Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ORFome decay in 293t and k562

ABSTRACT: ORFome decay in 293t and k562

PROVIDER: PRJNA522263 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR8571220.fastq.gz	Fastqsanger.gz
	SRR8571230.fastq.gz	Fastqsanger.gz
	SRR8571240.fastq.gz	Fastqsanger.gz
	SRR8571221.fastq.gz	Fastqsanger.gz
	SRR8571231.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 28

Similar Datasets

ORFome decay in 293t and k562

Project description:mRNA translation decodes nucleotide into amino acid sequences. However, translation has also been shown to affect mRNA stability depending on codon composition in model organisms, although universality of this mechanism remains unclear. Here, using three independent approaches to measure exogenous and endogenous mRNA decay, we define which codons are associated with stable or unstable mRNAs in human cells. We demonstrate that the regulatory information affecting mRNA stability is encoded in codons and not in nucleotides. Stabilizing codons tend to be associated with higher tRNA levels and higher charged/total tRNA ratios. While mRNAs enriched in destabilizing codons tend to possess shorter poly(A)-tails, the poly(A)-tail is not required for the codon-mediated mRNA stability. This mechanism depends on translation; however, the number of ribosome loads into a mRNA modulates the codon-mediated effects on gene expression. This work provides definitive evidence that translation strongly affects mRNA stability in a codon-dependent manner in human cells. 293T cells and k562 cells were infected with ORFome library to decay exodogenous gene mRNA decay. Stable infected cells were treated with actinmycin D at 6 well plate and samples were collected in duplicate every hour 0-6h for RNA-seq

2019-05-01 | GSE126521 | GEO

SLAM-seq for K562 endogenous mRNA decay

Project description:SLAM-seq for K562 endogenous mRNA decay

| PRJNA522262 | ENA

endogenous mRNA decay in 293t, hela, RPE cell line

Project description:endogenous mRNA decay in 293t, hela, RPE cell line

| PRJNA522261 | ENA

endogenous mRNA decay in 293t, hela, RPE cell line

Project description:mRNA endogenous decay profiles approach in 293T, HeLa and RPE cells. mRNA translation decodes nucleotide into amino acid sequences. However, translation has also been shown to affect mRNA stability depending on codon composition in model organisms, although universality of this mechanism remains unclear. Here, using three independent approaches to measure exogenous and endogenous mRNA decay, we define which codons are associated with stable or unstable mRNAs in human cells. We demonstrate that the regulatory information affecting mRNA stability is encoded in codons and not in nucleotides. Stabilizing codons tend to be associated with higher tRNA levels and higher charged/total tRNA ratios. While mRNAs enriched in destabilizing codons tend to possess shorter poly(A)-tails, the poly(A)-tail is not required for the codon-mediated mRNA stability. This mechanism depends on translation; however, the number of ribosome loads into a mRNA modulates the codon-mediated effects on gene expression. This work provides definitive evidence that translation strongly affects mRNA stability in a codon-dependent manner in human cells.

2019-05-01 | GSE126520 | GEO

Human Embryonic Kidney(293T) Cells: Control vs. Transfected

Project description:Transcriptional profiling of Human Embryonic Kidney(293T) Cells comparing control untreated 293T cells with 293T cells transfected with A) pcDNA 3.0(-) vector[Invitrogen] (Mock) and B) Expression vector pcDNA 3.0(-) containing cloned Influenza virus H5N1and H11N1-NS1 (Non-Structural1) gene.

2014-07-14 | GSE39155 | GEO

ChIP-seq and RIP-seq for SCML2 and SCML2 mutants in 293T-REx and K562 cells

Project description:ChIP-seq and RIP-seq for SCML2 and SCML2 mutants in 293T-REx and K562 cells

| PRJNA167619 | ENA

Genome-wide mapping of p53-binding in 293T cells

Project description:We report p53-target genes in response to DNA damage in 293T cells

2021-03-03 | GSE154103 | GEO

The immunopeptidome of HLA-A*11:01 expressed K562 cell line

Project description:The K562 cell line was obtained from ATCC (American Type Culture Collection, Manassas,VA). And the K562 cell line was transduced using a highly efficient retroviral vector coding HLA-A*11:01. The vectors were transfected into a 293T packaging cell line and replication-defective virus supernatants were harvested. After infection of K562 cells with the supernatant, antibody-directed flow cytometry sorting was done to obtain high expression for HLA-A*11:01. Cells were grown in T75 flasks to a density of 1e9 cells before purification of HLA-I peptides for MS experiments.

2020-12-07 | MSV000086567 | MassIVE

DNA methylation profiling for HEK-293T cells transfected with GFP and DMEΔ

Project description:Methylome data obtained from human embryonic kindey (HEK)-293T cells expressing a GFP (293T-GFP) or a truncated form of Arabidopsis DEMETER (DME) 5-methylcytosine (5mC) DNA glycosylase (293T-DMEΔ) analyzed on a Human Methylation 450K BeadChip platform (Illumina). These methylation array data revealed genome-wide DNA methylation patterns of the 293T-GFP cells (without direct 5mC excision activity) and 293T-DMEΔ cells (with artificially implemented direct 5mC excision activity).

2017-09-20 | GSE96864 | GEO

Expression data from 293T cell treated with ROCK inhibitor

Project description:We used microarray to determine the genes whose expression was changed at three or six hours after Y27632 treatment. Three-condition experiment; 293T control vs 293T treated with Y27632 for three hours, 293T control vs 293T treated with Y27632 for six hours.

2014-04-21 | E-GEOD-32024 | 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