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idr0001-study.txt
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idr0001-study.txt
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"# Section with generic information about the study including title, description, publication details (if applicable) and contact details"
# Study
Comment[IDR Study Accession] idr0001
Study Title A genomic Multiprocess survey of machineries that control and link cell shape, microtubule organization, and cell-cycle progression.
Study Type high content screen
Study Type Term Source REF EFO
Study Type Term Accession EFO_0007550
Study Description Understanding cells as integrated systems requires that we systematically decipher how single genes affect multiple biological processes and how processes are functionally linked. Here, we used multiprocess phenotypic profiling, combining high-resolution 3D confocal microscopy and multiparametric image analysis, to simultaneously survey the fission yeast genome with respect to three key cellular processes: cell shape, microtubule organization, and cell-cycle progression. We identify, validate, and functionally annotate 262 genes controlling specific aspects of those processes. Of these, 62% had not been linked to these processes before and 35% are implicated in multiple processes. Importantly, we identify a conserved role for DNA-damage responses in controlling microtubule stability. In addition, we investigate how the processes are functionally linked. We show unexpectedly that disruption of cell-cycle progression does not necessarily affect cell size control and that distinct aspects of cell shape regulate microtubules and vice versa, identifying important systems-level links across these processes.
Study Organism Schizosaccharomyces pombe
Study Organism Term Source REF NCBITaxon
Study Organism Term Accession NCBITaxon_4896
Study Screens Number 1
Study External URL www.sysgro.org
Study Public Release Date 2016-04-27
# Study Publication
Study PubMed ID 25373780
Study Publication Title A genomic Multiprocess survey of machineries that control and link cell shape, microtubule organization, and cell-cycle progression.
Study Author List Graml V, Studera X, Lawson JLD, Chessel A, Geymonat M, Bortfeld-Miller M, Walter T, Wagstaff L, Piddini E, Carazo Salas RE
Study PMC ID PMC4648281
Study DOI http://dx.doi.org/10.1016/j.devcel.2014.09.005
# Study License and Data DOI
Study License CC BY 4.0
Study License URL https://creativecommons.org/licenses/by/4.0/
Study Copyright Graml et al
# Study Contacts
Study Person Last Name Carazo Salas
Study Person First Name Rafael
Study Person Email rafael.carazosalas@bristol.ac.uk
Study Person Address School of Cellular and Molecular Medicine, University of Bristol, United Kingdom
Study Person Roles submitter
Term Source Name NCBITaxon EFO CMPO PATO GO Fbbi
Term Source URI http://purl.obolibrary.org/obo/ http://www.ebi.ac.uk/efo/ http://www.ebi.ac.uk/cmpo/ http://purl.obolibrary.org/obo/ http://purl.obolibrary.org/obo/ http://purl.obolibrary.org/obo/
"# Section containing all information relative to each screen in the study including materials used, protocols names and description, phenotype names and description. For multiple assays this section should be repeated."
# Screen; this section should be repeated if a study contains multiple screens
Screen Number 1
Comment[IDR Screen Name] idr0001-graml-sysgro/screenA
Screen Sample Type cell
Screen Description Primary screen of fission yeast knock out mutants looking for genes controlling cell shape, microtubules, and cell-cycle progression. 262 genes controlling specific aspects of those processes are identifed, validated, and functionally annotated.
Screen Size Plates: 192 5D Images: 109728 Planes: 3511296 Average Image Dimension (XYZCT): 1376 x 1040 x 16 x 2 x 1 Total Tb: 10.06
Screen Example Images https://idr.openmicroscopy.org/webclient/?show=well-592362 https://idr.openmicroscopy.org/webclient/img_detail/1239777/ JL_120809_S14B;H10
Screen Imaging Method spinning disk confocal microscopy
Screen Imaging Method Term Source REF Fbbi
Screen Imaging Method Term Accession FBbi_00000253
Screen Technology Type gene deletion screen
Screen Technology Term Source REF EFO
Screen Technology Term Accession EFO_0007552
Screen Type primary screen
Screen Type Term Source REF EFO
Screen Type Term Accession EFO_0007556
Screen Comments 3 plates have missing files and could not be correctly visualized. They have been deleted from the screen in the IDR: JL_120904_S32B, JL_130305_R1_6 and X_110227_S3) leaving 192 plates.
