Noi/NOTES/2012-5-20: Difference between revisions

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|-
| Ma15-21||172.9||6.94||Ma15-21||H5||13.06||1200.00||130.00||150.00
| Ma15-21||172.9||6.94||Ma15-21||H5||13.06||1200.00||130.00||150.00
|}
{| {{table}} border = 1
| align="center" style="background:#f0f0f0;"|'''Lab IDs'''
| align="center" style="background:#f0f0f0;"|'''Conc. (ng/ul)'''
| align="center" style="background:#f0f0f0;"|'''Volume for 1200ng'''
| align="center" style="background:#f0f0f0;"|'''LabID ID'''
| align="center" style="background:#f0f0f0;"|'''Well IDs'''
| align="center" style="background:#f0f0f0;"|'''H2O'''
| align="center" style="background:#f0f0f0;"|'''Total amount (ng)'''
| align="center" style="background:#f0f0f0;"|'''CT conversion reagent (ul)'''
| align="center" style="background:#f0f0f0;"|'''Total volume (ul)'''
|-
| SR-1||62.8||19.11||SR-1||A6||0.89||1200.00||130.00||150.00
|-
| SR-2||90.8||13.22||SR-2||B6||6.78||1200.00||130.00||150.00
|-
| SR-3||93.7||12.81||SR-3||C6||7.19||1200.00||130.00||150.00
|-
| SR-4||98.0||12.24||SR-4||D6||7.76||1200.00||130.00||150.00
|-
| SR-5||84.8||14.15||SR-5||E6||5.85||1200.00||130.00||150.00
|-
| SR-6||78.6||15.27||SR-6||F6||4.73||1200.00||130.00||150.00
|-
| SR-7||96.9||12.38||SR-7||G6||7.62||1200.00||130.00||150.00
|-
| SR-8||91.9||13.06||SR-8||H6||6.94||1200.00||130.00||150.00
|-
| SR-9||80.6||14.89||SR-9||A7||5.11||1200.00||130.00||150.00
|-
| SR-10||184.8||6.49||SR-10||B7||13.51||1200.00||130.00||150.00
|-
| SR-11||105.4||5.00||SR-11||C7||15.00||527.00||130.00||150.00
|-
| SR-12||181.4||6.62||SR-12||D7||13.38||1200.00||130.00||150.00
|-
| SR-13||270.0||4.44||SR-13||E7||15.56||1200.00||130.00||150.00
|-
| SR-14||33.0||15.00||SR-14||F7||5.00||495.00||130.00||150.00
|-
| SR-15||67.0||17.91||SR-15||G7||2.09||1200.00||130.00||150.00
|-
| SR-16||145.6||8.24||SR-16||H7||11.76||1200.00||130.00||150.00
|-
| SR-17||245.3||4.89||SR-17||A8||15.11||1200.00||130.00||150.00
|-
| SR-18||89.9||13.35||SR-18||B8||6.65||1200.00||130.00||150.00
|-
| SR-19||159.5||7.52||SR-19||C8||12.48||1200.00||130.00||150.00
|-
| SR-20||195.7||6.13||SR-20||D8||13.87||1200.00||130.00||150.00
|-
| SR-21||19.1||5.00||SR-21||E8||15.00||95.50||130.00||150.00
|-
| SR-22||14.0||5.00||SR-22||F8||15.00||70.00||130.00||150.00
|}
|}
  '''Program'''
  '''Program'''

