Work

Faculty Opinions recommendation of Approaches for integrating heterogeneous RNA-seq data reveal cross-talk between microbes and genes in asthmatic patients.

Year: 2020

Type: peer-review

Abstract: Sputum induction is a non-invasive method to evaluate the airway environment, particularly for asthma.RNA sequencing (RNA-seq) of sputum samples can be challenging to interpret due to the complex and heterogeneous mixtures of human cells and exogenous (microbial) material.In this study, we develop a pipeline that integrates dimensionality reduction and statistical modeling to grapple with the heterogeneity.LDA(Latent Dirichlet allocation)-link connects microbes to genes using reduced-dimensionality LDA topics.We validate our method with single-cell RNA-seq and microscopy and then apply it to the sputum of asthmatic patients to find known and novel relationships between microbes and genes.

Source: Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature

DOI: 10.3410/f.738181255.793576982

Author: Alejandro Schaffer

Institutions: National Institutes of Health, National Cancer Institute

Language: English

Topic: Single-cell and spatial transcriptomics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

SDG: Good health and well-being

Open Access status: green

Funders: Yale University, National Heart, Lung, and Blood Institute, U.S. National Library of Medicine