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Series GSE119931 Query DataSets for GSE119931
Status Public on Sep 17, 2019
Title Cell differentiation grade determines distinct FOXA2 contributions to the cis-regulatory networks of pancreatic cancer cells [RNA-seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Abnormal differentiation contributes to the spectrum of aberrant properties of tumor cells. Differentiation of both normal and tumor cells is controlled by regulatory networks enforced by transcription factors (TFs) involved in lineage specification. Among them, pioneer factors such as FOXA1/2, are able to bind and make accessible naïve chromatin, thus critically contributing to the establishment of gene regulatory networks. Pancreatic ductal adenocarcinoma (PDAC) is characterized by massive heterogeneity, with the coexistence at all disease stages of well- and poorly-differentiated cells with diverging transcriptional networks. We found that FOXA2, a TF controlling pancreas specification, was expressed in both well- and poorly-differentiated PDAC cells, but it controlled distinct gene expression programs and displayed extensively different genomic distributions because of its partnership with TFs expressed in a differentiation grade-specific manner, such as HNF1 and HOXB8/9 in well- and poorly-differentiated cells, respectively. These data suggest that pioneer TFs such as FOXA2 are versatile transcriptional regulators whose broad contribution to the gene regulatory networks of highly heterogeneous cancers such as PDACs, depends on the differential availability of partner TFs expressed in distinct tumor cells.
 
Overall design Total RNA from human pancreatic ductal adenocarcinoma cell lines was processed for multiparallel sequencing. Experiments were carried out in genome edited PANC1 cell line (3 FOXA2-deleted CRISPR-Cas9 bulk cell lines and 3 wt bulk) and CFPAC1 cell line silenced with Control-siRNA, FOXA1 and/or FOXA2 siRNA.
 
Contributor(s) Balestrieri C, Milan M, Natoli G
Citation(s) 31531882
Submission date Sep 13, 2018
Last update date Oct 16, 2019
Contact name Chiara Balestrieri
E-mail(s) balestrieri.c@gmail.com
Organization name IRCCS San Raffaele Scientific Institute
Lab Center for Omics Sciences
Street address Via Olgettina 58
City Milan
ZIP/Postal code 20132
Country Italy
 
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (18)
GSM3387462 PANC1.WT.Rep1
GSM3387463 PANC1.WT.Rep2
GSM3387464 PANC1.WT.Rep3
This SubSeries is part of SuperSeries:
GSE120017 Cell differentiation grade determines distinct FOXA2 contributions to the cis-regulatory networks of pancreatic cancer cells
Relations
BioProject PRJNA490732
SRA SRP161699

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE119931_CFPAC1.FOXA1FOXA2KD.genes.edgeR_results.txt.gz 1.1 Mb (ftp)(http) TXT
GSE119931_CFPAC1.FOXA1KD.genes.edgeR_results.txt.gz 1.1 Mb (ftp)(http) TXT
GSE119931_CFPAC1.FOXA2KD.genes.edgeR_results.txt.gz 1.1 Mb (ftp)(http) TXT
GSE119931_CFPAC1.FOXAKD.genes.counts.txt.gz 3.0 Mb (ftp)(http) TXT
GSE119931_PANC1.FOXA2KO.genes.counts.txt.gz 2.8 Mb (ftp)(http) TXT
GSE119931_PANC1.FOXA2KO.genes.edgeR_results.txt.gz 1013.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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