title: SLAM Project Data: Synthetic Lethality with zds2

description:
Internal identifier for dataset: SL/100623/13
Original datafile name: 255845A01_532.pair
Original datafile2 name: 255845A01_635.pair
SD of values from reference genes: 0.277
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.56 2.29 2.74
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 241 well C07 (strain 26509)


title: SLAM Project Data: Synthetic Lethality with spo11-rep2

status: Public on Feb 28 2013

type: genomic

city: Baltimore

first: Jef

last: Boeke

address: 733 N BROADWAY # 339

country: USA

institute: Johns Hopkins U

description:
Internal identifier for dataset: SL/090304/7
Original datafile name: 090304_7.gpr
Original datafile2 name: <none>
SD of values from reference genes: 0.508
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.27 1.48 1.59
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

hyb_protocol: Labeled extracts were hybridized overnight to Agilent 22k microarray slides at 42 degrees C.

scan_protocol: Images were acquired with a GenePix 4000B or 4200 AL scanner at 10 um resolution.

data_processing: Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 5.1 or higher). Annotations were reconstructed from data downloaded from the Saccharomyces Genome Database on 2008-11-15. Numerical data were obtained as the median of foreground signal intensities. Background signal intensities were not used. Custom R packages (hoptag v3.9-7; hoptagInfo02A v3.9-6) were used with their default options. See the software and PDF documentation included with this GEO Series submission for details. The VALUE column represents a dynamically weighted sum of data from the UpTag and DnTag probes for each gene.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Reference

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

growth_protocol: Cells were grown at 30 degrees C for approximately eight doublings using "Magic Marker" selectable medium supplemented with uracil.

extract_protocol: Genomic DNA was extracted by phenol extraction or by use of proprietary kits (e.g., Epicentre, Norgen).

tag: query gene

tag: knockout clone

value: Plate 217 well A03 (strain 20941)

tag: genetic background

tag: pool genotype

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX

source_name: Test

growth_protocol: Cells were grown without added uracil, using materials and procedures that were otherwise the same as those for Channel 1.


title: osteosarcoma cell line U-2 OS

type: RNA

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

description: human cell line

hyb_protocol: Standard Illumina ibridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: data were analysed using BeadStudio version 1.5.1.3;  rank invariant normalization was performed

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: osteosarcoma cell line

label_protocol: Biotilinated cRNA were prepared with the Ambion messageAmp for Illumina array

extract_protocol: Total RNA was extracted and purified from exponentially growing cells using the SV total RNA Isolation System (Promega,USA).

treatment_protocol: Exponentially growing cells were cultured for 48 hours in Iscove’s Modified Dulbecco Medium (Sigma, St. Louis, MO) supplemented with 1% Penicillin-Streptomycin-Amphotericin B Mixture (Lonza, Versviers Belgium), 1% L-Glutamine (Lonza, Versviers Belgium) and 10% Fetal Bovine Serum (Sigma, St. Louis, MO) at 37°C in humified 5% CO2 atmosphere.

tag: sample type

value: untreated

tag: cell line

value: U-2 OS


title: SLAM Project Data: Synthetic Lethality with yta7

description:
Internal identifier for dataset: SL/100302/7
Original datafile name: 100302NG264528A03_532.pair
Original datafile2 name: 100302NG264528A03_635.pair
SD of values from reference genes: 0.572
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.65 1.11 1.57
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

hyb_protocol: Labeled extracts were hybridized overnight to NimbleGen 72k 4-plex microarray slides at 42 degrees C.

scan_protocol: Images were acquired with a GenePix 4200AL scanner at 5 um resolution or an Agilent G2505C scanner at 2 um resolution

data_processing: Two-channel image files were analyzed with the NimbleScan software package (Roche NimbleGen, version 2.3.78 or higher). Annotations were reconstructed from data downloaded from the Saccharomyces Genome Database on 2008-11-15. Numerical data were obtained as the mean of the central pixels. Background signal intensities were not used. Custom R packages (hoptag v3.9-7; hoptagInfo07A v3.9-6) were used with their default options. See the software and PDF documentation included with this GEO Series submission for details. The VALUE column represents a dynamically weighted sum of data from the UpTag and DnTag probes for each gene.

value: Plate 238 well D11 (strain 25922)


title: SLAM Project Data: Synthetic Lethality with yta12

description:
Internal identifier for dataset: SL/100604/2
Original datafile name: 308116A02_532.pair
Original datafile2 name: 308116A02_635.pair
SD of values from reference genes: 0.403
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.30 2.55 2.34
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 239 well D10 (strain 26224)


title: SLAM Project Data: Synthetic Lethality with slm6-rep2

description:
Internal identifier for dataset: SL/051116/9
Original datafile name: 051116_212_D11.gpr
Original datafile2 name: <none>
SD of values from reference genes: 0.780
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.17 1.07 1.28
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 212 well D11 (strain 23406)


title: SLAM Project Data: Synthetic Lethality with sip3

description:
Internal identifier for dataset: SL/050104/6
Original datafile name: 050104_207_B11.gpr
Original datafile2 name: <none>
SD of values from reference genes: 0.966
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.12 0.74 1.15
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 207 well B11 (strain 21187)


title: SLAM Project Data: Synthetic Lethality with ysp1

description:
Internal identifier for dataset: SL/090224/5
Original datafile name: 090224NG142284A01_532.pair
Original datafile2 name: 090224NG142284A01_635.pair
SD of values from reference genes: 0.525
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.09 1.75 1.89
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 218 well D01 (strain 22849)


title: osteosarcoma cell line OS20

description: human cell line


title: osteosarcoma cell line OS19

description: human cell line


title: SLAM Project Data: Synthetic Lethality with sin3

description:
Internal identifier for dataset: SL/050505/7
Original datafile name: 050505_209_A03.gpr
Original datafile2 name: <none>
SD of values from reference genes: 0.764
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 0.54 1.16 1.15
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 209 well A03 (strain 21695)


title: WT.CTR.gamma.R2

city: Vienna

first: Pavel

last: Kovarik

address: Dr. Bohr-Gasse 9

department: Max F. Perutz Laboratories

country: Austria

institute: University of Vienna

description: SAMPLE 2

hyb_protocol: Agilent's SurePrint G3 Mouse GE 8x60K Microarray, (Agilent Microarray Design ID 028005).RNA quality was checked on RNA 6000 Nano chips using a Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA). Agilent’s Low Input Quick Amp Labeling Kit, one-color was used to generate fluorescent cRNA. The amplified cyanine 3-labeled cRNA samples were then purified using Promega’s SV Total RNA Isolation System and hybridized to Agilent Whole Mouse Genome Microarrays, 8x60K.

scan_protocol: Agilent Scanner, according to the standard protocol of the manufacturer

data_processing: Further analyses were performed using Bioconductor rooted in the statistical computing environment R. The raw intensities were imported into Bioconductor and further processed with the limma package. Quality Controls were performed using the arrayQualityMetrics package. The outlier array #10 [SA.CDK.gamma.R3] was removed from subsequent analysis. Normalization between arrays was performed using the quantile method, duplicate probes were averaged and a linear model also including a batch effect between Biological Replicates 1 and 2&3 was fitted due to a batch effect shown by the QA PCA plots. P-values were adjusted for multiple testing using the Benjamini & Hochberg method.

organism: Mus musculus

source_name: WT STAT1 mouse fibroblasts, 4 h interferon, siCtrl, replicate 2

growth_protocol: DMEM, 10% FCS, pen+strep

extract_protocol: Trizol

treatment_protocol: mouse interferon gamma, 10 ng/ml final concentration

tag: strain

tag: genotype/variation

value: WT STAT1

tag: sirna

value: control siRNA

tag: agent

value: IFN-gamma

tag: cell type

value: fibroblast

tag: replicate


title: SLAM Project Data: Synthetic Lethality with spf1

description:
Internal identifier for dataset: SL/061122/11
Original datafile name: 061122_214_F08.gpr
Original datafile2 name: <none>
SD of values from reference genes: 0.945
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 0.99 1.21 1.15
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 214 well F08 (strain 20272)


title: human primary osteoblasts HOB5

description: human primary osteoblasts

source_name: human primary osteoblasts

value: osteoblasts


title: osteosarcoma cell line OS17

description: human cell line


title: SLAM Project Data: Synthetic Lethality with ysc83

description:
Internal identifier for dataset: SL/100617/6
Original datafile name: 308385A02_532.pair
Original datafile2 name: 308385A02_635.pair
SD of values from reference genes: 0.466
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.90 1.64 1.92
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 240 well C09 (strain 26411)


title: SLAM Project Data: Synthetic Lethality with shu1

description:
Internal identifier for dataset: SL/080925/9
Original datafile name: 080925_217_B06_9.gpr
Original datafile2 name: <none>
SD of values from reference genes: 0.308
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.68 3.01 3.16
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 217 well B06 (strain 20957)


title: osteosarcoma cell line OS18

description: human cell line


title: osteosarcoma cell line OS10

description: human cell line


title: SLAM Project Data: Synthetic Lethality with yrm1

description:
Internal identifier for dataset: SL/091204/4
Original datafile name: 091204NG301642A04_532.pair
Original datafile2 name: 091204NG301642A04_635.pair
SD of values from reference genes: 0.500
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.01 1.58 1.96
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 223 well H08 (strain 22428)

