title: ECRG4 set: T185

description: Primary breast tumor


title: 7240 | IgG | IFN-high [Utz]

status: Public on Dec 02 2011

type: other

city: Oberlin

first: Jordan

last: Price

state: OH

address: 119 Woodland St

country: USA

institute: Oberlin College

description: IgG

hyb_protocol: Serum was diluted 1:250 from stocks (maintained at -80 deg. C. in) in PBS + 0.5% Tween 20 (Sigma-Aldrich, St. Louis, MO) and 2.5% fetal calf serum (Omega Scientific, Tarzana CA). Post primary incubation, washed arrays were incubated with 0.375ug/ml Goat anti-Human IgG conjugated to Cy5 (Jackson Immunoresearch, West Grove, PA).

scan_protocol: Arrays were scanned using an Axon digital scanning system (Molecular Devices, Sunnyvale, CA)

data_processing: Array images were analyzed using GenePix 6.0 software (Molecular Devices)

molecule: other

organism: Homo sapiens

source_name: systemic lupus erythematosus

tag: interferon signature category

value: IFN high


title: ECRG4 set: T172

type: RNA

city: Marseille

first: Pascal

last: FINETTI

state: BdR

address: 232 Bd Ste Marguerite

department: Centre de cancérologie de Marseille

country: France

institute: Institut Paoli-Calmettes

description: Primary breast tumor

hyb_protocol: see Affymetrix standard protocols (www.affymetrix.com)

data_processing: RMA using a quantile normalization (R package affy, v 1.20.0)

label: biotin

molecule: total RNA

source_name: human breast cancer tumors

extract_protocol: Guanidinium isothiocyanate and centrifugation over a cesium chloride gradient.

value: negative


title: ECRG4 set: T162

description: Primary breast tumor

scan_protocol: see Affymetrix standard protocols (www.affymetrix.com)


title: ECRG4 set: T183

description: Primary breast tumor

label_protocol: see Affymetrix standard protocols (www.affymetrix.com)

value: positive


title: ECRG4 set: T177

description: Primary breast tumor


title: lola_isoform_K_(ORC4)_rep6

status: Public on Dec 03 2011

city: Bethesda

first: Edward

last: Giniger

state: MD

department: NINDS

institute: NIH

hyb_protocol: Hybridization was performed using the Fred Hutchinson Cancer Research Center Genomics Resources standard protocol. Briefly, experimental and control labeled cDNA targets were co-hybridized to microarrays for 16 hrs at 63°C and sequentially washed at room temperature in 1 x SSC and 0.03% SDS for 2 min, 1 x SSC for 2 min, 0.2 x SSC with agitation for 20 min, and 0.05 x SSC with agitation for 10 min.  Arrays were immediately centrifuged until dry.

scan_protocol: Arrays were scanned using a GenePix 4000B scanner (Molecular Devices Corporation, Sunnyvale, CA).  Image analysis was performed using GenePix Pro 6.0.

data_processing: LOESS normalized, no background correction, scaled by median absolute deviation, all performed using limma package (Author, Gordon Smyth) within R statistical language.

organism: Drosophila melanogaster

source_name: lola C4-/- embryos, 10-12 hours after egg laying

label_protocol: First-strand cDNA synthesis and labeling were performed using the Fred Hutchinson Cancer Research Center Genomics Resources standard protocol. In brief, each total RNA sample (20-30 μg) was reverse transcribed using SuperScript II (Invitrogen) with aa-dUTP/dNTPs incorporation. The resulting cDNAs were subsequently coupled to either Cy3 or Cy5 fluorophores (GE Healthcare Bio-Sciences Corp., Piscataway, NJ).

growth_protocol: Embryos were collected for 2 hours at 25C on grape juice agar plates and incubated an additional 6 hours at 25C in a moist chamber. Embryos of the desired genotype were then hand-sorted with a fluorescent dissecting microscope based on positive GFP expression in the CNS. Sorted embryos were returned to 25C and allowed to develop until 10.0 hours after the end of egg collection. lola mutant and control embryos were collected concurrently.

extract_protocol: Experimental and control total RNA samples were extracted with Trizol (Invitrogen) per manufacturer’s instructions. Final RNA pellet was rinsed twice with 75% ethanol, air-dried 10 minutes, resuspended in 20μl RNase-free water at 60o and stored at -70o. Each RNA sample for microarrays was 20-30 μg of total RNA, derived from ~300 embryos.

treatment_protocol: Collected embryos were dechorionated with 50% bleach, rinsed once with 0.1 M Na phosphate pH 7.2; 0.3% Triton X-100, and rinsed twice with sterile water.

tag: strain

value: w1118; lolaORC4 sca-GAL4/lolaORC4 UAS-tau-eGFP

tag: developmental stage

value: embryonic, 10-12 hours after egg laying

source_name: ctrl embryos 10-12 hours after egg laying

value: w1118; sca-GAL4/UAS-tau-eGFP (control)


title: N2 exposed to OP50(E.coli), biological rep2

city: Laurel

first: Jada

last: Lewis

address: 8301 Muirkirk Road

institute: FDA

description: Gene expression data after 18 hours of exposure

hyb_protocol: Following fragmentation, cRNA were hybridized on GeneChip C.elegans Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station

scan_protocol: GeneChips were scanned using the GeneArray Scanner

data_processing: The data were analyzed with Partek Genomics Suite

organism: Caenorhabditis elegans

source_name: C. elegans after 18hours of exposure

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

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

treatment_protocol: 18 hours of exposure on bacteria seeded NGM plate

tag: agent

value: E.coli OP50

tag: growth stage


title: ECRG4 set: T173

description: Primary breast tumor


title: ECRG4 set: T160

description: Primary breast tumor


title: N2 exposed to OP50(E.coli), biological rep1


title: N2 exposed to OP50(E.coli), biological rep3


title: ECRG4 set: T161

description: Primary breast tumor


title: 7246 | IgG | IFN-high [Utz]

description: IgG


title: ECRG4 set: T152

description: Primary breast tumor


title: ECRG4 set: T155

description: Primary breast tumor


title: N2 exposed to E7946, biological rep2

value: V. cholerae E7946


title: N2 exposed to E7946, biological rep3


title: ECRG4 set: T150

description: Primary breast tumor


title: 7242 | IgG | IFN-high [Utz]

description: IgG


title: ECRG4 set: T184

description: Primary breast tumor


title: 7244 | IgG | IFN-high [Utz]

description: IgG


title: 7250 | IgG | IFN-high [Utz]

description: IgG


title: 7248 | IgG | IFN-high [Utz]

description: IgG


title: N2 exposed to E7946, biological rep1


title: ECRG4 set: T135

description: Primary breast tumor


title: ECRG4 set: T149

description: Primary breast tumor


title: N2 exposed to hemolysin mutant of E7946, biological rep3

value: V. cholerae hemolysin mutant of E7946


title: ECRG4 set: T146

description: Primary breast tumor


title: ECRG4 set: T134

description: Primary breast tumor


title: ECRG4 set: T130

description: Primary breast tumor


title: ECRG4 set: T131

description: Primary breast tumor


title: ECRG4 set: T117

description: Primary breast tumor


title: ECRG4 set: T120

description: Primary breast tumor


title: ECRG4 set: T123

description: Primary breast tumor


title: N2 exposed to CVD110, biological rep2

value: V. cholerae CVD110


title: ECRG4 set: T128

description: Primary breast tumor


title: N2 exposed to hemolysin mutant of E7946, biological rep1


title: N2 exposed to CVD110, biological rep3


title: ECRG4 set: T109

description: Primary breast tumor


title: ECRG4 set: T113

description: Primary breast tumor


title: N2 exposed to hemolysin mutant of E7946, biological rep2


title: ECRG4 set: T108

description: Primary breast tumor


title: ECRG4 set: T129

description: Primary breast tumor


title: ECRG4 set: T107

description: Primary breast tumor


title: N2 exposed to CVD110, biological rep1


title: ECRG4 set: T105

description: Primary breast tumor


title: ECRG4 set: T106

description: Primary breast tumor


title: N2 exposed to CVD109, biological rep2

value: V. cholerae CVD109


title: ECRG4 set: T104

description: Primary breast tumor


title: N2 exposed to CVD109, biological rep3


title: ECRG4 set: T98

description: Primary breast tumor


title: ECRG4 set: T95

description: Primary breast tumor


title: ECRG4 set: T100

description: Primary breast tumor


title: ECRG4 set: T77

description: Primary breast tumor


title: ECRG4 set: T94

description: Primary breast tumor


title: N2 exposed to CVD109, biological rep1


title: ECRG4 set: T70

description: Primary breast tumor


title: ECRG4 set: T79

description: Primary breast tumor


title: ECRG4 set: T73

description: Primary breast tumor


title: ECRG4 set: T72

description: Primary breast tumor


title: ECRG4 set: T76

description: Primary breast tumor


title: ECRG4 set: T71

description: Primary breast tumor


title: ECRG4 set: T68

description: Primary breast tumor


title: petiverana 156hr wingsection1 rep3

city: San Juan

first: Riccardo

last: Papa

address: Avenida Barbosa

department: Biology

country: Puerto Rico

institute: University of Puerto Rico

description: The color pattern in the butterfly used to dissect the three forewing sections is represented as: F1) basal black, F2) middle red, F3) apical black

hyb_protocol: Hybridization was performed by City of Hope Microarray Facility, Duarte, CA, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by City of Hope Microarray Facility, Duarte, CA USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: Raw data (.pair file)  from the NimbleGen arrays were compiled into a single data file, log2 transformed, run through quality control measures, loess normalized, and statistically analyzed using an ANOVA in JMP Genomics 4.0 (SAS Institute Inc., Cary, North Carolina, United States). On each array 855 randomly generated GC-adjusted DNA sequences were used to assess background hybridization noise. Additional quality control involved comparison of intensity distributions and principal components analysis across arrays. Pseudoimages were created to assess regions of uneven intensities and, when problematic, probe intensities for that region were removed and treated as missing data.

organism: Heliconius erato petiverana

source_name: Heliconius erato petiverana pupal forewings, apical pupal wings section, 156hr after pupation

label_protocol: Total RNA was reverse transcribed and amplified using the TransPlex Whole Transcriptome Amplification Kit 2 (Sigma-Aldrich, St. Louis, Missouri, United States). cDNA labeling was performed by City of Hope Microarray Facility, Duarte, CA, USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Each butterfly was reared from a caterpillar stage. Caterpillars were reared individually in cups under ambient light and humidity condition. The day of pupation was recorded with an approximation of 5 hours.

extract_protocol: Dissected tissues were stored in RNAlater (Qiagen Inc., Valencia, California, United States) at -80˚C until RNA extraction. Tissues were lysed using a Tissuelyser. Total RNA was purified using the RNAqueous Kit (Applied Biosystems, Carlsbad, California, United States) followed by DNA removal using the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the UCI Genomics facility  (UC Irvine, Irvine, CA USA).

