 |
 |
GEO help: Mouse over screen elements for information. |
|
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 |
GSM6065937 |
Human and chimpanzee 21 day embryoid bodies - replicate 1, lane 5 |
GSM6065938 |
Human and chimpanzee 21 day embryoid bodies - replicate 1, lane 6 |
GSM6065939 |
Human and chimpanzee 21 day embryoid bodies - replicate 1, lane 7 |
GSM6065940 |
Human and chimpanzee 21 day embryoid bodies - replicate 1, lane 8 |
GSM6065941 |
Human and chimpanzee 21 day embryoid bodies - replicate 1, lane 9 |
GSM6065942 |
Human and chimpanzee 21 day embryoid bodies - replicate 2, lane 1 |
GSM6065943 |
Human and chimpanzee 21 day embryoid bodies - replicate 2, lane 2 |
GSM6065944 |
Human and chimpanzee 21 day embryoid bodies - replicate 2, lane 3 |
GSM6065945 |
Human and chimpanzee 21 day embryoid bodies - replicate 2, lane 4 |
GSM6065946 |
Human and chimpanzee 21 day embryoid bodies - replicate 3, lane 1 |
GSM6065947 |
Human and chimpanzee 21 day embryoid bodies - replicate 3, lane 2 |
GSM6065948 |
Human and chimpanzee 21 day embryoid bodies - replicate 3, lane 3 |
GSM6065949 |
Human and chimpanzee 21 day embryoid bodies - replicate 3, lane 4 |
GSM6668355 |
Human/chimpanzee tetraploid hybrid 21 day embrypoid bodies - replicate 1, 10x lane 1 |
GSM6668356 |
Human/chimpanzee tetraploid hybrid 21 day embrypoid bodies - replicate 1, 10x lane 2 |
GSM6668357 |
Human/chimpanzee tetraploid hybrid 21 day embrypoid bodies - replicate 2, 10x lane 1 |
GSM6668358 |
Human/chimpanzee tetraploid hybrid 21 day embrypoid bodies - replicate 2, 10x lane 2 |
GSM6668359 |
Human/chimpanzee tetraploid hybrid 21 day embrypoid bodies - replicate 3, 10x lane 1 |
GSM6668360 |
Human/chimpanzee tetraploid hybrid 21 day embrypoid bodies - replicate 3, 10x lane 2 |
|
Relations |
BioProject |
PRJNA832107 |
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 |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
|
|
|
|
 |