Similar studies for GEO DataSets (Select 200134377) - GEO DataSets

Select item 2001343771.

Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and pervasive recursive splicing

(Submitter supplied) The coupled activities of RNA polymerase and the spliceosome are responsible for the abundance and isoform composition of mRNA in human cells. However, the dynamics of these megadalton enzymatic complexes working in concert on endogenous genes have not been described. Here, we establish a quasi-genome-scale platform for observing synthesis and processing kinetics of single nascent RNA molecules in real time. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing; Other

4 related Platforms
23 Samples

Download data: BED, CSV

Series

Accession:: GSE134377

ID:: 200134377

PubMed Full text in PMC Similar studies

Select item 2001781822.

Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and pervasive recursive splicing [pulse_chase_nascent RNA]

(Submitter supplied) The coupled activities of RNA polymerase and the spliceosome are responsible for the abundance and isoform composition of mRNA in human cells. However, the dynamics of these megadalton enzymatic complexes working in concert on endogenous genes have not been described. Here, we establish a quasi-genome-scale platform for observing synthesis and processing kinetics of single nascent RNA molecules in real time. more...

Organism:: Homo sapiens

Type:: Other

Platform:: GPL21697
6 Samples

Download data: XLSX

Series

Accession:: GSE178182

ID:: 200178182

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001781813.

Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and pervasive recursive splicing [Lariat seq]

(Submitter supplied) The coupled activities of RNA polymerase and the spliceosome are responsible for the abundance and isoform composition of mRNA in human cells. However, the dynamics of these megadalton enzymatic complexes working in concert on endogenous genes have not been described. Here, we establish a quasi-genome-scale platform for observing synthesis and processing kinetics of single nascent RNA molecules in real time. more...

Organism:: Homo sapiens

Type:: Other

Platform:: GPL20795
4 Samples

Download data: XLSX

Series

Accession:: GSE178181

ID:: 200178181

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001781804.

Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and pervasive recursive splicing [Nanopore]

(Submitter supplied) The coupled activities of RNA polymerase and the spliceosome are responsible for the abundance and isoform composition of mRNA in human cells. However, the dynamics of these megadalton enzymatic complexes working in concert on endogenous genes have not been described. Here, we establish a quasi-genome-scale platform for observing synthesis and processing kinetics of single nascent RNA molecules in real time. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL28975
2 Samples

Download data: GTF, TXT

Series

Accession:: GSE178180

ID:: 200178180

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001343945.

Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and pervasive recursive splicing [PARCLIP]

(Submitter supplied) The coupled activities of RNA polymerase and the spliceosome are responsible for the abundance and isoform composition of mRNA in human cells. However, the dynamics of these megadalton enzymatic complexes working in concert on endogenous genes have not been described. Here, we establish a quasi-genome-scale platform for observing synthesis and processing kinetics of single nascent RNA molecules in real time. more...

Organism:: Homo sapiens

Type:: Other

Platform:: GPL16791
2 Samples

Download data: CSV

Series

Accession:: GSE134394

ID:: 200134394

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001343936.

Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and pervasive recursive splicing [primer extension]

(Submitter supplied) The coupled activities of RNA polymerase and the spliceosome are responsible for the abundance and isoform composition of mRNA in human cells. However, the dynamics of these megadalton enzymatic complexes working in concert on endogenous genes have not been described. Here, we establish a quasi-genome-scale platform for observing synthesis and processing kinetics of single nascent RNA molecules in real time. more...

Organism:: Homo sapiens

Type:: Other

Platform:: GPL16791
1 Sample

Download data: BED

Series

Accession:: GSE134393

ID:: 200134393

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001343927.

Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and pervasive recursive splicing [nascent RNA profiling]

(Submitter supplied) The coupled activities of RNA polymerase and the spliceosome are responsible for the abundance and isoform composition of mRNA in human cells. However, the dynamics of these megadalton enzymatic complexes working in concert on endogenous genes have not been described. Here, we establish a quasi-genome-scale platform for observing synthesis and processing kinetics of single nascent RNA molecules in real time. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL16791
8 Samples

Download data: XLSX

Series

Accession:: GSE134392

ID:: 200134392

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001450928.

