GEO DataSets

(Submitter supplied) In this study, we performed laser capture microdissection (LCM) of PDAC samples to define their cancer- and stroma-specific molecular subtypes and identify a prognostic gene expression signature for short-term and long-term survival. LCM and RNA-seq analysis of cancer and adjacent stroma of 19 treatment-naïve PDAC tumors were performed. Gene expression signatures were tested for their robustness in a large independent validation set. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

38 Samples

Download data: TXT

(Submitter supplied) The single-cell RNA profiles of dissociated 10 pancreatic primary tumors and 6 metastatic biopsies were obtained using the 10x Genomics Chromium platform

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

16 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) This study used laser capture microdissection to obtain paired tumor epithelium and stroma RNA samples from human pancreatic ductal adenocarcinoma (PDA) frozen sections. Libraries were prepared using the Nugen Ovation RNA-Seq System V2 and sequenced to a depth of 30 million 100bp single-end reads. These data were used to model compartment-specific gene expression density on a genome-wide scale and build an algorithm for transcriptional devonvolution (ADVOCATE). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL20301

204 Samples

Download data: TXT

(Submitter supplied) Pancreatic tumors with small size can cause type3C Diabetes Mellitus (PCA-DM) but the mechanism is unknown. In this study we aimed at revealing the mRNA and long noncoding RNA (LncRNA) expression patterns of pancreatic tumors that triggered PCA-DM. Four pancreatic tumors from patients with PCA-DM (A1-A4), four pancreatic tumors from patients without PCA-DM (B1-B4), and four pancreatic tissues from patients with pancreatitis were individually profiled with Agilent microarrays(Arraystar Human LncRNA Array v3.0).

Organism:

Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platform:

GPL16956

12 Samples

Download data: TXT

(Submitter supplied) Most cancer deaths are caused by metastases, which are the end-results of circulating tumor cells (CTC) that detach from the cancer primary and succeed to survive in distant organs. The aim of the present study was to develop a gene signature of CTC and to assess its prognostic relevance after surgery for pancreatic ductaladenocarcinoma (PDAC). A negative depletion fluorescence activated cell sorting (FACS) procedure was developed and validated with spiking experiments using cancer cell lines in whole human blood samples. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4329

Platform:

GPL570

24 Samples

Download data: CEL

Analysis of circulating tumor cells (CTC) from patients who underwent surgery for PDAC. Most cancer deaths are caused by metastases, resulting from CTCs that detach from the primary cancer and survive in distant organs. Results provide insight into molecular characterization of CTC motility in PDAC.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 4 cell type, 6 individual sets

Platform:

GPL570

Series:

GSE18670

24 Samples

Download data: CEL

(Submitter supplied) Intratumoral heterogeneity (ITH) and tumor microenvironment (TME) of pancreatic ductal adenocarcinoma (PDAC) play important roles in tumor evolution and patient outcomes. However, the precise characterization of diverse cell populations and their crosstalk associated with PDAC progression and metastasis is still challenging. We performed single-cell RNA sequencing (scRNA-seq) of treatment-naive primary PDAC samples with and without paired liver metastasis samples to understand the interplay between ITH and TME in the PDAC evolution and its clinical associations. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

218 Samples

Download data: TXT

(Submitter supplied) To evaluate the prognostic relevance of molecular subtypes and key transcription factors in pancreatic ductal adenocarcinoma (PDAC), we performed gene expression analysis of whole-tumor tissue obtained from 118 surgically resected PDAC and 13 control samples.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13667

131 Samples

Download data: CEL

(Submitter supplied) Pancreatic cancer is characterized by abundant desmoplastic stroma. Despite numerous theoretical and experimental efforts, therapeutic approaches targeting pancreatic cancer stroma have been largely unsuccessful, highlighting the need for more comprehensive assessment of inter- and intratumoral stromal heterogeneity in a large series of clinical tumors. Quantitative computation of FAP-dominant fibroblasts, ACTA2-dominant fibroblasts, and intratumoral collagen in whole-tissue sections from 215 treatment-naïve pancreatic cancers allowed us to identify three distinct stroma types (FAP-dominant fibroblast-rich stroma [F-stroma], ACTA2-dominant fibroblast-rich stroma [A-stroma], and collgen-rich stroma [C-stroma]), which were differentially associated with patient outcomes, molecular characteristics and the immunosuppressive tumor microenvironment. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL23126

20 Samples

Download data: CEL

(Submitter supplied) Pancreatic ductal adenocarcinoma (PDAC) remains a lethal disease with a 5-year survival of 4%. A key hallmark of PDAC is extensive stromal involvement, which makes capturing precise tumor-specific molecular information difficult. Here, we have overcome this problem by applying blind source separation to a diverse collection of PDAC gene expression microarray data, which includes primary, metastatic, and normal samples. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL20769

