title: DRG_NT3KO-BaxKO_P0_TrkC-_rep2

description: NT3Bax P0 TrkC- 2

value: NT3-/- (Farinas et al., 1994)::Bax-/- (Deckwerth et al., 1996)::TrkCGFP (Gong et al., 2010)

tag: lumber/segmental level


title: Irf4#3

status: Public on Aug 23 2012

type: RNA

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

country: USA

institute: Harvard Medical School

hyb_protocol: Affymetrix WT Sense Target Labeling Kit.

scan_protocol: Affymetrix GeneChip Scanner.

data_processing: The datasets were pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: Lymph node, CD4+ Tconv, IRF4

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit.

extract_protocol: TRIzol.

tag: genetic background

tag: age

value: 8 weeks

tag: Sex

value: female

tag: tissue

value: lymph node

tag: cell type

value: conventional T cells (Tconv)

tag: transduced factors

tag: phenotype markers

tag: exclusion markers

tag: separation method

value: MoFlo Sorter


title: PC 538N

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81163.gif

hyb_protocol: not provided

scan_protocol: After hybridization, microarrays were imaged using an Axon GenePix 4000 scanner (Axon Instruments-Molecular Devices, LLC, Sunnyvale, CA, USA). Fluorescence ratios for array elements were extracted using GENEPIX software and uploaded into the Stanford Microarray Database for subsequent analysis.

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Homo sapiens

source_name: reference RNA

label_protocol: not provided

extract_protocol: not provided

tag: reference

growth_protocol:
All prostate samples used for this study were collected at the Stanford University Medical Center between 1999 and 2007 with patient's informed consent under an Institutional Review Board (IRB)-approved protocol. Multiple tissue samples were harvested from each prostate, flash-frozen and stored at 80oC. Frozen sections of each prostate sample were performed and evaluated by a genitourinary pathologist (JKM). The tumor and nontumor areas were marked and contaminating tissues were trimmed away from the block as described previously.48 Tumor samples in which at least 90% of the epithelial cells were cancerous were selected for extraction of DNA and RNA. In total, we selected 98 tumors from 86 patients that met these criteria. Associated clinical data were collected and included preoperative PSA levels, clinical stage, pathological stage, tumor Gleason grade and clinical follow-up. Recurrence was defined as a measurable serum PSA (>0.1ng/ml on two consecutive measurements) after surgery.
Gene-expression profiling was performed as reported. Briefly, Cy5-labeled cDNA was prepared by using 50ug of total RNA from prostate samples and Cy3-labeled cDNA was prepared by using common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines. For each experimental sample, Cy5- and Cy3-labeled samples were cohybridized to HEEBO spotted microarrays.49 HEEBO microarrays were manufactured in the Stanford Functional Genomics Facility at Stanford University and contained 44-544 70-mer probes.

tag: individual

value: PC 538N

tag: disease state

value: Normal

value: prostate


title: DRG_wildtype_P0_TrkC-_rep1

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

description: WT P0 TrkC- 1

hyb_protocol: The fragmented cRNA (15 µg) was used in a hybridization cocktail containing spiked controls (Affymetrix). A total of 200 µl of this hybridization cocktail was hybridized at 45°C for 16 hours to GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix).

scan_protocol: Following hybridization, the arrays were processed using a GeneChip Fluidics Station 400 according to recommended protocols (FS450_0001, Affymetrix). Fluorescent images of arrays were captured using the GeneChip Scanner 3000 7G (Affymetrix), and image data were acquired and analyzed using the Affymetrix GCC Scan Control v. 3.0.0.1214

data_processing: Raw data from CEL files was loaded into R using the R (v2.9) / Bioconductor (v1.6) package affy. Data was normalized with the rma function and present/absent calls were calculated using MAS5 normalization as implemented in the affy package.

label: biotin

label_protocol: Preparation of in vitro transcription (IVT) products was performed according to Affymetrix protocols (GeneChip Expression Analysis Technical manual, Rev. 5), with minor modifications.

extract_protocol: RNA extraction from isolated cells (Pico Pure RNA Isolation kit, KIT0204, Life Technologies)

treatment_protocol: DRG were exposed through dissection by ventral laminectomy and isolated in ice cold HBSS by pooling DRG from L1-L6 or separately by segmental level where needed (L1, L5). Isolated DRG were transferred to FCS-coated tubes using siliconized transfer pipettes, prior to dissociation in 0.25% trypsin/0.1% Collagenase H solution for 10 minutes at 37°C. HBSS was added to terminate enzymatic reaction, DRG pelleted by centrifugation (7 minutes, 800rpm), and resuspended in 1ml ice cold HBSS. Cells were dissociated by trituration using fire polished Pasteur pipettes to generate single cell suspension, and passed through 40 um gauze filters. For Fluorescent Activated Cell Sorting (FACS), a MoFlo (DAKO) high-speed 4-way cell sorter with a 3-laser setup (two water-cooled Coherent Enterprise II lasers; Model610 emitting at 488nm and Model653 allowing UV excitation; and one air-cooled Spectra Physics Helium-Neon laser emitting at 633nm) was used to separate GFPon from GFPoff cells.  To sort DRG sensory neurons, a 100μm nozzle was used at 20psi and sorted cells were collected in 1 ml Eppendorf tubes filled with 50μl Trizol to allow for subsequent RNA isolation. Average cell number used per data point was 350 for all experiments, except for L1/L5 p0 data sets, for which 100 cells were collected per sample.

tag: strain background

tag: genotype/variation

value: TrkCGFP (Gong et al., 2010)

value: dorsal root ganglion (DRG)

value: pooled (L1-L6)

value: FACS sorted DRG subpopulation


title: PC 26T2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-09/81251.gif

value: common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines

tag: ethnicity

value: Caucasian

tag: pre-operation treatment

value: PC 26T

tag: disease free survival


title: PC 339T2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-09/81281.gif

value: Tumor

value: PC 339T


title: DRG_NT3KO-BaxKO_P0_TrkC+_rep2

description: NT3Bax P0 TrkC+ 2

value: NT3-/- (Farinas et al., 1994)::Bax-/- (Deckwerth et al., 1996)::TrkCGFP (Gong et al., 2010)

tag: lumber/segmental level


title: DRG_NT3KO-BaxKO_P0_TrkC-_rep1

description: NT3Bax P0 TrkC- 1

tag: age


title: PC 627N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81099.gif

value: PC 627N


title: I+F#3

source_name: Lymph node, CD4+ Tconv, IRF4+FOXP3

tag: genetic background

value: 8 weeks

tag: Sex

value: female

value: lymph node


title: PC 26T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-09/81308.gif

value: PC 15T

tag: tissue


title: PC 47N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81089.gif

source_name: PC 47N2

value: PC 47N

value: Normal


title: DRG_NT3KO-BaxKO_P0_TrkC+_rep1

description: NT3Bax P0 TrkC+ 1

tag: cell type


title: PC 393T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81197.gif

value: PC 229T

value: prostate


title: PC 405T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/80899.gif

source_name: Human Reference RNA

source_name: PC 405T

value: PC 335T


title: I+F#2

value: conventional T cells (Tconv)

tag: transduced factors

tag: phenotype markers

value: MoFlo Sorter


title: DRG_BaxKO_P0_TrkC-_rep2

description: Bax P0 TrkC- 2

source_name: DRG_control mutant_P0

value: Bax-/- (Deckwerth et al., 1996)::TrkCGFP (Gong et al., 2010)

value: dorsal root ganglion (DRG)

value: pooled (L1-L6)

value: FACS sorted DRG subpopulation


title: PC 361T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81242.gif

value: common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines

value: Hispanic

value: PC 99T


title: PC 361T2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-09/81252.gif

value: Caucasian

value: PC 361T


title: DRG_BaxKO_P0_TrkC-_rep1

description: Bax P0 TrkC- 1


title: HIG+FIT#2

source_name: Lymph node, CD4+ Tconv, Helios+FOXP3

value: 8 weeks

value: female

value: lymph node

tag: exclusion markers

tag: separation method


title: PC 366N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81068.gif

tag: reference

tag: individual

value: PC 366N

value: Normal


title: PC 584N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81200.gif

value: PC 584N

tag: disease state

value: prostate


title: HIG#3

source_name: Lymph node, CD4+ Tconv, Helios

value: conventional T cells (Tconv)

value: Helios

value: MoFlo Sorter


title: HIG#2


title: DRG_BaxKO_P0_TrkC+_rep2

description: Bax P0 TrkC+ 2

tag: strain background

tag: genotype/variation

value: Bax-/- (Deckwerth et al., 1996)::TrkCGFP (Gong et al., 2010)

value: dorsal root ganglion (DRG)

value: pooled (L1-L6)


title: DRG_wildtype_P0_TrkC-_rep2

description: WT P0 TrkC- 2

value: TrkCGFP (Gong et al., 2010)

value: FACS sorted DRG subpopulation


title: PC 575N2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81237.gif

value: common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines

value: PC 575N


title: DRG_BaxKO_P0_TrkC+_rep1

description: Bax P0 TrkC+ 1


title: PC 21T3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-09/81253.gif

tag: ethnicity

value: Caucasian

tag: pre-operation treatment

value: PC 26T


title: PC 159T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81168.gif

value: PC 47T

tag: disease free survival


title: Gata1#2

source_name: Lymph node, CD4+ Tconv, GATA1

tag: age

value: 8 weeks

value: female

value: lymph node


title: PC 85T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81129.gif

source_name: PC 85T2

value: PC 610T

value: prostate


title: PC 339T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81247.gif

value: PC 339T

value: Tumor


title: HIG+FIT#3

tag: genetic background

value: conventional T cells (Tconv)

value: MoFlo Sorter


title: G+F#3

source_name: Lymph node, CD4+ Tconv, GATA1+FOXP3

tag: Sex


title: PC 405N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81135.gif

value: PC 405N

value: Normal

tag: tissue


title: G+F#2

tag: cell type


title: Foxp3+Pbx1#1

source_name: Lymph node, CD4+ Tconv, FOXP3+Pbx1

tag: transduced factors


title: PC 575N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81172.gif


title: PC 494T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81142.gif

value: PC 540T


title: PC 626T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81157.gif

value: common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines

value: PC 351T


title: Irf4#2

tag: phenotype markers


title: FIT#3

source_name: Lymph node, CD4+ Tconv, FOXP3

tag: exclusion markers


title: PC 574N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81146.gif

value: PC 574N


title: PC 547N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81192.gif

value: PC 547N


title: FIT#2

tag: separation method


title: PC 375N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/80873.gif

tag: reference

source_name: PC 375N RNA

value: PC 375N


title: PC 547T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81204.gif

value: Caucasian

tag: individual

value: PC 593T


title: PC 47T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81090.gif

source_name: PC 47T2

value: PC 482T


title: PC 97T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81117.gif

source_name: PC 97T2

value: PC 86T


title: PC 477T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81174.gif

value: PC 477T

value: prostate


title: PC 473T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81184.gif

value: Asian

value: PC 473T


title: Gata1#3

value: 8 weeks

value: female

value: lymph node

value: conventional T cells (Tconv)

value: MoFlo Sorter


title: PC 482T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/80937.gif

value: common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines

source_name: PC 482T

value: PC 494T


title: EOS#3

source_name: Lymph node, CD4+ Tconv, EOS

value: EOS


title: TIMP-1-GPI-7ng biological replicate 3

city: München

first: Carsten

last: Jäckel

address: Schillerstr 42

department: Klinische Biochemie

country: Germany

institute: Klinikum der Universität München, Klinische Biochemie

description: TIMP-1-GPI-7ng biological replicate 3

hyb_protocol: According to Affymetrix Protocols

scan_protocol: According to Affymetrix Protocols

data_processing: gcRMA

source_name: RCC cell line

label_protocol: According to Affymetrix Protocols

growth_protocol: Cells cultured in standard cell culture conditions

extract_protocol: According to Affymetrix Protocols

treatment_protocol: Cell were treated with rhTIMP1, empty vehicle or either 7ng or 14ng of TIMP1-GPI

value: kidney

value: renal cell carcinoma


title: PC 457T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81185.gif

source_name: reference RNA

value: Caucasian

value: PC 453T

tag: disease state

value: Tumor


title: TIMP-1-GPI-14ng biological replicate 3

description: TIMP-1-GPI-14ng biological replicate 3


title: TB 1872T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81140.gif

value: Positive


title: EOS#2


title: PC 634T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81087.gif

value: PC 389T

value: prostate


title: E+F#2

source_name: Lymph node, CD4+ Tconv, EOS+FOXP3


title: TIMP-1-GPI-14ng biological replicate 1

description: TIMP-1-GPI-14ng biological replicate 1


title: E+F#3


title: TIMP-1-GPI-7ng biological replicate 1

description: TIMP-1-GPI-7ng biological replicate 1


title: PC 474T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81182.gif

value: PC 474T


title: TIMP-1-GPI-7ng biological replicate 2

description: TIMP-1-GPI-7ng biological replicate 2


title: PC 248T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81166.gif

value: Asian

value: PC 547T


title: Gata1WT25+#2

source_name: Spleen, CD4+CD25hi Tregs, wildtype

value: wildtype

value: 8 weeks

value: female

value: spleen

value: regulatory T cells (Tregs)


