|
| Status |
Public on May 09, 2024 |
| Title |
F. columnare challenge hour4 white bass rep2 gill tissue |
| Sample type |
SRA |
| |
|
| Source name |
gill
|
| Organism |
Morone chrysops |
| Characteristics |
animal: white bass (WB)
tissue: gill
treatment: Flavobacterium columnare immersion
time: 4 hr after immersion
|
| Treatment protocol |
White bass (WB) and hybrid striped bass (HB) in the control group (t0hr) were given a mock treatment and sampled immediately prior to aquaria being challenged with 10 mL culture of Flavobacterium columnare isolate LSU-066-04 (0.70 absorbance at 550nm; 6.3X10^6 CFU/mL). Water was provided through the ultra-low-flow water delivery system at a rate of 30 ml/min for 24h then flow was increased to 200 mL/min. Fish were observed twice daily for the recording and removal of any dead or moribund fish, and fish were formally sampled at three timepoints after the challenge had been initiated, 1 hour post treatment (t1hr), 4 hours post treatment (t4hr), and 24 hours post treatment (t24hr).
|
| Growth protocol |
Fingerling white bass (WB) and hybrid striped bass (HB) (N=480 total, 240 of each) randomly selected from populations spawned indoors and reared in ponds to 2-3 months of age at the Harry K Dupree Stuttgart National Aquaculture Research Center (Stuttgart, Arkansas, USA) and stocked into 16 total replicate 18 L tanks (8 tanks for WB and 8 for HB, n=30 fish per tank). Fish were fed to apparent satiation 3 days per week, for 2 weeks prior to the study. Fish were not fed on the day before bacterial challenge or thereafter.
|
| Extracted molecule |
total 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.
Total RNA was standardized to 100 ng each sample. Sequencing libraries were then prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with the NEBNext Poly(A) mRNA Magnetic Isolation Module. Barcodes used were the NEBNext Multiplex Oligos for Illumina (Index Primers Sets 1 and 2).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
WB-2-t4hr
|
| 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 FastQC (v.0.11.8) and Trimmomatic (v.0.38). This was used to trim low-quality ends from reads and for Illumina adapter removal.
All reads were filtered for the removal of 18S, 5.8S, and 28S sequences using the STAR Gapped Mapper (v.2.7.8a) and Samtools (v.1.12) for alignment of sequences to the Morone 18S, 5.8S, and 28S sequences available on GenBank and output of unaligned reads used for subsequent analysis. This was completed as QC indicated the sequence reads WB-1-t4hr and HB-4-t4hr had 52.68% and 68.99% alignment to these sequences, respectively. These individuals were dropped from subsequent analysis.
The STAR Gapped Mapper (v.2.7.8a) and Samtools (v.1.12) were used to align all filtered reads generated for the other 46 samples to the white bass transcriptome using default parameters.
Read-counts were generated using the default parameters of HTSeq (v.0.9.0).
Gene expression fold-changes were determined between groups were determined in a pairwise fashion using edgeR (v.3.28.0) with TMM (Weighted trimmed mean of M-values) as the normalization method, Exact Test, and “robust” filter to strengthen estimations against potential outliers.
Assembly: All RNA transcripts from the white bass transcriptome shotgun assembly GAZY00000000.1 (GAZY01000001-GAZY01183659) in GenBank
Supplementary files format and content: tab-deliminated text file of read counts representing the total number of reads aligned to each genomic feature
|
| |
|
| Submission date |
Oct 23, 2023 |
| Last update date |
May 09, 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 |
GPL30659 |
| Series (1) |
| GSE246056 |
Gene expression profiles of white bass (Morone chrysops) and hybrid striped bass (M. chrysops x M. saxatilis) gill tissue over time following Flavobacterium covae exposure |
|
| Relations |
| BioSample |
SAMN37932539 |
| SRA |
SRX22182147 |
