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Sample GSM1380060 Query DataSets for GSM1380060
Status Public on Jan 01, 2015
Title P00145 Ischemic Left Ventricle
Sample type RNA
 
Source name heart left ventricle, ischemic
Organism Homo sapiens
Characteristics tissue: heart left ventricle
heart failure: yes
disease status: ischemic
gender: male
age: 56
Treatment protocol Explanted myocardium snap frozen in liquid nitrogen.
Growth protocol None
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol 100ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 RNA polymerase promoter. Second-strand cDNA synthesis was followed by in vitro transcription (Affymetrix One-Cycle Target Labeling Kit) for linear amplification and biotinylation of each transcript.
 
Hybridization protocol cDNAs were added to Affymetrix hybridization cocktails, heated at 99ºC for 2 min and hybridized for 16 h at 45ºC to Affymetrix Human Gene 1.1 ST Array GeneChips (Affymetrix Inc., Santa Clara, CA). The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.
Scan protocol A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.
Description P00145
PolyA mRNA
Data processing Microarray data were analyzed using the Oligo package available at the Bioconductor website (www.bioconductor.org). The raw data were first background-corrected by the Robust Multichip Average (RMA) method and then normalized by an invariant set method. Microarray Processing batch were controlled for using the R package Combat. Differential gene expression was analyzed by the Limma package available at the Bioconductor website. P-values obtained from the multiple comparison tests were corrected by false discovery rates.
 
Submission date May 06, 2014
Last update date Jan 01, 2015
Contact name Michael Patrick Morley
E-mail(s) mmorley@pennmedicine.upenn.edu
Phone 215-898-2026
Organization name Perelman School of Medicine at the University of Pennsylvania
Department Penn Cardiovascular Institute
Street address 3400 Civic Center Blvd, Bldg 421
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL11532
Series (2)
GSE57338 RNA-Seq Identifies Novel Myocardial Gene Expression Signatures of Heart Failure [microarray]
GSE57345 RNA-Seq Identifies Novel Myocardial Gene Expression Signatures of Heart Failure

Data table header descriptions
ID_REF
VALUE RMA log2 signal

Data table
ID_REF VALUE
7892501 3.303164388
7892502 3.489191619
7892503 3.168319163
7892504 7.434453979
7892505 3.073660207
7892506 2.776931776
7892507 4.197762931
7892508 6.452812949
7892509 10.30411481
7892510 3.561188487
7892511 2.842012227
7892512 5.175195194
7892513 2.633911149
7892514 10.15968915
7892515 8.404591207
7892516 2.401938748
7892517 6.57067701
7892518 2.960528215
7892519 3.69715483
7892520 8.26428749

Total number of rows: 33297

Table truncated, full table size 646 Kbytes.




Supplementary file Size Download File type/resource
GSM1380060_P00145_HuGene1.1ST.CEL.gz 4.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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