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Series GSE126112 Query DataSets for GSE126112
Status Public on Jan 29, 2020
Title 3D ATAC-PALM: Super-resolution Imaging of the Accessible Genome
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Spatial genome organization is essential to direct fundamental DNA-templated biological processes (e.g. transcription, replication, and repair), but the 3D in situ nanometer-scale structure of accessible cis-regulatory DNA elements within the crowded nuclear environment remains elusive. Here, we combined the recently developed Assay for Transposase-Accessible Chromatin with visualization (ATAC-see), PALM super-resolution imaging and lattice light-sheet microscope (a method termed 3D ATAC-PALM) to selectively image and quantitatively analyze key features of the 3D accessible genome in single cells. 3D ATAC-PALM reveals that accessible chromatin are non-homogeneously organized into spatially segregated clusters or accessible chromatin domains (ACDs). To directly link imaging and genomic data, we optimized multiplexed imaging of 3D ATAC-PALM with Oligopaint DNA-FISH, RNA-FISH and protein fluorescence. We found that ACDs colocalize with active chromatin and enclose transcribed genes. By applying these methods to analyze genetically purterbed cells, we demonstrated that genome architectural protein CTCF prevents excessive clustering of accessible chromatin and decompacts ACDs. These results highlight the 3D ATAC-PALM as a useful tool to probe the structure and organizing mechanism of the genome.
Overall design Examine accessible chromatin landscape (bulk ATAC-seq) in mouse embryonic stem cells under a variety of chemical/genetic purturbations. We performed at least two biological replicates for each condition. We also performed Micro-C experiment after acute auxin-induced acute CTCF depeltion for 6 hours.
Contributor(s) Xie L
Citation(s) 32203384
Submission date Feb 05, 2019
Last update date Apr 29, 2020
Contact name Robert Tjian
Organization name UC Berkeley/HHMI
Street address LKS
City Berkeley
State/province CA
ZIP/Postal code 94704
Country USA
Platforms (3)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
GPL21626 NextSeq 550 (Mus musculus)
Samples (14)
GSM3591784 Nextera_ATAC_seq
GSM3591785 PA549_Tn5_ATAC_seq
GSM3591786 WT_NoTSA_control_ATAC_seq
BioProject PRJNA521044
SRA SRP183765

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

Supplementary file Size Download File type/resource
GSE126112_CTCF-IAA.allValidPairs-004.txt.gz 3.7 Gb (ftp)(http) TXT
GSE126112_CTCF-IAA.hic 1.2 Gb (ftp)(http) HIC
GSE126112_CTCF-IAA.mcool 956.2 Mb (ftp)(http) MCOOL
GSE126112_CTCF-UT.allValidPairs-005.txt.gz 4.2 Gb (ftp)(http) TXT
GSE126112_CTCF-UT.hic 1.3 Gb (ftp)(http) HIC
GSE126112_CTCF-UT.mcool 1.1 Gb (ftp)(http) MCOOL
GSE126112_RAW.tar 1.2 Gb (http)(custom) TAR (of BW)
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Raw data are available in SRA
Processed data provided as supplementary file

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