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zenodo40/100

X-ray diffraction images of yeast 5-aminolevulinic acid dehydratase complexed with substrate 5-aminolevulinic acid.

X-ray diffraction images collected at the BW7B beamline at DESY (Hamburg) on 2 Jun 1998. More details in the notes.

opencc-by-4.0Jan 2017View details →

zenodo40/100

Data from: Stochastic phenotypic switching arises in response to directional selection in experimentally evolved multicellular yeast.

This BBC_2025__README.txt file was generated on 2025-09-24 by Beatriz Baselga Cervera GENERAL INFORMATION <ol> <li>Title of Dataset and code: Data from: Stochastic phenotypic switching arises in response to directional selection in experimentally evolved multicellular yeast.</li> </ol>   2. Author Information             Corresponding Investigator                         Name: Ph.D. Beatriz Baselga-Cervera                         Institution: University of Minnesota Twin cities, Minnesota, US.                         Email: <a href="mailto:bbaselga@umn.edu">bbaselga@umn.edu</a>; beabaselga@gmail.com             Co-investigator 1                         Name: Ph.D. Nahui Olin Medina-Chávez                         Institution: University of Minnesota Twin cities, Minnesota, US.                         Email: nmedinac@umn.edu             Co-investigator 2                         Name: Ph.D. Noah Gettle                         Institution: Wellcome Sanger Institute, Hinxton, UK.                         Email: nbgettle@gmail.com Co-investigator 3                         Name: Ph.D. Michael Travisano                         Institution: University of Minnesota Twin cities, Minnesota, US.                         Email: travisan@umn.edu     3. Data collectors: Ph.D. Beatriz Baselga-Cervera, Ph.D. Nahui Olin Medina-Chávez & Ph.D. Noah Gettle.   4. Date of data collection: 2022-2024   5. Geographic location of data collection: Saint Paul, US   6. Funding sources that supported the collection of the data: Fundación Alfonso Martín Escudero, Madrid, Spain (BBC).   7. Recommended citation for this dataset: Baselga-Cervera et al. (2024), Data from: Stochastic phenotypic switching arises in response to directional selection in experimentally evolved multicellular yeast.     DATA & FILE OVERVIEW   8. Description of dataset In this study, we address whether stochastic phenotypic switching can shape biological diversity contributing to evolutionary change across the transition from singles cells to multicellular clutters in Saccharomyces cerevisiae multicellular yeast system. Populations characterization was conducted with a Coulter Counter multisize 4, a FlowCam 3, under the optic microscope, via ACE2 gene sequencing and RNA sequencing and mathematical modeling. The populations studied were the genetically uniform diploid wild-type Saccharomyces cerevisiae Y55 strain clones, C1W8.1 and C1W8.2 multicellular evolved strains, constructed ACE2 gene knockouts, and strains containing the missense mutation (ACE2 c.1934 A>T).   9. File list: ●      Coulter Counter size distribution data:  o   File 1 name:  File_1_Coulter_Counter_Counts_20h.csv o   File 1 description: Size distributions of Saccharomyces cerevisiae Y55 strain clones, C1W8.1 and C1W8.2 multicellular evolved strains, constructed ACE2 gene knockout, and strains containing the missense mutation (ACE2 c.1934 A>T) in YPD at 20-hours growth. Data for: Fig. 1A, Fig. 3A and Fig. S2, Table S2 and Table S3.   o   File 2 name:  File_2_Coulter_Counter_Counts_24h.csv o   File 2 description: Size distributions of Saccharomyces cerevisiae Y55 strain clones, C1W8.1 and C1W8.2 multicellular evolved strains, constructed ACE2 gene knockout, and strains containing the missense mutation (ACE2 c.1934 A>T) in YPD at 24-hours growth. Data for: Fig. 1A, Fig. 3A, Fig. S2, Table S2 and Table S3.   o   File 3 name:  File_3_Coulter_Counter_Counts_48h.csv o   File 3 description: Size distributions of Saccharomyces cerevisiae Y55 strain clones, C1W8.1 and C1W8.2 multicellular evolved strains, constructed ACE2 gene knockout, and strains containing the missense mutation (ACE2 c.1934 A>T) in YPD at 48-hours growth. Data for: Fig. 1, Fig. 3A, Fig. S2, Table S2 and Table S3.   o   File name:  File_4_Coulter_Counter_Counts_Constructed_strains_diversity.csv o   File 4 description: Size distributions of the constructed ACE2 knockout and a strain containing the homozygous missense mutation (ACE2 c.1934 A>T) in YPD at 24h growth. Size distributions were obtained from populations before (initial) and five resuspended colonies obtained from small-size particles by plating the top fraction of the population after gravitational selection from three isolates per strain. Data for: Fig. 1, Fig. S2, Table S2 and Table S3.   o   File 5 name:  File_5_Coulter_Counter_Counts_Selection_Experiment.xlsx o   File 5 description: Size distributions of C1W8.1 and C1W8.2 multicellular evolved strains in YPD at 24h growth. Size distributions from the selection experiment for small-size particles by plating the top fraction of the population after gravitational selection over three cycles of selection. Data for: Fig. 2B and Fig. S6.   o   File 6 name:  File_6_Coulter_Counter_Counts_12h.xlsx o   File 6 description: Size distributions of C1W8.1 and C1W8.2 multicellular evolved strains, constructed ACE2 gene knockout, and strains containing the missense mutation (ACE2 c.1934 A>T) in YPD at 12-hours growth. Data for: Fig. 3A and Fig. S3.     ●      FlowCam data: o   File 7 name: File_7_Rawdata_FlowCam_all.csv o   File 7 description: FlowCam data from Saccharomyces cerevisiae Y55 strain clones, C1W8.1 and C1W8.2 multicellular evolved strains, constructed ACE2 gene knockouts, and strains containing the missense mutation (ACE2 c.1934 A>T) in YPD at 24h growth. Data for: Fig. S4.     ●      Data generated statistically: o   File 8 name: File_8_C1W8.2_overlapPairs_Selection_Experiment.csv o   File 8 description: overlapping indexes (η) of the KDE distributions were computed using the R-package ‘overlapping’ from the Coulter Counter data of the C1W8.2 derived strain over the selection experiment. Data for: Fig. S6D.   o   File 9 name: File_9_C1W8.1_overlapPairs_Selection_Experiment.csv o   File 9 description: overlapping indexes (η) of the KDE distributions were computed using the R-package ‘overlapping’ from the Coulter Counter data o   of the C1W8.1 derived strain over the selection experiment. Data for: Fig. S6C.     o   File 10 name: File_10_ overlapPairs_Constructed_strains_diversity.xlsx o   File 10 description: overlapping indexes (η) of the KDE distributions were computed using the R-package ‘overlapping’ from the Coulter Counter data of the constructed ACE2 knockout and a strain containing the homozygous missense mutation (ACE2 c.1934 A>T) in YPD at 24h growth. Size distributions were obtained from populations before (initial) and after gravitational selection of five resuspended colonies from three isolates per strain. Data for: Fig. S7.   ●      Data from ImageJ: o   File 11 name: File_11_ImageJ_analyses.xlsx o   File 11 description: ImageJ analyses of the microphotographs from Saccharomyces cerevisiae Y55 strain clones, C1W8.1 and C1W8.2 multicellular evolved strains, constructed ACE2 gene knockouts, and strains containing the missense mutation (ACE2 c.1934 A>T). Cultures were grown in culture tubes with 10 ml of media, 50 mL Erlenmeyer flasks with 10 mL and 30 mL of media, in YPD under non-shaking and shaking at 250 rpm. YPD media was used across all conditions. Cultures were assessed after 24 hours growth at 30°C.  Microphotographs of each condition and strain were obtained with a Nikon TE2000 microscope using 10x objective.   ●      Pictures: o   File 12 name: File_12_ FlowCam_Pictures.zip o   File 12 description FlowCam IMAGES from Saccharomyces cerevisiae Y55 strain clones, C1W8.1 and C1W8.2 multicellular evolved strains, constructed ACE2 gene knockouts, and strains containing the missense mutation (ACE2 c.1934 A>T) in YPD at 24h growth. Data for: Fig. 1B.   o   File 13 name: File_13_Microphotography_controled_experimental_conditions.zip o   File 13 description: Microphotographs from Saccharomyces cerevisiae Y55 strain clones, C1W8.1 and C1W8.2 multicellular evolved strains, constructed ACE2 gene knockouts, and strains containing the missense mutation (ACE2 c.1934 A>T). Cultures were grown in culture tubes with 10 mL of media, 50 mL Erlenmeyer flasks with 10 mL and 30 mL of media, in YPD under non-shaking and shaking at 250 rpm. YPD media was used across all conditions. Cultures were assessed after 24 hours of growth at 30°C. Pictures were obtained with a Nikon TE2000 microscope using 10x objective.     ●      Mathematical Model o   File 14 name: File_14_Mathematical_model.zip o   File 14 description: Mathematical model R code and generated values.   ●      ARN data o   File 15 name: File_15_rnaseq-final-results-Top_v_Bottom.xlsx o   File 15 description: RNA analyses final results Top vs Bottom phenotypic subdistributions. Top is used as control. o   File 16 name: File_16_Variant_Call_format_file.vcf o   File 16 description: Variant Calling analyses of the sample ARN sample Top 1. Adhesion number: SRR32105384.   ●      Time-lapse videos o   File 17 name: Supp. Video 1. C1W8.1 from 17 to 22 hours growth o   File 17 description: Supplementary Video 1. Experimentally evolved multicellular yeast video between 17 and 22 hours of growth (C1W8.1-derived strain) — time-lapse video of the formation of a single-cell propagule from a multicellular cluster. o   File 18 name: Supp. Video 2. Ace2x2KO over 26 hours growth. o   File 18 description: Supplementary Video 2. ace2Δ knockout constructed strain growth — time-lapse video of a single large multicellular cluster over 26 hours. o   File 19 name: Supp. Video 3. C1W8.1 over 6 hours growth o   File 19 description: Supplementary Video 3. Experimentally evolved multicellular yeast growth between 6 and 12 hours of growth (C1W8.1-derived strain). o   File 20 name: Supp. Video 4. C1W8.1 over 24 hours growth o   File 20 description: Supplementary Video 4. Experimentally evolved multicellular yeast growth over 24 hours (C1W8.1-derived strain) — cell division stops in small ancestral-like phenotypes. o   File 21 name: Supp. Video 5. Ace2x2KO over 24 hours growth o   File 21 description: Supplementary Video 5. ace2Δ knockout constructed strain growth — time-lapse video of multiple large multicellular clusters over 24 hours. o   File 22 name: Supp. Video 6. Ace2x2missense from 0 to 3h45m hours growth o   File 22 description: Supplementary Video 6. ace2Δ missense constructed strain growth — time-lapse video of multiple large multicellular clusters up to 3 hours 45 min.   METHODOLOGICAL INFORMATION Strains: ancestral wildtype (Y55 strains), C1W8.1 and C1W8.2 multicellular derived strains isolated after 60 days of selection in YPD media, constructed ACE2 gene knockouts, and strains containing the ACE2 missense mutation (ACE2 c.1934 A>T). Media: Growth media used in this study were Yeast Peptone Dextrose media (YPD; 1% (v/w) yeast extract, 2% (v/w) peptone, 2% (v/w) D-glucose, pH 5.8). Phenotypic characterization of the different strains was conducted in a Coulter Counter Multisizer 4 and FlowCam® 3.0 Fluid Imaging Technologies, optic microscopy and a mathematical model. Replicate populations of different individual isolates per strain were analyzed to obtain the population distributions in YPD media. RNA was extracted using an Invitrogen® PureLink RNA Mini Kit. Three out of four extracted samples per treatment with the highest RNA integrity score were submitted for TrueSeq Stranded RNA-Seq.     10. Detailed description ●      Coulter Counter size distribution data of all the populations:  o   File 1 name:  File_1_Coulter_Counter_Counts_20h.csv o   File 1 description: strains naming convention; strain_Isolate_run.pseudoreplicate. Strains: ace2x2m=strains containing the ACE2 missense mutation (ACE2 c.1934 A>T); ace2x2= ACE2 knockout; C1W8.1= C1W8.1 evolved multicellular strain; C1W8.2= C1W8.2 evolved multicellular strain; Y55= ancestral strain. §  Page 1: Column 1: Volume (um3) Column 2: Diameter (um2) Columns 3 to the last column: strains counts.   