GEO DataSets

(Submitter supplied) Isogenic UPF1+ or upf1- yeast strains were treated with 10 ug/ml thiolutin to inhibit global transcription. Targets were obtained from 16 time points: 0, 2, 4, 6, 8, 10, 12, 15, 20, 25, 30, 35, 40, 45, 50, 60 minutes after transcription inhibition. Three biological replicates of each were generated and the expression profiles were determined using Affymetrix YG-S98 arrays. Comparisons between the sample groups allow the identification of genes with differential expression over time between UPF1+ and upf1-. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Dataset:

GDS1611

Platform:

GPL90

96 Samples

Download data: CEL, CHP, EXP

Analysis of wild type and mutant upf1 strains up to 60 minutes after treatment with 10 ug/ml thiolutin, a global transcription inhibitor. Upf1 is an RNA helicase required for nonsense-mediated mRNA decay (NMD). Results identify genes with differential expression over time between the two strains.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, transformed count, 2 genotype/variation, 16 time sets

Platform:

GPL90

Series:

GSE3076

96 Samples

Download data: CEL, CHP, EXP

(Submitter supplied) We have generated 979 yeast strains in which the natural 3' UTR of essential gene mRNAs has been replaced by the same long 1.4 kb artificial 3' UTR (DAmP modification).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; Saccharomyces cerevisiae S288C

Type:

Expression profiling by array

Platform:

GPL18088

6 Samples

Download data: GPR

(Submitter supplied) We report a high resolution catalouge of NMD substrates using RNA-Seq. We discovered several hundred new substrates for NMD. Using published ribosome footprint profiling data, we measured ribosome densities of normal-looking NMD substrates and non-NMD substrates. NMD substrates exhibited a striking difference in normalized ribosome occupancy in wild-type and UPF1 cells. We also found that normal looking NMD substrates have higher ratio of out of frame reads, lower codon optimalites and a higher propensity to have long stretches of non-optimal codons.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21656

21 Samples

Download data: TXT

(Submitter supplied) Gene expression analysis requires accurate measurements of global RNA degradation rates, earlier problematic with methods disruptive to cell physiology. Recently, metabolic RNA labeling emerged as an efficient and minimally invasive technique applied in mammalian cells. Here, we have adapted SH-Linked Alkylation for the Metabolic Sequencing of RNA (SLAM-Seq) for a global mRNA stability study in yeast using 4-thiouracil pulse-chase labeling. more...

Organism:

Saccharomyces cerevisiae

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL19756

6 Samples

Download data: CSV

(Submitter supplied) Antisense long non-coding (aslnc)RNAs represent a substantial part of eukaryotic transcriptomes that are, in yeast, controlled by the Xrn1 exonuclease. Nonsense-Mediated Decay (NMD) destabilizes the Xrn1-sensitive aslncRNAs (XUT), but what determines their sensitivity remains unclear. We report that 3’ single-stranded (3’-ss) extension mediates XUTs degradation by NMD, assisted by the Mtr4 and Dbp2 helicases. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17342 GPL13272

36 Samples

Download data: GFF, TXT

(Submitter supplied) Small RNA produced by Dicer (Dcr1) are used to map dsRNA in wild-type strain and a xrn1-delta mutant of S. cerevisiae, inactivated for the cytoplasmic 5'-3' RNA decay pathway.

Organism:

Saccharomyces cerevisiae

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13272

4 Samples

Download data: TXT

(Submitter supplied) Nonsense-mediated mRNA decay (NMD) is a translation-dependent RNA quality-control pathway targeting transcripts such as messenger RNAs harboring premature stop-codons or short upstream open reading frame (uORFs). Our transcription start sites (TSSs) analysis of Saccharomyces cerevisiae cells deficient for RNA degradation pathways revealed that about half of the pervasive transcripts are degraded by NMD, which provides a fail-safe mechanism to remove spurious transcripts that escaped degradation in the nucleus. more...

