Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MAFK

Cell type

Cell type Class
Blood
Cell type
OCI-LY-7
Primary Tissue
Blood
Tissue Diagnosis
Lymphoma B-cell

Attributes by original data submitter

Sample

source_name
OCI-Ly7_P18
cell type
OCI-Ly7 lymphoma cells
chip antibody
P18 (MAFK)
chip antibody host/amount
Rabbit poly/5ug
chip antibody vendor
Santa Cruz

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP protocol: OCI-Ly7 cells were fixed with 1% formaldehyde, lysed and sonicated to generate fragments less than 500bp. Sonicated lysates were incubated with antibodies overnight and after increasing stringency washes immunocomplexes were recovered and DNA was isolated. Genomic DNA-fragment libraries were prepared using the Illumina ChIP-seq Library preparation Kit following the manufacture’s instructions (Illumina, CA). Briefly 10ng of purified ChIP DNA was end repaired by conversion of overhangs into phosphorylated blunt ends with the use of T4 DNA polymerase and E. coli DNA polymerase I Klenow fragment. Illumina single-end adapters were ligated to the ends of the DNA fragments. Ligation products were purified on a 2% agarose gel with a size selection of 200-300bp. Fifteen PCR cycles were performed with Illumina genomic DNA primers that anneal to the ends of the adapters. The purified PCR-amplified fragment libraries were quantified with the use of the PicoGreen dsDNA Quantitation Assay with the Qubit Fluorometer (Invitrogen, CA). The size range of libraries was validated on the Agilent Technologies 2100 Bioanalyzer with the High Sensitivity DNA Kit (Agilent, CA).

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg19

Number of total reads
17354297
Reads aligned (%)
80.2
Duplicates removed (%)
15.5
Number of peaks
6424 (qval < 1E-05)

hg38

Number of total reads
17354297
Reads aligned (%)
81.5
Duplicates removed (%)
14.9
Number of peaks
6397 (qval < 1E-05)

Base call quality data from DBCLS SRA