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Application of spectral library prediction for parallel reaction monitoring of viral peptides_PRM_data
<p><strong>Project description: </strong></p> <p>A major part of the analysis of parallel reaction monitoring (PRM) data is the comparison of observed fragment ion intensities to a library spectrum. Classically, these libraries are generated by data-dependent acquisition (DDA). Here we test Prosit, a published deep neural network algorithm, for its applicability in predicting spectral libraries for PRM. For this purpose, we targeted 1,529 precursors derived from synthetic viral peptides and analyzed the data with Prosit and DDA-derived libraries. Additionally, we used a spectral library predicted by Prosit and a DDA library to identify SARS-CoV-2 peptides from a simulated oropharyngeal swab.</p> <p> </p> <p><strong>Sample processing protocol:</strong></p> <p>A total of 1,569 crude synthetic viral peptides were ordered in six pools from JPT (Berlin, Germany). Synthetic peptides were separated on a 200 cm μPAC™ column (PharmaFluidics) by using an EASY-nLC1200 system (Thermo Fisher Scientific) equipped with a μPAC™ trapping column (PharmaFluidics). The flow rate was set to 300 nL/min and a stepped linear 160 min gradient was applied: 3-10% B in 22 min, 10-33%B in 95 min, 33-49% B in 23 min, 49-80% B in 10 min and 80% B for 10 min. Solvent A was 0.1% (v/v) formic acid (FA) in water, solvent B consisted of 80% (v/v) acetonitrile in 0.1% (v/v) FA. The column temperature was set to 50 °C. The Q Exactive Plus (Thermo Fisher Scientific) operated in Full MS/dd-MS2 or unscheduled PRM mode. For MS/dd-MS2 the following parameters were used. MS1 resolution was 70.000 with an AGC target of 3x10<sup>6</sup>, max. injection time of 20 ms and a scan range of 300-1650 m/z. MS2 resolution was 17.500 with an AGC target of 10<sup>5</sup>, max. injection time of 50 ms and an isolation window of 2 m/z. The analysis parameters in PRM mode were set as follows. MS1 parameters were identical to DDA. MS2 resolution was 17.500 with an AGC target of 10<sup>6</sup>, max. injection time of 55 ms and an isolation window of 1.4 m/z.</p> <p>Potential SARS-CoV-2 target peptides belonging to the N protein were identified by DDA of SARS-CoV-2 infected Calu-3 cells. Peptides were diluted in 0.1% TFA (0.2 µg/µL) and 5 µL were separated on a 50 cm μPAC™ column (PharmaFluidics) using an EASY-nLC1200 system (Thermo Fisher Scientific). The flow rate was set to 800 nL/min and a stepped 30 min gradient was applied: 6-11% B in 2:58 min, 11-30% B in 17:10 min, 30-35% B in 2:41 min, 35-47% B in 3:11 min, 47-80% B for 0:10 min, 80% B for 1:50 min, 80-0% B in 0:10 min and 100% A for 1:50 min. Solvent A was 0.1% (v/v) formic acid (FA) in water, solvent B consisted of 80% (v/v) acetonitrile in 0.1% (v/v) FA. The column temperature was set to 50 °C. The Q Exactive HF (Thermo Fisher Scientific) operated in Full MS/dd-MS2 (Top20) using the following parameters. MS1 resolution was 60.000 with an AGC target of 3x10<sup>6</sup>, max. injection time of 20 ms and a scan range of 300-1650 m/z. MS2 resolution was 17.500 with an AGC target of 10<sup>5</sup>, max. injection time of 50 ms and an isolation window of 2 m/z.</p> <p> </p> <p>To simulate a SARS-CoV-2 positive patient sample, we spiked cell-culture derived virus in a negative oropharyngeal swab and targeted the N protein by PRM. LC parameters were identical to DDA analysis of SARS-CoV-2 infected Calu-3 cells. The PRM parameters of the The Q Exactive HF (Thermo Fisher Scientific) were set as follows. MS1 parameters were identical to DDA. MS2 resolution was 45.000 with an AGC target of 10<sup>6</sup>, max. injection time of 100 ms and an isolation window of 1.4 m/z.</p> <p> </p> <p> </p> <p><strong>Data processing protocol:</strong></p> <p>DDA Raw files were searched with MaxQuant against the respective virus database (UniProt) with a peptide FDR of 1%. Detailed MaxQuant parameters can be found in the parameters.txt files of the according results. MaxQuant .msms output files were used to generate spectral libraries with BiblioSpec implemented in the Skyline environment using a cut-off score of 0.95. Peptide identification of PRM runs was done in Skyline using the top 6 fragment ions of the DDA spectral library or according Prosit derived library (Prosit_2020_intensity_model).</p>
