{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Richard Green"],"study_type":["transcription profiling by array"],"organism":["Homo sapiens"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-GEOD-34798"],"description":["This study determined key transcriptional signatures associated with HCV recurrence and eventual development of severe liver disease in infected transplant patient liver biopsies over time following transplant. We identified molecular signatures associated with severe fibrosis and liver injury prior to histologic evidence of disease progression. 111 liver biopsy specimens collected longitudinally from 57 HCV-infected liver transplant patients following organ transplant. Several batches of pooled normal liver RNA samples (Utah normal pool; UNP) are included."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Labeling - The Agilent Two-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA and Cy5-cDNA probe preparation.","Nucleic Acid Extraction - Biopsy specimens were disrupted in TRIzol reagent (Life Technologies, Carlsbad, CA) using a Polytron homogenizer (PowerGene 700; Fisher Scientific, Pittsburgh, PA).  Total RNA was isolated according to the manufacturer’s protocol.  All total RNA samples were amplified using the RiboAmp RNA Amplification Kit (Arcturus/MDS, Mountain View, CA).  The quality of amplified RNA was determined by capillary electrophoresis using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).","Hybridization - The Agilent Two-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred ng of each RNA sample was hybridized to one Agilent 22K Human oligo array.","Sample Processing - PCT study Utah Normal Pool (UNP): Liver biopsies used to compare transcriptional profiles of responders (with sustained virologic response:SVR) vs. non-responders to IFN treatment during HCV infection."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","Additional Files","MAGE-TAB Files","Array Designs"],"pubmed_authors":["Richard Green","Angela Rasmussen","Kathie Walters","Nathan Susnow","Matthew Yeh","Sean Proll","Deborah Diamond","Michael Katze","Marcus Korth","Nicolas Tchitchek","Anne Larson","Sharon Lederer","Alexei Krasnoselsky","Robert Carithers","Arndt Benecke"],"data_protocol":["Feature Extraction - The limma package was used. Background correction was performed (method=normexp, offset=1). Data was normalized within arrays with the loess method, then normalized between arrays with the quantile normalization method, and then log2 transformed.","Image Adquisition - Images were quantified using Agilent Feature Extraction Software (version A.8.1.1.1).","Assay Data Transformation - ID_REF = <br>VALUE = Normalized log2 (Cy5/Cy3) ratio","Image Adquisition - Scanned on an Agilent Scanner G2505B US23502338."],"additional_accession":[]},"is_claimable":false,"name":"Early transcriptional programming links progression to hepatitis C virus-induced severe liver disease in transplant patients","description":"This study determined key transcriptional signatures associated with HCV recurrence and eventual development of severe liver disease in infected transplant patient liver biopsies over time following transplant. We identified molecular signatures associated with severe fibrosis and liver injury prior to histologic evidence of disease progression. 111 liver biopsy specimens collected longitudinally from 57 HCV-infected liver transplant patients following organ transplant. Several batches of pooled normal liver RNA samples (Utah normal pool; UNP) are included.","dates":{"release":"2012-02-10T00:00:00Z","modification":"2022-11-25T19:51:59.796Z","creation":"2022-03-07T02:40:28.154Z"},"accession":"E-GEOD-34798","cross_references":{"GEO":["GSE34798"],"EFO":["EFO_0002768"]}}