Supplementary material for: Cell detachment rapidly induces changes in non-coding RNA expression in human mesenchymal stromal cells

Supplementary
Table 1 - List of assays used for qPCR analysis of candidate reference genes.
Information on RPLP0 reference gene analysis are reported within the text.
Supplementary
Table 2 – List of primers used for qPCR analysis of circular RNA for
validation of hybridization array results. The primers were used for qPCR
detection of circular RNAs with a SYBR green chemistry.
Supplementary
Table 3 – List of assays used for qPCR analysis of microRNA (miRNA) for
validation of RNAseq results. All assays are TaqMan Advanced miRNA Assays
from Thermo Fisher. hsa-miR-361-5p and hsa-miR-186-5p were used as reference
miRNA for normalization of gene expression.
Supplementary
Table 4 - List of differentially regulated miRNAs - 3D (trypsinised) vs. 2D
(monolayer) day 0 samples. Highlighted in bold the miRNAs with both p-value
and False Discovery Rate (FDR) <0.05.
Supplementary
Table 5 - List of differentially regulated piwi-RNAs - 3D (trypsinised) vs.
2D (monolayer) day 0 samples. *LTR derived; **LINE derived; ***SINE derived.
Highlighted in bold the piRNAs with both p-value and False Discovery Rate
(FDR) <0.05.
Supplementary
Table 6 - List of differentially regulated circular RNAs - 3D (trypsinised)
vs. 2D (monolayer) day 0 samples.
Supplementary
Table 7 - microRNA-binding sites in differentially expressed circular RNA
identified in 3D (trypsinised) vs. 2D (monolayer) day 0 samples.
Supplementary
Table 8 - Summary of results of geNorm, NormFinder, and comparative ΔCt
analyses for the stability of candidate reference genes in 3D (trypsinised)
vs. 2D (monolayer) day 0 samples. Genes were ranked from the most to the less
stable, based on the value calculated by the algorithms.
Supplementary
Table 9 - Summary of results of geNorm and NormFinder analyses for the
stability of selected miRNA endogenous controls in 3D (trypsinised) vs. 2D
(monolayer) day 0 samples.