title: Yeast DNA Integrity Network: Synthetic Lethality with hpr5

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.39 and 1.25 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX. The second-site ("query") mutation had the genotype hpr5::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- hpr5


title: Yeast DNA Integrity Network: Synthetic Lethality with hir1, expt 1

status: Public on Feb 16 2006

type: genomic

city: Baltimore

first: Daniel

last: Yuan

state: MD

address: 733 N. Broadway, Suite 351

department: Molecular Biology and Genetics

country: USA

institute: Johns Hopkins Univ School of Medicine

description: See above.

hyb_protocol: Labeled extracts were hybridized overnight to microarray slides at 42 degrees C. See PubMed ID 15994458.

scan_protocol: Images were acquired with a GenePix 4000B scanner.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.53 and 1.39 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Control

label_protocol: UpTag and DnTag sequences were amplified from genomic DNA by asymmetric PCR using labeled primers. See PubMed ID 15994458.

growth_protocol: Cells were grown at 30 degrees C to confluence on "Magic Marker" selection plates supplemented with uracil. See PubMed ID 15525520.

extract_protocol: Genomic DNA was prepared by extraction with phenol-chloroform and ethanol-precipitated. See PubMed ID 15525520.

tag: Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and selected to yield MATa haploid progeny. The parental strain was BY4743 (from S288C), with modifications resulting in the following genotype

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX. The second-site ("query") mutation had the genotype hir1::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- hir1

label_protocol: As in Channel 1.

growth_protocol: Cells were grown at 30 degrees C to confluence on "Magic Marker" selection plates lacking uracil. The aliquots of cells used for the two channels were split from the same source and were grown concurrently. See PubMed ID 15525520.

extract_protocol: As in Channel 1.

tag: As in Channel 1.


title: Yeast DNA Integrity Network: Synthetic Lethality with hir1, expt 2

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.15 and 1.41 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

growth_protocol: Cells were grown at 30 degrees C to confluence on "Magic Marker" selection plates supplemented with 100 micromolar uracil and 0.1% 5-fluoroorotic acid. See PubMed ID 15525520.


title: Yeast DNA Integrity Network: Synthetic Lethality with hex3

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.07 and 1.35 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX. The second-site ("query") mutation had the genotype hex3::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- hex3


title: Yeast DNA Integrity Network: Synthetic Lethality with hir2, expt 1

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.99 and 1.12 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX. The second-site ("query") mutation had the genotype hir2::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- hir2


title: Yeast DNA Integrity Network: Synthetic Lethality with elg1

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.26 and 1.64 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX. The second-site ("query") mutation had the genotype elg1::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- elg1


title: Yeast DNA Integrity Network: Synthetic Lethality with dun1, expt 4

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.58 and 1.18 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

growth_protocol: Cells were grown at 30 degrees C to confluence on "Magic Marker" selection plates supplemented with 100 micromolar uracil and 0.20% 5-fluoroorotic acid. See PubMed ID 15525520.

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX. The second-site ("query") mutation had the genotype dun1::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- dun1


title: Yeast DNA Integrity Network: Synthetic Lethality with eaf3

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.9 and 1.46 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX. The second-site ("query") mutation had the genotype eaf3::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- eaf3


title: Yeast DNA Integrity Network: Synthetic Lethality with dun1, expt 2

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.6 and 1.02 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

growth_protocol: Cells were grown at 30 degrees C to confluence on "Magic Marker" selection plates supplemented with 100 micromolar uracil and 0.10% 5-fluoroorotic acid. See PubMed ID 15525520.


title: Yeast DNA Integrity Network: Synthetic Lethality with ddc1, expt 2

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 0.96 and 0.87 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX. The second-site ("query") mutation had the genotype ddc1::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- ddc1


title: Yeast DNA Integrity Network: Synthetic Lethality with dun1, expt 1

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 2.24 and 2.08 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.


title: Yeast DNA Integrity Network: Synthetic Lethality with dun1, expt 3

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.4 and 1.12 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

growth_protocol: Cells were grown at 30 degrees C to confluence on "Magic Marker" selection plates supplemented with 100 micromolar uracil and 0.15% 5-fluoroorotic acid. See PubMed ID 15525520.


title: Yeast DNA Integrity Network: Synthetic Lethality with dia2

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 0.8 and 1.12 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX. The second-site ("query") mutation had the genotype dia2::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- dia2


title: Yeast DNA Integrity Network: Synthetic Lethality with mrc1, expt 2

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1 and 1.07 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX. The second-site ("query") mutation had the genotype mrc1::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- mrc1


title: Yeast DNA Integrity Network: Synthetic Lethality with dcc1

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.72 and 1.56 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX. The second-site ("query") mutation had the genotype dcc1::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- dcc1


title: Yeast DNA Integrity Network: Synthetic Lethality with ctf8

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.33 and 1.1 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX. The second-site ("query") mutation had the genotype ctf8::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- ctf8


title: Yeast DNA Integrity Network: Synthetic Lethality with ddc1, expt 1

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 2.1 and 1.8 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.


title: Yeast DNA Integrity Network: Synthetic Lethality with ctf4, expt 2

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 0.64 and 0.68 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX. The second-site ("query") mutation had the genotype ctf4::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- ctf4


title: Yeast DNA Integrity Network: Synthetic Lethality with csm3, expt 3

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.06 and 1.25 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX. The second-site ("query") mutation had the genotype csm3::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- csm3


title: Yeast DNA Integrity Network: Synthetic Lethality with csm3, expt 4

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.31 and 1.13 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.


