Similar studies for GEO DataSets (Select 200053693) - GEO DataSets

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Items: 20

Select item 2000536931.

Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation

(Submitter supplied) Identification of the coding elements in the genome is a fundamental step to understanding the building blocks of living systems. Short peptides (< 100 aa) have emerged as important regulators of development and physiology, but their identification has been limited by their size. We have leveraged the periodicity of ribosome movement on the mRNA to define actively translated ORFs by ribosome footprinting. more...

Organism:: Danio rerio

Type:: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:: GPL14875
30 Samples

Download data: TXT

Series

Accession:: GSE53693

ID:: 200053693

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Select item 2001196152.

Translation of upstream open reading frames in a model of neuronal differentiation

(Submitter supplied) Upstream open reading frames (uORFs) initiate translation within mRNA 5’ leaders,and have the potential to altermain coding sequence(CDS) translationontranscripts in which they reside. Ribosome profiling(RP)studies suggest that translating ribosomes are pervasive within 5’ leadersacross model systems. However, the significance of this observationremains unclear. To explore a role for uORF usage in neuronal differentiation, we performed RP on undifferentiated and differentiated human neuroblastoma cells. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11154
10 Samples

Download data: FPKM_TRACKING

Series

Accession:: GSE119615

ID:: 200119615

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Select item 2001832643.

Improved Super-Resolution Ribosome Profiling Reveals Prevalent Translation of Upstream ORFs and Small ORFs in Arabidopsis

(Submitter supplied) We used Ribo-seq (Ribosome profiling) combining with RNA-seq to explore the translational landscape of Arabidopsis Col-0 seedling. We generated 6 biological replicates of RNA-seq and Ribo-seq data for Arabidopsis Col-0 seedling. 3 of the replicates were collected after 20 minutes of 0.1% DMSO treatment and the other 3 samples were collected after 60 minutes of DMSO treatmeant. The resulting RNA-seq and Ribo-seq files were used to discover translated up-stream ORFs (uORFs) and analyze the translation efficiency of uORF-containing genes in Arabidopsis.

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing; Other

Platform:: GPL21785
12 Samples

Download data: RESULTS

Series

Accession:: GSE183264

ID:: 200183264

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Select item 2001370214.

Temperature-dependent regulation of upstream open reading frame translation in s. cerevisiae

(Submitter supplied) Translation of an mRNA in eukaryotes starts at AUG in most cases. Near-cognate codons (NCCs) such as UUG, ACG and AUU are also used as start sites at low levels in S. cerevisiae. Initiation from NCCs or AUGs in the 5’-untranslated regions (UTRs) of mRNAs can lead to translation of upstream open reading frames (uORFs) that might regulate expression of the main ORF (mORF). Although there is some circumstantial evidence that the translation of uORFs can be affected by environmental conditions, little is known about how it is affected by changes in growth temperature. more...

Organism:: Saccharomyces cerevisiae

Type:: Expression profiling by high throughput sequencing

Platform:: GPL13821
6 Samples

Download data: WIG

Series

Accession:: GSE137021

ID:: 200137021

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Select item 2000677415.

Ribosome profiling with translation inhibitors reveals pervasive translation in murine ES cells

(Submitter supplied) Ribosome profiling with translation inhibitors reveals pervasive translation in murine ES cells.

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing; Other

Platform:: GPL18061
10 Samples

Download data: TXT

Series

Accession:: GSE67741

ID:: 200067741

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Select item 2001050826.

RNA G-quadruplexes mark repressive upstream open reading frames in human mRNAs

(Submitter supplied) Translational control is a key determinant of protein abundance, which in turns defines the physiology and pathology of human cells. Initiation of translation is highly regulated in eukaryotes and is considered as the rate-limiting step of protein synthesis. mRNA secondary structures in 5’ untranslated region (UTR) and associated helicases have been characterised as key determinants of translation initiation. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing; Other

Platform:: GPL18573
24 Samples

Download data: BW, TXT

Series

Accession:: GSE105082

ID:: 200105082

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Select item 2000551957.

Ribosome profiling data obtained from HEK293T cells 30 minutes after treatment with arsenite to a final concentration of 40 µM

(Submitter supplied) Eukaryotic cells rapidly reduce protein synthesis in response to various stress conditions. This can be achieved by the phosphorylation-mediated inactivation of a key translation initiation factor, eIF2. However, the persistent translation of certain mRNAs is required for deployment of an adequate stress response. We carried out ribosome profiling of cultured human cells under conditions of severe stress induced with sodium arsenite. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing; Other

Platforms:: GPL15520 GPL11154
8 Samples

Download data: CSV, XLSX

Series

Accession:: GSE55195

ID:: 200055195

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Select item 2000996978.

Iron response of HepG2 cells

(Submitter supplied) RNA-seq of HepG2 cells in response to iron

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL16791
6 Samples

Download data: BEDGRAPH

Series

Accession:: GSE99697

ID:: 200099697

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Select item 2000060259.

eif3h/WT transcript level

(Submitter supplied) Microarray comparisons of transcript level in wild-type Arabidopsis and eif3h mutant plants. Goal: To detect any change in transcript level between WT and eif3h mutant. BACKGROUND: The eukaryotic translation initiation factor eIF3 has multiple roles during the initiation of translation of cytoplasmic mRNAs. However, the contributions of individual subunits of eIF3 to the translation of specific mRNAs remain poorly understood. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by array

Platform:: GPL198
4 Samples

Download data: CEL, EXP

Series

Accession:: GSE6025

ID:: 200006025

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Select item 20000602410.

eif3h/WT polysome loading

(Submitter supplied) Microarray comparisons of polysome loading in wild-type Arabidopsis and eif3h mutant Goal: To find the target mRNAs that are translationally regulated by eIF3h. BACKGROUND: The eukaryotic translation initiation factor eIF3 has multiple roles during the initiation of translation of cytoplasmic mRNAs. However, the contributions of individual subunits of eIF3 to the translation of specific mRNAs remain poorly understood. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by array

Platform:: GPL198
8 Samples

Download data: CEL, EXP

Series

Accession:: GSE6024

ID:: 200006024

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Select item 20014761911.

