biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsNares TrakooljulIllumina HiSeq 2000ATAC-seqGallus gallusGallus gallushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-14836This study investigated changes of chromatin accessibility of the gut associated with the removal and reduction of Phosphorus (P) (0 and 1 g P/kg feed) during the transition to egg production at 19 and 24 weeks (before and after the onset of laying, respectively) of Lohmann Brown (LB) and Lohmann Selected Leghorn (LSL) chickens. The experiment is a 2x2x2 factorial design, encompassing two strains, age groups, and diets and including a total of 80 (LB and LSL) hens. Unfortunately, two outliers were excluded from the final analysis based on quality control of library preparation and sequencing.biostudies-arrayexpressSample Collection - Forty LB and 40 LSL hatchlings were obtained from Lohmann Tierzucht GmbH, Cuxhaven, Germany. Hens were housed individually in metabolism crates starting at 15 or 20 weeks of age. The experimental diets were provided for four weeks before hens were slaughtered at weeks 19 and 24. This experiment had a 2×2×2-factorial arrangement of treatments with hen strain, hen age (19 and 24 weeks, representing before and after the onset of laying), and mineral P supplement (0 and 1 g P/kg of feed). Diets were maize-soybean meal-based, without a phytase supplement, and otherwise composed to contain all nutrients at recommended levels. The P concentration in the plant-based diet, without a mineral P supplement, was about 3 g/kg, equivalent to approximately 1.5 g/kg of NPP. Ten hens per strain and age were sampled, according to the diet treatments (80 hens in total), and each pen served as one experimental unit for all measurements in the statistical analysis. The hens were killed by electronic stunning and exsanguination from 07:00 to 13:00. Jejunum samples approximately 2 cm were collected from approximately 3 cm distal to the duodenal loop. The samples were cut open; the mucosa was thoroughly rinsed with a 0.9% NaCl solution, and scraped for each bird. The small intestinal mucosa (jejunum) samples were immediately frozen in liquid nitrogen and stored at -80 °C until analysis.Sequencing - The DNA libraries were sequenced for 2x100bp paired-end on a NextSeq 2000 sequencer (Illumina, San Diego, CA, USA).Library Construction - ATAC-seq libraries were generated using an already-established protocol for cryopreserved nuclei (Buenrostro et al., 2015; Halstead et al., 2020). Samples were collected, slowly frozen, and cryopreserved to keep the viability of cells. Density gradient centrifugation with iodexanol was employed to eliminate contaminating mitochondria. Nuclei were counted using Trypan solution to assess the optimal viable nuclei (>50,000) needed for transposition using Illumina Tagment DNA Enzyme and Buffer Kit (Tn5 Transposase/Tagment DNA Enzyme 1) according to the manufacturer's protocol (Illumina, San Diego, CA, USA). Tween 20 and Digitonin were added to the transposition reaction to increase nuclear permeabilization and efficiency. PCR was performed to amplify transposed fragments using the Illumina unique dual indexes. The libraries were quality control for fragment length distribution on DNA chip using Agilent Bioanalyzer 2100.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesNares TrakooljulSiriluck PonsuksilifalseChromatin accessibility profiling of the jejunum mucosa of two laying hen strains associated with low dietary PhosphorusThis study investigated changes of chromatin accessibility of the gut associated with the removal and reduction of Phosphorus (P) (0 and 1 g P/kg feed) during the transition to egg production at 19 and 24 weeks (before and after the onset of laying, respectively) of Lohmann Brown (LB) and Lohmann Selected Leghorn (LSL) chickens. The experiment is a 2x2x2 factorial design, encompassing two strains, age groups, and diets and including a total of 80 (LB and LSL) hens. Unfortunately, two outliers were excluded from the final analysis based on quality control of library preparation and sequencing.2026-04-24T00:00:00Z2026-04-24T08:01:11.671Z2025-02-13T23:36:52.936ZE-MTAB-14836ERP169225E-MTAB-14040EFO_0007045EFO_0004170EFO_0005518EFO_0004184