Antigen

Antigen Class

Unclassified

Antigen

Unclassified

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

C57BL/6J

tissue

Liver

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Tissues were dounce homogenized, and cross-linked nuclei were isolated and sorted by BD FACS Aria II using mCherry fluorescence. Sorted nuclei were sheared by Covaris E220 and used for ChIP for overnight. Immunoprecipitates were washed and subjected to elution and reverse crosslinking. DNA was then extracted by AMPure XP beads according to the manufacturer’s manual. Extracted DNA (1-10ng, or all if less) was used to generate sequencing libraries by following the “on-bead” sequencing library preparation method. Briefly, DNA was processed through end repair/phosphorylation using the End-It DNA End-Repair Kit (Epicentre), A-tailing using the Klenow Fragment (NEB M0212) and index adaptor ligation using the Quick Ligase (NEB M2200). AMPure XP beads were left in all the reactions to clean up the DNA using PEG(Polyethylene Glycol 8000)/NaCl solution. After ligation, DNA was eluted from AMPure XP beads and then PCR-amplified using the PfuUltra II Hotstart PCR Master Mix (Agilent 600850). Gel electrophoresis/extraction was performed using the E-Gel EX Agarose Gels (Invitrogen) and MinElute Gel Extraction (Qiagen) to select library fragments between 250 and 600bp. Quantity and quality of the libraries were analyzed by Qubit and Agilent Bioanalyzer, respectively, and the libraries were pooled at a final concentration of 12pM and sequenced by HiSeq2500 or NextSeq 500 systems.

Sequencing Platform

instrument_model

NextSeq 500

mm10

Number of total reads

22395963

Reads aligned (%)

98.3

Duplicates removed (%)

9.9

Number of peaks

152 (qval < 1E-05)

mm9

Number of total reads

22395963

Reads aligned (%)

98.1

Duplicates removed (%)

11.0

Number of peaks

150 (qval < 1E-05)