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| Status |
Public on Jan 10, 2022 |
| Title |
Regular Diet 3 |
| Sample type |
SRA |
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| Source name |
liver
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| Organism |
Mesocricetus auratus |
| Characteristics |
age: Four to six-week-old male Syrian Golden hamster
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| Treatment protocol |
Four to six-week-old male Syrian Golden hamsters (ENVIGO) were randomly assigned to either regular rodent chow (Teklad Global 16% Protein Rodent Diet, Envigo) or a HFHS diet for 16 weeks (Purina Chow #5001 with 11.5% Corn Oil, 11.5% Coconut Oil, 0.5% Cholesterol, 0.25% Deoxycholic Acid, and 10% Fructose: Dyets Inc., Dyet#615088)
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was collected from each sample and passed through Qiashredder column (Qiagen) at 21,000 x g for 2 min to homogenize any remaining genomic DNA in the aqueous phase. Aqueous phase was combined with 600 µL of RLT lysis buffer (Qiagen, Valencia, CA) with 1% beta mercaptoethanol (MilliporeSigma) and RNA was extracted using Qiagen AllPrep DNA/RNA 96-well system.
One hundred nanograms of RNA was used as input for rRNA depletion and NGS library preparation following the Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus workflow (Illumina)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
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| Description |
18749
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Raw fastq reads were trimmed of Illumina adapter sequences using cutadapt version 1.12
then trimmed and filtered for quality using the FASTX-Toolkit (Hannon Lab)
Remaining reads were aligned to the Mesocricetus auratus genome assembly version 1.0 using Hisat2 (Kim et al., 2015)
Reads mapping to genes were counted using htseq-count (Anders et al., 2015)
Differential expression analysis was performed using the Bioconductor package DESeq2 (Love et al., 2014)
Genome_build: Mesocricetus auratus genome assembly version 1.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
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| Submission date |
Jun 01, 2021 |
| Last update date |
Jan 10, 2022 |
| Contact name |
Dan Sturdevant |
| E-mail(s) |
dsturdevant@niaid.nih.gov
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| Phone |
4063639248
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| Organization name |
NIH
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| Department |
NIAID
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| Lab |
RTS
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| Street address |
903 S 4th street
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| City |
Hamilton |
| State/province |
MT |
| ZIP/Postal code |
59840 |
| Country |
USA |
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| Platform ID |
GPL29592 |
| Series (1) |
| GSE175943 |
High-fat high-sugar diet-induced changes in the lipid metabolism are associated with mildly increased COVID-19 severity and delayed recovery in the Syrian hamster |
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| Relations |
| BioSample |
SAMN19489684 |
| SRA |
SRX11041175 |
| 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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