User:David K. Barclay/Notebook/Controlling Pancreas Cell Fate Using Transcription Factors/2014/04/14

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==RNA Extraction==
 +
*Protocol taken from Dr. Haynes [01/27/2014 http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2014/01/27]
 +
 +
'''RNA Extraction'''
 +
* Use combined TRIzol/ spin column metod. Use RNeasy Mini Kit.
 +
 +
Samples (TRIzol-lysed U2OS samples from -80°C freezer)
 +
# Tube 1-A (+PcTF)
 +
# Tube 1-A (+PcTF)
 +
# Tube 4-A (mock)
 +
# Tube 4-A (mock)
 +
 +
Procedure notes (based on Carly's notes from [http://openwetware.org/wiki/Haynes_Lab:Notebook/Synthetic_Biology_and_Bioinformatics_for_Predictable_Control_of_Therapeutic_Gene2/2013/01/07 1/10/13])<br>
 +
'''TRIzol steps'''
 +
* Clean all work surfaces and pipettors with RNase-zap.
 +
* Thaw TRIzol-lysed cells at room temp
 +
* Under fume hood: Add '''100 μL chloroform''' to each sample
 +
* Shake vigorously (by inverting tubes) for 20 sec. Let sit at room temp. for 2 min.
 +
* Centrifuge in cold room (4°C) for 15 min @ 12,000G
 +
* Pipet off clear phase from organic phase (pink) into new tube (AVOID THE PINK PHASE)
 +
* Check volume of clear phase (in new tubes). Add same volume of 70% ethanol, RNase-free. Mix and incubate at room temp (refer to RNeasy protocol)
 +
'''Spin-column steps'''
 +
* Open up one pink, sealed spin-column (with attached cap) per sample, label it, and place into collection tube(s).
 +
* Transfer RNA/ethanol mix to each spin column.
 +
* Spin tubes at top speed for 30 sec (room temp).
 +
* Discard flow-through liquid and add 700μL of RW1 Buffer to the spin column.
 +
* Spin tubes at top speed for 30 sec (room temp).
 +
* Put collection vial in a fresh collection tube and discard the old one.
 +
* --> Add 500μL of RBE Buffer to the spin column.
 +
* Spin tubes at top speed for 30 sec (room temp) then discard the liquid flow-through.
 +
* Repeat the above two steps again. -->
 +
* Discard the flow-through and spin again.
 +
* Transfer liquid to a fresh 1.5 mL tube (RNase-free) and add 30 μL of RNase-free H<sub>2</sub>O.
 +
* Let tubes sit for 1 min at room temp.
 +
* Spin tubes for 1 min (room temp).
 +
 +
 +
'''Measure RNA Concentration'''
 +
* Use the BioTek Take3 plate/ reader
 +
 +
{|
 +
| Sample || OD 260 || 260/280 || ng/μL
 +
|-
 +
| 1. 1-A (+PcTF) || 1.007 || 2.1 || 805.8
 +
|-
 +
| 2. 1-A (+PcTF) || 0.843 || 2.1 || 674.0
 +
|-
 +
| 3. 4-A (+PcTF) || 0.992 || 2.1 || 793.9
 +
|-
 +
| 4. 4-A (+PcTF) || 0.959 || 2.1 || 767.0
 +
|}
 +
 +
* Keep on ice. Store stock RNA at -80°C after samples are used for cDNA synthesis.
 +
 +
 +
 +
'''cDNA Synthesis'''
 +
* Use Superscript III kit (freezer)
 +
* Pre-heat the heat block to 65°C. Use the PCR strip-tube-compatible block
 +
 +
Procedure notes
 +
* Kit components kept on ice: RNase H, SS III RT, and RNase out
 +
* Kit components thawed at Room temp: Oligo nT, RT Buffer, MgCl2, dNTP mix, water, DTT
 +
 +
* Label four 0.2 mL PCR strip-tubes
 +
* Make 8 μL solutions that contain 2.0 μg RNA
 +
** vol stock RNA (μL) = 2000 ng/ [RNA] from table
 +
** vol H<sub>2</sub>O = 8.0 μL - vol stock RNA
 +
* Make duplicates for each sample. Use RNA stocks #1 and #3.
 +
# Reaction 1: 2.5 μL Stock RNA #1 + 5.5 μL H<sub>2</sub>O = 2.5ug
 +
# Reaction 2: 2.5 μL Stock RNA #1 + 5.5 μL H<sub>2</sub>O = 2.5ug
 +
# Reaction 3: 2.5 μL Stock RNA #3 + 5.5 μL H<sub>2</sub>O = 2.5ug
 +
# Reaction 4: 2.5 μL Stock RNA #3 + 5.5 μL H<sub>2</sub>O = 2.5ug
 +
 +
'''Part 1'''
 +
* Add 1μL of primer (Oligo dT)
 +
* Add 1μL of dNTP
 +
* Total volume is 10 μL
 +
* Incubate for 5 min @ 65°C
 +
* Immediately place on ice and incubate for 1 min.
 +
 +
'''Part 2'''
 +
* Make a master mix for 4 rxns:
 +
** Single reaction = 2 μL RT Buffer, 4 μL MgCl2, 2 μL DTT, 1 μL RNaseOut, 1 μL SuperScript III
 +
** 4 reactions = 8 μL RT Buffer, 16 μL MgCl<sub>2</sub>, 8 μL DTT, 4 μL RNaseOut, and 4 μL SuperScript III
 +
* Carefully add 10μL of MM to each rxn tube
 +
* Mix tubes gently by flicking, centrifuge for a few seconds
 +
 +
'''Part 3'''
 +
* PCR Machine, set up as follows:
 +
# Stage 1: 50 min @ 50°C
 +
# Stage 2: 5 min @ 85°C
 +
# Stage 3: Infinity @ 4°C
 +
* While PCR machine is running, change heat block temp to 37°C
 +
* After PCR program is finished, add 1 μL of RNase H to each reaction. Mix by flicking the tubes.
 +
* Incubate @ 37°C for 20 min
 +
* Store at -20°C

