1. Deep Sequencing

The platform has an Illumina Miniseq System and a Nanopore MinION MK1B sequencer, 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:

In Nov. 2021, platform is equipped with a new instrument - Singleron Matrix^® automated single cell processing system. It can be used as an intergrated part for the preparation of single-cell sequencing libraries. The instrument can dispense the single cells in suspension into the proprietary SCOPE^™ microwell chip, and automatically complete the cell separation, cell lysis, and mRNA capture steps within 30 minutes. Our platform provides single-cell suspension preparation, sequencing library construction, and high-throughput sequencing services and technical support. 

Singleron Matrix® Single Cell Processing System

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. websites and databases

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.siais.shanghaitech.edu.cn/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.siais.shanghaitech.edu.cn  

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.

4. Training

The platform provides trainings on R programming, Linux basic programming, specific topic on data analysis, theoretical and experimental applications of high-throughput sequencing.

How to use?

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. 

Biomedical_Big_Data_Platform_High-throughput_Sequencing_Sample_Login_Form.docx

Biomedical_Big_Data_Platform_Data_Analysis_Submission_Form.docx

In order to manage and record the charge of services, we have put our services list online. In addition to the submission form above, you also need to go to ShanghaiTech University Instrument Sharing Platform website to submit your requirements (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