Comment[ArrayExpressAccession]	E-GEOD-29412
MAGE-TAB Version	1.1					
Public Release Date	2013-10-11
Investigation Title	To examine the influence of the early stress of maternal separation on the hippocampal transcriptome in young adulthood					
Comment[Submitted Name]	To examine the influence of the early stress of maternal separation on the hippocampal transcriptome in young adulthood
Experiment Description	In this study, we examined the consequences of the early stress (ES) of maternal separation on hippocampal gene expression in young adulthood. Young adult (2 months old) ES animals exhibit hippocampal transcriptome changes with a significant regulation of genes associated with intracellular signaling, MAP kinase signaling, plasma membrane function, neurotransmitter and neuropeptide receptors and cytoskeletal components. Agilent one-color experiment, Agilent-024724 Genotypic-designed Custom Rattus Norvegicus  8x15k; Organism: Rattus norvegicus; Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442); Biological replicates: 4 per treatment group.					
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	Suri	Suri	Vaidya			
Person First Name	Deepika	Deepika	Vidita			
Person Email	deepika@tifr.res.in					
Person Affiliation	TIFR					
Person Address	DBS, TIFR, Homi Bhabha Road, Mumbai, India					
Person Roles	submitter					
Protocol Name	P-GSE29412-1	P-GSE29412-4	P-GSE29412-5	P-GSE29412-2	P-GSE29412-3	P-GSE29412-6
Protocol Description	75th-percentile shift normalization was done using GeneSpring GX 11 Software. ID_REF =  VALUE = Normalized value (log base2)	The samples for gene expression were labeled using the Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the samples were incubated with reverse trancription mix at 40°C and converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned-up double-stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.	600 ng Cy3-labeled samples for 8x15 arrays were fragmented and hybridized. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent's Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327). RNA from each biological replicate was hybridized onto one array, making the total number of arrays 8.	The animals were subjected to the early stress (ES) of maternal separation. The litters were randomly assigned to the control or ES groups. Pups in the ES group were separated from the dams from postnatal day 2 (P2) to postnatal day 14 (P14) for a period of three hours at the same time each day, while pups of the control group were left undisturbed except for routine animal facility handling. Post P14 the ES animals were left undisturbed and all litters were weaned at P30. To determine the effects of early life adverse events on the hippocampal transcriptome in young adulthood, microarray analysis was performed.	At two months of age, control and ES animals (n = 4 per group) were sacrificed, the hippocampi were dissected and stored at -70 prior to use. RNA was extracted from these tissues. RNA was prepared using the Qiagen RNeasy mini kit following the manufacturer's recommendations. RNA was quantified using NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).	Scanned on an Agilent Technologies G2505C scanner. Images were quantified using Agilent Feature Extraction Software 10.5.1.1.
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	TREATMENT					
Experimental Factor Type	treatment					
Publication Title	Early stress evokes temporally distinct consequences on the hippocampal transcriptome, anxiety and cognitive behaviour.					
Publication Author List	Suri D, Bhattacharya A, Vaidya VA					
PubMed ID	24025219					
Publication DOI	10.1017/S1461145713001004					
Comment[SecondaryAccession]	GSE29412					
Comment[GEOReleaseDate]	2013-10-11					
Comment[ArrayExpressSubmissionDate]	2011-05-20					
Comment[GEOLastUpdateDate]	2013-10-12					
Comment[AEExperimentType]	transcription profiling by array					
SDRF File	E-GEOD-29412.sdrf.txt