Revision as of 17:46, 20 May 2012

DMR 330k BSPP capture of samples from Sergio

Sample list

New gDNA extracted from the cell pellet

on: http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-5-17
No. Sample ID Lab ID Conc. (ng/ul) Volume (ul) Yields (ug)
1 HUES2 p41 Ap15-1 110.0 250 27.5
2 ASThiPS4F1 p12 Ap15-2 139.1 250 34.8
3 ASThiPS4F2 p12 Ap15-3 145.1 250 36.3
4 HUES6 p39 Control TeSR Ap15-4 295.5 250 73.9
5 HUES6 p39 ACTIVIN Ap15-5 128.1 250 32.0
6 HUES6 p39 BMP-4 Ap15-6 153.9 250 38.5
7 HUES9 p39 Control TeSR Ap15-7 183.5 250 45.9
8 HUES9 p39 ACTIVIN Ap15-8 149.3 250 37.3
9 HUES9 p39 BMP-4 Ap15-9 111.2 250 27.8
10 HUES3 p36 Control TeSR Ap15-10 153.5 250 38.4
11 HUES3 p36 ACTIVIN Ap15-11 87.5 250 21.9
12 HUES3 p36 BMP-4 Ap15-12 109.7 250 27.4
13 H1 p54 Control TeSR Ap15-13 191.3 250 47.8
14 H1 p54 ACTIVIN Ap15-14 108.7 250 27.2
15 ASThiPS4F5 p16 Control TeSR Ap15-15 134.2 250 33.6
*16 ASThiPS4F5 p16 ACTIVIN Ap15-16 50.2 500 25.1
17 ASThiPS4F4 p36 Control TeSR Ap15-17 183.0 250 45.8
18 ASThiPS4F4 p36 ACTIVIN Ap15-18 82.6 250 20.7
19 ASThiPS4F4 p36 BMP-4 Ap15-19 263.4 250 65.9
20 H1 p48 Ma15-2 215.2 200 43.0
21 H9 p47 Ma15-3 252.0 200 50.4
22 HUES3 p33 Ma15-4 226.1 200 45.2
23 HUES6 p26 Ma15-5 238.7 200 47.7
24 HUES8 p35 Ma15-6 83.4 200 16.7
25 HUES9 p36 Ma15-7 236.8 200 47.4
26 ASThiPS4F3 p24 (derived from Astrocytes) Ma15-8 175.9 200 35.2
27 ASThiPS4F4 p16 (derived from Astrocytes) Ma15-9 164.3 200 32.9
28 FiPS4F2 p32 (derived from IMR90 fibroblasts) Ma15-10 205.9 200 41.2
29 FiPS4F5 p29 (derived from IMR90 fibroblasts) Ma15-11 97.6 200 19.5
30 KiPS4FA p54 (derived from keratinocytes) Ma15-12 129.5 200 25.9
31 Huv-iPS4F6 p23 (derived from HUVECs) Ma15-13 263.1 200 52.6
32 IMR90 p6 Ma15-14 76.1 200 15.2
33 Keratinocytes p3 Ma15-15 138.7 200 27.7
34 H1 p47 Control Ma15-16 216.4 200 43.3
35 H1 p47 BMP-4 Ma15-17 137.6 200 27.5
36 ASThiPS4F5 p12 Control Ma15-18 224.6 200 44.9
37 ASThiPS4F5 p12 BMP-4 Ma15-19 111.7 200 22.3
38 Huv-iPS4F6 p23 Control Ma15-20 289.9 200 58.0
39 Huv-iPS4F6 p23 BMP-4 Ma15-21 172.9 200 34.6
40 Huv-iPS4F6 p23 ACTIVIN Ma15-1 86.7 250 21.7

Old gDNA of samples have been captured in the previous experiments

  • Note:
    • Some of gDNA concentrations were re-measured and note that some of them have conc. lower than 50ng/ul, and some of them don't have enough amount for bisulfite conversion
    • Samples KERAT MMTA and KiPS4F #8 have high conc., but very little volume. I added ~17ul H2O then re-measured conc. again
    • ***I may not do bis-cvt on the two samples, SR-21 and SR22 since the amount of gDNA was too little
No Sample IDs Lab IDs Conc. (ng/ul)
1 H9 p43 mTeSR SR-1 62.8
2 H9 p43 ACTIVIN SR-2 90.8
3 H9 p43 BMP4 SR-3 93.7
4 HUV0iPS4F1 p19 SR-4 98.0
5 HUV-hiPS4F1 p20 ACTIVIN SR-5 84.8
6 HUV-hiPS4F1 p20 BMP4 SR-6 78.6
7 HUV-iPS4F3 F19 SR-7 96.9
8 HUV-hiPS4F3 p20 ACTIVIN SR-8 91.9
9 HUV-hiPS4F3 p20 BMP4 SR-9 80.6
10 aMSCs p7 SR-10 184.8
11 MSCiPS #8 p14 (~4 ul) SR-11 105.4
12 MSCiPS #4 p14 SR-12 181.4
13 hNiPS2F p23 SR-13 270.0
14 hKiPS3F-7 p24 (~15ul) SR-14 33.0
15 hNSC SR-15 67.0
16 hFiPS4F-7 p9 SR-16 145.6
17 HUVEC p2 SR-17 245.3
18 hiPS AST4F-4 p9 SR-18 89.9
19 KERAT MMTA SR-19 159.5
20 KiPS4F #8 SR-20 195.7
21 ***olf MSC 19.1ng/ul volume only 3-5ul SR-21 19.1
22 ***KiPS 14ng/ul volume only 3-5ul SR-22 14.0

