|
| Status |
Public on Dec 03, 2013 |
| Title |
WT PBS Rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
Lung tissue, WT, PBS
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
genotype/variation: wild-type
tissue: lung
treatment: PBS
|
| Treatment protocol |
The mice were intratracheally challenged with 100 micrograms of HDM in 50 microliters of PBS or 50 microliters of PBS alone 3 times per week for 3 weeks. Lung tissues were harvested 24 hours after the last challenge.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with the RNeasy MinElute kit (Qiagen) according to the manufacturer's specifications.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Description |
WP1
PBS-treated wild-type mice, rep1.
|
| Data processing |
Bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8.
Fastq sequences were aligned to mm10 using Tophat.
Number of read counts was calculated for each Entrez gene.
Differential expression analysis was performed using Deseq.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text file containing genes (Entrez Gene IDs) with raw counts for each Sample.
|
| |
|
| Submission date |
Jul 19, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Mario Medvedovic |
| Organization name |
University of Cincinnati
|
| Department |
Department of Environmental Health
|
| Lab |
Laboratory for Statistical Genomics and Systems Biology
|
| Street address |
3223 Eden Av. ML 56
|
| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45267-0056 |
| Country |
USA |
| |
|
| Platform ID |
GPL15103 |
| Series (1) |
| GSE49047 |
Overexpression of Dimethylarginine Dimethylaminohydrolase 1 Attenuates Airway Inflammation in a Mouse Model of Asthma |
|
| Relations |
| BioSample |
SAMN02261225 |
| SRA |
SRX326739 |
