CrossMP: Enabling Cross-Modality Translation between Single-Cell RNA-Seq and Single-Cell ATAC-Seq through Web-Based Portal

Lyu, Zhen; Dahal, Sabin; Zeng, Shuai; Wang, Juexin; Xu, Dong; Joshi, Trupti

doi:10.3390/genes15070882

CrossMP: Enabling Cross-Modality Translation between Single-Cell RNA-Seq and Single-Cell ATAC-Seq through Web-Based Portal

Journal Article · Fri Jul 05 00:00:00 EDT 2024 · Genes

DOI:https://doi.org/10.3390/genes15070882· OSTI ID:2471811

Lyu, Zhen ^[1]; Dahal, Sabin ^[2]; Zeng, Shuai ^[2]; ^[3]; ^[2]; ^[2]

University of Missouri, Columbia, MO (United States); OSTI
University of Missouri, Columbia, MO (United States)
Indiana University, Indianapolis, IN (United States)

In recent years, there has been a growing interest in profiling multiomic modalities within individual cells simultaneously. One such example is integrating combined single-cell RNA sequencing (scRNA-seq) data and single-cell transposase-accessible chromatin sequencing (scATAC-seq) data. Integrated analysis of diverse modalities has helped researchers make more accurate predictions and gain a more comprehensive understanding than with single-modality analysis. However, generating such multimodal data is technically challenging and expensive, leading to limited availability of single-cell co-assay data. Here, we propose a model for cross-modal prediction between the transcriptome and chromatin profiles in single cells. Our model is based on a deep neural network architecture that learns the latent representations from the source modality and then predicts the target modality. It demonstrates reliable performance in accurately translating between these modalities across multiple paired human scATAC-seq and scRNA-seq datasets. Additionally, we developed CrossMP, a web-based portal allowing researchers to upload their single-cell modality data through an interactive web interface and predict the other type of modality data, using high-performance computing resources plugged at the backend.

View Accepted Manuscript (DOE)

Research Organization:: University of Nebraska, Lincoln, NE (United States)

Sponsoring Organization:: Missouri Department of Health and Senior Services (MDHSS); National Institutes of Health (NIH); National Science Foundation (NSF); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: SC0023142

OSTI ID:: 2471811

Journal Information:: Genes, Journal Name: Genes Journal Issue: 7 Vol. 15; ISSN 2073-4425

Publisher:: MDPICopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
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CrossMP: Enabling Cross-Modality Translation between Single-Cell RNA-Seq and Single-Cell ATAC-Seq through Web-Based Portal

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