Dinh 2011/NOTES/2011-8-31
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Priorities[edit]
1) Nature method paper * (<6days) rebuttal - google doc - address issues - disclose and highlight probes design * demonstrate that probes will work on LC sciences oligos - $1100, 4K, 100 mer will take 2 weeks - (<6days)Target selections: epiMemory, epiMutation sets, +immunogenicity genes - Immunogenicity - Yang Xu paper: Hormad1, Zg16 A. Hormad1 - chr1:148,937,166-148,959,976 (~22kbp) DNA sequence [1] B. Zg16 - chr16:29,697,062-29,700,470 (~3kbp) DNA sequence [2] - Cross check with Ecker's cg_dmrs in ALL iPSCs versus ESCs list: File:Nature097980-s2-cg dmr alliPSCs.csv File:PGP1iPS memoryXList highPriority.txt - 41 File:PGP1iPS mutationXList highPriority.txt - 10 - Cross check with Ecker's cg_dmrs in any iPSCs versus ESCs list: File:Nature09798-s2-cg dmr.csv C. File:PGP1iPS memoryXList.txt - (include 41 from above) 236 (~16% of memory sites) D. File:PGP1iPS mutationXList.txt - (include 10 from above) 101 (~11% of memory sites) - All memory and mutation sites in PGP1iPS File:PGP1iPS memory methylMatrix.txt - 1476 sites File:PGP1iPS mutation methylMatrix.txt - 904 sites - how far does each spread? 1-6.4 kbp (ranges of cg_dmrs in files above) *Uniquely barcoded probes - (<10days)orig probes -> inverted probes + barcode -> bc probes -> prep + sanger validation
*Uniquely barcoded circles - (<7-10days) Uracil F primer-> 2 cycles PCR -> control elongation time and temperature * add limited amount of primers to improve ease of digestion. - USER digestion - Add short primer - continue for several cycles - clonal sequencing - 10 clones *2x2 Protocol test Zymo versus Imprint (perform bisulfite conversion using same DNA) Circles amplification with and without USER digestion
* Side project: Peak calling pipeline for 5cC enrichment analysis.
2) N37 10 tissues - data analysis
3) UPenn -> PCA, and mQTL (leave running for 2 weeks)
4) Episomal reprogramming 5) Sergio's samples
6) HIV