AlanFung:LabNotes/Human MDA Halotyping/2009-7-20

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Genomic DNA Extraction from GM18506 cells[edit]

Samples and Materials[edit]

  • 3 x 10^6 cells
  • Wizard Genomic DNA purification kit
  • 1.5mL microcentrifuge tubes
  • 15 mL centrifuge tubes
  • PBS
  • 37C water bath
  • Isopropanol
  • 70% ethanol
  • 65C water bath

Procedure[edit]

  • Harvest the cells and transfer them to a 1.5ml tube
  • Centrifuge at 16000g for 10sec to pellet the cells
  • Remove the supernatant
  • Add 200ul pbs to wash the cells repeat centrifuge and remove pbs
  • Vortex vigorously to resuspend cells
  • Add 600 ul of nuclei lysis solution and pipet to lyse the cells (pipet until no visible cell clumps remain)
  • add 3ul of rnase solution to the nuclear lysate and mix the sample by inverting the tube 5 times uncubate the mixture for 30m 37C allow the sample to cool to rt for 5m before proceeding
  • add 200ul of protein precipitation solution and vertex vugorously at high speed for 20sec
  • Chill sample on ice for 5m
  • centrifuge for 4n at 16000g
  • add 600ul rt isopropanol to a 1.5ml tube
  • transfer the supernatant containing the DNA to the 1.5ml tube
  • gently mix the solution by inversion until the white thread like strands of dna form a visible mass
  • centrifuge for 1m at 16000g at rt
  • decant the supertant
  • add 600ul of rt 70% ethanol and gently invert the tube several times to wash the dna
  • centrifuge for 1m at 16000g at rt
  • decant the supernatant
  • invert the tube on clean absorbent paper and air dry the pellet for 15m
  • add 100ul of dna rehydration solution
  • incubate at 65C for 1 hr periodialy mix the solution by gently tapping the tube
  • store dna at 4C


  • nanodrop

PCR validation for gDNA[edit]

sample and material[edit]

  • human genome specific primers
  • templates
  • Jurkat gdna
  • h2o
  • ntc h2o
  • econotaq

Procedures[edit]

' GM18506 Pos. Neg.
primer mix (f+r 10uM) 1 1 1
h2o 7 7 9
econotaq 2x 10 10 10
Gm template 1ng/ul 2 0 0
Jurkat template 0 2 0


  • Mix well the master mix by vortexing. Transfer 12 uL Master mix into each of 12 reactions.
  • Transfer 8 uL diluted primer into each reaction based on the arrangements
  • Gently vortex and spin down the PCR reaction tubes. Place in pcr machine immediately to PCR reaction.
  • Program: 94C 2min-> (94C 40sec-> 52C 40sec -> 72C 60 sec) x 30 -> 72C 10min -> 15C hold

PCR test on the whole set of human genome primers[edit]

Background[edit]

  • Testing if the human genome primers (f+r 10uM premixed) were degraded.


Procedures[edit]

  • Primers: Human genome specific primers set 1 (primer 1 to 24)
  • Templates: Pos (1 ng/uL gDNA)
                            1rxn  
  Primer mix (f+r 10 uM)    1.0     uL
  H2O                       7.0     uL
  Template                  2.0     uL
  Econo (2X)               10.0     uL
  ---------------------------------------------
                           20.0     uL

  Amplified at 52C for 40 cycles

Gel electrophoresis[edit]

  • 110mL (0.5X TBE) 2% agarose + 8 uL SYBR safe -> 2 middle gel with 26-well comb
  • Loading: Sample 7uL + 6X loading buffer 1.5 uL (Order: P1 -> P24 left to right)
  • Run at 135V for 20 min