Integrating spatial transcriptomic and single cell RNA-sequencing data

This is the repository of codes covering the second master internship of Qirong Mao, the aim is to integrate the spatial transcriptomic data and the single cell RNA-sequencing data.

Down stream analysis and generating figures: Code.R

Data source

ScRNA-seq data:

https://portal.brain-map.org/atlases-and-data/rnaseq

Allen Brain Map "MULTIPLE CORTICAL AREAS - SMART-SEQ (2019)"

47,432 cells with 50,821 transcripts profile.

Spatial transcriptomic data:

https://support.10xgenomics.com/spatial-gene-expression/datasets/1.1.0/V1_Human_Brain_Section_2

10X Genomics Visium Spatial Gene Expression Dataset- "V1 Human Brain Section 2"

4,972 spts with 36,601 transcripts profile.

Software

Novosparc

Code: https://github.com/rajewsky-lab/novosparc

Article: Nitzan, M., Karaiskos, N., Friedman, N. et al. Gene expression cartography. Nature 576, 132–137 (2019). https://doi.org/10.1038/s41586-019-1773-3

Cell2location

Code: https://cell2location.readthedocs.io/en/latest/

Article: https://www.biorxiv.org/content/10.1101/2020.11.15.378125v1

CellPhoneDB

Code: https://github.com/Teichlab/cellphonedb

Article: Efremova, M., Vento-Tormo, M., Teichmann, S.A. et al. CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes. Nat Protoc 15, 1484–1506 (2020). https://doi.org/10.1038/s41596-020-0292-x