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Sample GSM1364738 Query DataSets for GSM1364738
Status Public on Jul 01, 2014
Title HL-1_CON_6h_rep.4
Sample type RNA
 
Source name HL-1 cardiomyocytes, stimulated with murine control serum, 6h
Organism Mus musculus
Characteristics cell type: immortalized murine cardiomyocytes
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 HL-1
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.
 
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

Data table header descriptions
ID_REF
VALUE log2 normalized signals
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1212607 7.858537077 0.03383
ILMN_1212612 11.08864222 0
ILMN_1212619 7.233334611 0.49248
ILMN_1212628 7.10348037 0.72055
ILMN_1212632 7.309409141 0.38471
ILMN_1212636 12.56098989 0
ILMN_1212637 11.04087008 0
ILMN_1212645 7.269786792 0.43358
ILMN_1212648 10.2542273 0
ILMN_1212653 7.394521975 0.28571
ILMN_1212672 9.639934868 0
ILMN_1212682 7.845461817 0.03509
ILMN_1212683 7.268450047 0.43609
ILMN_1212685 7.210001799 0.53258
ILMN_1212692 7.14680804 0.64787
ILMN_1212693 8.301820009 0.00125
ILMN_1212695 7.04112261 0.80702
ILMN_1212698 7.359521797 0.31579
ILMN_1212702 10.7506063 0
ILMN_1212703 8.207086606 0.00376

Total number of rows: 25697

Table truncated, full table size 771 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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