|
| Status |
Public on Jun 09, 2021 |
| Title |
T48Is-1 |
| Sample type |
SRA |
| |
|
| Source name |
Intestine
|
| Organism |
Oncorhynchus mykiss |
| Characteristics |
tissue: Intestine
treatment: Intraperitoneal injection of IHNV
time: 48 hours after infection
|
| Treatment protocol |
The experimental and control groups were treated with IHNV and M199 for 48 hours, respectively.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by Trizol reagent kit (Invitrogen, Carlsbad, CA,USA), the RNA molecules in a size range of 18–30nt were enriched by polyacrylamide gel electrophoresis (PAGE).
cDNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
Rainbow trout
miRNAs_tpm_expression.txt
|
| Data processing |
Raw reads were further filtered according to the following rules: 1) Removing low quality reads containing more than one low quality (Q-value≤20) base or containing unknown nucleotides (N); 2) Removing reads without 3’adapters; 3) Removing reads containing 5’adapters; 4) Removing reads containing 3’ and 5’ adapters but no small RNA fragment between them; 5) Removing reads containing polyA in small RNA fragment; 6) Removing reads shorter than 18nt (not include adapters).
Low-quality raw reads and clean tags were identified as tRNA, rRNA, snoRNA, snRNA and scRNA using GenBank and Rfam database were removed and enriched clean tags were compared with the reference genome USDA_OmykA_1.1 and the reads mapped to exons, introns and repeat sequences were removed.
The expression profiles of miRNAs were calculated and normalized to transcripts per million (TPM), and the formula was TPM = Actual miRNA counts/Total counts of clean tags ×10 ^ 6, obtained the expression profiles of all miRNA of all samples.
Genome_build: Oncorhynchus mykiss USDA_OmykA_1.1
Supplementary_files_format_and_content: miRNAs_tpm_expression.txt: Tab-delimited text file includes counts and TPM values for each Sample.
|
| |
|
| Submission date |
Jun 08, 2021 |
| Last update date |
Jun 09, 2021 |
| Contact name |
Pan Yu Cai |
| E-mail(s) |
pyc@guizunyu.ntesmail.com
|
| Phone |
17693505396
|
| Organization name |
Gansu Agricultural University
|
| Department |
College of Animal Science and Technology
|
| Street address |
Yin Tan Road Street, An Ning District
|
| City |
Lan zhou |
| State/province |
Gansu |
| ZIP/Postal code |
730070 |
| Country |
China |
| |
|
| Platform ID |
GPL30022 |
| Series (2) |
| GSE176398 |
Integrative mRNA-miRNA interaction analysis associated with the immune response of rainbow trout Oncorhynchus mykiss to infectious hematopoietic necrosis virus infection [miRNA-seq] |
| GSE176399 |
Integrative mRNA-miRNA interaction analysis associated with the immune response of rainbow trout Oncorhynchus mykiss to infectious hematopoietic necrosis virus infection |
|
| Relations |
| BioSample |
SAMN19607897 |
| SRA |
SRX11094413 |
