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===09/03/2013=== Chris and I will be taking responsibility for MIDAS from here on. Started overnight MDA with Jeff and Chris observing. Loaded 8 arrays with PGP-1 chromosomes. * 2 conditions: ** 4 arrays with protease (trypsin) ** 4 arrays, [[Arichard:Protocols/MDA on microarray 2013 09 05|standard protocol]] except no freeze thaw Did not image prior to ALS because chromosomes were expected in every well due to high concentration. * Modification to standard protocol for protease treatment: ** Load 3 ul chromosomes. Add coverslip, let sit 10 min @ RT ** Load 3 ul 0.25% trypsin (1X) into protease condition arrays. Cover and let sit 5 min @ RT ** Load 4.5 ul ALS into all arrays. Cover and incubate 10 min @ 40 degC in thermocycler with plate adapter ** Load 4.5 ul NS into all arrays. *** Protocol based on Quake haplotype paper (Fan et al. 2010 NBT) * Protease condition master mix(per rxn/array): ** 15 ul template ** 1 ul 1 mM N6* ** 1 ul 25 mM dNTP (Epicentre) ** 2.3 ul 10X Phi29 buffer ** 0.1 ul 50X SYBR Green ** 1 ul 23X protease inhibitor (cOmplete) ** 1 ul H2O *** Total = 11.2 ul * No protease condition received 11.2 ul [[Arichard:Protocols/MDA on microarray 2013 09 05|standard MDA master mix]]
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