Supporting dataset of the reaction zones and marbles in the Mogok metamorphic belt
<p>The datasets include six tables. These tables include the information on the sample description, compositions of whole rocks and minerals, U-Th-Pb isotope data of baddeleyite and zircon, and mass-transfer calculation results for polycrystalline mineral reaction zones (PMRZs) in dolomite marbles from the Mogok metamorphic belt, Myanmar. The whole-rock compositions were determined by XRF and ICP-MS. The major elements of minerals were analyzed by EPMA, whereas the trace elements of minerals were analyzed by LA-ICP-MS. The U-Th-Pb isotope data were measured by SIMS.</p>
Solid state polymerization as a vitrimerization tool starting from available thermoplastics: the effect of reaction temperature
<p>Supplementary file</p>
Evaluation of rice landraces for brown planthopper resistance based on phenotypic reactions and biochemical attributes [DataSet]
<p>Data set for the publication: Evaluation of rice landraces for brown planthopper resistance based on phenotypic reactions and biochemical attributes</p>
Quinoline conjugated imidazopyridine and pyridopyrimidine synthesis in water as highly selective fluoride sensors via a catalyst-free four-component reaction
<p>Abstract</p> <p>A green and convenient procedure for the synthesis of quinoline-conjugated imidazopyridines and pyridopyrimidines has been developed by a simple one-pot reaction in the absence of any transition metal catalyst in water. This green process can be readily performed by reacting inexpensive starting materials of 2-chloroquinoline-3-carbaldehyde, malononitrile, 1,1-bis(methylthio)-2-nitroethylene, and diamine in aqueous solution. The present synthesis shows attractive characteristics, such as the use of water as reaction media, convenient one-pot operation, and reduced waste production without the use of any base or metal promoters. The products are purified by crystallization from ethanol, and the process does not involve any hazardous solvent. Also, the fluorescence study of these conjugated systems was also considered, which revealed that they have highly selective sensing of fluoride.</p>
The synthesis of SBA-Pr-3AP@Pd and its application as a highly dynamic, eco-friendly heterogeneous catalyst for Suzuki–Miyaura cross-coupling reaction
<p>The hexagonal mesoporous organic–inorganic hybrid as a new nanocatalyst was prepared by the treatment of SBA-15 with (3-chloropropyl)triethoxysilane, the 2,4,6-triamino pyrimidine ligand, and then PdCl2 to obtain the SBA-15-propyl-triamino pyrimidine@Pd called as SBA-Pr-3AP@Pd, which was examined through Suzuki–Miyaura cross-coupling reaction by several aryl halides and phenylboronic acid under mild conditions in high yield.</p>
Data from: Plasma assisted CO2 methanation: effects on the low-temperature activity of a Ni-Ce catalyst and reaction performance
Ni-Ce three-dimensional material with macropore diameter of 146.6±8.4 nm were synthesized and used for methanation catalyst. Firstly, H2-reduction of catalyst was conducted in thermal fixed bed and plasma reactor respectively, then X-ray diffraction (XRD) and CO2 Temperature Programmed Desorption (TPD) experiments on the two reduced samples were carried out to reveal the plasma effect on catalyst's physicochemical properties. It was found that plasma reduction created more abundant basic sites for CO2 adsorption, especially the medium basic sites were even doubled compared with the thermal reduced catalysts. The plasma reduced catalyst exhibited excellent low-temperature activity, ca. 50~60 oC lower than the thermal catalyst (the maximum CO2 conversion point). Based on the optimum reduced catalyst, plasma effect in the reactor level was further investigated under high gas hour space velocity (GHSV) ~50000 h-1. The plasma reactor showed higher CO2 conversion capacity and efficiency than the thermal reactor.
