Name	Sequence	Purpose	Step
qPCRctrl F	5′-TCAGTCAACCATTCAGTGGCCCAT-3′	PCR amplify ultraconserved genomic region	23
qPCRctrl R	5′-CAGGAAAGGGAATGCAGGGTTTGT-3′	PCR amplify ultraconserved genomic region	23
qPCRdsRed F	5′-GAGCGCGTGATGAACTTCGAGG-3′	PCR amplify dsRed transgenic region	23
qPCRdsRed R	5′-CAGCCCATAGTCTTCTTCTGCATTACG-3′	PCR amplify dsRed transgenic region	23
sgRNAl	5′TTCTAATACGACTCACTATAGACAGCAGTATCATCGACTAGTTTTAGAGCTAGA-3′	Synthesize sgRNA1 for CRISPR-Cas9 lineage barcoding by injection	27
sgRNA2	5′-TTCTAATACGACTCACTATAGAGAGCGCGCTCGTCGACTAGTTTTAGAGCTAGA-3′	Synthesize sgRNA2 for CRISPR-Cas9 lineage barcoding by injection	27
sgRNA3	5′-TTCTAATACGACTCACTATAGTCAGCA GTACTACTGACGAGTTTTAGAGCTAGA-3′	Synthesize sgRNA3 for CRISPR-Cas9 lineage barcoding by injection	27
sgRNA4	5′-TTCTAATACGACTCACTATAGACAGCAGTGTGTGAGTCTAGTTTTAGAGCTAGA-3′	Synthesize sgRNA4 for CRISPR-Cas9 lineage barcoding by injection	27
scGESTALT F	5′-TCGAGCTCAAGCTTCGG-3′	PCR amplify scGESTALT fragment for assessing editing efficiency	43
scGESTALT R	5′-CTGCCATTTGTCTCGAGGTC-3′	PCR amplify scGESTALT fragment for assessing editing efficiency	43
inDrops_GP6	5′-GAGGACTACACCATCGTGGAG-3′	PCR amplify long scGESTALT fragment from inDrops library	90
inDrops_PE1Sa	5′-CTCTTTCCCTACACGACGCTGGGTGTCGGGTGCAG-3′	PCR amplify long scGESTALT fragment from inDrops library	90
inDrops_GP12	5′-TCGTCGGCAGCGTCAGATGTGTATAA GAGACAG NNNNNNNNNTCGAGCTCAA GCTTCGGAC-3′, where N stands for a random base	PCR amplify short scGESTALT fragment from inDrops library	93
inDrops_PE1Sb	5′-CTCTTTCCCTACACGACGCT-3′	PCR amplify short scGESTALT fragment from inDrops library	93
R1-PCRix	5′-AATGATACGGCGACCACCGAGATCTACACxrefTCGTCGGCAGCGTC-3′, where xref is an index sequence for multiplexing (see Supplementary Table 2)	PCR amplify transcriptome or scGESTALT final sequencing library	97
R2-PCR	5′-CAAGCAGAAGACGGCATACGAGATGGGTGTCGGGTGCAG-3′	PCR amplify transcriptome or scGESTALT final sequencing library	97