Mus musculus
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: GSE26397
PROVIDER: PRJNA141689 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We performed two independent siRNA mediated knockdowns of Srf (Srf si1 & Srf si2) and an unspecific siRNA (siNon) in mouse cardiomyocytes HL-1 cells. Small RNAs were sequenced by Illumina/Solexa next-generation (single-end) sequencing technology. The sequence reads were mapped to the mouse reference genome (NCBI v37, mm9) using MicroRazerS. MicroRazerS searches for the longest possible prefix-match of each read, i.e. the longest possible contiguous match starting at the first base. Hence, it is robust to possible adapter sequence at the 3' end of a read and requires no adapter trimming. Small RNA-seq profiles of two siRNA mediated knockdowns of Srf and an unspecific siRNA in mouse cardiomyocytes
2011-01-03 | E-GEOD-19066 | biostudies-arrayexpress
Project description:We performed two independent siRNA mediated knockdowns of Srf (Srf si1 & Srf si2) and an unspecific siRNA (siNon) in mouse cardiomyocytes HL-1 cells. Small RNAs were sequenced by Illumina/Solexa next-generation (single-end) sequencing technology. The sequence reads were mapped to the mouse reference genome (NCBI v37, mm9) using MicroRazerS. MicroRazerS searches for the longest possible prefix-match of each read, i.e. the longest possible contiguous match starting at the first base. Hence, it is robust to possible adapter sequence at the 3' end of a read and requires no adapter trimming.
2011-01-03 | GSE19066 | GEO
Project description:Purpose: Common genetic variation at chromosome 4q25 lead to the strongest locus associated with atrial fibrillation (AF), the most frequent arrhythmia. The mechanism of association is currently unknown. We recently have identified a novel noncoding RNA expressed in the left atria. To determine the potential functional roles of the LNCRNA adjacent to PITX2 (PANCR) via knockdown in cardiomyocytes Methods and Results: H9 differentiated cardiomyocytes were treated with siRNA targeting PANCR and PITX2c and a scrambled control in triplicate. RNA and small RNA extracted and sent for sequencing. Approximately 50 million read fragments mapped to the transcriptome using STAR aligner to hg19 and fragments counted with htseq. EdgeR was used to quantify the differences between treatment groups. There were significant changes upon knocking down PITX2c or PANCR in the RNA sequencing with high concordance of effect sizes between the two treatments (r2 = 0.85). Similar to the RNAseq analysis, this miRNAseq analysis shows that the effects of PANCR knockdown on miRNA expression may be largely mediated by through its effect on PITX2c expression. Conclusion: PANCR knockdown decreased PITX2c expression in H9 differentiated cardiomyocytes, and altered the transcriptome similar to PITX2c knockdown. H9 derived cardiomyoctyes were treated with siRNA knockdown (scrambled control, PANCR, PITX2c) in triplicate and RNA and smallRNAs extracted for sequencing.
