Extended Data Fig. 5: Visualization of read pairs from a single transcribed molecule and detailed comparison of burst kinetics inference based on Smart-seq2-UMI and Smart-seq3 data.

(a) Visualization of read pairs sequenced from one molecule from the Cox7a2l locus. Top show the exons and introns in the Cox7a2l locus, with genomic coordinates (mm10). Each row shows a unique read pair, where orange boxes show the mapping of sequences onto the genomic loci, dotted lines indicate that the sequences are connected by the read pairs and solid lines indicate that the exon-intron junction was captured in the sequenced reads. Note, all read pairs combined span essentially the full transcript, meaning that for this molecule we could reconstruct the full transcript. (b) Coverage over CAST SNPs in 5’ UMI-containing read pairs in 369 mouse fibroblasts. Shown is the coverage in number of read pairs in a 10 bp sliding window of SNP distance relative to the TSS of their gene. Blue line indicates a loess fit of the data points. (c) Scatter plots showing the burst frequencies inferred for the C57 (x-axis) and CAST (y-axis) alleles for genes in mouse fibroblasts. The left plot shows the results based on Smart-seq3 data and the right panel shows the results from using Smart-seq2-UMI data. (d) Scatter plots show the burst sizes inferred for the C57 (x-axis) and CAST (y-axis) alleles for genes in mouse fibroblasts. The left plot shows the results based on Smart-seq3 data and the right panel shows the results from using Smart-seq2-UMI data.