Project description:Lungs were collected as soon as possible after thermal injury 30-40 mins post injury for neutrophil isolation. Lungs were minced in HBSS with 1% BSA (Sigma) and strained through a 40um nylon filter (BD). Samples were sorted using BD fusion machine. A 100um nozzle was used at a flow rate of 2.RNA was extracted from these neutrophils and microarray was performed.
Project description:Neutrophils are rapidly mobilized into circulation following sterile tissue injury, but the transcriptional heterogeneity of the peripheral blood neutrophil pool during this response is incompletely defined. To characterize how corneal injury reshapes the circulating neutrophil compartment, we performed droplet-based single-cell RNA sequencing on FACS-sorted peripheral blood neutrophils from mice at steady state (Pre-injury, normal) and one day after corneal injury (Day 1 post-corneal injury). Comparative analysis resolved distinct neutrophil states and revealed injury-associated shifts in subset composition. These data define the circulating neutrophil response to remote sterile corneal injury at single-cell resolution.
Project description:This data was used as an example to illustrate a computational method for assessing statistical significance in microarray experiments Contributed by 'The Inflammation and the Host Response to Injury Collaborative Research Program.' Keywords: Two group comparison Genomic response one day post traumatic injury was compared between patients having early or late respiratory recovery
Project description:To compare the transcriptome of ASCs and FAPs before and after injury, we performed quadriceps injury using glycerol in mice. We then isolated subcutaneous adipose tissue and quadriceps muscle and isolated ASCs and FAPs respectively (3 mice per condition). We then extracted RNA and performed RNA-seq.
Project description:This data was used as an example to illustrate a computational method for assessing statistical significance in microarray experiments Contributed by 'The Inflammation and the Host Response to Injury Collaborative Research Program.' Keywords: Two group comparison
Project description:The purpose of the experiment was to determine whole transcriptome changes after spinal cord injury (SCI) to understand how photobiomodulation promotes neuroprotection and functional recovery. SCI was performed at the thoracic (T) level T8, by crushing the dorsal columns using a calibrated watchmaker's forceps. Animals were then treated with photobiomodulation (PBM; 660nm wavelength) or sham control light, within 15 minutes of the injury. PBM or sham-treatment was treatment directed at the lesion site for 1 minute duration every 24hr for the first 3 days. Animals were then killed, tissues harvested and the RNA was extracted using RNEasy lipid tissue mini kit (Qiagen) according to the manufacture's instructions. Whole genome sequencing was outsourced to Qiagen RNA Sequencing Services (Germany).Library preparation was performed using the QIAseq Stranded Total RNA Library Kit with QIAseq FastSelect rRNA and globin depletion. QIAseq FastSelect rRNA HMR was used to reduce the amount of unwanted RNA species. After first and second strand synthesis, the cDNA was end-repaired and 3’ adenylated. Sequencing adapters were ligated to the overhangs. Adapted molecules were enriched using 16 cycles of PCR and purified by a bead-based cleanup. Library preparation was quality controlled using capillary electrophoresis (High Sensitivity Tape D1000) and high-quality libraries were pooled based on equimolar concentrations. The library pool(s) were quantified using qPCR and optimal concentration of the library pool used to generate the clusters on the surface of a flowcell before sequencing on a NovaSeq (Illumina Inc., Madison, USA) instrument (2x75, 2x10) according to the manufacturer instructions (Illumina Inc.). Raw data was de-multiplexed and FASTQ files for each sample were generated using the bcl2fastq software v2.20.0.422 (Illumina inc.).
Project description:The injury response in the skin is highly complex and involves input from multiple cell types. Single nuclei RNA sequencing was performed to broadly characterize changes in gene expression from all skin cell types early after injury compared to the unwounded state.
