Data Repository

To submit data to the repository, please complete this form.

Description Citation Data

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

Chimpanzee-human cortical expansion map. In vivo MRI data from 29 adult chimpanzees and 50 adult human subjects were analyzed. Vertex-wise and region-wise expansion was calculated in reference to the 114-region subdivision of the Desikan-Killiany atlas (DK-114). 

Genetic mapping and evolutionary analysis of human-expanded cognitive networks. Wei Y, de Lange SC, Scholtens LH, Watanabe K, Ardesch DJ, Jansen PR, Savage JE, Li L, PreussTM, Rilling JK, Posthuma D, van den Heuvel MP. Nat Commun. 2019 Oct 24;10(1):4839. doi: 10.1038/s41467-019-12764-8.

Wei et al., 2019 dataset

Diffusion MRI was used to reconstruct the connections of the cortical hemispheres of the chimpanzee and an exploratory analysis was performed of the grey matter structures of the chimpanzee cerebral cortex and their underlying white matter connectivity profiles. Results images are compatible with Connectome Workbench.

Concurrent analysis of white matter bundles and grey matter networks in the chimpanzee. Mars RB, O'Muircheartaigh J, Folloni D, Li L, Glasser MF, Jbabdi S, Bryant KL. Brain Struct Funct. 2019 Apr;224(3):1021-1033. doi: 10.1007/s00429-018-1817-8.

Mars et al., 2019 dataset

Connectivity matrix from chimpanzee DTI. Voxel-wise diffusion reconstructed using GQI, fibers reconstructed using deterministic fiber tracking (8 seeds per white matter voxel). Matrix describes group matrix based on 60% prevalence threshold.

Evolutionary expansion of connectivity between multimodal association areas in the human brain compared with chimpanzees. Ardesch DJ, Scholtens LH, Li L, Preuss TM, Rilling JK, van den Heuvel MP. Proc Natl Acad Sci U S A. 2019 Mar 18. pii: 201818512. doi: 10.1073/pnas.1818512116

Ardesch et al. 2019 dataset

Average microglial densities for the neocortex (NC: dorsolateral prefrontal cortex and midtemporal gyrus) and hippocampus (HC: CA1 and CA3) by morphological phenotype (ram: ramified, int: intermediate, amo: amoeboid), and tau-positive microglial densities (PHF1/Iba1-immunoreactive microglia) in aged chimpanzees (37-62 years old).

Microglia changes associated to Alzheimer's disease pathology in aged chimpanzees. Edler MK, Sherwood CC, Meindl RS, Munger EL, Hopkins WD, Ely JJ, Erwin JM, Perl DP, Mufson EJ, Hof PR, Raghanti MA. J Comp Neurol. 2018 Dec 15;526(18):2921-2936. doi: 10.1002/cne.24484

Edler et al. 2018 dataset

MRI-derived myelin maps and associated parcellations of humans, chimpanzees, and macaques. 

Development and Evolution of Cerebral and Cerebellar Cortex. Van Essen DC, Donahue CJ, Glasser MF. Brain Behav Evol. 2018;91(3):158-169. doi: 10.1159/000489943. 

Van Essen et al. 2018 dataset

MRI-derived cortical surfaces of many individual humans, chimpanzees, and macaques. The dataset presents two parcellation-based PFC delineations based on cytoarchitecture and function and show that a previously used morphological surrogate (cortex anterior to the genu of the corpus callosum) substantially underestimates PFC extent, especially in humans.

Quantitative assessment of prefrontal cortex in humans relative to nonhuman primates. Donahue CJ, Glasser MF, Preuss TM, Rilling JK, Van Essen DC. Proc Natl Acad Sci U S A. 2018 May 29;115(22):E5183-E5192. doi: 10.1073/pnas.1721653115.

Donahue et al. 2018 dataset

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
Volumes occupied by APP/Aβ (6E10-immunoreactive) plaques and vessels (%), volumes occupied by Aβ42 plaques and vessels (%), and AT8-immunoreactive pretangle, neurofibrillary tangle, and tau neuritic cluster densities (mm3) in the prefrontal cortex (layer III), middle temporal gyrus (layer III), and CA1 and CA3 subfields (pyramidal layer) of the hippocampus in aged chimpanzees (37-62 years).

