RNA-sequence analysis of Burkholderia vietnamiensis strain G4 exposed to ethylzingerone 4-(3-ethoxy-4-hydroxyphenyl) butan-2-one)
ABSTRACT: Burkholderia vietnamiensis strain G4, representative of a species routinely encountered as a contaminant of industrial product, was exposed to a proprietary preservative agent for 24 hours and gene expression analysed by RNA-seq.
Project description:In this study, we assess technical differences between commonly used single-cell RNA-Sequencing (scRNA-Seq) methods. We perform scRNA-seq on a homogenous population of mouse embryonic stem cells along with two kinds of control spike-in molecules to assess sensitivity and accuracy of these specific methods. In this dataset, we perform STRT-seq method on Fluidigm C1 system and generate single-cell libraries using Nextera XT kit. Please note the sample-data relationship format (SDRF) file for this submission contains only a high-level representation of all sample, library and run information, and not per cell. For meta-data at the level of individual cells, please refer to the supplementary file called single_cells_list.txt, which is included as part of this ArrayExpress submission.
Project description:Genome wide transcriptome analyses could reveal whether parasites causing severe malarial disease express different genes to those causing uncomplicated malaria. This knowledge could inform therapy and vaccine design targeting severe disease. Venous samples were collected from patients with severe (n=23) and uncomplicated (n=21) malaria attending a healthcare facility in Timika, Papua Province, Indonesia. This area has unstable malaria transmission with estimated annual parasite incidence of 450 per 1000 population and symptomatic illness in all ages. Severe malaria was defined as peripheral parasitaemia with at least one modified World Health Organization (WHO) criterion of severity. Erythrocytes were immediately isolated from whole blood, solubilised in RNA preservative and frozen. Libraries were 100 bp paired end sequenced on a 2500-HT Hiseq (Illumina) using RapidRun chemistry (Illumina).
Project description:In this study, we assess technical differences between commonly used single-cell RNA-Sequencing (scRNA-Seq) methods. We perform scRNA-seq on a homogenous population of mouse embryonic stem cells along with two kinds of control spike-in molecules to assess sensitivity and accuracy of these specific methods. In this dataset, we perform Smart-Seq2 method on Fluidigm C1 system and generate single-cell libraries using Nextera XT kit
Project description:In this study, we assess technical differences between commonly used single-cell RNA-Sequencing (scRNA-Seq) methods. We perform scRNA-seq on a homogenous population of mouse embryonic stem cells along with two kinds of control spike-in molecules to assess sensitivity and accuracy of these specific methods. In this dataset, we perform SMARTer method on Fluidigm C1 system and generate single-cell libraries using Nextera XT kit
Project description:The antimicrobial action of the curing agent NaNO2, which is added as a preservative to raw meat products, depends on its conversion to nitric oxide and other reactive nitrogen species under acidic conditions. In this study, we applied RNA-sequencing to analyze the acidified NaNO2 shock and adaptive response of Salmonella Typhimurium, a frequent contaminant in raw meat. Upon a 10 minute exposure to 150 mg/l NaNO2 in LB pH 5.5 acidified with lactic acid, genes involved in nitrosative stress protection together with several other stress related genes were induced. To the contrary, genes involved in translation, transcription, replication and motility were down-regulated. Induction of stress tolerance and reduction of cell proliferation obviously promote survival under harsh acidified NaNO2 stress. The subsequent adaptive response was characterized by up-regulation of NsrR-regulated genes and iron-uptake systems and down-regulation of genes involved in anaerobic respiratory pathways. Strikingly, amino acid decarboxylase systems, which contribute to acid tolerance, displayed increased transcript levels in response to acidified NaNO2. The induction of systems known to be involved in acid resistance indicates a nitrite mediated increase of acid stress. Transcriptome of Salmonella Typhimurium 14028, treated at OD600 = 0.80-0.85 with 150 mg/l NaNO2 (acidified by lactic acid in the growth medium) for 10 min (shock response) or until an OD600 = 1.45-1.55 is reached (1.5 - 2.0 h, adaptation response), was compared to respective control cultures without NaNO2. Amplified cDNA libraries for sequencing on the SOLiD 5500xl system were prepared from one culture per condition.
Project description:The adaptation of B. cenocepacia to the host environment was assessed in a rat chronic respiratory infection model and compared to that of high cell-density in vitro-grown cultures using transcriptomics
Project description:Differential hyper- and hypo-methylation regions in G0 versus G4/G5 CMP The goal of this study is to evaluate changes in CpG methylation profilings of telomere dysfunctional common myeloid progenitor cells (CMP) as compared to their wild type controls Genomic DNA was extracted from sorted CMP populations isolated from 3 pools of G0 or 2 pools of G5 mice using UltraPure Phenol:Chloroform:Isoamyl Alcohol according to manufacturer’s instructions (Life Technologies). 14,000 to 30,000 cells were available for each sample, resulting in a minimum of 45ng of DNA. Genome-wide DNA methylation profiling was performed by RRBS. Library preparation and sequencing were performed at the UT MD Anderson Cancer Center’s DNA Methylation Analysis Core and Sequencing and Microarray Facility, according to published protocols. RRBS sequencing data were aligned and methylation was called using Bismark v0.7.119. In brief, bisulphite-treated DNA was aligned to UCSC Genome Browser mm10 reference genome using Bowtie. In total 29-38 million reads were generated per sample with alignment rates around 63%. Next, MethylKit10 implemented with Fisher’s exact test was used to compare the cytosine methylation profiles of G0 and G5 CMP. Gene promoter regions were calculated based on RefSeq gene annotations with regions starting 1 kb upstream of the annotated transcription start site (TSS) and extending 500 base pairs downstream of TSS. Exons, introns, and CpG islands coordinates were collected from the UCSC Genome Browser mm10 version.
Project description:N6-methyladenosine (m6A) has been recently identified as a conserved epitranscriptomic modification of eukaryotic mRNAs, but its features, regulatory mechanisms, and functions in cell reprogramming are largely unknown. Here, we report m6A modification profiles in the mRNA transcriptomes of four cell types with different degrees of pluripotency. Comparative analysis reveals several features of m6A, especially gene- and cell-type-specific m6A mRNA modifications. We also show that microRNAs (miRNAs) regulate m6A modification via a sequence pairing mechanism. Manipulation of miRNA expression or sequences alters m6A modification levels through modulating the binding of METTL3 methyltransferase to mRNAs containing miRNA targeting sites. Increased m6A abundance promotes the reprogramming of mouse embryonic fibroblasts (MEFs) to pluripotent stem cells; conversely, reduced m6A levels impede reprogramming. Our results therefore uncover a role for miRNAs in regulating m6A formation of mRNAs and provide a foundation for future functional studies of m6A modification in cell reprogramming. m6A-seq in ESC, iPSC, NSC and sertoli cells.
Project description:The goal of this experiment was to study the alterations that occur in the adipose tissue of mice during a T. brucei infection. Gonadal adipose tissue from C57BL/6J mice infected with T. brucei AnTat 1.1E 90-13 parasites was collected at day 0 and 26 post-infection. Total RNA was extracted from 3 samples of non-infected adipose tissue and 2 samples of adipose tissue on day 26 post-infection. Day 6 post-infection adipose tissue samples (n=3) were already published (E-MTAB-4061).