Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Benchmark dataset relating to Kamrad et al "Interspecies interactions drive bacterial proteome reorganisation and emergent metabolism"

ABSTRACT: Three co-cultures containing gram-positive and -negative species at different ratios (1:1 to 1:9) were measured in quadruplicates, as well as the same number of corresponding mono-cultures. To isolate LC-MS matrix effects in the absence of biological proteome changes, we mixed mono-culture samples in the same ratio (co-measurement controls). Additionally, we mixed mono-cultures in the same ratio before protein extraction (co-extraction controls) to detect potential artefacts introduced during sample preparation. The results of this experiment are shown in the Extended Data Fig. 1.

INSTRUMENT(S):

ORGANISM(S): Bacteroides Thetaiotaomicron Peptoclostridium Difficile (strain 630) (clostridium Difficile) Agathobacter Rectalis

SUBMITTER: Stephan Kamrad

LAB HEAD: Kiran R Patil

PROVIDER: PXD072524 | Pride | 2026-02-02

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20250919_PRO1_AN_003_30-0099_StephanKamradCoEx_P01_D05.d.Zip	Other
	20250919_PRO1_AN_004_30-0099_StephanKamradCoEx_P01_H02.d.Zip	Other
	20250919_PRO1_AN_005_30-0099_StephanKamradCoEx_P01_C11.d.Zip	Other
	20250919_PRO1_AN_007_30-0099_StephanKamradCoEx_P01_F01.d.Zip	Other
	20250919_PRO1_AN_008_30-0099_StephanKamradCoEx_P01_B11.d.Zip	Other

Items per page:

1 - 5 of 49

Similar Datasets

Kamrad et al Interspecies interactions drive proteome reorganization and emergent metabolism in gut bacteria"

Project description:Inter-species interactions shape the function and dynamics of microbial communities. Yet, the understanding of how these interactions influence the molecular physiology of interacting species remains surprisingly limited. Here, we assembled 104 synthetic pairwise co-cultures of 15 diverse gut bacteria in vitro and examined responses using meta-proteomics and metabolomics. We detect a diversity of ecological interactions with an overall dominance of competition, amensalism and exploitation, yet with a circa 18% overall prevalence of positive interactions. The growth changes were accompanied by strong molecular changes, with typically more than 60% of the proteome of a species changing in response to at least one partner. We find that the magnitude of the proteome responses is influenced by proteome size, species abundance, and pH of the co-culture. Small-molecule transport and carbon metabolism are among the most responsive processes indicating pervasive metabolic interactions. Using metabolomics we identified likely cross-fed metabolites, emergent polyamine metabolism, and niche partitioning in amino acid utilization in co-cultures. Notably, many yet uncharacterized proteins were differentially abundant in co-cultures, suggesting a role of the ‘dark proteome’ in inter-species interactions. Clustering of these proteins with those with known biological function indicates an approach to leverage species interactions for functional genomics. Overall, our systematic approach demonstrates how bacterial interactions profoundly affect the physiology of participating cells, advancing our molecular understanding of ecological interactions.

2025-05-12 | PXD055395 | Pride

High-resolution proteomic analysis of medulloblastoma clinical samples identifies therapy resistant subgroups and MYC immunohistochemistry as a powerful outcome predictor

Project description:While international consensus and the 2021 WHO classification recognize multiple molecular medulloblastoma subgroups, these are difficult to identify in current clinical practice. As a result, biology driven risk stratification and therapy assignment for medulloblastoma constitutes a major challenge. Here, we report mass spectrometry analysis of clinical samples as a method for medulloblastoma subgroup discovery and identify MYC immunohistochemistry (IHC) as a clinically tractable method for improved risk stratification.

