biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsNares TrakooljulIllumina HiSeq 2000microRNA profiling by high throughput sequencingGallus gallusGallus gallushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-9138In this study, we deep-sequenced small RNAs of the jejunum mucosa in two laying hen strains (Lohmann Brown-Classic and Lohmann LSL-Classic) at 10, 16, 24, 30, and 60 weeks of age. These five time points span the initial, peak and end of the lay periods in which the hens critically experience physiological changes and need optimal diets to meet both growth and egg production requirements. Therefore, a comparative profiling of miRNAs, as key regulators of gene expression, in the jejunum mucosa may contribute to a better understanding of molecular mechanisms underlying genetics, age and nutrition factors of layers.biostudies-arrayexpressGrowth Protocol - The chicks were raised in group floor pens on deep litter bedding from hatchling until being moved to metabolic units at the age of 8, 14, 22, 28, and 58 weeks. All hens were fed standard corn-soybean meal-based diets according to the breeder’s recommendations and kept under comparable environments such as receiving 9 hours of light and 15 hours of darkness during 10 to 16 weeks of age, and 16 hours of light and 8 hours of darkness during 24 to 60 weeks of age.Library Construction - Small RNA sequencing libraries were generated from 1 µg of enriched small RNA using the SMARTer smRNA-Seq Kit for Illumina (Clontech Laboratories). Briefly, small RNA molecules were polyadenylated and reverse transcribed into first-strand cDNA using the MMLV-derived PrimeScript Reverse Transcriptase (RT). The SMART smRNA Oligo was then added to the 5´-end via the locked nucleic acid (LNA) technology. Illumina indexing adapters were incorporated during an additional PCR amplification to enable sample multiplexing. The smRNA-seq libraries were quality assessed for expected fragment length of a major peak at about 175bp using an Agilent High Sensitivity DNA kit and 2100 Bioanalyzer (Agilent Technology) and then size-selected using the BluePippin System and 3% agarose gel cassette with the internal Q2 DNA marker and size-selection parameters of 148 - 185bp (Sage Science). The molar concentration of the libraries was determined using a KAPA library quantification kit (KAPA Biosystem) and normalized to 2nM prior to sequencing.Sample Collection - The hens were slaughtered at the age of 10, 16, 24, 30, and 60 weeks for tissue sample collection. Before slaughtering, feed was deprived 2 h followed by 1 h ad libitum access to feed to standardize gut fill. The hens were individually stunned with a gas mixture of 35% CO2, 35% N2, and 30% O2 and killed by decapitation. The jejunum, terminal ileum, and ceca were identified and cut lengthwise. The digesta was gently removed and the gut was rinsed with saline. Jejunal mucosa was scraped off carefully using microscopic slides and flash frozen into liquid nitrogen, transported on dry ice to laboratory and subsequently stored at -80°C until analysis.Sequencing - Multiplexed libraries were parallel sequenced for 50bp single-reads using the high-output mode of an Illumina HiSeq2500 at the Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany. The base call (BCL) files from the sequencing run were de-multiplexed and converted into fastq files using the bcl2fastq2 conversion software, v2.19 (Illumina).Nucleic Acid Extraction - Total RNA was extracted from approximately 50 mg of tissue sample using Qiazol Lysis reagent (Qiagen) and further enriched for small RNAs using a miRNeasy Mini kit (Qiagen) according to the manufracturer’s recomendations. The integrity of total RNA was assessed using an Agilent RNA 6000 Nano kit and the enrichment and concentration of microRNAs were determined using an Agilent small RNA kit and the 2100 Bioanalyzer system (Agilent Technologies).OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesNares TrakooljulSiriluck PonsuksilifalsemicroRNA profiling of jejunum mucosa of two laying hen lines at five time points during egg production period between 10 to 60 weeks of ageIn this study, we deep-sequenced small RNAs of the jejunum mucosa in two laying hen strains (Lohmann Brown-Classic and Lohmann LSL-Classic) at 10, 16, 24, 30, and 60 weeks of age. These five time points span the initial, peak and end of the lay periods in which the hens critically experience physiological changes and need optimal diets to meet both growth and egg production requirements. Therefore, a comparative profiling of miRNAs, as key regulators of gene expression, in the jejunum mucosa may contribute to a better understanding of molecular mechanisms underlying genetics, age and nutrition factors of layers.2025-12-28T00:00:00Z2025-12-28T02:01:43.364Z2022-03-10T04:10:25.653ZE-MTAB-9138ERP122025E-MTAB-9137EFO_0002944EFO_0004170EFO_0003789EFO_0002896EFO_0005518EFO_0004184