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atcc a673 cells  (ATCC)


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    ATCC atcc a673 cells
    Atcc A673 Cells, supplied by ATCC, used in various techniques. Bioz Stars score: 96/100, based on 592 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    (A) MSH2 and Actin protein levels showed for <t>A673</t> (MSH2-wild-type), 319-N1-CI31 (Msh2-edited mouse small cell lung cancer cell line (see Figure S1)), and MSH2-edited A673-M1 and A673-M8 (right panel for A673-M8 cells performed in an independent blot, as stated by the break between the first three lanes and A673-M8). (B) Capillary electrophoresis histogram of microsatellite Bat26 locus for A673, A673-M1 and A673-M8. The most prominent peaks in the histogram determine the allele size is shown (solid blue). (C) Table of microsatellites assessed in A673 cells. Difference in the dominant allele size between the parental A673 and each MMR deficient cell line is indicated. Number of microsatellites affected in relation to the number of microsatellites studied displayed in the last column. (D) Number of somatic mutations present in A673-M1, and A673-M8 identified by exome sequencing. Parental A673 cells were used as a normal reference. Mutations with an allelic fraction (AF) higher or equal to 0.15 were reported. (E) Crystal violet staining of A673 (MSH2-wild-type), A673-M1 (MSH2-null), A673-M8 (MSH2-null), and HCT116 (MLH1-null) cells following compound selection. Concentrations used for selection shown in each panel. See also Figure S1 and S2.
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    (A) MSH2 and Actin protein levels showed for <t>A673</t> (MSH2-wild-type), 319-N1-CI31 (Msh2-edited mouse small cell lung cancer cell line (see Figure S1)), and MSH2-edited A673-M1 and A673-M8 (right panel for A673-M8 cells performed in an independent blot, as stated by the break between the first three lanes and A673-M8). (B) Capillary electrophoresis histogram of microsatellite Bat26 locus for A673, A673-M1 and A673-M8. The most prominent peaks in the histogram determine the allele size is shown (solid blue). (C) Table of microsatellites assessed in A673 cells. Difference in the dominant allele size between the parental A673 and each MMR deficient cell line is indicated. Number of microsatellites affected in relation to the number of microsatellites studied displayed in the last column. (D) Number of somatic mutations present in A673-M1, and A673-M8 identified by exome sequencing. Parental A673 cells were used as a normal reference. Mutations with an allelic fraction (AF) higher or equal to 0.15 were reported. (E) Crystal violet staining of A673 (MSH2-wild-type), A673-M1 (MSH2-null), A673-M8 (MSH2-null), and HCT116 (MLH1-null) cells following compound selection. Concentrations used for selection shown in each panel. See also Figure S1 and S2.
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    (A) MSH2 and Actin protein levels showed for <t>A673</t> (MSH2-wild-type), 319-N1-CI31 (Msh2-edited mouse small cell lung cancer cell line (see Figure S1)), and MSH2-edited A673-M1 and A673-M8 (right panel for A673-M8 cells performed in an independent blot, as stated by the break between the first three lanes and A673-M8). (B) Capillary electrophoresis histogram of microsatellite Bat26 locus for A673, A673-M1 and A673-M8. The most prominent peaks in the histogram determine the allele size is shown (solid blue). (C) Table of microsatellites assessed in A673 cells. Difference in the dominant allele size between the parental A673 and each MMR deficient cell line is indicated. Number of microsatellites affected in relation to the number of microsatellites studied displayed in the last column. (D) Number of somatic mutations present in A673-M1, and A673-M8 identified by exome sequencing. Parental A673 cells were used as a normal reference. Mutations with an allelic fraction (AF) higher or equal to 0.15 were reported. (E) Crystal violet staining of A673 (MSH2-wild-type), A673-M1 (MSH2-null), A673-M8 (MSH2-null), and HCT116 (MLH1-null) cells following compound selection. Concentrations used for selection shown in each panel. See also Figure S1 and S2.
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    (A) MSH2 and Actin protein levels showed for <t>A673</t> (MSH2-wild-type), 319-N1-CI31 (Msh2-edited mouse small cell lung cancer cell line (see Figure S1)), and MSH2-edited A673-M1 and A673-M8 (right panel for A673-M8 cells performed in an independent blot, as stated by the break between the first three lanes and A673-M8). (B) Capillary electrophoresis histogram of microsatellite Bat26 locus for A673, A673-M1 and A673-M8. The most prominent peaks in the histogram determine the allele size is shown (solid blue). (C) Table of microsatellites assessed in A673 cells. Difference in the dominant allele size between the parental A673 and each MMR deficient cell line is indicated. Number of microsatellites affected in relation to the number of microsatellites studied displayed in the last column. (D) Number of somatic mutations present in A673-M1, and A673-M8 identified by exome sequencing. Parental A673 cells were used as a normal reference. Mutations with an allelic fraction (AF) higher or equal to 0.15 were reported. (E) Crystal violet staining of A673 (MSH2-wild-type), A673-M1 (MSH2-null), A673-M8 (MSH2-null), and HCT116 (MLH1-null) cells following compound selection. Concentrations used for selection shown in each panel. See also Figure S1 and S2.
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    (A) MSH2 and Actin protein levels showed for <t>A673</t> (MSH2-wild-type), 319-N1-CI31 (Msh2-edited mouse small cell lung cancer cell line (see Figure S1)), and MSH2-edited A673-M1 and A673-M8 (right panel for A673-M8 cells performed in an independent blot, as stated by the break between the first three lanes and A673-M8). (B) Capillary electrophoresis histogram of microsatellite Bat26 locus for A673, A673-M1 and A673-M8. The most prominent peaks in the histogram determine the allele size is shown (solid blue). (C) Table of microsatellites assessed in A673 cells. Difference in the dominant allele size between the parental A673 and each MMR deficient cell line is indicated. Number of microsatellites affected in relation to the number of microsatellites studied displayed in the last column. (D) Number of somatic mutations present in A673-M1, and A673-M8 identified by exome sequencing. Parental A673 cells were used as a normal reference. Mutations with an allelic fraction (AF) higher or equal to 0.15 were reported. (E) Crystal violet staining of A673 (MSH2-wild-type), A673-M1 (MSH2-null), A673-M8 (MSH2-null), and HCT116 (MLH1-null) cells following compound selection. Concentrations used for selection shown in each panel. See also Figure S1 and S2.
    A141b1 Cell Line Atcc Crl 1423 A673 Cells Cell Line Atcc Crl, supplied by ATCC, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    (A) MSH2 and Actin protein levels showed for A673 (MSH2-wild-type), 319-N1-CI31 (Msh2-edited mouse small cell lung cancer cell line (see Figure S1)), and MSH2-edited A673-M1 and A673-M8 (right panel for A673-M8 cells performed in an independent blot, as stated by the break between the first three lanes and A673-M8). (B) Capillary electrophoresis histogram of microsatellite Bat26 locus for A673, A673-M1 and A673-M8. The most prominent peaks in the histogram determine the allele size is shown (solid blue). (C) Table of microsatellites assessed in A673 cells. Difference in the dominant allele size between the parental A673 and each MMR deficient cell line is indicated. Number of microsatellites affected in relation to the number of microsatellites studied displayed in the last column. (D) Number of somatic mutations present in A673-M1, and A673-M8 identified by exome sequencing. Parental A673 cells were used as a normal reference. Mutations with an allelic fraction (AF) higher or equal to 0.15 were reported. (E) Crystal violet staining of A673 (MSH2-wild-type), A673-M1 (MSH2-null), A673-M8 (MSH2-null), and HCT116 (MLH1-null) cells following compound selection. Concentrations used for selection shown in each panel. See also Figure S1 and S2.