2025-03-06 | PXD051319 | Pride

Combining data independent acquisition with spike-in SILAC (DIA-SiS) improves proteome coverage and quantification )

Project description:Data Independent Acquisition (DIA) is increasingly preferred over Data Dependent Acquisition (DDA) due to its higher throughput and fewer missing values. Whereas DDA often utilizes stable isotope labeling to improve quantification, DIA mostly relies on label-free approaches. Efforts to integrate DIA with isotope labeling include chemical methods like mTRAQ and dimethyl labeling, which, while effective, complicate sample preparation. Stable isotope labeling by amino acids in cell culture (SILAC) achieves high labeling efficiency through the metabolic incorporation of heavy labels into proteins in vivo. However, the need for metabolic incorporation limits the direct use in clinical scenarios. Spike-in SILAC methods utilize an externally generated heavy sample as an internal reference, enabling SILAC-based quantification even for samples that cannot be directly labeled. Here, we combine DIA with spike-in SILAC (DIA-SiS), leveraging the robust quantification of SILAC without the complexities associated with chemical labeling. We developed and rigorously validated DIA-SiS through a mixed-species benchmark to assess its performance in proteome coverage and quantification. We demonstrate that DIA-SiS significantly improves proteome coverage and quantification compared to label-free approaches and reduces the incidence of incorrectly quantified proteins. Additionally, DIA-SiS proves effective in analyzing proteins in low-input formalin-fixed paraffin-embedded (FFPE) tissue sections. DIA-SiS combines the precision of stable isotope-based quantification with the simplicity of label-free sample preparation, facilitating simple, accurate and comprehensive proteome profiling.

2024-10-14 | PXD052080 | Pride

RNA-sequencing of Clostridioides difficile WT and luxS mutant both during mono-culture biofilms and co-culture biofilms with Bacteroides fragilis

Project description:5 conditions for RNA-sequencing: Mono-culture biofilms of C. difficile WT, C. difficile luxS mutant (insertional ClosTron mutant as described in DOI: 10.1128/JB.01980-12), B. fragilis (PRJEB29695), and co-cultures biofilms of C. difficile WT and luxS mutant with B. fragilis. These were used to compare differences between C. difficile WT and luxS during mono-culture biofilms, as well transcriptomic differences for both C. difficile and B. fragilis during co-culture.

2018-12-16 | E-MTAB-7523 | biostudies-arrayexpress

Transcriptome response of Salmonella enterica subsp. enterica serovar Typhimurium N-15 and Bifidobacterium thermophilum RBL67 in co-culture

Project description:Bifidobacterium thermophilum RBL67 (RBL67), a human fecal isolate and promising probiotic candidate, showed antagonistic and protective effects against Salmonella and Listeria in vitro. However, the underlying mechanisms fostering these health-related effects remain unknown. Therefor the transcriptome response of RBL67 and Salmonella enterica subsp. enterica serovar Typhimurium N-15 (N-15) in co-culture compared to the response in their respective mono-cultures. RNA was extracted from culture samples taken after 4 (N-15) or 5 h (RBL67) and RNAseq was performed on an Illumina HiSeq 2000 sequencer. Three biological replciates were performed resulting in 12 data sets: 3 RBL67 mono culture, 3 N15 mono-culture, 3 RBL67 co-culture, 3 N15 co-culture. Our study provided first insights into probiotic-pathogen interaction on transcriptional level and suggests a mechanism for how probiotic organisms can protect the host from infections. RNA was extracted from culture samples taken after 4 (N-15) or 5 h (RBL67) and RNAseq was performed on an Illumina HiSeq 2000 sequencer. Three biological replciates were performed resulting in 12 data sets: 3 RBL67 mono culture, 3 N15 mono-culture, 3 RBL67 co-culture, 3 N15 co-culture.

2015-03-31 | E-GEOD-65716 | biostudies-arrayexpress

H2AZ extended acidic patch is necessary for formation specialized chromatin states in ESCs [RNA-Seq]

Project description:The H2A variant H2AZ is essential for embryonic development and for proper execution of developmental gene expression programs in embryonic stem cells (ESCs). Divergent regions in H2AZ are likely key for its functional specialization, but we know little about how these differences contribute to chromatin regulation. Here, we show that the extended acidic patch, specifically the three divergent residues in the C-terminal docking domain, is necessary for lineage commitment during ESC differentiation and proper execution of gene expression programs during ESC differentiation. Surprisingly, disruption of the acidic patch domain has a distinct consequence on cellular specification compared to H2AZ depletion. This is consistent with differences in gene expression profiles of H2AZ M-bM-^@M-^Sdepleted and acidic patch (AP) mutant ESCs during early lineage commitment. Interestingly, the distinct consequence of AP mutant expression on gene regulation is coincidence with an altered destabilized chromatin state and high chromatin mobility dependent on active transcription. Collectively, our data shows that the divergent residues within the acidic patch domain are key structural determinants of H2AZ function and links chromatin structure and dynamics with gene regulation and cell fate specification. H2AZ extended acidic patch was mutated, or H2AZ was KD in mouse embryonic stem cells and RNA-Seq analysis was performed on the resulting cultures. Characterization of H2AZ-WT and -AP3-mutant binding specificities were performed by ChIP-Seq.