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX


title: NT4 Knockout, biological rep1

city: Louisville

first: Tao

last: Huang

state: KY

address: 500 S Preston St, Rm1004

department: Anatomical Sciences and Neurobiology

institute: University of Louisville

description: Gene expression data from NT4 mutant geniculate ganglia at E14.5

hyb_protocol: Biotin-labeled cDNA was hybridized to Affymetrix Mouse Genome 430 2.0 arrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: dChip software was used to perform normalization and model-based expression value calculations. Different microarray samples were normalized using the baseline array that has a median probe signal, and the PM-MM difference model was applied for expression value calculation. Genes were considered to be differentially regulated if they met all 3 of the following criteria: 1) the fold change between knockout and wild-type mice exceeds 1.2; 2) the threshold for the absolute difference between knockout vs. wild type means is larger than 50; 3) the p-value of unpaired t-test is less than 0.05.

label: biotin

source_name: NT4 knockout geniculate ganglion at E14.5

label_protocol: Total RNA was amplified, fragmented, and biotinylated using WT-Ovation Pico RNA Amplification System.

extract_protocol: Total RNA was extracted from geniculate ganglion using RNeasy micro kit. DNase I treatment was applied to eliminate traces of DNA during the procedure.

tag: tissue

value: geniculate ganglion

tag: genotype

value: NT4 knockout

tag: age

value: Embryonic day 14.5

tag: background mouse strain


title: NT4 Knockout, biological rep3


title: NT4 Knockout, biological rep2


title: WT.CTR.0.R1

description: SAMPLE 1

source_name: WT STAT1 mouse fibroblasts, no interferon, siCtrl, replicate 1

value: untreated


title: SLAM Project Data: Synthetic Lethality with ser3

description:
Internal identifier for dataset: SL/081119/6
Original datafile name: 081119_215_G07_6.gpr
Original datafile2 name: <none>
SD of values from reference genes: 0.669
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.25 1.26 1.50
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 215 well G07 (strain 20221)


title: NT4 Wild Type, biological rep2

description: Gene expression data from NT4 wild-type geniculate ganglia at E14.5

source_name: Wild-type geniculate ganglion at E14.5

value: NT4 wild type


title: NT4 Wild Type, biological rep1


title: SLAM Project Data: Synthetic Lethality with yrb2

description:
Internal identifier for dataset: SL/100525/5
Original datafile name: 308501A01_532.pair
Original datafile2 name: 308501A01_635.pair
SD of values from reference genes: 0.718
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.22 0.57 1.06
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 237 well D06 (strain 21456)


title: osteosarcoma cell line MG-63

description: human cell line


title: SLAM Project Data: Synthetic Lethality with yra2

description:
Internal identifier for dataset: SL/100302/6
Original datafile name: 100302NG264528A02_532.pair
Original datafile2 name: 100302NG264528A02_635.pair
SD of values from reference genes: 0.310
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.38 1.83 1.99
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 235 well D10 (strain 25064)


title: NT4 Wild Type, biological rep3


title: SLAM Project Data: Synthetic Lethality with rts1

description:
Internal identifier for dataset: SL/050729/15
Original datafile name: 050729_280_A09.gpr
Original datafile2 name: <none>
SD of values from reference genes: 0.868
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 0.88 0.93 1.00
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 280 well A09 (strain 21790)


title: MET transformed HOB clones C18

description: MET transformed HOB clones

source_name: MET transformed HOB clones

value: stable transfected with MET oncogene

value: MET-HOB


title: SLAM Project Data: Synthetic Lethality with yra2-rep2

description:
Internal identifier for dataset: SL/100504/3
Original datafile name: 308154A03_532.pair
Original datafile2 name: 308154A03_635.pair
SD of values from reference genes: 0.433
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.30 1.29 1.57
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).


title: BDNF Knockout, biological rep3

description: Gene expression data from BDNF mutant geniculate ganglia at E14.5

source_name: BDNF knockout geniculate ganglion at E14.5

value: BDNF knockout


title: BDNF Knockout, biological rep2


title: SLAM Project Data: Synthetic Lethality with ypt6

description:
Internal identifier for dataset: SL/100317/21
Original datafile name: 100317NG300313A01_532.pair
Original datafile2 name: 100317NG300313A01_635.pair
SD of values from reference genes: 0.552
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.67 1.34 1.65
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 226 well A05 (strain 25171)


title: SLAM Project Data: Synthetic Lethality with rim101

description:
Internal identifier for dataset: SL/080923/3.1
Original datafile name: 080923_216_H12_3A_f8.gpr
Original datafile2 name: <none>
SD of values from reference genes: 0.463
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.90 1.55 1.95
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 216 well H12 (strain 20936)


title: SLAM Project Data: Synthetic Lethality with rev1-rep2

description:
Internal identifier for dataset: SL/050428/9
Original datafile name: 050428_208_E10.gpr
Original datafile2 name: <none>
SD of values from reference genes: 0.622
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.07 1.29 1.36
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 208 well E10 (strain 21643)


title: SLAM Project Data: Synthetic Lethality with rps17a

description:
Internal identifier for dataset: SL/050526/8
Original datafile name: 050526_204_A05.gpr
Original datafile2 name: <none>
SD of values from reference genes: 0.750
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 0.99 1.07 1.15
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 204 well A05 (strain 20549)


title: SLAM Project Data: Synthetic Lethality with ypt32

description:
Internal identifier for dataset: SL/100407/9
Original datafile name: 308438A01_532.pair
Original datafile2 name: 308438A01_635.pair
SD of values from reference genes: 0.372
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.21 2.38 2.79
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 228 well H08 (strain 24576)

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX


title: osteosarcoma cell line HOS

description: human cell line

value: HOS


title: SLAM Project Data: Synthetic Lethality with yps6

description:
Internal identifier for dataset: SL/100604/23
Original datafile name: 308127A03_532.pair
Original datafile2 name: 308127A03_635.pair
SD of values from reference genes: 0.650
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.52 1.23 1.51
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 238 well H05 (strain 25974)


title: osteosarcoma cell line OS9

description: human cell line

value: untreated


title: SLAM Project Data: Synthetic Lethality with yps5

description:
Internal identifier for dataset: SL/100407/21
Original datafile name: 308476A01_532.pair
Original datafile2 name: 308476A01_635.pair
SD of values from reference genes: 0.330
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.56 2.77 2.67
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 229 well B08 (strain 24626)


title: BDNF Wild Type, biological rep3

description: Gene expression data from BDNF wild-type geniculate ganglia at E14.5

value: geniculate ganglion

value: BDNF wild type

value: Embryonic day 14.5


title: BDNF Knockout, biological rep1


title: SLAM Project Data: Synthetic Lethality with rad54-rep2

description:
Internal identifier for dataset: SL/060318/7
Original datafile name: 060318_260_H5_C.gpr
Original datafile2 name: <none>
SD of values from reference genes: 0.772
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 0.80 1.10 1.26
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 260 well H05 (strain 24530)


title: SLAM Project Data: Synthetic Lethality with ypr197c

description:
Internal identifier for dataset: SL/100420/11
Original datafile name: 308371A03_532.pair
Original datafile2 name: 308371A03_635.pair
SD of values from reference genes: 0.357
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.51 1.79 2.37
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 231 well E06 (strain 25612)