title: Yeast DNA Integrity Network: Synthetic Lethality with ctf4, expt 1

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 0.59 and 0.68 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.


title: Yeast DNA Integrity Network: Synthetic Lethality with csm3, expt 2

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.68 and 1.4 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.


title: Yeast DNA Integrity Network: Synthetic Lethality with ctf18

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.45 and 1.5 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX. The second-site ("query") mutation had the genotype ctf18::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- ctf18


title: Yeast DNA Integrity Network: Synthetic Lethality with csm3, expt 1

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.41 and 1.34 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.


title: Yeast DNA Integrity Network: Synthetic Lethality with csm2

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.07 and 1.56 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX. The second-site ("query") mutation had the genotype csm2::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- csm2


title: Yeast DNA Integrity Network: Synthetic Lethality with cdc9, expt 1

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 0.87 and 1.08 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX. The second-site ("query") mutation had the genotype cdc9::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- cdc9


title: Yeast DNA Integrity Network: Synthetic Lethality with bre1

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.38 and 1.11 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

source_name: Control

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX. The second-site ("query") mutation had the genotype bre1::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- bre1


title: Yeast DNA Integrity Network: Synthetic Lethality with lys7

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 0.82 and 1.67 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX. The second-site ("query") mutation had the genotype lys7::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- lys7


title: Yeast DNA Integrity Network: Synthetic Lethality with ccr4

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.34 and 2.83 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX. The second-site ("query") mutation had the genotype ccr4::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- ccr4


title: Yeast DNA Integrity Network: Synthetic Lethality with ard1

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.18 and 1.46 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX. The second-site ("query") mutation had the genotype ard1::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- ard1


title: Yeast DNA Integrity Network: Synthetic Lethality with chk1

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 2.11 and 1.76 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX. The second-site ("query") mutation had the genotype chk1::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- chk1


title: Yeast DNA Integrity Network: Synthetic Lethality with cdc9, expt 2

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 0.55 and 0.59 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.


title: Yeast DNA Integrity Network: Synthetic Lethality with cac2

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 2.13 and 1.5 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX. The second-site ("query") mutation had the genotype cac2::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- cac2


title: Yeast DNA Integrity Network: Synthetic Lethality with asf1

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.19 and 1.24 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX. The second-site ("query") mutation had the genotype asf1::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- asf1


title: Yeast DNA Integrity Network: Synthetic Lethality with csm1

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1 and 1.62 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX. The second-site ("query") mutation had the genotype csm1::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- csm1


title: Yeast DNA Integrity Network: Synthetic Lethality with MMS 0.006%

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.23 and 1.12 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX. No second-site ("query") mutation was added. See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- methyl methanesulfonate 0.006%

growth_protocol: Cells were grown at 30 degrees C to confluence on "Magic Marker" selection plates supplemented with uracil and with methyl methanesulfonate 0.006% . The aliquots of cells used for the two channels were split from the same source and were grown concurrently. See PubMed ID 15525520.


title: Yeast DNA Integrity Network: Synthetic Lethality with MMS 0.004%

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.4 and 1.28 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

source_name: Experimental -- methyl methanesulfonate 0.004%

growth_protocol: Cells were grown at 30 degrees C to confluence on "Magic Marker" selection plates supplemented with uracil and with methyl methanesulfonate 0.004% . The aliquots of cells used for the two channels were split from the same source and were grown concurrently. See PubMed ID 15525520.


title: Yeast DNA Integrity Network: Synthetic Lethality with MMS 0.008%

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.13 and 1 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

source_name: Experimental -- methyl methanesulfonate 0.008%

growth_protocol: Cells were grown at 30 degrees C to confluence on "Magic Marker" selection plates supplemented with uracil and with methyl methanesulfonate 0.008% . The aliquots of cells used for the two channels were split from the same source and were grown concurrently. See PubMed ID 15525520.


title: Yeast DNA Integrity Network: Synthetic Lethality with HU 50 mM

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.08 and 1.03 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

source_name: Experimental -- hydroxyurea 50 mM

growth_protocol: Cells were grown at 30 degrees C to confluence on "Magic Marker" selection plates supplemented with uracil and with hydroxyurea 50 mM . The aliquots of cells used for the two channels were split from the same source and were grown concurrently. See PubMed ID 15525520.


title: Yeast DNA Integrity Network: Synthetic Lethality with MMS 0.001%

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.41 and 0.89 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

source_name: Experimental -- methyl methanesulfonate 0.001%

growth_protocol: Cells were grown at 30 degrees C to confluence on "Magic Marker" selection plates supplemented with uracil and with methyl methanesulfonate 0.001% . The aliquots of cells used for the two channels were split from the same source and were grown concurrently. See PubMed ID 15525520.


title: Yeast DNA Integrity Network: Synthetic Lethality with hst1

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.25 and 1.51 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX. The second-site ("query") mutation had the genotype hst1::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- hst1


title: Yeast DNA Integrity Network: Synthetic Lethality with HU 40 mM

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.18 and 1.17 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

source_name: Experimental -- hydroxyurea 40 mM

growth_protocol: Cells were grown at 30 degrees C to confluence on "Magic Marker" selection plates supplemented with uracil and with hydroxyurea 40 mM . The aliquots of cells used for the two channels were split from the same source and were grown concurrently. See PubMed ID 15525520.


