Question:
How does Single Cell Flex data generated from GEM-X chips compare to Flex data generated from NextGEM chips? Can I integrate Flex data generated from the two different chips?
Answer:
With all other factors controlled, we expect the complexity and mapping metrics to be comparable between similar Flex samples run on GEM-X and NextGEM chips.
Below is an example data comparison between PBMC samples run on GEM-X and NextGEM chips. At the same sequencing depth (reads per cell), sensitivity is comparable between the data from the two chips (Figure 1, left). The cell types and populations identified in the two datasets are also similar (Figure 1, right).
For heterogeneous sample types like PBMCs and dissociated tissue, we do not expect significant batch effects (Figure 2), and you can use Cell Ranger aggr (version 8.0 and above) for data integration without batch correction. Please see instructions on how to use Cell Ranger aggr for data integration provided on the support site.
Figure 2. UMAP projection colored by sample after integrating PBMC data generated from single cell Flex experiments run on GEM-X (black) and NextGEM (orange) chips. The analyses were performed with the same version of Cell Ranger and references. The plot was output from a Cell Ranger aggr pipestance without batch correction.
For highly homogeneous sample types like cell lines, batch effects may be observed (Figure 3). In this case, you may use Cell Ranger aggr (version 8.0 and above) with chemistry batch correction for data integration. The degree of correction may vary depending on the sample type and experimental conditions. Alternatively, you can use community developed tools for data integration and batch correction, some of which are discussed in an introductory analysis guide article: Batch Effect Correction.
Figure 3. UMAP projection colored by sample after integrating A20 cell line data generated from single cell Flex experiments run on GEM-X (black) and NextGEM (orange) chips. The analyses were performed with the same version of Cell Ranger and references. The plots were output from Cell Ranger aggr pipestance without (left) or with (right) chemistry batch correction.