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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 12, 2020 |
| Title |
35998 |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Peromyscus maniculatus |
| Characteristics |
stock: BW
diet: Chow Diet
age of animal at termination: 10 months
steatosis: No
Sex: Male
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| Treatment protocol |
Cohorts of 16 deer mice with 6 males (5 BWs and 1 SM2) on a regular diet, 7 males (5 BWs and 2 SM2s) and 3 females (all BWs) on HFD were used in this study. Deer mice were fed either a regular chow diet or a high fat diet (HFD, 58 kcal% fat and sucrose, Research Diets D12331) for 28 weeks, starting at 3-4 months of age. Body weight was measured every two weeks.
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| Growth protocol |
Deer mice, P. maniculatus were obtained from the Peromyscus Genetic Stock Center (PGSC), University of South Carolina (USC), Columbia, SC (RRID:SCR_002769). Deer mouse, P. maniculatus bairdii (BW Stock), was closed colony bred in captivity since 1948 and descended from 40 ancestors wild-caught near Ann Arbor, Michigan. Sonoran deer mouse, P. maniculatus sonoriensis (SM2 Stock), was derived from about 50 animals wild-caught by Jack Hayes in 1995 near White Mountain Research Station, CA (1).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Animals were sacrificed using isoflurane as an anesthetic followed by cervical dislocation, and the livers were collected. RNAs were extracted with a Qiagen RNeasy Plus Mini kit as per manufacturer’s recommendations (Qiagen, Valencia, CA)
RNA integrity was assessed using the Agilent Bioanalyzer and samples had a quality score ≥ 8.6. RNA libraries were prepared using established protocol with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, Lynn, MA). Each library was made with one of the TruSeq barcode index sequences and pooled together into one sample to be sequenced on the HiSeq 2x150bp pair-ended sequencing platform (Genewiz).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Sequences were aligned to the P. maniculatus genome (HU_Pman_2.1 (GCA_003704035.1)) in ensembl.org using STAR v2.7.2.
Reads were counted using the featureCounts function of the R Subreads package using Ensembl GTF and summarized at exon, transcript, or gene level.
Genome_build: HU_Pman_2.1
Supplementary_files_format_and_content: comma-separated values file with gene counts for each sample
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| Submission date |
Mar 11, 2020 |
| Last update date |
Mar 12, 2020 |
| Contact name |
Youwen Zhang |
| E-mail(s) |
youwen@email.sc.edu
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| Organization name |
University of South Carolina (Columbia)
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| Department |
Drug Discovery and Biomedical Sciences
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| Lab |
Dr. Hippokratis Kiaris
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| Street address |
715 Sumter Street CLS109
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| City |
Columbia |
| State/province |
South Carolina |
| ZIP/Postal code |
29208 |
| Country |
USA |
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| Platform ID |
GPL26686 |
| Series (1) |
| GSE146846 |
Whole Transcriptome Sequencing of Peromyscus maniculatus in Response to High Fat Diet |
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| Relations |
| BioSample |
SAMN14360978 |
| SRA |
SRX7898289 |
| 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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