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Links from GEO DataSets

Items: 20

1.

A high dimensional deep sequencing study of non-small cell lung adenocarcinoma in never-smoker Korean females [Seq]

(Submitter supplied) One of the most fertile applications of next generation sequencing will be in the field of cancer genomics. Here, we report a high-throughput multi-dimensional sequencing study of primary non-small cell lung adenocarcinoma tumors and adjacent normal tissues of 6 never-smoker Korean female patients. Our data encompass results from exome-seq, RNA-seq, small RNA-seq, and MeDIP-seq. We identified and validated novel genetic aberrations including 47 somatic mutations and 20 fusion transcripts. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform:
GPL10999
36 Samples
Download data: TXT, XLSX
Series
Accession:
GSE37764
ID:
200037764
2.

A high dimensional deep sequencing study of non-small cell lung adenocarcinoma in never-smoker Korean females

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Genome variation profiling by array; Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms:
GPL10153 GPL10999
48 Samples
Download data: TXT
Series
Accession:
GSE37765
ID:
200037765
3.

A high dimensional deep sequencing study of non-small cell lung adenocarcinoma in never-smoker Korean females [aCGH]

(Submitter supplied) One of the most fertile applications of next generation sequencing will be in the field of cancer genomics. Here, we report a high-throughput multi-dimensional sequencing study of primary non-small cell lung adenocarcinoma tumors and adjacent normal tissues of 6 never-smoker Korean female patients. Our data encompass results from exome-seq, RNA-seq, small RNA-seq, and MeDIP-seq. We identified and validated novel genetic aberrations including 47 somatic mutations and 20 fusion transcripts. more...
Organism:
Homo sapiens
Type:
Genome variation profiling by array
Platform:
GPL10153
12 Samples
Download data: TXT
Series
Accession:
GSE37759
ID:
200037759
4.

Molecular profiling of primary lung carcinomas

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by array; Genome variation profiling by genome tiling array
Platforms:
GPL6947 GPL4723
150 Samples
Download data: GPR
Series
Accession:
GSE29066
ID:
200029066
5.

Relation between smoking history and gene expression profiles in lung adenocarcinomas

(Submitter supplied) Lung cancer is the worldwide leading cause of death from cancer. Tobacco usage is the major pathogenic factor, however, not all lung cancers can be attributable to smoking. The genetic aberrations that differ between smokers' and never-smokers’ lung carcinomas remain to a large extent unclear. We analyzed 72 early-stage primary lung carcinomas including small cell lung cancers LCNEC, adenocarcinomas and squamous cell carcinomas by Illumina HT12 gene expression microarrays.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL6947
72 Samples
Download data: TXT, XLS
Series
Accession:
GSE29016
ID:
200029016
6.

Integrated genome-wide analysis of gene dosage and gene expression in Non Small Cell Lung Cancer

(Submitter supplied) Understanding the molecular events in non-small cell lung cancer (NSCLC) is essential to improve early diagnosis and treatment for this disease. We examined the effect of chromosomal copy number changes on gene expression in resected NSCLC patients. We identified a deletion on 14q32.2-33 as a common alteration in NSCLC (44%), which significantly influenced gene expression for HSP90AA1, residing on 14q32. more...
Organism:
Homo sapiens
Type:
Genome variation profiling by array
Platform:
GPL2827
32 Samples
Download data: XLS
Series
Accession:
GSE7878
ID:
200007878
7.

Human Large Airway Epithelial Cells from healthy never and current smoker and smokers with and without lung cancer

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by array; Expression profiling by high throughput sequencing
Platforms:
GPL13447 GPL10999
21 Samples
Download data: BEDGRAPH, CEL, TXT
Series
Accession:
GSE29007
ID:
200029007
8.

mRNA-seq of Human Airway Epithelial Cells

(Submitter supplied) mRNA expression was profiled from pooled bronchial airway epithelial cell brushings (n=3 patients/pool) obtained during bronchoscopy from healthy never (NS) and current smokers (S) and smokers with (C) and without (NC) lung cancer
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL10999
8 Samples
Download data: BEDGRAPH, GTF, TXT
Series
Accession:
GSE29006
ID:
200029006
9.