title: MET transformed HOB clones C8

description: MET transformed HOB clones

value: stable transfected with MET oncogene

value: MET-HOB


title: MET transformed HOB clones C6

description: MET transformed HOB clones


title: osteosarcoma cell line OS14

description: human cell line


title: SLAM Project Data: Synthetic Lethality with prc1

description:
Internal identifier for dataset: SL/041222/2
Original datafile name: 041222_206_C9.gpr
Original datafile2 name: <none>
SD of values from reference genes: 0.827
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 0.36 1.21 1.13
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 206 well C09 (strain 20885)


title: MET transformed HOB clones C16

description: MET transformed HOB clones


title: SLAM Project Data: Synthetic Lethality with prb1

description:
Internal identifier for dataset: SL/070725/14.1
Original datafile name: 070725_214_H09_14_B.gpr
Original datafile2 name: <none>
SD of values from reference genes: 0.850
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 0.82 1.01 1.01
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 214 well H09 (strain 20302)


title: SLAM Project Data: Synthetic Lethality with ypr196w

description:
Internal identifier for dataset: SL/100420/10
Original datafile name: 308371A02_532.pair
Original datafile2 name: 308371A02_635.pair
SD of values from reference genes: 0.600
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.52 1.09 1.47
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 231 well E05 (strain 25611)


title: SLAM Project Data: Synthetic Lethality with ypr195c

description:
Internal identifier for dataset: SL/100420/9
Original datafile name: 308371A01_532.pair
Original datafile2 name: 308371A01_635.pair
SD of values from reference genes: 0.608
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.61 1.18 1.51
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 231 well E04 (strain 25610)


title: SLAM Project Data: Synthetic Lethality with ppe1

description:
Internal identifier for dataset: SL/070711/10
Original datafile name: 070711_217_F08_10.gpr
Original datafile2 name: <none>
SD of values from reference genes: 0.412
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.61 1.32 1.76
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 217 well F08 (strain 21903)


title: BDNF Wild Type, biological rep1


title: SLAM Project Data: Synthetic Lethality with pol32

description:
Internal identifier for dataset: SL/050817/6
Original datafile name: 050817_248_F02_OS.gpr
Original datafile2 name: <none>
SD of values from reference genes: 0.701
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.14 0.82 1.07
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 248 well F02 (strain 26841)

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX


title: BDNF Wild Type, biological rep2


title: osteosarcoma cell line OS15

description: human cell line


title: SLAM Project Data: Synthetic Lethality with pic2

description:
Internal identifier for dataset: SL/070703/9
Original datafile name: 070703_215_E05_9.gpr
Original datafile2 name: <none>
SD of values from reference genes: 0.598
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.03 1.25 1.37
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 215 well E05 (strain 20188)


title: SLAM Project Data: Synthetic Lethality with ypr174c

description:
Internal identifier for dataset: SL/100420/1
Original datafile name: 308369A01_532.pair
Original datafile2 name: 308369A01_635.pair
SD of values from reference genes: 0.513
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.56 1.08 1.63
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 231 well C06 (strain 25589)


title: osteosarcoma cell line OS7

description: human cell line

value: untreated


title: osteosarcoma cell line Saos-2

description: human cell line


title: MET transformed HOB clones C42

description: MET transformed HOB clones


title: SLAM Project Data: Synthetic Lethality with pho80

description:
Internal identifier for dataset: SL/050505/6.1
Original datafile name: 050505_208_H12_FOA.gpr
Original datafile2 name: <none>
SD of values from reference genes: 0.793
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.18 1.24 1.44
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 208 well H12 (strain 21692)


title: SLAM Project Data: Synthetic Lethality with ypr172w

description:
Internal identifier for dataset: SL/100414/23
Original datafile name: 308110A03_532.pair
Original datafile2 name: 308110A03_635.pair
SD of values from reference genes: 0.483
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.57 1.89 1.95
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 231 well C04 (strain 25587)


title: MET transformed HOB clones C12

description: MET transformed HOB clones


title: SLAM Project Data: Synthetic Lethality with ypr170c

description:
Internal identifier for dataset: SL/100414/22
Original datafile name: 308110A02_532.pair
Original datafile2 name: 308110A02_635.pair
SD of values from reference genes: 0.336
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.06 2.08 2.36
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 231 well C02 (strain 25585)


title: Atxn1L HSC 1

city: Houston

first: Chad

middle: A.

last: Shaw

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: BCM

hyb_protocol: Affymetrix hybridization protocol

scan_protocol: Gene Chip Scanner 3000

data_processing: GC-RMA

label: dUTP-biotin

source_name: Atxn1L null murine HSCs

label_protocol: Ambion Message Amp kit to amplify and label mRNA

growth_protocol: No growth- purification of native HSCs from bone marrow of mice

extract_protocol: HSCss were extracted from bone marrow and purified using flow cytometry for KSL (lack of lineage marker expression (Lin-) and postive expression for c-Kit and Sca-1), expression of CD150 and included in the side population (Hoechst dye exclusion)

treatment_protocol: WT versus knock-out HSCs purified from 6-8 week old mice; KO allele described in Pub Med ID:  22013525

value: HSC


title: SLAM Project Data: Synthetic Lethality with otu2

description:
Internal identifier for dataset: SL/081119/11
Original datafile name: 081119_217_A11_BdPmx_11.gpr
Original datafile2 name: <none>
SD of values from reference genes: 0.723
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.05 1.09 1.25
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 217 well A11 (strain 20950)


title: WT HSC 3

source_name: wildtype murine HSCs

value: wildtype


title: SLAM Project Data: Synthetic Lethality with osh3

description:
Internal identifier for dataset: SL/081007/12
Original datafile name: 081007_217_F06_12_Bx.gpr
Original datafile2 name: <none>
SD of values from reference genes: 0.693
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.50 1.24 1.54
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 217 well F06 (strain 21901)


title: Atxn1L HSC 2


title: SLAM Project Data: Synthetic Lethality with ypr157w

description:
Internal identifier for dataset: SL/100414/19
Original datafile name: 308107A03_532.pair
Original datafile2 name: 308107A03_635.pair
SD of values from reference genes: 0.571
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.47 1.22 1.50
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 231 well B01 (strain 25572)


title: MET transformed HOB clones C15

description: MET transformed HOB clones

value: stable transfected with MET oncogene

value: MET-HOB


title: SLAM Project Data: Synthetic Lethality with ypr053c

description:
Internal identifier for dataset: SL/100625/10
Original datafile name: 255859A02_532.pair
Original datafile2 name: 255859A02_635.pair
SD of values from reference genes: 0.260
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.78 2.06 2.89
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 242 well C11 (strain 25472)


title: WT HSC 2


title: SLAM Project Data: Synthetic Lethality with opi1

description:
Internal identifier for dataset: SL/080923/8.1
Original datafile name: 080923_217_A05_8_f8.gpr
Original datafile2 name: <none>
SD of values from reference genes: 0.386
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.42 2.42 2.60
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 217 well A05 (strain 20943)


title: WT HSC 1


title: Hif-2αΔIE

city: Ann Arbor

first: XIANG

last: XUE

state: Michigan

address: 1301 E. Catherine Street

institute: Umich

description: Gene expression data from colons.

hyb_protocol: Following fragmentation, 16 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader.

data_processing: Data was analyzed using the affy Bioconductor packages implemented in the R-statistical environment. RMA was used to normalize the data and fit log2 transformed expression values.

source_name: Colon

label_protocol: Biotinylated aRNA were prepared according to the Ambion Premier kit protocol from 250 ng total RNA (MessageAmp Premier RNA Amplification Kit Instruction Manual, 2008, Ambion).

growth_protocol: All mice were C57BL/6 background and maintained in standard cages in a light and temperature-controlled room and were allowed standard chow and water ad libitum.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Colon mucosal scrapings were got from 6 to 8 weeks old mice treated with 3% DSS for 3 days

value: colon

value: 6 to 8 weeks old


title: SLAM Project Data: Synthetic Lethality with ypr045c

description:
Internal identifier for dataset: SL/100625/5
Original datafile name: 255856A01_532.pair
Original datafile2 name: 255856A01_635.pair
SD of values from reference genes: 0.270
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.37 1.51 2.14
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 242 well C04 (strain 25464)

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX


title: Mouse liver PB vs. Control 1.5X cDNA 8

city: Ottawa

first: Anna

middle: Francina

last: Jackson

state: Ontario

address: 50 Colombine Drive, Tunney's Pasture

department: Environmental Health Center

country: Canada

institute: Health Canada

description:
Pos_2_4_Dye_Cy5_Sample_53
Pos_2_4_Dye_Cy3_Sample_38

hyb_protocol: 1X (samples 1-8) or 1.5X (samples 9-16) cDNA was blocked with Agilent CGH-block and GE-blocking agent and hybridized to Agilent SurePrint GE 8x60 1.5 Mouse microarrays for 17 hours at 65C at 20rpm

scan_protocol: Arrays were washed and scanned on an Agilent G2505B Scanner according to manufacturer’s recommendations.