"# Library section. The library file should be supplied separately and it should contain the reagents description including, at the absolute minimum: reagent ID, sequences and position in the layout (= plate + position in the plate)"
Library File Name idr0001-screenA-library.txt
Library File Format tab-delimited text
Library Type haploid deletion library
Library Type Term Source REF EFO
Library Type Term Accession EFO_0007561
Library Manufacturer "Bioneer, Korea "
Library Version Bioneer haploid deletion library v.2 modified to generate a GFP-tubulin expressing library (Dixon et al., 2008). http://eng.bioneer.com/products/YeastGenome/Library-overview.aspx.
Library Experimental Conditions none
Library Experimental Conditions Term Source REF
Library Experimental Conditions Term Accession
Quality Control Description
# Protocols
Protocol Name growth protocol HCS library protocol HCS image acquistion and feature extraction protocol HCS data analysis protocol
Protocol Type growth protocol HCS library protocol HCS image acquistion and feature extraction protocol HCS data analysis protocol
Protocol Type Term Source REF EFO EFO EFO EFO
Protocol Type Term Accession EFO_0003789 EFO_0007571 EFO_0007572 EFO_0007573
Protocol Description KO mutants were grown exponentially for >48 hr and imaged in 96-well micro- plates (lectin-coated glass bottom, 10 mg/well) containing Cascade Blue Dextran-labeled YES medium (0.1 mg/ml). The Bioneer haploid deletion (knockout, KO) library v.2 (Bioneer, Korea) was modified to generate a GFP-tubulin expressing library (Dixon et al., 2008). Two-color images were acquired using an automated OperaLX spinning-disk confocal microscope (Perkin Elmer) with 603 water-immersion objective (NA 1.2). Six stacks of 16 z planes 0.4 mm separation were collected for each well. The entire genomic KO library was filmed twice. Customized software was used for image analysis and feature extraction. Cell shape or microtubule hits were KO strains with a: (1) low Kolmogorov- Smirnov p value relative to a mean wild-type for any one feature, or (2) signif- icant Euclidean distance deviation from a mean wild-type across many features. Cell-cycle progression hits were KOs with the proportion of cells in greater than two 2-cell cycle stages outside the 95% bootstrap confidence interval of the corresponding wild-type stages. Genotypic and visual quality controls were done for corroboration. Hits were large-scale validated with ten times independent rescreening (see Protocol) and if picked in R35% of cases kept as high-confidence hits for analysis. Support vector machine clas- sifiers assigned eight phenotypic classes to cell shape hits. ERA rates (Kafri et al., 2013) were calculated for cell-cycle progression hits. Clustering used R, functional GO assignments DAVID, Bayesian analysis, and the R package bnlearn (Scutari, 2010).
# Phenotypes
Phenotype Name abnormal microtubule cytoskeleton morphology during mitotic interphase long cytoplasmic microtubules short cytoplasmic microtubules microtubule bundles present in greater numbers viable curved vegetative cell viable elongated vegetative cell viable stubby vegetative cell viable vegetative cell with abnormal cell shape S-shaped cell viable pear-shaped vegetative cell viable spheroid vegetative cell abnormal mitotic cell cycle phase IP increased IP reduced SP increased SP reduced PAA increased PAA reduced IP2 increased
Phenotype Description We used two complementary strategies for detecting KO mu- tants with aberrant cell shape or microtubules (hits; Figures 1B, 1C, and S4). The first strategy identified mutants with a prominent alteration in a single feature (p value; Figure 1). The second strat- egy identified mutants with multiple subtle feature alterations (multiparametric profile scoring, Figure 1) We used two complementary strategies for detecting KO mu- tants with aberrant cell shape or microtubules (hits; Figures 1B, 1C, and S4). The first strategy identified mutants with a prominent alteration in a single feature (p value; Figure 1). The second strat- egy identified mutants with multiple subtle feature alterations (multiparametric profile scoring, Figure 1) We used two complementary strategies for detecting KO mutants with aberrant cell shape or microtubules (hits; Figures 1B, 1C, and S4). The first strategy identified mutants with a prominent alteration in a single feature (p value; Figure 1). The second strategy identified mutants with multiple subtle feature alterations (multiparametric profile scoring, Figure 1) We used two complementary strategies for detecting KO mu- tants with aberrant cell shape or microtubules (hits; Figures 1B, 1C, and S4). The first strategy identified mutants with a prominent alteration in a single feature (p value; Figure 1). The second strat- egy identified mutants with multiple subtle feature alterations (multiparametric profile scoring, Figure 1) Cell shape hit classification was