title: 15 dyn/cm2 0 Hz Rep 2

description: Amplified using AMBION Message Amp II kit

extract_protocol: AMBION PARIS kit


title: Cnidarian - algal symbiosis (Apo5_Cy5 vs Sym5_Cy3) slide 41

status: Public on Feb 21 2006

type: RNA

city: Corvallis

first: Mauricio

last: Rodriguez-Lanetty

state: OR

address: 3029 Cordley Hall

department: Zoology

country: USA

institute: Oregon State University

description: For statistical purposes, data was also normalized using the LOWESS transformation using the software MAANOVA (Bioconductor). But in this submission this transformation is not included. The value (Log Ratio) shown here has been normalized using only a global normalization method executed by GenePix Pro 6.0.

hyb_protocol: Array was pre-hybed  with the hybridization buffer (vial 7) from the Genisphere 3DNA 350 Kit with 0.1 mg/ml salmon sperm for 2 h at 50 degrees. cDNA hybridization was done using the same hybridization buffer (vial 7) plus blocker (supplied from Genisphere Kit). Hyb was carried out for 18h at 47 degrees. All washes were done as follow: 1) 2X SSC, 0.2% SDS at 60 degrees for 15 min; 2) 2X SSC at 23 degrees for 15 min; 3) 0.2X SSC at 23 degrees for 15 min; 4) Spin at 1000 rpm for 2 min. In the last wash after cDNA hybridization, array was dipped in Dye Saver 2 supplied from Genishere for 5 sec and spinned at 1000 rpm for 2 min.  Dye saver stops photobleaching of the dyes.

scan_protocol: Array scanned using Axon GenePix 4200  Software used GenePix Pro 6.0

molecule: polyA RNA

organism: Anthopleura elegantissima

source_name: Aposymbiotic sea anemone (Apo 5)

label_protocol: Sample was labeled using genisphere 3DNA 350 labeling Kit

growth_protocol: This anemone was acclimatized in the lab after collection at 14 degrees for 5 days at a day/night cycle of 12:12 h

extract_protocol:
Trizol for total RNA and
Micro mRNA purist (Ambion) for PolyA RNA

treatment_protocol: This was a natural treatment. This anemone was found aposymbiotic (lacking algal symbionts) naturally in the field (Oregon Coast)

tag: Sea anemone (lacking intracellular algal symbionts)

source_name: Symbiotic sea anemone (Sym5)

treatment_protocol: This was a natural treatment. This anemone was found harboring algal symbionts naturally in the field (Oregon Coast)

tag: Sea anemone harboring intracellular algal symbionts (dinoflagellates

value: Symbiodinium sp)


title: 15 dyn/cm2 0 Hz Rep 1

status: Public on Feb 22 2006

city: Durham

first: Heather

middle: Anne

last: Himburg

state: NC

address: PO Box 90281

department: Biomedical Engineering

institute: Duke Univeristy

description: Samples were amplified using Message AMP II kit

data_processing: Lowess Normalization

molecule: total RNA

organism: Sus scrofa

source_name: Sheared endothelial cells

growth_protocol: Cells were grown in M199 supplemented with antibiotic/mycotic and porcine serum.

extract_protocol: Ambion PARIS kit

treatment_protocol: Cells were sheared for 24 hours at 15 dyn/cm^2 in a parallel plate flow chamber.  The flow was steady, laminar.

tag: Cultured Porcine Aortic Endothelial Cells

source_name: Reference

growth_protocol: Cells were grown in M199 supplemented with antibiotic/mycotic, FBS, and porcine serum.

treatment_protocol: Static culture


title: 15 dyn/cm2 0 Hz Rep 3

description: Amplified with Message Amp II kit

tag: Passage 1-5


title: Cnidarian - algal symbiosis (Apo6_Cy5 vs Sym6_Cy3) slide 16

data_processing: The value (Log Ratio) shown here has been normalized using only a global normalization method executed by GenePix Pro 6.0.

source_name: Aposymbiotic sea anemone (Apo 6)

source_name: Symbiotic sea anemone (Sym6)


title: Cnidarian - algal symbiosis (Sym4_Cy5 vs Apo4_Cy3)_slide25

scan_protocol: Sample was labeled using genisphere 3DNA 350 labeling Kit  Hybridization protocol:

source_name: Symbiotic sea anemone (Sym 4)

source_name: Aposymbiotic sea anemone (Apo4)


title: 15 dyn/cm2 1 Hz Rep 3

description: Amplified with Message Amp II kit

source_name: Sheared Endothelial Cells

treatment_protocol: Cells were sheared for 24 hours at 15 dyn/cm^2 in a parallel plate flow chamber.  The flow was pulsatile, sinusoidal waveform with a frequency of 1 Hz.


