GENERAL INFORMATION 
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1. Dataset title: Dataset Sea bass rtp3 and its interaction with NNV


2. Authors: M. Carmen Alonso, Esther Garcia-Rosado, Julia Bejar, Patricia Moreno


3. Author contact information: M. Carmen Alonso (mdalonso@uma.es)


METHODOLOGICAL INFORMATION 
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1. Description of the methods for collection/generation of data: 

-Genomic DNA was obtained from sea bass caudal fin by saline precipitation, and cDNA was obtained from sea bass intraperitoneally injected with poly I:C. European sea bass rtp3 genes were amplified and sequenced.
-Injection of LPS, poly I:C and NNV in European sea bass. Brain and kidney were sampled at several times post-infection and processed for RNA extraction and rtp3 gene transcription analyses
-Cloning of rtp3 ORFs in expression vector and transfection in E-11 cells
- Inoculation of NNV in rtp3 expressing cells and evaluation of cellular survival (MTT and cristal violet), viral genome quantification (qPCR), viral titre, modulation of immune genes (qPCR)

2. Data processing methods

- Sequencing, aligment, phylogenetic analysis
- Sampling
- RNA extraction, cDNA sysnthesis and PCR amplification
- mRNA transcription of immunogenes
- cloning and transfection
- Viral genome quantification by absolute qPCR
- Viral titration

3. Software or instruments needed to interpret the data:
- Statistical analysis: data analyses were performed with GraphPad software GraphPad
- PCR amplifications were conducted with Lightcycler 96 thermocycler (Roche Diagnostics, S.L.U, Swiss) 
- Images analyses were perfomed with Fiji software

4. Standards and calibration information, if appropriate: not applicable

5. Environmental or experimental conditions:
- Virus propagation and cell culture: E-11 cells were grown in Leibovitz L-15 medium (Gibco, Paisley, UK) supplemented with 10% foetal bovine serum (FBS, Gibco, Paisley, UK), 100 unit/mL penicillin and 10 mg/mL streptomycin (Sigma) at 25 °C until confluence. 
The viral isolates SpDl-IAusc965.09 (DlNNV, RGNNV genotype) were propagated in E-11 cell in L-15 medium supplemented with 2% FBS, 100 units/mL penicillin and 10 mg/mL streptomycin at 25 ºC 
-Fish maintenance: fish were maintained under the following conditions for 30 days: 24 ± 0.5 ºC, pH 7.5 ± 0.5, salinity 38 ± 1 ppt, oxygen 6 ± 1 mg/l, NO2 < 3 mg/l, light 12 h.

FILE OVERVIEW 
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The dataset is distributed in 16 files in .pdf, .txt and .xlsx formats. This provides information on:
	- Aa alignment (.pdf)
	- Genetic characterization (.pdf)
	- Phylogenetic tree (.pdf)
	- Sequence (.pdf)
	- Growth curve Dlrtp3 X1-E11 (.xlsx)
	- Growth curve Dlrtp3 X2-E11 (.xlsx)
	- Growth curve Dlrtp3 X1+X2-E11 (.xlsx)
	- Immune genes modulation mx (.xlsx)
	- Immune genes modulation tnf alpha (.xlsx)
	- MTT cellular suvival assay MOI 0.01 (.xlsx)
	- Transcription Dl rtp3 X1 in vivo (.xlsx)
	- Transcription Dl rtp3 X2 in vivo (.xlsx)
	- Viral replication absolute qPCR (.xlsx)
	- Viral titre RGNNV MOI 0.01 (.xlsx)
	- Results Crystal Violet staining (.xlsx)
	- TUNEL assay (.txt)

DATA-SPECIFIC INFORMATION:
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1. Name File: Aa alignment (.pdf)

1.1. Variables list:
Variable name: Aminoacid
Description: Aminoacid alignment of European sea bass RTP3 proteins (X1 and X2) with other fish RTP3.
Units of measure or value labels: Not applicable

1.2. Codes or symbols: 
* total alignment
: partial alignment
	
1.3. Special formats or abbreviations used: Not applicable

2. Name File: Genetic characterization (.pdf)

2.1. Variables list:
Variable name: not applicable
Description: European sea bass rtp3 variant sequence analysis
Units of measure or value labels: Not applicable

2.2. Codes or symbols: 
Code or symbol: 
Exons are represented in boxes and introns with lines.
Coding regions are in black, the untranslated regions in white, and zinc-binding domain  are in blue. Size of each element are indicated by number (bp). 
	