Large airway epithelial cells from cigarette smokers with and without lung cancer undergoing flexible bronchoscopy in the operating room for resection of a suspicious lung nodule

(Submitter supplied) mRNA expression was assayed from bronchial epithelial cell samples from smokers with and without lung cancer. A subset of the samples (2 of the lung cancer samples and 3 of the no cancer samples) were pooled and underwent whole transcriptome sequencing. The goals were to compare whole transcriptome sequencing gene expression levels to gene expression levels derived from these samples run on the Affymetrix HGU133A 2.0 platform.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL13447
13 Samples
Download data: CEL
Series
Accession:
GSE28835
ID:
200028835
10.

The transcriptional landscape and mutational profile of lung adenocarcinoma

(Submitter supplied) Understanding the molecular signatures of cancer is important to apply appropriate targeted therapies. Here we present the first large scale RNA sequencing study of lung adenocarcinoma demonstrating its power to identify somatic point mutations as well as transcriptional variants such as gene fusions, alternative splicing events and expression outliers. Our results reveal the genetic basis of 200 lung adenocarcinomas in Koreans including deep characterization of 87 surgical specimens by transcriptome sequencing. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11154
164 Samples
Download data: TXT
Series
Accession:
GSE40419
ID:
200040419
11.

Field of Cancerization in Peripheral Airway Epithelium

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by array; Expression profiling by RT-PCR
Platforms:
GPL17039 GPL570
60 Samples
Download data: CEL
Series
Accession:
GSE54543
ID:
200054543
12.

Field of Cancerization in Peripheral Airway Epithelium: miRNA

(Submitter supplied) Field of cancerization in the airway epithelium has been increasing examined to understand early pathogenesis of non-small cell lung cancer. This study uses microarray high-throughput technologies to characterize the molecular aberrations in the terminal airway and bronchoalveolar cells in the context of field cancerization in high-risk smokers and lung cancer patients.
Organism:
Homo sapiens
Type:
Expression profiling by RT-PCR
Platform:
GPL17039
30 Samples
Download data: TXT
Series
Accession:
GSE54541
ID:
200054541
13.

Field of Cancerization in Peripheral Airway Epithelium: Gene Expresssion

(Submitter supplied) Field of cancerization in the airway epithelium has been increasing examined to understand early pathogenesis of non-small cell lung cancer. This study uses microarray high-throughput technologies to characterize the molecular aberrations in the terminal airway and bronchoalveolar cells in the context of field cancerization in high-risk smokers and lung cancer patients.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL570
30 Samples
Download data: CEL
Series
Accession:
GSE54495
ID:
200054495
14.

ADAM-28: A potential oncogene involved in asbestos-related lung adenocarcinomas

(Submitter supplied) To identify gene expression biomarkers associated with asbestos-related lung adenocarcinoma, we analyzed primary tumour gene expression for a total of 36 primary lung adenocarcinomas on 22,323 element microarrays, comparing 12 patients with lung asbestos body counts above levels associated with urban dwelling (ARLC-AC: asbestos-related lung cancer-adenocarcinoma) with 24 patients with no asbestos bodies (NARLC-AC: non-asbestos related lung cancer-adenocarcinoma).
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL3877
36 Samples
Download data: TXT
Series
Accession:
GSE20875
ID:
200020875
15.

Gene expression and lung tumors: screening for markers that discriminate tumor histology and genetic background.