357 Samples

Download data: TXT

(Submitter supplied) In this project we have used single cell RNA-seq to profile pancreatic cancer development in a mouse model, from pre-invasive stage to cancer, and in human PDAC sample. Using a reporter gene, we were able to dissect metaplastic acinar cell heterogeneity, profiled six different acinar metaplastic cell types and states, validated their localization to pre-invasive lesions and correlated findings with human PDAC. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19057 GPL16791 GPL17021

12 Samples

Download data: CSV, TXT

(Submitter supplied) We report the transcriptome changes that result from the transient knockdown of FAM83H-AS1 in Aspc1 cells and transient knockdown of LINC00673 in Panc1 cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

15 Samples

Download data: CSV, XLSX

(Submitter supplied) Through single-cell RNA sequencing (scRNA-seq), we identify substantial transcriptomic evolution of PDOs propagated from the parental tumor, which may alter predicted drug sensitivity. In addition, we performed an integrative analyses of PDAC biopsies and provide an in-depth characterization of the heterogeneity within the tumor microenvironment, including cancer-associated fibroblast (CAF) subclasses, and predicts for a multitude of ligand-receptor interactions, revealing potential targets for immunotherapy approaches.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

17 Samples

Download data: TAR

(Submitter supplied) Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer embedded in an extensive desmoplastic stroma. Since this challenges the molecular analyses of bulk tumor samples, we FACS-purified epithelial cells from PDAC and healthy human pancreas and performed genome-wide transcriptome and DNA methylome analyses. Clustering based on DNA methylation revealed two distinct groups of PDAC with different methylation levels at genomic regions encoding repeat elements. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

13 Samples

Download data: BED

(Submitter supplied) Pancreatic ductal adenocarcinoma (PDAC) is characterized by extensive desmoplasia, which challenges the molecular analyses of bulk tumor samples. Here we FACS-purified epithelial cells from human PDAC and normal pancreas and derived their genome-wide transcriptome and DNA methylome landscapes. Clustering based on DNA methylation revealed two distinct PDAC groups displaying different methylation patterns at regions encoding repeat elements. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array; Third-party reanalysis

Platform:

GPL21145

43 Samples

Download data: CSV, IDAT

(Submitter supplied) Pancreatic ductal adenocarcinoma (PDAC) is characterized by extensive desmoplasia, which challenges the molecular analyses of bulk tumor samples. Here we FACS-purified epithelial cells from human PDAC and normal pancreas and derived their genome-wide transcriptome and DNA methylome landscapes. Clustering based on DNA methylation revealed two distinct PDAC groups displaying different methylation patterns at regions encoding repeat elements. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

6 Samples

Download data: IDAT, TXT

(Submitter supplied) Pancreatic ductal adenocarcinoma (PDAC) is characterized by extensive desmoplasia, which challenges the molecular analyses of bulk tumor samples. Here we FACS-purified epithelial cells from human PDAC and normal pancreas and derived their genome-wide transcriptome and DNA methylome landscapes. Clustering based on DNA methylation revealed two distinct PDAC groups displaying different methylation patterns at regions encoding repeat elements. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

7 Samples

Download data: IDAT, TXT

(Submitter supplied) Pancreatic ductal adenocarcinoma (PDAC) is characterized by abundant stroma, the main cellular constituents of which are cancer-associated fibroblasts (CAFs). Heterogeneity in the PDAC CAF population was recently delineated demonstrating that both tumor-promoting and -suppressive activities co-exist in the stroma. Here, we aimed to identify biomarkers for the CAF population that contribute to a favorable outcome. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

2 Samples

Download data: MTX, TSV

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

Organism:

Mus musculus; Murid betaherpesvirus 1; JC polyomavirus; Human immunodeficiency virus 1; Human gammaherpesvirus 8; Homo sapiens; Human alphaherpesvirus 1; Human betaherpesvirus 5; human gammaherpesvirus 4; Betapolyomavirus macacae; Rattus norvegicus; Murid gammaherpesvirus 4; Betapolyomavirus hominis

Type:

Expression profiling by array; Non-coding RNA profiling by array; Genome variation profiling by SNP array

Platforms:

GPL6801 GPL7723 GPL570

96 Samples

Download data: CEL, CHP, GPR

(Submitter supplied) To perform an integrative profile of human pancreatic cancer (PDAC) to identify prognosis-significant genes and their related pathways. A concordant survival-based whole genome in silico array analysis of DNA copy number, and mRNA & micro RNA (miRNA) expression in 25 early stage PDAC was performed. A novel composite score simultaneously integrated gene expression with regulatory mechanisms to identify the signature genes with the most levels of prognosis-significant evidence. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL6801

32 Samples

Download data: CEL, CHP