data_processing: Agilent FE software, version 11 (one color protocol: GE1_1100_Jul11, or two-color protocol: GE2_1100_Jul11).

source_name: Phenobarbital-exposed mouse liver, 1.5X cDNA input, replicate 2.2

label_protocol: cDNA was labeled using the KREAtech ULS genomic DNA labeling kit (Agilent)

growth_protocol: 16-year-old FFPE liver tissue blocks were used

extract_protocol: RNA was extracted using the Qiagen FFPE Rneasy kit; cDNA was synthesized using the WTA2 kit (Sigma)

treatment_protocol: Mice were exposed to PB in drinking water (or drinking water alone) for ~4 weeks

value: 42 days

tag: gender

value: male

tag: organ

value: liver

tag: exposure

value: Phenobarbital

tag: cdna input

source_name: Control mouse liver, 1.5X cDNA input, replicate 2.2


title: Hif-2αF/F

description: Gene expression data from colons.


title: osteoblast differentiation 7 days [BM4_7]

description: osteoblast differentiation 7 days

data_processing: data were analysed using BeadStudio version 2;  rank invariant normalization was performed

source_name: osteoblast differentiation 7 days

extract_protocol: Total RNA was extracted from mesenchymal stem cells transfected osteogenic medium for 7,14 and 21 days

value: osteoblast

tag: time point

value: 7-day differentiated cells

value: MSC


title: SLAM Project Data: Synthetic Lethality with ypr039w

description:
Internal identifier for dataset: SL/100625/3
Original datafile name: 255851A03_532.pair
Original datafile2 name: 255851A03_635.pair
SD of values from reference genes: 0.268
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.55 2.16 2.76
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

tag: query gene

tag: knockout clone

value: Plate 242 well B11 (strain 25458)

tag: genetic background

tag: pool genotype


title: SLAM Project Data: Synthetic Lethality with nyv1

description:
Internal identifier for dataset: SL/041117/4
Original datafile name: 041117_203_C3.gpr
Original datafile2 name: <none>
SD of values from reference genes: 0.843
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.10 0.66 1.23
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 203 well C03 (strain 22704)


title: mesenchymal stem cells [BM5_msc]

description: mesenchymal stem cells

source_name: mesenchymal stem cells

value: primary mesenchymal stem cells

tag: cell line


title: SLAM Project Data: Synthetic Lethality with nmd2

description:
Internal identifier for dataset: SL/050223/3
Original datafile name: 050223_Upf2.gpr
Original datafile2 name: <none>
SD of values from reference genes: 0.532
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.74 1.56 1.95
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

source_name: Reference

value: Plate 217 well F10 (strain 21905)


title: SLAM Project Data: Synthetic Lethality with nmd2-rep2

description:
Internal identifier for dataset: SL/050311/4
Original datafile name: 050311_Upf2.gpr
Original datafile2 name: <none>
SD of values from reference genes: 0.575
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.17 1.44 1.68
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

source_name: Test


title: osteoblast differentiation 14 days [BM2_14]

description: osteoblast differentiation 14 days

source_name: osteoblast differentiation 14 days

value: 14-day differentiated cells


title: SLAM Project Data: Synthetic Lethality with ypl068c

description:
Internal identifier for dataset: SL/100413/7
Original datafile name: 308481A03_532.pair
Original datafile2 name: 308481A03_635.pair
SD of values from reference genes: 0.702
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.34 0.79 1.23
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 229 well F10 (strain 22760)


title: Mouse liver PB vs. Control 1.5X cDNA 7

description:
Pos_2_3_Dye_Cy5_Sample_52
Pos_2_3_Dye_Cy3_Sample_37

source_name: Phenobarbital-exposed mouse liver, 1.5X cDNA input, replicate 1

tag: strain

source_name: Control mouse liver, 1.5X cDNA input, replicate 1


title: osteoblast differentiation 7 days [BM2_7]

description: osteoblast differentiation 7 days

tag: cell type


title: SLAM Project Data: Synthetic Lethality with myo4-rep2

description:
Internal identifier for dataset: SL/040219/4
Original datafile name: 201C12b_1318.gpr
Original datafile2 name: <none>
SD of values from reference genes: 0.600
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.32 0.96 1.17
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 201 well C12 (strain 20379)


title: SLAM Project Data: Synthetic Lethality with mrs2-rep2

description:
Internal identifier for dataset: SL/050413/3
Original datafile name: 050413_208_E1.gpr
Original datafile2 name: <none>
SD of values from reference genes: 0.826
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 0.49 0.94 1.00
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 208 well E01 (strain 21631)


title: SLAM Project Data: Synthetic Lethality with ypl066w

description:
Internal identifier for dataset: SL/100413/8
Original datafile name: 308481A04_532.pair
Original datafile2 name: 308481A04_635.pair
SD of values from reference genes: 0.625
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.36 0.90 1.23
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 229 well F12 (strain 22762)


title: mesenchymal stem cells [BM4_msc]

description: mesenchymal stem cells


title: SLAM Project Data: Synthetic Lethality with ypl056c

description:
Internal identifier for dataset: SL/100413/15
Original datafile name: 308499A03_532.pair
Original datafile2 name: 308499A03_635.pair
SD of values from reference genes: 0.570
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.43 1.11 1.44
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 229 well G10 (strain 22772)

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX


title: SLAM Project Data: Synthetic Lethality with ypl062w

description:
Internal identifier for dataset: SL/100413/10
Original datafile name: 308496A02_532.pair
Original datafile2 name: 308496A02_635.pair
SD of values from reference genes: 0.529
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.52 1.04 1.53
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 229 well G04 (strain 22766)


title: mesenchymal stem cells [BM1_msc]

description: mesenchymal stem cells


title: Mouse liver PB vs. Control 1.5X cDNA 6

description:
Pos_2_2_Dye_Cy5_Sample_39
Pos_2_2_Dye_Cy3_Sample_54

source_name: Control mouse liver, 1.5X cDNA input, replicate 3

value: 42 days

value: male

value: liver

source_name: Phenobarbital-exposed mouse liver, 1.5X cDNA input, replicate 3


title: osteoblast differentiation 21 days [BM1_21]

description: osteoblast differentiation 21 days

source_name: osteoblast differentiation 21 days

value: osteoblast

value: 21-day differentiated cells


title: Mouse liver PB vs. Control 1.5X cDNA 3

description:
Pos_1_3_Dye_Cy5_Sample_38
Pos_1_3_Dye_Cy3_Sample_52

source_name: Control mouse liver, 1.5X cDNA input, replicate 2.1

source_name: Phenobarbital-exposed mouse liver, 1.5X cDNA input, replicate 1.1

value: Phenobarbital


title: SLAM Project Data: Synthetic Lethality with mec3-rep2

description:
Internal identifier for dataset: SL/050830/3
Original datafile name: 050830_226_C08.gpr
Original datafile2 name: <none>
SD of values from reference genes: 0.435
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.05 0.91 1.04
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 226 well C08 (strain 25198)


title: SLAM Project Data: Synthetic Lethality with nam7-rep3

description:
Internal identifier for dataset: SL/050223/2
Original datafile name: 050223_Upf1.gpr
Original datafile2 name: <none>
SD of values from reference genes: 0.479
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.54 1.88 2.55
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 239 well C11 (strain 26214)


title: SLAM Project Data: Synthetic Lethality with ypl041c

description:
Internal identifier for dataset: SL/100414/5
Original datafile name: 308093A01_532.pair
Original datafile2 name: 308093A01_635.pair
SD of values from reference genes: 0.473
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.30 1.26 1.95
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 230 well B03 (strain 22787)


title: Mouse liver PB vs. Control 1.5X cDNA 4

description:
Pos_1_4_Dye_Cy5_Sample_38
Pos_1_4_Dye_Cy3_Sample_52

source_name: Phenobarbital-exposed mouse liver, 1.5X cDNA input, replicate 1.2


title: osteoblast differentiation 21 days [BM5_21]

