Find research datasets worth reusing

opencc-by-4.0Feb 2020View details →

Data from: Genetic admixture increases phenotypic diversity in the nectar yeast Metschnikowia reukaufii,

Raw data and supplementary files for the manuscript "Genetic admixture increases phenotypic diversity in the nectar yeast Metschnikowia reukaufii." ------------------- Table S5.xlsx -- Pairwise correlations between phenotypic traits of Metschnikowia reukaufii. Table S6.xlsx -- Detailed results obtained in tests of phylogenetic signal for different phenotypic traits and indices of overall performance of Metschnikowia reukaufii. Table S7.xlsx -- Detailed model fitting results obtained for phenotypic traits and indices of overall performance of Metschnikowia reukaufii. mronlyvcf-renamed.vcf -- High coverage SNPs obtained from whole genome mapping of 73 Metschnikowia reukaufii strains to diploid reference (mean coverage = 47.9×, range 23 – 116×). MR_phenotypes.xlsx -- Phenotypic data obtained for 73 Metschnikowia reukaufii strains.

opencc-by-4.0May 2022View details →

Data for "Highly-Automated, High-Throughput Replication of Yeast-based Logic Circuit Design Assessments"

Flow Cytometry and plate reader data from "High Throughput Experimentation to replicate Yeast Gates Experiment," accompanied with jupyter noteboooks to replicate the analyses.  Sequencing data is <a href="https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA784977">available separately</a>. Files named <code>flow_cytometryax</code> should be concatenated: they are individual slices of a gzipped tar file. Concatenate them and then extract with <code>tar xzf filename</code>. The paper is available on <a href="https://biorxiv.org/cgi/content/short/2022.05.31.493627">Biorxiv</a>. The Jupyter notebooks used to analyze this data for the paper are <a href="https://github.com/rpgoldman/replication-paper-data-analysis">available on GitHub</a>.

opencc-by-4.0Jul 2018View details →

Metabolome and proteome dataset from yeast kinase knock-outs

The dataset comprised of processed data produced in Zelezniak at al, Cell Systems 2018 study, please see README.txt for the detailed description of files.

opencc-by-sa-4.0Aug 2017View details →

The molecular architecture of the yeast spindle pole body core determined by Bayesian integrative modeling

This repository pertains to the molecular architecture of the yeast spindle pole body (SPB), the structural and functional equivalent of the metazoan centrosome. Data from in vivo FRET and yeast two-hybrid, along with SAXS, X-ray crystallography, and electron microscopy were integrated by a Bayesian structure modeling approach. For more information about how to reproduce this modeling, see the <a href="https://salilab.org/spb/">Sali lab website</a> or the README file.

opencc-by-4.0Oct 2024View details →

The ScRAP yeast reference pangenome graphs

The yeast reference pangenome graphs deposited here are constructed by <a href="https://www.evomicslab.org/">Evomics Lab</a> using the high-quality genome assemblies of globally-sampled Saccharomyces cerevisiae strains described in both the original S. cerevisiae Reference Assembly Panel (ScRAP; See <a title="O&rsquo;Donnell et al. Nature Genetics, 2023" href="https://www.nature.com/articles/s41588-023-01459-y" target="_blank" rel="noopener">O’Donnell et al. Nature Genetics, 2023</a>) and its future extensions.  The detailed construction specification for each graphs are described below: 1) ScRAP_v20230121_163asm.minigraph.gfa This graph was built upon 163 yeast genome assemblies from 142 strains. Briefly, we took the S. cerevisiae reference genome (denoted as 'SGDref') retrieved from the Saccharomyces genome database (SGD) as well as 162 assemblies from our recently released S. cerevisiae Reference Assembly Panel (ScRAP; See <a title="O&rsquo;Donnell et al. Nature Genetics, 2023" href="https://www.nature.com/articles/s41588-023-01459-y" target="_blank" rel="noopener">O’Donnell et al. Nature Genetics, 2023</a>) to construct reference pangenome graph by using <a href="https://github.com/lh3/minigraph">minigraph</a> with the command ‘minigraph -cxggs -l 5000’. With the SGDref as the reference genome, we incrementally added those 162 assemblies of other S. cerevisiae strains into the graph according to their phylogenetic distances to SGDref. We further mapped each input assembly to the graph by minigraph with the command ‘minigraph -cxasm’ to calculate the corresponding mapping depth.

opencc-by-4.0May 2024View details →

Design of a new model yeast consortium for ecological studies of enological fermentation

