|
| Status |
Public on Sep 22, 2021 |
| Title |
IR rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Brain
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: brain
treatment: irradiated (10 Gy), 30 days
|
| Treatment protocol |
Mice were mock-irradiated or cranially irradiated AP (anterior-posterior) with an X-ray device (X-RAD 320, Precision X-ray; 250 kV, 15 mA, 1.65 mm Al filter, at 5 cm) fitted with a specifically designed collimator providing a 10.08 mm-diameter field size iso-dose exposure (total dose of 10 Gy).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At 30 days post-IR, mice were perfused with PBS and brains were dissected out. Total RNA was extracted from dissected whole brains using TRIzol (Invitrogen) according to the manufacturer's instructions. RNA quantity was then determined using a Qubit fluorometer (Thermo Fisher), and RNA quality was analyzed with an RNA tape on the 4200 TapeStation (Agilent).
TruSeq Stranded Total RNA Ribo-Zero kit (Illumina) was used to prepare sequencing libraries from 2 μg total RNA.
Sequencing was performed on the NextSeq500 using 75 nucleotide single end SBS chemistry, with ~30‐40 Million reads for each sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequence reads were aligned to the mouse transcriptome using TopHat.
Cufflinks package was used to quantify transcript levels
DEG analysis was performed using cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: whole genome FPKM matrix
|
| |
|
| Submission date |
Sep 20, 2021 |
| Last update date |
Sep 22, 2021 |
| Contact name |
Ralf Kittler |
| E-mail(s) |
Ralf.Kittler@UTSouthwestern.edu
|
| Organization name |
University of Texas Southwestern Medical Center
|
| Street address |
5323 Harry Hines Blvd
|
| City |
Dallas |
| State/province |
Texas |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE184451 |
Elimination of radiation-induced senescence in the brain tumor microenvironment attenuates glioblastoma recurrence |
|
| Relations |
| BioSample |
SAMN21522517 |
| SRA |
SRX12261279 |
