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Total RNA was harvested from mouse liver samples as described for microarray RNA isolation.
Mouse liver samples were homogenized in RIPA buffer (50mM Tris-HCl, 150mM NaCl, 2mM EDTA, 0.5% Sodium deoxycholate, 1% Igepal CA-630, 5mM DTT), containing protease inhibitor (SIGMA).
Mouse liver samples were blinded and shipped on ice.
A total of 14 mouse liver samples were used to prepare a pooled sample.
Mouse liver samples were retrieved from 11-week-old male C57BL/6 J mice.
Pathway interactions were investigated in the context of a transcriptomics dataset of mouse liver samples.
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Interestingly, the network corresponding to WT mouse liver sample contains almost double the number of edges (2073) as compared to the number of edges (1055) in the ob/ob mouse liver sample network.
Liver-specific genes are identified from mouse liver sample, and mouse embryo specific genes are identified from mouse day 9.5 embryo sample.
As a result, the GSC spikes AFFX-TrpnX-3_at, AFFX-DapX-3_at, AFFX-PheX-3_at, AFFX-LysX-3_at and AFFX-ThrX-3_at correspond approximately to 5.8, 17.3, 52.0, 156.0 and 468.1 copies per cell (per diploid DNA template) for mouse liver sample homogenates, where the spike factor = 0.2.
The following supplementary material is available for this article: Figure S1. A. RNA was extracted and profiled (4 μg total RNA) from a mouse liver sample, which was either preserved as fresh frozen (y-axis) or formalin-fixed, paraffin-embedded (FFPE) (x-axis).
Rey et al. [ 15] similarly performed a detailed study of the genome-wide binding of activator BMAL1 in the mouse liver sampled every four hours over one day (the list of ChIP-seq peaks and associated genes for each TF were provided in Text S2 of [ 15]).
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