|
| Status |
Public on Oct 01, 2014 |
| Title |
SCCA2KO SAL Rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
skin tissue
|
| Organism |
Mus musculus |
| Characteristics |
strain: BALB/C
genotype/variation: Serpinb3a-transgenic
tissue: skin
treatment: SAL
|
| Treatment protocol |
Day 0- shave a 2x2 cm2 patch on the back of all the mice. Day 1 - apply 200ug ASP extract on a gauze patch and tape onto the shaved back. Day-4 remove ASP patch. Day 5- sacrifice mice, collect skin from the patched area, place in 1 ml Trizol, homogenize and isolate RNA.
|
| Growth protocol |
All mice were maintained under pathogen-free conditions in the Veterinary Biosciences Department at Cincinnati Children's Hospital Medical Center
|
| 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 |
SAL-treated Serpinb3a-transgenic mice Rep 3
|
| Data processing |
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
fastq seqences 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: mm10
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns
|
| |
|
| Submission date |
Feb 03, 2014 |
| 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) |
| GSE54640 |
Serpinb3a contributes to early skin inflammation following allergen exposure |
|
| Relations |
| BioSample |
SAMN02630991 |
| SRA |
SRX467587 |
