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Series GSE201516 Query DataSets for GSE201516
Status Public on Apr 11, 2023
Title The relationship between regulatory changes in cis and trans and the evolution of gene expression in humans and chimpanzees
Organisms Pan troglodytes; Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary We used embryoid bodies to compare differences in gene expression between humans and chimpanzees in a large number of cell types
 
Overall design Single cell RNA-sequencing of human and chimpanzee embryoid bodies. We generated embryoid bodies from 3-6 human and 3 chimpanzee inividuals in three replicates. For each replicate, embryoid bodies from both species were dissociated and pooled prior to collecting ~40,000-60,000 cells with 10x scRNA-seq.

Single cell RNA-sequencing of human/chimpanzee tetraploid hybrid embryoid bodies. We generated embryoid bodies from one hybrid inividuals in three replicates. For each replicate, we collected ~20,000 cells and performed 10x 3' scRNA-seq v3.1.
 
Contributor(s) Barr K, Rhodes K, Gilad Y
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Apr 26, 2022
Last update date Apr 12, 2023
Contact name Yoav Gilad
Organization name University of Chicago
Department Genetic Medicine
Lab Yoav Gilad Lab
Street address 920 E. 58th St., CLSC 317A
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
 
Platforms (2)
GPL27803 Illumina HiSeq 4000 (Homo sapiens; Pan troglodytes)
GPL27804 Illumina NovaSeq 6000 (Homo sapiens; Pan troglodytes)
Samples (22)
GSM6065934 Human and chimpanzee 21 day embryoid bodies - replicate 1, lane 1
GSM6065935 Human and chimpanzee 21 day embryoid bodies - replicate 1, lane 3
GSM6065936 Human and chimpanzee 21 day embryoid bodies - replicate 1, lane 4
Relations
BioProject PRJNA832107

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
GSE201516_DataS1.csv.gz 46.1 Mb (ftp)(http) CSV
GSE201516_DataS2.csv.gz 10.6 Kb (ftp)(http) CSV
GSE201516_DataS3.csv.gz 449.1 Kb (ftp)(http) CSV
GSE201516_DataS4.h5Seurat 5.0 Gb (ftp)(http) H5SEURAT
GSE201516_HC.barcodes.csv.gz 584.7 Kb (ftp)(http) CSV
GSE201516_HC.counts.mtx.gz 1.2 Gb (ftp)(http) MTX
GSE201516_HC.features.csv.gz 96.8 Kb (ftp)(http) CSV
GSE201516_HC.metadata.csv.gz 2.9 Mb (ftp)(http) CSV
GSE201516_Hybrid.combined.barcodes.csv.gz 603.1 Kb (ftp)(http) CSV
GSE201516_Hybrid.combined.counts.mtx.gz 806.0 Mb (ftp)(http) MTX
GSE201516_Hybrid.combined.features.csv.gz 64.7 Kb (ftp)(http) CSV
GSE201516_Hybrid.combined.metadata.csv.gz 1.8 Mb (ftp)(http) CSV
GSE201516_Hybrid.human.barcodes.csv.gz 291.9 Kb (ftp)(http) CSV
GSE201516_Hybrid.human.counts.mtx.gz 1.1 Gb (ftp)(http) MTX
GSE201516_Hybrid.human.features.csv.gz 96.8 Kb (ftp)(http) CSV
GSE201516_Hybrid.human.metadata.csv.gz 1.6 Mb (ftp)(http) CSV
GSE201516_chimpanzee.orthologous.exons.gtf.gz 17.9 Mb (ftp)(http) GTF
GSE201516_chimpanzee.vcf.gz 526.7 Mb (ftp)(http) VCF
GSE201516_human.orthologous.exons.gtf.gz 17.9 Mb (ftp)(http) GTF
GSE201516_human.vcf.gz 3.0 Mb (ftp)(http) VCF
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Raw data are available in SRA
Processed data are available on Series record

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