Burn Injury (1-7d)
Ontology highlight
ABSTRACT:
ORGANISM(S): Rattus norvegicus
PROVIDER: GSE1860 | GEO | 2005/10/11
SECONDARY ACCESSION(S): PRJNA90481
REPOSITORIES: GEO
Similar Datasets
Project description:Animal experiments were performed with male Sprague-Dawley rats (Charles River Laboratories, Boston, MA) weighing 150 ? 200 grams. All experimental protocols used in this study were approved by the Subcommittee on Research Animal Care, Massachusetts General Hospital. Rats were individually housed in a temperature-controlled (25oC) and light-controlled room (12h light-dark cycle) and allowed to adjust to their new surroundings for at least 5 days prior to the experiment. Water and rat chow were provided ad libitum to the animals. On the day of the treatment, the animals were randomly divided into two groups, burned and sham-burned. The burn injury consisted of a full-skin-thickness scald burn of the dorsum, calculated to be ~ 20% of the rat?s total body surface area (TBSA), induced by immersing the designated area in boiling water for 10 s (45). Rats were resuscitated with an intra-peritoneal injection of sterile saline solution (1.5 mL/Kg body weight/% TBSA) immediately after burn. The mortality rate of this treatment was negligible. At each time point (1, 2, 4, and 7d), three animals belonging to each group were sacrificed, the liver and serum collected, and stored at ?80oC after being inflicted with 20% TBSA burn injury. Sham-burn rats (n=3) considered as the control were treated identically except that they were immersed into a 37oC water bath and immediately sacrificed to collect the livers.
2007-11-03 | E-GEOD-1860 | biostudies-arrayexpress
Project description:Type of experiment: Comparison of liver samples between sham (control) and 20% TBSA (total burn surface area) burn rats collected at 1h, 4h, 8h, and 24h. Experimental factors: Burn injury and time; Experiment design: All experimental liver samples collected after 1h, 4h, 8h, and 24h after burn injury were compared to a common reference (sham control treated as 0h time point); Bio source: Sprague-Drawley male rats weighing 150-200 g supplied through Charles river laboratories, MA (www.criver.com); Bio material manipulations: Rats (n=3 for each scald-burn and sham-burn time point) were individually housed in a temperature-controlled (25oC) and light-controlled room (12h light-dark cycle) and allowed to adjust to their new surroundings for at least 5 days prior to the experiment. Water and rat chow were provided ad libitum to the animals. On the day of the treatment, the animals were randomly divided into two groups, burned and sham-burned. The burn injury consisted of a full-skin-thickness scald burn of the dorsum, calculated to be ~ 20% of the ratâs total body surface area (TBSA), induced by immersing the designated area in boiling water for 10 s [Yamaguchi, 1997 #416]. Rats were resuscitated with an intra-peritoneal injection of sterile saline solution (1.5 mL/Kg body weight/% TBSA) immediately after burn. At each time point, three animals belonging to each group was sacrificed, the serum collected, and stored at â80oC. Hybridization extract: Total RNA was isolated from approximately 50 mg of pooled liver tissue using the Nucleospin II RNA isolation kit from Clontech (Palo Alto, CA), as per the manufacturerâs instructions. Labeling protocol: Labeling was performed as instructed by Affymetrix, Inc (www.affymetrix.com). In brief, 10 μg of total RNA was used for the double-stranded cDNA synthesis using the T7-oligo (dT) promoter primer kit (Affymetrix Inc.) and superscript RT II enzyme (Invitrogen). 1 μg of cDNA was labeled through invitro transcription reaction using T7 DNA polymerase in the presence of biotin labeled ribonucleotides. The cRNA was cleaned up using the Qiagen RNeasy columns following manufactures instructions. The cRNA (20 μg) was fragmented using the fragmentation buffer supplied as part of the Gene Chip Sample Cleanup Module (Affymetrix). Image analysis and raw data description: The images were analyzed using MAS V.0 software provided by Affymetrix, Inc. The raw data output consists of several metrices: Signal, Detection, Detection p-value, Stat pairs, Stat pairs used. Signal is a measure of the abundance of the transcript. Detection is call that indicates whether the transcript is detected (P, present), undetected (A, absent), or at the limit of detection (M, marginal). Detection p-value is a measure of the significance of the detection call. Stat pairs, is the number of probe pairs for a particular probe set on an array. Stat pairs used, is the number of probe pairs per probe set used in the analysis. Normalized and summarized data: All chips were scaled to a target intensity of 500 to account for differences between the replicate chips and their hybridization efficiencies using