All oligonucleotides used in this study were ordered from IDT with the indicated modifications.
Oligo name | Sequence (5’ to 3’) | Modification(s) |
---|---|---|
50dupex LAG | TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGACGCTGCCGAATTCTGGCTTGCTAGGACATTACAGGATCGTTCGGTCTC | None |
50duplex LAG dual biotin | TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGACGCTGCCGAA | Two biotin-modified thymidine residues in |
50duplex LEAD | GAGACCGAACGATCCTGTAATGTCCTAGCAAGCCAGAATTCGGCAGCGTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT*T*T*T*T*T*T | The six dT residues at the 3’ end are connected by phosphorothioate bonds (*) |
50duplex LAG2 | TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGACGCTGCCGAATTCTGGATTGCTAGGACATTACAGGATCGTTCGGTCTC | None |
50duplex LEAD2 dual biotin | GAGACCGAACGATCCTGTAATGTCCTAGCAA | Two biotin-modified thymidine residues in |
160mer duplex LEAD | AGAGAGTAGAGTTGAGTTGTGATGTGTAGAGTTGTTGTAGAGAAGAGTTGTGAAGTGTTGAGTAGAGAAGAGAAGAGAAGTGTTGTGATGTGTTGAGTAGTGTAGAGTTGAGAAGTAGAGATGTGTTGAGATGAGAAGAGTTGTAGTTGAGTTGAAGTGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT*T*T*T*T*T | The five dT residues at the 3’ end are connected by phosphorothioate bonds (*) |
160mer duplex LAG | TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCACTTCAACTCAACTACAACTCTTCTCATCTCAACACATCTCTACTTCTCAACTCTACACTACTCAACACATCACAACACTTCTCTTCTCTTCTCTACTCAACACTTCACAACTCTTCTCTACAACAACTCTACACATCACAACTCAACTCTACTCTCT | None |
Blocked Fork LEAD | ACCGGAGACCGAACGATCCTGTAATGTCCTAGCAAGCCAGAATTCGGCAGCGTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGGAAAGAATGTTGGTGAGGGTTGGGAAGTGGAAGGATGGGCTCGAGAGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTT*T*T*T*T*T | The five dT residues at the 3’ end are connected by phosphorothioate bonds (*) |
Blocked Fork LAG | TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGACGC | Two biotin-modified thymidine residues in |
Blocked Fork Primer | CCTCTCGAGCCCATCCTTCCACTTCCCAACCCTCACC | None |
C2 | CCTCTCGAGCCCATCCTTCCACTTCCCAACCCTCACC | None |
Oligonucleotide name | Sequence (5’ to 3’) |
---|---|
eYFP-F | CGGCGCGCCTCAGGTTCAGGTTCAGGTATGGTGAGCAAGGGCGAG |
eYFP-R | CGCGGCCGCTTACTTGTACAGCTCGTCCATGCCGAGAGTGATCCCGGC |
GFP-F | CGGCGCGCCTCAGGTTCAGGTTCAGGTATGGCTAGCAAAGGAGAAGAA |
GFP-R | CGCGGCCGCTTATTTGTAGAGCTCATCCATGCCATGTGTAATCCCAGCAGC |
SNAP-F | GGGCGCGCCTCAGGTTCAGGTTCAGGTATGGACAAAGACTGCGAAATG |
SNAP-R | CGAATTCTCATTAACCCAGCCCAGGCTTGCCCAGTCTG |
meYFP-F | CTACCAGTCCAAGCTGAGCAAAGAC |
meYFP-R | CTCAGGTAGTGGTTGTCG |
pOB-ezrA-up-F | TTTACGTACACTATCTGCAGATGCTTCTCCTCCTAATTTATCATT |
pOB-ezrA-up-R | ATTCGAGCTCGGTACCCGGGTTTTAAATTAATAAAAAAAACAC |
pOB-ezrA-down-F | CACTATAGAATACTCAAGCTTACTCCTTAATTTCCTCATAAATGATGA |