title: Yeast DNA Integrity Network: Synthetic Lethality with MMS 0.0004%

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.45 and 1.18 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

source_name: Experimental -- methyl methanesulfonate 0.0004%

growth_protocol: Cells were grown at 30 degrees C to confluence on "Magic Marker" selection plates supplemented with uracil and with methyl methanesulfonate 0.0004% . The aliquots of cells used for the two channels were split from the same source and were grown concurrently. See PubMed ID 15525520.


title: Yeast DNA Integrity Network: Synthetic Lethality with UVC 75 J/m2

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 0.97 and 1 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

source_name: Control

source_name: Experimental -- ultraviolet C irradiation 75 J/m2

growth_protocol: Cells were grown at 30 degrees C to confluence on "Magic Marker" selection plates supplemented with uracil and with ultraviolet C irradiation 75 J/m2 . The aliquots of cells used for the two channels were split from the same source and were grown concurrently. See PubMed ID 15525520.


title: Yeast DNA Integrity Network: Synthetic Lethality with CPT 5 ug/ml

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.06 and 0.93 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

source_name: Experimental -- camptothecin 5 ug/ml

growth_protocol: Cells were grown at 30 degrees C to confluence on "Magic Marker" selection plates supplemented with uracil and with camptothecin 5 ug/ml . The aliquots of cells used for the two channels were split from the same source and were grown concurrently. See PubMed ID 15525520.


title: Yeast DNA Integrity Network: Synthetic Lethality with UVC 50 J/m2

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.51 and 1.21 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

source_name: Experimental -- ultraviolet C irradiation 50 J/m2

growth_protocol: Cells were grown at 30 degrees C to confluence on "Magic Marker" selection plates supplemented with uracil and with ultraviolet C irradiation 50 J/m2 . The aliquots of cells used for the two channels were split from the same source and were grown concurrently. See PubMed ID 15525520.


title: Yeast DNA Integrity Network: Synthetic Lethality with MMS 0.002%

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.45 and 1.32 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

source_name: Experimental -- methyl methanesulfonate 0.002%

growth_protocol: Cells were grown at 30 degrees C to confluence on "Magic Marker" selection plates supplemented with uracil and with methyl methanesulfonate 0.002% . The aliquots of cells used for the two channels were split from the same source and were grown concurrently. See PubMed ID 15525520.


title: Yeast DNA Integrity Network: Synthetic Lethality with CPT 0.2 ug/ml

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.35 and 1.24 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

growth_protocol: Cells were grown at 30 degrees C to confluence on "Magic Marker" selection plates supplemented with uracil. See PubMed ID 15525520.

source_name: Experimental -- camptothecin 0.2 ug/ml

growth_protocol: Cells were grown at 30 degrees C to confluence on "Magic Marker" selection plates supplemented with uracil and with camptothecin 0.2 ug/ml . The aliquots of cells used for the two channels were split from the same source and were grown concurrently. See PubMed ID 15525520.


title: Yeast DNA Integrity Network: Synthetic Lethality with CPT 15 ug/ml

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.59 and 1.19 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

source_name: Experimental -- camptothecin 15 ug/ml

growth_protocol: Cells were grown at 30 degrees C to confluence on "Magic Marker" selection plates supplemented with uracil and with camptothecin 15 ug/ml . The aliquots of cells used for the two channels were split from the same source and were grown concurrently. See PubMed ID 15525520.


title: Yeast DNA Integrity Network: Synthetic Lethality with CPT 2 ug/ml

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.01 and 0.85 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

source_name: Experimental -- camptothecin 2 ug/ml

growth_protocol: Cells were grown at 30 degrees C to confluence on "Magic Marker" selection plates supplemented with uracil and with camptothecin 2 ug/ml . The aliquots of cells used for the two channels were split from the same source and were grown concurrently. See PubMed ID 15525520.


title: Yeast DNA Integrity Network: Synthetic Lethality with HU 15 mM

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 2.48 and 1.3 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

source_name: Experimental -- hydroxyurea 15 mM

growth_protocol: Cells were grown at 30 degrees C to confluence on "Magic Marker" selection plates supplemented with uracil and with hydroxyurea 15 mM . The aliquots of cells used for the two channels were split from the same source and were grown concurrently. See PubMed ID 15525520.


title: CGH_2006011805_der(X)_cell1

city: Leuven

first: Joris

middle: R

last: Vermeesch

address: Herestraat, 49

department: Center for Human Genetics

country: Belgium

institute: Katholic University Leuven

description: Analysis Phi29 amplified single-cell gDNA versus non-amplified gDNA

data_processing: Spot intensities were corrected for local background and only spots with signal intensities at least 1.2-fold above background were included in the analysis and log2 values were calculated. For each array, the normalised ratio was obtained by calculating the median of the log2 signal intensities over all the autosomal fragments with measurements from abnormal chromosomes masked out, and substracting this value from all the signal intensities of the spots on the array

organism: Homo sapiens

source_name: Amplified single-cell (number 1) gDNA (46,XX,der(X)t(X;14)(q21.3;q23.1)

label_protocol: One hundred and fifty nanogram of Phi29 amplified single-cell gDNA was labelled by random priming with Cy5-dUTP

tag: Single-cell gDNA following Phi29 whole genome amplification

source_name: Non-amplified reference gDNA (46,XX)

label_protocol: One hundred and fifty nanogram of gDNA was labelled by random priming with Cy3-dUTP

tag: Reference genomic DNA


title: Yeast DNA Integrity Network: Synthetic Lethality with HU 30 mM

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.63 and 1.23 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

source_name: Experimental -- hydroxyurea 30 mM

growth_protocol: Cells were grown at 30 degrees C to confluence on "Magic Marker" selection plates supplemented with uracil and with hydroxyurea 30 mM . The aliquots of cells used for the two channels were split from the same source and were grown concurrently. See PubMed ID 15525520.


