1. Quality assessment AATGCGTACATGCACCANTTCAG GTC TGTCANNTGCATTACATGCATTGA CC AATGCGTACATGCACCANTTCAG GTC TGTCTTTTGCATNACATGCAAAAA CC TGTCTTTTGCATNACATGCAGGG ACC Billion of short reads Detection of alternative splicing, differential expression (RNA-seq) Analysis of transcripts abundance Detection of novel splicing sites Small ncRNAs profiling Measure of differential gene expression Targeted resequencing Detection of alternative splicing, differential expression (RNA-seq) Analysis of transcripts abundance Detection of novel splicing sites Small ncRNAs profiling Measure of differential gene expression Targeted resequencing NGS Technologies Functional annotation Annotation of coding and non coding genes Functional domain prediction Molecular Function assignment an specification of Gene Ontology (GO) terms Mapping of proteins into metabolic pathway and reactions Functional annotation Annotation of coding and non coding genes Functional domain prediction Molecular Function assignment an specification of Gene Ontology (GO) terms Mapping of proteins into metabolic pathway and reactions Mapping to reference genome CHROMOSOMAL DNA RNA and DNA IP Whole genome & transcriptome De novo genome & transcriptome assembly Exome – enriched sequences SNP, indels, structural variation SNP, indels, structural variation Filtering / trimming Removing low quality reads. Trimming low quality ends. Filtering adapters, primers etc… OVERVIEW Starting in September 2009, this unit has contributed to different research projects by providing support and expertise in programming and advanced data analysis, focusing primarily on high-throughput genomics technologies including microarrays, genotyping and next-generation sequencing. The unit is open to all researchers at the PRBB and also to external users anywhere in the world. For further information please contact Ernesto Lowy (email: ernesto.lowy@crg.eu; phone: +933160181) MEMBERS Cozzuto, Luca Hermoso, Antonio Lowy, Ernesto Mancuso, Francesco MEMBERS Cozzuto, Luca Hermoso, Antonio Lowy, Ernesto Mancuso, Francesco Bioinformatics Tutorials & Workshops The unit is also focused on the education of biologists in the analysis and interpretation of their experimental data through the provision of custom advice and training in bioinformatics as well as in the acquisition of basic programming skills. Bioinformatics Unit Scientific data management platforms We develop and deploy easy-to-use lab data management systems and scientific collaborative platforms based on Wikipedia technology.. 2011 PUBLICATIONS: Mancuso FM, Montfort M, Carreras A, Alibes A, Roma G. HumMeth27QCReport: an R package for quality control and primary analysis of Illumina Infinium methylation data. BMC Research Notes 2011 Dec 19; 4:546. Mancuso FM, Montfort M, Carreras A, Alibes A, Roma G. HumMeth27QCReport: an R package for quality control and primary analysis of Illumina Infinium methylation data. BMC Research Notes 2011 Dec 19; 4:546. Mihailovich M, Wurth L, Zambelli F, Abaza I, Militti C, Mancuso FM, Roma G, Pavesi G, Gebauer F. Widespread generation of alternative UTRs contributes to sex-specific RNA binding by UNR. RNA. 2011 Nov 18;. [Epub ahead of print] Mihailovich M, Wurth L, Zambelli F, Abaza I, Militti C, Mancuso FM, Roma G, Pavesi G, Gebauer F. Widespread generation of alternative UTRs contributes to sex-specific RNA binding by UNR. RNA. 2011 Nov 18;. [Epub ahead of print] Uribesalgo I, Buschbeck M, Gutiérrez A, Teichmann S, Demajo S, Kuebler B, Nomdedéu JF, Martín-Caballero J, Roma G, Benitah SA, Di Croce L. E-box-independent regulation of transcription and differentiation by MYC. Nat Cell Biol. 2011 Oct 23. doi: 10.1038/ncb2355. [Epub ahead of print] Uribesalgo I, Buschbeck M, Gutiérrez A, Teichmann S, Demajo S, Kuebler B, Nomdedéu JF, Martín-Caballero J, Roma G, Benitah SA, Di Croce L. E-box-independent regulation of transcription and differentiation by MYC. Nat Cell Biol. 2011 