Because of rapid improvements in sequencing technologies, many types 15of transcriptomic, genomic and epigenomic data have been generated and made publicly available. Such data resources are potentially useful for the elucidation of biological systems and the development of medical tools by per-forming large-scale integrative analyses. Our mission is to promote such data-driven studies in the biomedical field and to develop component technologies to efficiently reuse large-scale biomedical data by employing data engineering technologies.We have been working on several research projects to develop data resources for transcriptional regulation studies. Transcription regulation is a fundamental process involving various types of molecules and biological phenomena includ-ing transcription, binding of transcription factors, epigenomic states, and ge-nomic variations. This means that treatment and integrative analysis of various heterogeneous datasets is required for understanding the complete mechanisms of transcriptional regulation.One of the data resources developed by our team is SCPortalen2 (https://single-cell.riken.jp/), which provides curated metadata and reprocessed data files for reusing single-cell data for further studies. This year, we expanded the original SCPortalen database to provide a comprehensive metadata search in-terface (SCDD, Single-cell Dataset Discovery) in addition to the interface for value-added datasets. We also expanded the database to collect 5’-end single-cell RNA-seq datasets for transcriptional regulation studies. The second data resource is refTSS4 (https://reftss.riken.jp/), which provides a reference set of transcription start sites (TSS). This year, we updated the reference and added a new function for GWAS-LD enrichment analysis at the TSS level. We have also begun to build a new database for cis-regulatory elements (CREs), named fanta.bio (https://fanta.bio/) (Figure). The new database provides genome-wide CRE information with genomic locations, activities in various cell types and states, and relationships to genomic variations.Along with these research projects, we provide and support the information infrastructure for several IMS laboratories to promote large-scale omics studies.Figure: Screenshot of the fanta.bio database siteThe screenshot of the home page of the fanta.bio web site (https://fanta.bio/). Users can search for CRE infor-mation using keywords and genomic positions.Recent Major PublicationsAbugessaisa I, Manabe RI, Kawashima T, Tagami M, Takahashi C, Okazaki Y, Bandinelli S, Kasukawa T, Ferrucci L. OVCH1 Antisense RNA 1 is differentially expressed between non-frail and frail old adults. Geroscience (2023)Yip CW, Hon CC, Yasuzawa K, Sivaraman DM, Ramilowski JA, Shibayama Y, Agrawal S, Prabhu AV, Parr C, Severin J, Lan YJ, Dostie J, Petri A, Nishiyori-Sueki H, Tagami M, Itoh M, López-Redondo F, Kouno T, Chang JC, Luginbühl J, Kato M, Murata M, Yip WH, Shu X, Abugessaisa I, Hasegawa A, Suzuki H, Kauppinen S, Yagi K, Okazaki Y, Kasukawa T, de Hoon M, Carninci P, Shin JW. Antisense-oligonucleotide-mediated perturbation of long non-coding RNA reveals functional features in stem cells and across cell types. Cell Rep 41, 111893 (2022)Abugessaisa I, Hasegawa A, Noguchi S, Cardon M, Watanabe K, Takahashi M, Suzuki H, Katayama S, Kere J, Kasukawa T. SkewC: Identifying cells with skewed gene body coverage in single-cell RNA sequencing data. iScience 25, 103777 (2022)Invited presentationsKasukawa T. “Database for reusing single-cell RNA-seq data”, NGS EXPO 2023 (Osaka, Japan) November 2023Kasukawa T. “fanta.bio database of genome-wide cis-regulatory elements for understandingthe transcriptional regulation” JBS2023 (Fukuoka, Ja-pan) November 2023Kasukawa T. “Development of an integrated data platform for understanding transcriptional regulation” RIKEN Hackathon 2023 Open symposium (Kobe, Japan) October 2023Kasukawa T. “Construction of the integrated transcrip-tional regulation data platform, INTRARED” Togo sympo-sium (Tokyo, Japan) October 2023Laboratory for Large-Scale Biomedical Data TechnologyTeam Leader: Takeya Kasukawa
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