|
| Status |
Public on Nov 18, 2021 |
| Title |
Peripheral Blood Mononuclear cells - rep_2 |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral Blood
|
| Organism |
Macaca mulatta |
| Characteristics |
cell type: Peripheral blood mononuclear cells
treatment: Untreated
facs marker: None
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single cells were prepared and loaded onto the 10x Genomics Chromium controller for a targeted cell recovery of 10,000 cells based on the 10x Genomics Chromium Next GEM Single Cell VDJ User Guide. cDNA amplification was carried out at 13 cycles of amplification for all samples. Concentration of resulting amplification was assayed through the use of an Agilent Bioanalyzer 2100 instrument and High Sensitivity DNA Kit.
10x Genomics 5’ GEX library construction and subsequent analysis through sequencing was also performed according to the 10x Genomics User Guide.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Raw sequencing data were demultiplexed using the 10x Genomics cellranger (v4.0.0) commands mkfastq command.
Reads were aligned to the RheMac10 genome annotation, and UMI-collapsed using the 10x Genomics cellranger (v4.0.0) count command.
Raw gene expression matrices were normalized and scaled using the SCTransform20 method with the Seurat R package (v3.1.5).
Genome_build: RheMac10
Supplementary_files_format_and_content: H5 files contain gene expression matrices of UMI counts from single cells.
|
| |
|
| Submission date |
Jul 08, 2021 |
| Last update date |
Oct 05, 2023 |
| Contact name |
Xinxia Peng |
| Organization name |
North Carolina State University
|
| Street address |
1060 William Moore Drive
|
| City |
Raleigh |
| ZIP/Postal code |
27607 |
| Country |
USA |
| |
|
| Platform ID |
GPL21120 |
| Series (1) |
| GSE179722 |
High-throughput Ig and TCR repertoire single-cell sequencing analysis in rhesus macaques |
|
| Relations |
| BioSample |
SAMN20118801 |
| SRA |
SRX11379622 |
