MOESM2 of Long noncoding RNA dysregulation in ischemic heart failure
Creators: name: Greco, Simona
name: Zaccagnini, Germana
name: Perfetti, Alessandra
name: Fuschi, Paola
name: Valaperta, Rea
name: Voellenkle, Christine
name: Castelvecchio, Serenella
name: Gaetano, Carlo
name: Finato, Nicoletta
name: Beltrami, Antonio
name: Menicanti, Lorenzo
name: Martelli, Fabio
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Hematology

description: Additional file 2: Figure S1. Cardiac hypertrophy of non end-stage patients. Sections were derived from FFPE LV biopsies of controls (A) and HF patients (B). Hematoxylin and eosin staining showed a clear cardiomyocyte hypertrophy. Representative pictures are shown (HF n=16; CTR n=4; calibration bar=100 µm; magnification 20X). The bar graphs show the RT-qPCR measurement of MYH6 and NPPA hypertrophy markers, that are down- and up-regulated as expected (HF=10; CTR=5; **p≤0.01; *** p≤0.001) (C and D). Figure S2: Quality control of RNA extracted from heart biopsies of patients and controls. Total RNA was extracted from LV samples derived from non end-stage HF (n=18, panel A), end-stage HF (n=11, panel B) or controls (n=17, panel C). Integrity and amount of RNAs were measured by Bioanalyzer electrophoresis. Representative patterns and RNA Integrity Numbers (RIN) are shown. Figure S3: LncRNAs profiling in non end-stage HF patients. (A) Profiling of lncRNAs by RT-qPCR in 13 HF patients and 12 age-and sex-matched controls. (B) Validation of significantly deregulated lncRNAs in 18 HF and 17 controls. The bar graph (A) and table (B) shows the average fold change values with respect to controls (*p≤0.05, **p≤0.01; *** p≤0.001). Figure S4: Transverse aortic constriction induces cardiac hypertrophy. LV pressure overload was induced by TAC in C57BL/6J mice and cardiac hypertrophy markers were measured by RT-qPCR, 7 days after surgery. As expected atp2a2 was down- modulated and nppa, nppb and acta were increased (TAC=10; CTR=8; *p≤0.05, **p≤0.01). Figure S5: Mouse-human genomic alignment of HF lncRNAs. Gene locations from GRCh38.p5 (GCA_000001405.20) and from GRCm38.p4 (GCA_000001635.6) human and mouse genome assemblies, respectively, were used to compare the lncRNA sequence alignment in human and mouse by using Clustal Omega (http://www.ebi.ac.uk/Tools/msa/clustalo/). The percentage of identity is indicated. Figure S6: LncRNA/mRNA correlation analysis in HF. HF lncRNAs levels correlated to the levels of the mRNA expressed in the same samples. The bar graph indicates the number of transcripts significantly correlated for each lncRNA, either positively (white) or negatively (black). Figure S7: Venn’s diagram of enriched pathways in common between LV and PBMCs in HF patients GSE26887, GSE9128 and GSE1869 GEO datasets. The comparison of the 89, 99 and 53 enriched pathways of GSE26887, GSE9128 and GSE1869 datasets, respectively, identified 43 enriched pathways in common. Transcriptomic changes observed in LV and PBMCs of HF patients were determined in the following GEO datasets: for LV, GSE26887, and for PBMCs, GSE9128 and GSE1869. Common deregulated pathways were plotted as a Venn’s diagram.