Similar studies for GEO DataSets (Select 200232216) - GEO DataSets

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Items: 15

Select item 2002322161.

Light-Assisted Single-Stranded Open-Chromatin Analysis in K562 and Spatially Localized Neuronal Single Cells

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Homo sapiens; Mus musculus

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

Platforms:: GPL18573 GPL19057 GPL17021
445 Samples

Download data: BED

Series

Accession:: GSE232216

ID:: 200232216

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Select item 2002322152.

K562 and human brain transcriptomes, and various epigenomes from K562 and human/mouse brain curated from public databases and re-analyzed for comparison with the single-stranded DNA open-chromatin detected by CHEX-seq

(Submitter supplied) To study the association of CHEX-seq with transcriptional activity, we downloaded and re-analyzed K562 bulk RNA-seq, single-cell RNA-seq, and GRO-seq data, as well as human brain single-cell RNA-seq data. To study the association of CHEX-seq with DNA replication, we downloaded and re-analyzed K562 replication origin data. To study the association of CHEX-seq with epigenomes, we downloaded and re-analyzed ATAC-seq, DNase-seq, FAIRE-seq, RRBS-seq, DRIP-seq, ChIP-seq and super-enhancer data from K562, human and/or mouse brain. more...

Organism:

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

Download data: XLS

Series

Accession:: GSE232215

ID:: 200232215

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Select item 2002317253.

Single-cell RNA-seq of astrocytes and neurons from primary culture of the mouse brain and of acute slice of interneurons from Patch-clamp pipette [RNA-seq mouse brain]

(Submitter supplied) To investigate the relationship between single-cell transcriptional activity and single-strand open-chromatin landscape in mouse brain, we performed single-cell RNA-seq.

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL19057 GPL17021
28 Samples

Download data: CSV

Series

Accession:: GSE231725

ID:: 200231725

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Select item 2002317194.

Light-Assisted Single-Stranded DNA Open-Chromatin Analysis in Single Spatially Localized Neuronal Cells Identifies the Capacity of Endogenous DNA to Act Catalytically [CHEX-seq]

(Submitter supplied) We report a novel chromatin structure analysis technique, named "CHEX-seq" (CHromatin EXposed), which couples oligonucleotide random annealing and nucleus-resolution photoactivation such that the single-stranded open-chromatin DNA is copied, reverse transcribed, amplified and sequenced.

Organism:: Mus musculus; Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL18573 GPL19057
417 Samples

Download data: BED, MTX, TXT

Series

Accession:: GSE231719

ID:: 200231719

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Select item 2001498075.

Strand-specific ChIP-seq at DNA breaks distinguishes single versus doubled stranded DNA binding and refutes single stranded nucleosomes

(Submitter supplied) In a first step of DNA double-strand break (DSB) repair by homologous recombination, DNA ends are resected such that single-stranded DNA (ssDNA) overhangs are generated. ssDNA is specifically bound by RPA and other factors, which constitutes a ssDNA-compartment on damaged chromatin. The molecular organization of this ssDNA- as well as the adjacent dsDNA-compartment is crucial during DSB signaling and repair. more...

Organism:: Saccharomyces cerevisiae

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL19756 GPL18085
314 Samples

Download data: BED, BEDGRAPH

Series

Accession:: GSE149807

ID:: 200149807

PubMed Similar studies SRA Run Selector

Select item 2001928226.

spKAS-seq reveals R-loop dynamics using low-input materials by detecting single-stranded DNA with strand specificity

(Submitter supplied) R-loops impact transcription and genome stability and are related to human diseases. Genome-wide R-loop mapping typically uses the S9.6 antibody or inactive RNase H, both requiring a large number of cells with varying results observed depending on the approach applied. Here, we present strand-specific KAS-seq (spKAS-seq) to map R-loops by taking advantage of the presence of a single-stranded DNA (ssDNA) in the triplex structure. more...

Organism:: Homo sapiens

Type:: Other

Platform:: GPL24676
46 Samples

Download data: BIGWIG

Series

Accession:: GSE192822

ID:: 200192822

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Select item 2000345927.

