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RNAseq Transcriptome Profile Project
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| Research Group - Dr. Fernanda Petersen, University of Oslo, Oslo, Norway
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Supplemental Information for Publication: A positive feedback loop mediated by Sigma X enhances
expression of the streptococcal regulator ComR. 2017. Khan R, Junges R, Åmdal HA, Chen T,
Morrison DA, Petersen F. Scientific Reports, in press.
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| Differential Gene Expresssion Analysis with JBrowse
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| Differential gene expression analysis between
Streptococcus mutans strain SM065 grown with and without XIP, the sigX-inducing peptide, was analyzed by two software packages:
Bioconductor's DESeq and
Cufflinks' Cuffdiff.
Click provided links below to see the gene expression tables.
In each table, links are provided
to view the differential transcription profiles in the JBrowse genome viewer.
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| RNAseq Profiles of Individual Samples
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The above differential gene expression study was based on 3 independently conducted experiments (Dag1-3)
for each of the two conditions (with or without XIP). RNASeq reads were mapped to the reference genome (S. mutans UA159, GenBank NC_004350.2) with the software
Bowtie and then mapped reads were separated by coding strands - forward (FW) or reverse-complement (RC).
The mapping results are viewed as 1) log2 read counts 2) read coverage and 3) read alignment in the JBrowse genome viewer.
For detail experimental design and analysis please refer to the above publication.
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SM065-XIP-Dag1 |
FW |
RC |
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SM065-XIP-Dag2 |
FW |
RC |
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SM065-XIP-Dag3 |
FW |
RC |
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