Affymetrix GENECHIP MAS V.0 software. The entire dataset is available at gene expression omnibus (http://www.ncbi.nlm.nih.gov/geo/) with the accession number GSE802. Three filters were serially used to obtain the list of annotated genes that demonstrated differential expression in intensity between sham and burn injured animals. In the first filter, only genes that were flagged as âpresentâ by the MAS V.0 analysis software in at least one of the time points in all replicate chips were considered for further analysis. This step eliminated all genes for which the expression data was not reproducible between the replicate chips. The genes that passed this criterion were subjected to a second filter where ANOVA was performed to test each gene independently for a statistical difference in expression between groups (0, 1, 4, 8 and 24 h). The output of the analysis is the probability (p value) that a difference in expression can be observed by chance i.e., probability of getting a false positive. While the occurrence of false positives can be controlled by choosing a higher significance level (0.01 or 0.001) it also concomitantly increases the false negatives. Therefore, in this study we have chosen to work with ANOVA p-value cut-off 0.05. To reduce the occurrence of the false positives, we have used the false discovery rate (FDR) method (33) which adjusts the ANOVA p-value (cut-off 0.05) while taking the dependencies between the genes into consideration. The 695 genes that demonstrated a significant ANOVA p-value were then selected and their expression values averaged. The third filter selected 339 genes that were either up-regulated or down-regulated by at least 2-fold between any one time point (1, 4, 8 or 24h) and the 0h time point (Sham control). To determine the temporal profiles in the data, gene expression values were hierarchically clustered using the dChip software (www.dChip.org). The expression values for a gene across all samples were standardized by setting the mean to 0 and standard deviation to 1. The software then builds a hierarchical cluster tree based on centroid-linkage method using Pearson correlation coefficient as the distance metric. A set of genes were assigned to cluster groups empirically based on visual inspection of their temporal expression patterns.
2007-10-11 | E-GEOD-802 | biostudies-arrayexpress
Project description:Type of experiment: Comparison of liver samples between sham (control) and 20% TBSA (total burn surface area) burn rats collected at 1h, 4h, 8h, and 24h. Experimental factors: Burn injury and time Experiment design: All experimental liver samples collected after 1h, 4h, 8h, and 24h after burn injury were compared to a common reference (sham control treated as 0h time point) Bio source: Sprague-Drawley male rats weighing 150-200 g supplied through Charles river laboratories, MA (www.criver.com) Bio material manipulations: Rats (n=3 for each scald-burn and sham-burn time point) were individually housed in a temperature-controlled (25oC) and light-controlled room (12h light-dark cycle) and allowed to adjust to their new surroundings for at least 5 days prior to the experiment. Water and rat chow were provided ad libitum to the animals. On the day of the treatment, the animals were randomly divided into two groups, burned and sham-burned. The burn injury consisted of a full-skin-thickness scald burn of the dorsum, calculated to be ~ 20% of the rat’s total body surface area (TBSA), induced by immersing the designated area in boiling water for 10 s [Yamaguchi, 1997 #416]. Rats were resuscitated with an intra-peritoneal injection of sterile saline solution (1.5 mL/Kg body weight/% TBSA) immediately after burn. At each time point, three animals belonging to each group was sacrificed, the serum collected, and stored at –80oC. Hybridization extract: Total RNA was isolated from approximately 50 mg of pooled liver tissue using the Nucleospin II RNA isolation kit from Clontech (Palo Alto, CA), as per the manufacturer’s instructions. Labeling protocol: Labeling was performed as instructed by Affymetrix, Inc (www.affymetrix.com). In brief, 10 μg of total RNA was used for the double-stranded cDNA synthesis using the T7-oligo (dT) promoter primer kit (Affymetrix Inc.) and superscript RT II enzyme (Invitrogen). 