Antigen

Antigen Class

Input control

Antigen

Input control

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

Kupffer cells with CD45.1 mark

strain

C57BL/6

tissue

Liver

cell type

Kupffer cells with CD45.1 mark

chip antibody

none (whole cell extract)

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Chromatin was eluted from the beads, then treated with RNase (Roche) for 30 min at 37°c and with Proteinase K (NEB) for 2 hrs at 37°c. Reverse cross-linking was performed at 65°c overnight. DNA was purified with SPRI beads (Agencourt AMPure XP beads, Beckman Coulter) at 2.3x ratio. Sequential steps of end-repair, A-base addition, adapter-ligation and amplification were performed, with DNA purification with SPRI beads after each step. Following the amplification step, DNA concentration was measured, and equivalent amounts of barcoded ChIPed DNA from each sample were pooled together. An additional size-selection step was performed Libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science Nat Protoc. 2013 Mar;8(3):539-54. doi: 10.1038/nprot.2013.023. PMID: 23429716

Sequencing Platform

instrument_model

Illumina HiSeq 1500

mm10

Number of total reads

8741282

Reads aligned (%)

98.3

Duplicates removed (%)

12.5

Number of peaks

294 (qval < 1E-05)

mm9

Number of total reads

8741282

Reads aligned (%)

98.1

Duplicates removed (%)

12.7

Number of peaks

250 (qval < 1E-05)