|
| Status |
Public on Dec 01, 2023 |
| Title |
HCHFD+PC rep3 |
| Sample type |
SRA |
| |
|
| Source name |
fed with a HCHFD plus Pulsatilla Chinensis
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Liver
sample type: treatment group
treatment: fed with a HCHFD plus Pulsatilla Chinensis
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions，Illumina TruSeq RNA Sample was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Demultiplexing and basecalling performed using CASAVA version 1.8.2.
QC was performed on the FASTQ files using FastQC(v0.11.5) software.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rat(Rnor_6.0) whole genome using HISAT2(v2.1.0).
Sequence reads aligned to the rat genome were imported into StringTie(v1.3.3b) for sequence read counting.
Sequence reads mapped to different isoforms of individual genes were pooled together, and then were input into the DESeq2(v1.28.0) differential expression analysis program to normalize and determine expression levels and differentially expressed genes.
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts for each gene per sample
|
| |
|
| Submission date |
Dec 10, 2021 |
| Last update date |
Dec 01, 2023 |
| Contact name |
ruijun wang |
| E-mail(s) |
W841684901@126.com
|
| Phone |
18518157361
|
| Organization name |
Tsinghua university
|
| Street address |
college of life science
|
| City |
beijing |
| ZIP/Postal code |
102206 |
| Country |
China |
| |
|
| Platform ID |
GPL25947 |
| Series (2) |
| GSE190630 |
RNA-Sequencing of rats treated with Chinese herbal medicine Pulsatilla Chinensis |
| GSE190631 |
RNA-Sequencing of HepG2 cells and rats treated with Chinese herbal medicine Pulsatilla Chinensis |
|
| Relations |
| BioSample |
SAMN23848731 |
| SRA |
SRX13374687 |
