ChIP-Atlas: SRX2364127

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: Control livers and tumors were disected and DNA was extracted from each individual sample using Phenol-chloroform protocol. Then, genomic DNA was used to analyze the DNA methylation profile by the EpiQuest™ Genome-Wide Full Service (Zymo Research Company). This included sample standardization, library preparation, bisulfite conversion, next-generation bisulfite sequencing, and bioinformatics pipeline. Libraries were prepared from 200-500ng of genomic DNA digested with 60 units of TaqαI and 30 units of MspI (NEB) sequentially and then extracted with Zymo Research DNA Clean and Concentrator™-5 kit (Cat#: D4003). 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 of 150–250bp and 250–350bp in size were recovered from a 2.5% NuSieve 1:1 agarose gel (Zymoclean™ Gel DNA Recovery Kit, Zymo Research Cat#: D4001). The fragments were then bisulfite-treated using the EZ DNA Methylation-Lightning™ Kit (Zymo Research, Cat#: D5020). Preparative-scale PCR was performed and the resulting products were purified (DNA Clean and Concentrator™ - Zymo Research, Cat#D4005) for sequencing on an Illumina HiSeq.