Journal: BMC Genomics

Article Title: Identification of candidate long non-coding RNAs in response to myocardial infarction

doi: 10.1186/1471-2164-15-460

Figure Lengend Snippet: Microarray analysis. Cardiac transcriptome of 4 sham-operated mice and 4 MI mice (derivation group) was characterized 24 hours after surgery using microarrays. A . Principal component analysis showing the ability of gene expression data to discriminate MI mice from sham-operated mice. B . M-A plot showing the distribution of the genes in the dataset. The vertical axis displays log2 transformed-fold change and the horizontal axis displays the average signal of each gene. C . Heatmap of differentially expressed genes. For B and C, red color indicates genes up-regulated in MI mice and green color indicates genes down-regulated in MI mice compared to sham mice. Black color indicates genes with comparable expression between MI and sham mice. Significance threshold was 2-fold with a q-value <5%.

Article Snippet: High-resolution microarray scanner (Agilent) and Feature Extraction software were used to scan the slide and extract raw microarrays data.

Techniques: Microarray, Expressing, Transformation Assay

Journal: BMC Genomics

Article Title: Identification of candidate long non-coding RNAs in response to myocardial infarction

doi: 10.1186/1471-2164-15-460

Figure Lengend Snippet: Effect of MI on lncRNAs expression in the heart. Microarrays performed with the 4 MI and 4 sham-operated mice (Derivation group) were mined for lncRNAs data. A . Analytical pipeline used to identify microarray probes recognizing lncRNAs. B . Percentage of probes on the microarray corresponding to mRNA and lncRNA transcripts. C . Heat-map of lncRNAs differentially expressed between MI and sham mice with a threshold fold-change of 2-fold and a q-value <5%. Red color indicates lncRNAs up-regulated in MI mice and green color indicates lncRNAs down-regulated in MI mice compared to sham mice.

Article Snippet: High-resolution microarray scanner (Agilent) and Feature Extraction software were used to scan the slide and extract raw microarrays data.

Techniques: Expressing, Microarray

Journal: BMC Genomics

Article Title: Identification of candidate long non-coding RNAs in response to myocardial infarction

doi: 10.1186/1471-2164-15-460

Figure Lengend Snippet: Quantitative assessment of lncRNAs in the heart. Expression of the top 10 lncRNAs identified as differentially expressed between MI and sham-operated mice in microarray experiments was quantified using quantitative RT-PCR, first (A) in the derivation group of 8 mice (4 sham and 4 MI), and then (B) in an independent validation group of 16 mice (8 sham and 8 MI). LncRNAs expression is shown relative to GAPDH (log scale). *P < 0.05; #P < 0.001 vs. sham-operated mice. (C) Time-course analysis of MIRT1 and MIRT2 in 21 additional mice subjected to coronary ligation and sacrificed after 1, 3, 6, 16, 24, 48, and 72 hours (n = 3 per time-point). *P < 0.05; #P < 0.001 vs 1 h time-point.

Article Snippet: High-resolution microarray scanner (Agilent) and Feature Extraction software were used to scan the slide and extract raw microarrays data.

Techniques: Expressing, Microarray, Quantitative RT-PCR, Ligation

Journal: BMC Genomics

Article Title: Identification of candidate long non-coding RNAs in response to myocardial infarction

doi: 10.1186/1471-2164-15-460

Figure Lengend Snippet: Correlation between lncRNAs and remodeling genes. Microarray data from the derivation group of 4 sham-operated and 4 MI mice were used in these analyses. A . Networks indicating the strength of the correlation between the lncRNAs MIRT1 and MIRT2 and 38 coding genes known to be involved in remodeling (“remodeling genes”). Remodeling genes differentially expressed between sham-operated and MI mice are coloured, with darker colour indicating a strong differential expression. Red colour indicates a higher level of expression in MI mice compared to sham-operated mice. Remodeling genes unaffected by MI are in white circles. A q-value <5% was used as threshold for differential expression between sham and MI mice (significance analysis of microarrays method). The thickness of the edges indicates the strength of the correlation between the lncRNAs and remodeling genes. Dotted lines indicate no correlation. A p-value <0.05 was used as significance threshold for correlation (Spearman’s rank correlation and Student’s test). B . List of the remodeling genes significantly (p < 0.05) correlated with lncRNAs and differentially expressed between sham-operated and MI mice. r indicates correlation coefficient and p indicates p-value. C . Kinetic of the expression of remodeling genes after MI. The 21 mice sacrificed at different time-points after MI were used in these analyses (n = 3 per time-point). P values obtained by ANOVA are indicated.

Article Snippet: High-resolution microarray scanner (Agilent) and Feature Extraction software were used to scan the slide and extract raw microarrays data.

Techniques: Microarray, Expressing