title: GSM3752661: RNA-seq_DKO_Rep4; Mus musculus; RNA-Seq
library_construction_protocol: WGBS: Genomic DNA was extracted with the AllPrep DNA/RNA Mini Kit (Qiagen). WGBS: 50 ng of genomic DNA were fragmented to 350 bp using a Covaris E220 sonicator. DNA was bisulfite-converted with the EZ DNA Methylation-Gold kit (Zymo Research) and WGBS libraries were prepared using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences) according to the manufacturer's instructions with 7 PCR cycles for the final amplification. The libraries were purified using Ampure XP beads (Beckman Coulter). RRBS: Genomic DNA was extracted with the AllPrep DNA/RNA Mini Kit (Qiagen). RRBS: RRBS libraries were prepared as described in Auclair et al., Genome Biol 15:545 (2014). Briefly, we digested genomic DNA 5 hours with MspI (Thermo Scientific), followed by end-repair and A-tailing (Klenow fragment, Thermo Scientific) and ligation to methylated adapters (T4 DNA ligase, Thermo Scientific) in Tango 1X buffer. Fragments between 150 and 400 bp were excised from a 3% agarose 0.5X TBE gel with the MinElute kit (Qiagen) and bisulfite-converted with the EpiTect Bisulfite kit (Qiagen) using two consecutive rounds of conversion. Final RRBS libraries were amplified with 14-16 cycles of PCR. The libraries were purified using Ampure XP beads (Beckman Coulter). RNA-seq: Total RNA was extracted with the AllPrep DNA/RNA Mini Kit (Qiagen). RNA-seq: RNA-Seq libraries were prepared with the TruSeq Stranded Total RNA Sample Prep Kit (Illumina) with Ribo-Zero depletion according to the manufacturer's instructions.
attributes.tag: GEO Accession
attributes.value: GSM3752661