(Submitter supplied) The success of targeted therapies creates a need to discriminate tumors accurately by their histological and genetic characteristics. Here, we used cDNA microarray analysis to identify gene expression profiles and single markers that recapitulate the pathological and genetic background (i.e., BRAF, EGFR, KRAS, LKB1, PIK3CA, and TP53 gene alterations) of non-small cell lung cancer (NSCLC). Gene expression profiles were determined for 6 normal lung tissues and 69 lung tumors from patients diagnosed with NSCLC. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL5645
75 Samples
Download data: GPR
Series
Accession:
GSE8569
ID:
200008569
16.

Conserved recurrent gene mutations correlate with pathway deregulation and clinical outcomes of lung adenocarcinoma in never-smokers

(Submitter supplied) Background. Novel and targetable mutations are needed for improved understanding and treatment of lung cancer in never-smokers. Methods. Twenty-seven lung adenocarcinomas from never-smokers were sequenced by both exome and mRNA-seq with respective normal tissues. Somatic mutations were detected and compared with pathway deregulation, tumor phenotypes and clinical outcomes. Results. Although somatic mutations in DNA or mRNA ranged from hundreds to thousands in each tumor, the overlap mutations between the two were only a few to a couple of hundreds. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11154
54 Samples
Download data: TXT
Series
Accession:
GSE87340
ID:
200087340
17.

Gene expression profiling of normal lung tissue adjacent to lung adenocarcinoma (ADCA)

(Submitter supplied) Individual variations in the transcriptional profile of normal lung tissue may reflect the lung ADCA patients’ predisposition to a specific clinical stage Associations between clinical outcome of cancer patients and the gene expression signature in primary tumors at time of diagnosis have been reported. To test whether gene expression patterns in the normal tissue surrounding the cancerous tissue might correlate with clinical stage, we compared transcriptome of normal lung samples of adenocarcinoma (ADCA) smoker patients of clinical stage I versus stage >I, and identified 55 differentially expressed genes. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL6947
24 Samples
Download data: TXT
Series
Accession:
GSE31267
ID:
200031267
18.

Smoking Status Impacts microRNA Mediated Prognosis and Lung Adenocarcinoma Biology

(Submitter supplied) Cigarette smoke is associated with the majority of lung cancers: however, 25% of lung cancer patients are non-smokers, and half of all newly diagnosed lung cancer patients are former smokers. Lung tumors exhibit distinct epidemiological, clinical, pathological, and molecular features depending on smoking status, suggesting divergent mechanisms underlie tumorigenesis in smokers and non-smokers. MicroRNAs (miRNAs) are integral contributors to tumorigenesis and mediate biological responses to smoking. more...
Organism:
Homo sapiens
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL11154
188 Samples
Download data: TXT
Series
Accession:
GSE62182
ID:
200062182
19.

Circulating RNAs profile in non-small cell lung cancer patients

(Submitter supplied) Circulating RNAs are a less invasive and easy accessed source of samples for biomedical research and clinical applications. However, circulating mRNA is mostly fragmented and less abundant. High throughput RNA sequencing (RSEQ) and DASL assay have been both applied to profile such fragmented RNA samples. In this study, we compared the ability of transcriptomic profiling of the two platforms. Circulating RNAs from three non-small cell lung cancer patients and three age-matched healthy controls were analyzed by RSEQ and DASL assay. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL14951
6 Samples
Download data: TXT
Series
Accession:
GSE69732
ID:
200069732
20.

Transcriptome of non-involved lung parenchyma from smoker lung adenocarcinoma patients from Milan, Italy.

(Submitter supplied) Scientific evidence indicates that genetic factors may contribute to differences in lung cancer risk for individuals with similar levels of tobacco exposure, which is the main environmental risk factor of lung cancer. Moreover, lung cancer patients show large differences in clinical staging and survival; these differences seem to be attributable, at least partially, to the genetic background. The analysis of the molecular properties (e.g., germline variations and genome-wide expression levels) of non-involved tissue from lung cancer patients may contribute in the identification of genetic factors involved in the development and progression of this pathology. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL10558
284 Samples
Download data: TXT
Series
Accession:
GSE71181
ID:
200071181
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