title: TIMP-1-GPI-14ng biological replicate 2

description: TIMP-1-GPI-14ng biological replicate 2


title: PC 498T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81180.gif

value: common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines

value: PC 551T


title: Vehicle biological rep 3

description: Vehicle biological rep 3

value: kidney

value: renal cell carcinoma


title: PC 452N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81195.gif

value: PC 452N

value: Normal


title: PC 448T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81179.gif

value: African American

value: PC 629T


title: PC 452T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81187.gif

value: Caucasian

value: PC 362T

value: prostate


title: PC 455T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81181.gif

value: PC 430T


title: Gata1KO25+#1

source_name: Spleen, CD4+CD25hi Tregs, Gata1 knockout

value: Gata1 knockout

value: MoFlo Sorter


title: EosWTCD25+#2

value: wildtype

value: 8 weeks

value: female


title: Gata1KO25+#2

value: spleen

value: regulatory T cells (Tregs)


title: Vehicle biological rep 1

description: Vehicle biological rep 1

value: kidney


title: rhTIMP1 biological rep 3

description: rhTIMP1 biological rep 3

value: renal cell carcinoma


title: Gata1WT25+#1


title: CCAA_Decoy_2

description:
Simple annotation: Cell-cycle, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2007-09/76670.gif
Genetic Modification: CCAATNNSNNNGCG

scan_protocol: GenePix Results 3

tag: cell line

value: HeLa


title: EosWTCD25+#1

tag: genotype/variation


title: rhTIMP1 biological rep 2

description: rhTIMP1 biological rep 2


title: rhTIMP1 biological rep 1

description: rhTIMP1 biological rep 1


title: Vehicle biological rep 2

description: Vehicle biological rep 2


title: TGCG_Decoy_1

description:
Simple annotation: Cell-cycle, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2007-09/76667.gif
Genetic Modification: TGCGCANK


title: msl1Δ_exp2

city: Seoul

first: Yong-Sun

last: Bahn

address: 134 Shinchon-dong Seodaemun-gu

department: Biotechnology

country: South Korea

institute: Yonsei University

description: Ctr vs.msl1Δ_exp2

hyb_protocol: Microarray Hybridization and Washing: A C. neoformans serotype D 70-mer microarray slide containing 7,936 probes (Duke University) was pre-hybridized at 42°C in 60 ml of pre-hybridization buffer (42.4 ml sterile distilled water, 2 ml 30% BSA (Sigma), 600 µl 10% SDS, 15 ml 20x SSC (Saline-Sodium Citrate, 3 M NaCl, 0.3 M Na-citrate, pH 7.0)), washed with distilled water and isopropanol, and dried by brief centrifugation (1000rpm, 2 min). The Cy3- and Cy5-labeled cDNA samples were combined, concentrated through a Microcon30 filter, and vacuum-dried. The dried cDNA samples were resuspended with 24 µl of 1x hybridization buffer (250 µl 50% formamide, 125 µl 20x SSC, 5 µl 10% SDS, 120 µl dH2O, total 500 µl), added with 1 µl polyA tail DNA (Sigma), further incubated at 100°C for 3 min and allowed to cool for 5 min at room temperature. The microarray slides were aligned into the hybridization chamber (DieTech), removed of any dust, and covered by Lifterslips (Erie Scientific). The Cy3/Cy5-labeled cDNA samples were applied in between Lifterslips and slides. To prevent slides from drying, 5 ml of 3x SSC buffer was applied into the hybridization chamber, which were subsequently incubated for 16 hr at 42°C. After incubation, the microarray slides were washed with three different washing buffers (wash buffer 1 (10 ml 20x SSC, 600 µl 10% SDS, 189.4 ml dH2O, preheated at 42°C), wash buffer 2 (3.5 ml 20x SSC, 346.5 ml dH2O), wash buffer 3 (0.88 ml 20x SSC, 349.12 ml dH2O)) for 2, 5, and 5 min, respectively, on an orbital shaker. Three independent DNA microarrays with 3 independent biological replicates were performed for each strain.

scan_protocol: After hybridization and washing, the microarray slides were scanned with a GenePix 4100A scanner (Axon Instrument) and the signals were analyzed with GenePix Pro (Ver. 4.0) and gal file (http://genome.wustl.edu/activity/ma/cneoformans).

data_processing: Since total RNAs isolated from serotype A C. neoformans strains were hybridized on microarray slides printed with serotype D 70-mer oligonucleotide sequences, the serotype A gene sequences were mapped to those of the serotype D using BLASTN. C. neoformans H99 gene sequences that were updated on 24 November 2008 were downloaded from the Broad institute (http://www.broad.mit.edu/annotation/genome/cryptococcus_neoformans). The serotype D C. neoformans JEC21 gene sequences that were updated on 27 April 2005 were downloaded from JCVI (ftp://ftp.tigr.org/pub/data/Eukaryotic_Projects/c_neoformans/). The functional category of each C. neoformans H99 gene was assigned using the NCBI KOG database (http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi). Using the serotype A gene sequence, each S. cerevisiae gene name or ID listed in the Supplementary Tables of the manuscript was identified by blastp search (e-value cut-off: e-6). For hierarchical and statistical analysis, data transported from GenePix software were analyzed with Acuity (Axon) by employing Lowess normalization (Lowess M log ratio (F532 Mean - B532, F635 Mean - B635)), reliable gene filtering, clustering (standard correlation and average linkage) and zero-transformation, and ANOVA analysis (P<0.05), and Microsoft Excel software (Microsoft).

organism: Cryptococcus neoformans

label_protocol: For cDNA synthesis, the total RNA concentration was adjusted to 1 µg/µl with DEPC-treated water, and 15 µl of the total RNA (15 µg) was added to 1 µl of 5 µg/µl oligo dT (5'-TTTTTTTTTTTTTTTTTTTTV-3')/pdN6 (Amersham, 1:1 mixture of 10 µg/µl, respectively), incubated at 70°C for 10 min, and place on ice for 10 min. Then, 15 µl of cDNA synthesis mixture (3 µl 0.1 M DTT, 0.3 µl RNase inhibitor (Intron), 1.2 µl aa-dUTP (5-(3-aminoallyl)-2'-deoxyuridine 5'-triphosphate)/dNTPs (a mixture of 6 µl dTTP (100 mM), 4 µl aa-dUTP (100 mM), 10 µl dATP (100 mM), 10 µl dCTP (100 mM), 10 µl dGTP (100 mM). 40 µl DEPC-treated water), 1.5 µl RevertAidTM H Minus M-MuLV Reverse Transcriptase (Fermentas), 6 µl RevertAidTM H Minus M-MuLV Reverse Transcriptase buffer, 3 µl DEPC-treated water) was added and incubated at 42°C for 2 hrs. Then, 10 µl of 1 N NaOH and 10 µl of 0.5 M EDTA (pH 8.0) were added and incubated at 65°C for 15 min. After incubation, 25 µl of 1 M HEPES buffer (pH 8.0) and 450 µl of DEPC-treated water were added, and the whole mixture was concentrated through a Microcon30 filter (Millipore) and vacuum-dried for 1 hr. For Cy3 and Cy5 (Amersham) labeling of the prepared cDNA, Cy3 and Cy5 were dissolved in 10 µl DMSO and 1 µl of each dye was aliquoted into separate tubes. The cDNAs prepared as described above were added to 9 µl of 0.05 M Na-bicarbonate (pH 8.0) and incubate at room temperature for 15 min. The cDNAs prepared from pooled reference RNAs were mixed with Cy5 as a control and the cDNAs prepared from each test RNA were mixed with Cy3. Each mixture was further incubated at room temperature for 1 hr in the dark and purified using the QIAquick PCR purification kit (QIAGEN).

growth_protocol: The wild-type H99 strain and msl1Δ (YSB13) mutant strain were grown in 50 ml YPD medium at 30°C for 16 h. Then, 2.5 ml of the overnight culture was inoculated into 50 ml of fresh YPD medium and further incubated for 4 h at 30°C to an optical density of 1.0 at 600 nm (OD600 =1.0).

extract_protocol: For total RNA isolation, the lyophilized cell pellets were added to 3 ml volume of sterile 3 mm glass bead (SIGMUND LINDER), homogenized by shaking, added to 4 ml of TRizol reagent (Tri reagent, Molecular Research Center), and allowed to incubate at room temperature for 5 min. Then, 800 µl of chloroform was added, incubated for 3 min at room temperature, transferred to 14 ml round-bottom tubes (SPL), and centrifuged by 10,000 rpm at 4°C for 15 min (Sorvall SS-34 rotor). Two milliliters of the supernatant was transferred to a new round-bottom tube, 2 ml isopropanol was added, inverted several times, and allowed to incubate for 10 min at room temperature. Then, the mixture was re-centrifuged at 10,000 rpm at 4°C for 10 min, and the pellet was washed with 4 ml of 75% ethanol diluted with diethylpyrocarbonate (DEPC)-treated water and centrifuged at 8,000 rpm at 4°C for 5 min. The pellet was dried and resuspended with 500 µl DEPC-treated water. Concentration and purity of total RNA samples were calculated by measuring OD260nm and gel-electrophoresis, respectively. For control total RNA, all total RNAs prepared from WT and msl1Δ mutant cells grown in conditions described above were pooled (pooled reference RNAs).

treatment_protocol: 50 ml culture was rapidly frozen in liquid nitrogen and lyophilized overnight. The lyophilized cells were subsequently used for total RNA isolation. As biological replicates for DNA microarrays, three independent cultures for each strain were prepared for total RNA isolation.

tag: strain

source_name: Pooled total RNA from all strains

tag: strain/background

value: H99 and YSB13

value: wild-type and msl1Δ

tag: sample type

value: reference


title: msl1Δ_exp1

description: Ctr vs.msl1Δ_exp1


title: E2F_Decoy_1

description:
Simple annotation: Cell-cycle, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2007-09/76663.gif
Genetic Modification: E2F


title: PC 470T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81176.gif

value: common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines

tag: ethnicity

value: Caucasian

tag: age

tag: pre-operation treatment

value: PC 470T

tag: disease free survival


title: KTGG_Decoy_1

description:
Simple annotation: Cell-cycle, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2007-09/76665.gif
Genetic Modification: KTGGYRSAGAA


title: EosKOCD25+#2

source_name: Spleen, CD4+CD25hi Tregs, Eos (Ikzf4) knockout

tag: genetic background

value: Eos (Ikzf4) knockout

tag: Sex

tag: tissue

tag: cell type


title: PC 166T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81186.gif

value: PC 252T

value: prostate


title: EosKOCD25+#1

tag: phenotype markers

tag: exclusion markers

tag: separation method

value: MoFlo Sorter


title: TGCG_Decoy_2

description:
Simple annotation: Cell-cycle, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2007-09/76668.gif
Genetic Modification: TGCGCANK


title: CCAA_Decoy_1

description:
Simple annotation: Cell-cycle, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2007-09/76669.gif
Genetic Modification: CCAATNNSNNNGCG


title: DLD1_PeptideTx_3

city: Plantagenet

first: Madeleine

middle: E.

last: Lemieux

state: ON

address: 275 Main St., Suite 252

country: Canada

institute: Bioinfo

description: Cells treated with 10 µM SAH-BCL9B for 12hrs

hyb_protocol: 12.5µg of fragmented, biotinylated cDNA was hybridized according to the standard Affymetrix protocol for the Human U133 Plus 2.0 array.

scan_protocol: Standard Affymetrix protocol.

data_processing: RMA probe summarization and normalization using the Bioconductor affy package (http://www.bioconductor.org).

source_name: DLD1 cells

label_protocol: Biotinylated cRNA was prepared from 100ng total RNA using the Affymetrix GeneChip 3’ IVT Express Kit according to the manufacturer's protocol.

extract_protocol: After treatment, cells were washed in PBS, resuspended in Trizol (Invitrogen) and purified according to manufacturer's instruction with the Qiagen RNeasy kit.

treatment_protocol: Triplicate cultures of 5x10^6 DLD1 cells were treated with 10µM DMSO or SAH-BCL9 peptides for 12 hrs prior to RNA extraction.

