Table 3 Real SLAMseq datasets and their corresponding analyses in this study
Samples | Description | Analysis | Figure |
|---|---|---|---|
GSM2666819-GSM2666839 | Chase-timecourse samples at 0, 0.5,1, 3, 6, 12 and 24 h with 3 replicates at each time point | Percentages of retained reads after mapping with standard and nucleotide-conversion aware scoring with DUNK. | 2b |
GSM2666816 | Single no 4SU 0 h replicate | Multimapper recovery count scatter vs unique mappers | 3c, S2b,c, S3 |
GSM2666816-GSM2666818 | 3 no 4SU 0 h replicates | Multimapper recovery correlation with RNAseq | 3a |
GSM2666816-GSM2666821 | 0 h no 4SU samples and 0 h chase samples with 3 replicates each | Evaluation of SNP calling and masking | 4a, c-d |
GSM2666816-GSM2666821, GSM2666828-GSM2666837 | 0 h no 4SU, 0, 3, 6, 12 and 24 h chase samples (3 replicates each) | Evaluation of QC diagnostics | 6 |