|
| Status |
Public on Jul 01, 2014 |
| Title |
NNC_CM_12h_rep.3 |
| Sample type |
RNA |
| |
|
| Source name |
isolated neonatal cardiomyocytes, 12h after stimulation with cytokine mix
|
| Organism |
Mus musculus |
| Characteristics |
cell type: isolated neonatal cardiomyocytes, murine
|
| Treatment protocol |
HL-1 cells and murine neonatal cardiomyocytes (NNC) were cultivated in 12- and 6-well plates, respectively, until required confluence was reached. For stimulation experiments the appropriate culture medium was prepared serum-free and supplemented with the following additives immediately before stimulation: a) 5 % murine control serum, b) 5 % murine PCI serum, c) 5 % murine control serum + 200 ng/ml LPS (from Escherichia coli 0111:B4; Sigma-Aldrich), d) 5 % murine control serum + cytokine mix. The mix consisted of (final concentrations): 50 ng/ml TNF-α, 10 ng/ml IL-1β, 50 ng/ml IL-6, 10 ng/ml IFN-γ (all cytokines purchased from Hiss/Novitec) and 100 ng/ml LPS. Stimulation was performed for 6 or 12 h at 37°C
|
| Growth protocol |
All cells were grown in an incubator at 37°C, in an atmosphere of 5 % CO2 and 95 % air at a relative humidity of approximately 95 %.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from cardiomyocytes (HL-1 cells, murine neonatal cardiomyocytes) using QIAcubeTM and RNeasy® Mini Kit from Qiagen in accordance to the Purification of Total RNA from Animal Cells Using Spin Technology protocol. RNA concentration and purity were determined with the NanoDrop® ND-2000c spectrophotometer and quality control was performed with the automated electrophoresis system ExperionTM (Bio-Rad Laboratories) according to the manufacturer’s specifications using the ExperionTM RNA StdSens Analysis Kit.
|
| Label |
biotin
|
| Label protocol |
Amplification and biotinylation of RNA were carried out using the TargetAmp™-Nano Labeling Kit for Illumina® Expression BeadChip® (Epicentre).
|
| |
|
| Hybridization protocol |
Hybridization was in agreement with the Whole-Genome Gene Expression Assay protocol from Illumina.
|
| Scan protocol |
Arrays were read with the detection system iScan from Illumina.
|
| Description |
NNC
|
| Data processing |
Raw data were pre-processed using GenomeStudio (v 1.9.0). Robust spline normalization (rsn) and detection filtering were performed by the lumi package within R statistics software and Bioconductor for HL-1 and NNC samples separately. One outlier LPS 12h (rep.4) was detected and removed.
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| |
|
| Submission date |
Apr 08, 2014 |
| Last update date |
Jul 01, 2014 |
| Contact name |
S. Lambeck |
| Organization name |
JUH
|
| Street address |
Erlanger Allee 101
|
| City |
Jena |
| ZIP/Postal code |
07743 |
| Country |
Germany |
| |
|
| Platform ID |
GPL6885 |
| Series (1) |
| GSE56584 |
Gene expression profiles of neonatal cardiomyocytes and immortalized heart muscle cells exposed to inflammatory stimuli |
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