value: Colorectal adenocarcinoma cell line

value: DLD1 cells

tag: treatment


title: KTGG_Decoy_2

description:
Simple annotation: Cell-cycle, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2007-09/76666.gif
Genetic Modification: KTGGYRSAGAA

tag: cell line


title: ACTW_Decoy_1

description:
Simple annotation: Cell-cycle, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2007-09/76671.gif
Genetic Modification: ACTWSNACTNY


title: PC 485T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81183.gif

tag: reference

tag: individual

value: PC 498T


title: DLD1_PeptideTx_2


title: msl1Δ_exp3

description: Ctr vs.msl1Δ_exp3

tag: strain

tag: genotype/variation

tag: strain/background


title: WT_exp3

description: Ctr vs.WT_exp3

organism: Cryptococcus neoformans H99

source_name: WT

value: wild-type

tag: sample type


title: PC 363N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81169.gif

value: PC 363N

tag: disease state

value: Normal


title: DLD1_PeptideTx_1


title: CD25+Xbp1WT

value: wildtype

tag: age

value: 8 weeks

value: female

value: spleen

value: regulatory T cells (Tregs)


title: ACTW_Decoy_2

description:
Simple annotation: Cell-cycle, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2007-09/76672.gif
Genetic Modification: ACTWSNACTNY

value: HeLa


title: PC 527N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81171.gif

value: common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines

value: PC 527N


title: PC 453T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81188.gif

tag: ethnicity

value: Caucasian

tag: pre-operation treatment

value: PC 375T

tag: disease free survival


title: CD25+Xbp1KO#2

source_name: Spleen, CD4+CD25hi Tregs, Xbp1 knockout

tag: genetic background

value: Xbp1 knockout

tag: Sex

tag: tissue

tag: cell type

value: MoFlo Sorter


title: PC 480N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/80964.gif

source_name: Human Reference RNA

source_name: PC 480N RNA

value: PC 480N

value: prostate


title: WT_exp1

description: Ctr vs.WT_exp1

value: wild-type

value: H99 and YSB13

value: wild-type and msl1Δ

value: reference


title: WT_exp2

description: Ctr vs.WT_exp2


title: DLD1_Vehicle_3

description: Control cells exposed for 12hrs to DMSO

value: Colorectal adenocarcinoma cell line

value: DLD1 cells

tag: treatment

value: vehicle


title: CD25+Xbp1WT#2

value: wildtype

value: 8 weeks

value: female

value: spleen

value: regulatory T cells (Tregs)

tag: phenotype markers

tag: exclusion markers

tag: separation method


title: PRO_96hr_femaleBrain_validation_2

status: Public on Aug 22 2012

city: Cincinnati

first: Rong-Lin

last: Wang

address: 26 W MLK Dr

institute: US EPA

description:
10938_1_4_rProcessedSignal
10938_1_4_gProcessedSignal
for gene classifier validation

hyb_protocol: Equal amounts of Cy3- and Cy5-labeled cRNA (750 ng each) were hybridized to a zebrafish oligo microarray for 17 h at 65C. The hybridized microarrays were then washed according to the manufacturer's protocol.

scan_protocol: Scanned by a 16-bit Agilent G2565BA scanner at 10-um resolution with the red and green photomultiplier tubes set to 100% and a scan area of 61 by 21.6 mm

data_processing:
Text output of individual samples (rProcessedSignal, gProcessedSignal) from Agilent Feature Extraction software were filtered according to Agilent recommendations (feature saturation, uniformity, pixel population consistency, signal strength relative to background; Agilent Technologies Training Manual, version 4.5).  Samples were then organized either by tissue types or combined. Missing data were imputed by KNNimputer (Troyanskaya et al., 2001, Bioinformatics). This was followed by thresholding, log2 transformation, per chip normalization to 75th percentile, and per gene normation to the median of all samples [available as Series supplementary files].

The biological samples for controls were duplicated between TRI_96hr_femaleOvary and TRI_96hr_femaleOvaryLowDose as well as between TRI_96hr_maleTestis and TRI_96hr_maleTestisLowDose. These redundant controls were therefore included only once in their respective matrix files (classifier_discovery_ovary.txt, classifier_discovery_testis.txt), giving rise to their odd number of columns. In total, there are five processed/normalized matrix files either for classifier discovery or validation:

The numeric identifiers in the data matrix column headers (Sample Description field above) correspond to the unique microarray identifiers in the file names of raw text files. For example, rProcessedSignal'612' for US23502387_251322310'612'_S01_22k.txt, and Ave'10237_1_2'rProcessedSignal for US23502303_2515064'10237'_S01_GE2-v5_95_Feb07_'1_2'.txt

classifier_discovery_brain.txt: 80 treated + 80 control
classifier_discovery_ovary.txt: 105 treated + 100 control
classifier_discovery_testis.txt: 84 treated + 79 control
classifier_discovery_allTissue.txt: all three tissues combined plus 21 liver samples, 290 treated + 290 control
classifier_validation.txt: 24 treated + 28 control.

The processed/normalized data files contain rProcessedSignal and gProcessedSignal (log2 transformed, per chip and per gene normalized) from the indicated samples.

organism: Danio rerio

source_name: brain_female_PRO_96 hr

label_protocol: Purified total RNA samples were shipped overnight on dryice to an Agilent-certified contract laboratory (Cogenics, Morrisville, NC 27560, USA), where all microarray gene expression profiling was performed. The quantity and quality of the RNA samples were assessed with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies,Wilmington, DE, USA) and an Agilent 2100 bioanalyzer. One microgram of total RNA from each sample was amplified and labeled with a fluorescent dye (either Cy3 or Cy5) with the use of a low-RNA input linear amplification labeling kit following the manufacturer's protocol). The quantity and purity of the resulting fluorescently labeled cRNA was evaluated with the Nanodrop ND-1000 spectrophotometer, and the size distribution was determined with an Agilent bioanalyzer.

growth_protocol: Reproductively mature fish were obtained from an onsite culture unit at the US EPA National Health and Human Effects Research laboratory. Three days before the initiation of exposure, fish were randomly loaded into tanks receiving a continuous flow of Lake Superior water (USA) pumped from 200 m offshore at a depth of 20 m (mesh size 1 um, flow rate 45 ml/min).  Each tank held 10 males and 10 females.

extract_protocol: Tissues were removed from RNAlater and placed on ice in 1.5-ml RNase-free microcentrifuge tubes (Ambion) containing 1 ml of TriReagent (Molecular Research Center,Cincinnati, OH)and then placed on ice for a short duration.  They were homogenized by physical disruption at 30 Hz for 5 min in a Retsch MM300 mixer mill (Retsch Laboratory Equipment, Newtown, PA, USA). Individual homogenates were immediately processed or stored at 80C in TriReagent. Total RNA was extracted following the manufacturer's protocol. Briefly, 100 ul of 1-bromo-3-chloropropane (BCP, Molecular Research Center) were added to each homogenized tissue in 1 ml of TriReagent, vortexed, and incubated at room temperature for 10 min. The BCP/TriReagent mixture was then centrifuged at 12,000 g for 15 min at 4C. The aqueous phase was transferred to a new RNase-free microcentrifuge tube containing 500 ul of 100% isopropanol and then gently agitated. Precipitated samples were centrifuged at 12,000 g for 10 min at 4C, and supernatants were decanted. One milliliter of 75% ethanol was added to the precipitant, and samples were spot vortexed and centrifuged for 10 min at 12,000 g at 4C. Supernatant was decanted, and the remaining volume was aspirated. The RNA pellets were resuspended in nuclease-free water (Ambion) by incubation at 4C for several hours. To remove any trace organic contaminants, RNA samples were reprecipitated using a 0.1 volume of 3 M sodium acetate (Ambion) and two volumes of 100% ethanol and then incubating at 80C for at least 20 min. Precipitated RNA was centrifuged at 12,000 g at 4C for 20 min, and the supernatant was removed. The RNA was resuspended in RNase-free water at 4C for several hours. The RNA was then quantified spectrophotometrically, and light absorbance at 260 and 280 nm was used as a measure of relative purity and quantity. The RNA samples were analyzed for structural integrity using either agarose gel electrophoresis or the Bioanalyzer NanoRNA kit (Agilent Technologies, Palo Alto, CA, USA). All RNA displayed 260:280-nm ratios of 1.7 or greater and had 28S:18S ratios of approximately two. Extracted total RNA was stored at 80C until subsequent use.

treatment_protocol: Reproductively mature male and female zebrafish were exposed to a continuous flow of test chemical (an analytically-confirmed concentration and a control), delivered in water (with no solvent), for 24, 48, or 96 hrs

tag: strain

value: AB

value: 5 months

tag: gender

value: brain

tag: treated with

value: PRO (prochloraz) 500 ug/L for 48hr

source_name: brain_female_water control_96 hr

value: in water control for 96 hr


title: PRO_96hr_femaleOvary_validation_2

description:
10938_1_3_rProcessedSignal
10938_1_3_gProcessedSignal
for gene classifier validation

source_name: ovary_female_PRO_96 hr

tag: genotype/variation

value: wild-type

value: ovary

value: PRO (prochloraz) 500 ug/L for 96hr

source_name: ovary_female_water control_96 hr


title: PRO_96hr_femaleOvary_validation_4

description:
10941_1_1_rProcessedSignal
10941_1_1_gProcessedSignal
for gene classifier validation


title: PRO_96hr_femaleOvary_validation_3

description:
10939_1_2_rProcessedSignal
10939_1_2_gProcessedSignal
for gene classifier validation


title: PRO_48hr_femaleOvary_validation_5

description:
10940_1_4_rProcessedSignal
10940_1_4_gProcessedSignal
for gene classifier validation

source_name: ovary_female_PRO_48 hr

source_name: ovary_female_water control_48 hr

value: in water control for 48 hr


title: PRO_96hr_femaleBrain_validation_3

description:
10939_1_3_rProcessedSignal
10939_1_3_gProcessedSignal
for gene classifier validation
both channels had the same biological control sample

value: water control for 96 hr


title: PRO_96hr_femaleBrain_validation_5

description:
10941_1_2_rProcessedSignal
10941_1_2_gProcessedSignal
for gene classifier validation


title: PRO_96hr_femaleBrain_validation_4

description:
10940_1_3_rProcessedSignal
10940_1_3_gProcessedSignal
for gene classifier validation


title: PRO_96hr_femaleBrain_validation_1

description:
10937_1_1_rProcessedSignal
10937_1_1_gProcessedSignal
for gene classifier validation


title: PRO_96hr_femaleOvary_validation_1

description:
10934_1_2_rProcessedSignal
10934_1_2_gProcessedSignal
for gene classifier validation


title: PRO_48hr_femaleOvary_validation_4

description:
10938_1_2_rProcessedSignal
10938_1_2_gProcessedSignal
for gene classifier validation


title: E2F_Decoy_2

description:
Simple annotation: Cell-cycle, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2007-09/76664.gif
Genetic Modification: E2F

tag: cell line

value: HeLa


title: PRO_48hr_femaleOvary_validation_3

description:
10937_1_4_rProcessedSignal
10937_1_4_gProcessedSignal
for gene classifier validation

tag: age


title: PRO_48hr_femaleBrain_validation_4

description:
10940_1_1_rProcessedSignal
10940_1_1_gProcessedSignal
for gene classifier validation

source_name: brain_female_PRO_48 hr

source_name: brain_female_water control_48 hr


title: PRO_48hr_femaleOvary_validation_1

description:
10935_1_4_rProcessedSignal
10935_1_4_gProcessedSignal
for gene classifier validation


title: PRO_48hr_femaleOvary_validation_2

description:
10937_1_2_rProcessedSignal
10937_1_2_gProcessedSignal
for gene classifier validation
both channels had the same biological control sample

value: water control for 48 hr


title: DLD1_Vehicle_1

description: Control cells exposed for 12hrs to DMSO

value: Colorectal adenocarcinoma cell line

value: DLD1 cells

value: vehicle


title: CD25+Xbp1KO

value: Xbp1 knockout

value: 8 weeks

value: female

value: spleen

value: MoFlo Sorter


title: PC 455N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81194.gif

source_name: reference RNA

tag: reference

value: common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines

tag: individual

value: PC 455N

tag: disease state

value: Normal

value: prostate


title: DLD1_Vehicle_2

description: Control cells exposed for 12hrs to DMSO


title: PRO_48hr_femaleBrain_validation_3

description:
10939_1_4_rProcessedSignal
10939_1_4_gProcessedSignal
for gene classifier validation

value: AB

value: wild-type

value: 5 months

value: brain

value: PRO (prochloraz) 500 ug/L for 48hr


title: FLU_96hr_femaleOvary_validation_5

description:
10941_1_3_rProcessedSignal
10941_1_3_gProcessedSignal
for gene classifier validation
both channels had the same biological control sample

value: ovary

value: water control for 96 hr

value: in water control for 96 hr


title: PRO_48hr_femaleBrain_validation_2

description:
10935_1_2_rProcessedSignal
10935_1_2_gProcessedSignal
for gene classifier validation

value: in water control for 48 hr


title: PRO_48hr_femaleBrain_validation_1

description:
10934_1_3_rProcessedSignal
10934_1_3_gProcessedSignal
for gene classifier validation


title: FLU_96hr_femaleOvary_validation_3

description:
10938_1_1_rProcessedSignal
10938_1_1_gProcessedSignal
for gene classifier validation