o   File 2 name:  File_2_Coulter_Counter_Counts_24h.csv o   File 2 description: strains naming convention; strain_Isolate_run.pseudoreplicate. Strains: ace2x2m=strains containing the ACE2 missense mutation (ACE2 c.1934 A>T); ace2x2= ACE2 knockout; C1W8.1= C1W8.1 evolved multicellular strain; C1W8.2= C1W8.2 evolved multicellular strain; Y55= ancestral strain. §  Page 1: Column 1: Volume (um3) Column 2: Diameter (um2) Columns 3 to the last column: strains counts.   o   File 3 name:  File_3_Coulter_Counter_Counts_48h.csv o   File 3 description: strains naming convention; strain_Isolate_run.pseudoreplicate. Strains: ace2x2m=strains containing the ACE2 missense mutation (ACE2 c.1934 A>T); ace2x2= ACE2 knockout; C1W8.1= C1W8.1 evolved multicellular strain; C1W8.2= C1W8.2 evolved multicellular strain; Y55= ancestral strain. §  Page 1: Column 1: Volume (um3) Column 2: Diameter (um2) Column 3 to the last column: strains counts.   o   File_4_Coulter_Counter_Counts_Constructed_strains_diversity.csv o   File 4 description: strains naming convention; strain_Isolate_colony_run.pseudoreplicate. Strains: ace2x2m=strains containing the ACE2 missense mutation (ACE2 c.1934 A>T); ace2x2= ACE2 knockout. §  Page 1: Column 1: Volume (um3) Column 2: Diameter (um2) Column 3 to the last column: strains counts.   o   File_5_Coulter_Counter_Counts_Selection_Experiment.xlsx o   File 5 description: strains naming convention; strain_colony.phenotype_selection.cycle_run.pseudoreplicate. Strains: C1W8.2= C1W8.2 evolved multicellular strain and C1W8.1= C1W8.1 evolved multicellular strain. §  Page 1: Column 1: Volume (um3) Column 2: Diameter (um2) Column 3 to the last column: strains counts.   o   File 6 name:  File_6_Coulter_Counter_Counts_12h.xlsx o   File 6 description: Size distributions of C1W8.1 and C1W8.2 multicellular evolved strains, constructed ACE2 gene knockout, and strains containing the missense mutation (ACE2 c.1934 A>T) in YPD at 12-hours growth. Data for: Fig. 3A and Fig. S3. §  Page 1: Column 1: Volume (um3) Column 2: Diameter (um2) Column 3: Time Column 4: replicate Column 5: Strain name (strain_f) Column 6: Isolate (isolate_f)         o   File 7 name: File_3_Rawdata_Flowcam_all.csv o   File 7 description: strains naming convention; ace2_isolate= ACE2 knockout; Ace2m_isolate= strain containing the ACE2 missense mutation (ACE2 c.1934 A>T); c1w82_isolate=C1W8.2 evolved multicellular strain; C1W81_isoalte C1W8.1 evolved multicellular strain; Y55_isolate=ancestral strain. §  Page 1:                                                                         Column 1: Particle ID                                                                         Column 2: Area ABD                                                                         Column 3: Aspect Ratio (Width/Length)                                                                         Column 4: Circle Fit                                                                         Column 5: Area base Diameter (ABD)                                                                         Column 6: Equivalent Spherical Diameter (ESD)                                                                         Column 7: Elongation                                                                         Column 8: Perimeter                                                                         Column 9: Roughness                         Column 10: Volume ABD-based                                                                         Column 11: Volume ESD-based                                                                         Column 12: Width                                                                         Column 13: Source. Name of the sample.   o   File 8 name: File_8_C1W8.2_overlapPairs_Selection_Experiment.csv o   File 8 description: C1W8.2 _lineage_selection.cycle= C1W8.2 evolved multicellular strain, lineage (A=ancestral, M1= lineage 1,  M2= lineage 2 , M3= lineage 3) and selection cycle  (0, 1, 2 and 3). §  Page 1: Column 1: Var1= strain 1 Column 2: Var2= strain 2 Column 3: overlap value of both strains compared.   o   File 9 name: File_9_C1W8.1_overlapPairs_Selection_Experiment.csv o   File 9 description: C1W8.1 _lineage_selection.cycle =C1W8.1 evolved multicellular strain, lineage (A=ancestral, M1= lineage 1,  M2= lineage 2 , M3= lineage 3) and selection cycle  (0, 1, 2 and 3). §  Page 1: Column 1: Var1= strain 1 Column 2: Var2= strain 2 Column 3: overlap value of both strains compared.   o   File 10 name: File_10_overlapPairs_Constructed_strains_diversity.xlsx o   File 10 description: variables naming convention; strain _isolate_colony.number. Strains; ace2x2m=strains containing the ACE2 missense mutation (ACE2 c.1934 A>T); ace2x2= ACE2 knockout. Isolate; 1,2 and 3. Colony.number; Initial=initial population and colony number (1,2,3,4 and 5). §  Page 1: Column 1: Var1= strain 1 Column 2: Var2= strain 2 Column 3: overlap value of both strains compared.   o   File 11 name: File_11_ ImageJ _analyses.xlsx o   File 11 description: ImageJ analyses of the microphotographs from Saccharomyces cerevisiae Y55 strain clones, C1W8.1 and C1W8.2 multicellular evolved strains, constructed ACE2 gene knockouts, and strains containing the missense mutation (ACE2 c.1934 A>T). Cultures were grown in culture tubes with 10 mL of media, 50 mL Erlenmeyer flasks with 10 mL and 30 mL of media, in YPD under non-shaking and shaking at 250 rpm. YPD media was used across all conditions. Cultures were assessed after 24 hours growth at 30°C.  