Comment[ArrayExpressAccession]	E-GEOD-47939
MAGE-TAB Version	1.1					
Public Release Date	2013-06-14
Investigation Title	MicroRNAs Expression Profiles and the target genes in Chinese Non-syndromic isolated Cleft Palate Patients					
Comment[Submitted Name]	MicroRNAs Expression Profiles and the target genes in Chinese Non-syndromic isolated Cleft Palate Patients
Experiment Description	MicroRNAs (miRNAs) play an important role in organ development. MicroRNA expression profiling is an effective method of acquiring novel and valuable information. In this study, using miRNA microarray technology, we finally validate three over-expressed miRNAs (hsa-miR-1246, hsa-miR-1323 and hsa-miR-93) and one under-expressed miRNA (hsa-miR-143*) in NSCP group. Target gene WNT5A of hsa-miR-143* was up-regulated, while target gene FGFR2 of hsa-miR-1246, hsa-miR-1323 and hsa-miR-93 was down-regulated in the NSCP group compared to the control group. The association of miRNAs expression levels with the risk of developing NSCP, the correlation with age and gender were analyzed. The risk analysis identified that odds ratio (95% CI) of hsa-miR-1246, hsa-miR-1323 and hsa-miR-93 was higher ranged from 9.75 (1.642-57.89) to 13.67 (2.480-75.30) and pM-oM-<M-^\0.05. Neither age nor gender was associated with the four miRNAs expression levels. In male cases, the association of hsa-miR-1246, hsa-miR-1323, hsa-miR-93 and hsa-miR-143* expression levels with NSCP was observed and the p value was 0.0012, 0.0008, 0.0088 and 0.0385, respectively. Bioinformatics approaches identified nine KEGG pathways enriched in predicted target genes. In summary, we firstly defined miRNAs profiles and target genes in human soft palate tissue. Four distinctive miRNAs and their target genes expression in NSCP will advance our understanding of the genetic progress of this complex disease. Further exploration will be needed to elucidate how these miRNAs and target genes modulate signaling pathways during palatogenesis. Two-condition experiment, control (normal development people) vs. NSCP patients. Biological replicates: 6 control replicates, 10 NSCP patients replicates.					
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	Wang	Wang	Zhang	Li		
Person First Name	Huijun	Huijun	Ping	Shouxia		
Person Email	huijunwang@fudan.edu.cn					
Person Affiliation	Children Hospital of Fudan University					
Person Phone	(8621)64931016					
Person Address	Translational Research Center for Development and Disease, Children Hospital of Fudan University, 399 Wanyuan Road,, Shanghai, Shanghai, China					
Person Roles	submitter					
Protocol Name	P-GSE47939-1	P-GSE47939-4	P-GSE47939-5	P-GSE47939-2	P-GSE47939-3	P-GSE47939-6
Protocol Description	The scanned images were analyzed with Agilent Feature Extraction Software 10.7 following the manufacturers instructions . ID_REF =  VALUE = Normalized signal intensity	AgilentM-bM-^@M-^Ys miRNA Complete Labeling and Hyb Kit (p/n 5190- 0456) generates fluorescent miRNA with a sample input of 100ng of total RNA. This method involves the ligation of one Cyanine 3- pCp molecule to the 3' end of a RNA molecule by using the Micro Bio- spin 6 columns for purification of the labeled miRNA. The sample must be completely dried after labeling.	Resuspend the dried labeled miRNA sample in 17 M-NM-<L of nuclease-free water when the Spike-In solution is used. Add 4.5 M-NM-<L of the 10X GE Blocking Agent and 22.5 M-NM-<L of 2X Hi-RPM Hybridization Buffer to each sample for a total of 45M-NM-<l.. Incubate at 100M-0C for 5 minutes and then immediately transfer to an ice water bath for 5 minutes.Quickly spin in a centrifuge to collect any condensation at the bottom of the tube. On completion of preparing the hybridization assembly, 45M-NM-<l of 1X hybridization buffer was added and hybridized to Agilent Microarray Hybridization Chamber Kit (G2534A) for 55M-0C for 20 hours in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute with 37M-0C GE Wash buffer 2 (Agilent).	All samples were cut off into small pieces and immediately transferred to RNA Later (Ambion, USA). After disposing in room temperature for 12hrs, samples were stored at -80M-bM-^DM-^C until the total RNA extraction.	Total RNA was extracted using TRIzolM-. Reagent (AmbionM-., Invitrogen, USA) according to the manufacturer instructions. RNA concentration was assessed with NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, USA) and RNA integrity was verified using an Agilent 2100 bioanalyzer (Agilent, USA).	Slides were scanned immediately after washing using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100% for XDR Hi and 5% for XDR Lo).
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	DEGREE	AGE	SEX	INDIVIDUAL		
Experimental Factor Type	degree	age	sex	individual		
Comment[SecondaryAccession]	GSE47939					
Comment[GEOReleaseDate]	2013-06-14					
Comment[ArrayExpressSubmissionDate]	2013-06-13					
Comment[GEOLastUpdateDate]	2013-06-16					
Comment[AEExperimentType]	transcription profiling by array					
Comment[AdditionalFile:Data1]	GSE47939_case_vs_control_FC2.0.txt					
Comment[AdditionalFile:Data2]	GSE47939_disease_vs_normal_FC2.0.txt					
Comment[AdditionalFile:Data3]	GSE47939_significant_miRNAs.txt					
SDRF File	E-GEOD-47939.sdrf.txt