source_name: ovary_female_FLU_96 hr

value: FLU (flutamide) 1700 ug/L for 96hr


title: FLU_96hr_femaleOvary_validation_4

description:
10939_1_1_rProcessedSignal
10939_1_1_gProcessedSignal
for gene classifier validation

value: female


title: FLU_96hr_femaleOvary_validation_2

description:
10935_1_3_rProcessedSignal
10935_1_3_gProcessedSignal
for gene classifier validation


title: FLU_48hr_femaleOvary_validation_5

description:
10941_1_4_rProcessedSignal
10941_1_4_gProcessedSignal
for gene classifier validation
both channels had the same biological control sample

value: water control for 48 hr


title: FLU_48hr_femaleOvary_validation_4

description:
10940_1_2_rProcessedSignal
10940_1_2_gProcessedSignal
for gene classifier validation

source_name: ovary_female_FLU_48 hr

value: FLU (flutamide) 1700 ug/L for 48hr


title: FLU_96hr_femaleOvary_validation_1

description:
10935_1_1_rProcessedSignal
10935_1_1_gProcessedSignal
for gene classifier validation


title: FLU_48hr_femaleOvary_validation_2

description:
10934_1_4_rProcessedSignal
10934_1_4_gProcessedSignal
for gene classifier validation


title: FLU_48hr_femaleOvary_validation_1

description:
10934_1_1_rProcessedSignal
10934_1_1_gProcessedSignal
for gene classifier validation


title: PC 501T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81178.gif

value: common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines

tag: ethnicity

value: Caucasian

tag: pre-operation treatment

value: PC 555T

tag: disease free survival


title: VIN_48hr_maleTestis_4

description:
Ave10249_1_3rProcessedSignal
Ave10249_1_3gProcessedSignal
for gene classifier discovery

source_name: testis_male_VIN_48 hr

value: male

tag: tissue

value: testis

value: VIN (vinclozolin) at 1000 ug/L for 48hr

source_name: testis_male_water control_48 hr


title: PC 423N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81170.gif

value: PC 423N

value: Normal

value: prostate


title: FLU_48hr_femaleOvary_validation_3

description:
10937_1_3_rProcessedSignal
10937_1_3_gProcessedSignal
for gene classifier validation

value: AB

value: wild-type

value: 5 months

value: ovary

tag: treatment


title: VIN_96hr_maleTestis_3

description:
Ave10246_1_2rProcessedSignal
Ave10246_1_2gProcessedSignal
for gene classifier discovery

source_name: testis_male_VIN_96 hr

value: VIN (vinclozolin) at 1000 ug/L for 96hr

source_name: testis_male_water control_96 hr

value: in water control for 96 hr


title: VIN_48hr_maleTestis_5

description:
Ave10250_1_4rProcessedSignal
Ave10250_1_4gProcessedSignal
for gene classifier discovery

value: in water control for 48 hr


title: VIN_48hr_maleTestis_2

description:
Ave10245_1_4rProcessedSignal
Ave10245_1_4gProcessedSignal
for gene classifier discovery


title: VIN_48hr_maleTestis_3

description:
Ave10246_1_3rProcessedSignal
Ave10246_1_3gProcessedSignal
for gene classifier discovery


title: VIN_96hr_maleTestis_2

description:
Ave10245_1_3rProcessedSignal
Ave10245_1_3gProcessedSignal
for gene classifier discovery


title: VIN_96hr_maleTestis_1

description:
Ave10233_1_3rProcessedSignal
Ave10233_1_3gProcessedSignal
for gene classifier discovery


title: VIN_96hr_maleTestis_5

description:
Ave10250_1_2rProcessedSignal
Ave10250_1_2gProcessedSignal
for gene classifier discovery


title: VIN_24hr_maleTestis_4

description:
Ave10249_1_2rProcessedSignal
Ave10249_1_2gProcessedSignal
for gene classifier discovery

source_name: testis_male_VIN_24 hr

value: VIN (vinclozolin) at 1000 ug/L for 24hr

source_name: testis_male_water control_24 hr

value: in water control for 24 hr


title: VIN_24hr_maleTestis_3

description:
Ave10246_1_4rProcessedSignal
Ave10246_1_4gProcessedSignal
for gene classifier discovery


title: VIN_24hr_maleTestis_5

description:
Ave10250_1_3rProcessedSignal
Ave10250_1_3gProcessedSignal
for gene classifier discovery


title: TRI_96hr_maleTestisLowDose_3

description:
Ave10332_1_3rProcessedSignal
Ave10332_1_3gProcessedSignal
for gene classifier discovery

source_name: testis_male_TRI_96 hr at low dose

value: TRI (trilostane) at 500 µg/liter for 96hr

value: in water control for 96 h


title: VIN_96hr_maleTestis_4

description:
Ave10249_1_4rProcessedSignal
Ave10249_1_4gProcessedSignal
for gene classifier discovery

value: male


title: TRI_96hr_maleTestisLowDose_1

description:
Ave10330_1_4rProcessedSignal
Ave10330_1_4gProcessedSignal
for gene classifier discovery

value: testis


title: TRI_96hr_maleTestis_2

description:
Ave10208_1_2rProcessedSignal
Ave10208_1_2gProcessedSignal
for gene classifier discovery
control sample identical to that of US23502303_251506410331_S01_GE2-v5_95_Feb07_1_2.txt

source_name: testis_male_TRI_96 hr

value: TRI (trilostane) at 2500 µg/liter for 96hr


title: VIN_24hr_maleTestis_1

description:
Ave10233_1_4rProcessedSignal
Ave10233_1_4gProcessedSignal
for gene classifier discovery


title: VIN_48hr_maleTestis_1

description:
Ave10233_1_2rProcessedSignal
Ave10233_1_2gProcessedSignal
for gene classifier discovery

value: VIN (vinclozolin) at 1000 ug/L for 48hr


title: VIN_24hr_maleTestis_2

description:
Ave10245_1_2rProcessedSignal
Ave10245_1_2gProcessedSignal
for gene classifier discovery


title: PC 430T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81175.gif

value: common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines

value: Caucasian

value: PC 343T


title: TRI_96hr_maleTestisLowDose_4

description:
Ave10333_1_3rProcessedSignal
Ave10333_1_3gProcessedSignal
for gene classifier discovery

value: AB

value: wild-type


title: TRI_96hr_maleTestisLowDose_2

description:
Ave10331_1_2rProcessedSignal
Ave10331_1_2gProcessedSignal
for gene classifier discovery

value: 5 months


title: TRI_96hr_maleTestisLowDose_5

description:
Ave10334_1_2rProcessedSignal
Ave10334_1_2gProcessedSignal
for gene classifier discovery


title: TRI_96hr_maleTestis_5

description:
Ave10212_1_2rProcessedSignal
Ave10212_1_2gProcessedSignal
for gene classifier discovery
control sample identical to that of US23502303_251506410334_S01_GE2-v5_95_Feb07_1_2.txt


title: TRI_96hr_maleTestis_3

description:
Ave10209_1_3rProcessedSignal
Ave10209_1_3gProcessedSignal
for gene classifier discovery
control sample identical to that of US23502303_251506410332_S01_GE2-v5_95_Feb07_1_3.txt


title: TRI_96hr_maleTestis_1

description:
Ave10207_1_4rProcessedSignal
Ave10207_1_4gProcessedSignal
for gene classifier discovery
control sample identical to that of US23502303_251506410330_S01_GE2-v5_95_Feb07_1_4.txt


title: TRI_96hr_maleTestis_4

description:
Ave10210_1_3rProcessedSignal
Ave10210_1_3gProcessedSignal
for gene classifier discovery
control sample identical to that of US23502303_251506410333_S01_GE2-v5_95_Feb07_1_3.txt


title: TRI_96hr_femaleOvaryLowDose_4

description:
Ave10333_1_2rProcessedSignal
Ave10333_1_2gProcessedSignal
for gene classifier discovery

source_name: ovary_female_TRI_96 hr at low dose

value: female

value: ovary


title: TRI_96hr_femaleOvaryLowDose_2

description:
Ave10331_1_3rProcessedSignal
Ave10331_1_3gProcessedSignal
for gene classifier discovery

source_name: ovary_female_water control_96 hr

value: in water control for 96 hr


title: TRI_48hr_maleTestis_4

description:
Ave10210_1_4rProcessedSignal
Ave10210_1_4gProcessedSignal
for gene classifier discovery

source_name: testis_male_TRI_48 hr

value: TRI (trilostane) at 2500 µg/liter for 48hr

value: in water control for 48 hr


title: TRI_96hr_femaleOvary_5

description:
Ave10334_1_3rProcessedSignal
Ave10334_1_3gProcessedSignal
for gene classifier discovery
control sample identical to that of US23502303_251506410334_S01_GE2-v5_95_Feb07_1_4.txt

source_name: ovary_female_TRI_96 hr


title: TRI_96hr_femaleOvaryLowDose_1

description:
Ave10330_1_2rProcessedSignal
Ave10330_1_2gProcessedSignal
for gene classifier discovery

value: TRI (trilostane) at 500 µg/liter for 96hr


title: TRI_96hr_femaleOvary_3

description:
Ave10332_1_2rProcessedSignal
Ave10332_1_2gProcessedSignal
for gene classifier discovery
control sample identical to that of US23502303_251506410332_S01_GE2-v5_95_Feb07_1_4.txt


title: TRI_24hr_maleTestis_5

description:
Ave10212_1_4rProcessedSignal
Ave10212_1_4gProcessedSignal
for gene classifier discovery

source_name: testis_male_TRI_24 hr

value: TRI (trilostane) at 2500 µg/liter for 24hr

value: in water control for 24 hr


title: TRI_24hr_maleTestis_2

description:
Ave10208_1_3rProcessedSignal
Ave10208_1_3gProcessedSignal
for gene classifier discovery

value: male

value: testis


title: TRI_48hr_maleTestis_2

description:
Ave10208_1_4rProcessedSignal
Ave10208_1_4gProcessedSignal
for gene classifier discovery


title: TRI_48hr_maleTestis_1

description:
Ave10207_1_3rProcessedSignal
Ave10207_1_3gProcessedSignal
for gene classifier discovery


title: TRI_24hr_maleTestis_4

description:
Ave10210_1_2rProcessedSignal
Ave10210_1_2gProcessedSignal
for gene classifier discovery


title: TRI_48hr_maleTestis_5

description:
Ave10212_1_3rProcessedSignal
Ave10212_1_3gProcessedSignal
for gene classifier discovery


title: TRI_24hr_maleTestis_1

description:
Ave10207_1_2rProcessedSignal
Ave10207_1_2gProcessedSignal
for gene classifier discovery


title: TRB_96hr_femaleLiver_1

description:
Ave10358_1_3rProcessedSignal
Ave10358_1_3gProcessedSignal
for gene classifier discovery

source_name: liver_female_TRB_96 hr

value: liver

value: TRB (17 -trenbolone) 3 ug/L for 96hr

source_name: liver_female_water control_96 hr


title: TRI_24hr_maleTestis_3

description:
Ave10209_1_4rProcessedSignal
Ave10209_1_4gProcessedSignal
for gene classifier discovery


title: TRB_96hr_femaleLiver_5

description:
Ave10362_1_3rProcessedSignal
Ave10362_1_3gProcessedSignal
for gene classifier discovery


title: TRB_96hr_femaleLiver_4

description:
Ave10361_1_4rProcessedSignal
Ave10361_1_4gProcessedSignal
for gene classifier discovery


title: TRB_96hr_femaleLiver_3

description:
Ave10360_1_2rProcessedSignal
Ave10360_1_2gProcessedSignal
for gene classifier discovery


title: PRO_96hr_maleTestis_5

description:
Ave10095_1_2rProcessedSignal
Ave10095_1_2gProcessedSignal
for gene classifier discovery

source_name: testis_male_PRO_96 hr

value: PRO (prochloraz) 500 ug/L for 96hr


title: PRO_96hr_maleTestis_4

description:
Ave10092_1_1rProcessedSignal
Ave10092_1_1gProcessedSignal
for gene classifier discovery


title: TRB_96hr_femaleLiver_2

description:
Ave10359_1_4rProcessedSignal
Ave10359_1_4gProcessedSignal
for gene classifier discovery


title: PRO_96hr_femaleBrain_5

description:
Ave10083_1_4rProcessedSignal
Ave10083_1_4gProcessedSignal
for gene classifier discovery

source_name: brain_female_PRO_96 hr

value: brain

source_name: brain_female_water control_96 hr


title: PRO_96hr_maleTestis_2

description:
Ave10074_1_1rProcessedSignal
Ave10074_1_1gProcessedSignal
for gene classifier discovery

value: AB


title: PRO_96hr_maleTestis_1

description:
Ave10073_1_4rProcessedSignal
Ave10073_1_4gProcessedSignal
for gene classifier discovery

value: wild-type


title: PRO_96hr_femaleBrain_4

description:
Ave10094_1_2rProcessedSignal
Ave10094_1_2gProcessedSignal
for gene classifier discovery

