GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE135465 Query DataSets for GSE135465
Status Public on Sep 05, 2019
Title Nucleome Dynamics during Retinal Development[Hi-C_Mm]
Organism Mus musculus
Experiment type Other
Summary The nuclei of rod photoreceptors in mice and other nocturnal species have an unusual inverted chromatin structure with centrally located heterochromatin that helps to focus light and improve photosensitivity. To gain a deeper understanding of this unique nuclear organization of rod photoreceptors, we have carried out Hi-C on retina at 3 stages of development and on purified rod photoreceptors. Predicted looping interactions from the Hi-C data were validated with fluorescent in situ hybridization (FISH). We discovered that a subset of genes important for retinal development, cancer and stress response in the retina are localized to the facultative heterochromatin domain in a developmental stage– and cell type–specific manner. We used machine learning to develop an algorithm based on our chromatin Hidden Markov Modeling (chromHMM) of retinal development to predict heterochromatin domains and study their dynamics during retinogenesis. FISH data for 264 genomic loci were used to train and validate the algorithm. These integrated data ( were used to identify a developmental stage- and cell type-specific core regulatory circuit super-enhancer (CRC-SE) upstream of the Vsx2 gene that is required for bipolar neuron expression. Deletion of the Vsx2 CRC-SE in mice led to the loss of bipolar neurons in the retina.
Overall design Examination of chromatin interaction profiles in 5 cell types
Contributor(s) Aldiri I, Xu B, Dyer MA
Citation(s) 31493975
Submission date Aug 06, 2019
Last update date Dec 15, 2020
Contact name Beisi Xu
Organization name St Jude Children's Research Hosipital
Department Center for Applied Bioinformatics
Street address 262 Danny Thomas Pl
City Memphis
State/province Tennessee
ZIP/Postal code 38105
Country USA
Platforms (2)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (11)
GSM4010832 HiC_Retina_Adult-Rep1
GSM4010833 HiC_Retina_Adult-Rep2
GSM4010834 HiC_Retina_Adult-Rep3
This SubSeries is part of SuperSeries:
GSE87064 The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis
BioProject PRJNA558977
SRA SRP217487

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
GSE135465_Proc.HiC_Retina_Adult.tar.gz 212.8 Kb (ftp)(http) TAR
GSE135465_Proc.HiC_Retina_E14.tar.gz 316.8 Kb (ftp)(http) TAR
GSE135465_Proc.HiC_Retina_GFPneg.tar.gz 241.5 Kb (ftp)(http) TAR
GSE135465_Proc.HiC_Retina_P0.tar.gz 370.6 Kb (ftp)(http) TAR
GSE135465_Proc.HiC_Rod_GFPpos.tar.gz 190.0 Kb (ftp)(http) TAR
GSE135465_hic_Retina_Adult.inter_30.hic 61.4 Gb (ftp)(http) HIC
GSE135465_hic_Retina_E14.5.inter_30.hic 84.8 Gb (ftp)(http) HIC
GSE135465_hic_Retina_GFPnegative.inter_30.hic 97.6 Gb (ftp)(http) HIC
GSE135465_hic_Retina_NRLGFPnegative.inter_30.hic 65.4 Gb (ftp)(http) HIC
GSE135465_hic_Retina_P0.inter_30.hic 78.7 Gb (ftp)(http) HIC
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap