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Series GSE124299 Query DataSets for GSE124299
Status Public on Feb 07, 2019
Title Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution
Organisms Macaca mulatta; Pan troglodytes; Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Third-party reanalysis
Summary Direct comparisons of human and non-human primate brain tissue have the potential to reveal molecular pathways underlying remarkable specializations of the human brain. However, chimpanzee tissue is largely inaccessible during neocortical neurogenesis when differences in brain size first appear. To identify human-specific features of cortical development, we leveraged recent innovations that permit generating pluripotent stem cell-derived cerebral organoids from chimpanzee. First, we systematically evaluated the fidelity of organoid models to primary human and macaque cortex, finding organoid models preserve gene regulatory networks related to cell types and developmental processes but exhibit increased metabolic stress. Second, we identified 261 genes differentially expressed in human compared to chimpanzee organoids and macaque cortex. Many of these genes overlap with human-specific segmental duplications and a subset suggest increased PI3K/AKT/mTOR activation in human outer radial glia. Together, our findings establish a platform for systematic analysis of molecular changes contributing to human brain development and evolution.
Overall design Single cell mRNA sequencing of iPS-derived neural and glial progenitor cells using the Fluidigm C1 system

This series includes re-analysis of publicly available data in accessions: phs000989.v3, GSE99951, GSE86207, GSE75140. Sample metadata and accession IDs for the re-analyzed samples are included in the file "GSE124299_metadata_on_processed_samples.xlsx" available on the foot of this record.

The following samples have no raw data due to data loss: GSM3569728, GSM3569738, GSM3571601, GSM3571606, GSM3571615, GSM3571621, GSM3571625, and GSM3571631
Contributor(s) Pollen A
Citation(s) 30735633
Submission date Dec 21, 2018
Last update date Apr 19, 2019
Contact name Christopher Villarreal
Organization name 444015
Department Genomics Institute
Lab Kent
Street address 1156 Hight Street, Engineering-2 Rm. 501, MS: GENOMICS INSTITUTE
City Santa Cruz
State/province CA
ZIP/Postal code 95064
Country USA
Platforms (3)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL19129 Illumina HiSeq 2500 (Macaca mulatta)
GPL19148 Illumina HiSeq 2500 (Pan troglodytes)
Samples (3096)
GSM3569575 S10.A10
GSM3569576 S10.A11
GSM3569577 S10.A12
BioProject PRJNA515930
SRA SRP180337

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
GSE124299_PrimaryOrganoidAndPublishedCPM.txt.gz 239.5 Mb (ftp)(http) TXT
GSE124299_metadata_on_processed_samples.xlsx 838.2 Kb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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