User:Behzad Damadzadeh/Notebook/PcTF Subcloning in E-coli/2013/06/06

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==06/06/2013==
==06/06/2013==
 +
<!-- Precede each finished task with a checkmark &#x2713; -->
 +
* &#x2713; Minipreps: FlpE (4)
 +
 +
----
 +
'''Minipreps'''<br>
 +
> Check with E, P, and E/P digests
 +
 +
{| {{table}} cellspacing="7"  width=700px
 +
|-valign="top"
 +
| <u>Reagent</u> || <u>1,4,7,10</u> || <u>2,5,8,11</u> || <u>3,6,9,12</u>
 +
| rowspan="7" | <u>Expected:</u><br>1. FlpE, E = 7160, 546<br>2. FlpE, P = 7706<br>3.FlpE, E/P=5649, 1511, 546
 +
| rowspan="7" | [[Image:Flp-E.jpg|300px|E/P digests 05/06/10]]<br>15 μL/lane; 1% agarose
 +
|-
 +
| DNA(plasmid) || 2.0 || 2.0 || 2.0
 +
|-
 +
| 10X buffer || 1.5 || 1.5 || 1.5
 +
|-
 +
| EcoRI || 1.0 || --- || 1.0
 +
|-
 +
| PstI || --- || 1.0 || 1.0
 +
|-
 +
| dH<sub>2</sub>O || 10.5 || 10.5 || 9.5
 +
|-
 +
| &nbsp;<br>&nbsp;<br>&nbsp;<br>&nbsp;||
 +
|}
 +
 +
15 μL --> 37°C/ ~15 min.
 +
 +
 +
--> Conclusion: Success! Combine 4 preps (300μL total) for DNA clean-up (tomorrow)<br>
 +
--> Streak clone (saved toothpick) onto 100 μg/mL Amp plate.<br>
 +
<!-- Precede each finished task with a checkmark &#x2713; -->
<!-- Precede each finished task with a checkmark &#x2713; -->
-
* &#x2713; Transfections: H3me reporters into cell lines KAH126-1, 130-2, 132-8
+
* &#x2713; Transfections: H3K27me3 reporters into cell lines BD002 (KAH201+KAH182+V0200)
* &#x2713; Polycomb-ATF negative control lines: colony plates
* &#x2713; Polycomb-ATF negative control lines: colony plates
----
----
 +
 +
'''1 day before transfection:'''<br>
 +
# Seed cultures in 6-well plates at ~2.5x10<suP>5</sup> so that cells will be ~5.0x10<sup>5</sup> at the time of transfection.
 +
'''Transfections'''<br>
'''Transfections'''<br>
-
> U2OS Flp-in T-REx lines (puro/zeo/blast) + Polycomb-ATF plasmids (hygro)<br>
+
 
