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San Raffaele Open Research Data Repository

IRCCS San Raffaele Scientific Institute Showcase

San Raffaele Open Research Data Repository (ORDR) is an institutional platform which allows to store preserve and share research data. ORDR is powered by the Digital Commons Data repository platform.

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1970 2024
110 results
  • QuantiGene Plex assay
    Preliminary data for the selection of housekeeping genes suitable for our cells to be used as normaliser for the full experiment that will allow us to identify genes potentially modified by the infection with ZIKV and counteracted with the heparin treatment. Instead of performing RNAseq analyses, we decided to opt for QuantiGene Plex (Thermofisher). This test incorporate branched DNA technology for accurate gene expression profiling. Branched DNA assays allow direct measurement of RNA transcripts using signal amplification (Luminex 200 technology) rather than target amplification. We decided to include 4 conditions: uninfected, uninfected + heparin, ZIKV and ZIKV + heparin, and three time points: 4, 24, 48 h post infection, for a total of 12 samples. We performed three 1:4 serial dilutions of all samples. Then, we load the plate with all undiluted samples + all dilutions made. We performed the experiment according to the manufacturer’s instructions (Thermofisher). Thanks to the Thermofisher free online software, we performed the analyses of the data we obtained from the Luminex reading. From the analyses file, we highlighted the data that were saturated (over 20000 reads), then we remove data from "uninfected + heparin 4h" and "ZIKV 4h" since the preparation was not perfect and the data were not reliable (incorrect serial dilution). We selected the samples in which genes are not saturated (dilution 1:64), and we performed the geometric mean (GEOMEAN) of all genes expressed by the same sample. We divided each values by its GEOMEAN and we calculated the standard deviation (SD). We selected the genes with the lower SD. This experiment allowed us to identify the best 4 housekeeping genes: the glyceraldehyde-3-phosphate dehydrogenase (GAPDH), phosphoglycerate kinase 1 (PGK1), ubiquitin C (UBC) and the ATPase H+ transporting the A subunit V1 (ATP6V1A) .
    • Dataset
  • ZIKV -Organoids
    Preliminary data of ZIKV infection in brain organoids. We perform immunostaining to characterise organoids grown in culture for 5 weeks. We identified neurons (MAP2) and astrocytes (GFAP). We tested the cytopathic effect of ZIKV in this 3D-system after infection with 1.000.000 infectious particles. We took pictures every 3 days post-infection by optic microscope and collected the supernatant for the retrotitration through plaque forming assay to check viral replication.
    • Dataset
  • Heparin Precursors with Reduced Anticoagulant Properties Retain Antiviral and Protective Effects That Potentiate the Efficacy of Sofosbuvir against Zika Virus Infection in Human Neural Progenitor Cells
    Raw data of the figures reported in the published related article:
    • Dataset
  • Heparin Protects Human Neural Progenitor Cells from Zika Virus-Induced Cell Death While Preserving Their Differentiation into Mature Neuroglial Cells
    Raw data of the figures reported in the published related article:
    • Dataset
  • Defining the role of HIF-2alpha in the pathogenesis of acute myeloid leukemia and exploiting its inhibition as a new therapeutic approach to promote leukemia differentiation and exhaustion
    This dataset represents findings obtained within a project supported by the Italian Ministry of Health (project code: RF-2019-12369841) and focused on investigating the mechanism of myeloid differentiation blockade by the transcription factor HIF-2alpha in acute myeloid leukemia (AML) and the consequences of its inhibition with novel targeted therapies. We found that in AML HIF-2alpha regulates a specific set of target genes involved in transcriptional repression, leading to inhibition of entire gene clusters linked to myeloid difefrentiation. As a consequence, HIF-2alpha blockade via genetic or pharmacologic approaches leads to myeloid differentiation and leukemia debulking. Also, we positioned HIF-2alpha under direct transcriptional control by the prodifferentiation agent all-trans retinoic acid (ATRA) and demonstrated that HIF-2alpha blockade cooperates with ATRA to trigger AML cell differentiation. Links related to this dataset contain: 1. A publication describing part of the results funded by this grant; 2. Source data linked to this publication and deposited in the BioStudies repository (accession number: S-SCDT-10_15252-EMMM_202317810); 3. Sequencing data deposited in the GEO repository.