description: osteoblast differentiation 21 days

value: MSC


title: Mouse liver PB vs. Control 1.5X cDNA 1

description:
Pos_1_1_Dye_Cy5_Sample_54
Pos_1_1_Dye_Cy3_Sample_39


title: Mouse liver PB vs. Control 1.5X cDNA 5

description:
Pos_2_1_Dye_Cy5_Sample_53
Pos_2_1_Dye_Cy3_Sample_38

source_name: Phenobarbital-exposed mouse liver, 1.5X cDNA input, replicate 2.1


title: SLAM Project Data: Synthetic Lethality with ypl039w

description:
Internal identifier for dataset: SL/100414/6
Original datafile name: 308093A02_532.pair
Original datafile2 name: 308093A02_635.pair
SD of values from reference genes: 0.569
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.67 1.49 1.70
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 230 well B05 (strain 22789)


title: SLAM Project Data: Synthetic Lethality with mkk2

description:
Internal identifier for dataset: SL/050920/8
Original datafile name: 050920_211_B07.gpr
Original datafile2 name: <none>
SD of values from reference genes: 0.699
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.03 0.53 1.01
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 211 well B07 (strain 22112)


title: osteoblast differentiation 14 days [BM3_14]

description: osteoblast differentiation 14 days

value: 14-day differentiated cells


title: SLAM Project Data: Synthetic Lethality with mak10-rep2

description:
Internal identifier for dataset: SL/061129/11
Original datafile name: 061129_214_H02.gpr
Original datafile2 name: <none>
SD of values from reference genes: 0.785
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 0.94 1.06 1.09
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 214 well H02 (strain 20294)


title: SLAM Project Data: Synthetic Lethality with mad2

description:
Internal identifier for dataset: SL/050916/15
Original datafile name: 050916_247_F07.gpr
Original datafile2 name: <none>
SD of values from reference genes: 0.581
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 0.78 1.03 1.07
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 243 well F07 (strain 21392)


title: SLAM Project Data: Synthetic Lethality with ypl035c

description:
Internal identifier for dataset: SL/100414/8
Original datafile name: 308093A04_532.pair
Original datafile2 name: 308093A04_635.pair
SD of values from reference genes: 0.469
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.94 1.82 2.08
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 230 well B08 (strain 22794)

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX


title: osteoblast differentiation 14 days [BM5_14]

description: osteoblast differentiation 14 days


title: SLAM Project Data: Synthetic Lethality with yor286w

description:
Internal identifier for dataset: SL/100305/18
Original datafile name: 100305NG301257A02_532.pair
Original datafile2 name: 100305NG301257A02_635.pair
SD of values from reference genes: 0.245
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 3.18 3.70 3.78
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 224 well H08 (strain 22542)


title: SLAM Project Data: Synthetic Lethality with yor285w

description:
Internal identifier for dataset: SL/100305/17
Original datafile name: 100305NG301257A01_532.pair
Original datafile2 name: 100305NG301257A01_635.pair
SD of values from reference genes: 0.320
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.91 2.32 2.99
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 224 well H07 (strain 22541)


title: Mouse liver PB vs. Control 1X cDNA 8

description:
Pos_2_4_Dye_Cy5_Sample_53
Pos_2_4_Dye_Cy3_Sample_38

hyb_protocol: 1X (samples 1-8) or 1.5X (samples 9-16) cDNA was blocked with Agilent CGH-block and GE-blocking agent and hybridized to Agilent SurePrint GE 8x60 mouse microarrays for 17 hours at 65C at 20rpm

source_name: Control mouse liver, 1X cDNA input, replicate 3.2

value: 42 days

value: male

value: liver

source_name: Phenobarbital-exposed mouse liver, 1X cDNA input, replicate 1.2


title: Mouse liver PB vs. Control 1.5X cDNA 2

description:
Pos_1_2_Dye_Cy5_Sample_37
Pos_1_2_Dye_Cy3_Sample_53

source_name: Phenobarbital-exposed mouse liver, 1.5X cDNA input, replicate 2

value: Phenobarbital


title: osteoblast differentiation 7 days [BM5_7]

description: osteoblast differentiation 7 days

source_name: osteoblast differentiation 7 days

value: osteoblast

value: 7-day differentiated cells


title: mesenchymal stem cells [BM3_msc]

description: mesenchymal stem cells

source_name: mesenchymal stem cells

value: primary mesenchymal stem cells


title: SLAM Project Data: Synthetic Lethality with yor283w

description:
Internal identifier for dataset: SL/100305/15
Original datafile name: 100305NG301253A03_532.pair
Original datafile2 name: 100305NG301253A03_635.pair
SD of values from reference genes: 0.268
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.74 3.09 3.33
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

source_name: Reference

value: Plate 224 well H05 (strain 22539)


title: SLAM Project Data: Synthetic Lethality with yor251c

description:
Internal identifier for dataset: SL/100305/10
Original datafile name: 100305NG301239A02_532.pair
Original datafile2 name: 100305NG301239A02_635.pair
SD of values from reference genes: 0.347
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.49 2.39 2.66
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 224 well F11 (strain 22507)

source_name: Test


title: MET transformed HOB clones [C15]

description: MET transformed HOB clones

source_name: MET transformed HOB clones

value: stable transfected with MET oncogene

value: MET-HOB


title: Mouse liver PB vs. Control 1X cDNA 6

description:
Pos_2_2_Dye_Cy5_Sample_39
Pos_2_2_Dye_Cy3_Sample_54

source_name: Control mouse liver, 1X cDNA input, replicate 2

source_name: Phenobarbital-exposed mouse liver, 1X cDNA input, replicate 3


title: osteoblast differentiation 7 days [BM3_7]

description: osteoblast differentiation 7 days

value: MSC


title: SLAM Project Data: Synthetic Lethality with yor277c

description:
Internal identifier for dataset: SL/100305/13
Original datafile name: 100305NG301253A01_532.pair
Original datafile2 name: 100305NG301253A01_635.pair
SD of values from reference genes: 0.284
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.84 2.77 3.18
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 224 well H01 (strain 22533)


title: MET transformed HOB clones [C42]

description: MET transformed HOB clones


title: SLAM Project Data: Synthetic Lethality with yor248w

description:
Internal identifier for dataset: SL/100305/9
Original datafile name: 100305NG301239A01_532.pair
Original datafile2 name: 100305NG301239A01_635.pair
SD of values from reference genes: 0.244
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 3.00 2.98 3.62
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 224 well F08 (strain 22504)


title: Mouse liver PB vs. Control 1X cDNA 4

description:
Pos_1_4_Dye_Cy5_Sample_37
Pos_1_4_Dye_Cy3_Sample_53

source_name: Phenobarbital-exposed mouse liver, 1X cDNA input, replicate 2.2

source_name: Control mouse liver, 1X cDNA input, replicate 1


title: Mouse liver PB vs. Control 1X cDNA 2

source_name: Phenobarbital-exposed mouse liver, 1X cDNA input, replicate 2


title: Mouse liver PB vs. Control 1X cDNA 7

description:
Pos_2_3_Dye_Cy5_Sample_52
Pos_2_3_Dye_Cy3_Sample_37

source_name: Phenobarbital-exposed mouse liver, 1X cDNA input, replicate 2.1


title: Mouse liver PB vs. Control 1X cDNA 5

description:
Pos_2_1_Dye_Cy5_Sample_53
Pos_2_1_Dye_Cy3_Sample_38

source_name: Phenobarbital-exposed mouse liver, 1X cDNA input, replicate 1


title: Mouse liver PB vs. Control 1X cDNA 3

description:
Pos_1_3_Dye_Cy5_Sample_38
Pos_1_3_Dye_Cy3_Sample_52

source_name: Control mouse liver, 1X cDNA input, replicate 3.1

source_name: Phenobarbital-exposed mouse liver, 1X cDNA input, replicate 1.1


title: #4:WT vs -STK(-) mutant [Exp2-rep2-dyeswap]

city: Columbus

first: Vijay

last: Pancholi

state: OH

address: 420W 12th Ave, TMRF-288

department: Pathology

institute: Ohio State University

description: Comparison of gene expression in the Sp-STK knockout mutant vs the parental strain M1 SF370

hyb_protocol: The labeled cDNA-probes (wild-type and mutant strains) were combined and purified using QIAquickTM PCR spin columns (Qiagen).  The labeled cDNA was hybridized with the array slide in  the hybridization buffer  (3xSSC, salmon testes (sonicated and denatured) DNA and 0.25% SDS) at 63C overnight using hybridization chamber (HybrChambTm, GeneMachines). The hybridized array slides were washed consecutively with 1 x SSC, 0.2 x SSC and 0.05 x SSC each with 0.03% SDS.