2015-04-15 | E-GEOD-67844 | biostudies-arrayexpress
Project description:Identification of Stat5 Target Genes by siRNA-mediated knockdown
| PRJNA108135 | ENA
Project description:Acute occlusion of a coronary artery results in swift tissue necrosis. Bordering areas of the infarcted myocardium may also experience impaired blood supply and reduced oxygen delivery leading to altered metabolic and mechanical processes. While transcriptional changes in hypoxic cardiomyocytes are well-studied, little is known about the proteins that are actively secreted from these cells. We established a novel secretome analysis of cardiomyocytes by combining stable isotope labeling and click chemistry with subsequent mass spectrometry analysis. Further functional validation experiments included ELISA measurement of human samples, murine LAD ligation and adeno-associated virus (AAV) 9-mediated in vivo overexpression in mice. The presented approach is feasible for the analysis of the secretome of primary cardiomyocytes without serum starvation. 1026 proteins were identified to be secreted within 24 hours, indicating a 5-fold increase in detection compared to former approaches. Among them, a variety of proteins have so far not been explored in the context of cardiovascular pathologies. One of the most strongly upregulated secreted factors upon hypoxia was proprotein convertase subtilisin/kexin type 6 (PCSK6). Validation experiments revealed an increase of PCSK6 on mRNA and protein level in hypoxic cardiomyocytes. PCSK6 expression was elevated in hearts of mice following 3 days of ligation of the left anterior descending artery, a finding confirmed by immunohistochemistry. ELISA measurements in human serum also indicate distinct kinetics for PCSK6 in patients suffering from acute myocardial infarction, with a peak on day 3 post-infarction. Transfer of PCSK6-depleted cardiomyocyte secretome resulted in decreased expression of collagen I and III in fibroblasts compared to control treated cells, and siRNA mediated knockdown of PCSK6 in cardiomyocytes impacted transforming growth factor-β activation and mothers against decapentaplegic homolog 3 (SMAD3) translocation in fibroblasts. An Adeno-associated virus (AAV) 9-mediated, cardiomyocyte-specific overexpression of PCSK6 in mice resulted in increased collagen expression and cardiac fibrosis as well as decreased left ventricular function after myocardial infarction. In conclusion, a novel mass spectrometry-based approach allows the investigation of the secretome of primary cardiomyocytes. Analysis of hypoxia-induced secretion led to the identification of PCSK6 to be crucially involved in cardiac remodeling after acute myocardial infarction. Secretome analysis was performed on neonatal rat ventricular cardiomyocytes (NRVCMs) which were incubated under hypoxic conditions (1.5% O2, 5% CO2, 93.5% N2) for 12 (Hypoxia 0-12h), 24 (Hypoxia 0-24h) and 30 (Hypoxia 24-30h) hours. Furthermore, knockdown (KD) of PCSK6 in vitro mediated by small interfering RNA (siRNA) was performed to investigate changes in the secretome of cardiomyocytes with PCSK6 KD vs. control (control siRNA) during 24 hours of hypoxia (PCSK6 KD 0-24h). Cells were pulse-labeled with AHA (L-azidohomoalanine) and SILAC (stable isotope labeling with amino acids in cell culture) for 12 (Hypoxia 0-12h), 24 (Hypoxia 0-24h/PCSK6 KD 0-24h) and 6 hours (Hypoxia 24-30h). For Hypoxia 0-12h 3 replicates, Hypoxia 0-24h 6 replicates, PCSK6 KD 0-24h 3 Replicates and Hypoxia 24-30h 2 replicates were performed with label-swap.
2020-03-05 | PXD016178 | Pride
Project description:Purpose: Common genetic variation at chromosome 4q25 lead to the strongest locus associated with atrial fibrillation (AF), the most frequent arrhythmia. The mechanism of association is currently unknown. We recently have identified a novel noncoding RNA expressed in the left atria. To determine the potential functional roles of the LNCRNA adjacent to PITX2 (PANCR) via knockdown in cardiomyocytes Methods and Results: H9 differentiated cardiomyocytes were treated with siRNA targeting PANCR and PITX2c and a scrambled control in triplicate. RNA and small RNA extracted and sent for sequencing. Approximately 50 million read fragments mapped to the transcriptome using STAR aligner to hg19 and fragments counted with htseq. EdgeR was used to quantify the differences between treatment groups. There were significant changes upon knocking down PITX2c or PANCR in the RNA sequencing with high concordance of effect sizes between the two treatments (r2 = 0.85). Similar to the RNAseq analysis, this miRNAseq analysis shows that the effects of PANCR knockdown on miRNA expression may be largely mediated by through its effect on PITX2c expression. Conclusion: PANCR knockdown decreased PITX2c expression in H9 differentiated cardiomyocytes, and altered the transcriptome similar to PITX2c knockdown.
2015-04-15 | GSE67844 | GEO
Project description:Identification of transcription factor Srf binding sites and histone 3 actetylated regions in mouse cardiomyocytes
| PRJNA141687 | ENA