CTR:Notebook/Migrant/2017/03/28: Difference between revisions

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|style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;"> Project name</span>
|style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;"> Project name</span>
|style="background-color: #F2F2F2" align="center"|<html><img src="/images/9/94/Report.png" border="0" /></html> [[{{#sub:{{FULLPAGENAME}}|0|-11}}|Main project page]]<br />{{#if:{{#lnpreventry:{{FULLPAGENAME}}}}|<html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>[[{{#lnpreventry:{{FULLPAGENAME}}}}{{!}}Previous entry]]<html>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</html>}}{{#if:{{#lnnextentry:{{FULLPAGENAME}}}}|[[{{#lnnextentry:{{FULLPAGENAME}}}}{{!}}Next entry]]<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html>}}
|style="background-color: #F2F2F2" align="center"|[[File:Report.png|frameless|link={{#sub:{{FULLPAGENAME}}|0|-11}}]][[{{#sub:{{FULLPAGENAME}}|0|-11}}|Main project page]]<br />{{#if:{{#lnpreventry:{{FULLPAGENAME}}}}|[[File:Resultset_previous.png|frameless|link={{#lnpreventry:{{FULLPAGENAME}}}}]][[{{#lnpreventry:{{FULLPAGENAME}}}}{{!}}Previous entry]]&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;}}{{#if:{{#lnnextentry:{{FULLPAGENAME}}}}|[[{{#lnnextentry:{{FULLPAGENAME}}}}{{!}}Next entry]][[File:Resultset_next.png|frameless|link={{#lnnextentry:{{FULLPAGENAME}}}}]]}}
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*Diluted samples 0874-05557 (BUOW) & 98N2049 (COYE) to 1ug of DNA in 100 uL total of Low TE
*Diluted samples 0874-05557 (BUOW) & 98N2049 (COYE) to 1ug of DNA in 100 uL total of Low TE


* Sonication (2017-03-28)
* Sonication (2017-04-10)
**BioRuptor NGS: 4 cycles of 30 seconds on, 90 seconds off, High Power
**BioRuptor NGS: 4 cycles of 30 seconds on, 90 seconds off, High Power
[[Image:BUOW COYE WG Sheared 03282017.JPG|150px]]  
[[Image:BUOW COYE Sheared 04102017.JPG|100px]]  


1) 2uL sheared BUOW
1) 2uL sheared BUOW
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<br>
<br>


* Dried down samples to get concentrated volume of 50 uL using SpeedVac (2017-03-28)
* Dried down samples to get concentrated volume of 50 uL using SpeedVac (2017-04-10)


* Clean-up fragmented DNA (2015-09-30)
* Clean-up fragmented DNA (2017-04-11)


* End Repair and Size Selection- edited to size select for 400bp (2015-09-30)
* End Repair and Size Selection- edited to size select for 400bp (2017-04-11)
**Made a diluted bead mixture with the ratio of 105ul beads: 79ul dH<sub>2</sub>O and added 160 ul of mixture to each tube
**Made a diluted bead mixture with the ratio of 109.25ul beads: 74.75ul dH<sub>2</sub>O and added 160 ul of mixture to each tube
[[Image:Sizeselect 20150930.jpg|150px]]  
[[Image:BUOW COYE sizeselect 04112017.JPG|100px]]  


1) 2uL YWAR
1) 2uL BUOW


2) 2uL 100bp low scale ladder,  
2) 2uL 100bp low scale ladder,  


3) 2uL WIFL
3) 2uL COYE


* Adenylate 3' Ends (2015-09-30)
* Adenylate 3' Ends (2017-04-12)
** Ran on JOHN thermocycler under program: SDCRKAD, Block B
** Ran on JOHN thermocycler under program: SDCRKAD, Block B


*Ligate Adapters (2015-09-30)
*Ligate Adapters (2017-04-12)
**Assigned Adapter 2 to YWAR and Adapter 4 to WIFL
**'''Assigned Adapter 3 to BUOW and Adapter 8 to COYE'''


