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>Noi (Created page with "= MONOD V1N3 BSPP capture (repeat sensitivity test) = '''Link to calendar: http://genome-tech.ucsd.edu/LabNotes/index.php/noi:DMR220k_LabNotes#2014''' * I repeated MONOD V...") |
>Noi |
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= MONOD V1N3 BSPP capture (repeat sensitivity test) = | = MONOD V1N3 BSPP capture (repeat sensitivity test) = | ||
'''Link to calendar: [[http://genome-tech.ucsd.edu/LabNotes/index.php/noi:DMR220k_LabNotes#2014]]''' | '''Link to calendar: [[http://genome-tech.ucsd.edu/LabNotes/index.php/noi:DMR220k_LabNotes#2014]]''' | ||
* I repeated MONOD V1N3 capture experiment on 3014-05-29. | * I repeated MONOD V1N3 capture experiment on 3014-05-29: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-5-29]] | ||
* I reduced capture volume to 10ul. | * I reduced capture volume to 10ul. | ||
* I reduced incubation time after adding SLN mix between 4-6h since I think that 20h is not necessary for polymerization and may cause more back ground if DNA template level is too low. | * I reduced incubation time after adding SLN mix between 4-6h since I think that 20h is not necessary for polymerization and may cause more back ground if DNA template level is too low. | ||
* I will add experimental procedures later | * I will add experimental procedures later | ||
== Bisulfite conversion == | |||
{| {{table}} border = 1 | |||
| align="center" style="background:#f0f0f0;"|'''Mix''' | |||
| align="center" style="background:#f0f0f0;"|'''82.1ng/ul JK DNA''' | |||
| align="center" style="background:#f0f0f0;"|'''H2O''' | |||
| align="center" style="background:#f0f0f0;"|'''Aliquot''' | |||
|- | |||
| 25ng||1.28||82.72||20.00 | |||
|- | |||
| 50ng||2.56||81.44||20.00 | |||
|- | |||
| 100ng||5.12||78.88||20.00 | |||
|- | |||
| 200ng||10.23||73.77||20.00 | |||
|} | |||
{| {{table}} border = 1 | |||
| align="center" style="background:#f0f0f0;"|'''Sample''' | |||
| align="center" style="background:#f0f0f0;"|'''Conc. (ng/ul)''' | |||
| align="center" style="background:#f0f0f0;"|'''Amount (ng)''' | |||
| align="center" style="background:#f0f0f0;"|'''Volume (ul)''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''H2O (ul)''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''Lightnig Conversion reagent''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''Total''' | |||
|- | |||
| JK-1||82.1||25||0.30||19.70||130||150.00 | |||
|- | |||
| JK-2||82.1||25||0.30||19.70||130||150.00 | |||
|- | |||
| JK-3||82.1||25||0.30||19.70||130||150.00 | |||
|- | |||
| JK-4||82.1||25||0.30||19.70||130||150.00 | |||
|- | |||
| JK-5||82.1||50||0.61||19.39||130||150.00 | |||
|- | |||
| JK-6||82.1||50||0.61||19.39||130||150.00 | |||
|- | |||
| JK-7||82.1||50||0.61||19.39||130||150.00 | |||
|- | |||
| JK-8||82.1||50||0.61||19.39||130||150.00 | |||
|- | |||
| JK-9||82.1||100||1.22||18.78||130||150.00 | |||
|- | |||
| JK-10||82.1||100||1.22||18.78||130||150.00 | |||
|- | |||
| JK-11||82.1||100||1.22||18.78||130||150.00 | |||
|- | |||
| JK-12||82.1||100||1.22||18.78||130||150.00 | |||
|- | |||
| JK-13||82.1||200||2.44||17.56||130||150.00 | |||
|- | |||
| JK-14||82.1||200||2.44||17.56||130||150.00 | |||