value: 5 months


title: TRI_48hr_maleTestis_3

description:
Ave10209_1_2rProcessedSignal
Ave10209_1_2gProcessedSignal
for gene classifier discovery

source_name: testis_male_water control_48 hr


title: PRO_96hr_femaleBrain_2

description:
Ave10073_1_2rProcessedSignal
Ave10073_1_2gProcessedSignal
for gene classifier discovery

value: female


title: PRO_96hr_femaleBrain_3

description:
Ave10092_1_2rProcessedSignal
Ave10092_1_2gProcessedSignal
for gene classifier discovery


title: PRO_96hr_femaleOvary_1

description:
Ave10074_1_3rProcessedSignal
Ave10074_1_3gProcessedSignal
for gene classifier discovery

source_name: ovary_female_PRO_96 hr

value: ovary


title: PRO_48hr_maleTestis_5

description:
Ave10095_1_1rProcessedSignal
Ave10095_1_1gProcessedSignal
for gene classifier discovery

source_name: testis_male_PRO_48 hr

value: PRO (prochloraz) 500 ug/L for 48hr


title: PRO_96hr_maleTestis_3

description:
Ave10075_1_1rProcessedSignal
Ave10075_1_1gProcessedSignal
for gene classifier discovery

source_name: testis_male_water control_96 hr

value: in water control for 96 hr


title: PRO_48hr_maleTestis_3

description:
Ave10075_1_2rProcessedSignal
Ave10075_1_2gProcessedSignal
for gene classifier discovery

value: in water control for 48 hr


title: PRO_48hr_femaleBrain_4

description:
Ave10083_1_2rProcessedSignal
Ave10083_1_2gProcessedSignal
for gene classifier discovery

source_name: brain_female_PRO_48 hr

source_name: brain_female_water control_48 hr


title: PRO_48hr_femaleBrain_5

description:
Ave10094_1_1rProcessedSignal
Ave10094_1_1gProcessedSignal
for gene classifier discovery


title: PRO_48hr_maleTestis_1

description:
Ave10073_1_1rProcessedSignal
Ave10073_1_1gProcessedSignal
for gene classifier discovery


title: MUS_96hr_femaleBrain_5

description:
Ave10325_1_3rProcessedSignal
Ave10325_1_3gProcessedSignal
for gene classifier discovery

source_name: brain_female_MUS_96 hr

value: MUS (muscimol) 500 ug/L for 96hr


title: MUS_96hr_maleBrain_5

description:
Ave10295_1_2rProcessedSignal
Ave10295_1_2gProcessedSignal
for gene classifier discovery

source_name: brain_male_MUS_96 hr

source_name: brain_male_water control_96 hr


title: MUS_96hr_maleBrain_4

description:
Ave10294_1_4rProcessedSignal
Ave10294_1_4gProcessedSignal
for gene classifier discovery


title: PRO_48hr_femaleBrain_3

description:
Ave10074_1_2rProcessedSignal
Ave10074_1_2gProcessedSignal
for gene classifier discovery


title: MUS_96hr_maleBrain_2

description:
Ave10276_1_3rProcessedSignal
Ave10276_1_3gProcessedSignal
for gene classifier discovery


title: MUS_96hr_femaleBrain_4

description:
Ave10324_1_4rProcessedSignal
Ave10324_1_4gProcessedSignal
for gene classifier discovery


title: MUS_96hr_femaleBrain_2

description:
Ave10319_1_4rProcessedSignal
Ave10319_1_4gProcessedSignal
for gene classifier discovery


title: PRO_48hr_maleTestis_2

description:
Ave10074_1_4rProcessedSignal
Ave10074_1_4gProcessedSignal
for gene classifier discovery


title: MUS_96hr_maleBrain_1

description:
Ave10275_1_4rProcessedSignal
Ave10275_1_4gProcessedSignal
for gene classifier discovery


title: PRO_48hr_maleTestis_4

description:
Ave10084_1_3rProcessedSignal
Ave10084_1_3gProcessedSignal
for gene classifier discovery


title: MUS_48hr_maleBrain_4

description:
Ave10294_1_3rProcessedSignal
Ave10294_1_3gProcessedSignal
for gene classifier discovery

source_name: brain_male_MUS_48 hr

value: MUS (muscimol) 500 ug/L for 48hr

source_name: brain_male_water control_48 hr


title: MUS_48hr_maleBrain_2

description:
Ave10276_1_4rProcessedSignal
Ave10276_1_4gProcessedSignal
for gene classifier discovery


title: MUS_48hr_femaleBrain_5

description:
Ave10325_1_4rProcessedSignal
Ave10325_1_4gProcessedSignal
for gene classifier discovery

source_name: brain_female_MUS_48 hr


title: MUS_96hr_femaleBrain_1

description:
Ave10277_1_3rProcessedSignal
Ave10277_1_3gProcessedSignal
for gene classifier discovery


title: MUS_48hr_maleBrain_5

description:
Ave10295_1_4rProcessedSignal
Ave10295_1_4gProcessedSignal
for gene classifier discovery


title: MUS_48hr_femaleBrain_4

description:
Ave10324_1_2rProcessedSignal
Ave10324_1_2gProcessedSignal
for gene classifier discovery


title: MUS_48hr_maleBrain_1

description:
Ave10275_1_2rProcessedSignal
Ave10275_1_2gProcessedSignal
for gene classifier discovery


title: MUS_48hr_femaleBrain_2

description:
Ave10319_1_3rProcessedSignal
Ave10319_1_3gProcessedSignal
for gene classifier discovery


title: MUS_48hr_femaleBrain_3

description:
Ave10320_1_4rProcessedSignal
Ave10320_1_4gProcessedSignal
for gene classifier discovery


title: PRO_48hr_femaleBrain_1

description:
Ave10072_1_1rProcessedSignal
Ave10072_1_1gProcessedSignal
for gene classifier discovery


title: MUS_48hr_maleBrain_3

description:
Ave10293_1_2rProcessedSignal
Ave10293_1_2gProcessedSignal
for gene classifier discovery


title: MUS_96hr_maleBrain_3

description:
Ave10293_1_3rProcessedSignal
Ave10293_1_3gProcessedSignal
for gene classifier discovery


title: KET_96hr_maleTestis_5

description:
Ave10337_1_4rProcessedSignal
Ave10337_1_4gProcessedSignal
for gene classifier discovery

source_name: testis_male_KET_96 hr

value: KET (ketoconazole) 370 ug/L for 96hr


title: MUS_48hr_femaleBrain_1

description:
Ave10277_1_2rProcessedSignal
Ave10277_1_2gProcessedSignal
for gene classifier discovery


title: PRO_48hr_femaleBrain_2

description:
Ave10073_1_3rProcessedSignal
Ave10073_1_3gProcessedSignal
for gene classifier discovery


title: KET_96hr_maleTestis_4

description:
Ave10336_1_3rProcessedSignal
Ave10336_1_3gProcessedSignal
for gene classifier discovery

value: male


title: KET_96hr_maleTestis_3

description:
Ave10335_1_2rProcessedSignal
Ave10335_1_2gProcessedSignal
for gene classifier discovery

value: testis


title: MUS_96hr_femaleBrain_3

description:
Ave10320_1_2rProcessedSignal
Ave10320_1_2gProcessedSignal
for gene classifier discovery


title: KET_96hr_maleTestis_2

description:
Ave10292_1_4rProcessedSignal
Ave10292_1_4gProcessedSignal
for gene classifier discovery


title: KET_96hr_maleTestis_1

description:
Ave10291_1_2rProcessedSignal
Ave10291_1_2gProcessedSignal
for gene classifier discovery


title: KET_96hr_maleLiver_5

description:
Ave10337_1_2rProcessedSignal
Ave10337_1_2gProcessedSignal
for gene classifier discovery

source_name: liver_male_KET_96 hr

value: liver

source_name: liver_male_water control_96 hr


title: KET_96hr_maleLiver_3

description:
Ave10335_1_3rProcessedSignal
Ave10335_1_3gProcessedSignal
for gene classifier discovery


title: KET_96hr_maleLiver_4

description:
Ave10336_1_4rProcessedSignal
Ave10336_1_4gProcessedSignal
for gene classifier discovery


title: KET_96hr_maleBrain_5

description:
Ave10295_1_3rProcessedSignal
Ave10295_1_3gProcessedSignal
for gene classifier discovery

source_name: brain_male_KET_96 hr


title: KET_96hr_maleBrain_3

description:
Ave10293_1_4rProcessedSignal
Ave10293_1_4gProcessedSignal
for gene classifier discovery


title: KET_96hr_maleBrain_2

description:
Ave10276_1_2rProcessedSignal
Ave10276_1_2gProcessedSignal
for gene classifier discovery


title: KET_96hr_maleBrain_4

description:
Ave10294_1_2rProcessedSignal
Ave10294_1_2gProcessedSignal
for gene classifier discovery


title: KET_96hr_maleLiver_1

description:
Ave10291_1_4rProcessedSignal
Ave10291_1_4gProcessedSignal
for gene classifier discovery


title: KET_96hr_maleLiver_2

description:
Ave10292_1_3rProcessedSignal
Ave10292_1_3gProcessedSignal
for gene classifier discovery


title: KET_96hr_femaleBrain_2

description:
Ave10319_1_2rProcessedSignal
Ave10319_1_2gProcessedSignal
for gene classifier discovery

source_name: brain_female_KET_96 hr

source_name: brain_female_water control_96 hr


title: KET_96hr_femaleBrain_1

description:
Ave10277_1_4rProcessedSignal
Ave10277_1_4gProcessedSignal
for gene classifier discovery


title: S 07 8980T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81189.gif

source_name: reference RNA

value: common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines

value: prostate


title: KET_96hr_femaleBrain_3

description:
Ave10320_1_3rProcessedSignal
Ave10320_1_3gProcessedSignal
for gene classifier discovery

value: brain


title: KET_96hr_femaleLiver_2

description:
Ave10292_1_2rProcessedSignal
Ave10292_1_2gProcessedSignal
for gene classifier discovery

source_name: liver_female_KET_96 hr

value: AB

source_name: liver_female_water control_96 hr


title: KET_96hr_femaleLiver_5

description:
Ave10344_1_2rProcessedSignal
Ave10344_1_2gProcessedSignal
for gene classifier discovery

value: wild-type


title: KET_96hr_femaleLiver_3

description:
Ave10335_1_4rProcessedSignal
Ave10335_1_4gProcessedSignal
for gene classifier discovery

value: 5 months


title: KET_96hr_femaleLiver_1

description:
Ave10291_1_3rProcessedSignal
Ave10291_1_3gProcessedSignal
for gene classifier discovery

value: female


title: KET_96hr_femaleBrain_4

description:
Ave10324_1_3rProcessedSignal
Ave10324_1_3gProcessedSignal
for gene classifier discovery


title: KET_96hr_femaleBrain_5

description:
Ave10325_1_2rProcessedSignal
Ave10325_1_2gProcessedSignal
for gene classifier discovery


title: KET_96hr_femaleLiver_4

description:
Ave10336_1_2rProcessedSignal
Ave10336_1_2gProcessedSignal
for gene classifier discovery


title: KET_96hr_maleBrain_1

description:
Ave10275_1_3rProcessedSignal
Ave10275_1_3gProcessedSignal
for gene classifier discovery


title: 26_HG1st_C12_con_upf17_upf

city: Perth

first: Sulev

last: Koks

state: Western Australia

address: 90 South Street

department: Centre for Molecular Medicine and Innovative Therapeutics

country: Australia

institute: Murdoch University

description:
26_C12
PBMC gene expression data.

hyb_protocol: 25 ng/ul fragmented and labeled DNA target was hybridized according to the standard protocol.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000.

data_processing: Images were processed using the Affymetrix Microarray Suite 5.0, CEL files were normalized with RMA and further analyzed using Bioconductor software based on the R language.

source_name: PBMC, healthy, upf17

label_protocol: 100 ng total RNA, Whole Transcript Sense Target Labeling assay.

growth_protocol: PBMCs were isolated from controls and psoriasis patients.

extract_protocol: Trizol-extracted RNA.

treatment_protocol: Two different antioxiative peptides (UPF1 and UPF17) were applied to the culture.

tag: disease status

value: healthy control

tag: cell type

value: peripheral blood mononuclear cells (PBMCs)

tag: drug treatment

tag: individual identifier


title: 27_HG1st_C32_con_upf17_upf

description:
27_C32
PBMC gene expression data.


title: 12_HG1st_P52_psor_upf17_upf

description:
12_P52
PBMC gene expression data.

source_name: PBMC, psoriasis, upf17

value: psoriasis


title: FLU_96hr_maleTestis_5

description:
Ave10080_1_1rProcessedSignal
Ave10080_1_1gProcessedSignal
for gene classifier discovery

source_name: testis_male_FLU_96 hr

tag: strain

tag: gender

value: FLU (flutamide) 1700 ug/L for 96hr

source_name: testis_male_water control_96 hr

value: in water control for 96 hr


title: 28_HG1st_C42_con_upf17_upf

description:
28_C42
PBMC gene expression data.


