Antigen

Antigen Class

TFs and others

Antigen

GFP

Cell type

Cell type Class

Pluripotent stem cell

Cell type

ES cells

NA

NA

Sample

source_name

Embryonic Stem Cells

strain background

129

cell type

Embryonic Stem Cells (ESCs)

genotype/variation

containing MLL2_N_GFP

chip antibody

Custom GFP antibody

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Experiments were performed with 3.3 million cells and 3 microgram antibody per ChIP. Crosslinking was performed on the culture plates for 20 min and ChIP’ed DNA was purified by Qiaquick PCR purification Kit (QIAGEN). DNA samples from ChIP-Seq were prepared for sequencing by end repair of 20 ng DNA as measured by Qubit (Invitrogen). Adaptors were ligated to DNA fragments, followed by size selection (~300 bp) and 14 cycles of PCR amplification. Integrity of DNA libraries was confirmed by running the products on a Bioanalyzer (BioRad). Cluster generation and sequencing (36 bp) was performed with the Illumina Genome Analyzer IIx (GAIIx) sequencing platform according to standard Illumina protocols.

Sequencing Platform

instrument_model

Illumina Genome Analyzer IIx

mm10

Number of total reads

16554507

Reads aligned (%)

89.0

Duplicates removed (%)

33.5

Number of peaks

2951 (qval < 1E-05)

mm9

Number of total reads

16554507

Reads aligned (%)

88.7

Duplicates removed (%)

33.7

Number of peaks

2903 (qval < 1E-05)