scan_protocol: Signals of the bound reagents on the microarray spots in terms of relative fluorescence values were measured and quantified by a laser scanner (GenePix 4100 ) at 10um/pixel resolution. The resulting images were processed using Gene Pix Pro  software (version 4.0, Axon instruments).

data_processing: The web application CARMAweb (Comprehensive R based microarray analysis web service) was used for the normalization and analysis of microarray data.  All raw data (in the form of  *. GPR files) were uploaded to the web application in the data directory. Using appropriate navigation tree, background correction from the foreground signals was applied and within microarray normalization was achieved using the Lowess method.  Genes flagged as bad spots by the scanning software were excluded from the analysis and all flagged spots were termed as "null".  The normalized data were then subjected to fold-change analysis and t-statistics using Bioconductor multtest package. This package employs the moderated t-statistics from the LIMMA package (liner models for micro array data) based on bayesian Significantly differentially expressed genes were those  showing log2 values > 0.6 ( up regualted) and Log2 values < 0.6 (down-regulated),   Bioconductors Multtest package provided suitable method  (e.g. Benjamini and Hochberg) adjust P values according to multiple hypothesis testing problems.

label: Alexafluor 647

organism: Streptococcus pyogenes

source_name: wild-type strain SF370

label_protocol: From the total RNA, cDNA was synthesized using random hexamer, dNTPs (except that  dTTP was replaced by the same amount of amino-allyl dUTP to incorporate dUTP into first-strand cDNA)  and each reverse transcriptase reaction (Superscript II Reverse Transcriptase, Invitrogen). The amino allyl-modified cDNA was purified using QIAquick PCR spin columns (Qiagen). Purified cDNA from the wild-type strain was labeled with Alexafluor-647 in 0.3M sodium carbonate (pH=9.0) for 1 h (dark) according to the manufacturer’s instructions (Molecular probes/Invitrogen,

growth_protocol: Streptococcal wild-type strain was grown in Todd-Hewitt broth to its late log phase, harvested by centrifugation and washed twice with sterile PBS.

extract_protocol: Washed streptococci were lysed with the amidase enzyme (lysin)  and total RNA was extracted using Qiagen RNeasy Mini kit ( cat# 74104). RNA was digested with RNAse-free DNase-I (Invitrogen) and RNA quality  and quantity was analyzed using Nucleic acid Bioanalyzer (Agilent technologies).

treatment_protocol: Streptococus pyogenes parent strain type M1 SF370 was obtained from ATCC (Jin H and Pancholi V[2006]J. Mol. Biol. 357:1351-1372).

tag: Streptococcus pyogenes wild-type M1 SF370 (#4)

label: Alexafluor 555

source_name: Sp-STK(-) mutant

label_protocol: From the total RNA, cDNA was synthesized using random hexamer, dNTPs (except that  dTTP was replaced by the same amount of amino-allyl dUTP to incorporate dUTP into first-strand cDNA)  and each reverse transcriptase reaction (Superscript II Reverse Transcriptase, Invitrogen). The amino allyl-modified cDNA was purified using QIAquick PCR spin columns (Qiagen). Purified cDNA from the mutant strain was labeled with Alexafluor-555 in 0.3M sodium carbonate (pH=9.0) for 1 h (dark) according to the manufacturer’s instructions (Molecular probes/Invitrogen,

growth_protocol: Streptococcal mutant strain was grown in Todd-Hewitt broth to its late log phase, harvested by centrifugation and washed twice with sterile PBS.

treatment_protocol: SP-STK knockout mutant was derived from S. pyogenes type M1 SF370 strain as described ( Jin H and Pancholi V[2006]J. Mol. Biol. 357:1351-1372)

tag: Streptococcus pyogenes SP-STK (-) mutant (#4)


title: MET transformed HOB clones [C12]

description: MET transformed HOB clones


title: #1:SP-STK(-) mutant vs WT [Exp1-rep1]

source_name: SP-STK(-) mutant

label_protocol: From the total RNA, cDNA was synthesized using random hexamer, dNTPs (except that  dTTP was replaced by the same amount of amino-allyl dUTP to incorporate dUTP into first-strand cDNA)  and each reverse transcriptase reaction (Superscript II Reverse Transcriptase, Invitrogen). The amino allyl-modified cDNA was purified using QIAquick PCR spin columns (Qiagen). Purified cDNA from the mutant was labeled with Alexafluor-647 in 0.3M sodium carbonate (pH=9.0) for 1 h (dark) according to the manufacturer’s instructions (Molecular probes/Invitrogen,

tag: Streptococcus pyogenes SP-STK(-) mutant

growth_protocol: Streptococcal wild-type parent strain was grown in Todd-Hewitt broth to its late log phase, harvested by centrifugation and washed twice with sterile PBS.

treatment_protocol: Streptococus pyogeens parent strain type M1 SF370 was obtained from ATCC (Jin H and Pancholi V[2006]J. Mol. Biol. 357:1351-1372).

tag: Streptococcus pyogenes M1 SF370


title: #5:SP-STK(-) mutant vs WT [Exp3-rep1]

label_protocol: From the total RNA, cDNA was synthesized using random hexamer, dNTPs (except that  dTTP was replaced by the same amount of amino-allyl dUTP to incorporate dUTP into first-strand cDNA)  and each reverse transcriptase reaction (Superscript II Reverse Transcriptase, Invitrogen). The amino allyl-modified cDNA was purified using QIAquick PCR spin columns (Qiagen). Purified cDNA from the mutant strain was labeled with Alexafluor-647 in 0.3M sodium carbonate (pH=9.0) for 1 h (dark) according to the manufacturer’s instructions (Molecular probes/Invitrogen,

tag: S. pyogenes SP-STK(-) mutant (#5)

label_protocol: From the total RNA, cDNA was synthesized using random hexamer, dNTPs (except that  dTTP was replaced by the same amount of amino-allyl dUTP to incorporate dUTP into first-strand cDNA)  and each reverse transcriptase reaction (Superscript II Reverse Transcriptase, Invitrogen). The amino allyl-modified cDNA was purified using QIAquick PCR spin columns (Qiagen). Purified cDNA from the wild-type strain was labeled with Alexafluor-555 in 0.3M sodium carbonate (pH=9.0) for 1 h (dark) according to the manufacturer’s instructions (Molecular probes/Invitrogen,

growth_protocol: Streptococcal  wild-type strain was grown in Todd-Hewitt broth to its late log phase, harvested by centrifugation and washed twice with sterile PBS.

tag: S. pyogenes wild-type M1 SF370 (#5)


title: #2:WT vs -STK(-) mutant [Exp1-rep2-dyeswap]

description: This is a dye swap experiment. Comparison of gene expression in the Sp-STK knockout mutant vs the parental strain M1 SF370

growth_protocol: Streptococcal M1 SF370 strain was grown in Todd-Hewitt broth to its late log phase, harvested by centrifugation and washed twice with sterile PBS.

tag: Streptocccus pyogenes M1 SF370 parent strain

label_protocol: From the total RNA, cDNA was synthesized using random hexamer, dNTPs (except that  dTTP was replaced by the same amount of amino-allyl dUTP to incorporate dUTP into first-strand cDNA)  and each reverse transcriptase reaction (Superscript II Reverse Transcriptase, Invitrogen). The amino allyl-modified cDNA was purified using QIAquick PCR spin columns (Qiagen). Purified cDNA from the mutant was labeled with Alexafluor-555 in 0.3M sodium carbonate (pH=9.0) for 1 h (dark) according to the manufacturer’s instructions (Molecular probes/Invitrogen,

growth_protocol: Streptococcal  mutant strain was grown in Todd-Hewitt broth to its late log phase, harvested by centrifugation and washed twice with sterile PBS.

tag: Streptococcus pyogenes mutant lacking SP-STK.


title: #3:SP-STK(-) mutant vs WT [Exp2-rep1]

tag: S. pyogenes SP-STK(-) mutant (#3)

tag: S. pyogenes wild-type strain SF370 (#3)


title: Human Esophageal Squamous Cell Carcinoma Cell Line Replicate 5

city: Beijing

first: Jia-Jie

last: Hao

address: 17 Panjiayuan Nanli

country: China

institute: Cancer Hospital (Institute), Chinese Academy of Medical Sciences

description:
KYSE510
Biological replicate 5 of 6.Human Esophageal squamous cell carcinoma cell line

hyb_protocol: Reference DNA probes and test DNA probes were combined and Human Cot-1 DNA (Invitrogen), 10 Blocking Agent and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, then samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential.

