|
| Status |
Public on Feb 23, 2022 |
| Title |
VhG2 |
| Sample type |
SRA |
| |
|
| Source name |
gill
|
| Organism |
Takifugu rubripes |
| Characteristics |
average size: 118 ± 7.5 g
treatment: Vibrio harveyi at concentration of 2.5x 10e7 CFU/mL
infection: Vibrio harveyi infection
tissue: gill
|
| Treatment protocol |
Fish were put into the aquaria with the bacteria at concentration of 2.5×10e7 CFU/mL for 12 h of immersion exposure. At 12 h fish were transferred to clean seawater and maintained for 7 days. Control groups were maintained in the clean seawater all the time. Spleen and gill tissues were collected in both symptomatic treatment fish and control fish at 7 day.
|
| Growth protocol |
T. rubripes (average size 118 ± 7.5 g) were obtained from a local supplier (Tianzheng Industrial, Dalian, China) and acclimated for approximately 7 days in a temperature controlled room (19 ± 1 ◦C).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA)
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 |
Illumina Casava1.8 software used for basecalling.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome (Takifugu_rubripes_Ensemble_92) using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: Takifugu_rubripes_Ensemble_92
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for all sample
|
| |
|
| Submission date |
Aug 08, 2020 |
| Last update date |
Feb 23, 2022 |
| Contact name |
dongxu gao |
| E-mail(s) |
gaodongxu@dlou.edu.cn
|
| Organization name |
Dalian Ocean University
|
| Street address |
Heishijiao
|
| City |
Dalian |
| ZIP/Postal code |
116000 |
| Country |
China |
| |
|
| Platform ID |
GPL28988 |
| Series (1) |
| GSE155911 |
RNA-sequencing analysis of Takifugu rubripes spleen and gill in response to Vibrio harveyi infection |
|
| Relations |
| BioSample |
SAMN15764879 |
| SRA |
SRX8911984 |
