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| Status |
Public on Dec 26, 2018 |
| Title |
SUB-EPA-3 |
| Sample type |
SRA |
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| Source name |
Subcutaneous Adipose Tissue (SAT5: SUB-EPA-3)
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL 6J (B6)
tissue: Subcutaneous Adipose
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| Treatment protocol |
C57BL/6J mice aged 5-6 week were fed on a high fat diet which consisted of 45%, 20% and 35% of energy from fat, protein and carbohydrate respectively for 11 weeks.
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| Extracted molecule |
total RNA |
| Extraction protocol |
At the end of 11 week feeding period, the mice were fasted for 4 hours and then euthanized by CO2 inhalation. Epidedimal (VAT), inguinal (SAT) and interscapular (BAT) adipose tissues were harvested, and snap frozen immediately in liquid N2, followed by storage at -80°C. Frozen adipose tissue samples (SAT, BAT, and VAT- 3 samples per group) were homogenized in QIAzol® (QIAGEN, Redwood City, CA). Total RNA was isolated according to manufacturer’s protocol using RNeasy Mini Kit.
Small RNA libraries were prepared using the Illumina small RNA protocol (Illumina, Inc., San Diego, CA)
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
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| Data processing |
Illumina small RNA adapter sequences were trimmed from the reads, and reads of length below 10nt or ending in homopolymers of length 9 nt or above were discarded.
Total usable number of reads for each sample was calculated.
The reads were mapped to the miRBase reference using BLAST; the abundance of each expressed microRNA was quantified as a fraction of the usable reads, and expressed as parts per million.
Genome_build: mm10
Supplementary_files_format_and_content: TAB-delimited text format, containing quantile normalized microRNA abundance
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| Submission date |
May 31, 2017 |
| Last update date |
Mar 23, 2020 |
| Contact name |
Naima Moustaid-Moussa |
| E-mail(s) |
naima.moustaid-moussa@ttu.edu
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| Phone |
8068347946
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| Organization name |
Texas Tech University
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| Department |
Nutritional Sciences & Obesity Research Institute
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| Lab |
Nutrigenomics Inflammation & Obesity Research lab
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| Street address |
1301 Akron Street
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| City |
Lubbock |
| State/province |
TX |
| ZIP/Postal code |
79409-1270 |
| Country |
USA |
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| Platform ID |
GPL9250 |
| Series (1) |
| GSE99506 |
MicroRNAs Regulated by Eicosapentaenoic Acid (EPA) in Brown, Subcutaneous, and visceral Adipose Tissue of Diet-Induced Obese Mice |
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| Relations |
| BioSample |
SAMN07180686 |
| SRA |
SRX2873436 |
| 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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