High-throughput RNA dataset of viral transcripts associated with chickens from various poultry farms in North and South Kuwait

Screening of poultry using RNA sequencing could enable the timely detection and identification of emerging viral pathogens, facilitating proactive measures to prevent and control potential outbreaks in the poultry industry. The reported dataset is of reads from RNA-Seq libraries consisting of approximately 130 gigabytes of RNA-sequencing data corresponding to blood, trachea and cloaca of chicken from various farms of North and South Kuwait regions. The sequences were quality-filtered and first mapped with the Chicken reference genome. The unmapped reads were aligned to the viral reference genomes. The aligned data was used for the quantification of viral transcripts across the samples. The RNA sequencing data could be useful for further meta-analysis and to extract valuable insights into the molecular landscape of poultry health. The insights gained from this research can guide the development of targeted diagnostic tools and strategies for effective poultry health management.


Value of the Data
• The RNA sequencing data is valuable for researchers involved in poultry transcriptome research.The dataset could be used to detect and identify emerging viral pathogens.• The dataset offers comprehensive insights into the molecular landscape of poultry health and understanding of viral diversity for effective surveillance and risk assessment.• The downstream analysis and interpretation of the results of the RNA sequencing data could serve as a valuable resource for researchers and provide molecular insights that support evidence-based decision-making for policymakers in the control and prevention of reemergent viral pathogens.

Background
The escalating threat of recurrent outbreaks and the potential emergence of highly pathogenic strains of viruses necessitate a proactive and vigilant approach to monitoring viral diseases in live birds.Early detection of viral pathogens is paramount in preventing major epidemics and safeguarding both the poultry industry and public health.In this context, employing advanced molecular diagnostic tools, particularly Next Generation Sequencing (NGS) based on RNA sequencing has emerged as a crucial component in comprehensive surveillance strategies.The main objective of the study was to explore the viral transcriptome associated with Chicken tissues from six different farms in North and South Kuwait regions.

Data Description
This article describes the dataset of the linked repository of around 130 Giga bytes of RNAsequencing data from various tissues (blood, trachea, and cloacal) of chickens from six different farms in North and South Kuwait.The sample information and the quality of the data are indicated in Tables 1 and 2 , respectively.
High-quality reads obtained after a thorough filtering process were processed further as described in the experimental design, materials and methods section to identify the viral transcripts in the samples.The read counts of identified viruses per sample are summarized in a bar-plot presented in Fig. 1 .Four viral transcripts viz., ASVP2257_gs1, FuSVgp1, lambdap54, and P4s05 corresponding to four viral species were identified that were distributed across the samples.ASVP2257_gs1 transcript from Y73 Avian sarcoma virus (PR2257 / PR2257/16) was identified in more samples (8/18) compared to others.Interestingly, this transcript is detected in all the blood samples from both North and South Kuwait farms, and tracheal swabs from two farms of North Kuwait.Another avian sarcoma viral transcript viz., FuSVgp1 from Fujinami sarcoma virus was detected in one blood (AT, South Kuwait) and one tracheal swab (NP, North Kuwait) samples.The next common transcript detected in four samples belonged to Escherichia phage Lambda (nat-host: Escherichia coli) and was detected in three tracheal swab samples of both Northern and Southern farms, and a cloacal swab sample (HA, North Kuwait).P4s05 from Enterobacteria-phage-P4 was found to be in high abundance comparatively, however it was detected only in one of the blood samples (NA, South Kuwait).Overall, across all samples, the abundance of the detected viral transcripts was low in most cases.

Sampling
Samples of blood, cloaca, and trachea were obtained from chickens from the local farms of Kuwait.Out of the six selected farms, three were chosen from the northern region and the remaining three were selected from the southern region of Kuwait ensuring a geographically diverse dataset.The samples were coded to protect the identity of the farms.Total RNA was isolated from chicken samples using QIAamp RNA extraction kit.RNA isolated from three randomly selected samples are combined to create a composite sample for each sample type.After the pooling of triplicate samples, a total of 18 composite samples representing six farms, and three sources (blood, cloaca & trachea) from two zones (north and south of Kuwait) were selected for downstream processing.Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads.RNA was fragmented and the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis.Samples were sequenced on an Illumina platform.Sequence data was processed using various bioinformatics tools.The highquality filtered reads were mapped against the Chicken reference genome.The unmapped reads were aligned to the viral reference genomes.The aligned reads were quantified.The read counts were considered for comparison across samples.Details of the analysis are provided in the subsequent sections.

Fig. 1 .
Fig. 1.Predominant group of viruses found in the poultry RNA samples.

Table 1
Sample information of the RNASeq libraries.

Table 2
Data quality summary.