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Sample GSM493837 Query DataSets for GSM493837
Status Public on Jan 01, 2011
Title myocyte_serum containing media_adeno-bGal_sample2
Sample type RNA
 
Source name Primary culture of neonatal rat ventricular cardiomyocytes, serum containing media
Organism Rattus norvegicus
Characteristics tissue: Neonatal cardiomyocytes
Treatment protocol Neonatal cardiomyocytes were isolated from 1-3 day old Sprague Dawley rat pups using the Neonatal Cardiomyocyte Isolation System (Worthington) according to the manufacturer’s instructions. Briefly, hearts were rinsed with ice cold HBSS, and trypsinised for 16 hrs at 4oC. Hearts were incubated with trypsin inhibitor at 37°C, and then incubated for 60 minutes with a collagenase solution at 37°C with gentle mixing. Cell pellet was triturated and resuspended in M199 media (invitrogen) containing 10% fetal calf serum. Cells were then pre-plated for 1 hr to deplete culture of fibroblasts, and non adherent cells were plated on gelatin coated culture dishes. Following plating cells were washed twice with culture media containing 10% fetal calf serum, infected with adenovirus encoding for beta-Galactosidase and grown for 48 hrs.
Extracted molecule total RNA
Extraction protocol RNA was extracted using RNeasy Fibrous Tissue kit (Qiagen) according to the manufacturer’s instructions.
Label biotin
Label protocol The Affymetrix Whole Transcript Sense Target Labeling Assay (Affymetrix) is used to create biotin – labeled sense -strand cDNA targets for hybridization to the Gene 1.0 ST Arrays.
 
Hybridization protocol Hybridization cocktail for a single probe array contained 2.5 ?g of fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 7% DMSO, and 1X Hybridization Buffer. GeneChip Rat Gene 1.0 ST Array– Affymetrix was hybridized at 45?C for 18 hours in the GeneChip Hybridization Oven 640 (Affymetrix)
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
Description Gene expression data from cardiomyocytes in 10% serum containing media, infected with adeno-beta-galactosidase
Data processing The data were analyzed with GeneSpring version 7.3 using RMA normalization, then normalized to median of all samples.
 
Submission date Jan 06, 2010
Last update date Jan 01, 2011
Contact name izhak kehat
E-mail(s) izhak.kehat@cchmc.org
Organization name CCHMC
Street address 3333 burnet ave
City cincinnati
State/province OH
ZIP/Postal code 45229
Country USA
 
Platform ID GPL6247
Series (1)
GSE19771 Neonat cardiomyocytes_hypertrophy_HDAC4

Data table header descriptions
ID_REF
VALUE The data were RMA normalized, then normalized to the median of all samples.

Data table
ID_REF VALUE
10701620 0.9256941
10701630 0.9854817
10701632 1.3862095
10701636 0.840408
10701643 0.84507245
10701648 0.9756117
10701654 0.93243426
10701663 0.7529046
10701666 0.904469
10701668 1.0282469
10701671 0.9773787
10701674 0.9981517
10701679 1.2243134
10701684 1.0922863
10701689 0.9522836
10701691 0.9052979
10701697 0.7096682
10701699 1.0800159
10701709 0.80171764
10701714 0.9237229

Total number of rows: 29215

Table truncated, full table size 545 Kbytes.




Supplementary file Size Download File type/resource
GSM493837.CEL.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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