Comment[ArrayExpressAccession] E-GEOD-36809 Public Release Date 2012-03-26 Investigation Title A genomic storm in critically injured humans Comment[Submitted Name] A genomic storm in critically injured humans Experiment Description Human survival from injury requires an appropriate inflammatory and immune response. We describe the circulating leukocyte transcriptome after severe trauma and show that the severe stress produce a global reprioritization affecting >80% of the cellular functions and pathways, a truly unexpected “genomic storm.” In severe blunt trauma, the early leukocyte genomic response is consistent with simultaneously increased expression of genes involved in the systemic inflammatory, innate immune, and compensatory antiinflammatory responses, as well as in the suppression of genes involved in adaptive immunity. Furthermore, complications like nosocomial infections and organ failure are not associated with any genomic evidence of a second hit and differ only in the magnitude and duration of this genomic reprioritization. Blood was sampled from 167 severe blunt trauma patients under the age of 55 yr who consented to blood sampling. The first blood sample was taken within 12 h of the injury and 1, 4, 7, 14, 21, and 28 d after injury. Study subjects were treated under the guidance of standard operating procedures developed, implemented, and audited across all participating centers to minimize treatment variation. In addition, 37 healthy control subjects were sampled. Total blood leukocytes were isolated according to protocols published previously. Total cellular RNA was extracted and hybridized onto an HU133 Plus 2.0 GeneChip (Affymetrix) according to the manufacturer’s recommendations. Date of Experiment Term Source Name EFO Term Source Version Term Source File http://www.ebi.ac.uk/efo/efo.owl Person Last Name Inflammation & the Host Response to Injury Xiao Mindrinos Seok Cuschieri Cuenca Gao Hayden Hennessy Moore Minei Bankey Johnson Sperry Nathens Billiar West Brownstein Mason Baker Finnerty Jeschke López Klein Gamelli Gibran Arnoldo Xu Zhang Calvano McDonald-Smith Schoenfeld Storey Cobb Warren Moldawer Herndon Lowry Maier Davis Tompkins Person First Name IDDC Wenzhong Michael Junhee Joseph Alex Hong Douglas Laura Ernest Joseph Paul Jeffrey Jason Avery Timothy Michael Bernard Philip Henry Celeste Marc M Matthew Richard Nicole Brett Weihong Yuping Steven Grace David John J H Lyle David Stephen Ronald Ronald Ronald Person Mid Initials N G L E P E L B R A H H V C G C B L S E P A D P S L N F V W G Person Email data_curator@gluegrant.org Person Affiliation Massachusetts General Hospital Person Phone 617 726 3447 Person Fax Person Address Department of Surgery, Massachusetts General Hospital, 55 Fruit Street, GRV 1302, Boston, MA, USA Person Roles submitter Person Roles Term Source REF Person Roles Term Accession Number Normalization Type Normalization Term Accession Number Normalization Term Source REF Replicate Type Replicate Term Accession Number Replicate Term Source REF Experimental Design Experimental Design Term Accession Number Experimental Design Term Source REF Quality Control Type Quality Control Term Accession Number Quality Control Term Source REF Protocol Name P-GSE36809-1 P-GSE36809-6 P-GSE36809-5 P-GSE36809-2 P-GSE36809-3 P-GSE36809-4 P-GSE36809-7 Protocol Description ID_REF =
VALUE = log2 RMA signal per Affymetrix Power Tools version 1.8.6 RMA model GeneChips were scanned using the Affymetrix Scanner G3000 Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station FS 4500, and used the standard solutions recommended by Affymetrix White blood cells were separated using a modified buffy coat isolation and red blood cell lysis method. This protocol recovers the plasma fraction, lyses RBCs, and allows recovery of the white blood cell fraction, eliminating the need to recover the buffy coat interfacial layer. Total RNA was purified using the Rneasy RNA Isolation kit standard protocol (Qiagen, Valencia, CA) Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2 ug RNA (Expression Analysis Technical Manual rev 3, 2002, Affymetrix) Affymetrix Power Tools version 1.8.6 RMA model Protocol Software Protocol Hardware Protocol Contact Protocol Type bioassay_data_transformation image_aquisition hybridization specified_biomaterial_action nucleic_acid_extraction labeling feature_extraction Protocol Term Source REF Protocol Term Accession Number Experimental Factor Name INJURY SEX AGE Experimental Factor Type injury Sex age Experimental Factor Term Source REF Experimental Factor Term Accession Number Publication Title Publication Author List PubMed ID 22110166 Publication DOI Publication Status Publication Status Term Source REF Publication Status Term Accession Number Comment[SecondaryAccession] GSE36809 Comment[GEOLastUpdateDate] 2012-03-27 Comment[AEExperimentType] transcription profiling by array Comment[GEOReleaseDate] 2012-03-26 Comment[ArrayExpressSubmissionDate] 2012-03-26 SDRF File E-GEOD-36809.sdrf.txt