ChIP-Seq Library Preparation and Analysis

Sequencing libraries were prepared from 1.0 ng of DNA subjected to ChIP and input samples by a Mondrian SP+ system (Nugen) with an Ovation SP ultralow DR multiplex system (Nugen). The libraries were further purified and size-selected using an AMPure XP kit (Beckman Coulter) and were quantified by a quantitative MiSeq (qMiSeq) method (65 (link)). The samples were sequenced on a HiSeq 2500 (Illumina) that generated 101-base reads. Sequencing data were aligned with the hg19 reference genome with Bowtie2 (66 (link)), and peaks were called with MACS2 (67 (link)). ChIP-seq peak visualization was done with Integrative Genomic Viewer (68 (link)).

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Sekine H., Okazaki K., Kato K., Alam M.M., Shima H., Katsuoka F., Tsujita T., Suzuki N., Kobayashi A., Igarashi K., Yamamoto M, & Motohashi H. (2018). O-GlcNAcylation Signal Mediates Proteasome Inhibitor Resistance in Cancer Cells by Stabilizing NRF1. Molecular and Cellular Biology, 38(17), e00252-18.

Publication 2018

Mondrian SP+ system Ovation SP ultralow DR multiplex system AMPure XP kit HiSeq 2500

Chip Chip seq Genomic

Corresponding Organization : Doshisha University

Other organizations : Tohoku Medical Megabank Organization, Saga University

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Variable analysis

independent variables

Sequencing libraries were prepared from 1.0 ng of DNA subjected to ChIP and input samples

dependent variables

Sequencing data were aligned with the hg19 reference genome with Bowtie2
Peaks were called with MACS2
ChIP-seq peak visualization was done with Integrative Genomic Viewer

control variables

Sequencing libraries were prepared by a Mondrian SP+ system (Nugen) with an Ovation SP ultralow DR multiplex system (Nugen)
The libraries were further purified and size-selected using an AMPure XP kit (Beckman Coulter)
The samples were sequenced on a HiSeq 2500 (Illumina) that generated 101-base reads

controls

No positive or negative controls were explicitly mentioned in the provided information.

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