RIKEN IMS AnnualReport 2020
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62Table1: Central services provided by the Genome Platform in 2020Library Preparationwhole genome sequencetarget sequencebulk RNA-seqSMART-SeqRamDA-seqssCAGETable2: Next-generation DNA sequencingIllumina SequencerNovaSeq6000HiSeq2500MiSeqPacBio SequelSequel ISequel IIMGI DNBSEQMGISEQ2000Figure: Two types of Individually Vented Cage systems in new SPF animal facilityation sequencing services to IMS researchers evolved to be-come the Genome Platform in September 2020. It supports each laboratory in the center in library preparation, sequencing and data analysis related to sequencing and plays a central role when large projects are adopted. For library preparation, we support whole-genome sequencing, targeted sequencing, CAGE, single-cell RNA-seq, and bulk RNA-seq. For sequencing, we support No-vaSeq6000, HiSeq2500, MiSeq, and PacBio Sequel runs. We plan to introduce DNBSEQ-T7, DNBSEQ-G400 and NextSeq2000 after April 2021. Data analysis is available for single-cell RNA-seq, bulk RNA-seq, Chip-Seq, and ATAC-seq.This year, we are working on 43 projects. The achievements in library preparation and sequencing are shown in Table 1. In a large project, we are conducting whole-genome sequencing analy-sis of 4,000 individuals for a dementia cohort study with the col-laboration of Kyushu University. In addition, we analyzed somatic mutations in acute myeloid leukemia (AML) patients using the target sequence method in collaboration with the Laboratory for Human Disease Models. Based on these results, we were able to clarify the pathogenesis of AML resistance to treatment and gain knowledge that will lead to personalized medicine (Nat Cancer).This platform enables users in IMS to obtain DNA libraries, sequence data and analysis data quickly and at a reasonable cost, pathogen-free (SPF) area and 1,500 mice in an isolated area. The SPF area also contains 550 germ-free or gnotobiotic mice in vinyl isolator rooms 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 “hu-manized mice”. Last year, a new SPF animal facility was completed and we have begun its management. The new facility has 32 vinyl isolators and 2 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 cryo-stocks of genetic resources (frozen embryos and sperm) for 748 lines. We also maintain relatively large colonies of several com-monly used strains, such as Rag1 KO and Cre deleters, and pro-vide them to users on demand. We have also provided technical assistance to generate knockout and transgenic mice (124 lines). In addition, we have created 18 lines of germ-free mice. We main-tain flexibility so that we can provide space in the animal facility for new experiments, e.g., behavioral testing for 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 thus empowering their research. We expect that the intramural interactions fostered by the Genome Platform among the Divi-sions of Human Immunology, Disease Systems Biology, Cancer Immunology, and Genome Medicine will greatly enhance IMS research activities.large genomic fragments containing human genes encoding the 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.# of Samples4,00020,896322,8802,40076# of Runs10770118# of Runs80232# of Runs110Genome Platform and related activitiesThe Sequence Platform that originally provided next-gener-Animal FacilityWe continue to maintain over 50,000 mice in the specific-

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