done using eight support vector machine classifiers trained to recognize eight basic phenotypic classes on an individual cell basis: stubby (wide), banana (curved), orb (round), kinky (S-shaped), long (elongated), skittle (with one side wider than the other), and T-shaped (branched). Cell shape hit classification was done using eight support vector machine classifiers trained to recognize eight basic phenotypic classes on an individual cell basis: stubby (wide), banana (curved), orb (round), kinky (S-shaped), long (elongated), skittle (with one side wider than the other), and T-shaped (branched). Cell shape hit classification was done using eight support vector machine classifiers trained to recognize eight basic phenotypic classes on an individual cell basis: stubby (wide), banana (curved), orb (round), kinky (S-shaped), long (elongated), skittle (with one side wider than the other), and T-shaped (branched). Cell shape hit classification was done using eight support vector machine classifiers trained to recognize eight basic phenotypic classes on an individual cell basis: stubby (wide), banana (curved), orb (round), kinky (S-shaped), long (elongated), skittle (with one side wider than the other), and T-shaped (branched). Cell shape hit classification was done using eight support vector machine classifiers trained to recognize eight basic phenotypic classes on an individual cell basis: stubby (wide), banana (curved), orb (round), kinky (S-shaped), long (elongated), skittle (with one side wider than the other), and T-shaped (branched). Cell shape hit classification was done using eight support vector machine classifiers trained to recognize eight basic phenotypic classes on an individual cell basis: stubby (wide), banana (curved), orb (round), kinky (S-shaped), long (elongated), skittle/pear (with one side wider than the other), and T-shaped (branched). Cell shape hit classification was done using eight support vector machine classifiers trained to recognize eight basic phenotypic classes on an individual cell basis: stubby (wide), banana (curved), orb (round), kinky (S-shaped), long (elongated), skittle (with one side wider than the other), and T-shaped (branched). To detect KO mutants (hits) with altered cell-cycle progression, we used bootstrap statistics to estimate the typical proportions of wild-type cells in each cell-cycle stage, scoring as hits KOs where at least two cell-cycle stages were statistically disproportionate with respect to the wild-type (i.e., under- or overrepresented; Figure 1D). To detect KO mutants (hits) with altered cell-cycle progression, we used bootstrap statistics to estimate the typical proportions of wild-type cells in each cell-cycle stage, scoring as hits KOs where at least two cell-cycle stages were statistically disproportionate with respect to the wild-type (i.e., under- or overrepresented; Figure 1D). To detect KO mutants (hits) with altered cell-cycle progression, we used bootstrap statistics to estimate the typical proportions of wild-type cells in each cell-cycle stage, scoring as hits KOs where at least two cell-cycle stages were statistically disproportionate with respect to the wild-type (i.e., under- or overrepresented; Figure 1D). To detect KO mutants (hits) with altered cell-cycle progression, we used bootstrap statistics to estimate the typical proportions of wild-type cells in each cell-cycle stage, scoring as hits KOs where at least two cell-cycle stages were statistically disproportionate with respect to the wild-type (i.e., under- or overrepresented; Figure 1D). To detect KO mutants (hits) with altered cell-cycle progression, we used bootstrap statistics to estimate the typical proportions of wild-type cells in each cell-cycle stage, scoring as hits KOs where at least two cell-cycle stages were statistically disproportionate with respect to the wild-type (i.e., under- or overrepresented; Figure 1D). To detect KO mutants (hits) with altered cell-cycle progression, we used bootstrap statistics to estimate the typical proportions of wild-type cells in each cell-cycle stage, scoring as hits KOs where at least two cell-cycle stages were statistically disproportionate with respect to the wild-type (i.e., under- or overrepresented; Figure 1D). To detect KO mutants (hits) with altered cell-cycle progression, we used bootstrap statistics to estimate the typical proportions of wild-type cells in each cell-cycle stage, scoring as hits KOs where at least two cell-cycle stages were statistically disproportionate with respect to the wild-type (i.e., under- or overrepresented; Figure 1D). To detect KO mutants (hits) with altered cell-cycle progression, we used bootstrap statistics to estimate the typical proportions of wild-type cells in each cell-cycle stage, scoring as hits KOs where at least two cell-cycle stages were statistically disproportionate with respect to the wild-type (i.e., under- or overrepresented; Figure 1D).