    • Dataset
  • Data for "CD32 captures committed haemogenic endothelial cells during human embryonic development"
    During embryonic development, blood cells emerge from specialized endothelial cells, named hemogenic endothelial cells (HECs). As HECs are rare and transiently found during very early development, it remains difficult to distinguish them from endothelial cells. Here, we performed transcriptomic analysis of 28-32 day human embryos, and observed that the expression of Fc receptor CD32 (FCGR2B), is highly enriched in the endothelial cell population that contains HECs. Functional analyses using human embryonic and hPSC-derived endothelial cells revealed that robust multilineage hematopoietic potential is harbored within CD32+ endothelial cells and showed that 90% of CD32+ endothelial cells are bona fide HECs. Remarkably, these analyses indicated that HECs progress through different states, culminating in FCGR2B expression, at which point cells are irreversibly committed to a hematopoietic fate. These findings provide a precise method for isolating HECs from human embryos and hPSC cultures, thus allowing the efficient generation of hematopoietic cells in vitro.
    • Dataset
  • Circulating hematopoietic stem/progenitor cell subsets contribute to human hematopoietic homeostasis
    In physiological conditions, few circulating hematopoietic stem/progenitor cells (cHSPC) are present in the peripheral blood but their contribution to hematopoietic homeostasis in humans remain unsolved. By integrating advanced immunophenotyping, cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq), functional single-cell assays and integration site (IS) clonal tracking, we unveiled the phenotypic composition, the transcriptional features and the biological role of human cHSPC subpopulations in relationship to their bone marrow (BM) counterpart. We found that cHSPC progressively reduced in cell count over aging and are enriched for primitive, lymphoid and erythroid subpopulations, showing pre-activated transcriptional and functional state. Moreover, cHSPC have low expression of multiple BM-retention molecules, but maintain their homing potential after xenotransplantation. By generating a comprehensive Human Organ-Resident HSPC (HuOR) dataset based on scRNAseq data, we detected organ-specific seeding properties of the distinct trafficking HSPC subpopulations. Of note, circulating multi-lymphoid progenitors (MLP) are primed for seeding the thymus and actively contribute to T-cell production at steady state in patients treated with HSPC-gene therapy (GT). Human clonal tracking data from GT patients also showed that cHSPC connect distant BM niches and participate to steady-state hematopoietic production, with primitive cHSPC having the highest re-circulation capability to travel in and out the BM. Finally, in case of hematopoietic impairment, cHSPC composition reflects the BM-HSPC content and might represent a biomarker of the BM state for clinical and research purposes. Overall, our comprehensive work unveiled fundamental insights into the in vivo dynamics of human HSPC trafficking and its role in sustaining hematopoietic homeostasis.
    • Dataset
  • Dual specificity kinase DYRK3 regulates cell migration by influencing the stability of protrusions
    Plasma membrane-associated platforms (PMAPs) form at specific sites of plasma membrane by scaffolds including ERC1 and Liprin-1. We identify a mechanism regulating PMAPs assembly, with consequences on motility/invasion. Silencing Ser/Thr kinase DYRK3 in invasive breast cancer cells inhibits their motility and invasive capacity. Similar effects on motility were observed by increasing DYRK3 levels, while kinase-dead DYRK3 had limited effects. DYRK3 overexpression inhibits PMAPs formation nad has negative effects on stability of lamellipodia and adhesions in migrating cells. Liprin-1 depletion results in unstable lamellipodia and impaired cell motility. DYRK3 causes increased Liprin-1 phosphorylation. Increasing levels of Liprin-1 rescue the inhibitory effects of DYRK3 on cell spreading, suggesting that an equilibrium between Liprin-1 and DYRK3 levels is required for lamellipodia stability and tumor cell motility. Our results show that DYRK3 is relevant to tumor cell motility, and identify a PMAP target of the kinase, highlighting a new mechanism regulating cell edge dynamics. Upon request, the corresponding author is available to provide the data in different formats if it is not possible to open data files with open-source softwares.
