10.25402/BTN.9995504.v1 Martin J. Stoddart Martin J. Stoddart Elena Della Bella Elena Della Bella Supplementary material for: Cell detachment rapidly induces changes in non-coding RNA expression in human mesenchymal stromal cells Future Science Group 2019 human mesenchymal stem cells RNA sequencing non-coding RNA circular RNA microrna piwi-RNA reference gene stability loss of anchorage cell detachment trypsinization Protein Trafficking Proteomics and Intermolecular Interactions (excl. Medical Proteomics) Biochemistry and Cell Biology not elsewhere classified Gene Expression (incl. Microarray and other genome-wide approaches) Genetics not elsewhere classified 2019-10-17 13:17:54 Dataset https://future-science-group.figshare.com/articles/dataset/Supplementary_material_for_Cell_detachment_rapidly_induces_changes_in_non-coding_RNA_expression_in_human_mesenchymal_stromal_cells/9995504 <div> <table> <tr> <td> <p>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.</p> <p>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.</p> <p>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.</p> <p>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.</p> <p>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.</p> <p>Supplementary Table 6 - List of differentially regulated circular RNAs - 3D (trypsinised) vs. 2D (monolayer) day 0 samples.</p> <p>Supplementary Table 7 - microRNA-binding sites in differentially expressed circular RNA identified in 3D (trypsinised) vs. 2D (monolayer) day 0 samples.</p> <p>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.</p> <p>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.</p> </td> </tr> </table> </div>