Aged chimpanzees exhibit pathologic hallmarks of Alzheimer's disease. Edler MK, Sherwood CC, Meindl RS, Hopkins WD, Ely JJ, Erwin JM, Mufson EJ, Hof PR, Raghanti MA. Neurobiol Aging. 2017 Nov;59:107-120. doi: 10.1016/j.neurobiolaging.2017.07.006. 

Edler et al. 2017 dataset
Total neuron and choline acetyltransferase-immunoreactive axon length densities for select regions within the striatum and globus pallidus. Percentage of striatal cholinergic neuron morphological subtypes (unipolar, bipolar, or multipolar). Species included are human, chimpanzee, gorilla, olive baboon, pigtailed macaque, and tufted capuchin. Cholinergic innervation of the basal ganglia in humans and other anthropoid primates. Stephenson AR, Edler MK, Erwin JM, Jacobs B, Hopkins WD, Hof PR, Sherwood CC, Raghanti MA. J Comp Neurol. 2017 Feb 1;525(2):319-332. doi: 10.1002/cne.24067. Stephenson et al. 2017 dataset
Tyrosine hydroxylase-immunoreactive axon length density/total neuron densities in select regions of striatum and globus pallidus for human, chimpanzee, gorilla, olive baboon, pigtailed macaque, and capuchin monkey. Human-specific increase of dopaminergic innervation in a striatal region associated with speech and language: A comparative analysis of the primate basal ganglia. Raghanti MA, Edler MK, Stephenson AR, Wilson LJ, Hopkins WD, Ely JJ, Erwin JM, Jacobs B, Hof PR, Sherwood CC. J Comp Neurol. 2016 Jul 1;524(10):2117-29. doi: 10.1002/cne.23937. Raghanti et al. 2016 dataset
Amygdala nuclei volumes and serotonin transporter (SERT)-immunoreactive axon densities of bonobos and chimpanzees. Also included are SERT-immunoreactive axon densities for the middle temporal gyrus and caudate nucleus. Differential serotonergic innervation of the amygdala in bonobos and chimpanzees. Stimpson CD, Barger N, Taglialatela JP, Gendron-Fitzpatrick A, Hof PR, Hopkins WD, Sherwood CC. Soc Cogn Affect Neurosci. 2016 Mar;11(3):413-22. doi: 10.1093/scan/nsv128. Stimpson et al. 2016 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

Linear metrics (cerebral lobe dimensions and sulcal lengths) and principal component scores of cortical shape variation in 206 chimpanzees and 218 human brains.

Relaxed genetic control of cortical organization in human brains compared with chimpanzees. Gómez-Robles A, Hopkins WD, Schapiro SJ, Sherwood CC. Proc Natl Acad Sci U S A. 2015 Dec 1;112(48):14799-804. doi: 10.1073/pnas.1512646112. Gomez-Robles 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

3D landmark coordinates describing cortical and subcortical anatomy in 189 chimpanzee and 189 human brains.

