cell lung cancer (NSCLC) patients diagnosed with stage I-IV. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

106 Samples

Download data: TXT, XLSX

(Submitter supplied) We’ve undertaken a genome-wide approach to identify and test genes in fibroblasts that are both induced upon interaction with basal breast cancer cells in culture and upregulated in stromal cells from primary human breast cancers. Several of the upregulated genes encode secreted growth factors or cytokines. Using RNAi and a co-injection tumorigenicity assay, we determined that the majority of secreted factors selected for functional validation played significant, yet functionally diverse, roles in promoting tumorigenicity. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4762

Platform:

GPL6244

80 Samples

Download data: CEL, TXT

Analysis of fibroblasts (HFF1, HFF2, Wi38, CCD1112Sk) and breast cancer epithelial cells (Cal51, MDA-MB-231) FACS-sorted from 6-day cocultures. Cancer-associated fibroblasts can promote tumor formation and growth. Results provide insight into tumor-fibroblast interactions involved in tumorigenicity.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 cell type, 14 protocol sets

Platform:

GPL6244

Series:

GSE41678

80 Samples

Download data: CEL

(Submitter supplied) Tumorigenesis depends on intricate interactions between genetically altered tumor cells and their surrounding tumor microenvironment (TME). Investigation of tumor cell-TME interactions could be greatly facilitated by models that mimic human disease on both the genotypic and phenotypic levels. Three dimensional (3D) cultures represent an important means to study the impact of tumor cell-TME interactions on specific aspects of neoplastic phenotypes. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

6 Samples

Download data: CEL, TXT