Comment[ArrayExpressAccession]	E-GEOD-52875
MAGE-TAB Version	1.1											
Public Release Date	2013-12-04
Investigation Title	Expression signatures in heart tissues of mice simulating posttraumatic stress disorder (PTSD)											
Comment[Submitted Name]	Expression signatures in heart tissues of mice simulating posttraumatic stress disorder (PTSD)
Experiment Description	This SuperSeries is composed of the SubSeries listed below. Refer to individual Series											
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl										
Person Last Name	Cho											
Person First Name	Ji-Hoon											
Person Email	jcho@systemsbiology.org											
Person Affiliation	Institute for Systems Biology											
Person Address	Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, USA											
Person Roles	submitter											
Protocol Name	P-GSE52875-2	P-GSE52875-4	P-GSE52875-1	P-GSE52875-3	P-GSE52875-7	P-GSE52875-10	P-GSE52875-8	P-GSE52875-11	P-GSE52875-5	P-GSE52875-6	P-GSE52875-12	P-GSE52875-9
Protocol Description	Scanned data was processed using AnalyzerDG software. For the preprocessing of two-channel microarray data in each experimental group,  Hy3 and Hy5 (high energy scanned) intensities were concatenated, normalized using LOWESS (within-array normalization) and normalized using the quantile method (between-array normalization). ID_REF =  VALUE = Since there are four identical replicated probes for each miRNA in the Exiqon microarray platform, they were consolidated by taking the median expression value over the replicated probes to remove redundancy.	Scanned data was processed using Agilent Feature Extraction. For the preprocessing of two-channel microarray data,  gProcessedSignal and rProcessedSignal intensities were concatenated and they were normalized using quantile method. ID_REF =  VALUE = Since there are four identical replicated probes for each miRNA in the Exiqon microarray platform, they were consolidated by taking the median expression value over the replicated probes to remove redundancy.	The scanned images of the arrays were converted and imported into the Institute for Systems BiologyM-bM-^@M-^Ys Systems Biology Experiment Analysis System (SBEAMS) for array data normalization and further analyses. ID_REF =  VALUE = Quantile normalized and log2-transformed gene expression values. Each dataset for each condition was independently processed	The scanned images of the arrays were converted and imported into the Institute for Systems BiologyM-bM-^@M-^Ys Systems Biology Experiment Analysis System (SBEAMS) for array data normalization and further analyses. ID_REF =  VALUE = Quantile normalized and log2-transformed gene expression values.	Total RNA was reverse transcribed and followed by generation of cDNAs. The resulting cDNAs were transcribed and labeled with cyanine 3-CTP.	Total RNA from the heart tissue was labeled with either Hy3 or Hy5 dye with labeling kits from Exiqon then hybridized at 56M-0C for 16 h.	The labeled antisense cRNAs were purified and hybridized to microarrays. The hybridization was carried out for 16 h at 45M-0C.	Labeled samples were hybridized to Exiqon 5th generation miRCURY LNA microRNA array according to the manufacturer's protocol.	The experimental animals were kept in a wire mesh box inside the aggressorM-4s cage for 6 hours a day for either 5 or 10 consecutive days. Animals were randomly assigned to aggressors cages. Each subject mouse was randomly placed 3-5 times within the home cage of an aggressor mouse and received bites/attacks for up to 2 min (or until 10 attacks/bites occurred, whichever came first. Each day the stress procedure occurred at different times and different resident mice were used for each aggressor. Body weight and temperature of the experimental mice were measured every day prior the beginning of the social defeat period and the return to their home cages. Control mice were kept inside of the wired mesh boxes inside of a large cage without any aggressor.	Total RNA was isolated from individual mouse heart samples by homogenization in TRIzol reagent per the manufacturerM-bM-^@M-^Ys protocol (Invitrogen, Gran Island, NY). The quality and quantity of the RNA samples were evaluated using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific, Waltham, MA) and Agilent 2100 BioAnalyzer (Agilent, Santa Clara, CA).	After hybridization, the slides were washed and scanned with a scanner from Agilent (Santa Clara, CA).	The arrays were washed and scanned using an Agilent scanner.
Protocol Type	normalization data transformation protocol	normalization data transformation protocol	normalization data transformation protocol	normalization data transformation protocol	labelling protocol	labelling protocol	hybridization protocol	hybridization protocol	sample treatment protocol	nucleic acid extraction protocol	array scanning protocol	array scanning protocol
Experimental Factor Name	ORGANISM PART											
Experimental Factor Type	organism part											
Comment[SecondaryAccession]	GSE52875											
Comment[GEOReleaseDate]	2013-12-04											
Comment[ArrayExpressSubmissionDate]	2013-12-02											
Comment[GEOLastUpdateDate]	2013-12-05											
Comment[AEExperimentType]	transcription profiling by array											
SDRF File	E-GEOD-52875.sdrf.txt