Protocols: Tissue samples were dissected from the animals following an anatomical reference guide. The samples were immediately flash frozen in liquid nitrogen and kept at -80 °C until 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. The r nomenclature in the files stands for run not read. Files are single end technical replicates. 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 at 37 °C for 7 hours with 100U MspI (New England Biolabs) and then at 65 °C overnight with 50U TaqαI (New England Biolabs). The DNA fragments 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 PAGE to recover DNA inserts around 40-240bp. The adapter-ligated DNA libraries was subjected to a bisulfite conversion using EpiTect Bisulfite kit (Qiagen) according to the manufacturer's protocols. 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).
ENA first public
2022-06-15
ENA last update
2022-06-15
External Id
SAMEA9349149
INSDC center alias
Leibniz-Institute for Farm Animal Biology (FBN) Institute of Genome Biology/ Genomics Unit
INSDC center name
Leibniz-Institute for Farm Animal Biology (FBN) Institute of Genome Biology/ Genomics Unit
INSDC first public
2022-06-15T00:13:31Z
INSDC last update
2022-06-15T00:13:31Z
INSDC status
public
Submitter Id
E-MTAB-10640:Hip2635
age
147 to 167
broker name
ArrayExpress
clinical information
castrated
common name
pig
developmental stage
adult
genotype
wild type genotype
organism part
hippocampus
sample name
E-MTAB-10640:Hip2635
sex
male
strain
German Landrace