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===Before starting protocols=== 1. Check if have enough reagents etc for the protocol *lysis buffer *nextera transposomes *transposase/transposome *IVT reaction mixture *cells etc *blocking primer, RNase III, PolyA Polymerase, ATP, taq polymerase, other primers 2. Purify GM12878 DNA from GM12878 cells with DNeasy blood and tissue kit for cells (USE PROTEINASE K (invitrogen) AND protease (qiagen) AND RNAase A). quanititate DNA with nanodrop. GM12878 DNA purification method used (followed DNeasy kit protocol for washes etc): a. pellet cells b. resuspend in: 1. 100 ul PBS 2. 10 uL proteinase K 3. 3 uL 5 AU Qiagen protease 4. 4 uL A797A promega RNase solution (RNase A) c. add 200 uL buffer AL, incuabate at 56C for 10 minutes d. step 3 in DNeasy kit protocol until finish 3. samples this time: Samples: 1. 1000 cells IVT 2. 500 cells IVT 3. 100 cells IVT 4. 6 ng purified DNA IVT 5. 3 ng purified DNA IVT 6. 600 pg purified DNA IVT 17. 1000 cells lysed without transposome complex IVT 18. pure DNA only (6 ng) IVT 19. Nuclease free H20 only IVT 23. 1000 cells IVT (double [NT] for IVT)
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