Sample information curated by ChIP-Atlas

Antigen

Antigen Class
DNase-seq
Antigen
DNase-Seq

Cell type

Cell type Class
Blood
Cell type
Pre-B cells
NA
NA

Attributes by original data submitter

Sample

source_name
pre-B lymphocyte
transfection
inducible Ikaros
time
6h
treatment
4-OHT
dose
0.5 uM
cell line
B3
cell type
pre-B lymphocyte

Sequenced DNA Library

library_strategy
DNase-Hypersensitivity
library_source
GENOMIC
library_selection
DNase
library_construction_protocol
B3 cells containing inducible Ikaros were plated at a density of 0.5 million cells/ml in IMDM medium supplemented with 10% FCS and 1% penicillin/streptomycin. Time point samples were collected by 5 min centrifugation at 1200 rpm. Cell pellets were washed 2 times in PBS, frozen in liquid nitrogen and storaged at -80. Control vector-ERt2 B3 cells were plated at a density of 0.5 million cells/ml in IMDM medium supplemented with 10% FCS and 1% penicillin/streptomycin. Samples were collected by 5 min centrifugation at 1200 rpm. Cell pellets were washed 2 times in PBS, frozen in liquid nitrogen and storaged at -80. DNase-seq libraries were generatedas previously described (Myers protocol: http://myers.hudsonalpha.org/documents/Myers%20Lab%20Sequencing%20Library%20Protocol%20061508.pdf). Libraries were sequenced as 43bp paired-end on the NextSeq 500 Illumina platform. DNase-seq libraries were sequenced to a minimum depth of ~20 million reads per each biological replicate.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
122548374
Reads aligned (%)
87.2
Duplicates removed (%)
8.4
Number of peaks
35227 (qval < 1E-05)

mm9

Number of total reads
122548374
Reads aligned (%)
87.1
Duplicates removed (%)
8.8
Number of peaks
35352 (qval < 1E-05)

Base call quality data from DBCLS SRA