title: Cnidarian - algal symbiosis (Apo1_Cy5 vs Sym1_Cy3) Slide 12

scan_protocol: Array scanned using Axon GenePix 4200 and Software used GenePix Pro 6.0

source_name: Aposymbiotic sea anemone (Apo 1)

label_protocol: Sample was labeled using genisphere 3DNA 350 labelling Kit

source_name: Symbiotic sea anemone (Sym1)


title: Cnidarian - algal symbiosis (Sym1_Cy5_vs_Apo1_Cy3) Slide 09

source_name: Symbiotic sea anemone (Sym 1)

extract_protocol:
Tryzol for total RNA and
Micro mRNA purist (Ambion)

source_name: Aposymbiotic sea anemone (Apo1)

extract_protocol:
Tryzol for total RNA and
mRNA purist (Ambion)


title: Cnidarian - algal symbiosis (Sym2_Cy5 vs Apo2_Cy3) slide14

source_name: Symbiotic sea anemone (Sym 2)

source_name: Aposymbiotic sea anemone (Apo2)


title: 15 dyn/cm2 1 Hz Rep 1

description: Amplified with Message Amp II kit


title: 7.5 dyn/cm^2 0 Hz Rep 2

description: Amplified with Message Amp II kit

extract_protocol: AMBION Paris Kit

treatment_protocol: Cells were sheared for 24 hours at 7.5 dyn/cm^2 in a parallel plate flow chamber. The flow was steady, laminar.

tag: Cultured Porcine Aortic endothelial cells

tag: Passages 1-6.


title: Cnidarian - algal symbiosis (Apo3_Cy5 vs Sym3_Cy3) slide 28

source_name: Aposymbiotic sea anemone (Apo 3)

source_name: Symbiotic sea anemone (Sym3)


title: SW-900

type: genomic

city: Bethesda

first: William

middle: Wallace

last: Lockwood

state: MD

address: 50 South Drive

institute: National Human Genome Research Institute

description:
cyanine 5 = sample
cyanine 3 = reference

label: Cyanine 5

molecule: genomic DNA

organism: Homo sapiens

source_name: SW-900 Squamous Cell Carcinoma Cell Line

tag: ATCC catalogue number HTB59

label: cyanine 3

source_name: Male genomic

tag: NOVAGEN POOLED MALE REFERENCE GENOMIC DNA


title: HCC2450

source_name: HCC2450 Squamous Cell Carcinoma Cell Line


title: SK-MES-1

source_name: SK-MES-1 Squamous Cell Carcinoma Cell Line

tag: ATCC Catalouge Number HTB-58


title: H520

source_name: H520 Squamous Cell Carcinoma Cell Line

tag: ATCC Catalogue Number HTB182


title: 7.5 dyn/cm^2 3 Hz Rep 1

description: Amplification with Message AMP II kit

source_name: Sheared endothelial cells

extract_protocol: AMBION Paris kit

treatment_protocol: Cells were sheared for 24 hours at 7.5 dyn/cm^2 in a parallel plate flow chamber. The flow was pulsatile with a sinusoidal frequency of 3 Hz.

tag: Passages 1-6

source_name: Reference


title: H2009

description:
Cyanine 5 = sample
Cyanine 3 = reference

source_name: H2009 Adenocarcinoma Cell Line

tag: ATCC catalogue number CRL-5911

label: Cyanine 3


title: Pooled Rheumatoid Arthritis C442MC

status: Public on Feb 18 2006

city: Oklahoma City

first: Parima

last: Pathipvanich

state: OK

address: 755 Research Parkway, Suite 464

department: Arthritis/Immunology

institute: Oklahoma Medical Research Foundation

description: none.

hyb_protocol: Ventana Discovery 9h, 58 C washed to 0.1xSSC

scan_protocol: scanned on Agilient G2505B scanner. Imagene 5.0

data_processing: Dozmorov I, Centola M, Bioinformatics 19:2004-2011, 2003

source_name: B-Lymphocytes from 8 RA patients

label_protocol: Jarvis, JN, et al. Arthritis Res. Ther 2004, 6:R15-R32

growth_protocol: none.

