Comment[ArrayExpressAccession]	E-GEOD-45475
MAGE-TAB Version	1.1							
Public Release Date	2013-10-01
Investigation Title	The formation of the intestine at the juvenile stage is raised by the Hox10 gene through the migration of endodermal strand cells in ascidian							
Comment[Submitted Name]	The formation of the intestine at the juvenile stage is raised by the Hox10 gene through the migration of endodermal strand cells in ascidian
Experiment Description	Hox cluster genes play crucial roles in the establishment of the body plan along the antero-posterior axis during animal development. Hox genes are expressed in the chordate endodermal tissues, and unraveling functions there is necessary for elucidating the mechanisms of endoderm specification. In the invertebrate chordate Ciona intestinalis, the endodermal tissues are in the premature state at the larval stage, and they form the differentiated digestive tract during metamorphosis. In this study, we showed that a Hox gene Ci-Hox10 is required for the formation of the intestine during metamorphosis. To know the downstream genes that are controlled by Hox10, microarray analysis of Hox10 knock-down embryos was performed. Gene expressions in the tail region of Hox10 knockdown embryos that were injected with Hox10 morpholino (MO) and control embryos of Ciona intestinalis were examined by comparative analysis with two color detection. Dye-swap analysis was carried out.							
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	Hamada	Kawai	Ogura	Ikuta	Saiga	Hamada	Satoh	Sasakura
Person First Name	Mayuko	Narudo	Yosuke	Tetsuro	Hidetoshi	Mayuko	Nori	Yasunori
Person Email	hamadam@oist.jp							
Person Affiliation	Okinawa Institute of Science and Technology							
Person Phone	098-921-2242							
Person Fax	098-934-5622							
Person Address	Okinawa Institute of Science and Technology, 12-22 Suzaki, Uruma, Okinawa, Japan							
Person Roles	submitter							
Protocol Name	P-GSE45475-1	P-GSE45475-5	P-GSE45475-6	P-GSE45475-2	P-GSE45475-3	P-GSE45475-4	P-GSE45475-7	
Protocol Description	The intensity of probes was extracted from scanned microarray images using Feature Extraction 10.5 software (Agilent Technologies). All algorithms and parameters used in this analysis were the default conditions of the software. Some probes which were judged beyond analysis by Feature Extraction 10.5 software were eliminated from the analysis. ID_REF =  VALUE = Lowess-normalized log10 ratio (Cy5/Cy3)	Cyanine-5 (Cy5) or cyanine-3 (Cy3) labeled cRNAs were synthesized from 200 ng total RNA using the Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.	A set of fluorescently labeled cRNA targets (750ng for each sample) was employed in a hybridization reaction. Hybridization and washing were performed using the GE Hybridization Kit and GE Wash Pack (Agilent Technologies). The protocols were according to the manufacturer's instructions.	Approximately 250 Hox10 morpholino(MO) (0.64mM)-injected embryos and control embryos at the tailbud stage (18 hours after fertilization) were cut between the tail and the trunk, and each of the tail regions was collected.	Ciona intestinalis were obtained from the National BioResource Project in Japan.	Total RNA was extracted from each of the tail regions by the acid guanidium thiocyanate-phenol-chloroform method.	Hybridized microarrays were scanned on an Agilent Technologies G2565BA Microarray Scanner System.	
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol	
Experimental Factor Name	TREATMENT							
Experimental Factor Type	treatment							
Comment[SecondaryAccession]	GSE45475							
Comment[GEOReleaseDate]	2013-10-01							
Comment[ArrayExpressSubmissionDate]	2013-03-25							
Comment[GEOLastUpdateDate]	2013-10-02							
Comment[AEExperimentType]	transcription profiling by array							
SDRF File	E-GEOD-45475.sdrf.txt