pOB-ezrA-down-R | GGATCAACTTTGGGAGAGAGAAACTAGTATGTAGTTATACTTAAA |
pOB-TetR-F | TAAATTAGGAGGAGAAGCATCTGCAGATAGTGTACGTAAAAAGA |
pOB-TetR-R | GTATAACTACATACTAGTTTCTCTCTCCCAAAGTTGATCCC |
ftsZ-eyfp-F | ACATGGCCATGTCAGGTTCAG |
ftsZ-eyfp-R | GGCGCGCCTTATTTATATAATTC |
FGFtsZXhoI-F | CTCGAGATGTTAGAATTTGAACAAGG |
FGFtsZEcoRI-R | TTAGAATTCACGTCTTGTTCTTCTTGAA |
FGFtsZNheI-F | GTTGCTAGCATGTTAGAATTTGAACAAGG |
FGFtsZAscI-R | GTTGGCGCGCCTTATCCCAGACCCGGTTTAC |
Mouse primers | Oligonucleotide sequences (5’−3’) | |
---|---|---|
Forward | TGAGCAAATCCTCCACAGCCCTGTTC | |
Reverse | CTGCTAAAGCGCATGCTCCAGACTG | |
Forward | TCTCTGACCAGCTTTCCAACCTTCAG | |
Reverse | CTCAAACCAGCACCACCTCCATATTG | |
Forward | TCAGCAAGACTCTGGGCAAGCTCT | |
Reverse | CTCAAAATCTGAGCCACTCCCTC | |
Forward | CCTGGAAAATGCTTCTGTCCGT | |
Reverse | GTGTCCACATAGTCATTGGCAGAGTG | |
Forward | AGCTGACCCTGAAGTTCATCTG | |
Reverse | GTCGTCCTTGAAGAAGATGGTG | |
Forward | GCTGCAGGCGCGGAGAAGGGCTCTC | |
Reverse | CTTCACGTACACCTTGGAGC | |
IL2 (internal control) | Forward | GCCTAGAAGATGAACTTGGACCTCTG |
Reverse | GTGGAAGGATTCACTTGCACAGTGAC | |
Human RPE primers | ||
Forward | CGTACCCGCACTTGCACAAC | |
Reverse | TCTCGCTCTCGTTCAGAAGTC | |
Forward | TGCCCGCTGCTGTCTAAT | |
Reverse | TCTCCGCTCTGAGCAAGG | |
β- | Forward | CCAACCGCGAGAAGATGA |
Reverse | CCAGAGGCGTACAGGGATAG |
Mouse primers | Oligonucleotide sequences (5’−3’) | |
---|---|---|
Forward | TGAGCAAATCCTCCACAGCCCTGTTC | |
Reverse | CTGCTAAAGCGCATGCTCCAGACTG | |
Forward | TCTCTGACCAGCTTTCCAACCTTCAG | |
Reverse | CTCAAACCAGCACCACCTCCATATTG | |
Forward | TCAGCAAGACTCTGGGCAAGCTCT | |
Reverse | CTCAAAATCTGAGCCACTCCCTC | |
Forward | CCTGGAAAATGCTTCTGTCCGT | |
Reverse | GTGTCCACATAGTCATTGGCAGAGTG | |
Forward | AGCTGACCCTGAAGTTCATCTG | |
Reverse | GTCGTCCTTGAAGAAGATGGTG | |
Forward | GCTGCAGGCGCGGAGAAGGGCTCTC | |
Reverse | CTTCACGTACACCTTGGAGC | |
IL2 (internal control) | Forward | GCCTAGAAGATGAACTTGGACCTCTG |
Reverse | GTGGAAGGATTCACTTGCACAGTGAC | |
Human RPE primers | ||
Forward | CGTACCCGCACTTGCACAAC | |
Reverse | TCTCGCTCTCGTTCAGAAGTC | |
Forward | TGCCCGCTGCTGTCTAAT | |
Reverse | TCTCCGCTCTGAGCAAGG | |
β- | Forward | CCAACCGCGAGAAGATGA |
Reverse | CCAGAGGCGTACAGGGATAG |
Sequence (5ʹ → 3ʹ) | Description |
---|---|
CRISPR hairpin target* | |
Mini-CRISPR array | |
CAATACCTACCTCAATATTTCAATCCACGCACCC | RC† |
CGTAGCTGAGGACCACCAGAACAG TTTT | 15-nt 3ʹ overhang prespacer, 4-nt between duplex and PAM†† |
CGTAGCTGAGGACCACCAGAACAG TT | 2-nt between duplex and PAM |
CGTAGCTGAGGACCACCAGAACAG TTTTTT | 6-nt between duplex and PAM |
CGTAGCTGAGGACCACCAGAACAG TTTTTTTT | 8-nt between duplex and PAM |
CTGTTCTGGTGGTCCTCAGCTACG TTTT | RC of previous four oligos |
CRISPR DNA substrate | |
TCAATATTTCAATCCACGCACCCATGAAGAGTGCGACAGCGAAAATC | RC |
