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Series GSE192773 Query DataSets for GSE192773
Status Public on Apr 26, 2023
Title Molecular features driving cellular and regulatory complexity of human brain evolution [RNA-seq]
Organisms Macaca mulatta; Pan troglodytes; Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Genomic changes acquired in human evolution contribute to the unique abilities of human brain. However, characterizing the molecular underpinnings of human-specific traits is a multifaceted challenge due to the cellular heterogeneity of human brain and complex regulation of gene expression. Here, we performed single-nuclei RNA-sequencing (snRNA-seq) and single-nuclei ATAC-seq (snATAC-seq) in human, chimpanzee, and rhesus macaque brain tissue (brodmann area 23, posterior cingulate cortex). Human-specific changes were distinct among neuronal subtypes indicating that human brain evolution was accompanied by molecular alterations in finer cellular resolution. We also observed more human-specific alterations in epigenome compared to transcriptome. Interestingly, human-specific accessibility changes in neurons were not as concordant with gene expression changes in comparison to other species, partially explaining this discrepancy. These cis-regulatory elements were enriched for immediate early gene motifs, identifying accelerated evolution of activity regulated genes in humans. We also uncovered associations between human evolution and brain disease genes at the cell type level. Together, these results reveal multiple mechanisms for human brain evolution at cell type resolution and establish the first direct evidence for accelerated human-specificity of activity-dependent molecular changes.
 
Overall design Brodmann Area 23 was dissected from human, chimpanzee and rhesus macaque (Macaca Mulatta). Each species contained 4 adult, post-mortem samples. Each sample was obtained from a different individual. Droplet-based single-nuclei RNA-seq libraries were prepared using the Chromium Single Cell 3’ v3.1 (1000121, 10x Genomics) according to the manufacturer’s protocol. Libraries were sequenced using an Illumina NovaSeq 6000.
 
Contributor(s) Caglayan E, Ayhan F, Preuss TM, Yi SV, Konopka G
Citation(s) 37468639
Submission date Dec 29, 2021
Last update date Jun 28, 2024
Contact name Genevieve Konopka
E-mail(s) gena@alum.mit.edu
Organization name UT Southwestern Medical Center
Department Neuroscience
Street address 5323 Harry Hines Blvd.
City Dallas
State/province TX
ZIP/Postal code 75390-9111
Country USA
 
Platforms (6)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL19129 Illumina HiSeq 2500 (Macaca mulatta)
GPL19148 Illumina HiSeq 2500 (Pan troglodytes)
Samples (12)
GSM5765186 RNA_Human_BA23_H1
GSM5765187 RNA_Human_BA23_H2
GSM5765188 RNA_Human_BA23_H3
This SubSeries is part of SuperSeries:
GSE192774 Molecular features driving cellular and regulatory complexity of human brain evolution
Relations
BioProject PRJNA793060

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
GSE192773_All_Species_UMI_Count_Matrix_Barcodes.txt.gz 783.0 Mb (ftp)(http) TXT
GSE192773_All_Species_UMI_Count_Matrix_Genes.txt.gz 1.9 Mb (ftp)(http) TXT
GSE192773_All_Species_UMI_Count_Matrix_MetaData.txt.gz 87.2 Kb (ftp)(http) TXT
GSE192773_All_Species_UMI_Count_Matrix_snRNAseq.mtx.gz 1.2 Mb (ftp)(http) MTX
GSE192773_Seq_Template_EvolutionPaper_RNA_Updated.xlsx 47.3 Kb (ftp)(http) XLSX
GSE192773_Seurat_Astrocyte_RNA.RDS.gz 503.7 Mb (ftp)(http) RDS
GSE192773_Seurat_Excitatory_RNA.RDS.gz 3.9 Gb (ftp)(http) RDS
GSE192773_Seurat_Inhibitory_RNA.RDS.gz 1.5 Gb (ftp)(http) RDS
GSE192773_Seurat_Microglia_RNA.RDS.gz 247.5 Mb (ftp)(http) RDS
GSE192773_Seurat_OPCOli_RNA.RDS.gz 2.5 Gb (ftp)(http) RDS
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Raw data are available in SRA
Processed data are available on Series record

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