2013-09-23 | E-GEOD-40064 | biostudies-arrayexpress

Braveheart is a long non-coding RNA necessary for cardiac lineage commitment

Project description:Purpose: Long non-coding RNAs (lncRNAs) display development-specific gene expression patterns, yet we know little about their precise roles in lineage commitment. Here, we discover a novel mammalian heart-associated lncRNA, AK143260, necessary for cardiac lineage specification. Methods: Gene expression profiles of mouse ESCs and differentiated organs were analyzed for master regulators of lineage commitment. The AK143260 transcript was shown to be strongly expressed in mESCs and in cells undergoing cardiac differentiation. Its role in cardiac differentiation was examined using depletion and in vitro differentiation systems, with morphological and gene expression profiling at different time-points. Results: mESCs depleted of AK143260, named Braveheart, fail to differentiate into cardiomyocytes and to activate a core cardiac gene regulatory network including key transcription factors driving cardiogenesis. We show that Braveheart functions upstream of MesP1 (mesoderm posterior 1), a transcription factor critical for specification of the earliest known multi-potent cardiovascular progenitor and in promoting epithelial-mesenchymal transition (EMT). Consistent with this, Braveheart depletion leads to morphological defects and loss of cardiogenic potential in a defined in vitro cardiomyocyte differentiation system. Furthermore, Braveheart is necessary to maintain myocardial gene expression and myofibril organization in neonatal cardiomyocytes. Conclusions: These findings reveal that Braveheart is an important regulator of cardiac commitment and implicate lncRNAs as potential therapeutic targets for cardiac disease and regeneration. Gene expression profiles from control and Bravheart-depleted mESCs were obtained by RNA-Seq on an Illumina HiSeq2000 instruments at Days 0,3,6 and 9. Gene expression profiles from mESCs, MEFs, partially reprogrammed MEFs and miPS cells were obtained by RNA-Seq on Illumina GAII/GAIIx instruments.

2013-01-30 | E-GEOD-39656 | biostudies-arrayexpress

Genome-wide analysis of sperm DNA methylation from monozygotic twin bulls

Project description:Epigenetics (DNA methylation) profiling of sperm from Monozygotic (MZ) twin bull brothers comparing with each other Two-condition experiment, DNA methylation analysis of sperm from Monozygotic twin bull brothers which were hybridized as dye-swap in two-color arrays in a dye-balanced design.

2015-12-31 | E-GEOD-74200 | biostudies-arrayexpress

Identification of transcripts regulated by CEBPA protein and its P30 isoform in K562

Project description:To investigate the effect of CEBPA and its mutant isoform P30 on the expression of mRNAs and long non-coding RNAs (lncRNAs), we utilized the K562 AML cell line carrying a stable and Tet-on inducible CEBPA or P30 allele. Based on the expression of known CEBPA transcriptional targets, we selected RNA extracted from 48 hours of induction (CEBPA or P30) together with RNA extracted from control-induced cells (CTR). 2 biological replicates for each sample have been utilized.

2015-06-10 | E-GEOD-65235 | biostudies-arrayexpress

Latent infection of an active giant endogenous virus in a unicellular green alga

Project description:Latency is a common strategy in a wide range of viral lineages, but its prevalence in giant viruses remains unknown. Here we describe the activity and viral production from a 617 kbp integrated giant viral element in the model green alga Chlamydomonas reinhardtii. We resolve the integrated viral region using long-read sequencing and show that viral particles are produced and released in otherwise healthy cultures. A diverse array of viral-encoded selfish genetic elements are expressed during GEVE reactivation and produce proteins that are packaged in virions. In addition, we show that field isolates of Chlamydomonas sp. harbor latent giant viruses related to the C. reinhardtii GEVE that exhibit similar infection dynamics, demonstrating that giant virus latency is prevalent in natural host communities. Our work reports the largest temperate virus documented to date and the first active GEVE identified in a unicellular eukaryote, substantially expanding the known limits of viral latency.

2025-06-16 | PXD060118 | Pride