Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

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.

Attributes by original data submitter

Sample

dev stage
unknown
cell type
dendritic cell
treatments
treatment_term_id: CHEBI:16412; treatment_term_name: Lipopolysaccharide; treatment_type: chemical; duration_units: hour;
sex
not collected
sample type
in vitro differentiated cells
donor ID
ENCDO088XVR
age
unknown
lab
Manuel Garber, UMass

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
general protocol: https://www.encodeproject.org/documents/342b2d20-53cf-4698-b7db-48fefe735f56/@@download/attachment/Luban_lab_ChIP_protocol.pdf extraction method: TruChIP chromatin shearing reagent kit Covaris cat# 520154, sonication Covaris M220, IP (home protocol), DNA isolation with QIAquick PCR Purification Kit cat# 28104.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
24690342
Reads aligned (%)
88.4
Duplicates removed (%)
43.2
Number of peaks
19916 (qval < 1E-05)

hg19

Number of total reads
24690342
Reads aligned (%)
87.7
Duplicates removed (%)
43.5
Number of peaks
19768 (qval < 1E-05)

Base call quality data from DBCLS SRA