scan_protocol: Scanned on an Agilent G2565B Scanner Images were quantified using Agilent Feature Extraction Software (version 9.1.3.1).

data_processing:
Agilent Feature Extraction Software (version 9.1.3.1) was used for background subtraction and Linear normalization.
Agilent Genomic Workbench Lite Edition 5.0 use centralization algorithm to normalize the data of arrays and use ADM-2 algorithm to analyze the aberration data.

label_protocol: The digested test and reference DNA fragments were labeled with Cy3-dUTP and Cy5-dUTP using Agilent Genomic DNA Enzymatic Labeling Kit (Agilent p/n 5190-0449), respectively. Then Microcon YM-30 (Millipore) was used to clear up the labeled probes.

growth_protocol: Each cell line was cultured in RPMI-1640 (Invitrogen) supplemented with 10% fetal calf serum at 37℃ with 5% CO2.

extract_protocol:
Genomic DNA extracted using Qiagen DNeasy Blood & Tissue Kit following manufacturer's instructions
1 μg the reference commercial genomic DNA (promega) and the same amount of the test (cell line) DNA were digested with Alu I (promega) and RSA I (promega) following Agilent's instructions (Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol Version 6.1, August 2009)

tag: tissue

tag: age

tag: Sex

value: Femaie

tag: location

value: Esophagus

source_name: Commercial Human Genomic DNA: Female

tag: company

value: Promega

tag: catalog


title: SLAM Project Data: Synthetic Lethality with yor228c

description:
Internal identifier for dataset: SL/100223/7
Original datafile name: 100223NG261129A03_532.pair
Original datafile2 name: 100223NG261129A03_635.pair
SD of values from reference genes: 0.483
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.03 1.65 1.93
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

tag: query gene

tag: knockout clone

value: Plate 224 well D12 (strain 22484)

tag: genetic background

tag: pool genotype

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX


title: SLAM Project Data: Synthetic Lethality with yor246c

description:
Internal identifier for dataset: SL/100305/7
Original datafile name: 100305NG300043A03_532.pair
Original datafile2 name: 100305NG300043A03_635.pair
SD of values from reference genes: 0.300
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.70 2.75 3.02
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 224 well F06 (strain 22502)


title: SLAM Project Data: Synthetic Lethality with yor225w

description:
Internal identifier for dataset: SL/100223/3
Original datafile name: 100223NG261128A03_532.pair
Original datafile2 name: 100223NG261128A03_635.pair
SD of values from reference genes: 0.303
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.68 2.95 3.31
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 224 well D09 (strain 22481)


title: Mouse liver PB vs. Control 1X cDNA 1

description:
Pos_1_1_Dye_Cy5_Sample_54
Pos_1_1_Dye_Cy3_Sample_39

value: 42 days

tag: gender

value: male

tag: strain

tag: organ

value: liver

tag: exposure

value: Phenobarbital

tag: cdna input

source_name: Control mouse liver, 1X cDNA input, replicate 3


title: Phenobarbital-exposed mouse liver, 1.5X cDNA input, replicate 1

source_name: Whole liver, 0.05% PB in drinking water, ~4 weeks, archival FFPE


title: Control mouse liver, 1.5X cDNA input, replicate 1

source_name: Whole liver, not-exposed, archival FFPE


title: Human Esophageal Squamous Cell Carcinoma Cell Line Replicate 4

description:
KYSE450
Biological replicate 4 of 6.Human Esophageal squamous cell carcinoma cell line

value: Male

source_name: Commercial Human Genomic DNA: Male


title: SLAM Project Data: Synthetic Lethality with yor223w

description:
Internal identifier for dataset: SL/090211/14
Original datafile name: 090211NG142277A02_532.pair
Original datafile2 name: 090211NG142277A02_635.pair
SD of values from reference genes: 0.368
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.39 2.70 2.76
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

source_name: Reference

value: Plate 270 well B02 (strain 22479)

source_name: Test


title: Human Esophageal Squamous Cell Carcinoma Cell Line Replicate 6

description:
YES-2
Biological replicate 6 of 6.Human Esophageal squamous cell carcinoma cell line


title: SLAM Project Data: Synthetic Lethality with yor215c

description:
Internal identifier for dataset: SL/100122/5
Original datafile name: 100122NG258815A01_532.pair
Original datafile2 name: 100122NG258815A01_635.pair
SD of values from reference genes: 0.424
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.39 1.52 2.22
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 224 well C12 (strain 22471)


title: Human Esophageal Squamous Cell Carcinoma Cell Line Replicate 3

description:
KYSE180
Biological replicate 3 of 6.Human Esophageal squamous cell carcinoma cell line


title: Phenobarbital-exposed mouse liver, 1.5X cDNA input, replicate 3


title: SLAM Project Data: Synthetic Lethality with yor214c

description:
Internal identifier for dataset: SL/100122/4
Original datafile name: 100122NG255783A04_532.pair
Original datafile2 name: 100122NG255783A04_635.pair
SD of values from reference genes: 0.364
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.83 2.41 2.91
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 224 well C11 (strain 22470)


title: Control mouse liver, 1.5X cDNA input, replicate 2


title: Mouse 7 KO-CR1

city: Nagasaki

first: Isao

last: Shimokawa

address: 1-12-4 Sakamoto

department: Basic Medical Science

country: Japan

institute: Nagasaki University Graduate School of Biomedical Sciences

description: Total probes are 36227. The quality tag of probes consists of G (signal intensity was above noise levels), L (fluorescence intensity of spots is as low as noise levels), I (shape of spots is irregular), S (fluorescence intensities of most pixels in a spot is saturated), C (background area of spots is contaminated), P (spots are contaminated), and M (spots designated as "elimination from the analysis" by the maker).

hyb_protocol: After incubation, slides were washed, and stained with Cy5-streptavidin for microarray (GE Healthcara Bio-Science Corp., Piscataway, NJ).

scan_protocol: Arrays were scanned by GenePix4000B (Molecular Devices LLC., Sunnyvale, CA).

data_processing: Array images were processed using CodeLink ™ Expression Analysis v5.0 (Applied Microarray Inc.). Each slide was subjected to quantile normalization.

source_name: liver, Npy KO, DR

label_protocol: Labeled cRNA was applied to the CodeLink Mouse Whole Genome Bioarrays (Applied Microarrays, Inc., Tempe, AZ) for 18 hours at 37°C. Individual samples from two mice of each group were run on separate microarrays.

extract_protocol: RNA, extracted from liver tissues, that passed the Agilent Technologies 2100 Bioanalyzer quality control test, was used to generate biotin-labeled cRNA with a MessageAmpTM II-Biotin Enhanced Kit (Ambion, Inc., Austin, TX ).

tag: strain/background

value: mixed (129S-Npytm1Rpa/J and 129S6/SvEvTac)

tag: genotype

value: Npy-/-

tag: feeding

value: dietary restriction


title: SLAM Project Data: Synthetic Lethality with yor205c

description:
Internal identifier for dataset: SL/100115/8
Original datafile name: 100115NG301673A04_532.pair
Original datafile2 name: 100115NG301673A04_635.pair
SD of values from reference genes: 0.674
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.13 1.12 1.23
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 224 well C02 (strain 22461)


title: Human Esophageal Squamous Cell Carcinoma Cell Line Replicate 2

description:
KYSE150
Biological replicate 2 of 6.Human Esophageal squamous cell carcinoma cell line

tag: tissue

tag: age

value: Femaie

value: Esophagus

value: Promega


title: SLAM Project Data: Synthetic Lethality with yor200w

description:
Internal identifier for dataset: SL/100115/7
Original datafile name: 100115NG301673A03_532.pair
Original datafile2 name: 100115NG301673A03_635.pair
SD of values from reference genes: 0.713
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.29 1.28 1.37
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 224 well B10 (strain 22456)

