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

Transcriptomic comparison of Listeria monocytogenes and its derivative mutant strain with inactivated lmo0946 gene in stationary phase of growth

ABSTRACT: To elucidate whole-transcriptome changes in stationary-phase of growth of L. monocytogenes induced by inactivation of lmo0946 gene, we performed transcriptome comparison of wild-type and its derivative mutant in lmo0946 gene. The analysis revealed very high abundance of two non-coding RNAs, namely Rli47 (sRNA) and SsrA (tmRNA) in both studied strains.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Listeria monocytogenes EGD-e

SUBMITTER: Agata Krawczyk-Balska

PROVIDER: E-MTAB-10810 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcriptomic comparison of Listeria monocytogenes and its derivative mutant strain with inactivated lmo0946 gene in exponential phase of growth

Project description:To gain comprehensive knowledge on role of Lmo0946 in physiology of L. monocytogenes, we set on analyzing whole-transcriptome changes induced by inactivation of lmo0946 gene. Remarkably, we identified for the first time a global effect of lmo0946 inactivation on transcriptome of L. monocytogenes with highly induced genes belonging to SOS regulon in absence of any environmental stress.

2023-08-05 | E-MTAB-10809 | biostudies-arrayexpress

Platelets favor the outgrowth of established metastases

Project description:Despite abundant evidence demonstrating that platelets foster metastasis, anti- platelet agents have low therapeutic potential due to the risk of hemorrhages. In addition, whether platelets can regulate metastasis at the late stages of the disease remains unknown. In this study, we subjected syngeneic models of metastasis to various thrombocytopenic regimes to show that platelets provide a biphasic contribution to metastasis. While potent intravascular binding of platelets to tumor cells efficiently promotes metastasis, platelets further support the outgrowth of established metastases via immune suppression. Genetic depletion and pharmacological targeting of the platelet-specific receptor GPVI in humanized mouse models efficiently reduced the growth of established metastases, independently of active platelet binding to tumor cells in the bloodstream. Our study is the first to demonstrate therapeutic efficacy when targeting animals bearing growing metastases. It further identifies GPVI as the first molecular target whose inhibition can impair metastasis without inducing collateral hemostatic perturbations.

2024-03-10 | E-MTAB-13864 | biostudies-arrayexpress

Epstein-Barr virus protein EB2 stimulates translation initiation of mRNAs through direct interactions with both PABP and eIF4G

Project description:Epstein-Barr virus (EBV) expresses several mRNAs produced from intronless genes that could be unfavorably translated in front of cellular spliced mRNAs. To overpass these limitations, the virus encodes a RNA-binding protein (RBP), EB2, which is already known to facilitate nuclear mRNAs export and to increase their translational yield. Here we show that EB2 binds both nuclear and cytoplasmic cap-binding complexes (respectively, CBC and eIF4F), and the poly(A)-binding protein (PABP) to enhance translation initiation of a given mRNP. Interestingly, such effect can be obtained only if EB2 was initially bound to the native mRNPs in the nucleus. We also demonstrate that the EB2-eIF4F-PABP association renders the translation of these mRNPs less sensitive to inhibitors of initiation. Taken together, our new data suggest that EB2 binds and stabilizes cap-binding complexes to increase mRNP translation and demonstrate the importance of the mRNP assembly process in the nucleus to promote translation in the cytoplasm.

2022-03-03 | PXD003800 | Pride

RNA-seq of Streptococcus pneumoniae serotype 6B; wild type strain and 2 different double mutants grown in Todd-Hewitt media supplemented with 0.5% yeast extract (THY)

Project description:RNA-seq was performed in this study in order to identify whether the introduction of a gene mutation in S. pneumoniae, has any effect increase or decrease expression of any S. pneumoniae genes in the mutant strains that previous publications suggest might affect the safe use of these strains in humans.

2021-08-31 | E-MTAB-10076 | biostudies-arrayexpress

Transition of embryonic stem cells from ground state pluripotency (RNA-seq)

Project description:Mouse embryonic stem cells were maintained in minimal and chemically-defined culture conditions supporting naive pluripotency. Inhibitors of the Gsk3 (CHIR99021) and Mek/Erk (PD0325901) pathways were withdrawn, cultures maintained for 24 hours, and subsequently sorted by flow cytometry based on fluorescence of a short-half-life Rex1(Zfp42)::GFP reporter into two populations: Rex1-high cells, functionally capable of reversion to naive pluripotency, and Rex1-low cells that have exited the naive state.

