AlanFung:LabNotes/Capturing/2014-1-14: Difference between revisions
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*nanodrop result 37.9ng/ul * 12ul = 454.8ng/ul | *nanodrop result 37.9ng/ul * 12ul = 454.8ng/ul | ||
*PAGE | *PAGE | ||
==Re-amplify illumina_JurkatCT 01/28/2014== | |||
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8<\hiddentext> | |||
|- style="font-size:12pt;font-weight:bold" align="center" | |||
| width="105" height="15" | Probes | |||
| width="71" | illumina_155 | |||
|- style="font-size:12pt;font-weight:bold" align="center" | |||
| height="15" | Sample | |||
| Jurkat_CT | |||
|- style="font-size:12pt;font-weight:bold" align="center" | |||
| height="15" | Index | |||
| align="center" | 1 | |||
|- style="font-size:12pt" align="center" | |||
|style="font-weight:bold" height="15" | Captured Template | |||
| align="center" | 4 | |||
|- style="font-size:12pt" align="center" | |||
|style="font-weight:bold" height="15" | 10uM AmpF6.4Sol | |||
| align="center" | 1 | |||
|- style="font-size:12pt" align="center" | |||
|style="font-weight:bold" height="15" | 10uM AmpR6.3Ind1 | |||
| align="center" | 1 | |||
|- style="font-size:12pt" align="center" | |||
|style="font-weight:bold" height="15" | 2X KAPA SYBR MM | |||
| align="center" | 25 | |||
|- style="font-size:12pt" align="center" | |||
|style="font-weight:bold" height="15" | H2O | |||
| align="center" | 19 | |||
|- style="font-size:12pt" align="center" | |||
|style="font-weight:bold" height="15" | Total | |||
| align="center" | 50 | |||
|} | |||
Program (Eppendorf Realplex stored under Alan/ampF6.4_template) | |||
98C 30s -> (98C 10s -> 58C 20s -> 72C 20s)x8 -> (98C 10s -> 72C 20s)x30 -> 72C 3min | |||
[[File:01282014.JPG|600px]] | |||
*Minelute with 15ul EB Buffer | |||
*14.3ng/ul *15ul = 214.5ng | |||
==PAGE Size Selection== | |||
*Lowmass-Ladder: 1ul + 12ul h2o + 13ul loading dye | |||
*Library:13ul library + 13ul 6x loading dye | |||
*One well in a 5 well TBE gel, run at 200V for 30 mins | |||
[[File:ZhangLab_2 2014-01-28 15hr 26min.jpg|400px]] | |||
==HL-BSPP-illumina_155pp_CTJurkat-Jan14 Sequencing at illumina== | |||
===Prepare sequencing primer=== | |||
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8<\hiddentext> | |||
|- style="font-size:12pt;font-weight:bold" align="center" | |||
| width="116" height="15" | Read | |||
| width="263" | Primer | |||
|- align="center" | |||
|style="font-size:12pt;font-weight:bold" height="16" | Read 1 | |||
|style="font-size:13pt" | SolSeq6.3.3 | |||
|- align="center" | |||
|style="font-size:12pt;font-weight:bold" height="16" | Index Read | |||
|style="font-size:13pt" | AmpR6.3IndSeq | |||
|- align="center" | |||
|style="font-size:12pt;font-weight:bold" height="16" | Read 2 | |||
|style="font-size:13pt" | SolSeqV6.3.2r | |||
|} | |||
*Spike in (100uM) primer to Miseq cartridge (1mL) | |||
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8<\hiddentext> | |||
|- style="font-size:12pt" align="center" | |||
