ChIP-Atlas: SRX818190

Antigen

Cell type Class: Blood
Cell type: Dendritic Cells
MeSH Description: ANTIGEN-PRESENTING CELLS of dendritic cell morphology found in the LYMPH NODES and other lymphoid tissues.

library_strategy: ChIP-Seq
library_source: GENOMIC
library_selection: ChIP
library_construction_protocol: DNA from infected and non-infected DCs was extracted using the PureGene DNA extraction kit (Gentra Systems). Samples from infected and non-infected DCs from two individuals were crosslinked with 1% w/v formaldehyde for 10 min at RT and immediately quenched for 5 min with 125mM Glycine at RT. The formaldehyde fixed samples were then sonicated to 100-400 bp using a Bioruptor (Diagenode) and then ChIP-DNA prepared using the IP-Star Compact (Diagenode) Indirect method with an Antibody-Antigen incubation of 10 hr, Bead incubation of 2 hr, and 4x 20 min wash steps. Approximately 1 million cells were used for each ChIP and ~50,000 cells for the input. The following antibodies were used: H3K4me1 (Company: CST, Cat. No.: 5326P, Lot No.: 1), H3K4me3 (CST, 9751BC, 7), H3K9me3 (MABI, 0318, 13001), H3K27me3 (MABI, 0323, 13001), H3K27ac (Abcam, Ab4729, GR119051), and H3K36me3 (MABI, 0333, 12003). ChIP and Input libraries were prepared using the Illumina Truseq Nano DNA kit, with alterations including: PCR enrichment (14 cycles) prior to size selection and utilizing the PippinPrep method (SAGE Science) instead of the SPRI method for size selection (200-400 bp).