Meiotic crossover hotspots contained in haplotype block boundaries of the mouse genome

Kauppi et al. 10.1073/pnas.0701965104.

Supporting Information

Files in this Data Supplement:

SI Table 1
SI Table 2
SI Table 3




Table 1. Universal primers used for PCR and sequencing, in 5' to 3' orientation

Boundary 1

M1/143.7754F ATAGCACCTTGCCGTATGTG

M1/143.7760F ACCTGAGAGCTACCAAGCCC

M1/143.7773F GCAGAGAGCTGGCTTAATGG

M1/143.7779F GCCAATGTTCCTAACGTTGTG

M1/143.7785F GCTTTTCAGAGGCAGACTAG

M1/143.7748F GCTGCATGCAGTGTAGGTGG

M1/143.7774R AGCAGATACATGTGCAGGCC

Boundary 2

M2/143.9183F GTATCAAGCCATTCAGGGTGG

M2/143.9189Fs CCGTTGTCACCACCTAGGAC

M2/143.9195Fs TTCCCAGTGCTTATCATGCC

M2/143.9190R AGCAGCCTGGGCTTCAAAC

M2/143.9202UF CCATCACAATCCTGATCTGAC

M2/143.9208R TAAGCTGGAAGTAGCTTCATG

M2/143.9211Fs CTCCATGGAGATGTAAGTGAC

M2/143.9232Fs TTTGAGACAGGCCCGTGGTC

M2/143.9234Rs CTGCACATCTAAGCTCTTCTC

M2/143.9248Fs CCAGAGACCTAAAGACCCTC

M2/143.9249Rs CAGTCAAAAGCCAGCAGGAG

M2/143.9270R ACAGGGACAGTACGACTTAG

M2/143.9269F CAGACATATGACGTCCCACAC

M2/143.9212R GTCACTTACATCTCCATGGAG

M2/143.9269F CAGACATATGACGTCCCACAC

M2/143.9276Fs TGCTGTCAGCTCCATAAGAG

M2/143.9283Fs GAAATCGTTGGTGTGTGCAC

M2/143.9290F TTAGCTTGCCTTGCTCTCTG

M2/143.9300R TGCGCAGAAGCACATTCCTG

M2/143.9306R CGATATATCAGGTACCACGGG

Boundary 3

M3/144.7936F GGCATACAGACAGCATGCAAG

M3/144.0801UF CAGAGCTATCTCTCCGGCCTAGTT

M3/144.0812R GACATCTGACTACCAAACACC

M3/144.0812Fs CTTGAGTCATCTCCTAGCCC

M3/144.0818Fs TTGGAGAAGGAATCTCCCAC

M3/144.0824Fs CCCCTTAGCAACTCTAAAGC

M3/144.0831Fs CAGAAACAGCTTTCCTAACCC

M3/144.0837Fs TAGATTCCCATGAAGATTCC

M3/144.0851R CCTTCATCCGCAGAAGCATC

M3/144.0857Rs CCTCTAAATCAATCATGGCTC

M3/144.0862F CAGCCATAGCTTACCTTATGC

M3/144.0863Rs TTCACTTTGGTTATCCACAAC

M3/144.0886F GGAATAAGTGCAGGAGCAGA

M3/144.0902R CGTAGGTTGACTCTGCACCC

M3/144.0869UR CCTGGCTCTTCATTGCACCCAAG

Boundary 9

M9/145.2801F CTCCTACACAATGCCATTTACC

M9/145.2806UF GGTACACATAGGACAGTAAGTCAC

M9/145.2809UF GTAGAACTGGGATTCAGCCCAA

M9/145.2811F ACTGACTTGTCTTGTCTGGCC

M9/145.2812R GAAGGCCAGACAAGACAAGTC

M9/145.2822F ACCTGCTGCCTGGACCTTCC

M9/145.2825R CTAGAATGATCAGACACATTTGG

M9/145.2828UR GGTACTAAATATCCTGCGGTTG

M9/145.2832R GAGAGAACCATTTAGTGCCC

M9/145.2837R AGTCTCACTGGAGTGTTCGC

M9/145.2866UR CTGGATGCATTAGTACCACTCTGC

M9/145.2866F GAGTGGTACTAATGCATCCAG





Table 2. Nucleotide sequences of allele-specific and universal PCR primers (in 5' to 3' orientation), plus cycling conditions used in the crossover assays

