|
| Status |
Public on Dec 15, 2021 |
| Title |
HFr1 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Chlorocebus sabaeus |
| Characteristics |
diet: High fructose
gender: female
|
| Treatment protocol |
Prior to the study, all animals were maintained on a chow diet. In the study, 5 animals were fed a high fructose diet and 5 were fed a chow diet.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Liver tissue was flash frozen in liquid nitrogen immediately after collection and stored at -80oC. Total RNA was extracted from vervet monkey livers using the Zymo Direct-zol RNA MiniPrep kit.
RNA-Seq libraries were prepared from 500 ng of total RNA according to the Illumina TruSeq stranded mRNA protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
wfv_rna_seq_1
|
| Data processing |
Raw sequences were de-multiplexed using the Illumina Casava v1.8 software.
FastQC and FASTX-toolkit were used for QC. Sequence reads with Phred scores ≥ Q30 were retained.
Sequence reads were aligned against the vervet reference genome (ChlSab1.1) using STAR 2.5.3a.
Aligned reads were quantified using an expectation-maximization algorithm in Partek Flow and annotated using the Ensembl release 93 gene model.
Transcript abundances were normalized by the Trimmed mean of M-values method.
Genome_build: ChlSab1.1
Supplementary_files_format_and_content: Matrix table of transcript counts before normalization for all genes in 10 samples.
Supplementary_files_format_and_content: Matrix table of transcript counts after normalization for all genes in 10 samples.
|
| |
|
| Submission date |
Jun 10, 2021 |
| Last update date |
Dec 15, 2021 |
| Contact name |
Jeannie Chan |
| E-mail(s) |
jchan@wakehealth.edu
|
| Organization name |
Wake Forest School of Medicine
|
| Department |
Internal Medicine
|
| Street address |
Medical Center Boulevard
|
| City |
Winston-Salem |
| State/province |
NC |
| ZIP/Postal code |
27157 |
| Country |
USA |
| |
|
| Platform ID |
GPL18770 |
| Series (1) |
| GSE176576 |
Efffect of a high fructose diet on gene expression in vervet monkey livers. |
|
| Relations |
| BioSample |
SAMN19658771 |
| SRA |
SRX11116143 |
