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Series GSE61266 Query DataSets for GSE61266
Status Public on May 21, 2015
Title Genome-wide Definition of Promoter and Enhancer Usage During Neural Induction of Human Embryonic Stem Cells [gene expression profile]
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Genome-wide mapping of transcriptional regulatory elements are essential tools for the understanding of the molecular events orchestrating self-renewal, commitment and differentiation of stem cells. We combined high-throughput identification of nascent, Pol-II-transcribed RNAs by Cap Analysis of Gene Expression (CAGE-Seq) with genome-wide profiling of histones modifications by chromatin immunoprecipitation (ChIP-seq) to map active promoters and enhancers in a model of human neural commitment, represented by embryonic stem cells (ESCs) induced to differentiate into self-renewing neuroepithelial-like stem cells (NESC). We integrated CAGE-seq, ChIP-seq and gene expression profiles to discover shared or cell-specific regulatory elements, transcription start sites and transcripts associated to the transition from pluripotent to neural-restricted stem cell. Our analysis showed that >90% of the promoters are in common between the two cell types, while approximately half of the enhancers are cell-specific and account for most of the epigenetic changes occurring during neural induction, and most likely for the modulation of the promoters to generate cell-specific gene expression programs. Interestingly, the majority of the promoters activated or up-regulated during neural induction have a “bivalent” histone modification signature in ESCs, suggesting that developmentally-regulated promoters are already poised for transcription in ESCs, which are apparently pre-committed to neuroectodermal differentiation. Overall, our study provide a collection of differentially used enhancers, promoters, transcription starts sites, protein-coding and non-coding RNAs in human ESCs and ESC-derived NESCs, and a broad, genome-wide description of promoter and enhancer usage and gene expression programs occurring in the transition from a pluripotent to a neural-restricted cell fate.
Overall design ESCs (H9 NIH code WA09, ISL1 Ds-Red) were kindly provided by the group of K.R. Chien. Neural differentiation was induced by the method of embryoid bodies following a published protocol [1]. Briefly, 4-days embryoid bodies were transferred to polyornithine-coated dishes and propagated in N2-supplemented DMEM/F12 (Invitrogen). Total RNA was extracted from 1-2x10^6 cells from three different cultures of ESCs and NESCs, transcribed into biotinylatedcRNA and hybridized onto GeneChip® HG-U133 Plus 2.0 Arrays (Affymetrix) according to the protocol supplied by the manufacturer (Affymetrix, Santa Clara, CA).
Contributor(s) Poletti V, Carri AD, Tagliazucchi GM, Petiti L, Mazza EM, Peano C, De Bellis G, Bicciato S, Miccio A, Cattaneo E, Mavilio F
Citation(s) 25978676
Submission date Sep 09, 2014
Last update date May 23, 2015
Contact name Silvio Bicciato
Phone +39-049-827-6108
Organization name University of Padova
Department Molecular Medicine
Street address via U. Bassi 59/b
City Padova
ZIP/Postal code 35131
Country Italy
Platforms (1)
GPL19171 Affymetrix GeneChip Human Genome U133 Array Set HG-U133 Plus2 based on a custom CDF (GeneAnnot version 2.2.0)
Samples (6)
GSM1501178 Human embryonic stem cells (H9), replicate A
GSM1501179 Human embryonic stem cells (H9), replicate B
GSM1501180 Human embryonic stem cells (H9), replicate C
This SubSeries is part of SuperSeries:
GSE61267 Genome-wide Definition of Promoter and Enhancer Usage During Neural Induction of Human Embryonic Stem Cells
BioProject PRJNA260623

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Supplementary file Size Download File type/resource
GSE61266_RAW.tar 40.3 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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