8 samples of bis-cvt gDNA from Dinh

  • The list will be filled later and need to re-measure of the conc. with ssDNA Qubit assay

Bisulfite conversion

Reagent prep
Add the following reagents to CT Conversion Reagent
  -  H2O                   9.0mL
  - M-Dissolving Buffer    500ul
  - M-Dilution Buffer      3.0mL
Mix at room temperature with frequent vortexing or shaking for 15 minutes
Add 144 ml of 100% ethanol to the 36 ml M-Wash Buffer concentrate before use
Lab IDs Conc. (ng/ul) Volume for 1200ng LabID ID Well IDs H2O Total amount (ng) CT conversion reagent (ul) Total volume (ul)
Ap15-1 110.0 10.91 Ap15-1 A1 9.09 1200.00 130.00 150.00
Ap15-2 139.1 8.63 Ap15-2 B1 11.37 1200.00 130.00 150.00
Ap15-3 145.1 8.27 Ap15-3 C1 11.73 1200.00 130.00 150.00
Ap15-4 295.5 4.06 Ap15-4 D1 15.94 1200.00 130.00 150.00
Ap15-5 128.1 9.37 Ap15-5 E1 10.63 1200.00 130.00 150.00
Ap15-6 153.9 7.80 Ap15-6 F1 12.20 1200.00 130.00 150.00
Ap15-7 183.5 6.54 Ap15-7 G1 13.46 1200.00 130.00 150.00
Ap15-8 149.3 8.04 Ap15-8 H1 11.96 1200.00 130.00 150.00
Ap15-9 111.2 10.79 Ap15-9 A2 9.21 1200.00 130.00 150.00
Ap15-10 153.5 7.82 Ap15-10 B2 12.18 1200.00 130.00 150.00
Ap15-11 87.5 13.71 Ap15-11 C2 6.29 1200.00 130.00 150.00
Ap15-12 109.7 10.94 Ap15-12 D2 9.06 1200.00 130.00 150.00
Ap15-13 191.3 6.27 Ap15-13 E2 13.73 1200.00 130.00 150.00
Ap15-14 108.7 11.04 Ap15-14 F2 8.96 1200.00 130.00 150.00
Ap15-15 134.2 8.94 Ap15-15 G2 11.06 1200.00 130.00 150.00
Ap15-16 50.2 23.90 Ap15-16 H2 -3.90 1200.00 130.00 150.00
Ap15-17 183.0 6.56 Ap15-17 A3 13.44 1200.00 130.00 150.00
Ap15-18 82.6 14.53 Ap15-18 B3 5.47 1200.00 130.00 150.00
Ap15-19 263.4 4.56 Ap15-19 C3 15.44 1200.00 130.00 150.00
Ma15-1 86.7 13.84 Ma15-1 D3 6.16 1200.00 130.00 150.00
Ma15-2 215.2 5.58 Ma15-2 E3 14.42 1200.00 130.00 150.00
Ma15-3 252.0 4.76 Ma15-3 F3 15.24 1200.00 130.00 150.00
Ma15-4 226.1 5.31 Ma15-4 G3 14.69 1200.00 130.00 150.00
Ma15-5 238.7 5.03 Ma15-5 H3 14.97 1200.00 130.00 150.00
Ma15-6 83.4 14.39 Ma15-6 A4 5.61 1200.00 130.00 150.00
Ma15-7 236.8 5.07 Ma15-7 B4 14.93 1200.00 130.00 150.00
Ma15-8 175.9 6.82 Ma15-8 C4 13.18 1200.00 130.00 150.00