| align="center" width="116" height="16" | | |||
|style="font-weight:bold" width="263" | Stock Primer 100uM | |||
|style="font-weight:bold" width="179" | Spike into Total Volume (ul) | |||
|style="font-weight:bold" width="156" | Final Concentration (uM) | |||
|- style="font-size:12pt" align="center" | |||
|style="font-weight:bold" height="16" | Volume (ul) | |||
| align="center" | 5 | |||
| align="center" | 1000 | |||
| align="center" | 0.5 | |||
|} | |||
===Prepare Sequencing Library=== | |||
*Library concentration '''1.69nM''' (qPCR), we normally load it at 10pM |
Latest revision as of 15:20, 29 January 2014
Capturing Bisulfite Converted Jurkat gDNA w GP1 V6 probe set[edit]
- probes prep notes LabNotes/Probe/2014-1-7
[[1]]
Capturing Jurkat gDNA w ppMALT1 ordered form IDT[edit]
Bisulfite Conversion of Jurkat gDNA[edit]
- Bisulfite conversion with zymo methylation gold
- Convert 500ng of Jurkat gDNA (2 rxn, 100ng total)
- Add 130ul of lighting conversion reagent to 5ul of jurkat gDNA and 15ul of ddH2O
- Mix and centrifuge
1. 98°C for 8 minutes 2. 54°C for 60 minutes 3. 4°C hold
- Add 600ul M-binding buffer to column
- load the sample into column, mix by inverting column and centrifuge at 14000rpm for 30sec
- discard flow through
- add 100ul m-wash buffer to the column and centrifuge at 14000rpm for 30sec
- add 200ul L-Desulphonation buffer to the column and sit at RT for 20 minutes and centrifuge at 14000rpm for 30sec
- add 200ul of m-wash buffer to the column and centrifuge at 14000rpm for 30sec
- Add 10ul of EBuffer to column sit for 5 mintues and centrifuge at 14000rpm for 30sec (2 rxn total)
ssDNA Qubit assay[edit]
- 47.1ng/ul *20ul = 942ng
- Stored in Maytag -20C (Alan Misc. #9)
Probe calculations[edit]
illumina methylation seq pool 155[edit]
ppMALAT1[edit]
GP1_V6[edit]
Capture setup[edit]
GP1_V6 | ||||||
Sample | Conc. (ng/ul) | Volume for 200ng (ul) | H2O | GP1_V6 | 10X ampligase Buffer | Total |
CT Jurkat | 47.1 | 4.25 | 11.47 | 2.28 | 2 | 20 |
illumina methylation seq pool | ||||||
Sample | Conc. (ng/ul) | Volume for 200ng (ul) | H2O | illumina methylation seq pool | 10X ampligase Buffer | Total |
CT Jurkat | 47.1 | 4.25 | 10.38 | 3.37 | 2.00 | 20 |
ppMALAT1 | ||||||
Sample | Conc. (ng/ul) | Volume for 200ng (ul) | H2O | ppMALAT1 | 10X ampligase Buffer | Total |
Jurkat | 100 | 2 | 15.34 | 0.66 | 2.00 | 20 |
Negative Control | n/a | n/a | 17.34 | 0.66 | 2.00 | 20 |
illumina methylation seq pool 155 probes setup[edit]
Program stored under Alan/aCPG -> 95c 30sec -> cool down to 55C at 0.02C/sec -> 58C 20h -> add 3ul SLN mix (2U/ul AmpliTaq Stoffel fragment; 0.5U/ul AmpLigase; 100uM dNTP) -> 55C 20h-> 94C 2min -> add 2ul Exo I/III mix-> 37C 2h -> 94C 2min -> 4C hold.
GP1_V6 & ppMALAT1 setup[edit]
Program stored under Kun/CPG -> 95c 30sec -> cool down to 55C at 0.02C/sec -> 55C 20h -> add 3ul SLN mix (2U/ul AmpliTaq Stoffel fragment; 0.5U/ul AmpLigase; 100uM dNTP) -> 55C 20h-> 94C 2min -> add 2ul Exo I/III mix-> 37C 2h -> 94C 2min -> 4C hold.
