ChIP-Atlas: SRX760615

Antigen

Cell type Class: Liver
Cell type: Kupffer Cells
MeSH Description: Specialized phagocytic cells of the MONONUCLEAR PHAGOCYTE SYSTEM found on the luminal surface of the hepatic sinusoids. They filter bacteria and small foreign proteins out of the blood, and dispose of worn out red blood cells.

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