GCGTAGCTGAGGACCACCAGAACAGTTTT | 25-nt 3ʹ overhang prespacer |
GCGTAGCTGAGGACCACCAGAACAG | 25 bp duplex |
CTGTTCTGGTGGTCCTCAGCTACGC | RC |
GCGTAGCTGAGGACCTTTTTTTTTTTTT | T-rich ssDNA prespacer |
CAAGCTTGTCGACCTGAAAAAAAAAAAAAATTCAAAAAAAAAAAAA | RC |
CTAGTATGATCATGTCCAACGAATCAATACCTACCTCAATGAACGGAT | 48 bp duplex |
ATCCGTTCATTGAGGTAGGTATTGATTCGTTGGACATGATCATACTAG | RC |
GCGTAGCTGAGGACCTTTTTTTTTTTTTTTTTT | 3 PAM sites interspersed in 2-nt |
TGTCGCAAGCTTGTCAAAAAAAAAAAAAAAAAATTCAATTCAATTCA | RC |
GCGTAGCTGAGGACCTTTTTTTTTTTTTTTTTTTT | 3 PAM sites without spacing |
TGTCGCAAGCTTGTCAAAAAAAAAAAAAAAAAAAATTCTTCTTCAAA | RC |
GCGTAGCTGAGGACCTTTTTTTTTT | 3 PAM sites interspersed with 10-nt |
TGTCGCAAGCTTGTCAAAAAAAAAATTCAAAAAAAAAATTCAAAAA | RC |
GCGTAGCTGAGGACCTTTTTTTTTTTT | 3 PAM sites interspersed with 8-nt |
TGTCGCAAGCTTGTCAAAAAAAAAAAATTCAAAAAAAATTCAAAAAAAA | RC |
GCGTAGCTGAGGACCTTTTTTTTTTTTTT | 3 PAM sites interspersed with 6-nt |
TGTCGCAAGCTTGTCAAAAAAAAAAAAAATTCAAAAAATTCAAAA | RC |
GCGTAGCTGAGGACCTTTTTTTTTTTTTTTT | 3 PAM sites interspersed with 4-nt |
TGTCGCAAGCTTGTCAAAAAAAAAAAAAAAATTCAAAATTCAAAA | RC |
GCGTAGCTGAGGACCTATATATATATAT | AT-rich ssDNA prespacer |
CAAGCTTGTCGACCTGTATATATATATATATTCATATATATAT | RC |
GCGTAGCTGAGGACCTTGGTATTCAACA | Non-T-rich upstream/T rich downstream ssDNA prespacer |
CAAGCTTGTCGACCTGAAAAAAAAAAAAAATTCTGTTGAATACCAAG | RC |
GCGTAGCTGAGGACCTTTTTTTTTTTTT | T-rich upstream/non T-rich downstream ssDNA prespacer |
CAAGCTTGTCGACCTGCTGTTGAATACGAGTTCAAAAAAAAAAAAA | RC |
GCGTAGCTGAGGACCTTGGTATTCAACA | Non-T-rich up- and downstream ssDNA prespacer |
CAAGCTTGTCGACCTGCTGTTGAATACGAGTTCTGTTGAATACCAA | RC |
GCGTAGCTGAGGACC | Primer used for ddNTP Sanger sequencing |
GCGTAGCTGAGGACCCGTGGCACCGACATGGCATTTTTNNNN | NNNN on upstream region |
GCGTAGCTGAGGACCCGTGGCACCGACATGGCAGTTTTTNNN | NNN on upstream region |
GCGTAGCTGAGGACCCGTGGCACCGACATGGCAGGTTTTTNN | NN on upstream region |
GCGTAGCTGAGGACCCGTGGCACCGACATGGCAGGCTTTTTN | N on upstream region |
GCGTAGCTGAGGACCCGTGGCACCGACATGGCATTTTT | NNNN on downstream region |
GCGTAGCTGAGGACCCGTGGCACCGACATGGCATTTTT | NNN on downstream region |
GCGTAGCTGAGGACCCGTGGCACCGACATGGCATTTTT | NN on downstream region |
GCGTAGCTGAGGACCCGTGGCACCGACATGGCATTTTT | N on downstream region |
CAAGCTTGTCGACCTG | Primer used for primer extension |
TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCAAGCTTGTCGACCTG | Primer used for amplification-Forward |
GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGCGTAGCTGAGGACC | Primer used for amplification-Reverse |
*For CRISPR oligonucleotides, leader is in italics, repeat is in bold, and spacer is in plain uppercase font. For hairpin, the loop region is in lowercase.
