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Status |
Public on Dec 31, 2022 |
Title |
DE_07_076_DE_L |
Sample type |
SRA |
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Source name |
lung
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Organism |
Rattus norvegicus |
Characteristics |
strain: Sprague-Dawley Sex: Male age: Adult tissue: Lung treatment chemical: Diesel exhaust dose of diesel exhaust: 200 ug/m3 treatment duration: 6hr/day for 4 days post-exposure timepoint: 7 days
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Treatment protocol |
The rats were exposed by whole-body inhalation to filtered air or an aerosol containing DEP at concentrations of 200 or 1000 ug/m3, 6 hours/day for 4 days. The control and DEP-exposed rats were euthanized at post-exposure time intervals of 1, 7, or 27 days.
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Growth protocol |
Male Sprague-Dawley rats (Hilltop Lab Animals, Scottdale, PA), weighing approximately 200-250 g were used in this study which was conducted in an Association for Assessment and Accreditation of Laboratory Animal Care International approved animal facility (NIOSH, Morgantown, WV) following a protocol approved by the Animal Care and Use Committee. The rats were housed in pairs and maintained on a 12-hour light-dark cycle in a temperature (68-72°F) and humidity (30-70%) controlled room with free access to filtered tap water and HaCXan Teklad Global 18% protein rodent diet (Harlan Teklad; Madison, WI).
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was isolated from a piece of the lung tissue using the miRNeasy Mini Kit (Qiagen, Inc, Valencia, CA) following the procedure provided by the manufacturer. One microgram total RNA/sample was used to create sequencing libraries using the Illumina TruSeq® Stranded Total RNA Library Prep (Illumina, Inc., San Diego, CA) following the manufacturer's protocol. Briefly, following depletion of ribosomal RNA (rRNA), the RNA samples were purified, fragmented (68°C for 5 minutes), and primed for cDNA synthesis. The denatured and cleaved RNA fragments were purified using a bead cleanup and reverse transcribed into first strand cDNA using reverse transcriptase and random primers. While synthesizing the double stranded cDNA, dUPT was incorporated in place of dTTP followed by the addition of a single ‘A’ nucleotide to the 3 prime ends to facilitate proper adapter ligation to each sample. Indexing adapters provided in the library preparation kit were ligated to the ends of the ds cDNA. After adapter ligation, the samples were PCR amplified (12 cycles) to enrich the DNA fragments containing the adapter molecules and to enhance the amount of DNA in the library using a Veriti™ 96 Well Thermal Cycler (Applied Biosystems; Foster City, CA).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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Description |
processed data file: DE_HisatCounts_all.csv
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Data processing |
Basecalls were performed using bcl2fastq/2.19. Sequence reads were trimmed using Trimmomatic/0.35 with the following parameters ILLUMINACLIP:TruSeq2-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:60 All sequences were aligned to the Rattus norvegicus Rnor 6.0 genome from NCBI downloaded July 31, 2015 using HiSat2/2.1.0. Raw gene counts were assigned using Samtools/1.8, Python/2.7.3 and HTSeq/0.6.1. Genome_build: Rnor6.0 Supplementary_files_format_and_content: DE_HisatCounts_all.csv: Comma-separated text file including raw counts in a matrix.
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Submission date |
Jun 17, 2020 |
Last update date |
Dec 31, 2022 |
Contact name |
Christina M Umbright |
Organization name |
DHHS/PHS/CDC/NIOSH
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Department |
HELD
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Lab |
L-4324
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Street address |
1095 Willowdale Road
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City |
Morgantown |
State/province |
WV |
ZIP/Postal code |
26505 |
Country |
USA |
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Platform ID |
GPL18694 |
Series (1) |
GSE152720 |
Pulmonary effects of inhaled diesel particles in rats |
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Relations |
BioSample |
SAMN15307186 |
SRA |
SRX8570891 |
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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