tag: genotype

value: pure H. erato petiverana

tag: phenotype

value: red band in the middle of the forewing on a black backround and a completely black hindwing

tag: slide number and position of the samples in each array

tag: origin of the colony

value: Panama

tag: wing phenotype

value: black

tag: tissue

value: apical pupal wings section

value: 156 hours after pupation

tag: colony rearing location


title: ECRG4 set: T59

description: Primary breast tumor


title: petiverana 156hr wingsection2 rep3

source_name: Heliconius erato petiverana pupal forewings, middle pupal wings section, 156hr after pupation

value: red

value: middle pupal wings section


title: ECRG4 set: T63

description: Primary breast tumor

value: positive


title: ECRG4 set: T57

description: Primary breast tumor


title: ECRG4 set: T54

description: Primary breast tumor


title: ECRG4 set: T45

description: Primary breast tumor

value: negative


title: petiverana 156hr wingsection3 rep3


title: ECRG4 set: T49

description: Primary breast tumor


title: ECRG4 set: T40

description: Primary breast tumor


title: ECRG4 set: T44

description: Primary breast tumor


title: petiverana 156hr wingsection2 rep1


title: ECRG4 set: T41

description: Primary breast tumor


title: petiverana 156hr wingsection2 rep2


title: ECRG4 set: T48

description: Primary breast tumor


title: petiverana 156hr wingsection1 rep2

source_name: Heliconius erato petiverana pupal forewings, basal pupal wings section, 156hr after pupation

value: basal pupal wings section


title: petiverana 156hr wingsection3 rep1


title: petiverana 156hr wingsection3 rep2


title: petiverana 156hr wingsection1 rep1


title: ECRG4 set: BC266

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: RMA using a quantile normalization

label_protocol: Affymetrix standard protocol

tag: age at diagnosis

tag: histology

value: IDC

tag: pt

tag: pn

tag: sbr grade

tag: er ihc

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)

tag: molecular subtype

value: Basal

value: breast cancer tumor


title: petiverana 180hr wingsection3 rep3

source_name: Heliconius erato petiverana pupal forewings, apical pupal wings section, 180hr after pupation

tag: genotype

tag: phenotype

tag: slide number and position of the samples in each array

tag: developmental stage

value: 180 hours after pupation


title: ECRG4 set: BC262

tag: tissue


title: ECRG4 set: BC260

tag: age at diagnosis

value: other

value: Normal


title: ECRG4 set: BC264

tag: histology


title: ECRG4 set: BC261

tag: pt


title: petiverana 180hr wingsection1 rep3

source_name: Heliconius erato petiverana pupal forewings, basal pupal wings section, 180hr after pupation

value: pure H. erato petiverana

tag: origin of the colony

tag: wing phenotype

tag: colony rearing location


title: TAX577605 (HumanOmni2.5)

type: genomic

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

hyb_protocol: Standard Illumina protocol for HumanOmni 2.5 Quad Beadchip

data_processing: Copy number (Log R) and B allele frequency estimates were obtained from GenomeStudio (Illumina). Genomic profiles from 2.5M data were partitioned using the R implementation (DNAcopy) of Circular Binary Segmentation (CBS) with an alpha value of 0.001. Change points were analyzed using the SDundo option in CBS with a standard deviation threshold of 1.

label: C-Bio and A-DNP

molecule: genomic DNA

source_name: Breast tumor

extract_protocol: Genomic DNA from fresh frozen breast tumor tissue was extracted using overnight digestion with proteinase K at 55C, followed by repeated phenol-chloroform purification steps.

tag: disease state

value: Breast cancer (HER2+)

tag: er

tag: osbin

tag: os

tag: age

tag: ln

tag: primary

tag: grade


title: petiverana 180hr wingsection1 rep2

tag: genotype

tag: phenotype

value: red band in the middle of the forewing on a black backround and a completely black hindwing

tag: slide number and position of the samples in each array

value: Panama


title: ECRG4 set: BC263

tag: age at diagnosis

tag: pn

tag: sbr grade

tag: er ihc

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)

tag: molecular subtype

tag: tissue


title: ECRG4 set: BC265

tag: histology

tag: pt


title: TAX577422 (HumanOmni2.5)

scan_protocol: Standard Illumina protocol for HumanOmni 2.5 Quad Beadchip

tag: disease state

tag: er

tag: osbin

tag: os

tag: age

tag: ln

tag: primary

tag: grade


title: ECRG4 set: BC259

tag: age at diagnosis

value: ILC

tag: pn

tag: sbr grade

tag: er ihc

tag: pr ihc


title: TAX577721 (HumanOmni2.5)

label_protocol: Standard Illumina protocol for HumanOmni 2.5 Quad Beadchip


title: TAX577719 (HumanOmni2.5)


title: ECRG4 set: BC258

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)

tag: molecular subtype


title: petiverana 180hr wingsection1 rep1

tag: genotype

tag: phenotype

tag: slide number and position of the samples in each array

tag: origin of the colony

tag: wing phenotype

value: black

tag: tissue

tag: developmental stage

tag: colony rearing location


title: ECRG4 set: BC255

tag: age at diagnosis

tag: histology

tag: pt

tag: pn


title: ECRG4 set: BC256

tag: sbr grade

tag: er ihc

tag: pr ihc

tag: p53 ihc

value: LuminalA


title: petiverana 180hr wingsection2 rep3

source_name: Heliconius erato petiverana pupal forewings, middle pupal wings section, 180hr after pupation

value: red

value: middle pupal wings section


title: petiverana 180hr wingsection3 rep2

value: apical pupal wings section


title: ECRG4 set: BC254

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)

tag: molecular subtype


title: TAX577716 (HumanOmni2.5)

tag: disease state

tag: er

tag: osbin

tag: os

tag: age

tag: ln

tag: primary

tag: grade


title: cya_3

city: Kyoto

first: Masayuki

last: Inui

address: 9-2 Kizugawadai, Kizugawa

country: Japan

institute: Research institute of Innovative Technology for the Earth (RITE)

hyb_protocol: Fifty microlitres of each Cy3- and Cy5-labelled DNA was mixed and added to 100 µl 2x hybridization buffer [12x saline sodium citrate (SSC), 0.4 % SDS, 10x Denhardt's solution, 0.2 mg ml–1 denatured salmon sperm DNA]. All steps, from hybridizing to washing and drying, were automatically performed using a Lucidea Automated Slide Processor (Amersham Biosciences). The hybridization solution, which was heated at 95 °C for 2 min and cooled to room temperature, was added to hybridization buffer to a final combined volume of 200 µl. The DNA microarray was inserted into the Lucidea Automated Slide Processor and hybridization at 60 °C with the whole-genome DNA microarray was allowed to proceed for 14 h. The hybridization arrays were subsequently washed (once at 35 °C for 6 min in 2x SSC and 0.2 % SDS, once at 35 °C for 6 min in 0.2x SSC and 0.2 % SDS), rinsed (twice at 35 °C in 0.2x SSC and once at 37 °C in isopropanol) and dried.

scan_protocol: The slides were scanned at 532 nm for Cy3 and at 635 nm for Cy5 with a Fujifilm Fluorescent Image Analyser FLA-8000 (Fuji).

data_processing: Images were analysed with a GenePix Pro 5.0 instrument (Axon Instruments). Individual spots were located, the Cy3 and Cy5 fluorescence intensity at each spot was measured, and the background signal intensities were determined. Data was normalized with a GenePix Pro 5.0. Each data was normalized so that the mean of the ratio of means of all of the features, except the flagged ones, is equal to 1.

organism: Corynebacterium glutamicum

label_protocol: DNA samples were blunted with T4 DNA polymerase, ligated to linkers, and amplified by PCR. Amplified DNA from reference DNA and immunoprecipitated DNA were differentially labeled with Cy3 and Cy5, respectively, by using CGH labeling kit (Invitrogen) according to the manufacture’s instruction.

growth_protocol: C. glutamicum was grown in A medium containing 1% glucose at 33oC under aeration for 240min to reach the late-exponential phase of growth.

extract_protocol: Exponentially-growing C. glutamicum cultures (35 ml) at the OD610 of up to 2.5 were treated with formaldehyde (at the final concentration of 1%) and incubate for 20 min at room temperature. The cross-linking was quenched by addition of glycine (at the final concentration of 125 mM) and incubation for 10 min at room temperature. Cells were then collected by centrifugation, washed twice with Tris-buffered saline (20 mM Tris-HCl pH 7.5, 150 mM NaCl) and stored at -80˚C. Pellets were resuspended in 2 ml IP buffer (50 mM HEPES-KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, Roche Antiprotease mini). The cells were mechanically disrupted for nine cycles of 25 s at a speed rating of 6.5 with a FastPrep™ FP120 (BIO 101, Thermo Savant) at room temperature with intermittent cooling on ice for 5 min. The supernatant after centrifugation was sonicated on ice to shear DNA to an average size to 600-1,000 bp. A 50 μl fraction of the supernatant was saved for later analysis (reference DNA). The remainder was subjected to immunoprecipitation with 100μl of magnetic beads coated with Protein G (Invitrogen), which was coupled to the monoclonal anti-Strep-tag II antibody (Qiagen). The mixture was incubated overnight on a rotating platform at 4˚C. The beads were washed once with IP buffer, twice with IP buffer containing 400 mM NaCl, eight times with RIPA buffer (50 mM HEPES pH7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Sodium deoxycholate), and twice with TE buffer with 50 mM NaCl. Immunoprecipitated complexes were eluted from the beads by treatment with 210 μl elution buffer (50 mM Tris-HCl pH8.0, 10 mM EDTA, 1% SDS) at 65˚C for 20 min. Cross-links of immunoprecipitated samples and of total DNA samples were reversed by incubation overnight at 65˚C. Samples were then treated with RNase A and proteinase K for 2 h at 55˚C. DNA was extracted with phenol-chloroform and purified with QIAquick PCR purification mini Elute kit (Qiagen).

treatment_protocol: Formaldehyde was added to cultures at a final concentration of 1% (v/v) and incubation was continued for 20 min

tag: genotype

value: glxR::Strep-tag II, ΔcyaB

tag: strain

tag: antibody

value: anti-Strep-tag II

tag: antibody vendor

value: Qiagen

tag: antibody catalog #

tag: antibody lot #

source_name: Reference genomic DNA, input


title: cya_4


title: petiverana 180hr wingsection2 rep2

tag: phenotype

tag: slide number and position of the samples in each array

tag: origin of the colony

tag: wing phenotype

tag: tissue

tag: developmental stage

tag: colony rearing location


title: TAX577002 (HumanOmni2.5)

tag: disease state

tag: er

tag: osbin

tag: os

tag: age


title: cya_2

tag: genotype

tag: strain


title: cya_1

tag: antibody

tag: antibody vendor


title: TAX577683 (HumanOmni2.5)

tag: ln

tag: primary

tag: grade


title: ECRG4 set: BC252

tag: age at diagnosis

tag: histology

value: IDC

tag: pt

tag: pn

tag: sbr grade

tag: er ihc

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)

tag: molecular subtype

value: Basal

value: breast cancer tumor


title: ECRG4 set: BC253

tag: tissue


title: ECRG4 set: BC250


title: petiverana 180hr wingsection2 rep1

tag: genotype

tag: phenotype

tag: slide number and position of the samples in each array

tag: origin of the colony

tag: wing phenotype

tag: developmental stage

value: 180 hours after pupation

tag: colony rearing location


title: TAX577354 (HumanOmni2.5)

tag: disease state

tag: er

tag: osbin

tag: os

tag: age

tag: ln

tag: primary

tag: grade


title: TAX577544 (HumanOmni2.5)


title: ECRG4 set: BC251

tag: age at diagnosis

tag: histology

tag: pt

tag: pn

tag: sbr grade

tag: er ihc

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)

tag: molecular subtype


title: ECRG4 set: BC247

tag: tissue


title: WT_3

tag: genotype

value: glxR::Strep-tag II

tag: strain

tag: antibody

tag: antibody vendor

tag: antibody catalog #

tag: antibody lot #


title: ECRG4 set: BC246

tag: age at diagnosis

tag: histology

tag: pt


title: ECRG4 set: BC248

tag: pn

tag: sbr grade

tag: er ihc


title: petiverana 180hr wingsection3 rep1

value: pure H. erato petiverana

tag: phenotype

tag: slide number and position of the samples in each array

tag: origin of the colony

tag: wing phenotype

tag: developmental stage

tag: colony rearing location


title: WT_2

tag: genotype

tag: strain


title: ECRG4 set: BC243

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)

