10.6084/m9.figshare.7587476.v1
Louise Porter
Louise
Porter
Neil Saptarshi
Neil
Saptarshi
Yongxiang Fang
Yongxiang
Fang
Sonika Rathi
Sonika
Rathi
Anneke Hollander
Anneke
Hollander
Eiko Jong
Eiko
Jong
Simon Clark
Simon
Clark
Paul Bishop
Paul
Bishop
Timothy Olsen
Timothy
Olsen
Triantafillos Liloglou
Triantafillos
Liloglou
Venkata Chavali
Venkata
Chavali
Luminita Paraoan
Luminita
Paraoan
Additional file 1: of Whole-genome methylation profiling of the retinal pigment epithelium of individuals with age-related macular degeneration reveals differential methylation of the SKI, GTF2H4, and TNXB genes
Springer Nature
2019
donor RPE cells
EWAS discovery cohort
Table S 9. Histone modifications
2H
age-related macular degeneration
Table S 8. SNPs
sample cohort
Literature search results
Non-Coding Genetic Variation
CRE
SKI
AREDS
AMD
differentially methylated CpG loci
ENCODE
Table S 12. Target differentially methylated CpG probes
expression studies cohort
MGS
candidate gene CpG site
Table S 5. Comparison
Table S 10. Histone modifications enrichment
GTF
Differentially Methylated Regions
Table S 3. Model parameters
Table S 11. Analysis
Single-Nucleus-RNA-Seq Reveal Cis-Regulatory Elements
TNXB genes Table S 1. Minnesota Grading System
Table S 2. Demographic characteristics
Table S 4. Bisulfite Pyrosequencing primer sequences
Table S 7. Candidate Genes
Table S 6. RT-qPCR primer sequences
DOCX 115 kb
2019-01-14 05:00:00
Journal contribution
https://springernature.figshare.com/articles/journal_contribution/Additional_file_1_of_Whole-genome_methylation_profiling_of_the_retinal_pigment_epithelium_of_individuals_with_age-related_macular_degeneration_reveals_differential_methylation_of_the_SKI_GTF2H4_and_TNXB_genes/7587476
Table S1. Minnesota Grading System (MGS) â based on the AREDS grading system. Table S2. Demographic characteristics of all RPE samples used in the study including EWAS discovery cohort, independent sample cohort, and expression studies cohort. Table S3. Model parameters used for data analysis. Table S4. Bisulfite Pyrosequencing primer sequences. Table S5. Comparison of demographic characteristics between AMD cases and normal human donor RPE cells in our EWAS discovery cohort, independent sample cohort and combined cohorts. Table S6. RT-qPCR primer sequences. Table S7. Candidate Genes: Literature search results. Table S8. SNPs associated with candidate gene CpG site. Table S9. Histone modifications enriched at differentially methylated CpG loci in various cell types and cell lines represented in the ENCODE data. Table S10. Histone modifications enrichment in Differentially Methylated Regions in AMD. Table S11. Analysis of differentially methylated CpG loci in relation to proposed Cis-Regulatory Elements (CRE) in the RPE/Choroid from the data of T. Cherry et al. (doi: https://doi.org/10.1101/412361, http://biorxiv.org/cgi/content/short/412361v1 , Epigenomic Profiling and Single-Nucleus-RNA-Seq Reveal Cis-Regulatory Elements in Human Retina, Macula and RPE and Non-Coding Genetic Variation). Table S12. Target differentially methylated CpG probes in relation to ATAC-Seq peaks in identified in RPE tissue in Wang et al, 20187. (DOCX 115 kb)