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Items: 20

1.

R-loop dependent promoter-proximal termination ensures genome stability [ATAC-seq]

(Submitter supplied) Precise regulation of transcription is essential to maintain genome integrity, yet key mechanisms coordinating transcription, genome stability and downstream cellular functions remain incomplete. Here we report the identification of SOSS-INTAC, a stable association of the genome stability regulator Sensor of Single-stranded DNA (ssDNA) (SOSS) complex and transcription regulator Integrator-PP2A (INTAC). more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24676
4 Samples
Download data: BW
Series
Accession:
GSE223992
ID:
200223992

PubMed Full text in PMC Similar studies

2.

R-loop dependent promoter-proximal termination ensures genome stability

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24676
111 Samples
Download data: BW
Series
Accession:
GSE223997
ID:
200223997

PubMed Full text in PMC Similar studies

3.

R-loop dependent promoter-proximal termination ensures genome stability [PRO-seq]

(Submitter supplied) Precise regulation of transcription is essential to maintain genome integrity, yet key mechanisms coordinating transcription, genome stability and downstream cellular functions remain incomplete. Here we report the identification of SOSS-INTAC, a stable association of the genome stability regulator Sensor of Single-stranded DNA (ssDNA) (SOSS) complex and transcription regulator Integrator-PP2A (INTAC). more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24676
4 Samples
Download data: BW
Series
Accession:
GSE223996
ID:
200223996

PubMed Full text in PMC Similar studies

4.

R-loop dependent promoter-proximal termination ensures genome stability [KAS-seq]

(Submitter supplied) Precise regulation of transcription is essential to maintain genome integrity, yet key mechanisms coordinating transcription, genome stability and downstream cellular functions remain incomplete. Here we report the identification of SOSS-INTAC, a stable association of the genome stability regulator Sensor of Single-stranded DNA (ssDNA) (SOSS) complex and transcription regulator Integrator-PP2A (INTAC). more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24676
4 Samples
Download data: BW
Series
Accession:
GSE223995
ID:
200223995

PubMed Full text in PMC Similar studies

5.

R-loop dependent promoter-proximal termination ensures genome stability [ChIP-seq]

(Submitter supplied) Precise regulation of transcription is essential to maintain genome integrity, yet key mechanisms coordinating transcription, genome stability and downstream cellular functions remain incomplete. Here we report the identification of SOSS-INTAC, a stable association of the genome stability regulator Sensor of Single-stranded DNA (ssDNA) (SOSS) complex and transcription regulator Integrator-PP2A (INTAC). more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24676
49 Samples
Download data: BW
Series
Accession:
GSE223994
ID:
200223994

PubMed Full text in PMC Similar studies

6.

R-loop dependent promoter-proximal termination ensures genome stability [CUT&Tag]

(Submitter supplied) Precise regulation of transcription is essential to maintain genome integrity, yet key mechanisms coordinating transcription, genome stability and downstream cellular functions remain incomplete. Here we report the identification of SOSS-INTAC, a stable association of the genome stability regulator Sensor of Single-stranded DNA (ssDNA) (SOSS) complex and transcription regulator Integrator-PP2A (INTAC). more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24676
50 Samples
Download data: BW
Series
Accession:
GSE223993
ID:
200223993

PubMed Full text in PMC Similar studies

7.

The Integrator complex controls the termination of transcription at diverse classes of gene targets

(Submitter supplied) Complexes containing INTS3 and either NABP1 or NABP2 were initially characterized in DNA damage responses, but their biochemical function remained unknown. Using affinity purifications and HIV Integration Targeting-Sequencing (HIT-Seq), we find that these complexes are part of the Integrator complex, which binds RNA Polymerase II and regulates specific target genes. Integrator cleaves snRNAs as part of their processing to their mature form in a mechanism that is intimately coupled with transcription termination. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL13112 GPL11002
11 Samples
Download data: BED
Series
Accession:
GSE65090
ID:
200065090

PubMed Full text in PMC Similar studies SRA Run Selector

8.

