GEO DataSets

(Submitter supplied) Gastric cancer (GC) is the world's third leading cause of cancer mortality. In spite of significant therapeutic improvement, the clinical outcome for patients with advanced GC is poor; thus, the identification and validation of novel targets is extremely important from a clinical point of view. We generated a wide, multi-level platform of GC models, comprising 100 Patient-derived xenografts (PDXs), primary cell lines and organoids. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

42 Samples

Download data: TXT

(Submitter supplied) Expression profiling of frozen primary and patient derived xenograft gastric cancer

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

102 Samples

Download data: TXT

(Submitter supplied) Gastric cancers with mismatch repair (MMR) inactivation are characterised by microsatellite instability (MSI). In this study, the transcriptional profile of 38 gastric cancers with and without MSI was analysed. Unsupervised analysis showed that the immune and apoptotic gene networks efficiently discriminated these two cancer types. Hierarchical clustering analysis revealed numerous gene expression changes associated with the MSI phenotype. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

69 Samples

Download data: CEL

(Submitter supplied) PURPOSE: Although epidermal growth factor receptor (EGFR) mutated adenocarcinomas initially have very high response rates to EGFR tyrosine kinase inhibitors (TKIs), most atients eventually develop resistance. Patient derived xenografts (PDXs) are considered preferred preclinical models to study the biology of patient tumors. EGFR-mutant PDX models may be valuable tools to study the biology of these tumors and to elucidate mechanisms of resistance to EGFR-targeted therapies. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by array

Platform:

GPL14951

25 Samples

Download data: TXT

(Submitter supplied) Experimental set accompanying Giacomini et al publication "A legacy gene-expression signature of genetic instability in colon cancer". Includes 18 colon cancer cell line training set, 13 colon cancer cell line test set, and 3 cell lines (HCT116, HCT116+ch2, HCT116+ch3) used to evaluate signature after correcting underlying genetic instability. Experiments were performed by comparing mRNA from each colon cancer cell line (Cy5; channel 2) to a "universal" mRNA reference (Cy3; channel 1). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL2002 GPL2001

34 Samples

Download data

(Submitter supplied) Background: In high-grade serous ovarian cancer (HGSOC) intrinsic and/or acquired resistance against platinum-containing chemotherapy is a major obstacle for successful treatment. A low frequency of somatic mutations, but frequent epigenetic alterations including DNA methylation in HGSOC tumors, presents the cancer epigenome as a relevant target for innovative therapy. Patient-derived xenografts (PDXs) supposedly are good preclinical models for identifying novel drug targets. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

22 Samples

Download data: IDAT

(Submitter supplied) Samples were taken from surgically resected tumor specimens from patients with proximal colon cancer. The expression profiles were determined using the Affymetrix GeneChip Human Exon 1.0 ST Array version 2. APC gene mutation status was determined using Sanger sequencing. A classifier for APC mutation status was trained using these expression data.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5175

52 Samples

Download data: CEL

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by SNP array

Platforms:

GPL570 GPL6801

89 Samples

Download data: CEL

(Submitter supplied) There is a strong need to develop patient-derived xenograft (PDX) tumor models for studying new treatment options for gastric cancer (GC). With low engraftment success, few collections of GC PDX have been reported and molecular basis of the model establishment remain largely unknown. Here we established n=27 PDX models from n=100 GC tumors and compared their characteristics to GC patient tumors based on the recent work done by ACRG and TCGA, to evaluate the representativeness and relevance of the collection for drug testing. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL6801

62 Samples

Download data: CEL, TXT

(Submitter supplied) There is a strong need to develop patient-derived xenograft (PDX) tumor models for studying new treatment options for gastric cancer (GC). With low engraftment success, few collections of GC PDX have been reported and molecular basis of the model establishment remain largely unknown. Here we established n=27 PDX models from n=100 GC tumors and compared their characteristics to GC patient tumors based on the recent work done by ACRG and TCGA, to evaluate the representativeness and relevance of the collection for drug testing. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

