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Series GSE61264 Query DataSets for GSE61264
Status Public on May 21, 2015
Title Genome-wide Definition of Promoter and Enhancer Usage During Neural Induction of Human Embryonic Stem Cells [CAGE-seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
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.
Investiagtion of promoters usage changes during ESCs neural induction
Overall design ESCs and NESCs promoter usage profiling by CAGE-seq
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 15, 2019
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)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
Samples (1)
GSM1501174 Level 2 promoters in human ESCs and NESCs
This SubSeries is part of SuperSeries:
GSE61267 Genome-wide Definition of Promoter and Enhancer Usage During Neural Induction of Human Embryonic Stem Cells
BioProject PRJNA260622
SRA SRP046749

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

Supplementary file Size Download File type/resource
GSE61264_RAW.tar 160.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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