ChIP-Atlas: SRX6762249

Antigen

Cell type Class: Liver
Cell type: Liver
MeSH Description: A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.

library_strategy: Bisulfite-Seq
library_source: GENOMIC
library_selection: RANDOM
library_construction_protocol: Livers were surgically retrieved, frozen in dry ice, and stored at -80°C. Pelleted minced tissue was homogenized further with sterile disposable pestles using a hand-held motor (Kimble) in the presence of 1 mL of Trizol reagent (Invitrogen) and fractionated according to the manufacturer's instructions to obtain total RNA, genomic DNA, and protein fractions. WGBS libraries were constructed from starting 1ug genomic DNA and 50ng phage lambda, sheared via BioRuptor, subjected to bisulfite conversion (EZ DNA methylation kit; Zymo research), ligated and amplified with methylated adapters (TruSeq RNA v2; Illumina) and low-input DNA ligation chemistry (HyperPrep; KAPA Biosystems). RNAseq libraries were constructed starting with poly-A-selected RNA from 1 µg of DNaseI-treated total RNA input using a magnetic poly-dT bead hybridization capture (Illumina), eluted in 10µL of nuclease-free H2O, transferred as magnetically isolated supernatant to RNase-free wells of a 96-well reaction plate, and used directly for rRNA-free library assembly using a KAPA Stranded RNA-Seq with RiboErase commercial kit (KAPA Biosystems).