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]
- HL095: [11]
- HL101: [12]
- HL108: [13]
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>