|
| Status |
Public on Nov 01, 2021 |
| Title |
SP CD3 Control scRNA-seq (WT) |
| Sample type |
SRA |
| |
|
| Source name |
Spleen
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: CD4-Cre+ PRMT5fl/fl
cell type: T cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single-cell suspensions were harvested from fresh tissues according to standard procedures and surface-stained in FACS buffer with monoclonal antibodies. Related T cell subsets from mice spleen or thymus were sorted with FACS Aria II Cell Sorter.
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3’ V3.1 Reagent Kits (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10xGenomics Single Cell 3’ V3.1 Library Gel Bead Kit and prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8
cellranger (v3.1.0) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 20% passed the cell quality filtering and mitochondria genes were removed in the expression table. Seurat package (version: 2.3.4 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data. PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10 principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. lnFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Genome_build: mm10
Supplementary_files_format_and_content: MTX file and TSV file contain counts for each barcodes and genes
|
| |
|
| Submission date |
Oct 27, 2021 |
| Last update date |
Nov 03, 2021 |
| Contact name |
zheyi chen |
| E-mail(s) |
zheyi_chen0601@163.com, chenzheyi@sjtu.edu.cn
|
| Organization name |
Shanghai Jiao Tong University School of Medicine
|
| Street address |
1665 Kong Jiang Road
|
| City |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE186699 |
PRMT5 deficiency enforces the transcriptional and epigenetic programs of Klrg1+CD8+ terminal effector T cells [scRNA-seq] |
| GSE186863 |
PRMT5 deficiency enforces the transcriptional and epigenetic programs of Klrg1+CD8+ terminal effector T cells |
|
| Relations |
| BioSample |
SAMN22602062 |
| SRA |
SRX12798609 |
