411265empowering their research. We expect that the intramural interac-tions fostered by the Genome Platform among the Divisions of Human Immunology, Disease Systems Biology, Cancer Immunol-ogy, and Genome Medicine will greatly enhance IMS research activities.Table1: Central services provided by the Genome Platform in 2021large 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 with confirmed expression of human genes on a C57BL/6 background and have backcrossed them onto the NSG mouse background using the speed-congenic method.supports each laboratory in the Center in library prepara-tion, sequencing and data analysis related to sequencing and plays a central role when large projects are adopted. In FY2021, we in-stalled a 10xGenomincs Chromium Controller to perform single-cell RNA-seq analysis. We also support library preparation for this analysis. As for the sequencer, we have newly introduced the NextSeq2000, which is a middle output (40~330GB) sequencer. In addition, we also support the registration of data in public da-tabases.This year, we are working on 40 projects. The achievements in library preparation and sequencing are shown in Table 1. A key contribution is that we analyzed gene expression in mouse primi-tive endoderm stem cells using the single-cell sequencing method in collaboration with the Laboratory for Developmental Genet-ics. Based on the results, we were able to clarify the establishment of primitive endoderm stem cells and gain knowledge that will lead to understanding the mechanisms for primitive endoderm specification (Ohinata Y et al., Science. 2022). In addition, we are developing an off-target analysis method for gene editing with the RIKEN Program for Drug Discovery and Medical Technology Platforms (DMP).This platform enables users in IMS to quickly obtain DNA li-braries, sequence data and analysis data at a reasonable cost, thus and 1,500 mice in an isolated area. The SPF area also con-tains 550 germ-free or gnotobiotic mice in vinyl isolator rooms and in vinyl isolation bio-bubble rooms. The former is used by several IMS research groups, in particular the mucosal immu-nologists, and the latter is for “humanized mice”. In addition, a new SPF animal facility was completed in 2019. The new facility has 32 vinyl isolators and two Individually Vented Cage systems (IVCs) (Figure) and has the capacity to breed 1,500 mice. We introduce mouse lines into the SPF area via a combination of in vitro fertilization (IVF) and embryo transfer methods and have also generated cryostocks of genetic resources (frozen embryos and sperm) for 944 lines. We also maintain relatively large colo-nies of several commonly used strains, such as Rag1 KO and Cre deleters, and provide them to users on demand. We have also pro-vided technical assistance to generate knockout and transgenic mice (163 lines). In addition, we have created 17 lines of germ-free mice. We maintain flexibility so that we can provide space for new experiments 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 into NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mice by better “hu-manizing” the host strain. For this purpose, we have introduced # of Samples1,78137,347104341,34448014028# of Runs8774141# of RunsLibrary Preparationwhole genome sequencetargeted sequencebulk RNA-seqIg-seqSMART-SeqRamDA-seqssCAGE10x 3’GETable2: Next-generation DNA sequencingIllumina SequencerNovaSeq6000HiSeq2500MiSeqPacBio SequelSequel ISequel IIFigure: Vinyl isolators and two types of Individually Vented Cage systems in the new SPF animal facilityGenome Platform and related activitiesThe Genome Platform was launched in September 2020. It Animal FacilityWe continue to maintain over 50,000 mice in the SPF area
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