Phenotype Score Type automated automated automated automated automated automated automated automated automated automated automated automated automated automated automated automated automated automated automated
Phenotype Term Source REF CMPO CMPO CMPO CMPO CMPO CMPO CMPO CMPO CMPO CMPO CMPO CMPO CMPO CMPO CMPO CMPO CMPO CMPO CMPO
Phenotype Term Name abnormal microtubule cytoskeleton morphology during mitotic interphase elongated cytoplasmic microtubules phenotype shortened cytoplasmic microtubules phenotype increased number of microtubule bundle phenotype curved cell phenotype elongated cell phenotype stubby cell phenotype abnormal cell shape phenotype S-shaped cell phenotype pear-shaped cell phenotype round cell phenotype abnormal mitotic cell cycle phase phenotype more cells with interphase microtubule arrays phenotype fewer cells with interphase microtubule arrays phenotype more cells with metaphase microtubule spindles phenotype fewer cells with metaphase microtubule spindles phenotype more cells with G1 phase microtubule arrays phenotype fewer cells with G1 phase microtubule arrays phenotype more cells with S phase microtubule arrays phenotype
Phenotype Term Accession CMPO_0000438 CMPO_0000370 CMPO_0000371 CMPO_0000372 CMPO_0000365 CMPO_0000077 CMPO_0000367 CMPO_0000116 CMPO_0000364 CMPO_0000366 CMPO_0000118 CMPO_0000437 CMPO_0000383 CMPO_0000388 CMPO_0000378 CMPO_0000387 CMPO_0000412 CMPO_0000410 CMPO_0000413
Phenotype Term Source REF CMPO
Phenotype Term Name more cells with G1 phase microtubule arrays phenotype
Phenotype Term Accession CMPO_0000412
# Raw Data Files
Raw Image Data Format Evotec/PerkinElmer Opera Flex
Raw Image Organization The genome wide screen was repeated twice and then a follow up replicates focussed on genes which showed possible phentoypes in the first two replicates. 35 x 96 well plates in the first replicate, 68 in the second and 92 in the third (total 195 plates). Approximately 6 images taken per well (fields). 3 plates have missing files and could not be correctly visualized. They have been deleted from the screen in the IDR: JL_120904_S32B, JL_130305_R1_6 and X_110227_S3) leaving 192 plates.
# Feature Level Data Files (give individual file details unless there is one file per well)
Feature Level Data File Name sysgroFeature_repeat1.tsv
Feature Level Data File Format tab-delimited text
Feature Level Data File Description Each line is one single cell segmented in one particular image. 153 columns. See Table S1 of the PubMed:25373780 paper for more detail on what each measurement is.
Feature Level Data Column Name reference name description alternativeName experimentName imageName plateName well strainID extent maxThetaConvex nbSkelEnds widthLeft predictedLong sumGreen avgValNCBlack nbSymmEle meanCurvnessConcave h3s relGradient sampleStdIrglBlack meanCurvnessConvex curvatureCircLong z10 h13s z12 lenConvex z11 z14 z13 z16 solidity z15 sumGreen112 z18 z17 z19 h4s maxTheta nbConvex z21 nbConcave z20 nbSeg h12s z23 z22 z25 z24 z27 sampleStdIrglWhite avgValNCWhite z26 z29 sampleMeanIrglWhite z28 predictedBanana widthRatio curvatureCircLength sampleMeanIrglBlack h5s sampleMeanNCWhite avgValIrglBlack z30 widthRight maxThetaConcave curvatureCirc h6s meanTheta eccentricity coordinates predictedMT width h7s h10 h12 h11 maxValIrglBlack h13 f1 f2 f3 f4 f5 meanThetaConvex minLen meanThetaConcave predictedWt sumGreen36 lenConcave maxLen area h8s predictedSeg equivdiameter predictedTshape perimeter minTheta maxValNCBlack maxValIrglWhite sampleStdNCBlack curvatureCircLongLength h9s relLengthGradient skelLength h1 h2 h1s h3 predictedSkittle h4 h5 predictedStubby h6 h7 h8 h9 avgValIrglWhite h11s predictedOrb predictedKinky nbSkelJunc orientation relStretchGradient h2s length centroid_x centroid_y maxValNCWhite sampleStdNCWhite z1 z2 z3 z4 meanLen z5 z6 sampleMeanNCBlack h10s z7 z8 z9 mt_maxCurvature mt_orientation mt_maxIntensity mt_meanCurvature mt_meanIntensity mt_minDistFirstCellEnd mt_length mt_totalCurvature mt_totalIntensity mt_minDistSecondCellEnd mt_count