Data from: Within-family parent-offspring co-adaptation in a wild bird: on static traits, behavioural reaction norms and sex differences
Parental care, a central component of reproduction in a wide range of animal species, often involves elaborate behavioural interactions between parents and their offspring. Due to the reciprocal nature of these interactions, it has been hypothesized that parental and offspring behaviours (e.g. parental food provisioning and offspring begging) are not only target but also agent of selection. These traits are therefore expected to co-evolve, ultimately leading to co-adaptation of parent and offspring behaviours within families. However, empirical data on such parent-offspring co-adaptation are limited, particularly for wild populations. Furthermore, mean levels of behaviour (as measured in previous studies) may not adequately describe the dynamic nature of the reciprocal interplay between parents and their offspring, and instead rather the behavioural reaction norms for provisioning and begging may be co-adapted. We applied a large-scale cross-fostering study over 3 consecutive breeding seasons to investigate whether provisioning behaviour of wild blue tit (Cyanistes caeruleus) parents co-varies with the begging behaviour of their genetic, cross-fostered offspring. We simultaneously analysed parent and offspring behaviours, both as static traits (mean levels) and behavioural reaction norms (offspring begging as a function of food deprivation and parental provisioning as a function of short-term experimental changes in brood size). Neither maternal nor paternal provisioning rates co-varied with the begging intensity of their genetic offspring when analysed as mean levels of behaviour. However, the slopes of the reaction norms for provisioning and begging were negatively correlated between male, but not female, parents and their genetic offspring. Thus, fathers that change their provisioning rate strongly with brood size sire offspring whose level of begging only weakly increases with hunger, and vice versa. The observed co-variation suggests the existence of sex-specific optima for parent-offspring trait combinations. Thus, our study not only highlights the importance of a behavioural reaction norm approach when investigating parent-offspring interactions, but also stresses the relevance of considering parents as separate units, at least for biparental species.
Data from: Defining the alloreactive T cell repertoire using high-throughput sequencing of mixed lymphocyte reaction culture
The cellular immune response is the most important mediator of allograft rejection and is a major barrier to transplant tolerance. Delineation of the depth and breadth of the alloreactive T cell repertoire and subsequent application of the technology to the clinic may improve patient outcomes. As a first step toward this, we have used MLR and high-throughput sequencing to characterize the alloreactive T cell repertoire in healthy adults at baseline and 3 months later. Our results demonstrate that thousands of T cell clones proliferate in MLR, and that the alloreactive repertoire is dominated by relatively high-abundance T cell clones. This clonal make up is consistently reproducible across replicates and across a span of three months. These results indicate that our technology is sensitive and that the alloreactive TCR repertoire is broad and stable over time. We anticipate that application of this approach to track donor-reactive clones may positively impact clinical management of transplant patients.
Inferring quantity and qualities of superimposed reaction rates from single molecule survival time distributions
<div> <p>Actions of molecular species, for example binding of transcription factors to chromatin, may comprise several superimposed reaction pathways. The number and the rate constants of such superimposed reactions can in principle be resolved by inverse Laplace transformation of the corresponding distribution of reaction lifetimes. However, current approaches to solve this transformation are challenged by photobleaching-prone fluorescence measurements of lifetime distributions. Here, we present a genuine rate identification method (GRID), which infers the quantity, rates and amplitudes of dissociation processes from fluorescence lifetime distributions using a dense grid of possible decay rates. In contrast to common multi-exponential analysis of lifetime distributions, GRID is able to distinguish between broad and narrow clusters of decay rates. We validate GRID by simulations and apply it to CDX2-chromatin interactions measured by live cell single molecule fluorescence microscopy. GRID reveals well-separated narrow decay rate clusters of CDX2, in part overlooked by multi-exponential analysis. We discuss the amplitudes of the decay rate spectrum in terms of frequency of observed events and occupation probability of reaction states. We further demonstrate that a narrow decay rate cluster is compatible with a common model of TF sliding on DNA.</p> </div>
Data from: Green approach for synthesis of bioactive Hantzsch 1,4-dihydropyridine derivatives based on thiophene moiety via multicomponent reaction
A novel green and efficient one-pot multicomponent reaction of dihydropyridine derivatives was reported as having good to excellent yield. In the presence of the catalyst ceric ammonium nitrate (CAN), different 1,3-diones and same starting materials as 5-bromothiophene-2-carboxaldehyde and ammonium acetate were used at room temperature under solvent-free condition for the Hantzsch pyridine synthesis within a short period of time. All compounds were evaluated for their in vitro antibacterial and antifungal activity and, interestingly, we found that 5(b–f) show excellent activity compared with Ampicillin, whereas only the 5e compound shows excellent antifungal activity against Candida albicans compared with griseofulvin. The cytotoxicity of all compounds has been assessed against breast tumour cell lines (BT-549), but no activity was found. The X-ray structure of one such compound, 5a, viewed as a colourless block crystal, corresponded accurately to a primitive monoclinic cell.
