|
| Status |
Public on Apr 26, 2023 |
| Title |
RNA_Chimpanzee_BA23_C1 |
| Sample type |
SRA |
| |
|
| Source name |
Post-mortem brain, Brodmann Area 23
|
| Organism |
Pan troglodytes |
| Characteristics |
tissue: brain
brain region: Brodmann Area 23
Sex: M
age: 27
humanized_age: 53
molecule subtype: nuclear RNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Nuclei for snRNA-seq were isolated from human, chimpanzee, and macaque BA23 brain tissue. Debris was removed with a density gradient centrifugation using the Nuclei PURE 2M Sucrose Cushion Solution and Nuclei PURE Sucrose Cushion Buffer from Nuclei PURE Prep Isolation Kit (#NUC201-1KT, Sigma Aldrich).
Droplet-based single-nuclei RNA-seq libraries were prepared using the Chromium Single Cell 3’ v3.1 (1000121, 10x Genomics) according to the manufacturer’s protocol81. Libraries were sequenced using an Illumina NovaSeq 6000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
All_Species_UMI_Count_Matrix_snRNAseq.mtx
All_Species_UMI_Count_Matrix_MetaData.txt
All_Species_UMI_Count_Matrix_Genes.txt
All_Species_UMI_Count_Matrix_Barcodes.txt
Seurat_Astrocyte_RNA.RDS
Seurat_Excitatory_RNA.RDS
Seurat_Inhibitory_RNA.RDS
Seurat_Microglia_RNA.RDS
Seurat_OPCOli_RNA.RDS
|
| Data processing |
Barcode correction, alignment are performed using cellranger count (Software: 10x Genomics Cell Ranger 3.1.0)
Chimpanzee, macaque reads were mapped to human (CrossMap)
Reads counted per gene (featureCounts) and gene-cell matrix was constructed (umi-tools)
Ambient RNA contamination removed (CellBender)
Low quality cell barcodes, doublets were removed (Refer to supplementary methods)
Genome_build: Human: GRCh38, Chimpanzee: panTro5 (Pan_tro 3.0), Rhesus Macaque: rheMac10 (Mmul_10)
Supplementary_files_format_and_content: processed expression matrix: mtx files, gene and barcode information are in separate files
Supplementary_files_format_and_content: Cell barcode meta data
|
| |
|
| Submission date |
Dec 29, 2021 |
| Last update date |
Apr 26, 2023 |
| Contact name |
Genevieve Konopka |
| E-mail(s) |
gena@alum.mit.edu
|
| Organization name |
UT Southwestern Medical Center
|
| Department |
Neuroscience
|
| Street address |
5323 Harry Hines Blvd.
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390-9111 |
| Country |
USA |
| |
|
| Platform ID |
GPL19148 |
| Series (2) |
| GSE192773 |
Molecular features driving cellular and regulatory complexity of human brain evolution [RNA-seq] |
| GSE192774 |
Molecular features driving cellular and regulatory complexity of human brain evolution |
|
| Relations |
| BioSample |
SAMN24500102 |
| SRA |
SRX13554493 |