- GP1_V6-Jurkat Stored in Maytag -20C (Alan Misc. #24)
- illumina_155-Jurkat Stored in Maytag -20C (Alan Misc. #25, remove for amplification done on 01282014)
- ppMALTA1-Jurkat Stored in Maytag -20C (Alan Misc. #26)
- ppMALTA1-H2O Stored in Maytag -20C (Alan Misc. #27)
Prepare SLN Mix[edit]
SLN Mix | |||||
Components | Stock Concentration | Unit | Final Concentration | Unit | Prepare Volume (ul) |
AmpliTaq Stoffel | 10 | U/ul | 2 | U/ul | 2.6 |
Ampligase | 5 | U/ul | 0.5 | U/ul | 1.3 |
dNTP | 1 | mM | 100 | uM | 1.3 |
10X Ampligase Buffer | 10 | X | 1 | X | 1.3 |
H2O | n/a | n/a | n/a | n/a | 6.5 |
Total | n/a | n/a | n/a | n/a | 13 |
Prepare Exo Mix[edit]
- Mix 1:1 Exo I & Exo III (9ul total)
PCR Amplification[edit]
(AmpF6.4Sol and AmpR6.3 for GP1_V6 & illumina_155)[edit]
(ISB_CA_AF and ISB_CA_AR_T2 for ppMALTA1) stored in #18, #19 Alan Misc. -20C[edit]
Probes | BSPP_GP1_V6 | illumina_155 |
Sample | Jurkat_CT | Jurkat_CT |
Index | 1 | 2 |
Components | 1x rxn | 1x rxn |
Captured Template | 20 | 20 |
10uM AmpF6.4Sol | 1 | 1 |
10uM AmpR6.3Indx | 1 | 1 |
2X KAPA SYBR MM | 25 | 25 |
H2O | 3 | 3 |
Probes | ppMALTA1 | ppMALTA1 |
Sample | Jurkat_gDNA | -ve control |
Components | 1x rxn | 1x rxn |
Captured Template | 20 | 20 |
10uM ISB_CA_AF | 1 | 1 |
10uM ISB_CA_AR_T2 | 1 | 1 |
2X KAPA SYBR MM | 25 | 25 |
H2O | 3 | 3 |
Program (Eppendorf Realplex stored under Alan/ampF6.4_template) 98C 30s -> (98C 10s -> 58C 20s -> 72C 20s)x8 -> (98C 10s -> 72C 20s)x15 -> 72C 3min
- After the 8+15 cycle only GP1_V6 captured seq library got amplified
- After meeting with Dr. Zhang, he suggests adding more cycles to the remaining 3 captured product
- Amplification happened immediately for all 3 captures, that includes the negative control, which makes me think it is unspecific amplification. I will run a PAGE gel to verify the amplicon size
- GP1_V6 amplicon Stored in Maytag -20C (Alan Misc. #20)
- illumina_155 amplicon Stored in Maytag -20C (Alan Misc. #21, removed for gel size selection)
- ppMALTA1_Jurkat amplicon Stored in Maytag -20C (Alan Misc. #22)
- ppMALTA1_H2O amplicon Stored in Maytag -20C (Alan Misc. #23)
PAGE Gel[edit]
File:ZhangLab 2 2014-01-21 13hr 54min.jpg
- LM-GP1_V6-illumina_155-ppMALAT1-ppMALAT1_Negative
- illumina_155: probe:99nt, gap:99nt, primer: Dr. Zhang agrees that the amplicon at around 300bp should be the captured product. We will perform a size selection and send it to illumina for miseq run
Perform PAGE Size Selection on illumina_155pp-CT_Jurkat[edit]
- Purify amplicon using minelute, elute with 12ul EB buffer
- nanodrop result 37.9ng/ul * 12ul = 454.8ng/ul
- PAGE
Re-amplify illumina_JurkatCT 01/28/2014[edit]
Probes | illumina_155 |
Sample | Jurkat_CT |
Index | 1 |
Captured Template | 4 |
10uM AmpF6.4Sol | 1 |
10uM AmpR6.3Ind1 | 1 |
2X KAPA SYBR MM | 25 |
H2O | 19 |
Total | 50 |
Program (Eppendorf Realplex stored under Alan/ampF6.4_template) 98C 30s -> (98C 10s -> 58C 20s -> 72C 20s)x8 -> (98C 10s -> 72C 20s)x30 -> 72C 3min
- Minelute with 15ul EB Buffer
- 14.3ng/ul *15ul = 214.5ng
PAGE Size Selection[edit]
- Lowmass-Ladder: 1ul + 12ul h2o + 13ul loading dye
- Library:13ul library + 13ul 6x loading dye
- One well in a 5 well TBE gel, run at 200V for 30 mins
File:ZhangLab 2 2014-01-28 15hr 26min.jpg
HL-BSPP-illumina_155pp_CTJurkat-Jan14 Sequencing at illumina[edit]
Prepare sequencing primer[edit]
Read | Primer |
Read 1 | SolSeq6.3.3 |
Index Read | AmpR6.3IndSeq |
Read 2 | SolSeqV6.3.2r |
- Spike in (100uM) primer to Miseq cartridge (1mL)
Stock Primer 100uM | Spike into Total Volume (ul) | Final Concentration (uM) | |
Volume (ul) | 5 | 1000 | 0.5 |
Prepare Sequencing Library[edit]
- Library concentration 1.69nM (qPCR), we normally load it at 10pM