GEO DataSets

(Submitter supplied) Lineage plasticity is a prominent feature of pancreatic ductal adenocarcinoma (PDA) cells, which can occur via deregulation of lineage-specifying transcription factors. Here, we show that the zinc finger protein ZBED2 is aberrantly expressed in PDA and regulates tumor cell identity in this disease. Unexpectedly, our epigenomic experiments reveal that ZBED2 is a sequence-specific transcriptional repressor of interferon-stimulated genes, which occurs through antagonism of Interferon Regulatory Factor 1 (IRF1)-mediated transcriptional activation at co-occupied promoter elements. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

8 Samples

Download data: BIGWIG

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL18573 GPL11154

74 Samples

Download data: BIGWIG

(Submitter supplied) Lineage plasticity is a prominent feature of pancreatic ductal adenocarcinoma (PDA) cells, which can occur via deregulation of lineage-specifying transcription factors. Here, we show that the zinc finger protein ZBED2 is aberrantly expressed in PDA and regulates tumor cell identity in this disease. Unexpectedly, our epigenomic experiments reveal that ZBED2 is a sequence-specific transcriptional repressor of interferon-stimulated genes, which occurs through antagonism of Interferon Regulatory Factor 1 (IRF1)-mediated transcriptional activation at co-occupied promoter elements. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL11154

66 Samples

Download data: TXT

(Submitter supplied) The activation of cellular quality control pathways to maintain metabolic homeostasis and mitigate diverse cellular stresses is emerging as a critical growth and survival mechanism in many cancers. Autophagy, a highly conserved cellular self-degradative process, is a key player in the initiation and maintenance of pancreatic ductal adenocarcinoma (PDA). However, the regulatory circuits that activate autophagy, and how they enable reprogramming of PDA cell metabolism are unknown. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

6 Samples

Download data: FPKM_TRACKING

(Submitter supplied) We perform ChIPseq, ATACseq, and RNAseq to characterize the role of ID1 in PDA cells.

Organism:

Mus musculus; Homo sapiens

Type:

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

Platforms:

GPL17021 GPL16791

43 Samples

Download data: CSV, TDF

(Submitter supplied) Determine methylation pattern in PDAC a genome-wide analysis was performed in a cohort of 167 PDAC and 29 adjacent pancreatic tissues samples using the Infinium 450k methylation arrays (Illumina).

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

196 Samples

Download data: IDAT, 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) 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) The aberrant expression of squamous lineage markers in pancreatic ductal adenocarcinoma (PDA) has been correlated with poor clinical outcomes. However, the functional role of this putative trans-differentiation event in PDA pathogenesis remains unclear. Here, we show that expression of the transcription factor TP63 (ΔN isoform) is sufficient to install and sustain the enhancer landscape and transcriptional signature of the squamous lineage in human PDA cells. more...

Organism:

Homo sapiens; Mus musculus

Type:

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

Platforms:

GPL11154 GPL18573 GPL19057

92 Samples

Download data: BIGWIG

(Submitter supplied) The aberrant expression of squamous lineage markers in pancreatic ductal adenocarcinoma (PDA) has been correlated with poor clinical outcomes. However, the functional role of this putative trans-differentiation event in PDA pathogenesis remains unclear. Here, we show that expression of the transcription factor TP63 (ΔN isoform) is sufficient to install and sustain the enhancer landscape and transcriptional signature of the squamous lineage in human PDA cells. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL11154 GPL19057

42 Samples

Download data: TXT

(Submitter supplied) The aberrant expression of squamous lineage markers in pancreatic ductal adenocarcinoma (PDA) has been correlated with poor clinical outcomes. However, the functional role of this putative trans-differentiation event in PDA pathogenesis remains unclear. Here, we show that expression of the transcription factor TP63 (ΔN isoform) is sufficient to install and sustain the enhancer landscape and transcriptional signature of the squamous lineage in human PDA cells. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

50 Samples

Download data: BIGWIG

(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:

Homo sapiens; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19057 GPL18573

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) 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:

Mus musculus; Homo sapiens

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) PANC-1Tet/ZIC2 and PANC-1Tet/empty were established from human pancreatic cancer cell line PANC-1. PANC-1Tet/ZIC2 cells express FLAG-tagged human ZIC2 on the withdrawal of DOX. On the other hand, PANC-1Tet/empty was transfected an empty vector for the control experiment. To identify ZIC2 target genes, total RNAs were purified from the cells before and 48 hours after the DOX withdrawal. Gene expression profiles were analyzed by AGILENT human 4x44k cDNA microarray. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL10332

6 Samples

Download data: TXT