SnapShot-Seq: a method for extracting genome-wide, in vivo mRNA dynamics from a single total RNA sample (Q35107880)

6 August 2017

SnapShot-Seq: a method for extracting genome-wide, in vivo mRNA dynamics from a single total RNA sample (English)

1 reference

6 August 2017

0 references

1 reference

Nimrod Miller

7

0 references

Sarah A Boswell

Sarah A Boswell

3

0 references

Yong-Chao Ma

Yong-Chao Ma

9

0 references

Nicole Cloonan

Nicole Cloonan

4

0 references

Sean Grimmond

Sean M Grimmond

11

0 references

Michael Springer

12

Michael Springer

1 reference

6 August 2017

Jesse M Gray

1

1 reference

6 August 2017

David A Harmin

2

1 reference

6 August 2017

Thomas E Mullen

5

1 reference

6 August 2017

Joseph J Ling

6

1 reference

6 August 2017

Scott Kuersten

8

1 reference

6 August 2017

Steven A McCarroll

10

1 reference

6 August 2017

language of work or name

English

0 references

publication date

26 February 2014

1 reference

6 August 2017

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6 August 2017

9

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6 August 2017

2

1 reference

6 August 2017

e89673

1 reference

Creative Commons Attribution 4.0 International

6 August 2017

start time

26 February 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells

1 reference

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mRNA decapping factors and the exonuclease Xrn2 function in widespread premature termination of RNA polymerase II transcription

9 July 2018

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Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation

9 July 2018

1 reference

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Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

Coupled pre-mRNA and mRNA dynamics unveil operational strategies underlying transcriptional responses to stimuli.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

RNA sequencing reveals two major classes of gene expression levels in metazoan cells

9 July 2018

1 reference

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Oncogenic fusion protein EWS/FLI1 down-regulates gene expression by both transcriptional and posttranscriptional mechanisms

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

Nascent transcript sequencing visualizes transcription at nucleotide resolution

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

RiboSys, a high-resolution, quantitative approach to measure the in vivo kinetics of pre-mRNA splicing and 3'-end processing in Saccharomyces cerevisiae.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

The differential interaction of snRNPs with pre-mRNA reveals splicing kinetics in living cells

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

Alternative expression analysis by RNA sequencing

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

Gene-specific RNA polymerase II phosphorylation and the CTD code

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

Comprehensive comparative analysis of strand-specific RNA sequencing methods

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

Global coordination of transcriptional control and mRNA decay during cellular differentiation

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

Widespread transcription at neuronal activity-regulated enhancers

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

Tumor transcriptome sequencing reveals allelic expression imbalances associated with copy number alterations

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

A wave of nascent transcription on activated human genes

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

Rates of in situ transcription and splicing in large human genes

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

Co-transcriptional splicing of constitutive and alternative exons

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

Transcriptome analysis by strand-specific sequencing of complementary DNA.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

Spinal muscular atrophy: why do low levels of survival motor neuron protein make motor neurons sick?

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

Conserved principles of mammalian transcriptional regulation revealed by RNA half-life

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

Alternative isoform regulation in human tissue transcriptomes

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

The biflavonoid isoginkgetin is a general inhibitor of Pre-mRNA splicing

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

RNA-binding proteins and post-transcriptional gene regulation

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

In vivo dynamics of RNA polymerase II transcription.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

Genome-wide mapping of in vivo protein-DNA interactions

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

Microarray analysis of newly synthesized RNA in cells and animals

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

Pre-mRNA splicing and retinitis pigmentosa

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

The Ro autoantigen binds misfolded U2 small nuclear RNAs and assists mammalian cell survival after UV irradiation

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

Coexpression of neighboring genes in Caenorhabditis elegans is mostly due to operons and duplicate genes

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

In vivo kinetics of mRNA splicing and transport in mammalian cells

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

The splicing of U12-type introns can be a rate-limiting step in gene expression

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

Clustering of housekeeping genes provides a unified model of gene order in the human genome

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

The human transcriptome map: clustering of highly expressed genes in chromosomal domains

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

Regulation of adjacent yeast genes

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

Dissecting the regulatory circuitry of a eukaryotic genome

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

A genome-wide transcriptional analysis of the mitotic cell cycle

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

Order of intron removal during splicing of endogenous adenine phosphoribosyltransferase and dihydrofolate reductase pre-mRNA.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

In vivo transcriptional pausing and cap formation on three Drosophila heat shock genes

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

Splice site selection, rate of splicing, and alternative splicing on nascent transcripts

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

Cell type-specific analysis of mRNA synthesis and decay in vivo with uracil phosphoribosyltransferase and 4-thiouracil

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

Cotranscriptional spliceosome assembly occurs in a stepwise fashion and requires the cap binding complex.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935918

Global Analysis of Nascent RNA Reveals Transcriptional Pausing in Terminal Exons

27 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0089673

Biosynthetic labeling of RNA with uracil phosphoribosyltransferase allows cell-specific microarray analysis of mRNA synthesis and decay

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24586954

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Spliceosome mutations in hematopoietic malignancies

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24586954

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0089673

1 reference

6 August 2017

0 references

1 reference

6 August 2017

1 reference