extract_protocol: Trizol/Qiagen RNeasy

treatment_protocol: none.

tag: tissue

value: b-lymphocytes from 3 male, 5 female Rheumatoid Arthritis patients.

tag: mean age

tag: mean disease duration


title: C57BL/6 H.pylori vs. C57BL/6

status: Public on Feb 17 2006

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description: Total RNA was prepared using the RNeasy protocol with on-column DNAse digestion (Qiagen, Hilden, Germany) and confirmed to be intact and free of contaminating DNA using an Agilent 2100 bioanalyzer and a RNA 6000 Nano LabChip kit (Agilent Technologies, Palo Alto, CA). A custom tailored 'in situ' synthesized 60-mer oligonucleotide microarray (Agilent) comprising 8014 murine genes with immunological focus was used for expression profiling. RNA was amplified and labeled using a reverse-transcriptase/T7 polymerase linear amplification labeling kit (Agilent), and 1.5 mg of respective cRNAs labeled either with Cy3 or Cy5 were hybridized for 16 h at 65°C. Slides were used and processed according to the manufacturer's manuals.

data_processing: Features were extracted with an Image Analysis software (Version A.7.5.1, Agilent). Intensities were normalized by local background correction and by rank consistency filtering with a combination of linear and LOWESS normalization. Data analysis was performed with Rosetta Resolver Biosoftware (Build 5.1.0.0.163, Rosetta Biosoftware, Seattle, WA).

organism: Mus musculus

source_name: C57BL/6 H.pylori

tag: Female C57BL/6 mice (6 weeks old, Charles River, Sulzfeld, Germany) were infected with a single oral dose of 9.5 × 10e8 Hp76 cells suspended in PBS and 0.2 M NaHCO3. The stomach was removed, and the stomach mucosa was scraped off with a sterile scalpel blade on liquid nitrogen until ~2/3 of the tissue was removed.

tag: Female C57BL/6 mice (6 weeks old, Charles River, Sulzfeld, Germany). The stomach was removed, and the stomach mucosa was scraped off with a sterile scalpel blade on liquid nitrogen until ~2/3 of the tissue was removed.


title: C57BL/6 vs. C57BL/6 H.pylori


title: C57BL/6 Cholesterol H.pylori vs. C57BL/6

source_name: C57BL/6 Cholesterol H.pylori


title: HCC1195

description: cy 5 = sample cy 3= reference

source_name: HCC1195 adenocarcinoma cell line

tag: HCC1195 adenocarcinoma cell line

source_name: normal male

tag: NOVAGEN POOLED NORMAL MALE REFERENCE GENOMIC DNA


title: C57BL/6 vs. C57BL/6 Cholesterol H.pylori


title: Pooled Control C441MC

description: none.

