Center for High Throughput Sequencing, Core Facility for Protein Research

Institute of Biophysics

Chinese Academy of Sciences

15 Datun Road, Chaoyang District

Beijing 100101, China

---

Chen Xiaowei: chenxiaowei(at)ibp.ac.cn

Fan Zhen: fanzhen(at)ibp.ac.cn

1. SpatialDB: a database for spatially resolved transcriptomes. (https://www.spatialomics.org/SpatialDB/)

Spatially resolved transcriptomics providing gene expression profiles with positional information is key to tissue function and fundamental to disease pathology. SpatialDB is the first public database that specifically curates spatially resolved transcriptomic data from published papers, aiming to provide a comprehensive and accurate resource of spatial gene expression profiles in tissues. Currently, SpatialDB contains detailed information of 24 datasets generated by 8 spatially resolved transcriptomic techniques. SpatialDB allows users to browse the spatial gene expression profile of all the 8 techniques online and compare the spatial gene expression profile of any two datasets generated by the same or different techniques side by side. It provides spatially variable (SV) genes identified by SpatialDE and trendsceek, as well as functional enrichment annotation of SV genes.

Citation:

1. Fan Zhen, Chen Runsheng, Chen Xiaowei. SpatialDB: a database for spatially resolved transcriptomes. Nucleic Acids Research. 2019. doi: 10.1093/nar/gkz934.

---

2. LncVar: a database of genetic variation associated with long non-coding genes. (http://159.226.118.31/LncVar/)

Long noncoding RNAs (lncRNAs) have been identified in various species, and play essential roles in many molecular processes. Genetic variations, including single nucleotide polymorphisms (SNPs) and structural variations, are widely distributed in the genome. Variations in the long noncoding gene loci may affect lncRNA transcripts from sequences, structures, expression levels to biological functions.Therefore we constructed LncVar, a database of long noncoding genes associated genetic variations in 6 species (human, mouse, zebrafish, worm, fruitfly, Arabidopsis).

Citation:

1. Chen X., et al. LncVar: a database of genetic variation associated with long non-coding genes. Bioinformatics. 2017 Jan 1;33(1):112-118. doi: 10.1093/bioinformatics/btw581. Epub 2016 Sep 6. PubMed PMID: 27605101.

2. Chen X., et al. LncVar: Deciphering Genetic Variations Associated with Long Noncoding Genes. Methods Mol Biol. 2019;1870:189-198. doi:10.1007/978-1-4939-8808-2_14. PubMed PMID: 30539556.

---

3. 发明专利名称：一种预测影响长非编码RNA生物学功能的SNP位点的方法，发明人：陈小伟；范珍；陈润生，专利号：ZL 2018 1 0122529.9，专利保护期：2018年12月7日至2038年12月7日

---

4. 发明专利名称：基于染色体空间相互作用预测长非编码RNA生物学功能的方法，发明人：范珍；陈小伟；陈润生，专利号：ZL 2018 1 0082985.5，2018年12月14日至2038年12月14日