Data from: Mathematical modelling of the vitamin C clock reaction
Chemical clock reactions are characterised by a relatively long induction period followed by a rapid `switchover' during which the concentration of a \emph{clock chemical} rises rapidly. In addition to their interest in chemistry education, these reactions are relevant to industrial and biochemical applications. A substrate-depletive, non-autocatalytic clock reaction involving household chemicals (vitamin C, iodine, hydrogen peroxide and starch) is modelled mathematically via a system of nonlinear ordinary differential equations. Following dimensional analysis the model is analysed in the phase plane and via matched asymptotic expansions. Asymptotic approximations are found to agree closely with numerical solutions in the appropriate time regions. Asymptotic analysis also yields an approximate formula for the dependence of switchover time on initial concentrations and the rate of the slow reaction. This formula is tested via `kitchen sink chemistry' experiments, and is found to enable a good fit to experimental series varying in initial concentrations of both iodine and vitamin C. The vitamin C clock reaction provides an accessible model system for mathematical chemistry.
Data from: Distal-less activates butterfly eyespots consistent with a reaction diffusion process
Eyespots on the wings of nymphalid butterflies represent colorful examples of pattern formation, yet the developmental origins and mechanisms underlying eyespot center differentiation are still poorly understood. Using CRISPR-Cas9 we re-examine the function of Distal-less (Dll) as an activator or repressor of eyespots, a topic that remains controversial. We show that the phenotypic outcome of CRISPR mutations depends upon which specific exon is targeted. In Bicyclus anynana, exon 2 mutations are associated with both missing and ectopic eyespots and also exon-skipping. Exon 3 mutations, which do not lead to exon-skipping, produce only null phenotypes including missing eyespots, lighter wing coloration and loss of scales. Reaction-diffusion modeling of Dll function, using Wnt and Dpp as candidate morphogens, accurately replicates these complex crispant phenotypes. These results provide new insight into the function of Dll as a potential activator of eyespot development, scale growth, and melanization, and suggest that the tuning of Dll expression levels can generate a diversity of eyespot phenotypes, including their appearance on the wing.
Data from: Experimental evolution for generalists and specialists reveals multivariate genetic constraints on thermal reaction norms
Theory predicts the emergence of generalists in variable environments and antagonistic pleiotropy to favour specialists in constant environments, but empirical data seldom support such generalist–specialist trade-offs. We selected for generalists and specialists in the dung fly Sepsis punctum (Diptera: Sepsidae) under conditions that we predicted would reveal antagonistic pleiotropy and multivariate trade-offs underlying thermal reaction norms for juvenile development. We performed replicated laboratory evolution using four treatments: adaptation at a hot (31 °C) or a cold (15 °C) temperature, or under regimes fluctuating between these temperatures, either within or between generations. After 20 generations, we assessed parental effects and genetic responses of thermal reaction norms for three correlated life-history traits: size at maturity, juvenile growth rate and juvenile survival. We find evidence for antagonistic pleiotropy for performance at hot and cold temperatures, and a temperature-mediated trade-off between juvenile survival and size at maturity, suggesting that trade-offs associated with environmental tolerance can arise via intensified evolutionary compromises between genetically correlated traits. However, despite this antagonistic pleiotropy, we found no support for the evolution of increased thermal tolerance breadth at the expense of reduced maximal performance, suggesting low genetic variance in the generalist–specialist dimension.
Data from: Variation in continuous reaction norms: quantifying directions of biological interest
Thermal performance curves are an example of continuous reaction norm curves of common shape. Three modes of variation in these curves-- Vertical shift, horizontal shift, and generalist-specialist tradeoffs-- are of special interest to evolutionary biologists. Since two of these modes are nonlinear, traditional methods such as Principal Component Analysis fail to decompose the variation into biological modes and to quantify the variation associated with each mode. Here we present the results of a new method, Template Mode of Variation (TMV), that decomposes the variation into predetermined modes of variation for a particular set of thermal performance curves. We illustrate the method using data on thermal sensitivity of growth rate in Pieris rapae caterpillars. The TMV model explains 67% of the variation in thermal performance curves among families; generalist-specialist tradeoffs account for 38% of the total between-family variation. The TMV method implemented here is applicable to both differences in mean and patterns of variation, and can be used with either phenotypic or quantitative genetic data for thermal performance curves or other continuous reaction norms that have a template shape with a single maximum. The TMV approach may also apply to growth trajectories, age-specific life history traits and other function-valued traits.
