Spreadsheet: 994f8885-a278-4bc9-80a2-614b6769646d
Sheet: Sheet1

Primers to identify new B/C3 polymorphisms in scaffold 8254711 | DNA sequence 5' to 3'
4711 MaeI SNP L | TCATTAACGATGCGTGTTTC
4711 MaeI SNP R | AATTAATTTGCAAAAGTTAAAATGG
4711 indel L | [NAME]
4711 indel R | TTGTATTAATGTCAACACAATCTTTG
RT-PCR MTA primers to verify one continuous transcript
SB210 Somatic 1,301 L
SB210 Somatic 3,166 R
SB210 Somatic 3,166 L
SB210 Somatic 5,249 R
Primers to amplify MTA-TM  from somatic nucleus for northern probe
SB210 Somatic 6 | GCTCTCCCTCGCTTTCTTAGAT
SB210 Somatic 1526 | GTTTGAGAAATCCCTCTGGTATTG
Primers to amplify MTB-TM from somatic nucleus for northern probe
SB210 Somatic 10,960 | CAACAGGAGGTGCTGCTTAATC
SB210 Somatic 12,493 | AAGATTGCATGGATGCACAAAG
Primers to create gene pair knockout construct
SB210 Somatic -930 upstream  L | GCATCATAAGACGAATATTAACTAAG
SB210 Somatic  -66 upstream R (neo) | AAGGAAACATGTAGAAGTGCTTGCTTTCAACTAGAGTCA
SB210 Somatic +98 downstream L (neo) | GAATTCGATATCAAGCTTTGAGAGTGCATTTAATTGCTT
SB210 Somatic +818 downstream R | TTGGGGTTTAAGATTTCAAAG
neoL | ACTTCTACATGTTTCCTTTCTTATTATTAC
neoR | AAGCTTGATATCGAATTCAGATC
Overlapping PCR was done with primers
SB210 Somatic -930 upstream  L and SB210 Somatic +818 downstream R
Primers to create MTA knockout construct
upstream and [NAME] primers listed above
SB210 Somatic 5,175 L (neo) | CTGAATTCGATATCAAGCTTCAATTTTTTACTTAGTATTTTTCTTTTG
SB210 Somatic 5,866 R | TTTCTTTGCAATATTGAATAACA
Overlapping PCR was done with primers
SB210 Somatic -930 upstream  L and SB210 Somatic 5,866 R
Primers to create MTB knockout construct
SB210 Somatic 6,110 L | TATGCAATCAATCTATTGAGTCTTTAC
SB210 Somatic 6,784 R (neo) | GAAAGGAAACATGTAGAAGTTGATCAATTCTTCTATGTTTATTTTAAG
SB210 Somatic +98 downstream L (neo) | GAATTCGATATCAAGCTTTGAGAGTGCATTTAATTGCTT
SB210 Somatic +818 downstream R | TTGGGGTTTAAGATTTCAAAG
Neo primers listed above
Overlapping PCR was done with primers
SB210 Somatic 6,110 L and SB210 Somatic +818 downstream R
Primers to monitor assortment of knockout transformants
MTA
SB210 Somatic 1,623 L | TATTAACTAAAAACCCTACTAAAA
SB210 Somatic 1,972 R | GATTAAAGTTTTCTTCTAGTATC
MTB
SB210 Somatic 10,270 L | GTTTTAGTAACTCCTTCCA
SB210 Somatic 10,805 R | TTAATCCCAGTAATTTTTAACAAA
Neo for gene pair knockout and MTA knockout:
SB210 Somatic -992 L | TTTGTGTATTTTCATTCATTCGTTCAC
Neo | GTAATAATAAGAAAGGAAACATGTAGAAGT
Neo for MTB knockout
SB210 Somatic 5,250 L | GTTTGCCCATGCAATAGATTCTG
Neo | GTAATAATAAGAAAGGAAACATGTAGAAGT
RT-PCR MTA primers - flank introns and products are specific to the somatic nucleus
SB210 Somatic 1,197 L | TGAAGGCGAACATGACAAGC
SB210 Somatic 1,842 R | TTTCTAGCTTCGCAATAATGTCTCAG
RT-PCR MTB  primers - flank introns and products are specific to the somatic nucleus
SB210 Somatic 10,673 L | GCCTTTTGTTCTCCACCTGTTT
SB210 Somatic 11,600 R | AGAGGGGAATCAGCAGTGTC
Primers to amplify mt-specific Southern probes
II SB210 Germline 13,932 L | GACCTATAAATCCCAGTAAAGCC
II SB210 Germline 15,538 R | GCTGAAGAATTGCATGTTGC
III SB210 Germline 80,422 L | CCAAACTAAGTCTGTGTTGGTG
III SB210 Germline 82,98 6R | TTCTGGTGCAGACTTTTTGCA G
IV SB210 Germline 52,153 L | GGATAAGAAGGTACTAAGCTT
IV SB210 Germline 54,175 R | TGA ATGTTGCATTCA ACTGC
V SB210 Germline 26,886 L | AATACATCCAAATTTTCTCCCAAA AAC
V SB210 Germline 30,618 R | [NAME]
VI SB210 Germline 38,280 L | GTTTGCGGAGGAGGAGAAGG