Revision as of 15:51, 15 April 2014

Cell Fate Switch by Synthetic Transcription Factors Main project page
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RNA extraction

Set up

  • TRIzol added to treated/untreated cell pair at time points
3U 3 day untreated
6T 6 day treated
6U 6 day untreated
10T 10 day treated
10U 10 day untreated

RNA Extraction

RNA Extraction

  • Use combined TRIzol/ spin column metod. Use RNeasy Mini Kit.

Samples (TRIzol-lysed U2OS samples from -80°C freezer)

  1. Tube 1-A (+PcTF)
  2. Tube 1-A (+PcTF)
  3. Tube 4-A (mock)
  4. Tube 4-A (mock)

Procedure notes (based on Carly's notes from 1/10/13)
TRIzol steps

  • Clean all work surfaces and pipettors with RNase-zap.
  • Thaw TRIzol-lysed cells at room temp
  • Under fume hood: Add 100 μL chloroform to each sample
  • Shake vigorously (by inverting tubes) for 20 sec. Let sit at room temp. for 2 min.
  • Centrifuge in cold room (4°C) for 15 min @ 12,000G
  • Pipet off clear phase from organic phase (pink) into new tube (AVOID THE PINK PHASE)
  • Check volume of clear phase (in new tubes). Add same volume of 70% ethanol, RNase-free. Mix and incubate at room temp (refer to RNeasy protocol)

Spin-column steps

  • Open up one pink, sealed spin-column (with attached cap) per sample, label it, and place into collection tube(s).
  • Transfer RNA/ethanol mix to each spin column.
  • Spin tubes at top speed for 30 sec (room temp).
  • Discard flow-through liquid and add 700μL of RW1 Buffer to the spin column.
  • Spin tubes at top speed for 30 sec (room temp).
  • Put collection vial in a fresh collection tube and discard the old one.
  • --> Add 500μL of RBE Buffer to the spin column.
  • Spin tubes at top speed for 30 sec (room temp) then discard the liquid flow-through.
  • Repeat the above two steps again. -->
  • Discard the flow-through and spin again.
  • Transfer liquid to a fresh 1.5 mL tube (RNase-free) and add 30 μL of RNase-free H2O.
  • Let tubes sit for 1 min at room temp.
  • Spin tubes for 1 min (room temp).


Measure RNA Concentration

  • Use the BioTek Take3 plate/ reader
Sample OD 260 260/280 ng/μL
1. 1-A (+PcTF) 1.007 2.1 805.8
2. 1-A (+PcTF) 0.843 2.1 674.0
3. 4-A (+PcTF) 0.992 2.1 793.9
4. 4-A (+PcTF) 0.959 2.1 767.0
  • Keep on ice. Store stock RNA at -80°C after samples are used for cDNA synthesis.


cDNA Synthesis

  • Use Superscript III kit (freezer)
  • Pre-heat the heat block to 65°C. Use the PCR strip-tube-compatible block

Procedure notes

  • Kit components kept on ice: RNase H, SS III RT, and RNase out
  • Kit components thawed at Room temp: Oligo nT, RT Buffer, MgCl2, dNTP mix, water, DTT
  • Label four 0.2 mL PCR strip-tubes
  • Make 8 μL solutions that contain 2.0 μg RNA
    • vol stock RNA (μL) = 2000 ng/ [RNA] from table
    • vol H2O = 8.0 μL - vol stock RNA
  • Make duplicates for each sample. Use RNA stocks #1 and #3.
  1. Reaction 1: 2.5 μL Stock RNA #1 + 5.5 μL H2O = 2.5ug
  2. Reaction 2: 2.5 μL Stock RNA #1 + 5.5 μL H2O = 2.5ug
  3. Reaction 3: 2.5 μL Stock RNA #3 + 5.5 μL H2O = 2.5ug
  4. Reaction 4: 2.5 μL Stock RNA #3 + 5.5 μL H2O = 2.5ug

Part 1

  • Add 1μL of primer (Oligo dT)
  • Add 1μL of dNTP
  • Total volume is 10 μL
  • Incubate for 5 min @ 65°C
  • Immediately place on ice and incubate for 1 min.

Part 2

  • Make a master mix for 4 rxns:
    • Single reaction = 2 μL RT Buffer, 4 μL MgCl2, 2 μL DTT, 1 μL RNaseOut, 1 μL SuperScript III
    • 4 reactions = 8 μL RT Buffer, 16 μL MgCl2, 8 μL DTT, 4 μL RNaseOut, and 4 μL SuperScript III
  • Carefully add 10μL of MM to each rxn tube
  • Mix tubes gently by flicking, centrifuge for a few seconds

Part 3

  • PCR Machine, set up as follows:
  1. Stage 1: 50 min @ 50°C
  2. Stage 2: 5 min @ 85°C
  3. Stage 3: Infinity @ 4°C
  • While PCR machine is running, change heat block temp to 37°C
  • After PCR program is finished, add 1 μL of RNase H to each reaction. Mix by flicking the tubes.
  • Incubate @ 37°C for 20 min
  • Store at -20°C



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