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Links from GEO DataSets

Items: 14

1.

RiboSeq and mSeq of two yeast strains

(Submitter supplied) We report on how the absence of expansion segment 7S from the yeast ribosome alters A-site occupancy along transcripts. This has consequence for local translation rates and protein fidelity.
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing; Other
Platform:
GPL26302
11 Samples
Download data: TXT
Series
Accession:
GSE220642
ID:
200220642
2.

mSeq of total and polysome bound mRNAs in two yeast strains

(Submitter supplied) We report on how the association of mRNA to translating ribosomes changes due to the absence of the expansion segment 27L in S. cerevisiae. We observe specific enrichment and depletion of mRNA sets from rmutant ribosomes which reshapes the proteome.
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23014
12 Samples
Download data: TXT
Series
Accession:
GSE134774
ID:
200134774
3.

Lso2 is a conserved ribosome-bound protein required for translational recovery in yeast

(Submitter supplied) Ribosome binding proteins function broadly in protein synthesis, gene regulation and cellular homeostasis but the complete complement of functional ribosome-bound proteins remains unknown. Using quantitative mass spectrometry we identified Late-annotated short open reading frame 2 (Lso2) as a ribosome-associated protein that is broadly conserved in eukaryotes. Genome-wide crosslinking and immunoprecipitation of Lso2 and its human ortholog CCDC124 recovered 25S rRNA in a region near the A site that overlaps the GTPase activating center. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing; Other
Platforms:
GPL17342 GPL13821 GPL19756
25 Samples
Download data: BED, BEDGRAPH, FASTA, GFF, TXT, WIG
Series
Accession:
GSE109343
ID:
200109343
4.

mRNA seq of total and polysome associated mRNAs in three different conditions

(Submitter supplied) We report on how the presence or absence of a 18 nt long ribosome-bound RNA affects the translation in S. cerevisiae. We observe that translation of all mRNAs is downregulated when the RNA is present.
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23014
16 Samples
Download data: TXT
Series
Accession:
GSE135475
ID:
200135475
5.

Loss of a Conserved tRNA Anticodon Modification Perturbs Cellular Signaling

(Submitter supplied) Transfer RNA (tRNA) modifications enhance the efficiency, specificity and fidelity of translation in all organisms. The anticodon modification mcm5s2U34 is required for normal growth and stress resistance in yeast; mutants lacking this modification have numerous phenotypes. Mutations in the homologous human genes are linked to neurological disease. The yeast phenotypes can be ameliorated by overexpression of specific tRNAs, suggesting that the modifications are necessary for efficient translation of specific codons. more...
Organism:
Saccharomyces cerevisiae
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL13272
24 Samples
Download data: TXT
Series
Accession:
GSE45366
ID:
200045366
6.

Regulation of Translation Elongation Revealed by Ribosome Profiling

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Caenorhabditis elegans; Saccharomyces cerevisiae; Homo sapiens
Type:
Other
Platforms:
GPL16791 GPL18245 GPL17342
56 Samples
Download data: WIG
Series
Accession:
GSE115162
ID:
200115162
7.

Regulation of Translation Elongation Revealed by Ribosome Profiling [Dataset_4]

(Submitter supplied) Ribosomes undergo substantial conformational changes during translation elongation to accommodate incoming aminoacyl-tRNAs and translocate along the mRNA template. We used multiple elongation inhibitors and chemical probing to define ribosome conformational states corresponding to different sized ribosome-protected mRNA fragments (RPFs) generated by ribosome profiling. We show using various genetic and environmental perturbations that the previously identified 20-22 nucleotide (nt) RPFs correspond predominantly to ribosomes in a pre-accommodation state with an open 40S ribosomal A site while the classical 27-29 nt fragments correspond to ribosomes in a pre-translocation state with an occupied 40S ribosomal A site. more...
Organism:
Saccharomyces cerevisiae; Homo sapiens; Caenorhabditis elegans
Type:
Other
Platforms:
GPL16791 GPL18245 GPL17342
28 Samples
Download data: CSV, WIG
Series
Accession:
GSE115161
ID:
200115161
8.

Regulation of Translation Elongation Revealed by Ribosome Profiling [Dataset_3]

(Submitter supplied) Ribosomes undergo substantial conformational changes during translation elongation to accommodate incoming aminoacyl-tRNAs and translocate along the mRNA template. We used multiple elongation inhibitors and chemical probing to define ribosome conformational states corresponding to different sized ribosome-protected mRNA fragments (RPFs) generated by ribosome profiling. We show using various genetic and environmental perturbations that the previously identified 20-22 nucleotide (nt) RPFs correspond predominantly to ribosomes in a pre-accommodation state with an open 40S ribosomal A site while the classical 27-29 nt fragments correspond to ribosomes in a pre-translocation state with an occupied 40S ribosomal A site. more...
Organism:
Saccharomyces cerevisiae
Type:
Other
Platform:
GPL17342
7 Samples
Download data: CSV
Series
Accession:
GSE115160
ID:
200115160
9.

