Noi/NOTES/2012-8-1: Difference between revisions
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= WGBS sequencing library preparation using KAPA protocol (Eppendorf) and epMotion (Repeat!) = | = WGBS sequencing library preparation using KAPA protocol (Eppendorf) and epMotion (Repeat!) = | ||
* The step of library sequencing prep will be filled soon. | * The step of library sequencing prep will be filled soon. | ||
== Amplification == | |||
* Test qPCR | |||
* Loaded 2.5 ul of bis-cvt DNA and 2.5ul of amplified amplicons | |||
[[File:ZhangLab_2 2012-08-02 11hr 31min-HAPMAP-bis-test.jpg| 400px]] <br> | [[File:ZhangLab_2 2012-08-02 11hr 31min-HAPMAP-bis-test.jpg| 400px]] <br> | ||
{| {{table}} | |||
| width="80pt" align="center" style="background:#f0f0f0;"|'''Sample ID''' | |||
| width="70pt" align="center" style="background:#f0f0f0;"|'''Labeling''' | |||
| align="center" style="background:#f0f0f0;"|'''Indx''' | |||
|- | |||
| WGBS.GM12891||#1||PCR_R.N2Indx1 | |||
|- | |||
| WGBS.GM12892||#2||PCR_R.N2Indx2 | |||
|- | |||
| WGBS.GM10861||#3||PCR_R.N2Indx3 | |||
|- | |||
| WGBS.GM11994||#4||PCR_R.N2Indx4 | |||
|- | |||
| WGBS.GM11995||#5||PCR_R.N2Indx5 | |||
|- | |||
| WGBS.GM18506||#6||PCR_R.N2Indx6 | |||
|- | |||
| WGBS.GM18507||#7||PCR_R.N2Indx7 | |||
|- | |||
| WGBS.GM18505||#8||PCR_R.N2Indx8 | |||
|} | |||
* Purified sequencing libraries with 0.8x vol AMPure bead with epMotion (3 strips), eluted with 25ul EB for each well -> total volume at the end ~70ul | * Purified sequencing libraries with 0.8x vol AMPure bead with epMotion (3 strips), eluted with 25ul EB for each well -> total volume at the end ~70ul | ||
[[File:ZhangLab_2 2012-08-02 16hr 05min_bead-HAPMAP-WGBS.jpg| 400px]] <br> | [[File:ZhangLab_2 2012-08-02 16hr 05min_bead-HAPMAP-WGBS.jpg| 400px]] <br> | ||
== PAGE quantification of 400-600bp fragments == | == PAGE quantification of 400-600bp fragments == | ||
* Perform PAGE size-selection of the size range 400-600bp for a small scale sequencing | * Perform PAGE size-selection of the size range 400-600bp for a small scale sequencing. Then pooled 60ng of each library and performed PAGE size-selection. | ||
[[File:ZhangLab_2 2012-08-02 16hr 05min_bead-HAPMAP-WGBS-400-600bp_PQ.jpg| 400px]]<br> | [[File:ZhangLab_2 2012-08-02 16hr 05min_bead-HAPMAP-WGBS-400-600bp_PQ.jpg| 400px]]<br> | ||
{| {{table}} | {| {{table}} border = 1 | ||
| width = "60pt" align="center" style="background:#f0f0f0;"|'''Lab IDs''' | | width="60pt" align="center" style="background:#f0f0f0;"|'''Lab IDs''' | ||
| align="center" style="background:#f0f0f0;"|'''Final conc. | | align="center" style="background:#f0f0f0;"|'''Final conc. | ||
of 400-600bp (ng/ul)''' | |||
| align="center" style="background:#f0f0f0;"|'''Total yields in 70ul (ng)''' | | align="center" style="background:#f0f0f0;"|'''Total yields in 70ul (ng)''' | ||
| align="center" style="background:#f0f0f0;"|'''Volume for 60ng (ul)''' | |||
|- | |- | ||
| #1||13.50||945.28 | | #1||13.50||945.28||4.44 | ||
|- | |- | ||
| #2||9.66||675.94 | | #2||9.66||675.94||6.21 | ||
|- | |- | ||
| #3||11.24||786.94 | | #3||11.24||786.94||5.34 | ||
|- | |- | ||
| #4||13.64||955.09 | | #4||13.64||955.09||4.40 | ||
|- | |- | ||
| #5||13.85||969.55 | | #5||13.85||969.55||4.33 | ||
|- | |- | ||
| #6||8.95||626.85 | | #6||8.95||626.85||6.70 | ||
|- | |- | ||
| #7||12.40||867.78 | | #7||12.40||867.78||4.84 | ||
|- | |- | ||
| #8||11.29||790.44 | | #8||11.29||790.44||5.31 | ||
|} | |} |
Revision as of 01:06, 3 August 2012
WGBS sequencing library preparation using KAPA protocol (Eppendorf) and epMotion (Repeat!)
- The step of library sequencing prep will be filled soon.
Amplification
- Test qPCR
- Loaded 2.5 ul of bis-cvt DNA and 2.5ul of amplified amplicons
File:ZhangLab 2 2012-08-02 11hr 31min-HAPMAP-bis-test.jpg
Sample ID | Labeling | Indx |
WGBS.GM12891 | #1 | PCR_R.N2Indx1 |
WGBS.GM12892 | #2 | PCR_R.N2Indx2 |
WGBS.GM10861 | #3 | PCR_R.N2Indx3 |
WGBS.GM11994 | #4 | PCR_R.N2Indx4 |
WGBS.GM11995 | #5 | PCR_R.N2Indx5 |
WGBS.GM18506 | #6 | PCR_R.N2Indx6 |
WGBS.GM18507 | #7 | PCR_R.N2Indx7 |
WGBS.GM18505 | #8 | PCR_R.N2Indx8 |
- Purified sequencing libraries with 0.8x vol AMPure bead with epMotion (3 strips), eluted with 25ul EB for each well -> total volume at the end ~70ul
File:ZhangLab 2 2012-08-02 16hr 05min bead-HAPMAP-WGBS.jpg
PAGE quantification of 400-600bp fragments
- Perform PAGE size-selection of the size range 400-600bp for a small scale sequencing. Then pooled 60ng of each library and performed PAGE size-selection.
File:ZhangLab 2 2012-08-02 16hr 05min bead-HAPMAP-WGBS-400-600bp PQ.jpg
Lab IDs | Final conc.
of 400-600bp (ng/ul) |
Total yields in 70ul (ng) | Volume for 60ng (ul) |
#1 | 13.50 | 945.28 | 4.44 |
#2 | 9.66 | 675.94 | 6.21 |
#3 | 11.24 | 786.94 | 5.34 |
#4 | 13.64 | 955.09 | 4.40 |
#5 | 13.85 | 969.55 | 4.33 |
#6 | 8.95 | 626.85 | 6.70 |
#7 | 12.40 | 867.78 | 4.84 |
#8 | 11.29 | 790.44 | 5.31 |