{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Lillian Nanney"],"study_type":["transcription profiling by array"],"organism":["Homo sapiens"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-GEOD-8056"],"description":["Thermal injury incites inflammatory responses that often transcend the local environment and lead to structural deficiencies in skin that give way to scar formation. We hypothesized that extensive perturbations within burned skin following thermal insult and during subsequent events of wound repair induce vast alterations in gene expression that likely serve as a wound and systemic healing deterrent. A high-throughput microarray experiment was designed to analyze genetic expression patterns and identify potential genes to target for therapeutic augmentation or silencing. The study compares gene expression from burn wound margins at various times following thermal injury to expression observed in normal skin. Utilizing this design, we report that the totality of gene expression alterations is indeed enormous. Further, we observed that the differential expression of many inflammatory and immune response genes appear to be continually up-regulated in burn wound margins seven days or more after initial thermal insult. As it is well established that the inflammatory process must abate for wound healing to proceed, the finding of ongoing local inflammation is cause for further investigation. To our knowledge, this is the first report of the gene expression alterations induced by thermal injury of human skin. As such, it provides a wealth of data to mine with the ultimate goal of better understanding the local pathophysiologic changes at the site of thermal injury that not only affect wound healing capacity, but may also contribute to systemic derangements within the burn patient. Keywords: time course, disease state analysis The study compares gene expression from burn wound margins at various times following thermal injury to expression observed in normal skin. All skin specimens were obtained in the operating room within minutes of being removed from the patient. Burn specimens were taken from wound margins. Harvested tissue at the burn wound margin maximized the capture of viable cells from the multiple lineages important to the healing process and minimized the inclusion of non-viable cells destroyed by full-thickness injury. After isolation, RNA samples were pooled equally by mass as to contain RNA from 5 tissue specimens for each array replicate."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Hybridization - Hybridized cRNA was detected using streptavidin coupled to phycoerythrin and visualized using GeneChip Scanner 3000 7G.","Nucleic Acid Extraction - At the time of isolation, tissues were chopped into small pieces at -20M-0C. Samples were weighed and 1ml Trizol (Invitrogen, Carlsbad, CA) was added per 100mg of sample. RNA was extracted using QiagenM-bM-^@M-^Ys Rnase-free DNase Set (Valencia, CA) supplied protocol with the following modification. RNA was precipitated with 0.25 volumes isopropanol (Fisher Scientific, Fairlawn, NJ) and 0.25 volumes of RNA precipitation solution (7% NaCl / 21% disodium citrate). DNase treatment was performed following the first Trizol isolation using QiagenM-bM-^@M-^Ys RNase-free DNase Set. ManufacturerM-bM-^@M-^Ys protocol was modified and 10M-5l DNase in 70M-5l Buffer RDD was added to every 100M-5l of sample. Following DNase treatment the Trizol isolation was repeated once or occasionally twice to remove the DNase as well as any remaining fats or salts. RNA was re-suspended in RNase/DNase free H2O. A small aliquot of each sample was sent to the Microarray Core for quantification and bioanalysis. If the sample met the Microarray CoreM-bM-^@M-^Ys standards, samples were pooled equally by mass as to contain RNA from 5 tissue specimens for each array replicate. Pooled RNA samples were then resubmitted for bioanalysis quality assurance followed by microarray labeling and replicate hybridization.","Labeling - Following quality control, the RNA was prepared for microarray analysis using the standard Affymetrix protocol (Affymetrix Inc, Santa Clara, CA). Briefly, a total of 5 M-5g of total RNA was reverse transcribed to double-stranded (ds) cDNA using an oligo-dT primer coupled to a T7 promoter. In vitro transcription from the ds cDNA was then carried out using T7 polymerase and incorporating biotin-modified CTP and UTP ribonucleotides."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","MAGE-TAB Files","Array Designs"],"pubmed_authors":["Alonda Pollins","Lillian Nanney","Lauren Sims","Braden Boone","Joseph Greco III"],"data_protocol":["Image Adquisition - GeneChips were scanned using GeneChip Scanner 3000 7G and GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA). Default values were used to grid images (.DAT) and generate .CEL and .CHP files and to generate gene expression values and ratios of gene expression between the hybridized samples","Feature Extraction - For statistical analysis, CEL files (raw Affymetrix data) were imported in GeneSpring 7.0 (Agilent Technologies) and transformed by RMA (Robust Multichip Analysis).","Assay Data Transformation - ID_REF = <br>VALUE = RMA-calculated Signal intensity"],"additional_accession":[]},"is_claimable":false,"name":"Gene Expression Profiles in Thermally Injured Human Skin: A Temporal Microarray Analysis","description":"Thermal injury incites inflammatory responses that often transcend the local environment and lead to structural deficiencies in skin that give way to scar formation. We hypothesized that extensive perturbations within burned skin following thermal insult and during subsequent events of wound repair induce vast alterations in gene expression that likely serve as a wound and systemic healing deterrent. A high-throughput microarray experiment was designed to analyze genetic expression patterns and identify potential genes to target for therapeutic augmentation or silencing. The study compares gene expression from burn wound margins at various times following thermal injury to expression observed in normal skin. Utilizing this design, we report that the totality of gene expression alterations is indeed enormous. Further, we observed that the differential expression of many inflammatory and immune response genes appear to be continually up-regulated in burn wound margins seven days or more after initial thermal insult. As it is well established that the inflammatory process must abate for wound healing to proceed, the finding of ongoing local inflammation is cause for further investigation. To our knowledge, this is the first report of the gene expression alterations induced by thermal injury of human skin. As such, it provides a wealth of data to mine with the ultimate goal of better understanding the local pathophysiologic changes at the site of thermal injury that not only affect wound healing capacity, but may also contribute to systemic derangements within the burn patient. Keywords: time course, disease state analysis The study compares gene expression from burn wound margins at various times following thermal injury to expression observed in normal skin. All skin specimens were obtained in the operating room within minutes of being removed from the patient. Burn specimens were taken from wound margins. Harvested tissue at the burn wound margin maximized the capture of viable cells from the multiple lineages important to the healing process and minimized the inclusion of non-viable cells destroyed by full-thickness injury. After isolation, RNA samples were pooled equally by mass as to contain RNA from 5 tissue specimens for each array replicate.","dates":{"release":"2010-05-22T00:00:00Z","modification":"2023-10-02T21:49:16.66Z","creation":"2022-02-07T21:54:17.972Z"},"accession":"E-GEOD-8056","cross_references":{"GEO":["GSE8056"],"EFO":["EFO_0002768"]}}