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| Status |
Public on Jun 20, 2018 |
| Title |
Rat-Control4-WTTS |
| Sample type |
SRA |
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| Source name |
Hypothalamus
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Long-Evans
tissue: Hypothalamus
developmental stage: Adult
disease state: control
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was harvested using using Qiagen RNeasy Micro Purification Kit
WTTS libraries were constructed based on our previous protocols. The WTTS method includes several major steps: fragmentation, poly(A)+ RNA enrichment, 1st strand cDNA synthesis, Size selection and PCR amplication.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent PGM |
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| Data processing |
WTTS reads were trimmed for adaptor sequence, and masked for low-quality sequence using FASTX-Toolkit.
WTTS reads were mapped to rat genome using the aligner Bowtie2 version 2.2.3 with setting"bowtie2 -L 25 -N 0 -i S,1,1.15 --no-unal".
The ends of mapped reads within 24bp of each other on the same strand were clustered to detect poly(A) sites .
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: mapped reads
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| Submission date |
Jun 22, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Zhihua Jiang |
| E-mail(s) |
[email protected]
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| Organization name |
Washington State University
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| Department |
Animal Science
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| Lab |
Jianglab
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| Street address |
Veterinary and Biomedical Research Building, Room 151
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| City |
Pullman |
| State/province |
WA |
| ZIP/Postal code |
99164-7620 |
| Country |
USA |
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| Platform ID |
GPL20670 |
| Series (1) |
| GSE100349 |
Detailing Novel Epigenetic Events Associated with Diet-Induced Obesity in the Rat |
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| Relations |
| BioSample |
SAMN07268455 |
| SRA |
SRX2946174 |
| 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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