Data from: Smooth enlargement of human standing sway by instability due to weak reaction floor and noise
Human quiet standing is accompanied by body sway. The amplitude of this body sway is known to be larger than would be predicted from simple noise effects, and sway characteristics are changed by neurological disorders. This large sway is thought to arise from nonlinear control with prolonged periods of no control (intermittent control), and a nonlinear control system of this kind has been predicted to exhibit bifurcation. The presence of stability-dependent transition enables dynamic reaction that depends on the stability of the environment, and can explain the change in sway characteristics that accompanies some neurological disorders. This research analyses the characteristics of a system model that induces transition, and discusses whether human standing reflects such a mechanism. In mathematical analysis of system models, (intermittent control-like) nonlinear control with integral control is shown to exhibit Hopf bifurcation. Moreover, from the analytical solution of the system model with noise, noise is shown to work to smooth the enlargement of sway around the bifurcation point. This solution is compared with measured human standing sway on floors with different stabilities. By quantitatively comparing the control parameters between human observation and model prediction, enlargement of sway is shown to appear as predicted by the model analysis.
Data from: Evolutionary change in continuous reaction norms
Understanding the evolution of reaction norms remains a major challenge in ecology and evolution. Investigating evolutionary divergence in reaction norm shapes between populations and closely related species is one approach to provide insights. Here we use a meta-analytic approach to compare divergence in reaction norms of closely related species or populations of animals and plants, across types of traits and environments. We quantified mean-standardized differences in overall trait means (Offset) and reaction norm shape (including both Slope and Curvature). These analyses revealed that differences in shape (Slope and Curvature together) were generally greater than differences in Offset. Additionally, differences in Curvature were generally greater than differences in Slope. The type of taxon contrast (species vs. population), trait, organism, and the type and novelty of environments all contributed to the best fitting models, especially for Offset, Curvature and the total differences (Total) between reaction norms. Congeneric species had greater differences in reaction norms than populations, and novel environmental conditions increased the differences in reaction norms between populations or species. These results show that evolutionary divergence of curvature is common and should be considered an important aspect of plasticity together with slope. Biological details about traits and environments, including cryptic variation expressed in novel environmental conditions, may be critical to understanding how reaction norms may evolve in novel and rapidly changing environments.
Data from: Variation in thermal performance and reaction norms among populations of Drosophila melanogaster
The major goal of evolutionary thermal biology is to understand how variation in temperature shapes phenotypic evolution. Comparing thermal reaction norms among populations from different thermal environments allows us to gain insights into the evolutionary mechanisms underlying thermal adaptation. Here, we have examined thermal adaptation in six wild populations of the fruit fly (Drosophila melanogaster) from markedly different natural environments by analyzing thermal reaction norms for fecundity, thorax length, wing area and ovariole number under ecologically realistic fluctuating temperature regimes in the laboratory. Contrary to expectation, we found only minor differences in the thermal optima for fecundity among populations. Differentiation among populations was mainly due to differences in absolute (and partly also relative) thermal fecundity performance. Despite significant variation among populations in the absolute values of morphological traits, we observed only minor differentiation in their reaction norms. Overall, the thermal reaction norms for all traits examined were remarkably similar among different populations. Our results therefore suggest that thermal adaptation in D. melanogaster predominantly involves evolutionary changes in absolute trait values rather than in aspects of thermal reaction norms.
Data from: Dispersal propensity in Tetrahymena thermophila ciliates – a reaction norm perspective
Dispersal and phenotypic plasticity are two main ways for species to deal with rapid changes of their environments. Understanding how genotypes (G), environments (E) and their interaction (genotype and environment; G x E) each affects dispersal propensity is therefore instrumental for predicting the ecological and evolutionary responses of species under global change. Here we used an actively dispersing ciliate to quantify the contributions of G, E, and G x E on dispersal propensity, exposing 44 different genotypes to three different environmental contexts (densities in isogenotype populations). Moreover, we assessed the condition-dependence of dispersal, i.e. whether dispersal is related to morphological, physiological or behavioral traits. We found that genotypes showed marked differences in dispersal propensity and that dispersal is plastically adjusted to density, with the overall trend for genotypes to exhibit negative density-dependent dispersal. A small, but significant G x E interaction indicates genetic variability in plasticity and therefore some potential for dispersal plasticity to evolve. We also show evidence consistent with condition-dependent dispersal suggesting that genotypes also vary in how individual condition is linked to dispersal under different environmental contexts thereby generating complex dispersal behavior due to only three variables (genes, environment, and individual condition).