    Journal: Cell chemical biology

    Article Title: Engineering forward genetics into cultured cancer cells for chemical target identification

    doi: 10.1016/j.chembiol.2019.06.006

    Figure Lengend Snippet: (A) MSH2 and Actin protein levels showed for A673 (MSH2-wild-type), 319-N1-CI31 (Msh2-edited mouse small cell lung cancer cell line (see Figure S1)), and MSH2-edited A673-M1 and A673-M8 (right panel for A673-M8 cells performed in an independent blot, as stated by the break between the first three lanes and A673-M8). (B) Capillary electrophoresis histogram of microsatellite Bat26 locus for A673, A673-M1 and A673-M8. The most prominent peaks in the histogram determine the allele size is shown (solid blue). (C) Table of microsatellites assessed in A673 cells. Difference in the dominant allele size between the parental A673 and each MMR deficient cell line is indicated. Number of microsatellites affected in relation to the number of microsatellites studied displayed in the last column. (D) Number of somatic mutations present in A673-M1, and A673-M8 identified by exome sequencing. Parental A673 cells were used as a normal reference. Mutations with an allelic fraction (AF) higher or equal to 0.15 were reported. (E) Crystal violet staining of A673 (MSH2-wild-type), A673-M1 (MSH2-null), A673-M8 (MSH2-null), and HCT116 (MLH1-null) cells following compound selection. Concentrations used for selection shown in each panel. See also Figure S1 and S2.

    Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Msh2 [D24B5] XP rabbit mAb Cell Signaling Technology Cat#2017 Anti-β-actin (8H10D10) mouse mAb Cell Signaling Technologies Cat#3700 IRDye 800CW donkey anti-rabbit IgG (H+L) LI-COR Cat#926-32213 IRDye 680RD donkey anti-mouse IgG (H+L) LI-COR Cat#926-68072 Bacterial and Virus Strains Biological Samples Chemicals, Peptides, and Recombinant Proteins Bortezomib Selleck Chemicals Cat#S1013; CAS ID: 179324-69-7 Etoposide Sigma-Aldrich Cat#E1383; CAS ID: 33419-42-0 CD437 Sigma-Aldrich Cat#C5865; CAS ID: 125316-60-1 MLN4924 ApexBio Cat#B1036; CAS ID: 905579-51-3 Critical Commercial Assays CellTiter-Glo luminescent cell viability assay Promega Cat#G7571 Deposited Data WES from human and mouse cell lines This paper SRA ID: PRJNA543281 Experimental Models: Cell Lines Ewing sarcoma A673 cell lines ATCC ATCC® CRL-1598™ Trp53fl/fl; Rb1fl/fl; Rbl2fl/fl; RosaLSL-Tomato/+ murine SCLC cell lines This paper N/A 293T/17 ATCC ATCC® CRL-11268™ Experimental Models: Organisms/Strains Mouse: Trp53 fl/fl Rb fl/fl P130 fl/fl Schaffer et al., 2010 Mouse: Trp53 fl/fl JAX: 008462 Mouse: Rb fl/fl JAX: 008186 Mouse: P130 fl/fl JAX: 008177 Oligonucleotides Primers for PCR and sequencing of PSMB5 and POLA1 , see Table S3 This paper N/A Recombinant DNA LentiCRISPR V2 plasmid Addgene Cat#52961 psPAX2 plasmid Addgene Cat#12260 pMD2.G plasmid Addgene Cat#12259 Software and Algorithms Genome Analysis Toolkit (GATK, v3.8-0) DePristo et al., 2011 ; McKenna et al., 2010 N/A NGS QC Toolkit (v2.3.3) Patel and Jain, 2012 N/A Burrows-Wheeler Aligner (BWA, v0.7.15a) Li and Durbin, 2009 N/A Picard (v2.12.0) N/A https://broadinstitute.github.io/picard HaplotypeCaller N/A N/A MuTect2 Cibulskis et al., 2013 N/A Annomen N/A https://github.com/jiwoongbio/Annomen SAMtools ( Li et al., 2009 ) N/A Other Open in a separate window KEY RESOURCES TABLE MSH2 deletion induces hypermutation in mammalian cancer cell lines.

    Techniques: Electrophoresis, Sequencing, Staining, Selection

    (A) Cell Titer Glo assay of MLN4924 10-point DRC for parental A673-M1 cells and MLN4924-resistant clones A, C, D, E, F, and H. Data are represented as mean ± SD. (B) Table showing EC50 for MLN4924 from parental A673-M1 and each resistant clone. (C) UBA3 is the only gene mutated in all six clones. (D) UBA3 mutations identified in MLN4924-resistant clones. DRC, dose response curve.

    Journal: Cell chemical biology

    Article Title: Engineering forward genetics into cultured cancer cells for chemical target identification

    doi: 10.1016/j.chembiol.2019.06.006

    Figure Lengend Snippet: (A) Cell Titer Glo assay of MLN4924 10-point DRC for parental A673-M1 cells and MLN4924-resistant clones A, C, D, E, F, and H. Data are represented as mean ± SD. (B) Table showing EC50 for MLN4924 from parental A673-M1 and each resistant clone. (C) UBA3 is the only gene mutated in all six clones. (D) UBA3 mutations identified in MLN4924-resistant clones. DRC, dose response curve.

    Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Msh2 [D24B5] XP rabbit mAb Cell Signaling Technology Cat#2017 Anti-β-actin (8H10D10) mouse mAb Cell Signaling Technologies Cat#3700 IRDye 800CW donkey anti-rabbit IgG (H+L) LI-COR Cat#926-32213 IRDye 680RD donkey anti-mouse IgG (H+L) LI-COR Cat#926-68072 Bacterial and Virus Strains Biological Samples Chemicals, Peptides, and Recombinant Proteins Bortezomib Selleck Chemicals Cat#S1013; CAS ID: 179324-69-7 Etoposide Sigma-Aldrich Cat#E1383; CAS ID: 33419-42-0 CD437 Sigma-Aldrich Cat#C5865; CAS ID: 125316-60-1 MLN4924 ApexBio Cat#B1036; CAS ID: 905579-51-3 Critical Commercial Assays CellTiter-Glo luminescent cell viability assay Promega Cat#G7571 Deposited Data WES from human and mouse cell lines This paper SRA ID: PRJNA543281 Experimental Models: Cell Lines Ewing sarcoma A673 cell lines ATCC ATCC® CRL-1598™ Trp53fl/fl; Rb1fl/fl; Rbl2fl/fl; RosaLSL-Tomato/+ murine SCLC cell lines This paper N/A 293T/17 ATCC ATCC® CRL-11268™ Experimental Models: Organisms/Strains Mouse: Trp53 fl/fl Rb fl/fl P130 fl/fl Schaffer et al., 2010 Mouse: Trp53 fl/fl JAX: 008462 Mouse: Rb fl/fl JAX: 008186 Mouse: P130 fl/fl JAX: 008177 Oligonucleotides Primers for PCR and sequencing of PSMB5 and POLA1 , see Table S3 This paper N/A Recombinant DNA LentiCRISPR V2 plasmid Addgene Cat#52961 psPAX2 plasmid Addgene Cat#12260 pMD2.G plasmid Addgene Cat#12259 Software and Algorithms Genome Analysis Toolkit (GATK, v3.8-0) DePristo et al., 2011 ; McKenna et al., 2010 N/A NGS QC Toolkit (v2.3.3) Patel and Jain, 2012 N/A Burrows-Wheeler Aligner (BWA, v0.7.15a) Li and Durbin, 2009 N/A Picard (v2.12.0) N/A https://broadinstitute.github.io/picard HaplotypeCaller N/A N/A MuTect2 Cibulskis et al., 2013 N/A Annomen N/A https://github.com/jiwoongbio/Annomen SAMtools ( Li et al., 2009 ) N/A Other Open in a separate window KEY RESOURCES TABLE MSH2 deletion induces hypermutation in mammalian cancer cell lines.

    Techniques: Glo Assay, Clone Assay

    (A) Cell Titer Glo assay of bortezomib 10-point dose response curve (DRC) for parental A673 cells and bortezomib-resistant clones A, B, C, and D. Data are represented as mean ± SD. (B) Table showing EC50 for bortezomib from parental A673-M1 and each bortezomib-resistant clone. Mutations detected in exon 2 of PSMB5 reported for each resistant clone. (C) Cell Titer Glo assay of bortezomib in 10-point dose response curve (DRC) for parental 319-N1 cells and bortezomib-resistant clones A, B, C, D, E, F and G. Data are represented as mean ± SD. (D) Table showing EC50 for bortezomib from parental 319-N1-CI31 and each bortezomib-resistant clone. Mutations found in exon 2 of Psmb5 showed for each resistant clone. (E) Sequencing trace for V90G mutation found in Psmb5 from mSCLC clone G. (F) Crystal structure of PSMB5 bound to bortezomib (Protein Data Bank accession 5L5Z). Depicted all mutated codons found in bortezomib-resistant clones from Ewing sarcoma and mSCLC clones (red). See also Figure S3 A–B.

    Journal: Cell chemical biology

    Article Title: Engineering forward genetics into cultured cancer cells for chemical target identification

    doi: 10.1016/j.chembiol.2019.06.006

    Figure Lengend Snippet: (A) Cell Titer Glo assay of bortezomib 10-point dose response curve (DRC) for parental A673 cells and bortezomib-resistant clones A, B, C, and D. Data are represented as mean ± SD. (B) Table showing EC50 for bortezomib from parental A673-M1 and each bortezomib-resistant clone. Mutations detected in exon 2 of PSMB5 reported for each resistant clone. (C) Cell Titer Glo assay of bortezomib in 10-point dose response curve (DRC) for parental 319-N1 cells and bortezomib-resistant clones A, B, C, D, E, F and G. Data are represented as mean ± SD. (D) Table showing EC50 for bortezomib from parental 319-N1-CI31 and each bortezomib-resistant clone. Mutations found in exon 2 of Psmb5 showed for each resistant clone. (E) Sequencing trace for V90G mutation found in Psmb5 from mSCLC clone G. (F) Crystal structure of PSMB5 bound to bortezomib (Protein Data Bank accession 5L5Z). Depicted all mutated codons found in bortezomib-resistant clones from Ewing sarcoma and mSCLC clones (red). See also Figure S3 A–B.

    Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Msh2 [D24B5] XP rabbit mAb Cell Signaling Technology Cat#2017 Anti-β-actin (8H10D10) mouse mAb Cell Signaling Technologies Cat#3700 IRDye 800CW donkey anti-rabbit IgG (H+L) LI-COR Cat#926-32213 IRDye 680RD donkey anti-mouse IgG (H+L) LI-COR Cat#926-68072 Bacterial and Virus Strains Biological Samples Chemicals, Peptides, and Recombinant Proteins Bortezomib Selleck Chemicals Cat#S1013; CAS ID: 179324-69-7 Etoposide Sigma-Aldrich Cat#E1383; CAS ID: 33419-42-0 CD437 Sigma-Aldrich Cat#C5865; CAS ID: 125316-60-1 MLN4924 ApexBio Cat#B1036; CAS ID: 905579-51-3 Critical Commercial Assays CellTiter-Glo luminescent cell viability assay Promega Cat#G7571 Deposited Data WES from human and mouse cell lines This paper SRA ID: PRJNA543281 Experimental Models: Cell Lines Ewing sarcoma A673 cell lines ATCC ATCC® CRL-1598™ Trp53fl/fl; Rb1fl/fl; Rbl2fl/fl; RosaLSL-Tomato/+ murine SCLC cell lines This paper N/A 293T/17 ATCC ATCC® CRL-11268™ Experimental Models: Organisms/Strains Mouse: Trp53 fl/fl Rb fl/fl P130 fl/fl Schaffer et al., 2010 Mouse: Trp53 fl/fl JAX: 008462 Mouse: Rb fl/fl JAX: 008186 Mouse: P130 fl/fl JAX: 008177 Oligonucleotides Primers for PCR and sequencing of PSMB5 and POLA1 , see Table S3 This paper N/A Recombinant DNA LentiCRISPR V2 plasmid Addgene Cat#52961 psPAX2 plasmid Addgene Cat#12260 pMD2.G plasmid Addgene Cat#12259 Software and Algorithms Genome Analysis Toolkit (GATK, v3.8-0) DePristo et al., 2011 ; McKenna et al., 2010 N/A NGS QC Toolkit (v2.3.3) Patel and Jain, 2012 N/A Burrows-Wheeler Aligner (BWA, v0.7.15a) Li and Durbin, 2009 N/A Picard (v2.12.0) N/A https://broadinstitute.github.io/picard HaplotypeCaller N/A N/A MuTect2 Cibulskis et al., 2013 N/A Annomen N/A https://github.com/jiwoongbio/Annomen SAMtools ( Li et al., 2009 ) N/A Other Open in a separate window KEY RESOURCES TABLE MSH2 deletion induces hypermutation in mammalian cancer cell lines.

    Techniques: Glo Assay, Clone Assay, Sequencing, Mutagenesis

    (A) Cell Titer Glo assay of CD437 10-point DRC for parental cell line and CD437-resistant clones A, B, C, and D. Data are represented as mean ± SD. (B) Table showing EC50 for CD437 from parental A673-M1 and each CD437-resistant clone. POLA1 mutations reported for each resistant clone. (C) Cell Titer Glo assay of CD437 10-point DRC for parental cell line and clones A, B, C, D, E, F, G, H, I and J. Data are represented as mean ± SD. (D) Table showing EC50 for CD437 from parental 319-N1-Cl31 and each CD437-resistant clone. Polal mutations detected in each resistant clone. (E) Sequencing trace for I768S mutation found in Pola1 from mSCLC clone A. (F) Crystal structure of POLA1 (Protein Data Bank accession 5IUD). Mutated codons found in CD437-resistant clones from Ewing sarcoma and mSCLC (red). See also Figure S3 C–D.

    Journal: Cell chemical biology

    Article Title: Engineering forward genetics into cultured cancer cells for chemical target identification

    doi: 10.1016/j.chembiol.2019.06.006

    Figure Lengend Snippet: (A) Cell Titer Glo assay of CD437 10-point DRC for parental cell line and CD437-resistant clones A, B, C, and D. Data are represented as mean ± SD. (B) Table showing EC50 for CD437 from parental A673-M1 and each CD437-resistant clone. POLA1 mutations reported for each resistant clone. (C) Cell Titer Glo assay of CD437 10-point DRC for parental cell line and clones A, B, C, D, E, F, G, H, I and J. Data are represented as mean ± SD. (D) Table showing EC50 for CD437 from parental 319-N1-Cl31 and each CD437-resistant clone. Polal mutations detected in each resistant clone. (E) Sequencing trace for I768S mutation found in Pola1 from mSCLC clone A. (F) Crystal structure of POLA1 (Protein Data Bank accession 5IUD). Mutated codons found in CD437-resistant clones from Ewing sarcoma and mSCLC (red). See also Figure S3 C–D.

    Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Msh2 [D24B5] XP rabbit mAb Cell Signaling Technology Cat#2017 Anti-β-actin (8H10D10) mouse mAb Cell Signaling Technologies Cat#3700 IRDye 800CW donkey anti-rabbit IgG (H+L) LI-COR Cat#926-32213 IRDye 680RD donkey anti-mouse IgG (H+L) LI-COR Cat#926-68072 Bacterial and Virus Strains Biological Samples Chemicals, Peptides, and Recombinant Proteins Bortezomib Selleck Chemicals Cat#S1013; CAS ID: 179324-69-7 Etoposide Sigma-Aldrich Cat#E1383; CAS ID: 33419-42-0 CD437 Sigma-Aldrich Cat#C5865; CAS ID: 125316-60-1 MLN4924 ApexBio Cat#B1036; CAS ID: 905579-51-3 Critical Commercial Assays CellTiter-Glo luminescent cell viability assay Promega Cat#G7571 Deposited Data WES from human and mouse cell lines This paper SRA ID: PRJNA543281 Experimental Models: Cell Lines Ewing sarcoma A673 cell lines ATCC ATCC® CRL-1598™ Trp53fl/fl; Rb1fl/fl; Rbl2fl/fl; RosaLSL-Tomato/+ murine SCLC cell lines This paper N/A 293T/17 ATCC ATCC® CRL-11268™ Experimental Models: Organisms/Strains Mouse: Trp53 fl/fl Rb fl/fl P130 fl/fl Schaffer et al., 2010 Mouse: Trp53 fl/fl JAX: 008462 Mouse: Rb fl/fl JAX: 008186 Mouse: P130 fl/fl JAX: 008177 Oligonucleotides Primers for PCR and sequencing of PSMB5 and POLA1 , see Table S3 This paper N/A Recombinant DNA LentiCRISPR V2 plasmid Addgene Cat#52961 psPAX2 plasmid Addgene Cat#12260 pMD2.G plasmid Addgene Cat#12259 Software and Algorithms Genome Analysis Toolkit (GATK, v3.8-0) DePristo et al., 2011 ; McKenna et al., 2010 N/A NGS QC Toolkit (v2.3.3) Patel and Jain, 2012 N/A Burrows-Wheeler Aligner (BWA, v0.7.15a) Li and Durbin, 2009 N/A Picard (v2.12.0) N/A https://broadinstitute.github.io/picard HaplotypeCaller N/A N/A MuTect2 Cibulskis et al., 2013 N/A Annomen N/A https://github.com/jiwoongbio/Annomen SAMtools ( Li et al., 2009 ) N/A Other Open in a separate window KEY RESOURCES TABLE MSH2 deletion induces hypermutation in mammalian cancer cell lines.

