Antigen

Antigen Class

Bisulfite-Seq

Antigen

Bisulfite-Seq

Cell type

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.

Sample

source_name

liver

strain

offspring of C57BL/6N dam and C3H/HeN sire

Sex

male

replicate animal

3

Sequenced DNA Library

library_strategy

Bisulfite-Seq

library_source

GENOMIC

library_selection

RANDOM

library_construction_protocol

Frozen liver tissues were quickly pulverized with BioPulverizer (Bio Spec Products Inc.) on dry ice. DNA was extracted with Allprep DNA/RNA/Protein Mini Kit (Qiagen) according to the manufacturer's protocol. DNA was further purified by phenol-chloroform extraction followed by ethanol precipitation. DNA (1 µg) was spiked with 1ng unmethylated lambda DNA (Promega), fragmented using a Covaris E210 (intensity 5, duty cycle 10%, cycles per burst 200; average size 300 bp), end-repaired, A-tailed, and adapter-ligated using Truseq DNA sample prep kit (Illumina) according to the manufacturer's protocol. Adapter-ligated DNA was size selected on a Pippin Prep (Sage Science; 1.5% agarose cassette; targeted DNA size 430bp +/- 120bp). After cleaning up DNA with AMPure XP beads, bisulfite conversion was performed using EpiTect Bisulfite kit (Qiagen) with the following thermal cycles, 95°C 5 minutes, 60°C 25 minutes, 95°C 5 minutes, 60°C 85 minutes, 95°C 5 minutes, 60°C 175 minutes, 95°C 5 minutes, 60°C 180 minutes. After cleaning up DNA with AMPure XP beads DNA was eluted in 17.5 ul. Two 4 ul aliquots of bisulfite converted DNA were amplified with PfuTurbo Cx Hotstart DNA Polymerase with following thermal cycles, 95°C 5 minutes, 98°C 30 seconds, 12 cycles of (98°C 10 seconds, 65°C 30 seconds, 72°C 30 seconds), 72°C 5 minutes. The two amplification reactions were pooled, cleaned with AMpure XP beads, and stored at -20°C until use.

Sequencing Platform

instrument_model

Illumina HiSeq 2000

mm10

Number of total reads

584857282

Reads aligned (%)

85.8

Coverage rate (×)

16.5

Number of hyper MRs

247727 (qval < 1E-05)

mm9

Number of total reads

584857282

Reads aligned (%)

87.0

Coverage rate (×)

16.5

Number of hyper MRs

247392 (qval < 1E-05)