Comment[ArrayExpressAccession]	E-MEXP-3866
Investigation Title	Estrogen regulation of microRNA in the zebrafish liver																									
Comment[Submitted Name]	Estrogen regulation of microRNA in the zebrafish liver
Comment[AEExperimentDisplayName]	microRNA profiling by array of Danio rerio samples originating from livers of male fish exposed to 17-beta estradiol																									
Comment[MIAMExpressLogin]	amiton																									
Comment[MIAMExpressSubmissionID]	8670																									
Experiment Description	Microarrays displaying zebrafish microRNA specific probes were hybridized using RNA samples originating from livers of male zebrafish exposed to 17-beta estradiol (E2) for 0, 24 and 48 hours.																									
Experimental Design	reference design	co-expression_design	time series design	compound treatment design																						
Comment[AEExperimentType]	microRNA profiling by array																									
Experimental Factor Name	COMPOUND	DOSE	TIME																							
Experimental Factor Type	compound	dose	time																							
Person Last Name	Cohen																									
Person First Name	Amit																									
Person Email	acohe04@yahoo.com																									
Person Phone	-523218177																									
Person Affiliation	Hebrew University of Jerusalem																									
Person Address	Genomic Data Analysis Unit, Hadassah Medical School P.O. Box 12272, Jerusalem, Jerusalem, 91120, Israel																									
Person Roles	submitter																									
Person Roles Term Source REF	EFO																									
Quality Control Type	biological replicate																									
Public Release Date	2013-06-02																									
Comment[ArrayExpressSubmissionDate]	2013-04-11 09:44																									
PubMed ID	23767875
Publication Author List	Cohen A, Smith Y 
Publication Title	Estrogen Regulation of MicroRNAs, Target Genes, and MicroRNA Expression Associated with Vitellogenesis in the Zebrafish																									
Publication Status	submitted																									
Protocol Name	P-MTAB-31620	P-MTAB-31621	P-MTAB-31622	P-MTAB-31623	P-MTAB-31624	P-MTAB-31625
Protocol Description	To create a common reference pool, Exiqon pooled all samples per experiment for the use of Hy5 signals. The common reference was a pool of RNA composed of ten samples: four control samples, three samples of 24 hrs after E2 treatment and three samples of 48 hrs after E2 treatment. 	The hybridization was performed according to the miRCURY LNA array manual using a Tecan HS4800 hybridization station (Tecan). Each Hy3(tm)-labeled sample was mixed with the Hy5(tm)-labeled reference RNA sample and then hybridized on the miRCURY LNA(tm) miRNA Arrays (v.11.0) following the common reference design. (Parameters: Chamber type = OTHER: Tecan HS4800 hybridization station, Quantity of label target used = 1, Mass unit = Micro gram, time = 16, Tiny time unit = hours, Volume unit = Nano litre, temperature = 56)	Male zebrafish were exposed to 17beta-estradiol (E2) (Sigma) by immersion. The concentration used was 5 ug/L (18 nM). Ten fish were kept in each aquarium (5L in volume) under static conditions. E2 (dissolved in 50 % Ethanol) was added and tissue samples were collected at each time point (0, 24, 48 hrs) after treatment. Water was changed and E2 was refreshed once a day during the incubation period. Only Ethanol was added to control (0 hrs) fish. Samples were frozen instantly in liquid nitrogen and stored at -80C.	Total RNA samples (1 ug) and reference RNA samples were labeled with Hy3(tm) and Hy5(tm) fluorescent labels, respectively, using the miRCURY(tm) LNA Array power labeling kit (Exiqon Vedbaek), following the procedure described by the manufacturer. (Parameters: Amount of nucleic acid labeled = 1, Amplification = none, Mass unit = Micro gram)	Add 1 ml Trizol to tissue sample and homogenize with machine in Corex tube. Incubate at RT for 5 min and freeze in M-^V80. Continue with RNA extraction using ultracentrifuge: Rotor ss-34 code 05. After the removal of the RNA phase for recovery of small RNAs: X2 volume of isopropyl alcohol and placing the solution at -80C for two hours before centrifuge. (Parameters: Extracted product = total_RNA, Amplification = none)	The miRCURY LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies). The microarray slides were scanned and stored in an ozone-free environment in order to prevent potential bleaching of the fluorescent dyes. Image analysis was carried out using the ImaGene 8.0 software (BioDiscovery). (Parameters: Scanning hardware = G2565BA DNA microarray scanner [Agilent], Scanning software = AIDA [Raytest GmbH])																				
Protocol Type	pool	hybridization protocol	treatment protocol	nucleic acid labeling protocol	nucleic acid extraction protocol	array scanning protocol																				
Protocol Term Source REF	EFO	EFO	EFO	EFO	EFO	EFO																				
Term Source Name	EFO
Term Source File	http://www.ebi.ac.uk/efo/																									
SDRF File	E-MEXP-3866.sdrf.txt