    Techniques: Glo Assay, Clone Assay, Sequencing, Mutagenesis

    KEY RESOURCES TABLE

    Journal: Cell chemical biology

    Article Title: Engineering forward genetics into cultured cancer cells for chemical target identification

    doi: 10.1016/j.chembiol.2019.06.006

    Figure Lengend Snippet: KEY RESOURCES TABLE

    Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Msh2 [D24B5] XP rabbit mAb Cell Signaling Technology Cat#2017 Anti-β-actin (8H10D10) mouse mAb Cell Signaling Technologies Cat#3700 IRDye 800CW donkey anti-rabbit IgG (H+L) LI-COR Cat#926-32213 IRDye 680RD donkey anti-mouse IgG (H+L) LI-COR Cat#926-68072 Bacterial and Virus Strains Biological Samples Chemicals, Peptides, and Recombinant Proteins Bortezomib Selleck Chemicals Cat#S1013; CAS ID: 179324-69-7 Etoposide Sigma-Aldrich Cat#E1383; CAS ID: 33419-42-0 CD437 Sigma-Aldrich Cat#C5865; CAS ID: 125316-60-1 MLN4924 ApexBio Cat#B1036; CAS ID: 905579-51-3 Critical Commercial Assays CellTiter-Glo luminescent cell viability assay Promega Cat#G7571 Deposited Data WES from human and mouse cell lines This paper SRA ID: PRJNA543281 Experimental Models: Cell Lines Ewing sarcoma A673 cell lines ATCC ATCC® CRL-1598™ Trp53fl/fl; Rb1fl/fl; Rbl2fl/fl; RosaLSL-Tomato/+ murine SCLC cell lines This paper N/A 293T/17 ATCC ATCC® CRL-11268™ Experimental Models: Organisms/Strains Mouse: Trp53 fl/fl Rb fl/fl P130 fl/fl Schaffer et al., 2010 Mouse: Trp53 fl/fl JAX: 008462 Mouse: Rb fl/fl JAX: 008186 Mouse: P130 fl/fl JAX: 008177 Oligonucleotides Primers for PCR and sequencing of PSMB5 and POLA1 , see Table S3 This paper N/A Recombinant DNA LentiCRISPR V2 plasmid Addgene Cat#52961 psPAX2 plasmid Addgene Cat#12260 pMD2.G plasmid Addgene Cat#12259 Software and Algorithms Genome Analysis Toolkit (GATK, v3.8-0) DePristo et al., 2011 ; McKenna et al., 2010 N/A NGS QC Toolkit (v2.3.3) Patel and Jain, 2012 N/A Burrows-Wheeler Aligner (BWA, v0.7.15a) Li and Durbin, 2009 N/A Picard (v2.12.0) N/A https://broadinstitute.github.io/picard HaplotypeCaller N/A N/A MuTect2 Cibulskis et al., 2013 N/A Annomen N/A https://github.com/jiwoongbio/Annomen SAMtools ( Li et al., 2009 ) N/A Other Open in a separate window KEY RESOURCES TABLE MSH2 deletion induces hypermutation in mammalian cancer cell lines.

    Techniques: Recombinant, Cell Viability Assay, Sequencing, Plasmid Preparation, Software

    (A) MSH2 and Actin protein levels showed for A673 (MSH2-wild-type), 319-N1-CI31 (Msh2-edited mouse small cell lung cancer cell line (see Figure S1)), and MSH2-edited A673-M1 and A673-M8 (right panel for A673-M8 cells performed in an independent blot, as stated by the break between the first three lanes and A673-M8). (B) Capillary electrophoresis histogram of microsatellite Bat26 locus for A673, A673-M1 and A673-M8. The most prominent peaks in the histogram determine the allele size is shown (solid blue). (C) Table of microsatellites assessed in A673 cells. Difference in the dominant allele size between the parental A673 and each MMR deficient cell line is indicated. Number of microsatellites affected in relation to the number of microsatellites studied displayed in the last column. (D) Number of somatic mutations present in A673-M1, and A673-M8 identified by exome sequencing. Parental A673 cells were used as a normal reference. Mutations with an allelic fraction (AF) higher or equal to 0.15 were reported. (E) Crystal violet staining of A673 (MSH2-wild-type), A673-M1 (MSH2-null), A673-M8 (MSH2-null), and HCT116 (MLH1-null) cells following compound selection. Concentrations used for selection shown in each panel. See also Figure S1 and S2.

    Journal: Cell chemical biology

    Article Title: Engineering forward genetics into cultured cancer cells for chemical target identification

    doi: 10.1016/j.chembiol.2019.06.006

    Figure Lengend Snippet: (A) MSH2 and Actin protein levels showed for A673 (MSH2-wild-type), 319-N1-CI31 (Msh2-edited mouse small cell lung cancer cell line (see Figure S1)), and MSH2-edited A673-M1 and A673-M8 (right panel for A673-M8 cells performed in an independent blot, as stated by the break between the first three lanes and A673-M8). (B) Capillary electrophoresis histogram of microsatellite Bat26 locus for A673, A673-M1 and A673-M8. The most prominent peaks in the histogram determine the allele size is shown (solid blue). (C) Table of microsatellites assessed in A673 cells. Difference in the dominant allele size between the parental A673 and each MMR deficient cell line is indicated. Number of microsatellites affected in relation to the number of microsatellites studied displayed in the last column. (D) Number of somatic mutations present in A673-M1, and A673-M8 identified by exome sequencing. Parental A673 cells were used as a normal reference. Mutations with an allelic fraction (AF) higher or equal to 0.15 were reported. (E) Crystal violet staining of A673 (MSH2-wild-type), A673-M1 (MSH2-null), A673-M8 (MSH2-null), and HCT116 (MLH1-null) cells following compound selection. Concentrations used for selection shown in each panel. See also Figure S1 and S2.

