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Sample GSM3418157 Query DataSets for GSM3418157
Status Public on Mar 27, 2019
Title fWBI Animal 3, White Matter
Sample type SRA
Source name Brain
Organism Macaca mulatta
Characteristics brain sub-region tissue: White matter, centrum semiovale
irradiation group: Fractionated whole brain irradiation
radiation dose to brain: 40 Gy, (8x5 Gray fractions)
animal: fWBI Animal 3
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 39
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
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
BioSample SAMN10182288
SRA SRX4803664

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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