|
| Status |
Public on May 01, 2024 |
| Title |
TOQX_3 |
| Sample type |
SRA |
| |
|
| Source name |
testes
|
| Organism |
Trachinotus ovatus |
| Characteristics |
tissue: testes
genotype: TOQX
treatment: Remove testicular tissue
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. 0.4 ug of total RNA was used for the construction of sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
clean data (clean reads) were obtained by trimming reads containing adapter, ploy-N or with low quality from raw data
Index of the reference genome was built using hisat2-2.0.4 and paired-end clean reads were mapped to the reference genome.
Stringtie-1.3.3b was used to count the read numbers mapped to each gene. And then FPKM was calculated.It normalizes for both sequencing depth and genome size
Assembly: 173339
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.
|
| |
|
| Submission date |
Apr 26, 2024 |
| Last update date |
May 01, 2024 |
| Contact name |
Honghua Chen |
| E-mail(s) |
19876388857m@sina.cn
|
| Phone |
19876388857
|
| Organization name |
Chinese Academy of Fishery Sciences
|
| Street address |
Haizhu District - 6-7/F, Xinhai Building, No. 231 Xingang West Road
|
| City |
Guangzhou |
| ZIP/Postal code |
510300 |
| Country |
China |
| |
|
| Platform ID |
GPL34418 |
| Series (1) |
| GSE265938 |
Molecular characterization and differential expression profiles of transcription factor Sox gene family between ovaries and testes from golden pompano （Trachinotus ovatus） |
|
| Relations |
| BioSample |
SAMN41098289 |
| SRA |
SRX24382709 |
