Quality assessment

1. Bioinformatics Unit 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 NGS Technologies Scientific data management platforms We develop and deploy easy-to-use lab data management systems and scientific collaborative platforms based on Wikipedia technology. . RNA and DNA IP Whole genome & transcriptome Exome – enriched sequences Quality assessment Request page: Researchers can fill themselves the request to be submitted. Billion of short reads AATGCGTACATGCACCANTTCAGGTC TGTCANNTGCATTACATGCATTGACC TGTCANNTGCATTACATGCATTGACC AATGCGTACATGCACCANTTCAGGTC TGTCTTTTGCATNACATGCAAAAACC TGTCTTTTGCATNACATGCAGGGACC • Filtering / trimming • Removing low quality reads. • Trimming low quality ends. • Filtering adapters, primers etc… Schematic workflow behind Lab Service wiki De novo genome & transcriptome assembly Experiment page: Lab members enter individually or collaboratively all the data related to the ongoing experiments. • 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 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. • 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 CHROMOSOMAL DNA SNP, indels, structural variation 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. • 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 Versatile databasedesign. Wecanimportandinterlinkdiversedatasourcesintoacommonstoragepoint. Userscandecidewhichisthemostconveniententrypointforthem. MIcroarrays 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 Preprocessing Normalization Raw Data Filtering for differentially expressed genes Data inspection & Quality Control Superfly.Work for Johannes Jaeger’s group. • FUNCTIONAL ANALYSIS • David (GO, KEGG, other ontologies) • Ingenuity • GSEA • Motif analysis (known and de-novo) • Specific request Modern webdevelopment. We develop using different web technologies with an integrative outlook. Weworkforprovidingthebestuserexperincewhenaccessingcomplexscientificdata. Statistical testing Functional analysis Methylation arrays (*) With Infinium arrays we make use of the in-house developed R package HumMeth27QCReport. Preprocessing (*) 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. GoldenGate Methylation Assay Infinium HumanMethylation27 Infinium HumanMethylation450 Raw Data Data inspection & Quality Control • STATISTICAL TESTING • Linear Discriminant Analysis (lda) • Principal Component Analysis (PCA) • Clustering • Specific requests Normalization Statistical testing Other type of arrays - Comparative genomic hybridization (CGH) array: to survey DNA copy-number variations across whole genome. Background correction & Normalization Segmentation 2011 PUBLICATIONS: • Mancuso FM, Montfort M, Carreras A, Alibes A, Roma G. HumMeth27QCReport: an R package for quality control and primary analysis of IlluminaInfiniummethylation 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] • 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) • 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] Background correction & Normalization Polymorphism call - Single Nucleotide Polymorphism (SNP) array: to detect polymorphism within a population and chromosomal aberrations across the genome Segmentation