|
| Status |
Public on Nov 19, 2020 |
| Title |
amygdala1-1 |
| Sample type |
SRA |
| |
|
| Source name |
nucleus
|
| Organism |
Macaca mulatta |
| Characteristics |
tissue: amygdala
passage: 0
|
| Growth protocol |
The tissues samples of amygdala were surgically removed and the frozen tissue was used to intact nucleus isolation. The nucleus was isolated and purified as previously described with some modifications.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The scRNA-Seq libraries were generated using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V2 Reagent Kits (10X Genomics, Pleasanton, USA). Briefly, cells nuclei were concentrated to 1000 nuclei/μL and approximately 15000 nuclei were loaded into each channel to generate single-cell Gel Bead-In-Emulsions (GEMs), which results into expected mRNA barcoding of 9000 single nucleus for each sample. After the RT step, GEMs were broken and barcoded-cDNA was purified and amplified.
The amplified barcoded cDNA was fragmented, A-tailed, ligated with adaptors and index PCR amplified. The final libraries were quantified using the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific, USA) and the size distribution of the libraries were determined using a High Sensitivity DNA chip on a Bioanalyzer 2200 (Agilent, USA). All libraries were sequenced by HiSeq Xten (Illumina, USA) on a 150 bp paired-end run.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Rhesus macaques
Nuclear RNA
snRNA-Seq
S001_1-1
processed data file: RDS.RawData.txt
|
| Data processing |
We applied fastp with default parameter filtering the adaptor sequence and removed the low-quality reads to achieve clean data. Feature-barcode matrices were obtained by aligning reads to the rhesus monkey genome (Version: Mmul 10, Ensembl) using CellRanger v3.0.0. In order to minimize the sample batch, we applied the down sample analysis among samples sequenced according to the mapped barcoded reads per cell of each sample and achieved the aggregated matrix eventually. Nucleus contained over 200 expressed genes and mitochondria UMI rate below 20% passed the quality filtering and mitochondria genes were removed in the expression table but used for nucleus expression regression to avoid the effect of the nucleus status for clustering analysis and marker analysis of each cluster.
Genome_build: GRCH38 (Ensembl Version91)
Supplementary_files_format_and_content: RDS.RawData.txt includes counts.
|
| |
|
| Submission date |
Feb 23, 2020 |
| Last update date |
Nov 19, 2020 |
| Contact name |
yanyong cheng |
| E-mail(s) |
cheng_yanyong@163.com
|
| Organization name |
Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine
|
| Department |
Department of Anesthesiology
|
| Street address |
639 Zhizaoju Road
|
| City |
shanghai |
| ZIP/Postal code |
200011 |
| Country |
China |
| |
|
| Platform ID |
GPL27943 |
| Series (1) |
| GSE145765 |
Single-cell RNA-sequencing analysis for the molecular taxonomy of primate amygdala |
|
| Relations |
| BioSample |
SAMN14167301 |
| SRA |
SRX7785028 |
