SCIENZE OMICHE IN MICROBIOLOGIA
Academic Year 2022/2023 - Teacher: VIVIANA CAFISOExpected Learning Outcomes
The course aim to provide the basic elements for the analysis of “omic” data obtained by high-throughput sequencing and Proteomics in microbiology.
Course Structure
Analysis of NGS data and proteomics in bacteriology.
Detailed Course Content
Bacterial Genomics: NGS sequencing methods and file formats. De-multiplexing, Sequence Quality Control (FastQC) and Read Trimmming. Strategies and software for read mapping, for de-novo assembly, samtools, Re-sequencing and variant calling from .bam files. Gene prediction and Genome annotation of bacterial genomes. On-line Bioinformatic tools for the analysis of bacterial genomes. Species identification, Virulome and acquired Resistome -Single Nucleotide Polymorphisms (SNPs) and acquired genes-. Detection and validation of specific SNPs by real time qPCR and High Resolution Meelting Analysis. Determination of in silico-MLST and SNP phylogenetic analysis. In silico MLST determination, genomic epidemiology and phylogeny by analysis of whole genome SNPs e core SNPs.
Bacterial RNAomes and Transcriptomics: Bacterial RNAomes and transcriptome analysis from RNA-seq raw data, read Trimming, de-novo transcript assembly and reference-genome transcript assembly. Normalization of data obtained from different experiments, analysis of differentially expressed genes and small non coding RNAs, determination of operon structures using bacterial transcriptome dedicated tools, Enrichment analysis and tools. Statistical data analysis by EdgeR or other software. Data validation by real time qPCR. Viewing results in IGV genome browser.
Gene Ontology: KEGG database, Go-consortium tools, analysis "functional protein association networks" by STRING Consortium tool.
Microbiomes: Analysis of Targeted Amplicon-Based Next Generation Sequencing of 16S rDNA and ITS for the study of bacterial microbiomes by the generation of OTU, descriptive (alpha-diversity and beta-diversity) and statistical analysis of microbiomes (QIIME). and Overview of Metagenomics.
Bacterial Proteomics: Spatial, temporal and environmental Proteomes. Methods for the proteome study (Two-dimensional electrophoresis (2-DE): IEF Separation by pI (isoelectric point), SDS-PAGE (separation by molecular mass), Image analysis (scanner), Mass spectrometry, Charge / mass ratios, Protein databases: EMBL, GenBank, SWISS PROT.
Metagenomics and Metatranscriptomics: Basics.
Textbook Information
Scientific papers
Course Planning
| Subjects | Text References | |
|---|---|---|
| 1 | Genomica Batterica:Metodi di sequenziamento NGS, formati di file. De-multiplexing, Sequence quality control (FastQC), Read trimming. Strategie e software per read mapping, de novo assembly, samtools, Re-sequencing e variant calling da file bam. Strategie e software per gene prediction and Genome annotation di genomi batterici. | Materiale fornito dal docente |
| 2 | Genomica Batterica: Strumenti web per l'analisi dei genomi batterici, identificazione, studio del viruloma del resistoma in termini di ''acquired'' genes e SNPs. Ricerca e validazione di specifici SNPs mediante High Resolution Meelting. In silico determinazione di MLST, genomic epidemiology ed analisi filogenetiche mediante analisi di whole genome SNPs e core SNPs. | Materiale fornito dal docente |
| 3 | Analisi di RNAomi e trascrittomi batterici da RNA-seq data, read trimming, de-novo transcript assembly, reference genome transcripts assembly, normalizzazione di dati ottenuti da esperimenti diversi, analisi di geni differenzialmente espressi e small non coding RNA, determinazione di operoni mediante tools dedicati ai trascrittomi batterici. Tools per analisi di Enrichment. Analisi statistica dei dati ottenuti mediante EdgeR o software opportuni. Analisi di validazione dei dati mediante real time qPCR. Visu | Materiale fornito dal docente |
| 4 | Gene Ontology: KEGG database, Go-consortium tools, analisi di "functional protein association networks" mediante STRING Consortium Tool. | Materiale fornito dal docente |
| 5 | Microbiomi: Analisi di Targeted Amplicon-Based Next Generation Sequencing delle 16S rDNA and ITS per lo studio dei Microbiomi batterici mediante la generazione di OTU, analisi descrittiva (alpha-diversity and beta-diversity) ed analisi statistica dei microbiomi (QIIME). | Materiale fornito dal docente |
| 6 | Proteoma batterico: spaziale, temporale ed ambientale. Strumenti per lo studio del proteoma (Elettroforesi bidimensionale (2-DE): IEF Separazione per pI (punto isoelettrico), SDS-PAGE (separazione per massa molecolare), Analisi di immagine (scanner), Spettrometria di massa (MALDI-TOF; ESI), Rapporti carica/massa, database Proteici: EMBL, GenBank, SWISS-PROT. | Materiale fornito dal docente |
| 7 | Metagenomica e Metatrascrittomica: Cenni su analisi di base. | Materiale fornito dal docente |