    • Dataset
  • IL-10-producing regulatory cells impact on Celiac Disease evolution
    In the manuscript "IL-10-producing regulatory cells impact on celiac disease evolution" (doi: 10.1016/j.clim.2024.109923), we showed that IL-10-producing cells are fundamental in controlling pathological T-cell responses to gluten. In brief, our major findings are: 1) Gluten ingestion induces systemic inflammation in CD patients; 2) Gliadin-specific IFN-g+ T cells are present in patients regardless of tissue damage; 3) The presence of DC-10 in mucosal infiltrates is a hallmark of potential CD patients; 4) In potential CD, DC-10 maintain mucosal homeostasis and protect the gut from damage. The datasets here loaded contain all the clinical and immunological data, supporting our conclusions, that have been used to build the manuscript. An additional file (raw_data_description) contains the main guidelines to correctly associate the raw data with the corresponding figure/table in the manuscript.
    • Dataset
  • New orphan disease therapies from the proteome of industrial plasma processing waste- a treatment for aceruloplasminemia
    Raw data associated to the paper Zanardi, Nardini, et al. Communications Biology (see link). - Proteomics raw data for protein identification associated to Figure 1 of the manuscript are deposited in dedicated repository indicated in the paper (see "link") - Folder " 64CUkCP Biodistribution ": raw data associated to Fig 5 panel (a) and Supplementary Figure 8 describing labelled Cp biodistribution in the brain and blood of mice - Folder "Images choroid plexus": collection of the histochemistry images of choroid plexus stained for iron deposition used to generate data of figure 5 panels (g and h) - Folder "Images Purkinje": collection of the histochemistry images of cerbellum used to count thenumber of Purkinje neurons reported on figure 5 panels (i and j) - Folder "Images liver": collection of the histochemistry images of liver stained with hematoxylin-eosin used to generate figure 7 panels (c and d) - Folder Immunohistochemistry images Cerebellum => Autofluor Purkinje Cells Density: images used to generate data in figure 5 panels (k and l) - Folder Immunohistochemistry images Cerebellum => Astrocyte Density in Arbor Vitae: images used to generate data in figure 6 panels (a and b) - Folder Immunohistochemistry images Cerebellum => GFAP expression in Arbor Vitae: images used to generate data in figure 6 panel (c) - Folder Immunohistochemistry images Cerebellum => Microglia Density in Arbor Vitae: images used to generate data in figure 6 panels (a and d) - Folder Immunohistochemistry images Cerebellum => IBA1 expression in Arbor Vitae: images used to generate data in figure 6 panel (e) - Folder Immunohistochemistry images Hippocampus => Astrocyte Density in CA1 SR: images used to generate data in figure 6 panels (f and g) - Folder Immunohistochemistry images Hippocampus => GFAP expression in CA1 SR: images used to generate data in figure 6 panel (h) - Folder Immunohistochemistry images Hippocampus => Microglia Density in CA1 SR: images used to generate data in figure 6 panels (i and j) - Folder Immunohistochemistry images Hippocampus => IBA1 expression in CA1 SR: images used to generate data in figure 6 panel (k) - Folder Immunohistochemistry images Hippocampus => Neuron Density in CA1 SP: images used to generate data in figure 6 panels (l and m) - Folder Immunohistochemistry images Hippocampus => Thickness of CA1 SP: images used to generate data in figure 6 panel (n) - Folder Immunohistochemistry images Hippocampus => Autofluor Neurons Density in CA1 SP: images used to generate data in figure 6 panel (o) - Folder "WT+CP database ": raw data associated to Supplementary Figure 6 describing the evaluation of toxicity induction in wild-type (WT) mice treated for 4 months with purified ceruloplasmin
    • Dataset