Feature Level Data Column Description information on the gene/strain which was in the well information on the gene/strain which was in the well information on the gene/strain which was in the well information on the gene/strain which was in the well information of what (physical) well the image that cell is from was in. In particular, the image with that cell is: experimentName/plateName/imageName.flex information of what (physical) well the image that cell is from was in. In particular, the image with that cell is: experimentName/plateName/imageName.flex information of what (physical) well the image that cell is from was in. In particular, the image with that cell is: experimentName/plateName/imageName.flex information of what (physical) well the image that cell is from was in. In particular, the image with that cell is: experimentName/plateName/imageName.flex information on the gene/strain which was in the well numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature coordinates in pixel of the outline of that cell numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature numerical feature
# Processed Data Files
Processed Data File Name idr0001-screenA-processed.txt
Processed Data File Format tab-delimited text
Processed Data File Description This file contains information about the phenotypes observed, their reproducibility per gene and conservation across species.
Processed Data Column Name Gene Identifier Gene Symbol Reproducibility of Shape Hits Reproducibility of microtubule hits Reproducibility of cell cycle progression hits Visual Shape Hit Visual Microtubule Hit Conservation in S. cerevisiae Conservation in Vertebrates Conservation in H. sapiens Mineotaur Hit Type Has Phenotype Phenotype Annotation Level Phenotype 1 Phenotype 2 Phenotype 3 Phenotype 4 Phenotype 5 Phenotype 6 Phenotype 7 Phenotype 8 Phenotype 9 Phenotype 10 Phenotype 11 Phenotype 12 Phenotype 13 Phenotype 14 Phenotype 15 Phenotype 16 Phenotype 17 Phenotype 18 Phenotype 19
Processed Data Column Type gene identifier gene symbol data data data data data data data data data other other phenotype phenotype phenotype phenotype phenotype phenotype phenotype phenotype phenotype phenotype phenotype phenotype phenotype phenotype phenotype phenotype phenotype phenotype phenotype
Processed Data Column Annotation Level multiple replicates of reagent multiple replicates of reagent multiple replicates of reagent gene gene gene gene gene phenotype gene gene gene gene gene gene gene gene gene gene gene gene gene gene gene gene gene gene gene
Processed Data Column Description The identifier for the target gene The target gene that has been knocked out in the strain How many screening rounds provided sufficient data for analysis of shape and for how many of these a particular deletion was detected as a hit How many screening rounds provided sufficient data for analysis of microtubules and for how many of these a particular deletion was detected as a hit How many screening rounds provided sufficient data for analysis of cell cycle progression and for how many of these a particular deletion was detected as a hit Whether it was visually corroborated in the first genomic screen by a human observer Whether it was visually corroborated in the first genomic screen by a human observer The genes' conservation in other S. cerevisiae The genes' conservation in vertebrates The genes' conservation in H. sapiens Classification of the hit type for the Mineotaur software to use as hit type labels. Whether there is a phenotype associated with the entity in the row. The level of entity that is annotated with the phenotype. Phenotype observed among cells with this gene deletion Phenotype observed among cells with this gene deletion Phenotype observed among cells with this gene deletion Phenotype observed among cells with this gene deletion Phenotype observed among cells with this gene deletion Phenotype observed among cells with this gene deletion Phenotype observed among cells with this gene deletion Phenotype observed among cells with this gene deletion Phenotype observed among cells with this gene deletion Phenotype observed among cells with this gene deletion Phenotype observed among cells with this gene deletion Phenotype observed among cells with this gene deletion Phenotype observed among cells with this gene deletion Phenotype observed among cells with this gene deletion Phenotype observed among cells with this gene deletion Phenotype observed among cells with this gene deletion Phenotype observed among cells with this gene deletion Phenotype observed among cells with this gene deletion Phenotype observed among cells with this gene deletion
Processed Data Column Link To Library File Gene Identifier