Brandon:LabNotes/Project1/2012-5-7: Difference between revisions

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>Bsos
>Bsos
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*also in reference to [http://genome-tech.ucsd.edu/LabNotes/index.php/Athurva_Gore:LabNotes/2012-4-26 Athurva's summary]
*also in reference to [http://genome-tech.ucsd.edu/LabNotes/index.php/Athurva_Gore:LabNotes/2012-4-26 Athurva's summary]
*new technique of only annealing sequences for form full mosaic ends and adding adaptors.
*new technique of only annealing sequences for form full mosaic ends and adding adaptors.
*would result in 100% efficiency of capture of sequence upon insertion, including single insertions.


Summary and primers to order:
Summary:


  5’- [A][TTAATACGACTCACTATAGGG][T][CCTCCCTCGCGCCATCA][G][AGATGTGTATAAGAGACAG] -3’  
  5’- [A][TTAATACGACTCACTATAGGG][T][CCTCCCTCGCGCCATCA][G][AGATGTGTATAAGAGACAG] -3’  
Line 12: Line 13:
    
    
         5’- ATTAATACGACTCACTATAGGGTCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAG -3’
         5’- ATTAATACGACTCACTATAGGGTCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAG -3’
                                            3'-[ddC] CTACACATATTCTCTGTC [Phos]-5'
                                                3'- TCTACACATATTCTCTGTC [Phos]-5'
   
   
  5'- [phos] CTGTCTCTTATACACATC [ddC]-3'
  5'- [phos] CTGTCTCTTATACACATCT -3'
       3’-  GACAGAGAATATGTGTAGAGACTACCGCGCTCCCTCCTGGGATATCACTCAGCATAATTA -5’
       3’-  GACAGAGAATATGTGTAGAGACTACCGCGCTCCCTCCTGGGATATCACTCAGCATAATTA -5’
   
   
Line 25: Line 26:
   
   
   
   
  Second adapter to anneal:
  Upon single insertion, T7 still present in either direction of insertion, IVT off top strand, and bottom:
 
NNNNN------ CTGTCTCTTATACACATC -3'              5’- ATTAATACGACTCACTATAGGGTCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAG NNNNNN
---NNNNNNNN GACAGAGAATATGTGTAGAGACTACCGCGCTCCCTCCTGGGATATCACTCAGCATAATTA -5’              3'- CTACACATATTCTCTGTC ------NNNN
After fill in with T4 DNA polymerase, or BST or w/e
5’- A[TTAATACGACTCACTATAGGG]TCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAG NNNNNNNN
3'- T[AATTATGCTGAGTGATATCCC]AGGAGGGAGCGCGGTAGTCTCTACACATATTCTCTGTC ------NNNN
 
 
NNNNN------ CTGTCTCTTATACACATCTCTGATGGCGCGAGGGAGGA[CCCTATAGTGAGTCGTATTAA]T -3'
---NNNNNNNN GACAGAGAATATGTGTAGAGACTACCGCGCTCCCTCCT[GGGATATCACTCAGCATAATT]A -5’
  read primers/amplification etc
5’- ATTAATACGACTCACTATAGGGTCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAG NNNNNNNNNNNNN CTGTCTCTTATACACATCTCTGATGGAGCGGGCTGGCAAGGCAGACCGATC -3’
                      5'- TCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAG -3' read primer 1
                                                                           
 
Experiments needed to be done for proof of concept
should now be ready for IVT.
ask rui
===left over notes===
 
  Second adapter to anneal:
   
   
                                                                     [phos] -5' CTGTCTCTTATACACATCTCTGATGGAGCGGGCTGGCAAGGCAGACCGATC -3’
                                                                     [phos] -5' CTGTCTCTTATACACATCTCTGATGGAGCGGGCTGGCAAGGCAGACCGATC -3’
Line 41: Line 72:
  3'- CTAGCCAGACGGAACGGTCGGGCGAGGTAGTCTCTACACATATTCTCTGTC NNNNNNNNNNNNN GACAGAGAATATGTGTAGAGACTACCGCGCTCCCTCCTGGGATATCACTCAGCATAATTA -5’  
  3'- CTAGCCAGACGGAACGGTCGGGCGAGGTAGTCTCTACACATATTCTCTGTC NNNNNNNNNNNNN GACAGAGAATATGTGTAGAGACTACCGCGCTCCCTCCTGGGATATCACTCAGCATAATTA -5’  
   
   
  read primers/amplification etc
5’- ATTAATACGACTCACTATAGGGTCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAG NNNNNNNNNNNNN CTGTCTCTTATACACATCTCTGATGGAGCGGGCTGGCAAGGCAGACCGATC -3’
                      5'- TCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAG -3' read primer 1
                                                                            3'- GACAGAGAATATGTGTAGAGACTACCTCGCCCGACCGT -5' read primer 2
AGCGGGCTGGCAAGGCAGACCGATC -3’