INTAC endonuclease and phosphatase modules differentially regulate transcription by RNA polymerase II

(Submitter supplied) Gene expression in metazoans is controlled by promoter-proximal pausing of RNA polymerase II, which can undergo productive elongation or early termination. Integrator-PP2A (INTAC) plays a crucial role in determining the fate of paused polymerases, but the underlying mechanisms remain unclear. Here we establish a rapid degradation system to dissect the direct functions of INTAC RNA endonuclease and phosphatase modules. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other
Platform:
GPL24676
72 Samples
Download data: BW, TXT
Series
Accession:
GSE223265
ID:
200223265

PubMed Similar studies

9.

Integrator is a genome-wide attenuator of non-productive transcription

(Submitter supplied) Termination of RNA polymerase II (RNAPII) transcription in metazoans relies largely on the Cleavage and Polyadenylation (CPA) and Integrator (INT) complexes originally found to act at the ends of protein-coding and snRNA genes, respectively. Here we monitor CPA- and INT-dependent termination activities genome-wide, including at thousands of previously unannotated transcription units (TUs), producing unstable RNA. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Other
Platforms:
GPL11154 GPL18573
40 Samples
Download data: BW
Series
Accession:
GSE151919
ID:
200151919

PubMed Full text in PMC Similar studies Analyze with GEO2RSRA Run Selector

10.

Stabilization of Pol II protein, orchestration of transcription cycles, and maintenance of enhancer landscape by general transcription regulator SPT5 [TT-seq]

(Submitter supplied) Transcription machinery progression is governed by multitasking regulators including SPT5, an evolutionarily conserved factor implicated in virtually all transcriptional steps from enhancer activation to termination. Yet its mechanistic understanding in human cells remains incomplete. Here we utilize rapid degradation system and reveal crucial function of SPT5 in maintaining cellular and chromatin Pol II levels. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20795
6 Samples
Download data: BW
Series
Accession:
GSE183506
ID:
200183506

PubMed Similar studies Analyze with GEO2RSRA Run Selector

11.

Stabilization of Pol II protein, orchestration of transcription cycles, and maintenance of enhancer landscape by general transcription regulator SPT5 [PRO-seq]

(Submitter supplied) Transcription machinery progression is governed by multitasking regulators including SPT5, an evolutionarily conserved factor implicated in virtually all transcriptional steps from enhancer activation to termination. Yet its mechanistic understanding in human cells remains incomplete. Here we utilize rapid degradation system and reveal crucial function of SPT5 in maintaining cellular and chromatin Pol II levels. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20795
25 Samples
Download data: BW
Series
Accession:
GSE183505
ID:
200183505

PubMed Similar studies SRA Run Selector

12.

Stabilization of Pol II protein, orchestration of transcription cycles, and maintenance of enhancer landscape by general transcription regulator SPT5

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms:
GPL24676 GPL20795
69 Samples
Download data: BW
Series
Accession:
GSE180845
ID:
200180845

PubMed Similar studies

13.

Stabilization of Pol II protein, orchestration of transcription cycles, and maintenance of enhancer landscape by general transcription regulator SPT5 [ATAC-seq]

(Submitter supplied) Transcription machinery progression is governed by multitasking regulators including SPT5, an evolutionarily conserved factor implicated in virtually all transcriptional steps from enhancer activation to termination. Yet its mechanistic understanding in human cells remains incomplete. Here we utilize rapid degradation system and reveal crucial function of SPT5 in maintaining cellular and chromatin Pol II levels. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL20795
4 Samples
Download data: BW
Series
Accession:
GSE180844
ID:
200180844

PubMed Similar studies SRA Run Selector

14.

Stabilization of Pol II protein, orchestration of transcription cycles, and maintenance of enhancer landscape by general transcription regulator SPT5 [RNA-seq]

(Submitter supplied) Transcription machinery progression is governed by multitasking regulators including SPT5, an evolutionarily conserved factor implicated in virtually all transcriptional steps from enhancer activation to termination. Yet its mechanistic understanding in human cells remains incomplete. Here we utilize rapid degradation system and reveal crucial function of SPT5 in maintaining cellular and chromatin Pol II levels. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20795
6 Samples
Download data: BW
Series
Accession:
GSE180843
ID:
200180843

PubMed Similar studies SRA Run Selector

15.

