|
| Status |
Public on Jan 25, 2019 |
| Title |
Proton100.S7 |
| 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: 100 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 |
SAMN07816826 |
| SRA |
SRX3305797 |