1 μg of cDNA was labeled through invitro transcription reaction using T7 DNA polymerase in the presence of biotin labeled ribonucleotides. The cRNA was cleaned up using the Qiagen RNeasy columns following manufactures instructions. The cRNA (20 μg) was fragmented using the fragmentation buffer supplied as part of the Gene Chip Sample Cleanup Module (Affymetrix). Image analysis and raw data description: The images were analyzed using MAS V.0 software provided by Affymetrix, Inc. The raw data output consists of several metrices: Signal, Detection, Detection p-value, Stat pairs, Stat pairs used. Signal is a measure of the abundance of the transcript. Detection is call that indicates whether the transcript is detected (P, present), undetected (A, absent), or at the limit of detection (M, marginal). Detection p-value is a measure of the significance of the detection call. Stat pairs, is the number of probe pairs for a particular probe set on an array. Stat pairs used, is the number of probe pairs per probe set used in the analysis. Normalized and summarized data: All chips were scaled to a target intensity of 500 to account for differences between the replicate chips and their hybridization efficiencies using Affymetrix GENECHIP MAS V.0 software. The entire dataset is available at gene expression omnibus (http://www.ncbi.nlm.nih.gov/geo/) with the accession number GSE802. Three filters were serially used to obtain the list of annotated genes that demonstrated differential expression in intensity between sham and burn injured animals. In the first filter, only genes that were flagged as ‘present’ by the MAS V.0 analysis software in at least one of the time points in all replicate chips were considered for further analysis. This step eliminated all genes for which the expression data was not reproducible between the replicate chips. The genes that passed this criterion were subjected to a second filter where ANOVA was performed to test each gene independently for a statistical difference in expression between groups (0, 1, 4, 8 and 24 h). The output of the analysis is the probability (p value) that a difference in expression can be observed by chance i.e., probability of getting a false positive. While the occurrence of false positives can be controlled by choosing a higher significance level (0.01 or 0.001) it also concomitantly increases the false negatives. Therefore, in this study we have chosen to work with ANOVA p-value cut-off 0.05. To reduce the occurrence of the false positives, we have used the false discovery rate (FDR) method (33) which adjusts the ANOVA p-value (cut-off 0.05) while taking the dependencies between the genes into consideration. The 695 genes that demonstrated a significant ANOVA p-value were then selected and their expression values averaged. The third filter selected 339 genes that were either up-regulated or down-regulated by at least 2-fold between any one time point (1, 4, 8 or 24h) and the 0h time point (Sham control). To determine the temporal profiles in the data, gene expression values were hierarchically clustered using the dChip software (www.dChip.org). The expression values for a gene across all samples were standardized by setting the mean to 0 and standard deviation to 1. The software then builds a hierarchical cluster tree based on centroid-linkage method using Pearson correlation coefficient as the distance metric. A set of genes were assigned to cluster groups empirically based on visual inspection of their temporal expression patterns. Keywords = Rat Keywords = burn Keywords = microarrays Keywords = fatty acids Keywords = cholesterol Keywords = inflammation Keywords: time-course
2004-05-07 | GSE802 | GEO
Project description:Burn injury induces a systemic hyperinflammatory response with detrimental side effects. Studies have described the biochemical changes induced by severe burns, but the transcriptome response is not well characterized. The goal of this work is to characterize the blood transcriptome after burn injury. Burn patients presenting to a regional center between 2012-2017 were prospectively enrolled. Blood was collected on admission and at predetermined time points (hours 2, 4, 8, 12, 24). RNA was isolated and transcript levels were measured with a gene expression microarray. To identify differentially regulated genes (FDR≤0.1) by burn injury severity, patients were grouped by total body surface area (TBSA) above or below 20% and statistically enriched pathways were identified. Sixty-eight patients were analyzed, most patients were male with a median age of 41 (IQR, 30.5-58.5) years, and TBSA of 20% (11-34%). Thirty-five patients had %TBSA injury ≥20%, and this group experienced greater mortality (26% vs. 3%, p=0.008). Comparative analysis of genes from patients with </≥20% TBSA revealed 1505, 613, 380, 63, 1357, and 954 differentially expressed genes at hours 0, 2, 4, 8, 12 and 24 respectively. Pathway analysis revealed an initial upregulation in several immune/inflammatory pathways within the ≥20% TBSA groups followed by shutdown. Severe burn injury is associated with an early proinflammatory immune response followed by shutdown of these pathways. Examination of the immunoinflammatory response to burn injury through differential gene regulation and associated immune pathways by injury severity may identify mechanistic targets for future intervention.
