|
| Status |
Public on May 21, 2019 |
| Title |
HFD+HT_59 |
| Sample type |
SRA |
| |
|
| Source name |
After rats were fed with high-fat diet alone for 4 weeks, hawk tea extract (HT) were co-supplemented with HFD for further 11 weeks.
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: SD
tissue: Liver
Sex: male
age: 6-8 weeks
diet: high-fat
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
After rats were fed with high-fat diet alone for 4 weeks, hawk tea extract (HT) were co-supplemented with HFD for further 11 weeks.
|
| Data processing |
Raw image data files obtained from high throughput sequencing was delivered to Phred base calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rat whole genome using HISAT2 software.
Fragments Per Kilobase of exon per Million fragments (FPKM) were calculated using Stringtie-1.3.3b . In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Rat reference genome (rn6) for read alignment
Supplementary_files_format_and_content: tab-delimited text files include raw and normalized counts or FPKM values for each Sample.
|
| |
|
| Submission date |
Jan 14, 2019 |
| Last update date |
May 21, 2019 |
| Contact name |
Juan Feng |
| E-mail(s) |
fengjuansdu@126.com
|
| Phone |
13240774409
|
| Organization name |
Tsinghua University
|
| Department |
School of Medicine
|
| Street address |
No.30, Shuangqing Road, Haidian District
|
| City |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
| |
|
| Platform ID |
GPL24688 |
| Series (1) |
| GSE125084 |
RNA-seq-based transcriptome profiling of hawk tea extract (HTE)-fed hypercholesterolemic rat livers |
|
| Relations |
| BioSample |
SAMN10743298 |
| SRA |
SRX5249212 |
