 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 05, 2024 |
| Title |
Rat 5 |
| Sample type |
SRA |
| |
|
| Source name |
Lung
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Lung
genotype: Male
treatment: Air
|
| Treatment protocol |
To mimic the deployment of common fire line shifts (modified Kelly schedule), rats were exposed to whole-body eucalyptus smoke over the course of two weeks. Exposure occurred for 4 consecutive days on week 1, followed by a 3-day break, and 3 subsequent days of smoke exposure on week 2. Rats (n=24) were randomized by weight into three groups based on body weight (n = 8/group): filtered air, low smoke, and high smoke concentrations. The smoke exposures were set to a target CO concentration of 10 ppm for the low smoke group and 20 ppm for the high smoke group.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen lung tissue (~35 mg) was homogenized in TRIzol reagent (ThermoFisher Scientific, Waltham, MA). Total RNA was isolated using the Direct-Zol RNA Miniprep Kit (Zymo Research, Irvine, CA) and quantified by a Qubit fluorometer (ThermoFisher Scientific). RNA quality was verified using a Bioanalyzer (Agilent Technologies, Santa Clara, CA). All RNA samples (n =7 – 8 /group) used for sequencing had an RIN ≥ 9.0.
RNA samples (1 µg) were processed on an Apollo324 system (Takara Bio USA, Inc. Mountain View, CA). Notably, one sample from the filtered-air exposed group was removed from further processing due to poor quality. Sequencing libraries were prepared using the PrepX RNA-seq Library Kit for Illumina following the manufacturer’s protocol. Resulting cDNA libraries were amplified by polymerase chain reaction (PCR) with index primers and subsequently assessed using a Qubit and Bioanalyzer. Pooled libraries were diluted to a final concentration of 1.8 pM + 2% PhiX and then sequenced on the NextSeq 500 platform (Illumina Inc., San Diego, CA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RPI12_S5
|
| Data processing |
RNA sequencing data were demultiplexed and trimmed using Partek Flow NGS analysis software (version 10.0.21.0312, St. Louis, MO).
Generated reads were aligned to the rat genome (rn6) using STAR 2.7.3a and raw read counts were normalized by median ratio with DESeq2.
A Storey Q-value cutoff ≤ 0.05 was implemented to identify differentially expressed genes (DEGs).
Assembly: rn6
Supplementary files format and content: tab-delimited text file contains normalized values for each sample
|
| |
|
| Submission date |
Jul 13, 2023 |
| Last update date |
Jun 05, 2024 |
| Contact name |
Colette Miller |
| E-mail(s) |
Miller.Colette@epa.gov
|
| Organization name |
U.S. Environmental Protection Agency
|
| Street address |
109 TW Alexander
|
| City |
Research Triangle Park |
| State/province |
NC |
| ZIP/Postal code |
27711 |
| Country |
USA |
| |
|
| Platform ID |
GPL20084 |
| Series (1) |
| GSE237251 |
Repeated Exposure to Wood Smoke Alters Pulmonary Gene and Metabolic Profiles |
|
| Relations |
| BioSample |
SAMN36430148 |
| SRA |
SRX21004431 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
