Similar studies for GEO DataSets (Select 200041785) - GEO DataSets

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Items: 20

Select item 2000417851.

Global analysis of Upf1 in mESCs reveals expanded scope of nonsense-mediated mRNA decay

(Submitter supplied) Nonsense-mediated mRNA decay (NMD) is a conserved RNA surveillance pathway that is an important modulator of disease pathology and is required for embryonic development. Despite significant research effort, the rules that govern NMD remain incompletely understood. Here we used a combined¬ approach, integrating RNA-Seq, ribosome footprinting, and CLIP-Seq analysis of the essential NMD factor Upf1, to provide a more complete picture of the role of NMD in modulating gene expression in murine embryonic stem cells (mESCs). more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing; Other

Platforms:: GPL11002 GPL13112
23 Samples

Download data: BED, FPKM_TRACKING

Series

Accession:: GSE41785

ID:: 200041785

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001263852.

Divergent effects of eRF3 and Upf1 on the expression of uORF carrying mRNAs and ribosome protein genes

(Submitter supplied) In addition to its role in translation termination, eRF3 has been implicated in the nonsense-mediated mRNA decay (NMD) pathway through its interaction with Upf1. NMD is a RNA quality control mechanism, which detects and degrades aberrant mRNAs as well as some normal transcripts including those that harbor upstream open reading frames in their 5' leader sequence and long 3′ UTR. In this study, we used RNA-sequencing and ribosome profiling to perform a genome wide analysis of the effect of either eRF3 or Upf1 depletion in human cells. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing; Other

Platform:: GPL18573
12 Samples

Download data: XLSX

Series

Accession:: GSE126385

ID:: 200126385

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000861483.

RNA-seq of KD, rescues of NMD factors, and UPF1-flag CLIP-seq in HeLa cells.

(Submitter supplied) This study aims at confidently identifying endogenous nonsense mediated decay (NMD) targets. To achieve this purpose, we performed KD of a few NMD factors in HeLa cells. Additionally, we performed rescue experiments for each factor, expressing an RNAi-resistant version of the gene from a plasmid. To determine transcripts bound by UPF1 in HeLa cells, A construct with a C-terminally flag tagged version of UPF1 was expressed. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL16791
35 Samples

Download data: CSV

Series

Accession:: GSE86148

ID:: 200086148

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

Select item 2000600454.

A post-translational regulatory switch on UPF1 controls targeted mRNA degradation.

(Submitter supplied) Nonsense-mediated mRNA decay (NMD) controls the quality of eukaryotic gene expression and also degrades physiologic mRNAs. How NMD targets are identified is incompletely understood. A central NMD factor is the ATP-dependent RNA helicase UPF1. Neither the distance in space between the termination codon and the poly(A) tail nor the binding of steady-state, largely hypophosphorylated UPF1 is a discriminating marker of cellular NMD targets, unlike for PTC-containing reporter mRNAs when compared to their PTC-free counterparts. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL16791
6 Samples

Download data: BED

Series

Accession:: GSE60045

ID:: 200060045

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001761975.

Effects of pan-UPF1 knockdown on RNA abundance

(Submitter supplied) Flp-In T-REx-293 cells transfected with non-targeting control siRNA or UPF1-specific siRNA as indicated and used for total RNA-seq.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24676
6 Samples

Download data: TXT

Series

Accession:: GSE176197

ID:: 200176197

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001626996.

Condition- and isoform-dependent UPF1 activity

(Submitter supplied) HEK-293 cells transfected with non-targeting control siRNA or UPF1LL-specific siRNA were treated with vehicle control, puromycin, or thapsigargin as indicated and used for total RNA-seq.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24676
48 Samples

Download data: TXT

Series

Accession:: GSE162699

ID:: 200162699

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

Select item 2000695867.

Target discrimination in nonsense-mediated mRNA decay requires Upf1 ATPase activity

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

Organism:: Homo sapiens

Type:: Other

Platform:: GPL11154
14 Samples

Download data: RPKM

Series

Accession:: GSE69586

ID:: 200069586

PubMed Full text in PMC Similar studies

Select item 2000695858.

Target discrimination in nonsense-mediated mRNA decay requires Upf1 ATPase activity (RIP-Seq)

(Submitter supplied) RNA quality control pathways serve to get rid of faulty RNAs and therefore must be able to discriminate these RNAs from those that are normal. Here we present evidence that the ATPase cycle of SF1 Helicase Upf1 is required for mRNA discrimination during Nonsense-Mediated Decay (NMD). Mutations affecting the Upf1 ATPase cycle disrupt the mRNA selectivity of Upf1, leading to indiscriminate accumulation of NMD complexes on both NMD target and non-target mRNAs. more...

Organism:: Homo sapiens

Type:: Other

Platform:: GPL11154
8 Samples

Download data: RPKM

Series

Accession:: GSE69585

ID:: 200069585

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

Select item 2000695849.

Target discrimination in nonsense-mediated mRNA decay requires Upf1 ATPase activity (CLIP-Seq)

Organism:: Homo sapiens

Type:: Other

Platform:: GPL11154
6 Samples

Download data: BAM

Series

Accession:: GSE69584

ID:: 200069584

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20004797610.

Translation-dependent displacement of UPF1 from coding sequences causes its enrichment in 3’ UTRs

(Submitter supplied) The RNA helicase UPF1 is best known for its key function in mRNA nonsense-mediated mRNA decay (NMD), but has also been implicated in additional mRNA turnover mechanisms, telomere homeostasis, and DNA replication. In NMD, UPF1 recruitment to target mRNAs is thought to occur through interaction with release factors at terminating ribosomes, but evidence for translation-independent interaction of UPF1 with the 3’ untranslated region (UTR) of mRNAs has also been reported. more...

