|
| Status |
Public on Nov 17, 2020 |
| Title |
Lung - mRNA_CB_Day1_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
lung homogenate
|
| Organism |
Mus musculus |
| Characteristics |
treatment: carbon black
strain: C57BL/6
gender: male
tissue: lung
age: 8-12 weeks
genotype: wild type
|
| Treatment protocol |
8 week old male C57BL/6 mice were randomly divided into four groups ( air, carbon black, ozone and carbon black + ozone) and exposed to 2 ppm ozone (O3) for 3 hours, 10 mg/m3 carbon black (CB) for 3 hours, 10 mg/m3 CB and 2ppm ozone co-exposure (CB+O3) for 3 hours daily up to 4 days.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated from whole lung homogenate after pulverizing the lung tissues at -80 ° C. Total RNA was isolated using RNeasy Mini Kit (Qiagen 74106) and reverse transcription was performed using manufacturer’s protocol.
Libraries were built with the TruSeq® Stranded mRNA Library Prep Kit (Illumina, San Diego, CA) and run on the HiSeq 2500 (Illumina) in 51bp paired end reads. Fastq files were mapped and quantified using the mapping-based mode of Salmon 1.1.0.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
CB_Day1_S2
|
| Data processing |
A mouse decoy-aware index was created using both the Ensembl primary assembly (release 99) and the transcriptome (release 99) through Salmon 1.1.0.
The index was then used to map the 51 bp paired end reads for quantification, specifying options “--validateMappings” and “gcBias” through Salmon 1.1.0.
Quantification files were imported into R (v3.6.3) using tximeta.
Differential gene expression performed through DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: quantification files produced by Salmon 1.1.0
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample
|
| |
|
| Submission date |
Nov 16, 2020 |
| Last update date |
Nov 17, 2020 |
| Contact name |
Quincy Alexander Hathaway |
| E-mail(s) |
qahathaway@mix.wvu.edu
|
| Phone |
724-255-4637
|
| Organization name |
West Virginia University
|
| Department |
Exercise Physiology
|
| Lab |
Hollander Lab
|
| Street address |
1 Medical Center Road
|
| City |
Morgantown |
| State/province |
WV |
| ZIP/Postal code |
26505 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE161538 |
Next Generation Sequencing of lung homogenate mRNA from 8-12 week male C57BL/6 mice following Sham, Carbon Black, Ozone, or Carbon Black-Ozone Co-exposure. |
|
| Relations |
| BioSample |
SAMN16809681 |
| SRA |
SRX9514709 |
