For the best experience on the Abcam website please upgrade to a modern browser such as Google Chrome

Hello. We're improving abcam.com and we'd welcome your feedback.

Hello. We're improving abcam.com and we'd welcome your feedback.

Infomation icon

We haven't added this to the BETA yet

New BETA website

New BETA website

Hello. We're improving abcam.com and we'd welcome your feedback.

Take a look at our BETA site and see what we’ve done so far.

Switch on our new BETA site

Now available

Search and browse selected products

  • A selection of primary antibodies

Purchase these through your usual distributor

In the coming months

  • Additional product types
  • Supporting content
  • Sign in to your account
  • Purchase online
United States
Your country/region is currently set to:

If incorrect, please enter your country/region into the box below, to view site information related to your country/region.

Call (888) 77-ABCAM (22226) or contact us
Need help? Contact us

  • My account
  • Sign out
Sign in or Register with us

Welcome

Sign in or

Don't have an account?

Register with us
My basket
Quick order
Abcam homepage

  • Research Products
    By product type
    Primary antibodies
    Secondary antibodies
    ELISA and Matched Antibody Pair Kits
    Cell and tissue imaging tools
    Cellular and biochemical assays
    Proteins and Peptides
    By product type
    Proteomics tools
    Agonists, activators, antagonists and inhibitors
    Cell lines and Lysates
    Multiplex miRNA assays
    Multiplex Assays
    By research area
    Cancer
    Cardiovascular
    Cell Biology
    Epigenetics
    Metabolism
    Developmental Biology
    By research area
    Immunology
    Microbiology
    Neuroscience
    Signal Transduction
    Stem Cells
  • Customized Products & Partnerships
    Customized Products & Partnerships

    Customized products and commercial partnerships to accelerate your diagnostic and therapeutic programs.

    Customized products

    Partner with us

  • Support
    Support hub

    Access advice and support for any research roadblock

    View support hub

    Protocols

    Your experiments laid out step by step

    View protocols

  • Events
    • Conference calendar
    • Cancer
    • Cardiovascular
    • Epigenetics & Nuclear signaling
    • Immunology
    • Neuroscience
    • Stem cells
    • Tradeshows
    • Scientific webinars
    Keep up to date with the latest events

    Full event breakdown with abstracts, speakers, registration and more

    View global event calendar

  • Pathways
    Cell signalling pathways

    View all pathways

    View all interactive pathways

RNA isolation and reverse transcription protocol for cells in culture

Related

  • RNA immunoprecipitation (RIP) protocol
    • Non-coding RNAs guide
      • RNA interference - a comprehensive overview
        • Video protocols library

          ​Procedure for the isolation, DNase treatment and reverse transcription of RNA from cell culture.

          Reviewed November 11, 2021

          Download or print this protocol.

          Contents 

          • Reagents
          • RNA isolation procedure for cells
          • DNase treatment of RNA samples
          • Reverse transcription of DNase treated RNA


          ​Reagents

          • Ice-cold PBS
          • TRIzol
          • Chloroform
          • Isopropanol
          • 75% ethanol
          • DEPC treated H2O/water
          • DEPC treated TE buffer
          • DNase cocktail: Rq1 RNase free DNase, DNase 10X reaction buffer, DEPC-treated H2O, RNase Out
          • RT sample: DEPC-treated water, 5X first stand buffer, DTT 0.1M, primers with 0.1ug/ul or 1/30 dilution of 3 ug/ul, BSA


          Method

          1. RNA isolation procedure for cells

          1.1 Using at least 106 cells, aspirate the media and wash once with ice-cold PBS (1–2 ml).

          1.2 Aspirate the PBS (remove as much as possible) and add 1 ml TRIzol.

          1.3 Scrape the plate briefly, then remove the TRIzol with a pipette and deposit the TRIzol/cell lysate into a 1.5 ml Eppendorf tube.

