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Series GSE139420 Query DataSets for GSE139420
Status Public on Feb 15, 2020
Title In situ capture of global transcription dynamics and enhancer activity with high accuracy and sensitivity 
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Transcription is a highly dynamic process that generates the majority of single-stranded DNA in the genome as ‘transcription bubbles’. Here we describe a kethoxal-assisted single-stranded DNA sequencing (KAS-seq), which marks single-stranded DNA in situ for genome-wide capture and sequencing, based on the fast and specific reaction between N3-kethoxal and guanines in single-stranded DNA in live cells. KAS-seq enables rapid (within 5 min) and sensitive detection of the position, relative level, and dynamics of ssDNA, as a readout of transcriptionally engaged RNA polymerases, with 1,000 cells. KAS-seq defines a group of enhancers that are single-stranded, which confers higher transcription factor binding density, more enhancer-promotor interactions, and higher ability to activate transcription. Under protein condensation inhibition condition, KAS-seq reveals unprecedented, rapid release of RNA polymerase II (Pol II) from a group of promotors, and reveals gene sets with different extents of responses, which correlate with Pol II C-terminal domain (CTD) serine 5 phosphorylation (S5P) level at TSS under no treatment condition. KAS-seq thus facilitates fast, comprehensive, and accurate analysis of transcription dynamics and enhancer activities simultaneously in a low input and high-throughput manner.
Overall design Examination of N3-kethoxal labeling ssDNA pattern in 2 HEK293 and mESCs.

Examination of N3-kethoxal labeling ssDNA pattern in mouse liver tissue.
Contributor(s) Lyu R, Wu T
Citation(s) 32251394
Submission date Oct 25, 2019
Last update date May 17, 2020
Contact name Ruitu Lyu
Organization name The University of Chicago
Department Chemistry
Lab Chuan He
Street address 929 E 57th Street
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
Platforms (4)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (78)
GSM4141407 HEK293_Ctrl_KAS-Input.rep1
GSM4141408 HEK293_Ctrl_KAS-Input.rep2
GSM4141409 HEK293_Ctrl_KAS-IP.rep1
BioProject PRJNA579592
SRA SRP227038

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Supplementary file Size Download File type/resource
GSE139420_RAW.tar 7.8 Gb (http)(custom) TAR (of BED, BIGWIG, XLS)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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