source_name: B-Lymphocytes from 8 age/sex matched controls

tag: tissue b-lymphocytes from 3 male, 5 female controls


title: H226

source_name: H226 Squamous Cell Carcinoma Cell Line

tag: ATTC catalogue number CRL-5826


title: H2087

description: cy 5 = sample cy 3= reference

source_name: H2087 adenocarcinoma cell line

tag: ATTC catalogue number CRL-5922


title: H1819

description: cy 5 = sample cy 3= reference

source_name: H1819 adenocarcinoma cell line

tag: ATTC catalogue number CRL-5897

tag: NOVAGEN POOLED NORMAL REFERENCE GENOMIC DNA


title: H157

source_name: Squamous Cell Carcinoma Cell Line H157

tag: Squamous Cell Carcinoma Cell Line H157

source_name: male genomic

tag: NOVAGEN POOLED MALE REFERENCE GENOMIC DNA


title: H2170

source_name: Squamous Cell Carcinoma Cell Line H2170

tag: ATCC Catalogue Number CRL-5928

source_name: Male genomic


title: H2347

description: cy 5 = sample cy 3= reference

source_name: H2347 adenocarcinoma cell line

tag: ATTC catalogue number CRL-5942


title: HCC78

description: cy 5 = sample cy 3= reference

source_name: HCC78 adenocarcinoma cell line


title: HCC95

source_name: HCC95 Squamous Cell Carcinoma Cell Line

tag: HCC95 Squamous Cell Carcinoma Cell Line


title: HCC15

source_name: HCC15 Squamous Cell Carcinoma Cell Line

tag: HCC15 Squamous Cell Carcinoma Cell Line


title: H1395

description:
cy 5 = sample
cy 3 = reference

source_name: H1395 adenocarcinoma cell line

tag: ATCC catalogue number CRL-5868

tag: NOVAGEN POOLED NORMAL MALE GENOMIC DNA


title: HCC193

description: cy 5 = sample cy 3= reference

source_name: HCC193 adenocarcinoma cell line


title: HCC366

description: cy 5 = sample cy 3= reference

source_name: HCC366 adenocarcinoma cell line


title: HCC1833

description: cy 5 = sample cy 3= reference

source_name: HCC1833 adenocarcinoma cell line

tag: HCC1833 adenocarcinoma cell line


title: H1648

description: cy 5 = sample cy 3= reference

source_name: H1648 adenocarcinoma cell line

tag: ATTC catalogue number CRL-5882

source_name: normal male


title: H2122

description: cy 5 = sample cy 3= reference

source_name: H2122 adenocarcinoma cell line

tag: ATTC catalogue number CRL-5985


title: H1993

description: cy 5 = sample cy 3= reference

source_name: H1993 adenocarcinoma cell line

tag: ATTC catalogue number CRL-5909

tag: NOVAGEN POOLED NORMAL MALE REFERENCE GENOMIC DNA


title: H1155

description:
cy 5 = sample
CY3 = reference

source_name: H1155 large cell carcinoma line

tag: ATTC catalogue number CRL-5818


title: HCC461

description: cy 5 = sample cy 3= reference

source_name: HCC461 adenocarcinoma cell line


title: Yeast DNA Integrity Network: Synthetic Lethality with dpb4

status: Public on Feb 16 2006

city: Baltimore

first: Daniel

last: Yuan

address: 733 N. Broadway, Suite 351

department: Molecular Biology and Genetics

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 1.05 and 1.42 (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.

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 dpb4::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- dpb4

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 dpb3

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 1.1 and 1.36 (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 dpb3::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- dpb3


title: BT-474

city: Vancouver

first: Ashleen

last: Shadeo

state: BC

address: 675 west 10th Ave

country: Canada

institute: British Columbia Cancer Research Center

description: Competitive hybridization of differentially labeled pooled female genomic DNA and BT-474 genomic DNA

source_name: Novagen Catalogue Number: 70605-3

tag: Novagen Catalogue Number

tag: Pooled female genomic DNA


title: Yeast DNA Integrity Network: Synthetic Lethality with xrs2

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 1.22 and 0.72 (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 xrs2::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- xrs2


title: UACC-893

description: Competitive hybridization of differentially labeled pooled female genomic DNA and UACC-893 genomic DNA

source_name: ATCC UACC-893

tag: ATCC

source_name: Novagen 70605-3


title: Yeast DNA Integrity Network: Synthetic Lethality with tof1, 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 1.21 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.

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 tof1::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- tof1


title: Yeast DNA Integrity Network: Synthetic Lethality with tsa1

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 0.92 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 tsa1::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- tsa1


title: Yeast DNA Integrity Network: Synthetic Lethality with trf4

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 1.27 and 2.57 (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 trf4::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- trf4


title: MCF7

description: Competitive hybridization of differentially labeled pooled female genomic DNA and MCF7 genomic DNA


title: SKBR3

description: Competitive hybridization of differentially labeled pooled female genomic DNA and SKBR3 genomic DNA

source_name: ATCC Catalogue Number: HTB-30D

tag: ATCC Catalogue Number

source_name: Novagen


title: MDA-MB-231

description: pooled female genomic DNA competitively hybridized against MDA-MB-231 cell line genomic DNA

source_name: ATCC (HTB-26D)

tag: ATCC catalogue number

source_name: Pooled female genomic DNA


title: Patient-99-199_HR-CGH (Experiment-ID: 36559)

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 breakpoints of large aberrations causing the respective disease.

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).

source_name: Genomic DNA isolated from a lymphoblast cell line

tag: Patient with 22Q11DS (VCFS); lymphoblast cell line.

