Will I see a batch effect if I split nuclei from a single tissue slice into multiple lanes for sequencing?
Will I see a batch effect if I split nuclei from a single tissue slice into multiple lanes for sequencing?
We have observed minimal lane-to-lane batch effect, so integration across different lanes is not required. Nevertheless, consistent normalization should be performed on the merged dataset. We recommend redoing normalization on the merged dataset, either through counts per million (CPM) or SCT (from Seurat) methods, [AR1] [PH2] before performing in-depth analysis.