GSM8783754: 100254, 2 Kidney,OxBS (DNA Oxidation); Rattus norvegicus; Bisulfite-Seq
DNA was isolated from 4-week-old male HSRA-C (n=6) and HSRA-S (n=6) kidney samples using the PureLink Genomic DNA Mini Kit (Invitrogen) and quantified with the Qubit High-Sensitivity DNA Assay Kit. A total of 100 ng of genomic DNA was used as input for each sample in duplicate and libraries were processed using the Ovation RRBS Methylseq System 1-16 per manufacturer's instruction with a single adapter/index. Paired samples were subjected to either bisulfite conversion (RRBS) as well as the optional DNA oxidation procedure (oxRRBS). This allowed for the determination of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) modifications of genomic DNA. RRBS measures 5mC and 5hmC but does not differentiate between the two, while oxRRBS only measures 5mC modifications. Final libraries were validated by bioanalyzer (QIAxcel-DNA High Sensitivity) and concentrations were measured by fluorescence (Qubit HS DNA Assay Kit). Final libraries averaged ~300 base pairs in length and were normalized to 10nM for sequencing. Libraries were sequenced on Illumina NextSeq 2000 per Ovation RRBS Methyl-Seq specifications (100 PE reads) using a P2 200 cycle reagent kit.