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

tissue

Liver

strain

C57/bl

gender

male

age

3w

condition

NORMAL

Sequenced DNA Library

library_strategy

Bisulfite-Seq

library_source

GENOMIC

library_selection

RANDOM

library_construction_protocol

DNA was isolated from snap-frozen mouse tissues or from frozen human samples (purchased from Cancer Center Tissue and Tumor Bank of UMass Medical School) and incubated in lysis buffer (25  mM Tris-HCl (pH  8), 2  mM EDTA, 0.2% SDS, 200  mM NaCl) supplemented with 300 μg/ml proteinase K (Roche) followed by phenol:chloroform extraction and ethanol precipitation. Unmethylated lamba phage DNA was spiked in for a final concentration of 0.5%. 1 μg of gDNA was sonicated using The Covaris S2 Sonicator (Covaris Inc, Woburn MA) to the desired size range of approximately 125 bp median size, with the majority of insert sizes falling within the range of 100-200bp as determined by Agilent Bioanalyzer examination and quantified using the Kapa Biosystems kit. End repair, A-tailing, and adapter ligation are carried out using the standard Illumina TruSeq protocol. Adapters used were the methylated bar coded adapters included in the Illumina TruSeq DNA sample preparation kit. Sodium bisulfite conversion of all DNA samples following adapter ligation was performed using the EZ DNA Methylation-Gold Kit or the EZ DNA Methylation-Lightning kit (Zymo Research). 4-8 rounds of PCR were performed using the KAPA HiFi +Uracil DNA polymerase (Kapa Biosystems). AMPure XP purification (Agencourt) was used to retain fragments with insert sizes between 100-200bp, and this insert size range was verified post-sequencing.

Sequencing Platform

instrument_model

Illumina HiSeq 2000

mm10

Number of total reads

355290011

Reads aligned (%)

85.2

Coverage rate (×)

6.3

Number of hyper MRs

231338 (qval < 1E-05)

mm9

Number of total reads

355290011

Reads aligned (%)

86.5

Coverage rate (×)

6.3

Number of hyper MRs

231183 (qval < 1E-05)