Synchronized reagent delivery in double emulsions for triggering chemical reactions and gene expression
<p>Data underlying the figures in the publication “Synchronized reagent delivery in double emulsions for triggering chemical reactions and gene expression”, published in Small Methods.</p> <p>Table of contents:</p> <p>1. Figure 2C; Origin file containing all data and analysis for Figure 2C. Requires Origin Software to open.</p> <p>2. Figure 3; FlowJo Workspace for data analysis and fcs raw data acquired from flow cytometer for Figure 3B and 3C. Requires FlowJo software to open.</p> <p>Raw data file names:</p> <p>200721 FDG in PVA after prod_FDG sample 6_006.fcs</p> <p>200721 FDG in PVA&SDS 4 h after prod_FDG sample 4 PVA shake_002.fcs</p> <p>200721 FDG in PVA&SDS 4 h after prod_FDG sample 4 SDS 001 shake_004.fcs</p> <p>200721 FDG in PVA&SDS 22 h after prod_FDG sample 4 PVA shake_002.fcs</p> <p>200721 FDG in PVA&SDS 22 h after prod_FDG sample 4 SDS 001 shake_004.fcs</p> <p>3. Figure 4BC; Origin file containing all data and analysis for Figure 4B and 4C. Requires Origin Software to open.</p> <p>4. Figure 5; Origin file containing all data and analysis for Figure 5D. Requires Origin Software to open.</p> <p>File Figure 5_201215-new LUVs 500 mM DH5alpha: FlowJo Workspace for data analysis and fcs raw data acquired from flow cytometer for Figure 5B. Requires FlowJo software to open.</p> <p>Raw data file names:</p> <p>201215-new LUVs 500 mM-DH5alpha_sample 1 18h after prod_012.fcs</p> <p>201215-new LUVs 500 mM-DH5alpha_sample 3 18h after prod- 05%SDS_018.fcs</p> <p>5. Figure S2; PDF files, report from DLS instrument.</p> <p>6. Figure S4; Excel file containing the values extracted from microscopy images for Figure S4.</p> <p>7. Figure S5; FlowJo Workspace for data analysis and fcs raw data acquired from flow cytometer for Figure S5. Requires FlowJo software to open.</p> <p>Raw data file names:</p> <p>200721 FDG in PVA after prod_FDG sample 6_006.fcs</p> <p>200721 FDG in PVA&SDS 4 h after prod_FDG sample 4 SDS 001 shake_004.fcs</p> <p>200721 FDG in PVA&SDS 4 h after prod_FDG sample 5 SDS 01 shake_008.fcs</p> <p>200721 FDG in PVA&SDS 4 h after prod_FDG sample 6 SDS 0001 shake_006.fcs</p> <p>200721 FDG in PVA&SDS 22 h after prod_FDG sample 4 SDS 001 shake_004.fcs</p> <p>200721 FDG in PVA&SDS 22 h after prod_FDG sample 5 SDS 01 shake_008.fcs</p> <p>200721 FDG in PVA&SDS 22 h after prod_FDG sample 6 SDS 0001 shake_006.fcs</p> <p>8. Figure S6; Origin file containing all data and analysis for Figure S6 left-Requires Origin Software to open-, and Excel file containing the values from 96 well plate measurements used for Figure S6 right.</p> <p>9. Figure S7; Excel files containing the values from 96 well plate measurements used for Figure S7 left, and the values extracted from microscopy images for Figure S7 right.</p> <p>10. Figure S9; FlowJo Workspace for data analysis and fcs raw data acquired from flow cytometer for Figure S9. Requires FlowJo software to open.</p> <p>Raw data file names:</p> <p>201215-new LUVs 500 mM-DH5alpha_sample 1 3h30min after prod_005.fcs</p> <p>201215-new LUVs 500 mM-DH5alpha_sample 1 18h after prod_012.fcs</p> <p>201215-new LUVs 500 mM-DH5alpha_sample 1 30min after prod_001.fcs</p> <p>201215-new LUVs 500 mM-DH5alpha_sample 3 3h30min after prod - 05%SDS_008.fcs</p> <p>201215-new LUVs 500 mM-DH5alpha_sample 3 18h after prod- 05%SDS_018.fcs</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.