title: FLU_96hr_maleTestis_3

description:
Ave10078_1_1rProcessedSignal
Ave10078_1_1gProcessedSignal
for gene classifier discovery

tag: genotype/variation

tag: treated with


title: 20_HG1st_P11_psor_upf1_upf

description:
20_P11
PBMC gene expression data.

source_name: PBMC, psoriasis, upf1


title: FLU_96hr_maleTestis_4

description:
Ave10078_1_3rProcessedSignal
Ave10078_1_3gProcessedSignal
for gene classifier discovery

tag: age


title: 13_HG1st_C10_con_nupf_no

description:
13_C10
PBMC gene expression data.

source_name: PBMC, healthy, treatment control

value: control


title: 24_HG1st_C21_con_upf1_upf

description:
24_C21
PBMC gene expression data.

source_name: PBMC, healthy, upf1


title: 22_HG1st_C52_con_upf17_upf

description:
22_C52
PBMC gene expression data.


title: 23_HG1st_C20_con_nupf_no

description:
23_C20
PBMC gene expression data.


title: 29_HG1st_C40_con_nupf_no

description:
29_C40
PBMC gene expression data.


title: 15_HG1st_C50_con_nupf_no

description:
15_C50
PBMC gene expression data.


title: 30_HG1st_P22_psor_upf17_upf

description:
30_P22
PBMC gene expression data.


title: 16_HG1st_P51_psor_upf1_upf

description:
16_P51
PBMC gene expression data.


title: 14_HG1st_P12_psor_upf17_upf

description:
14_P12
PBMC gene expression data.


title: 19_HG1st_P10_psor_nupf_no

description:
19_P10
PBMC gene expression data.

source_name: PBMC, psoriasis, treatment control


title: 21_HG1st_C51_con_upf1_upf

description:
21_C51
PBMC gene expression data.


title: 25_HG1st_P50_psor_nupf_no

description:
25_P50
PBMC gene expression data.


title: 18_HG1st_C11_con_upf1_upf

description:
18_C11
PBMC gene expression data.


title: FLU_96hr_maleTestis_2

description:
Ave10076_1_4rProcessedSignal
Ave10076_1_4gProcessedSignal
for gene classifier discovery


title: 09_HG1st_P32_psor_upf17_upf

description:
09_P32
PBMC gene expression data.


title: 08_HG1st_P41_psor_upf1_upf

description:
08_P41
PBMC gene expression data.


title: 17_HG1st_C30_con_nupf_no

description:
17_C30
PBMC gene expression data.


title: 11_HG1st_P42_psor_upf17_upf

description:
11_P42
PBMC gene expression data.


title: 07_HG1st_P31_psor_upf1_upf

description:
07_P31
PBMC gene expression data.


title: 10_HG1st_P21_psor_upf1_upf

description:
10_P21
PBMC gene expression data.


title: FLU_96hr_maleTestis_1

description:
Ave10076_1_2rProcessedSignal
Ave10076_1_2gProcessedSignal
for gene classifier discovery


title: 06_HG1st_P30_psor_nupf_no

description:
06_P30
PBMC gene expression data.


title: 05_HG1st_C41_con_upf1_upf

description:
05_C41
PBMC gene expression data.


title: FLU_48hr_maleTestis_5

description:
Ave10080_1_2rProcessedSignal
Ave10080_1_2gProcessedSignal
for gene classifier discovery

source_name: testis_male_FLU_48 hr

value: FLU (flutamide) 1700 ug/L for 48hr

source_name: testis_male_water control_48 hr

value: in water control for 48 hr


title: FLU_48hr_maleTestis_4

description:
Ave10079_1_1rProcessedSignal
Ave10079_1_1gProcessedSignal
for gene classifier discovery

value: male

value: testis


title: FLU_48hr_maleTestis_3

description:
Ave10078_1_2rProcessedSignal
Ave10078_1_2gProcessedSignal
for gene classifier discovery


title: FLU_48hr_maleTestis_1

description:
Ave10075_1_4rProcessedSignal
Ave10075_1_4gProcessedSignal
for gene classifier discovery


title: 03_HG1st_P20_psor_nupf_no

description:
03_P20
PBMC gene expression data.


title: septum_mat_rep6

city: Bar Harbor

first: Michael

middle: C.

last: Saul

state: ME

address: 600 Main St

institute: The Jackson Laboratory

description:
High maternal aggression mice were derived by selective breeding from hsd:ICR mice, an outbred strain of mice sold by Harlan Labs (Madison, WI).
39M

hyb_protocol: Samples were hybridized to arrays at 45 degrees C for 16 hours following procedures outlined in the GeneChip WT Terminal Labeling and Hybridization Use Manual , Rev. 4.

scan_protocol: Arrays were scanned on the Affymetrix GC3000 G7 scanner, and data were extracted and processed using Affymetrix Command Console v3.1.1.1229.

data_processing: Raw array data were normalized and summarized at the probeset level using Affymetrix Power Tools v1.12.0 with default settings for PLIER with GC-bin background correction.  Summarized data were analyzed using limma for BioConductor v3.6.9.

source_name: septum, lactating adult female mice

label_protocol: 200ng of each total RNA sample were labeled with an Ambion GeneChip WT Expression Kit (Ambion, Austin, TX, USA) according to the manufacturer's specifications.

growth_protocol: The strain of mice used was selectively bred in our lab for high maternal aggression.  Maternal mice were housed with a breeder male for two weeks while virgin mice were co-housed with 2 other female mice for the same amount of time.  After two weeks, the females in both conditions were individually housed.  Tissue was collected between postpartum days 6-8 in lactating females, and virgin females were age-matched.

extract_protocol: Total RNA was extracted using the Aurum Total RNA Fatty and Fibrous Tissue Kit (Bio-Rad, Hercules, CA, USA), which uses a guanidinium thiocyanate-phenol-chloroform extraction followed by a spin column cleanup and purification.  RNA purity and concentration were assessed using a NanoDrop spectrophotometer, and RNA integrity was assessed using an RNA Pico Chip on an Agilent BioAnalyzer 2100.

treatment_protocol: Prior to RNA extraction, all mice were euthanized by cervical dislocation followed by decapitation under deep isofluorane anaesthesia in accordance with UW-Madison IACUC guidelines.  Brains were removed and flash-frozen in isopentane on dry ice.  Brain tissue was then sectioned on a cryostat, and samples of lateral septum were microdissected using a hole punch.  Frozen tissue was stored for no more than 12 weeks prior to nucleic acid extraction.

value: microdissected septum

value: high maternal aggression

tag: maternal state

value: lactating


title: septum_vir_rep6

description:
High maternal aggression mice were derived by selective breeding from hsd:ICR mice, an outbred strain of mice sold by Harlan Labs (Madison, WI).
40V

source_name: septum, virgin adult female mice

value: virgin


title: 01_HG1st_P40_psor_nupf_no

description:
01_P40
PBMC gene expression data.


title: septum_vir_rep1

description:
High maternal aggression mice were derived by selective breeding from hsd:ICR mice, an outbred strain of mice sold by Harlan Labs (Madison, WI).
03V


title: septum_mat_rep5

description:
High maternal aggression mice were derived by selective breeding from hsd:ICR mice, an outbred strain of mice sold by Harlan Labs (Madison, WI).
35M


title: septum_vir_rep2

description:
High maternal aggression mice were derived by selective breeding from hsd:ICR mice, an outbred strain of mice sold by Harlan Labs (Madison, WI).
05V


title: FLU_48hr_maleTestis_2

description:
Ave10076_1_3rProcessedSignal
Ave10076_1_3gProcessedSignal
for gene classifier discovery

value: AB

value: wild-type


title: 04_HG1st_C31_con_upf1_upf

description:
04_C31
PBMC gene expression data.


title: septum_mat_rep4

description:
High maternal aggression mice were derived by selective breeding from hsd:ICR mice, an outbred strain of mice sold by Harlan Labs (Madison, WI).
25M


title: FLU_24hr_maleTestis_5

description:
Ave10362_1_4rProcessedSignal
Ave10362_1_4gProcessedSignal
for gene classifier discovery

source_name: testis_male_FLU_24 hr

value: 5 months

value: FLU (flutamide) 1700 ug/L for 24hr

source_name: testis_male_water control_24 hr

value: in water control for 24 hr


title: septum_vir_rep3

description:
High maternal aggression mice were derived by selective breeding from hsd:ICR mice, an outbred strain of mice sold by Harlan Labs (Madison, WI).
20V


title: septum_vir_rep5

description:
High maternal aggression mice were derived by selective breeding from hsd:ICR mice, an outbred strain of mice sold by Harlan Labs (Madison, WI).
32V


title: septum_vir_rep4

description:
High maternal aggression mice were derived by selective breeding from hsd:ICR mice, an outbred strain of mice sold by Harlan Labs (Madison, WI).
22V


title: 02_HG1st_C22_con_upf17_upf

description:
02_C22
PBMC gene expression data.

value: healthy control

value: peripheral blood mononuclear cells (PBMCs)


title: septum_mat_rep1

description:
High maternal aggression mice were derived by selective breeding from hsd:ICR mice, an outbred strain of mice sold by Harlan Labs (Madison, WI).
02M


title: Streptococcus mutans biofilm treated with cranberry proanthocyanidins replicate 3

city: Ithaca

first: Guoping

last: Feng

state: NY

address: 262 Stocking Hall

department: Food Science

institute: Cornell University

scan_protocol: The fluorescence intensity of the probed microarray was acquired and processed by a GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA) according to the procedures supplied by the manufacturer.

data_processing: After the slides were scanned, single-channel images were loaded into JCVI Spotfinder software (http://www.tm4.org/spotfinder.html) and overlaid. A spot grid was created according to JCVI specifications and then manually adjusted to fit all spots within the grid. The intensity values of each spot were measured and saved into ".mev" files. Data were normalized using LOWESS and standard deviation regularization with default settings, followed by in-slide replicate analysis using the JCVI microarray data analysis software MIDAS (http://www.tm4.org/midas.html). Spots that were flagged as having either low intensity values or low signal saturation were automatically discarded. The statistical analysis was carried out using BRB-ArrayTools (version 3.8.1; http://linus.nci.nih.gov/BRB-ArrayTools.html) with a cutoff P value of 0.001 for class prediction and P value of 0.001 and 0.010.05 for class comparison.

organism: Streptococcus mutans UA159

source_name: biofilm RNA

label_protocol: The experimental RNAs from biofilms were used to generate cDNA according to the protocol provided by JCVI at http://pfgrc.jcvi.org/index.php/microarray/protocols.html

extract_protocol: Cury, J. A., and H. Koo. 2007. Extraction and purification of total RNA from Streptococcus mutans biofilms. Anal. Biochem. 365:208-214

tag: rna

value: 50h old biofilm treated with cranberry proanthocyanidins in 15% ethanol

tag: sample type

value: biofilm

value: cranberry proanthocyanidins in 15 pct. ethanol

source_name: mid-log RNA planktonic culture

label_protocol: The reference RNAs from biofilms were used to generate cDNA according to the protocol provided by JCVI at http://pfgrc.jcvi.org/index.php/microarray/protocols.html

value: mid-log growth phase of planktonic culture

value: planktonic culture

value: reference


title: Streptococcus mutans biofilm control replicate 4

value: 50h old biofilm treated with control vehicle (15% ethanol)

value: 15 pct. ethanol


title: Streptococcus mutans biofilm treated with cranberry proanthocyanidins replicate 1


title: septum_mat_rep3

description:
High maternal aggression mice were derived by selective breeding from hsd:ICR mice, an outbred strain of mice sold by Harlan Labs (Madison, WI).
17M

value: microdissected septum

value: high maternal aggression

value: lactating


title: Streptococcus mutans biofilm control replicate 3


title: septum_mat_rep2

description:
High maternal aggression mice were derived by selective breeding from hsd:ICR mice, an outbred strain of mice sold by Harlan Labs (Madison, WI).
04M


title: TRB_96hr_femaleOvary_1

description:
rProcessedSignal605
gProcessedSignal605
for gene classifier discovery

source_name: ovary_female_TRB_96 hr

value: AB

value: wild-type

value: female

value: ovary

value: TRB (17 -trenbolone) 3 ug/L for 96hr

source_name: ovary_female_water control_96 hr

value: in water control for 96 hr


title: TRB_96hr_femaleBrain_5

description:
rProcessedSignal602
gProcessedSignal602
for gene classifier discovery

source_name: brain_female_TRB_96 hr

value: 5 months

value: brain

source_name: brain_female_water control_96 hr


title: TRB_96hr_femaleOvary_3

description:
rProcessedSignal607
gProcessedSignal607
for gene classifier discovery


title: TRB_96hr_femaleOvary_4

description:
rProcessedSignal638
gProcessedSignal638
for gene classifier discovery


