platforms 72 platforms 73 During 2023, the bioinformatics platform consolidated its role of support for the community by performing more than 80 analyses, including bulk and single-cell RNAseq, ChIPseq, ATACseq, GWAS, and eQTL analysis. The platform also collaborated on more specific and custom projects, including the optimization of the pipeline for demultiplexing sequencing data (Genomics platform), the development of a customised DB mining pipeline for a laboratory studying the interaction between proteins and lipids, and the implementation of a tool to detect rare events of Internal Tandem Duplications in amplicon sequencing data for the CHU human genetics service. Beside these analysis and developments, the bioinformatics platform organised 132h of training sessions on programming languages (python and R) and NGS data analysis. These sessions have been followed by 80 GIGA members from several research and platform teams. These courses received highly positive feedback from participants. The platform also gave support to the community in their usage of mass storage and High Performance Computing (HPC) infrastructures. Indeed, more than 1000 users have used the mass storage, with a total of 403 million files occupying 2000 Tb of disk space. Moreover, GIGA members and collaborators have run more than 4 million jobs on the GIGA HPC Cluster, for a cumulated calculation time (CPU time) of 1 million hours. Beside the support to these users, the SEGI and the bioinformatics platform have increased the storage capacity of the mass storage and of the cluster thanks to a fund from the University (CURV). With over 5 years of experience, the platform aims now to solidify its position in the field and has started to prepare for new challenges ahead. Recently, the platform has strengthened its expertise in multi-omics data integration, particularly focusing on single-cell resolution. Recent advances in single-cell analysis have enabled unprecedented precision in understanding biological processes. Leveraging GIGA’s technological platforms and underutilized public datasets, the platform is working on developing tools for the community. Additionally, the bioinformatics platform participates actively in a collaborative GIGA effort to bring “spatial-omics” technologies to the researchers, with the team ready to address this upcoming challenge. In 2023 Alice Mayer, GIGA-Bioinformatics Manager alice.mayer@uliege.be www.gigabioinformatics.uliege.be Contact Services Bulk RNAseq Messenger RNA, total RNA, small RNA Mapping to genome, count normalisation Differential expression, alternative splicing, cell type deconvolution Single-cell RNAseq 10x, Rhapsody, SmartSeq, etc From whole cells or nuclei Samples demultiplexing according to tags or genome Mapping to genome, counts normalisation, clustering Cluster caracterisation, sample or cluster compraisons TCR and BCR profiling Other analysis ATACseq and ChIPseq Genome-Wide Association Studies (GWAS, i.e. association between SNP and a given phenotype) Expression Quantitative Trait Loci analysis (eQTL, i.e. association between SNP and gene expression in different conditions) RNA methylation (native RNA sequencing with nanopore technology) Tools development and bioinformatics trainings Nextflow pipelines Fully customized scripts to extract information from databases and answer specific questions Interactive graphical user interfaces (Python/Shiny) Trainings in R, Python, NGS data analysis, etc x
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