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX


title: Human Esophageal Squamous Cell Carcinoma Cell Line Replicate 1

description:
KYSE30
Biological replicate 1 of 6.Human Esophageal squamous cell carcinoma cell line

tag: Sex

tag: location


title: Control mouse liver, 1.5X cDNA input, replicate 3

value: 42 days


title: Phenobarbital-exposed mouse liver, 1X cDNA input, replicate 3

value: male


title: Mouse 6 KO-AL2

source_name: liver, Npy KO, AL

value: liver

value: ad libitum


title: Mouse 8 KO-CR2


title: Mouse 5 KO-AL1


title: Control mouse liver, 1X cDNA input, replicate 3


title: SLAM Project Data: Synthetic Lethality with yor170w

description:
Internal identifier for dataset: SL/091201/14
Original datafile name: 091201NG301639A02_532.pair
Original datafile2 name: 091201NG301639A02_635.pair
SD of values from reference genes: 0.311
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.86 2.68 3.03
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 223 well H06 (strain 22426)


title: SLAM Project Data: Synthetic Lethality with yor199w

description:
Internal identifier for dataset: SL/100115/6
Original datafile name: 100115NG301673A02_532.pair
Original datafile2 name: 100115NG301673A02_635.pair
SD of values from reference genes: 0.318
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.75 2.34 2.93
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 224 well B09 (strain 22455)


title: Phenobarbital-exposed mouse liver, 1X cDNA input, replicate 2

value: Phenobarbital


title: Mouse 2 WT-AL2

source_name: liver, WT, AL

value: Npy+/+


title: Phenobarbital-exposed mouse liver, 1.5X cDNA input, replicate 2


title: Gene expression analysis following methionine addition to wild type cells

city: Nanjing

first: Yakun

last: Wan

address: Sipailou #2

institute: Southeast University

description: Two color microarrays, comparing RNA from the experimental condition (WT cells grown in medium containing 200 µg/mL methionine) to RNA from the control (WT cells grown in medium lacking methionine), were performed using Agilent whole-genome S. cerevisiae arrays.

hyb_protocol: Agilent yeast gene expression array protocol

data_processing:
Differentially expressed genes were identified by maximum-likelihood analysis (Ideker et al., 2000 and Smith et al., 2002) with lambda ≥ 100, with the exception of sth1-deplete 2hr and sth1-reinduction 4hr (lambda ≥ 50).  Significantly affected genes in each condition were identified by a ≥ 2-fold change in gene expression when compared to the corresponding control strain.
Please refer to the following links for the .clone file-format:
http://db.systemsbiology.net/software/VERAandSAM/doc/VERAandSAM_win.html
http://db.systemsbiology.net/software/VERAandSAM/doc/fileFormat.html

source_name: WT minus methionine

growth_protocol: Wild type, nup157∆, nup170∆, and nup188∆ cells were cultured at 30˚C in YPD medium to an OD600 of 0.8 and harvested.  PMET3-HA3-STH1 cells were grown at 30˚C in synthetic complete (SC) medium lacking methionine to mid-logarithmic phase (0 h) and STH1 was repressed by the addition of methionine to a final concentration of 200 µg/mL for 8 hrs.  Following 8 hrs of repression, methionine was removed by extensive washes with SC medium lacking methionine and STH1 was reinduced by growth in SC medium lacking methionine for an additional 4 hrs.  Cells were harvested at 0 hr, 2 hr and following 4 hrs of reinduction.

extract_protocol: Total RNA was isolated using hot acidic phenol extraction.

tag: genotype/variation

value: BY4742 (MATα  his3∆1 leu2∆0 ura3∆0 lys2∆0)

source_name: WT plus methionine


title: Sth1p reinduction 4hr gene expression analysis

description: Two color microarrays, comparing RNA from PMET3-HA3-STH1 cells grown in the experimental condition (medium containing 200 µg/mL methionine to deplete Sth1p for 8 hrs followed by growth in medium lacking methionine to reinduce Sth1p for an additional 4 hrs) to RNA from PMET3-HA3-STH1 cells grown in the control condition (medium lacking methionine), were performed using Agilent whole-genome S. cerevisiae arrays.

scan_protocol: Agilent yeast gene expression array protocol

source_name: Sth1p depeltion 0hr

value: TMY1452 (MATa  his3∆1 leu2∆0 ura3∆0 lys2∆0 sth1::kanR-PMET3-HA3-STH1)

source_name: Sth1p reinduction 4hr

value: TMY1452 (MATα  his3∆1 leu2∆0 ura3∆0 lys2∆0 sth1::kanR-PMET3-HA3-STH1)


title: nup188∆ gene expression analysis

description: Two color microarrays, comparing RNA from the experimental condition (nup188∆ cells grown in YPD) to RNA from the control (WT cells grown in YPD), were performed using Agilent whole-genome S. cerevisiae arrays.

source_name: wild type

label_protocol: Agilent yeast gene expression array protocol

value: DVY1172 (MATa  his3∆1 leu2∆0 ura3∆0 met15∆0)

value: DVY1136 (MATα  his3∆1 leu2∆0 ura3∆0 lys2∆0 nup188∆::kanR)


title: nup170∆ gene expression analysis

description: Two color microarrays, comparing RNA from the experimental condition (nup170∆ cells grown in YPD) to RNA from the control (WT cells grown in YPD), were performed using Agilent whole-genome S. cerevisiae arrays.

value: DVY1174 (MATa  his3∆1 leu2∆0 ura3∆0 lys2∆0)

value: DVY1173 (MATa  his3∆1 leu2∆0 ura3∆0 met15∆0 nup170∆::kanR)


title: Sth1p depletion 2hr gene expression analysis

description: Two color microarrays, comparing RNA from PMET3-HA3-STH1 cells grown in the experimental condition (medium containing 200 µg/mL methionine to deplete Sth1p for 2 hrs) to RNA from PMET3-HA3-STH1 cells grown in the control condition (medium lacking methionine), were performed using Agilent whole-genome S. cerevisiae arrays.

source_name: Sth1p depletion 0hr

source_name: Sth1p deplete 2hr


title: nup157∆ gene expression analysis

description: Two color microarrays, comparing RNA from the experimental condition (nup157∆ cells grown in YPD) to RNA from the control (WT cells grown in YPD), were performed using Agilent whole-genome S. cerevisiae arrays.

value: DVY1134 (MATa  his3∆1 leu2∆0 ura3∆0 nup157∆::URA3)


title: SLAM Project Data: Synthetic Lethality with yor186w

description:
Internal identifier for dataset: SL/100108/8
Original datafile name: 100108NG301667BA04_532.pair
Original datafile2 name: 100108NG301667BA04_635.pair
SD of values from reference genes: 0.263
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.45 2.68 3.08
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

tag: query gene

value: Plate 224 well A08 (strain 22442)

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX


title: Mouse 3 WT-CR1

source_name: liver, WT, DR

value: mixed (129S-Npytm1Rpa/J and 129S6/SvEvTac)

value: male

value: dietary restriction


title: lung_PolyIC_7d_H5

status: Public on Feb 27 2013

city: Gaithersburg

first: Sriram

last: Sridhar

state: MD

address: 1 MedImmune Way

department: Translational Medicine

institute: MedImmune

hyb_protocol: Array washing, staining and scanning was performed according to standard Affymetrix protocols.

data_processing: Probe level data was curated by first mapping individual probe sequences to their most current genome sequences. Probes which were non-uniquely mapped to specific genes or contained outdated mappings were discarded, and the remaining probes were summarized into probesets and normalized using Robust Multi-array Average (RMA). Probes expressed at low levels across all samples were subsequently discarded.

source_name: PolyIC, 7d

label_protocol: Purified total RNA was amplified and labeled using NuGen Ovation kits (NuGEN Technologies, Inc., San Carlos, CA) and RNA from samples was hybridized to Affymetrix Mouse 430 2.0 arrays.

extract_protocol: Total RNA was isolated from the mouse lung tissue of poly I:C and saline treated mice across 7 time points (2, 6, 24, 48, 72, 96, and 168 hours, n=6 per group) and homogenized in QIAzol reagent.

treatment_protocol: Mice were intranasally treated with poly I:C or saline once prior to RNA extraction from lung tissue at subsequent timepoints.

tag: agent

value: PolyIC

tag: time point

value: BALB/cJ

value: Male

value: lung homogenate


title: SLAM Project Data: Synthetic Lethality with yor238w

description:
Internal identifier for dataset: SL/100302/17
Original datafile name: 100302NG300007A01_532.pair
Original datafile2 name: 100302NG300007A01_635.pair
SD of values from reference genes: 0.468
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.79 1.40 1.76
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

tag: knockout clone

value: Plate 224 well E10 (strain 22494)

tag: genetic background

tag: pool genotype


title: Mouse 4 WT-CR2

value: Npy+/+

tag: gender

value: liver