tag: molecular subtype

tag: tissue


title: TAX577423 (HumanOmni2.5)

tag: disease state

value: Breast cancer (HER2+)

tag: er

tag: osbin

tag: os

tag: age

tag: ln

tag: primary

tag: grade


title: WT_1

tag: genotype

tag: antibody

tag: antibody vendor

tag: antibody catalog #

tag: antibody lot #


title: ECRG4 set: BC245

tag: age at diagnosis

tag: histology

tag: pt

tag: pn

tag: sbr grade

tag: er ihc

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt


title: TAX577277 (HumanOmni2.5)

tag: disease state

tag: er

tag: osbin

tag: os

tag: age

tag: ln

tag: primary


title: TAX577715 (HumanOmni2.5)

tag: grade


title: TAX577678 (HumanOmni2.5)


title: ECRG4 set: BC244

tag: age at diagnosis

tag: histology

tag: dfs time (months)

tag: molecular subtype

tag: tissue


title: TAX577421 (HumanOmni2.5)


title: petiverana 108hr wingsection2 rep3

source_name: Heliconius erato petiverana pupal forewings, middle pupal wings section, 108hr after pupation

tag: genotype

tag: phenotype

value: red band in the middle of the forewing on a black backround and a completely black hindwing

tag: slide number and position of the samples in each array

tag: origin of the colony

value: Panama

tag: wing phenotype

tag: developmental stage

value: 108 hours after pupation

tag: colony rearing location


title: petiverana 108hr wingsection1 rep3

source_name: Heliconius erato petiverana pupal forewings, basal pupal wings section, 108hr after pupation

value: black

value: basal pupal wings section


title: ECRG4 set: BC257

tag: pt

tag: pn

tag: sbr grade

tag: er ihc

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt


title: ECRG4 set: BC241

tag: age at diagnosis

tag: histology

tag: dfs time (months)

tag: molecular subtype


title: petiverana 108hr wingsection3 rep3

source_name: Heliconius erato petiverana pupal forewings, apical pupal wings section, 108hr after pupation

tag: genotype

tag: phenotype

tag: slide number and position of the samples in each array

tag: tissue


title: ECRG4 set: BC242

value: ILC

value: LuminalA


title: ECRG4 set: BC240


title: ECRG4 set: BC239


title: petiverana 108hr wingsection1 rep2

tag: origin of the colony

tag: wing phenotype

tag: developmental stage

tag: colony rearing location


title: TAX577652 (HumanOmni2.5)

tag: disease state

tag: er

tag: osbin

tag: os

tag: age

tag: ln

tag: primary

tag: grade


title: petiverana 108hr wingsection3 rep2

value: apical pupal wings section


title: TAX577703 (HumanOmni2.5)


title: ECRG4 set: BC238

tag: age at diagnosis

tag: histology

value: other

tag: pt

tag: pn

tag: sbr grade

tag: er ihc

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)

tag: molecular subtype


title: ECRG4 set: BC236

value: LuminalB

tag: tissue


title: TAX577705 (HumanOmni2.5)

tag: disease state

tag: er

tag: osbin

tag: os

tag: age


title: TAX577717 (HumanOmni2.5)

tag: ln

tag: primary

tag: grade


title: ECRG4 set: BC231

tag: age at diagnosis

tag: histology

value: IDC

tag: pt

tag: pn

tag: sbr grade


title: ECRG4 set: BC237

tag: er ihc

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt


title: petiverana 108hr wingsection2 rep1

tag: genotype

tag: phenotype

tag: slide number and position of the samples in each array

tag: origin of the colony

tag: wing phenotype

value: red

tag: tissue

value: middle pupal wings section

tag: developmental stage

tag: colony rearing location


title: ECRG4 set: BC232

tag: age at diagnosis

tag: histology

tag: dfs time (months)

tag: molecular subtype

value: breast cancer tumor


title: ECRG4 set: BC234

tag: pt

tag: pn

tag: sbr grade

tag: er ihc


title: petiverana 108hr wingsection2 rep2


title: petiverana 108hr wingsection1 rep1


title: petiverana 108hr wingsection3 rep1


title: ECRG4 set: BC235

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt


title: TAX577691 (HumanOmni2.5)

tag: disease state

tag: er

tag: osbin

tag: os

tag: age

tag: ln

tag: primary

tag: grade


title: ECRG4 set: BC249

tag: age at diagnosis

tag: histology

tag: dfs time (months)

tag: molecular subtype

value: Basal

tag: tissue


title: ECRG4 set: BC230

value: TUB

tag: pt

tag: pn

tag: sbr grade

tag: er ihc

tag: pr ihc


title: MCF7_hypoxia_9h_Pontin_shRNA_rep1

city: Pohang

first: Bhin

last: Jin-hyuk

address: Ji-gok research center, hyoja-dong, Nam-gu

department: Department of Chemical engineering

country: South Korea

institute: POSTECH

description: MCF7 cells transfected with Pontin shRNA and grown in Hypoxia 9h

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Illumina BeadScan 500 System

data_processing: The data were normalised using quantile normalization method with beadarray version 1.10 and lumi version 1.8.3 in R/Bioconductor package.

growth_protocol: Media: DMEM, 2mM L-Glutamine and 10% Fetal Bovine Serum

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were transfected with Pontin shRNA and grown in Hypoxia for 6 to 9 hours

tag: cell line

tag: treatment

value: hypoxia

tag: time

tag: transfection

value: shRNA (shPontin)


title: MCF7_hypoxia 6h_Pontin_shRNA_rep2

description: MCF7 cells transfected with Pontin shRNA and grown in Hypoxia 6h

label_protocol: Standard Illumina hybridization protocol


title: petiverana 60hr wingsection1 rep3

source_name: Heliconius erato petiverana pupal forewings, basal pupal wings section, 60hr after pupation

tag: genotype

value: pure H. erato petiverana

tag: phenotype

value: red band in the middle of the forewing on a black backround and a completely black hindwing

tag: slide number and position of the samples in each array

tag: origin of the colony

value: Panama

tag: wing phenotype

tag: developmental stage

value: 60 hours after pupation

tag: colony rearing location


title: petiverana 60hr wingsection3 rep3

source_name: Heliconius erato petiverana pupal forewings, apical pupal wings section, 60hr after pupation

value: black

tag: tissue


title: ECRG4 set: BC228

source_name: human breast cancer tumors

tag: age at diagnosis

tag: histology

value: ILC

tag: pt

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)

tag: molecular subtype

value: LuminalA


title: ECRG4 set: BC226

tag: pn

tag: sbr grade

tag: er ihc

tag: pr ihc


title: TAX577700 (HumanOmni2.5)

tag: disease state

value: Breast cancer (HER2+)

tag: er

tag: osbin

tag: os

tag: age

tag: ln

tag: primary

tag: grade


title: ECRG4 set: BC227

tag: age at diagnosis

tag: histology

tag: pt

tag: p53 ihc

tag: tissue


title: ECRG4 set: BC225

tag: pn

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)

tag: molecular subtype

value: LuminalB


title: petiverana 60hr wingsection1 rep2

tag: genotype

tag: phenotype

tag: slide number and position of the samples in each array

tag: origin of the colony

tag: wing phenotype

value: basal pupal wings section

tag: developmental stage

tag: colony rearing location


title: ECRG4 set: BC222

tag: age at diagnosis

value: IDC

tag: sbr grade

tag: er ihc

tag: pr ihc


title: ECRG4 set: BC233

tag: histology

tag: pt

tag: p53 ihc

tag: tissue


title: ECRG4 set: BC224

tag: pn

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)


title: MCF7_hypoxia 6h_Pontin_shRNA_rep1

tag: cell line

tag: treatment

tag: time

tag: transfection


title: MCF7_normoxia_Pontin_shRNA_rep1

description: MCF7 cells transfected with Pontin shRNA and grown in Normoxia

value: normoxia


title: ECRG4 set: BC221

tag: molecular subtype

value: breast cancer tumor


title: MCF7_normoxia_Pontin_shRNA_rep2


title: ECRG4 set: BC223

tag: age at diagnosis


title: ECRG4 set: BC229

tag: sbr grade


title: petiverana 60hr wingsection3 rep2

tag: genotype

tag: phenotype

tag: slide number and position of the samples in each array

tag: origin of the colony

tag: wing phenotype

value: apical pupal wings section

tag: developmental stage

tag: colony rearing location


title: ECRG4 set: BC219

tag: histology

tag: pn

tag: er ihc

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

tag: tissue


title: ECRG4 set: BC220

value: other

tag: pt

tag: dfs evt

tag: dfs time (months)

tag: molecular subtype


title: MCF7_hypoxia_9h_rep1

description: MCF7 cells grown in Hypoxia 9h

tag: cell line

tag: treatment

value: hypoxia

tag: time

tag: transfection

value: control shRNA (shNS)


title: petiverana 60hr wingsection2 rep3

source_name: Heliconius erato petiverana pupal forewings, middle pupal wings section, 60hr after pupation

tag: genotype

value: pure H. erato petiverana

tag: phenotype

tag: slide number and position of the samples in each array

tag: origin of the colony

tag: wing phenotype

value: red

value: middle pupal wings section

tag: developmental stage


title: petiverana 60hr wingsection2 rep2

value: red band in the middle of the forewing on a black backround and a completely black hindwing

value: Panama

value: 60 hours after pupation

tag: colony rearing location


title: ECRG4 set: BC218

tag: age at diagnosis

tag: histology

tag: pn

tag: sbr grade

tag: er ihc

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

value: Basal


title: petiverana 60hr wingsection1 rep1

value: black

tag: tissue


title: MCF7_hypoxia_9h_rep2

description: MCF7 cells grown in Hypoxia 9h

tag: cell line

tag: treatment

tag: time

tag: transfection


title: petiverana 60hr wingsection3 rep1

tag: genotype

tag: phenotype

tag: slide number and position of the samples in each array

tag: origin of the colony


title: ECRG4 set: BC213

tag: age at diagnosis

tag: pt

tag: dfs evt

tag: molecular subtype

value: LuminalB


title: MCF7_hypoxia_9h_Pontin_shRNA_rep2

value: shRNA (shPontin)


title: MCF7_hypoxia_6h_rep1

description: MCF7 cells grown in Hypoxia 6h


title: ECRG4 set: BC217

tag: histology

tag: pn

tag: sbr grade

tag: er ihc

tag: dfs time (months)

value: LuminalA


title: petiverana 60hr wingsection2 rep1

tag: wing phenotype

tag: tissue

tag: developmental stage

tag: colony rearing location


title: MCF7_hypoxia_6h_rep2

description: MCF7 cells grown in Hypoxia 6h

tag: cell line

tag: treatment

tag: time

tag: transfection


title: ECRG4 set: BC216

tag: age at diagnosis

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc


title: MCF7_normoxia_rep1

description: MCF7 cells grown in Normoxia

value: normoxia


title: ECRG4 set: BC214

tag: histology

value: IDC

tag: pt

tag: dfs evt

tag: molecular subtype

value: breast cancer tumor


title: petiverana 12hr wingsection2 rep3

source_name: Heliconius erato petiverana pupal forewings, middle pupal wings section, 12hr after pupation

tag: genotype

tag: phenotype

tag: slide number and position of the samples in each array

tag: origin of the colony

value: 12 hours after pupation


title: TAX577280 (HumanOmni2.5)

tag: disease state

value: Breast cancer (HER2+)

tag: er

tag: osbin

tag: os

tag: age

tag: ln

tag: primary

tag: grade


title: ECRG4 set: BC215

tag: age at diagnosis

value: MUC

tag: pn

tag: sbr grade

tag: er ihc

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

tag: dfs time (months)

tag: tissue


title: ECRG4 set: BC211

tag: histology

tag: pt

tag: dfs evt

tag: molecular subtype


title: ECRG4 set: BC208


title: ECRG4 set: BC210

value: TUB


title: ECRG4 set: BC206


title: ECRG4 set: BC209


title: petiverana 12hr wingsection3 rep3

source_name: Heliconius erato petiverana pupal forewings, apical pupal wings section, 12hr after pupation

tag: genotype

value: pure H. erato petiverana

tag: phenotype

tag: slide number and position of the samples in each array

tag: origin of the colony

tag: wing phenotype

value: apical pupal wings section

tag: developmental stage

tag: colony rearing location


title: ECRG4 set: BC212

tag: age at diagnosis

value: MIX

tag: pn

tag: sbr grade

tag: er ihc

value: Normal


title: ECRG4 set: BC207

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc


title: petiverana 12hr wingsection2 rep2

value: red band in the middle of the forewing on a black backround and a completely black hindwing

value: Panama

value: red

tag: tissue

value: middle pupal wings section


title: ECRG4 set: BC205

tag: histology

tag: dfs evt

tag: dfs time (months)


title: petiverana 12hr wingsection3 rep2

tag: genotype

tag: phenotype

value: black


title: MCF7_normoxia_rep2

description: MCF7 cells grown in Normoxia

tag: cell line

tag: treatment

tag: transfection

value: control shRNA (shNS)


title: Aortic Endothelial Cells treated with Winter07 APM for 3 hr

city: Davis

first: Hnin

middle: H

last: Aung

state: CA

address: 451 E Health Science Dr., GBSF 5404

department: Internal Medicine

institute: University of California, Davis

description: Gene expression data from Aortic Endothelial cell treated with winter2007 APM