Microphotographs of each condition and strain were obtained with a Nikon TE2000 microscope using 10x objective. §  Page 1: Column 1: Var1= strain 1 Column 2: Var2 = strain 2 Column 3: overlap value of both strains compared.     o   File 12 name: File_12_ FlowCam_Pictures.zip o   File 12 description: FlowCam runs, images, and raw data of Saccharomyces cerevisiae Y55 strain clones, C1W8.1 and C1W8.2 multicellular evolved strains, constructed ACE2 gene knockouts, and strains containing the missense mutation (ACE2 c.1934 A>T) in YPD at 24h growth. Data for: Fig. 1B.   o   File 13 name: File_13_Microphotography_controled_experimental_conditions.zip o   File 13 description: 149 microphotographs. § Folder 1:  Images of Erlenmeyer flasks with 30ml of YPD § Folder 2:  Images of Erlenmeyer’s and tubes with 10ml of YPD   o   File 14 name: File_14_Mathematical_model.zip o   File 14 description: Mathematical model, R code, and generated values. §  Document 1:  R code of the model §  Document 2:  Resulted data from the mathematical model with different inset values of k, alpha, and beta. §  Document 2:  Resulted data from the mathematical model with different inset values of k, alpha, gamma, and beta.       o   File 15 name: File_15_rnaseq-final-results-Top_v_Bottom.xlsx o   File 15 description: §  Page 1: Column 1: number Column 2: ID Column 3: protID             Column 4: gene_symbol                     Column 5: chr             Column 6: chr_latin Column 7: location Column 8: baseMean             Column 9: log2FoldChange Column 10: lfcSE Column 11: stat             Column 12: pvalue     padj Column 13: test Column 14: log10padj             Column 15: log10baseMean Column 16: blast_pident Column 17: transcript_length             Column 18: blast_evalue Column 19: blast_bitscore Column 20: rnaID             Column 21: feature Column 22: accession Column 23: strain             Column 24: gene_accession   o   File 16 name: File_16_Variant_Call_format_file.vcf o   File 16 description: Variant Calling analyses of the  ARN sample Top 1. Adhesion number: SRR32105384.   o   File 17 name: Supp. Video 1. C1W8.1 from 17 to 22 hours growth o   File 17 description: Supplementary Video 1. Experimentally evolved multicellular yeast video between 17 and 22 hours of growth (C1W8.1-derived strain) — time-lapse video of the formation of a single-cell propagule from a multicellular cluster. The time-lapse video captures growth dynamics over this period, highlighting the formation of a single-cell propagule from a multicellular cluster on two occasions (visible in the lower left region of the frame). Images were acquired every 15 minutes using a 10x objective lens.  o   File 18 name: Supp. Video 2. Ace2x2KO over 26 hours of growth. o   File 18 description: Supplementary Video 2. ace2Δ knockout constructed strain growth — time-lapse video of a single large multicellular cluster over 26 hours. The video captures large, multicellular clusters that produce both large, multicellular and small, ancestral-like clusters. The video shows a single large multicellular cluster fragmenting into two large multicellular clusters at ~ 13 hours of growth (from 02:09 to 02:10 minutes in the time-lapse) and generating two small ancestral-like propagules at ~19 hours of growth (from 03:07 to 03:09 minutes in the time-lapse). Microphotographs were obtained at 3-minute intervals under a 10x objective over 26 hours.   o   File 19 name: Supp. Video 3. C1W8.1 over 6 hours growth o   File 19 description: Supplementary Video 3. Experimentally evolved multicellular yeast growth between 6 and 12 hours of growth (C1W8.1-derived strain). The time-lapse video captures large, multicellular clusters of the C1W8.1 strains, which produce both large, multicellular and small, ancestral-like clusters. Additionally, small ancestral-like clusters are observed undergoing cellular division —no separation is observed— during the first 2 to 3 hours, followed by a cessation of division for the remainder of the time-lapse. Images were acquired every 30 seconds using a 10x objective lens. o   File 20 name: Supp. Video 4. C1W8.1 over 24 hours growth o   File 20 description: Supplementary Video 4. Experimentally evolved multicellular yeast growth over 24 hours (C1W8.1-derived strain) — cell division stops in small ancestral-like phenotypes. The footage captures multiple large multicellular clusters undergoing fragmentation into propagules. Additionally, a small ancestral-like cluster is observed undergoing division during the first 2 to 3 hours, followed by a cessation of division for the remainder of the time-lapse (visible in the lower left region of the frame). This early division phase is evident during the first 10 seconds of the video. Images were acquired every 5 minutes using a 10x objective lens.  o   File 21 name: Supp. Video 5. Ace2x2KO over 24 hours growth o   File 21 description: Supplementary Video 5. ace2Δ knockout constructed strain growth — time-lapse video of multiple large multicellular clusters over 24 hours. The video shows multiple large multicellular clusters fragmenting into large clusters and several small ancestral-like clusters being dragged by Brownian motion and evaporation of the sample. Microphotographs were obtained at fixed intervals of 3 minutes under the 10x objective over 24 hours.  o   File 22 name: Supp. Video 6. Ace2x2missense from 0 to 3h45m hours growth o   File 22 description: Supplementary Video 6. ace2Δ missense constructed strain growth — time-lapse video of multiple large multicellular clusters up to 3 hours 45 min. The video shows multiple large multicellular clusters fragmenting into large clusters, generating two small ancestral-like propagules before being dragged by Brownian motion and evaporation of the sample. Microphotographs were obtained at 3-minute intervals under the 10x objective.

