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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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  • Pancreas and spleen were microdissected from wild type (C57B6/SV129 background) E14.5 embryos and P0 newborn pups. Pools of 30-60 tissues were used. Tissues were digested for 1 hour at 37°C in HBSS/0.1% collagenase A/20 µg/ml DNase I, followed by dissociation of the cell clusters into single cells using a non-enzymatic dissociation medium (Sigma). Single cell suspensions were blocked with mouse IgGs and anti-CD16/32 Abs and immunostained with biotin-anti-CD11b (Biolegend) and RPE-conjugated goat anti-CCR2 (R&D Systems), followed by Cy5.5 conjugated streptavidin. CD11b+CCR2+ cell were then isolated by FACS sorting. mRNA from purified cells was prepared using the RNAeasy kit (Qiagen) and run on a MouseWG-6 v2.0 Expression BeadChip.
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  • Hydrostatic pressure is one of the main mechanical stimuli cartilage cells are submitted to during joint loading. If moderate hydrostatic pressure is known to be beneficial to cartilage differentiation, excessive pressure, on the other hand, induces changes in cartilage similar to those observed in osteoarthritic cartilage. Therefore, the purpose of the experiment is to identify new target genes of high hydrostatic pressure in chondrocyte precursor cells.
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  • Gastrulation represents a pivotal point in mammalian development, when the basic body plan is established and cells are specified into one of the three germ layers. This is followed by rapid diversification into specific lineages and the appearance of the various cell types required to build each of the organs. The rich variety of cell types present at this stage has never been rigorously characterised in any mammalian organism, and thus insight into cell fate decisions and the underlying regulatory networks have been inaccessible. We have used droplet based single-cell RNA-sequencing to address this by profiling ~20000 cells from C57BL/6 E8.25 mouse embryos.
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  • Breast cancer was one of the first cancer types where molecular subtyping led to explanation of interpersonal heterogeneity and resulted in improvement of treatment regimen. Several multigene classifiers have been developed and in particular those defining molecular signatures of early breast cancers possess significant prognostic information. Hence since 2014, molecular subtyping of primary breast cancers was implemented as a part of routine diagnostics with direct impact of therapy assignment. In this study, we evaluate direct and potential benefits of molecular subtyping in low-risk breast cancers as well as present the advantages of a robust molecular signature in regard to patient work-up among high-risk breast cancers.
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