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SRX4803642: GSM3418135: TBI Animal 1, Hippocampus; Macaca mulatta; RNA-Seq
4 ILLUMINA (NextSeq 500) runs: 32.7M spots, 2.5G bases, 1Gb downloads

Submitted by: NCBI (GEO)
Study: Evaluation of Transcriptomic Change in Late-Delayed Radiation following Fractionated Whole Brain Irradiation and High Dose Total Body Irradiation in Non-Human Primates
show Abstracthide Abstract
Fractionated whole-brain irradiation for the treatment of intracranial neoplasia causes progressive neurodegeneration and neuroinflammation. The long-term consequences of high single dose brain irradiation are unknown. In order to assess the late effects of brain irradiation we have compared transcriptomic gene expression profiles from nonhuman primates (rhesus macaques, Macaca mulatta) receiving single dose total body irradiation to those given fractionated whole brain radiotherapy and control comparators. Gene expression profiles from the dorsolateral prefrontal cortex (Brodmann area 46), hippocampus, and deep white matter (centrum semiovale) were compared. The goals of this study were to identify novel potential molecular effects of radiation-induced brain injury, to evaluate regional differences in the cerebral radiation response, and to assess whether animals receiving high dose total body irradiation demonstrated similar transcriptomic patterns as those observed in animals receiving fractionated whole brain irradiation. Overall design: 3x3 design in which 3 brain regions [dorsolateral prefrontal cortex (brodmann area 46), hippocampus, and deep whiter matter (centrum semiovale)] were evaluated from three treatment groups: thorax-only irradiated control animals (10 Gy, estimated dose to the brain < 0.1 Gy), animals receiving fractionated whole brain irradiation (n=5, 40 Gy, 8x5 Gy fractions; 12 months prior to necropsy) and animals receiving high, single dose, total body irradiation (n=5, 6.75 - 8.05 Gy, 6-9 years prior to necropsy). The effects of brain region and irradiation status on differential gene expression were evaluated.
Sample: TBI Animal 1, Hippocampus
SAMN10182322 • SRS3882590 • All experiments • All runs
Organism: Macaca mulatta
Library:
Instrument: NextSeq 500
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: SINGLE
Construction 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).
Experiment attributes:
GEO Accession: GSM3418135
Links:
Runs: 4 runs, 32.7M spots, 2.5G bases, 1Gb
Run# of Spots# of BasesSizePublished
SRR79704088,158,750614.9M262.2Mb2019-03-28
SRR79704097,943,826598.8M257.6Mb2019-03-28
SRR79704108,354,205629.7M265.1Mb2019-03-28
SRR79704118,246,297621.6M261.1Mb2019-03-28

ID:
6489056

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