Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Ikzf1

Cell type

Cell type Class
Blood
Cell type
BH1
NA
NA

Attributes by original data submitter

Sample

source_name
BH1 cell line
cell line
Pre B cell line (BH1)
strain
C57BL/6
chip antibody
anti-Ikaros Polyclonal rabbit made in house

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The ChIP protocol was adapted from the Millipore ChIP Assay Kit (17-295) with minor modifications. Cells were washed in PBS and 100 000 000 cells were cross-linked at 37° C for 10 min in 5ml PBS/0.5%BSA/1% ultra-pure formaldehyde(Electron Microscopy Sciences). Quenching with 125mM glycine and a cold PBS wash (containig 1 protease inhibitor cocktail (PIC); Roche) was followed by cell lysis in 5ml of 1% Triton X-100, 50mM MgCl2, 100mM Tris-HCl pH 7.1, 11% sucrose, 1 PIC for 10 min on ice. Nuclei were pelleted and were lysed in 500 ml of 1% SDS, 50mM Tris-HCl, 10mM EDTA, 1 PIC. Chromatin was sonicated to 500–300 bp using a Bioruptor 200 (Diagenode), cleared by centrifugation and sonication efficiency was verified. Libraries were prepared according to standard Illumina protocols and were validated with the Agilent Bioanalyzer

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
44954542
Reads aligned (%)
98.0
Duplicates removed (%)
35.9
Number of peaks
3916 (qval < 1E-05)

mm9

Number of total reads
44954542
Reads aligned (%)
97.5
Duplicates removed (%)
31.7
Number of peaks
2345 (qval < 1E-05)

Base call quality data from DBCLS SRA