2025-07-18
ENA first public
ERC000011
ENA-CHECKLIST
Research Institute for Farm Animal Biology (FBN)
INSDC center name
public
INSDC status
ERS18930045
SRA accession
E-MTAB-14007:15W33974
Submitter Id
60
week
age
ArrayExpress
broker name
not collected
collection date
chicken
common name
Protocols: Tissue samples were dissected from the animals following an anatomical reference guide. 2 cm long jejunum sample was taken about 3 cm distal to the duodenal loop of each bird, cut open and rinsed with sterilized saline buffer to remove digesta residues. The intestinal epithelium was scraped using sterilized razor blades. The mucosa sample was frozen on dry ice and stored at -80°C upon DNA extraction. All animal care and sample collection procedures were in compliance with the German Animal Protection Law and approved by the FBN animal care committee.  Genomic DNA was extracted from samples using a DNeasy kit (Qiagen) according to the manufacturer’s recommendation including proteinase K digestion and RNase A treatment to obtain high purity DNA.  2 µg of DNA was spiked-in with 1% DNA control of unmethylated cl857 Sam7 Lambda DNA (Promega) and digested for 7 hours with 100U MspI (New England Biolabs) and then overnight with 50U TaqαI. The DNA fragments (double-enzyme digested) were end-repaired, A-tailed and ligated to TruSeq DNA adapters using a TruSeq Nano DNA library prep kit (Illumina) according to the manufacturer’s protocols. Size-selection of the adapter-ligated DNA fragments were achieved by using sample purification beads (TruSeq Nano DNA library prep kit) to recover DNA inserts around 40–240bp. The adapter-ligated DNA libraries was subjected to a bisulfite conversion using an EZ DNA Methylation-Gold Kit according to the manufacturer’s protocols (Zymo Research). Library amplification was performed using a PfuTurbo Cx Hotstart DNA Polymerase kit (Stratagene). The quality of libraries was assessed on 2100 Bioanalyzer using a high-sensitive DNA chip (Agilent Technologies).
description
adult
developmental stage
wild type genotype
genotype
not collected
geographic location (country and/or sea)
not applicable
isolate
Gallus gallus
organism
Gallus gallus
organism
jejunum mucosa
organism part
Gallus gallus
scientific_name
female
sex
Lohmann LSL-Classic
strain
15W33974
title