Reconstruction of the tumor spatial microenvironment along the malignant-boundary-nonmalignant axis

Published: 25 January 2023| Version 1 | DOI: 10.17632/m5s3zjrs6j.1
Contributor:
Zhenzhen Xun

Description

To evaluating Cottrazm's performance on deconvolution and reconstruction of spatial spots, simulated data was generated from CRC scRNA-seq data based on the spatial location that dissected before and cell-type distribution patterns in tumor microenvironment. In the simulated ST dataset, each spot consists of mixture of 6-10 cells randomly picked from scRNA-seq data. The simulated data was divided into malignant region with 1000 spots, tumor boundary region with 500 spots, non-malignant region with 1,000 spots, and tertiary lymphoid structure regions with 250 spots. The cell composition of spots in each region based on random selection of the results obtained from deconvolution result.

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Institutions

Shanghai Jiao Tong University

Categories

Transcriptomics

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