TABLE 5.
3′-adapter template oligonucleotide sequences
| Name | Sequence | RNA nucleotides | UMI trimmed |
|---|---|---|---|
| c3t_NoUMI_6RNA (Upton et al. 2021) |
/5Cy5/ACACTCTTTCCCTACACGACGCTCTTCCrGrArUrCrUrC | 6 | C |
| c3t_C3N_6RNA | /5Cy5/ACACTCTTTCCCTACACGACGCTCTTCCGATrCrUrNrNrNrC | 6 | NNNC |
| c3t_CY5N_6RNA (Ferguson et al. 2023) |
/5Cy5/ACACTCTTTCCCTACACGACGCTCTTCCGATCTNrNrNrNrNrYrC | 6 | NNNNNYC |
| c3t_CA5N_6RNA | /5Cy5/ACACTCTTTCCCTACACGACGCTCTTCCGATCTNrNrNrNrNrArC | 6 | NNNNNAC |
| c3t_CG5N_6RNA | /5Cy5/ACACTCTTTCCCTACACGACGCTCTTCCGATCTNrNrNrNrNrGrC | 6 | NNNNNGC |
| c3t_CR5N_6RNA | /5Cy5/ACACTCTTTCCCTACACGACGCTCTTCCGATCTNrNrNrNrNrRrC | 6 | NNNNNRC |
| c3t_CY5N_2RNA | /5Cy5/ACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNrYrC | 2 | NNNNNYC |
| c3t_CD5N_1RNA | /5Cy5/ACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNDrC | 1 | NNNNNDC |
| c3t_ddCD5N | /5Cy5/ACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNND/3ddC/ | 0 | NNNNNDC |
| c3t_ddCA5N | /5Cy5/ACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNA/3ddC/ | 0 | NNNNNAC |
| c3t_ddCG5N | /5Cy5/ACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNG/3ddC/ | 0 | NNNNNGC |
| c3t_ddCR5N* | /5Cy5/ACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNR/3ddC/ | 0 | NNNNNRC |
| c3t_ddCR5N_barcoded** | /5Cy5/ACACTCTTTCCCTACACGACGCTCTTCCGAT CTNNNNNXXXXXXNNNNNR/3ddC/ | 0 | NNNNNXXXXXXNNNNNRC |
-
Citations for previously introduced oligonucleotides are included below the names if applicable. The final column refers to the UMI sequence that will need to be trimmed from the 5′ end of the Read1 sequencing reads. (*) Current recommendation for OTTR buffer 4B2 (Fig. 1; Supplemental Fig. 5). (**) Current recommendation for barcoded OTTR 3′ddC adapter template, with a constant sequence (indicated by X) that defines for example, a specific well- or cell-identifier.
