We clustered 4,481 DeepCAGE promoters into three clusters, and extracted three subsets filtered by low, medium and high gene expression level.
In the present study, we found that conditioned medium (CM) of osteoblasts induced gene expression level changes of OSCC cells [ 17], for example, Twist1, was up-regulated in these cells after such treatment.
The gene expression values (continuous variable) were discretized into three distinct levels, "H", "L" or "M", representing high, low or medium gene expression, respectively.
Cell-conditioned medium (CM) was obtained to assess the effects of secreted factors produced by osteoblasts and CRPC cells on gene expression level, proliferation and mineralization.
The gene expression level was quantified using RSEM (Li and Dewey 2011).
The gene expression level was calculated based on the transcript/gene ratio.
Gene expression level of (A) COL1A1, (B) COL2A1, (C) COL3A1 and (D) COL10A1 were determined in monocultures supplemented with OAB-conditioned mediusinging plasmid standard curves.
To test the relationship of DNAm and gene expression, we classified the genes into four categories according to gene expression levels: high expression (RPKM: 10 1,000), medium expression (RPKM: 1 10), low expression (RPKM: 0 1) and silent expression (RPKM: 0).
Interestingly, MSCs cultured in the presence of FBS and IFN-γ displayed lower IDO1 gene expression levels than cells grown in serum-free medium (Fig. 3F).
Fig. 5 Output of target products and gene expression levels obtained using ultrasound treatment in the systems with PDB medium (a, b) and the treated resting cells (c, d).