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

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


title: T47D

description: Competitive hybridization of differentially labeled pooled female genomic DNA and T47D genomic DNA

source_name: Breast Cancer Cell LineT47D


title: Patient-97-122_HR-CGH (Experiment-ID: 36230)

tag: Patient with Der22/ES; lymphoblast cell line.


title: ZR-75-30

description: Competitive hybridization of differentially labeled pooled female genomic DNA and ZR-75-30 genomic DNA

source_name: ATCC: CRL-1504D


title: Patient-97-237_HR-CGH (Experiment-ID: 38797)

description: High resolution comparative genome hybridization (HR-CGH) was performed in order to identify the exact breakpoints of large aberrations causing the respective disease (VCFS).


title: Patient-99-023_HR-CGH (Experiment-ID: 38603)

source_name: Genomic DNA isolated from blood

tag: Patient with 22Q11DS (VCFS); blood.


title: Yeast DNA Integrity Network: Synthetic Lethality with slx8

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 1.65 (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 slx8::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- slx8


title: Patient-98-135_HR-CGH (Experiment-ID: 38661)


title: Patient-01-242_HR-CGH (Experiment-ID: 39336)


title: Yeast DNA Integrity Network: Synthetic Lethality with sic1, 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 0.9 and 1.63 (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 sic1::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- sic1


title: Yeast DNA Integrity Network: Synthetic Lethality with slx1

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 1.76 and 2.01 (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 slx1::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- slx1


title: Yeast DNA Integrity Network: Synthetic Lethality with rtt107

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 0.98 and 0.92 (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 rtt107::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- rtt107


title: Yeast DNA Integrity Network: Synthetic Lethality with sic1, 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 1.79 (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 sae2

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 1.2 and 0.95 (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 sae2::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- sae2


title: Patient-00-120_HR-CGH (Experiment-ID: 36338)

tag: Patient with CES; lymphoblast cell line.


title: Yeast DNA Integrity Network: Synthetic Lethality with rtt101

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 1.14 and 0.91 (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 rtt101::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- rtt101


title: Yeast DNA Integrity Network: Synthetic Lethality with slx4

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 1.11 (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.

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 slx4::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- slx4


title: Yeast DNA Integrity Network: Synthetic Lethality with rpn10

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 1.12 and 1.91 (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 rpn10::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- rpn10


title: Patient-04-018_HR-CGH_rep2 (Experiment-ID: 38516)


title: Patient-03-154_HR-CGH (Experiment-ID: 36297)

tag: Patient with 22Q11DS (VCFS).


title: Yeast DNA Integrity Network: Synthetic Lethality with rpn4

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 1.12 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.

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 rpn4::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- rpn4


title: Patient-97-159_HR-CGH (Experiment-ID: 38793)


title: Patient-04-018_HR-CGH_rep1 (Experiment-ID: 36320)

description: HR-CGH was performed in order to identify the exact breakpoints of large aberrations causing the respective disease.

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: Yeast DNA Integrity Network: Synthetic Lethality with rmd7

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 1.12 and 0.79 (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 rmd7::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- rmd7


title: Patient-04-018_HR-CGH_rep3 (Experiment-ID: 42719)


title: Patient-05-050_HR-CGH (Experiment-ID: 42762)

tag: Patient with Dup22; lymphoblast cell line.


title: Yeast DNA Integrity Network: Synthetic Lethality with rad9, 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 1.12 and 1.14 (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 rad9::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- rad9


title: Yeast DNA Integrity Network: Synthetic Lethality with rlf2

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 1.12 and 1.74 (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 rlf2::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- rlf2


title: Yeast DNA Integrity Network: Synthetic Lethality with rad9, 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 1.34 and 1.43 (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 tof1, 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 0.92 and 0.76 (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.

source_name: Experimental -- tof1


title: Yeast DNA Integrity Network: Synthetic Lethality with rad6

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 0.74 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.

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 rad6::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- rad6


title: Yeast DNA Integrity Network: Synthetic Lethality with rad5

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 0.62 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.

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 rad5::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- rad5


title: Yeast DNA Integrity Network: Synthetic Lethality with rad53

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 0.78 and 0.78 (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 lacking uracil. 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 rad53::NatR. To enable propagation of rad53 mutants, a third-site mutation with genotype sml1::TEF1pr-URA3 was included.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- rad53

growth_protocol: Cells were grown at 30 degrees C to confluence on "Magic Marker" selection plates with 50 micrograms/ml nourseothricin and 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.


title: Yeast DNA Integrity Network: Synthetic Lethality with rad2

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 1.2 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.

