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== Qubit ssDNA assay == * Sample in assay 1ul, dilution 200x {| {{table}} border =1 | align="center" style="background:#f0f0f0;"|'''Sample''' | align="center" style="background:#f0f0f0;"|'''LabID ID''' | align="center" style="background:#f0f0f0;"|'''Well IDs''' | align="center" style="background:#f0f0f0;"|'''Concentration in the Qubit''' | align="center" style="background:#f0f0f0;"|'''''' | align="center" style="background:#f0f0f0;"|'''Final conc. (ng/ul)''' | align="center" style="background:#f0f0f0;"|'''Yields in 16ul (ng)''' | align="center" style="background:#f0f0f0;"|'''LabID ID''' | align="center" style="background:#f0f0f0;"|'''Well IDs''' | align="center" style="background:#f0f0f0;"|'''Repeated samples''' |- | 1.00||Ap15-1||A1||57.00||ng/mL||11.40||182.40||Ap15-1||A1||X |- | 2.00||Ap15-2||B1||62.20||ng/mL||12.44||199.04||Ap15-2||B1||X |- | 3.00||Ap15-3||C1||81.70||ng/mL||16.34||261.44||Ap15-3||C1||X |- | 4.00||Ap15-4||D1||75.40||ng/mL||15.08||241.28||Ap15-4||D1||X |- | 5.00||Ap15-5||E1||59.60||ng/mL||11.92||190.72||Ap15-5||E1||X |- | 6.00||Ap15-6||F1||74.50||ng/mL||14.90||238.40||Ap15-6||F1||X |- | 7.00||Ap15-7||G1||76.40||ng/mL||15.28||244.48||Ap15-7||G1||X |- | 8.00||Ap15-8||H1||76.40||ng/mL||15.28||244.48||Ap15-8||H1||X |- | 9.00||Ap15-9||A2||76.10||ng/mL||15.22||243.52||Ap15-9||A2||X |- | 10.00||Ap15-10||B2||60.10||ng/mL||12.02||192.32||Ap15-10||B2||X |- | 11.00||Ap15-11||C2||56.40||ng/mL||11.28||180.48||Ap15-11||C2||X |- | 12.00||Ap15-12||D2||59.00||ng/mL||11.80||188.80||Ap15-12||D2||X |- | 13.00||Ap15-13||E2||72.50||ng/mL||14.50||232.00||Ap15-13||E2||X |- | 14.00||Ap15-14||F2||74.30||ng/mL||14.86||237.76||Ap15-14||F2||X |- | 15.00||Ap15-15||G2||58.90||ng/mL||11.78||188.48||Ap15-15||G2||X |- | 16.00||Ap15-16||H2||45.10||ng/mL||9.02||144.32||Ap15-16||H2||X |- | 17.00||Ap15-17||A3||76.40||ng/mL||15.28||244.48||Ap15-17||A3||X |- | 18.00||Ap15-18||B3||54.90||ng/mL||10.98||175.68||Ap15-18||B3||X |- | 19.00||Ap15-19||C3||78.90||ng/mL||15.78||252.48||Ap15-19||C3||X |- | 20.00||Ma15-1||D3||44.10||ng/mL||8.82||141.12||Ma15-1||D3||X |- | 21.00||Ma15-2||E3||49.80||ng/mL||9.96||159.36||Ma15-2||E3||X |- | 22.00||Ma15-3||F3||51.60||ng/mL||10.32||165.12||Ma15-3||F3||X |- | 23.00||Ma15-4||G3||58.20||ng/mL||11.64||186.24||Ma15-4||G3||X |- | 24.00||Ma15-5||H3||60.10||ng/mL||12.02||192.32||Ma15-5||H3||X |- | 25.00||Ma15-6||A4||40.60||ng/mL||8.12||129.92||Ma15-6||A4||X |- | 26.00||Ma15-7||B4||59.90||ng/mL||11.98||191.68||Ma15-7||B4||X |- | 27.00||Ma15-8||C4||54.50||ng/mL||10.90||174.40||Ma15-8||C4||X |- | 28.00||Ma15-9||D4||43.60||ng/mL||8.72||139.52||Ma15-9||D4||X |- | 29.00||Ma15-10||E4||73.10||ng/mL||14.62||233.92||Ma15-10||E4||X |- | 30.00||Ma15-11||F4||49.70||ng/mL||9.94||159.04||Ma15-11||F4||X |- | 31.00||Ma15-12||G4||36.90||ng/mL||7.38||118.08||Ma15-12||G4||X |- | 32.00||Ma15-13||H4||60.00||ng/mL||12.00||192.00||Ma15-13||H4||X |- | 33.00||Ma15-14||A5||28.00||ng/mL||5.60||89.60||Ma15-14||A5||X |- | 34.00||Ma15-15||B5||27.70||ng/mL||5.54||88.64||Ma15-15||B5||X |- | 35.00||Ma15-16||C5||53.50||ng/mL||10.70||171.20||Ma15-16||C5||X |- | 36.00||Ma15-17||D5||51.10||ng/mL||10.22||163.52||Ma15-17||D5||X |- | 37.00||Ma15-18||E5||53.60||ng/mL||10.72||171.52||Ma15-18||E5||X |- | 38.00||Ma15-19||F5||51.40||ng/mL||10.28||164.48||Ma15-19||F5||X |- | 39.00||Ma15-20||G5||48.90||ng/mL||9.78||156.48||Ma15-20||G5||X |- | 40.00||Ma15-21||H5||55.40||ng/mL||11.08||177.28||Ma15-21||H5||X |- | 1.00||H9 p43 mTeSR||SR-1||108.00||ng/mL||21.60||345.60||SR-1||A6||- |- | 2.00||H9 p43 ACTIVIN ||SR-2||64.90||ng/mL||12.98||207.68||SR-2||B6||X |- | 3.00||H9 p43 BMP4||SR-3||133.00||ng/mL||26.60||425.60||SR-3||C6||- |- | 4.00||HUV0iPS4F1 p19||SR-4||140.00||ng/mL||28.00||448.00||SR-4||D6||- |- | 5.00||HUV-hiPS4F1 p20 ACTIVIN||SR-5||95.40||ng/mL||19.08||305.28||SR-5||E6||- |- | 6.00||HUV-hiPS4F1 p20 BMP4||SR-6||135.00||ng/mL||27.00||432.00||SR-6||F6||- |- | 7.00||HUV-iPS4F3 F19||SR-7||134.00||ng/mL||26.80||428.80||SR-7||G6||- |- | 8.00||HUV-hiPS4F3 p20 ACTIVIN||SR-8||96.10||ng/mL||19.22||307.52||SR-8||H6||- |- | 9.00||HUV-hiPS4F3 p20 BMP4||SR-9||120.00||ng/mL||24.00||384.00||SR-9||A7||- |- | 10.00||aMSCs p7||SR-10||53.90||ng/mL||10.78||172.48||SR-10||B7||X |- | 11.00||MSCiPS #8 p14 (~4 ul)||SR-11||71.60||ng/mL||14.32||229.12||SR-11||C7||Can\'t repeat |- | 12.00||MSCiPS #4 p14||SR-12||94.60||ng/mL||18.92||302.72||SR-12||D7||- |- | 13.00||hNiPS2F p23||SR-13||29.60||ng/mL||5.92||94.72||SR-13||E7||X |- | 14.00||hKiPS3F-7 p24 (~15ul)||SR-14||7.13||ng/mL||1.43||22.82||SR-14||F7||X |- | 15.00||hNSC ||SR-15||70.90||ng/mL||14.18||226.88||SR-15||G7||X |- | 16.00||hFiPS4F-7 p9||SR-16||23.10||ng/mL||4.62||73.92||SR-16||H7||X |- | 17.00||HUVEC p2||SR-17||50.80||ng/mL||10.16||162.56||SR-17||A8||X |- | 18.00||hiPS AST4F-4 p9||SR-18||131.00||ng/mL||26.20||419.20||SR-18||B8|| |- | 19.00||KERAT MMTA ||SR-19||19.80||ng/mL||3.96||63.36||SR-19||C8||X |- | 20.00||KiPS4F #8||SR-20||19.00||ng/mL||3.80||60.80||SR-20||D8||X |- | 21.00||olf MSC 19.1ng/ul volume only 3-5ul||SR-21||4.60||ng/mL||0.92||14.72||SR-21||E8||can\'t repeat |- | 22.00||KiPS 14ng/ul volume only 3-5ul||SR-22||7.42||ng/mL||1.48||23.74||SR-22||F8||can\'t repeat |} * From the yields of bis-cvt gDNA, many samples have the yields lower than 300ng or 200ng which is the amount the acceptable for capture with BSPP. I checked the yields of the old samples I have processed before (SR-1 - SR-9) to see if this is the technical error of this batch. I got the total yields of SR-1 -15 pretty much the same as I got before. This suggested that there are not the batch effect, but may be the quality of gDNA. I need to repeat bis-cvt again to get enough yield for capture. However, there are some sample that has no more gDNA or has very low concentration, and I don't expected to get higher yield from those samples. * Continued on: http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-5-21
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