Intron looping is mediated by U1 snRNP and RNA polymerase II co-transcriptionally

(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:: GPL11154
18 Samples

Download data: BEDGRAPH, BW, TXT

Series

Accession:: GSE145092

ID:: 200145092

PubMed Full text in PMC Similar studies

Select item 2001449069.

Intron looping is mediated during transcription by U1 snRNP and RNA polymerase II [RNA-Seq]

(Submitter supplied) In the earliest step of spliceosome assembly, the two splice sites flanking an intron are brought into proximity by U1 snRNP and U2AF. The mechanism that facilitates this intron looping is poorly understood. Using a CRISPR interference-based approach to halt RNA polymerase II transcription in the middle of introns, we discovered that the 5 splice site base pairs with a U1 snRNA that is tethered to RNA polymerase II during intron synthesis. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11154
1 Sample

Download data: TXT

Series

Accession:: GSE144906

ID:: 200144906

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20014490510.

Intron looping is mediated during transcription by U1 snRNP and RNA polymerase II [RIP-seq]

(Submitter supplied) In the earliest step of spliceosome assembly, the two splice sites flanking an intron are brought into proximity by U1 snRNP and U2AF. The mechanism that facilitates this intron looping is poorly understood. Using a CRISPR interference-based approach to halt RNA polymerase II transcription in the middle of introns, we discovered that the 5 splice site base pairs with a U1 snRNA that is tethered to RNA polymerase II during intron synthesis. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11154
10 Samples

Download data: BEDGRAPH, BW

Series

Accession:: GSE144905

ID:: 200144905

PubMed Full text in PMC Similar studies Analyze with GEO2R SRA Run Selector

Select item 20014487411.

Intron looping is mediated by U1 snRNP and RNA polymerase II co-transcriptionally [ChIP-seq]

(Submitter supplied) In the earliest step of spliceosome assembly, the two splice sites flanking an intron are brought into proximity by U1 snRNP and U2AF. The mechanism that facilitates this intron looping is poorly understood. Using a CRISPR interference-based approach to halt RNA polymerase II transcription in the middle of introns, we discovered that the 5 splice site base pairs with a U1 snRNA that is tethered to RNA polymerase II during intron synthesis. more...

Organism:: Homo sapiens

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

Platform:: GPL11154
7 Samples

Download data: BW

Series

Accession:: GSE144874

ID:: 200144874

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20017833512.

Global alternative splicing analysis of mutations in two new spliceosome components KIN17 and PRCC in C. elegans

(Submitter supplied) Mutant alleles of KIN17 (dxbp-1) and PRCC (prcc-1) were identifed in a forward genetic screen for suppressors of cryptic splice site activation

Organism:: Caenorhabditis elegans

Type:: Expression profiling by high throughput sequencing

Platform:: GPL26672
15 Samples

Download data: TXT

Series

Accession:: GSE178335

ID:: 200178335

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20015407913.

Revealing nascent RNA processing dynamics with nano-COP

(Submitter supplied) During maturation, eukaryotic precursor RNAs undergo processing events including intron splicing, 3’-end cleavage, and polyadenylation. Here, we describe nanopore analysis of CO-transcriptional Processing (nano-COP), a method for probing the timing and patterns of RNA processing. An extension of native elongating transcript sequencing (NET-seq), which quantifies transcription genome-wide through short-read sequencing of nascent RNA 3’ ends, nano-COP uses long-read nascent RNA sequencing to observe global patterns of RNA processing. more...

Organism:: Homo sapiens; synthetic construct

Type:: Other

Platforms:: GPL24106 GPL25738
11 Samples

Download data: TSV, TXT

Series

Accession:: GSE154079

ID:: 200154079

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20010468114.