Ma15-9 164.3 7.30 Ma15-9 D4 12.70 1200.00 130.00 150.00
Ma15-10 205.9 5.83 Ma15-10 E4 14.17 1200.00 130.00 150.00
Ma15-11 97.6 12.30 Ma15-11 F4 7.70 1200.00 130.00 150.00
Ma15-12 129.5 9.27 Ma15-12 G4 10.73 1200.00 130.00 150.00
Ma15-13 263.1 4.56 Ma15-13 H4 15.44 1200.00 130.00 150.00
Ma15-14 76.1 15.77 Ma15-14 A5 4.23 1200.00 130.00 150.00
Ma15-15 138.7 8.65 Ma15-15 B5 11.35 1200.00 130.00 150.00
Ma15-16 216.4 5.55 Ma15-16 C5 14.45 1200.00 130.00 150.00
Ma15-17 137.6 8.72 Ma15-17 D5 11.28 1200.00 130.00 150.00
Ma15-18 224.6 5.34 Ma15-18 E5 14.66 1200.00 130.00 150.00
Ma15-19 111.7 10.74 Ma15-19 F5 9.26 1200.00 130.00 150.00
Ma15-20 289.9 4.14 Ma15-20 G5 15.86 1200.00 130.00 150.00
Ma15-21 172.9 6.94 Ma15-21 H5 13.06 1200.00 130.00 150.00
Lab IDs Conc. (ng/ul) Volume for 1200ng LabID ID Well IDs H2O Total amount (ng) CT conversion reagent (ul) Total volume (ul)
SR-1 62.8 19.11 SR-1 A6 0.89 1200.00 130.00 150.00
SR-2 90.8 13.22 SR-2 B6 6.78 1200.00 130.00 150.00
SR-3 93.7 12.81 SR-3 C6 7.19 1200.00 130.00 150.00
SR-4 98.0 12.24 SR-4 D6 7.76 1200.00 130.00 150.00
SR-5 84.8 14.15 SR-5 E6 5.85 1200.00 130.00 150.00
SR-6 78.6 15.27 SR-6 F6 4.73 1200.00 130.00 150.00
SR-7 96.9 12.38 SR-7 G6 7.62 1200.00 130.00 150.00
SR-8 91.9 13.06 SR-8 H6 6.94 1200.00 130.00 150.00
SR-9 80.6 14.89 SR-9 A7 5.11 1200.00 130.00 150.00
SR-10 184.8 6.49 SR-10 B7 13.51 1200.00 130.00 150.00
SR-11 105.4 5.00 SR-11 C7 15.00 527.00 130.00 150.00
SR-12 181.4 6.62 SR-12 D7 13.38 1200.00 130.00 150.00
SR-13 270.0 4.44 SR-13 E7 15.56 1200.00 130.00 150.00
SR-14 33.0 15.00 SR-14 F7 5.00 495.00 130.00 150.00
SR-15 67.0 17.91 SR-15 G7 2.09 1200.00 130.00 150.00
SR-16 145.6 8.24 SR-16 H7 11.76 1200.00 130.00 150.00
SR-17 245.3 4.89 SR-17 A8 15.11 1200.00 130.00 150.00
SR-18 89.9 13.35 SR-18 B8 6.65 1200.00 130.00 150.00
SR-19 159.5 7.52 SR-19 C8 12.48 1200.00 130.00 150.00
SR-20 195.7 6.13 SR-20 D8 13.87 1200.00 130.00 150.00
SR-21 19.1 5.00 SR-21 E8 15.00 95.50 130.00 150.00
SR-22 14.0 5.00 SR-22 F8 15.00 70.00 130.00 150.00
Program
   98°C for 10 minutes
   64°C for 2.5 hours
   4°C storage up to 20 hours
Measure conc. with ssDNA Qubit assay (used 1ul of bis-cvt gDNA)