Antigen

Antigen Class

Histone

Antigen

H3K4me3

Cell type

Cell type Class

Pluripotent stem cell

Cell type

iPSC derived neural cells

NA

NA

Sample

source_name

HD Sample H3K4me3 ChIP-Seq

subject status

huntington's disease (HD)

cell type

iPSC-derived medium spiny neuron-like cells

chip antibody

H3K4me3 (Millipore, 07-473)

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Chromatin was digested with 150 units of MNase (NEB, M0247S) for 10min at 37°C. The digestion reaction was stopped with 10mM EDTA. The chromatin was incubated with 1ul of k4me3 (Millipore, 07-473) overnight and 20ul of Protein G beads (ThermoFisher, 10004D) were added for 2hr incubation at 4°C on the following day Immunoprecipitated DNA and nonspecific IgG-bound DNA were prepared for high-throughput sequencing according to Illumina's instructions and sequenced on an Illumina platform following the manufacturer's standard protocol.

Sequencing Platform

instrument_model

Illumina HiSeq 2000

hg38

Number of total reads

17314325

Reads aligned (%)

100.0

Duplicates removed (%)

0.4

Number of peaks

2121 (qval < 1E-05)

hg19

Number of total reads

17314325

Reads aligned (%)

99.4

Duplicates removed (%)

1.4

Number of peaks

2146 (qval < 1E-05)