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with GeneChip Operating System (GCOS) 1.4 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Human Aortic Endothelial Cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix One Cycle Sample Preparation protocol from 9 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Aortic Endothelial Cell and Bronchial Epithelial Cells were cultured in EGM-2 bullet kit (EBM-2 plus SingleQuot of growth supplements) and BEGM-2 bullet kit. Tissue cells were grown to confluent 80 %. Experiments were conducted with cells at passages 4-6.

extract_protocol: Total RNA was extracted using TRIzol® Reagent followed by RNeasy Mini Kit including the DNA digestion step as described by the manufacturer. performed according to the manufacturer's instructions.

treatment_protocol: Confluence HAEC or HBEC were treated with control H2O or 10 ug/mL of summer 2006 APM or winter 2007 APM for 3 h. After treatment, cells were washed twice with PBS (without Ca and Mg) and scraped into cold PBS. Cell pellets were placed in Trizol.

tag: cell type

value: Aortic Endothelial Cells


title: ECRG4 set: BC204

tag: age at diagnosis

value: IDC

tag: molecular subtype

value: LuminalB


title: Bronchail Epithelial Cells treated with Winter07 APM for 3 hr

description: Gene expression data from Bronchail Epithelial cells treated with winter2007 APM

source_name: Human Bronchail Epithelial Cells

value: Bronchail Epithelial Cells


title: petiverana 12hr wingsection1 rep3

source_name: Heliconius erato petiverana pupal forewings, basal pupal wings section, 12hr after pupation

tag: slide number and position of the samples in each array

tag: origin of the colony

tag: wing phenotype

value: basal pupal wings section

tag: developmental stage

value: 12 hours after pupation

tag: colony rearing location


title: Bronchail Epithelial Cells treated with Winter07 H2O for 3 hr

description: Gene expression data from Bronchail Epithelial cells treated with  winter2007 H2O


title: ECRG4 set: BC202

tag: pt

tag: pn

tag: sbr grade

tag: er ihc

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

tag: tissue

value: breast cancer tumor


title: Bronchail Epithelial Cells treated with Sum06 APM for 3 hr

description: Gene expression data from Bronchail Epithelial cells treated with Summer2006 APM


title: ECRG4 set: BC203

tag: histology

value: other

tag: dfs evt

tag: dfs time (months)

value: Basal


title: ECRG4 set: BC199

tag: age at diagnosis

tag: molecular subtype


title: Bronchail Epithelial Cells treated with Sum06 H2O for 3 hr

description: Gene expression data from Bronchail Epithelial cells treated with Summer2006 H2O

tag: cell type


title: Aortic Endothelial Cells treated with Winter07 H2O for 3 hr

description: Gene expression data from Aortic Endothelial cell treated with winter2007 H2O


title: ECRG4 set: BC200


title: petiverana 12hr wingsection3 rep1

tag: genotype

value: pure H. erato petiverana

tag: phenotype

tag: slide number and position of the samples in each array

tag: origin of the colony

tag: wing phenotype

value: apical pupal wings section


title: petiverana 12hr wingsection1 rep1

value: red band in the middle of the forewing on a black backround and a completely black hindwing

tag: developmental stage

tag: colony rearing location


title: ECRG4 set: BC201

value: ILC

tag: pn

tag: sbr grade

tag: er ihc

tag: pr ihc

value: Normal


title: ECRG4 set: BC198

tag: histology

tag: pt

tag: p53 ihc

tag: ki67 ihc

value: LuminalA

tag: tissue


title: Aortic Endothelial Cells treated with Sum06 APM for 3 hr

description: Gene expression data from Aortic Endothelial cells treated with Summer2006 APM

tag: cell type


title: petiverana 12hr wingsection1 rep2

tag: genotype

value: Panama

value: black


title: ECRG4 set: BC197

tag: age at diagnosis

tag: dfs evt

tag: dfs time (months)

tag: molecular subtype


title: Aortic Endothelial Cells treated with Sum06 H2O for 3 hr

description: Gene expression data from Aortic Endothelial cells treated with Summer2006 H2O

value: Aortic Endothelial Cells


title: Daptomycin non-suceptible strain DAPR 5 hours growth replicate 3

type: mixed

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

description: Staphylococcus aureus daptomycin non-suceptible strain 701 DAPR versus Staphylococcus aureus gDNA pool

hyb_protocol: A mixture of RNA from WT or DAPR strains and gDNA pool was diluted in 50 µl Agilent hybridization buffer, and hybridized at a temperature of 60°C for 17 hours in a dedicated hybridization oven.

scan_protocol: 100% PMT using Agilent scanner

data_processing: Local background-subtracted signals were corrected for unequal dye incorporation or unequal load of labelled product. The algorithm consisted of a rank consistency filter and a curve fit using the default LOWESS (locally weighted linear regression) method.

label: cyanine 3

organism: Staphylococcus aureus

source_name: S. aureus 701 DAPR

label_protocol: Incorporation during reverse transcription

growth_protocol: 5 hours growth in Muller-Hinton

extract_protocol: RNAprotectTM Bacteria Reagent (Qiagen, Hilden, Germany) and immediately incubated on ice. After centrifugation for 10 min at 6.000 x g and 4°C, the supernatant was discarded and the pellet resuspended in 1 ml RLT-buffer (Qiagen) supplemented with 1 % (vol/vol) β-mercaptoethanol. Cells were disrupted in Lysing Matrix E (MP Biomedicals) using a FastPrep®-24 (MP Biomedicals, Solon, OH, USA), followed by cooling on ice for 2 min. After brief centrifugation, the supernatant was purified using RNeasy®Mini Kit. Final treatment with DNase for 1 h at 37°C and again purified with RNeasy®Mini Kit.

treatment_protocol: no treatments

tag: strain

label: cyanine 5

source_name: gDNA pool

tag: reference

value: Staphylococcus aureus gDNA mixture


title: ECRG4 set: BC196

tag: pn

value: LuminalB


title: Daptomycin non-suceptible strain DAPR 5 hours growth replicate 2


title: Daptomycin non-suceptible strain DAPR 5 hours growth replicate 1


title: hybrid 156hr wingsection1 rep3

description: The color pattern in the butterfly used to dissect the three forewing sections is represented as: F1) basal red, F2) middle yellow, F3) apical black

organism: Heliconius erato etylus x Heliconius himera

source_name: Heliconius erato hybrid pupal forewings, basal pupal wings section, 156hr after pupation

value: hybrid butterfly obtained crossing H. erato etylus and H. himera

tag: phenotype

value: red basal forewing with a yellow middle forewing band and red rays in the hindwing on a black backround

tag: slide number and position of the samples in each array

tag: origin of the colony

value: Ecuador

tag: wing phenotype

value: red

tag: developmental stage

value: 156 hours after pupation

tag: colony rearing location

value: Puerto Rico


title: ECRG4 set: BC194

tag: histology

value: IDC

tag: sbr grade

tag: er ihc

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

value: breast cancer tumor


title: ECRG4 set: BC195

tag: age at diagnosis

tag: pt

tag: dfs evt

tag: dfs time (months)

value: Basal

tag: tissue


title: ECRG4 set: BC193

tag: pn

tag: molecular subtype


title: Daptomycin suceptible strain WT 5 hours growth replicate 3

description: Staphylococcus aureus daptomycin suceptible strain 616 WT versus Staphylococcus aureus gDNA pool

source_name: S. aureus 616 WT

tag: strain

tag: reference


title: ECRG4 set: BC191


title: hybrid 156hr wingsection1 rep2

tag: genotype

tag: phenotype

tag: slide number and position of the samples in each array

tag: origin of the colony

tag: wing phenotype

value: basal pupal wings section

tag: developmental stage


title: ECRG4 set: BC192

tag: histology

tag: sbr grade

tag: er ihc

tag: pr ihc

tag: p53 ihc


title: Daptomycin suceptible strain WT 5 hours growth replicate 1


title: ECRG4 set: BC188

tag: age at diagnosis

value: other

tag: pt

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)


title: ECRG4 set: BC189

value: MIX

tag: pn

tag: molecular subtype

value: LuminalA

tag: tissue


title: ECRG4 set: BC187


title: ECRG4 set: BC186

value: Normal


title: ECRG4 set: BC185


title: petiverana 12hr wingsection2 rep1

tag: genotype

value: pure H. erato petiverana

tag: phenotype

value: red band in the middle of the forewing on a black backround and a completely black hindwing

tag: slide number and position of the samples in each array

value: Panama

value: middle pupal wings section

value: 12 hours after pupation

tag: colony rearing location


title: hybrid 156hr wingsection1 rep1

value: hybrid butterfly obtained crossing H. erato etylus and H. himera

value: red basal forewing with a yellow middle forewing band and red rays in the hindwing on a black backround

tag: origin of the colony

value: Ecuador

tag: wing phenotype

tag: developmental stage


title: ECRG4 set: BC190

tag: histology

tag: sbr grade

tag: er ihc

tag: pr ihc


title: hybrid 156hr wingsection3 rep3

source_name: Heliconius erato hybrid pupal forewings, apical pupal wings section, 156hr after pupation

value: black

value: apical pupal wings section

value: 156 hours after pupation

value: Puerto Rico


title: hybrid 156hr wingsection2 rep3

source_name: Heliconius erato hybrid pupal forewings, middle pupal wings section, 156hr after pupation

value: yellow


title: ECRG4 set: BC183

tag: age at diagnosis

value: IDC

tag: p53 ihc

tag: ki67 ihc

value: breast cancer tumor


title: Daptomycin suceptible strain WT 5 hours growth replicate 2

tag: strain

tag: reference

value: Staphylococcus aureus gDNA mixture


title: ECRG4 set: BC184

tag: pt

tag: pn

tag: dfs evt

tag: dfs time (months)

tag: molecular subtype

value: Basal

tag: tissue


title: hybrid 156hr wingsection3 rep2

tag: genotype

tag: phenotype

tag: slide number and position of the samples in each array

tag: origin of the colony

tag: wing phenotype

tag: colony rearing location


title: ECRG4 set: BC182

tag: age at diagnosis

tag: histology

tag: sbr grade

tag: er ihc

tag: pr ihc


title: ECRG4 set: BC178

tag: pt

tag: p53 ihc

tag: ki67 ihc


title: ECRG4 set: BC180

tag: pn

tag: dfs evt

tag: dfs time (months)

value: LuminalA


title: Col-0 treated with 9-KOT vs Col-0 treated with water, after both treated with PstDC3000 48h Rep 4

city: Madrid

first: Jorge

last: Vicente

address: Darwin

country: Spain

institute: CSIC

description: Biological replicate 4 of 4. Gene expression of Col-0 treated with 9-KOT vs  Col-0 treated with water, after both treated with Pst DC3000, 48h

hyb_protocol: The hybridization experiment was performed according to the manufacture's protocol (Agilent technologies, Agilent 60-mer oligo microarray processing protocol: Two color microarray based gene expression analysis, G4140-90050 ver 5.7)

scan_protocol: Images from Cy3 and Hyper5 channels were equilibrated and captured with a GenePix 4000B (Axon) and spots were converted into numerical data using GenPix software (Axon).

