|
| Status |
Public on Sep 05, 2024 |
| Title |
HFSD2 (high-fat and sucrose diet) |
| Sample type |
SRA |
| |
|
| Source name |
Retina
|
| Organism |
Oryctolagus cuniculus |
| Characteristics |
tissue: Retina
genotype: WT
treatment: High-fat and sucrose diet for six months
|
| Treatment protocol |
Male adult Chinchilla rabbits fed with a regular control diet (ND, standard rabbit chow), HFD (adding 10% lard and 0.5% cholesterol in the standard chow), HSD (adding 40% sucrose in the standard chow), and HFSD (adding 10% lard, 0.5% cholesterol, and 35% sucrose in the standard chow) for six months
|
| Growth protocol |
Male Chinchilla rabbits at the age 12-16 weeks old (3.5±0.5kg) (Dongfang Breeding Co., Pizhou, China) were housed in individual cages and a room with controlled humidity (45±5%) and temperature (22±6 C) under 12/12-h light-dark cycle
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted from dissected rabbit retinas using TRIzol (Thermo Fisher) and treated with RNAse-free DNAse I (New England Biolabs) to remove genomic DNA. The yield of total RNA was assessed using NanoDrop Microvolume Spectrophotometers (NanoDrop Technologies).
The cDNA libraries were prepared using an Illumina TruSeq RNA sample preparation kit, and the quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
M4_6_2.fq.gz
|
| Data processing |
the sequencing quality was first assessed using FastQC, and poor-quality 5′ end reads were trimmed using a Perl script and then mapped onto the rat genome using TopHat2, allowing for up to 2 mismatches as default settings.
Reads mapped onto multiple genomic locations were discarded, and a custom R script was used to calculate the fragments per kilobase million (FPKM) of each gene and obtain the expression profile of each sample
Assembly: orycun2
|
| |
|
| Submission date |
Sep 05, 2024 |
| Last update date |
Sep 05, 2024 |
| Contact name |
Danian Chen |
| E-mail(s) |
dchen@lunenfeld.ca
|
| Phone |
86-18980605810
|
| Organization name |
West China Hospital, Sichuan University
|
| Street address |
37 Guoxue Xiang Street
|
| City |
Chengdu |
| ZIP/Postal code |
610041 |
| Country |
China |
| |
|
| Platform ID |
GPL21255 |
| Series (1) |
| GSE276438 |
High-fat and High-sucrose Diets Synergistically Induce reticular pseudo-drusen (RPD)-like Lesions in Rabbits |
|
| Relations |
| BioSample |
SAMN43511799 |
| SRA |
SRX25977189 |
