Replication Data for: Circulating miRNAome of avian influenza-infected ruddy turnstones (Arenaria interpres) (doi:10.18710/PYOFFX)

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Replication Data for: Circulating miRNAome of avian influenza-infected ruddy turnstones (Arenaria interpres)

doi:10.18710/PYOFFX

DataverseNO

2024-12-12

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Brand, Anne-Fleur, 2024, "Replication Data for: Circulating miRNAome of avian influenza-infected ruddy turnstones (Arenaria interpres)", https://doi.org/10.18710/PYOFFX, DataverseNO, V1

Replication Data for: Circulating miRNAome of avian influenza-infected ruddy turnstones (Arenaria interpres)

doi:10.18710/PYOFFX

Brand, Anne-Fleur (NTNU – Norwegian University of Science and Technology)

Jaspers, Veerle

Brand, Anne-Fleur

Andreassen, Rune

Klaassen, Marcel

Wille, Michelle

Fernandes, Jorge

Waugh, Courtney

NTNU – Norwegian University of Science and Technology

2022-07-01

Cutadapt

FastQC

MultiQC

miRDeep2

bowtie

STAR

Rsubread

DESeq2

R

LightCycler 96 analysis software

LinRegPCR

BLASTN

302205

DataverseNO

NTNU – Norwegian University of Science and Technology

Jaspers, Veerle

Brand, Anne-Fleur

2024-12-12

https://doi.org/10.18710/PYOFFX

Medicine, Health and Life Sciences, microRNA, small RNA sequencing, circulating microRNA, shorebird, qPCR, avian influenza, Arenaria interpres

<p>This dataset contains the data required to reproduce the analysis and the figures in the paper: Circulating miRNAome of avian influenza-infected ruddy turnstones (<i>Arenaria interpres</i>) (doi: 10.1111/jav.03404). </p> <p><strong>Article abstract: </strong></p> <p>MicroRNAs (miRNAs) are highly conserved small noncoding RNAs that regulate gene expression post-transcriptionally. Circulating miRNAs - miRNAs that have been released from cells and circulate in the bloodstream - are relatively stable and interesting molecules for wildlife research, where they may form a proxy for gene expression as a function of the animal’s state under a variety of environmental challenges. Aiming at providing initial baseline data on the circulating miRNAome in avian wildlife, we assessed the miRNA profiles of wild ruddy turnstones (<i>Arenaria interpres</i>) on their Australian non-breeding grounds. The ruddy turnstone is a long-distant migrant and a significant reservoir species for low pathogenic avian influenza virus (LPAIV). We therefore investigated both LPAIV-infected and uninfected individuals for their specific miRNA profiles to potentially elucidate the species’ molecular mechanisms underlying its response to LPAIV infection. De novo miRNA characterisation in the ruddy turnstone genome identified 161 conserved and two novel, bird-specific miRNAs, with liver-enriched miRNA-122 being the most abundant. Z chromosome-linked miR-2954-3p was significantly more abundant in serum from males (ZZ) than from females (ZW). Furthermore, we found a sex- and age-associated effect of LPAIV infection on miRNA abundance in serum samples, including one novel miRNA. This circulating miRNA signature may reflect sex- and age-specific differences in the host response, indicating that circulating miRNAs could serve as a valuable non-destructive analytical tool for enhancing our understanding of avian infections in a wildlife context and should be explored further.</p> <p> The data analysis pipeline for processing the sequencing data is contained in the script 01_MicroRNA_Sequencing_Analysis.sh. This script utilizes raw sequencing reads, which have been deposited in the European Nucleotide Archive (ENA) under accession numbers ERR10462083-94 (project accession PRJEB47802), as input data. The pipeline includes steps for quality control, adapter trimming, read filtering, <i>de novo</i> microRNA discovery, and differential expression analysis. The script 02_Coding_Article_Figures.sh contains the code used to generate the figures in the article. </p> <p>For mapping and quantification, the file 03_ain_miRNAome.fasta, which contains the mature mioRNA sequences from ruddy turnstones (<i>Arenaria interpres</i>), is required. 04_Fastqc_Sequence_Length_Distribution_Plot.tsv is required to create Figure 2. The file 05_FeatureCounts_output.tsv contains the feature counts used for differential expression analysis. Figure 4, Table 3 and 4 in the article, and Supplemental Information Figure S3 were generated based on the results from this pipeline. The files 06_eff.RTS.csv and 07_mcmc.RTS.csv were used to generate Figure 5, Supplemental Information Figure S4 and Table S8.</p>

miRBase 22.1 RNA Central v20 Genbank Reference RNA sequence database release 211

<a href="http://creativecommons.org/publicdomain/zero/1.0">CC0 1.0</a>

Raw sequencing reads have been deposited in the European Nucleotide Archive (ENA) under accession numbers ERR10462083-94 (project accession PRJEB47802). The ruddy turnstone (Arenaria interpres) genome was downloaded from: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/399/435/GCA_013399435.1_ASM1339943v1/GCA_013399435.1_ASM1339943v1_genomic.fna.gz The mature and hairpin sequences from microRNAs in miRBase were downloaded from: ftp://mirbase.org/pub/mirbase/CURRENT/mature.fa.gz ftp://mirbase.org/pub/mirbase/CURRENT/hairpin.fa.gz

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00_README.txt

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01_MicroRNA_Sequencing_Analysis.sh

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This script outlines a bioinformatics pipeline for processing and analyzing RNA sequencing data of microRNAs (miRNAs) in ruddy turnstones, including quality checks, adapter trimming, read filtering, mapping, feature counting, and differential expression analysis.

text/x-sh

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02_Coding_Article_Figures.sh

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This file contains the scripts used for generating the manuscript figures.

text/x-sh

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03_ain_miRNAome.fasta

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This file contains mature microRNA (miRNA) sequences from ruddy turnstones (Arenaria interpres). Each sequence represents a different miRNA arm, either the 3' or 5' arm, and is associated with a specific miRNA family. The file is formatted in FASTA, where each sequence is preceded by a header line starting with >, followed by a description or identifier for that sequence.

application/octet-stream

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04_Fastqc_Sequence_Length_Distribution_Plot.tsv

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This file, extracted from the MultiQC report, summarizes the sequence length distribution of the clean small RNA-seq reads for each sample after FastQC quality assessment. This file was used to generate Figure 2 of the manuscript, which visually presents the distribution of read lengths (18-25 nt) across all the samples.

text/tsv

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05_FeatureCounts.tsv

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This file, generated from the featureCounts function, contains miRNA counts, derived from a set of BAM files. The file provides raw counts for each miRNA feature, with each row corresponding to a unique miRNA ID, and each column representing a sample.

text/tsv

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06_eff.RTS.csv

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This file contains amplification efficiencies for each miRNA target. These efficiencies, which represent the amplification factor per PCR cycle, are essential for accurate data normalization in qPCR analysis.

text/comma-separated-values

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07_mcmc.RTS.csv

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This file contains qPCR data and metadata for each sample, including the bird's sex, age, and AIV infection status, for use with the mcmc.qpcr package.

text/comma-separated-values