data_processing: Raw intensities were background-substracted by NORMEXP method with a offset of 50. Signals (in log2 scale) were then normalized by LOWESS algorithm (intra-arrays normalization) followed by adjustment of their quantiles (inter-arrays normalization).

organism: Arabidopsis thaliana

label_protocol: 5 ug of aminoallyl-labeled aRNA were resuspended in 0.1 M Na2CO3 (pH 9.0) and labeled with Hyper5 and Cy3 Mono NHS Ester (CyTMDye Post-labeling Reactive Dye Pack, Amersham). Samples were purified following the manufacturer's instructions for Megaclear TM (Ambion) and Hyper5  and Cy3 incorporation was measured using 1 ul of the probe in the Nanodrop

growth_protocol: Seeds were sown on soil, vernalized for three days at 4°, and grown in chamber at 22° and 70% relative humidity under a 14 hours light, 10 hours dark photoperiod at 250 uE m-2 sec-1 fluorescent illumination. Plants were treated and examined between 3 and 4 weeks after seed germination.

extract_protocol: The frozen plant tissue (~100 mg) was ground in tiny mortars dipped in liquid nitrogen. The frozen powder was carefully transfered into 1.5 ml microcentrifuge tubes using small funnels and rubber spatulas also cooled with liquid nitrogen. Total RNA was extracted using TRIzol reagent (Invitrogen, 15596-026) according to manufacturer's instructions and purified with an RNeasy mini kit (Qiagen, 74104).1 ug of total RNA was amplified via the aRNA MessageAmp II kit (Ambion, 1751)

treatment_protocol: The plants were treated and with 150uM 9-KOT or water; the plants were treated and with 150uM 9-KOT or water and after both with PstDC3000 (106ufc/ml)

tag: ecotype

source_name: water/Pst DC3000/48h


title: hybrid 156hr wingsection3 rep1

tag: genotype

tag: phenotype

tag: tissue

tag: developmental stage


title: hybrid 156hr wingsection2 rep2

tag: slide number and position of the samples in each array

tag: origin of the colony

tag: wing phenotype

tag: colony rearing location


title: Col-0 treated with 9-KOT vs Col-0 treated with water, after both treated with PstDC3000 48h Rep 2

description: Biological replicate 2 of 4. Gene expression of Col-0 treated with 9-KOT vs  Col-0 treated with water, after both treated with Pst DC3000, 48h


title: Col-0 treated with 9-KOT vs Col-0 treated with water, after both treated with PstDC3000 48h Rep 3

description: Biological replicate 3 of 4. Gene expression of Col-0 treated with 9-KOT vs  Col-0 treated with water, after both treated with Pst DC3000, 48h


title: ECRG4 set: BC176

tag: age at diagnosis

tag: histology

tag: sbr grade

tag: er ihc

tag: molecular subtype


title: ECRG4 set: BC175

tag: pt

tag: pn

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc


title: hybrid 180hr wingsection3 rep3

source_name: Heliconius erato hybrid pupal forewings, apical pupal wings section, 180hr after pupation

tag: genotype

tag: phenotype

value: 180 hours after pupation


title: ECRG4 set: BC172

tag: dfs evt

tag: dfs time (months)

tag: tissue


title: ECRG4 set: BC177

value: LuminalB


title: ECRG4 set: BC173


title: hybrid 156hr wingsection2 rep1

tag: slide number and position of the samples in each array

tag: origin of the colony

tag: wing phenotype

value: middle pupal wings section

tag: developmental stage


title: Col-0 treated with 9-KOT vs Col-0 treated with water, after both treated with PstDC3000 48h Rep 1

description: Biological replicate 1 of 4. Gene expression of Col-0 treated with 9-KOT vs  Col-0 treated with water, after both treated with Pst DC3000, 48h

tag: ecotype


title: ECRG4 set: BC170

tag: age at diagnosis

tag: histology

tag: sbr grade

tag: er ihc


title: Col-0 treated with 9-KOT vs Col-0 treated with water, after both treated with PstDC3000 24h Rep 4

description: Biological replicate 4 of 4. Gene expression of Col-0 treated with 9-KOT vs  Col-0 treated with water, after both treated with Pst DC3000, 24h

source_name: water/Pst DC3000/24h


title: hybrid 180hr wingsection2 rep3

source_name: Heliconius erato hybrid pupal forewings, middle pupal wings section, 180hr after pupation

tag: colony rearing location


title: hybrid 180hr wingsection1 rep3

source_name: Heliconius erato hybrid pupal forewings, basal pupal wings section, 180hr after pupation

value: red

value: basal pupal wings section


title: ECRG4 set: BC169

source_name: human breast cancer tumors

tag: pt

tag: pn

tag: pr ihc

tag: p53 ihc

tag: molecular subtype


title: ECRG4 set: BC165

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)


title: Col-0 treated with 9-KOT vs Col-0 treated with water, after both treated with PstDC3000 24h Rep 2

description: Biological replicate 2 of 4. Gene expression of Col-0 treated with 9-KOT vs  Col-0 treated with water, after both treated with Pst DC3000, 24h


title: ECRG4 set: BC179

tag: tissue


title: hybrid 180hr wingsection3 rep2

source_name: Heliconius erato hybrid pupal forewings, apicalpupal wings section, 180hr after pupation

tag: genotype

value: hybrid butterfly obtained crossing H. erato etylus and H. himera

tag: phenotype

value: red basal forewing with a yellow middle forewing band and red rays in the hindwing on a black backround

tag: slide number and position of the samples in each array

tag: origin of the colony

tag: wing phenotype

value: apicalpupal wings section


title: ECRG4 set: BC171

tag: age at diagnosis

tag: histology

tag: sbr grade


title: ECRG4 set: BC163

tag: pt

tag: er ihc


title: ECRG4 set: BC166

tag: pn

tag: pr ihc


title: Col-0 treated with 9-KOT vs Col-0 treated with water 24h Rep 4

description: Biological replicate 4 of 4. Gene expression of Col-0 treated with 9-KOT vs  Col-0 treated with water, 24h

tag: ecotype


title: ECRG4 set: BC168

tag: p53 ihc

tag: ki67 ihc

tag: molecular subtype


title: ECRG4 set: BC167

tag: dfs evt

tag: dfs time (months)

tag: tissue


title: Col-0 treated with 9-KOT vs Col-0 treated with water, after both treated with PstDC3000 24h Rep 1

description: Biological replicate 1 of 4. Gene expression of Col-0 treated with 9-KOT vs  Col-0 treated with water, after both treated with Pst DC3000, 24h


title: hybrid 180hr wingsection2 rep2

tag: genotype

tag: phenotype

tag: slide number and position of the samples in each array

value: Ecuador

tag: developmental stage

tag: colony rearing location


title: ECRG4 set: BC164

tag: age at diagnosis

tag: histology

tag: sbr grade


title: ECRG4 set: BC161

tag: pt

tag: pn

tag: er ihc


title: ECRG4 set: BC162

tag: pr ihc

tag: p53 ihc


title: Col-0 treated with 9-KOT vs Col-0 treated with water, after both treated with PstDC3000 24h Rep 3

description: Biological replicate 3 of 4. Gene expression of Col-0 treated with 9-KOT vs  Col-0 treated with water, after both treated with Pst DC3000, 24h

tag: ecotype


title: hybrid 180hr wingsection1 rep1

tag: origin of the colony

tag: wing phenotype


title: hybrid 180hr wingsection1 rep2

tag: tissue


title: ECRG4 set: BC159

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)

tag: molecular subtype


title: ECRG4 set: BC158


title: ECRG4 set: BC160


title: hybrid 180hr wingsection2 rep1

tag: genotype

tag: phenotype

tag: slide number and position of the samples in each array

tag: developmental stage

tag: colony rearing location


title: Col-0 treated with 9-KOT vs Col-0 treated with water 24h Rep 2

description: Biological replicate 2 of 4. Gene expression of Col-0 treated with 9-KOT vs  Col-0 treated with water, 24h


title: ECRG4 set: BC156

tag: age at diagnosis

tag: histology

tag: pt

tag: pn

tag: sbr grade

value: Normal


title: Col-0 treated with 9-KOT vs Col-0 treated with water 24h Rep 1

description: Biological replicate 1 of 4. Gene expression of Col-0 treated with 9-KOT vs  Col-0 treated with water, 24h

tag: ecotype


title: ECRG4 set: BC153

tag: er ihc

tag: pr ihc

tag: p53 ihc


title: hybrid 180hr wingsection3 rep1

tag: origin of the colony

tag: wing phenotype

value: black

tag: tissue

value: apical pupal wings section

value: Puerto Rico


title: hybrid 108hr wingsection1 rep3

source_name: Heliconius erato hybrid pupal forewings, basal pupal wings section, 108hr after pupation

tag: genotype

value: 108 hours after pupation


title: hybrid 108hr wingsection3 rep3

source_name: Heliconius erato hybrid pupal forewings, apical pupal wings section, 108hr after pupation

tag: phenotype


title: hybrid 108hr wingsection2 rep3

source_name: Heliconius erato hybrid pupal forewings, middle pupal wings section, 108hr after pupation

tag: slide number and position of the samples in each array

value: yellow


title: Col-0 treated with 9-KOT vs Col-0 treated with water 8h Rep 3

description: Biological replicate 3 of 4. Gene expression of Col-0 treated with 9-KOT vs  Col-0 treated with water, 8h


title: Col-0 treated with 9-KOT vs Col-0 treated with water 8h Rep 2

description: Biological replicate 2 of 4. Gene expression of Col-0 treated with 9-KOT vs  Col-0 treated with water, 8h


title: ECRG4 set: BC157

value: IDC

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)

tag: molecular subtype

value: Basal

value: breast cancer tumor


title: ECRG4 set: BC151

tag: age at diagnosis

tag: histology

tag: pt

value: LuminalA


title: ECRG4 set: BC150

tag: pn

tag: sbr grade


title: ECRG4 set: BC154

tag: er ihc

tag: pr ihc


title: ECRG4 set: BC152

tag: p53 ihc


title: Col-0 treated with 9-KOT vs Col-0 treated with water 8h Rep 1

description: Biological replicate 1 of 4. Gene expression of Col-0 treated with 9-KOT vs  Col-0 treated with water, 8h

tag: ecotype


title: Col-0 treated with 9-KOT vs Col-0 treated with water 8h Rep 4

description: Biological replicate 4 of 4. Gene expression of Col-0 treated with 9-KOT vs  Col-0 treated with water, 8h


title: Col-0 treated with 9-KOT vs Col-0 treated with water 2h Rep 4

description: Biological replicate 4 of 4. Gene expression of Col-0 treated with 9-KOT vs  Col-0 treated with water, 2h


