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===Before starting protocols=== 1. Check if have enough reagents etc for the protocol *nextera transposomes *transposase/transposome *IVT reaction mixture *cells etc *blocking primer, RNase III, PolyA Polymerase 2. Purify GM12878 DNA from Gm12878 cells with DNeasy blood and tissue kit for cells (uses proteinase). quanititate DNA and aliquot to a standard concentration of 60 ng or a multiple of that. 3. Have to raise off MEFs with trypsin 1. suck off media 2. add 5 mL PBS/wash 3. suck off 4. 2 mL trypsin 5. put in 37C, 2 minutes 6. dilute with PBS, 10 mL 7. spin down and resuspend. 4. samples Samples: 1. 1000 cells IVT 2. 500 cells IVT 3. 100 cells IVT 4. 6 ng purified DNA IVT 5. 600 pg purified DNA IVT 6. 60 pg purified DNA IVT 7. 1000 cells nextera tagmentation 8. 500 cells nextera tagmentation 9. 100 cells nextera tagmentation 10. 6 ng purified DNA nextera tagmentation 11. 600 pg purified DNA nextera tagmentation 12. 60 pg purified DNA nextera tagmentation 13. 1000 cells MEFs IVT 14. 1000 cells MEFs nextera tagmentation 15. 1000 cells lysed without transposome complex IVT 16. pure DNA only (6 ng) IVT 17. Nuclease free H20 only IVT 18. 1000 cells lysed without transposome complex nextera tagmentation 19. pure DNA only (6 ng) nextera tagmentation 20. Nuclease free H20 only nextera tagmentation
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