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

Journal: PLoS ONE

Article Title: Genome-Wide Transcription Study of Cryptococcus neoformans H99 Clinical Strain versus Environmental Strains

doi: 10.1371/journal.pone.0137457

Figure Lengend Snippet: (A) Pairwise correlation matrix. Four C . neoformans strains (H99, H4, S48B and S68B) were compared. Two independent samples were prepared for each fungal strain. Rep1–2: replicates of samples. Numbers in the box represents correlation coefficient values among groups. Dark box: high correlation; light box: low correlation. (B) Gene expression heat map. Dendrogram represents the colour-coded expression levels of the significantly regulated genes. The groups of genes which showed differential expressions in H99 versus other strains were as indicated. Low levels in H99 category indicates the genes with low expression levels in H99 (green) but high expression in the environmental strains (red). In contrast, high levels in H99 category indicates the genes with high expression levels in H99 (red) but show low expression in the environmental strains (green). Hierachrical cluster was performed with Euclidean distance metric and Ward’s Linkage rule clustering. Colour range represents log 10 (FC) of the microarray intensities.

Article Snippet: The slide was washed and scanned on a High Resolution Microarray Scanner C-model (Agilent Technologies).

Techniques: Expressing, Microarray

Journal: bioRxiv

Article Title: Pleiotropic Roles for the Plasmodium berghei RNA Binding Protein UIS12 in Transmission and Oocyst Maturation

doi: 10.1101/2020.12.21.423818

Figure Lengend Snippet: Shown are mean values of microarray results of total RNA isolated from mixed infected erythrocytes from uis12(-) (clone 1) - and WT-infected mice from two biological replicates. (A) Shown is a volcano-plot illustrating the fold change of the expression levels and the negative log p -values of all analyzed 2,890 P. berghei genes. The dotted black line represents a p -value of 0.05 and all transcripts with a P -value <0.05 are shown in red. Exemplary transcripts are highlighted and labeled in blue. (B) Pie charts displaying the proportions of up- (green >2), non- (grey), and down- (orange <-2) regulated transcripts amongst all transcripts (upper left), blood stage-specific transcripts (center) and gametocyte-specific transcripts (upper right) . Exemplary transcripts are listed in the respective region of the chart. The number of transcripts analyzed is shown in a white circle inside the center. (C) Pie charts displaying the proportions of up- (green >2), non- (grey), and down- (orange <-2) regulated transcripts amongst female (left) and male (right) gametocyte-specific transcripts . The number of transcripts analyzed is shown in a white circle inside the center.

Article Snippet: Scanning of the microarrays was performed with 5 µm resolution and the extended mode using a ‘High Resolution Microarray Laser Scanner’ (G2505, Agilent Technologies).

Techniques: Microarray, Isolation, Infection, Expressing, Labeling

Journal: bioRxiv

Article Title: Pleiotropic Roles for the Plasmodium berghei RNA Binding Protein UIS12 in Transmission and Oocyst Maturation

doi: 10.1101/2020.12.21.423818

Figure Lengend Snippet: Quantitative RT-PCR on selected blood stage and gametocyte transcripts validate the results of the microarray analysis. Shown are -fold changes of steady state mRNA levels of uis12(-) clone 1 compared to wild-type mixed blood stages for selected genes ( Puf1, P28, MDV, DOZI, Actin II, UIS1/IK2, SET, MSP1 , and AMA1 ). qRT-PCR data were normalized to the steady state levels of HSP70 mRNA. The microarray data represent mean values of biological replicate 1 and 2 ±SD.

Article Snippet: Scanning of the microarrays was performed with 5 µm resolution and the extended mode using a ‘High Resolution Microarray Laser Scanner’ (G2505, Agilent Technologies).

Techniques: Quantitative RT-PCR, Microarray

Journal: bioRxiv

Article Title: Pleiotropic Roles for the Plasmodium berghei RNA Binding Protein UIS12 in Transmission and Oocyst Maturation

doi: 10.1101/2020.12.21.423818

Figure Lengend Snippet: (A) Shown is a graphic display of the 10-nucleotide U-rich motif found in the ORF of transcripts that are up-regulated in absence of UIS12 in the microarray with biological replicate 1. The size of the depicted nucleotide represents its probability at the respective position. (B) Venn diagram comparing shared down-regulated transcripts of the gametocyte microarray analyses performed for dozi(-) and cith(-) with a -fold change lower than -1 ( Mair et al ., 2010 ) and down-regulated transcripts in mixed blood stages of uis12(-) with a mean -fold change lower than -2.

Article Snippet: Scanning of the microarrays was performed with 5 µm resolution and the extended mode using a ‘High Resolution Microarray Laser Scanner’ (G2505, Agilent Technologies).

Techniques: Microarray