The platform has a MGI G99 Sequencer, an Illumina Miniseq System and a Nanopore MinION MK1B sequencer, 10X Genomics Chromium single cell System and Visium CytAssist Spatial System, as well as a full set of instruments related to library construction and quality control. Our platform can provide high-throughput sequencing services and technical supports, including consultation, sample quality control, library construction and high throughput sequencing services.
Instruments list:
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| MGI G99 Sequencer | 10X Genomics Chromium single cell System | 10X Genomics Visium CytAssist Spatial System |
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Nanopore MinION Sequencer | Illumina Miniseq System | NanoDrop One |
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Agilent Bioanalyzer 2100 | Qubit 4.0 | Lonza FlashGel System |
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| Dolomite μEncapsulator | BioRad 96-deep well PCR | Bioruptor Pico |
2. Bioinformatics
The platform provides general sequence analysis, data mining for open source databases or other kinds of source, functional analysis for omics data of the next and third generation sequencing, omics data analysis, such as Hi-c data analysis, Genome assembly, Genome annotation, RNA-seq data analysis, ATAC-seq data analysis, CRISPR g-RNA screening, proteomics data analysis, single-cell RNA-seq data analysis, BCR/TCR/Antibody library analysis, genome sequencing mutation analysis, DNA Encoding Library (DEL) sequencing data analysis, etc.
We also provides the usage of a commercial software, CLC Genomics Workbench, a bioinformatics integrated analysis tool for Genomics and transcriptome data analysis.
Examples of works:
3.1 crispr-surfaceome
A website constructed to facilitate CRISPR guide RNA design, with special focus on genes encoding proteins expressed on the surface of cells.
URL : https://crispr-surfaceome.gdgyygljj.com/home
Note: currently we only have data on human. You are welcome to request design of gRNAs for other species.
3.2 singlecell-IVD
A website designed for single cell data interactive visualization and analysis (after cell clustering).
Functions of this website include:
1, Interactive data visualization and analysis based on cellxgene vip https://github.com/interactivereport/cellxgene_VIP）.
2, Manage, share of private projects by project owner, for example before a publication.
3, Reuse of published data from yourself or others. Once put online as a public project, researchers all over the world can query and search the database.
URL：https://singlecell.gdgyygljj.com
Note: You can vote for publicly available datasets interest you the most. We can work together to make the data processed and put them online.
The platform provides trainings on R programming, Linux basic programming, specific topic on data analysis, theoretical and experimental applications of high-throughput sequencing.
If you have a requirement of high-throughput sequencing or data analysis, please download the sample or data analysis submission form, fill in the requirements, print and sign it, finally submit it to us. Or you can contact us for consulting, submit the form after communication and comfirmation.
https://eshare.shanghaitech.edu.cn/).
Notes: The instrument sharing platform is availabe to both people on campus and outside the campus. People on campus can login with a unified identity. People outside the campus can submit service requirements through new user registration. You can contact us if there is any problem.
Contact: Lichun Jiang, phD
Email：jianglch@@shanghaitech.edu.cn
Address: Room B101, Ren Building, No.393 Middle Huaxia Road, Shanghai, 201210
Tel: 021-20684479
