Noi/NOTES/2014-4-4: Difference between revisions
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= MONOD test on human plasma/serum = | |||
* Continued from : [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-3-11]] | |||
* From last time lab meeting, Dr. Zhang suggested to do capture on serum DNA before continuing to capture with real cancer/tumor samples. | * From last time lab meeting, Dr. Zhang suggested to do capture on serum DNA before continuing to capture with real cancer/tumor samples. | ||
: - The sample #2-S-CS I had highest yield last time has ~25ng left after quantification. I extracted more DNA from plasma and serum of sample #3 to increase DNA yield. | : - The sample #2-S-CS I had highest yield last time has ~25ng left after quantification. I extracted more DNA from plasma and serum of sample #3 to increase DNA yield. | ||
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:: #3-P-CS = 0.246ug/mL or ng/ul, yield = 28ul * 0.246ng/ul = 6.89ng | :: #3-P-CS = 0.246ug/mL or ng/ul, yield = 28ul * 0.246ng/ul = 6.89ng | ||
:: #3-S-CS = 7.630ug/mL or ng/ul, yield = 28ul * 7.630ng/ul = 213ng | :: #3-S-CS = 7.630ug/mL or ng/ul, yield = 28ul * 7.630ng/ul = 213ng | ||
---- | |||
=== Bisulfite conversion (Zymo Lightning kit) === | === Bisulfite conversion (Zymo Lightning kit) === | ||
: - I used 25ul of #3-S-CS for bisulfite conversion (190.75ng). Since the volume exceed 20ul, I adjust Lightning Conversion Reagent accordingly to the input volume. | : - I used 25ul of #3-S-CS for bisulfite conversion (190.75ng). Since the volume exceed 20ul, I adjust Lightning Conversion Reagent accordingly to the input volume. | ||
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- Follow bisulfite conversion of EZ DNA Methylation-Lightning™ Kit | - Follow bisulfite conversion of EZ DNA Methylation-Lightning™ Kit | ||
- Elute with 15ul of Elution buffer --> volume after spin is ~14ul | - Elute with 15ul of Elution buffer --> volume after spin is ~14ul | ||
==== <u>Qubit ssDNA assay< | ==== <u>Qubit ssDNA assay</u> ==== | ||
: - I used 1ul for Qubit ssDNA assay (200x dilution) | : - I used 1ul for Qubit ssDNA assay (200x dilution) | ||
:: - bis-#3-S-CS = 7.43ng/ul, yield = 14ul * 7.43ng/ul =104.02 | :: - bis-#3-S-CS = 7.43ng/ul, yield = 14ul * 7.43ng/ul =104.02 | ||
:: - Recovery rate = (104.02 * 100)/190.75 = 54.53% | :: - Recovery rate = (104.02 * 100)/190.75 = 54.53% | ||
:: - Amount left in 13ul for BSPP capture = 96.59ng | :: - Amount left in 13ul for BSPP capture = 96.59ng |
Latest revision as of 20:37, 5 April 2014
MONOD test on human plasma/serum[edit]
- Continued from : [[1]]
- From last time lab meeting, Dr. Zhang suggested to do capture on serum DNA before continuing to capture with real cancer/tumor samples.
- - The sample #2-S-CS I had highest yield last time has ~25ng left after quantification. I extracted more DNA from plasma and serum of sample #3 to increase DNA yield.
ChargeSwitch® gDNA 1 ml Serum kit[edit]
Procedures[edit]
- - Add plasma or serum to 1.5mL tube (adjust to total 600ul).
- #3-P-CS : plasma volume 560 (pooled 4tubes) + 40ul 1x PBS
- #3-S-CS : serum volume 420ul (pooled 3 tubes) + 180ul
- - Note: the volume of sample could be up to 1000ul
- - Add plasma or serum to 1.5mL tube (adjust to total 600ul).
- - Mix 840ul of Lysis Buffer + 60 Proteinase K (420:30, 2 tubes)
- - Add 450ul of Lysis Buffer and Proteinase K mix soulution (420ul of Lysis Buffer and 30ul of Proteinase K for 600ul sample)
- - Pipette up & down 5x to mix
- - Incubate at RT for 20min to lyse the sample.
- Binding DNA
- - Vortex the tube containing ChargeSwitch Magnetic beads
- - In 1.5 mL tube, mix 150ul of ChargeSwitch Purification Buffer + 18ul of ChargeSwitch Magnetic beads for 2.1 rxn (315ul buffer + 37.8ul beads)
- - Add 168ul of ChargeSwitch Purification Buffer and ChargeSwitch Magnetic beads mix to the digested sample
- - Pipette up & down 5x to mix (use p1000 pipette, avoid generating bubbles)
- - Incubate at RT for 2 min to allow DNA bind to magnetic beads
- - Place the sample tube in the MagnaRack for 3 min or until the bead forming a tight pellet. )
- - Carefully remove the spnt without disturbing the bead pellet
- Washing DNA
- - Remove sample tube from magnetic rack
- - Add 600ul of ChargeSwitch Wash Buffer to the tube and pipette up & down 5x gently & avoid bubbles
- - Place the sample tube in the MagnaRack for 2 min or until the bead forming a tight pellet
- - Carefully remove the spnt without disturbing the bead pellet
- - Repeat washing step
- - I dried up the bead for 2 min
- Eluting DNA
- - Remove sample tube from magnetic rack (there should be no spnt in the tube)
- - Add 26ul of ChargeSwitch Elution Buffer to the tube and pipette up & down gently 10x to resuspend magnetic beads
- - Wait for 2 min
- # Do not use H2O for elution
- - Place the sample tube in the MagnaRack for 1 min or until the bead forming a tight pellet
- - Carefully transfer eluted DNA to 1.5mL tube
- - The actual volume left was 28ul. This might be due to the left over washing buffer.
Qubit dsDNA HS assay[edit]
- - I used 2ul for assay (100x)
- #3-P-CS = 0.246ug/mL or ng/ul, yield = 28ul * 0.246ng/ul = 6.89ng
- #3-S-CS = 7.630ug/mL or ng/ul, yield = 28ul * 7.630ng/ul = 213ng
Bisulfite conversion (Zymo Lightning kit)[edit]
- - I used 25ul of #3-S-CS for bisulfite conversion (190.75ng). Since the volume exceed 20ul, I adjust Lightning Conversion Reagent accordingly to the input volume.
- Add 162.5ul of Lightning Conversion Reagent to 25ul extracted DNA and mix by pipetting 10X - Follow bisulfite conversion of EZ DNA Methylation-Lightning™ Kit - Elute with 15ul of Elution buffer --> volume after spin is ~14ul
Qubit ssDNA assay[edit]
- - I used 1ul for Qubit ssDNA assay (200x dilution)
- - bis-#3-S-CS = 7.43ng/ul, yield = 14ul * 7.43ng/ul =104.02
- - Recovery rate = (104.02 * 100)/190.75 = 54.53%
- - Amount left in 13ul for BSPP capture = 96.59ng