|
| 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 |
May 15, 2019 |
| Contact name |
Alisa Mo |
| E-mail(s) |
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)
|
|
| Relations |
| BioProject |
PRJNA294311 |
| SRA |
SRP063015 |
| 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) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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