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Sample GSM493835 Query DataSets for GSM493835
Status Public on Jan 01, 2011
Title myocyte_serum free media_adeno-HD4_sample2
Sample type RNA
 
Source name Primary culture of neonatal rat ventricular cardiomyocytes, serum free 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 serum free culture media, infected with adenovirus encoding for HDAC4 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 serum free media, infected with adeno-HDAC4
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 0.99636656
10701630 0.97278434
10701632 1.2172397
10701636 0.76148
10701643 0.8866133
10701648 0.8548712
10701654 1.1415647
10701663 0.9975648
10701666 0.86653155
10701668 1.1191174
10701671 1.2037022
10701674 1.1187129
10701679 0.7951159
10701684 1.1766181
10701689 0.8106465
10701691 1.0765738
10701697 1.0324589
10701699 0.8317965
10701709 1.036239
10701714 1.0980129

Total number of rows: 29215

Table truncated, full table size 543 Kbytes.




Supplementary file Size Download File type/resource
GSM493835.CEL.gz 4.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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