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Links from GEO DataSets

Items: 17

1.

Oligodendrocyte differentiation alters tRNA modifications and codon-dependent mRNA decay [QuantMseq]

(Submitter supplied) Oligodendrocytes are specialized cells that confer neuronal myelination. Leukodystrophies associated with oligodendrocyte and hypomyelination are known to result when a number of tRNA metabolism genes are mutated. Thus, for unknown reasons, oligodendrocytes may be hypersensitive to perturbations in tRNA biology. In this study, we survey the tRNA transcriptome in the murine oligodendrocytes cell lineage in an effort to understanding the molecular underpinning for human disease. more...
Organism:
Mus musculus
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL21626
7 Samples
Download data: CSV
Series
Accession:
GSE182808
ID:
200182808
2.

Oligodendrocyte differentiation alters tRNA modifications and codon-dependent mRNA decay [QuantM-seq II]

(Submitter supplied) Oligodendrocytes are specialized cells that confer neuronal myelination. Leukodystrophies associated with oligodendrocyte and hypomyelination are known to result when a number of tRNA metabolism genes are mutated. Thus, for unknown reasons, oligodendrocytes may be hypersensitive to perturbations in tRNA biology. In this study, we survey the tRNA transcriptome in the murine oligodendrocytes cell lineage in an effort to understanding the molecular underpinning for human disease. more...
Organism:
Saccharomyces cerevisiae
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL26302
8 Samples
Download data: CSV
Series
Accession:
GSE198271
ID:
200198271
3.

Oligodendrocyte differentiation alters tRNA modifications and codon-dependent mRNA decay

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Saccharomyces cerevisiae; Mus musculus
Type:
Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other
Platforms:
GPL26302 GPL17021 GPL21626
49 Samples
Download data
Series
Accession:
GSE182811
ID:
200182811
4.

Oligodendrocyte differentiation alters tRNA modifications and codon-dependent mRNA decay [RiboSeq]

(Submitter supplied) Oligodendrocytes are specialized cells that confer neuronal myelination. Leukodystrophies associated with oligodendrocyte and hypomyelination are known to result when a number of tRNA metabolism genes are mutated. Thus, for unknown reasons, oligodendrocytes may be hypersensitive to perturbations in tRNA biology. In this study, we survey the tRNA transcriptome in the murine oligodendrocytes cell lineage in an effort to understanding the molecular underpinning for human disease. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Other
Platform:
GPL17021
8 Samples
Download data: TXT
Series
Accession:
GSE182810
ID:
200182810
5.

Oligodendrocyte differentiation alters tRNA modifications and codon-dependent mRNA decay [DecaySeq]

(Submitter supplied) Oligodendrocytes are specialized cells that confer neuronal myelination. Leukodystrophies associated with oligodendrocyte and hypomyelination are known to result when a number of tRNA metabolism genes are mutated. Thus, for unknown reasons, oligodendrocytes may be hypersensitive to perturbations in tRNA biology. In this study, we survey the tRNA transcriptome in the murine oligodendrocytes cell lineage in an effort to understanding the molecular underpinning for human disease. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
26 Samples
Download data: TXT
Series
Accession:
GSE182809
ID:
200182809
6.

Quantitative tRNA-sequencing uncovers metazoan tissue-specific tRNA regulation

(Submitter supplied) Transfer RNAs (tRNA) are quintessential in deciphering the genetic code; disseminating nucleic acid triplets into correct amino acid identity. While this decoding function is clear, an emerging theme is that tRNA abundance and functionality can powerfully impact protein production rate, folding, activity, and messenger RNA stability. Importantly, however, the expression pattern of tRNAs (in even simple systems) is obliquely known. more...
Organism:
Mus musculus; Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL21626 GPL21697
29 Samples
Download data: CSV
Series
Accession:
GSE141436
ID:
200141436
7.

Oligodendrocyte-lineage cell-secreted L-type prostaglandin D synthase promotes oligodendrocyte differentiation and myelination

(Submitter supplied) We used RNA sequencing to examine the transcriptional changes in differentiated oligodendrocytes, oligodendrocyte precursor cells, astroctytes, and microglia after blocking exocytosis from oligodendrocyte-lineage cells
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21103
24 Samples
Download data: XLSX
Series
Accession:
GSE168569
ID:
200168569
8.

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
9.

Selective gene expression maintains human tRNA anticodon pools during differentiation

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Other
Platforms:
GPL24676 GPL18573
97 Samples
Download data: BEDGRAPH, BROADPEAK, NARROWPEAK
Series
Accession:
GSE227928
ID:
200227928
10.

