Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Oxygen-dependent translation efficiency (TE) and mRNA expression analysis

ABSTRACT: mRNA TE and steady-state levels were measured in U87MG cells subjected to 21% or 1% oxygen followed by ribosome density fractionation.

ORGANISM(S): Homo sapiens

PROVIDER: GSE128547 | GEO | 2020/04/23

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Hypoxia-Acidosis translation efficiency (TE) and mRNA expression analysis

Project description:mRNA TE and steady-state levels were measured in normoxic, normoxia-acidosis, hypoxia, hypoxia acidosis U87MG from RNA seq of ribosome density fractionation.

2020-04-23 | GSE139233 | GEO

HuR-dependent translation efficiency (TE) and mRNA expression analysis in hypoxia.

Project description:mRNA TE and steady-state levels were measured in hypoxic U87MG cells treated with non-silencing control or HuR-specific siRNA pools followed by ribosome density fractionation.

2020-04-23 | GSE128541 | GEO

HIF-2α- and HIF-1α-dependent translation efficiency (TE) and mRNA expression analysis in hypoxia.

Project description:mRNA TE and steady-state levels were measured in hypoxic U87MG cells treated with non-silencing control or HIF-2α-specific or HIF-1α-specific siRNA pools followed by ribosome density fractionation.

2020-04-23 | GSE128555 | GEO

Oxygen-dependent translation efficiency (TE) and mRNA expression analysis

Project description:Oxygen-dependent translation efficiency (TE) and mRNA expression analysis

| PRJNA528083 | ENA

Hypoxia-Acidosis translation efficiency (TE) and mRNA expression analysis

Project description:Hypoxia-Acidosis translation efficiency (TE) and mRNA expression analysis

| PRJNA578854 | ENA

Cycloheximide can distort measurements of mRNA levels and translation efficiency

Project description:Regulation of the efficiency with which an mRNA is translated into proteins represents a key mechanism for controlling gene expression. Such regulation impacts the number of actively translating ribosomes per mRNA molecule, referred to as translation efficiency (TE), which can be monitored using ribosome profiling and RNA-seq, or by evaluating the position of an mRNA in a polysome gradient. Here we show that in budding yeast, under nutrient limiting conditions, the commonly used translation inhibitor cycloheximide induces rapid transcriptional upregulation of hundreds of genes involved in ribosome biogenesis. Cycloheximide also prevents translation of these newly transcribed messages, leading to an apparent drop in TE of these genes under conditions that include key transitions of the yeast metabolic cycle, meiosis, and amino acid starvation; an effect which is abolished when cycloheximide pretreatment is omitted. This response requires TORC1 signaling, and is modulated by the genetic background as well as the vehicle used to deliver the drug. The present work highlights an important caveat to the use of translation inhibitors when measuring TE, and will hopefully aid in future experimental design as well as interpretation of prior results

2019-03-08 | GSE125038 | GEO

HuR-dependent translation efficiency (TE) and mRNA expression analysis in hypoxia.

Project description:HuR-dependent translation efficiency (TE) and mRNA expression analysis in hypoxia.

| PRJNA528039 | ENA

Translation Profiling +/- miR-124

Project description:Ribosome Occupancy Experiments: for these experiments Channel 1 is amplified RNA (aRNA) from mRNA unbound to any ribosomes. Channel 2 is aRNA from mRNA associated with ribosomes. Ribosome Density Experiments: for these experiments Channel 1 is amplified RNA (aRNA) from mRNA present in the light fractions of the polysome. Channel 2 is aRNA from mRNA associated with ribosomes deep in the polysome. Experiments are biological replicates of ribosome occupancy and density 12 hours post mock transfection or miR-124 transfection.

2010-06-20 | E-GEOD-18836 | biostudies-arrayexpress

N6-methyladenosine Modulates Messenger RNA Translation Efficiency

Project description:N6-methyladenosine (m6A) is the most abundant internal messenger (mRNA) modification in mammalian mRNA. This modification is reversible and non-stoichiometric, which potentially adds an additional layer of variety and dynamic control of mRNA metabolism. The m6A-modified mRNA can be selectively recognized by the YTH family “reader” proteins. The preferential binding of m6A-containing mRNA by YTHDF2 is known to reduce the stability of the target transcripts; however, the exact effects of m6A on translation has yet to be elucidated. Here we show that another m6A reader protein, YTHDF1, promotes ribosome loading of its target transcripts. YTHDF1 forms a complex with translation initiation factors to elevate the translation efficiency of its bound mRNA. In a unified mechanism of translation control through m6A, the YTHDF2-mediated decay controls the lifetime of target transcripts; whereas, the YTHDF1-based translation promotion increases the translation efficiency to ensure effective protein production from relatively short-lived transcripts that are marked by m6A. PAR-CLIP and RIP was used to identify YTHDF1 binding sites followed by ribosome profling and RNA seq to assess the consequences of YTHDF1 siRNA knock-down

2015-06-09 | E-GEOD-63591 | biostudies-arrayexpress

HIF-2α- and HIF-1α-dependent translation efficiency (TE) and mRNA expression analysis in hypoxia.

Project description:HIF-2α- and HIF-1α-dependent translation efficiency (TE) and mRNA expression analysis in hypoxia.

| PRJNA528091 | ENA