Supplementary Materials

Gene essentiality and synthetic lethality in haploid human cells

Vincent A. Blomen, Peter Májek, Lucas T. Jae, Johannes W. Bigenzahn, Joppe Nieuwenhuis, Jacqueline Staring, Roberto Sacco, Ferdy R. van Diemen, Nadine Olk, Alexey Stukalov, Caleb Marceau, Hans Janssen, Jan E. Carette, Keiryn L. Bennett, Jacques Colinge, Giulio Superti-Furga, Thijn R. Brummelkamp

Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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  • Materials and Methods
  • Supplementary Text
  • Figs. S1 to S23
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Table S1
Essential Genes in KBM7 cells. For each gene we list insertion counts in sense and antisense orientation for the non-overlapping part of the gene's pre-mRNA. Biased genes that pass the noise-filter criterion for essentiality are listed with "YES" and the P-values and Q-values based on the noise-model are listed per gene. In addition, all insertion numbers for each independent replicate are listed in a separate tab.
Table S2
Essential Genes in HAP1 cells. For each gene we list insertion counts in sense and antisense orientation for the non-overlapping part of the gene's pre-mRNA. Biased genes that pass the noise-filter criterion for essentiality are listed with "YES" and the P-values and Q-values based on the noise-model are listed per gene. In addition, all insertion numbers for each independent replicate are listed in a separate tab.
Table S3
Shared and unique essential genes. A list of 'core' essential genes that are required for fitness of both HAP1 and KBM7 cells, in addition to genes that are essential uniquely in either cell type. Genes in orange are identified to have a fitness-effect in KBM7 cells and genes in green for HAP1.
Table S4
Essential genes and their yeast orthologs. A list of core essential genes that are detected via Ensembl to be homologous to genes essential in yeast or to genes important for fitness in yeast (1).
Table S5
Analysis of protein complexes with proteins encoded by essential genes. This table reports all the proteins identified in every pulldown with a multiple hypothesis-corrected P-value that was used to filter true from unlikely interactions. Bait AC = UniProtKB/Swissprot accession code of a bait; Prey AC = UniProtKB/Swissprot accession code of the preys; Interaction P-value = P-value according to the Decontaminator statistical model (see Materials and Methods); Prey adjusted P-value = a corrected P-value for the multiple hypotheses represented by the many potential preys identified for a bait; Bait and prey gene names are the official gene symbols; Replicate Ids = CeMM pulldown numbers identifying each replicate used in the data analysis; Spectral counts in replicates are the number of spectra identifying each protein in each replicate; Total spectral counts are the sums of the counts in each replicate; psm.mascot_scores=Mascot protein scores in each replicate; psm.phenyx_scores = Phenyx protein scores in each replicate; same columns for the negative control pulldowns; is_contaminant = known contaminants are maked with "TRUE"; is_carryover = when the bait of the previous pulldown is found as a prey for the next bait, this column contains a "TRUE" to indicate likely carryover due to high abundance in the previous sample; is_true_binder ="TRUE" if not a contaminant, not carryover, and the adjusted P-value<0.05.
Table S6
Overview of the number of mapped insertion sites preand post-normalization in each replicate for the synthetic lethality network. All datasets were normalized to the aggregated insertion counts of four wild-type HAP1 datasets; see Materials and Methods for normalization details. All gold transcripts of a gene are listed here, the first transcript of each gene is identified by the gene name, any additional transcripts are distinguished with suffixes ~2, ~3, etc.
Table S7
Functional link of the identified network genes to the secretory pathway. Genes identified in the synthetic lethality network were analyzed for their function. This table lists genes that could be linked to the secretory pathway with a reference to the published literature or online databases.
Table S8
Summary of read counts for all performed screens and the number of mapped unique insertion sites.