GSM1155957 - GEO DataSets

Select item 2000720891.

Validation of THS-seq method, and comparison of published ENCODE DNase-seq data, self-generated ATAC-seq data and published ATAC-seq data, and THS-seq data for quantitation of chromatin accessibility.

(Submitter supplied) Chromatin accessibility captures the binding status of protein factors to chromosomes in vivo, and has been considered a highly informative proxy for functional protein-DNA interactions. Existing DNase I and Tn5 transposase based assays generally require tens of thousands to millions of fresh cells. Applying Tn5 tagmentation to single cells yields very sparse maps. Here we present a transposome hypersensitive sites sequencing assay (THS-seq) for highly sensitive characterizations of chromatin accessibility.

Organism:: Homo sapiens

Type:: Third-party reanalysis; Other; Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL15520 GPL16791
11 Samples

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Series

Accession:: GSE72089

ID:: 200072089

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000663862.

High-resolution nucleosome positioning from ATAC-seq chromatin accessibility data

(Submitter supplied) We describe the NucleoATAC algorithm for high-resolution nucleosome positioning and occupancy determination using ATAC-seq.

Organism:: Schizosaccharomyces pombe; Saccharomyces cerevisiae; Homo sapiens

Type:: Other

4 related Platforms
32 Samples

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Series

Accession:: GSE66386

ID:: 200066386

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000477533.

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(Submitter supplied) We describe an assay for transposase-accessible chromatin using sequencing (ATAC-seq), based on direct in vitro transposition of sequencing adaptors into native chromatin, as a rapid and sensitive method for integrative epigenomic analysis. ATAC-seq captures open chromatin sites using a simple two-step protocol with 500–50,000 cells and reveals the interplay between genomic locations of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution. more...