|
| Status |
Public on Apr 16, 2024 |
| Title |
Liver, HS-3 |
| Sample type |
SRA |
| |
|
| Source name |
the experimental group is subjected to heat stress by treating the rainbow trout liver in 24°C for a duration of 8 h
|
| Organism |
Oncorhynchus mykiss |
| Characteristics |
tissue: Liver
treatment: heat stress
|
| Treatment protocol |
the control group involve placing rainbow trout liver in 20°C
the experimental group is subjected to heat stress by treating the rainbow trout liver in 24°C for a duration of 8 h
|
| Extracted molecule |
nuclear RNA |
| Extraction protocol |
According to the manufacturer's protocol, RFs from the liver of rainbow trout was extracted using RNA Clean and Concentrator-25 kit (Zymo Research, Beijing, China). .
Ribo-seq libraries were assembled utilizing the NEBNext® Multi-Small RNA Library Prep Set for Illumina®
Ribosome profiling sequencing
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Sequencing was performed on an Illumina HiSeq™ X10 platform at Gene Denovo Biotechnology
The raw Ribo-seq data underwent quality control to remove low-quality sequences and rRNA. Clean reads were then aligned to the chromosome-level genome of the rainbow trout (www.ncbi.nlm.nih.gov/genome/?term=oncorhynchus+mykiss) using Bowtie2 software
DEGs were identified using the edgeR package, defined as having an absolute fold change values ≥ 2 and FDR < 0.05,
The three-nucleotide periodic distribution was successfully constructed using the riboWaltz R package
Assembly: Oncorhynchus mykiss Omyk_1.1
Supplementary files format and content: ribo-CG-vs-HS.txt (includes count values and FPKM values for each Sample)
Library strategy: Ribo-seq
|
| |
|
| Submission date |
Apr 09, 2024 |
| Last update date |
Apr 16, 2024 |
| Contact name |
guiyan zhao |
| E-mail(s) |
zhaogy@st.gsau.edu.cn
|
| Phone |
18893812949
|
| Organization name |
Gansu Agricultural University
|
| Street address |
Yingmen Village 1
|
| City |
Lanzhou |
| ZIP/Postal code |
730070 |
| Country |
China |
| |
|
| Platform ID |
GPL30022 |
| Series (1) |
| GSE263547 |
Integrated transcriptome and Ribosome Profiling analyses elucidate the liver response of rainbow trout (Oncorhynchus mykiss) to heat stress [Ribo-seq] |
|
| Relations |
| BioSample |
SAMN40894150 |
| SRA |
SRX24196658 |