opencc-by-4.0Sep 2024View details →

zenodo40/100

CX-MS Datasets for "Comprehensive Structure and Functional Adaptations of the Yeast Nuclear Pore Complex"

This repository contains chemical cross-linking mass spectrometry data of affinity-purified Yeast nuclear pore complexes. Data Files Description: NPC_XL_Identification_Inter_Crosslinked.csv: Inter-protein cross-links identified by pLink 2. NPC_XL_spectra.mgf: MS2 spectra data for the identified cross-links. NPC_XL_proteins.fasta : Protein sequences used for search. Sample Processing: NPCs were immuno-purified from Mlp1 tagged S. cerevisiae strains (Kim et al., 2018). After native elution, 1.0 mM disuccinimidyl suberate (DSS) was added and the sample was incubated at 25ºC for 40 min with shaking (1,200 rpm). The reaction was quenched by adding a final concentration of 50 mM freshly prepared ammonium bicarbonate and incubating for 20 min with shaking (1,200 rpm) at 25ºC. The sample (50 µg) was then concentrated and denatured at 98ºC for 5 min in a solubilization buffer (10% solution of 1-dodecyl-3-methylimidazolium chloride (C12-mim-Cl) in 50 mM ammonium bicarbonate, pH 8.0, 100 mM DTT). After denaturation, the sample was centrifuged at 21,130 g for 10 min and the supernatant was transferred to a 100 kDa MWCO ultrafiltration unit (MRCF0R100, Microcon). The sample was quickly spun at 1,000 g for 2 min and washed twice with 50 mM ammonium bicarbonate. After alkylation (50 mM iodoacetamide), the cross-linked NPC in-filter was digested by trypsin and lysC O/N at 37ºC. After proteolysis, the sample was recovered by centrifugation and peptides were fractionated into 10-12 fractions by using a stage tip self-packed with basic C18 resins (Dr. Masch GmbH). Fractionated samples were pooled prior to LC/MS analysis. Desalted cross-link peptides were dissolved in the sample loading buffer (5% Methanol, 0.2% FA), separated with an automated nanoLC device (nLC1200, Thermo Fisher), and analyzed by an Orbitrap Q Exactive HFX (Pharma mode) mass spectrometer (Thermo Fisher) as previously described (Xiang et al., 2020; Xiang et al., 2021). Briefly, peptides were loaded onto an analytical column (C18, 1.6 μm particle size, 100 Å pore size, 75 μm × 25 cm; IonOpticks) and eluted using a 120-min liquid chromatography gradient. The flow rate was approximately 300 nl/min. The spray voltage was 1.7 kV. The QE HF-X instrument was operated in the data-dependent mode, where the top 10 most abundant ions (mass range 380 – 2,000, charge state 4 - 8) were fragmented by high-energy collisional dissociation (HCD). The target resolution was 120,000 for MS and 15,000 for tandem MS (MS/MS) analyses. The quadrupole isolation window was 1.8 Th; the maximum injection time for MS/MS was set at 200 ms. Data Processing: The raw data were searched with pLink2 (Chen et al., 2019b). An initial MS1 search window of 5 Da was allowed to cover all isotopic peaks of the cross-linked peptides. The data were automatically filtered using a mass accuracy of MS1 ≤ 10 ppm (parts per million) and MS2 ≤ 20 ppm of the theoretical monoisotopic (A0) and other isotopic masses (A+1, A+2, A+3, and A+4) as specified in the software. Other search parameters included cysteine carbamidomethyl as a fixed modification and methionine oxidation as a variable modification. A maximum of two trypsin missed-cleavage sites was allowed. The initial search results were obtained using a default 5% false discovery rate (FDR) expected by the target-decoy search strategy. Spectra were manually verified to improve data quality (Kim et al., 2018; Shi et al., 2014). Cross-linking data were analyzed and plotted with CX-Circos (http://cx-circos.net).