    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Msh2 [D24B5] XP rabbit mAb Cell Signaling Technology Cat#2017 Anti-β-actin (8H10D10) mouse mAb Cell Signaling Technologies Cat#3700 IRDye 800CW donkey anti-rabbit IgG (H+L) LI-COR Cat#926-32213 IRDye 680RD donkey anti-mouse IgG (H+L) LI-COR Cat#926-68072 Bacterial and Virus Strains Biological Samples Chemicals, Peptides, and Recombinant Proteins Bortezomib Selleck Chemicals Cat#S1013; CAS ID: 179324-69-7 Etoposide Sigma-Aldrich Cat#E1383; CAS ID: 33419-42-0 CD437 Sigma-Aldrich Cat#C5865; CAS ID: 125316-60-1 MLN4924 ApexBio Cat#B1036; CAS ID: 905579-51-3 Critical Commercial Assays CellTiter-Glo luminescent cell viability assay Promega Cat#G7571 Deposited Data WES from human and mouse cell lines This paper SRA ID: PRJNA543281 Experimental Models: Cell Lines Ewing sarcoma A673 cell lines ATCC ATCC® CRL-1598TM Trp53fl/fl; Rb1fl/fl; Rbl2fl/fl; RosaLSL-Tomato/+ murine SCLC cell lines This paper N/A 293T/17 ATCC ATCC® CRL-11268TM Experimental Models: Organisms/Strains Mouse: Trp53 fl/fl Rb fl/fl P130 fl/fl Schaffer et al., 2010 Mouse: Trp53 fl/fl JAX: 008462 Mouse: Rb fl/fl JAX: 008186 Mouse: P130 fl/fl JAX: 008177 Oligonucleotides Primers for PCR and sequencing of PSMB5 and POLA1 , see Table S3 This paper N/A Recombinant DNA LentiCRISPR V2 plasmid Addgene Cat#52961 psPAX2 plasmid Addgene Cat#12260 pMD2.G plasmid Addgene Cat#12259 Software and Algorithms Genome Analysis Toolkit (GATK, v3.8-0) DePristo et al., 2011 ; McKenna et al., 2010 N/A NGS QC Toolkit (v2.3.3) Patel and Jain, 2012 N/A Burrows-Wheeler Aligner (BWA, v0.7.15a) Li and Durbin, 2009 N/A Picard (v2.12.0) N/A https://broadinstitute.github.io/picard HaplotypeCaller N/A N/A MuTect2 Cibulskis et al., 2013 N/A Annomen N/A https://github.com/jiwoongbio/Annomen SAMtools ( Li et al., 2009 ) N/A Other Open in a separate window KEY RESOURCES TABLE MSH2 deletion induces hypermutation in mammalian cancer cell lines.

    Techniques: Electrophoresis, Sequencing, Staining, Selection

    (A) Cell Titer Glo assay of MLN4924 10-point DRC for parental A673-M1 cells and MLN4924-resistant clones A, C, D, E, F, and H. Data are represented as mean ± SD. (B) Table showing EC50 for MLN4924 from parental A673-M1 and each resistant clone. (C) UBA3 is the only gene mutated in all six clones. (D) UBA3 mutations identified in MLN4924-resistant clones. DRC, dose response curve.

    Journal: Cell chemical biology

    Article Title: Engineering forward genetics into cultured cancer cells for chemical target identification

    doi: 10.1016/j.chembiol.2019.06.006

    Figure Lengend Snippet: (A) Cell Titer Glo assay of MLN4924 10-point DRC for parental A673-M1 cells and MLN4924-resistant clones A, C, D, E, F, and H. Data are represented as mean ± SD. (B) Table showing EC50 for MLN4924 from parental A673-M1 and each resistant clone. (C) UBA3 is the only gene mutated in all six clones. (D) UBA3 mutations identified in MLN4924-resistant clones. DRC, dose response curve.

    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Msh2 [D24B5] XP rabbit mAb Cell Signaling Technology Cat#2017 Anti-β-actin (8H10D10) mouse mAb Cell Signaling Technologies Cat#3700 IRDye 800CW donkey anti-rabbit IgG (H+L) LI-COR Cat#926-32213 IRDye 680RD donkey anti-mouse IgG (H+L) LI-COR Cat#926-68072 Bacterial and Virus Strains Biological Samples Chemicals, Peptides, and Recombinant Proteins Bortezomib Selleck Chemicals Cat#S1013; CAS ID: 179324-69-7 Etoposide Sigma-Aldrich Cat#E1383; CAS ID: 33419-42-0 CD437 Sigma-Aldrich Cat#C5865; CAS ID: 125316-60-1 MLN4924 ApexBio Cat#B1036; CAS ID: 905579-51-3 Critical Commercial Assays CellTiter-Glo luminescent cell viability assay Promega Cat#G7571 Deposited Data WES from human and mouse cell lines This paper SRA ID: PRJNA543281 Experimental Models: Cell Lines Ewing sarcoma A673 cell lines ATCC ATCC® CRL-1598TM Trp53fl/fl; Rb1fl/fl; Rbl2fl/fl; RosaLSL-Tomato/+ murine SCLC cell lines This paper N/A 293T/17 ATCC ATCC® CRL-11268TM Experimental Models: Organisms/Strains Mouse: Trp53 fl/fl Rb fl/fl P130 fl/fl Schaffer et al., 2010 Mouse: Trp53 fl/fl JAX: 008462 Mouse: Rb fl/fl JAX: 008186 Mouse: P130 fl/fl JAX: 008177 Oligonucleotides Primers for PCR and sequencing of PSMB5 and POLA1 , see Table S3 This paper N/A Recombinant DNA LentiCRISPR V2 plasmid Addgene Cat#52961 psPAX2 plasmid Addgene Cat#12260 pMD2.G plasmid Addgene Cat#12259 Software and Algorithms Genome Analysis Toolkit (GATK, v3.8-0) DePristo et al., 2011 ; McKenna et al., 2010 N/A NGS QC Toolkit (v2.3.3) Patel and Jain, 2012 N/A Burrows-Wheeler Aligner (BWA, v0.7.15a) Li and Durbin, 2009 N/A Picard (v2.12.0) N/A https://broadinstitute.github.io/picard HaplotypeCaller N/A N/A MuTect2 Cibulskis et al., 2013 N/A Annomen N/A https://github.com/jiwoongbio/Annomen SAMtools ( Li et al., 2009 ) N/A Other Open in a separate window KEY RESOURCES TABLE MSH2 deletion induces hypermutation in mammalian cancer cell lines.

