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Series GSE69098 Query DataSets for GSE69098
Status Public on Jun 16, 2015
Title MPE-seq, a New Method for the Genome-wide Analysis of Chromatin Structure
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary In this study we developed MPE-seq, a method for the genome-wide characterization of chromatin that involves the digestion of nuclei with methidiumpropyl-EDTA-Fe(II) [MPE-Fe(II)] followed by massively parallel sequencing. Like micrococcal nuclease (MNase), MPE-Fe(II) preferentially cleaves the linker DNA between nucleosomes. We also performed MNase-seq as a comparison. We further performed ChIP-seq using chromatin samples obtained by MPE-Fe(II) or MNase digestion of nuclei.
Overall design Nuclei from J1 mouse embryonic stem cells were treated with MPE-Fe(II) or MNase. The isolated DNA was sequenced by Illumina HiSeq sequencers. Some of the digested chromatin was studied by performing ChIP-seq using antibodies against histone H2B or H3.
Contributor(s) Ishii H, Kadonaga JT, Ren B
Citation(s) 26080409
Submission date May 20, 2015
Last update date May 15, 2019
Contact name Haruhiko Ishii
Phone 858-534-2793
Organization name Ludwig Institute for Cancer Research
Street address 9500 Gilman Drive
City La Jolla
State/province California
ZIP/Postal code 92093-0653
Country USA
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (27)
GSM1692813 MPE-seq 10 min rep1
GSM1692814 MPE-seq 10 min rep2
GSM1692815 MPE-seq 20 min rep1
BioProject PRJNA284528
SRA SRP058542

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE69098_MNase.101_140.center_60.normalized.bedgraph.bz2 444.0 Mb (ftp)(http) BEDGRAPH
GSE69098_MNase.141_160.center_60.normalized.bedgraph.bz2 315.2 Mb (ftp)(http) BEDGRAPH
GSE69098_MNase.141_190.center_60.normalized.bedgraph.bz2 424.5 Mb (ftp)(http) BEDGRAPH
GSE69098_MNase.161_190.center_60.normalized.bedgraph.bz2 106.9 Mb (ftp)(http) BEDGRAPH
GSE69098_MNase.1_100.center_60.normalized.bedgraph.bz2 152.1 Mb (ftp)(http) BEDGRAPH
GSE69098_MNase_ChIP_H2B.101_140.center_60.normalized.bedgraph.bz2 77.2 Mb (ftp)(http) BEDGRAPH
GSE69098_MNase_ChIP_H2B.141_190.center_60.normalized.bedgraph.bz2 98.2 Mb (ftp)(http) BEDGRAPH
GSE69098_MNase_ChIP_H2B.1_100.center_60.normalized.bedgraph.bz2 38.2 Mb (ftp)(http) BEDGRAPH
GSE69098_MNase_ChIP_H3.101_140.center_60.normalized.bedgraph.bz2 67.1 Mb (ftp)(http) BEDGRAPH
GSE69098_MNase_ChIP_H3.141_190.center_60.normalized.bedgraph.bz2 76.9 Mb (ftp)(http) BEDGRAPH
GSE69098_MNase_ChIP_H3.1_100.center_60.normalized.bedgraph.bz2 35.4 Mb (ftp)(http) BEDGRAPH
GSE69098_MNase_ChIP_Input.101_140.center_60.normalized.bedgraph.bz2 47.3 Mb (ftp)(http) BEDGRAPH
GSE69098_MNase_ChIP_Input.141_190.center_60.normalized.bedgraph.bz2 259.8 Mb (ftp)(http) BEDGRAPH
GSE69098_MNase_ChIP_Input.1_100.center_60.normalized.bedgraph.bz2 50.5 Mb (ftp)(http) BEDGRAPH
GSE69098_MNase_low.101_140.center_60.normalized.bedgraph.bz2 56.7 Mb (ftp)(http) BEDGRAPH
GSE69098_MNase_low.141_160.center_60.normalized.bedgraph.bz2 196.8 Mb (ftp)(http) BEDGRAPH
GSE69098_MNase_low.141_190.center_60.normalized.bedgraph.bz2 546.5 Mb (ftp)(http) BEDGRAPH
GSE69098_MNase_low.161_190.center_60.normalized.bedgraph.bz2 346.5 Mb (ftp)(http) BEDGRAPH
GSE69098_MNase_low.1_100.center_60.normalized.bedgraph.bz2 20.7 Mb (ftp)(http) BEDGRAPH
GSE69098_MPE.101_140.center_60.normalized.bedgraph.bz2 450.3 Mb (ftp)(http) BEDGRAPH
GSE69098_MPE.141_160.center_60.normalized.bedgraph.bz2 361.9 Mb (ftp)(http) BEDGRAPH
GSE69098_MPE.141_190.center_60.normalized.bedgraph.bz2 911.5 Mb (ftp)(http) BEDGRAPH
GSE69098_MPE.161_190.center_60.normalized.bedgraph.bz2 556.8 Mb (ftp)(http) BEDGRAPH
GSE69098_MPE.1_100.center_60.normalized.bedgraph.bz2 180.8 Mb (ftp)(http) BEDGRAPH
GSE69098_MPE_ChIP_H2B.101_140.center_60.normalized.bedgraph.bz2 49.1 Mb (ftp)(http) BEDGRAPH
GSE69098_MPE_ChIP_H2B.141_190.center_60.normalized.bedgraph.bz2 92.4 Mb (ftp)(http) BEDGRAPH
GSE69098_MPE_ChIP_H2B.1_100.center_60.normalized.bedgraph.bz2 29.0 Mb (ftp)(http) BEDGRAPH
GSE69098_MPE_ChIP_H3.101_140.center_60.normalized.bedgraph.bz2 46.2 Mb (ftp)(http) BEDGRAPH
GSE69098_MPE_ChIP_H3.141_190.center_60.normalized.bedgraph.bz2 78.7 Mb (ftp)(http) BEDGRAPH
GSE69098_MPE_ChIP_H3.1_100.center_60.normalized.bedgraph.bz2 32.6 Mb (ftp)(http) BEDGRAPH
GSE69098_MPE_ChIP_Input.101_140.center_60.normalized.bedgraph.bz2 111.3 Mb (ftp)(http) BEDGRAPH
GSE69098_MPE_ChIP_Input.141_190.center_60.normalized.bedgraph.bz2 114.7 Mb (ftp)(http) BEDGRAPH
GSE69098_MPE_ChIP_Input.1_100.center_60.normalized.bedgraph.bz2 142.4 Mb (ftp)(http) BEDGRAPH
GSE69098_RNA_seq_data.txt.bz2 688.6 Kb (ftp)(http) TXT
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Processed data are available on Series record

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