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| Status |
Public on Jun 01, 2023 |
| Title |
Brain, beaver, rep 2 |
| Sample type |
SRA |
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| Source name |
Brain
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| Organism |
Castor canadensis |
| Characteristics |
tissue: Brain
Sex: male
age: adult
genotype: wild type
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| Treatment protocol |
The 39 organ samples for young adults of baboon (Papio anubis), beaver (Castor canadensis), and long-tailed macaque (Macaca fascicularis) were collected from the Southwest National Primate Research Center (SNPRC). The 9 organ samples for young adults of chipmunk (Tamias sibiricus), American black bear (Ursus americanus), sugar glider (Petaurus breviceps), tube-nosed bat (Murina leucogaster), and white-footed mouse (Peromyscus leucopus) were collected as previously described (Fushan et al., 2015).
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| Extracted molecule |
total RNA |
| Extraction protocol |
After sacrifice, organs were removed and frozen on dry ice. RNA was extracted from tissues with PureLink RNA Mini Kit and passed to sequencing.
Sequencing libraries were prepared as described in (Fushan et al., 2015)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Beaver_2_Brain
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| Data processing |
To generate reference sequences and identify species-specific ortholog gene sets, pipeline from (Ma et al., 2016) was utilized. Published annotated genomes in Ensembl or NCBI were used if available. Otherwise, de novo transcriptomes were assembled with Trinity.
Reads were mapped to the species-specific ortholog sets using STAR (Dobin et al., 2013).Read counting was performed by featureCounts (Liao et al., 2014).
Supplementary files format and content: comma-separated values file includes gene counts for each sample
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| Submission date |
Mar 14, 2023 |
| Last update date |
Jun 01, 2023 |
| Contact name |
Alexander Tyshkovskiy |
| E-mail(s) |
alex.tyshkovskiy@gmail.com
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| Organization name |
Brigham & Women's Hospital, Harvard Medical School
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| Street address |
77 Avenue Louis Pasteur
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| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL33250 |
| Series (2) |
| GSE227359 |
Gene expression signatures of mammalian longevity across species |
| GSE227360 |
Distinct longevity mechanisms across and within species and their association with aging |
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| Relations |
| BioSample |
SAMN33760417 |
| SRA |
SRX19677056 |
| 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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