M1 assay

 

Primary PCR

  

143773310FG

GTTGGTGATGAATTGCCCG

143779724RC

ggcCAACTTGCAAAATACCG

8 times (96°C 20 sec, 61°C 30 sec, 65°C 7 min 30 sec)

 

10 times (96°C 20 sec, 60°C 30 sec, 65°C 7 min 30 sec)

 

8 times (96°C 20 sec, 59°C 30 sec, 65°C 7 min 30 sec)

 

Secondary PCR

  

143774191FG

GTGAGGAGTTTCTAAGCG

143779715RA/Ad

gtctacgtagtcagctctgGCAAAATACCGTAAGTCATT

Adap

GTCTACGTAGTCAGCTCTGG

30 times (96°C 20 sec, 59°C 30 sec, 65°C 7 min)

 

Tertiary PCR

  

M1/143.7742UF

CTAACCTGGGCACAGCAGGCATGC

M1/143.7796UR

CTACTCACACTTTGGCTAAACTCC

23 times (96°C 20 sec, 62°C 30 sec, 65°C 7 min 30 sec)

 

M2 assay

 

Primary PCR

  

143919254FC

CCTCTATGAGCTGGTAGGTC

143929742RC

ggGTCTTTTTTGAATGCAGGGG

10 times (96°C 20 sec, 62°C 30 sec, 65°C 12 min)

 

15 times (96°C 20 sec, 61°C 30 sec, 65°C 12 min)

 

Secondary PCR

  

143919650FA

GGTTACAGAGAGGCAACGCA

143928551RC

CTTCCAGAAGACCCTGTCG

32 times (96°C 20 sec, 62°C 30 sec, 65°C 12 min)

 

Tertiary PCR

  

M2/143.9197UF

CACCTTATGGCAGCCAGGCATC

M2/143.9285UR

GGCTTCAAATTGGCATTCCTG

10 times (96°C 20 sec, 62°C 30 sec, 65°C 10 min)

 

17 times (96°C 20 sec, 60°C 30 sec, 65°C 10 min)

 

Boundary 3 assay

  

Primary PCR

  

144079888FT

ccGACATCAATATTGGCCAGT

144089161RT2

GCTCACAGAGTGCACA

8 times (96°C 20 sec, 63°C 30 sec, 65°C 11 min)

 

19 times (96°C 20 sec, 62°C 30 sec, 65°C 11 min)

 

Secondary PCR

  

144080078G3

CAATGGGTGGGAGCCG

144088790G

cgCCTTACTCCTTTTAAGCCC

8 times (96°C 20 sec, 63°C 30 sec, 65°C 11 min)

 

22 times (96°C 20 sec, 62°C 30 sec, 65°C 11 min)

 

Boundary 9 assay

  

Primary PCR

  

145280120FC

CTCCATGAGCATTGTTGCTAC

145287174RG

GGCTGTGGACCAGAAGAC

5 times (96°C 20 sec, 63°C 30 sec, 65°C 8 min)

 

10 times (96°C 20 sec, 62°C 30 sec, 65°C 8 min)

 

10 times (96°C 20 sec, 61°C 30 sec, 65°C 8 min)

 

Secondary PCR

  

145281025FA

GAACCTAATTTTTCAAGGAAA

145286752RT

ACCTACCCCACCCTATGA

8 times (96°C 20 sec, 58°C 30 sec, 65°C 7 min 30 sec)

 

24 times (96°C 20 sec, 56°C 30 sec, 65°C 7 min 30 sec)

 

Bases in lower case are 5' extensions used to boost GC content and are not part of genomic sequence. Adap is a longer extension primer, used along with the extended allele-specific primer to improve PCR efficiency.

This Article

  1. Published online before print August 9, 2007, doi: 10.1073/pnas.0701965104 PNAS August 14, 2007 vol. 104 no. 33 13396-13401
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