Dataset Available

RNA-seq data for mice (Mus musculus) treated with oil/dispersants

Authors: Liu, Yao-Zhong and Gilbert Morris

Published On: Jan 13 2021 22:21 UTC

DOI: https://doi.org/10.7266/J892KQFR

UDI: R6.x821.000:0003

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Project Information

Funded By:
Gulf of Mexico Research Initiative

Funding Cycle:
RFP-VI

Research Group:
Impact of Oil Spill to Human Lung Health: Next Generation Sequencing and Mouse Model Based Analyses

Point of Contact

Yao-Zhong Liu
Tulane University / School of Public Health and Tropical Medicine
yliu8@tulane.edu

Theme keywords

BP oil spill, dispersant, Corexit 9500, Corexit 9527, K-ras mouse, RNA-seq, lung cancer, tumorigenesis, Mus musculus

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Abstract:

In this experiment, K-ras mice (Mus musculus) were treated with oil, Corexit 9500, Corexit 9527, 9500+oil, 9527+oil, and saline (the control group). Each treatment group contained 3/4 mice of each gender. RNA-seq of the lungs of the treated mice was performed. The raw RNA-seq data have been submitted to the NCBI GEO (Gene Expression Omnibus) for public access. The dataset was assigned a GEO access number GSE148895.

Suggested Citation:

Liu, Yao-Zhong and Gilbert Morris. 2021. RNA-seq data for mice (Mus musculus) treated with oil/dispersants. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/J892KQFR

Purpose:

The purpose of the data was to identify genes/pathways of K-ras mice (Mus musculus) lung that are differentially regulated under oil and dispersants.

Data Parameters and Units:

The headers are Sample name, title, source name, organism (Mus musculus), characteristics: strain (K-ras), characteristics: gender (M/F), characteristics: treatment (saline, oil, 9500, 9500+oil, 9527, 9527+oil), molecule, (total RNA), processed data file (counts_ALL.csv), raw file and GEO accession number.

Methods:

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. Specifically, the concentrations of substances in different treatments are listed below. 1. Oil treatment group: concentration of oil is 1:200 2. Corexit 9500/9527 treatment groups: concentration of Corexit is 1:400 3. Oil + 9500/9527 treatment groups: concentration of oil is 1:200; concentration of Corexit is 1:400 The data was generated using next generation sequencing technology. The treated mice's lung was processed for RNA extraction, followed by RNA-seq analysis. Differential expression analysis was performed on the RNA-seq data to identify differentially regulated genes/pathways.