Investigation Title	Cardiac gene expression and systemic cytokine profile are complementary in a murine model of post ischemic heart failure	
Comment[Submitted Name]	Cardiac gene expression and systemic cytokine profile are complementary in a murine model of post ischemic heart failure	
Experimental Design	transcription profiling by array	
Experimental Design Term Source REF	EFO	
Comment[SecondaryAccession]		
Comment[SecondaryAccession]	GSE18703	
Comment[ArrayExpressReleaseDate]	2010-06-20	
Comment[AEMIAMESCORE]	4	
Comment[ArrayExpressAccession]	E-GEOD-18703	
Comment[MAGETAB TimeStamp_Version]	2010-08-03 16:06:40 Last Changed Rev: 13058	
Experimental Factor Name	BIOSOURCEPROVIDER	TISSUE	
Experimental Factor Type	BioSourceProvider	tissue	
Experimental Factor Term Source REF	
Person Last Name	Iacobas	Costa	Lachtermacher	Esporcatte	Montalvão	Iacobas	Iacobas	Spray	Dohmann	Campos de Carvalho	Goldenberg	Rodrigues	Rabischoffisky	Belem	Vasconcellos	Faria Neto	
Person First Name	Dumitru	P	S	B	F	D	S	D	H	A	R	D	A	L	R	H	
Person Mid Initials	Andrei	C		L		A		C	F	C	C	C				C	
Person Email	diacobas@aecom.yu.edu	
Person Phone	718-430-4138	
Person Fax	718-430-8594	
Person Address	Neuroscience, Albert Einstein College of Medicine, 1300 Morris Parc Avenue, Bronx, NY, USA	
Person Affiliation	Albert Einstein College of Medicine	
Person Roles	submitter	
Person Roles Term Source REF	The MGED Ontology	
Quality Control Type	
Quality Control Term Source REF	
Replicate Type	
Replicate Term Source REF	
Normalization Type	
Normalization Term Source REF	
Date of Experiment	
Public Release Date	2010-06-20	
PubMed ID	
Publication DOI	
Publication Author List	
Publication Title	
Publication Status	
Publication Status Term Source REF	
Experiment Description	After myocardial infarction (MI) activation of the immune system and inflammatory mechanisms, among others, can lead to ventricular remodeling and heart failure (HF). Interaction between these systemic alterations and corresponding changes in the heart has not been extensively examined in the setting of chronic ischemia. The main purpose of this study was to investigate alterations in cardiac gene and systemic cytokine profile in mice with post-ischemic HF. Plasma was tested for IgM and IgG anti-heart reactive repertoire and inflammatory cytokines. Heart samples were assayed for gene expression. Ischemic HF significantly increased the levels of serum IgM (by 5.2 fold) and IgG (by 3.6 fold) associated with remarkable content of anti-heart specificity. Comparable increase was observed in levels of circulating pro-inflammatory cytokines, such as IL-1β (3.8x) and TNF-α (6.0x). IFN-gamma was also increased in the MI group by 3.1x. However, IL-4 and IL-10 showed no significant difference between MI and sham groups. Chemokines such as MCP-1 and IL-8 were enhanced in the plasma of infarcted mice. We identified 2079 well annotated unigenes that were significantly regulated by the post-ischemic HF. Complement activation and immune response was among the most up-regulated processes. Interestingly, 21 out of the 101 quantified unigenes involved in inflammatory response were significantly up-regulated and none were down-regulated. These data indicate that post-ischemic heart remodeling is accompanied by immune mediated mechanisms that act both systemically and locally. We compared RNA samples extracted from whole hearts of control and infarcted mice samples by analyzing hybridization to AECOM 32k mouse microarrays (http://microarray1k.aecom.yu.edu/) spotted with Operon version 3.0 70-mer oligonucleotides. The hybridization protocol, the slide type and the scanner settings were uniform throughout the entire experiment to minimize the technical noise. Control (sham) and infarcted red-labeled heart samples were hybridized against an in-house prepared green-labeled universal mouse reference.	
