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
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<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>
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