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== May 22nd, 2015 == * order the IDT control oligo - [[File:DD15_idt_dna_epimark_ctrl_order.png | 600px]] * contact Nature Protocol papers authors to ask about the controls - contacted Dr. Balasubramanian from the oxBS paper. ** Dr. Balasubramanian: "If you followed the protocol exactly, 5hmC should undergo very little conversion to U. Supplies of d5hmCTPs are often contaminated with some dCTP which gets incorporated much faster than d5hmCTP itself during the PCR - so this is worth checking out (ideally by LC-MS analysis). You might also wish to try the commercial oxBS kits, now provided by CEGX (http://www.cambridge-epigenetix.com/) who have optimised the formulations, workflow and controls to make them even more robust (we actually used their oxidant formulation in the Nat protocols paper). Best wishes for your experiments." * put the BSPP dual index design on wiki: fixed the sequencing primer designs from last time, http://genome-tech.ucsd.edu/LabNotes/index.php/Illumina_GA/Oligo_info#Library_Free_Multiplexing_Primers_for_Dual-Index * use H1 for TAB experiment comparing ngTet, mTet2, and Wisegene mTet1: would Dr. Bejar & Brian be able to share with us his CRISPR plasmids so we can do Tet2 and DNMT3a knockout on H1 and then differentiate towards definitive endoderm?
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