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Series GSE158327 Query DataSets for GSE158327
Status Public on Nov 13, 2020
Title Efficient transcription-coupled chromatin accessibility mapping in situ
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Chromatin accessibility mapping is a powerful approach to identify potential regulatory elements. In the popular ATAC-seq method, Tn5 transposase inserts sequencing adapters into accessible DNA (‘tagmentation’). CUT&Tag is a tagmentation-based epigenomic profiling method in which antibody tethering of Tn5 to a chromatin epitope of interest profiles specific chromatin features in small samples and single cells. Here we show that by simply modifying the tagmentation conditions for histone H3K4me2/3 CUT&Tag, antibody-tethered tagmentation of accessible DNA sites is redirected to produce accessible DNA maps that are indistinguishable from the best ATAC-seq maps. Thus, DNA accessibility maps can be produced in parallel with CUT&Tag maps of other epitopes with all steps from nuclei to amplified sequencing-ready libraries performed in single PCR tubes in the laboratory or on a home workbench. As H3K4 methylation is produced by transcription at promoters and enhancers, our method identifies transcription-coupled accessible regulatory sites.
 
Overall design We used Cleavage under targets and Tagmentation (Cut-and-Tag), a chromatin profiling strategy in which antibody-targeted controlled integration of DNA sequencing adapters produces libraries for paired-end DNA sequencing.
 
Contributor(s) Henikoff S, Kaya-Okur HS, Ahmad K
Citation(s) 33191916
Submission date Sep 21, 2020
Last update date Mar 08, 2021
Contact name Jorja Henikoff
E-mail(s) jorja@fhcrc.org
Phone 206-667-4850
Organization name Fred Hutchinson Cancer Research Center
Department Basic Sciences
Lab Henikoff
Street address 1100 Fairview AV N, A1-162
City Seattle
State/province WA
ZIP/Postal code 98109-1024
Country USA
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (143)
GSM4797822 H1_K4me2_p-w_60_(20200402_SH_Hs_H1_K4m2E_60_0810)
GSM4797823 K562_H2AZ_rem10_(20200617_SH_Hs_H2AZ_10_0801)
GSM4797824 K562_H2AZ_(20200402_SH_Hs_H2AZ_0801)
Relations
BioProject PRJNA664814
SRA SRP284358

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Supplementary file Size Download File type/resource
GSE158327_CUTnTag-direct_v2_Protocols.io.pdf 2.7 Mb (ftp)(http) PDF
GSE158327_CUTnTag-direct_v3_Protocols.io.pdf 2.5 Mb (ftp)(http) PDF
GSE158327_RAW.tar 8.6 Gb (http)(custom) TAR (of BED, BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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