Protocol Name	P-GSE18703-2	P-GSE18703-3	P-GSE18703-4	P-GSE18703-5	P-GSE18703-6	P-GSE18703-7	P-GSE18703-8	P-GSE18703-9	P-GSE18703-1	
Protocol Type	specified_biomaterial_action	grow	nucleic_acid_extraction	labeling	labeling	hybridization	image_aquisition	feature_extraction	bioassay_data_transformation	
Protocol Description	Permanent myocardial infarcts were produced by ligation of the descending branch of the left coronary artery. Animals were anesthetized by an intraperitoneal injection with ketamine (40mg/kg) and xylazine (80mg/kg), placed in a supine position and intubated. Mice were ventilated with a volume-cycled ventilator (100 cycles/min, Harvard Apparatus; Holliston, MA) with volume sufficient to adequately expand but not overexpand the lungs. After a left anterior thoracotomy, the heart was exposed and the suture (8-0 mononylon) was passed under the artery at a position ~1mm from the tip of the normally positioned left auricle. The chest was then closed and the skin sutured with 5-0 nylon. Sham operations were created by the same method but without tying the suture in LAD.	Mice were housed at controlled temperature (23ºC) with 12:12-hour light-dark cycle and received standard mouse chow and water ad libitum.	total RNA was extracted using the TRIzol® protocol (Invitrogen, CA). RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE)	30ug total RNA extracted from each heart was reverse transcribed into cDNA incorporating fluorescent Alexa Fluor®_647–aha-dUTP using SuperScriptTM Plus Direct cDNA Labeling System (Invitrogen, CA).	30ug total RNA extracted from each heart was reverse transcribed into cDNA incorporating fluorescent Alexa Fluor®_555–aha-dUTP using SuperScriptTM Plus Direct cDNA Labeling System (Invitrogen, CA).	Alexa Fluor®_647-labeled cDNA was co-hybridized with Alexa Fluor®_555-labeled universal mouse reference prepared in our lab from ten adult mouse tissues (aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, and stomach - equal amounts from males and females) overnight at 50°C on a MO3 AECOM mouse oligonucleotide array spotted with 32k Operon 70-mer oligonucleotides V3.0 (GPL5371).	After washing (0.1% SDS and 1% SSC) to remove the non-hybridized cDNAs, each array was scanned WITH A 4000B scanner (MDS, Toronto, Canada)) and images were primarily analyzed with GenePixPro 6.0 (Axon Instruments, CA).	Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al. Physiol Genomics 2005.	ID_REF = <br>X = X-coordinate of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image<br>Y = Y-coordinate of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image<br>Dia. = diameter of the feature-indicator<br>F635 Median = median feature pixel intensity for Alexa Fluor®_647 channel<br>F635 Mean = mean feature pixel intensity for Alexa Fluor®_647 channel<br>F635 SD = standard deviation of feature pixel intensity for Alexa Fluor®_647 channel<br>B635 Median = median background pixel intensity for Alexa Fluor®_647 channel<br>B635 Mean = mean background pixel intensity for Alexa Fluor®_647 channel<br>B635 SD = standard deviation of background pixel intensity for Alexa Fluor®_647 channel<br>F635 % Sat. = percent saturated pixels for Alexa Fluor®_647 channel<br>F532 Median = median feature pixel intensity for Alexa Fluor®_555 channel<br>F532 Mean = mean feature pixel intensity for Alexa Fluor®_555 channel<br>F532 SD = standard deviation of feature pixel intensity for Alexa Fluor®_555 channel<br>B532 Median = median background pixel intensity for Alexa Fluor®_555 channel<br>B532 Mean = mean background pixel intensity for Alexa Fluor®_555 channel<br>B532 SD = standard deviation of background pixel intensity for Alexa Fluor®_555 channel<br>F532 % Sat. = percent saturated pixels for Alexa Fluor®_555 channel<br>FLAG = A feature was considered as valid (0 value) if there are no local corruption, no saturated pixels and the foreground signal is at least 2x larger than the background signal. Negative values indicate substandard feature.<br>VALUE = normalized to the green channel log2 ratio of the background subtracted signal of that feature and the median of the background subtracted signals of all valid features of the block (700 features) in the red channel. A NULL indicates that the feature was not valid (negative FLAG)	
Protocol Parameters	
Protocol Hardware	
Protocol Software	
Protocol Contact	
Protocol Term Source REF	The MGED Ontology	The MGED Ontology	The MGED Ontology	The MGED Ontology	The MGED Ontology	The MGED Ontology		The MGED Ontology	The MGED Ontology	
SDRF File	E-GEOD-18703.sdrf.txt	
Term Source Name	NCBI Taxonomy		The MGED Ontology	ArrayExpress	EFO	The MGED Ontology	
Term Source File	http://www.ncbi.nlm.nih.gov/Taxonomy/		http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/arrayexpress	http://www.ebi.ac.uk/efo/	http://mged.sourceforge.net/ontologies/MGEDontology.php	
Term Source Version