opencc-by-4.0Nov 2021View details →

zenodo40/100

Annotated images from yeast cell lifespans - Training & Test sets - DetecDiv (id01)

This dataset has been generated by manual annotation from timelapse images of yeast cells dividing using the DetecDiv software (see below). It contains ~250 000 images from 250 cellular lifespans (each lifespan is made of between 700 and 1000 images). Each image is classified between 6 classes: "1. unbudded", "2. small", "3. large", "4. dead", "5. empty", "6. clog", according to the subfolder of the image. Besides, this folder also contains a .mat file containing 250 timeseries of classes corresponding to the lifespan of the 200 cells.   The dataset used for training (200 cellular lifespans) is in the folder /trainingset, while the dataset used for testing (50cellular lifespans) is in the folder /testset It has been used to train the network <a href="https://doi.org/10.5281/zenodo.5553862">doi.org/10.5281/zenodo.5553862</a> from the software DetecDiv: <a href="https://github.com/gcharvin/DetecDiv">github.com/gcharvin/DetecDiv</a> <a href="https://biorxiv.org/content/10.1101/2021.10.05.463175v1">biorxiv.org/content/10.1101/2021.10.05.463175v1</a>   Data type: 3D microscopy images (3 stacks brightfield) (.tif) + annotation (.mat) Microscopy data type: Brightfield images with 3 stacks, each stack representing a color of RGB. Imaging: 20x 0.45 NA brightfield, 6.5µm*6.5µm sCMOS Cell type: Budding yeast wild type cell (BY4742) File format: .tif (16-bit RGB, 1 color per z-stack) + .mat Image size: 60x60x1 (Pixel size: x,y: 325 nm, 3*z: 3*1325 nm)   Author(s): Théo, ASPERT Contact email: theo.aspert@gmail.com Affiliation: IGBMC, Université de Strasbourg Funding bodies: This work was supported by the Agence Nationale pour la Recherche, the grant ANR-10-LABX-0030-INRT, a French State fund managed by the Agence Nationale de la Recherche under the frame program Investissements d'Avenir ANR-10-IDEX-0002-02.

opencc-by-4.0Oct 2021View details →

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Data from: Photoinactivation of Yeast and Biofilm Communities of Candida albicans Mediated by ZnTnHex-2-PyP4+ Porphyrin

Data supporting the figures presented in the research article Photoinactivation of Yeast and Biofilm Communities of Candida albicans Mediated by ZnTnHex-2-PyP4+ Porphyrin.   Candida albicans is the main cause of superficial candidiasis. While the antifungals available are defied by biofilm formation and resistance emergence, antimicrobial photodynamic inactivation (aPDI) arises as an alternative antifungal therapy. The tetracationic metalloporphyrin Zn(II) meso-tetrakis(N-n-hexylpyridinium-2-yl)porphyrin (ZnTnHex-2-PyP4+) has high photoefficiency and improved cellular interactions. We investigated the ZnTnHex-2-PyP4+ as a photosensitizer (PS) to photoinactivate yeasts and biofilms of C. albicans strains (ATCC 10231 and ATCC 90028) using a blue light-emitting diode. The photoinactivation of yeasts was evaluated by quantifying the colony forming units. The aPDI of ATCC 90028 biofilms was assessed by the MTT assays, propidium iodide (PI) labeling, and scanning electron microscopy. Mammalian cytotoxicity was investigated in Vero cells using MTT assay. The aPDI (4.3 J/cm2) promoted eradication of yeasts at 0.8 and 1.5 µM of PS for ATCC 10231 and ATCC 90028, respectively. At 0.8 µM and same light dose, aPDI-treated biofilms showed intense PI labeling, about 89% decrease in the cell viability, and structural alterations with reduced hyphae. No considerable toxicity was observed in mammalian cells. Our results introduce the ZnTnHex-2-PyP4+ as a promising PS to photoinactivate both yeasts and biofilms of C. albicans, stimulating studies with other Candida species and resistant isolates.

opencc-by-4.0May 2022View details →

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Processed and annotated yeast gene expression data from yeast2 and ygs98 platforms

This dataset contains the following files: <ul> <li>yeast2_processed_rds.tar.gz - processed gene expression matrices from the yeast2 platform. The data is stored in binary R format (.rds).</li> <li>ygs98_processed_rds.tar.gz - processed gene expression matrices from the yeast2 platform. The data is stored in binary R format (.rds).</li> <li>yeast2-curated-annotations.txt - metadata for the yeast2 platform.</li> <li>ygs98-curated-annotations.txt - metadata for the ygs98 platform.</li> </ul>

opencc-by-4.0Aug 2017View details →

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Data from: Mutations in yeast are deleterious on average regardless of the degree of adaptation to the testing environment