    Techniques: Glo Assay, Clone Assay

    (A) Cell Titer Glo assay of bortezomib 10-point dose response curve (DRC) for parental A673 cells and bortezomib-resistant clones A, B, C, and D. Data are represented as mean ± SD. (B) Table showing EC50 for bortezomib from parental A673-M1 and each bortezomib-resistant clone. Mutations detected in exon 2 of PSMB5 reported for each resistant clone. (C) Cell Titer Glo assay of bortezomib in 10-point dose response curve (DRC) for parental 319-N1 cells and bortezomib-resistant clones A, B, C, D, E, F and G. Data are represented as mean ± SD. (D) Table showing EC50 for bortezomib from parental 319-N1-CI31 and each bortezomib-resistant clone. Mutations found in exon 2 of Psmb5 showed for each resistant clone. (E) Sequencing trace for V90G mutation found in Psmb5 from mSCLC clone G. (F) Crystal structure of PSMB5 bound to bortezomib (Protein Data Bank accession 5L5Z). Depicted all mutated codons found in bortezomib-resistant clones from Ewing sarcoma and mSCLC clones (red). See also Figure S3 A–B.

    Journal: Cell chemical biology

    Article Title: Engineering forward genetics into cultured cancer cells for chemical target identification

    doi: 10.1016/j.chembiol.2019.06.006

    Figure Lengend Snippet: (A) Cell Titer Glo assay of bortezomib 10-point dose response curve (DRC) for parental A673 cells and bortezomib-resistant clones A, B, C, and D. Data are represented as mean ± SD. (B) Table showing EC50 for bortezomib from parental A673-M1 and each bortezomib-resistant clone. Mutations detected in exon 2 of PSMB5 reported for each resistant clone. (C) Cell Titer Glo assay of bortezomib in 10-point dose response curve (DRC) for parental 319-N1 cells and bortezomib-resistant clones A, B, C, D, E, F and G. Data are represented as mean ± SD. (D) Table showing EC50 for bortezomib from parental 319-N1-CI31 and each bortezomib-resistant clone. Mutations found in exon 2 of Psmb5 showed for each resistant clone. (E) Sequencing trace for V90G mutation found in Psmb5 from mSCLC clone G. (F) Crystal structure of PSMB5 bound to bortezomib (Protein Data Bank accession 5L5Z). Depicted all mutated codons found in bortezomib-resistant clones from Ewing sarcoma and mSCLC clones (red). See also Figure S3 A–B.

    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Msh2 [D24B5] XP rabbit mAb Cell Signaling Technology Cat#2017 Anti-β-actin (8H10D10) mouse mAb Cell Signaling Technologies Cat#3700 IRDye 800CW donkey anti-rabbit IgG (H+L) LI-COR Cat#926-32213 IRDye 680RD donkey anti-mouse IgG (H+L) LI-COR Cat#926-68072 Bacterial and Virus Strains Biological Samples Chemicals, Peptides, and Recombinant Proteins Bortezomib Selleck Chemicals Cat#S1013; CAS ID: 179324-69-7 Etoposide Sigma-Aldrich Cat#E1383; CAS ID: 33419-42-0 CD437 Sigma-Aldrich Cat#C5865; CAS ID: 125316-60-1 MLN4924 ApexBio Cat#B1036; CAS ID: 905579-51-3 Critical Commercial Assays CellTiter-Glo luminescent cell viability assay Promega Cat#G7571 Deposited Data WES from human and mouse cell lines This paper SRA ID: PRJNA543281 Experimental Models: Cell Lines Ewing sarcoma A673 cell lines ATCC ATCC® CRL-1598TM Trp53fl/fl; Rb1fl/fl; Rbl2fl/fl; RosaLSL-Tomato/+ murine SCLC cell lines This paper N/A 293T/17 ATCC ATCC® CRL-11268TM Experimental Models: Organisms/Strains Mouse: Trp53 fl/fl Rb fl/fl P130 fl/fl Schaffer et al., 2010 Mouse: Trp53 fl/fl JAX: 008462 Mouse: Rb fl/fl JAX: 008186 Mouse: P130 fl/fl JAX: 008177 Oligonucleotides Primers for PCR and sequencing of PSMB5 and POLA1 , see Table S3 This paper N/A Recombinant DNA LentiCRISPR V2 plasmid Addgene Cat#52961 psPAX2 plasmid Addgene Cat#12260 pMD2.G plasmid Addgene Cat#12259 Software and Algorithms Genome Analysis Toolkit (GATK, v3.8-0) DePristo et al., 2011 ; McKenna et al., 2010 N/A NGS QC Toolkit (v2.3.3) Patel and Jain, 2012 N/A Burrows-Wheeler Aligner (BWA, v0.7.15a) Li and Durbin, 2009 N/A Picard (v2.12.0) N/A https://broadinstitute.github.io/picard HaplotypeCaller N/A N/A MuTect2 Cibulskis et al., 2013 N/A Annomen N/A https://github.com/jiwoongbio/Annomen SAMtools ( Li et al., 2009 ) N/A Other Open in a separate window KEY RESOURCES TABLE MSH2 deletion induces hypermutation in mammalian cancer cell lines.

    Techniques: Glo Assay, Clone Assay, Sequencing, Mutagenesis

    (A) Cell Titer Glo assay of CD437 10-point DRC for parental cell line and CD437-resistant clones A, B, C, and D. Data are represented as mean ± SD. (B) Table showing EC50 for CD437 from parental A673-M1 and each CD437-resistant clone. POLA1 mutations reported for each resistant clone. (C) Cell Titer Glo assay of CD437 10-point DRC for parental cell line and clones A, B, C, D, E, F, G, H, I and J. Data are represented as mean ± SD. (D) Table showing EC50 for CD437 from parental 319-N1-Cl31 and each CD437-resistant clone. Polal mutations detected in each resistant clone. (E) Sequencing trace for I768S mutation found in Pola1 from mSCLC clone A. (F) Crystal structure of POLA1 (Protein Data Bank accession 5IUD). Mutated codons found in CD437-resistant clones from Ewing sarcoma and mSCLC (red). See also Figure S3 C–D.

    Journal: Cell chemical biology

    Article Title: Engineering forward genetics into cultured cancer cells for chemical target identification

    doi: 10.1016/j.chembiol.2019.06.006

    Figure Lengend Snippet: (A) Cell Titer Glo assay of CD437 10-point DRC for parental cell line and CD437-resistant clones A, B, C, and D. Data are represented as mean ± SD. (B) Table showing EC50 for CD437 from parental A673-M1 and each CD437-resistant clone. POLA1 mutations reported for each resistant clone. (C) Cell Titer Glo assay of CD437 10-point DRC for parental cell line and clones A, B, C, D, E, F, G, H, I and J. Data are represented as mean ± SD. (D) Table showing EC50 for CD437 from parental 319-N1-Cl31 and each CD437-resistant clone. Polal mutations detected in each resistant clone. (E) Sequencing trace for I768S mutation found in Pola1 from mSCLC clone A. (F) Crystal structure of POLA1 (Protein Data Bank accession 5IUD). Mutated codons found in CD437-resistant clones from Ewing sarcoma and mSCLC (red). See also Figure S3 C–D.