 +
> U2OS Flp-in T-REx lines (puro/zeo/blast) + FRT-marked mammalian transfection vector (hygro)<br>
--> Note: co-transfect with FlpE (1:3); hygro resistance replaces zeo resistance after "Flp" in<br>
--> Note: co-transfect with FlpE (1:3); hygro resistance replaces zeo resistance after "Flp" in<br>
> Use Lipofectamine, 6-well format<br>
> Use Lipofectamine, 6-well format<br>
> Plates:
> Plates:
-
# KAH126-1 Flp-in T-REx
+
# BD002 (3:1) Flp-in T-REx
-
# KAH130-2 Flp-in T-REx
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#BD002 (4:1) Flp-in T-REx
-
# KAH132-8 Flp-in T-REx
+
 +
BD002 (3:1) = 339 ng/μl
 +
BD002 (4:1) = 317 ng/μl
 +
KAH187 = 441.5 ng/μl
 +
FlpE = 192 ng/μl
-
{| class="wikitable" border="0" cellspacing="5" <!-- Transfection table -->
+
{| {{table}} cellspacing="7" width=700px
|-
|-
-
| <u>Plate-Well</u> || <u>Plasmid</u> || <u>DNA</u> || <u>Volume</u> || <u>Lipo</u>  || <u>Opti-MEM (total)</u>
+
| Plate-Well || Plasmid || DNA || Volume|| dH2O|| Lipo || PLUS reagent || <u>Opti-MEM (total)</u>
|-
|-
-
| 1-1            || KAH96/V0201 + FlpE  || 1.5 + 0.5 μg || 2.4 + 1.4 μL || 4 μL      || 500 μL
+
| 1-1            || BD002 (3:1) + FlpE  || 1.5 + 0.5 μg || 4.42 + 2.60 μL || 12.98μL|| 2.5μL|| 7.5 μL      || 570 μL
|-
|-
-
| 1-2            || KAH142/V0201 + FlpE || "          || 2.4 + 1.4 μL  || "             || "
+
| 1-2            || BD002 (4:1) + FlpE || "          || 4.73 + 2.60 μL  || 12.67μL|| "  ||    "       || "
|-
|-
-
| 1-3           || KAH146/V0201 + FlpE || "          || 6.4 + 1.4 μL   || "             || "
+
| 1-3 (-) Ctrl    || BD002 (3:1) + --- || 2 μg      || 4.42 + --- μL || 15.58μL || "    ||  "     || "
|-
|-
-
| 1-4           || KAH147/V0201 + FlpE || "          || 9.6 + 1.4 μL   || "             || "
+
| 1-4 (-)Ctrl      || --- + --- || 0 μg        || --- + --- μL || 20.0μL|| "    ||   "   || "
|-
|-
-
| ---
+
|1-5             || KAH187    ||  20 μg        ||  4.53 || 15.46μL||     " || "||"
-
|-
+
-
| 2-1            || KAH96/V0201 + FlpE  || 1.5 + 0.5 μg || 2.4 + 1.4 μL || 4 μL      || 500 μL
+
-
|-
+
-
| 2-2            || KAH142/V0201 + FlpE || "          || 2.4 + 1.4 μL   || "            || "
+
-
|-
+
-
| 2-3            || KAH146/V0201 + FlpE || "          || 6.4 + 1.4 μL   || "            || "
+
-
|-
+
-
| 2-4           || KAH147/V0201 + FlpE || "          || 9.6 + 1.4 μL  || "            || "
+
-
|-
+
-
| ---
+
-
|-
+
-
| 3-1            || KAH96/V0201 + FlpE || 1.5 + 0.5 μg || 2.4 + 1.4 μL || 4 μL      || 500 μL
+
-
|-
+
-
| 3-2            || KAH142/V0201 + FlpE || "         || 2.4 + 1.4 μL  || "             || "
+
-
|-
+
-
| 3-3            || KAH146/V0201 + FlpE || "          || 6.4 + 1.4 μL  || "            || "
+
-
|-
+
-
| 3-4            || KAH147/V0201 + FlpE || "          || 9.6 + 1.4 μL  || "            || "
+
|}
|}
-
> Add 16 μL (4x) Lipo to 1000 μL (4x) Opti-MEM --> R.T/ 5 min. <br>
+
# Prepare DNA-Lipofectamine complexes (600 μl per sample) as follows:
-
> Add DNA to 250 μL Opti-MEM <br>
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## Label sterile microfuge (1.5 ml) tubes.
-
> Add 250 Lipo mix into each 250 DNA mix --> R.T./ 20 min. <br>
+
## Add '''570 μL Opti-MEM''' to each 20 μL DNA sample.
-
> Add 500 μL complexes to each 3.5 mL well (4 ml med. total each); Grow cells at 37&deg;C<br>
+
## Add '''2.5 μL PLUS reagent''' to each DNA+Opti-MEM sample. Incubate for 5 minutes at room temperature.
-
> Refresh medium after 5 hours (ab-free)<br>
+
## Add '''7.5 μL Lipofectamine LTX''' to each DNA+Opti-MEM+PLUS reagent sample. Incubate for 30 minutes at room temperature.
-
> Grow for one/two days, then plate dilution cultures in selection medium (+hygro)
+
# Add the total 600 μL of DNA+Opti-MEM+PLUS reagent+Lipofectamine mixture '''drop-wise''' to each appropriate well of cells.
 +
# Incubate cells at 37°C in a CO<sub>2</sub> incubator
 +
# (Optional) To reduce toxicity, after 5-6 hours wash cells once with warm 1xPBS to remove excess DNA-Lipo complexes. Add fresh antibiotic-free growth medium.
 +
Transgene expression should be detectable after 18 hours.
-
----
 
