biostudies-arrayexpressUnknownTranscriptomicsGenomicsProteomicsNares TrakooljulNextSeq 2000RNA-seq of coding RNAGallus gallusGallus gallushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-14546Co-infections with nematodes and protozoa occur frequently in free-ranging chickens and lead to complex local and systemic physiological responses, particularly in immune and metabolic pathways. This study aimed to investigate tissue-specific transcriptomic regulation in chickens co-infected with Ascaridia galli and Heterakis gallinarum, later developing a Histomonas meleagridis infection. The study focused on male birds of three chicken strains with different growth rates i.e. Lohmann Brown-LB, Lohmann Dual-LD, and Ross-308 and on three tissues; jejunum, caecum, and liver as these organs are predilection sites for the parasite life cycle, and are central in host nutrient absorption, local and systemic immune responses, and metabolic regulation.biostudies-arrayexpressSample Collection - Birds (n =12 per strain) were assigned to infection or control groups in a 3 × 2 factorial design. The infected group (n = 18 birds) were inoculated orally with 0.2 mL NaCl with 500 infective eggs of A. galli and H. gallinarum at one week of age while the control group (n = 18 birds) was given a placebo (0.2 mL saline solution). Two weeks after inoculation, birds were killed and tissue samples were dissected, snap frozen in liquid nitrogene and stored at -80 °C.Library Construction - Total RNA of one microgram (RIN > 8) was used for library preparation using an Illumina Stranded mRNA Prep, Ligation kit with a 10 PCR-cycle of amplification according to the manufacture's recommendation (Illumina). The libraries were quality checked on Bionalyzer for fragment length distribution and normalized to an equal concentration of 10nM prior to pooling.Sequencing - DNA libraries were pooled and paired-end sequenced for 2x59bp reads at 750 pM concentration on the NextSeq 2000 system using a P3 flowcell at the sequencing facility of the Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany. Raw sequencing reads (fastq) were generated using dragen bcl convert v3.10.11 and quality-checked using FastQC version 0.11.9 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Data preprocessing was performed using Trim Galore v.0.6.10 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Low quality reads (a mean Q-score < 20) and short reads (<20bp) were removed. Adapter-like sequences at the 3'-end of sequence reads were trimmed.Nucleic Acid Extraction - Frozen tissue samples from the jejunum, caecum, and liver (n = 108) were homogenized in liquid nitrogen to extract total RNA. Total RNA was extracted from approximately 40 mg of each sample, with subsequent steps of TRI reagent-based extraction (Sigma-Aldrich, Taufkirchen, Germany), DNaseI treatment (Roche Diagnostics, Mannheim, Germany ), and RNA purification (NucleoSpin RNA kit; Macherey-Nagel, Düren, Germany) according to the manufacturer's instructions. The RNA concentration was determined through spectrophotometry using the NanoDrop ND-2000 (Peqlab, Erlangen, Germany) and RNA quality of final RNA was analyzed with the Bioanalyzer 2100 device (Agilent Technologies, Waldbronn, Germany).OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesHenry ReyerNares TrakooljulGürbüz DaşfalseTissue-specific transcriptome regulation during intestinal nematode infection in chickens with different levels of growth performanceCo-infections with nematodes and protozoa occur frequently in free-ranging chickens and lead to complex local and systemic physiological responses, particularly in immune and metabolic pathways. This study aimed to investigate tissue-specific transcriptomic regulation in chickens co-infected with Ascaridia galli and Heterakis gallinarum, later developing a Histomonas meleagridis infection. The study focused on male birds of three chicken strains with different growth rates i.e. Lohmann Brown-LB, Lohmann Dual-LD, and Ross-308 and on three tissues; jejunum, caecum, and liver as these organs are predilection sites for the parasite life cycle, and are central in host nutrient absorption, local and systemic immune responses, and metabolic regulation.2025-10-14T00:00:00Z2025-10-14T01:02:06.218Z2024-10-21T20:09:18.164ZE-MTAB-14546ERP165347EFO_0002944EFO_0004170EFO_0005518EFO_0003738EFO_0004184