|- | |||
| JK-15||82.1||200||2.44||17.56||130||150.00 | |||
|- | |||
| JK-16||82.1||200||2.44||17.56||130||150.00 | |||
|} | |||
* Elute with 10ul Elution buffer | |||
* Use 1ul for Qubit ssDNA assay | |||
==== Qubit ssDNA assay results ==== | |||
* I did many bisulfite conversion reactions to compare the recovery rate with different inputs | |||
{| {{table}} class = wikitable | |||
| align="center" style="width:120px;background:#f0f0f0;"|'''Sample''' | |||
| align="center" style="width:100px;background:#f0f0f0;"|'''Conc. in the Qubit''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''Unit''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''uL used''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''Dilution''' | |||
| align="center" style="width:100px;background:#f0f0f0;"|'''Sample conc. (ng/ul)''' | |||
| align="center" style="width:100px;background:#f0f0f0;"|'''Yield in 9ul (ng)''' | |||
| align="center" style="width:100px;background:#f0f0f0;"|'''Input DNA (ng)''' | |||
| align="center" style="width:100px;background:#f0f0f0;"|'''% Recovery''' | |||
|- | |||
| JK-1||3.8||ng/mL||1||200||0.760||6.84||bgcolor="lightcyan"|25||bgcolor="lightcyan"|27.36 | |||
|- | |||
| JK-2||4.9||ng/mL||1||200||0.980||8.82||bgcolor="lightcyan"|25||bgcolor="lightcyan"|35.28 | |||
|- | |||
| JK-3||2.5||ng/mL||1||200||0.500||4.50||bgcolor="lightcyan"|25||bgcolor="lightcyan"|18.00 | |||
|- | |||
| JK-4||5.11||ng/mL||1||200||1.022||9.20||bgcolor="lightcyan"|25||bgcolor="lightcyan"|36.79 | |||
|- | |||
| JK-5||10.8||ng/mL||1||200||2.160||19.44||bgcolor="PaleTurquoise"|50||bgcolor="PaleTurquoise"|38.88 | |||
|- | |||
| JK-6||9.06||ng/mL||1||200||1.812||16.31||bgcolor="PaleTurquoise"|50||bgcolor="PaleTurquoise"|32.62 | |||
|- | |||
| JK-7||12.3||ng/mL||1||200||2.460||22.14||bgcolor="PaleTurquoise"|50||bgcolor="PaleTurquoise"|44.28 | |||
|- | |||
| JK-8||11.2||ng/mL||1||200||2.240||20.16||bgcolor="PaleTurquoise"|50||bgcolor="PaleTurquoise"|40.32 | |||
|- | |||
| JK-9||25||ng/mL||1||200||5.000||45.00||bgcolor="aqua"|100||bgcolor="aqua"|45.00 | |||
|- | |||
| JK-10||26.7||ng/mL||1||200||5.340||48.06||bgcolor="aqua"|100||bgcolor="aqua"|48.06 | |||
|- | |||
| JK-11||28.4||ng/mL||1||200||5.680||51.12||bgcolor="aqua"|100||bgcolor="aqua"|51.12 | |||
|- | |||
| JK-12||24.3||ng/mL||1||200||4.860||43.74||bgcolor="aqua"|100||bgcolor="aqua"|43.74 | |||
|- | |||
| JK-13||90.1||ng/mL||1||200||18.020||162.18||bgcolor="DeepSkyBlue"|200||bgcolor="DeepSkyBlue"|81.09 | |||
|- | |||
| JK-14||89||ng/mL||1||200||17.800||160.20||bgcolor="DeepSkyBlue"|200||bgcolor="DeepSkyBlue"|80.10 | |||
|- | |||
| JK-15||79.7||ng/mL||1||200||15.940||143.46||bgcolor="DeepSkyBlue"|200||bgcolor="DeepSkyBlue"|71.73 | |||
|- | |||
| JK-16||85.4||ng/mL||1||200||17.080||153.72||bgcolor="DeepSkyBlue"|200||bgcolor="DeepSkyBlue"|76.86 | |||
|} | |||
== BSPP capture set up == | |||
{| {{table}} border = 1 | |||
| align="center" style="width:180px;background:#f0f0f0;"|'''strip 1''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''5:500''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''5:500''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''10:500''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''10:500''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''25:500''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''25:500''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''50:500''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''50:500''' | |||
