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  • DNA microarray analysis was performed on RNA from a strain of Mycobacterium tuberculosis H37Rv in which the essential whiB1 gene was deleted from the chromosome but partially complemented by a wild type allele on a plasmid, compared to RNA from H37Rv wild type containing the same plasmid.
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  • To understand the regulation of cytotoxicity by decidual CD8+ T cells (CD8+ dT) at the maternal-fetal interface, gene expression analysis of CCR7-CD45RA- effector-memory CD8+ T cells isolated from peripheral blood of unrelated healthy controls and decidual tissue from first trimester (6-12 weeks) and term (>37 weeks) pregnancy was performed. Furthermore, first trimester decidual effector-memory CD8+ T cells were stimulated with anti-CD3/CD28 in the presence of IL-2 for 12 hours or 72 hours. RNA was isolated and gene expression profiles were generated by employing Affymetrix HG_U133_Plus 2 arrays on the Affymetrix Geneatlas system.
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  • Comparison of Ebf2-expressing bone marrow mesenchymal cells from Ebf2-GFP heterozgous and Ebf2-GFP homozygous (=knock-out) mice
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  • Transcription profiling of differential light treated Nematostella exposed to 12hr light: 12hr dark compared with 24hr complete darkness
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  • We performed an RNA-seq analysis on FACS-sorted CD4+ memory T cells (Tmem, CD4+CD25-CD45RA-) stimulated in vitro with anti-CD3/CD28 coated beads (1:5), IL-2 (100 U/mL) in the presence of a TNF-alpha inhibitor (Etanercept, ETN, 5 μg/mL) or recombinant human TNF-alpha (rhTNF-alpha, 50 ng/mL) treatment. The cells were cultured for three days at 37°C and 5% CO2. On day three Tmem were lysed (Buffer RLT supplemented with DTT, QIAGEN) and RNA extraction was performed (RNeasy Plus Micro kit), followed by sample preparation with TruSeq (polyA) mRNA kits (Illumina), RNA sequencing (carried out by an Illumina HiSeq2500), and the alignment of trimmed fastQ files to GRCh38 human reference genome. We also performed a Quality control (QC). This was done using the tool FastQC FastQC/0.11.3-Java-1.7.0_80. QC metrics were calculated for the aligned reads using Picard-tools picard/1.130-Java-1.7.0_80, CollectRnaSeqMetrics, MarkDuplicates, CollectInsertSize-Metrics and SAMtools/1.2-foss-2015b flagstat. Finally, we carried out a Differential expression gene (DEG) analysis using DESeq2, in order to evaluate the impact of ETN and rhTNF-alpha on Transcriptome profiling of stimulated CD4+ Tmem. Principal Component Analysis (PCA) was carried out to visualise the samples given their entire transcriptome and any remaining batch effects.
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  • Meningococcal sepsis is an overwhelming form of the sepsis syndrome which may cause mortality within 12-24 hours in previously healthy children and adults, where the causative infectious agent is N. meningitidis, an obligate human pathogen. The genomic changes induced by N. meningitidis are modulated by the anti-inflammatory cytokine interleukin-10 (IL-10), which is present in large quantities in plasma from patients with meningococcal sepsis. This present study investigated kinase activities in human monocytes stimulated by N. meningitidis and IL-10. The first aim was to identify array peptides that could indicate which signaling pathways were activated or inhibited by the host response to the meningococci. The second aim was to detect whether IL-10 affected N. meningitidis-nduced phosphorylation of array peptides, in order to identify potential targets of the IL-10 anti-inflammatory response. We approached this using a strategy where elutriation-purified human monocytes are stimulated in vitro with N. meningitidis and IL-10, with concentrations corresponding to previously measured levels in patients with fulminant meningococcal septicemia. This work examined activation or inhibition of signaling pathways mediated by tyrosine kinases when purified human monocytes are in vitro incubated with N. meningitidis in the presence or absence of IL-10.
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  • The Polycomb group gene BMI1 is essential for efficient muscle regeneration in a mouse model of Duchenne Muscular Dystrophy and its enhanced expression in adult skeletal muscle satellite cells ameliorates the muscle strength in this model. In this experiment, we investigated the impact of mild BMI1 overexpression in human cells. We showed translation between observed mouse and human phenotypes. In human myoblasts, BMI1 overexpression increases mitochondrial activity leading to an enhanced energetic state with increased ATP production and concomitant protection against DNA damage both in vitro and upon xenografting in a severe dystrophic mouse model. These preclinical data in mouse models and in human cells provide a strong rationale for the development of pharmacological approaches to target BMI1-mediated mitochondrial regulation and protection from DNA damage to sustain the regenerative potential of the skeletal muscle in conditions of chronic muscle wasting. This ArrayExpress record is for the RNA-seq data from three independently prepared normal and DMD myoblasts cell cultures infected with GFP and BMI1Over lentiviral particles and induced to differentiate for 2 days. Please note that each biological sample has one library, and each library is sequenced with two NextSeq runs, each run on identical 4 lane configurations. Hence for each biological sample, there are 16 raw fastq files. The run and lane information has been captured in the “run batch” and “lane batch” attributes respectively in the samples table, and should be used for bath corrections during analysis.
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  • Seedlings are grown on a mesh covering MS media without carbon source, and subsequently transferred at 9 DAS to control media without sucrose or medium supplemented with 15 mM sucrose. 3 hours and 24 hours after transfer, seedlings were harvested and the third leaf micro-dissected for RNA extraction.
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  • To assess natural variation in the ability to respond to changes in gibberellin metabolism, we examined the effect of the ectopic expression of GA20ox1 in 10 Arabidopsis thaliana accessions. RNA-seq was performed on the sixth leaf, which was micro-dissected (size < 0.25 mm2) at the beginning of the transition from cell proliferation to cell expansion.
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  • MV130 is a commercially polyvalent bacterial preparation, which has shown to reduce the the rate of respiratory infections in patients suffering from recurrent respiratory tract infections. However, the immunological mechanisms associated to this clinical benefit remain unknown. We wanted to identify immunological mechanisms in human monocytes-derived dendritic cells (hmoDCs) from 4 healthy donors treated with MV130 compared to control. Global comparative transcription by DNA technology, allows us to detect genes, pathways and clusters that are differentially expressed with the treatment (MV130) respect to control.
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