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Sample GSM1380004 Query DataSets for GSM1380004
Status Public on Jan 01, 2015
Title C02168 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: 54
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 C02168
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 2.29830735
7892502 3.719030432
7892503 2.573829149
7892504 7.110779846
7892505 2.922957974
7892506 2.885503815
7892507 3.737769176
7892508 5.733922107
7892509 10.1403054
7892510 4.236809014
7892511 3.069769413
7892512 5.202960563
7892513 2.674789001
7892514 9.265239341
7892515 7.892137327
7892516 2.412035122
7892517 6.159748731
7892518 2.95349217
7892519 3.638640707
7892520 7.587169039

Total number of rows: 33297

Table truncated, full table size 646 Kbytes.




Supplementary file Size Download File type/resource
GSM1380004_C02168_HuGene1.1ST.CEL.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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