|- | |||
| BIS-DNA required (ng)||5||5||10||10||25||25||50||50 | |||
|- | |||
| JK #||JK-1||JK-2||JK-5||JK-6||JK-9||JK-10||JK-13||JK-14 | |||
|- | |||
| Conc.||0.760||0.980||2.160||1.812||5.000||5.340||18.020||17.800 | |||
|- | |||
| Volume (ul)||6.58||5.10||4.63||5.52||5.00||4.68||2.77||2.81 | |||
|- | |||
| H2O (ul)||0.27||1.75||2.07||1.18||1.25||1.57||2.72||2.69 | |||
|- | |||
| V1N3 amount (ng)||0.11||0.11||0.22||0.22||0.55||0.55||1.10||1.10 | |||
|- | |||
| V1N3 conc. (ng/ul)||0.73||0.73||0.73||0.73||0.73||0.73||0.73||0.73 | |||
|- | |||
| V1N3 volume (ul)||0.15||0.15||0.30||0.30||0.75||0.75||1.50||1.50 | |||
|- | |||
| 10X Ampligase Buffer||1.00||1.00||1.00||1.00||1.00||1.00||1.00||1.00 | |||
|- | |||
| H2O in Mix||2.00||2.00||2.00||2.00||2.00||2.00||2.00||2.00 | |||
|- | |||
| Total||10.00||10.00||10.00||10.00||10.00||10.00||10.00||10.00 | |||
|} | |||
<br> | |||
{| {{table}} border = 1 | |||
| align="center" style="width:180px;background:#f0f0f0;"|'''strip 2''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''5:1000''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''5:1000''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''10:1000''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''10:1000''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''25:1000''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''25:1000''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''50:1000''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''50:1000''' | |||
|- | |||
| BIS-DNA required (ng)||5||5||10||10||25||25||50||50 | |||
|- | |||
| JK #||JK-4||JK-5||JK-7||JK-8||JK-11||JK-12||JK-15||JK-16 | |||
|- | |||
| Conc.||1.022||2.160||2.460||2.240||5.680||4.860||15.940||17.080 | |||
|- | |||
| Volume (ul)||4.89||2.31||4.07||4.46||4.40||5.14||3.14||2.93 | |||
|- | |||
| H2O (ul)||1.81||4.38||2.33||1.93||1.09||0.35||0.85||1.06 | |||
|- | |||
| V1N3 amount (ng)||0.22||0.22||0.44||0.44||1.10||1.10||2.20||2.20 | |||
|- | |||
| V1N3 conc. (ng/ul)||0.73||0.73||0.73||0.73||0.73||0.73||0.73||0.73 | |||
|- | |||
| V1N3 volume (ul)||0.30||0.30||0.60||0.60||1.50||1.50||3.01||3.01 | |||
|- | |||
| 10X Ampligase Buffer||1.00||1.00||1.00||1.00||1.00||1.00||1.00||1.00 | |||
|- | |||
| H2O in Mix||2.00||2.00||2.00||2.00||2.00||2.00||2.00||2.00 | |||
|- | |||
| Total||10.00||10.00||10.00||10.00||10.00||10.00||10.00||10.00 | |||
|} | |||
<br> | |||
{| {{table}} border = 1 | |||
| align="center" style="width:140px;background:#f0f0f0;"|'''strip 3''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''NTC:500''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''NTC:1000''' | |||
|- | |||
| BIS-DNA required (ng)||0||0 | |||
|- | |||
| JK #||0||0 | |||
|- | |||
| Conc.||0||0 | |||
|- | |||
| Volume (ul)||0.00||0.00 | |||
|- | |||
| H2O (ul)||5.50||3.99 | |||
|- | |||
| V1N3 amount (ng)||1.10||2.20 | |||
|- | |||
| V1N3 conc. (ng/ul)||0.73||0.73 | |||
|- | |||
| V1N3 volume (ul)||1.50||3.01 | |||
|- | |||