title: CGH_2006011806_der(X)_cell3

source_name: Amplified single-cell (number 3) gDNA (46,XX,der(X)t(X;14)(q21.3;q23.1)


title: Yeast DNA Integrity Network: Synthetic Lethality with UVC 150 J/m2

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 0.96 and 0.96 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

source_name: Experimental -- ultraviolet C irradiation 150 J/m2

growth_protocol: Cells were grown at 30 degrees C to confluence on "Magic Marker" selection plates supplemented with uracil and with ultraviolet C irradiation 150 J/m2 . The aliquots of cells used for the two channels were split from the same source and were grown concurrently. See PubMed ID 15525520.


title: Yeast DNA Integrity Network: Synthetic Lethality with UVC 200 J/m2

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.46 and 1.4 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

source_name: Experimental -- ultraviolet C irradiation 200 J/m2

growth_protocol: Cells were grown at 30 degrees C to confluence on "Magic Marker" selection plates supplemented with uracil and with ultraviolet C irradiation 200 J/m2 . The aliquots of cells used for the two channels were split from the same source and were grown concurrently. See PubMed ID 15525520.


title: CGH_2006011804_der(X)_cell2

source_name: Amplified single-cell (number 2) gDNA (46,XX,der(X)t(X;14)(q21.3;q23.1)

source_name: Non-amplified reference gDNA (46,XY)


title: Yeast DNA Integrity Network: Synthetic Lethality with UVC 125 J/m2

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.29 and 1.19 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

source_name: Control

source_name: Experimental -- ultraviolet C irradiation 125 J/m2

growth_protocol: Cells were grown at 30 degrees C to confluence on "Magic Marker" selection plates supplemented with uracil and with ultraviolet C irradiation 125 J/m2 . The aliquots of cells used for the two channels were split from the same source and were grown concurrently. See PubMed ID 15525520.


title: CGH_2006011805_der(X)_cell2


title: CGH_2006011802_del(4q)_cell2

source_name: Amplified single-cell (number 2) gDNA (46,XX,del(4)(q13.1q22.3)


title: Yeast DNA Integrity Network: Synthetic Lethality with UVC 100 J/m2

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.43 and 1.27 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

source_name: Experimental -- ultraviolet C irradiation 100 J/m2

growth_protocol: Cells were grown at 30 degrees C to confluence on "Magic Marker" selection plates supplemented with uracil and with ultraviolet C irradiation 100 J/m2 . The aliquots of cells used for the two channels were split from the same source and were grown concurrently. See PubMed ID 15525520.


title: CGH_2006011803_del(4q)_cell3

source_name: Amplified single-cell (number 3) gDNA (46,XX,del(4)(q13.1q22.3)


title: CGH_2006011803_der(X)_cell1


title: Patient-05-029_HR-CGH_alternativeHDarray (Experiment-ID: 43076)

city: New Haven

first: Jan

middle: Oliver

last: Korbel

state: CT

address: 266 Whitney Avenue

institute: Yale University

description: High resolution comparative genome hybridization (HR-CGH) was performed in order to identify the exact deletion breakpoints in the beta-globin locus.

data_processing: For each spot on the array log2-ratios of the Cy3-labeled test sample versus the Cy5-labeled reference sample were calculated. Fluorescence intensity normalization was performed using the Qspline algorithm (Workman et al 2002; PMID: 12225587), implemented as normalize.qspline in the Bioconductor package (www.bioconductor.org).

source_name: Genomic DNA isolated from blood

tag: Patient with beta-thalassemia; DNA isolated from blood.

source_name: Genomic DNA from 7 normal male individuals (Promega)

tag: Pooled genomic DNA from 7 normal male individuals (Promega); used as control.


title: Yeast DNA Integrity Network: Synthetic Lethality with CPT 0.5 ug/ml

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.18 and 1.31 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

source_name: Experimental -- camptothecin 0.5 ug/ml

growth_protocol: Cells were grown at 30 degrees C to confluence on "Magic Marker" selection plates supplemented with uracil and with camptothecin 0.5 ug/ml . The aliquots of cells used for the two channels were split from the same source and were grown concurrently. See PubMed ID 15525520.


title: Yeast DNA Integrity Network: Synthetic Lethality with CPT 0.1 ug/ml

description: See above.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 1.28 and 1.08 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.

source_name: Experimental -- camptothecin 0.1 ug/ml

growth_protocol: Cells were grown at 30 degrees C to confluence on "Magic Marker" selection plates supplemented with uracil and with camptothecin 0.1 ug/ml . The aliquots of cells used for the two channels were split from the same source and were grown concurrently. See PubMed ID 15525520.


title: Patient-05-029_HR-CGH_rep2 (Experiment-ID: 38257)

description: High resolution comparative genome hybridization (HR-CGH) was performed in order to identify the exact deletion breakpoints in the beta-globin locus. (Replicate number 2.)

data_processing: For each spot on the array log2-ratios of the Cy3-labeled test sample versus the Cy5-labeled reference sample were calculated. Fluorescence intensity normalization was performed using the Qspline algorithm (Workman et al. 2002; PMID: 12225587), implemented as normalize.qspline in the Bioconductor package (www.bioconductor.org).

tag: Patient with beta-thalassemia; blood.


title: Patient-05-029_HR-CGH_rep1 (Experiment-ID: 38590)

description:
High resolution comparative genome hybridization (HR-CGH) was performed in order to identify the exact deletion breakpoints in the beta-globin locus.  Repetitive elements were identified using RepeatMasker [1] and oligonucleotide probes were designed to represent the nonrepetitive DNA sequence.

