Antigen

Antigen Class

Unclassified

Antigen

Unclassified

Cell type

Cell type Class

Blood

Cell type

KOPN-8

Primary Tissue

Blood

Tissue Diagnosis

Leukemia

Sample

source_name

Leukemia cell line (KOPN-8)

cell line

Leukemia cell line; KOPN-8

cell type

Infant pre B-cell line derived from ALL with t(11;19)(q23;p13) translocation

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

ChIP-seq: Fixed cells were lysed in 1% SDS lysis buffer. Samples were sonicated and protein-DNA complexes were isolated with antibody. Nascent RNA-seq: 108 4sU-treated cells were lysed in 10ml Trizol. RNA was extracted using chloroform and precipitated with EtOH. 4sU RNA was biotinylated with 1mg/ml Biotin-HPDP and nascent RNA was enriched for using streptavidin-coated beads. Libraries were prepared according to Illumina's protocol accompanying the DNA Library Prep Master Mix Set (Part# E6040) or Ultra RNA Library Prep Master Mix Set (Part# E7530).

Sequencing Platform

instrument_model

Illumina HiSeq 2000

hg38

Number of total reads

17347184

Reads aligned (%)

99.0

Duplicates removed (%)

6.1

Number of peaks

400 (qval < 1E-05)

hg19

Number of total reads

17347184

Reads aligned (%)

98.2

Duplicates removed (%)

6.3

Number of peaks

334 (qval < 1E-05)