*Gel of Final Library:
*Gel of Final Library:
[[Image:Finallibrary 20150930.jpg|150px]]  
[[Image:BUOW COYE final 04122017.JPG|100px]]  


1) 2uL YWAR
1) 2uL BUOW


2) 2uL 100bp low scale ladder,  
2) 2uL 100bp low scale ladder,  


3) 2uL WIFL
3) 2uL COYE


* Picogreen:
* Qubit:
**YWAR: 7.42 ng/μL
**'''BUOW: 7.72 ng/μL'''
**WIFL: 6.72 ng/μL
**'''COYE: 7.12 ng/μL'''


*Run 1μL of sample + 2μL of dH<sub>2</sub>O on BioAnalyzer DNA High Sensitivity Chip (2015-09-30)
*Run 1μL of sample + 2μL of dH<sub>2</sub>O on BioAnalyzer DNA High Sensitivity Chip (2017-04-12)
**YWAR
**BUOW
[[Image:YWAR Bioanalyzer.png|550px]]
[[Image:BUOW WG Bioanalyzer.JPG|500px]]
*WIFL
*COYE
[[Image:WIFL bioanalyzer.jpg|550px]]
[[Image:COYE WG Bioanalyzer.JPG|500px]]


*[http://openwetware.org/images/5/51/SmitT-Winnie-100115-2100_expert_High_Sensitivity_DNA_Assay_DE72905009_2015-10-01_09-57-14_%282%29.pdf Bioanalyzer Results]
*[http://www.openwetware.org/wiki/Image:BUOW_COYE_WG_Bioanalyzer_04122017.pdf Bioanalyzer Results]


*Sent 10nM to Berkeley for sequencing (Illumina HiSeq 250 PER (Rapid Mode)) (2015-10-01)
*Sent 10nM to Berkeley for sequencing (Illumina HiSeq 250 PER (Rapid Mode)) (2017-04-16)


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Latest revision as of 02:17, 27 September 2017

Project name Main project page
Previous entry      Next entry

Whole Genome Sequencing PCR-Free Library Prep for BUOW & COYE

  • Used TruSeq Library Prep Kit
  • Diluted samples 0874-05557 (BUOW) & 98N2049 (COYE) to 1ug of DNA in 100 uL total of Low TE
  • Sonication (2017-04-10)
    • BioRuptor NGS: 4 cycles of 30 seconds on, 90 seconds off, High Power

1) 2uL sheared BUOW

2) 2uL 100bp low scale ladder,

3) 2uL sheared COYE →Sheared DNA to ~400bp.

  • Dried down samples to get concentrated volume of 50 uL using SpeedVac (2017-04-10)
  • Clean-up fragmented DNA (2017-04-11)
  • End Repair and Size Selection- edited to size select for 400bp (2017-04-11)
    • Made a diluted bead mixture with the ratio of 109.25ul beads: 74.75ul dH2O and added 160 ul of mixture to each tube

1) 2uL BUOW

2) 2uL 100bp low scale ladder,

3) 2uL COYE

  • Adenylate 3' Ends (2017-04-12)
    • Ran on JOHN thermocycler under program: SDCRKAD, Block B
  • Ligate Adapters (2017-04-12)
    • Assigned Adapter 3 to BUOW and Adapter 8 to COYE
  • Gel of Final Library:

1) 2uL BUOW

2) 2uL 100bp low scale ladder,

3) 2uL COYE

  • Qubit:
    • BUOW: 7.72 ng/μL
    • COYE: 7.12 ng/μL
  • Run 1μL of sample + 2μL of dH2O on BioAnalyzer DNA High Sensitivity Chip (2017-04-12)
    • BUOW

  • COYE

  • Sent 10nM to Berkeley for sequencing (Illumina HiSeq 250 PER (Rapid Mode)) (2017-04-16)
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