Abstract:

This proposal addressed the theme of “impact of oil spills on public health”. Specifically, the proposal addressed the general hypothesis, which is: upon oil/dispersant respiratory exposure there will be a higher carcinogenic potential of lung tissue. To test this hypothesis, we profiled and confirmed the existence of molecular signatures of carcinogenesis through RNA-seq analysis of a mouse model treated with instilled oil/dispersants. We exposed the wild-type C57BL/6 (B6) mice to BP crude oil, dispersant 9500, dispersant 9527, oil + 9527, oil + 9500 and H2O (as control) using intratracheal instillation method for 2 weeks. We then performed RNA-seq analysis of the lung tissue from the mice to identify differentially expressed (DEx) genes (DEGs) in the treated mice vs. the control mice. These DEGs were functionally annotated to search for GO terms and pathways related to carcinogenesis. For each treatment group, 3 male and 3 female mice were used. Therefore, we generated RNA-seq data for a total of 36 animals (6 animals/group x 6 treatment group). We have submitted the RNA-seq data to NCBI's GEO (Gene Expression Omnibus) online database (https://www.ncbi.nlm.nih.gov/geo/). The dataset is now assigned a GEO series number GSE137204. In the GEO website, RNA-seq data are organized under three types: the metadata, the processed data and the raw data files. The metadata describes the treatment group and other information related to a sample. The processed data files contain raw counts of sequencing reads for transcripts. The raw data files are the raw fastq data files generated in the RNA-seq experiments. This dataset supports the publication: Liu, Yao-Zhong; Charles A. Miller; Yan Zhuang; Sudurika S. Mukhopadhyay; Shigeki Saito; Edward B. Overton; and Gilbert F. Morris. 2020. The Impact of the Deepwater Horizon Oil Spill upon Lung Health—Mouse Model-Based RNA-Seq Analyses. International Journal of Environmental Research and Public Health, 17(15), 5466. doi:10.3390/ijerph17155466

Suggested Citation:

Liu, Yao-Zhong. 2020. RNA sequencing of house mice (Mus musculus) exposed to BP crude oil, dispersant 9500, and dispersant 9527. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-6r9v-ek39

Publications:

Liu, Y.-Z., Miller, C. A., Zhuang, Y., Mukhopadhyay, S. S., Saito, S., Overton, E. B., & Morris, G. F. (2020). The Impact of the Deepwater Horizon Oil Spill upon Lung Health—Mouse Model-Based RNA-Seq Analyses. International Journal of Environmental Research and Public Health, 17(15), 5466. doi:10.3390/ijerph17155466

Purpose:

This dataset addresses the general hypothesis, which is: upon oil/dispersant respiratory exposure there will be a higher carcinogenic potential of lung tissue.

Data Parameters and Units:

The sequencing data is the count data that contain number of counts for each gene/transcript. The count data do not have units. Dataset consists of 1 Excel file with the following headers- Sample name; title; source name; organism; characteristics: strain; characteristics: gender; characteristics: treatment; molecule; description; processed data file; raw file; and GEO accession number.

Methods:

Revised: To prepare WAFs (water-accommodated fractions) for BP crude oil and dispersants, the following procedure was performed. First, the mixture of crude oil/dispersants with saline was made using the following volume ratios: 1) a 1:20 ratio (crude oil: saline) for the WAF of crude oil only, 2) a 1:40 ratio (Corexit dispersant: saline) for the WAF of Corexit dispersants only, and 3) a 2:1:40 ratio (crude oil: Corexit dispersant: saline) for WAF-dispersed oil (oil-dispersant mixture). In the treatment experiments, we further diluted WAF using saline by a 1:10 ratio for mouse treatment. Please see NCBI GEO website for detailed descriptions (https://www.ncbi.nlm.nih.gov/geo/), search GEO accession number GSM4072941 for dataset.

Individual Files: