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| Status |
Public on Jan 11, 2018 |
| Title |
GRC303_15 |
| Sample type |
SRA |
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| Source name |
serum
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Wistar Kyoto rats
diet: normal
exposure: air
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| Treatment protocol |
Male Wistar Kyoto (WKY) rats were purchased from Charles Rivers Laboratories (Raleigh, NC) and brought to our AAALAC-approved animal facility at 4 wks old. Animals were housed two/cage in polycarbonate cages with beta chip bedding and kept on a 12h light/dark cycle. All experimental protocols were approved by the U.S. EPA's Institutional Animal Care and Use Committee (IACUC). Animals were fed either our normal facility food (Rodent Chow 5001, Ralston Purina Laboratories, St. Louis, MO) or a diet enriched with 6% by weight fish oil (Teklad Custom Research Diets #TD.140729, Harlan Laboratories, Inc.). Animals were given water and food ad libitum starting at 4 weeks old for 8 weeks until exposure. Animals were exposed to either filtered air or 0.8 ppm ozone for 4h/day for 2 consecutive days. The average (mean ± SEM) air temperature (75.01 ± 0.21), relative humidity (49.84 ± 0.30), and ozone concentration (0.8045 ± 0.0027 ppm) were monitored continuously.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Serum and EDTA plasma samples were collected from the abdominal aorta. 100 µl of serum thawed on ice were centrifuged at 3000 X g for 5 min. Small RNA was isolated using miRCURY RNA Isolation Biofluids Kit following manufacturer's instructions, including an optional on-column DNase digestion (Exiqon, Woburn, MA).
Indexed small RNA sequencing libraries were prepared using CleanTag Small RNA Library Prep Kit (TriLink BioTechnologies, San Diego, CA) with 10 ng of purified input RNA following manufacturer's instructions. Libraries were quantified using Bioanalyzer High-Sensitivity DNA chip, pooled, and were sequenced using a NextSeq 500 sequencer on High Output mode (Illumina, San Diego, CA) using 50 cycles of single-end reads.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
small RNA
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| Data processing |
Basecalling was performed using RTA v2
Fastq files generated using bcl2fastq with the following options: --ignore-missing-bcls --ignore-missing-filter --ignore-missing-positions --ignore-missing-controls --auto-set-to-zero-barcode-mismatches --find-adapters-with-sliding-window --adapter-stringency 0.9 --mask-short-adapter-reads 35 --minimum-trimmed-read-length 35 -R "/data/scratch/workspace/RunFolder" --sample-sheet "/data/scratch/workspace/RunFolder/SampleSheet.csv" -o "/data/scratch/workspace/RunFolder/Analysis/Fastq" -i "/data/scratch/workspace/RunFolder/Data/Intensities/BaseCalls"
Illumina adapters were trimmed using the Illumina Basespace app FASTQ Toolkit version 2.0.0. keeping sequences 16 bp and greater. Reads were further trimmed on quality score in Partek Flow (Build version 6.0.17.0723) with default settings except Min read length was set to 15
Trimmed reads were aligned to the rat genome (rn5) in Partek Flow using Bowtie v 1.0.0 with default setting except Seed mismatch limit was set 1 and Seed length was set to 10.
Aligned reads were quantified to miRBase mature microRNAs (version 21) in Parek Flow using Partek E/M with default settings
Raw microRNA counts were normalized in Partek Flow using the trimmed mean of M-values (TMM) method, then adding 1.0E-4 to all counts
Genome_build: rn5
Supplementary_files_format_and_content: All_Samples_microRNA_Normalized_counts.txt is a tab-delimited text file containing normalized counts for all processed samples
Supplementary_files_format_and_content: All_Samples_Raw_microRNA_counts.txt is a tab-delimited text file containing raw microRNA counts for all samples
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| Submission date |
Jul 28, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Brian Norris Chorley |
| E-mail(s) |
[email protected]
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| Organization name |
US Environmental Protection Agency
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| Department |
ORD
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| Lab |
NHEERL
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| Street address |
109 TW Alexander Dr
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| City |
Research Triangle Park |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
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| Platform ID |
GPL20084 |
| Series (1) |
| GSE102015 |
Ozone-Induced Vascular Contractility and Pulmonary Injury are Differentially Impacted by Diets Enriched with Coconut Oil, Fish Oil, and Olive Oil |
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| Relations |
| BioSample |
SAMN07423515 |
| SRA |
SRX3046044 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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