ABSTRACT: MADLI MS imaging dataset of developing maize root tips grown in 13C or unlabeled glucose. Manuscript is being submitted and the citation will be made once it is published.
Project description:This dataset is part of a study aimed at developing algorithms for the quantification of stable isotope content in microorganisms after labeling them with stable isotope-labeled substrates. In this dataset Escherichia coli cultures were labeled with different percentages (1% or 10%) of either single-carbon 13C glucose (13C2) or fully-labeled 13C glucose (13C1-6). Labeled cells were subsequently mixed with unlabeled E. coli cells in fixed ratios (50%, 90%, 95%, 99%). Cultures of E. coli were grown in M9 minimal medium in which a percentage of the glucose was replaced with 13C2 or 13C1-6 glucose for >10 generations to achieve close to complete labeling of cells. Triplicate cultures were grown for each percentage. Please note that the unlabeled glucose that was used of course had a natural content of 13C of around 1.1%, thus the 0% added label samples have an actual 13C content of 1.1% and all added label is on top of this value. We included a tab delimited table with this submission providing details on all raw files.
Project description:This dataset is part of a study aimed at developing algorithms for the quantification of stable isotope content in microorganisms in microbial communities after labeling them with stable isotope-labeled substrates. For this dataset Escherichia coli cultures were labeled with different percentages (1, 5 and 10%) of fully labeled 13C glucose (13C1-6) and spiked-in into a mock microbial community consisting of 32 species of bacteria, archaea, eukaryote and bacteriophages (UNEVEN Community described in Kleiner et al. 2017 Nat Communications 8(1):1558). The community also contained unlabeled E. coli cells and labeled/unlabeled E. coli cells in the spike-in sample were at a 1:1 ratio. Cultures of E. coli were grown in M9 minimal medium in which a percentage of the glucose was replaced with 13C1-6 glucose for >10 generations to achieve close to complete labeling of cells. The following percentages of 13C1-6 glucose were added 1, 5 and 10%. Triplicate cultures were grown for each percentage. Please note that the unlabeled glucose that was used of course had a natural content of 13C of around 1.1%, thus the 0% added label samples have an actual 13C content of 1.1% and all added label is on top of this value. We included a tab delimited table with this submission providing details on all raw files.
Project description:Ethanolic extracts of unlabeled and fully 13C labeled yeast (Pichia pastoris) and mixtures thereof were measured on HILIC and C18 (Dual injection system with HILIC eluting until 15 min and RPC after 15 min).
Project description:The root system is fundamental for maize growth and yield. The primary root system is the most important structure of maize seedlings and is the first organ that emerges at germination, providing water and nutrients for the growing seedlings. However, it is difficult to characterize them at single cell level, due to their complex and heterogeneous cell types. In this study, we profiled the transcriptomes of more than 7000 cells derived from maize root tips of seedlings grown on media with (nitrate+) or without nitrate (nitrate-).
Project description:Ethanolic extracts of unlabeled and fully 13C labeled yeast (Pichia pastoris) and mixtures thereof were measured on HILIC and C18 (Dual injection system with HILIC eluting until 15 min and RPC after 15 min).
Project description:This dataset is part of a study aimed at developing algorithms for the quantification of stable isotope content in microorganisms after labeling them with stable isotope-labeled substrates. In this dataset Escherichia coli and Bacillus subtilis cultures were labeled with different percentages of fully labeled 13C glucose (13C6). Cultures of B. subtilis and E. coli were grown in Bacillus minimal medium or M9 minimal medium (E. coli) in which a percentage of the glucose was replaced with 13C6 glucose for >10 generations to achieve close to complete labeling of cells. The following percentages of 13C6 glucose were added 0, 0.01, 0.025, 0.1, 0.25, 1, 5 and 10%. Triplicate cultures were grown for each percentage. Please note that the unlabeled glucose that was used of course had a natural content of 13C of around 1.1%, thus the 0% added label samples have an actual 13C content of 1.1% and all added label is on top of this value. We included a tab delimited table with this submission providing details on all raw files.
Project description:In this study, we monitored glycolysis in mouse lymphoma and lung tumors by measuring the conversion of hyperpolarized [U-2H, U-13C]glucose to lactate using 13C magnetic resonance spectroscopy and spectroscopic imaging. We observed labeled lactate only in tumors and not in surrounding normal tissue or other tissues in the body and found that it was markedly decreased at 24 h after treatment with a chemotherapeutic drug. We also detected an increase in a resonance assigned to 6-phosphogluconate in the pentose phosphate pathway. This technique could provide a new way of detecting early evidence of tumor treatment response in the clinic and of monitoring tumor pentose phosphate pathway activity.
Project description:Higher 13C-lactate labeling was seen in the more aggressive tumors, including all triple negative breast cancers. There was a significant correlation between lactate labeling and expression of the monocarboxylate transporter (MCT1), which mediates tumor cell pyruvate uptake, and a weaker correlation with expression of LDHA, which catalyzes label exchange between the injected pyruvate and the endogenous lactate pool.