title: FLU_24hr_maleTestis_4

description:
Ave10361_1_2rProcessedSignal
Ave10361_1_2gProcessedSignal
for gene classifier discovery

value: male

value: testis

value: FLU (flutamide) 1700 ug/L for 24hr

value: in water control for 24 hr


title: FLU_24hr_maleTestis_3

description:
Ave10360_1_4rProcessedSignal
Ave10360_1_4gProcessedSignal
for gene classifier discovery


title: TRB_96hr_femaleOvary_2

description:
rProcessedSignal606
gProcessedSignal606
for gene classifier discovery


title: FLU_24hr_maleTestis_1

description:
Ave10358_1_2rProcessedSignal
Ave10358_1_2gProcessedSignal
for gene classifier discovery


title: FLU_24hr_maleTestis_2

description:
Ave10359_1_3rProcessedSignal
Ave10359_1_3gProcessedSignal
for gene classifier discovery


title: TRB_96hr_femaleOvary_5

description:
rProcessedSignal665
gProcessedSignal665
for gene classifier discovery


title: Streptococcus mutans biofilm treated with cranberry proanthocyanidins replicate 2

value: 50h old biofilm treated with cranberry proanthocyanidins in 15% ethanol

value: biofilm

value: cranberry proanthocyanidins in 15 pct. ethanol

value: mid-log growth phase of planktonic culture

value: planktonic culture

value: reference


title: Streptococcus mutans biofilm treated with cranberry proanthocyanidins replicate 4


title: TRB_96hr_femaleBrain_3

description:
rProcessedSignal600
gProcessedSignal600
for gene classifier discovery

value: AB

value: wild-type


title: Streptococcus mutans biofilm control replicate 1

value: 50h old biofilm treated with control vehicle (15% ethanol)

value: 15 pct. ethanol


title: TRB_96hr_femaleBrain_4

description:
rProcessedSignal601
gProcessedSignal601
for gene classifier discovery

value: female

value: TRB (17 -trenbolone) 3 ug/L for 96hr

value: in water control for 96 hr


title: FIP_96hr_maleTestis_5

description:
Ave10088_1_2rProcessedSignal
Ave10088_1_2gProcessedSignal
for gene classifier discovery

source_name: testis_male_FIP_96 hr

value: 5 months

value: male

value: FIP (fipronil) 5 ug/L for 96hr

source_name: testis_male_water control_96 hr


title: FIP_96hr_maleTestis_4

description:
Ave10088_1_1rProcessedSignal
Ave10088_1_1gProcessedSignal
for gene classifier discovery

value: testis


title: Advanced stage ovarian carcinoma T318

type: genomic

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description:
reference DNA is pooled DNA from the blood of 18 healthy individuals
raw data files: US22502676_251901512335_S01_CGH-v4_95_Feb07_1_1.txt, US22502676_251901512335_S01_CGH-v4_95_Feb07_1_2.txt

hyb_protocol: Hybridization protocol available via www.agilent.com

scan_protocol: Slides were scanned using the Agilent microarray scanner, protocol according to Agilent.

data_processing: Dewaving: The data have been de-waved as described in Van de Wiel et al. (2009) using the R package NoWaves. This is available from www.few.vu.nl/~mavdwiel/nowaves.html. Agilent 105K normals were used as calibration. Normalization: mode normalization.

molecule: genomic DNA

source_name: Tumor

label_protocol: DNA labeling protocol according to Enzo Life Sciences

extract_protocol: DNAzol (Invitrogen) according to manufacturer's protocol

value: Female

value: ovarian carcinoma tissue

tag: sample

tag: Stage

value: IIIc

tag: type

value: S

tag: grade

tag: ct

value: yes

tag: status

value: Dead

tag: os (months)

tag: progression

tag: pfs (months)

source_name: Female reference DNA

value: blood pooled from 18 healthy individuals


title: TRB_96hr_femaleBrain_2

description:
rProcessedSignal599
gProcessedSignal599
for gene classifier discovery

tag: strain

value: AB

value: wild-type

tag: tissue

value: brain

tag: treatment


title: TRB_96hr_femaleBrain_1

description:
rProcessedSignal598
gProcessedSignal598
for gene classifier discovery

tag: genotype/variation

tag: gender

value: female

tag: treated with


title: Advanced stage ovarian carcinoma T317

description:
reference DNA is pooled DNA from the blood of 18 healthy individuals
raw data files: US22502676_251901512335_S01_CGH-v4_95_Feb07_1_2.txt, US22502676_251901512335_S01_CGH-v4_95_Feb07_1_2.txt

tag: age


title: FIP_96hr_maleTestis_3

description:
Ave10087_1_4rProcessedSignal
Ave10087_1_4gProcessedSignal
for gene classifier discovery


title: Streptococcus mutans biofilm control replicate 2

tag: rna

value: 50h old biofilm treated with control vehicle (15% ethanol)

tag: sample type

value: biofilm

value: 15 pct. ethanol

value: mid-log growth phase of planktonic culture

value: planktonic culture

value: reference


title: FAD_96hr_maleBrain_5

description:
rProcessedSignal663
gProcessedSignal663
for gene classifier discovery

source_name: brain_male_FAD_96 hr

value: 5 months

value: male

value: FAD (fadrozole) 25 ug/L for 96hr

source_name: brain_male_water control_96 hr

value: in water control for 96 hr


title: FIP_96hr_maleTestis_2

description:
Ave10087_1_3rProcessedSignal
Ave10087_1_3gProcessedSignal
for gene classifier discovery

value: testis

value: FIP (fipronil) 5 ug/L for 96hr


title: Advanced stage ovarian carcinoma T316

description:
reference DNA is pooled DNA from the blood of 18 healthy individuals
raw data files: US22502676_251901512061_S01_CGH-v4_95_Feb07_1_1.txt, US22502676_251901512061_S01_CGH-v4_95_Feb07_1_2.txt

value: Female

value: ovarian carcinoma tissue

tag: sample

tag: Stage

value: IV

value: S

value: yes

value: Alive

value: blood pooled from 18 healthy individuals


title: FAD_96hr_maleBrain_4

description:
rProcessedSignal661
gProcessedSignal661
for gene classifier discovery

value: AB

value: wild-type

value: brain


title: FIP_96hr_maleTestis_1

description:
Ave10087_1_2rProcessedSignal
Ave10087_1_2gProcessedSignal
for gene classifier discovery


title: FAD_96hr_maleBrain_2

description:
rProcessedSignal610
gProcessedSignal610
for gene classifier discovery


title: FAD_96hr_maleBrain_3

description:
rProcessedSignal611
gProcessedSignal611
for gene classifier discovery


title: FAD_96hr_maleBrain_1

description:
rProcessedSignal608
gProcessedSignal608
for gene classifier discovery


title: FAD_96hr_femaleOvary_5

description:
rProcessedSignal667
gProcessedSignal667
for gene classifier discovery

source_name: ovary_female_FAD_96 hr

value: female

value: ovary


title: FAD_96hr_femaleBrain_4

description:
rProcessedSignal656
gProcessedSignal656
for gene classifier discovery

source_name: brain_female_FAD_96 hr

value: 5 months


title: FAD_96hr_femaleOvary_3

description:
rProcessedSignal660
gProcessedSignal660
for gene classifier discovery

value: FAD (fadrozole) 25 ug/L for 96hr


title: FAD_96hr_femaleOvary_2

description:
rProcessedSignal659
gProcessedSignal659
for gene classifier discovery

value: in water control for 96 hr


title: FAD_96hr_femaleBrain_5

description:
rProcessedSignal657
gProcessedSignal657
for gene classifier discovery


title: Advanced stage ovarian carcinoma T313

description:
reference DNA is pooled DNA from the blood of 18 healthy individuals
raw data files: US22502676_251901512059_S01_CGH-v4_95_Feb07_1_1.txt, US22502676_251901512059_S01_CGH-v4_95_Feb07_1_2.txt

value: III

tag: type

value: M

tag: grade

value: Dead


title: Advanced stage ovarian carcinoma T314

description:
reference DNA is pooled DNA from the blood of 18 healthy individuals
raw data files: US22502676_251901512060_S01_CGH-v4_95_Feb07_1_1.txt, US22502676_251901512060_S01_CGH-v4_95_Feb07_1_2.txt

value: Female

value: ovarian carcinoma tissue

tag: ct

tag: status


title: Advanced stage ovarian carcinoma T312

value: IIIb

value: E

tag: os (months)

tag: progression


title: Advanced stage ovarian carcinoma T315

value: IIIc

value: S

value: yes

value: Alive

value: no

tag: pfs (months)


title: FAD_96hr_femaleOvary_1

description:
rProcessedSignal658
gProcessedSignal658
for gene classifier discovery

tag: strain

value: AB

value: wild-type

value: female

tag: tissue


title: FAD_48hr_femaleOvary_2

description:
rProcessedSignal649
gProcessedSignal649
for gene classifier discovery

source_name: ovary_female_FAD_48 hr

tag: genotype/variation

value: 5 months

value: ovary

value: FAD (fadrozole) 25 ug/L for 48hr

source_name: ovary_female_water control_48 hr

tag: treatment

value: in water control for 48 hr


title: FAD_48hr_femaleOvary_4

description:
rProcessedSignal651
gProcessedSignal651
for gene classifier discovery

tag: gender

tag: treated with


title: FAD_48hr_femaleOvary_3

description:
rProcessedSignal650
gProcessedSignal650
for gene classifier discovery

tag: age


title: FIP_48hr_maleTestis_5

description:
Ave10086_1_4rProcessedSignal
Ave10086_1_4gProcessedSignal
for gene classifier discovery

source_name: testis_male_FIP_48 hr

value: male

value: testis

value: FIP (fipronil) 5 ug/L for 48hr

source_name: testis_male_water control_48 hr


title: FIP_48hr_maleTestis_4

description:
Ave10085_1_2rProcessedSignal
Ave10085_1_2gProcessedSignal
for gene classifier discovery


title: FAD_96hr_femaleBrain_3

description:
rProcessedSignal655
gProcessedSignal655
for gene classifier discovery

value: brain

value: FAD (fadrozole) 25 ug/L for 96hr

value: in water control for 96 hr


title: Advanced stage ovarian carcinoma T311

description:
reference DNA is pooled DNA from the blood of 18 healthy individuals
raw data files: US22502676_251901512058_S01_CGH-v4_95_Feb07_1_1.txt, US22502676_251901512058_S01_CGH-v4_95_Feb07_1_2.txt

value: Female

value: ovarian carcinoma tissue

value: IIIc

value: E

value: Dead

value: blood pooled from 18 healthy individuals


title: FAD_48hr_femaleOvary_5

description:
rProcessedSignal652
gProcessedSignal652
for gene classifier discovery

value: AB

value: wild-type

value: female


title: FAD_48hr_femaleBrain_5

description:
rProcessedSignal647
gProcessedSignal647
for gene classifier discovery

source_name: brain_female_FAD_48 hr

value: 5 months

value: FAD (fadrozole) 25 ug/L for 48hr

source_name: brain_female_water control_48 hr


title: FAD_96hr_femaleBrain_1

description:
rProcessedSignal653
gProcessedSignal653
for gene classifier discovery


title: FAD_48hr_femaleBrain_4

description:
rProcessedSignal646
gProcessedSignal646
for gene classifier discovery

value: in water control for 48 hr


title: Advanced stage ovarian carcinoma T308

description:
reference DNA is pooled DNA from the blood of 18 healthy individuals
raw data files: US22502676_251901512058_S01_CGH-v4_95_Feb07_1_2.txt, US22502676_251901512058_S01_CGH-v4_95_Feb07_1_2.txt

value: IV

value: yes


title: Advanced stage ovarian carcinoma T309

description:
reference DNA is pooled DNA from the blood of 18 healthy individuals
raw data files: US22502676_251901512059_S01_CGH-v4_95_Feb07_1_2.txt, US22502676_251901512059_S01_CGH-v4_95_Feb07_1_2.txt


title: FIP_48hr_maleTestis_3

description:
Ave10082_1_4rProcessedSignal
Ave10082_1_4gProcessedSignal
for gene classifier discovery

value: male

value: testis

value: FIP (fipronil) 5 ug/L for 48hr


title: FAD_48hr_femaleBrain_3

description:
rProcessedSignal644
gProcessedSignal644
for gene classifier discovery

value: brain


title: Advanced stage ovarian carcinoma T306

description:
reference DNA is pooled DNA from the blood of 18 healthy individuals
raw data files: US22502676_251901512074_S01_CGH-v4_95_Feb07_1_1.txt, US22502676_251901512074_S01_CGH-v4_95_Feb07_1_2.txt

value: Female

value: ovarian carcinoma tissue

value: IIIa

value: C

value: Alive

value: no


title: Advanced stage ovarian carcinoma T310

description:
reference DNA is pooled DNA from the blood of 18 healthy individuals
raw data files: US22502676_251901512061_S01_CGH-v4_95_Feb07_1_2.txt, US22502676_251901512061_S01_CGH-v4_95_Feb07_1_2.txt

