|
| Status |
Public on Mar 27, 2019 |
| Title |
TBI Animal 5, White Matter |
| Sample type |
SRA |
| |
|
| Source name |
Brain
|
| Organism |
Macaca mulatta |
| Characteristics |
brain sub-region tissue: White matter, centrum semiovale
irradiation group: Total body irradiation
radiation dose to brain: 8.05 Gy
animal: TBI Animal 5
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Animals were humanely euthanized in accordance with the American Veterinary Medical Association’s Guidelines on Euthanasia by deep anesthesia with pentobarbital, followed by exsanguination and perfusion of the vascular system with 2 liters of cold normal saline. The brain was removed intact, and sectioned coronally in 4 mm intervals using a stainless steel brain matrix with cutting guides. Sections were immediately frozen on dry ice. 100 mg of brain tissue was homogenized in QIAzol lysis reagent, and aliquots of homogenized lysates equivalent to 40 mg tissue were extracted for total RNA using the RNeasy Microarray Tissue Mini kit (Qiagen). Extracted RNA was DNase-treated and purified using the RNA Clean and Concentrator-5 kit (Zymo Research), then assessed for RNA quality using an Agilent 2100 Bioanalyzer and the RNA 6000 Nano Kit (Agilent Technologies). RIN values for the RNA samples ranged from 7.1 to 9.3.
Total RNA was used to prepare cDNA libraries using the Illumina® TruSeq Stranded Total RNA with Ribo-Zero Gold Preparation kit (Illumina Inc.) and the SciClone NGS Work Station (Perkin Elmer).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Sample 30
Total RNA, ribosomal RNA depleted
processed data file: Counts_All.txt
|
| Data processing |
Raw read quality was assessed by FASTQC analysis (Babraham Bioinformatics). Uniquely mapped reads ranged from 21M-36M reads per sample.
Reads with >Q20 quality score were aligned to the Ensembl Macaca mulatta genome build Mmul_1 using the STAR aligner.
Gene counts determined by featureCounts software.
Differentially expressed genes (DEGs) were identified by DESeq2, irradiated groups were compared to thorax-only irradiated controls.
Genome_build: Mmul_1
Supplementary_files_format_and_content: Counts_All.txt: Tab-delimited matrix of raw counts generated by featureCounts.
|
| |
|
| Submission date |
Oct 05, 2018 |
| Last update date |
Mar 27, 2019 |
| Contact name |
Rachel N Andrews |
| E-mail(s) |
[email protected]
|
| Phone |
3367161561
|
| Organization name |
Wake Forest University
|
| Department |
Pathology, Section on Comparative Medicine
|
| Lab |
Cline
|
| Street address |
Medical Center Boulevard
|
| City |
Winston-Salem |
| State/province |
North Carolina |
| ZIP/Postal code |
27103 |
| Country |
USA |
| |
|
| Platform ID |
GPL21120 |
| Series (1) |
| GSE120901 |
Evaluation of Transcriptomic Change in Late-Delayed Radiation following Fractionated Whole Brain Irradiation and High Dose Total Body Irradiation in Non-Human Primates |
|
| Relations |
| BioSample |
SAMN10182292 |
| SRA |
SRX4803655 |