          1.4 Leave at room temperature for 5 min.

          1.5 Add 250 µl chloroform and shake the tube vigorously for about 15 sec.

          1.6 Leave at room temperature for 5 min.

          1.7 Centrifuge at 10,000 rpm for 5 min.

          1.8 At this point, there will be three layers in each tube:

          Top layer: clear, aqueous

          Middle layer/interphase: white precipitated DNA

          Bottom layer: pink organic phase

          Carefully remove the aqueous phase using a pipette. Leave behind some of the aqueous phase (about 1 mm above DNA layer to prevent DNA contamination). Place in another 1.5 ml Eppendorf tube.

          Tip: Avoid working with large pipettes here, as it is harder to control the rate and force of fluid withdrawal and this increases the likelihood of drawing some of the organic or DNA phase.

          1.9 Add 550 µl isopropanol to the aqueous phase and mix gently. Leave at room temperature for 5 min.

          1.10 Centrifuge at maximal speed (14,000 rpm) for 20 min. If a low yield is expected, centrifuge for 30 min.

          1.11 Place samples on ice. There should be a pellet barely visible at the base of each tube. Pour off the isopropanol and add 1 ml 75% ethanol in DEPC treated H2O. Mix gently. Recentrifuge at 9,500 rpm for 5 min.

          1.12 Pour off the ethanol and let the pellets air-dry. This is a critical step; if the pellets dry out too much, the RNA crystallizes and is very difficult to resolubilize. If not enough of the ethanol evaporates, this also prevents the RNA from going into the solution.

          1.13 After pouring off the bulk of the ethanol wash, there will be approximately 30–40 µl left in the bottom of the Eppendorf tube. To quicken the evaporation, centrifuge the tubes briefly to force the remaining fluid on the side of the tube to the bottom, then pipette off as much of the ethanol as is feasible. The best time to add DEPC treated water to the RNA pellet is when there is only a tiny meniscus of solution left around the pellet itself.

          1.14 Add approximately 15–25 µl (depending on yield) of either DEPC treated TE buffer or water to the RNA pellet. To a small Eppendorf tube, dilute the RNA 1/40 (1.2 µl in 48.8 µl of TE buffer) and add to a microcuvette (path length = 1 cm). Then measure the absorbance at 260 nm. The 260/280 ratio should be greater than 1.8. If less than 1.5–1.6 or so, the RNA is likely to be at least partially degraded. Lower ratios also suggest DNA or thiocyanate contamination. The concentration is essentially the equivalent of the OD at 260 nm (in µg/µl).

          Alternative: RNA isolation procedure for tissue

          The only difference from the procedure in cells is the first few steps: 

          1.1  Add 1 ml TRIzol to a sterile culture tube (preferably 12x75 mm). To this tube, add the frozen tissue (try not to add more than approximately 20 mg).

          1.2 On ice, pulverize the tissue with a homogenizer at a setting of 25 out of 30 for a total of 2 X 10 sec.

          1.3 Pour the TRIzol solution into a 1.5 ml Eppendorf tube and then proceed as above from Step 1.4.
          ​

          2. DNase treatment of RNA samples

          The DNase cocktail consists of the following (per sample):

          • RQ1 RNase free DNase: 1 µl
          • DNase 10x reaction buffer: 2 µl
          • DEPC-treated H2O: 6 µl
          • RNase Out: 0.5 µl

          2.1 Make a master mix of the above based on the number of RNA samples being treated.

          2.2 Prepare the RNA in the following way: Add 2 µg of RNA (calculated by 2 µg/the concentration in µg/µl) to a small Eppendorf tube. Bring the total volume of the RNA to 11 µl by adding additional DEPC treated water.

          For example, if your RNA concentration is 1 µg/µl, add 2 µl of the RNA to 9 µl of DEPC water.


          2.3 Add 9 µl of the DNase master mix to the RNA bringing the total volume to 20 µl.

          2.4 Using a thermal cycler, incubate the samples at 37°C for 15 min, followed by 65°C for 20 min, then place on ice.

          2.5 Briefly centrifuge each sample to assure all of the volume lies in the bottom of the tube. The DNase treated RNA can then be used immediately for the reverse transcription reaction.

