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| Status |
Public on May 11, 2021 |
| Title |
Non-survivor 2 (Irradiated) (B1) |
| Sample type |
SRA |
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| Source name |
Lung
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| Organism |
Macaca mulatta |
| Characteristics |
tissue: Lung
age at irradiation (years): 4.76
treatment: irradiated
survival status: Non-survivor
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 40-80 mg frozen lung tissues from three different affected regions of the lung from eight irradiated animals (4 non-survivors and 4 survivors) and from two different randomly selected regions from three unirradiated control animals. Tissue was placed into a 1.4 mm ceramic bead tube with 1 ml QIAzol lysis reagent and homogenized using a bead mill (Bead Ruptor 24, Omni International, Kennesaw, GA). The tissue sample tube was processed on the Bead Ruptor for 1 cycle at a speed of 5.5 m/s for 20 sec; and repeated up to six times until the sample was completely homogenized. All homogenized lysates were extracted for total RNA using the RNeasy Microarray Tissue Mini kit (Qiagen, Germantown, MD). Extracted RNA was DNase-treated and purified using the RNA Clean and Concentrator-5 kit (Zymo Research, Irvine, CA), then assessed for RNA quality using an Agilent 2100 Bioanalyzer and the RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA)
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
7R-B1
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| Data processing |
Raw read quality was assessed by FASTQC analysis (Babraham Bioinformatics).
Reads with >Q20 quality score were aligned to the Ensembl Macaca mulatta genome build Mmul_1 using the STAR sequence aligner
Gene counts were extracted using feature Counts software
Differentially expressed genes (DEGs) were analyzed using limma-voom
Genome_build: Mmul_1
Supplementary_files_format_and_content: Gene counts
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| Submission date |
May 10, 2021 |
| Last update date |
May 11, 2021 |
| Contact name |
J. Mark Thakur |
| E-mail(s) |
jmcline@wakehealth.edu
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| Phone |
+1-336-716-1564
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| Organization name |
Wake Forest School of Medicine
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| Department |
Pathology-Comparative Medicine
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| Street address |
Medical Center Boulevard
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| City |
Winston-Salem |
| State/province |
North Carolina |
| ZIP/Postal code |
27157-1040 |
| Country |
USA |
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| Platform ID |
GPL21120 |
| Series (1) |
| GSE174196 |
RNA sequencing analysis of lung samples of control and irradiated animals |
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| Relations |
| BioSample |
SAMN19101951 |
| SRA |
SRX10830903 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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