Investigation Title A large-scale clinical study of gene expression response to severe burn injury Comment[Submitted Name] A large-scale clinical study of gene expression response to severe burn injury Experimental Design transcription profiling by array Experimental Design Term Source REF EFO Comment[AEExperimentType] transcription profiling by array Comment[AEExperimentDisplayName] Gene expression of blood samples from pediatric and adult patients with severe burns collected at an early and middle stage after injury. Comment[AEMIAMESCORE] 4 Comment[SecondaryAccession] Comment[SecondaryAccession] GSE19743 Comment[ArrayExpressReleaseDate] 2010-06-16 Comment[ArrayExpressAccession] E-GEOD-19743 Comment[MAGETAB TimeStamp_Version] 2010-08-04 06:56:38 Last Changed Rev: 13058 Experimental Factor Name injury sampling time point developmental stage Experimental Factor Type injury sampling time point developmental stage Experimental Factor Term Source REF Person Last Name Xu Xiao Tompkins Person First Name Weihong Wenzhong Ron Person Mid Initials Person Email wxiao1@partners.org Person Phone Person Fax Person Address Person Affiliation Person Roles submitter Person Roles Term Source REF 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 2010-06-16 PubMed ID 20479259 Publication DOI 10.1073/pnas.1002757107 Publication Author List Zhou B, Xu W, Herndon D, Tompkins R, Davis R, Xiao W, Wong WH, Inflammation and Host Response to Injury Program, Toner M, Warren HS, Schoenfeld DA, Rahme L, McDonald-Smith GP, Hayden D, Mason P, Fagan S, Yu YM, Cobb JP, Remick DG, Mannick JA, Lederer JA, Gamelli RL, Silver GM, West MA, Shapiro MB, Smith R, Camp DG 2nd, Qian W, Storey J, Mindrinos M, Tibshirani R, Lowry S, Calvano S, Chaudry I, West MA, Cohen M, Moore EE, Johnson J, Moldawer LL, Baker HV, Efron PA, Balis UG, Billiar TR, Ochoa JB, Sperry JL, Miller-Graziano CL, De AK, Bankey PE, Finnerty CC, Jeschke MG, Minei JP, Arnoldo BD, Hunt JL, Horton J, Cobb JP, Brownstein B, Freeman B, Maier RV, Nathens AB, Cuschieri J, Gibran N, Klein M, O'Keefe G Publication Title Analysis of factorial time-course microarrays with application to a clinical study of burn injury. Publication Status published Publication Status Term Source REF EFO Publication Status Term Accession Number EFO_0001796 Experiment Description To understand the age-dependent response to burn injury, blood samples from pediatric and adult patients were collected at different times after severe burn injury. Gene expression was measured using Affymetrix U133 Plus 2.0 arrays for both patient samples and healthy controls. Time points were binned into two groups: early stage for <11 days and middle stage for 11-49 days. 114 arrays for 57 patients (2 time points per patient) and 63 arrays for 63 healthy controls. Protocol Name P-GSE19743-2 P-GSE19743-3 P-GSE19743-4 P-GSE19743-5 P-GSE19743-6 P-GSE19743-1 Protocol Type nucleic_acid_extraction labeling hybridization image_acquisition feature_extraction bioassay_data_transformation Protocol Description Peripheral blood was collected and lysis buffer (bicarbonate-buffered ammonium chloride solution, 0.826%NH4Cl, 0.1% KHC03, 0.0037%Na4EDTA in H2O) was added at a ratio of 20:1 (lysis buffer:blood). Samples were then incubated at room temperature until erythrocyte lysis was complete (5–7 min). Leukocytes were recovered by centrifugation (400 g, 48C) and washed once in ice-cold phosphate buffered saline. Leukocyte pellets were then resuspended in 8ml RLT buffer (Qiagen) and the samples sheared ten times with an 18-gauge needle attached to a 10-ml syringe. Samples were then immediately frozen and kept at 270 8C until RNA extraction was required. Total cellular RNA was isolated from the leukocyte pellets using a commercial kit (RNeasy, Qiagen). Biotinylated cRNA were prepared following the standard Affymetrix protocol from 4 ug total RNA. According to the standard Affymetrix protocol, with some modifications. Affymetrix GeneChip 3000 7G scanner The data were processed using dChip (Build: April 9 2009) using default analysis setting and invariant set normalization. ID_REF =
VALUE = Model based expression index (MBEI) from dChip Protocol Parameters Protocol Hardware Protocol Software Protocol Contact Protocol Term Source REF The MGED Ontology The MGED Ontology The MGED Ontology The MGED Ontology The MGED Ontology SDRF File E-GEOD-19743.sdrf.txt Term Source Name The MGED Ontology ArrayExpress EFO The MGED Ontology Term Source File http://mged.sourceforge.net/ontologies/MGEDontology.php http://www.ebi.ac.uk/arrayexpress http://www.ebi.ac.uk/efo/ http://mged.sourceforge.net/ontologies/MGEDontology.php Term Source Version