Rui:Haplotyping: Difference between revisions

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>RuiLiu
m (Created page with '==Progress== ===Summary=== {| {{table}} border=1 | align="center" style="background:#f0f0f0;"|'''''' | align="center" style="background:#f0f0f0;"|'''''' | align="center" style="b…')
 
>RuiLiu
 
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| library ID||||RL-Hap_RNAseq-1_13-Jun6||RL_hap1-12_9.2.11;RL_hap13-23_9.2.11;MC_hap1-11_9.2.11||RL-Hap-73_80-Nov8
| library ID||||RL-Hap_RNAseq-1_13-Jun6||RL_hap1-12_9.2.11;RL_hap13-23_9.2.11;MC_hap1-11_9.2.11||RL-Hap-73_80-Nov8
|-
|-
| sequence||||HL095||HL101, SE60||HL108, SE40
| sequence||||HL095, SE80||HL101, SE60||HL108, SE40
|-
|-
| note link||lib. Prep.||[http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Haplotyping/2011-6-4]||[http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Haplotyping/2011-8-23]||[http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Haplotyping/2011-11-3]
| note link||lib. Prep.||[http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Haplotyping/2011-6-4]||[http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Haplotyping/2011-8-23]||[http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Haplotyping/2011-11-3]

Latest revision as of 17:56, 12 March 2012

Progress[edit]

Summary[edit]

' ' 6/4/11 8/23/11 11/3/11
cell ID GM40231 GM12878 M-GM12878p15
lysis cell # 5 10 10
lysis V. (ul) 30 60 60
Aliquot pg/tube ~1pg ~1pg ~1pg
aliquot # 12 24+12 8 (from 20)
Ptnase treatment yes yes
dALS V. (ul) 1ul
dNS V. (ul) 1ul
N6 MDA V. (ul) 7ul
MDA hours 1.7(1); 2.2(1); 2.7(2); 3(4)
Purification EtOH, elute in 4ul
MDA yeilding 30; 70; 6; 30-100ng
Tagmentation DNA ~1pg ~1pg ~1-20ng
Trp-I (1:50) 0.4 0.4 1
Ptnase treatment 1ul 1:500d
PCR w/ BO up 20ct 16ct
stop 28ct 22ct
Purification beads 0.7X 0.8X
elute 10ul
PCR w/ barcode DNA 9ul beads 1-20ng
up 1ct 4ct
stop 5ct 5ct 12ct
fold change
library ID RL-Hap_RNAseq-1_13-Jun6 RL_hap1-12_9.2.11;RL_hap13-23_9.2.11;MC_hap1-11_9.2.11 RL-Hap-73_80-Nov8
sequence HL095, SE80 HL101, SE60 HL108, SE40
note link lib. Prep. [1] [2] [3]
[4] [5] [6]
seq. analysis [7] [8] [9]

Sequencing analysis[edit]

  • Dr. Zhang's link on haplotyping analysis [10]

Notes[edit]

  • "Methylation haplotyping on few cells" project: May 27th email [14]
  • Human gDNA samples: Kun's stack - the box at the left up corner (-20C), Rui's box (4C) with GC DNA and Africa's DNA.
  • Prepare ABD mixture: 9 mL 40% acrylamide, 1 ml Acrylamide/Bis (19:1), 200 mg DATD in 15 mL tube. Shake to dissolve DATD. Use a 3 cc syringe and .22 um filter to 1 mL of ABD into 1.5 mL tube. The rest can be saved at 4C for 1 week

Protocol[edit]

2011[edit]

<calendar> name=Rui:LabNotes/Haplotyping format=%name/%year-%month-%day date=2011/10/1 view=oneyear </calendar>