Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Multi-omics reveals molecular responses to aneuploidy in Leishmania

ABSTRACT: Integrated genomics, transcriptomics, proteomics and metabolomics experiment of aneuploid Leishmania donovani strains. This submission concerns the proteomic data.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Leishmania Donovani Ld 2001

SUBMITTER: Bart Cuypers

LAB HEAD: Kris Laukens

PROVIDER: PXD028521 | Pride | 2022-08-26

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	LFQintensities_submission.txt	Txt
	SampleIDs.txt	Txt
	sample1.raw	Raw
	sample10.raw	Raw
	sample11.raw	Raw

Items per page:

1 - 5 of 44

Similar Datasets

Proteomic changes in oocytes after in vitro maturation in lipotoxic conditions are different from those in cumulus cells

Project description:Sensitivity of cumulus enclosed-oocytes to metabolic stress during in vitro maturation. A proteomic insight

2019-04-02 | PXD012141 | Pride

Proteomics analysis of Bemisia tabaci (MED) saliva

Project description:The saliva from Bemisia tabaci (MED biotype) adults was collected using an artificial feeding system and analyzed using an LC-MS/MS proteomics analysis.

2024-01-26 | PXD033180 | Pride

RNA-seq of Mycobacterium smegmatis mc2-155 SMR5 wild-type vs. a pafBC deletion strain under different growth/stress conditions

Project description:The goal of the experiment is to obtain a differential gene expression profile for Mycobacterium smegmatis mc2-155 SMR5 (Msm) wild-type in comparison to a pafBC deletion strain (MSMEG_3888 and MSMEG_3889). In addition, the gene expression is to be analyzed with respect to different growth/stress conditions. Four groups were etablished: (1) Msm wild-type under standard conditions (2) Msm delta-pafBC under standard conditions (3) Msm wild-type treated with mitomycin C (4) Msm delta-pafBC treated with mitomycin C.

2018-06-17 | E-MTAB-6497 | biostudies-arrayexpress

LC-MS/MS analysis of HD5-interacting proteins

Project description:Human enteric α-defensin 5 (HD5) acts as a “double-edged sword” in host immunity due to its prominent role in promoting pathogen infections, yet the mechanistic basis of its infection-enhancing operation remains unclarified. Here we show that HD5 induces abundant filopodial extensions in epithelial cells which capture Shigella, a major human enteroinvasive pathogen that exploits filopodia for invasion, at high efficiency, suggesting a novel human-specific mechanism of HD5-augmented bacterial invasion. Using multi-omics screening and both gut-on-chip and in vivo models, we identify the HD5 receptor as P2Y11, a purinergic receptor distributed apically on the luminal surface of human colonic epithelium, which to our knowledge is the first HD5 receptor for a specific cellular function. cAMP-PKA signaling was identified to be the main pathway mediating the cytoskeleton-regulating activity of HD5, whose critical residues involved were also determined. In illuminating this mechanism of Shigella invasion, our findings raise the possibility of new intervention strategies against HD5-augmented infections.

2024-12-16 | PXD057885 | Pride

Cyberlindnera jadinii yeast as a functional protein source: Modulation of immunoregulatory pathways in the intestinal proteome of zebrafish (Danio rerio)

Project description:Cyberlindnera jadinii yeast is a potential sustainable novel feed ingredient for aquaculture industries. Yeasts contain bio-active components and proteins such as beta-glucans, mannans, nucleic acids and proteins that can enhance fish immunity against the disease. In our study, we focused on the characterization of intestinal immunoregulatory pathways in zebrafish (Danio rerio) by quantifying the intestine proteins with isobaric tags for relative and absolute quantitation (iTRAQ) and 2D LC-MS/MS approach. Zebrafish were fed either a control diet (C) or a diet supplemented with autolyzed C. jadinii (ACJ). The KEGG pathways analysis revealed that compared with the control diet, the ACJ yeast diet induced an increased abundance of proteins related to arginine and proline metabolism, phagosome, C-lectin receptor signalling pathway, ribosome pathway and PPAR signalling pathway, which can modulate and enhance the innate response of zebrafish. Moreover, fish fed ACJ yeast diet also showed decreased abundance of proteins associated with inflammatory pathways including apoptosis, necroptosis and ferroptosis pathways. These findings support a mobilization of the innate immune response and a control of inflammatory-related pathways in the intestine of zebrafish. Our findings in the well annotated proteome of zebrafish enabled a detailed investigation of intestinal responses and provide insight into the health-beneficial effects of the yeast species C. jadinii relevant for aquaculture species.

2024-05-24 | PXD040431 | Pride

Role of Fnr1 and Fnr3 in transcriptional regulation under oxygen limitation in Herbaspirillum seropedicae

Project description:To determine the direct promoter targets of Fnr proteins, we correlated transcriptional changes observed in single fnr1 and fnr3 mutants (E-MTAB-5741) with ChIP-Seq analysis, taking advantage of C-terminally 3xFlag fnr alleles engineered into the H. seropedicae genome. ChIP-seq data were obtained from cultures grown under limited oxygen availability. Using this approach, DNA-binding targets for the H. seropedicae Fnr1 and Fnr3 proteins were unambiguously revealed and correlated with transcript profiles to determine the specific regulons of each protein.

