Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Streptococcus pneumoniae membrane proteomics of WT and scRNA mutants

ABSTRACT: We studied the membrane protein compositions of Streptococcus pneumoniae WT and scRNA mutant strains, with or without the CSP1 induction into competence state.

INSTRUMENT(S): Dionex instrument model

ORGANISM(S): Streptococcus Pneumoniae Serotype 2 (strain D39 / Nctc 7466)

SUBMITTER: Jingjun Lin

LAB HEAD: Gee W Lau

PROVIDER: PXD054463 | Pride | 2024-08-19

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	14-142-Gee-Lau-ScRNA-CSP.raw	Raw
	14-142-Gee-Lau-ScRNA.raw	Raw
	14-142-Gee-Lau-WT.raw	Raw
	14-142-Gee-Lau-WTCSP.raw	Raw
	WT.pl	Other

Items per page:

1 - 5 of 8

Similar Datasets

Essential role of proline synthesis and the one-carbon metabolism pathways for systemic virulence of Streptococcus pneumoniae

Project description:Rapid adaptation to grow within the physiological conditions found in the host environment is an essential but poorly understood virulence requirement for systemic pathogens such as Streptococcus pneumoniae. We have now demonstrated an essential role for the one-carbon metabolism pathway and a conditional role depending on strain background for proline biosynthesis for S. pneumoniae growth in serum or CSF and therefore for systemic virulence. RNAseq data demonstrated that loss of one carbon metabolism or proline biosynthesis both have profound but differing effects on S. pneumoniae metabolism in human serum, identifying the metabolic processes dependent on each pathway during systemic infection. These data provide a more detailed understanding of the adaptations required by systemic bacterial pathogens in order to cause infection, and demonstrate that the requirement for some of these adaptations vary between strains from the same species and could therefore underpin strain variations in virulence potential.

2023-09-10 | E-MTAB-13289 | biostudies-arrayexpress

scRNA-seq of sea lamprey (Petromyzon marinus) brain regions

Project description:scRNA-seq was used in order to produce a cell type atlas of the larval and adult sea lamprey (Petromyzon marinus) brain. This resource enabled us to reveal the cell type composition and molecular organization of a representative of a lineage (i.e., the cyclostomes) that diverged from the rest of vertebrates around 500 million years ago, and lays the foundations for a better comprehension of vertebrate brain evolution

2021-12-13 | E-MTAB-11087 | biostudies-arrayexpress

Transcriptomic response of Anoxybacillus sp. SK 3-4 to aluminum exposure

Project description:By comparing the gene expression profiling in Anoxybacillus sp. SK 3-4 with and without aluminum exposure, the sets of gene up-regulated and down-regulated by aluminum were identified. The function of genes or proteins induced under these conditions can a reflection of the mechanism of resistance. Transcriptome profiling of Anoxybacillus sp. SK 3-4 treated by aluminum would allow a better understanding of the gene involving in tolerance and removal of aluminum. Global transcriptomic response of Anoxybacillus sp. SK 3-4 to aluminum exposure

2016-08-05 | E-GEOD-78908 | biostudies-arrayexpress

Single-cell RNA sequencing of MAIT cells from young and aged mice

Project description:In this study, we performed single-cell RNA sequencing (scRNA-seq) on MAIT cells extracted from the intestines of young and aged mice. For each age group, MAIT cells from five individual mice were pooled before sequencing.

2024-11-26 | E-MTAB-14483 | biostudies-arrayexpress

Single cell RNA sequencing (scRNA-seq) of human embryoid body (day 4 of culture)

Project description:Human Primordial Germ Cell (PGC)-like cells (PGCLC) were specified in vitro from naive-like hiPS cell lines. To evaluate the first steps of PGCLC differentiation, we performed scRNA-seq (droplet-based technology, 10x) on cell suspension from embryoid body (EB) obtained after EB aggregation followed by 4 days of culture (EBd4) with cocktail of cytokines (BMP4, LIF, SCF, EGF and ROCK inhibitor) supplemented with 0.1 mM 2-mercaptoethanol and 15% KSR. In this study, two pools of embryoid bodies (EBD4_A, EBD4_B) were cultured independently for for further encapsulation and sequencing.