†RC = reverse complement of previous oligonucleotide.
††For cleavage substrates, PAM sequences are underlined.
Restriction enzyme recognition sequences are capitalised. BsaI overhangs are underlined. Introduced mutations are in bolded capital letters. Additional oligonucleotides used for site-directed mutagenesis are listed in Tables S1 and S2 of
Name | Sequence (5’ to 3’) | Function |
---|---|---|
F2-pUC19-BsaI | gcgAGATCT | |
R3-pUC19-MfeI-SpeI | actgcgACTAGTCAATTGattaatgcagctggcacgac | |
F-800Right | actgcgCAATTGagaccccggaagacatcag | |
R-800Right | actgcgTCTAGAcattgcgaagttcaagcgta | |
F2-gtsB-F | actgcgGGTCTCa | Conserved |
R3-gtsB-R | actgcgGGTCTCc | Conserved |
4845-M13F | GTAAAACGACGGCCAGTTCCGACAGGCTGTAGTCCTT | |
R2-M13R-gtsB | GGAAACAGCTATGACCATGTGGTCCTCAGCTCGGAATA | |
SP1 | ACCACACCGAACAGGAAGTC | 5’ RACE cDNA synthesis |
B-SP2 | ACTGCGTCTAGAGACCAAGGTGATACCGATAAACA | 5’ RACE |
B-SP3 | ACTGCGTCTAGACGAACAAGGCCAGGTTTTT | 5’ RACE |
A-SP2 | ACTGCGTCTAGATTTCTTGTCGAGCAGGGAGT | 5’ RACE |
A-SP3 | ACTGCGTCTAGATTCTTCTTTGGCGACGTCTT | 5’ RACE |
Name | Sequence | Reference |
---|---|---|
agr-a | This study | |
agr-b | This study | |
agr-c | This study | |
agr-d | This study |
Name | Sequence (5´→3´) |
---|---|
JR163 | GCGCCCATGGCTAAGGCATCCATTTCAATAGACGAGAAG |
JR164 | GCGCGTCGACTTATTCTTTTTCCGTATCCATTTGCTGTA |
JR169 | GCGCCCATGGATTCAAAAGATCAAACAATGTTTTACAACTTC |
JR170 | GCGCGTCGACTCATTTCTCACCAATTTCGTTATTTTTCAG |
JR197 | GCGCGGATCCCAATTATTTCGAATGGTGCGGTGTC |
JR198 | TCCTTATTCGTCGACCATCTTTCCTCAGTCCCTTCCTG |
JR199 | GGAAAGATGGTCGACGAATAAGGAATAAATCCTAGTTAGTAGGG |
JR200 | CGCGCGAATTCCCAAGACTCAACCTCTTTCACTC |
JR249 | GCGCCTGCAGAAAAAATTATTGTACGCGGTGGAAAAC |
JR250 | GCGCGGTACCGCGAATAAAGACGCTAAGTTTGTTACATCG |
JR253 | GCGCTCTAGAAAAGGCATCCATTTCAATAGACGAG |
JR254 | GCGCGGTACCTCTTTTTCCGTATCCATTTGCTG |
JR255 | GCGCTCTAGATTCAAAAGATCAAACAATGTTTTACAAC |
JR256 | GCGCGGTACCTTCTCACCAATTTCGTTATTTTTCAG |
