Table 1. Mapping summary of the sequencing experiment. Reads were first aligned to the NCBI mRNA RefSeq database allowing up to 2 mismatches. Unmapped reads were later aligned to the mouse genome including mitochondria. Multireads refer to reads that mapped to more than one transcript/genomic locations. TR refers to technical replicates.
| Lane 1 | Lane 2 | Lane 3 | Lane 4 | Lane 6 | Lane 7 | |
|---|---|---|---|---|---|---|
| Serum Free Media | SB-431542 | Activin A (3 ng/mL) | Activin A (15 ng/mL) TR1 | Activin A (15 ng/mL) TR2 | Activin A (100 ng/mL) | |
| Total reads | 33.4 M | 35.2 M | 32.8 M | 29.4 M | 25.1 M | 30.0 M |
| Unique reads (mRNA Refseq) | 58.20% | 56.80% | 59.20% | 59.10% | 59.50% | 58.20% |
| Multireads (Isoform group only, mRNA Refseq) | 13.52% | 13.37% | 13.45% | 13.20% | 13.19% | 13.05% |
| Multireads (mRNA refseq) | 5.47% | 5.63% | 5.45% | 6.20% | 5.71% | 5.45% |
| Genomic (Unique) | 12.16% | 13.33% | 10.63% | 10.76% | 11.01% | 12.16% |
| Genomic (Multireads) | 2.10% | 2.12% | 1.98% | 1.98% | 2.03% | 2.09% |
| Genomic and Mitochondria | 2.49% | 3.51% | 4.52% | 4.41% | 3.92% | 4.52% |
| Mitochondria (Unique) | 0.59% | 0.64% | 1.06% | 0.74% | 0.75% | 0.84% |
| Unmappable | 5.38% | 4.44% | 3.61% | 3.47% | 3.73% | 3.59% |
| Transcripts (Unique reads > = 10) | 11792 | 11565 | 11508 | 11409 | 11097 | 11401 |
| Transcripts (Multireads > = 10) | 6401 | 6293 | 6329 | 6265 | 6167 | 6215 |
| Binding Sites (Unique reads > = 10) | 126844 | 125775 | 117587 | 110069 | 96060 | 109109 |