Comment[ArrayExpressAccession]	E-GEOD-41859
MAGE-TAB Version	1.1										
Public Release Date	2014-10-01
Investigation Title	miRNA-mRNA networks in mouse testis during the 1st wave of spermatogenesis										
Comment[Submitted Name]	miRNA-mRNA networks in mouse testis during the 1st wave of spermatogenesis
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	Kumar										
Person First Name	Pradeep										
Person Mid Initials	G										
Person Email	kumarp@rgcb.res.in										
Person Affiliation	Rajiv Gandhi Centre for Biotechnology										
Person Address	Molecular Reproduction, Rajiv Gandhi Centre for Biotechnology, Thycaud, Poojappura, Trivandrum, Kerala, India										
Person Roles	submitter										
Protocol Name	P-GSE41859-2	P-GSE41859-1	P-GSE41859-6	P-GSE41859-9	P-GSE41859-10	P-GSE41859-7	P-GSE41859-3	P-GSE41859-4	P-GSE41859-5	P-GSE41859-8	P-GSE41859-11
Protocol Description	The raw data .cel file were normalized by ExonRMA16 summarization with All Confidence level: ALL followed by Quantile normalization and Baseline Transformation to median of all samples ID_REF =  VALUE = Normalized Data	Raw data values were thresholded to 1.0 for all those less than 0.0 and normalized by 75 percentile shift method. ID_REF =  VALUE = Normalized Data	The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile. One M-5g total RNA from sample and reference was labelled with Hy3M-bM-^DM-" and Hy5M-bM-^DM-" fluorescent label, respectively, using the miRCURYM-bM-^DM-" LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer.	Biotinylated cDNAs were prepared according to the GeneChip Whole Transcript Sense Target Labeling protocol (Affymetrix).	Following fragmentation, cDNAs were hybridized for 17 hr at 45M-0C on Affymetrix Mouse Gene 1.0 ST Arrays. GeneChips were washed and stained in the GeneChip Fluidics Station 450 (Affymetrix).	The Hy3M-bM-^DM-"-labeled samples and a Hy5M-bM-^DM-"-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURYM-bM-^DM-" LNA array version 11.0 (Exiqon, Denmark), which contains capture probes targeting all miRNAs for human, mouse or rat registered in the miRBASE version 13.0 at the Sanger Institute. . The hybridization was performed according to the miRCURYM-bM-^DM-" LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria).	None. Animals were reared in normal temperature, 26 M-11M-KM-^ZC and humidity controlled environment under 14h light: 10h dark conditions.	Male Swiss albino mice were obtained from an inbred line maintained in animal house facility.	Total RNA extraction was performed using Guanidine Thiocyanate (GTC) based QIAzol lysis reagent, miRNeasy Mini Kit according to the manufacturer's instructions.	After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURYM-bM-^DM-" LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA).	GeneChips were scanned using the GeneChip Scanner 3000 7G (Affymetrix).
Protocol Type	normalization data transformation protocol	normalization data transformation protocol	labelling protocol	labelling protocol	hybridization protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol	array scanning protocol
Publication Title	Dramatic Changes in 67 miRNAs During Initiation of First Wave of Spermatogenesis in Mus musculus Testis: Global Regulatory Insights Generated by miRNA-mRNA Network Analysis.										
Publication Author List	Sree S, Radhakrishnan K, Indu S, Kumar PG										
PubMed ID	25122060										
Publication DOI	10.1095/biolreprod.114.119305										
Comment[SecondaryAccession]	GSE41859										
Comment[GEOReleaseDate]	2014-10-01										
Comment[ArrayExpressSubmissionDate]	2012-10-26										
Comment[GEOLastUpdateDate]	2014-10-01										
Comment[AEExperimentType]	transcription profiling by array										
SDRF File	E-GEOD-41859.sdrf.txt