2018-02-26 | E-MTAB-6395 | biostudies-arrayexpress

The expression profiles of 30 transcription factors in 17 inducible gain-of-function lines after activation of overexpression, including 5 time points

Project description:We performed a large-scale expression analysis with inducible gain-of-function (GOF) lines which contain a C-terminal fusion protein of the TF of interest and a glucocorticoid receptor (GR) domain, driven by a constitutive 35S promoter. Such fusion proteins reside in the cytosol and can only translocate to the nucleus in the presence of dexamethasone (DEX), enabling the TF to regulate its downstream target genes (Corrado and Karali, 2009). In total 18 GOF lines were used of the following TFs: ERF-1 (AT4G17500), ERF2 (AT5G47220), ERF5 (AT5G47230), ERF6 (AT4G17490), ERF11 (AT1G28370), ERF8 (AT1G53170), ERF9 (AT5G44210), ERF59 (AT1G06160), ERF98 (AT3G23230), MYB51 (AT1G18570), STZ (AT1G27730), WRKY28 (AT4G18170), WRKY33 (AT2G38470), WRKY15 (AT2G23320), ZAT6 (AT5G04340), WRKY48 (AT5G49520), RAP2.6L (AT5G13330) and the control 35S::GFP-GR. To get an indication of which genes are direct or indirect targets of the induced TF, we performed a time-course experiment. All GOF lines were transferred at 15 DAS to DEX-containing medium and the third leaf was harvested at 1 h, 2 h, 4 h, 8 h and 24 h after transfer. The expression of 30 TFs (17 TFs listed above and WRKY6 (AT1G62300), WRKY30 (AT5G24110) and WRKY40 (AT1G80840), GA2OX6 (AT1G02400), GA20OX1 (AT4G25420), ACS6 (AT4G11280), MPK3 (AT3G45640), DEL1 (AT3G48160), UVI4 (AT2G42260), CYCA3;1 (AT5G43080), CYCB1;2 (AT5G06150), XET (AT1G10550), EXPA5 (AT3G29030)) was measured with nCounter Nanostring (Geiss et al, 2008). The time-course experiment gives an indication of whether a gene is putatively a direct, and thus induced during the early time points, or an indirect target of the induced TF.

2017-11-28 | E-MTAB-6209 | biostudies-arrayexpress

Multi-modal single-cell sequencing of differentiating mESCs using Smart-seq3 and scATAC-seq

Project description:We report dynamics of X-chromosome upregulation (XCU) along X-chromosome inactivation (XCI) in mESCs as they differentiate into EpiSCs. F1 hybrid C57BL6/J × CAST/EiJ male and female mESCs were grown in serum/LIF conditions were differentiated using Fgf2 and Activin A for 1, 2, 4 and 7 days to induce random XCI in female cells. Multi-modal single-cell sequencing was performed using scATAC on nuclei and Smart-seq3 to assay chromatin accessibility and poly-A+ RNA expression, respectively. Allelic resolution is achieved using strain-specific SNPs in the data. We reveal dynamic balancing of X alleles as cells undergo XCI to compensate dosage imbalances between sexes as well as between X and autosomes. Furthermore, we reveal that female naïve mESCs with two active X chromosomes lack XCU on both alleles which has major implications for reprogramming studies. Finally, we estimate allelic transcriptional burst kinetics from the data and find that progressively increased burst frequencies underlies the XCU process.

2022-02-14 | E-MTAB-10714 | biostudies-arrayexpress

Calibrating ChIP-seq with nucleosomal internal standards to measure histone modification density genome-wide

Project description:Despite serving as a central experimental technique in epigenetics research, chromatin immunoprecipitation (ChIP) suffers from several serious drawbacks: it is a relative measurement untethered to any external scale that obviates fair comparison amongst experiments; it employs antibody reagents that have differing affinity and specificity for target epitopes, which are in turn variable in abundance; and it is frequently not reproducible. To address these problems, we developed internal standard calibrated ChIP (ICeChIP), a method of spiking a native chromatin sample with nucleosomes reconstituted from recombinant and semisynthetic histones on barcoded DNA prior to immunoprecipitation. ICeChIP measures local histone modification densities on a biologically meaningful scale, enabling unbiased trans-experimental comparisons and revealing a correlation between the apparent symmetry of H3K4me3 in promoter nucleosomes and gene expression. Direct in situ assessment of immunoprecipitation accommodates for a number of experimental pitfalls, and provides a critical examination of untested assumptions inherent in conventional ChIP. Examination of spiked-in semi-synthetic nucleosomes in ICeChIP-seq experiments performed for HEK293, mESC E14 and DM S2 cell line

2015-05-07 | E-GEOD-60378 | biostudies-arrayexpress

A positive feedback loop between Atoh7 and a Notch effector regulates cell cycle progression and neurogenesis in retina

Project description:The microarray analysis was designed to test the effects of HES5.3 siRNAs, Atoh7 siRNAs and nt siRNAs on gene expression in embryonic chick retina.

2013-03-01 | E-MTAB-1430 | 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