Genomic Data

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Description Citation Data

R script and associated files for analysis of species differences in DNA methylation of the prefrontal cortex and cerebellum in humans, chimpanzees, and rhesus macaques.

Comparative analysis of humans, chimpanzees, and rhesus macaques reveals distinctive epigenetic features of the human prefrontal cortex and cerebellum. Guevara EE, Hopkins WD, Hof PR, Ely JJ, Bradley BJ, Sherwood CC. in review

Guevara et al. dataset

R script and associated files for analysis of epigenetic aging of the prefrontal cortex and cerebellum in humans, chimpanzees, and rhesus macaques.

Epigenetic aging of the prefrontal cortex and cerebellum in humans, chimpanzees, and rhesus macaques. Guevara EE, Hopkins WD, Hof PR, Ely JJ, Bradley BJ, Sherwood CC. in review

NCBI GEO Accession number GSE154403, Guevara et al. dataset

422 polyA-selected RNA-seq samples were obtained from 33 brain regions representing all major brain structures from four adult cognitively healthy human individuals, three chimpanzees, three bonobos, and three rhesus macaques

Single-cell-resolution transcriptome map of human, chimpanzee, bonobo, and macaque brains. Khrameeva E, Kurochkin I, Han D, Guijarro P, Kanton S, Santel M, Qian Z, Rong S, Mazin P, Sabirov M, Bulat M, Efimova O, Tkachev A, Guo S, Sherwood CC, Camp JG, Pääbo S, Treutlein B, Khaitovich P. Genome Res. 2020 May;30(5):776-789. doi: 10.1101/gr.256958.119.

NCBI GEO Accession number GSE127898

Cell-type-specific transcriptome profiling of sorted nuclei from prefrontal cortex (Brodmann area 46) of chimpanzees and rhesus macaques. Cell-type-specific whole-transcriptome data were obtained using fluorescence-activated nuclei sorting (FANS) with antibodies to either NeuN or OLIG2 to isolate neurons (NeuN+) or oligodendrocytes and their precursors (OLIG2+). 

Accelerated evolution of oligodendrocytes in the human brain. Berto S, Mendizabal I, Usui N, Toriumi K, Chatterjee P, Douglas C, Tamminga CA, Preuss TM, Yi SV, Konopka G. Proc Natl Acad Sci U S A. 2019 Nov 26;116(48):24334-24342. doi: 10.1073/pnas.1907982116.

NCBI GEO Accession number GSE123936

Deep sequenced mRNAs and small noncoding RNAs from 16 brain regions of chimpanzees and rhesus macaques, and compared to the complementary human BrainSpan dataset. Transcriptional profiles come from 247 tissue samples representing hippocampus, amygdala, striatum, mediodorsal nucleus of thalamus, cerebellar cortex, and 11 areas of the neocortex from six humans, five chimpanzees, and five macaques.


Molecular and cellular reorganization of neural circuits in the human lineage. Sousa AMM, Zhu Y, Raghanti MA, Kitchen RR, Onorati M, Tebbenkamp ATN, Stutz B, Meyer KA, Li M, Kawasawa YI, Liu F, Perez RG, Mele M, Carvalho T, Skarica M, Gulden FO, Pletikos M, Shibata A, Stephenson AR, Edler MK, Ely JJ, Elsworth JD, Horvath TL, Hof PR, Hyde TM, Kleinman JE, Weinberger DR, Reimers M, Lifton RP, Mane SM, Noonan JP, State MW, Lein ES, Knowles JA, Marques-Bonet T, Sherwood CC, Gerstein MB, Sestan N. Science. 2017 Nov 24;358(6366):1027-1032. doi: 10.1126/science.aan3456.

