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Series GSE86981 Query DataSets for GSE86981
Status Public on May 03, 2017
Title The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis [ChIP-Seq_Hs]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary In the developing retina, as in many other regions of the central nervous system, multipotent neural progenitor cells undergo unidirectional changes to produce differentiated cells in a precise spatiotemporal order. Here we profile the epigenetic and transcriptional changes that occur during retinal development in mice and humans. Although some progenitor genes and cell cycle genes were epigenetically silenced during retinogenesis, the most dramatic change was derepression of cell type–specific differentiation programs. We identified developmental stage–specific superenhancers and showed that the majority of epigenetic changes during murine retinal development are conserved in the human retina. To determine how the epigenome changes during tumorigenesis and reprogramming, we performed the same integrated epigenetic analysis of murine and human retinoblastomas and iPSCs derived from murine rod photoreceptors. The retinoblastoma epigenome mapped to the developmental stage when retinal progenitors switch from a neurogenic to a terminal pattern of cell division and murine retinoblastomas initiate earlier in development than human tumors. The epigenome of retinoblastomas was far more similar to that of normal retina than was the epigenome of retinal-derived iPSCs but we were able to identify retinal specific epigenetic memory. Together, these data provide an in depth view of the dynamic epigenome during neurogenesis and how that relates to developmental tumors and epigenetic memory in iPSCs produced from neurons.
 
Overall design Examination of 8 different histone modifications and 3 transcription factors, transcriptome, DNA methylation in 23 cell types
 
Contributor(s) Aldiri I, Xu B, Wang L, Chen X, Hiler D, Griffiths L, Valentine M, Shirinifard A, Barabas M, Zhang J, Johnson D, Frase S, Easton J, Zhang J, Mardis ER, Wilson RK, Downing JR, Dyer MA
Citation(s) 28472656
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 CA168875 Molecular Targeted Therapy for Retinoblastoma ST. JUDE CHILDREN'S RESEARCH HOSPITAL MICHAEL A DYER
R01 EY014867 Cell type-specific roles of Rb in retinal differentiation ST. JUDE CHILDREN'S RESEARCH HOSPITAL MICHAEL A DYER
R01 EY018599 Proliferation and Differentiation of Retinal Stem Cells ST. JUDE CHILDREN'S RESEARCH HOSPITAL MICHAEL A DYER
Submission date Sep 15, 2016
Last update date May 15, 2019
Contact name Beisi Xu
E-mail(s) beisi.xu@stjude.org
Organization name St Jude Children's Research Hosipital
Department Computational Biology
Street address 262 Danny Thomas Pl
City Memphis
State/province Tennessee
ZIP/Postal code 38105
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (72)
GSM2316298 BRD4-AB1-FW13
GSM2316299 BRD4-AB1-FW15
GSM2316300 BRD4-AB1-FW20
This SubSeries is part of SuperSeries:
GSE87064 The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis
Relations
BioProject PRJNA343125
SRA SRP089967

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
GSE86981_INPUT-FW13_14.bw 513.2 Mb (ftp)(http) BW
GSE86981_INPUT-FW15_16.bw 483.1 Mb (ftp)(http) BW
GSE86981_INPUT-FW18_20.bw 500.4 Mb (ftp)(http) BW
GSE86981_INPUT-FW23_24.bw 340.0 Mb (ftp)(http) BW
GSE86981_RAW.tar 13.2 Gb (http)(custom) TAR (of BW)
GSE86981_RB-CTCF.bw 416.2 Mb (ftp)(http) BW
GSE86981_RB-H3K36me3.bw 630.1 Mb (ftp)(http) BW
GSE86981_RB-H3K4me2.bw 557.9 Mb (ftp)(http) BW
GSE86981_RB-H3K9-14Ac.bw 392.0 Mb (ftp)(http) BW
GSE86981_RB-INPUT.bw 546.7 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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