Comment[ArrayExpressAccession] E-GEOD-46960 MAGE-TAB Version 1.1 Public Release Date 2013-06-01 Investigation Title Comprehensive gene expression profile of human livers from patients with biliary atresia at the time of diagnosis and the corresponding disease and normal controls Comment[Submitted Name] Comprehensive gene expression profile of human livers from patients with biliary atresia at the time of diagnosis and the corresponding disease and normal controls Experiment Description Liver biopsy samples were obtained from 64 infants with biliary atresia at the time of intraoperative cholangiogram. Liver biopsy samples were obtained from 14 age-matched infants with other causes of intrahepatic cholestasis, and from 7 deceased-donor children. GeneChip® Human Gene 1.0 ST Array (Affymetrix, CA) were used to screen mRNAs whose expression was specifically regulated in the livers from patients with biliary atresia. Gene expression profiling: Liver biopsy samples obtained from infantas with other causes of intrahepatic cholestasis were served as diseased control. Liver tissue obtained from deceased-donor children were served as normal control. A molecular signataure of biliary atresia at the time of diagnosis was identified by comparing hepatic gene expression profile from biliary atresia to those from diseased and normal controls. This dataset is part of the TransQST collection. 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 Bezerra Bessho Mourya Shivakumar Walters McGee Jegga Rao Person First Name Jorge Kazuhiko Reena Pranavkumar Stephanie John Anil Marepalli Person Mid Initials A G Person Email jorge.bezerra@cchmc.org Person Affiliation Cincinnati Children's Hospital Medical Center Person Address Gastroenterology, Hepatology & Nutrition , Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave. , Cincinnati, OH, USA Person Roles submitter Protocol Name P-GSE46960-1 P-GSE46960-3 P-GSE46960-4 P-GSE46960-2 P-GSE46960-5 Protocol Description Expression data (Affymetrix .CEL format) imported to GeneSpring software: 1. Normalized all data using RMA (Robust Muti-array Average) methods. 2. Performed baseline transformation to median of 7 normal control samples. There was no other option to specifically normalize data across all samples. ID_REF = VALUE = Normalized signal intensity Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 400 ng total RNA amplified with TargetAmp1-Round Aminoallyl-aRNA Amplification Kit 101 (Epicentre, WI) using both the TargetAmp t7-Oligo (dT) Primer A (Epicentre, WI) and the Full Spectrum MultiStart Primers for T7 IVT (10X) (SBI System Biosciences, CA) along with SuperScript III Reverse Transcriptase (Invitrogen, CA). Following chemical fragmentation of biotinylated-labeled cRNA, 10ug of cRNA were hybridized for 16hr at 45˚C on the GeneChip� Human Gene 1.0 ST Array (Affymetrix, CA). Gene Chips were washed and stained in the Affymetrix Fluidics Station 450. Wedge liver biopsy samples were obtained from infants with biliary atresia during intraoperative cholangiogram. Wedge or needle liver biopsy samples from other causes of intrahepatic cholestasis were obtained during diagnostic procedures. Liver biopsy samples from deceased-donor children were obtained during procedure to confirm the eligibiity of the patients as a donor. Biopsy samples were snap frozen in liquid nitrogen, and stored at -80˚C by the time of RNA isolation. Total RNA was isolated from liver biopsy samples using RNeasy Mini Kit, according to the manufacturer’s protocol (QIAGEN, CA). RNA integrity was verified using the Agilent 2100 Bioanalyser (Agilent Technologies, Inc., CA). GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Protocol Type normalization data transformation protocol labelling protocol hybridization protocol nucleic acid extraction protocol array scanning protocol Experimental Factor Name disease Experimental Factor Type disease Comment[SecondaryAccession] GSE46960 Comment[GEOReleaseDate] 2013-06-01 Comment[ArrayExpressSubmissionDate] 2013-05-15 Comment[GEOLastUpdateDate] 2013-06-05 Comment[AEExperimentType] transcription profiling by array SDRF File E-GEOD-46960.sdrf.txt PubMed ID 24493287 Publication DOI 10.1002/hep.27045 Publication Author List Bessho K, Mourya R, Shivakumar P, Walters S, Magee JC, Rao M, Jegga AG, Bezerra JA Publication Title Gene expression signature for biliary atresia and a role for interleukin-8 in pathogenesis of experimental disease