title: ECRG4 set: BC148

tag: tissue


title: ECRG4 set: BC145


title: ECRG4 set: BC147


title: ECRG4 set: BC149


title: hybrid 108hr wingsection3 rep2

description: The color pattern in the butterfly used to dissect the three forewing sections is represented as: F1) basal red, F2) middle yellow, F3) apical black

tag: genotype

tag: origin of the colony

tag: wing phenotype

tag: developmental stage

tag: colony rearing location


title: Col-0 treated with 9-KOT vs Col-0 treated with water 24h Rep 3

description: Biological replicate 3 of 4. Gene expression of Col-0 treated with 9-KOT vs  Col-0 treated with water, 24h


title: ECRG4 set: BC146

value: MIX

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)

value: LuminalB


title: ECRG4 set: BC144

tag: age at diagnosis

tag: histology

tag: molecular subtype


title: ECRG4 set: BC143

tag: pt

tag: pn

tag: sbr grade


title: hybrid 108hr wingsection1 rep2

tag: phenotype

tag: slide number and position of the samples in each array

value: red

value: basal pupal wings section


title: hybrid 108hr wingsection2 rep2

value: hybrid butterfly obtained crossing H. erato etylus and H. himera

value: red basal forewing with a yellow middle forewing band and red rays in the hindwing on a black backround

tag: tissue

value: middle pupal wings section


title: hybrid 108hr wingsection3 rep1

tag: genotype

value: Ecuador


title: Col-0 treated with 9-KOT vs Col-0 treated with water 2h Rep 2

description: Biological replicate 2 of 4. Gene expression of Col-0 treated with 9-KOT vs  Col-0 treated with water, 2h

tag: ecotype


title: ECRG4 set: BC142

tag: er ihc

tag: pr ihc

tag: p53 ihc


title: Col-0 treated with 9-KOT vs Col-0 treated with water 30min Rep 4

description: Biological replicate 4 of 4. Gene expression of Col-0 treated with 9-KOT vs  Col-0 treated with water, 30min

source_name: 9-KOT/30 min

source_name: water/30 min


title: hybrid 108hr wingsection1 rep1

tag: origin of the colony

tag: wing phenotype

tag: developmental stage

tag: colony rearing location


title: hybrid 108hr wingsection2 rep1


title: ECRG4 set: BC139

tag: age at diagnosis

tag: histology

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)


title: hybrid 60hr wingsection3 rep3

source_name: Heliconius erato hybrid pupal forewings, apical pupal wings section, 60hr after pupation

tag: phenotype

value: black

value: 60 hours after pupation


title: hybrid 60hr wingsection2 rep3

source_name: Heliconius erato hybrid pupal forewings, middle pupal wings section, 60hr after pupation

tag: slide number and position of the samples in each array

value: Puerto Rico


title: Col-0 treated with 9-KOT vs Col-0 treated with water 30min Rep 1

description: Biological replicate 1 of 4. Gene expression of Col-0 treated with 9-KOT vs  Col-0 treated with water, 30min


title: Col-0 treated with 9-KOT vs Col-0 treated with water 2h Rep 1

description: Biological replicate 1 of 4. Gene expression of Col-0 treated with 9-KOT vs  Col-0 treated with water, 2h


title: ECRG4 set: BC137

tag: pt

tag: pn

tag: sbr grade

tag: molecular subtype

value: Normal

tag: tissue


title: ECRG4 set: BC134

tag: er ihc

tag: pr ihc

tag: p53 ihc


title: Col-0 treated with 9-KOT vs Col-0 treated with water 2h Rep 3

description: Biological replicate 3 of 4. Gene expression of Col-0 treated with 9-KOT vs  Col-0 treated with water, 2h

tag: ecotype


title: ECRG4 set: BC135


title: ECRG4 set: BC138

value: ILC


title: ECRG4 set: BC136

value: IDC


title: hybrid 60hr wingsection2 rep2

tag: genotype

tag: origin of the colony

tag: wing phenotype

value: yellow

tag: developmental stage

tag: colony rearing location


title: hybrid 60hr wingsection2 rep1


title: Col-0 treated with 9-KOT vs Col-0 treated with water 30min Rep 2

description: Biological replicate 2 of 4. Gene expression of Col-0 treated with 9-KOT vs  Col-0 treated with water, 30min


title: ECRG4 set: BC132

tag: age at diagnosis

tag: histology

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)

value: breast cancer tumor


title: ECRG4 set: BC131

tag: pt

tag: pn

tag: sbr grade

value: Basal


title: hybrid 60hr wingsection1 rep3

source_name: Heliconius erato hybrid pupal forewings, basal pupal wings section, 60hr after pupation

tag: phenotype

tag: slide number and position of the samples in each array

tag: tissue


title: ECRG4 set: BC129

tag: er ihc

tag: pr ihc

tag: p53 ihc

tag: molecular subtype


title: ECRG4 set: BC133

value: LuminalA


title: Col-0 treated with 9-KOT vs Col-0 treated with water 30min Rep 3

description: Biological replicate 3 of 4. Gene expression of Col-0 treated with 9-KOT vs  Col-0 treated with water, 30min

tag: ecotype


title: ECRG4 set: BC130


title: Blood_15mg silica, 4 week post-exposure_rep6

city: Morgantown

first: Rajendran

last: Sellamuthu

state: WV

address: 1095 Willowdale Rd

department: HELD

description: The labeling and hybridization of microarray were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

hyb_protocol: Employing materials and protocols provided by Illumina, Inc (San Diego, CA), each labeled cRNA sample was hybridized to RatRef-12 v1.0 expression beadchip (Illumina, Inc) for 20 hrs at 580C. Following hybridization, microarrays were washed to remove unbound and non-specifically hybridized target molecules and stained with Cy3-streptavidin conjugate (Illumina, Inc). This was followed by a non-stringent washing to remove unbound conjugate.

scan_protocol: The arrays were scanned with the Illumina BeadStation 500 platform, following the protocol provided by the manufacturer (Illumina, Inc, San Diego, CA).

data_processing: Array data were extracted using Illumina's BeadStudio software (Framework version 3.0.19.0). Normalization and statistical analysis of the expression data were carried out in R/Bioconductor using the 'lumi' and 'limma' packages. The 'lumi' Bioconductor package covered the data input, quality control, force positive background correction, variance stabilization, normalization and gene annotation (http://bioconductor.org/packages/2.2/bioc/vignettes/lumi/inst/doc/lumi.pdf). Robust spline normalization was used to generate the values in the matrix table. After normalization, Lumi code deletes undetected genes, resulting in a subset of genes detected on the array. A linear model analysis using the 'limma' package in R was conducted to identify differentially expressed genes. p values were calculated and log fold changes were converted to standard fold changes. Resulting raw p-values were corrected for false discovery rate using the Benjamini-Hochberg method.

organism: Rattus norvegicus

source_name: 15mg/m3 silica, 4 week post-exposure rat 38 blood

label_protocol: Biotin-labeled cRNA was generated from 375 ng RNA samples each by employing the Illumina TotalPrep RNA Amplification Kit (Ambion, Inc, Austin, TX).

growth_protocol: Rats were housed in the animal facility at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV. The animals were kept under controlled lighting (12-hour light-dark cycle), temperature (72± 50 F), and humidity (50 ± 20%) with free access to food and water.

extract_protocol: Total RNA was isolated from the blood samples using Mouse RibopureTM Blood isolation kit (Ambion Inc, Austin, TX) following the protocol provided by the kit manufacturer. The total RNA isolated was digested with RNase-free DNase and further purified using RNeasy Mini kit (Qiagen Inc, Valencia, CA) following the recommendations of the supplier. The globin mRNA present in abundance in the blood RNA samples was depleted using the GlobinclearTM – Mouse/Rat globin mRNA removal kit (Ambion Inc, Austin, TX).

treatment_protocol: Rats were exposed to air (control) or crystalline silica by inhalation (1, 2, or 15 mg/m3, 6 hours/day, 5 days). Rats exposed to 1 or 2 mg/m3, 6 hours/day, 5 days and the corresponding control were sacrificed at 16-hours following the last silica exposure. Rats exposed to 15 mg/m3, 6 hours/day, 5 days and corresponding controls were sacrificed at post-exposure time intervals of 0, 1, 2, 4, 8, and 16 weeks.

tag: strain

value: CDF Fisher 344

tag: gender

value: male

tag: age

value: 3 mo

value: blood

tag: treatment

value: 15mg silica

tag: time

value: 4 week post-exposure


title: Blood_15mg silica, 8 week post-exposure_rep4

institute: National Institute for Occupational Safety and Health

source_name: 15mg/m3 silica, 8 week post-exposure rat 20 blood

value: 8 week post-exposure


title: ECRG4 set: BC155

tag: age at diagnosis

tag: histology

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)


title: ECRG4 set: BC126

tag: pt

tag: pn

tag: sbr grade


title: hybrid 60hr wingsection3 rep2

tag: genotype

value: hybrid butterfly obtained crossing H. erato etylus and H. himera

tag: phenotype

value: red basal forewing with a yellow middle forewing band and red rays in the hindwing on a black backround

tag: slide number and position of the samples in each array

tag: origin of the colony

value: Ecuador

tag: wing phenotype

value: black

tag: tissue

value: apical pupal wings section

tag: developmental stage

tag: colony rearing location


title: ECRG4 set: BC141

value: IDC

tag: er ihc

tag: pr ihc

tag: p53 ihc

tag: molecular subtype


title: ECRG4 set: BC127

tag: age at diagnosis

tag: histology

tag: ki67 ihc

tag: dfs evt


title: Blood_15mg silica, 2 week post-exposure_rep4

source_name: 15mg/m3 silica, 2 week post-exposure rat 52 blood

tag: strain

tag: gender

tag: age

tag: treatment

tag: time

value: 2 week post-exposure


title: ECRG4 set: BC128

tag: pt

tag: pn

tag: sbr grade

tag: dfs time (months)

value: Normal

value: breast cancer tumor


title: ECRG4 set: BC124

tag: er ihc

value: LuminalB

tag: tissue


title: hybrid 60hr wingsection1 rep2

tag: genotype

tag: phenotype

tag: slide number and position of the samples in each array

tag: origin of the colony

tag: wing phenotype

value: red

value: basal pupal wings section

tag: developmental stage

value: 60 hours after pupation

tag: colony rearing location

value: Puerto Rico


title: ECRG4 set: BC125

tag: age at diagnosis

tag: histology

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt

tag: molecular subtype

value: LuminalA


title: Blood_15mg silica, 16 week post-exposure_rep3

source_name: 15mg/m3 silica, 16 week post-exposure rat 3 blood

tag: strain

value: CDF Fisher 344

tag: gender

value: male

tag: age

value: 3 mo

value: blood

tag: treatment

value: 15mg silica

tag: time

value: 16 week post-exposure


title: ECRG4 set: BC121

tag: pt

tag: pn

tag: sbr grade

tag: er ihc

tag: dfs time (months)

tag: tissue


title: ECRG4 set: BC123

tag: age at diagnosis

tag: histology


title: ECRG4 set: BC122

tag: pr ihc

tag: p53 ihc


title: hybrid 60hr wingsection1 rep1

tag: genotype

value: hybrid butterfly obtained crossing H. erato etylus and H. himera

tag: phenotype

value: red basal forewing with a yellow middle forewing band and red rays in the hindwing on a black backround

tag: slide number and position of the samples in each array

tag: origin of the colony

value: Ecuador

tag: wing phenotype

tag: developmental stage

tag: colony rearing location


title: hybrid 60hr wingsection3 rep1

value: black

value: apical pupal wings section


title: ECRG4 set: BC119

value: IDC

tag: pt

tag: ki67 ihc

tag: dfs evt

tag: molecular subtype

value: LuminalB

value: breast cancer tumor


title: hybrid 12hr wingsection1 rep2

source_name: Heliconius erato hybrid pupal forewings, basal pupal wings section, 12hr after pupation