2022-11-29 | E-MTAB-12089 | biostudies-arrayexpress

Clustered regulatory signals at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe

Project description:Sequencing of mononucleosomal DNA during asynchronous mitosis and 0, 3 and 5 hours into meiosis in Schizosaccharomyces pombe. Two samples from mononucleosomal DNA from asynchronous mitosis (haploid 972 h- and diploid pat1.114) and three samples from 0, 3 and 5 hours into meiosis (from diploid pat1.114) were sequenced (Illumina Genome Analyzer IIx) using the single-end read protocol.

2013-11-25 | E-GEOD-41772 | biostudies-arrayexpress

Expression changes after loss of Dot1l in murine MLL-AF9 leukemia cells

Project description:MLL-fusions may induce leukemogenic gene expression programs by recruiting the histone H3K79 methyltransferase to MLL-target promoters. We evaluated gene expression changes after cre-mediated loss of Dot1l in leukemia cells obtained from mice injected with MLL-9 transformed lineage negative bone marrow cells. MLL-AF9 murine leukemia cells carrying two conditional Dot1l alleles were retrovirally transduced with Cre or empty control vector, and gene expression changes were monitored on day 3, 5, and 7 after transduction.

2011-09-12 | E-GEOD-25911 | biostudies-arrayexpress

Dual RpoH sigma factors in Sinorhizobium meliloti

Project description:Sinorhizobium meliloti can live as a soil saprophyte, and can engage in a nitrogen fixing symbiosis with plant roots. To succeed in such diverse environments, the bacteria must continually adjust gene expression. Transcriptional plasticity in eubacteria is often mediated by alternative sigma factors interacting with core RNA polymerase. The S. meliloti genome encodes 14 of these alternative sigmas, including two putative RpoH (heat shock) sigmas. We used custom Affymetrix Symbiosis Chips to characterize the global transcriptional response of S. meliloti rpoH1, rpoH2 and rpoH1 rpoH2 mutants during heat shock and stationary phase growth. Under these conditions, expression of over 300 genes is dependent on rpoH1 and rpoH2. Gene expression profiling of Sinorhizobium meliloti Rm1021 and its isogenic rpoH1, rpoH2, and rpoH1rpoH2 mutants, subjected to heat shock or stationary phase growth, was performed using custom Affymetrix GeneChips

2012-10-02 | E-GEOD-36186 | biostudies-arrayexpress

Post-transcriptional buffering of low nascent RNA transcription by Puf5

Project description:Gene expression is a dynamic process regulated on several layers starting with transcription, mRNA export, translation and finally, mRNA degradation. While subsequent layers heavily influence each other, it is not clear if the most extreme layers, chromatin architecture and mRNA decay are linked. Here, we show that changes in nascent transcription mediated by mutating H3K56 to alanine are buffered at a post-transcriptional level by the Pumilio protein Puf5, which stabilizes transcripts in a context-dependent manner. Depleting Puf5 in an H3K56A background leads to downregulation of its direct targets, largely consisting of ribosomal protein genes. This is followed by a decrease in translation efficiency and finally, cell cycle arrest. Importantly, we show that this phenomenon of post-transcriptional buffering is not only linked to H3K56A, but might be a more widespread phenomenon to ensure physiological mRNA levels and to maintain cellular homeostasis.

2021-07-19 | E-MTAB-10107 | biostudies-arrayexpress

Comparison of gene expression in MGAS315 and its isogenc mtsR mutant

Project description:RATIONALE: mtsR is a regulator of genes involved in ion aquisition in S. pyogenes that has been suggested to be involved in development of invasive infections. We wanted to identify mtsR regulon. EXPERIMENT: We compared global gene expression in wild type strain MGAS315 with expression in its isogenc mtsR mutant. Experiment was performed with bacteria in exponential (EXP) and at late exponential phase (Late EXP) grown in THY medium Keywords: strain comparison 1. Three independent cultures of WT or mutant strain bacteria at exponential phase of growth (OD60=0.5, biological replicates) served as source of total RNA. RNA was transcribed into cDNA, fragmented and labeled using standard Affymetrix protocol for prokaryotic target preparation. Hybridization with custom Affymetrix array and scaning was performed using protocol recomended by manufacturer. Hybridizaton values aquired by GCOS (in CHP files) are normalized to global hybridization intesity. 2. Analogous experiment was performed with bacteria grown to OD600=1.2 representing late exponential growth phase

2010-05-06 | E-GEOD-10252 | 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