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= Bisulfite conversion = {| {{table}} border = 1 | align="center" style="background:#f0f0f0;"|'''Sample ID''' | align="center" style="background:#f0f0f0;"|'''concentration (ng/ul)''' | align="center" style="background:#f0f0f0;"|'''New code''' | align="center" style="background:#f0f0f0;"|'''volume for 1500ng (ul)''' | align="center" style="background:#f0f0f0;"|'''H20 (ul)''' | align="center" style="background:#f0f0f0;"|'''Total amount for bis-cvt (ng)''' | align="center" style="background:#f0f0f0;"|'''CT conversion reagent (ul)''' | align="center" style="background:#f0f0f0;"|'''Total volume (ul)''' |- | Scr-1||117.10||T1||12.81||7.19||1500.00||130.00||150.00 |- | Sh3513-1||116.50||T2||12.88||7.12||1500.00||130.00||150.00 |- | Sh1-1||80.30||T3||18.68||1.32||1500.00||130.00||150.00 |- | Scr-2||235.00||T4||6.38||13.62||1500.00||130.00||150.00 |- | Sh3513-2||313.00||T5||4.79||15.21||1500.00||130.00||150.00 |- | Sh1-2||142.00||T6||10.56||9.44||1500.00||130.00||150.00 |- | Mock||117.00||T7||12.82||7.18||1500.00||130.00||150.00 |- | TET2-35#||113.00||T8||13.27||6.73||1500.00||130.00||150.00 |- | TET2-75#||138.00||T9||10.87||9.13||1500.00||130.00||150.00 |- | HMEC-Scr||215.00||T10||6.98||13.02||1500.00||130.00||150.00 |- | HMEC-Sh3513||246.00||T11||6.10||13.90||1500.00||130.00||150.00 |- | HMEC-Sh1||51.30||T12||20.00||0.00||1026.00||130.00||150.00 |- | PGP1F||250.00||S13||6.00||14.00||1500.00||130.00||150.00 |- | PGP1 CD1 iPS P16||31.40||S14||20.00||0.00||628.00||130.00||150.00 |- | hHCT116||40.90||S16||20.00||0.00||818.00||130.00||150.00 |- | hHCT116 DKO||250.00||S17||6.00||14.00||1500.00||130.00||150.00 |- | MSCs P7||184.80||S18||8.12||11.88||1500.00||130.00||150.00 |- | MSCiPS #4 P14||181.40||S19||8.27||11.73||1500.00||130.00||150.00 |- | MSCiPS #8 P14||105.40||S20||14.23||5.77||1500.00||130.00||150.00 |- | H1 P47||54.60||S21||20.00||0.00||1092.00||130.00||150.00 |- | H9 P45||24.50||S22||20.00||0.00||490.00||130.00||150.00 |- | cAWS1||130.00||S23||11.54||8.46||1500.00||130.00||150.00 |}<br> * Note: cAWS1, and PGP1 CD1 iPS did 4bis-cvt reactions === Qubit ss-DNA assay === {| {{table}} border = 1 | align="center" style="background:#f0f0f0;"|'''sample ID''' | align="center" style="background:#f0f0f0;"|'''Sample code''' | align="center" style="background:#f0f0f0;"|'''Conc. In Qubit (ng/mL)''' | align="center" style="background:#f0f0f0;"|'''Final conc. (ng/ul)''' | align="center" style="background:#f0f0f0;"|'''Volume (ul)''' | align="center" style="background:#f0f0f0;"|'''Yields (ng)''' |- | Scr-1||T1||366.00||73.20||30.00||2196.00 |- | Sh3513-1||T2||369.00||73.80||30.00||2214.00 |- | Sh1-1||T3||233.00||46.60||30.00||1398.00 |- | Scr-2||T4||102.00||20.40||30.00||612.00 |- | Sh3513-2||T5||116.00||23.20||30.00||696.00 |- | Sh1-2||T6||164.00||32.80||30.00||984.00 |- | Mock||T7||282.00||56.40||30.00||1692.00 |- | TET2-35#||T8||212.00||42.40||30.00||1272.00 |- | TET2-75#||T9||227.00||45.40||30.00||1362.00 |- | HMEC-Scr||T10||147.00||29.40||30.00||882.00 |- | HMEC-Sh3513||T11||140.00||28.00||30.00||840.00 |- | HMEC-Sh1||T12||122.00||24.40||30.00||732.00 |- | PGP1F||S13||151.00||30.20||15.00||453.00 |- | PGP1 CD1 iPS P16||S14||103.00||20.60||60.00||1236.00 |- | hHCT116||S16||122.00||24.40||30.00||732.00 |- | hHCT116 DKO||S17||302.00||60.40||30.00||1812.00 |- | MSCs P7||S18||73.00||14.60||30.00||438.00 |- | MSCiPS #4 P14||S19||164.00||32.80||30.00||984.00 |- | MSCiPS #8 P14||S20||226.00||45.20||30.00||1356.00 |- | H1 P47||S21||181.00||36.20||30.00||1086.00 |- | H9 P45||S22||60.60||12.12||30.00||363.60 |- | cAWS1||S23||60.50||12.10||60.00||726.00 |}<br> * Dr. Zhang used to suggested to put more bis-cvt gDNA (about 400ng) in capture reaction, but use the same amount of probe * To be consistent, Sergio's samples were captured only with DMR220k probes * I used 15ul of elution buffer in each bis-cvt reaction, so the samples were a little bit diluted. To put 400ng of bis-cvt gDNA in captured reaction, the total volume was larger than usual (approx. 20-25ul).
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