Table 1. Sequences of template and primers.

Name	Sequence
Spike in	GAGTGGGTGTTGGTGTTTGTATTTAAATACGATTAAATAATATTAATATATTATCGATTAAATAATAATTAATTAATATTTGATGTGATGGGTGGTATGG
H1	GAGTGGGTGTTGGTGTTTGT
H2	CCATACCACCCATCACATCA
RRBS1	AcAcTcTTTcccTAcAcGAcGcTcTTccGATc(x)T
RRBS2	(p)GATcGGAAGAGcAcAcGTcTGAAcTccAGTcA
PE1	CAAGCAGAAGACGGCATACGAGATX{8}GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT (where X{8} is an index sequence for multiplexing libraries)
PE2	AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
P5	AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACAATGATACGGCGACCACCGA
P7	CAAGCAGAAGACGGCATACGAGATCAAGCAGAAGACGGCATACGA
Single cell poly-T primers	/5Acryd/iSpPC/CGATGACGTAATACGACTCACTATAGGGATACCACCATGGCTCTTTCCCTACACGACGCTCTTCCGATCT-N{7–10}-GAGTGATTGCTTGTGACGCCTT-N{8}-UMI{NNNNN}-TTTTTTTTTTTTTTTTTTTV 5Acryd—an Acrydite modification that allows incorporation into polyacrylamide gel iSpPC—photo-cleavable spacer N{7–10} and N{8} are barcodes
Bulk T7RTPolyT	CGATGACGTAATACGACTCACTATAGGGATACCACCATGGCTCTTTCCCTACACGACGCTCTTCCGATCT-N{10}-TTTTTTTTTTTTTTTTTTTVN N{10} is any nucleotide and V can be any nucleotide but T
PvG748-SBS12-RT	AGACGTGTGCTCTTCCGATCTNNNNNN