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Series GSE112356 Query DataSets for GSE112356
Status Public on Sep 25, 2018
Title A genomic study of the contribution of DNA methylation to regulatory evolution in primates
Organisms Macaca mulatta; Pan troglodytes; Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary A long-standing hypothesis is that changes in gene regulation play an important role in adaptive evolution, notably in primates. Yet, in spite of the evidence accumulated in the past decade that regulatory changes contribute to many species-specific adaptations, we still know remarkably little about the mechanisms of regulatory evolu tion. In this study we focused on DNA methylation, an epigenetic mechanism whose contribution to the evolution of gene expression remains unclear. To interrogate the methylation status of the vast majority of cytosines in the genome, we performed whole-genome bisulfite conversion followed by high-throughput sequencing across 4 tissues (heart, kidney, liver and lung) in 3 primate species (human, chimpanzee and macaque). In parallel, we collected gene expression profiles using RNA-seq from the same tissue samples, allowing us to perform a high resolution scan for genes and pathways whose regulation evolved under natural selection. We integrated these datasets to characterize better the genome features whose methylation status leads to expression changes, and we developed a statistical model to quantify the proportion of variation in gene expression levels across tissues and species.
Overall design We extracted RNA and genomic DNA followed by high-throughput sequencing across 4 tissues (heart, kidney, liver and lung) in 4 individuals per primate species (human, chimpanzee and macaque).
Contributor(s) Roux J, Blake LE, Hernando-Herraez I, Hsiao CJ, Banovich NE, Garcia Perez R, Chavarria C, Mitrano A, Pritchard JK, Marques-Bonet T, Gilad Y
Citation(s) 30333510, 31953346
Submission date Mar 26, 2018
Last update date Mar 23, 2020
Contact name Lauren Elizabeth Blake
Organization name University of Chicago
Department Human Genetics
Lab Yoav Gilad
Street address 920 E. 58th Street, CLSC 317
City Chicago
State/province Illinois
ZIP/Postal code 60615
Country USA
Platforms (3)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL19129 Illumina HiSeq 2500 (Macaca mulatta)
GPL19148 Illumina HiSeq 2500 (Pan troglodytes)
Samples (159)
GSM3068272 C1H
GSM3068273 C1K
GSM3068274 C1Li
BioProject PRJNA445737
SRA SRP136499

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Supplementary file Size Download File type/resource
GSE112356_RNA_counts.txt.gz 1.7 Mb (ftp)(http) TXT
GSE112356_combined.RDa.gz 2.5 Gb (ftp)(http) RDA
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Raw data are available in SRA
Processed data are available on Series record

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