Barrick Lab :: DsRNAprepbacteria

---+ Isolation of dsRNA  from bacteria

---+++ Materials and Reagents

Use filter tips. Keep all solutions, reagents and plastics to be used for RNA work separate from general supplies. Solutions need to be certified RNase free.

Equipment:

   * A bench top centrifuge. Refrigerated centrifuge at 4°C is recommended.
   * Nanodrop or Qubit

Solutions:

   * RNase free water
   * 1x PBS (prepared with RNase free water)
   * 150mM NaCl (prepared  with RNase free water)
   * DNase 1 solution for on-column digestion (from Zymo, cat #E1010) (Optional)
   * Ethanol, 95-100% (from Biosci store is fine)
   * Ethanol, 75% (diluted from above with 1x PBS)

---+++ Protocol

   * This protocol starts with a pellet of bacteria cells. Depending on your experiment you will need to spin cells from a saturated 1mL liquid culture (e.g. E. coli) or from resuspended cells grown on an agar plate (e.g. S. alvi). If the pellet comes from -80C storage, make sure it is totally thaw on ice.
   * *Critical* _Rapidly_ resuspend cell pellet in 500ul of RNA extraction solution. Use pipette tip to dislodge a frozen pellet, break apart and triturate until homogeneous. Work quickly to avoid RNase degradation.
   * Incubate sample at 95°C for 7min to lyse cells. Place a weight on top of tubes (or use tube locks) to prevent pressure from opening tubes.
   * Pellet the warm sample by centrifuging at 16 000 x g for 5min at room temperature.
   * Transfer 200ul of supernatant containing RNA to a fresh tube and continue with below RNA clean up. Store the remaining ~300ul at -80°C, as a back up.

The following uses the Zymo clean and concentrator kit:

   * Add 2 volumes (400ul) of RNA Binding Buffer to each volume of RNA sample and mix well.
   * Add 1 volume (600ul) ETOH (95-100%) to the mixture and mix well.
   * Transfer half the mixture to the Zymo-Spin IIC column in a collection tube and centrifuge at &gt;12,000 x g for 1 min. Discard the flow through.
   * Load the remaining half and repeat spin, discard.
   * During this spin, prepare the DNase 1 cocktail for use. Per reaction: 
      * 5ul RNase-Free DNase I
      * 75ul Reaction Buffer
   * Add 400ul of 80% ethanol to the Zymo-Spin IIC column in a collection tube and centrifuge at &gt;12,000 x g for 30 secs. Discard the flow through.
   * Add 80ul DNase I cocktail directly to the matrix of the Zymo-Spin IIC column.
   * Incubate the column at 25-370C for &gt; 15 mins (optimal temp for DNase I is 370C).
   * Centrifuge &gt; 12,000 x g for 30 seconds. Discard the flow through.
   * Add 400ul RNA Prep Buffer to the column and centrifuge at 12,000 x g for 1 minute. Discard the flow trough.
   * Add 800ul RNA Wash Buffer to the column and centrifuge at &gt; 12,000 x g for 30 seconds. Discard the flow through. 
   * Add 400ul RNA Wash Buffer to the column and centrifuge at &gt; 12,000 x g for 2 minutes. Discard the flow through. Remove the column carefully from the collection tube and transfer to new RNase-free tube.
   * Add 30 ul of DNase/RNase-Free water directly to the column matrix and let stand for 1 minute at room temperature.
   * Centrifuge at 10,000 x g for 1 min.
   * Use the eluted RNA immediately or store at -80C.

---+++ Quality check RNA

Assess the RIN and quantity of RNA eluted using the Tapestation (load ~100ng) and Qubit (a dilution of 1/10 will be required to reach linear range), respectively.

-- Main.SimonDAlton - 23 Jan 2017
This topic: Lab > WebHome > ProtocolList > DsRNAprepbacteria
Topic revision: r3 - 2024-05-01 - LucioNavarro