27 Samples

Download data: CEL

(Submitter supplied) We report the correlation of transcript abundance with response to EP in 19 PDX models of SCLC

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

19 Samples

Download data: XLSX

(Submitter supplied) Purpose: Study the changes in cell transcriptome in breast cancer with respect to normal breast tissue in association with somatic mutations Methods: RNA was extracted from frozen normal breast tissues and PDXs cells Results: We found over-expression of oncogenic pathways associated with oncogenic mutations in PDXs

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

21 Samples

Download data: XLSX

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

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; Expression profiling by high throughput sequencing

Platforms:

GPL21290 GPL22678 GPL16791

20 Samples

Download data: TXT

(Submitter supplied) Prostate cancer translational research has been hampered by the lack of comprehensive and tractable models that represent the genomic landscape of clinical disease. Metastatic castrate-resistant prostate cancer (mCRPC) patient derived xenografts (PDXs) recapitulate the genetic and phenotypic diversity of the disease. We sought to establish a representative, preclinical platform of PDX-derived organoids that is experimentally facile for high throughput and mechanistic analysis.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21290 GPL16791

8 Samples

Download data: TXT

(Submitter supplied) Prostate cancer translational research has been hampered by the lack of comprehensive and tractable models that represent the genomic landscape of clinical disease. Metastatic castrate-resistant prostate cancer (mCRPC) patient derived xenografts (PDXs) recapitulate the genetic and phenotypic diversity of the disease. We sought to establish a representative, preclinical platform of PDX-derived organoids that is experimentally facile for high throughput and mechanistic analysis.

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL22678

12 Samples

Download data: SEG

(Submitter supplied) Engraftment of primary pancreas ductal adenocarcinomas (PDAC) in mice to generate patient derived xenograft (PDX) models is a promising platform to for biological and therapeutic studies in this disease. However, these models are still incompletely characterized. Here, we measured the impact of the murine environment on the gene expression of the engrafted human tumoral cells. We have analyzed gene expression profiles from 35 new PDX models and compared them with previously published microarray data from PDAC and hepatocellular carcinoma (HCC). more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Third-party reanalysis

Platform:

GPL570

37 Samples

Download data: CEL, TXT

(Submitter supplied) Tumors from pancreatic cancer specimens obtained at surgery were used for efficacy testing and biologic analysis Keywords: Pharmacogenetics

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

36 Samples

Download data: CEL

(Submitter supplied) Reliable identification of cancer markers can have substantial implications to early detection of cancer. We report here an integrated computational and experimental study on identification of gastric cancer markers in patients’ tissue and sera based on (i) genome-scale transcriptomic analyses on 80 paired gastric cancer/reference tissues, with the aim of identifying abnormally expressed genes at various subtypes/stages of gastric carcinoma (ii) a computational identification of differentially expressed genes that may have their proteins secreted into blood circulation, followed by experimental validations.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5175

160 Samples

Download data: CEL

(Submitter supplied) Gastric cancer (GC) heterogeneity between and within tumors represents a barrier to disease management. We generated a comprehensive single-cell atlas of GC comprising 31 primary gastric tumor samples representing clinical stages I-IV and histological subtypes. We identified 34 distinct cell-lineage states, related by developmental trajectories and previously unreported rare cell populations. Many lineage states exhibited a distinctive tumor-associated expression profile, each contributing individually to a combined tumor-wide molecular collage. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

40 Samples

Download data: CSV

(Submitter supplied) Gastric cancer (GC) is a challenging malignant disease among gastrointestinal tumors. The clinical treatments for GC include surgery, neoadjuvant therapy and adjuvant chemotherapy. As patients’ response to chemotherapeutic drugs varies, an approach to predict the efficacy of chemotherapeutic treatment is urgently needed. Here, a biorepository of 17 human gastric tumor organoids (GTOs) and 9 normal organoids (GNOs) derived from GC patients was established, which contains the intestinal, diffuse and mixed-type of GC. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

30 Samples

Download data: VCF