Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Cannot find NOME-Seq data

    Hello,

    I am trying to find some NOME-Seq data, but I cannot locate it.

    Here is the study ...

    Genome Research 2012
    "Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules"
    Theresa K. Kelly, Yaping Liu, Fides D. Lay, Gangning Liang, Benjamin P. Berman, and Peter A. Jones

    Here is the information about Data Access ...

    NOMe-seq tracks for genomic viewers (Fig. 2; Supplemental Fig. S2)
    are available as a supplemental document and at http://epigenome.
    usc.edu and the NCBI Gene Expression Omnibus (GEO) (http://
    www.ncbi.nlm.nih.gov/geo/) under accession number GSE21823.
    All source code tools are available at http://sourceforge.net/projects/
    uecgatk/. See Supplemental Material for instructions on using these
    tools. The tool and source code for the new module of the IGV
    viewer to display NOMe-seq data from raw BAMalignment files are
    publicly available for download at the IGV project website, http://
    www.broadinstitute.org/igv/.

    I can only find MNase-Seq data at GEO. I can't find publically available BAM files either. I just want a processed file with coordinates and fractions of methylated GpCs and CpGs to infer occupancy and % CpG methylation.

  • #2
    When you click on a GSE record, there is a contact e-mail for the person who created the record. You should ask him.

    Comment


    • #3
      Here is the GEO file for that paper:
      NCBI's Gene Expression Omnibus (GEO) is a public archive and resource for gene expression data.


      feel free to contact me
      USC Epigenome Center

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Recent Advances in Sequencing Analysis Tools
        by seqadmin


        The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
        Today, 07:48 AM
      • seqadmin
        Essential Discoveries and Tools in Epitranscriptomics
        by seqadmin




        The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
        04-22-2024, 07:01 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Today, 07:17 AM
      0 responses
      11 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 05-02-2024, 08:06 AM
      0 responses
      19 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-30-2024, 12:17 PM
      0 responses
      20 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-29-2024, 10:49 AM
      0 responses
      28 views
      0 likes
      Last Post seqadmin  
      Working...
      X