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