SMU Data Science Review

The Transcript Profile Changes With Developmental Maturation of Fetal Lung Type 2 Cells: An Analysis of RNAseq Data

Heber C. Nielsen, Southern Methodist UniversityFollow
Volodymyr Orlov, Southern Methodist UniversityFollow
Rebecca Holsapple, Southern Methodist UniversityFollow
Monnie McGee, Southern Methodist UniversityFollow

Abstract

In this paper, we utilize next-generation sequencing (NGS) data from the LungMap project to identify and characterize the developmental RNA transcriptome in alveolar epithelial type II cells of embryonic mouse lungs of gestational ages embryonic days 16 (E16) and 18 (E18). Late gestation lung cellular maturation is necessary for survival at birth. Using R and the BioConductor packages for RNAseq analysis, we analyze changes in the mouse lung RNA transcriptome as this maturation process takes place. We particularly identify the cluster of genes whose expression changes markedly between immature (E16) and mature (E18) lungs which can be used to define cell pathways that appear critical for the maturation process. Our results show that there are 98 differentially expressed genes with 82 genes where differences in counts cannot be attributed to difference in sample origin. We were surprised to identify substantial differences in RNA expression between 2 experienced lab groups using identical protocols. We have leveraged data analytical capabilities to create new insight into the development of the lung in preparation for survival afterbirth.

Recommended Citation

Nielsen, Heber C.; Orlov, Volodymyr; Holsapple, Rebecca; and McGee, Monnie (2020) "The Transcript Profile Changes With Developmental Maturation of Fetal Lung Type 2 Cells: An Analysis of RNAseq Data," SMU Data Science Review: Vol. 3: No. 2, Article 7.
Available at: https://scholar.smu.edu/datasciencereview/vol3/iss2/7