Oct 23. doi: 10.1038/ncb2355. [Epub ahead of print] Luis NM, Morey L, Mejetta S, Pascual G, Janich P, Kuebler B, Cozzuto L, Roma G, Nascimento E, Frye M, Di Croce L, Benitah SA. Regulation of Human Epidermal Stem Cell Proliferation and Senescence Requires Polycomb- Dependent and -Independent Functions of Cbx4 Cell Stem Cell. 2011 Sep 2;9(3):233-46. (Erratum in Cell Stem Cell, Volume 9, Issue 5, 486, 4 November 2011) Luis NM, Morey L, Mejetta S, Pascual G, Janich P, Kuebler B, Cozzuto L, Roma G, Nascimento E, Frye M, Di Croce L, Benitah SA. Regulation of Human Epidermal Stem Cell Proliferation and Senescence Requires Polycomb- Dependent and -Independent Functions of Cbx4 Cell Stem Cell. 2011 Sep 2;9(3):233-46. (Erratum in Cell Stem Cell, Volume 9, Issue 5, 486, 4 November 2011) Hummel M, Bonnin S, Lowy E, Roma G. TEQC: an R-package for quality control in target capture experiments. Bioinformatics. 2011 Mar 12. doi: 10.1093/bioinformatics/btr122 [Epub ahead of print] Hummel M, Bonnin S, Lowy E, Roma G. TEQC: an R-package for quality control in target capture experiments. Bioinformatics. 2011 Mar 12. doi: 10.1093/bioinformatics/btr122 [Epub ahead of print] Modern web development. We develop using different web technologies with an integrative outlook. We work for providing the best user experince when accessing complex scientific data. Experiment page: Lab members enter individually or collaboratively all the data related to the ongoing experiments. Request page: Researchers can fill themselves the request to be submitted. Schematic workflow behind Lab Service wiki Database and Scientific Web development We can plan different ways to convert your raw experimental data into structured information which can become available to third parties or the whole scientific community via the WWW. Versatile database design. We can import and interlink diverse data sources into a common storage point. Users can decide which is the most convenient entry point for them. We collaborate with other Cores facilities to deploy this technology in order to improve their workflows. We use advanced wiki systems for boosting and tracking the collaboration in global genome initiatives we are involved. Superfly.Work for Johannes Jaeger’s group. Gene expression arrays STATISTICAL TESTING between compared sample groups Fold-change for the size of the change P-values and false discovery rates for the reliability of the change FUNCTIONAL ANALYSIS David (GO, KEGG, other ontologies) Ingenuity GSEA Motif analysis (known and de-novo) Specific request Raw Data Preprocessing Statistical testing Normalization Data inspection & Quality Control Filtering for differentially expressed genes Functional analysis Methylation arrays (*) With Infinium arrays we make use of the in-house developed R package HumMeth27QCReport. GoldenGate Methylation Assay Infinium HumanMethylation27 Infinium HumanMethylation450 Raw Data Preprocessing (*) Data inspection & Quality Control Normalization Statistical testing STATISTICAL TESTING Linear Discriminant Analysis (lda) Principal Component Analysis (PCA) Clustering Specific requests Other type of arrays - Comparative genomic hybridization (CGH) array: to survey DNA copy-number variations across whole genome. - Single Nucleotide Polymorphism (SNP) array: to detect polymorphism within a population and chromosomal aberrations across the genome Background correction & Normalization Segmentation Background correction & Normalization Segmentation Polymorphism call Detection of enriched regions (Chip-seq, RIP-seq) Statistical evaluation of enriched regions Data visualization in a genome browser Detection of enriched motifs in binding sites Analysis of gene enrichment Detection of enriched regions (Chip-seq, RIP-seq) Statistical evaluation of enriched regions Data visualization in a genome browser Detection of enriched motifs in binding sites Analysis of gene enrichment MIcroarraysMIcroarrays