VI SB210 Germline 40,363 R | CAGAATCTATTGCATGGGCAA AC
VII SB210 Germline 64,817 L | GAGACA AGTTTA AGAGCGGAGCA
VII SB210 Germline  67,405 R | CAA AGTACGCTCTAA ATAGGTAG
Primers for PCR to amplify gaps in assembled SB210 mat germline sequence
SB210  Germline -2,106 L | AGTTATGGCTCGCCCAGTTG
SB210  Germline 1,650 R | TTATACCTCTAATAA ATCTTA ACCTCTCAA AAG C
SB210  Germline 15,485 L | GTAGTCTATCATAAGATGGG
SB210  Germline 18,049 R | GGGTTTATTACCTCTTTTG
SB210  Germline 30,495 L | TATCCTTCGGTCCTTAATCA
SB210  Germline 32,769 R | GGGTATTCTATGGTATACTTTCATC
SB210  Germline 50,233 L | GTAAAGATAAAGATCTGACTGTA
SB210  Germline 52,153 R | AAGCTTAGTACCTTCTTATCC
SB210  Germline 60,293 L | GATCAGTTTTCA ACTTGTGCTTCA TC
SB210  Germline 63,836 R | TCTATGAATATGCTCATCCTTCCTTTATC
SB210  Germline 71,858 L | GTGGCTTTTCGACACTAA ACA ACT
SB210  Germline 74,345 R | TTAATCAAAGTTGGTTCTTGTTTTAATTATC
SB210  Germline 87,988 L | CATCCCAACTTGTGTCCTTGTTG
SB210  Germline +818 R | TTGGGGTTTAAGATTTCA AAGGC
Primers for PCR to determine position of IESs
SB210  Germline 5,366 L | GAATCAATTTTTAAATTGTTTAAAGCTTTACAATCC
SB210  Germline 11,350 R | AGTTTAGATTTACTTGATAGCA
SB210  Germline 13,130 L | GGGGATAGTAACCATTAAAACCAT
SB210  Germline 13,932 R | GGCTTTACTGGGATTTATAGGTC
SB210  Germline 17,968 L | ACCAGAGGGATTTCTCAA AC
SB210  Germline 21,916 R | AACTTATACTAACAACTGATTCAAGTGGAGTG
SB210  Germline 32,563 L | TATTAACTAAAAACCCTACTAAAA
SB210  Germline 37,087 R | [NAME] AGTTTTCTTCTAGTATC
SB210  Germline 45,385 L | GTTTTAGTA ACTCCTTCCA
SB210  Germline 50,295 R | TTA ATCCCAGTA ATTTTTAACAAA
SB210  Germline 74,283 L | ACCAGAGGGATTTCTCAA AC
SB210  Germline 82,059 R | GATAGACGTTAA AAATTA AACTTCAA
Primers to amplify MTA-TM
[NAME] 5 L | GCTCTCCCTCGCTTTCTTAGAT
A2 mt II SB210 Germline 10,870 R | CACGCTATCTAAATGCCTTTAAATAG
A3 gMTA2-TM SB210 Germline 634 L | ATTCGCTAACCACGCAATTC
A4 mt II SB210 Germline 1,650 R | [NAME]
A5 left of mat SB210 Germline -904 L | GCATCATAAGACGAATATTAACTAAG
[NAME] Germline 80,417 R | CACCAACACAGACTTAGTTTGG
A7 left of mat SB210 Germline -238 L | CTAAAATAGAGAAACAGACATACA
[NAME] 52,153 R | AAGCTTAGTACCTTCTTATCC
A9 gMTA2-TM SB210 Germline 490 L | AGAGTGCTCAATGCACAAGCTC
A10 mt V SB210 Germline 21,916 | AACTTATACTAACAACTGATTCAAGTGGAGTG
A11 mt VI SB210 Germline 36,957 R | TTTCTAGCTTCGCAATAATGTCTCAG
A12 mt VII SB210 Germline 63,836 R | TCTATGAATATGCTCATCCTTCCTTTATC
Primers to amplify MTB-TM
B1 mt II SB210 Germline 15,538 L | GCAACATGCAATTCTTCAGCTTTAAG
B2 gMTB3-TM SB210 Germline 90,267 R | AAGATTGCATGGATGCACAAAG
[NAME] Germline 74,340 L | GATAATTAAAACAAGAACCAACTTTGA
B4 right of mat SB210 Germline +299 R | AGATAGATATATAAATTGGTTGATTGATAGACGAC
[NAME] Germline 88,136 L | CTACTAATCAGAGGTTTTGTTTTCGCAT
[NAME] 60,294 R | TGAAGCACAAGTTGAAAACTGAT
[NAME] 30,618 L | TCACGTGTAGTACTCCTAATCTGACC
[NAME] Germline 45,788 L | GCCTTTTGTTCTCCACCTGTTT
B9 mt VII SB210 Germline 71,858 L | GTGGCTTTTCGACACTAAACAACT
RT-PCR  primers to amplify MTB-TM from cDNA of isogenic mature strains
B4 right of mat SB210 Germline +299 R used for all reactions | AGATAGATATATAAATTGGTTGATTGATAGACGAC
B1 mt II SB210 Germline 15,538 L | GCAACATGCAATTCTTCAGCTTTAAG
[NAME] Germline 88,136 L | CTACTAATCAGAGGTTTTGTTTTCGCAT
SB210  Germline 60,293 L mt IV | GATCAGTTTTCA ACTTGTGCTTCA TC
[NAME]  30,000 L | GCTTGACCTAAAACAACATCATCT
B9 mt VII SB210 Germline 71,858 L | GTGGCTTTTCGACACTAAACAACT