Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ribosome profiling and RNA-seq of in vitro differentiated human CD4+ Th1 cells.

ABSTRACT: We investigated the translatome of in vitro differentiated human CD4+ Th1 cells.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Homo sapiens

SUBMITTER: Roberta Alfieri

PROVIDER: E-MTAB-5961 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Ribosome Profiling of mouse skin squamous tumours

Project description:Purpose: Ribosome profiling has revolutionized systems-based analysis and which produces a âglobal snapshotâ of all the ribosomes translationally active in a cell at a particular moment. The goals of this study are to first apply ribosome profiling to in vivo samples for the first time and in particular to stem cells and tumours and second to determine which mRNAs are being actively translated in these particular situations. Although much is known about gene expression regulation, little is known about how protein translation regulation can affect stem cell differentiation and tumour progression. Methods: several replicates of ribosome and mRNA profiles of wild-type (WT) and NSun2 -/- mouse skin squamous tumours were generated by deep sequencing, using Illumina HiSeq platform. Results: Our analyses reveal that activation of stress response pathways in vivo drives both a global reduction of protein synthesis and altered translation of specific mRNAs that together promote stem cell functions and tumourigenesis. Ribosome profiles of wild-type (WT) and NSun2 -/- mouse skin squamous tumours

2016-06-16 | E-GEOD-72066 | biostudies-arrayexpress

Ribo-Seq transcriptomic analysis of human RD cells infected with enterovirus strains EV7, EV71, and PV1.

Project description:Ribosome profiling (Ribo-Seq) (maps positions of translating ribosomes on the transcriptome) analysis of human (RD) cells infected with enterovirus strains EV7, EV71, and PV1.

2018-10-19 | E-MTAB-6180 | biostudies-arrayexpress

Ribo-seq of iPSC-derived neurons with TDP-43 knockdown

Project description:TDP-43 is a key splicing regulator. Here, we perform ribosome profiling on iPSC-derived neurons to examine how translation is affected by TDP-43 knockdown.

2022-02-28 | E-MTAB-10235 | biostudies-arrayexpress

Stem cell function and sensitivity to genotoxic stress is controlled by protein translation rates

Project description:Whether protein synthesis and cellular stress response pathways interact to control stem cell functions is currently unknown. Here, we show that skin stem cells synthesise less protein than their immediate progenitors in vivo, even when forced to proliferate in a tumour model. Our analyses reveal that activation of stress response pathways drives both a global reduction of protein synthesis and altered translation of specific mRNAs that together promote stem cell functions and tumourigenesis. Mechanistically we show that inhibition of post-transcriptional cytosine-5 methylation locks stem cells in this distinct translational inhibition programme. Paradoxically, this stress-induced translation inhibition renders stem cells hypersensitive to genotoxic stress, as tumour regeneration after treatment with 5-fluorouracil is blocked. Thus, stem cells must revoke translation inhibition pathways to regenerate a tissue or tumour. This SuperSeries is composed of the SubSeries listed below.

2016-06-16 | E-GEOD-72067 | biostudies-arrayexpress

Widespread regulation of translation by elongation pausing in heat shock

Project description:RNA-seq and ribosome footprinting libraries of mouse 3T3 and human 293T cellsrelated to Shalgi et al. 2013 36bases paired-end RNA-seq, and ribosome footprinting libraries for: 3T3 cells - Control, 8 hours of mild heat shock (42) and 2 hours of severe heat shock (44) - in replicates, as well as 3T3 cells treated by mild followed by severe heat shock. In addition, 3T3 cells treated with Hsp70 inhibitor VER-155008 (Massey et al. 2010), and 293T cells transfected with Hspa1a or GFP, before and after 2 hours of severe heat shock.

2013-01-03 | E-GEOD-32060 | biostudies-arrayexpress

RIL-seq analysis of MG1655 Escherichia coli experiencing long-term nitrogen starvation in Gutnick minimal media

Project description:RNA interaction by ligation and sequencing (RIL-seq) was carried out to compare the Hfq-RNA-RNA interactome of MG1655 E coli bacteria that grown in Gutnick minimal media. Wild-type and hfq::3xFLAG tagged K12 E.coli were grown in Gutnick minimal media with 3mM NH4Cl as the sole nitrogen source, and cell samples were taken during exponential growth (N+), ~20min following N-runout and induction of growth arrest (N-), 24hr following N-runout and induction of growth arrest (N-24) and 2hr following addition of NH4Cl to N-24 cells (N-24+2). All sampling was performed in triplicate for each strain and condition

2023-12-01 | E-MTAB-13403 | biostudies-arrayexpress

Analysis of Zika Virus gene expression by Ribosome profiling and RNA sequencing

Project description:Ribosome profiling (Ribo-Seq) (maps positions of translating ribosomes on the transcriptome) and RNA-Seq (quantifies the transcriptome) analysis of African green monkey (Vero E6) cells and Aedes albopictus (C6/36) cells infected with Zika Virus (ZIKV) strain PE243. Cells were harvested at 24 h post infection (p.i.) and Ribo-Seq and RNA-Seq libraries were prepared and deep sequenced.

2018-06-30 | E-MTAB-5418 | biostudies-arrayexpress

An integrated approach combining RNA-seq, Ribo-seq and Proteomics identifies the coding potential of Mycobacterium abscessus

Project description:The objective of this study is to develop an integrated map for the M. abscessus ATCC19977 organism. Among the data types contributing to the development of this map are next-generation RNA-sequencing, differential RNA-sequencing, ribosome profiling, and mass spectrometry. The design of the study consists of two biological samples, each with one technical replication; both biological samples were subjected to identical conditions.

2016-03-30 | E-GEOD-72996 | biostudies-arrayexpress

Ribosome profiling of the retrovirus murine leukemia virus

2018-01-17 | E-MTAB-6231 | biostudies-arrayexpress

Reduced representation bisulfite sequencing from G0 & G4/G5 CMP

Project description:Differential hyper- and hypo-methylation regions in G0 versus G4/G5 CMP The goal of this study is to evaluate changes in CpG methylation profilings of telomere dysfunctional common myeloid progenitor cells (CMP) as compared to their wild type controls Genomic DNA was extracted from sorted CMP populations isolated from 3 pools of G0 or 2 pools of G5 mice using UltraPure Phenol:Chloroform:Isoamyl Alcohol according to manufacturer’s instructions (Life Technologies). 14,000 to 30,000 cells were available for each sample, resulting in a minimum of 45ng of DNA. Genome-wide DNA methylation profiling was performed by RRBS. Library preparation and sequencing were performed at the UT MD Anderson Cancer Center’s DNA Methylation Analysis Core and Sequencing and Microarray Facility, according to published protocols. RRBS sequencing data were aligned and methylation was called using Bismark v0.7.119. In brief, bisulphite-treated DNA was aligned to UCSC Genome Browser mm10 reference genome using Bowtie. In total 29-38 million reads were generated per sample with alignment rates around 63%. Next, MethylKit10 implemented with Fisher’s exact test was used to compare the cytosine methylation profiles of G0 and G5 CMP. Gene promoter regions were calculated based on RefSeq gene annotations with regions starting 1 kb upstream of the annotated transcription start site (TSS) and extending 500 base pairs downstream of TSS. Exons, introns, and CpG islands coordinates were collected from the UCSC Genome Browser mm10 version.

2015-04-09 | E-GEOD-62392 | 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