Investigation Title	Expression profiles of (40,XX) and (39,XO) females	
Comment[Submitted Name]	Expression profiles of (40,XX) and (39,XO) females	
Experimental Design	transcription profiling by array	
Experimental Design Term Source REF	EFO	
Comment[AEMIAMESCORE]	3	
Comment[SecondaryAccession]	GSE13520	
Comment[ArrayExpressReleaseDate]	2010-04-07	
Comment[Publication DOI]	10.1186/1471-2164-11-82	
Comment[ArrayExpressAccession]	E-GEOD-13520	
Comment[MAGETAB TimeStamp_Version]	2010-07-30 11:31:51 Last Changed Rev: 13058	
Experimental Factor Name	
Experimental Factor Type	
Experimental Factor Term Source REF	
Person Last Name	Bauer	Ojarikre	Burgoyne	Affara	Sargent	Lopes	Lopes	
Person First Name	Julien	Andrew	Paul	Nabeel	Carole	Alexandra	Alexandra	
Person Mid Initials			S	A		M	M.	
Person Email							alopes@ipatimup.pt	
Person Phone	
Person Fax	
Person Address							IPATIMUP, R. Dr. Roberto Frias s/n, Porto, Portugal	
Person Affiliation							IPATIMUP	
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	2010-04-07	
PubMed ID	20122165	
Publication DOI	20122165	
Publication Author List	Lopes AM, Burgoyne PS, Ojarikre A, Bauer J, Sargent CA, Amorim A, Affara NA	
Publication Title	Transcriptional changes in response to X chromosome dosage in the mouse: implications for X inactivation and the molecular basis of Turner Syndrome.	
Publication Status	journal_article	
Publication Status Term Source REF	The MGED Ontology	
Experiment Description	Gobal expression analysis in four somatic tissues (brain, liver, kidney and muscle) of adult 40,XX and 39,XO mice with the aim of identifying which genes are expressed from both X chromosomes as well as those genes deregulated in X chromosome monosomy.  Keywords: Expression profiling by array For each tissue, the RNA samples of seven 40,XX, eight 39,XpO and eight 39,XmO mice were pooled by genotype into 9 groups, representing 3 biological replicates per genotype, as follows: 39,XpO-1 and 39,XpO-2 (3 pooled individuals each), 39,XpO-3 (2 pooled individuals); 39,XmO-1 and 39,XmO-2 (3 pooled individuals each), 39,XmO-3 (2 pooled individuals); 40,XX-1 and 40,XX-2 (3 pooled individuals each) 40,XX-3 (2 pooled individuals)	
Protocol Name	P-GSE13520-2	P-GSE13520-3	P-GSE13520-4	P-GSE13520-1	
Protocol Type	nucleic_acid_extraction	labeling	hybridization	bioassay_data_transformation	
Protocol Description	Total RNA was isolated from homogenized tissues using Trizol reagent and purified using a column based centrifugation method (Qiagen) according to the manufacturer’s instructions.	Biotin-16 UTP of in vitro transcribed RNA. Used Illumina RNA amplification kit (Cat # 1755 Ambion US)	1500ng of cRNA from each sample was hybridized to each of the six microarrays on the platform for 16 hours at 58 degrees celsius.   1500ng of cRNA from each sample was hybridized to each of the six microarrays on the platform for 15 hours at 55 degrees celsius. The microarrays were washed and then stained with streptavidin conjugated to Cy3 fluorescent dye. The staining procedure relies on the affinity of streptavidin to biotin which is incorporated into the UTP residues of the hybridised cRNA sample. Arrays were then washed again and air dried.	The values for each bead in the array were imported into the Illumina software BeadStudio for preliminary quality checks, summarized according to bead type and then exported into R. Normalization across all arrays was performed on a log scale using the quantile normalization method implemented in the Lumi normalization package from the bioconductor repository (www.bioconductor.org). ID_REF = <br>VALUE = log2 normalised intensity signal	
Protocol Parameters	
Protocol Hardware	
Protocol Software	
Protocol Contact	
Protocol Term Source REF				The MGED Ontology	
SDRF File	E-GEOD-13520.sdrf.txt	
Term Source Name	NCBI Taxonomy	The MGED Ontology	ArrayExpress	EFO	The MGED Ontology	
Term Source File	http://www.ncbi.nlm.nih.gov/Taxonomy/	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/arrayexpress	http://www.ebi.ac.uk/efo/	http://mged.sourceforge.net/ontologies/MGEDontology.php	
Term Source Version