Noi/NOTES/2012-7-6

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Preparation of sheared gDNA for WGBS[edit]

Below table are HAPMAP samples I have processed by capturing with BSPP

Catalog ID Sex Family Relationship Whole genome sequnces RNA Seq
GM10860 Male 1362 father no no
GM11992 Male 1362 paternal grandfather yes yes
GM11993 Female 1362 paternal grandmother yes yes
GM10861 Female 1362 mother no no
GM11994 Male 1362 maternal grandfather yes yes
GM11995 Female 1362 maternal grandmother yes yes
GM12801 Male 1454 father no no
GM12812 Male 1454 paternal grandfather yes yes
GM12813 Female 1454 paternal grandmother yes yes
GM12802 Female 1454 mother no no
GM12814 Male 1454 maternal grandfather yes yes
GM12815 Female 1454 maternal grandmother yes yes
  • At the end he told me to include the trios in family 1363 one trios from the table above (I chose family 1362) and the trios from Yoruba (but not the one listed in the grant proposal because the samples were not available)

Sample list[edit]

  • Sample preparation to shear DNA at BioGem, UCSD
    • Prepare DNA in total volume either 50ul or 130ul in H2O or EB buffer is fine (I used 50ul following Alice's suggestion and her set up).
    • Size ~400bp
Labeled on the tube Sample IDs Family Relationship Population Position in HAPMAP PT01 plate Conc. (ng/ul) Volume for 1000ng (ul) H2O Total volume (ul)
1 GM12891 1463 Maternal grandfather CEU G8 250.00 8.00 42.00 50.00
2 GM12892 1463 Maternal grandmother CEU B12 250.00 8.00 42.00 50.00
3 GM10861 1362 Mother CEU A9 250.00 8.00 42.00 50.00
4 GM11994 1362 Maternal grandfather CEU G9 250.00 8.00 42.00 50.00
5 GM11995 1362 Maternal grandmother CEU G7 250.00 8.00 42.00 50.00
6 GM18506 Y009 Child YRI Tube from Dr. Zhang 190.00 10.52 39.48 50.00
7 GM18507 Y009 Father YRI Tube from Dr. Zhang 263.00 7.60 42.40 50.00
8 GM18505 Y009 Mother YRI Tube from Dr. Zhang 218.30 9.17 40.83 50.00
Follow up the set up for Covaris shearing (From BioGem and Alan's note: [[1]]
Target BP 400
Tube Micro
Duty Factor 10%
Peak Incident Power (w) 140
Cycle per Burst 200
Time (secs) 55
Volume 50ul
Temperature (c) 7 
Intensifier Yes
Technique of pipeeting DNA samples from 0.2mL tube to microtube (purchase at BioGem) (suggested by Alice)
Since Microtube can not be uncapped, I need to used p200 pipette transfer DNA to microtube by puncture the rubber on the top of the tube. I need to check if the top of the tube is clean to prevent contamination
After shearing sheared DNA should be transfered to a clean 0.2mL tube. This time Alice suggested to used p10 pipette instead of p200 to transfer DNA (5 times of pipeting for each sample) due to the pressure issue. Don't forget to spin the tube before transferring DNA
If the samples are not process within a week, the sheared DNA should be stored in -20C