Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Long-RNA sequencing and ribosome profiling of inflamed beta-cells reveal an extensive translatome landscape

ABSTRACT: Long-RNA sequencing and ribosome profiling of inflamed beta-cells reveal an extensive translatome landscape

PROVIDER: PRJNA703954 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13762817.fastq.gz	Fastqsanger.gz
	SRR13762818.fastq.gz	Fastqsanger.gz
	SRR13762819.fastq.gz	Fastqsanger.gz
	SRR13762820.fastq.gz	Fastqsanger.gz
	SRR13762821.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 30

Similar Datasets

Long-RNA sequencing and ribosome profiling of inflamed beta-cells reveal an extensive translatome landscape

Project description:Using a transcriptome-wide profiling approach to map translation initiation start sites in human beta-cells under standard and inflammatory conditions, we identifies non-canonical start sites and translation initiation within lncRNA.

2021-02-23 | GSE167223 | GEO

Extensive oscillatory gene expression during C. elegans larval development [Ribosome footprinting]

Project description:We report the presence of extensive, transcriptionally controlled oscillations in the C. elegans, developmental transcriptome. Furthermore, using ribosome profiling, we show that these oscillating transcripts are actively translated. Ribosome-profiling analysis of a timecourse that was collected over C. elegans development

2014-03-01 | E-GEOD-52905 | biostudies-arrayexpress

Functional translatome proteomics reveal converging regulation by mTORC1 and eIF2α

Project description:Regulation of the translatome is essential during stress. However, the precise sets of translational targets regulated by the key translational stress responses –integrated stress response (ISR) and mTORC1 – remain elusive. We developed multiplexed enhanced protein dynamics (mePROD) proteomics, combining dynamic SILAC, multiplexing, and signal amplification, to enable measuring acute changes in protein synthesis. Treating cells with ISR/mTORC1-modulating stressors, we showed extensive translatome modulation and ~20% of proteins synthesized at highly reduced rates. Comparing translation-deficient sub-proteomes revealed an extensive overlap demonstrating that target specificity is achieved on protein level and not by pathway activation. Titrating inhibition of cap-dependent translation confirmed that synthesis of individual proteins is controlled by intrinsic properties responsive to global translation inhibition. This study reports a method to measure translation rates at the nascent chain level and provides insight into how the ISR and mTORC1, two key cellular pathways, regulate the translatome to guide cellular survival upon stress.

2019-12-06 | PXD014377 | Pride

Functional Translatome Proteomics Reveal Converging and Dose-Dependent Regulation by mTORC1 and eIF2α

2019-12-09 | PXD015438 | Pride

Extensive oscillatory gene expression during C. elegans larval development [Ribosome footprinting]

2014-03-01 | GSE52905 | GEO

Translatome of A549, H1299 and HBE cells

Project description:We performed translatome and transcriptome sequencing of A549, H1299 and HBE cells and analyzed the translation ratio (TR) of all genes Total RNA and ribosome-bound RNA were extracted from A549, H1299 and HBE cells, and the polyA+ mRNA was sequenced using Illumina GAIIx and HiSeq-2000. The reads were mapped to RefSeq RNA reference sequences and the expression level were quantified by rpkM calculation.

2013-03-05 | E-GEOD-42006 | biostudies-arrayexpress

Translatome analysis of Mycobacterium tuberculosis

Project description:We present the data obtained from high-resolution ribosome profiling analysis of Mycobacterium tuberculosis grown under standard conditions (log phase) and cells subjected to oxidative stress (50 µM cumene hydroperoxide) and pH stress (pH 4.5). Our data shows pervasive ribosome pausing in the M. tb translatome. A large number of genes show very high pause immediately downstream to the translation start site. Moreover, serines and alanines in the E site of the ribosome exhibit highest pause scores.

2021-06-02 | GSE151718 | GEO

Ribosome profiling of LS180 cells

Project description:A combination of ribosome profiling and RNA-seq was used to analyze the translatome of LS180 colon adenocarcinoma cells

2024-06-30 | GSE211536 | GEO

Sex differences in the developmental patterns of the cortical astroglial cell translatome

Project description:Employing translating ribosome affinity purification with RNA sequencing (TRAPseq) on cortical tissue to isolate astroglial-specific translatome from Aldh1l1-L10-GFP mice and examine sex (male + female) and age (postnatal days 1, 4, 7, 14, 35; adults (9 weeks)) dependent changes in the astroglial translatome.

2022-02-01 | GSE192490 | GEO

Ribosome hibernation factor promotes Staphyloccocal survival and differentially represses translation

Project description:We sequenced a total of 16 cDNA libararies derived from fragmented total mRNA and ribosome protected mRNAs from S. aureus hpf mutant (NE838) and its parental strain JE2 grown in tryptic soy broth (TSB) or minimal medium (MM). The data represented 2 independent biological replicates. Examination of the impact of hpf on global S.aureus translatome, mRNA abundance and the ribosome density along the transcripts.

2016-03-29 | E-GEOD-74197 | 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