| 10X Ampligase Buffer||1.00||1.00 | |||
|- | |||
| H2O in Mix||2.00||2.00 | |||
|- | |||
| Total||10.00||10.00 | |||
|} | |||
<u>'''V1N3 & Ampligase Buffer mix</u> | |||
{| {{table}} | |||
| align="center" style="width:140px;background:#f0f0f0;"|'''Mix 0.11''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''1x''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''4x''' | |||
|- | |||
| Diluted V1N3||0.15||0.60 | |||
|- | |||
| 10X Ampligase Buffer||1.00||4.00 | |||
|- | |||
| H2O||2.00||8.00 | |||
|- | |||
| Sum||3.15|| | |||
|} | |||
{| {{table}} | |||
| align="center" style="width:140px;background:#f0f0f0;"|'''Mix 0.22''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''1x''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''6x''' | |||
|- | |||
| Diluted V1N3||0.30||1.80 | |||
|- | |||
| 10X Ampligase Buffer||1.00||6.00 | |||
|- | |||
| H2O||2.00||12.00 | |||
|- | |||
| Sum||3.30|| | |||
|} | |||
{| {{table}} | |||
| align="center" style="width:140px;background:#f0f0f0;"|'''Mix 0.44''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''1x''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''4x''' | |||
|- | |||
| Diluted V1N3||0.60||2.40 | |||
|- | |||
| 10X Ampligase Buffer||1.00||4.00 | |||
|- | |||
| H2O||2.00||8.00 | |||
|- | |||
| Sum||3.60|| | |||
|} | |||
{| {{table}} | |||
| align="center" style="width:140px;background:#f0f0f0;"|'''Mix 0.55''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''1x''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''4x''' | |||
|- | |||
| Diluted V1N3||0.75||3.00 | |||
|- | |||
| 10X Ampligase Buffer||1.00||4.00 | |||
|- | |||
| H2O||2.00||8.00 | |||
|- | |||
| Sum||3.75|| | |||
|} | |||
{| {{table}} | |||
| align="center" style="width:140px;background:#f0f0f0;"|'''Mix 1.1''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''1x''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''6x''' | |||
|- | |||
| Diluted V1N3||1.50||9.00 | |||
|- | |||
| 10X Ampligase Buffer||1.00||6.00 | |||
|- | |||
| H2O||2.00||12.00 | |||
|- | |||
| Sum||4.50|| | |||
|} | |||
{| {{table}} | |||
| align="center" style="width:140px;background:#f0f0f0;"|'''Mix 2.2''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''1x''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''4x''' | |||
|- | |||
| Diluted V1N3||3.01||12.04 | |||
|- | |||
| 10X Ampligase Buffer||1.00||4.00 | |||
|- | |||
| H2O||2.00||8.00 | |||
|- | |||
| Sum||6.01|| | |||
|} | |||
'''Program''' | |||
-> 95c 30sec -> cool down to 55C at 0.02C/sec -> 55C 20h | |||
-> add 1ul SLN mix (2U/ul Hemo Klentaql fragment; 0.5U/ul AmpLigase; 100uM dNTP) | |||
-> 55C 4:40h-> 94C 2min -> add 1.5ul Exo I/III mix (1ul of 20U/ul ExoI & 0.5ul of 200U/ul of ExoIII)-> 37C 2h -> 94C 2min -> 4C hold.''' | |||
== Amplification == | |||
* I used 10ul of captured DNA in total 75ul PCR reaction. | |||
:{| {{table}} | |||
| align="center" style="background:#f0f0f0;"|'''Components''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''1x rxn''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''20 rxn mix''' | |||
|- | |||
| Captured template||10.00||0.00 | |||
|- | |||
| 10uM AmpF6.4Sol||1.50||30.00 | |||
|- | |||
| 10uM AmpR6.3.IndX (X=57-72)||1.50||0.00 | |||
|- | |||