Stabilization of Pol II protein, orchestration of transcription cycles, and maintenance of enhancer landscape by general transcription regulator SPT5 [ChIP-seq]

(Submitter supplied) Transcription machinery progression is governed by multitasking regulators including SPT5, an evolutionarily conserved factor implicated in virtually all transcriptional steps from enhancer activation to termination. Yet its mechanistic understanding in human cells remains incomplete. Here we utilize rapid degradation system and reveal crucial function of SPT5 in maintaining cellular and chromatin Pol II levels. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24676
28 Samples
Download data: BW
Series
Accession:
GSE180842
ID:
200180842

PubMed Similar studies SRA Run Selector

16.

Genome-wide maps of double strand breaks after siRNA knockdown of DDX41 in HCT116 cells

(Submitter supplied) We report the first genome-wide mapping of fragility hotspots after siRNA-mediated knockdown of the DEAD-box helicase DDX41 in HCT116 cells using sBLISS. DDX41 defficient cells display elevated levels of genomic instability. sBLISS analysis revealed that hotspots for genomic instability in the absence of DDX41 are located around the transcription start site of transcribed genes.
Organism:
Homo sapiens
Type:
Other
Platform:
GPL18573
4 Samples
Download data: BED, BW
Series
Accession:
GSE183147
ID:
200183147

PubMed Full text in PMC Similar studies SRA Run Selector

17.

Genome wide mapping of DDX41 chromatin binding using a targeted nuclease approach in U2OS cells after expression

(Submitter supplied) Purpose: Investigation of DDX41 chromatin binding sites in U2OS cells Method: Expression of DDX41-GFP was induced for 48 hours before crosslinking using 1µg/ml docycycline. Control cells were not induced with doxycline. Cells were mildly crosslinked using 1% FA for 2 min at RT. Concanavalin A-coated beads were activated in Binding Buffer (20 mM Hepes-KOH pH 7.9, 10 mM KCl, 1mM CaCl2, 1 mM MnCl2).1*10^6 U2OS cells were washed twice with Wash Buffer (Hepes-NaOH pH7.5, 150 mM NaCl, 0.5 mM Spermidine, 1 mM protease inhibitor) at room temperature and afterwards immobilized on the activated beads in 1 ml Wash Buffer. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18573
4 Samples
Download data: BW
Series
Accession:
GSE183083
ID:
200183083

PubMed Full text in PMC Similar studies SRA Run Selector

18.

Genome wide mapping of native R-loops using a targeted nuclease approach in HCT116 cells after DDX41 siRNA knockdown (MapR)

(Submitter supplied) Purpose: Investigation of genome-wide changes in R-loop levels after knockdown of DDX41 HCT116 cells in comparison to a control knockdown. Method: Concanavalin A-coated beads were activated in Binding Buffer (20 mM Hepes-KOH pH 7.9, 10 mM KCl, 1mM CaCl2, 1 mM MnCl2). 1*10^6HCT116 cells were washed twice with Wash Buffer (Hepes-NaOH pH7.5, 150 mM NaCl, 0.5 mM Spermidine, 1 mM protease inhibitor) at room temperature and afterwards immobilized on the activated beads in 50 µl Wash Buffer containing 0.05% Digitonin. more...
Organism:
Homo sapiens
Type:
Other
Platform:
GPL18573
12 Samples
Download data: BW
Series
Accession:
GSE183081
ID:
200183081

PubMed Full text in PMC Similar studies SRA Run Selector

19.

MapR in U2OS and HCT116 cells and RNA-seq in U2OS

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Other; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18573
48 Samples
Download data: BED, BW, TSV
Series
Accession:
GSE168173
ID:
200168173

PubMed Full text in PMC Similar studies

20.

RNA-seq after DDX41 knockdown in U2OS cells

(Submitter supplied) Purpose: Investigating transcriptome changes after depletion of DDX41. Methods: mRNA profiles after DDX41 knockdown compared to control knockdown were generated in 5 biological replicates. Samples were mapped using STAR (v2.7) against hg38 with the Gencode annotation. Reads per gene were counted using featureCounts (v.1.6). The differential expression analysis was performed using Bioconductor (v2.46)/DESeq2 (v1.26). more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
10 Samples
Download data: BW, TSV
Series
Accession:
GSE168171
ID:
200168171

PubMed Full text in PMC Similar studies Analyze with GEO2RSRA Run Selector

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