Rui:Haplotying: Difference between revisions

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==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===
* Dr. Zhang's link on haplotyping analysis [http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/Haplotyping]
* HL095: [http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/Haplotyping/2011-6-14]
* HL101: [http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/Haplotyping/2011-9-7]
* HL108: [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:Hap_analysis_on_HL108]
===Notes===
* "Methylation haplotyping on few cells" project: May 27th email [http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/Haplotyping/2011-5-12]
* 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>

Latest revision as of 00:56, 7 December 2011