Long-read sequencing of nascent RNA in S. pombe reveals coupling among RNA processing events

(Submitter supplied) Splicing and expression profiling of nascent and mRNA by RNA sequencing This SuperSeries is composed of the SubSeries listed below.

Organism:: Schizosaccharomyces pombe

Type:: Expression profiling by high throughput sequencing; Other

Platforms:: GPL17225 GPL21481
18 Samples

Download data: BED, BEDGRAPH

Series

Accession:: GSE104681

ID:: 200104681

PubMed Full text in PMC Similar studies

Select item 20013788315.

Ultra-deep sequencing reveals pre-mRNA splicing as a sequence driven high-fidelity process

(Submitter supplied) Alternative splicing diversifies mRNA transcripts in human cells. While the spliceosome pairs exons with a high degree of accuracy, the rates of rare aberrant and non-canonical pre-mRNA splicing have not been evaluated at the nucleotide level to determine the quantity and identity of these events across splice junctions. Using ultra-deep sequencing the frequency of aberrant and non-canonical splicing events for three splice junctions flanking exon 7 of SMN1 were determined at single nucleotide resolution. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11154
1 Sample

Download data: TXT

Series

Accession:: GSE137883

ID:: 200137883

PubMed Full text in PMC Similar studies Analyze with GEO2R SRA Run Selector

Select item 20022018616.

FUBP1 is a core splicing factor that facilitates 3' splice site recognition and splicing of long introns

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

Organism:: synthetic construct; Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL11154 GPL19424 GPL18573
61 Samples

Download data: BW

Series

Accession:: GSE220186

ID:: 200220186

PubMed Similar studies

Select item 20022018417.

FUBP1 is a core splicing factor that facilitates 3' splice site recognition and splicing of long introns [In vivo iCLIP]

(Submitter supplied) Splicing is a central process in metazoans and greatly expands their proteome by alternative splicing of pre-mRNA transcripts. An essential regulatory step during early spliceosome assembly is the recognition of cis-regulatory RNA motifs in pre-mRNAs. Here, we identified the RNA binding protein FUBP1 as a novel core splicing factor with a ubiquitous footprint on pre-mRNAs. FUBP1 binds to a previously unknown cis-regulatory motif upstream of the branch point of human introns. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11154
27 Samples

Download data: BW

Series

Accession:: GSE220184

ID:: 200220184

Select item 20022018318.

FUBP1 is a core splicing factor that facilitates 3' splice site recognition and splicing of long introns [In vitro iCLIP]

(Submitter supplied) Splicing is a central process in metazoans and greatly expands their proteome by alternative splicing of pre-mRNA transcripts. An essential regulatory step during early spliceosome assembly is the recognition of cis-regulatory RNA motifs in pre-mRNAs. Here, we identified the RNA binding protein FUBP1 as a novel core splicing factor with a ubiquitous footprint on pre-mRNAs. FUBP1 binds to a previously unknown cis-regulatory motif upstream of the branch point of human introns. more...

Organism:: synthetic construct

Type:: Expression profiling by high throughput sequencing

Platform:: GPL19424
18 Samples

Download data: BED, BW

Series

Accession:: GSE220183

ID:: 200220183

PubMed Similar studies

Select item 20022018019.

FUBP1 is a core splicing factor that facilitates 3' splice site recognition and splicing of long introns [RNA-Seq]

(Submitter supplied) Splicing is a central process in metazoans and greatly expands their proteome by alternative splicing of pre-mRNA transcripts. An essential regulatory step during early spliceosome assembly is the recognition of cis-regulatory RNA motifs in pre-mRNAs. Here, we identified the RNA binding protein FUBP1 as a novel core splicing factor with a ubiquitous footprint on pre-mRNAs. FUBP1 binds to a previously unknown cis-regulatory motif upstream of the branch point of human introns. more...