GEO DataSets

(Submitter supplied) We report systematical profiling of translation efficiency in stress conditions of NIH3T3 cells.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL19057

8 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) In cell stress, mRNA in the cytoplasm is sequestered to the insoluble ribonucleoprotein (RNP) compartments containing stress granules. These RNP granules are known to be involved in the control of mRNA processing and decay, but it has been elusive whether the mRNA redistribution in cell stress is universal or specific to a subset of transcripts. Here we provide a transcriptome-wide profiles of the RNP granules in cell stress and show that mRNA accumulation in stress granule differentially affects individual  transcripts. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

24 Samples

Download data: TXT

(Submitter supplied) Ribonucleoprotein (RNP) granules are non-membrane bound organelles thought to assemble by protein-protein interactions of RNA-binding proteins. We present evidence that a wide variety of RNAs self-assemble in vitro into either liquid-liquid phase separations or more stable assembles, referred to as RNA tangles. Self-assembly in vitro is affected by RNA length, ionic conditions, and sequence. Remarkably, self-assembly of yeast RNA in vitro under physiological salt mimics the composition of mRNAs within yeast stress granules. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19756

6 Samples

Download data: XLS

(Submitter supplied) Stress granules are mRNA-protein assemblies formed on nontranslating mRNAs. Stress granules are important in the stress response, related to neuronal mRNP granules, and aberrant stress granules contribute to some degenerative diseases. By RNA-Seq and single molecule FISH, we describe the stress granule transcriptome in both yeast and mammalian cells. This reveals that while essentially every mRNA, and some ncRNAs, can be targeted to stress granules, the efficiency of targeting can vary from <1% to 73%. more...

Organism:

Saccharomyces cerevisiae; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19756 GPL18573

12 Samples

Download data: TXT

(Submitter supplied) The eukaryotic cytosol contains multiple RNP granules including P-bodies and stress granules. Three different methods have been used to describe the transcriptome of stress granules or P-bodies, but how these methods compare, and how RNA partitioning occurs between P-bodies and stress granules has not been addressed. Herein, we compare the analysis of the stress granule transcriptome based on differential centrifugation, with and without subsequent stress granule immunopurification. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

24 Samples

Download data: DIFF

(Submitter supplied) Stress granules (SGs) are highly dynamic cytoplasmic membrane-less organelles that assemble when cells are challenged by stress. At different stages of assembly, various RNA molecules are sorted into SGs where they play important roles in maintaining the structural stability of SGs and regulating gene expression. Despite recent efforts of fluorescence microscopy and biochemical fractionation analysis, there still lacks a complete description of the dynamic changes in the molecular inventory of SG components during different stages of assembly and disassembly. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

61 Samples

Download data: XLSX

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

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

18 Samples

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(Submitter supplied) Analysis of Tdrd7 deficiency in mouse lens epithelial-derived cell line at gene expression level. The hypothesis tested was that Tdrd7 is involved in post-transcriptional control of gene expression in the lens. Results provide evidence for differential regulation of genes involved in lens homeostasis and cataract formation in the absence of Tdrd7. In eukaryotic cells, cytoplasmic RNA granules (RGs) function in the post-transcriptional control of gene expression. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

6 Samples

Download data: TXT

(Submitter supplied) Analysis of Tdrd7 deficiency in mouse lens epithelial-derived cell line at gene expression level. The hypothesis tested was that Tdrd7 is involved in post-transcriptional control of gene expression in the lens. Results provide evidence for differential regulation of genes involved in lens homeostasis and cataract formation in the absence of Tdrd7. In eukaryotic cells, cytoplasmic RNA granules (RGs) function in the post-transcriptional control of gene expression. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

6 Samples

Download data: TXT

(Submitter supplied) Analysis of Tdrd7 deficiency in mouse lens epithelial-derived cell line at gene expression level. The hypothesis tested was that Tdrd7 is involved in post-transcriptional control of gene expression in the lens. Results provide evidence for differential regulation of genes involved in lens homeostasis and cataract formation in the absence of Tdrd7. In eukaryotic cells, cytoplasmic RNA granules (RGs) function in the post-transcriptional control of gene expression. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

