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Series GSE229169 Query DataSets for GSE229169
Status Public on Oct 31, 2023
Title Comparative single cell epigenomic analysis of gene regulatory programs in the rodent and primate motor cortex
Organisms Callithrix jacchus; Macaca mulatta; Homo sapiens; Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Sequence divergence of cis-regulatory elements drives species-specific traits, but how this manifests in the evolution of neocortex at the molecular and cellular level remains to be elucidated. We investigated the gene regulatory programs in the primary motor cortex of human, macaque, marmoset, and mouse with single cell multiomics assays, generating gene expression, chromatin accessibility, DNA methylome and chromosomal conformation profiles from a total of over 180,000 cells. For each modality, we determined species-specific, divergent, and conserved gene expression and epigenetic features at multiple levels. We find that cell type-specific gene expression evolves more rapidly than broadly expressed genes, and that epigenetic status at distal candidate cis-regulatory elements (cCREs) evolves faster than promoters. Strikingly, transposable elements (TEs) contribute to nearly 80% of the human-specific cCREs in cortical cells. Through machine learning, we develop sequence-based predictors of cCREs in different species, and demonstrate that the genomic regulatory syntax is highly preserved from rodents to primates. Lastly, we show that epigenetic conservation combined with sequence similarity help uncover functional cis-regulatory elements and enhance our ability to interpret genetic variants contributing to neurological disease and traits.
Overall design Analysis of single cell multiome ATAC + gene expression (10x Genomics) of motor cortex from human, macaque, marmoset, and mouse
Contributor(s) Zemke NR, Ren B
Citation(s) 38092918
Submission date Apr 07, 2023
Last update date Dec 15, 2023
Contact name Bing Ren
Organization name UCSD
Street address 9500 Gilman Drive
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
Platforms (5)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (46)
GSM7156218 M1_donor3 (Multiome ATAC)
GSM7156219 M1_donor3 (Multiome Gene Expression)
GSM7156220 M1_donor3_rep2 (Multiome ATAC)
BioProject PRJNA953340

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
GSE229169_barcodes.tar.gz 1.0 Mb (ftp)(http) TAR
GSE229169_features.tar.gz 60.8 Mb (ftp)(http) TAR
GSE229169_human_filtered_barcodes.tsv.gz 184.7 Kb (ftp)(http) TSV
GSE229169_human_filtered_features.tsv.gz 127.5 Kb (ftp)(http) TSV
GSE229169_human_filtered_matrix.mtx.gz 356.9 Mb (ftp)(http) MTX
GSE229169_human_filtered_metadata.tsv.gz 240.1 Kb (ftp)(http) TSV
GSE229169_macaque_filtered_barcodes.tsv.gz 149.4 Kb (ftp)(http) TSV
GSE229169_macaque_filtered_features.tsv.gz 76.7 Kb (ftp)(http) TSV
GSE229169_macaque_filtered_matrix.mtx.gz 257.8 Mb (ftp)(http) MTX
GSE229169_macaque_filtered_metadata.tsv.gz 198.8 Kb (ftp)(http) TSV
GSE229169_marmoset_filtered_barcodes.tsv.gz 152.0 Kb (ftp)(http) TSV
GSE229169_marmoset_filtered_features.tsv.gz 77.1 Kb (ftp)(http) TSV
GSE229169_marmoset_filtered_matrix.mtx.gz 255.0 Mb (ftp)(http) MTX
GSE229169_marmoset_filtered_metadata.tsv.gz 209.2 Kb (ftp)(http) TSV
GSE229169_matrix.tar.gz 10.1 Gb (ftp)(http) TAR
GSE229169_mouse_filtered_barcodes.tsv.gz 204.4 Kb (ftp)(http) TSV
GSE229169_mouse_filtered_features.tsv.gz 115.4 Kb (ftp)(http) TSV
GSE229169_mouse_filtered_matrix.mtx.gz 338.7 Mb (ftp)(http) MTX
GSE229169_mouse_filtered_metadata.tsv.gz 282.2 Kb (ftp)(http) TSV
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