[1] Smit, A.F.A., Hubley, R. & Green, P., RepeatMasker Open-3.0, 1996-2004.

data_processing: For each spot on the array log2-ratios of the Cy3-labeled test sample versus the Cy5-labeled reference sample were calculated. Fluorescence intensity normalization was performed using the Qspline algorithm (Workman et al 2002), implemented as normalize.qspline in the Bioconductor package (www.bioconductor.org).


title: CGH_2006011804_der(X)_cell3


title: CGH_2006011802_del(4q)_cell1

source_name: Amplified single-cell (number 1) gDNA (46,XX,del(4)(q13.1q22.3)


title: mesothelioma_cell_lines

type: RNA

city: Nancy

first: Bertrand

last: Rihn

address: 5 rue A Lebrun

department: Faculté de Pharmacie

country: France

institute: Université de Lorraine

description: The balance coefficient between Cy3/Cy5 fluorescence equaled 0,97. cDNA was hybridized on Incte Pharmaceuticals array containing 6969 probes (3962 human genes, 3007 human ESTs)

hyb_protocol: "The arrayed cDNA clones were hybridized with a 1:1 mixture of Cy3- or Cy5-labeled first-strand cDNAs generated from poly(A)1 RNA from various tissues, including both normal and tumor tissues, using the protocol provided by Incyte. The fluorescence intensity was scanned, and data were analyzed using Incyte GEMTOOLS software."

scan_protocol: inclusion criteria : signal to background ratio > 2,5			                     grid location coverage > 40%

data_processing: enzyme, function or pathway cluster analysis were performed using a Gemtools software (v2,4,2, Incyte Pharmaceuticals, freemont, Ca, USA). In this sutdy, genes were considered differentially expressed if the change was  >2,0-fold.

molecule: total RNA

source_name: Met-5A (mesothelial cell lines)

label_protocol: cDNA produce by reverse transcription were labeled either with Cy3 (MSTO-211H) or Cy5 (Met-5A) dUTP as described previously (M. Shena et al (1995), Science 270, 467-470.)

growth_protocol: Met-5A and MSTO-211H were respectively grown in M199 and RPMI 1640 supplemented with fetal claf serum (10%) according to the instructions of ATCC and described previously (Ke, Y., Reddel et al (1989), Am. J. Pathol. 134, 979-991)

extract_protocol: when cells reached confluence, the medium was replaced and 18 h later, total RNA was harvested using TrizolTM (Gibco BRL, Grand Island, NY, USA). Ployadenylated mRNAs were isolated with OligotexTM (Qiagen S.A., Courtaboeuf, France).

treatment_protocol: No treatment

tag: "ATCC® Number

tag: Designations

tag: Depositors

value: The United States of America

tag: Biosafety Level

value: 2 [CELLS CONTAIN PAPOVAVIRUS]

tag: Shipped

value: frozen

tag: Medium & Serum

value: See Propagation

tag: Growth Properties

value: adherent

tag: Organism

value: Homo sapiens (human)

tag: Morphology

value: epithelial

tag: Source

tag: Cell type

value: epithelial; virus transformed"

source_name: MSTO-211H (mesthelioma cell lines)

value: G Bepler

value: fibroblast

value: Disease:biphasic mesothelioma

tag: Derived from metastatic site

value: lung"


title: Muscle-AMPKgamma3-mutant(R225Q)transgenic-4

status: Public on Feb 15 2006

city: Göteborg

first: Elisabeth

middle: C

last: Nilsson

address: Arvid Wallgrens Backe 20

country: Sweden

institute: Arexis AB

description: Expression profiles generated from the white portion of the gastrocnemicus muscle from AMPK gamma3 mutant (R225Q) transgenic mice

data_processing: Quantile normalization and RMA (using GeneTraffic Uno version 3.2-11)

label: Biotin

organism: Mus musculus

source_name: White portion of the gastrocnemius muscle

tag: Strain

tag: Genotype

value: AMPK gamma3 mutant (R225Q) transgenic

tag: Generation

tag: Gender

value: male

tag: Tissue

value: white portion of the gastrocnemius muscle

tag: Feeding condition

value: fasted


title: Muscle-AMPKgamma3-wt-6

description: Expression profiles generated from the white portion of the gastrocnemicus muscle from wild type littermates to AMPK gamma3 knock-out mice

value: wild type

tag: Tissue:	white portion of the gastrocnemius muscle


title: Muscle-AMPKgamma3-mutant(R225Q)transgenic-6


title: Muscle-AMPKgamma3-wt-8

description: Expression profiles generated from the white portion of the gastrocnemicus muscle from wild type littermates to AMPK gamma3 mutant (R225Q) transgenic mice


