|
| 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.
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| |
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| 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.
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| |
|
| 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 |
| E-mail(s) |
hishii@ucsd.edu
|
| 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 |
| |
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| Platforms (2) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
|
| Samples (27)
|
|
| Relations |
| BioProject |
PRJNA284528 |
| SRA |
SRP058542 |
| 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 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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