65Table1: Central services provided by the Genome Platform in 2023Library PreparationWhole genome sequenceWhole exome sequenceTarget sequenceBulk RNA-seqRamDA-seqNET-CAGE10x 3’ GETable2: Next-generation DNA sequencingIllumina SequencerNovaSeq6000NextSeq2000MiSeqPacBio SequelSequel IIFigure: The vinyl isolator roomsThis platform enables users in IMS to obtain DNA librar-ies, sequence data and analysis data quickly and at a reasonable cost, thus empowering their research. For library preparation, we support whole-genome sequencing, targeted sequencing, CAGE, single-cell RNA-seq, and bulk RNA-seq. For sequencing, we sup-port NovaSeq6000, NextSeq2000, MiSeq, and PacBio Sequel runs. Data analysis is available for whole-genome sequencing, targeted sequencing, CAGE, single-cell RNA-seq, bulk RNA-seq, Chip-Seq, and ATAC-seq. In addition, we also support the registration of data in public databases.In FY2023, we have begun to support microbiome experi-ments. The genome platform enabled users to receive analysis data online by using the HOKUSAI SS data science platform. In addition, the Illumina DRAGEN Bio-IT platform makes routine data analysis fast and easy and enables data to be provided to users in a short period of time. PacBio Revio has been installed at the RIKEN Center for Sustainable Resource Science (CSRS), and CSRS has kindly agreed to make Revio available to IMS.This year, we are working on 57 projects. The achievements in library preparation and sequencing are shown in Table 1. Con-tinued from last year, we conducted whole-genome sequencing analysis of 800 individuals for an Atrial Fibrillation Study in col-laboration with the University of Tokyo.and 1,500 mice in an infected animal area. The SPF area also contains 1,000 germ-free or gnotobiotic mice in vinyl isola-tor rooms (Figure) and in vinyl isolation bio-bubble rooms. The former are used by several IMS research groups, in particular the mucosal immunologists, and the latter are for “humanized mice”. In addition, for COVID-19 research, a new animal biosafety level 3 (ABSL3) room was completed in 2021. The ABSL3 room has high negative pressure and Individually Vented Cage systems (IVCs) and has the capacity to breed 150 mice. We introduce mouse lines into the SPF area via a combination of in vitro fertil-ization (IVF) and embryo transfer methods and have also gener-ated cryo-stocks of genetic resources (frozen embryos and sperm) for 775 lines. We also maintain relatively large colonies of several commonly used strains, such as Rag1 KO and Cre deleters, and provide them to users on demand. We have also provided tech-nical assistance to generate knockout and transgenic mice (92 lines). In addition, we have created 9 lines of germ-free mice. We maintain flexibility so that we can provide space for new experi-ments in the animal facility, e.g., behavioral testing of germ-free mice.We have generated genetically modified mice to improve the efficiency of transplantation of human hematopoietic stem cells We expect that the intramural interactions fostered by the Genome Platform among the Divisions of Human Immunol-ogy, Disease Systems Biology, Cancer Immunology, and Genome Medicine will greatly enhance IMS basic and translational re-search activities.into NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mice by better “hu-manizing” the host strain. For this purpose, we have introduced large genomic fragments containing human genes encoding MHC, cytokines, adhesion molecules, virus receptors, and others into the NSG mice. We maintain such transgenic and knock-in mice.# of Samples488260914661815664219# of Runs14241231# of Runs10Genome Platform and related activitiesThe Genome Platform was launched in September 2020. Animal FacilityWe continue to maintain over 60,000 mice in the SPF area
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