title: Muscle-AMPKgamma3-mutant(R225Q)transgenic-2


title: Muscle-AMPKgamma3-wt-7


title: Muscle-AMPKgamma3-wt-10

tag: train


title: Muscle-AMPKgamma3-wt-11


title: Muscle-AMPKgamma3-mutant(R225Q)transgenic-3


title: Muscle-AMPKgamma3-wt-12


title: Muscle-AMPKgamma3-wt-9


title: Signal transduction analysis in sugarcane leaves (LB x HB replicate 1, dye swap)

status: Public on Feb 14 2006

city: Campinas

first: Renato

last: Vicentini

state: SP

address: Cidade Universitaria "Zeferino Vaz"

department: Centro de Biologia Molecular e Engenharia Genetica - CBMEG

country: Brazil

institute: Universidade Estadual de Campinas - UNICAMP

description:
Hybridization: micro_Manual Hyb; Manual Hybridization of microarrays
Scan_protocol: Model - Generation III Scanner; ArrayVision; Image scan
RNA extraction: Trizol
Labeling: Micro_First Strand_dT. Cyscribe First strand cDNA labeling kit, Amersham Biosciences. Using OLIGO-dT primers only.

organism: Saccharum officinarum

source_name: HB Lv_c3

value: The first leaf with a visible dewlap (leaf+1) was collected from at the 9 months time point from the seven individuals of each group and pooled. This sample has high sugar content. The leaf was sectioned in small 1-2 cm pieces that were frozen in liquid nitrogen and stored at -80oC

source_name: LB Lv_c3

value: The first leaf with a visible dewlap (leaf+1) was collected from at the 9 months time point from the seven individuals of each group and pooled. This sample has low sugar content. The leaf was sectioned in small 1-2 cm pieces that were frozen in liquid nitrogen and stored at -80oC


title: Muscle-AMPKgamma3-mutant(R225Q)transgenic-1


title: Muscle-AMPKgamma3-mutant(R225Q)transgenic-5


title: Muscle-AMPKgamma3-wt-4


title: Muscle-AMPKgamma3-ko-4

description: Expression profiles generated from the white portion of the gastrocnemicus muscle from AMPK gamma3 knock-out mice

value: AMPK gamma3 knock-out


title: Muscle-AMPKgamma3-wt-5


title: Signal transduction analysis in sugarcane leaves (LB x HB replicate 2, dye swap)


title: Muscle-AMPKgamma3-ko-6


title: Muscle-AMPKgamma3-ko-3


title: Muscle-AMPKgamma3-wt-3


title: Muscle-AMPKgamma3-wt-1


title: Muscle-AMPKgamma3-wt-2


title: Muscle-AMPKgamma3-ko-2


title: Muscle-AMPKgamma3-ko-5


title: Muscle-AMPKgamma3-ko-1


title: SOCS1-/-IFNg-/- + 48h IFNg

city: Parkville

first: Sam

last: Wormald

state: Victoria

address: 1G Royal Parade

department: Cancer and Haematology

country: Australia

institute: The Walter and Eliza Hall Institute

hyb_protocol: Samples were hybridized to MGU74Av2  microarrays as instructed by Affymetrix

scan_protocol: Samples were scanned using an Affymetrix GeneArray Scanner, as instructed by Affymetrix

data_processing: Raw probe data were quantile-normalized, background corrected and summarized using the Affy package for the R statistical programming environment

label: biotin-phycoerythrin

source_name: SOCS1-/-IFNg-/- liver + 48h IFNg

label_protocol: Biotin-labelled cRNA was generated as instructed by Affymetrix

extract_protocol: Total RNA was extracted with Trizol (Invitrogen), and cleaned with RNeasy (Qiagen)

treatment_protocol: Mice were IP injected with 100 ul (4ug) of recombinant interferon-gamma or 100 ul of phosphate-buffered saline (PBS), and livers were taken at 0h, 0.5h, 1h, 2h, 4h, 12h, 16h, 24h or 48h.

tag: Suppressor of Cytokine Signalling 1-/-, Interferon-gamma-/- liver


title: SOCS1-/-IFNg-/- + 24h IFNg

source_name: SOCS1-/-IFNg-/- liver + 24h IFNg


title: Signal transduction analysis in sugarcane leaves  (HB x LB replicate 1)


title: Signal transduction analysis in sugarcane leaves  (HB x LB replicate 2)


title: IFNg-/- + 4h IFNg

hyb_protocol: Samples were hybridized to MGU74Av2 microarrays as instructed by Affymetrix

label: Biotin-phycoerythrin

source_name: IFNg-/- liver + 4h IFNg

treatment_protocol: Mice were IP injected with 4ug (100ul) of recombinant interferon-gamma or 100ul phosphate-buffered saline (PBS), and livers were taken at various timepoints afterwards.