| 2X KAPA SYBR MM||37.50||750.00 | |||
|- | |||
| H2O||24.50||490.00 | |||
|- | |||
| Total||75.00|| | |||
|} | |||
:- Aliquot 63.5ul + 1.5ul AmpR6.3 IndX + 10ul template | |||
:- Set cycle number maximum at 27X | |||
'''Program (Eppendorf Realplex)''' | |||
98C 30s -> (98C 10s -> 58C 20s -> 72C 20s)x8 -> (98C 10s -> 72C 20s)x19 -> 72C 3min | |||
:{| {{table}} border = 1 | |||
| align="center" style="width:100px;background:#f0f0f0;"|'''Sample''' | |||
| align="center" style="width:80px;background:#f0f0f0;"|'''Index''' | |||
| align="center" style="width:100px;background:#f0f0f0;"|'''Sample''' | |||
| align="center" style="width:80px;background:#f0f0f0;"|'''Index''' | |||
|- | |||
| 500:1_5ng_1||Ind_57||1000:1_5ng_1||Ind_65 | |||
|- | |||
| 500:1_5ng_2||Ind_58||1000:1_5ng_2||Ind_66 | |||
|- | |||
| 500:1_10ng_1||Ind_59||1000:1_10ng_1||Ind_67 | |||
|- | |||
| 500:1_10ng_2||Ind_60||1000:1_10ng_2||Ind_68 | |||
|- | |||
| 500:1_25ng_1||Ind_61||1000:1_25ng_1||Ind_69 | |||
|- | |||
| 500:1_25ng_2||Ind_62||1000:1_25ng_2||Ind_70 | |||
|- | |||
| 500:1_50ng_1||Ind_63||1000:1_50ng_1||Ind_71 | |||
|- | |||
| 500:1_50ng_2||Ind_64||1000:1_50ng_2||Ind_72 | |||
|} | |||
==== PAGE verification ==== | ==== PAGE verification ==== | ||
* Loaded 4ul of PCR products in 6% TBE gel | * Loaded 4ul of PCR products in 6% TBE gel | ||
[[File:ZhangLab_2 2014-06-03 16hr 20min_V1N3_500to1.jpg| 450px]] <br> | [[File:ZhangLab_2 2014-06-03 16hr 20min_V1N3_500to1.jpg| 450px]] <br> | ||
<br> | |||
[[File:ZhangLab_2 2014-06-03 16hr 20min_V1N3_1000to1.jpg| 450px]] | [[File:ZhangLab_2 2014-06-03 16hr 20min_V1N3_1000to1.jpg| 450px]] | ||
* Dr. Zhang suggested to do sequencing on 5ng and 10ng input. | |||
* I pooled PCR product by using the gel image intensity to get equimolar ratio of each libraries, including 5ng-1000:1 rep 1 &2 and 10ng-1000:1 rep1 and 2. | |||
* Purified pooled PCR products with 0.8X AMPure beads and eluted with 40ul EB buffer. | |||
* Loaded in 2-wells of 5-well 6% TBE gel | |||
[[File:ZhangLab_2 2014-06-06 09hr 53min_PAGE-SS_V1N3-5-10ng.jpg|250px]] | |||
* Resuspend sequencing libraries in 20ul H2O | |||
'''Sequencing library ID:''' NP-BSPP-MNV1N3-5-10ng, Jun1, 2014 | |||
:- Conc. by Qubit dsDNA HS = 0.644ng/ul (Alan did not have enough room for more libraries in qPCR) | |||
:- Run: HL188 (required ~300k/library) | |||
:- Length: 375bp | |||
:- Index: 65-68 (5ng-rep1, 5ng-rep2, 10ng-rep1, 10ng-rep2) | |||
:- They all used probe:target = 1000:1 | |||
:{| {{table}} border = 1 | |||
| align="center" style="width:80px;background:#f0f0f0;"|'''Index''' | |||
| align="center" style="width:100px;background:#f0f0f0;"|'''Sample''' | |||
|- | |||
| Ind_65||JK_5ng_1 | |||
|- | |||
| Ind_66||JK_5ng_2 | |||
|- | |||
| Ind_67||JK_10ng_1 | |||
|- | |||
| Ind_68||JK_10ng_2 | |||
|} | |||
:- JK = Jurkat DNA |
Latest revision as of 20:19, 8 June 2014
MONOD V1N3 BSPP capture (repeat sensitivity test)[edit]
Link to calendar: [[1]]
- I repeated MONOD V1N3 capture experiment on 3014-05-29: [[2]]
- I reduced capture volume to 10ul.
- I reduced incubation time after adding SLN mix between 4-6h since I think that 20h is not necessary for polymerization and may cause more back ground if DNA template level is too low.