value: red

value: basal pupal wings section

value: 12 hours after pupation


title: hybrid 12hr wingsection2 rep2

source_name: Heliconius erato hybrid pupal forewings, middle pupal wings section, 12hr after pupation

value: yellow

value: middle pupal wings section

value: Puerto Rico


title: Blood_15mg silica, 1 week post-exposure_rep6

source_name: 15mg/m3 silica, 1 week post-exposure rat 70 blood

tag: strain

value: CDF Fisher 344

tag: gender

value: male

tag: age

value: 3 mo

value: blood

tag: treatment

tag: time

value: 1 week post-exposure


title: ECRG4 set: BC120

source_name: human breast cancer tumors

tag: age at diagnosis

tag: histology

tag: pn

tag: sbr grade

tag: er ihc

tag: pr ihc

tag: p53 ihc

tag: dfs time (months)

value: LuminalA

tag: tissue


title: ECRG4 set: BC115

tag: pt

tag: ki67 ihc


title: Blood_0mg silica, 0 week post-exposure_rep3 (control for 1mg silica)

source_name: 0mg/m3 silica, 0 week post-exposure rat 139 blood (control for 1mg/m3 silica)

value: 0mg silica

value: 0 week post-exposure


title: ECRG4 set: BC113

value: IDC

tag: dfs evt

tag: molecular subtype


title: Blood_0mg silica, 0 week post-exposure_rep2 (control for 2mg silica)

source_name: 0mg/m3 silica, 0 week post-exposure rat 106 blood (control for 2mg/m3 silica)

tag: strain

tag: gender


title: ECRG4 set: BC114

value: LuminalB


title: ECRG4 set: BC118

value: TUB

value: breast cancer tumor


title: ECRG4 set: BC116

value: MIX


title: ECRG4 set: BC111

value: ILC

value: Normal


title: Blood_1mg silica, 0 week post-exposure_rep6

source_name: 1mg/m3 silica, 0 week post-exposure rat 134 blood

tag: age

tag: treatment

value: 1mg silica


title: ECRG4 set: BC112

tag: age at diagnosis

value: other

value: Basal


title: Blood_15mg silica, 0 week post-exposure_rep6

source_name: 15mg/m3 silica, 0 week post-exposure rat 86 blood

value: CDF Fisher 344

value: male

value: 15mg silica

tag: time


title: hybrid 12hr wingsection1 rep1

source_name: Heliconius erato hybrid pupal forewings, basal pupal wings sectiong, 12hr after pupation

tag: genotype

value: hybrid butterfly obtained crossing H. erato etylus and H. himera

tag: phenotype

value: red basal forewing with a yellow middle forewing band and red rays in the hindwing on a black backround

tag: slide number and position of the samples in each array

tag: origin of the colony

value: Ecuador

tag: wing phenotype

value: red

value: basal pupal wings sectiong

tag: developmental stage

value: 12 hours after pupation

tag: colony rearing location

value: Puerto Rico


title: hybrid 12hr wingsection2 rep1

value: yellow

tag: tissue

value: middle pupal wings section


title: hybrid 12hr wingsection3 rep1

source_name: Heliconius erato hybrid pupal forewings, apical pupal wings section, 12hr after pupation

value: black

value: apical pupal wings section


title: Blood_1mg silica, 0 week post-exposure_rep5

source_name: 1mg/m3 silica, 0 week post-exposure rat 133 blood

value: 3 mo

value: blood

value: 1mg silica

value: 0 week post-exposure


title: ECRG4 set: BC140

tag: histology

value: ILC

tag: pt

tag: pn

tag: sbr grade

tag: er ihc

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

tag: dfs time (months)

value: LuminalA

value: breast cancer tumor


title: ECRG4 set: BC107

tag: age at diagnosis

value: IDC

tag: dfs evt

tag: molecular subtype

value: Basal


title: ECRG4 set: BC108


title: ECRG4 set: BC110

value: Normal


title: ECRG4 set: BC109


title: ECRG4 set: BC117

value: LuminalB


title: ECRG4 set: BC106


title: Blood_2mg silica, 0 week post-exposure_rep7

source_name: 2mg/m3 silica, 0 week post-exposure rat 103 blood

tag: strain

value: CDF Fisher 344

tag: gender

value: male

tag: age

tag: treatment

value: 2mg silica

tag: time


title: healthy vs coagulase - negative Staphylococci 16

city: Berlin

first: Pawel

last: Lisowski

address: Hannoversche Str. 28

country: Germany

institute: Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association

description:
3,4 lactation is a second experimental group consisting of pooled RNA from cow in 3rd and 4th stage of lactation.
Biological replicate 4 of 4, technical replicate 2 of 2

hyb_protocol: Standard Agilent hybridization protocol.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Background correction method normexp was used and followed by loess method for within array normalization. Between array normalization was performed with the Aquantile method. Mean values of channels intensities were taken as an input and a median of background signal for background correction calculations.

organism: Bos taurus

source_name: quarter of mammary gland

label_protocol: 1000 ng of total RNA was using to labeling reaction with Quick Amp Labeling Kit, Two Color with Cy5 i Cy3 (Agilent ) according to the manufacturer’s protocol

extract_protocol: Total RNA extracted using Rnasy mini kit  following manufacturer's instructions Quantity and quality of each RNA sample was estimated by Nanodrop (Nanodrop, USA) and Bioanalyzer (Agilent, USA).

tag: breed

value: Holstein Friesian

tag: disease state

value: healthy tissue in 1,2,3,4 lactation

value: tissue infected with CoNS in 3,4 lactation


title: Blood_1mg silica, 0 week post-exposure_rep8

source_name: 1mg/m3 silica, 0 week post-exposure rat 136 blood

value: 3 mo

tag: tissue


title: Blood_15mg silica, 0 week post-exposure_rep8

source_name: 15mg/m3 silica, 0 week post-exposure rat 88 blood

value: blood

value: 15mg silica


title: hybrid 12hr wingsection3 rep2

tag: genotype

value: hybrid butterfly obtained crossing H. erato etylus and H. himera

tag: phenotype

value: red basal forewing with a yellow middle forewing band and red rays in the hindwing on a black backround

tag: slide number and position of the samples in each array

tag: origin of the colony

value: Ecuador

tag: wing phenotype

value: black

value: apical pupal wings section

tag: developmental stage

value: 12 hours after pupation

tag: colony rearing location

value: Puerto Rico


title: Blood_0mg silica, 0 week post-exposure_rep4 (control for 1mg silica)

source_name: 0mg/m3 silica, 0 week post-exposure rat 140 blood (control for 1mg/m3 silica)

value: 0mg silica

value: 0 week post-exposure


title: coagulase - negative Staphylococci vs healthy 15

description:
3,4 lactation is a second experimental group consisting of pooled RNA from cow in 3rd and 4th stage of lactation.
Biological replicate 4 of 4, technical replicate 1 of 2


title: healthy vs coagulase - negative Staphylococci 14

description:
3,4 lactation is a second experimental group consisting of pooled RNA from cow in 3rd and 4th stage of lactation.
Biological replicate 3 of 4, technical replicate 2 of 2


title: ECRG4 set: BC104

tag: age at diagnosis

tag: histology

value: IDC

tag: pt

tag: pn

tag: sbr grade

tag: er ihc

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)

value: LuminalA

value: breast cancer tumor


title: ECRG4 set: BC100

tag: molecular subtype

tag: tissue


title: ECRG4 set: BC105


title: ECRG4 set: BC102

value: Basal


title: Blood_15mg silica, 16 week post-exposure_rep8

source_name: 15mg/m3 silica, 16 week post-exposure rat 8 blood

tag: strain

value: CDF Fisher 344

tag: gender

value: male

tag: age

tag: treatment

tag: time

value: 16 week post-exposure


title: ECRG4 set: BC97

tag: age at diagnosis

tag: histology


title: ECRG4 set: BC103

value: TUB

tag: pt

tag: pn


title: coagulase - negative Staphylococci vs healthy 13

description:
3,4 lactation is a second experimental group consisting of pooled RNA from cow in 3rd and 4th stage of lactation.
Biological replicate 3 of 4, technical replicate 1 of 2

tag: breed

value: Holstein Friesian

tag: disease state

value: tissue infected with CoNS in 3,4 lactation

value: healthy tissue in 1,2,3,4 lactation


title: coagulase - negative Staphylococci vs healthy 11

description:
1,2 lactation is an first experimental group consisting of pooled RNA from cows in 1st and 2nd stage of lactation
Biological replicate 4 of 4, technical replicate 1 of 2

value: tissue infected with CoNS in 1,2 lactation


title: Blood_15mg silica, 8 week post-exposure_rep3

source_name: 15mg/m3 silica, 8 week post-exposure rat 19 blood

value: 3 mo

value: blood

value: 15mg silica

value: 8 week post-exposure


title: Blood_1mg silica, 0 week post-exposure_rep7

source_name: 1mg/m3 silica, 0 week post-exposure rat 135 blood

value: 1mg silica

value: 0 week post-exposure


title: ECRG4 set: BC99

value: IDC

tag: sbr grade

tag: er ihc

tag: pr ihc

tag: p53 ihc


title: healthy vs coagulase - negative Staphylococci 10

description:
1,2 lactation is an first experimental group consisting of pooled RNA from cows in 1st and 2nd stage of lactation
Biological replicate 3 of 4, technical replicate 2 of 2


title: ECRG4 set: BC101

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)

tag: molecular subtype

value: Normal

value: breast cancer tumor


title: ECRG4 set: BC96

value: LuminalA

tag: tissue


title: healthy vs coagulase - negative Staphylococci 12

description:
1,2 lactation is an first experimental group consisting of pooled RNA from cows in 1st and 2nd stage of lactation
Biological replicate 4 of 4, technical replicate 2 of 2


title: ECRG4 set: BC98

value: MIX


title: ECRG4 set: BC94

value: LuminalB


title: Blood_2mg silica, 0 week post-exposure_rep4

source_name: 2mg/m3 silica, 0 week post-exposure rat 100 blood

tag: strain

value: CDF Fisher 344

tag: gender

value: male

tag: age

tag: treatment

value: 2mg silica


title: ECRG4 set: BC95

source_name: human breast cancer tumors

tag: age at diagnosis

tag: histology

tag: pt


title: Blood_15mg silica, 2 week post-exposure_rep5

source_name: 15mg/m3 silica, 2 week post-exposure rat 53 blood

tag: time

value: 2 week post-exposure


title: Blood_0mg silica, 0 week post-exposure_rep1 (control for 2mg silica)

source_name: 0mg/m3 silica, 0 week post-exposure rat 105 blood (control for 2mg/m3 silica)

value: 0mg silica


title: Blood_15mg silica, 4 week post-exposure_rep7

source_name: 15mg/m3 silica, 4 week post-exposure rat 39 blood

value: 3 mo

value: 4 week post-exposure


title: healthy vs coagulase - positive Staphylococci 4

description:
1,2 lactation is an first experimental group consisting of pooled RNA from cows in 1st and 2nd stage of lactation
Biological replicate 2 of 4, technical replicate 2 of 2

tag: breed

value: Holstein Friesian

tag: disease state

value: healthy tissue in 1,2,3,4 lactation

value: tissue infected with CoPS in 1,2 lactation


title: ECRG4 set: BC88

tag: pn

tag: sbr grade

tag: er ihc

tag: pr ihc

value: Basal


title: Blood_2mg silica, 0 week post-exposure_rep6

source_name: 2mg/m3 silica, 0 week post-exposure rat 102 blood

value: blood

value: 0 week post-exposure


title: ECRG4 set: BC84

value: IDC

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)