          3. Reverse transcription of DNase treated RNA

          3.1 Under most circumstances, each sample of RNA (1 µg, or 10 µl from the DNase treatment reaction) will be run with reverse transcriptase with the second 1 µg aliquot being used for a no-RT control. 

          3.2 For each sample, mix together the following:


          • 13 µl DEPC treated water
          • 16 µl 5X first strand buffer
          • 7 µl DTT (0.1 M)
          • 8 µl random primers (concentration = 0.1 µg/µl or a 1/30 dilution of the 3 µg/µl)
          • 8 µl BSA 
          • 3 µl dNTPs
          • ​1 µl RNase Out

          3.3 The total from the above reagents is 56 µl. Mix by vortexing.

          3.4 Aliquot 28 µl each into two separate 0.5 ml Eppendorf tubes. One tube will serve as the RT reaction (to which 2 µl of the MMLV reverse transcriptase is added) and the other, the no-RT control, to which 2 µl of H2O is added.

          3.5 To each tube, add 10 µl of the DNase treated RNA from above.

          3.6 Mix well by pipetting.

          3.7 Incubate all samples at 37°C for 1 hr, then 95°C for 5 min. The latter step fully inactivates remaining enzymes (i.e. MMLV RT and any remaining DNase). 

          3.8 Use immediately for PCR or store at -20°C first thing the next day.

          Alternative: a total of 20 µl of the non-RT containing mix is required per sample

          3.1 Randomly select two or three samples from a group and prepare no-RT controls by aliquoting out 28 µl per sample into 0.5 ml tubes and adding 1 µg of RNA to each along with an additional 2 µl of DEPC treated H2O (this is optional).

          3.2 To the remaining RT master mix, add 2 µl of MMLV RT/sample being prepared, mix by vortexing, and then aliquot 30 µl per tube for each sample.

          • For example, if you have a total of 10 samples, you will reverse transcribe all 10, but want 2 or 3 samples additionally for no RT controls to assure that the DNase treatment step worked. Thus, you would multiply the above master mix by 7 or 8. 1X the master mix is for two samples.
          • If you'll need a total of 12 reactions (for both RT and no-RT reactions) then you will need 6X master mix cocktail.

          3.3 Once made, aliquot the two no-RT samples (28 µl each), add 20 µl of the MMLV RT (2 µl/sample) to the master mix. Vortex the mix, then aliquot 30 µl per tube for 10 tubes. To each, add the corresponding 1 µg (10 µl) of RNA and incubate as above.


          Download or print the full protocol


          Get resources and offers direct to your inbox Sign up
          A-Z by research area
          • Cancer
          • Cardiovascular
          • Cell biology
          • Developmental biology
          • Epigenetics & Nuclear signaling
          • Immunology
          • Metabolism
          • Microbiology
          • Neuroscience
          • Signal transduction
          • Stem cells
          A-Z by product type
          • Primary antibodies
          • Secondary antibodies
          • Biochemicals
          • Isotype controls
          • Flow cytometry multi-color selector
          • Kits
          • Loading controls
          • Lysates
          • Peptides
          • Proteins
          • Slides
          • Tags and cell markers
          • Tools & Reagents
          Help & support
          • Support
          • Make an Inquiry
          • Protocols & troubleshooting
          • Placing an order
          • RabMAb products
          • Biochemical product FAQs
          • Training
          • Browse by Target
          Company
          • Corporate site
          • Investor relations
          • Company news
          • Careers
          • About us
          • Blog
          Events
          • Tradeshows
          • Conferences
          International websites
          • abcam.cn
          • abcam.co.jp

          Join with us

          • LinkedIn
          • facebook
          • Twitter
          • YouTube
          • Terms of sale
          • Website terms of use
          • Cookie policy
          • Privacy policy
          • Legal
          • Modern slavery statement
          © 1998-2023 Abcam plc. All rights reserved.