GSM3379780: cohort1.P2C3.fastq.gz; Rattus norvegicus; Bisulfite-Seq
The first buccal swab was collected from both cheeks of each pup prior to randomization on P2, using Hydraflock swab (Puritan diagnostics, LLC). After an hour's rest with their mother, a  second buccal swab was collected, enabling sufficient DNA from each pup. Pups were then randomized to controls or LBN cages. During P3-P9,  behaviors of dams in both control and adversity/LBN cages was observed daily, to ascertain the generation of fragmented unpredictable caring patterns by the adverse environment (Molet et al. 2016; Davis et al. 2017). On P10, buccal swabs were collected as described for P2, then all litters were transferred to normal bedded cages. The Buccal swab was placed into the DNA shields™ (Zymo research) immediately after swabbing. DNA was prepared from the DNA shields solution using the Quick-gDNA™ MiniPrep kit (Zymo Research) following  the manufacturer's protocol. The quantity of double stranded DNA was analyzed using Qubit, and RRBS Libraries were prepared from 40 ng of genomic DNA digested with Msp I and then extracted with DNA Clean & Concentrator™-5 kit (Zymo Research). Fragments were ligated to pre-annealed adapters containing 5'-methyl-cytosine instead of cytosine according to Illumina's specified guidelines (www.illumina.com). Adaptor-ligated fragments were then bisulfite-treated using the EZ DNA Methylation-Lightning™ Kit (Zymo Research). Preparative-scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator for sequencing. Amplified RRBS libraries were quantified and qualified by Qubit, Bioanalyzer (Agilent), and Kapa library quant (Kapa systems), and then sequenced on the Illumina NextSeq 500 platform.
GEO Accession
GSM3379780