SUPR
Decoding spatial transcripton in gastric cancer
Dnr:

NAISS 2024/23-631

Type:

NAISS Small Storage

Principal Investigator:

Xingqi Chen

Affiliation:

Uppsala universitet

Start Date:

2024-10-30

End Date:

2025-10-01

Primary Classification:

30107: Medical Genetics

Webpage:

Allocation

Abstract

This application is intend to Takeover storage from our current project on Alvis (NAISS 2024/22-1126). Here comes detail description. We have single cell RNA-seq data and spatial transcripton data from 10x spatial transcriptomics technique to decoding the tumor cells heterogeniety. We are going to use Cell2location to deciphering the cell type population in each spatial location in each sample. We have sequenced 30 tumor samples using the 10x spatial transcriptomics technique to explore tumor cell heterogeneity. To analyze these samples, we used Cell2location, a tool designed to identify cell type populations in each spatial location within each sample. Since Cell2location relies on machine learning algorithms implemented in PyTorch, it requires GPU resources for efficient processing. The Cell2location software involves the following key steps: Simulating the abundance of cell types across spatial locations. Simulating the expected multi-cell mRNA expression of genes across locations. Simulating multi-cell mRNA integer counts, accounting for differences in technology effects. Our request for the computational resource was already approved, and we need to get the storage for the project as well. We would like to get 5000GiB for our data storage and connect to the computational recourse on Alvis.