The role of spontaneous mutations in evolution depends on the distribution of their effects on fitness. Despite a general consensus that new mutations are deleterious on average, a handful of mutation accumulation experiments in diverse organisms instead suggest that of beneficial and deleterious mutations can have comparable fitness impacts, i.e., the product of their respective rates and effects can be roughly equal. We currently lack a general framework for predicting when such a pattern will occur. One idea is that beneficial mutations will be more evident in genotypes that are not well adapted to the testing environment. We tested this prediction experimentally in the laboratory yeast Saccharomyces cerevisiae by allowing nine replicate populations to adapt to novel environments with complex sets of stressors. After >1000 asexual generations interspersed with 41 rounds of sexual reproduction, we assessed the mean effect of induced mutations on yeast growth in both the environment to which they had been adapting and the alternative novel environment. The mutations were deleterious on average, with the severity depending on the testing environment. However, we find no evidence that the adaptive match between genotype and environment is predictive of mutational fitness effects.

opencc-zeroApr 2024View details →

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Data from: The limit to evolutionary rescue depends on ploidy in yeast exposed to nystatin

<h4>Data package about haploid vs diploid adaptation to nystatin in yeast</h4> <div>This package contains files and scripts related to the publication "The limit to evolutionary rescue depends on ploidy in yeast exposed to nystatin". Raw data and analyses are included.</div>

opencc-by-4.0Apr 2024View details →

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Manual quantification of peroxisome counts in yeast from 2-channel fluorescence Z-stacks

This dataset contains fluorescence microscopy imaging data from various strains of Saccharomyces cerevisiae. The images were used to test software called perox-per-cell, which automatically quantifies peroxisome features in yeast cells based on microscopy data. There are 44 imaging instances in the dataset, each consisting of two Z-stacks, one capturing signal from calcofluor white to identify cell boundaries (blue channel), and one capturing signal from GFP tagged with peroxisome targeting sequence 1 (PTS1) to locate peroxisomes (green channel). These raw microscopy imaging sets are provided as ZVI files in Zstacks.zip. We compared perox-per-cell's automatically-generated peroxisome counts to those derived manually by two individuals. For manual counting, images were deconvolved with theoretically generated point spread functions using Axiovision software V4.9.1 SP2 followed by the generation of maximum intensity Z-projections (MIP) of both blue and green channels. All the deconvolved MIP images from WT and mutant strains were blinded and labelled as ‘1-44’, and their grey levels were set to ‘best fit’ in the Axiovision software prior to providing them to two individuals who manually counted peroxisomes in cells using the ‘measure events’ tool in Axiovision. The maximum intensity projection images used for manual counting are provided as ZVI files in MaxIntensityProjections.zip. Each individual's manual counts are included in this dataset within the CSV file ManualPeroxisomeCounts.csv. Please note that cell IDs in this file are only indicative of the order in which each individual counted peroxisomes, they do not indicate a specific cell within an image. For example, "Cell5" in Image 3 that was processed by manual counter 1 may not be the same cell as "Cell5" in Image3 processed by manual counter 2. These two entries have the same cell ID only because for both manual counters, they were the 5th cell counted. For our software test, we used wild-type (WT) yeast strains as well as several mutant strains with known peroxisomal defects. The strains used for each image are indicated in the ImageAndStrainTable.csv file. Experimental details: Saccharomyces cerevisiae cells were grown in synthetic defined medium (SD: 6.7 g/L Yeast nitrogen base without amino acids + 0.79 g/L CSM) with 2% Dextrose in flask cultures shaken at 250 rpm at 30 °C until log phase after which they were pelleted and resuspended in 50 µg/ml calcofluor white stain (Sigma, Cat No. 18909) for 5-10 min followed by imaging at room temperature. 3D images consisting of 26 XY images with a Z-slice spacing of 0.204 µm (total Z-stack thickness 5.1 µm) were acquired at 100× magnification using a fluorescence microscope (Axioskop 2 MOT plus, Carl Zeiss, Inc.) equipped with a Plan Apochromat 100×/1.4 Oil DIC objective, an Axio Cam HRm camera and an HBO 100 Mercury lamp. Identical exposure times (50 ms) were used to acquire the green channel images whereas the exposure time for blue channel was adjusted for individual images based on the intensity of calcofluor staining.

opencc-by-4.0May 2024View details →

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Figure 2 in Weathering of Torula Yeast Borax Food Bait and Capture of Oriental, Mediterranean, and Melon Fruit Flies in Hawaii (Diptera: Tephritidae)

Figure 2. Captures of Mediterranean fruit flies (males and females combined) in Multilure traps baited with torula yeast borax weathered 3, 6, 9, or 12 d. Traps operated for 2 d at weekly intervals over 5 consecutive weeks. Symbols represent means + 1 SE (N = 10 traps/treatment/sampling period).

opencc-by-4.0Dec 2022View details →

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Figure 1 in Weathering of Torula Yeast Borax Food Bait and Capture of Oriental, Mediterranean, and Melon Fruit Flies in Hawaii (Diptera: Tephritidae)

Figure 1. Captures of oriental fruit flies (males and females combined) in Multilure traps baited with torula yeast borax weathered 3, 6, 9, or 12 d. Traps operated for 2 d at weekly intervals over 8 consecutive weeks. Symbols represent means + 1 SE (N = 10 traps/treatment/sampling period).

opencc-by-4.0Dec 2022View details →

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Figure 3 in Weathering of Torula Yeast Borax Food Bait and Capture of Oriental, Mediterranean, and Melon Fruit Flies in Hawaii (Diptera: Tephritidae)

Figure 3. Captures of melon flies (males and females combined) in Multilure traps baited with torula yeast borax weathered 3, 6, 9, or 12 d. Traps operated for 2 d at weekly intervals over 4 consecutive weeks. Symbols represent means + 1 SE (N = 10 traps/treatment/sampling period).

