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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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In the current study, we have performed a multi-factorial integrative analysis of genome-wide chromatin immunoprecipitation-sequencing (ChIP-seq) on multiple histone marks, as well as RNA-Sequencing (RNA-seq) and DNA methylation studies to generate new knowledge on the epigenetic landscapes underlying the heterogeneity of PDAC tissue grown as patient-derived tumor xenografts (PDTXs).
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Mycobacterium tuberculosis (Mtb) is one of the most successful pathogens in human history and remains the second leading cause of death from an infectious agent worldwide. The major reason of Mtb success principally relies on its ability to perfectly adapt to the host, by establishing latent infection and evading from the control driven by immune system. Accordingly, both innate and adaptive immune responses are required to control TB progression and pathogenesis and in particular dendritic cells (DC), as professional antigen presenting cells, are one of the major cellular effectors of the anti-mycobacterial response. In this context, we performed a microarray analysis to characterize the de-regulation of cellular miRNAs during Mtb infection of human DC. Human DC were prepared from human peripheral blood mononuclear cells of anonymous healthy blood donors and infected with Mtb for 3, 8 and 24 hours. This data set contains the global miRNA expression profiling in uninfected and Mtb-infected DC cultures to identify altered signature of miRNAs potentially implicated in Mtb-mediated immune evasion strategies.
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Pancreatic adenocarcinoma (PDAC) is one of the most lethal human malignancies and a major health problem. Patient-derived xenografts (PDX) are appearing as a prime approach for preclinical studies despite being insufficiently characterized as a model of the human disease and its diversity. We generated subcutaneous PDX from PDAC samples obtained either surgically or using diagnostic biopsies (endoscopic ultrasound guided fine needle aspirate). The extensive multiomics characterization of the xenografts demonstrated that PDX is a suitable model for preclinical studies, representing the diversity of the primary cancers. We generated subcutaneous PDX from PDAC samples obtained either surgically or using diagnostic biopsies (endoscopic ultrasound guided fine needle aspirate). The variable 'MultiOmicsClassification' indicates the resulting sample's group. 'CIMPclass' is the CpG island methylator phenotype as estimated from the methylation arrays analysis. In this dataset, Illumina Infinium HumanCode-24 BeadChips SNP arrays were used to analyze the DNA xenografts samples from pancreatic ductal adenocarcinoma.
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17α-Ethinylestradiol (EE2) is a ubiquitous aquatic contaminant shown to decrease fish fertility at low concentrations, especially in fish exposed during development. The mechanisms of the decreased fertility are not fully understood. In this study, we perform transcriptome analysis by RNA sequencing of testes from zebrafish with previously reported lowered fertility due to exposure to low concentrations of EE2 during development. Fish were exposed to 1.2 and 1.6 ng/L (measured concentration) of EE2 from fertilization to 80 days of age, followed by 82 days of remediation in clean water.
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Keloid disease (KD) is a fibroproliferative cutaneous tumour characterised by heterogeneity, excess collagen deposition and aggressive local invasion. Normal and keloid scar tissues were analysed with a site-specific in situ approach through combined laser capture microdissection, as well as whole tissue biopsy and monolayer cell culture techniques.
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After performing an in-vivo screening with U87 glioblastoma cells transduced with a knockdown library several genes could be identified. LAPTM5 which was one of the candidates was further evaluated. Single knockdown of LAPTM5 in U87MG conferred a pro-invasive phenotype in-vitro and in-vivo. To decipher the underlying pathways U87MG control cells (U87RNAi) and U87shLAPTM5 were analyzed after in-vitro culture by a transcription profiling Array.
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