|
| Status |
Public on Feb 04, 2022 |
| Title |
PBMCs-Post-IS (Pre-Tx) |
| Sample type |
SRA |
| |
|
| Source name |
monkey peripheral blood mononuclear cells
|
| Organism |
Macaca mulatta |
| Characteristics |
tissue: whole blood
cell type: peripheral blood mononuclear cells (PBMCs)
time: before transplantation
treatment: Post-IS (after immunosuppression)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were harvested and resuspended in PBS with 0.04% BSA at 1×10^6 cells per milliliter. Then, cell suspensions were loaded on a Chromium Single Cell Controller (10x Genomics) to generate single-cell gel beads in emulsion (GEMs) by using ChromiumTM Single Cell 5' Library & Gel Bead Kit V1 (10x Genomics, 1000006). Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs.
Barcoded cDNAs were pooled and underwent cleanup by using DynaBeads MyOne Silane Beads (Invitrogen, 37002D) and then amplified and cleanup for further next generation library construction. Single-cell RNA seq libraries were prepared using ChromiumTM Single Cell 5' Library Construction Kit V1 (10x Genomics, 1000020) following instructions provided by the manufacturer. Sequencing was performed on an Illumina HiSeq X Ten (Illumina, San Diego, CA, USA) with pair end 150bp.
Single-cell RNA sequencing
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
after immunosuppression and before cell transplant
|
| Data processing |
The clean single-cell RNA-seq data was mapped to macaca mulatta reference genome Mmul_10 using Cell Ranger v3.1.0.
Cell quality control was performed by R package scater v1.14.0.
The raw UMI counts were then normalized by R package scran v1.14.1 .
Seurat v3.2.3 was used for downstream analysis including identifying cell types.
Genome_build: Mmul_10
Supplementary_files_format_and_content: .tar.gz files containing cellranger output
.csv files containing raw count matrix or cell metadata
|
| |
|
| Submission date |
Sep 29, 2021 |
| Last update date |
Feb 04, 2022 |
| Contact name |
Yaqi Wang |
| E-mail(s) |
yaqi_wang@pku.edu.cn
|
| Organization name |
Peking University
|
| Street address |
No.5 Yiheyuan Road Haidian District
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
| |
|
| Platform ID |
GPL24522 |
| Series (2) |
| GSE185037 |
Human Pluripotent Stem Cell-derived Islets Ameliorate Diabetes in Nonhuman Primates [monkey_singlecell] |
| GSE185038 |
Human Pluripotent Stem Cell-derived Islets Ameliorate Diabetes in Nonhuman Primates |
|
| Relations |
| BioSample |
SAMN21903843 |
| SRA |
SRX12405091 |