2017-02-22 | E-MTAB-5305 | biostudies-arrayexpress

RNAseq data of blood samples from children with pneumonia, M. pneumoniae pneumonia and Healthy Controls used to validate transcriptomic signatures of M.pneumoniae penumonia

Project description:Pneumonia remains the leading cause of death in children under five, but existing diagnostic methods frequently lead to innecessary or mistaken treatment. M. pneumoniae lacks cellular wall so it does not respond to common firs-line antibiotic. Our study aims to guide the diagnosis and treatment by identifying host transcriptomic biomarkers in the blood of children with Mycoplasma pneumoiae pneumonia. Using RNA sequencing, we identified and validated 8 different n-transcript signature that accurately differentiates M. pneumoniae pneumonia from the rest of pneumonias. A strand specific library preparation was completed using NEBNext® Ultra™ II mRNA kit (NEB) and NEB rRNA/globin depletion probes following manufacturer’s recommendations. Individual libraries were normalized using Qubit, pooled together and diluted. The sequencing was performed using a 150 or 75 paired-end configuration in a Novaseq6000 or HiSeq 4000 platforms. Quality control of raw data was carried out using FastQC, alignment and read counting were performed using STAR, alignment filtering was done with SAMtools and read counting was carried out using FeatureCounts. RNAseq data was processed for batch correction using control samples and COMBAT-Seq package.

2024-12-08 | E-MTAB-14588 | biostudies-arrayexpress

In vivo cleavage rules and target repertoire of RNase III in Escherichia coli

Project description:In this study we generated 5'P libraries in wt and RNAse III mutant strains, grown to exponential and stationary phases. Libraries that retain short RNA fragments were also generated in both growth phases. After sequencing by Illumina NextSeq 500 system, reads were mapped to E. coli genome NC_000913.3. By comparing the read start counts per position in the wt and mutant strain libraries we identified the cleavage sites of RNase III.

2018-09-30 | E-MTAB-6704 | biostudies-arrayexpress

RNA sequencing of the non-hematopoietic microenvironment of aspirates from Multiple Myeloma patients at diagnosis and after treatment versus non-cancer controls

Project description:By generating a paired single cell RNA-sequencing database of the tumor niche from 10 newly diagnosed MM patients, we created a unique dataset allowing the in-depth analyses of stromal-immune interactions within the tumor microenvironment (see related accession number). Using this database, we identified the presence of inflammatory stromal fibroblasts in the bone marrow of Myeloma patients.The stromal inflammation was associated with NF-κB signaling, and sources of IL-1β or TNFα were specific immune subsets previously shown to be altered in MM, suggesting the presence of an immune cell-mediated feed-forward loop of bone marrow inflammation in MM. By tracking inflammatory signatures over time in individual patients undergoing first-line treatment using bulk RNA sequencing, we show that bone marrow inflammation is not reverted by successful anti-tumor therapy (this dataset), suggesting a role for stromal fibroblasts and bone marrow inflammation in disease persistence or relapse. Raw sequencing data files will be deposited to EGA.

2021-02-01 | E-MTAB-9285 | biostudies-arrayexpress

RNA-seq of Solanum Lycopersicum and Solanum Pennellii parents and crosses up to the F4 generation

Project description:This study investigates changes in gene expression among 2 Tomato species and their hybrids. This was used to investigate changes in gene (small-RNA-Seq data in separate submission) and sRNA expression after hybridisation.

2022-04-25 | E-MTAB-10660 | biostudies-arrayexpress

RNA-seq of livers from glucagon receptor knock-out (GcgrKO) mice compared to wildtype littermates

Project description:Glucagon is a key regulator of glucose homeostasis, amino acid catabolism, and lipid metabolism. Glucagon receptor knock-out (GcgrKO) mice have slightly reduced blood glucose levels whereas plasma levels of amino acids are vastly increased reflecting disruption of hepatic amino acid catabolism. To dissect the molecular mechanisms underlying this effect, RNA sequencing of livers from male GcgrKO mice and wild-type littermates were performed. The mice were 10 weeks of age and were subjected to a short-term fast of 4 h before anesthesia with 2.5% isoflurane.

2022-10-11 | E-MTAB-12060 | 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