2.3. Special formats or abbreviations used: not applicable

3. Name File: Phylogenetic tree (.pdf)

3.1. Variables list:
Variable name: sequence
Description: Neighbour-joining phylogenetic tree based on complete amino acid sequences of fish rtp3 gene, using human (Homo sapiens) and mouse (Mus musculus) as outgroup. The evolutionary distances were computed using the Poisson correction method.
Units of measure or value labels: Not applicable

3.2. Codes or symbols: 
Code or symbol: bar indicate 0.1 amino acid substitutions per site.  

3.3. Special formats or abbreviations used: not applicable

4. Name File: Sequence (.pdf)

4.1. Variables list:
Variable name: Secuence
Description: alignment of nucleotide sequence of the European sea bass rtp3 genes X1 and X2. 
Units of measure or value labels: not appicable

4.2. Codes or symbols:
Start and stop codons are indicated in blue boxes 
ATTTA sequence with brown boxes 
poly A signal sequence in a green box
Introns are represented in the sequence with a yellow line
* total alignment
: partial alignment

4.3. Special formats or abbreviations used: not applicable

5. Name File: Growth curve Dlrtp3 X1-E11 (.xlsx)
5.1. Variables list:
Variable name: Cell growth
Description: Growth curves of Dlrtp3 X1-Ell cell line compared to non-transfected E-11 cells
Units of measure or value labels: cell/ml

Variable name: sampling time
Units of measure or value labels: days after cell were seeded

5.2. Codes or symbols: No specific codes have been used 

5.3. Special formats or abbreviations used: Not applicable

6. Name File: Growth curve Dlrtp3 X2-E11 (.xlsx)

6.1. Variables list:
Variable name: Cell growth
Description: Growth curves of Dlrtp3 X2-Ell cell line compared to non-transfected E-11 cells
Units of measure or value labels: cells/ml

Variable name: sampling time
Units of measure or value labels: days after cell were seeded

6.2. Codes or symbols: No specific codes have been used 

6.3. Special formats or abbreviations used: Not applicable


7. Name File: Growth curve Dlrtp3 X1+X2-E11 (.xlsx)

7.1. Variables list:
Variable name: Cell growth
Description: Growth curves of Dlrtp3 X1+X2-Ell cell line compared to non-transfected E-11 cells
Units of measure or value labels: cell/ml

Variable name: sampling time
Units of measure or value labels: days after cell were seeded

7.2. Codes or symbols: No specific codes have been used 

7.3. Special formats or abbreviations used: Not applicable

8. Name File: Immune genes modulation mx (.xlsx)

8.1. Variables list:
Variable name: poly I:C inoculation
Description: Analysis of the endogenous mx gene transcription in E-11 cells and rtp3 expressing cells inoculated with poly I:C
Units of measure or value labels: Quantitative values ​​expressed as Cq (mx and endogenous gen, beta-actin)

Variable name: sampling time
Units of measure or value labels: hours after inoculation

8.2. Codes or symbols: No specific codes have been used 

8.3. Special formats or abbreviations used: Not applicable.


9. Name File: Immune genes modulation tnf alpha (.xlsx)

9.1. Variables list:
Variable name: bacterial extract inoculation
Description: Analysis of the endogenous mx gene transcription in E-11 cells and rtp3 expressing cells inoculated with bacterial extracts
Units of measure or value labels: Quantitative values ​​expressed as Cq (mx and endogenous gen, beta-actin)

Variable name: sampling time
Units of measure or value labels: hours after inoculation

9.2. Codes or symbols: No specific codes have been used 

9.3. Special formats or abbreviations used: Not applicable.


10. Name File: MTT cellular suvival assay MOI 0.01 (.xlsx)

10.1. Variables list:
Variable name: NNV inoculation
Description: Analysis of cellular survival of E-11 and rtp3 expressing cells in response to NNV. Cellular survival was measured by MTT method
Units of measure or value labels: Quantitative values ​​expressed as measurements of the optical density at 550nm or OD550  of absorbance.

