Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Choosing the best hexamer sequences for custom adapters?

    I have two sets of adapters that I am using for my library preparations. Both are custom adapters.

    Universal Y-shaped Adapter 1:
    ACACTCTTTCCCTACACGACGCTCTTCCGATC*T
    Adapter 1 barcode:
    /5Phos/GATCGGAAGAGCACACGTCTGAACTCCAGTCACCXXXXXXTCTCGTATGCCGTCTTCTGCTTG
    IDT recommended barcodes:
    TATGCG
    AACACC
    AACCAG
    AACGGA
    AAGAGG
    AAGCCT
    AAGGTC
    AATCGC
    ACAACG
    ACCGAT

    I then PCR amplify these barcoded libraries, adding an extra barcode to the amplicon. I use the following primers:

    PCR primer 1:
    CAAGCAGAAGACGGCATACGAGA*T
    PCR primer adapters:
    AATGATACGGCGACCACCGAGATCTACACXXXXXXACACTCTTTCCCTACACG
    IDT recommended barcodes:
    ACCTCA
    ACGCAA
    ACGTGT
    ACTCTG
    AGAAGC
    AGCATG
    AGCTAC
    AGGACA
    AGTGAG
    ATGTCC

    My question is, does anyone have any experience in choosing the hexamer barcodes, for use with Next-Seq?

    I emailed IDT, and they recommended specific hexamer sequences (shown above). I simply want to know why these sequences were chosen, they have not been able to explain why. The only thing I can see, is the correct balance of AT to CG in the hexamer? Are there other considerations?

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, 03-27-2024, 06:37 PM
0 responses
13 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-27-2024, 06:07 PM
0 responses
11 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
53 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
69 views
0 likes
Last Post seqadmin  
Working...
X