Difference between revisions of "User:Behzad Damadzadeh/Notebook/PcTF Subcloning in E-coli/2012/11/16"

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|style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;">PcTF Subcloning in E. coli</span>
 
|style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;">PcTF Subcloning in E. coli</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>}}
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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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=Date=
+
=11/16/12=
  
'''List title'''
+
*'''[[User:Karmella Haynes|---Karmella]] 13:51, 16 November 2012 (EST)''': Here is my suggested procedure for trying the PcTF fusion cloning...
# List items
+
 
 +
----
 +
'''Assemblies''': Shown as Part/cuts/purified fragment size
 +
# KAH109/pT7CFE1-CHis: KAH109/(E/P)/1132 + pT7CFE1-CHis/(E/P)/3600
 +
# KAH111/pT7CFE1-CHis: KAH184/(E/S)/1123 + "
 +
# KAH112/pT7CFE1-CHis: KAH187/(E/S)/1123 + "
 +
# KAH115/pT7CFE1-CHis: KAH188/(E/S)/931 + "
 +
# KAH148/pT7CFE1-CHis: KAH189/(E/S)/967 + "
 +
# KAH150/pT7CFE1-CHis: KAH190/(E/S)/967 + "
 +
# KAH151/pT7CFE1-CHis: KAH191/(E/S)/967 + "
 +
 
 +
* Note: KAH109 is being re-done as an internal control to trouble-shoot the ligation<br>
 +
* Note: KAH111-KAH151 are all cut and purified already
 +
 
 +
 
 +
'''Digest (Fermentas FD)'''<br>
 +
# pT7CFE1-CHis, E/P
 +
# KAH109 E/P
 +
# KAH111 E/P
 +
# KAH112 E/P
 +
# KAH115 E/P
 +
# KAH148 E/P
 +
# KAH150 E/P
 +
# KAH151 E/P
 +
 
 +
{| class="wikitable" border="0" cellspacing="3" <!-- Digest rxn. table -->
 +
|- valign="top"
 +
| <u>Reagent</u> || <u>Volume</u> || &nbsp;
 +
| rowspan="9" |  [[Image:PcTF_in-vitro_Expression.png‎|350px|Cloning digest ]]<br>30 μL/lane, 1% agarose
 +
|-
 +
| DNA (plasmid) || 25.0 μL
 +
|-
 +
| 10x buffer || 3.0
 +
|-
 +
| EcoRI || 1.0
 +
|-
 +
| PstI || 1.0
 +
|-
 +
| dH<sub>2</sub>O || 0
 +
|-
 +
| &nbsp; || 30 μL --> 37°C/ ~30 min.
 +
|}
 +
 
 +
 
 +
 
 +
'''Measure concentration(s)'''
 +
{| class="wikitable" border="0" cellspacing="3" <!-- [DNA] table -->
 +
|-
 +
| <u>Sample</u> || <u>OD260</u> || <u>260/280</u> || <u>ng/μL</u>
 +
|-
 +
| 1. pT7CFE1-CHis (E/P) || --- || 1.829 || 57.344
 +
|-
 +
| 2. KAH109  (E/P) || --- || 2.354 || 36.072
 +
|-
 +
| 3. KAH111  (E/P) || --- || 2.238 || 15.003
 +
|-
 +
| 4. KAH112  (E/P) || --- || 1.862 || 22.857
 +
|-
 +
| 5. KAH115  (E/P) || --- || 2.096 || 18.312
 +
|-
 +
| 6. KAH148  (E/P) || --- || 2.389 || 23.735
 +
|-
 +
| 7. KAH150  (E/P) || --- || 1.99 || 19.822
 +
|-
 +
| 8. KAH151  (E/P) || --- || 1.9 || 19.701
 +
|}
 +
 
 +
 
 +
'''Ligations''' (trouble shooting suggestions)
 +
* Note: Use 50 ng of vector this time (instead of 20)
 +
* Note: Use a 3:1 ratio of insert to vector... x μL insert = 3 * (bp of insert/ bp of vector) * 50 ng vector / (concentration of insert ng/μL)
 +
 
 +
{| class="wikitable" border="0" cellspacing="3" <!-- Ligation rxn table -->
 +
| &nbsp;            || 1    || 2    || 3    || 4    || 5    || 6    || 7    || 8 
 +
|-
 +
| Insert Name      || KAH109  || KAH111  || KAH112  || KAH115  || KAH148  || KAH150  || KAH151  || N/A
 +
|-
 +
| Insert DNA        || 1.3  || 3.12 || 2.05  || 2.12  || 1.7 || 2.03  || 2.05  || 0
 +
|-
 +
| Vector DNA        || 0.87  || 0.87  || 0.87  || 0.87  || 0.87  || 0.87  || 0.87  || 0.87
 +
|-
 +
| 2x lgn buf (Roche) || 5.0  || 5.0  || 5.0  || 5.0  || 5.0  || 5.0  || 5.0  || 5.0
 +
|-
 +
| T4 ligase (NEB)    || 1.0  || 1.0  || 1.0  || 1.0  || 1.0  || 1.0  || 1.0  || 1.0
 +
|-
 +
| dH<sub>2</sub>O    || 1.83  || 0.01  || 1.08  || 1.01  || 1.43  || 1.1  || 1.08  || 3.13
 +
|-
 +
| &nbsp;            || 10 μL || 10 μL || 10 μL || 10 μL || 10 μL || 10 μL || 10 μL || 10 μL
 +
|}
 +
 
