Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1027882 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26380010_1.fastq.gz | Fastqsanger.gz | |||
| SRR26380010_2.fastq.gz | Fastqsanger.gz | |||
| SRR26380011_1.fastq.gz | Fastqsanger.gz | |||
| SRR26380011_2.fastq.gz | Fastqsanger.gz | |||
| SRR26380012_1.fastq.gz | Fastqsanger.gz |
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Project description:Rationale: Despite shortening vasopressor use in shock, hydrocortisone administration remains controversial, with potential harm on the immune system. Few studies assessed hydrocortisone impact on the transcriptional response in shock, and we are lacking data in burns. Objectives: To assess the hydrocortisone-induced transcriptional modulation in severe burn shock, particularly on the immune response. Methods: We collected whole blood samples (n= 117) during a randomized controlled trial assessing the efficacy of hydrocortisone administration on burn shock. Using whole genome microarrays, we first compared burn patients from the placebo group (n=15) to healthy volunteers (n=13) to describe the transcriptional modulation induced by burn shock over the first week. Then we compared burn patients randomized for either hydrocortisone administration (n=15) or placebo (n=15) to assess hydrocortisone-induced modulation. Measurements and Main Results: Study groups were similar in terms of severity and major outcomes, but shock duration (significantly reduced in the hydrocortisone group). Many genes (n=2250) were differentially expressed between burn patients and healthy volunteers, with 85% of them exhibiting a profound and persistent modulation over seven days. Interestingly, we showed that hydrocortisone enhanced the shock-associated repression of adaptive, but also innate immunity. Conclusions: We found that the initial host response to burn shock encompasses a wide and persistent modulation of gene expression, with profound modulation of pathways associated with metabolism and immunity. Importantly, hydrocortisone administration may worsen the immunosuppression associated with severe injury. These data should be taken into account in the risk ratio of hydrocortisone administration in patients with inflammatory shock.
2017-07-02 | GSE77791 | GEO
Project description:The erythroblastic island (EBI) functions as a niche where erythroblastic island macrophages (EBIMφ) are positioned within rings of erythroblasts, providing support and signals that orchestrate efficient erythropoiesis. Herein, we postulated burn injury impacts the EBI, given the nearly universal presence of anemia and inflammation in burn patients, and a divergent myeloid transcriptional signature we observed in murine bone marrow following burn injury, where G-CSF secretion increased neutrophil and monocyte transcripts but reduced EBIMφ transcripts. We utilized flow cytometry to investigate EBIMφ after imaging flow cytometry confirmed the heme induced transcription factor Spi-C as a robust marker of EBIMφ in Spicigfp/igfp mice. Two populations referred to as Spic+ macrophages and Spic+ Gr1 low monocytes possessed cell intrinsic GFP, with Spic+ macrophages distinguished by higher levels of GFP, F4/80, autofluorescence, and negligible CD115 staining compared to Gr1 low monocytes. Further, at least 50% of the Spic+ macrophages stained for CD163 while staining was negligible on Gr1 low monocytes. Since CD163 distinguished the populations and macrophage remnants could convolute flow cytometry analysis, total CD163 protein was quantified in marrow aspirates to corroborate results. Application of Spicigfp/igfp mice in studies revealed a G-CSF dependent reduction of Spic+ macrophages in post burn marrow that coincided with a loss of erythroid cells and that recombinant G-CSF alone was sufficient to reduce Spic+ macrophages in the marrow. These results provide the first evidence that burn injuries impact the EBI niche through G-CSF dependent depletion of EBIMφ and support the use of Spicigfp/igfp mice in investigation of EBIMφ.
2024-12-09 | GSE263318 | 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:Here we developed a new high-throughput polymorphism detection and genotyping method based on identifying restriction cut site polymorphisms using a microarray platform. We compared the genomes of 20 individual urchins; 10 from the northern part of the species range (Boiler Bay, OR) and 10 from the southern part of the range (San Diego, CA).
2010-03-13 | GSE20857 | GEO
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. Keywords = Burn Liver microarray genechip time course Keywords: time-course
2005-10-11 | GSE1860 | GEO
Project description:1) Bacteria 2) Southern Appalachian Peat Bogs Raw sequence reads
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Project description:Iron and light are typically recognized as major limiting factors controlling phytoplankton growth in the Southern Ocean. Recent field-based evidence suggests, however, that manganese concentrations in this region can be low enough to impact phytoplankton physiology and primary productivity. Our study examined the interactive influence of combined iron and manganese deprivation on protein expression and photophysiology in Phaeocystis antarctica, a key Antarctic phytoplankter, and provide taxon-specific proteomic evidence that natural Southern Ocean Phaeocystis populations regularly experience stress due to combined low manganese and iron availability. In culture, combined low iron and manganese induced large scale changes in the Phaeocystis proteome and resulted in reorganization of key components of the photosynthetic apparatus; these differences were largely distinct from those arising from changes in irradiance. These results implicate manganese availability as an important driver of Southern Ocean productivity and demonstrate the utility of peptide mass spectrometry as a tool for mapping of manganese contributions to HNLC conditions in this region.
2019-06-25 | PXD010974 | Pride