line data analysis  (MathWorks Inc)

Journal: Molecular oncology

Article Title: miRNA profiling identifies deregulated miRNAs associated with osteosarcoma development and time to metastasis in two large cohorts.

doi: 10.1002/1878-0261.12154

Figure Lengend Snippet: Fig. 2. Unsupervised hierarchical cluster analysis. The expression value (log2) for each detectable miRNA (Cq < 37) was used to determine the clustering of the samples. Red: primary OS samples; yellow: OS cell lines; blue: OB cell lines.

Article Snippet: See the T erm s and C onditions (https://onlinelibrary.w iley.com /term s-and-conditions) on W iley O nline L ibrary for rules of use; O A articles are governed by the applicable C reative C om m ons L icense Discovery Cohort 23 OS samples (Fresh frozen) Normal control: 3 OB cell lines Validation Cohort 78 OS samples (FFPE) Normal control: 3 OB cell lines Cohorts RNA extraction cDNA synthesis Quality control miRNA analysis Data analysis miRNeasy Mini Kit (Qiagen) miRNAeasy FFPE Kit (Qiagen) 50 ng RNA Universal cDNA Synthesis Kit II (Exiqon) 65 ng RNA Universal cDNA Synthesis Kit II (Exiqon) QC of cDNA Expression of: miR-103; miR-191-5p; miR-423 (Cq<32) UniSp6 (Spike-in) (Cq:16-18) QC of cDNA Expression of: miR-191-5p; miR-423-5p (Cq<30); UniSP4, UniSp5, UniSp6 (Spike-ins) 752 miRNAs analysed microRNA Ready-to-Use PCR, Human Panel I+II v2 (Exiqon) cDNA diluted 1:100 33 miRNAs analysed Pick&Mix microRNA PCR Panels (Exiqon) cDNA diluted 1:20 Analysis in GenEx Software (MultiD) Normalization: Mean global expression Analysis in GenEx Software (MultiD) Normalization: 5 reference miRs 78 miRs diff. expressed (OS samples vs OB cell lines) 5 reference miRs identified 29 miRs diff. expressed (OS samples vs OB cell lines) 33 miRs diff. expressed Exclusion of miRs with no expr. diff. btw.

Techniques: Expressing

Journal: Molecular oncology

Article Title: miRNA profiling identifies deregulated miRNAs associated with osteosarcoma development and time to metastasis in two large cohorts.

doi: 10.1002/1878-0261.12154

Figure Lengend Snippet: Fig. 4. Network of validated target genes. Network of validated target genes associated with the terms ‘Cell Death and Survival, Cancer, Hematological System Development and Function’. The relation of 29 validated target genes (miRWalk2.0) assembled in a network associated with 11 miRNAs altered in OS in this study. Eight genes were downregulated and 21 upregulated. Red: downregulated; blue: upregulated. Gray lines: association between genes; Red lines: association between gene and miRNA; continuous line: direct association; dashed line: indirect association.

Article Snippet: See the T erm s and C onditions (https://onlinelibrary.w iley.com /term s-and-conditions) on W iley O nline L ibrary for rules of use; O A articles are governed by the applicable C reative C om m ons L icense Discovery Cohort 23 OS samples (Fresh frozen) Normal control: 3 OB cell lines Validation Cohort 78 OS samples (FFPE) Normal control: 3 OB cell lines Cohorts RNA extraction cDNA synthesis Quality control miRNA analysis Data analysis miRNeasy Mini Kit (Qiagen) miRNAeasy FFPE Kit (Qiagen) 50 ng RNA Universal cDNA Synthesis Kit II (Exiqon) 65 ng RNA Universal cDNA Synthesis Kit II (Exiqon) QC of cDNA Expression of: miR-103; miR-191-5p; miR-423 (Cq<32) UniSp6 (Spike-in) (Cq:16-18) QC of cDNA Expression of: miR-191-5p; miR-423-5p (Cq<30); UniSP4, UniSp5, UniSp6 (Spike-ins) 752 miRNAs analysed microRNA Ready-to-Use PCR, Human Panel I+II v2 (Exiqon) cDNA diluted 1:100 33 miRNAs analysed Pick&Mix microRNA PCR Panels (Exiqon) cDNA diluted 1:20 Analysis in GenEx Software (MultiD) Normalization: Mean global expression Analysis in GenEx Software (MultiD) Normalization: 5 reference miRs 78 miRs diff. expressed (OS samples vs OB cell lines) 5 reference miRs identified 29 miRs diff. expressed (OS samples vs OB cell lines) 33 miRs diff. expressed Exclusion of miRs with no expr. diff. btw.

Techniques: