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Series GSE64558 Query DataSets for GSE64558
Status Public on Jan 18, 2016
Title Dissection of transcriptional and cis-regulatory control of differentiation in human pancreatic cancer [RNA-seq]
Organism Homo sapiens
Experiment type Expression 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 Poly(A) fraction of the total RNA from human pancreatic ductal adenocarcinoma cell lines was extracted and subjected to by multiparallel sequencing. Experiments were carried out in unmodified cells in duplicate, genome edited clonal CFPAC1 cells (2 KLF5-deleted CRISPR-Cas9 clones, 3 ELF3-deleted CRISPR-Cas9 clones and 2 wt clones) and CFPAC1 cells ectopically expressing ZEB1 or empty vector control (in duplicate).
 
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 IRCCS San Raffaele Scientific Institute
Department Center for Omics Sciences
Street address Via Olgettina 58
City Milan
ZIP/Postal code 20132
Country Italy
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (29)
GSM1574293 AsPC1.rep1
GSM1574294 AsPC1.rep2
GSM1574295 BxPc3.rep1
This SubSeries is part of SuperSeries:
GSE64560 Dissection of transcriptional and cis-regulatory control of differentiation in human pancreatic cancer.
Relations
BioProject PRJNA271301
SRA SRP051606

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
GSE64558_ELF3-KO_KLF5-KO_ZEB1-OE.gene_exp.diff.gz 7.9 Mb (ftp)(http) DIFF
GSE64558_ELF3-KO_KLF5-KO_ZEB1-OE.genes.fpkm_tracking.gz 2.4 Mb (ftp)(http) FPKM_TRACKING
GSE64558_Lo-G-PDACs_vs_Hi-G-PDACs.gene_exp.diff.gz 853.3 Kb (ftp)(http) DIFF
GSE64558_PDACs.genes.fpkm_tracking.gz 3.1 Mb (ftp)(http) FPKM_TRACKING
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Raw data are available in SRA
Processed data are available on Series record

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