Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Humans and other commonly used model organisms are resistant to cycloheximide-mediated biases in ribosome profiling experiments

ABSTRACT: Humans and other commonly used model organisms are resistant to cycloheximide-mediated biases in ribosome profiling experiments

PROVIDER: PRJNA564089 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10072555.fastq.gz	Fastqsanger.gz
	SRR10072556.fastq.gz	Fastqsanger.gz
	SRR10072557.fastq.gz	Fastqsanger.gz
	SRR10072558.fastq.gz	Fastqsanger.gz
	SRR10072559.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 33

Similar Datasets

Humans and other commonly used model organisms are resistant to cycloheximide-mediated biases in ribosome profiling experiments

Project description:Ribosome profiling measures genome-wide translation dynamics at sub-codon resolution. Cycloheximide (CHX), a widely used translation inhibitor to arrest ribosomes in these experiments, has been shown to induce biases in yeast, questioning its use. However, whether such biases are present in datasets of other organisms including humans is unknown. Here we compare different CHX-treatment conditions in human cells and yeast in parallel experiments using an optimized protocol. We find that human ribosomes are not susceptible to conformational restrictions by CHX, nor does it distort gene-level measurements of ribosome occupancy, measured decoding speed or the translational ramp. Furthermore, CHX-induced codon-specific biases on ribosome occupancy are not detectable in human cells or other model organisms. This shows that reported biases of CHX are species-specific and that CHX does not affect the outcome of ribosome profiling experiments in most settings. Our findings provide a solid framework to conduct and analyze ribosome profiling experiments.

2021-07-28 | GSE136940 | GEO

Humans and other commonly used model organisms are resistant to cycloheximide-mediated biases in ribosome profiling experiments.

| S-EPMC8384890 | biostudies-literature

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

Ribosome profiling data of HEK293T cells treated with C13-benzamidyl cycloheximide

Project description:We performed ribosome profiling in HEK293T cells with treatment with either C13-benzamidyl cycloheximide (hereafter "benzamide") or cycloheximide.

2021-09-28 | GSE184519 | GEO

Cycloheximide treatment with 15 uM for 2 h

Project description:The number and type of synthetic chemicals that are being produced worldwide continues to increase significantly. While these industrial chemicals provide numerous benefits, there is no doubt that some have potential to damage the environment and health. Toxicity must be evaluated and use must be carefully controlled and monitored in order to minimize potential damage. DNA microarray technology has become an important new technique in toxicology. We are using the yeast Saccharomyces cerevisiae as a model organism for toxicological study because it is a simple, fast-growing eukaryote that has been thoroughly characterized. In order to evaluate toxicity by newly synthesized or mixture chemicals, toxicity-induced gene expression alteration profiles by known chemicals should be collected. In our study, cells need to be exposed with same experimental cellular condition, semi lethal (IC50), respectively. In the case of cycloheximide (CAS; 66-81-9), the exposure dose was decided as 15 uM by growth curve with continuously diluted exposure. Cycloheximide is an inhibitor of protein biosynthesis in eukaryotic organisms that is recognized as a developmental toxicant and suspected to be a kidney toxicant. Keywords: stress response

2007-11-01 | GSE9458 | GEO

Effects of cycloheximide (CHX) on ribosome profiling experiments in Schizosaccharomyces pombe

Project description:Effects of cycloheximide (CHX) on ribosome profiling experiments in Schizosaccharomyces pombe

| PRJEB21099 | ENA

Expression data from Murine T cell in response to cycloheximide treatment

Project description:Cycloheximide has been used for inhibiting protein synthesis in order to identify IL-2 direct targeted genes in T cells, but the effects of cycloheximide itself on genomewide genes are not well defined We conducted a global analysis of cycloheximide regulated genes in mouse T cell line CTLL-2 using Affymetrix mouse genome array, and identified 213 genes differentially expressed (?1.5-fold change) in response to cycloheximide 30min after adding cylcoheximide to T cells cultured without IL-2 for 14 hours. These genes involve in a number biological processes. Keywords: stress response

2009-01-10 | GSE6084 | GEO

organisms

Project description:organisms Raw sequence reads

| PRJNA825711 | ENA

A novel approach uncovering the biological signal in Hi-C data affected by technical biases

Project description:The chromatin interaction assays, particularly Hi-C, enabled detailed studies of chromatin architecture in multiple organisms and model systems, resulting in a deeper understanding of gene expression regulation mediated by epigenetics mechanisms. However, the analysis and interpretation of Hi-C data remain challenging due to technical biases, limiting direct comparisons of datasets obtained in different experiments and laboratories. As a result, removing biases from Hi-C-generated chromatin contact matrices is a critical data analysis step. Our novel approach HiConfidence eliminates biases from the Hi-C data by weighing chromatin contacts according to their consistency between replicates so that low-quality replicates do not influence the result. The algorithm is effective for the analysis of global changes in chromatin structures such as compartments and TADs. We apply the HiConfidence approach to several Hi-C datasets with significant technical biases that could not be analyzed effectively using existing methods, and obtain meaningful biological conclusions. In particular, HiConfidence aids in the study of how changes in the histone acetylation pattern affect chromatin organization in Drosophila cells.

2023-02-05 | GSE200078 | GEO

Genomic characterization of five commonly used endometrial cancer cell lines

Project description:Genomic characterization of five commonly used endometrial cancer cell lines

| PRJNA635126 | ENA