Antigen

Antigen Class

Input control

Antigen

Input control

Cell type

Cell type Class

Blood

Cell type

Leukemia, Lymphoid

MeSH Description

Leukemia associated with HYPERPLASIA of the lymphoid tissues and increased numbers of circulating malignant LYMPHOCYTES and lymphoblasts.

Sample

source_name

106A cell line

cell line

106A cell line

chip antibody

Input

sample type

Cytokine independent

strain

C57BL/6

cell type

NUP98-PHF23 pre-T LBL derived cell line

source

NUP98-PHF23 pre-T LBL derived cell line, mouse 106

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

ChIP was performed using a ChIP-IT kit from Active Motif (Carlsbad, CA), following the manufacturer’s recommended protocol with minor modifications as described in supplementary methods. Antibodies used were: anti-H3K4me3 (17-614, Millipore), anti-H3K27me3 (07-449, Millipore), anti-V5 (R960-25, Life Technologies), anti-FLAG (M2. Sigma Aldrich) and anti RNA Polymerase II (CTD4H8, Santa Cruz). ChIP DNA (10 ng) was end-repaired and phosphorylated using T4 polymerase, Klenow, and T4 Polynucleotide Kinase. An A-overhang was introduced using exo-Klenow and then ligated to Illumina paired-end adapters with DNA ligase. Ligated products were size selected on a Caliper LabChip XT to a mean size of 240bp +/- 20%. The libraries were amplified with Illumina PCR Primer InPE1.0, PCR Primer InPE2.0 and PCR Primer Indexes and sequenced on Illumina GAIIx or MiSeq sequencers under a single-end run protocol.

Sequencing Platform

instrument_model

Illumina Genome Analyzer IIx

mm10

Number of total reads

24948437

Reads aligned (%)

92.6

Duplicates removed (%)

14.3

Number of peaks

716 (qval < 1E-05)

mm9

Number of total reads

24948437

Reads aligned (%)

92.4

Duplicates removed (%)

14.4

Number of peaks

758 (qval < 1E-05)