|
Status |
Public on Jan 25, 2019 |
Title |
Proton150.S9 |
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: 150 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 |
SAMN07816817 |
SRA |
SRX3305799 |