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| Status |
Public on Jun 08, 2021 |
| Title |
Transgenic rabbits fed High cholesterol diet |
| Sample type |
SRA |
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| Source name |
vascular
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| Organism |
Oryctolagus cuniculus |
| Characteristics |
strain: JW/CSK
tissue: aorta media
treatment: hight cholesterol diet
genotype: PGC1-alpha (mouse gene) transgenic
age: 9 months
Sex: male
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| Treatment protocol |
Non-transgenic rabbits fed with chow diet were served as the ctrl group, and transgenic or non-transgenic rabbits fed with high cholesterol diet for 20 weeks were the experimental groups. For each group, RNA from 5 rabbits were included and pooled together.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the aortic media of the 9-month-old male non-transgenic and transgenic rabbits using the TruSeq RNA Sample Preparation Kit (Illumina, Cat#FC-122-1001) according to the manufacture’s protocol.
Briefly, mRNA was first enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
S170554-3_HCJW5CCXY_L2
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| Data processing |
Basic analysis mainly included raw data filtering and quality control, reference genome comparison, alignment homogeneity analysis, saturation analysis, sample correlation analysis, expression analysis, and differential gene analysis.
Advanced analyses mainly included KEGG Pathway and GO Enrichments for the differential expressed genes, in which fpkm>=30 and fold change cutoff =1.5.
Genome_build: OryCun2.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
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| Submission date |
Jun 07, 2021 |
| Last update date |
Jun 08, 2021 |
| Contact name |
Xiaohong jiang |
| E-mail(s) |
xiaohongjiang@nju.edu.cn
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| Phone |
86-025-89681280
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| Organization name |
Nanjing university
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| Lab |
3M lab
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| Street address |
Xianlin Road
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| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210000 |
| Country |
China |
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| Platform ID |
GPL18453 |
| Series (1) |
| GSE176340 |
RNA-Seq of rabbits treated with normal diet or high cholesterol diet |
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| Relations |
| BioSample |
SAMN19597876 |
| SRA |
SRX11085700 |
| 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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