Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • flutterfly28
    replied
    Hey favwiz, did you ever figure out what was wrong?
    I seem to be having the same problem with my ATAC-Seq run...

    Leave a comment:


  • RickC7
    replied
    We have successfully sequenced ATAC-Seq libraries on the Next-Seq. I need to look back at my notes, but we did not use the custom primers. Loosely based off Pamela Milani (Fraenkel Lab) We used the Nextera DNA Library Kit and Nextera Index primers. Sequencing run worked fine. Did you use PhiX on the run? That would give you some indication...

    Leave a comment:


  • pmiguel
    replied
    No reads, or no clusters?
    Nextera sequencing primers aren't included in HiSeq High Output chemstry reagents. But they are in MiSeq/HiSeq Rapid chemsitry and so should be in the NextSeq reagent kits.
    So my next thought would be that your adapters have an error in them that is preventing any sequence from being generated. You should go to the oligonucleotide synthesis company's specification sheet for your oligos and verify the sequence provided is the Nextera adapter sequence.
    --
    Phillip

    Leave a comment:


  • favwiz
    started a topic Can't sequence ATAC-Seq libraries

    Can't sequence ATAC-Seq libraries

    We have prepared ATAC libraries for 24 samples following the protocol from Buenrostro et.al, using their custom Nextera-like primers and we have attempted to sequence these on NextSeq.
    We're essentially getting no reads and can't figure out why. The libraries show good fragment distribution on Tapestation, and we have also run a library quantification qPCR which also shows that there is sufficient sequenceable material.
    We're completely stuck, and Illumina as well as the ATAC forum have been of little help...
    If anyone can help, it would be very much appreciated!

Latest Articles

Collapse

  • seqadmin
    Exploring the Dynamics of the Tumor Microenvironment
    by seqadmin




    The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
    07-08-2024, 03:19 PM
  • seqadmin
    Exploring Human Diversity Through Large-Scale Omics
    by seqadmin


    In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
    06-25-2024, 06:43 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 07-19-2024, 07:20 AM
0 responses
38 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-16-2024, 05:49 AM
0 responses
49 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-15-2024, 06:53 AM
0 responses
61 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-10-2024, 07:30 AM
0 responses
43 views
0 likes
Last Post seqadmin  
Working...
X