opencc-by-4.0Dec 2022View details →

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Data from: Live-cell analysis of IMPDH protein levels during yeast colony growth provides insights into the regulation of GTP synthesis

Here we present real-time, live-cell analysis of accumulation of the Imd2 isoform of IMPDH in Saccharomyces cervisiae yeast cells forming a monolayer colony in a microfluidic device over a 50-hour time course. We observe two distinct phases of increased Imd2 accumulation: a guanine-insensitive phase early in outgrowth and a guanine-sensitive phase later, when cells become crowded. We show that the IMPDH inhibitor mycophenolic acid enhances both phases of increase. Deletion of a transcription attenuator upstream of the mRNA start site that decreases Imd2 mRNA synthesis in the presence of high GTP increases the baseline level of Imd2 protein ten-fold and abolishes guanine-sensitive but not guanine-insensitive induction. Our results suggest that at least two mechanisms of yeast Imd2 regulation exist, the known GTP-dependent attenuation of RNA polymerase II elongation and a GTP concentration-independent pathway that may be controlled by cell growth state.

opencc-zeroJun 2024View details →

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Figure 2 in EVALUATION OF THE EFFECTIVENESS OF USING A UNIVERSAL METHOD FOR ISOLATING GENOMIC dsDNA BY SALTING OUT TECHNIQUE ACCORDING TO THE S.M. ALJANABI AND I. MARTINEZ PROTOCOL FOR YEAST SACCHAROMYCES CEREVISIAE

Figure 2. Quantification of extracted Saccharomyces cerevisiae DNA by UVVis Spectrophotometry (DNA samples: 1–15).

opencc-by-4.0Dec 2022View details →

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Fig. 1 in Capture of Zeugodacus cucurbitae (Diptera: Tephritidae) in traps baited with torula yeast solution versus cucumber volatile plugs

Fig. 1. Captures of melon flies, Zeugodacus cucurbitae, in Multilure traps bait- ed with torula yeast borax solution or cucumber volatile plugs at low-capture sites (B, C, and E). Data were pooled among sites and over sampling weeks as described in the text. Bar heights represent means (± 1 SE) of 270 values (3 sites × 15 traps per trap type × 6 wk).

opencc-by-4.0Mar 2017View details →

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Fig. 2 in Capture of Zeugodacus cucurbitae (Diptera: Tephritidae) in traps baited with torula yeast solution versus cucumber volatile plugs

Fig. 2. Captures of melon flies, Zeugodacus cucurbitae, in Multilure traps bait- ed with torula yeast borax solution or cucumber volatile plugs over an 8 wk period at the intermediate-capture site (A). Points represent means (± 1 SE) of 15 traps per lure type.

opencc-by-4.0Mar 2017View details →

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Fig. 3 in Capture of Zeugodacus cucurbitae (Diptera: Tephritidae) in traps baited with torula yeast solution versus cucumber volatile plugs

Fig. 3. Captures of melon flies, Zeugodacus cucurbitae, in Multilure traps baited with torula yeast borax solution or cucumber volatile plugs over a 6 wk period at the high-capture site (D). Points represent means (± 1 SE) of 10 traps per lure type.

opencc-by-4.0Mar 2017View details →

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Fig. 3 in Isolation and characterization of unrecorded yeasts species in the family Metschnikowiaceae and Bulleribasidiaceae in Korea

Fig. 3. Phylogenetic tree derived from neighbor-joining analysis based on the D1/D2 domains of the LSU rRNA gene sequences, showing the placement of strains YP355, YP230 and YP366 in the genus Hannaella. Bulleromyces albus CBS 500T was used as outgroup. Bootstrap values of above 50% are given at nodes based on 1,000 replicates. Bar, 0.02 substitutions per site.

opencc-by-4.0Dec 2020View details →

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Fig. 2 in Isolation of wild yeasts from soils collected in Pochoen-si, Korea and characterization of unrecorded yeasts

Fig. 2. Neighbor-joining phylogenetic tree based on 26S rRNA gene sequences shows the relationship between the strains isolated in this study and their relatives of the genus Leucosporidium. Bar: 0.005 substitutions per site.

opencc-by-4.0Dec 2020View details →

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Fig. 2 in Isolation and characterization of unrecorded yeasts species in the family Metschnikowiaceae and Bulleribasidiaceae in Korea

Fig. 2. Phylogenetic tree derived from neighbor-joining analysis based on the D1/D2 domains of the LSU rRNA gene sequences, showing the placement of strain YI7 in the Kodamaea clade. Candida melibiosica CBS 5814T was used as outgroup. Bootstrap values of above 50% are given at nodes based on 1,000 replicates. Bar, 0.02 substitutions per site.

opencc-by-4.0Dec 2020View details →

ScienceDex guides

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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.

allen-brain-atlas

neuroscienceopenDocumentation, web resources, and API references are available online.

Last verified 2026-04-30Open record

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.

abode-home-cage

behavioral-neuroscienceopenThe DataShare record exposes download links for annotations, documentation, license text, and the zipped per-snippet data directory.

Last verified 2026-04-30Open record

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.

dandi-nwb

electrophysiologyopenPublished Dandiset metadata and archive endpoints are available through the production DANDI API.

Last verified 2026-04-30Open record

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.

ibl

behavioral-neuroscienceopenPublic sessions can be searched and loaded from the IBL public data server through ONE.

Last verified 2026-04-29Open record

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.

openneuro

neuroscienceopenPublished datasets are available on demand over the internet.

Last verified 2026-04-29Open record