- I will add experimental procedures later
Bisulfite conversion[edit]
Mix | 82.1ng/ul JK DNA | H2O | Aliquot |
25ng | 1.28 | 82.72 | 20.00 |
50ng | 2.56 | 81.44 | 20.00 |
100ng | 5.12 | 78.88 | 20.00 |
200ng | 10.23 | 73.77 | 20.00 |
Sample | Conc. (ng/ul) | Amount (ng) | Volume (ul) | H2O (ul) | Lightnig Conversion reagent | Total |
JK-1 | 82.1 | 25 | 0.30 | 19.70 | 130 | 150.00 |
JK-2 | 82.1 | 25 | 0.30 | 19.70 | 130 | 150.00 |
JK-3 | 82.1 | 25 | 0.30 | 19.70 | 130 | 150.00 |
JK-4 | 82.1 | 25 | 0.30 | 19.70 | 130 | 150.00 |
JK-5 | 82.1 | 50 | 0.61 | 19.39 | 130 | 150.00 |
JK-6 | 82.1 | 50 | 0.61 | 19.39 | 130 | 150.00 |
JK-7 | 82.1 | 50 | 0.61 | 19.39 | 130 | 150.00 |
JK-8 | 82.1 | 50 | 0.61 | 19.39 | 130 | 150.00 |
JK-9 | 82.1 | 100 | 1.22 | 18.78 | 130 | 150.00 |
JK-10 | 82.1 | 100 | 1.22 | 18.78 | 130 | 150.00 |
JK-11 | 82.1 | 100 | 1.22 | 18.78 | 130 | 150.00 |
JK-12 | 82.1 | 100 | 1.22 | 18.78 | 130 | 150.00 |
JK-13 | 82.1 | 200 | 2.44 | 17.56 | 130 | 150.00 |
JK-14 | 82.1 | 200 | 2.44 | 17.56 | 130 | 150.00 |
JK-15 | 82.1 | 200 | 2.44 | 17.56 | 130 | 150.00 |
JK-16 | 82.1 | 200 | 2.44 | 17.56 | 130 | 150.00 |
- Elute with 10ul Elution buffer
- Use 1ul for Qubit ssDNA assay
Qubit ssDNA assay results[edit]
- I did many bisulfite conversion reactions to compare the recovery rate with different inputs
Sample | Conc. in the Qubit | Unit | uL used | Dilution | Sample conc. (ng/ul) | Yield in 9ul (ng) | Input DNA (ng) | % Recovery |
JK-1 | 3.8 | ng/mL | 1 | 200 | 0.760 | 6.84 | 25 | 27.36 |
JK-2 | 4.9 | ng/mL | 1 | 200 | 0.980 | 8.82 | 25 | 35.28 |
JK-3 | 2.5 | ng/mL | 1 | 200 | 0.500 | 4.50 | 25 | 18.00 |
JK-4 | 5.11 | ng/mL | 1 | 200 | 1.022 | 9.20 | 25 | 36.79 |
JK-5 | 10.8 | ng/mL | 1 | 200 | 2.160 | 19.44 | 50 | 38.88 |
JK-6 | 9.06 | ng/mL | 1 | 200 | 1.812 | 16.31 | 50 | 32.62 |
JK-7 | 12.3 | ng/mL | 1 | 200 | 2.460 | 22.14 | 50 | 44.28 |
JK-8 | 11.2 | ng/mL | 1 | 200 | 2.240 | 20.16 | 50 | 40.32 |
JK-9 | 25 | ng/mL | 1 | 200 | 5.000 | 45.00 | 100 | 45.00 |
JK-10 | 26.7 | ng/mL | 1 | 200 | 5.340 | 48.06 | 100 | 48.06 |
JK-11 | 28.4 | ng/mL | 1 | 200 | 5.680 | 51.12 | 100 | 51.12 |
JK-12 | 24.3 | ng/mL | 1 | 200 | 4.860 | 43.74 | 100 | 43.74 |
JK-13 | 90.1 | ng/mL | 1 | 200 | 18.020 | 162.18 | 200 | 81.09 |
JK-14 | 89 | ng/mL | 1 | 200 | 17.800 | 160.20 | 200 | 80.10 |
JK-15 | 79.7 | ng/mL | 1 | 200 | 15.940 | 143.46 | 200 | 71.73 |
JK-16 | 85.4 | ng/mL | 1 | 200 | 17.080 | 153.72 | 200 | 76.86 |
BSPP capture set up[edit]