tag: Interferon-gamma-/- liver


title: SOCS1-/-IFNg-/- + 16h IFNg

source_name: SOCS1-/-IFNg-/- liver + 16h IFNg


title: SOCS1-/-IFNg-/- + 2h IFNg

source_name: SOCS1-/-IFNg-/- liver + 2h IFNg


title: SOCS1-/-IFNg-/- + 1h IFNg

source_name: SOCS1-/-IFNg-/- liver + 1h IFNg


title: SOCS1-/-IFNg-/- + 4h PBS

source_name: SOCS1-/-IFNg-/- liver + 4h PBS


title: IFNg-/- + 48h IFNg

source_name: IFNg-/- liver + 48h IFNg


title: SOCS1-/-IFNg-/- + 4h IFNg

source_name: SOCS1-/-IFNg-/- liver + 4h IFNg


title: SOCS1-/-IFNg-/- + 12h PBS

source_name: SOCS1-/-IFNg-/- liver + 12h PBS


title: SOCS1-/-IFNg-/- + 12h IFNg

source_name: SOCS1-/-IFNg-/- liver + 12h IFNg


title: SOCS1-/-IFNg-/- + 0.5h IFNg

source_name: SOCS1-/-IFNg-/- liver + 0.5h IFNg


title: IFNg-/- + 16h IFNg

source_name: IFNg-/- liver + 16h IFNg


title: IFNg-/- + 24h IFNg

source_name: IFNg-/- liver + 24h IFNg


title: IFNg-/- + 12h IFNg

source_name: IFNg-/- liver + 12h IFNg


title: mouse VILI ovlps5 20K

status: Public on Feb 12 2006

city: Pittsburgh

first: Tamas

last: Dolinay

state: PA

department: Pulmonary, Allergy and Critical Care

institute: Univerisity of Pittsburgh Medical Center

description: mouse lps+high pressure ventilation treatment5

data_processing: CodeLink Expression Analysis 2.3 (10K) and 4.1. (20K) sofware for initial analysis. Raw data was log2 base transformed and normalized with the Cyclic Loess method implemented in Bioconductor.  Cyclic Loess is described by Wu W, Dave N, Tseng G, Richards T, Xing EP, and Kaminski N.  in their publication entitled Comparison of normalization for Codelink bioarray data, published in BMC Bioinformatics 6: 309, 2005. The data submitted is median normalized.

source_name: BALB/c lung tissue

tag: BALB/c male, 22-30g


title: IFNg-/- + 12h PBS

source_name: IFNg-/- liver + 12h PBS


title: IFNg-/- + 1h IFNg

source_name: IFNg-/- liver + 1h IFNg


title: mouse VILI ovlps4 20K

description: mouse lps+high pressure ventilation treatment4


title: SOCS1-/-IFNg-/- (negative control)

source_name: SOCS1-/-IFNg-/- liver (untreated)


title: IFNg-/- + 4h PBS

source_name: IFNg-/- liver + 4h PBS


title: IFNg-/- (negative control)

source_name: IFNg-/- liver (untreated)


title: IFNg-/- + 2h IFNg

source_name: IFNg-/- liver + 2h IFNg


title: mouse VILI ovlps2 20K

description: mouse lps+high pressure ventilation treatment2


title: mouse VILI ov3 20K

description: mouse high pressure ventilation treatment6

tag: BALB/c male,22-30g


title: mouse VILI ovlps3 20K

description: mouse lps+high pressure ventilation treatment3


title: mouse VILI ov1 20K

description: mouse high pressure ventilation treatment4

tag: BALB/c male 22-30g


title: mouse VILI ovlps1 20K

description: mouse lps+high pressure ventilation treatment1


title: mouse VILI ov2 20K

description: mouse high pressure ventilation treatment5


title: mouse VILI lps4 20K

description: mouse lps treatment7

tag: BALB/C male, 22-30g


title: mouse VILI lps5 20K

description: mouse lps treatment8


title: mouse VILI lps3 20K

description: mouse lps treatment6


title: mouse VILI c4 20K

description: mouse control 7


title: Mouse VILI c1 10K

description: mouse control1

source_name: BALB/C lung tissue

tag: BALb/c male, 22-30g


title: mouse VILI lps1 20K

description: mouse lps treatment4


title: mouse VILI c2 20K

description: mouse control 5


title: mouse VILI lps3 10K

description: mouse lps treatment3


title: mouse VILI lps1 10K

description: mouse lps treatment1


title: mouse VILI ov2 10K

description: mouse high pressure ventilation treatment2


title: mouse VILI lps2 20K

description: mouse lps treatment5


title: mouse VILI c3 10K

description: mouse control3


title: mouse VILI c2 10K

description: mouse control2


title: mouse VILI ov1 10K

description: mouse high pressure ventilation treatment1


title: mouse VILI ov3 10K

description: mouse high pressure ventilation treatment3


title: mouse VILI c3 20K

description: mouse control 6


title: mouse VILI c1 20K

description: mouse control 4


title: SBC-5

status: Public on Feb 10 2006

city: Tokyo

first: Akihiko

last: Gemma

address: Bumkyo-ku

country: Japan

institute: Nippon Medical School

description: small cell cancer cell line

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

label: biotin

source_name: human cancer cell line

label_protocol: Approximately 1µg of mRNA was processed to produce biotinylated cRNA targets.

extract_protocol: Total RNA was extracted from the cell lysate using TRIsol reagent (Invitrogen).mRNA was purified from total RNA with oligo-dT-magnetic beads (Toyobo)

tag: small cell cancer cell line


title: IFNg-/- + 0.5h IFNg

source_name: IFNg-/- liver + 0.5h IFNg


title: LC-1F

description: squamous cell cancer cell line

tag: squamous cell cancer cell line


title: SQ-5

description: squamous cell cancer cell line


title: MS-1

description: small cell cancer cell line


title: LC1/sq

description: squamous cell cancer cell line


title: LC2/ad

description: adenocarcinoma cell line(Non-small)

tag: adenocarcinoma cell line(Non-small)


title: QG-56

description: squamous cell cancer cell line


title: EBC-1

description: squamous cell cancer cell line


title: ABC-1

description: adenocarcinoma cell line(Non-small)


title: RERF LC-KJ

description: adenocarcinoma cell line(Non-small)


