ChIP-seq Analysis of Histone Modifications

ChIP-seq libraries were prepared using standard protocols provided by Illumina (www.illumina.com). Libraries were sequenced (Solexa, Illumina) in two successive runs and output from each sample was used for analysis. The resulting sequence outputs (bases 2-42) were aligned to the reference mouse genome (version mm9) using bowtie 0.12.7 (19 (link)).
The peaks were filtered for P < 10⁻²⁰, next, peak calling and annotation were done by using Model-based Analysis of ChIP-Seq (MACS, version 1.4) (20 (link)) and peakAnnotator (version 1.4) (21 (link)), respectively. The published ChIP-seq data from Gene Expression Omnibus (GEO) database were acquired to analyze the binding targets of H3K9me2 and H3K9me3 (accession number GSE82144) (22 (link)), RELA (GSE36099) (23 (link)), and KDM4A and KDM4C in mouse acute myeloid leukemia (AML) cells (GSE81300) (24 (link)).

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Hung K.H., Woo Y.H., Lin I.Y., Liu C.H., Wang L.C., Chen H.Y., Chiang B.L, & Lin K.I. (2018). The KDM4A/KDM4C/NF-κB and WDR5 epigenetic cascade regulates the activation of B cells. Nucleic Acids Research, 46(11), 5547-5560.

Publication 2018

Solexa

Acute myeloid leukemia Cells Chip seq Gene expression Genome Mouse Rela

Corresponding Organization : Genomics Research Center, Academia Sinica

Other organizations : King Abdullah University of Science and Technology, Academia Sinica, Kaohsiung Medical University, Taipei Tzu Chi Hospital, National Taiwan University Hospital, National Taiwan University

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Variable analysis

independent variables

ChIP-seq libraries prepared using standard Illumina protocols
Sequencing of the libraries in two successive runs

dependent variables

Binding targets of H3K9me2, H3K9me3, RELA, KDM4A, and KDM4C in mouse AML cells

control variables

Reference mouse genome (version mm9) used for alignment
Bowtie 0.12.7 used for sequence alignment
Peak filtering at P < 10^-20
MACS version 1.4 used for peak calling
PeakAnnotator version 1.4 used for peak annotation

Annotations

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