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. 2022 Sep 23;4(12):100592. doi: 10.1016/j.jhepr.2022.100592

Fig. 6.

Fig. 6

Increased SOCS1 expression in iPSCs attributed to epigenetic regulation.

(A) UCSC Genome Browser screenshot of SOCS1 gene with promoter, CpG island and Genehancer tracks displayed (B) qPCR analysis of mRNA levels for baseline expression of SOCS1 in iPSCs and HepaRG cells. Data from repeated experiments in triplicate were averaged and are expressed as mean and standard deviation values (error bar) presented with an unpaired Student’s t test with Welch’s correction used to determine the p values. A p value <0.05 was considered significant. ∗p <0.05, ∗∗p <0.001, ∗∗∗p <0.0001, n.s., non-significant. (C) ENCODE data on RNA sequencing for SOCS1 gene expression in H1 embryonic stem cells and in liver cells with legend for colored-coded gene regulatory elements. (D) Reduced representation bisulfate sequencing for DNA methylation status of SOCS1 gene (mapped to GRCh37/hg19) in iPSCs and HepaRG cells. Red indicates methylated CpG bases and blue indicates unmethylated CpG bases. (E) qPCR analysis of chromatin-immunoprecipitation for binding events of histone modifications H3K4me1, H3K4me3, and H3K27ac in iPSCs and HepaRG cells. Three genomic regions of SOCS1 gene were mapped to GRCh37/hg19; Region 1: 11,347,874-11,348,373bp. Region 2: 11,348,390-11,348,889bp. Region 3: 11,348,920-11,349,444bp in comparison to data using a negative (Neg) control primer. Data from repeated experiments in triplicate were averaged and are expressed as mean and standard deviation values (error bar) presented with an unpaired Student’s t test with Welch’s correction used to determine the p values. A p value <0.05 was considered significant. ∗p <0.05, ∗∗p <0.001, ∗∗∗p <0.0001, n.s., non-significant. ENCODE integrative analysis (PMID: 22955616; PMCID: PMC3439153) ENCODE portal (PMID: 29126249; PMCID: PMC5753278). UCSC Genome Browser SessionURL(SOCS1):http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr16%3A11347831%2D11350479&hgsid=1280379467_j7ViSdKoDWUyqakJN2IuPyL2H5Yz.