GEO DataSets

(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) 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) 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) Pancreatic ductal adenocarcinoma (PDAC) is known by its aggressiveness and lack of effective therapeutic options. Thus, improvement in current knowledge of molecular changes associated with pancreatic cancer is urgently needed to explore novel venues of diagnostics and treatment of this dismal disease. While there is mounting evidence that long noncoding RNAs (ncRNAs) transcribed from intronic and intergenic regions of the human genome may play different roles in the regulation of gene expression in normal and cancer cells, their expression pattern and biological relevance in pancreatic cancer is currently unknown. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL3985

38 Samples

Download data

(Submitter supplied) Purpose: Transcriptome analysis of pancreatic ductal adenocarcinoma (PDAC) has been useful to identify gene expression changes that sustain malignant phenotypes. Yet, most studies examined only tumor tissues and focused on protein-coding genes, leaving long non-coding RNAs (lncRNAs) largely underexplored. Methods: We generated total RNA-Seq data from patient-matched tumor and nonmalignant pancreatic tissues and implemented a computational pipeline to survey known and novel lncRNAs. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18460 GPL16791

30 Samples

Download data: FA, TXT

(Submitter supplied) Three PDAC tissue samples and their matched adjacent non-tumor samples were obtained and were used for microarray assay.

Organism:

Homo sapiens

Type:

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

Platform:

GPL16956

6 Samples

Download data: TXT

(Submitter supplied) Purpose: Patients with locally advanced prostate cancer after radical prostatectomy are candidates for secondary therapy. However, this higher risk population is heterogeneous. Many cases do not metastasize even when conservatively managed. Given the limited specificity of pathological features to predict metastasis, newer risk prediction models are needed. We report a validation study of a genomic classifier that predicts metastasis after radical prostatectomy in a high risk population. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

235 Samples

Download data: CEL

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

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array; Expression profiling by array

Platforms:

GPL10152 GPL14550

20 Samples

Download data: TXT

(Submitter supplied) Neuroendocrine prostate cancer (NEPC) is proliferative, invasive, and untreatable. Its molecular pathogenesis remains poorly understood but appears to require TP53 and RB1 aberration. In this study we modeled the development of NEPC from conventional prostatic adenocarcinoma using a unique patient-derived xenograft and identified up-regulation of the placental gene PEG10. We found that the androgen receptor and the E2F/RB pathway dynamically regulate distinct post-transcriptional and post-translational isoforms of PEG10 at different stages of NEPC development. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL10152

6 Samples

Download data: TXT

(Submitter supplied) Neuroendocrine prostate cancer (NEPC) is proliferative, invasive, and untreatable. Its molecular pathogenesis remains poorly understood but appears to require TP53 and RB1 aberration. In this study we modeled the development of NEPC from conventional prostatic adenocarcinoma using a unique patient-derived xenograft and identified up-regulation of the placental gene PEG10. We found that the androgen receptor and the E2F/RB pathway dynamically regulate distinct post-transcriptional and post-translational isoforms of PEG10 at different stages of NEPC development. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL14550

14 Samples

Download data: TXT

(Submitter supplied) Purpose: Clinicopathologic features and biochemical recurrence are sensitive, but not specific, predictors of metastatic disease and lethal prostate cancer. We hypothesize that a genomic expression signature detected in the primary tumor represents true biological potential of aggressive disease and provides improved prediction of early prostate cancer metastasis. Methods: A nested case-control design was used to select 639 patients from the Mayo Clinic tumor registry that underwent radical prostatectomy between 1987 and 2001. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

545 Samples

Download data: CEL, 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) 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) We report the scRNAseq profiles of three mouse models of pancreatic cancer: KIC, KPfC, KPC. Analyses demonstrate the existence of 2 molecular subtypes of cancer cells, 2 molecular subtypes of cancer associated fibroblasts, and 2 molecular subtypes of cancer associated macrophages.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

5 Samples

Download data: MTX, TSV

(Submitter supplied) Long non-coding RNAs are emerging as key regulators of cancer cell activities. In this study, our goal was to perform a stringent profiling of breast cancer cell lines that represented a progression series. We used the MCF-10 series, which includes the normal-like MCF-10A, HRAS-transformed MCF-10AT1 (early-stage), and MCF-10CA1a (malignant). We have identified expressed mRNAs and lncRNAs within each cell type. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL18460

15 Samples

Download data: TXT

(Submitter supplied) We performed high throughput transcriptome of breast cancer and normal tissues, identifying lincRNA associated molecular subtype with powerful capacity to distinct breast cancer population and predict prognosis. We also identified subtype-specific lincRNAs that may be a useful complement to intrinsic molecular subtype classification when divergence emerges among pathologists.Paired-end transcriptome sequencing were carried out on a cohort of 33 breast tissues from 11 groups including five breast cancer subtypes including luminal A (LA), luminal B (HER2 negative)(LB, HER2-), luminal B (HER2 positive) (LB, HER2+), HER2 and tripple negative breast cancer (TNB), adjacent noncancerous breast tissue (ANT, three samples for each subtype) and the complete normal breast tissues (three samples)

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9115

33 Samples

Download data: TXT

(Submitter supplied) Portal vein tumor thrombosis is a strong poor indication of HCC. Characterizing the molecular alterations of these metastatic HCCs is important for understanding the molecular mechanisms during HCC progression and metastasis. Previous genomic studies mainly focus on single molecular layer, such as gene expressions or exonic mutations. In this study, we systematically examined the copy number variation (CNV), DNA methylation, miRNA and transcriptome of matched adjacent normal tissues, primary tumors and PVTTs from 19 HCC patients. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

60 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing; Methylation profiling by genome tiling array; Genome variation profiling by high throughput sequencing; Genome variation profiling by SNP array; Expression profiling by high throughput sequencing

Platforms:

GPL13534 GPL16131 GPL16791

240 Samples

Download data: CEL, CYCHP, IDAT, TXT

(Submitter supplied) Portal vein tumor thrombosis is a strong poor indication of HCC. Characterizing the molecular alterations of these metastatic HCCs is important for understanding the molecular mechanisms during HCC progression and metastasis. Previous genomic studies mainly focus on single molecular layer, such as gene expressions or exonic mutations. In this study, we systematically examined the copy number variation (CNV), DNA methylation, miRNA and transcriptome of matched adjacent normal tissues, primary tumors and PVTTs from 19 HCC patients. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL16131

60 Samples

Download data: CEL, CYCHP

(Submitter supplied) Portal vein tumor thrombosis is a strong poor indication of HCC. Characterizing the molecular alterations of these metastatic HCCs is important for understanding the molecular mechanisms during HCC progression and metastasis. Previous genomic studies mainly focus on single molecular layer, such as gene expressions or exonic mutations. In this study, we systematically examined the copy number variation (CNV), DNA methylation, miRNA and transcriptome of matched adjacent normal tissues, primary tumors and PVTTs from 19 HCC patients. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

60 Samples

Download data: IDAT, TXT