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Series GSE96833 Query DataSets for GSE96833
Status Public on Sep 05, 2019
Title Archaic and modern bone DNA methylation maps from the Neanderthal, Denisovan, modern human and chimpanzee
Organisms Pan troglodytes; Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Third-party reanalysis
Summary Regulatory changes are broadly accepted as key drivers of phenotypic divergence. However, identifying regulatory changes that underlie human-specific traits has proven very challenging. Here, we use 63 DNA methylation maps of ancient and present-day humans, as well as of six chimpanzees, to detect differentially methylated regions that emerged in modern humans after the split from Neanderthals and Denisovans. We show that genes affecting the face and vocal tract went through particularly extensive methylation changes. Specifically, we identify widespread hypermethylation in a network of face- and voice-affecting genes (SOX9, ACAN, COL2A1, NFIX and XYLT1). We propose that these repression patterns appeared after the split from Neanderthals and Denisovans, and that they might have played a key role in shaping the modern human face and vocal tract
 
Overall design DNA methylation maps were reconstructed from several human groups, including two Neanderthals, one Denisovan and five anatomically modern humans (Ust Ishim, Stuttgart, Loschbour, I1583 and La Braña 1). Additionally, present-day DNA methylation maps were produced from two present-day human bones (WGBS) and two chimpanzee bones (WGBS and RRBS).

The metadata for the following samples are included in the supplementary file 'GSE96833_metadata_reanalysis_samples.xls':
- Altai Neanderthal Reconstructed Methylome
- Denisovan Reconstructed Methylome
- Modern Human (Ust Ishim) Reconstructed Methylome
- Modern Human (Stuttgart) Reconstructed Methylome
- Modern Human (Loschbour) Reconstructed Methylome
- Vindija Neanderthal Reconstructed Methylome
 
Contributor(s) Carmel L, Gokhman D, Marques-Bonet T, Meissner A, Lalueza-Fox C, Reich D, Meshorer E, Pinhasi R, Vidal JM, Prada ME, Liebergall M, Kandel L, Mjungu D, Stone AC, Quillen EE, Bontrop R, Kondova I, Lipende I, Gelabert P, Ferrando-Bernal M, Gu H, Novak M, Alpaslan-Roodenberg S, Rohland N, Li H, Nieves-Colón MA, Mallick S, Nissim-Rafinia M, García-Pérez R, Housman G, Agranat-Tamir L
Citation(s) 31539495
Submission date Mar 20, 2017
Last update date Jul 25, 2021
Contact name David Gokhman
E-mail(s) david.gokhman@mail.huji.ac.il
Organization name The Hebrew University of Jerusalem
Street address Givat Ram, Safra Campus
City Jerusalem
ZIP/Postal code 91904
Country Israel
 
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL16809 Illumina HiSeq 2000 (Pan troglodytes)
Samples (6)
GSM2637886 Modern Human (La Brana 1) Reconstructed Methylome
GSM2637887 Modern Human Bone WGBS 1
GSM2637888 Modern Human Bone WGBS 2
Relations
BioProject PRJNA387623
SRA SRP107883

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
GSE96833_Altai_Neanderthal_MethylationMap.bedgraph.gz 156.8 Mb (ftp)(http) BEDGRAPH
GSE96833_Denisovan_MethylationMap.bedgraph.gz 149.9 Mb (ftp)(http) BEDGRAPH
GSE96833_Loschbour_MethylationMap.bedgraph.gz 153.5 Mb (ftp)(http) BEDGRAPH
GSE96833_RAW.tar 789.1 Mb (http)(custom) TAR (of BEDGRAPH)
GSE96833_Stuttgart_MethylationMap.bedgraph.gz 155.0 Mb (ftp)(http) BEDGRAPH
GSE96833_Ust_Ishim_MethylationMap.bedgraph.gz 157.3 Mb (ftp)(http) BEDGRAPH
GSE96833_Vindija_Neanderthal_MethylationMap.bedgraph.gz 135.7 Mb (ftp)(http) BEDGRAPH
GSE96833_metadata_reanalysis_samples.xls.gz 7.7 Kb (ftp)(http) XLS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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