Investigation Title	Comparative genomic hybridization of zebra finch and common whitethroat samples using a Affymetrix custom array designed for the zebra finch	
Comment[Submitted Name]	An Affymetrix microarray for large scale genomic and transcriptional analyses of the zebra finch_Taenopygia guttata_and other passerines	
Experimental Design	comparative_genome_hybridization_design	quality_control_testing_design	species_design	comparative genomic hybridization by array	
Experimental Design Term Source REF	mo		mo	EFO	
Comment[ArrayExpressReleaseDate]	2007-09-30	
Comment[AEMIAMESCORE]	4	
Comment[ArrayExpressAccession]	E-MEXP-1181	
Comment[MAGETAB TimeStamp_Version]	2010-08-09 19:51:20 Last Changed Rev: 13058	
Experimental Factor Name	species	
Experimental Factor Type	organism	
Experimental Factor Term Source REF	
Person Last Name	Naurin	
Person First Name	Sara	
Person Mid Initials	
Person Email	sara.naurin@zooekol.lu.se	
Person Phone	 46 (0) 46 222 37 06	
Person Fax	
Person Address	Ecology building	
Person Affiliation	Department of Ecology	
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	2007-09-30	
PubMed ID	
Publication DOI	
Publication Author List	Sara Naurin, Staffan Bensch, Bengt Hansson, Tomas Johansson, David F. Clayton, Ann-Sofie Albrekt, Torbjörn von Schantz, Dennis Hasselquist	
Publication Title	A microarray for large scale genomic and transcriptional analyses of the zebra finch (Taenopygia guttata) and other passerines	
Publication Status	
Publication Status Term Source REF	
Experiment Description	We have conducted a Cross-Species Microarray analysis by hybridizing genomic DNA from the common whitethroat (Sylivia communis) on a newly developed Affymetrix costum array designed for the zebra finch (Taeniopygia guttata), the Lund-zf array. We have also quality tested the Lund-zf array by hybridizing zebra finch genomic DNA to the platform.	
Protocol Name	P-MEXP-74987	P-MEXP-74920	P-MEXP-72042	P-MEXP-72046	P-MEXP-74988	P-MEXP-74991	P-AFFY-6	
Protocol Type	grow	grow	nucleic_acid_extraction	labeling	hybridization	feature_extraction	feature_extraction	
Protocol Description	The common whitethroat (Sylvia communis) is a warbler (Sylvidae), a seasonal breeder and a long distance migratory bird. The species breed in Europe (May-July) and winter in Africa south of Sahara (Oct-April). Birds were caught in the wild in southern Sweden (Skåne: 55o42’16 N, 13o25’52 E) in may 2006. The Swedish field is situated on the southern tip of Sweden and is constituted of typical breeding habitat, bush-land with open clearings surrounded by cultivated, open areas. Birds were caught using mist-nets and playback song close to the net. Males will fly into the net defending their territory. 80 microliters of blood was collected from the jugular vein and extracted for Comparative Genome Hybridizations (CGH) of Genomic DNA on the Lund-zf530237N array. Birds were then re-released on their territories.	Zebra Finches were kept in same-sexed cages (size: 80*40*80 cm) with up to five individuals each in a room (size 3*4 meters) with about 150 individuals of both sexes. Temperature was kept at 20 +- 2 degrees and the photoperiod was constant at 14 hours light and 10 hours dark (full spectrum light). Food (commercial seed mixture, Exoten, Tropical), water and cuttle bone was provided ad libitum. 80 microliters of blood was collected from the jugular vein and extracted for Hybridizations of Genomic DNA on the Lund-zf530237N array.	DNA was extracted from 20 ul blood from one adult zebra finch male and one adult common whitethroat male with standard phenol-chloroform-isoamylalcohol extraction (Sambrook et al. 1989, Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning, a laboratory manual. Cold Spring Harbor:Cold Spring Harbor Laboratory Press) .	DNA was labeled and fragmented according to Step 7 and Step 8 of an Affymetrix standard protocol, the GeneChip Mapping 10K 2.0 Assay Manual (www.affymetrix.com). 	The biotin labeled DNA samples were used in the regular hybridization mix for GeneChip Arrays and hybridized onto the Lund-zf530237N Affymertix array overnight in the GeneChip® Hybridisation oven 640 using standard procedures. 	The arrays were washed and then stained in a GeneChip® Fluidics Station 450. Scanning was carried out with the GeneChip® Scanner 3000 and image analysis was performed using GeneChip® Operating Software. 	Title: Affymetrix CEL analysis. Description: 	
Protocol Parameters			Extracted product;Amplification;	Amplification;Amount of nucleic acid labeled;Label used;	Chamber type;Quantity of label target used;temperature;	
Protocol Hardware						GeneChip Scanner 3000 [Affymetrix]	
Protocol Software						Scanning software	MicroArraySuite 5.0	
Protocol Contact	
Protocol Term Source REF						The MGED Ontology	
SDRF File	E-MEXP-1181.sdrf.txt	
Term Source Name	mo	The MGED Ontology		ArrayExpress	mo	EFO	The MGED Ontology	
Term Source File	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://mged.sourceforge.net/ontologies/MGEDontology.php		http://www.ebi.ac.uk/arrayexpress	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/efo/	http://mged.sourceforge.net/ontologies/MGEDontology.php	
Term Source Version