Fig. 5
Treatment of the Reh cell line with PMA induces global THE1B LTR activation. a Treatment of Reh cells with 2 ng/ml PMA for 8 or 16 h followed by measurement of CSF1R-LTR expression by qPCR. Three biological replicates. (p < 0.05 PMA treated vs. untreated, paired Student's t-test) b CBFA2T3 gene expression measured by qPCR following treatment of Reh cells with 2 ng/ml PMA for 8 or 16 h. Three biological replicates (p < 0.05 PMA treated vs. untreated, paired Student's t-test). c UCSC genome browser screenshot showing alignment of RACE-Seq reads to the CSF1R-LTR following PMA treatment of Reh cells. d Overlap of RACE-Seq LTR peaks from Reh cells±PMA treatment with merged peaks from the 3 HRS cell lines. e Hierarchical unsupervised clustering of Pearson correlation of gene expression patterns. f Fold-change of gene expression before and after PMA treatment with the presence of active LTRs close to these genes plotted based on the gene expression fold-change axis. g Fold-change of gene expression obtained by RNA-Seq for each HRS cell line over Reh with the presence of active PMA induced LTRs close to these genes plotted based on the gene expression fold-change axis. Significance of LTRs associated with upregulated genes tested using a hypergeometric test