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 rad2::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- rad2


title: Yeast DNA Integrity Network: Synthetic Lethality with rad51, 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 1.7 and 1.71 (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 rad51::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- rad51


title: Yeast DNA Integrity Network: Synthetic Lethality with rad27, 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 1.43 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 rad27::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- rad27


title: Yeast DNA Integrity Network: Synthetic Lethality with rad18

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 0.52 and 0.74 (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 rad18::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- rad18


title: Yeast DNA Integrity Network: Synthetic Lethality with pop2, 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 1.3 and 2.84 (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 pop2::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- pop2


title: Yeast DNA Integrity Network: Synthetic Lethality with rad17, 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 1.61 and 1.86 (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 rad17::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- rad17


title: Yeast DNA Integrity Network: Synthetic Lethality with rad54, 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 1.92 and 1.6 (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 rad54::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- rad54


title: Yeast DNA Integrity Network: Synthetic Lethality with pop2, 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 1.33 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.


title: Yeast DNA Integrity Network: Synthetic Lethality with rad51, 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 1.52 and 2.22 (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 pol32, 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 0.89 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.

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 pol32::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- pol32


title: Yeast DNA Integrity Network: Synthetic Lethality with rad52

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 1.37 and 2.05 (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 rad52::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- rad52


title: Yeast DNA Integrity Network: Synthetic Lethality with rad17, 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 1.04 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.


title: Yeast DNA Integrity Network: Synthetic Lethality with rad24, 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 1.18 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.

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 rad24::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- rad24


title: Yeast DNA Integrity Network: Synthetic Lethality with rad27, 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 0.78 and 0.86 (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 rad50

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 1.2 and 1.2 (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 rad50::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- rad50


title: Yeast DNA Integrity Network: Synthetic Lethality with rad54, 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 1.18 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.


title: Yeast DNA Integrity Network: Synthetic Lethality with mus81

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 0.98 and 0.65 (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 mus81::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- mus81


title: Yeast DNA Integrity Network: Synthetic Lethality with rad24, 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 0.97 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.


title: Yeast DNA Integrity Network: Synthetic Lethality with rad55

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 1.03 and 1.22 (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 rad55::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- rad55


title: Yeast DNA Integrity Network: Synthetic Lethality with pol32, 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 1.25 and 1.37 (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 rad57

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 1.16 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 rad57::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- rad57


title: Yeast DNA Integrity Network: Synthetic Lethality with msi1

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 1.8 and 1.77 (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 msi1::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- msi1


title: Yeast DNA Integrity Network: Synthetic Lethality with npt1

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 1.2 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 npt1::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- npt1


title: Yeast DNA Integrity Network: Synthetic Lethality with nat1

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 1.77 (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 nat1::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- nat1


title: Yeast DNA Integrity Network: Synthetic Lethality with mre11

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 1.23 (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.

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 mre11::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- mre11


title: Yeast DNA Integrity Network: Synthetic Lethality with mec3, 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 1.58 and 1.66 (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 mec3::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- mec3


title: Yeast DNA Integrity Network: Synthetic Lethality with mrc1, 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 1.79 and 2.01 (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 mdm39

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 1.7 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 mdm39::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- mdm39


title: Yeast DNA Integrity Network: Synthetic Lethality with mms22

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 1.27 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.

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 mms22::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- mms22


title: Yeast DNA Integrity Network: Synthetic Lethality with mec3, 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 0.86 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.


title: Yeast DNA Integrity Network: Synthetic Lethality with mec1

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 0.9 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.

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 mec1::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- mec1


title: Yeast DNA Integrity Network: Synthetic Lethality with mms1

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 1.15 (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 mms1::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- mms1


title: Yeast DNA Integrity Network: Synthetic Lethality with lge1

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 0.68 and 0.94 (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 lge1::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- lge1


title: Yeast DNA Integrity Network: Synthetic Lethality with hst4, 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 1.31 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 hst4::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- hst4


title: Yeast DNA Integrity Network: Synthetic Lethality with hst3, 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 1.24 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 hst3::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- hst3


title: Yeast DNA Integrity Network: Synthetic Lethality with hst4, 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 2.18 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.


title: Yeast DNA Integrity Network: Synthetic Lethality with hir2, 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 0.88 and 0.58 (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 hst3, 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 0.98 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.


title: Yeast DNA Integrity Network: Synthetic Lethality with lrs4

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 1.01 (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 lrs4::TEF1pr-URA3.  See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).

source_name: Experimental -- lrs4