The greater the number of cells captured, the more types of cells can be detected, and the more accurate the differences between sub-populations can be annotated. Singleron has developed a high-density microfluidic chip based on its own GEXSCOPE® platform, which can effectively capture more than 30,000 cells on a single chip, breaking the limit of 10,000 cells at a time on the standard high-throughput single-cell platform.
The Singleron high-density (HD) chip single-cell sequencing technology can produce more precise and accurate results for cell clustering and cell type annotation. Currently, high-density (HD) chips have been used in a variety of tissue types with excellent results. It is especially suitable for atlas study and rare cell subtype discovery.
Capturing Rare Cell Types
Mouse embryonic cells were captured by Singleron high-density chip. At the sequencing depth of 21.9K reads/cell, the total number of cells detected was 42,628, the median number of genes was 1677, and the cumulative number of detected genes was 31917. Clustering analysis showed that it enabled detection of rare cell types (about 0.15% in total cell population), in this case the Endoderm cells. Other detected cells include endothelial cells, kidney epithelial cells, T and B immune cells, granulocyte macrophage progenitor, red blood cells, bile duct cells, megakaryocyte, liver cells, neutrophils, microglia, and 16 other important cell types.
Fig. 2. Display of mouse embryonic cell clustering
A: Demonstration of different cell types;
B: Demonstration of the proportion of different cell types
To evaluate the consistency between samples, 3 testis samples from mice were selected for high-density chip single-cell sequencing. At the sequencing depth of 13.2K reads/cell, the average number of cells detected was 21289, the mean median gene number was 1350, and the cumulative average gene number was 31116. The data of three samples were analyzed jointly, and the cell types were labeled after clustering. According to the cell atlas, 25 clusters were detected in the sample, including spermatogonia, spermatocyte, spermatocyte, round-headed spermatocyte, testicular stromal cell, Sertoli's cell, macrophage, and stromal cell. The cell types of the three samples were similar, and the main cell types were spermatocytes and spermatocytes. Combined with the figure below, it can be seen that the 3 samples had excellent reproducibility.
Fig. 3. Display of mouse testicular cell population
A: Display of 3 mouse testis samples clustered by cell type;
B: Display of the proportion of each cell type in 3 testicular samples.
Low Doublet Rate
In order to evaluate the doublet rate of the high density chip, we analyzed a 293T+ Mouse testicle cell line and the high density chip single cell sequencing was performed. Data showed that at the sequencing depth of 14.8K reads/cell, the total number of detected cells was 14,929, the median number of single-cell genes was 2051, the cumulative number of detected genes was 56,431, and the double-cell rate was only 2.68% (Figure 4A,B,C). The proportion of Mapped reads in the exon region of the genome is as high as 96.5% (Figure 4D). The human and mouse mixed cell lines can also achieve high data quality from high density chips.
Figure 4. Data quality control results