|
| Status |
Public on Nov 15, 2016 |
| Title |
Mapping of Long-Range Chromatin Interactions using Proximity Ligation Assisted ChIP-seq |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
We report Proximity Ligation Assisted ChIP-sequencing (PLAC-seq), a method for comprehensive detection of long-range interactions associated with proteins of interest. PLAC-seq requires up to 500-fold less starting material compared to ChIA-PET and using experimentally determined input as control precisely reveals protein associated interaction upto single-element resolution. Application of PLAC-seq to mouse embryonic stem cells revealed a comprehensive map of regulatory interactions.
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| |
|
| Overall design |
PLAC-seq experiments against H3k4me3 (2M cells), Pol2 (5M cells), H3k27ac (0.5M, 2.5M cells) and in situ Hi-C experiment in mouse embryonic stem cell (F123)
PLAC-Seq data can be visualized at 3D Genome Browser (3dgenome.org)
|
| |
|
| Contributor(s) |
Fang R, Yu M, Ren B |
| Citation(s) |
27886167 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| U54 HG006997 |
Center for Mammalian Regulatory Genomics |
Ludwig Institute for Cancer Research Ltd |
REN |
| U54 DK107977 |
San Diego Center for 4D Nucleome Research |
Ludwig Institute for Cancer Research Ltd |
MURRE, REN |
|
| |
| Submission date |
Aug 28, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Rongxin Fang |
| E-mail(s) |
r3fang@ucsd.edu
|
| Organization name |
Ludwig Institute for Cancer Research
|
| Lab |
Ren Lab
|
| Street address |
9500 Gilman Dr #3080
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
|
| Samples (9)
|
| GSM2295898 |
H3K27Ac PLAC-seq 2.5 million of cells rep1 |
| GSM2295899 |
H3K27Ac PLAC-seq 2.5 million of cells rep2 |
| GSM2295900 |
H3K27Ac PLAC-seq 0.5 million of cells rep1 |
|
| Relations |
| BioProject |
PRJNA340368 |
| SRA |
SRP083136 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE86150_Mouse.ESF123.placseq.H3k27ac.05M.fithic.interactions.bed.gz |
1.1 Mb |
(ftp)(http) |
BED |
| GSE86150_Mouse.ESF123.placseq.H3k27ac.25M.fithic.interactions.bed.gz |
2.3 Mb |
(ftp)(http) |
BED |
| GSE86150_Mouse.ESF123.placseq.H3k27ac.PLACE.interactions.bed.gz |
554.3 Kb |
(ftp)(http) |
BED |
| GSE86150_Mouse.ESF123.placseq.H3k4me3.PLACE.interactions.bed.gz |
793.3 Kb |
(ftp)(http) |
BED |
| GSE86150_Mouse.ESF123.placseq.H3k4me3.fithic.interactions.bed.gz |
4.7 Mb |
(ftp)(http) |
BED |
| GSE86150_Mouse.ESF123.placseq.Pol2.fithic.interactions.bed.gz |
1.1 Mb |
(ftp)(http) |
BED |
| GSE86150_RAW.tar |
13.0 Gb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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