GEO DataSets

(Submitter supplied) Translatome analysis by sucrose gradient centrifugation of cell lysates followed by microarray profiling of the polysomal and subpolysomal RNA fractions represents a way of both studying translational control networks and better approximating the proteomic representation of cells. It is an established notion that translational control takes place essentially at the translation initiation level, therefore the variation in abundance of a given mRNA species on polysomes can be directly related to the variation in abundance of the corresponding protein. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

18 Samples

Download data: TXT

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

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array; Other

Platforms:

GPL7662 GPL8546

60 Samples

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(Submitter supplied) In this study, we systematically identified RNAs associated with ribosomes. To identify ribosome associated RNAs, C-terminal ZZ-tagged Rpl16a or Rpl16b, expressed under control of thier native promoter, were affinity purified from whole cell extracts of cultures grown to mid-log phase in minimal medium. Extracts were incubated with immunoglobulin G (IgG) coupled microbeads, washed, and ribosomes were eluted by tobacco etch virus (TEV) protease treatment. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL8546

8 Samples

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(Submitter supplied) In this study, we systematically identified ribosome associated RNAs. To identify ribosome associated RNAs, C-terminal ZZ-tagged Rpl16a, expressed under control of its native promoter, was affinity purified from whole cell extracts of cultures grown to mid-log phase. Extracts were incubated with immunoglobulin G (IgG) coupled microbeads, washed, and ribosomes were eluted by tobacco etch virus (TEV) protease treatment. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array; Other

Platform:

GPL7662

52 Samples

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(Submitter supplied) Sequencing of total RNA and polysomal RNA of two cell lines, MCF7 (tumoral) and MCF10A (non-tumoral)

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9115

12 Samples

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(Submitter supplied) RNA-Seq analyses of GSC line NSC11 after 2Gy irradiation in the transcriptome and the translatome to evaluate radiation-induced changes in alternative splicing.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

24 Samples

Download data: TXT

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

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL13160

8 Samples

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(Submitter supplied) Soil salinity is one of the primary causes of yield decline in rice. Pokkali (Pok) is a highly salt-tolerant landrace whereas IR29, is salt-sensitive but a widely cultivated cultivar. Comparative analysis of these genotypes may offer better understandings of the salinity tolerance mechanism. The published reports largely underscored the importance of transcriptional regulation during salt stress in these genotypes, while, the regulation at translational level is also critically important. more...

Organism:

Oryza sativa

Type:

Other

Platform:

GPL13160

4 Samples

Download data: XLSX

(Submitter supplied) Soil salinity is one of the primary causes of yield decline in rice. Pokkali (Pok) is a highly salt-tolerant landrace whereas IR29, is salt-sensitive but a widely cultivated cultivar. Comparative analysis of these genotypes may offer better understandings of the salinity tolerance mechanism. The published reports largely underscored the importance of transcriptional regulation during salt stress in these genotypes, while, the regulation at translational level is also critically important. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13160

4 Samples

Download data: XLSX

(Submitter supplied) Transcriptome and translatome analyses of 6 and 24 hours imbibed seeds dormant and non-dormant seeds of NILDOG1-Cvi with and without addition of the transcription inhibitor Cordycepin. NILDOG1-Cvi is the Ler WT containing an introgression of the Cvi accession on chromosome 5, which includes the DOG1 gene (Bentsink et al., 2006).

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL17134

45 Samples

Download data: CEL

(Submitter supplied) Translation efficiencies of Jurkat mRNAs in control and in cells treated with thapsigargin 10microM for 1h and 3h.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

3 Samples

Download data: TXT

(Submitter supplied) Translation efficiencies of mouse mRNAs in control and in cells treated with thapsigargin 10microM for 3h.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL4134

2 Samples

Download data: TXT

(Submitter supplied) Mammalian gene expression displays widespread circadian oscillations. Rhythmic transcription underlies the core clock mechanism, but it cannot explain numerous observations made at the level of protein rhythmicity. We have used ribosome profiling in mouse liver to measure the translation of mRNAs into protein around-the-clock and at high temporal and nucleotide resolution. Transcriptome-wide, we discovered extensive rhythms in ribosome occupancy, and identified a core set of ≈150 mRNAs subject to particularly robust daily changes in translation efficiency. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

48 Samples

Download data: TXT

(Submitter supplied) COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which infected >200 million people resulting in >4 million deaths. However, temporal landscape of the SARS-CoV-2 translatome and its impact on the human genome remain unexplored. Here, we report a high-resolution atlas of the translatome and transcriptome of SARS-CoV-2 for various time points after infecting human cells. more...

Organism:

Chlorocebus aethiops; Homo sapiens; Severe acute respiratory syndrome coronavirus 2

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL29105 GPL29166

127 Samples

Download data: BW

(Submitter supplied) We sequenced the total mRNA and translating mRNA (RNC-mRNA) of three hepatocellular carcinoma cell lines Hep3B, HCCLM3 and MHCC97H

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL11154

6 Samples

Download data: XLS

(Submitter supplied) BACKGROUND: The daily gene expression oscillations that underlie mammalian circadian rhythms show striking differences between tissues and involve post-transcriptional regulation. Both aspects remain poorly understood. We have used ribosome profiling to explore the contribution of translation efficiency to temporal gene expression in kidney, and contrasted our findings with liver data available from the same mice. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL17021

48 Samples

Download data: TXT

(Submitter supplied) Analysis of estrogen receptor (ER)-positive MCF7 cell total RNA expression and polysome-assiciated RNA expression following treatment with estradiol (E2) and vehicle (etoh). We used expression microarrays to measure polysome association and total RNA abundance in E2 treated MCF7. These data, along with previously published data, show that genes that are upregulated by estrogen treatment are biased towards association with polysomes.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

18 Samples

Download data: CEL

(Submitter supplied) Defining radioresponse using the translatome and the transcriptome to identify functional consequences of radiation. We used microarrays to detail the changes in glioblastoma stem-like cells (GSCs) in both the translatome and transcriptome after irradiation.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL571

54 Samples

Download data: CEL, CHP

(Submitter supplied) Purpose: mRNA translation into protein is highly regulated, but the role of mRNA isoforms, noncoding RNAs (ncRNAs), and genetic variants has yet to be systematically studied. Using high-throughput sequencing (RNA-seq), we have measured cellular levels of mRNAs and ncRNAs, and their isoforms, in lymphoblast cell lines (LCL) and in polysomal fractions, the latter shown to yield strong correlations of mRNAs with expressed protein levels. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing

Platform:

GPL17303

6 Samples

Download data: TXT

(Submitter supplied) Genome-wide analysis of translation has the potential to provide major contributions in understanding the pathophysiology of infection processes, given the complex interplay between pathogens and host cells. This study uncovers the reshaping undergoing in the translational control system of the host in response to staphylococcal α-hemolysin oligomers (rAHL). Keywords: translatome profiling, polysomal profiling, polysomal RNA, translational control, translational profiling, polysome profiling, post-transcriptional regulation, staphylococcal α-hemolysin, pore forming toxins, PTF.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

12 Samples

Download data: TXT