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Sample GSM8126673

Query DataSets for GSM8126673

Status

Public on Mar 05, 2024

Title

Male Heart, 0.1 mg/kg/day MOPA, Animal 122

Sample type

SRA

Source name

Heart

Organism

Rattus norvegicus

Characteristics

Sex: Male
tissue: Heart
strain: Sprague Dawley
age: 10-12 weeks post acclimation
treatment: 0.1 mg/kg/day MOPA, 5-day repeat exposure, oral gavage
treatment: dose: 0.1 mg/kg/day
treatment: dose group: 2
treatment: chemical name: Perfluoro-3-methoxypropanoic acid (MOPA)
treatment: route of_exposure: Oral gavage
sample qc_issue: No Issue

Treatment protocol

For oral gavage studies, at least four male and four female rats per dose group receive the vehicle alone or test article in vehicle via gavage (5 or 10 ml/kg) for five days. Animals are weighed daily prior to administration and are observed twice daily, once during administration and once in the late afternoon, at least six hours apart, for assessment of moribundity and mortality. Formal clinical observations are performed on the first day post-dosing and prior to necropsy. Moribund animals or animals exhibiting overt clinical toxicity are removed from the study. The temperature in the experimental animal room is maintained at a target of 22°C (± 3°C) with a relative humidity that is ideally between 50-60% but is at least 30% and preferably not to exceed 70% other than during room cleaning. Lighting is artificial with a sequence of 12 hours light, 12 hours dark. Animals are housed individually or caged in small groups of no more than three animals of the same sex in accordance with local institutional animal care and use requirements.

Growth protocol

Male and female Sprague Dawley (Crl:CD IGS, Charles River Laboratory) rats are purchased at 6 – 8 weeks of age. Upon receipt, the animals are placed on a standard, purified laboratory diet and reverse osmosis treated drinking water ad libitum. The specific brand and type of food and source of the water should be noted in Appendix II (Detailed Animal Study Report) of the individual assessment. After a 7- to 14-day quarantine and acclimation period, the animals are weighed and randomly assigned by weight to chemical exposure and control groups. Only clinically healthy animals are used in the study. The target age for initiating exposure is 8 - 10 weeks.

Extracted molecule

total RNA

Extraction protocol

Treated and control animals are necropsied approximately 24 hours after the last exposure. Carbon dioxide asphyxiation is used as the method of euthanasia, with death confirmed by a secondary method such as exsanguination or cervical dislocation. The following tissues were dissected from each animal: kidney, liver, adrenal gland, brain, heart, lung, ovary (females), spleen, testis (males), thyroid, thymus, and uterus (females). Tissue samples were collected within ten minutes of termination. The left liver lobe, right kidney, left lung, both testis, uterus, heart, spleen, thymus and whole brain were sectioned into 5mm^3 pieces. Samples from these larger tissues were then individually divided into at least 3 cryovials. At least two of the samples from each tissue in each animal were preserved in RNAlater™ (Thermo Fisher Scientific) at 4°C overnight and then frozen at approximately -20°C for up to 3 weeks before transferring to approximately -80°C. At least one sample from each larger tissue is frozen immediately in liquid nitrogen and stored at approximately -80°C. The smaller bilateral tissues: adrenal glands, thyroid gland, and ovaries (female) are placed into two cryovials and preserved in RNALater with the left side of the tissue or gland going into the first cryovial and the right side going into the second cryovial. The first tube of RNALater preserved tissue is submitted for sequencing. For each tissue undergoing transcriptomic analysis, total RNA is extracted from one of the aliquots stored in RNAlater™.
The isolated total RNA is used to perform targeted RNA sequencing (RNA-seq) using the BioSpyder TempO-Seq rat S1500+ assay (v1.2) according to manufacturer’s instructions. No specific RNA purity or integrity criteria are applied to the RNA samples as the TempO-Seq assay has been designed to provide high quality gene expression measurements on whole cell lysates, purified RNA, and formalin-fixed paraffin embedded tissue.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Description

etap_mopa_heart_male_counts.csv
Plate_30_MOPA_heartm_122h

Data processing

Raw sequencing reads (FASTQ files) were aligned to known probe sequences listed in the TempO-Seq probe manifest using HISAT2 to compute a matrix of read counts for each probe in each sample.
Assembly: TempO-seq Rat S1500+ v1.2
Supplementary files format and content: Count table CSV files contain a row for each known probe and a column for each sample. Each cell contains the number of reads from a single cell uniquely aligned to a single probe sequence
Supplementary files format and content: Probe manifest CSV file contains a row for each known probe with the probe name, sequence, and target gene

Submission date

Mar 05, 2024

Last update date

Mar 05, 2024

Contact name

Logan J Everett

Organization name

U.S. Environmental Protection Agency

Department

Office of Research and Development

Lab

Center for Computational Toxicology and Exposure