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Sample GSM1320477 Query DataSets for GSM1320477
Status Public on Oct 01, 2014
Title SCCA2KO SAL Rep 1
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 1
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 SAMN02630987
SRA SRX467585

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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