Sequencing-based ssDNA detection

(Submitter supplied) Meiotic DNA double stranded breaks (DSBs) initiate genetic recombination in discrete areas of the genome called recombination hotspots. Although DSBs can be directly mapped using ChIP-Seq and antibody against ssDNA-associated proteins, genome-wide mapping of recombination hotspots in mammals is still a challenge due to the low frequency of recombination, high heterogeneity of the germ cell population and the relatively low efficiency of ChIP. more...

Organism:: Mus musculus

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL9250 GPL13112
11 Samples

Download data: BED, WIG

Series

Accession:: GSE34592

ID:: 200034592

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Select item 2000040998.

Single stranded DNA formation during S phase in the presence of hydroxyurea in S. cerevisiae and S. pombe

(Submitter supplied) We have developed a method to analyze single-stranded DNA (ssDNA) formation on a genomic scale by using microarrays. Using this technique we have assessed the location and the amount of ssDNA in S. cerevisiae during DNA replication. We have observed that when replication is impeded by hydroxyurea, ssDNA formation can be detected in both wild type and the checkpoint-deficient rad53 cells. However, while wild type cells showed ssDNA formation at only a subset of origins, rad53 cells formed ssDNA at virtually all known origins. more...

Organism:: Schizosaccharomyces pombe; Saccharomyces cerevisiae

Type:: Other

Platforms:: GPL3398 GPL3388
10 Samples

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Series

Accession:: GSE4099

ID:: 200004099

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000391669.

Strand-specific ChIP-seq profiling of Rad52 localization

(Submitter supplied) We report the development of a novel strand-specific ChIP-seq strategy and application of this strategy in studying genome instability events

Organism:: Schizosaccharomyces pombe

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL9453
66 Samples

Download data: BED

Series

Accession:: GSE39166

ID:: 200039166

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20006344410.

RNA processing proteins regulate Mec1/ATR activation by promoting generation of RPA-coated ssDNA.

(Submitter supplied) Eukaryotic cells respond to DNA double-strand breaks (DSBs) by activating a checkpoint that depends on the protein kinases Tel1/ATM and Mec1/ATR. Mec1/ATR is activated by RPA-coated single-stranded DNA (ssDNA), which arises upon nucleolytic degradation (resection) of the DSB. Emerging evidences indicate that RNA processing factors play critical, yet poorly understood, roles in genomic stability. Here, we provide evidence that the Saccharomyces cerevisiae RNA decay factors Xrn1, Rrp6 and Trf4 regulate Mec1/ATR activation by promoting generation of RPA-coated ssDNA. more...

Organism:: Saccharomyces cerevisiae

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17342
12 Samples

Download data: TXT

Series

Accession:: GSE63444

ID:: 200063444

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Select item 20013942011.

In situ capture of global transcription dynamics and enhancer activity with high accuracy and sensitivity

(Submitter supplied) 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. more...

Organism:: Homo sapiens; Mus musculus

Type:: Expression profiling by high throughput sequencing; Other; Genome binding/occupancy profiling by high throughput sequencing

4 related Platforms
78 Samples

Download data: BED, BIGWIG, XLS

Series

Accession:: GSE139420

ID:: 200139420

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20020243312.

uscfDNA-oriented sequencing pipeline profiling the cell-free DNA populations in plasma

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Homo sapiens

Type:: Other

Platform:: GPL24676
23 Samples

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Series

Accession:: GSE202433

ID:: 200202433

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Select item 20020243213.

Digestion treatment of uscfDNA extracted by SPRI Method

(Submitter supplied) We report the application of an uscfDNA-oriented sequencing pipeline profiling the cell-free DNA populations in plasma. The uscfDNA sequencing pipeline include two uscfDNA-optimized extraction methods (QiaM and SPRI) and one control extraction method (QiaC). Final libraries are made with a single-stranded library prepartion kit. We generate genome-wide maps revealing the presence of an uscfDNA population (25-99bp) in addition to the mncfDNA (100-250bp).