Modular structure facilitates mosaic evolution of the brain in chimpanzees and humans. Gómez-Robles A, Hopkins WD, Sherwood CC. Nat Commun. 2014 Jul 22;5:4469. doi: 10.1038/ncomms5469. Gómez-Robles et al. 2014 dataset
Cortical neuropeptide Y-immunoreactive axon and varicosity densities/total neuron densities for pigtailed macaque, moor macaque, olive baboon, squirrel monkey, tufted capuchin, gorilla, chimpanzee, and human. Humans and great apes share increased neocortical neuropeptide Y innervation compared to other haplorhine primates. Raghanti MA, Edler MK, Meindl RS, Sudduth J, Bohush T, Erwin JM, Stimpson CD, Hof PR, Sherwood CC. Front Hum Neurosci. 2014 Feb 28;8:101. doi: 10.3389/fnhum.2014.00101. Raghanti et al. 2014 dataset
Stereologic estimates of shrinkage-corrected volumes for left insula and its subdivisions (granular, dysgranular, agranular insular cortices). Frontoinsula (FI) is part of agranular insular cortex that is defined by the presence of von Economo neurons. Body mass estimates (Smith and Jungers, 1997) and population group sizes (Nunn and van Schaik, 2001; Nunn, 2002) were collected from previously published literature. A volumetric comparison of the insular cortex and its subregions in primates. Bauernfeind AL, de Sousa AA, Avasthi T, Dobson SD, Raghanti MA, Lewandowski AH, Zilles K, Semendeferi K, Allman JM, Craig AD, Hof PR, Sherwood CC. J Hum Evol. 2013 Apr;64(4):263-79. Bauernfeind et al. 2013 dataset
3D landmark coordinates describing cortical anatomy in 72 chimpanzee and 73 human brains. Increased morphological asymmetry, evolvability and plasticity in human brain evolution. Gómez-Robles A, Hopkins WD, Sherwood CC. Proc Biol Sci. 2013 Apr 24;280(1761):20130575. doi: 10.1098/rspb.2013.0575. Gómez-Robles et al. 2013 dataset
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
MRI based volumetric data across adult lifespan for whole brain, neocortical gray, neocortical white, frontal lobe gray, frontal lobe white, and hippocampus in chimpanzees and humans. Aging of the cerebral cortex differs between humans and chimpanzees. Sherwood CC, Gordon AD, Allen JS, Phillips KA, Erwin JM, Hof PR, Hopkins WD. Proc Natl Acad Sci U S A. 2011 Aug 9;108(32):13029-34. doi: 10.1073/pnas.1016709108. Sherwood et al. 2011 dataset
The density of Von Economo Neurons (VENS) in the anterior cingulate cortex that express activating-transcription factor 3 (ATF3), interleukin 4 receptor (IL4Ra) and neuromedin B (NMB) proteins in humans and great apes.      Biochemical specificity of von Economo neurons in hominoids. Stimpson CD, Tetreault NA, Allman JM, Jacobs B, Butti C, Hof PR, Sherwood CC. Am J Hum Biol. 2011 Jan-Feb;23(1):22-8. doi: 10.1002/ajhb.21135. Stimpson et al. 2011 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

Total neuron and length densities of tyrosine hydroxylase (TH), choline acetyltransferase (ChAT), and serotonin transporter (SERT)-immunoreactive axons in the frontal cortex (areas 4, 9, and 32) of humans, chimpanzees, and moor macaques.

Cortical dopaminergic innervation among humans, chimpanzees, and macaque monkeys: a comparative study. Raghanti MA, Stimpson CD, Marcinkiewicz JL, Erwin JM, Hof PR, Sherwood CC. Neuroscience. 2008 Jul 31;155(1):203-20.

Cholinergic innervation of the frontal cortex: differences among humans, chimpanzees, and macaque monkeys. Raghanti MA, Stimpson CD, Marcinkiewicz JL, Erwin JM, Hof PR, Sherwood CC. J Comp Neurol. 2008 Jan 20;506(3):409-24.

Differences in cortical serotonergic innervation among humans, chimpanzees, and macaque monkeys: a comparative study. Raghanti MA, Stimpson CD, Marcinkiewicz JL, Erwin JM, Hof PR, Sherwood CC. Cereb Cortex. 2008 Mar;18(3):584-97. Epub 2007 Jun 22.

Raghanti et al. 2008 datasets

Stereologic counts of neuron and glial cell densities from dorsolateral prefrontal cortex (area 9) layers II/III in 18 species of anthropoid primates.

Evolution of increased glia-neuron ratios in the human frontal cortex. Sherwood CC, Stimpson CD, Raghanti MA, Wildman DE, Uddin M, Grossman LI, Goodman M, Redmond JC, Bonar CJ, Erwin JM, Hof PR. Proc Natl Acad Sci U S A. 2006 Sep 12;103(37):13606-11. Sherwood et al. 2006 dataset


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


Subscribe to Email Updates