Bio-Med Big Data Center (BMDC) assisted the research that established Long-Term Expansion of Pancreatic Islet Organoids from Resident Procr+ Progenitors2020-03-20
A novel endocrine progenitor in adult mouse pancreas and an in-vitro method for the induction and long-term expansion of islet-like organoids were establishes for the first time by the research group led by Prof. Yi Arial Zeng, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, CAS. The study was published by CELL on the 19th of March, 2020 (Long-Term Expansion of Pancreatic Islet Organoids from Resident Procr+ Progenitors, https://doi.org/10.1016/j.cell.2020.02.048 ). Omics Core of BMDC assisted the research with the construction of single-cell RNA library, and the analysis of single-cell RNA sequencing data. In the meantime, the relevant data were deposited and published at the NODE database.More
On February 10, an automatic analysis cloud platform for virus genome identification (VIC), jointly developed by Institut Pasteur of Shanghai , CAS and Bio-Med Big Data Center, SINH, CAS using Huawei cloud computing technology, was released. Its service can be accessed at https://biosino.org/vic/.More
The platform takes Illumina-based RNAseq data as inputs, has following key functions (refer to the left figure):
1) Automatic data quality control;
2) Genome mapping and assembly;
3) Virus composition and abundance analysis for various viruses, including novel coronavirus COVID-19.
Enhancements added to v3 NODE submission portal include:More
1: Batch upload: "step by step-multiple" creates batch-upload for samples, experiments and archive records;
2: Multi-omics submission: users can now upload raw data of multiple omics data types into one project;
3: Append new data to an existing project: users can use "step by step-multiple" to append new samples and experiments to an existing projects.
Bio-Med Big Data Center (BMDC) assists the research that reveals crucial function of circular-RNA in innate immune process2019-04-26
A latest research on circular-RNA and its role in innate immune regulation, by Prof. Li Yang’s laboratory of CAS-MPG Partner Institute for Computational Biology, was published in a prestigious scientific journal “Cell” (Structure and degradation of circular RNAs regulate PKR activation in innate immunity, DOI: 10.1016/j.cell.2019.03.046). Study’s nucleic sequence data were produced by Multi-Omics Core Facility of BMDC, and managed by NODE database, a new generation of data hub for multi-omics big data.More
Prof. Yixue Li, the director of BMDC, co-authored a research article with Prof. Hui Yang of Key Laboratory of Primate Neurobiology, CAS and Lars M. Steinmetz of Stanford University on a novel off-target analysis technique “genome-wide off-target analysis by two-cell embryo injection” (GOTI), published on Feb. 28th 2019 in Science (Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos, DOI: 10.1126/science.aav9973). By using this technique, they observed the occurrence of a large number of unpredictable off-target single-nucleotide editing events, suggesting the serious safety risk of base-editing technique.More
NODE database has been accepted by FAIRsharing as a recommended international biological data source2018-09-07
The National Omics Data Encyclopedia ( NODE ), developed and maintained by Bio-Med Big Data Center at CAS-MPG Partner Institute for Computational Biology, was publicly released in September 2018. Its registry at FAIRsharing was recently upgraded its status to “R” (https://fairsharing.org/FAIRsharing.EivZJw), an indicator of the maturity of a database by the standard of FAIRshing principles: findable, accessible, interoperable and reproducible. FAIRsharing is an international curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies ( https://fairsharing.org ).More
Bio-Med Big Data Center (BMDC) assisted the discovery of the mechanism of Haematopoietic stem and progenitor cells (HSPCs) homing2018-11-21
A complete and dynamic process of HSPC homing was revealed for the first time by the research group led by Prof. Weijun Pan, Shanghai Institute of Nutrition and Health, CAS. This study was published byMore
on the 20th of November, 2018 (VCAM-1+ macrophages guide the homing of HSPCs to a vascular niche, DOI: 10.1038/s41586-018-0709-7) . Uli Schwarz Quantitative Biology Core Facility of BMDC assisted with the long-time, muliti-sample, in vivo imaging technique, ensured the work completed successfully. In the meantime, the interactive 3D- reconstruction models and the videos of the in-vivo imaging were delivered and published at the NODE database.
A collaboration between research teams of Li Yang at CAS-MPG Partner Institute for Computational Biology and Jia Chen, Xingxu Huang at Shanghai Sci.-Tech. University has developed a series of CRISPR/Cpf1 (Cas12a)-based base-editors (dCpf1-BE) (published in Nature Biotechnology, Base editing with a Cpf1-cytidine deaminase fusion, DOI: 10.1038/nbt.4102 ). Sample data used in the study are available at NODE database.More
Transcriptomic data from somatic-cloned macaque monkey was successfully deposited and made public at NODE2018-01-31
Twenty GBs of transcriptomic sequencing data from somatic-cloned macaque money samples were simultaneously released at NODE (http://www.biosino.org/node/cloneMonkey) and NCBI. The somatic-cloning research was conducted jointly by Muming Pu, Qiang Sun and team at Institute of Neuroscience, CAS. The work was published in Cell (Cloning of macaque monkeys by somatic Cell nuclear transfer, DOI： 10.1016/j.cell.2018.01.020 ).More
The birth of world first somatic-cloned monkey - a new era for non-human primate experimental animal2018-01-30
Zhongzhong and Huahua, the first somatic-cloned monkeys, were given birth at the Institute of Neuroscience, CAS, as reported online as a cover article by Cell on January 25th, 2018 (Cloning of macaque monkeys by somatic Cell nuclear transfer, DOI： 10.1016/j.cell.2018.01.020 ). This 5 year-long milestone work in the area of non-human primate experimental animal, authored by Qiang Sun and his/her team, has paved a new path for mechanism research, clinical intervention, diagnostic and treatment applications for human brain diseases.More