Mining Spatial Transcriptomics Datasets using DeepSpaceDB

0 просмотров

10:16 мин.

5 сентября 2025 г.

0 просмотров

Nupura Prabhune¹^,² , Yilin Du¹^,³ , Afeefa Zainab⁴ , Satoru Ebihara³ , Shinji Takeoka² , Shinpei Kawaoka¹^,⁵ , Alexis Vandenbon⁴^,⁶

¹Department of Integrative Bioanalytics, Institute of Development, Aging and Cancer, Tohoku University, ²Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, ³Department of Rehabilitation Medicine, Tohoku University Graduate School of Medicine, ⁴Institute for Life and Medical Sciences, Kyoto University, ⁵Inter-Organ Communication Research Team, Institute for Life and Medical Sciences, Kyoto University, ⁶Institute for Liberal Arts and Sciences, Kyoto University

This article introduces a protocol for using DeepSpaceDB, a dynamic, interactive database for spatial transcriptomics, offering analysis workflows and examples to explore tissue organization and disease-related gene expression.

Больше видео

Gene Expression Patterns

DeepSpaceDB Database

Tissue Slice Analysis

Spatially Variable Genes

Differential Gene Expression

Tumor Microenvironment

Mouse Brain Sample

Colorectal Cancer Metastasis

Bioinformatics Tools

Chapters in this video

0:00

Introduction

1:36

Analysis of a Mouse Brain Sample

5:26

Identification of Differentially Expressed Genes in Metastatic Regions of Colorectal Origin in Mouse Livers

8:25

Results