Facilities available to PhD students

Each PhD student has an office workstation, equipped with a PC, and a reserved space in the laboratory. Doctoral students who also carry out clinical care activities have access to the relevant hospital facilities. The following are available to students: -cellular and molecular biology laboratories equipped with modern equipment that allow carrying out both basic and translational research relating to the doctoral topics and human genetics and genomics laboratories engaged in the management and study of genetic diseases through integrated molecular diagnostic and experimental research. Specialist instruments for conducting molecular biology, cell biology, microbiology, biochemistry and genetics experiments include: optical microscopes, fluorescence microscopes, spectrophotometers, chemical hoods, Real-Time PCR machines, sonicators, luminometers, agarose gel electrophoresis apparatus and polyacrylamide, BSL2 biological safety cabinets, CO2 incubators, centrifuges, refrigerators and freezers, equipment for handling class 1 MOGMs (e.coli, immortalized human cell lines), ultracentrifuges, supercentrifuges, mass spectrometer, thermal cyclers, automatic sequencers multicapillary, digitaldroplet PCR, molecular imaging tools, nucleic acid quantification systems, cell sorter, cytometer; - hardware IT equipment for scientific computing and data storage (workstations, desktop computers, 1 HPC cluster, data storage servers, GPU graphics cards). For activities relating to research projects, specialist software for statistical analysis, big data, Next Generation Sequencing data, sequence and fragment analysis, machine learning, virtualization, molecular dynamics simulations and workflow management systems are also available. : Ingenuity Pathway Analysis, Amber, Transcriptome Analysis Console, Integrative Genomics Viewer, PyTorch, Docker, VEP, Snakemake, NextFlow, Anaconda, Salmon, EdgeR, DESeq2, Haplogrep 3, Mitoverse, Burrow-Wheeler Aligner, bowtie2, htseq-count, hisat2 , STAR, cutadapt, MACS2, Genrich, IDR, MetaPhlAn, samtools, bedtools, SRAtoolkit, GNU parallel, "R" statistical software with 403 R packages including AnnotationDbi, ATACseqQC, DESeq2, edgeR, enrichR, ggplot2, harmony, monocle3, Seurat , Proteome Discoverer, Thermo, GraphPad Prism, Flowjo, Biorender, SeqScape, Genescan, Genotyper, Genemapper; - scientific equipment for mass spectrometric analysis (managed at the National Institute for Infectious Diseases IRCCS “Lazzaro Spallanzani”), laboratory animal enclosure (at the Department of Molecular Medicine to which the doctorate belongs).

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