Sousa et al. 2017 dataset
Raw and normalized gene and protein expression data for anterior cingulate cortex (ACC) and caudate nucleus (CN) tissue from humans and chimpanzees. Evolutionary divergence of gene and protein expression in the brains of humans and chimpanzees. Bauernfeind AL, Soderblom EJ, Turner ME, Moseley MA, Ely JJ, Hof PR, Sherwood CC, Wray GA, Babbitt CC. Genome Biol Evol. 2015 Jul 10;7(8):2276-88. doi: 10.1093/gbe/evv132. Bauernfeind et al. 2015 dataset
Region-specific protein expression data for humans and chimpanzees. Each tab in the spreadsheet represents human or chimpanzee expression data from anterior cingulate cortex (ACC; layers 3, 5), primary motor cortex (M1; layers 3, 5), primary sensory cortex (S1; layers 3, 4, 5), primary visual cortex (V1; layers 3, 4a, 4b, 4c, 5), caudate nucleus (CN; gray matter), or cerebellum (CB; granule cell layer). High spatial resolution proteomic comparison of the brain in humans and chimpanzees. Bauernfeind AL, Reyzer ML, Caprioli RM, Ely JJ, Babbitt CC, Wray GA, Hof PR, Sherwood CC. J Comp Neurol. 2015 Oct 1;523(14):2043-61. doi: 10.1002/cne.23777. Bauernfeind et al. 2015 dataset
Expression patterns of 20 synaptic genes from the prefrontal cortex of 12 primate species. The genes investigated included glutamate receptors, scaffolding proteins, synaptic vesicle components, as well as factors involved in synaptic vesicle release and structural components of the nervous system.   Analysis of synaptic gene expression in the neocortex of primates reveals evolutionary changes in glutamatergic neurotransmission. Muntané G, Horvath JE, Hof PR, Ely JJ, Hopkins WD, Raghanti MA, Lewandowski AH, Wray GA, Sherwood CC. Cereb Cortex. 2015 Jun;25(6):1596-607. doi: 10.1093/cercor/bht354. Muntané et al. 2015 dataset

Gene expression profiling of samples of prefrontal cortex (PFC), primary visual cortex (VC), cerebellar cortex (CBC), kidney and skeletal muscle of humans, chimpanzees, macaques and mice. The data accompanies a large set of metabolite and lipidome measurements of the same tissue samples.

Exceptional evolutionary divergence of human muscle and brain metabolomes parallels human cognitive and physical uniqueness. Bozek K, Wei Y, Yan Z, Liu X, Xiong J, Sugimoto M, Tomita M, Pääbo S, Pieszek R, Sherwood CC, Hof PR, Ely JJ, Steinhauser D, Willmitzer L, Bangsbo J, Hansson O, Call J, Giavalisco P, Khaitovich P. PLoS Biol. 2014 May 27;12(5):e1001871. doi: 10.1371/journal.pbio.1001871.

NCBI GEO Accession number GSE49379
Differential gene expression and gene co-expression modules in the frontopolar cortex of humans, chimpanzees, and rhesus macaques.    Human-specific transcriptional networks in the brain. Konopka G, Friedrich T, Davis-Turak J, Winden K, Oldham MC, Gao F, Chen L, Wang GZ, Luo R, Preuss TM, Geschwind DH. Neuron. 2012 Aug 23;75(4):601-17. doi: 10.1016/j.neuron.2012.05.034. Konopka et al. 2012 dataset

Whole-genome mapping of DNA methylation in humans and chimpanzees.

Divergent whole-genome methylation maps of human and chimpanzee brains reveal epigenetic basis of human regulatory evolution. Zeng J, Konopka G, Hunt BG, Preuss TM, Geschwind D, Yi SV. Am J Hum Genet. 2012 Sep 7;91(3):455-65. doi: 10.1016/j.ajhg.2012.07.024. Zeng et al. 2012 dataset

Differential gene expression regulation by human and chimpanzee FOXP2.

Human-specific transcriptional regulation of CNS development genes by FOXP2. Konopka G, Bomar JM, Winden K, Coppola G, Jonsson ZO, Gao F, Peng S, Preuss TM, Wohlschlegel JA, Geschwind DH. Nature. 2009 Nov 12;462(7270):213-7. doi: 10.1038/nature08549. Konopka et al. 2009 dataset


National Chimpanzee Brain Resoure is supported by NIH - National Institute of Neurological Disorders and Stroke


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