{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Nares Trakooljul"],"instrument_platform":["Illumina HiSeq 2500"],"study_type":["RNA-seq of coding RNA"],"organism":["Gallus gallus"],"species":["Gallus gallus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-9188"],"description":["In this study, we deep-sequenced the transcriptomic profile of the ileum 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 transcriptome profiling of the ileum mucosa may lead to a better understanding of molecular mechanisms underlying genetics, age and nutrition factors of layers."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Growth 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.","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. Ileum 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.","Library Construction - 2 µg of total RNA with RIN > 8 was used for library preparation using a TruSeq Stranded mRNA Kit with 11 cycles of PCR-amplification according to the manufacture’s recommendation (Illumina).","Nucleic Acid Extraction - Intestinal tissue samples were ground into powder in liquid nitrogen, and approximately 50 mg of the sample was homogenized in 1 ml of TRIzol Reagent (Invitrogen, Karlsruhe, Germany). Total RNA was extracted according to the manufacturer’s instructions. Extracted RNA was additionally treated with DNaseI using RNase-Free DNase Set (Qiagen) and purified using the RNeasy Mini Kit (Qiagen). The RNA quantity and quality was assessed using a NanoDrop ND-1000 (Peqlab) and a Bioanalyzer 2100 (Agilent Technologies), respectively.","Sequencing - Multiplexed DNA libraries were sequenced for 2x101bp paired-end reads except for 8 samples of age 60 weeks (2x71bp paired-end)   using the illumina HiSeq SBS Kit v4 in the high-output mode according to the manufacturer’s recommendation using an Illumina HiSeq 2500 instrument at the Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Nares Trakooljul","Michael Oster","Klaus Wimmers"],"additional_accession":[]},"is_claimable":false,"name":"Ileum mucosa transcriptome profiling of two laying hen strains at five time points spanning egg production phases during 10 to 60 weeks of age","description":"In this study, we deep-sequenced the transcriptomic profile of the ileum 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 transcriptome profiling of the ileum mucosa may lead to a better understanding of molecular mechanisms underlying genetics, age and nutrition factors of layers.","dates":{"release":"2025-12-28T00:00:00Z","modification":"2025-12-28T02:01:43.365Z","creation":"2022-02-23T15:40:40.842Z"},"accession":"E-MTAB-9188","cross_references":{"ENA":["ERP122141"],"Biostudies":["E-MTAB-9137"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0003738","EFO_0004184"]}}