Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Blood
Cell type
B cells
NA
NA

Attributes by original data submitter

Sample

source_name
Tonsillar Naïve B cells
cell type
Tonsillar naive B cells
treatment
NA
chip antibody
none
purification
Cells purified from normal fresh human tonsillectomy specimens by magnetic bead cell separation based on the expression the phenotypic marker IgD

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed as previously described (Ci et al., Blood, 2009). Briefly, 108 cells were fixed with 1% formaldehyde, lysed, and sonicated (Branson Sonicator; Branson) leading to a DNA average size of 200 bp. Five µg of antibodies were added to the precleared sample and incubated overnight at 4°C. The complexes were purified using protein-A beads (Roche) followed by elution from the beads and decrosslinking. DNA was purified using PCR purification columns (QIAGEN). ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT™ dsDNA HS Assay (Life Technologies)

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg38

Number of total reads
39380553
Reads aligned (%)
98.5
Duplicates removed (%)
14.0
Number of peaks
1852 (qval < 1E-05)

hg19

Number of total reads
39380553
Reads aligned (%)
97.5
Duplicates removed (%)
15.4
Number of peaks
1762 (qval < 1E-05)

Base call quality data from DBCLS SRA