  To order:
  to stop nonspecific amplification in shendure protocol
  5’-[Phos]- CTGTCTCTTATACACATC -3’ [ddC - 3' to block ends]
  5’-[Phos]- CTGTCTCTTATACACATC -3’ [ddC - 3' to block ends]

Revision as of 20:28, 7 May 2012

Adaptation of transposition method for inserting T7

  • in reference to shendure paper transposition
  • also in reference to Athurva's summary
  • new technique of only annealing sequences for form full mosaic ends and adding adaptors.
  • would result in 100% efficiency of capture of sequence upon insertion, including single insertions.

Summary:

5’- [A][TTAATACGACTCACTATAGGG][T][CCTCCCTCGCGCCATCA][G][AGATGTGTATAAGAGACAG] -3’ 
   spcr     T7 forward       spcr   read sequence  spcr         ME 

 
       5’- ATTAATACGACTCACTATAGGGTCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAG -3’
                                                3'- TCTACACATATTCTCTGTC [Phos]-5'

5'- [phos] CTGTCTCTTATACACATCT -3'
      3’-  GACAGAGAATATGTGTAGAGACTACCGCGCTCCCTCCTGGGATATCACTCAGCATAATTA -5’


Fragments created after transposition:


5’- ATTAATACGACTCACTATAGGGTCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAG NNNNNNNN------ CTGTCTCTTATACACATC -3'
                                          3'- CTACACATATTCTCTGTC ------NNNNNNNN GACAGAGAATATGTGTAGAGACTACCGCGCTCCCTCCTGGGATATCACTCAGCATAATTA -5’ 


Upon single insertion, T7 still present in either direction of insertion, IVT off top strand, and bottom:
NNNNN------ CTGTCTCTTATACACATC -3'               5’- ATTAATACGACTCACTATAGGGTCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAG NNNNNN
---NNNNNNNN GACAGAGAATATGTGTAGAGACTACCGCGCTCCCTCCTGGGATATCACTCAGCATAATTA -5’               3'- CTACACATATTCTCTGTC ------NNNN


After fill in with T4 DNA polymerase, or BST or w/e

5’- A[TTAATACGACTCACTATAGGG]TCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAG NNNNNNNN
3'- T[AATTATGCTGAGTGATATCCC]AGGAGGGAGCGCGGTAGTCTCTACACATATTCTCTGTC ------NNNN


NNNNN------ CTGTCTCTTATACACATCTCTGATGGCGCGAGGGAGGA[CCCTATAGTGAGTCGTATTAA]T -3'
---NNNNNNNN GACAGAGAATATGTGTAGAGACTACCGCGCTCCCTCCT[GGGATATCACTCAGCATAATT]A -5’


  read primers/amplification etc

5’- ATTAATACGACTCACTATAGGGTCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAG NNNNNNNNNNNNN CTGTCTCTTATACACATCTCTGATGGAGCGGGCTGGCAAGGCAGACCGATC -3’
                      5'- TCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAG -3' read primer 1
                                                                           
Experiments needed to be done for proof of concept

should now be ready for IVT.

ask rui 

left over notes

 Second adapter to anneal:

                                                                    [phos] -5' CTGTCTCTTATACACATCTCTGATGGAGCGGGCTGGCAAGGCAGACCGATC -3’
5’- ATTAATACGACTCACTATAGGGTCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAG NNNNNNN------ CTGTCTCTTATACACATC -3'    X   X XXX X XXXX X XX  XX
             XX  XX X XXXX X XXX X   X    3'- CTACACATATTCTCTGTC ------NNNNNNN GACAGAGAATATGTGTAGAGACTACCGCGCTCCCTCCTGGGATATCACTCAGCATAATTA -5’ 
         3'- CTAGCCAGACGGAACGGTCGGGCGAGGTAGTCTCTACACATATTCTCTGTC [phos] -5' 


Strands after fill-in, ligation, separation

top strand
5’- ATTAATACGACTCACTATAGGGTCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAG NNNNNNNNNNNNN CTGTCTCTTATACACATCTCTGATGGAGCGGGCTGGCAAGGCAGACCGATC -3’

bottom strand
3'- CTAGCCAGACGGAACGGTCGGGCGAGGTAGTCTCTACACATATTCTCTGTC NNNNNNNNNNNNN GACAGAGAATATGTGTAGAGACTACCGCGCTCCCTCCTGGGATATCACTCAGCATAATTA -5’ 

to stop nonspecific amplification in shendure protocol
5’-[Phos]- CTGTCTCTTATACACATC -3’ [ddC - 3' to block ends]