|
| Status |
Public on May 16, 2024 |
| Title |
sample_011: Intestine from NVSel strain fish exposed to IHNV at timepoint 0 hrs post challenge |
| Sample type |
SRA |
| |
|
| Source name |
Intestine
|
| Organism |
Oncorhynchus mykiss |
| Characteristics |
FISH strain: NVSel
pathogen strain: IHNV
time post pathogen challenge: 0 hrs
tissue: Intestine
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Tissue samples were placed in RNAlater and stored at -80°C until usage. Total RNA was extracted with the Qiagen RNeasy Mini Kit per the manufacturer's recommendation. Total RNA was treated with Amplification Grade DNase I from Sigma-Aldrich and then precipitated prior to library construction.
Library for RNA-Seq was prepared according to KAPA Stranded mRNA-Seq poly-A selected kit with 200-300bp insert size (KAPA Biosystems, Wilmington, MA) using 250 ng total RNAs as input. Final library quality and quantity was analyzed by Agilent Bioanalyzer 2100 and Life Technologies Qubit 3.0 Fluorometer. The RNA integrity was checked by Agilent Bioanalyzer 2100 and samples with clean rRNA peaks were used for further experiments.
RNA-Seq of 150 bp PE (paired end) reads were sequenced on Illumina HiSeq 4000 (Illumina Inc., San Diego, CA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Base-calling and demultiplexing were performed using the native Illumina software by the sequencing service provider.
Raw reads were processed for quality control using fqC v0.11.5 and TrimGalore! software v0.6.4_dev. This software was used to trim low-quality ends from reads, for Illumina adapter removal, and for removal of excess poly(A)-tails.
STAR v2.7.7a was used for alignment of reads to the rainbow trout genome using the default alignment parameters recommended by the STAR software.
Gene counts for reverse-stranded preparations were provided by STAR v2.7.7a using default parameters recommended by the STAR software.
Read counts output from the STAR v2.7.7a software were used to calculate fold-change using the DESeq2 package 1.24.0 in R-BiocManager Release 1.30.10.
Genome_build: All unmasked sequences from the rainbow trout primary assembly in Ensemble (Oncorhynchus_mykiss.Omyk_1.0.dna.primary_assembly)
Supplementary_files_format_and_content: Tab-delimited text files of effective read counts, rounded to the nearest whole number
|
| |
|
| Submission date |
Nov 08, 2021 |
| Last update date |
May 16, 2024 |
| Contact name |
Jason Abernathy |
| Organization name |
USDA-ARS
|
| Lab |
Aquatic Animal Health Research Unit
|
| Street address |
990 Wire Road
|
| City |
Auburn |
| State/province |
AL |
| ZIP/Postal code |
36832 |
| Country |
USA |
| |
|
| Platform ID |
GPL24430 |
| Series (1) |
| GSE188423 |
Underlying mechanisms for selected disease resistance and enhanced non-specific resistance in rainbow trout |
|
| Relations |
| BioSample |
SAMN22988465 |
| SRA |
SRX13062973 |