Organism:

Saccharomyces cerevisiae BY4741

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18330

40 Samples

Download data: BED, WIG

(Submitter supplied) The goal of this experiment was to identify transcripts associated with the S. cerevisiae Upf1 protein. Keywords: RNA IP

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL90

8 Samples

Download data: CEL, CHP

(Submitter supplied) The goal of this set of experiments was to identify transcripts that are differentially expressed upon reactivation of NMD in an nmd2::HIS3 strain by galactose-induced expression of the NMD2 gene. Keywords: Genetic modification and time course

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL90

40 Samples

Download data: CEL

(Submitter supplied) Time course after the addition of the transcriptional inhibitor thiolutin at 3 and 10 µg/mL to an exponential growing culture of S. cerevisiae in YPD. Keywords: time course, mRNA stability analysis

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL3763

6 Samples

Download data

(Submitter supplied) Time course after the addition of the transcriptional inhibitor thiolutin at 3µg/mL to an exponential growing culture of S. cerevisiae in YPD. Keywords: time course, mRNA stability analysis

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL3763

5 Samples

Download data

(Submitter supplied) To analyze the effect of global translation initiation inhibition associated to glucose deprivation on cytoplasmic lncRNAs levels, we performed RNA-Seq using WT, xrn1-delta and upf1-delta cells grown in glucose-containing complete synthetic medium (CSM) and then shifted for 16 min in glycerol- and ethanol-containing medium. In parallel, control cells were maintained for the same time in glucose-containing CSM. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27812

16 Samples

Download data: TSV

(Submitter supplied) Despite being predicted to lack coding potential, cytoplasmic long non-coding (lnc)RNAs can associate with ribosomes. However, the landscape and biological relevance of lncRNAs translation remains poorly studied. In yeast, cytoplasmic Xrn1-sensitive lncRNAs (XUTs) are targeted by the Nonsense-Mediated mRNA Decay (NMD), suggesting a translation-dependent degradation process. Here, we report that XUTs are pervasively translated, which impacts their decay. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27812

40 Samples

Download data

(Submitter supplied) To define the translational landscape of Xrn1-sensitive lncRNAs in yeast, we performed Ribo-Seq in WT and upf1 mutant cells, in native conditions or upon treatment with translation elongation inhibitor (cycloheximide).

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27812

8 Samples

Download data: TSV

(Submitter supplied) To investigate the role of translation in the decay of cytoplasmic lncRNAs, we performed RNA-Seq in WT and upf1-delta yeast cells, treated or not with CHX.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27812

8 Samples

Download data: TSV

(Submitter supplied) To investigate the role of translation in the decay of cytoplasmic lncRNAs, we performed RNA-Seq in WT and upf1-delta yeast cells, treated or not with CHX.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27812

8 Samples

Download data: TSV

(Submitter supplied) The goal of the project was to study synthesis rates (SR) and mRNA levels (RA) genome wide in a series of aneuploid strains to check for the posible variation in SR and RA in the genes of the aneuploid chromosome withe regard to the rest of the genome. We used Genomic Run-On (GRO) experiment to mesaure SR and RA values.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL24366

24 Samples

Download data: TXT

(Submitter supplied) In order to maintain the appropriate level of mRNA it is necessary coordinate simultaneously all the steps along the mRNA life cycle. It has been shown that several factors act in the regulation of gene expression as global coordinators. Thus, some kind of information is transferred from the nucleus to the cytoplasm, imprinted in the mRNA. In this way, it is conceivable the existence of mechanisms that ensure the balance between mRNA synthesis and degradation through the information flow from the cytoplasm to the nucleus and vice versa, as a crosstalk among both process to ensure the proper mRNA homeostasis in the cell. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL13620

18 Samples

Download data: TXT

(Submitter supplied) HeLa cells were treated with siRNA directed against Luciferase or RENT1 in duplicate (as described in Mendell et al., Science, 2002; PubMed ID:12228722). Transcripts that are differentially expressed between the two experimental conditions are putatively regulated by RENT1. Keywords: repeat sample

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS705

Platform:

GPL8300

4 Samples

Download data: CEL, EXP, RPT