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Global brain gene expression profiles from mice 145 days post-inoculation, with either mock inoculum or the RML prion strain, were compared applying a 1.3-fold change as the lower limit, lower 90% confidence boundary of fold change and p values of <0.05.
Differentially expressed genes were identified by defining the appropriate filtering criteria in the dCHIP software as: lower 90% confidence boundary of fold change between the group means exceeded twofold; the absolute difference between the two groups exceeded 100; the P value threshold of the unpaired t-test was 0.05.
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(a) MA plot of fold change of ATAC read density at individual sites across the genome.
(g) MA plot of fold change of RNAP2 read density at individual sites across the genome.
(c) MA plot of fold change of H3K4me1 read density at individual sites across the genome.
(e) MA plot of fold change of H3K27ac read density at individual sites across the genome.
Linear regression analysis of fold change data between qRT-PCR and RNA-seq.
Gene symbol, fold change, direction of fold change, and presence of CRE sites (CRE) are indicated.
The correlation of fold changes was 0.62.
In this validation, 22 out of the 27 measurements (81%) of the qPCR measurements are within the boundaries of the fold change intervals for both RNA-Seq fold change measurements.
We observed that 480 of the proteins quantified in the iTRAQ experiment were outside the selected boundaries of significant fold change (+/− log2 (0.58)), but we cannot from this experiment conclude if any of these proteins represent a true biological change in abundance without additional verification.
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