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Translation inhibition with CHX in mouse embryonic stem cells in bulk

ABSTRACT: Translation inhibition with CHX in mouse embryonic stem cells in bulk

PROVIDER: PRJNA1134767 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29791040_1.fastq.gz	Fastqsanger.gz
	SRR29791040_2.fastq.gz	Fastqsanger.gz
	SRR29791041_1.fastq.gz	Fastqsanger.gz
	SRR29791041_2.fastq.gz	Fastqsanger.gz
	SRR29791042_1.fastq.gz	Fastqsanger.gz

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Translation inhibition with CHX in mouse embryonic stem cells

Project description:Translation inhibition with CHX in mouse embryonic stem cells

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Translation inhibition with CHX in mouse embryonic stem cells in bulk

Project description:Gene-expression noise can influence cell-fate choices across pathology and physiology. However, a crucial question persists: do regulatory proteins or pathways exist that control noise independently of mean expression levels? Our integrative approach, combining single-cell RNA sequencing with proteomics and regulator enrichment analysis, reveals 32 putative noise regulators. The approach utilizes global translation inhibition (i.e., potential protein regulators), and single-cell RNA sequencing (scRNA-seq) to quantify the changes in noise of all transcripts (i.e., potential mRNA targets). This dataset corresponds to a control bulk RNAseq experiment experiment upon translation inhibition with cycloheximide to validate the changes in mean observed with single-cell.

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Cytoplasmic lncRNAs accumulate upon CHX-induced translation elongation inhibition

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Translation inhibition with CHX in mouse embryonic stem cells

Project description:Gene-expression noise can influence cell-fate choices across pathology and physiology. However, a crucial question persists: do regulatory proteins or pathways exist that control noise independently of mean expression levels? Our integrative approach, combining single-cell RNA sequencing with proteomics and regulator enrichment analysis, reveals 32 putative noise regulators. The approach utilizes global translation inhibition (i.e., potential protein regulators), and single-cell RNA sequencing (scRNA-seq) to quantify the changes in noise of all transcripts (i.e., potential mRNA targets). This dataset corresponds to the aforementioned scRNA-seq experiment upon translation inhibition with cycloheximide.

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Cytoplasmic lncRNAs accumulate upon ANS-induced translation elongation inhibition

Project description:To investigate the role of translation in the decay of cytoplasmic lncRNAs, we performed RNA-Seq in WT and upf1-delta yeast cells, treated or not with CHX.

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

Project description:CHX is an inhibitor of translation elongation often used in ribosome profiling experiments. There is evidence that CHX treatment of cells may cause artefacts in the distribution of ribosomes on mRNAs. We investigate this possibility in S. pombe by performing ribosome profiling in the presence and absence of this drug.

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Effect of global translation initiation inhibition associated to glucose starvation on cytoplasmic lncRNAs levels

Project description:To analyze the effect of global translation initiation inhibition associated to glucose deprivation on cytoplasmic lncRNAs levels, we performed RNA-Seq using WT, xrn1-delta and upf1-delta cells grown in glucose-containing complete synthetic medium (CSM) and then shifted for 16 min in glycerol- and ethanol-containing medium. In parallel, control cells were maintained for the same time in glucose-containing CSM. For the WT strains, we also included a treatment of 15 min with CHX (100 μg/ml final concentration) or an equal volume of DMSO (Mock).

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Project description:NIH-3T3 cells were pretreated for 15 min with either DMSO (mock) or cycloheximide followed by addition of either mock, 100 U/ml IFNalpha or 100 U/ml IFNgamma for 1h. During the last 30 min, 500 µM 4-thiouridine was added to cell culture medium. Total cellular RNA was isolated using Trizol reagent and nascent RNA was purified as described (Dölken et al. RNA 2008) . Three replicates of nascent RNA were analyzed by Affymetrix Mouse Gene ST 1.0 arrays Primary (translation independent) from secondary (translation dependent) IFN-mediated differential gene expression were studied in NIH-3T3 fibroblasts by studying studying differential gene expression in presence and absence of Cycloheximide (CHX). In addition, the effect of 75 min CHX during the last 30 min of treatment was studied in nascent RNA.

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