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Series GSE72550 Query DataSets for GSE72550
Status Public on Mar 07, 2016
Title Epigenomic Landscapes of Retinal Rods and Cones
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Both rod and cone photoreceptors are critical for mammalian vision yet they have important functional differences. In this study, we investigate patterns of DNA methylation and chromatin accessibility in mouse rods and cones. Unexpectedly, we find that a substantial fraction of hypo-methylated regions in the rod methylome are in inaccessible chromatin. These regions show marks of active regulatory regions earlier in neuronal development and could remain undermethylated in adult rods due to their highly compact chromatin. We further identify rod- and cone-enriched regions of accessible chromatin that correspond with cell type-specificity of nearby photoreceptor gene expression. We predict novel DNA signatures of rod and cone specificity and show that NR2E3 function is necessary for rods to gain their complete ensemble of epigenomic features. Taken together, our data capture the epigenomic landscapes of retinal rods and cones, including differences relevant to chromatin structure and photoreceptor biology.
 
Overall design RNA-seq, MethylC-seq, ATAC-seq, and native histone ChIP-seq in the retina
 
Contributor(s) Mo A, Luo C, Davis FP, Mukamel E, Eddy SR, Ecker JR, Nathans J
Citation(s) 26949250
Submission date Aug 31, 2015
Last update date Mar 21, 2019
Contact name Alisa Mo
E-mail amo4@jhmi.edu
Phone 410 955 4679
Organization name Johns Hopkins University School of Medicine
Department Molecular Biology and Genetics
Lab Jeremy Nathans
Street address 725 N. Wolfe St. PCTB805
City Baltimore
State/province MD
ZIP/Postal code 21205
Country USA
 
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (33)
GSM1864999 RNA-seq_WT_rods_rep1
GSM1865000 RNA-seq_WT_rods_rep2
GSM1865001 RNA-seq_rd7_rods_rep1
Relations
BioProject PRJNA294311
SRA SRP063015

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
GSE72550_ChIP-seq_H3K27ac_WT_rods_SICER_peaks.txt.gz 390.4 Kb (ftp)(http) TXT
GSE72550_ChIP-seq_H3K27me3_WT_rods_SICER_peaks.txt.gz 184.3 Kb (ftp)(http) TXT
GSE72550_ChIP-seq_H3K4me1_WT_rods_SICER_peaks.txt.gz 500.8 Kb (ftp)(http) TXT
GSE72550_ChIP-seq_H3K4me3_WT_rods_SICER_peaks.txt.gz 81.9 Kb (ftp)(http) TXT
GSE72550_MethylC-seq_DMRs_DSS_WT_cones_vs_rd7_rods_hypo_in_Cones.txt.gz 39.3 Kb (ftp)(http) TXT
GSE72550_MethylC-seq_DMRs_DSS_WT_cones_vs_rd7_rods_hypo_in_rd7.txt.gz 16.5 Kb (ftp)(http) TXT
GSE72550_MethylC-seq_DMRs_DSS_WT_rods_vs_WT_cones_hypo_in_Cones.txt.gz 53.0 Kb (ftp)(http) TXT
GSE72550_MethylC-seq_DMRs_DSS_WT_rods_vs_WT_cones_hypo_in_Rods.txt.gz 86.4 Kb (ftp)(http) TXT
GSE72550_MethylC-seq_DMRs_DSS_WT_rods_vs_rd7_rods_hypo_in_Rods.txt.gz 11.3 Kb (ftp)(http) TXT
GSE72550_MethylC-seq_DMRs_DSS_WT_rods_vs_rd7_rods_hypo_in_rd7.txt.gz 2.4 Kb (ftp)(http) TXT
GSE72550_MethylC-seq_WT_cones_UMRs_LMRs.txt.gz 683.7 Kb (ftp)(http) TXT
GSE72550_MethylC-seq_WT_rods_UMRs_LMRs.txt.gz 854.1 Kb (ftp)(http) TXT
GSE72550_MethylC-seq_rd7_rods_UMRs_LMRs.txt.gz 736.0 Kb (ftp)(http) TXT
GSE72550_RAW.tar 28.5 Gb (http)(custom) TAR (of BW, TAR, TXT)
Raw data are available in SRA
Processed data provided as supplementary file
Processed data is available on Series record

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