Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

Cell type Class
Blood
Cell type
Plasmablasts
NA
NA

Attributes by original data submitter

Sample

source_name
in vitro differentiated plasmablasts
cell type
plasmablasts
origin
differentiation of NBC from buffy coat (healthy donor)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Genomic DNA was extracted using the AllPrep DNA/RNA mini kit (Qiagen) after cell-sorting (FACS Aria, BD) of blood or lymph node naive B cells and of in vitro differentiated plasmablasts (day 6 of the culture). For ChIP experiments, cells were fixed with 1% formaldehyde prior to cell sorting. Genomic DNA (7 μg) from naïve B cells and plasmablasts was fragmented to 200 to 500 bp by sonication (Bioruptor, Diagenode) before incubation with β-glucosyltransferase and azide-glucose. Glucosylated 5hmCs were then labeled with biotin before enrichment of the biotinylated DNA fragments with streptavidin-coated magnetic beads. All steps used reagents from the Hydroxymethyl Collector kit (Active Motif). After elution from the beads, purified DNA was precipitated and processed for sequencing on a Highseq2000 (Illumina). Library preparations and sequencing reactions were run at the IGBMC genomic platform (Strasbourg, France). ChIP-seq was performed in P1 cells as follows. Cells were fixed for 8 minutes in 1% formaldehyde at room temperature and chromatin was sonicated for 15 minutes with the Bioruptor Sonication System (Diagenode). Immunoprecipitation was carried out with antibodies from Diagenode against H3K4me1 (pAb-194-050, lot: A1863-001P) and H3K27ac (pAb-196-050, lot: A1723-0041D) using approximately 500,000 cells per antibody. ChIP-seq libraries were constructed using the Kapa Hyper Prep Kit (Kapa Biosystems) and sequenced with an Illumina HiSeq1500 sequencer.

Sequencing Platform

instrument_model
Illumina HiSeq 1500

hg38

Number of total reads
39181802
Reads aligned (%)
93.3
Duplicates removed (%)
17.2
Number of peaks
20235 (qval < 1E-05)

hg19

Number of total reads
39181802
Reads aligned (%)
92.7
Duplicates removed (%)
18.1
Number of peaks
20277 (qval < 1E-05)

Base call quality data from DBCLS SRA