value: IIIb

value: E

value: Dead

value: blood pooled from 18 healthy individuals


title: Advanced stage ovarian carcinoma T305


title: Advanced stage ovarian carcinoma T304

description:
reference DNA is pooled DNA from the blood of 18 healthy individuals
raw data files: US22502676_251901512073_S01_CGH-v4_95_Feb07_1_1.txt, US22502676_251901512073_S01_CGH-v4_95_Feb07_1_2.txt

value: III


title: Advanced stage ovarian carcinoma T303

description:
reference DNA is pooled DNA from the blood of 18 healthy individuals
raw data files: US22502676_251901512074_S01_CGH-v4_95_Feb07_1_2.txt, US22502676_251901512074_S01_CGH-v4_95_Feb07_1_2.txt

value: IV


title: Advanced stage ovarian carcinoma T302

description:
reference DNA is pooled DNA from the blood of 18 healthy individuals
raw data files: US22502676_251901512073_S01_CGH-v4_95_Feb07_1_2.txt, US22502676_251901512073_S01_CGH-v4_95_Feb07_1_2.txt

value: yes


title: FAD_48hr_femaleOvary_1

description:
rProcessedSignal648
gProcessedSignal648
for gene classifier discovery

value: AB

value: wild-type

value: 5 months

value: female

value: ovary

value: FAD (fadrozole) 25 ug/L for 48hr

value: in water control for 48 hr


title: FAD_48hr_femaleBrain_1

description:
rProcessedSignal640
gProcessedSignal640
for gene classifier discovery

value: brain


title: FAD_48hr_femaleBrain_2

description:
rProcessedSignal641
gProcessedSignal641
for gene classifier discovery


title: FIP_48hr_maleTestis_1

description:
Ave10081_1_1rProcessedSignal
Ave10081_1_1gProcessedSignal
for gene classifier discovery

value: male

value: testis

value: FIP (fipronil) 5 ug/L for 48hr


title: FIP_48hr_maleTestis_2

description:
Ave10081_1_3rProcessedSignal
Ave10081_1_3gProcessedSignal
for gene classifier discovery


title: FIP_48hr_maleBrain_5

description:
Ave10087_1_1rProcessedSignal
Ave10087_1_1gProcessedSignal
for gene classifier discovery

source_name: brain_male_FIP_48 hr

source_name: brain_male_water control_48 hr


title: FIP_48hr_maleBrain_4

description:
Ave10085_1_4rProcessedSignal
Ave10085_1_4gProcessedSignal
for gene classifier discovery


title: EE2_96hr_maleTestis_5

description:
rProcessedSignal630
gProcessedSignal630
for gene classifier discovery

source_name: testis_male_EE2_96 hr

value: EE2 (17α-ethynyl estradiol) 30 ng/L for 96hr

value: in water control for 96 hr


title: EE2_96hr_maleTestis_4

description:
rProcessedSignal629
gProcessedSignal629
for gene classifier discovery


title: EE2_96hr_maleTestis_3

description:
rProcessedSignal628
gProcessedSignal628
for gene classifier discovery


title: EE2_96hr_maleTestis_2

description:
rProcessedSignal627
gProcessedSignal627
for gene classifier discovery


title: FIP_48hr_maleBrain_2

description:
Ave10081_1_2rProcessedSignal
Ave10081_1_2gProcessedSignal
for gene classifier discovery


title: mucosa-normal-rep3c

city: Ashland

first: David

middle: Michael

last: Coppola

state: Virginia

address: 304 Caroline

department: Biology

institute: Randolph Macon College

hyb_protocol: Fragmented aRNA was hybridized at 42 Cº overnight using the HybBag mixing system with 1X OneArray Hybridization Buffer (Phalanx Biotech), 0.01 mg/ml sheared salmon sperm DNA (Promega, Madison, WI, USA), at a concentration of 0.025 mg/ml labeled target. After hybridization, the arrays were washed according to the standard OneArray protocol.

scan_protocol: Raw intensity signals for each microarray were captured using a Molecular Dynamics™ Axon 4100A scanner, measured using GenePixPro™ Software, and stored in GPR format (Axon Instruments, Sunnyvale, CA, USA).

data_processing:
The data from all microarrays were then analyzed using Rosetta Resolver (Rosetta Biosoftware).
Control and missing features were removed before normalization. The remaining signals were quantile normalized and transformed to log2 values.

source_name: olfactory mucosa

label_protocol: RNA was converted to double-stranded cDNA and amplified using in vitro transcription that included amino-allyl UTP, and the aRNA product was subsequently conjugated with with Cy5™ NHS ester (GEH Lifesciences, Piscataway, NJ, USA).

growth_protocol: Mice were kept in standard group animal room housing from birth through extraction of tissue

extract_protocol: Total RNA was extracted using Qiagen RNAeasy kit. Tissue was homogenized in 2ml dounce homogenizers and Qiashredders (Qiagen, Inc.) were used for tissue disruption. Other procedures followed the manufacturers instructions without modification.

treatment_protocol: Mice were either unilateral naris occluded with cautery or given shame cautery on mussle

value: FVB strain

value: Female

value: 25 Days Old

tag: condition

value: normal


title: FIP_48hr_maleBrain_1

description:
Ave10080_1_3rProcessedSignal
Ave10080_1_3gProcessedSignal
for gene classifier discovery

value: AB


title: Early stage ovarian carcinoma T117

description:
reference DNA is pooled DNA from the blood of 18 healthy individuals
raw data files: MAL_251901510439_S01_CGH-v4_95_Feb07_1_1.txt, MAL_251901510439_S01_CGH-v4_95_Feb07_1_2.txt

value: ovarian carcinoma tissue

tag: sample

value: Ic ascites positive

value: S

value: no

value: Dead

value: yes

value: blood pooled from 18 healthy individuals


title: EE2_96hr_maleTestis_1

description:
rProcessedSignal626
gProcessedSignal626
for gene classifier discovery

value: wild-type

value: 5 months

value: male

source_name: testis_male_water control_96 hr


title: Early stage ovarian carcinoma T114

description:
reference DNA is pooled DNA from the blood of 18 healthy individuals
raw data files: MAL_251901510436_S01_CGH-v4_95_Feb07_1_1.txt, MAL_251901510436_S01_CGH-v4_95_Feb07_1_2.txt

source_name: Tumor

tag: Stage

value: Ia

value: M

value: Alive


title: EE2_96hr_maleBrain_5

description:
rProcessedSignal625
gProcessedSignal625
for gene classifier discovery

source_name: brain_male_EE2_96 hr

value: brain

value: EE2 (17α-ethynyl estradiol) 30 ng/L for 96hr

value: in water control for 96 hr


title: FIP_48hr_maleBrain_3

description:
Ave10085_1_1rProcessedSignal
Ave10085_1_1gProcessedSignal
for gene classifier discovery

value: AB

value: FIP (fipronil) 5 ug/L for 48hr

value: in water control for 48 hr


title: mucosa-normal-rep3b

value: FVB strain

value: Female

value: 25 Days Old

value: normal


title: Early stage ovarian carcinoma T115

value: ovarian carcinoma tissue

tag: type

value: S

value: yes

value: no

source_name: Female reference DNA

value: blood pooled from 18 healthy individuals


title: Early stage ovarian carcinoma T116

value: Ia

tag: grade


title: mucosa-normal-rep3a


title: EE2_96hr_maleBrain_4

description:
rProcessedSignal624
gProcessedSignal624
for gene classifier discovery

value: wild-type

value: 5 months

value: male

source_name: brain_male_water control_96 hr


title: mucosa-open-rep3c

value: open


title: mucosa-open-rep3a


title: FAD_96hr_femaleOvary_4

description:
rProcessedSignal666
gProcessedSignal666
for gene classifier discovery

source_name: ovary_female_FAD_96 hr

value: AB

value: female

value: ovary

value: FAD (fadrozole) 25 ug/L for 96hr

source_name: ovary_female_water control_96 hr

value: in water control for 96 hr


title: mucosa-occluded-rep3c

value: FVB strain

value: Female

value: 25 Days Old

value: occluded


title: EE2_96hr_maleBrain_3

description:
rProcessedSignal623
gProcessedSignal623
for gene classifier discovery

value: brain

value: EE2 (17α-ethynyl estradiol) 30 ng/L for 96hr


title: mucosa-open-rep3b


title: EE2_96hr_maleBrain_2

description:
rProcessedSignal622
gProcessedSignal622
for gene classifier discovery


title: Early stage ovarian carcinoma T113

description:
reference DNA is pooled DNA from the blood of 18 healthy individuals
raw data files: MAL_251901510437_S01_CGH-v4_95_Feb07_1_1.txt, MAL_251901510437_S01_CGH-v4_95_Feb07_1_2.txt

value: ovarian carcinoma tissue

value: Ic capsule ruptured

value: M

tag: ct

value: no

value: Alive

value: blood pooled from 18 healthy individuals


title: mucosa-occluded-rep3a


title: mucosa-normal-rep2b

value: normal


title: FIP_48hr_femaleBrain_5

description:
Ave10092_1_3rProcessedSignal
Ave10092_1_3gProcessedSignal
for gene classifier discovery

source_name: brain_female_FIP_48 hr

value: AB

value: wild-type

value: 5 months

value: female

value: FIP (fipronil) 5 ug/L for 48hr

value: in water control for 48 hr


title: mucosa-normal-rep2c

value: FVB strain

value: Female

value: 25 Days Old


title: Early stage ovarian carcinoma T111

description:
reference DNA is pooled DNA from the blood of 18 healthy individuals
raw data files: MAL_251901510132_S01_CGH-v4_95_Feb07_1_1.txt, MAL_251901510132_S01_CGH-v4_95_Feb07_1_2.txt

value: Ic ovarian surface

value: E

tag: status


title: FIP_48hr_femaleBrain_4

description:
Ave10086_1_2rProcessedSignal
Ave10086_1_2gProcessedSignal
for gene classifier discovery

value: brain


title: EE2_96hr_femaleOvary_5

description:
rProcessedSignal637
gProcessedSignal637
for gene classifier discovery

source_name: ovary_female_EE2_96 hr

value: ovary

value: EE2 (17α-ethynyl estradiol) 30 ng/L for 96hr

value: in water control for 96 hr


title: Early stage ovarian carcinoma T109

description:
reference DNA is pooled DNA from the blood of 18 healthy individuals
raw data files: MAL_251901510135_S01_CGH-v4_95_Feb07_1_1.txt, MAL_251901510135_S01_CGH-v4_95_Feb07_1_2.txt

value: ovarian carcinoma tissue

value: Ib

value: yes

value: Alive

tag: os (months)

value: no

value: blood pooled from 18 healthy individuals


title: EE2_96hr_maleBrain_1

description:
rProcessedSignal621
gProcessedSignal621
for gene classifier discovery

value: AB

value: wild-type

value: 5 months

value: male


title: mucosa-open-rep2c

value: FVB strain

value: Female

value: 25 Days Old

value: open


title: mucosa-occluded-rep3b

value: occluded


title: Early stage ovarian carcinoma T112

value: Ic capsule ruptured

value: E

tag: progression


title: Early stage ovarian carcinoma T105

description:
reference DNA is pooled DNA from the blood of 18 healthy individuals
raw data files: MAL_251901510437_S01_CGH-v4_95_Feb07_1_2.txt, MAL_251901510437_S01_CGH-v4_95_Feb07_1_2.txt

value: ovarian carcinoma tissue

value: Ia

value: C

tag: pfs (months)


title: Early stage ovarian carcinoma T108

description:
reference DNA is pooled DNA from the blood of 18 healthy individuals
raw data files: MAL_251901510439_S01_CGH-v4_95_Feb07_1_2.txt, MAL_251901510439_S01_CGH-v4_95_Feb07_1_2.txt

value: yes

value: Alive


title: mucosa-normal-rep2a

tag: strain

value: normal


title: Early stage ovarian carcinoma T106

description:
reference DNA is pooled DNA from the blood of 18 healthy individuals
raw data files: MAL_251901510438_S01_CGH-v4_95_Feb07_1_2.txt, MAL_251901510438_S01_CGH-v4_95_Feb07_1_2.txt

tag: tissue

value: no

value: blood pooled from 18 healthy individuals


title: Early stage ovarian carcinoma T104

description:
reference DNA is pooled DNA from the blood of 18 healthy individuals
raw data files: MAL_251901510436_S01_CGH-v4_95_Feb07_1_2.txt, MAL_251901510436_S01_CGH-v4_95_Feb07_1_2.txt

value: Dead


title: EE2_96hr_femaleOvary_4

description:
rProcessedSignal635
gProcessedSignal635
for gene classifier discovery

value: AB

tag: genotype/variation

value: wild-type

value: 5 months

value: female

value: ovary

value: EE2 (17α-ethynyl estradiol) 30 ng/L for 96hr

value: in water control for 96 hr