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Sample GSM2825350 Query DataSets for GSM2825350
Status Public on Jan 25, 2019
Title Proton200.S10
Sample type SRA
 
Source name aorta
Organism Mus musculus
Characteristics strain: C57BL/6
developmental stage: adult
Sex: male
age: 10 to 12 week
genetic alteration: wildtype
radiation: Proton
radiation dose: 200 cGy
Treatment protocol 10 mice were treated with ten different centigrays of gamma radiation and 10 mice were treated with ten different centigrays of high energy protons (0 cGy, 5 cGy, 10 cGy, 25 cGy, 50 cGy, 75 cGy, 100 cGy, 125 cGy, 150 cGy, 200 cGy). Treated at the same time, same day. Sacrificed 4 hours after irradiation.
Growth protocol Mice were housed in groups on a 12 hour light, 12 hour dark schedule. feed type : regular chow; diet availability : ad libitum; diet supplements : none; water supply type : bottle; water type : tap
Extracted molecule total RNA
Extraction protocol RNA was extracted using Trizol and Qiagen Rneasy Mini kit.
Library construction was carried out using Illumina TruSeq RNA Sample Prep kit and SBS kit v3. Samples were handled in a blinded fashion. Selection strategy: polyA
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description master_list_gene_counts_MIN.sense.Gamma_Proton_radiation.txt.gz
Data processing CASAVA-1.8.1 was used to demultiplex pooled samples and convert BCL to FASTQ.
RNA-Seq data were aligned to the mouse genome build mm9 by STAR_2.5.2a.
Data were normalized at the gene-level, using a resampling strategy, the code is available at https://github.com/itmat/Normalization
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file from gene-level normalization contains counts from unique reads that only map to one gene.
 
Submission date Oct 19, 2017
Last update date May 15, 2019
Contact name Gregory Robert Grant
E-mail(s) ggrant@upenn.edu
Phone 215-573-3736
Organization name University of Pennsylvania
Department Genetics
Lab ITMAT Bioinformatics
Street address 3400 Civic Center Blvd.
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL17021
Series (1)
GSE105266 Distinct vascular genomic effects of proton and gamma radiation
Relations
BioSample SAMN07816821
SRA SRX3305800

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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