Rui:Haplotying: Difference between revisions

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==Progress==
==Progress==
===Summary===
{| {{table}} border=1
| align="center" style="background:#f0f0f0;"|''''''
| align="center" style="background:#f0f0f0;"|''''''
| align="center" style="background:#f0f0f0;"|'''6/4/11'''
| align="center" style="background:#f0f0f0;"|'''8/23/11'''
| align="center" style="background:#f0f0f0;"|'''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||16
|-
| 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||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]
|-
| ||||[http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Haplotyping/2011-6-6]||[http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Haplotyping/2011-8-24]||[http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Haplotyping/2011-11-4]
|-
| ||seq. analysis||[http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/Haplotyping/2011-6-14]||[http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/Haplotyping/2011-9-7]||[http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:Hap_analysis_on_HL108]
|}
===Sequencing analysis===
===Sequencing analysis===
* Dr. Zhang's link on haplotyping analysis [http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/Haplotyping]
* Dr. Zhang's link on haplotyping analysis [http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/Haplotyping]

Revision as of 18:42, 15 November 2011

Progress

Summary

' ' 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 16
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 HL101, SE60 HL108, SE40
note link lib. Prep. [1] [2] [3]
[4] [5] [6]
seq. analysis [7] [8] [9]

Sequencing analysis

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

Notes

  • "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

2011

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