Regulation of Translation Elongation Revealed by Ribosome Profiling [Dataset_2]

(Submitter supplied) Ribosomes undergo substantial conformational changes during translation elongation to accommodate incoming aminoacyl-tRNAs and translocate along the mRNA template. We used multiple elongation inhibitors and chemical probing to define ribosome conformational states corresponding to different sized ribosome-protected mRNA fragments (RPFs) generated by ribosome profiling. We show using various genetic and environmental perturbations that the previously identified 20-22 nucleotide (nt) RPFs correspond predominantly to ribosomes in a pre-accommodation state with an open 40S ribosomal A site while the classical 27-29 nt fragments correspond to ribosomes in a pre-translocation state with an occupied 40S ribosomal A site. more...
Organism:
Saccharomyces cerevisiae
Type:
Other
Platform:
GPL17342
6 Samples
Download data: TSV
Series
Accession:
GSE115159
ID:
200115159
10.

Regulation of Translation Elongation Revealed by Ribosome Profiling [Dataset_1]

(Submitter supplied) Ribosomes undergo substantial conformational changes during translation elongation to accommodate incoming aminoacyl-tRNAs and translocate along the mRNA template. We used multiple elongation inhibitors and chemical probing to define ribosome conformational states corresponding to different sized ribosome-protected mRNA fragments (RPFs) generated by ribosome profiling. We show using various genetic and environmental perturbations that the previously identified 20-22 nucleotide (nt) RPFs correspond predominantly to ribosomes in a pre-accommodation state with an open 40S ribosomal A site while the classical 27-29 nt fragments correspond to ribosomes in a pre-translocation state with an occupied 40S ribosomal A site. more...
Organism:
Saccharomyces cerevisiae
Type:
Other
Platform:
GPL17342
15 Samples
Download data: TSV
Series
Accession:
GSE115158
ID:
200115158
11.

The extent of ribosome queuing in budding yeast

(Submitter supplied) Ribosome queuing is a fundamental phenomenon suggested to be related to topics such as genome evolution, synthetic biology, gene expression regulation, intracellular biophysics, and more. However, this phenomenon hasn't been quantified yet at a genomic level. Nevertheless, methodologies for studying translation (e.g. ribosome footprints) are usually calibrated to capture only single ribosome protected footprints (mRPFs) and thus limited in their ability to detect ribosome queuing. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing; Other
Platform:
GPL19756
3 Samples
Download data: TSV
Series
Accession:
GSE107718
ID:
200107718
12.

Improved ribosome-footprint and mRNA measurements provide insights into dynamics and regulation of yeast translation

(Submitter supplied) Ribosome-footprint profiling provides genome-wide snapshots of translation, but technical challenges can confound its analysis. Here, we use improved methods to obtain ribosome-footprint profiles and mRNA abundances that more faithfully reflect gene expression in Saccharomyces cerevisiae. Our results support proposals that both the beginning of coding regions and codons matching rare tRNAs are more slowly translated. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing; Third-party reanalysis
Platform:
GPL13821
3 Samples
Download data: TXT
Series
Accession:
GSE75897
ID:
200075897
13.

Optimization of codon translation rates via tRNA modifications maintains proteome integrity

(Submitter supplied) Proteins begin to fold as they emerge from translating ribosomes. The kinetics of ribosome transit along a given mRNA can influence nascent chain folding, but the extent to which individual codon translation rates impact proteome integrity remains unknown. Here, we show that slower decoding of discrete codons elicits widespread protein aggregation in vivo. Using ribosome profiling, we find that loss of anticodon wobble uridine (U34) modifications in a subset of tRNAs leads to ribosome pausing at their cognate codons in S. more...
Organism:
Caenorhabditis elegans; Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL19959 GPL19958
98 Samples
Download data: TXT
Series
Accession:
GSE67387
ID:
200067387
14.

VELCRO-IP RNA-seq reveals ribosome expansion segment function in translation genome-wide

(Submitter supplied) Roles for ribosomal RNA (rRNA) in gene regulation remain largely unexplored. With hundreds of rDNA units positioned across multiple loci, it is not possible to genetically modify rRNA in mammalian cells, hindering understanding of ribosome function. It remains elusive whether expansion segments (ESs), tentacle-like rRNA extensions that vary in sequence and size across eukaryotic evolution, may have functional roles in translation control. more...
Organism:
Mus musculus
Type:
Other
Platform:
GPL21626
7 Samples
Download data: TXT
Series
Accession:
GSE141382
ID:
200141382
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