Aggregate read coverage in Pdpk1 in two cell types, Vip and Sst, further separated according to the ‘batch’ metadata label into two groups. The first group contains cells from batches R8S4-180530 and, while the second group contains the remaining batches. Cells from different batches belong to different mice and were processed on different dates. In all groups, coverage decreases rapidly in the 3’ UTR of the isoform with the longest 3’ UTR, eventually reaching zero. Additionally, the relative coverage in this region compared to the rest of the gene (seeming to originate from a different isoform with a short 3’ UTR) varies drastically across batches, and consistently in different cell types. In principle, this could be due to biological differences between mice from different batches, but an explanation based on technical factors such as amplification bias may be more plausible.