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Series GSE86150 Query DataSets for GSE86150
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.
 
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

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
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data is available on Series record

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