Appropriate results were previously obtained for these control mouse samples using Western blot and ECLISA.
FISH was used to detect M. tuberculosis in infected mouse samples using fluorescent M. tuberculosis probes MTB187, MTB223 and MTB1284.
Detailed analysis of the rat and mouse samples using this protocol was published in a separate paper.
The gene expression level was normalized relative to GAPDH expression level for chicken samples and relative to HPRT expression level for mouse samples using a ΔCt approach.
Several recent studies have compared transcript expression levels measured in human and mouse samples using both conventional microarrays and RNA-Seq [ 13, 16].
For example, Lee et al. [ 109] conducted a comprehensive survey of miRNA sequence variations from human and mouse samples using RNA-Seq.
For relative quantification of transcripts, Ct values for each sample were normalized to GAPDH and ALDOA for human samples, and HPRT1 and β-actin for mouse samples, using the Data Assist software (Applied Biosystems).
The first column is the time-point during T. gondii infection for the mouse forebrain samples used for RNA extraction.
With the exception of mouse, the samples used for the Hi-C libraries were the same as the material used for CTCF ChIP-seq (Schmidt et al., 2012).
Given the absence of these factors from the dataset, this further suggests that the mouse ICM samples used reflect an earlier stage of blastocyst development.