6 Samples

Download data: TXT

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

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25244

45 Samples

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(Submitter supplied) RNA-binding proteins and messenger RNAs assemble into ribonucleoprotein granules that regulate mRNA trafficking, local translation, and turnover. The dysregulation of RNA-protein condensation disturbs synaptic plasticity and neuron survival, and has been widely associated with human neurological disease. Neuronal granules are thought to condense around particular proteins that dictate the identity and composition of each granule type. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25244

18 Samples

Download data: TSV, XLSX

(Submitter supplied) RNA-binding proteins and messenger RNAs assemble into ribonucleoprotein granules that regulate mRNA trafficking, local translation, and turnover. The dysregulation of RNA-protein condensation disturbs synaptic plasticity and neuron survival, and has been widely associated with human neurological disease. Neuronal granules are thought to condense around particular proteins that dictate the identity and composition of each granule type. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25244

3 Samples

Download data: TXT

(Submitter supplied) RNA-binding proteins and messenger RNAs assemble into ribonucleoprotein granules that regulate mRNA trafficking, local translation, and turnover. The dysregulation of RNA-protein condensation disturbs synaptic plasticity and neuron survival, and has been widely associated with human neurological disease. Neuronal granules are thought to condense around particular proteins that dictate the identity and composition of each granule type. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25244

4 Samples

Download data: TXT

(Submitter supplied) RNA-binding proteins and messenger RNAs assemble into ribonucleoprotein granules that regulate mRNA trafficking, local translation, and turnover. The dysregulation of RNA-protein condensation disturbs synaptic plasticity and neuron survival, and has been widely associated with human neurological disease. Neuronal granules are thought to condense around particular proteins that dictate the identity and composition of each granule type. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25244

20 Samples

Download data: TSV, TXT

(Submitter supplied) We report here transcriptome wide changes in S. cerevisiae in response to sodium azide treatment. The observed changes are consistent with those observed in response to oxidative stress such as H2O2. We also identify transcripts that are specifically affected by Scd6 and/or Sbp1. Some of these mRNAs could be direct targets of Scd6/Sbp1.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17342

12 Samples

Download data: TXT

(Submitter supplied) Stress granules are dynamic non-membrane bound organelles made up of untranslating messenger ribonucleoproteins (mRNPs) that form when cells integrate stressful environmental cues resulting in stalled translation initiation complexes. Although stress granules dramatically alter mRNA and protein localization, understanding these complexes has proven to be challenging through conventional imaging, purification, and crosslinking approaches. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL20301

37 Samples

Download data: CSV

(Submitter supplied) RNAs interact with networks of proteins to form complexes (RNPs) that govern many biological processes, but inter-protein networks on RNA are currently impossible to examine in a comprehensive way. We developed a live-cell RNP-MaP (RNP network analysis by mutational profiling) chemical probing strategy for mapping simultaneous binding by and cooperative interactions among multiple proteins with single RNA molecules at nucleotide resolution. more...

Organism:

Homo sapiens; Mus musculus

Type:

Other

4 related Platforms

87 Samples

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(Submitter supplied) Stress granules are phase separated assemblies formed around mRNAs that have now been identified after stress granule purification from cell culture. Here, we present a purification free method to detect stress granules RNAs in single cells and in tissues, including those displaying cell heterogeneity. We adapted TRIBE (Target of RNA-binding proteins Identified by Editing) to detect stress-granule RNAs by fusing a stress-granule RNA-binding protein (FMR1) to the catalytic domain of an RNA-editing enzyme (ADAR). more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19132

16 Samples

Download data: CSV, TSV, TXT

(Submitter supplied) To understand affected genes by overexpression of origouridylate binding protein 1b (UBP1b) under heat stress conditions, transcriptional profiling of UBP1box and control plants were analyzed under normal and heat stress (40°C) conditions using Arabidopsis custom microarrays.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL20796

12 Samples

Download data: TXT