Project description:Motor unit remodelling involving repeated denervation and re-innervation occurs throughout life. The efficiency of this process declines with age contributing to neuromuscular deficits. We investigated differentially expressed genes (DEG) in muscle following peroneal nerve crush to model of motor unit remodelling in C57Bl6 mice. Muscle RNA was isolated at 3 days post-crush, RNA libraries were generated using poly-A selection, sequenced.
Project description:The RNA sequencing experiment is part of the study: “Modulating Redox Balance Restores Azacytidine Efficacy in Hypomethylating Agent Resistant Disease.” In the study we generated myelodysplastic syndrome/acute myeloid leukemia (MDS/AML) OCI-M2 cell line that is resistant to hypomethylating therapy by 5-azacytidine (AZA). By modulation of the redox environment via modification of redox sensor KEAP1 using sulforaphane (SFN) in these cells we were able to restore sensitivity to AZA. We used RNA sequencing to define transcriptomic differences between AZA sensitive (AZA-S) and AZA resistant (AZA-R) cells and to characterize how the transcriptome is changing upon treatment of these cells with AZA, SFN and combination of both.
Project description:The changes in the transcriptome of leaves between 0, 9, 13 and 17 days of cold acclimation were analyzed using RNA-Seq in Veyo and Falster genotypes of perennial ryegrass.
Project description:What are the effects of Microcystis aeruginosa and cyanotoxin on the grass carp intestine? 16S rRNA sequencing is needed to analyze the gut microbiota.
Project description:Chronic inflammation is a hallmark of obesity type II diabetes (T2D) accompanied by increased circulating inflammatory T-cells. Diabetic cardiomyopathy (dbCM) is characterised by systemic inflammation, disrupted metabolism and impaired cardiac function. However, whether T-cell mediated cardiac autoimmunity is present in dbCM and causally linked to cardiac metabolic remodelling remains unknown. We used db/db transgenic mouse model of dbCM and an integrated in vivo and ex vivo experimental approach to examine the impact of T-cell mediated inflammation on cardiac function and metabolic disturbances in T2D. Furthermore, we used glucokinase activator AZD1656 drug intervention for six weeks in db/db mice to examine whether we can improve metabolic remodeling and cardiac inflammation in dbCM. This drug has been previously shown to target metabolism of T cells and with anti-inflammatory effect. In this data set, we used RNA extracted from the snap-frozen hearts (control, db/db and AZD1656-treated db/db hearts, n=5/group) analysed by massive analysis of cDNA End (MACE-Seq, 1x75 bps Illumina; MACE: 5 Million reads / library).
Project description:LLC-OVA lung carcinoma cells were used to establish subcutaneous tumors in C57BL/6J mice. One million LLC-OVA cells were injected subcutaneously into each mouse. Tumor-bearing mice were divided into two treatment groups: three mice received mifepristone (60 mg/kg body weight) administered via oral gavage on alternate days, and four mice received vehicle control (olive oil) on the same schedule. Treatments were continued for 18 days. On day 19, mice were sacrificed and tumors were harvested for immune profiling. Tumor-infiltrating NK cells were isolated and subjected to bulk RNA-sequencing to assess transcriptional changes induced by glucocorticoid receptor antagonism within the tumor microenvironment.
Project description:DNA double-strand breaks (DSBs) are toxic to mammalian cells. However, during meiosis, more than 200 DSBs are generated deliberately, to ensure reciprocal recombination and orderly segregation of homologous chromosomes. If left unrepaired, meiotic DSBs can cause aneuploidy in gametes and compromise viability in offspring. Oocytes in which DSBs persist are therefore eliminated by the DNA-damage checkpoint. The checkpoint’s downstream effectors that trigger oocyte death, thereby preserving genome stability across the generations, are unknown. Here we show that the DNA-damage checkpoint eliminates oocytes via the pro-apoptotic BCL-2 pathway members Puma, Noxa and Bax. Deletion of these factors prevents oocyte elimination in recombination-repair mutants, even when the abundance of unresolved DSBs is high. Remarkably, surviving oocytes can extrude a polar body and be fertilised, despite chaotic chromosome segregation at the first meiotic division. Our findings raise the possibility that allelic variants of the BCL-2 pathway could influence the risk of embryonic aneuploidy.
Project description:This study employed an unbiased forward genetic screen to identify suppressors of the maternal-effect lethal phenotype caused by tost-1 dysfunction in Caenorhabditis elegans. The temperature-sensitive tost-1(xf196 ts) mutant exhibits complete embryonic lethality at the restrictive temperature (25°C), providing a robust screening platform. Following EMS mutagenesis of L4 larvae, we screened F2 progeny for viable individuals at 25°C, indicating suppression of the lethal phenotype. After backcrossing to confirm heritability, we performed whole genome sequencing on 21 suppressor strains to identify causative mutations. Additionally we also sequenced the strain used for the mutagenesis as the reference genome.
Project description:Human valvular endothelial cells were co-cultured with THP-1 monocytes in high glucose (33mM) or normal glucose (5mM) levels for 2 hours. Afterwards cells were lysed and total cellular RNA was extracted using TRIzol reagent.
Project description:This study used formalin-fixed paraffin-embedded (FFPE) human tissue collected for the Integrated teChnologies for Improved polyp SurveillancE (INCISE) collaborative from polypectomies performed within the Scottish BCSP in the NHS Greater Glasgow and Clyde health board between 2009-2016 in patients who underwent further colonoscopy between 6 months and 6 years after the index colonoscopy. The extracted DNA was then passed to the Genomics Innovation Alliance (formerly Glasgow Precision Oncology Laboratory; GPOL) for genomic sequencing using their bespoke Cancer Plus panel. Some patients had metachronous polyps, and synchronous polyps sequenced, in addition to their largest index polyp. The output from the sequencing is FASTQ files and VCF files.