Difference between revisions of "Haynes Lab:Notebook/Jan/2013/10/18"

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|style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;"> Project name</span>
 
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|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>}}
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|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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<!-- ##### DO NOT edit above this line unless you know what you are doing. ##### -->
 
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==Entry title==
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==Extraction and Verification of mCh==
* Insert content here...
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* Name: mCh / BBa_J176005
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** Date of culture inoculation: [http://openwetware.org/wiki/Haynes_Lab:Notebook/Jan/2013/09/26 10/17/13]
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** Results for Cultures 1 and 2: Mixture is cloudy so growth in both. Success.
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** Results for Streaks 1 and 2: Growth in both areas along zig-zag line, although more growth in colony 1 streak than colony 2 streak. Overall success.
 +
 
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* Sample 1: mCh/V0120 colony 1; BBa_J176005; part = 705 bp; vector = 3200 bp
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* Sample 2: mCh/V0120 colony 2; same
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* Sample 3: mCh/V0120 (control DNA); BBa_J176005; part = 705 bp; vector = 3200 bp
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'''DNA Concentration Data'''
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<!-- Wiki code notes: The {| is the opening tag for tables. {{table}} is an OWW template that creates thin grey border lines and cell margins.
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<!-- Each |- starts a new row. There are three rows. bgcolor=#cfcfcf *colors* the *background* of the first row grey.  -->
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<!-- Below that, each | starts a row of cells. -->
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<!-- The symbol || separates cells in a row. Replace the --- in each cell with your data. -->
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<!-- If you have only one plasmid, delete the |- under Plasmid 1's row, and delete the entire row for Plasmid 2.-->
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{| {{table}}
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|- bgcolor=#cfcfcf
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| Plasmid || OD260 || OD260/280 || ng/μL
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|-
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| 1. Plasmid 1 || 0.12 || 1.84 || 120
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|-
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| 2. Plasmid 2 || 0.026 || 1.656 || 26
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|}
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'''Restriction Digest Table'''<br>
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* Checked plasmid minipreps with EcoRI/PstI digests
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{| {{table}} border="1" cellspacing="3"
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<!-- Editing: the coding for this table is a bit more advanced. -->
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<!-- valign="top" aligns all the text in the first row to the top.  -->
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<!-- The | symbols on the next two lines start new cells in the same row. This does the same thing as ||, but you have to use | on new lines to set formatting for cells. -->
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<!-- bgcolor=#cfcfcf *colors* the *background* of the Reagent and Volume cells grey.  -->
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<!-- The next two "rowspan=7" cells span  all 7 rows in the table so that they can fit the "Expected" list and a gel image. rowspan is how you create merged rows in Wiki code. -->
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<!-- Replace Plasmid 1 and 2 with the names of your plasmids. Replace insert size and vector size with appropriate information for your plasmids. If you only have one Plasmid, delete all the text for Plasmid 2
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|- valign="top"
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| bgcolor=#cfcfcf | Reagent
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| bgcolor=#cfcfcf | Volume
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| rowspan="7" | <u>Expected:</u><br>1. Plasmid 1 = 705 bp, 3200 bp<br>2. Plasmid 2 = 705 bp, 3200 bp<br>
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| rowspan="7" | [[Image:Jan_Simper_mCh_DNA_Boot_Camp.jpg|400px|Today's gel]]<br>15 μL/lane; 1% agarose; [http://openwetware.org/wiki/Image:KAH_Fermentas_GeneRuler_1kbplus.jpg Ladder]
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|-
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| DNA(plasmid) || 3.0 μL
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|-
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| 10X buffer || 1.5
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|-
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| EcoRI || 1.0
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|-
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| PstI || 1.0
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|-
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| dH<sub>2</sub>O || 8.5
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|-
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| &nbsp; || 15 μL --> 37°C/ 15 min.
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|}
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Both samples 1 and 3 had a band slightly above the 3000 bp band, which was probably the 3200 bp vector. In addition, both samples 1 and 3 had a band slightly above the 700 bp band, which was likely the 705 bp plasmid. Overall, there is evidence to conclude that Sample 1 is the cloned plasmid DNA because of its similarities to the control DNA. Sample 2 had no bands of any sort and there was likely no DNA there in the first place due to a bad miniprep. Sample 1 was submitted for DNA sequencing to confirm that it is in fact the cloned plasmid DNA.
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'''DNA Sequencing Samples'''
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<!-- * signs create an automatically bulleted list. Replace 'date' with the date you submitted the samples -->
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<!-- The Order Number is shown at the top of your sequencing order form. Record in the indicated spot below -->
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* Submitted to DNASU on: '10/21/13'
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* Order Number: 8258
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<!-- # signs create an automatically numbered list. Replace Plasmid 1 & 2 with the names of your plasmids. Replace 'name' with the appropriate name of each primer. -->
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# mCh - forward primer 'P0001' -- 705 matches, thus 100% matching across the sequence. DNA cloning successful.
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# mCh - reverse primer 'P0002' -- 705 matches, so 100% match. DNA cloning successful.
  
  

Latest revision as of 23:29, 26 September 2017

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Extraction and Verification of mCh

  • Name: mCh / BBa_J176005
    • Date of culture inoculation: 10/17/13
    • Results for Cultures 1 and 2: Mixture is cloudy so growth in both. Success.
    • Results for Streaks 1 and 2: Growth in both areas along zig-zag line, although more growth in colony 1 streak than colony 2 streak. Overall success.
  • Sample 1: mCh/V0120 colony 1; BBa_J176005; part = 705 bp; vector = 3200 bp
  • Sample 2: mCh/V0120 colony 2; same
  • Sample 3: mCh/V0120 (control DNA); BBa_J176005; part = 705 bp; vector = 3200 bp


DNA Concentration Data

Plasmid OD260 OD260/280 ng/μL
1. Plasmid 1 0.12 1.84 120
2. Plasmid 2 0.026 1.656 26


Restriction Digest Table

  • Checked plasmid minipreps with EcoRI/PstI digests
Reagent Volume Expected:
1. Plasmid 1 = 705 bp, 3200 bp
2. Plasmid 2 = 705 bp, 3200 bp
Today's gel
15 μL/lane; 1% agarose; Ladder
DNA(plasmid) 3.0 μL
10X buffer 1.5
EcoRI 1.0
PstI 1.0
dH2O 8.5
  15 μL --> 37°C/ 15 min.

Both samples 1 and 3 had a band slightly above the 3000 bp band, which was probably the 3200 bp vector. In addition, both samples 1 and 3 had a band slightly above the 700 bp band, which was likely the 705 bp plasmid. Overall, there is evidence to conclude that Sample 1 is the cloned plasmid DNA because of its similarities to the control DNA. Sample 2 had no bands of any sort and there was likely no DNA there in the first place due to a bad miniprep. Sample 1 was submitted for DNA sequencing to confirm that it is in fact the cloned plasmid DNA.


DNA Sequencing Samples

  • Submitted to DNASU on: '10/21/13'
  • Order Number: 8258
  1. mCh - forward primer 'P0001' -- 705 matches, thus 100% matching across the sequence. DNA cloning successful.
  2. mCh - reverse primer 'P0002' -- 705 matches, so 100% match. DNA cloning successful.