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| Status |
Public on Dec 31, 2022 |
| Title |
MW_045_026_AA |
| Sample type |
SRA |
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| Source name |
lung
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Fischer 344
tissue: lung
treatment: air
mwcnt concentration (mg/m3): 0
outlier in subsequent analyses: no
molecule subtyoe: total RNA including microRNAs
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| Treatment protocol |
Exposures were performed in a whole-body inhalation chamber. Groups (n=6) were exposed to air (controls) or MWCNT (6 hours/day, 3 days) to result in cumulative doses of 180, 90, 45, 22.5, or 11.25 mg/m3.
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| Growth protocol |
This experiment was conducted in an animal facility (NIOSH, Morgantown, WV) accredited by AAALAC International following a protocol approved by the Institutional Animal Care and Use Committee (IACUC). Male Fischer (CDF®) rats (F344/DuCrl) 3 months of age were purchased from Charles River Laboratories (Wilmington, MA). Rats were housed 3 per cage and maintained on a 12-hour light-dark cycle in a temperature (68-72oF) and humidity (30-70%) controlled room with free access to filtered tap water and Teklad rodent diet (Envigo, Indianapolis, IN).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA, including miRNA and other small RNA molecules, 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, including optional DNase treatment with RNase-Free DNase (Qiagen, Inc.; Valencia, CA).
One microgram total RNA/sample was used to create sequencing libraries using the IlluminaTruSeq Stranded mRNA Library Prep Kit (Illumina, Inc., San Diego, CA) following the manufacturer's protocol. 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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| Data processing |
Basecalls were performed using bcl2fastq/2.19.
Sequence reads were trimmed for adaptor sequence low-quality using Trimmomatic/0.35 with the following parameters ILLUMINACLIP:TruSeq2-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:60
Sequences were mapped to Rnor6.0 whole genome using Hisat2/2.1.0 with the following parameters: -q --downstream-transcriptome-assembly --dta-cufflinks --fr --no-mixed --time --met-file
Aligned sequences were identified, sorted, and counted using Samtools/1.8 and HTSeq/0.11.2
Genome_build: Rnor6.0
Supplementary_files_format_and_content: tab-delimted text file including raw counts in a matrix containing all samples
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| Submission date |
Apr 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) |
| GSE148869 |
Lung response to multi-walled carbon nanotube exposure in rats. |
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| Relations |
| BioSample |
SAMN14614553 |
| SRA |
SRX8133151 |
| 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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