Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Nascent Transcriptome of Cycloheximide (CHX)-arrested Xenopus laevis Embryos from 5-7.5 hpf

ABSTRACT: Nascent Transcriptome of Cycloheximide (CHX)-arrested Xenopus laevis Embryos from 5-7.5 hpf

PROVIDER: PRJNA833148 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR18969064_1.fastq.gz	Fastqsanger.gz
	SRR18969064_2.fastq.gz	Fastqsanger.gz
	SRR18969065_1.fastq.gz	Fastqsanger.gz
	SRR18969065_2.fastq.gz	Fastqsanger.gz
	SRR18969066_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

Nascent Transcriptome of Cycloheximide (CHX)-arrested Xenopus laevis Embryos from 5-7.5 hpf

Project description:To characterize the effect of cell cyle elongation on nascent transcription during zygotic genome activation (ZGA) of Xenopus laevis embryos, we microinjected 5-ethynyl uridine (EU) into 1-cell stage embryos and treated the embryos with 0.2 mg/ml of cycloheximide (CHX) to arrest them in interphase from 5 hpf to 7.5 hpf. Control and CHX-arrested embryos were collected for isolating total RNAs, followed by biotinylation using disulfide biotin azide via click reaction and purification of nascent transcripts using streptavidin beads. Libraries were constructed and sequenced on illumina NextSeq 500.

2022-08-22 | GSE201834 | 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

α-arrestin-dependent endocytosis after cycloheximide treatment

Project description:To identify new plasma membrane (PM) proteins that require α-arrestins for endocytosis, we performed an iTRAQ-based quantitative proteomic screening. We analysed and compared the PM proteome for each arrestin knockout (art∆) strain to a WT strain after a 90 min cycloheximide (CHX) treatment. CHX is a translation inhibitor and can trigger the endocytosis of several transporters in a substrate-independent manner. We searched for proteins that underwent CHX-induced endocytosis in a WT strain but that remained stabilized at the PM in an art∆ strain.

2019-09-25 | PXD014695 | Pride

Analysis of the effect of CHX on the cultured podocyte proteome

Project description:We analyzed the effect of Cycloheximide (CHX) on the podocyte proteome in both the differentiated and undifferentiated state.

2018-05-01 | PXD006886 | Pride

ATAC-seq and H4K16ac ChIP-seq profiles of E14 ES cells treated with cycloheximide

Project description:ATAC-seq and H4K16ac ChIP-seq profiles of E14 ES cells before and after treatment with cycloheximide (CHX, 1 ug/ml) for 3 hours.

2017-07-23 | GSE98358 | GEO

Ath_Agilent_v2_Riechmann array expression profile AP1-GR ap1cal inflorescences - chx experiment

Project description:This experiment describes gene expression after the activation of APETALA1-GR, to study and identify AP1 target genes. We used a 35S:AP1-GR ap1 cal line to induce a synchronized response activating the AP1-GR fusion protein in ap1 cal inflorescence-like meristems through dexamethasone or dexamethasone+cycloheximide treatment. Tissue samples were collected at 3hrs after the treatment. The expression profiles of the individual samples were then analyzed by gene expression profiling using whole-genome oligonucleotide arrays (Agilent, custom-commercial). We treated inflorescences of 35S:AP1-GR ap1-1 cal-1 plants with a dexamethasone-containing or a mock solution, or with identical solutions that contained in addition 10 M-NM-<M cycloheximide. Tissue was collected 3 hours after the treatment. Samples from each of the four biological replicates resulted in a set of four hybridization pairs: Mock vs. Dex, Mock vs. Chx, Mock vs. Dex+Chx, and Chx vs. Dex+Chx. Dye polarities were switched between biological replicates.

2011-01-01 | E-GEOD-20175 | biostudies-arrayexpress

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.

2017-09-05 | E-MTAB-5794 | biostudies-arrayexpress

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

jaw-D;pTCP4::mTCP4:GR_Cycloheximide + Dexamethasone microarray

Project description:9-day-old jaw-D;pTCP4::mTCP4:GR treated with Cycloheximide (CHX, control) and the combination of Cycloheximide and Dexamethasone (CHX DEX, treated).

2021-05-20 | GSE174702 | GEO

Transcription profiling by array of Arabidopsis thaliana shoots treated with either DEX or CHX to identify STM-regulated target genes

Project description:Global expression of the Arabidopsis transcriptional regulator SHOOT MERISTEMLESS (STM) in a 35S:STM-GR transgenic line was induced for 3 hours with dexamethasone (DEX) compared to mock-induced (DMSO) control. Additionally,to identify direct targets, plants were treated with the protein synthesis inhibitor cycloheximide (CHX) together with DEX, compared to CHX treatment alone.

2018-05-29 | E-MTAB-6786 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data