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

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posted on 17.10.2019 by Martin J. Stoddart, Elena Della Bella

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.

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