Journal: Scientific Reports

Article Title: Time and phenotype-dependent transcriptome analysis in AAV-TGFβ1 and Bleomycin-induced lung fibrosis models

doi: 10.1038/s41598-022-16344-7

Figure Lengend Snippet: Longitudinal assessment of transcriptomic changes in AAV-TGFβ1 and Bleomycin induced fibrosis. Total RNA was extracted from the mice treated as described in Fig. and applied to RNA-sequencing. ( a ) unsupervised hierarchical clustering (Z-scored FPKMs) of all mRNAs showing differential expression (log 2 FC ≥ 0.6, q ≤ 0.05) at ≥ two contrasts across all time points and models (n = 6010). The genes within the color-coded clusters were applied to ( b ) Reactome pathway enrichment analysis. Cluster 1, n = 148 genes; cluster 2, n = 552; cluster 3, n = 186, cluster 4, n = 403 and cluster 5, n = 275. ( c ) Expression profiles of the top 3 differentially expressed genes in each cluster. ( d ) Total number of differentially expressed genes over time for both models. ( e ) Correlation plots for genes showing differential expression either exclusively in one model or commonly in both models, as defined by expression cutoffs (log 2 FC = 0.6). The coefficient of determination (R 2 ) is show for each set of genes under the graphs. Legend as in ( f ). ( f ) Significance of enrichment ( p -value) for selected KEGG pathways over time, obtained and plotted for the gene sets defined in ( e ). TLR = toll-like receptor. ECM = extracellular matrix. Heatmap created with TIBCO Spotfire Analyst 10.3.2.

Article Snippet: Heatmap created with TIBCO Spotfire Analyst 10.3.2.

Techniques: RNA Sequencing Assay, Expressing

Journal: BMC Medical Genomics

Article Title: Identification of protein-coding and non-coding RNA expression profiles in CD34 + and in stromal cells in refractory anemia with ringed sideroblasts

doi: 10.1186/1755-8794-3-30

Figure Lengend Snippet: Validation of gene expression data of CD34 + cells by real-time RT-PCR . Comparison of gene expression levels by real-time RT-PCR (black bars) and microarray experiments (gray bars) for eight select genes (names indicated at bottom) in CD34 + cells of MDS-RARS patients and healthy individuals. Positive and negative fold change values indicate the up- or down-regulation of expression in MDS-RARS patients in relation to the expression in healthy individuals, respectively.

Article Snippet: Data were normalized among the samples by quantile [ ] using Spotfire DecisionSite ® for Microarray Analysis (TIBCO Software Inc, Somerville, MA, USA).

Techniques: Biomarker Discovery, Gene Expression, Quantitative RT-PCR, Comparison, Microarray, Expressing

Journal: BMC Medical Genomics

Article Title: Identification of protein-coding and non-coding RNA expression profiles in CD34 + and in stromal cells in refractory anemia with ringed sideroblasts

doi: 10.1186/1755-8794-3-30

Figure Lengend Snippet: Validation of gene expression data of stromal cells by real-time RT-PCR . Comparison of gene expression obtained from real-time RT-PCR (black bars) and microarray experiments (gray bars) for four select genes (names indicated at bottom) in stromal cells of MDS-RARS patients and of healthy individuals. The positive and negative fold change values indicate up- or down-regulation of expression in MDS-RARS patients in relation to the expression in healthy individuals, respectively.

Article Snippet: Data were normalized among the samples by quantile [ ] using Spotfire DecisionSite ® for Microarray Analysis (TIBCO Software Inc, Somerville, MA, USA).

Techniques: Biomarker Discovery, Gene Expression, Quantitative RT-PCR, Comparison, Microarray, Expressing