Transfer RNA pools in human cells are controlled by selective gene expression [tRNA-Seq]

(Submitter supplied) Transfer RNAs are required for translating genetic information into protein sequence. The human genome contains hundreds of tRNA genes, many of which in multiple copies. How their expression is regulated to control functional tRNA levels is unknown. Here, we combined quantitative tRNA profiling and ChIP-Seq to measure tRNA expression upon differentiation of human induced pluripotent stem cells (hiPSC) into neuronal and cardiac cells. more...
Organism:
Homo sapiens
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL18573
8 Samples
Download data: CSV
Series
Accession:
GSE227927
ID:
200227927
11.

Transfer RNA pools in human cells are controlled by selective gene expression [Ribo-seq]

(Submitter supplied) Transfer RNAs are required for translating genetic information into protein sequence. The human genome contains hundreds of tRNA genes, many of which in multiple copies. How their expression is regulated to control functional tRNA levels is unknown. Here, we combined quantitative tRNA profiling and ChIP-Seq to measure tRNA expression upon differentiation of human induced pluripotent stem cells (hiPSC) into neuronal and cardiac cells. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Other
Platform:
GPL18573
5 Samples
Download data: CSV
Series
Accession:
GSE227926
ID:
200227926
12.

Transfer RNA pools in human cells are controlled by selective gene expression [RNA-seq]

(Submitter supplied) Transfer RNAs are required for translating genetic information into protein sequence. The human genome contains hundreds of tRNA genes, many of which in multiple copies. How their expression is regulated to control functional tRNA levels is unknown. Here, we combined quantitative tRNA profiling and ChIP-Seq to measure tRNA expression upon differentiation of human induced pluripotent stem cells (hiPSC) into neuronal and cardiac cells. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
8 Samples
Download data: CSV, TXT
Series
Accession:
GSE227925
ID:
200227925
13.

Transfer RNA pools in human cells are controlled by selective gene expression [ChIP-seq]

(Submitter supplied) Transfer RNAs are required for translating genetic information into protein sequence. The human genome contains hundreds of tRNA genes, many of which in multiple copies. How their expression is regulated to control functional tRNA levels is unknown. Here, we combined quantitative tRNA profiling and ChIP-Seq to measure tRNA expression upon differentiation of human induced pluripotent stem cells (hiPSC) into neuronal and cardiac cells. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24676
68 Samples
Download data: BEDGRAPH, BROADPEAK, NARROWPEAK
Series
Accession:
GSE227924
ID:
200227924
14.

Transfer RNA pools in human cells are controlled by selective gene expression [ATAC-seq]

(Submitter supplied) Transfer RNAs are required for translating genetic information into protein sequence. The human genome contains hundreds of tRNA genes, many of which in multiple copies. How their expression is regulated to control functional tRNA levels is unknown. Here, we combined quantitative tRNA profiling and ChIP-Seq to measure tRNA expression upon differentiation of human induced pluripotent stem cells (hiPSC) into neuronal and cardiac cells. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18573
8 Samples
Download data: CSV, NARROWPEAK
Series
Accession:
GSE227923
ID:
200227923
15.

Deciphering the reading of the genetic code by near-cognate tRNA

(Submitter supplied) Some codons of the genetic code can be read not only by cognate, but also by near-cognate tRNAs. This flexibility is thought to be conferred mainly by a mismatch between the third base of the codon and the first of the anticodon (the so-called wobble position). However, this simplistic explanation underestimates the importance of nucleotide modifications in the decoding process. Using a system in which only near-cognate tRNAs can decode a specific codon, we investigated the role of six modifications of the anticodon, or adjacent nucleotides, of the tRNAs specific for Tyr, Gln, Lys, Trp, Cys and Arg in Saccharomyces cerevisiae. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17342
2 Samples
Download data: TXT
Series
Accession:
GSE108772
ID:
200108772
16.

DM-tRNA-seq of mock and MHV68-infected mouse MC57G fibroblasts

(Submitter supplied) We applied a tRNA-specific sequencing pipeline to analyze tRNA expression during infection of MC57G fibroblasts with the gammaherpesvirus MHV68. We find that expression of 14% of tRNA genes is significantly upregulated during infection. By mapping reads to either premature tRNA (pre-tRNA) or mature tRNA sequences, we find that increased expression of tRNA genes is manifested at the level of the pre-tRNA only, indicating a homeostatic mechanism to maintain the size and composition of mature tRNA pools.
Organism:
Mus musculus
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL21103
8 Samples
Download data: TXT
Series
Accession:
GSE142393
ID:
200142393
17.

Effect of Rheb depletion of Rheb and Ribo-HA knock-in on gene expression of neurons

(Submitter supplied) To examine the effect of neuronal Rheb on brain myelination, we generated a conditional neuronal Rheb knockout mouse line.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
6 Samples
Download data: XLSX
Series
Accession:
GSE230354
ID:
200230354
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