Antigen

Antigen Class

Unclassified

Antigen

Unclassified

Cell type

Cell type Class

Blood

Cell type

CCRF-CEM

Primary Tissue

Blood

Tissue Diagnosis

Leukemia Acute Lymphocytic

Sample

source_name

Leukemia cell line (CCRF-CEM)

cell line

Leukemia cell line; CCRF-CEM

cell type

Paediatric immature T-cell line derived from ALL with t(5;14)(q35.1;q32.2)

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

33223746

Reads aligned (%)

99.0

Duplicates removed (%)

2.1

Number of peaks

931 (qval < 1E-05)

hg19

Number of total reads

33223746

Reads aligned (%)

98.1

Duplicates removed (%)

2.2

Number of peaks

685 (qval < 1E-05)