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| Status |
Public on Nov 11, 2020 |
| Title |
16Con5 |
| Sample type |
SRA |
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| Source name |
Control_casein_liver
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Zucker rat
diet: Control _casein
tissue: Liver
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from liver tissues was isolated using the Trizol reagent (ThermoFisher, Waltham, MA) and then the quality of isolated RNA was first assessed using the conventional A260/280 ratio and A260/230 ratio measurement (SpectraMax i3x; Molecular Devices, Sunnyvale, CA, USA) which were all satisfactory. In addition, RNA Integrity Number (also known as RIN) was assessed using the RNA R6K assay for the Agilent 2200 TapeStation (Agilent Technology, Santa Clara, CA, USA) in which RINs ranged between 8.5 and 9.5 hence satisfactory.
Illumina TruSeq RNA Library Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
9L-Con16_S35_L005
Control diet #5
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| Data processing |
Sequenced reads were performed quality assessment using FastQC.
Sequenced reads were then aligend to Rattus norvegicus Rnor_6.0 reference genome using ArrayStar
Raw read counts then obtained from ArrayStar were then analyzed using DESeq2
N/A
N/A
Genome_build: Rattus norvegicus Rnor_6.0
Supplementary_files_format_and_content: normalized counts for each sample and expression data.
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| Submission date |
Sep 25, 2020 |
| Last update date |
Nov 11, 2020 |
| Contact name |
Byung-whi Kong |
| E-mail(s) |
bkong@uark.edu
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| Phone |
479-575-5494
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| Organization name |
University of Arkansas
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| Department |
Poultry Science
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| Street address |
1260 W. Maple, POSC, L-426
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| City |
Fayetteville |
| State/province |
AR |
| ZIP/Postal code |
72701 |
| Country |
USA |
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| Platform ID |
GPL22396 |
| Series (1) |
| GSE158553 |
Long-Term Soy Protein Isolate Intake Reduces Liver Steatosis through Changes in Global Gene Expression in Obese Zucker Rats |
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| Relations |
| BioSample |
SAMN16262117 |
| SRA |
SRX9190607 |
| 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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