 +
'''Plates Nomenclature
 +
# BD-116, (KAH109)
 +
# BD-117, (KAH111)
 +
# BD-118, (KAH112)
 +
# BD-119, (KAH115)
 +
# BD-120, (KAH148)
 +
# BD-121, (KAH150)
 +
# BD-122, (KAH151)
 +
# CTRL
 +
 
 +
* Add total ligation reaction to 30 μL DH5α-Turbo cells
 +
* Follow routine "fast" transformation procedure
 +
* Plate onto 100 ug/mL Amp agar plates

Latest revision as of 21:16, 26 September 2017

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11/16/12

  • ---Karmella 13:51, 16 November 2012 (EST): Here is my suggested procedure for trying the PcTF fusion cloning...

Assemblies: Shown as Part/cuts/purified fragment size

  1. KAH109/pT7CFE1-CHis: KAH109/(E/P)/1132 + pT7CFE1-CHis/(E/P)/3600
  2. KAH111/pT7CFE1-CHis: KAH184/(E/S)/1123 + "
  3. KAH112/pT7CFE1-CHis: KAH187/(E/S)/1123 + "
  4. KAH115/pT7CFE1-CHis: KAH188/(E/S)/931 + "
  5. KAH148/pT7CFE1-CHis: KAH189/(E/S)/967 + "
  6. KAH150/pT7CFE1-CHis: KAH190/(E/S)/967 + "
  7. KAH151/pT7CFE1-CHis: KAH191/(E/S)/967 + "
  • Note: KAH109 is being re-done as an internal control to trouble-shoot the ligation
  • Note: KAH111-KAH151 are all cut and purified already


Digest (Fermentas FD)

  1. pT7CFE1-CHis, E/P
  2. KAH109 E/P
  3. KAH111 E/P
  4. KAH112 E/P
  5. KAH115 E/P
  6. KAH148 E/P
  7. KAH150 E/P
  8. KAH151 E/P
Reagent Volume   Cloning digest
30 μL/lane, 1% agarose
DNA (plasmid) 25.0 μL
10x buffer 3.0
EcoRI 1.0
PstI 1.0
dH2O 0
  30 μL --> 37°C/ ~30 min.


Measure concentration(s)

Sample OD260 260/280 ng/μL
1. pT7CFE1-CHis (E/P) --- 1.829 57.344
2. KAH109 (E/P) --- 2.354 36.072
3. KAH111 (E/P) --- 2.238 15.003
4. KAH112 (E/P) --- 1.862 22.857
5. KAH115 (E/P) --- 2.096 18.312
6. KAH148 (E/P) --- 2.389 23.735
7. KAH150 (E/P) --- 1.99 19.822
8. KAH151 (E/P) --- 1.9 19.701


Ligations (trouble shooting suggestions)

  • Note: Use 50 ng of vector this time (instead of 20)
  • Note: Use a 3:1 ratio of insert to vector... x μL insert = 3 * (bp of insert/ bp of vector) * 50 ng vector / (concentration of insert ng/μL)
  1 2 3 4 5 6 7 8
Insert Name KAH109 KAH111 KAH112 KAH115 KAH148 KAH150 KAH151 N/A
Insert DNA 1.3 3.12 2.05 2.12 1.7 2.03 2.05 0
Vector DNA 0.87 0.87 0.87 0.87 0.87 0.87 0.87 0.87
2x lgn buf (Roche) 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0
T4 ligase (NEB) 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
dH2O 1.83 0.01 1.08 1.01 1.43 1.1 1.08 3.13
  10 μL 10 μL 10 μL 10 μL 10 μL 10 μL 10 μL 10 μL

Plates Nomenclature

  1. BD-116, (KAH109)
  2. BD-117, (KAH111)
  3. BD-118, (KAH112)
  4. BD-119, (KAH115)
  5. BD-120, (KAH148)
  6. BD-121, (KAH150)
  7. BD-122, (KAH151)
  8. CTRL
  • Add total ligation reaction to 30 μL DH5α-Turbo cells
  • Follow routine "fast" transformation procedure
  • Plate onto 100 ug/mL Amp agar plates