Curated Sample Data


Genome
mm9
Antigen Class
DNase-seq
Antigen
DNase-Seq
Cell type Class
Blood
Cell type
Pro-B cells

Cell type information


NA
NA

Attributes by Original Data Submitter


source_name
pre-B lymphocyte
transfection
control
time
2h
treatment
4-OHT
dose
0.5 uM
cell line
B3
cell type
pre-B lymphocyte

Metadata from Sequence Read Archive

Library Description


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.

Platform Information


instrument_model
NextSeq 500

External Database Query

Logs in read processing pipeline


Number of total reads
44862414
Reads aligned (%)
91.3
Duplicates removed (%)
7.1
Number of peaks
1291 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA