Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • RNA-Seq on FFPE samples : Illumina TruSeq RNA exome or Roch Kapa HMR kit

    Hi,

    I've ~300 FFPE samples to analyzed using RNA-Seq. I've two possibilities for the library prep depending on the sequencing center I will chose.

    Either :

    Illumina TruSeq RNA Exome : https://emea.illumina.com/content/il...na-access.html

    or

    Roche Kapa HMR

    Both libraries will be sequenced at 2x100bp - 50M reads

    Any experience with these kits with FFPE samples ?

    Thank you

  • #2
    similar situation here, also would like to know the answer.
    Thank you!

    Comment


    • #3
      Both are fine choices so the decision will likely come down to what sort of transcripts you are interested in looking at. The TruSeq RNA Exome kit is going to give you significantly higher coverage of coding transcripts but you will not have any non-coding RNA data to analyze. Depending on the starting RNA quality, the Roche Kapa HMR kit (or similar) will yield somewhere between 20-40% alignment rates to exonic regions.

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Strategies for Sequencing Challenging Samples
        by seqadmin


        Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
        03-22-2024, 06:39 AM
      • seqadmin
        Techniques and Challenges in Conservation Genomics
        by seqadmin



        The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

        Avian Conservation
        Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
        03-08-2024, 10:41 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 06:37 PM
      0 responses
      10 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      9 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      50 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      67 views
      0 likes
      Last Post seqadmin  
      Working...
      X