2021-10-31 | GSE182616 | GEO
Project description:Severe burn results in muscle wasting affecting quality of life in both children and adults. Biologic metabolic profiles are noticeably distinctive in childhood. We posit that muscle gene expression profiles are differentially regulated in response to severe burns in young animals. Twelve C57BL6 male mice, including young (5 weeks-old) and adults (11 weeks-old), received either scald burn, or sham procedure. Mouse muscle tissue was harvested 24 hours later for Next Generation Sequence (NGS) analysis. Our results showed 662 downregulated and 450 upregulated genes in gastrocnemius of young mice compared to adults without injury. After injury, we found 74/75 downregulated genes and 107/128 upregulated genes in both burned groups compared to respective uninjured age groups. VEGFA-VEGFR2, focal adhesion, and nuclear receptor meta-pathways were the top 3 gene pathways undergoing a differential change in response to age. Of note, the proteasome degradation pathway showed the most similar changes in both adult and young burned animals. This study demonstrates the characteristic profile of gene expression in skeletal muscle in young and adult burned mice. Prominent age effects were revealed in transcriptional levels with increased alterations of genes, miRNAs, pathways, and interactions.
2022-11-04 | GSE208548 | GEO
Project description:The study investigated ethanol-induced alterations in the transcriptome of adult male Wistar rats. The study was divided into two parts. Part 1: 10 animals were single housed during 8 weeks and exposed to 6% ethanol solution and water simultaneously or just water (24 hours/day, 7 days/week). Fluid intake and body weight were recorded twice weekly during 8 weeks. Animals were sacrificed immediately after the last consumption measurement and the nucleus accumbens were dissected and snap frozen until further processing. Part 2: 12 rats were single housed and exposed to continuous access to ethanol and water (24 hours/day, 7 days/week). After 4 weeks, animals were divided into 2 groups, equally balanced based on previous ethanol intake, and were given additional ethanol or water through a gavage tube daily during 3 weeks. This was followed by an additional 2 weeks of continuous ethanol access and then animals were immediately sacrificed and the nucleus accumbens were dissected and snap frozen until further processing. Next, the RNA was extracted from the cells using Qiagen RNeasy Lipid tissue mini kit and the RNA concentration and quality was measured using a BioAnalyzer. RNAseq was performed using standard Illumina protocols in collaboration with SciLifeLab, Stockholm, Sweden. No difference in gene expression was detected between any groups. Keywords: RNAseq, Gene expression profiles, Ethanol consumption, Rat.
2017-06-01 | GSE73627 | GEO
Project description:Twelve-week-old rats underwent bilateral ovariectomy (OVX) or sham surgery. Four weeks after surgery, the animals underwent the following treatments for 4 weeks: subcutaneous injection of teriparatide (TPTD) or saline 3 times weekly. All rats were anesthetized and sacrificed at the end of the experimental period. The L4-5 dorsal root ganglia (DRG) were harvested.
2020-03-30 | GSE121109 | GEO
Project description:The experimental design included three biological replicates for each of the three conditions: Sham-Sham, Sham-CLP and burn-CLP. Liver samples were collected from the rats and the total RNA was analyzed on a Affymetrix RAE230A chip. No technical replicates were included in the study Keywords: other
2005-09-20 | GSE1781 | GEO
Project description:The experimental design included three biological replicates for each of the three conditions: Sham-Sham, Sham-CLP and burn-CLP. Liver samples were collected from the rats and the total RNA was analyzed on a Affymetrix RAE230A chip. No technical replicates were included in the study
2007-11-03 | E-GEOD-1781 | biostudies-arrayexpress
Project description:Mice were exposed to cardiac ischemia/reperfusion injury and sacrificed after 1 or 4 days. Hearts were stained with Evans blu/TTC to isolate the at risk area. Hearts were divided into 1mm slices, the at risk area of any slice were pooled together before RNA extraction. Mice were divided into 3 different groups: Sham animals have been subjected to the surgical procedure without the induction of the ischemia and reperfusion injury and represent the control animals; LAD group is represented by animals subjected to the surgical procedure and the induction of the ischemia and reperfusion imjury; MLAD group is represented by animals subjected to the surgical procedure and the induction of the ischemia and reperfusion injury, followed by myriocin treatment (SLN/Myr) at the beginning of reperfusion.
2019-07-07 | GSE133913 | GEO