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Series GSE64557 Query DataSets for GSE64557
Status Public on Jan 18, 2016
Title Dissection of transcriptional and cis-regulatory control of differentiation in human pancreatic cancer [ChIP-seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The histological grade of carcinomas describes the ability of tumor cells to organize differentiated epithelial structures and has prognostic impact. Molecular control of differentiation in normal and cancer cells relies on lineage-determining transcription factors (TFs) that activate the repertoire of cis-regulatory elements controlling cell type-specific transcriptional outputs. TF recruitment to cognate genomic DNA binding sites results in the deposition of histone marks characteristic of enhancers and other cis-regulatory elements. Here we integrated transcriptomics and genome-wide analysis of chromatin marks in human pancreatic ductal adenocarcinoma (PDAC) cells of different grade to identify first, and then experimentally validate the sequence-specific TFs controlling grade-specific gene expression. We identified a core set of TFs with a pervasive binding to the enhancer repertoire characteristic of differentiated PDACs and controlling different modules of the epithelial gene expression program. Defining the regulatory networks that control the maintenance of epithelial differentiation of PDAC cells will help determine the molecular basis of PDAC heterogeneity and progression.
 
Overall design Chromatin from human pancreatic ductal adenocarcinoma cell lines was immunoprecipitated with different antibodies for histone modifications and transcription factors and subjected to multiparallel sequencing. Experiments were carried out in unmodified cells and genome edited clonal CFPAC1 cells.
 
Contributor(s) Balestrieri C, Diaferia G, Natoli G
Citation(s) 26769127
Submission date Dec 29, 2014
Last update date May 15, 2019
Contact name Chiara Balestrieri
E-mail(s) balestrieri.c@gmail.com
Organization name Humanitas University
Lab Transcription and Chromatin Lab
Street address Via Rita Montalcini
City Pieve Emanuele (MI)
ZIP/Postal code 20090
Country Italy
 
Platforms (2)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (56)
GSM1574235 H3K27ac.CAPAN1
GSM1574236 H3K27ac.CAPAN2
GSM1574237 H3K27ac.CFPAC1
This SubSeries is part of SuperSeries:
GSE64560 Dissection of transcriptional and cis-regulatory control of differentiation in human pancreatic cancer.
Relations
BioProject PRJNA271302
SRA SRP051604

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
GSE64557_RAW.tar 48.5 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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