Variable name: cellular type
Units of measure or value labels: absorbance 

10.2. Codes or symbols: No specific codes have been used 

10.3. Special formats or abbreviations used: Not applicable.


11. Name File: Transcription Dl rtp3 X1 in vivo (.xlsx)

11.1. Variables list:
Variable name: injection
Description: Naive fish were sampled to analysed basal transcription and, additionally, fish were injected with L-15, LPS, poly I:C and RGNNV to evaluate rtp3 transcription in vivo.
Units of measure or value labels: Quantitative values expressed as Cq (rtp3 and endogenous gen, 18S)

Variable name: organ (brain and head kidney) and sampling time
Units of measure or value labels: days after injection

11.2. Codes or symbols: No specific codes have been used 

11.3. Special formats or abbreviations used: Not applicable.


12. Name File: Transcription Dl rtp3 X2 in vivo (.xlsx)

12.1. Variables list:
Variable name: injection
Description: Naive fish were sampled to analysed basal transcription and, additionally, fish were injected with L-15, LPS, poly I:C and RGNNV to evaluate rtp3 transcription in vivo.
Units of measure or value labels: Quantitative values expressed as Cq (rtp3 and endogenous gen, 18S)

Variable name: organ (brain and head kidney) and sampling time
Units of measure or value labels: days after injection

12.2. Codes or symbols: No specific codes have been used 

12.3. Special formats or abbreviations used: Not applicable.


13. Name File: Viral replication absolute qPCR (.xlsx)

13.1. Variables list:
Variable name: inoculation
Description: E-11 cells and European sea bass rtp3 expressing cells were inoculated with NNV and viral genome was quantified to analyse viral propagation.
Units of measure or value labels: Quantitative values expressed as Cq (RNA1 segment and RNA2 segment)

Variable name: sampling time
Units of measure or value labels: days after inoculation

13.2. Codes or symbols:
The standard curve is represented as Cq corresponding to a specific log of copy number of plasmid containing viral segment.

13.3. Special formats or abbreviations used: Not applicable.


14. Name File: Viral titre RGNNV MOI 0.01 (.xlsx)

14.1. Variables list:
Variable name: inoculation
Description: E-11 cells and European sea bass rtp3 expressing cells were inoculated with NNV and viral particles released in the supernantants were quantified to analyse viral propagation.
Units of measure or value labels: TCID50/ml

Variable name: sampling time
Units of measure or value labels: days after inoculation

14.2. Codes or symbols: No specific codes have been used 

14.3. Special formats or abbreviations used: Not applicable.


15. Name File: Results Crystal Violet staining (.xlsx)

15.1. Variables list:
Variable name: NNV inoculation
Description: Analysis of cellular survival of E-11 and rtp3 expressing cells in response to NNV. Cellular survival was measured by crystal violet staining
Units of measure or value labels: Quantitative data were obtained defining the % of area stained.  A maximum area of study was defined, and was the same for all cell lines

Variable name: cellular type
Units of measure or value labels: % of area stained

15.2. Codes or symbols: No specific codes have been used 

15.3. Special formats or abbreviations used: Not applicable.

16. Name File: TUNEL assay (.txt)

16.1. Variables list:
Variable name: Apoptosis 
Description: Apoptosis signal in infected and non-infected E-11, Dlrtp3X1-E11, Dlrtp3X2-E11 and Dlrtp3X1+X2-E11 cells was evaluated at 5 days post-infection using the TUNEL assay. 
Units of measure or value labels: Apoptotic signal was quantitatively analysed with the ImageJ software (NIH), and expressed as percentage of nuclei showing FITC fluorescence relative to the total number of nuclei. 

Variable name: cellular type
Units of measure or value labels: 

16.2. Codes or symbols: Referenced to number of nuclei detected 
Label 
Area	Area of the nuclei
Mean	Promedium value of intensity of GFP signal detected
StdDev	Desvest
Min	Minimum value of intensity of GFP signal detected
Max	Maximum value of intensity of GFP signal detected
IntDen	Intermediate density of GFP signal detected

16.3. Special formats or abbreviations used: Not applicable.


MORE INFORMATION

These data derived from the project "Interplay between nodavirus virulence and innate response in sea bass and sea bream (INTERNODASS)" (Proyectos de I+D+i Retos Investigación, PID2020-115954RB-I00), and it has been published in Moreno et al. (2023) Genomic characterization and transcription analysis of European sea bass
(Dicentrarchus labrax) rtp3 genes, Molecular Immunology, 163, 243-248 (https://doi.org/10.1016/j.molimm.2023.10.009), and in Moreno et al. (2026) Functional assessment of European sea bass RTP3 proteins and their effect
on RGNNV replication, Fish and Shellfish Immunology, 168, 111002 (https://doi.org/10.1016/j.fsi.2025.111002)
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