Fractions of liver biopsy specimens obtained by transjugular route, and primarily processed for clinical pathology, were stored in diethyl pyrocarbonate (DEPC) solution for mRNA isolation using the RNeasy kit (Qiagen). 250 ng of highly pure and preserved RNA were deeply analyzed using the Illumina Whole Genome-DASL assay, which quantifies approximately 24,000 transcripts. The microarray data were deposited and stored in GEO (GSE77627).
Illumina were processed using lumi package quantile normalisation [27 (link)]. Coefficient for age, derived from a linear model using probe set expression versus age and gender adjusted [28 (link)], was employed as a metric score to evaluate the influence of age in the gene expression from cirrhotic liver tissue. We performed pre-ranked gene set enrichment analysis (GSEA) using the canonical pathways MSigDB collection signatures [29 (link)].
Ethics Committee of the Barcelona Hospital Clinic approved the experimental protocol (HCB/2011/6814). Experimental groups were defined considering patients’ age: young (n=7, mean age 42 ± 5 years old, range 33-48), old (n=7, mean age 62 ± 4, range 58-70).
Illumina were processed using lumi package quantile normalisation [27 (link)]. Coefficient for age, derived from a linear model using probe set expression versus age and gender adjusted [28 (link)], was employed as a metric score to evaluate the influence of age in the gene expression from cirrhotic liver tissue. We performed pre-ranked gene set enrichment analysis (GSEA) using the canonical pathways MSigDB collection signatures [29 (link)].
Ethics Committee of the Barcelona Hospital Clinic approved the experimental protocol (HCB/2011/6814). Experimental groups were defined considering patients’ age: young (n=7, mean age 42 ± 5 years old, range 33-48), old (n=7, mean age 62 ± 4, range 58-70).
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