Organism:: Homo sapiens

Type:: Other

Platform:: GPL11154
5 Samples

Download data: BED

Series

Accession:: GSE47976

ID:: 200047976

Select item 20005988411.

PTBP1 excludes UPF1 to protect long 3'UTRs from nonsense-mediated mRNA decay

(Submitter supplied) RNA-seq analysis of human 293 Tet-off cells depleted of PTBP1 and UPF1 alone and in tandem with specific siRNAs.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11154
8 Samples

Download data: TXT

Series

Accession:: GSE59884

ID:: 200059884

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

Select item 20024648512.

UPF1 ATPase autoinhibition and activation modulate RNA binding kinetics and NMD efficiency

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

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24676
96 Samples

Download data

Series

Accession:: GSE246485

ID:: 200246485

PubMed Full text in PMC Similar studies

Select item 20024648413.

UPF1 ATPase autoinhibition and activation modulate RNA binding kinetics and NMD efficiency 2

(Submitter supplied) The RNA helicase UPF1 interacts with mRNAs, mRNA decay machinery, and the terminating ribosome to promote nonsense-mediated mRNA decay (NMD). Structural and biochemical data have revealed that UPF1 exists in an enzymatically autoinhibited “closed” state. Upon binding the NMD protein UPF2, UPF1 undergoes an extensive conformational change into a more enzymatically active “open” state, which exhibits enhanced ATPase and helicase activity. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24676
48 Samples

Download data: TXT

Series

Accession:: GSE246484

ID:: 200246484

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20024648314.

UPF1 ATPase autoinhibition and activation modulate RNA binding kinetics and NMD efficiency 1

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24676
48 Samples

Download data: TXT

Series

Accession:: GSE246483

ID:: 200246483

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20010092915.

Global characterization of direct substrates of nonsense-mediated mRNA decay in Caenorhabditis elegans

(Submitter supplied) Purpose: We present a genome-wide investigation to distinguish mRNA substrates directly regulated by nonsense-mediated mRNA decay (NMD) from indirect secondary effects using true NMD null alleles Methods: mRNA profiles of wild type (N2), smg-1(r910), and smg-1(r910) smg-2(r915) animals were generated by deep sequencing, in triplicate, using Illumina HiSeq2000. We further performed deep sequencing in triplicate on RNAs that co-immunoprecipitate with the central effector of NMD, SMG-2, in both smg-1(r910) and smg-1(r910) smg-2(r915) mutant animals. more...

Organism:: Caenorhabditis elegans

Type:: Expression profiling by high throughput sequencing; Other

Platform:: GPL13657
15 Samples

Download data: GTF, TXT

Series

Accession:: GSE100929

ID:: 200100929

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20005395416.

Expression analysis of DamP mRNAs using expressed molecular barcodes

(Submitter supplied) We have generated 979 yeast strains in which the natural 3' UTR of essential gene mRNAs has been replaced by the same long 1.4 kb artificial 3' UTR (DAmP modification). Nonsense mediated mRNA decay (NMD) of these mRNA reporters was tested by using Agilent barcode microarrays by taking advantage of molecular barcodes introduced just downstream the stop codon during strain construction. We introduced in each DAmP strain either a neutral mutation (deletion of YEL068C) or the deletion of essential factors for NMD: NAM7 and NMD2. more...

Organism:: Saccharomyces cerevisiae S288C; Saccharomyces cerevisiae

Type:: Expression profiling by array

Platform:: GPL18088
6 Samples

Download data: GPR

Series

Accession:: GSE53954

ID:: 200053954

Select item 20014634017.

Transcriptome and translatome profiling of Arabidopsis upf1-3 pad4 mutant

(Submitter supplied) Goal of the study is to decipher the role of UPF1 in maintaining transcriptome and translatome homeostasis in Arabidopsis

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17639
18 Samples

Download data: CSV

Series

Accession:: GSE146340

ID:: 200146340

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20009087018.

RNA sequencing of synaptic and cytoplasmic Upf1-bound transcripts supports contribution of nonsense-mediated decay to epileptogenesis

(Submitter supplied) Immunoprecipitation of Upf1-bound RNA from the cytoplasmic and synaptosomal compartments followed by RNA sequencing identified unique populations of NMD-associated transcripts and altered levels after status epilepticus.

Organism:: Mus musculus

Type:: Other

Platform:: GPL13112
4 Samples

Download data: DIFF

Series

Accession:: GSE90870

ID:: 200090870

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20005675119.

MOV10 Is a 5' to 3' RNA Helicase Contributing to UPF1 mRNA Target Degradation by Translocation along 3'UTRs

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

Organism:: Homo sapiens

Type:: Other; Expression profiling by high throughput sequencing

Platforms:: GPL16791 GPL11154
10 Samples

Download data: BED

Series

Accession:: GSE56751

ID:: 200056751

PubMed Similar studies

Select item 20005674820.

MOV10 Is a 5' to 3' RNA Helicase Contributing to UPF1 mRNA Target Degradation by Translocation along 3'UTRs (expression)

(Submitter supplied) RNA helicases are important regulators of gene expression that act by remodeling RNA secondary structures and as RNA-protein interactions. Here, we demonstrate that MOV10 has an ATP-dependent 5' to 3' in vitro RNA unwinding activity and determine the RNA-binding sites of MOV10 and its helicase mutants using PAR-CLIP. We find that MOV10 predominantly binds to 3' UTRs upstream of regions predicted to form local secondary structures and provide evidence that MOV10 helicase mutants are impaired in their ability to translocate 5' to 3' on their mRNA targets. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL16791
6 Samples

Download data: TXT

Series

Accession:: GSE56748

ID:: 200056748

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