Dataset describing the characterization of a new 6-species yeast consortium representative of wine yeast diversity, as well as its application as proof-of-concept to explore the diversity-functionnality relationship in microbial community. It includes the data, scripts, figures, tables, and additional informations pertaining to the article "Design of a new model yeast consortium for ecological studies of enological fermentation" to be submitted.

opencc-by-4.0Aug 2021View details →

Data for: Sequential infection of Daphnia magna by a gut microsporidium followed by a haemolymph yeast decreases transmission of both parasites

This dataset supports the findings presented in: Manzi, F., Halle, S., Seemann, L., Ben-Ami, F., & Wolinska, J. (2021). Sequential infection of Daphnia magna by a gut microsporidium followed by a haemolymph yeast decreases transmission of both parasites. Parasitology, 1-42. doi:10.1017/S0031182021001384

opencc-by-4.0Nov 2022View details →

Anti-inflammatory compounds in probiotic yeast revealed by untargeted metabolomics

Abstract The saccharomyces strain Saccharomyces cerevisiae var. boulardii has exhibited efficacy in ameliorating symptoms of gastrointestinal disorders, including inflammatory diseases. The molecular origin of the anti-inflammatory activity has remained largely elusive to this day. Earlier studies suggest a small, secreted, yet undefined, molecule as the active principle and thus an untargeted metabolomics approach towards its identification was adopted. We used LCMS-analysis to interrogate the secreted metabolome of S. cerevisiae var. boulardii in comparison to a S. cerevisiae reference strain. Statistical analysis of the data revealed several compounds unique to S. cerevisiae var. boulardii, that were partially annotated and confirmed by comparison with authentic standards. Furthermore, anti-inflammatory properties were experimentally assigned to several small molecules, indicating that this property of the yeast variant is due to several factors. Our data suggest that the anti-inflammatory properties of S. cerevisiae var. boulardii can be linked to the activity of small molecules in its secreted metabolome.

opencc-by-4.0Apr 2023View details →

The mycobiome of the gut of willow wood borer, Xiphydria prolongata (Hymenoptera: Xiphydriidae): a rich source of rare yeasts

A high-throughput amplicon sequencing as a culture-independent approach was used to identify the gut mycobiome of the willow wood borer Xiphydria prolongata. The findings of this study are significance in terms of the insect-fungal interactions and indicate the unexpected richness of the mycobiome and the presence of many rare yeast species in the wood borer gut. A total of 40 fungal genera were found, and among them, only one endophytic fungi, Daldinia (Hypoxylaceae), has been previously reported in Xiphydria. Zygosaccharomyces siamensis is the most prevalent ascomycete species, while Rhodosporidiobolus colostri is the most abundant basidiomycetous yeast in X. prolongata. Some of the species identified in here was known as very rare fungus such as Skoua fertilis, Chaetomium nepalense, R. colostri and Vustinia terrae. This study is also the first report to S. fertilis and V. terrae in the insect gut flora. These funguses most likely aid in the digestion of lignocellulose in the gut of wood borer. Therefore, further researches are required to know the source of acquisition and functional role of these yeast and their industrial potential.

opencc-by-4.0Jan 2020View details →

Dataset 'Yeast facilitates the multiplication of Drosophila bacterial symbionts but has no effect on the form or parameters of Taylor's law'

Dataset from the manuscript 'Yeast facilitates the multiplication of Drosophila bacterial symbionts but has no effect on the form or parameters of Taylor’s law' (2020) Each line corresponds to a single experimental unit.

opencc-by-4.0Jul 2020View details →

data for "A disordered encounter complex is central to the yeast Abp1p SH3 domain binding pathway"

Protein-protein interactions are involved in a wide range of cellular processes. These interactions often involve intrinsically disordered proteins (IDPs) and protein binding domains. However, the details of IDP binding pathways are hard to characterize using experimental approaches, which can rarely capture intermediate states present at low populations. SH3 domains are common protein interaction domains that typically bind proline-rich disordered segments and are involved in cell signaling, regulation, and assembly. We hypothesized, given the flexibility of SH3 binding peptides, that their binding pathways include multiple steps important for function. Molecular dynamics simulations were used to characterize the steps of binding between the yeast Abp1p SH3 domain (AbpSH3) and a proline-rich IDP, ArkA. Before binding, the N-terminal segment 1 of ArkA is pre-structured and adopts a polyproline II helix, while segment 2 of ArkA (C-terminal) adopts a 310 helix, but is far less structured than segment 1. As segment 2 interacts with AbpSH3, it becomes more structured, but retains flexibility even in the fully engaged state. Binding simulations reveal that ArkA enters a flexible encounter complex before forming the fully engaged bound complex. In the encounter complex, transient nonspecific hydrophobic and long- range electrostatic contacts form between ArkA and the binding surface of SH3. The encounter complex ensemble includes conformations with segment 1 in both the forward and reverse orientation, suggesting that segment 2 may play a role in stabilizing the correct binding orientation. While the encounter complex forms quickly, the slow step of binding is the transition from the disordered encounter ensemble to the fully engaged state. In this transition, ArkA makes specific contacts with AbpSH3 and buries more hydrophobic surface. Simulating the binding between ApbSH3 and ArkA provides insight into the role of encounter complex intermediates and nonnative hydrophobic interactions for other SH3 domains and IDPs in general.