-
 
-
'''Polycomb-ATF negative control lines: colony plates'''<br>
 
-
> For each line make 2 plates: ~1x10<sup>5</sup> and 5x10<sup>4</sup> cells<br>
 
-
> 25 ml 1 μg/mL puro, 15 μg/mL blast, 200 μg/mL zeo<br>
 
-
> Also make 6-well back-up plate for all transfections (~3x10<sup>5</sup> cells in selection medium)
 
 +
----
<!-- ##### DO NOT edit below this line unless you know what you are doing. ##### -->
<!-- ##### DO NOT edit below this line unless you know what you are doing. ##### -->
-
|}
 
__NOTOC__
__NOTOC__

Current revision

PcTF Subcloning in E. coli Main project page
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06/06/2013

  • ✓ Minipreps: FlpE (4)

Minipreps
> Check with E, P, and E/P digests

Reagent 1,4,7,10 2,5,8,11 3,6,9,12 Expected:
1. FlpE, E = 7160, 546
2. FlpE, P = 7706
3.FlpE, E/P=5649, 1511, 546
E/P digests 05/06/10
15 μL/lane; 1% agarose
DNA(plasmid) 2.0 2.0 2.0
10X buffer 1.5 1.5 1.5
EcoRI 1.0 --- 1.0
PstI --- 1.0 1.0
dH2O 10.5 10.5 9.5
 
 
 
 

15 μL --> 37°C/ ~15 min.


--> Conclusion: Success! Combine 4 preps (300μL total) for DNA clean-up (tomorrow)
--> Streak clone (saved toothpick) onto 100 μg/mL Amp plate.


  • ✓ Transfections: H3K27me3 reporters into cell lines BD002 (KAH201+KAH182+V0200)
  • ✓ Polycomb-ATF negative control lines: colony plates



1 day before transfection:

  1. Seed cultures in 6-well plates at ~2.5x105 so that cells will be ~5.0x105 at the time of transfection.

Transfections

> U2OS Flp-in T-REx lines (puro/zeo/blast) + FRT-marked mammalian transfection vector (hygro)
--> Note: co-transfect with FlpE (1:3); hygro resistance replaces zeo resistance after "Flp" in
> Use Lipofectamine, 6-well format
> Plates:

  1. BD002 (3:1) Flp-in T-REx
  2. BD002 (4:1) Flp-in T-REx

BD002 (3:1) = 339 ng/μl BD002 (4:1) = 317 ng/μl KAH187 = 441.5 ng/μl FlpE = 192 ng/μl

Plate-Well Plasmid DNA Volume dH2O Lipo PLUS reagent Opti-MEM (total)
1-1 BD002 (3:1) + FlpE 1.5 + 0.5 μg 4.42 + 2.60 μL 12.98μL 2.5μL 7.5 μL 570 μL
1-2 BD002 (4:1) + FlpE " 4.73 + 2.60 μL 12.67μL " " "
1-3 (-) Ctrl BD002 (3:1) + --- 2 μg 4.42 + --- μL 15.58μL " " "
1-4 (-)Ctrl --- + --- 0 μg --- + --- μL 20.0μL " " "
1-5 KAH187 20 μg 4.53 15.46μL " ""
  1. Prepare DNA-Lipofectamine complexes (600 μl per sample) as follows:
    1. Label sterile microfuge (1.5 ml) tubes.
    2. Add 570 μL Opti-MEM to each 20 μL DNA sample.
    3. Add 2.5 μL PLUS reagent to each DNA+Opti-MEM sample. Incubate for 5 minutes at room temperature.
    4. Add 7.5 μL Lipofectamine LTX to each DNA+Opti-MEM+PLUS reagent sample. Incubate for 30 minutes at room temperature.
  2. Add the total 600 μL of DNA+Opti-MEM+PLUS reagent+Lipofectamine mixture drop-wise to each appropriate well of cells.
  3. Incubate cells at 37°C in a CO2 incubator
  4. (Optional) To reduce toxicity, after 5-6 hours wash cells once with warm 1xPBS to remove excess DNA-Lipo complexes. Add fresh antibiotic-free growth medium.

Transgene expression should be detectable after 18 hours.




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