strip 1 | 5:500 | 5:500 | 10:500 | 10:500 | 25:500 | 25:500 | 50:500 | 50:500 |
BIS-DNA required (ng) | 5 | 5 | 10 | 10 | 25 | 25 | 50 | 50 |
JK # | JK-1 | JK-2 | JK-5 | JK-6 | JK-9 | JK-10 | JK-13 | JK-14 |
Conc. | 0.760 | 0.980 | 2.160 | 1.812 | 5.000 | 5.340 | 18.020 | 17.800 |
Volume (ul) | 6.58 | 5.10 | 4.63 | 5.52 | 5.00 | 4.68 | 2.77 | 2.81 |
H2O (ul) | 0.27 | 1.75 | 2.07 | 1.18 | 1.25 | 1.57 | 2.72 | 2.69 |
V1N3 amount (ng) | 0.11 | 0.11 | 0.22 | 0.22 | 0.55 | 0.55 | 1.10 | 1.10 |
V1N3 conc. (ng/ul) | 0.73 | 0.73 | 0.73 | 0.73 | 0.73 | 0.73 | 0.73 | 0.73 |
V1N3 volume (ul) | 0.15 | 0.15 | 0.30 | 0.30 | 0.75 | 0.75 | 1.50 | 1.50 |
10X Ampligase Buffer | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
H2O in Mix | 2.00 | 2.00 | 2.00 | 2.00 | 2.00 | 2.00 | 2.00 | 2.00 |
Total | 10.00 | 10.00 | 10.00 | 10.00 | 10.00 | 10.00 | 10.00 | 10.00 |
strip 2 | 5:1000 | 5:1000 | 10:1000 | 10:1000 | 25:1000 | 25:1000 | 50:1000 | 50:1000 |
BIS-DNA required (ng) | 5 | 5 | 10 | 10 | 25 | 25 | 50 | 50 |
JK # | JK-4 | JK-5 | JK-7 | JK-8 | JK-11 | JK-12 | JK-15 | JK-16 |
Conc. | 1.022 | 2.160 | 2.460 | 2.240 | 5.680 | 4.860 | 15.940 | 17.080 |
Volume (ul) | 4.89 | 2.31 | 4.07 | 4.46 | 4.40 | 5.14 | 3.14 | 2.93 |
H2O (ul) | 1.81 | 4.38 | 2.33 | 1.93 | 1.09 | 0.35 | 0.85 | 1.06 |
V1N3 amount (ng) | 0.22 | 0.22 | 0.44 | 0.44 | 1.10 | 1.10 | 2.20 | 2.20 |
V1N3 conc. (ng/ul) | 0.73 | 0.73 | 0.73 | 0.73 | 0.73 | 0.73 | 0.73 | 0.73 |
V1N3 volume (ul) | 0.30 | 0.30 | 0.60 | 0.60 | 1.50 | 1.50 | 3.01 | 3.01 |
10X Ampligase Buffer | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
H2O in Mix | 2.00 | 2.00 | 2.00 | 2.00 | 2.00 | 2.00 | 2.00 | 2.00 |
Total | 10.00 | 10.00 | 10.00 | 10.00 | 10.00 | 10.00 | 10.00 | 10.00 |
strip 3 | NTC:500 | NTC:1000 |
BIS-DNA required (ng) | 0 | 0 |
JK # | 0 | 0 |
Conc. | 0 | 0 |
Volume (ul) | 0.00 | 0.00 |
H2O (ul) | 5.50 | 3.99 |
V1N3 amount (ng) | 1.10 | 2.20 |
V1N3 conc. (ng/ul) | 0.73 | 0.73 |
V1N3 volume (ul) | 1.50 | 3.01 |
10X Ampligase Buffer | 1.00 | 1.00 |
H2O in Mix | 2.00 | 2.00 |
Total | 10.00 | 10.00 |
V1N3 & Ampligase Buffer mix
Mix 0.11 | 1x | 4x |
Diluted V1N3 | 0.15 | 0.60 |
10X Ampligase Buffer | 1.00 | 4.00 |
H2O | 2.00 | 8.00 |
Sum | 3.15 |
Mix 0.22 | 1x | 6x |
Diluted V1N3 | 0.30 | 1.80 |
10X Ampligase Buffer | 1.00 | 6.00 |
H2O | 2.00 | 12.00 |
Sum | 3.30 |
Mix 0.44 | 1x | 4x |
Diluted V1N3 | 0.60 | 2.40 |
10X Ampligase Buffer | 1.00 | 4.00 |
H2O | 2.00 | 8.00 |
Sum | 3.60 |
Mix 0.55 | 1x | 4x |