JR257 | GCGCCTGCAGGGAAAAAATTATTGTACGCGGTGGAAAAC |
JR264 | GCGCAGATCTGGCAAATACAGCATTGAACTATGTG |
JR265 | GCGCGGATCCAATCGAAGCACCTCATTCCTTC |
JR266 | GCGCGGATCCATGAGAATAATGGGTTTAGATGTCGGC |
JR267 | GCGCGTCGACGCTAGGAATGTAGCAAGGATTTCTTC |
SHW815 | GATCTATCGATGCATGCCATGGGCTAAATGACCAAGGAATTACCG |
SHW816 | CGCGTCGGGCGATATCGGATCCTTTCTTCCGCGTTTTGGTAACG |
SHW817 | CAATCATCATTTTAAAAGCACCTCACTATTTTTCAG |
SHW818 | TGCTTTTAAAATGATGATTGGTAAGCGATTAAGC |
SHW819 | GATCTATCGATGCATGCCATGGAGATAGAGGCAGAATAAGACATC |
SHW820 | CGCGTCGGGCGATATCGGATCCGGTATTTACAACCACTACGTCG |
SHW821 | CGTTCTTATTTCATGAAGCATCCCTCCCTTTC |
SHW822 | TGCTTCATGAAATAAGAACGGAGGAAATGTGCTG |
SHW830 | GCGCGCTCTAGATGGACGATTTACGCAAAGAGCTCAG |
SHW831 | GCGCGCGGTACCTTAGCTTTTACTTTTTTAGAGGTTGTTTTC |
SHW832 | GCGCGCTCTAGAAATTCCAACAGTAATTGAACAAACTAGC |
SHW833 | GCGCGCGGTACCCCTTTTAAGCCAGATTTATTAATGATAATATC |
SW77 | GTAAAACATTGCTTGATCTTTTGAATCCATGGGTTTCAC |
SW78 | GATCAAGCAATGTTTTACAACTTCGGCGATGATTC |
SW79 | GTAAAACATGTCTTGATCTTTTGAATCCATGGGTTTCAC |
SW80 | GATCAAGACATGTTTTACAACTTCGGCG ATGATTC |
SW110 | GCGCGCGGATCCATGCATGCAGAATTTAGAACAGATAG |
SW111 | GCGCGCGTCGACTCATGAAGCATCCCTCCCTTTC |
SW112 | GCGCGCGGATCCATGATGATTGGTAAGCGATTAAGCG |
SW113 | GCGCGCGTCGACTTAATTTGGATAAGGGACTGTACCTTC |
SW136 | CTAAACGAGCTATCATACTTCTAGCATCCTTGTGAC |
SW137 | GTATGATAGCTCGTTTAGAACGAGATGAAATTATCGAG |
SW138 | AATTTCATCTGCTTCTAAACGACGTATCATACTTCTAGC |
SW139 | GTTTAGAAGCAGATGAAATTATCGAGGAACTTGTCAAAG |
SW144 | CCTTGTGAGCAGGAATATAAGCAGGATCGCCTG |
SW145 | TATATTCCTGCTCACAAGGATGCTAGAAGTATGATAC |
SW146 | GTATCATACTTGCAGCATCCTTGTGACGAGGAATATAAG |
SW147 | GGATGCTGCAAGTATGATACGTCGTTTAGAACGAG |
Lmo1503F | GCTATACCATGGATTCAAAAGATCAAACAATGTTTTACAAC |
Lmo1503R | CGATATCTCGAGTCATTTCTCACCAATTTCGTTATTTTTCAG |
PrkAF | GCTATACCATGGCAATGATGATTGGTAAGCGATTAAGCG |
PrkAR | CGATATCTCGAGTCATTTTTTCTTTTTCTTATCTTTTTTCTCCTCAGG |
PrpCF | GCTATACCATGGCAATGCATGCAGAATTTAGAACAGATAGAG |
PrpCR | CGATATCTCGAGTCATGAAGCATCCCTCCCTTTC |