|
| Status |
Public on Apr 26, 2023 |
| Title |
Human_BA23_H1 |
| Sample type |
SRA |
| |
|
| Source name |
Post-mortem brain, Brodmann Area 23
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: brain
brain region: Brodmann Area 23
Sex: F
age: 53
humanized_age: 53
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei for snATAC-seq were isolated from human, chimpanzee, and macaque BA23 brain tissue as previously described: https://www.protocols.io/view/isolation-of-nuclei-from-frozen-tissue-for-atac-se-6t8herw
Droplet-based single-nuclei ATAC-seq libraries were prepared using the Chromium Single Cell ATAC Library kit (1000110, 10x Genomics) according to the manufacturer’s protocols. Libraries were sequenced using an Illumina NovaSeq 6000.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Human_Count_Matrix_snATACseq_Barcodes.txt
Human_Count_Matrix_snATACseq_Genes.txt
Human_Count_Matrix_snATACseq_MetaData.txt
Human_Count_Matrix_snATACseq.mtx
Seurat_Astrocyte_ATAC_Human.RDS
Seurat_Excitatory_ATAC_Human.RDS
Seurat_Inhibitory_ATAC_Human.RDS
Seurat_Microglia_ATAC_Human.RDS
Seurat_OPCOli_ATAC_Human.RDS
|
| Data processing |
Barcode correction, alignment are performed using cellranger count (Software: 10x Genomics Cell Ranger ATAC 1.1.0)
Supplementary_files_format_and_content: Read duplicates were removed (picard MarkDuplicates)
Peak calling (macs2 --nomodel, --keep-dup all, extsize 200, --shift –100 )
Common peak identification across samples and species (Refer to supplementary methods)
Peak-cell matrix generation (custom scripts)
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 binarized peak-cell matrix: mtx file, peak 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 |
GPL16791 |
| Series (2) |
| GSE192772 |
Molecular features driving cellular and regulatory complexity of human brain evolution [ATAC-seq] |
| GSE192774 |
Molecular features driving cellular and regulatory complexity of human brain evolution |
|
| Relations |
| BioSample |
SAMN24501191 |
| SRA |
SRX13554628 |
