Question: Are batch effects observed across Chip A?
Answer: We don't observe batch effects when comparing the same sample run across multiple chips. In general, the largest source of technical variability originates from differences in sequencing depth between samples. This can be addressed by using the Cell Ranger pipeline to normalize sequencing reads across samples (https://support.10xgenomics.com/single-cell/software/pipelines/latest/using/aggregate).
The table and plot below highlight the robustness of the Chromium system. Shown are four Single Cell sample libraries (A-D) that were prepared on the same day using the same tube of PBMCs. The four libraries were generated by running three different chips and sequenced on two different HiSeq 4000 flow cells. The number of cells recovered and the cell clustering are very similar across all four libraries.
For more information on sources of biological and technical variation in Single Cell Gene Expression experiments, please see the Technical Note: https://support.10xgenomics.com/single-cell-gene-expression/index/doc/technical-note-biological-and-technical-variation-in-single-cell-gene-expression-experiments
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