opencc-by-4.0Feb 2020View details →

Computed results for Bayesian genome scale modelling temperature effect on yeast metabolism

This repository contains the computed results for reproducing the figures in the manuscript "Li G., et al. Bayesian genome scale modelling identifies thermal determinants of yeast metabolism". The scripts can be found in Github (<a href="https://github.com/Gangl2016/BayesianGEM">https://github.com/Gangl2016/BayesianGEM</a>)

opencc-by-4.0Oct 2020View details →

Analysing the Yeast Complexome - The Complex Portal rising to the challenge

Datasets of complexes and co-complexes used in the analysis for this paper: Analysing the Yeast Complexome - The Complex Portal rising to the challenge.

opencc-byNov 2020View details →

SpEDIT: A fast and efficient CRISPR/Cas9 method for fission yeast

Underlying data and extended data for: SpEDIT: A fast and efficient CRISPR/Cas9 method for fission yeast

opencc-by-4.0Sep 2016View details →

MAD diffraction images for yeast 5-aminolevulinic acid dehydratase (ALAD).

Selenomethionine multiwavelength anomalous dispersion (MAD) diffraction images for the original structure determination of 5-aminolevulinic acid dehydratase (ALAD) from yeast collected at the bending magnet beamline BM14, ESRF, Grenoble (25-27 Sept 1996). There are separate folders for the data from different wavelengths (l1 is the edge dataset, l4 is the edge inverse beam, l2 is the peak, l5 and l55 are the peak inverse beam (l55 is an overlapping continuation of l5 due to beam loss), l3 is the remote and l6 is the remote inverse beam). The seoa folder contains the selenium 'optimised anomalous' peak data. The images were collected with a Mar Research image plate and each folder has a file called 'mos.com' giving the data collection parameters for that run except for the exposure times which were 45 seconds per image for both l1 and l2, 55 seconds per image for the remote l3 and 120 seconds per image for the optimised anomalous collection (seoa). The latter dataset does not have a file listing the parameters which were: crystal-to-detector distance 275mm, delta-phi 1 degree, wavelength 0.9791 Angstroms, big-MAR format (note other datasets were collected in small-MAR format).

Diffraction images for yeast 5-aminolevulinic acid dehydratase complexed with the inhibitor 5-hydroxylevulinic acid.

Diffraction images for a co-crystal of 5-aminolaevulinic acid dehydratase (ALAD) from yeast with the competitive inhibitor 5-hydroxylevulinic acid extending to a resolution of 1.9 Å. The data were collected at beamline ID29 at ESRF in Feb 2002 using an ADSC detector.

X-ray diffraction images for yeast 5-aminolevulinic acid dehydratase complexed with 4-oxosebacic acid.

X-ray diffraction images for yeast 5-aminolaevulinic acid dehydratase complexed with 4-oxosebacic acid which were collected using beamline ID14-2 at the ESRF (Grenoble) in Feb 2001.

X-ray diffraction images for yeast 5-aminolevulinic acid dehydratase complexed with 4-keto-5-aminohexanoic acid.

X-ray diffraction images which were collected at the EMBL beamline BW7B, DESY (Hamburg) on 28th June 1999 using a Marresearch 345 image plate detector. The data were collected in three passes, images in the first main one having file prefix hykah, the second being a low-resolution run (lr) and, the last, a very high resolution (vhr) pass. More details are given in the notebook pages.

X-ray diffraction images for yeast 5-aminolevulinic acid dehydratase complexed with succinylacetone.

X-ray diffraction images which were collected on 28th March 1999 at the EMBL beamline BW7B at DESY (Hamburg) using a Marresearch 345 image plate detector. More information in the notes.