GEO DataSets

(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) 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 SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19057 GPL18573

136 Samples

Download data: BIGWIG, TXT

(Submitter supplied) Pancreatic ductal adenocarcinoma (PDA) is one of the most lethal human malignancies, owing in part to its propensity for metastasis. Here, we used an organoid culture system to investigate how transcription and the enhancer landscape become altered during each stage of PDA progression. This approach revealed that the metastatic transition is accompanied by massive, and recurrent alterations in enhancer activity. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL19057

36 Samples

Download data: TXT

(Submitter supplied) Pancreatic ductal adenocarcinoma (PDA) is one of the most lethal human malignancies, owing in part to its propensity for metastasis. Here, we used an organoid culture system to investigate how transcription and the enhancer landscape become altered during each stage of PDA progression. This approach revealed that the metastatic transition is accompanied by massive, and recurrent alterations in enhancer activity. more...

Organism:

Mus musculus; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL18573 GPL19057

90 Samples

Download data: BIGWIG

(Submitter supplied) Pancreatic ductal adenocarcinoma (PDA) is one of the most lethal human malignancies, owing in part to its propensity for metastasis. Here, we used an organoid culture system to investigate how transcription and the enhancer landscape become altered during each stage of PDA progression. This approach revealed that the metastatic transition is accompanied by massive, and recurrent alterations in enhancer activity. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

10 Samples

Download data: BIGWIG

(Submitter supplied) This study used Illumina single-end RNA-sequencing to examine gene expression differences between 2 mouse-derived pancreatic stellate cell lines (PSC4, PSC5) grown either in 2D monolayers, as 3D quiescent cultures, or as 3D activated transwell cocultures with 2 mouse tumor-derived pancreatic ductal organoid lines (T4, T5). Mouse pancreatic stellate cell (PSC) lines were derived from the pancreata of wild-type C57Bl/6J mice. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

8 Samples

Download data: 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) 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) We utilized biomaterial scaffolds to identify a unique gene expression signature of immune cells in tumor-bearing mice. Single cell RNA sequencing analysis then revealed two distinct macrophage populations that exist at both the primary tumor and systemically in both mice and pancreatic cancer patients, marked by the expression of C1qa, C1qb, and Trem2.

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24247 GPL24676 GPL21103

15 Samples

Download data: H5, MTX, TSV

(Submitter supplied) CUT&RUN for IgG, H3K4me3 and HA-SPDEF in human PDA HPAF-II cells and CUT&RUN HA-Spdef in murine KPC 2D FC1245 cells We performed CUT&RUN assay in human and murine PDA cells to profile the direct binding of SPDEF to target genes.

Organism:

Mus musculus; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL18573 GPL19057

12 Samples

Download data: BED, BW

(Submitter supplied) This study used Illumina RNA-sequencing to examine gene expression differences following Spdef deletion in hF27, CFPAC1 and HPAF-II orthotopically grafted tumor models.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

29 Samples

Download data: RESULTS

(Submitter supplied) This study used 10X Genomics, single-cell RNA-sequencing to examine the differentiation states of cancer cells present in tumors derived from the KrasLSL-G12D; Trp53LSL-R172H; Pdx1-Cre (KPC) mouse model of pancreatic ductal adenocarcinoma. The study analyzed tumors from 8 different mice.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

8 Samples

Download data: CSV, H5, RDS

(Submitter supplied) This study used Illumina strand-specific, paired-end RNA-sequencing to examine gene expression differences following Spdef deletion and re-instatement in epithelial organoid cultures of primary tumor cells from KrasLSLG12D/+; Trp53LSLR172H/+; Pdx1-Cre (KPC) mice.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

12 Samples

Download data: RESULTS

(Submitter supplied) The mechanisms involved in promoting metastasis of pancreatic ductal adenocarcinoma have yet to be elucidated. Here, we show that AnnexinA2 regulates the secretion of Semaphorin3D from pancreatic tumor cells allowing it to bind to its receptor PlexinD1 on the surface of the tumor cell, which induces invasion and metastasis. Knockdown of AnnexinA2 or Semaphorin3D decreases the metastatic potential of pancreatic tumor cells, while over expression of AnnexinA2 or Semaphorin3D is sufficient to rescue the invasion capacity of these cells. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6096

2 Samples

Download data: CEL

(Submitter supplied) Pancreatic stellate cells (PSC) are one source of cancer-associated fibroblasts (CAF) and play, therefore, an essential role in pancreatic ductal adenocarcinoma (PDA). Paracrine signalling between PDA cancer cells and CAF has been widely studied, yet external influences on paracrine crosstalk are poorly understood. This study aimed to gain a deeper insight into the communication of PSC and cancer cells under different co-culture conditions via analysis of PSC gene expression profiles. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

24 Samples

Download data: TXT

(Submitter supplied) Pancreatic cancer (PC) is the fourth leading cause of cancer death with an overall 5-year survival rate of < 5%, a statistic that has changed little in almost 50 years. A deeper understanding of the underlying molecular pathophysiology is expected to advance the urgent need to develop novel therapeutic and early detection strategies for this disease. Genomic characterisation of PC has previously relied on targeted PCR based exome sequencing of small cohorts of mixed primary and metastatic lesions propagated as xenografts or cell lines (Jones et al, Science 321:1801-1806), leaving the true mutational spectrum of the clinical disease largely unresolved. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

91 Samples

Download data: TXT

(Submitter supplied) Aldh1b1 expressing, adult mouse pancreatic stem cells, were isolated and subjected to single cell RNA Seq. 

Organism:

synthetic construct; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL19604

856 Samples

Download data: TSV

(Submitter supplied) Analysis of induced E47 expression on PDA cells at the gene expression level.The hypothesis tested in the present study was that PDA cells can be reprogrammed to revert to their original quiescent acinar cell phenotype by stimulating a tamoxifen inducible form of E47 fused to a modified estrogen (E47-ER) receptor . Results provide important information on the remarkable ability of E47ER to trigger reactivation of the acinar cell differentiation program and cell cycle arrest in PDA cells.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

12 Samples

Download data: TXT

(Submitter supplied) To understand the molecular process associated with tissue morphogenesis of pancreatic epithelial cells, we profiled the transcriptomes of normal or malignant pancreatic organoids formed in three-dimenstional reconsitututed basement membrance (rBM). Cell monolayers cultured on rBM-coated culture plastics were used as controls.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

12 Samples

Download data: CEL, CHP