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Old 04-03-2013, 04:33 PM   #1
cutcopy11
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Location: Purdue University

Join Date: Nov 2009
Posts: 19
Default 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.
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Old 04-03-2013, 06:00 PM   #2
Dario1984
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Location: Sydney, Australia

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Posts: 123
Default

When you click on a GSE record, there is a contact e-mail for the person who created the record. You should ask him.
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Old 04-04-2013, 08:13 AM   #3
DNAase
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Location: Los Angeles

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Here is the GEO file for that paper:
http://www.ncbi.nlm.nih.gov/geo/quer...i?acc=GSE21823

feel free to contact me
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