    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Msh2 [D24B5] XP rabbit mAb Cell Signaling Technology Cat#2017 Anti-β-actin (8H10D10) mouse mAb Cell Signaling Technologies Cat#3700 IRDye 800CW donkey anti-rabbit IgG (H+L) LI-COR Cat#926-32213 IRDye 680RD donkey anti-mouse IgG (H+L) LI-COR Cat#926-68072 Bacterial and Virus Strains Biological Samples Chemicals, Peptides, and Recombinant Proteins Bortezomib Selleck Chemicals Cat#S1013; CAS ID: 179324-69-7 Etoposide Sigma-Aldrich Cat#E1383; CAS ID: 33419-42-0 CD437 Sigma-Aldrich Cat#C5865; CAS ID: 125316-60-1 MLN4924 ApexBio Cat#B1036; CAS ID: 905579-51-3 Critical Commercial Assays CellTiter-Glo luminescent cell viability assay Promega Cat#G7571 Deposited Data WES from human and mouse cell lines This paper SRA ID: PRJNA543281 Experimental Models: Cell Lines Ewing sarcoma A673 cell lines ATCC ATCC® CRL-1598TM Trp53fl/fl; Rb1fl/fl; Rbl2fl/fl; RosaLSL-Tomato/+ murine SCLC cell lines This paper N/A 293T/17 ATCC ATCC® CRL-11268TM Experimental Models: Organisms/Strains Mouse: Trp53 fl/fl Rb fl/fl P130 fl/fl Schaffer et al., 2010 Mouse: Trp53 fl/fl JAX: 008462 Mouse: Rb fl/fl JAX: 008186 Mouse: P130 fl/fl JAX: 008177 Oligonucleotides Primers for PCR and sequencing of PSMB5 and POLA1 , see Table S3 This paper N/A Recombinant DNA LentiCRISPR V2 plasmid Addgene Cat#52961 psPAX2 plasmid Addgene Cat#12260 pMD2.G plasmid Addgene Cat#12259 Software and Algorithms Genome Analysis Toolkit (GATK, v3.8-0) DePristo et al., 2011 ; McKenna et al., 2010 N/A NGS QC Toolkit (v2.3.3) Patel and Jain, 2012 N/A Burrows-Wheeler Aligner (BWA, v0.7.15a) Li and Durbin, 2009 N/A Picard (v2.12.0) N/A https://broadinstitute.github.io/picard HaplotypeCaller N/A N/A MuTect2 Cibulskis et al., 2013 N/A Annomen N/A https://github.com/jiwoongbio/Annomen SAMtools ( Li et al., 2009 ) N/A Other Open in a separate window KEY RESOURCES TABLE MSH2 deletion induces hypermutation in mammalian cancer cell lines.

    Techniques: Glo Assay, Clone Assay, Sequencing, Mutagenesis

    KEY RESOURCES TABLE

    Journal: Cell chemical biology

    Article Title: Engineering forward genetics into cultured cancer cells for chemical target identification

    doi: 10.1016/j.chembiol.2019.06.006

    Figure Lengend Snippet: KEY RESOURCES TABLE

    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Msh2 [D24B5] XP rabbit mAb Cell Signaling Technology Cat#2017 Anti-β-actin (8H10D10) mouse mAb Cell Signaling Technologies Cat#3700 IRDye 800CW donkey anti-rabbit IgG (H+L) LI-COR Cat#926-32213 IRDye 680RD donkey anti-mouse IgG (H+L) LI-COR Cat#926-68072 Bacterial and Virus Strains Biological Samples Chemicals, Peptides, and Recombinant Proteins Bortezomib Selleck Chemicals Cat#S1013; CAS ID: 179324-69-7 Etoposide Sigma-Aldrich Cat#E1383; CAS ID: 33419-42-0 CD437 Sigma-Aldrich Cat#C5865; CAS ID: 125316-60-1 MLN4924 ApexBio Cat#B1036; CAS ID: 905579-51-3 Critical Commercial Assays CellTiter-Glo luminescent cell viability assay Promega Cat#G7571 Deposited Data WES from human and mouse cell lines This paper SRA ID: PRJNA543281 Experimental Models: Cell Lines Ewing sarcoma A673 cell lines ATCC ATCC® CRL-1598TM Trp53fl/fl; Rb1fl/fl; Rbl2fl/fl; RosaLSL-Tomato/+ murine SCLC cell lines This paper N/A 293T/17 ATCC ATCC® CRL-11268TM Experimental Models: Organisms/Strains Mouse: Trp53 fl/fl Rb fl/fl P130 fl/fl Schaffer et al., 2010 Mouse: Trp53 fl/fl JAX: 008462 Mouse: Rb fl/fl JAX: 008186 Mouse: P130 fl/fl JAX: 008177 Oligonucleotides Primers for PCR and sequencing of PSMB5 and POLA1 , see Table S3 This paper N/A Recombinant DNA LentiCRISPR V2 plasmid Addgene Cat#52961 psPAX2 plasmid Addgene Cat#12260 pMD2.G plasmid Addgene Cat#12259 Software and Algorithms Genome Analysis Toolkit (GATK, v3.8-0) DePristo et al., 2011 ; McKenna et al., 2010 N/A NGS QC Toolkit (v2.3.3) Patel and Jain, 2012 N/A Burrows-Wheeler Aligner (BWA, v0.7.15a) Li and Durbin, 2009 N/A Picard (v2.12.0) N/A https://broadinstitute.github.io/picard HaplotypeCaller N/A N/A MuTect2 Cibulskis et al., 2013 N/A Annomen N/A https://github.com/jiwoongbio/Annomen SAMtools ( Li et al., 2009 ) N/A Other Open in a separate window KEY RESOURCES TABLE MSH2 deletion induces hypermutation in mammalian cancer cell lines.

    Techniques: Virus, Recombinant, Cell Viability Assay, Sequencing, Plasmid Preparation, Software