Diluted V1N3 | 0.75 | 3.00 |
10X Ampligase Buffer | 1.00 | 4.00 |
H2O | 2.00 | 8.00 |
Sum | 3.75 |
Mix 1.1 | 1x | 6x |
Diluted V1N3 | 1.50 | 9.00 |
10X Ampligase Buffer | 1.00 | 6.00 |
H2O | 2.00 | 12.00 |
Sum | 4.50 |
Mix 2.2 | 1x | 4x |
Diluted V1N3 | 3.01 | 12.04 |
10X Ampligase Buffer | 1.00 | 4.00 |
H2O | 2.00 | 8.00 |
Sum | 6.01 |
Program -> 95c 30sec -> cool down to 55C at 0.02C/sec -> 55C 20h -> add 1ul SLN mix (2U/ul Hemo Klentaql fragment; 0.5U/ul AmpLigase; 100uM dNTP) -> 55C 4:40h-> 94C 2min -> add 1.5ul Exo I/III mix (1ul of 20U/ul ExoI & 0.5ul of 200U/ul of ExoIII)-> 37C 2h -> 94C 2min -> 4C hold.
Amplification[edit]
- I used 10ul of captured DNA in total 75ul PCR reaction.
Components 1x rxn 20 rxn mix Captured template 10.00 0.00 10uM AmpF6.4Sol 1.50 30.00 10uM AmpR6.3.IndX (X=57-72) 1.50 0.00 2X KAPA SYBR MM 37.50 750.00 H2O 24.50 490.00 Total 75.00
- - Aliquot 63.5ul + 1.5ul AmpR6.3 IndX + 10ul template
- - Set cycle number maximum at 27X
Program (Eppendorf Realplex) 98C 30s -> (98C 10s -> 58C 20s -> 72C 20s)x8 -> (98C 10s -> 72C 20s)x19 -> 72C 3min
Sample Index Sample Index 500:1_5ng_1 Ind_57 1000:1_5ng_1 Ind_65 500:1_5ng_2 Ind_58 1000:1_5ng_2 Ind_66 500:1_10ng_1 Ind_59 1000:1_10ng_1 Ind_67 500:1_10ng_2 Ind_60 1000:1_10ng_2 Ind_68 500:1_25ng_1 Ind_61 1000:1_25ng_1 Ind_69 500:1_25ng_2 Ind_62 1000:1_25ng_2 Ind_70 500:1_50ng_1 Ind_63 1000:1_50ng_1 Ind_71 500:1_50ng_2 Ind_64 1000:1_50ng_2 Ind_72
PAGE verification[edit]
- Loaded 4ul of PCR products in 6% TBE gel
File:ZhangLab 2 2014-06-03 16hr 20min V1N3 500to1.jpg
File:ZhangLab 2 2014-06-03 16hr 20min V1N3 1000to1.jpg
- Dr. Zhang suggested to do sequencing on 5ng and 10ng input.
- I pooled PCR product by using the gel image intensity to get equimolar ratio of each libraries, including 5ng-1000:1 rep 1 &2 and 10ng-1000:1 rep1 and 2.
- Purified pooled PCR products with 0.8X AMPure beads and eluted with 40ul EB buffer.
- Loaded in 2-wells of 5-well 6% TBE gel
File:ZhangLab 2 2014-06-06 09hr 53min PAGE-SS V1N3-5-10ng.jpg
- Resuspend sequencing libraries in 20ul H2O
Sequencing library ID: NP-BSPP-MNV1N3-5-10ng, Jun1, 2014
- - Conc. by Qubit dsDNA HS = 0.644ng/ul (Alan did not have enough room for more libraries in qPCR)
- - Run: HL188 (required ~300k/library)
- - Length: 375bp
- - Index: 65-68 (5ng-rep1, 5ng-rep2, 10ng-rep1, 10ng-rep2)
- - They all used probe:target = 1000:1
Index Sample Ind_65 JK_5ng_1 Ind_66 JK_5ng_2 Ind_67 JK_10ng_1 Ind_68 JK_10ng_2
- - JK = Jurkat DNA