|
| Status |
Public on Apr 11, 2023 |
| Title |
Human/chimpanzee tetraploid hybrid 21 day embrypoid bodies - replicate 3, 10x lane 2 |
| Sample type |
SRA |
| |
|
| Source name |
human/chimpanzee tetraploid hybrid
|
| Organisms |
Pan troglodytes; Homo sapiens |
| Characteristics |
cell type: iPS-derived Embryoid Body cells
individuals: HLI-25
|
| Growth protocol |
iPSCs were dissociated and EBs were generated at 1000 cells per EB using Aggrewell micropatterned plates. EBs were formed in Aggrewell EB formation medium. They were half-fed with 1mL Aggrewell EB formation medium at 24 hours. After 48 hours they were transferred to Corning ultra-low adherence plates in E6 media. Media was replaced every other day until 21 days were met.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
EBs were dissocated in Accumax, pooled, and collected on a 10x Chromium controller.
Libraries were constructed using 10x 3' scRNA-seq v3.1 according to manufacturer directions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Hybrid.human.counts.mtx.gz
Hybrid.human.features.tsv.gz
Hybrid.human.barcodes.tsv.gz
Hybrid.human.metadata.tsv.gz
Hybrid.combined.counts.mtx.gz
Hybrid.combined.features.tsv.gz
Hybrid.combined.barcodes.tsv.gz
Hybrid.combined.metadata.tsv.gz
DataS1.tsv.gz
|
| Data processing |
Samples were aligned to the human genome using cellranger from 10x genomics.
Aligned UMI count matrices were loaded in R using the Seurat package. Samples were normalized using the SCTransform pipeline and aligned to an external reference using Harmony.Cells types were assigned by proximity to reference cell types in harmony-corrected PCA space
Samples were aligned to a set of orthologous exons in the combined human/chimpanzee genome using cellranger. We only kept reads that uniquely aligned to either the human or chimpanzee genome.
We used cell-type assignmnts from the human-aligned data to annotate the allele specific reads from the combined species alignment.
We assessed differential expression in each cell type using the paired Wilcoxon signed-ranks test.
We computed the percent of DE due to allele-secific changes between species for each gene in each cell type
Assembly: hg38
Assembly: panTro6
Supplementary files format and content: the mtx file contains UMI counts for every gene and cell
Supplementary files format and content: The features tsv contains the row names (genes) while the barcodes tsv contains the colun names (cell barcodes) for the counts matrix. The metadata tsv contains individual and species calls.
Supplementary files format and content: The GTFs contain the orthologous exons used for mapping to human or chimpanzee genomes
Supplementary files format and content: DataS1 contains the results of differential expression analysis
Supplementary files format and content: DataS2 contains a list of tissue-specific differentially expressed genes
|
| |
|
| Submission date |
Oct 21, 2022 |
| Last update date |
Apr 11, 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 |
| |
|
| Platform ID |
GPL27804 |
| Series (1) |
| GSE201516 |
The relationship between regulatory changes in cis and trans and the evolution of gene expression in humans and chimpanzees |
|
| Relations |
| BioSample |
SAMN31405652 |
| SRA |
SRX17989590 |
