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

From ZhangLabWiki
Jump to navigation Jump to search
>Noi
(Created page with "* http://genome-tech.ucsd.edu/LabNotes/index.php/noi:DMR220k_LabNotes '''Link to calendar''' = DMR 330k BSPP capture of samples from Sergio = == Sample list == == New gDNA...")
 
>Noi
No edit summary
Line 149: Line 149:
== 8 samples of bis-cvt gDNA from Dinh ==
== 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
* 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
  - 
{| {{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)'''
|-
| 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
|}

Revision as of 17:28, 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
 -  


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