Nonetheless, the fact that neither citrate synthase activity nor VDAC content changed between torpor and IBE, in either isolated mitochondria or permeabilized liver, allow us to conclude with confidence that total mitochondrial content does not change between torpor and IBE.
Our group had previously conducted whole-genome gene expression profiling in a larger set (N = 206) of these liver samples, which allowed us to determine to what extent the identified miR-eQTLs influence global gene expression as mRNA eQTLs [ 17].
The massive amount of sequencing reads obtained from L. menadoensis liver and testis allowed us to apply stringent filtering criteria, both in the processing of raw sequencing reads and in the filtering of assembled contigs, in order to achieve a final set of high quality transcripts and to overcome the most common pitfalls of NGS assemblies.
Our genome-wide data for CTCF binding in livers of five eutherian species allowed us to identify de novo DNA sequences associated with CTCF binding at hundreds of thousands of locations.
Hi-C maps from liver cells of different species allowed us to ask how the evolutionary dynamics of CTCF correlate with conservation or divergence of domain structure.
While our assumptions allowed us to model liver regeneration in humans, other alternative hypotheses about the differences in liver regeneration between rats and humans remain possible.
The search and identification of HFE transcripts in a range of human tissues (heart, duodenum, small intestine, liver, spleen, kidney, ovary and testis) allowed us to distinguish, besides the full length, seven alternative splicing transcripts.
We have previously also sequenced the NMR transcriptome, which allowed us to compare liver gene expression profiles between NMRs and wild-derived mice (Yu et al., 2011).
According to Correa et al., 2007, in vitro ischemia-reperfusion in rodent livers, allowed detection of succinate in extracellular fluids, and this phenomenon played an important role in the activation of HSCs (Fig. 3).
The model comprises kinetics for transport processes and metabolic enzymes as well as population liver expression data allowing us to assess the impact of inter-individual variability of concentrations of key proteins.
