NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE139109 Query DataSets for GSE139109
Status Public on Feb 20, 2020
Title CAPTURE-3C-seq analysis of cis-element-mediated long-range DNA interactions in K562 and G1E-ER4 cells
Organisms Homo sapiens; Mus musculus
Experiment type Other
Summary The spatiotemporal control of 3D chromatin structure is fundamental for gene regulation, yet it remains challenging to obtain high-resolution chromatin interacting profiles at cis-regulatory elements (CREs) by chromatin conformation capture (3C)-based methods. Here, we describe the redesigned dCas9-based CAPTURE method for multiplexed, high-throughput and high-resolution analysis of locus-specific chromatin interactions. Using C-terminally biotinylated dCas9, endogenous biotin ligase and pooled sgRNAs, the new system enables quantitative analysis of the spatial configuration of a few to hundreds of enhancers or promoters in a single experiment, enabling systematic comparisons across CREs within and between gene clusters. We reveal the hierarchical structure of super-enhancers (SEs) and distinct modes of SE-gene interactions. Multiplexed capture of temporal dynamics of promoter-centric interactions establishes the instructive function of enhancer-promoter looping in transcriptional regulation during lineage differentiation. These applications illustrate the ability of multiplexed CAPTURE for decoding the organizational principles of genome structure and function.
 
Overall design We combined the chromatin interaction assays (Chromatin Conformation Capture or 3C) with the high affinity dCas9 purification approach to unbiasedly identify single genomic locus-associated long-range interactions (CAPTURE-3C-seq).
 
Contributor(s) Liu X, Chen Y, Zhang Y, Xu J
Citation(s) 32138752
Submission date Oct 18, 2019
Last update date Mar 16, 2020
Contact name Jian Xu
E-mail(s) Jian.Xu@stjude.org
Phone 9015955208
Organization name St. Jude Children's Research Hospital
Department Pathology
Street address 262 Danny Thomas Place, MS 345
City Memphis
State/province Tennessee
ZIP/Postal code 38105
Country USA
 
Platforms (2)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (31)
GSM4131114 CAPTURE-3C-seq_K562_sgHS1-5_rep1
GSM4131115 CAPTURE-3C-seq_K562_sgHS1-5_rep2
GSM4131116 CAPTURE-3C-seq_K562_sgHS1-5-combined
This SubSeries is part of SuperSeries:
GSE139117 Analysis of CRE-mediated chromatin interactions by CAPTURE2.0
Relations
BioProject PRJNA578398
SRA SRP226228

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
GSE139109_CAPTURE-3C-seq_G1E-ER4_sgPromoter_0hr_combined_interaction.txt.gz 321.6 Kb (ftp)(http) TXT
GSE139109_CAPTURE-3C-seq_G1E-ER4_sgPromoter_12hr_combined_interaction.txt.gz 331.4 Kb (ftp)(http) TXT
GSE139109_CAPTURE-3C-seq_G1E-ER4_sgPromoter_24hr_combined_interaction.txt.gz 407.0 Kb (ftp)(http) TXT
GSE139109_CAPTURE-3C-seq_G1E-ER4_sgPromoter_2hr_combined_interaction.txt.gz 372.4 Kb (ftp)(http) TXT
GSE139109_CAPTURE-3C-seq_G1E-ER4_sgPromoter_6hr_combined_interaction.txt.gz 323.5 Kb (ftp)(http) TXT
GSE139109_CAPTURE-3C-seq_K562_sgHS1-5_combined_interaction.txt.gz 29.0 Kb (ftp)(http) TXT
GSE139109_CAPTURE-3C-seq_K562_sgSE_combined_interaction.txt.gz 2.0 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap