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Figure 1. Workflow of the analysis to estimate the number of true human miRNAs. Samples containing NGS data were ... Figure 1. Workflow of the analysis.

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Presentation on theme: "Figure 1. Workflow of the analysis to estimate the number of true human miRNAs. Samples containing NGS data were ... Figure 1. Workflow of the analysis."— Presentation transcript:

1 Figure 1. Workflow of the analysis to estimate the number of true human miRNAs. Samples containing NGS data were ... Figure 1. Workflow of the analysis to estimate the number of true human miRNAs. Samples containing NGS data were collected from SRA, TCGA and data uploaded to miRMaster, and the obtained samples and reads were filtered. Three sets of miRNAs were created: miRBase high-confidence (HC), miRBase low-confidence set (LC) and other (Other). Using in silico high-throughput validation and experimental low-throughput validation steps, the probabilities that a miRNA will pass the validation procedure have been calculated for each miRNA set respectively. Finally, the number of true miRNAs was estimated using the original miRNA counts and the computed probabilities. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact Nucleic Acids Res, Volume 47, Issue 7, 01 March 2019, Pages 3353–3364, The content of this slide may be subject to copyright: please see the slide notes for details.

2 Figure 2. Northern blots of endogenous miRNAs
Figure 2. Northern blots of endogenous miRNAs. (A) The 11 analyzed cell lines that are indicated on top of the figure ... Figure 2. Northern blots of endogenous miRNAs. (A) The 11 analyzed cell lines that are indicated on top of the figure were derived from lung (A549), liver (HUH-7), bone marrow (SHSY-5Y), keratinocytes (HaCaT), cervix (HeLa), mammary gland (MCF7), placenta (JEG-3), Testis (Tera-1), prostate (PC-3), B-lymphocytes (DG-75) and T-lymphocytes (Jurkat). HEK-293T RNA was used as a reference to compare signals to exogenously expressed miRNAs. The endogenous mature forms are shown for the miRNAs indicated on the left side of the figure. (B) The number of mature and premature forms of the endogenous miRNA expressed in the 12 cells lines as indicated in Figure 2A. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact Nucleic Acids Res, Volume 47, Issue 7, 01 March 2019, Pages 3353–3364, The content of this slide may be subject to copyright: please see the slide notes for details.

3 Figure 3. Representative NB results for a positive, questionable and negative miRNA in HEK 293T cells. (A) NB for ... Figure 3. Representative NB results for a positive, questionable and negative miRNA in HEK 293T cells. (A) NB for hsa-miR-155–5p from high-confidence set A showing distinct bands for its precursor (p) and mature (m) form. (B) Hybridization against hsa-miR-1260a (low-confidence set B) detects two small RNA fragments with similar signal intensities for the control. (C) Probing for hsa-miR-6776–5p (low-confidence set B) did not result in any specific bands. Ethidium bromide staining of RNA gels was used as a loading control. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact Nucleic Acids Res, Volume 47, Issue 7, 01 March 2019, Pages 3353–3364, The content of this slide may be subject to copyright: please see the slide notes for details.

4 Figure 4. Comparison of exogenous and endogenous miRNA expression by northern blotting. The mature form is indicated by ... Figure 4. Comparison of exogenous and endogenous miRNA expression by northern blotting. The mature form is indicated by ‘m’ and the premature form by ‘p’. The left part of the figure shows exogenous expression of miR-148a-3p in HEK 293T cells. HEK 293T cells that were transfected with an empty vector are shown as a control (ctrl). The right part of the figure shows endogenous expression of miR-148a-3p in 12 cells lines as specified in Figure 2A. To show endogenous miRNAs, the signal intensity of the endogenous miRNAs apparently is enhanced as compared to the signal intensity of the exogenous miRNAs due to the very strong signal of overexpressed miR-148a-3p (compare backgrounds of exo- and endogenous northern blots and see the comparison between HEK 293T cells that were used as a control for the transfection analysis (ctrl) shown in the left part of the figure and the HEK 293T cells that were compared with other cells shown in the right part of the figure). As described in the ‘Materials and Methods’ section, contrast and brightness were adjusted by the software during scanning according to the darkest spot on the blot. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact Nucleic Acids Res, Volume 47, Issue 7, 01 March 2019, Pages 3353–3364, The content of this slide may be subject to copyright: please see the slide notes for details.

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