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SRX22521238: GSM7899062: Muscle, acrolein (M15R1_S10); Rattus norvegicus; RNA-Seq
1 ILLUMINA (NextSeq 500) run: 25.3M spots, 1.9G bases, 766.7Mb downloads

External Id: GSM7899062_r1
Submitted by: Kodavanti, CPHEA/PHITD/CIB, U.S. EPA
Study: Acrolein-induced transcriptomic alterations in male Wistar-Kyoto rats
show Abstracthide Abstract
Acute acrolein inhalation in male rats resulted in multi-tissue transcriptomic alterations that were observed through Illumina mRNA sequencing. Specifically, site-specific respiratory expression profile differences were noted between air- and acrolein-exposed groups. Nasal epithelial tissue demonstrated 452 differentially expressed genes (DEGs) (310 up-regulated and 142 down-regulated)and lung tissue demonstrated 95 DEGs (80 up-regulated and 15 down-regulated). Notable transcriptomic alterations were also observed in liver tissue of acrolein-exposed rats, with 1699 identified DEGs (788 up-regulated and 911 down-regulated). A variety of mRNA expression profile differences resulting from acute acrolein inhalation was observed in other peripheral tissues, including adipose, muscle, adrenals, hippocamus, and hypothalamus. Gene changes were largely representative of oxidative and inflammatory response in the nose, as well as xenobiotic metabolism changes in the lung. Liver changes, which were most numerous, included alterated metabolic signaling (Sirtuin and FXR signaling), as well as alterated oxidoreductive, GPCR, and glucocorticoid pathways. Together, these data demonstrate acrolein, a well-characterized respiratory irritant, induces systemic neuroendocrine immunological and metabolic stress. Overall design: Adult male Wistar-Kyoto rats were exposed to air (0ppm) or acrolein nose-only for 4hr total exposure duration. For the first 30 minutes of exposure, increasing half-log exposure concentrations were used at 0, 0.1, 0.316, and 1 ppm, such that each concentration was employed for 7.5 minutes, with this 30 minute window being followed by 3.5 hours at the highest concentration of acrolein of 3.16 ppm. Exposures were conducted ~0700-1100 AM and performed under general room temperature and humidity. Immediately after exposure, rats were necropsied, tissues collected and flash frozen in liquid nitrogen, and frozen for later analysis. Later, RNA was extracted and sequenced.
Sample: Muscle, acrolein (M15R1_S10)
SAMN38249629 • SRS19532685 • All experiments • All runs
Library:
Name: GSM7899062
Instrument: NextSeq 500
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: SINGLE
Construction protocol: Uniform portions of frozen tissue were sectioned and processed with RNeasy non-fibrous, fibrous, or lipid tissue mini kits (Qiagen, Valencia, CA) following manufacturer directions (kit dependent upon tissue type). RNA quantity and purity (260/230 and 260/280 ratios) were spectrophotometrically quantified using a Nanodrop 1000 (ThermoFisher Scientific Inc., Waltham, MA). RNA integrity was assessed by the RNA 6000 LabChip® kit and a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) using a RIN cutoff of 7. Samples processing for mRNA sequencing was performed on the Apollo324 automated system (Takara Bio Inc., Kusatsu, Japan) for library prep with PrepX mRNA 48 protocol v19, using the PrepXTM RNA-seq for Illumina Library Kit (Takara), SuperScript III reverse transcriptase (ThermoFisher), and AMPure XP Beads (Agilent). PCR amplification with 48 index primers was run for 16 cycles and resulting PCR product quality was analyzed again via Qubit (ThermoFisher) and bioanalyzer. An RNA-seq library was prepared with Wafergen's PrepX mRNA 48 protocol and dsDNA products were prepared from cDNA. Each library was sequenced according to Illumina NextSeq 500, with a final concentration of 2.2 pM + 2% PhiX and run for 75 cycles (Illumina Inc., San Diego, CA).
Runs: 1 run, 25.3M spots, 1.9G bases, 766.7Mb
Run# of Spots# of BasesSizePublished
SRR2682447625,268,6151.9G766.7Mb2023-11-16

ID:
30512391

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