Tests towards #10

testdata/E-MEXP-31.idf.txt

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+Investigation Title	Transcription profiling of mammalian male germ cells undergoing mitotic growth, meiosis and gametogenesis in highly enriched cell populations	
+Comment[Submitted Name]	Rat Spermatogenesis	
+Experimental Design	development_or_differentiation_design	cell_type_comparison_design	transcription profiling by array	
+Experimental Design Term Source REF	mo:1.3.1.1	mo	EFO	
+Comment[ArrayExpressReleaseDate]	2004-03-01	
+Comment[AEMIAMESCORE]	4	
+Comment[ArrayExpressAccession]	E-MEXP-31	
+Comment[MAGETAB TimeStamp_Version]	2011-01-23 09:46:49 Last Changed Rev: 14857	
+Experimental Factor Name	targeted cell type	
+Experimental Factor Type	cell_type	
+Experimental Factor Term Source REF	
+Person Last Name	Primig
+Person First Name	Michael
+Person Mid Initials	
+Person Email	[email protected]
+Person Phone	+33 2 23 23 61 78
+Person Fax	+33 2 23 23 50 55
+Person Address	INSERM GERHM U625, University of Rennes 1, Campus de Beaulieu, 35042 Rennes, France
+Person Affiliation	bioinformatics
+Person Roles	submitter
+Person Roles Term Source REF	mo
+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	2004-03-01	
+PubMed ID	14718556	
+Publication DOI	14718556	
+Publication Author List	Ulrich Schlecht, Philippe Demougin, Reinhold Koch, Leandro Hermida, Christa Wiederkehr, Patrick Descombes, Charles Pinneau, Bernard Jegou, Michael Primig	
+Publication Title	Expression profiling of mammalian male meiosis and gamete development identifies novel candidate genes for roles in the regulation of fertility	
+Publication Status	journal_article	
+Publication Status Term Source REF	mo	
+Experiment Description	We report a comprehensive large-scale expression profiling analysis of mammalian male germ cells undergoing mitotic growth, meiosis and gametogenesis using High Density Oligonucleotide Microarrays and highly enriched cell populations. Among 11955 rat loci investigated, 1268 were identified as differentially transcribed in germ cells at subsequent developmental stages as compared to total testis, somatic Sertoli cells as well as brain and skeletal muscle controls. The loci were organized into four expression clusters that correspond to somatic, mitotic, meiotic and post-meiotic cell types. This work provides information about expression patterns of approximately 200 genes known to be important during male germ cell development. Approximately 40 of those are included in a group of 121 transcripts for which we report germ cell expression and lack of transcription in three somatic control cell types. Moreover, we demonstrate the testicular expression and transcriptional induction in mitotic, meiotic and/or post-meiotic germ cells of 293 as yet uncharacterized transcripts some of which are likely to encode factors involved in spermatogenesis and fertility. This group also contains numerous potential germ cell specific targets for innovative contraceptives. A graphical display of the data is conveniently accessible through the GermOnline database at http://www.germonline.org.	
+Protocol Name	P-MEXP-1359	P-MEXP-1358	P-MEXP-1360	Affymetrix:Protocol:Hybridization-EukGE-WS2v4[]	P-AFFY-6	Affymetrix:Protocol:ExpressionStat
+Protocol Type	nucleic_acid_extraction	pool	labeling	hybridization	feature_extraction	bioassay_data_transformation	
+Protocol Description	Total RNA was purified using the RNeasy kit (Qiagen) following the manufacturer’s instructions.  The RNA was immediately snap frozen in liquid nitrogen and stored at –80°C. 	Pachytene spermatocytes and early spermatids were prepared by centrifugal elutriation to a purity greater than 90% from 8 rats at 90 dpp as previously described except that cells were mechanically dispersed (28).  Purified cells were centrifuged, snap frozen in liquid nitrogen and stored at - 80°C.  Total testicular samples were produced by excising and snap freezing testes from three Sprague-Dawley rats at 90 dpp in liquid nitrogen.  The outermost connective tissue capsule was then surgically removed on the frozen organs before they were manually ground using a ceramic mortar and pistil.  Total RNA was purified using the RNeasy kit (Qiagen) following the manufacturer’s instructions.  The RNA was immediately snap frozen in liquid nitrogen and stored at –80°C.   Samples from brain (Lewis, 60 dpp) and skeletal muscle (Wistar, 70 dpp) were isolated from adult rats according to standard procedures. 	Total RNA was prepared using RNeasy Mini-Spin columns (Qiagen) using standard protocols.  RNA quality was monitored with  RNA Nano 6000 Chips and the 2100 Bioanalyzer (Agilent).  Labeling of total RNA was performed as described in the Expression Analysis Technical Manual (Affymetrix) with minor modifications as indicated below.  Double-stranded (ds) cDNA was synthesized from 13 µg of total RNA using the Superscript II kit (Invitrogen Life Technologies) and a T7-(dT)24-VN primer 5'GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-(T)24-VN3' [V = G, A, or C, N = G, A, C or T].  The in vitro transcription (IVT) reaction was carried out with 50% of the ds cDNA synthesized with the Bioarray HighYield RNA Transcript Labeling Kit (Enzo).  Subsequently, the biotin-labeled cRNAs were purified by using RNeasy Mini spin columns and analysed on RNA Nano 6000 Chips. The cRNA target was then incubated at 94°C for 35 minutes; the resulting fragments of 50-150 nucleotides were monitored using the Bionalyzer.	Title: Affymetrix EukGE-WS2v4 Hybridization. Description: 	Title: Affymetrix CEL analysis. Description: 	Title: Affymetrix CHP Analysis (ExpressionStat). Description: 	
+Protocol Parameters	Extracted product;Amplification;		Amplification;Label used;Amount of nucleic acid labeled;
+Protocol Hardware	
+Protocol Software				MicroArraySuite 5.0	MicroArraySuite 5.0	MicroArraySuite 5.0	
+Protocol Contact	
+Protocol Term Source REF		mo		mo
+SDRF File	E-MEXP-31.sdrf.txt	
+Term Source Name		mo	ArrayExpress	mo:1.3.1.1	mo	EFO	
+Term Source File		http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/arrayexpress	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/efo/	
+Term Source Version				1.3.1.1