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Sample GSM1380086 Query DataSets for GSM1380086
Status Public on Jan 01, 2015
Title P00271 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: 65
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 P00271
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 2.377830995
7892502 3.640733923
7892503 2.455088145
7892504 7.040915767
7892505 2.135865411
7892506 2.70676416
7892507 4.266075662
7892508 6.304846348
7892509 9.940050016
7892510 4.99220058
7892511 2.930526488
7892512 4.866887895
7892513 3.145123632
7892514 9.528082302
7892515 7.79778059
7892516 2.589449465
7892517 6.37348754
7892518 2.367349161
7892519 3.313466917
7892520 7.773885487

Total number of rows: 33297

Table truncated, full table size 646 Kbytes.




Supplementary file Size Download File type/resource
GSM1380086_P00271_HuGene1.1ST.CEL.gz 4.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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