Data from: Phenotypic stutter steps in experimentally evolved multicellularity

This BBC_2024__README.txt file was generated on 2024-09-25 by Beatriz Baselga Cervera

GENERAL INFORMATION

1. Title of Dataset and code: Data from: Phenotypic stutter steps in experimentally evolved multicellularity.

2. Author Information

            Corresponding Investigator

                        Name: Dr Beatriz Baselga-Cervera

                        Institution: University of Minnesota Twin Cities, Minnesota, US.

                        Email: [e-mail]; [e-mail]

            Co-investigator 1

                        Name: Dr Nahui Olin Medina-Chávez

                        Institution: University of Minnesota Twin Cities, Minnesota, US.

                        Email: [e-mail]

            Co-investigator 2

                        Name: Dr Michael Travisano

                        Institution: University of Minnesota Twin Cities, Minnesota, US.

                        Email:[e-mail]

4.Data collectors: Dr Beatriz Baselga-Cervera & Dr. Nahui Olin Medina-Chávez.

5. Date of data collection: 2023-2024

6. Geographic location of data collection: Saint Paul, US

5. Funding sources that supported data collection: Fundación Alfonso Martín Escudero, Madrid, Spain (BBC).

6. Recommended citation for this dataset: Baselga-Cervera et al. (2024), Data from: Phenotypic stutter steps in experimentally evolved multicellularity. Zenodo. Data set.

DATA & FILE OVERVIEW

1. Description of dataset

In this study, we address whether stochastic phenotypic switching can shape biological diversity contributing to evolutionary change across the transition from single cells to multicellular clutters in Saccharomyces cerevisiae multicellular yeast system. Population's characterization was conducted with a Coulter Counter multisize 4, and a FlowCam 3, by colony morphology, under the optic microscope, via ACE2 gene sequencing and RNA sequencing. 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).

2. File list:

Coulter Counter size distribution data: 

File 1 name:  File_1_Coulter_Counter_Counts_20h.csv

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 20hgrowth. 

File 2 name:  File_2_Coulter_Counter_Counts_24h.csv

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 24h growth. 

File 3 name:  File_3_Coulter_Counter_Counts_48h.csv

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 48h growth. 

File name:  File_4_Coulter_Counter_Counts_Constructed_strains_diversity.csv

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 after gravitational  selection of five resuspended colonies from three isolates per strain.

File 5 name:  File_5_Coulter_Counter_Counts_Selection_Experiment.xlsx

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 and maintaining lineages based on colony morphology.

FlowCam data:

File 6 name: File_6_Rawdata_Flowcam_all.csv

File 6 desciption: 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 generated statistically:

File 7 name: File_7_C1W8.2_overlapPairs_Selection_Experiment.csv

File 7 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.

File 8 name: File_8_C1W8.1_overlapPairs_Selection_Experiment.csv

File 8 description: overlapping indexes (η) of the KDE distributions were computed using the R-package ‘overlapping’ from the Coulter Counter data of the C1W8.1 derived strain over the selection experiment.

File 9 name: File_9_ overlapPairs_Constructed_strains_diversity.xlsx

File 9 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.

Pictures:

File 10 name: File_8_Colonies_Pictures_Constructed_strains.zip

File 10 description: constructed ACE2 knockout and a strain containing the homozygous missense mutation (ACE2 c.1934 A>T) YPD agar plates and magnifications when dilution plating the small size fraction of the population.

ARN data

File 11 name: File_11_rnaseq-final-results-Top_v_Bottom.xlsx

File 11 description: RNA analyses top vs. bottom phenotypic subdistributions' final results. The Top subdistribution is used as control.

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) and Standard minimal (SD; Yeast nitrogen base with amino acids (YNB w/AA) 6.7 g L-1, 0.5% (v/w) D-glucose).

Phenotypic characterization of the different strains was conducted in a Coulter Counter Multisizer 4 and FlowCam® 3.0 Fluid Imaging Technologies, colony morphology, and optic microscopy. 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 of four extracted samples per treatment with the highest RNA integrity score were submitted for TrueSeq Stranded RNA-Seq.

3. Detailed description

Coulter Counter size distribution data of all the populations: 

File 1 name:  File_1_Coulter_Counter_Counts_20h.csv

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.

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Column 1: Volumen (um3)

Column 2: Diameter (um2)

Columns 3 to the last column: strains counts.

File 2 name:  File_2_Coulter_Counter_Counts_24h.csv

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.

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Column 1: Volumen (um3)

Column 2: Diameter (um2)

Columns 3 to the last column: strains counts.

File 3 name:  File_3_Coulter_Counter_Counts_48h.csv

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.

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Column 1: Volumen (um3)

Column 2: Diameter (um2)

Column 3 to the last column: strains counts.

File_4_Coulter_Counter_Counts_Constructed_strains_diversity.csv

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.

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Column 1: Volumen (um3)

Column 2: Diameter (um2)

Column 3 to the last column: strains counts.

File_5_Coulter_Counter_Counts_Selection_Experiment.xlsx

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.

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Column 1: Volumen (um3)

Column 2: Diameter (um2)

Column 3 to the last column: strains counts.

File 6 name: File_3_Rawdata_Flowcam_all.csv

File 6 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.

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                                                                        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.

File 7 name: File_7_C1W8.2_overlapPairs_Selection_Experiment.csv

File 7 description: C1W8.2 _lineage_selection.cycle= C1W8.2 evolved multicellular strain, lineage (A=ancestral, M1= rugose colony morphology lineage 1,  M2= rugose colony morphology lineage 2 , M3= rugose colony morphology lineage 3 , U1= rough colony morphology lineage 1, U2= rough colony morphology lineage 2, U3= rough colony morphology lineage 3) and selection cycle  (0, 1, 2 and 3).

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Column 1: Var1= strain 1

Column 2: Var2= strain 2

Column 3: overlap value of both strains compared.

File 8 name: File_8_C1W8.1_overlapPairs_Selection_Experiment.csv

File 8 description: C1W8.1 _lineage_selection.cycle =C1W8.1 evolved multicellular strain, lineage (A=ancestral, M1= rugose colony morphology lineage 1,  M2= rugose colony morphology lineage 2 , M3= rugose colony morphology lineage 3 , U1= rough colony morphology lineage 1, U2= rough colony morphology lineage 2, U3= rough colony morphology lineage 3) and selection cycle  (0, 1, 2 and 3).

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Column 1: Var1= strain 1

Column 2: Var2= strain 2

Column 3: overlap value of both strains compared.

File 9 name: File_9_overlapPairs_Constructed_strains_diversity.xlsx

File 9 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).

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Column 1: Var1= strain 1

Column 2: Var2= strain 2

Column 3: overlap value of both strains compared.

File 10 name: File_10_Colonies_Pictures_Constructed_strains.zip

File 10 description: colony pictures by strain. Strains: Strains; ace2x2 m=strains containing the ACE2 missense mutation (ACE2 c.1934 A>T); ace2x2= ACE2 knockout.

File 11 name: File_11_rnaseq-final-results-Top_v_Bottom.xlsx

File 11 description:

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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