title: Lu130

description: small cell cancer cell line


title: PC-1

description: squamous cell cancer cell line


title: H69

description: small cell cancer cell line


title: Lu139

description: small cell cancer cell line


title: PC-6

description: small cell cancer cell line


title: Lu165

description: small cell cancer cell line


title: A549

description: adenocarcinoma cell line(Non-small)


title: RERF-LC-AI

description: squamous cell cancer cell line


title: SBC3

description: small cell cancer cell line


title: RERF LC-MS

description: adenocarcinoma cell line(Non-small)


title: LU135

description: small cell cancer cell line


title: LU65

description: adenocarcinoma cell line(Non-small)


title: N231

description: small cell cancer cell line


title: PC-3

description: adenocarcinoma cell line(Non-small)


title: LK2

description: squamous cell cancer cell line


title: PC7

description: adenocarcinoma cell line(Non-small)


title: PC9

description: adenocarcinoma cell line(Non-small)


title: carcinoma-1 - mAdbID:51664

status: Public on Feb 09 2006

city: Bethesda

first: Stuart Yuspa

last: Adam Glick

address: 9000 Rockville Pike

department: National Cancer Institute

institute: National Institutes of Health

description: mAdb experiment ID: 51664

hyb_protocol: cDNA Microarray Hybridization Other: 1 ¶l COT-1 DNA (8-10 ug/ul) and 1 ul poly A (8-10 ug/ul) were added to the labelled cDNA and then denatured at 100øC for 1 minute, followed by snap cooling on ice. (Final volume should be 20 ul.) Freshly made 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) was warmed to 42øC just before adding to samples. 20 ul of 2X F-hyb buffer to samples, and the total 40 ul of sample added to the microarray. 20 ul of 3X SSC was added to wells in hybridization chamber to maintain humidity. Array slides were incubated overnight (12-16 hours) at 42øC in water bath or hybridization oven. After hybridization of slides, slides were washed for 2 minute in 2X SSC with 0.1% SDS (with occasional plunging), for 2 minute in 1X SSC (with occasional plunging), for 2 minutes in 0.2X SSC (with occasional plunging), for 1 minute in 0.05X SSC, and spun for 3 minutes at 450 rpm to dry.

data_processing: After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.

source_name: ST 221- control 8

label_protocol:
Cy5 Labeling
Label amount: 40000 pmol dye
Label method: Aminoallyl Coupling Method
Other: Protocol Similar to that found at the J. David Gladstone Institutes Genomic Core Laboratory (SOP #P004). Used CyeDye Post-Labelling Reactive Dye Pack.

extract_protocol:
RNA Extraction
Extraction method: Trizol-QIAgen RNeasy Kit
Other: Tumors were Homogenized in TRIzol, and RNA purified with the Quiagen RNeasy clean up kit.

treatment_protocol:
Treatment type: compound
Agent: Doxycycline
Treatment dose: 1 gram / kg chow
Treatment time: 48 hours
In-vivo treatment: Mice with tumors were treated with 1 gram/Kg doxycycline chow (Bio-Serve) after a 3-hour fast and tumors harvested after 48 hrs.
Treatment type: compound
Agent: DMBA/TPA
In-vivo treatment: Mice were shaved and initiated topically with 100ug of DMBA in 200ul of acetone. After 1 week mice were treated topically with 5 ug TPA in 200 ul acetone twice a week for 20 weeks. Benign tumors developed by 12-14 weeks of promotion, and SCC between 25-35 weeks after start of promotion. Tumor stage was verified by analysis of H&E stained sections.

tag: Strain

value: FVB

tag: Age

value: 7-12 Weeks

value: chemically-derived skin tumor

tag: Developmental stage

value: adult

tag: Disease state

value: Squamous Cell Carcinoma

tag: Genotype/Genetic variation

label_protocol:
Cy3 Labeling
Label amount: 40000 pmol dye
Label method: Aminoallyl Coupling Method
Other: Protocol Similar to that found at the J. David Gladstone Institutes Genomic Core Laboratory (SOP #P004). Used CyeDye Post-Labelling Reactive Dye Pack.

value: K5rTA tetOTGFbeta


title: papilloma-4 - mAdbID:51021

description: mAdb experiment ID: 51021

source_name: ST 257B - control 2 - Cy3

tag: Tissue

value: Papilloma

source_name: DT 228A-Cy5


title: papilloma-5 - mAdbID:51022

description: mAdb experiment ID: 51022

source_name: ST 257CE - control 3 - Cy3

source_name: DT 228B-Cy5


title: papilloma-3 - mAdbID:51663

description: mAdb experiment ID: 51663


title: PC-10

description: squamous cell cancer cell line


title: carcinoma-4 - mAdbID:45849

description: mAdb experiment ID: 45849

source_name: ST 241A- control 10-Cy5


title: carcinoma-5 - mAdbID:45720

description: mAdb experiment ID: 45720

source_name: ST 257A- control 11-Cy5


title: carcinoma-3 - mAdbID:47345

description: mAdb experiment ID: 47345

source_name: ST 242- control 9


title: papilloma-8 - mAdbID:45847

description: mAdb experiment ID: 45847

source_name: ST 257CE - control 3 - Cy5

source_name: DT 228B-Cy3


title: papilloma-1 - mAdbID:50815

description: mAdb experiment ID: 50815

source_name: ST 2000E - control 1

source_name: DT 228A-Cy3


title: papilloma-11 - mAdbID:37657

description: mAdb experiment ID: 37657