This track represents the first epigenome map of human fetal and iPSC-derived retinal pigment epithelium (RPE). This hub includes four super tracks:
- ATAC-seq (four tracks): fetal RPE peaks (visible by default); iPSC-RPE peaks (visible); fetal RPE signal (bigWig, hidden); iPSC-RPE signal (bigWig from five lines, hidden)
- ChIP-seq (four tracks): fetal RPE peaks (visible by default); iPSC-RPE peaks (visible); fetal RPE signal (bigWig, hidden); iPSC-RPE signal (bigWig from six lines, nine total ChIP-seq experiments, hidden)
- RNA-seq TPM barplots (two tracks, visible): fetal RPE (one sample); iPSC-RPE (from six lines)
- RNA-seq signal (two tracks, hidden): fetal RPE signal (bigWig); iPSC-RPE signal (bigWig from six lines)
Display Conventions and Configuration
iPSC-RPE and fetal RPE tracks are displayed using the following colors:
- Dark Red - fetal RPE - ATAC-seq
- Light Red - iPSC-RPE - ATAC-seq
- Dark Blue - fetal RPE - ChIP-seq (H3K27ac)
- Light Blue - iPSC-RPE - ChIP-seq (H3K27ac)
- Dark Green - fetal RPE - RNA-seq
- Light Green - iPSC-RPE - RNA-seq
iPSC lines were reprogrammed as part of the iPSCORE resource.
Derivation of iPSC-RPEs
iPSC-RPEs were differentiated using a slightly modified version of the protocol developed by Maruotti et al.
RNA-seq pipeline is described in DeBoever et al.
ATAC-seq reads were aligned to the genome using STAR. Peaks were called using macs2.
ChIP-seq reads were aligned to the genome using BWAS-mem. Peaks were called using macs2.
iPSC-RPE data is currently unpublished.
Data were generated and processed at the Frazer lab at UC San Diego. For inquiries, please contact us at the following address: firstname.lastname@example.org
Panopoulos AD, D'Antonio M, Benaglio P, Frazer KA et al.
iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types.
Stem Cell Reports. 2017.
DeBoever C, Li H, Jakubosky D, Frazer KA et al.
Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced Pluripotent Stem Cells Resource Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced Pluripotent Stem Cell.
CEll Stem Cell. 2017.
Maruotti J, Sripathi SR, Bharti K, Fuller J et al.
Small-molecule-directed, efficient generation of retinal pigment epithelium from human pluripotent stem cells.
CEll Stem Cell. 2017.