Developmental regulation of Canonical and small ORF translation from mRNAs

(Submitter supplied) We present a genome-wide assessment of the translation of small open reading frames (smORF) in Drosophila melanogaster mRNAs, using ribosomal profiling of polysomal fractions in three contiguous temporal windows, which encopass all of embryogenesis. We also performed the same protocol using S2 cells. In this way, mRNAs bound by multiple ribosomes can be isolated and distinguished from mRNAs bound by sporadic, putatively non-productive single ribosomes or ribosomal subunits.

Organism:: Drosophila melanogaster

Type:: Other

Platforms:: GPL19132 GPL16479
13 Samples

Download data: CSV

Series

Accession:: GSE147619

ID:: 200147619

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Select item 20010912212.

Transcripts from downstream alternative transcription start sites evade uORF-mediated inhibition of gene expression during blue light exposure in Arabidopsis

(Submitter supplied) uORF-mediated translation reguration

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing; Other

Platform:: GPL21785
8 Samples

Download data: TXT

Series

Accession:: GSE109122

ID:: 200109122

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Select item 20012496213.

The landscape of mRNA translation in tomato roots

(Submitter supplied) We used Ribo-seq (Ribosome profiling) combining with RNA-seq to explore the translational landscape of tomato roots. We generated three biological replicates of RNA-seq and Ribo-seq data for tomato roots. We next used the RNA-seq result for de novo transcriptome assembly and Ribo-seq to identify novel translated open reading frames (ORFs). Our data revealed more than three hundreds of novel translated ORFs on previously unannotated transcripts. more...

Organism:: Solanum lycopersicum

Type:: Other

Platform:: GPL25655
6 Samples

Download data: BED, GTF

Series

Accession:: GSE124962

ID:: 200124962

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Select item 20010771814.

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

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Select item 20009861015.

Ribosome footprints sequencing from Arabidopsis thaliana roots during Pi starvation

(Submitter supplied) Post-transcriptional gene regulation plays a significant role in the response to Pi starvation. Here, we utilized advances in next-generation sequencing technology to examine changes in transcriptional control, RNA association with translating ribosomes in 14-day-old Arabidopsis seedlings subjected to 7 days of Pi starvation.

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing; Other

Platform:: GPL13222
7 Samples

Download data: TXT

Series

Accession:: GSE98610

ID:: 200098610

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Select item 20014997316.

Decoding SARS-CoV-2 coding capacity

(Submitter supplied) SARS-CoV-2 is a coronavirus responsible for the COVID-19 pandemic. Although the SARS-CoV-2 trascriptome was reported recently, its coding capacity and the relative production of different viral proteins remained unclear. Utilizing a suit of ribosome profiling techniques, we present a high resolution map of the SARS-CoV-2 coding regions.

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

Type:: Expression profiling by high throughput sequencing; Other

Platforms:: GPL28867 GPL28488 GPL28866
26 Samples

Download data: TAB, WIG

Series

Accession:: GSE149973

ID:: 200149973

PubMed Similar studies SRA Run Selector

Select item 20020473917.

Translation and Natural Selection of long non-canonical RNA micropeptides

(Submitter supplied) Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides but lacking canonical coding sequences. Apparently unable to produce peptides, lncRNA function seems to only involve RNA sequence and structure. Here, we exhaustively detect in-vivo translation of small open reading frames (small ORFs) within lncRNAs using Ribosomal profiling during Drosophila melanogaster embryogenesis. We show that around 30% of lncRNAs contain small ORFs engaged by ribosomes, leading to regulated translation of 100 to 300 micropeptides. more...

Organism:: Drosophila melanogaster

Type:: Non-coding RNA profiling by high throughput sequencing

Platform:: GPL30203
9 Samples

Download data: XLSX

Series

Accession:: GSE204739

ID:: 200204739

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Select item 20015585418.

DAP5 enables main ORF translation on mRNAs with structured and uORF-containing 5’ leaders

(Submitter supplied) Half of mammalian transcripts contain short upstream open reading frames (uORFs) that potentially regulate translation of the downstream coding sequence (CDS). The molecular mechanisms governing these events remain poorly understood. Here, we find that the non-canonical initiation factor Death-associated protein 5 (DAP5 or eIF4G2) is required for translation initiation on select transcripts. Using ribosome profiling and luciferase-based reporters coupled with mutational analysis we show that DAP5-dependent translation occurs on messenger RNAs (mRNAs) with long, structure-prone 5′ leader sequences and persistent uORF translation. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing; Other

Platform:: GPL21290
8 Samples

Download data: TXT

Series

Accession:: GSE155854

ID:: 200155854

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Select item 20005462519.

Polysomes from DENR knockdown cells

(Submitter supplied) The aim was to identify transcripts that are poorly translated upon knockdown of DENR. Lysates from control (GFP) and DENR knockdown S2 cells were run on polysome gradients. RNA from the (80S peak + polysome peaks) was isolated and analyzed by microarrays. In parallel, total RNA from the cells was also profiled as a normalization control and profiled. The 'translation score' of translated mRNA to total RNA was then calculated for control and DENR knockdown cells.