How do intestinal microbiota interact with host genome-encoded
processes to impact vertebrate health and disease
?

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Camp Frank 2014 Data

                          

Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape.
J. Gray Camp, Christopher L. Frank, Colin R. Lickwar, Harendra Guturu, Tomas Rube,
Aaron M. Wenger, Jenny Chen, Gill Bejerano, Gregory E. Crawford, and John F. Rawls.
Genome Research 2014.
PMID 24963153    GEO GSE57919     UCSC Track Hub       Supplemental Data  
All data mapped to the mm9 genome

-UCSC Track Hub Directions
1. Click UCSC Track Hub link
2. Load Data from IEC Microbiota Section (eg. DNase parzen>"Full", etc.)

The trackHub contains the following composite tracks:
"DNase raw" - displays raw summed coverage for 5-prime end of each mapped read (the end cleaved by DNase I) mapped to mm9 by BWA.
"DNase parzen" - displays kernel density smoothened DNase-seq data generated by F-seq (for more information, please see PMID:18784119)
"DNase peaks" - displays top 100,000 peak calls from F-seq for each DNase-seq sample. Darker bars represent higher-scoring peaks.
"RNA-seq" - displays raw summed coverage for paired-end RNA-seq reads mapped to mm9 by Tophat.

Each composite track header can be clicked on to further specify individual sample display settings.

3. Search for your favorite locus in the UCSC search field

UCSC Track Hubs Help
UCSC Browser Help

-Manual Track Hub Information
http://trackhub.genome.duke.edu/crawfordlab/publications/CampFrank2014/hub.txt
hub myHub
shortLabel IEC Microbiota
longLabel CR vs. GF vs. CV IECs from Camp and Frank, et al. 2014
genomesFile genomes.txt
email greg.crawford@duke.edu
descriptionUrl http://rawlslab.duhs.duke.edu/data/index.html