value: breast cancer tumor


title: coagulase - positive Staphylococci vs healthy 7

description:
3,4 lactation is a second experimental group consisting of pooled RNA from cow in 3rd and 4th stage of lactation.
Biological replicate 2 of 4, technical replicate 1 of 2

value: tissue infected with CoPS in 3,4 lactation


title: ECRG4 set: BC91

tag: molecular subtype

value: LuminalA

tag: tissue


title: coagulase - positive Staphylococci vs healthy 5

description:
3,4 lactation is a second experimental group consisting of pooled RNA from cow in 3rd and 4th stage of lactation.
Biological replicate 1 of 4, technical replicate 1 of 2


title: ECRG4 set: BC83

value: MIX


title: ECRG4 set: BC93


title: ECRG4 set: BC80

value: ILC

value: Normal


title: healthy vs coagulase - positive Staphylococci 8

description:
3,4 lactation is a second experimental group consisting of pooled RNA from cow in 3rd and 4th stage of lactation.
Biological replicate 2 of 4, technical replicate 2 of 2


title: ECRG4 set: BC87


title: ECRG4 set: BC86


title: Blood_15mg silica, 1 week post-exposure_rep7

source_name: 15mg/m3 silica, 1 week post-exposure rat 71 blood

tag: strain

value: CDF Fisher 344

tag: gender

value: male

tag: age

tag: treatment

value: 15mg silica

value: 1 week post-exposure


title: coagulase - negative Staphylococci vs healthy 9

description:
1,2 lactation is an first experimental group consisting of pooled RNA from cows in 1st and 2nd stage of lactation
Biological replicate 3 of 4, technical replicate 1 of 2

value: Holstein Friesian

value: tissue infected with CoNS in 1,2 lactation


title: ECRG4 set: BC85

tag: age at diagnosis

tag: histology

tag: pt


title: ECRG4 set: BC89

tag: pn

value: LuminalB


title: healthy vs coagulase - positive Staphylococci 2

description:
1,2 lactation is an first experimental group consisting of pooled RNA from cows in 1st and 2nd stage of lactation
Biological replicate 1 of 4, technical replicate 2 of 2

tag: breed

tag: disease state

value: healthy tissue in 1,2,3,4 lactation

value: tissue infected with CoPS in 1,2 lactation


title: Blood_2mg silica, 0 week post-exposure_rep5

source_name: 2mg/m3 silica, 0 week post-exposure rat 101 blood

value: 3 mo

value: blood

value: 2mg silica

tag: time

value: 0 week post-exposure


title: healthy vs coagulase - positive Staphylococci 6

description:
3,4 lactation is a second experimental group consisting of pooled RNA from cow in 3rd and 4th stage of lactation.
Biological replicate 1 of 4, technical replicate 2 of 2

value: tissue infected with CoPS in 3,4 lactation


title: ECRG4 set: BC90

value: IDC

tag: sbr grade

tag: er ihc

tag: pr ihc

tag: p53 ihc

value: LuminalA

value: breast cancer tumor


title: Blood_15mg silica, 8 week post-exposure_rep8

source_name: 15mg/m3 silica, 8 week post-exposure rat 24 blood

value: CDF Fisher 344

value: 8 week post-exposure


title: ECRG4 set: BC81

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)

tag: molecular subtype


title: coagulase - positive Staphylococci vs healthy 3

description:
1,2 lactation is an first experimental group consisting of pooled RNA from cows in 1st and 2nd stage of lactation
Biological replicate 2 of 4, technical replicate 1 of 2


title: ECRG4 set: BC92

value: ILC

tag: tissue


title: Blood_15mg silica, 16 week post-exposure_rep2

source_name: 15mg/m3 silica, 16 week post-exposure rat 2 blood

tag: strain

tag: gender

value: male

tag: age

tag: treatment

value: 15mg silica

value: 16 week post-exposure


title: Blood_0mg silica, 0 week post-exposure_rep3 (control for 2mg silica)

source_name: 0mg/m3 silica, 0 week post-exposure rat 107 blood (control for 2mg/m3 silica)

value: 0mg silica


title: Blood_2mg silica, 0 week post-exposure_rep2

source_name: 2mg/m3 silica, 0 week post-exposure rat 98 blood


title: ECRG4 set: BC77

tag: age at diagnosis

tag: histology

tag: pt

tag: pn

value: Normal


title: ECRG4 set: BC76

tag: sbr grade

value: Basal


title: coagulase - positive Staphylococci vs healthy 1

description:
1,2 lactation is an first experimental group consisting of pooled RNA from cows in 1st and 2nd stage of lactation
Biological replicate 1 of 4, technical replicate 1 of 2

source_name: quarter of mammary gland

tag: breed

value: Holstein Friesian

tag: disease state

value: tissue infected with CoPS in 1,2 lactation

value: healthy tissue in 1,2,3,4 lactation


title: D105-3C-WT

city: Iowa City

first: Thomas

middle: B

last: Bair

state: IA

address: 335 EMRB

institute: University of Iowa

description: Gene expression data from nascent tumor cells

hyb_protocol: According to manf. protocol

scan_protocol: According to manf. Protocol Genechip 3000 Scanner

data_processing: Affymetrix Microarray Analysis Suite version 5.0., arrays were then imported into PartekGS (Partek Inc) and RMA normalized using default settings

organism: Mus musculus

source_name: Day 105, whole tissue

label_protocol: RNA from both PC and OG samples were put through two rounds of linear amplification using Affymetrix’s GeneChip 2-cycle cDNA Synthesis Kit according to the manufacturer’s protocol. The quality of the amplified and fragmented RNAs was assessed by the RNA 6000 Nano Labchip /2100  Bioanalyzer (Agilent). 20-50 ng of total intact RNA was labeled, fragmented and biotin labled.

growth_protocol: 8 week old mice

extract_protocol: Frozen sections of ip oil granulomata were fixed in 70% ethanol for 20 seconds, stained to identify plasma cells using methyl green pyronin (MGP) (Sigma)17 that also contained 300 U/mL of an RNase inhibitor (Superasin, Ambion) for two minutes with slight agitation, destained by a quick dip in RNAase-free water followed by two changes of 100% ethanol (3 and 30 seconds, respectively), dehydrated in two changes of xylene for 2 minutes each, and allowed to air dry. MGP-positive cells were microdissected on a Leica LMD6000 into 0.5 mL RNase-free tube caps containing 50 μL of RLT extraction buffer (Qiagen). Total RNA from both laser-microdissected MGP-positive cells (PC samples) and whole, undissected tissue (OG samples) sections was isolated using Allprep DNA/RNA Micro kits (Qiagen) according to the manufacturer’s protocol. RNA integrity was assessed via both NanoDrop 2000 Spectrophotometer (Thermo) and Agilent’s RNA 6000 Pico Labchip and 2100 Bioanalyzer. Samples showing degradation were not used in this investigation.

treatment_protocol: Two independent cohorts of BALB/c.iMycEμ mice were aged at least 8 weeks, allocated to 2 study groups and injected intraperitoneally with 0.5 ml of pristane (2,6,10,14-tetramethylpentadecane) oil.

tag: background strain

tag: tissue type

value: Whole tissue sections of ip oil granulomata

tag: experiment

value: study 2


title: ECRG4 set: BC73

value: MIX

tag: er ihc

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)


title: D105-1C-WT


title: ECRG4 set: BC74

value: IDC

tag: molecular subtype

tag: tissue


title: Blood_15mg silica, 2 week post-exposure_rep3

description: The labeling and hybridization of microarray were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 15mg/m3 silica, 2 week post-exposure rat 51 blood

tag: strain

tag: gender

tag: age

value: 3 mo

value: blood

tag: treatment

tag: time

value: 2 week post-exposure


title: ECRG4 set: BC70

tag: age at diagnosis

tag: histology

tag: pt

tag: pn

tag: sbr grade

value: LuminalB

value: breast cancer tumor


title: D49-3B-WT

source_name: Day 49, whole tissue

tag: background strain

tag: tissue type

tag: experiment


title: ECRG4 set: BC78

value: ILC

tag: er ihc

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt

value: LuminalA


title: D49-2A-WT


title: ECRG4 set: BC66

tag: dfs time (months)

tag: molecular subtype

tag: tissue


title: ECRG4 set: BC75


title: ECRG4 set: BC67


title: Blood_1mg silica, 0 week post-exposure_rep2

source_name: 1mg/m3 silica, 0 week post-exposure rat 130 blood

tag: strain

value: CDF Fisher 344

tag: gender

value: male

tag: age

tag: treatment

value: 1mg silica

tag: time

value: 0 week post-exposure


title: Blood_15mg silica, 4 week post-exposure_rep8

source_name: 15mg/m3 silica, 4 week post-exposure rat 40 blood

value: 15mg silica

value: 4 week post-exposure


title: ECRG4 set: BC72

source_name: human breast cancer tumors

tag: age at diagnosis

tag: histology

tag: pt

tag: pn

tag: sbr grade


title: ECRG4 set: BC79

tag: er ihc

tag: pr ihc

value: Basal


title: ECRG4 set: BC71

tag: p53 ihc

tag: ki67 ihc


title: ECRG4 set: BC69

tag: dfs evt

tag: dfs time (months)


title: Blood_2mg silica, 0 week post-exposure_rep1

source_name: 2mg/m3 silica, 0 week post-exposure rat 97 blood

tag: tissue

value: 2mg silica


title: D105-2B-WT

tag: background strain

tag: tissue type

value: Whole tissue sections of ip oil granulomata

tag: experiment

value: study 2


title: Blood_15mg silica, 1 week post-exposure_rep5

source_name: 15mg/m3 silica, 1 week post-exposure rat 69 blood

tag: strain

tag: gender

tag: age

value: 3 mo

tag: treatment

value: 1 week post-exposure


title: ECRG4 set: BC68

tag: age at diagnosis

tag: histology

value: IDC

tag: pt

tag: molecular subtype


title: ECRG4 set: BC65

tag: pn

tag: sbr grade

tag: er ihc

tag: pr ihc


title: ECRG4 set: BC64

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)


title: Blood_1mg silica, 0 week post-exposure_rep1

source_name: 1mg/m3 silica, 0 week post-exposure rat 129 blood

tag: tissue

value: blood

tag: time


title: Blood_0mg silica, 0 week post-exposure_rep1 (control for 1mg silica)

source_name: 0mg/m3 silica, 0 week post-exposure rat 137 blood (control for 1mg/m3 silica)

tag: strain

tag: gender

value: 0mg silica


title: D33-2A-WT

source_name: Day 33, whole tissue

tag: background strain

tag: tissue type

tag: experiment


title: D33-3A-WT


title: ECRG4 set: BC61

tag: age at diagnosis

tag: histology

tag: pt

value: LuminalB

value: breast cancer tumor


title: ECRG4 set: BC62

tag: pn

tag: sbr grade

tag: molecular subtype

value: LuminalA


title: ECRG4 set: BC60

tag: er ihc

tag: pr ihc

tag: p53 ihc


title: Blood_0mg silica, 0 week post-exposure_rep4 (control for 2mg silica)

source_name: 0mg/m3 silica, 0 week post-exposure rat 108 blood (control for 2mg/m3 silica)

value: CDF Fisher 344

value: male

tag: age

tag: treatment


title: ECRG4 set: BC57

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)

tag: tissue


title: D33-1C-WT

tag: background strain

tag: tissue type


title: ECRG4 set: BC55

tag: age at diagnosis


title: D17-2A-WT

source_name: Day 17, whole tissue

tag: experiment


title: ECRG4 set: BC58

tag: histology

tag: pt


title: D49-1A-WT


title: D17-3B-WT


title: ECRG4 set: BC59

value: MIX

tag: pn

tag: sbr grade


title: ECRG4 set: BC54

tag: er ihc

tag: molecular subtype


title: ECRG4 set: BC56

tag: pr ihc

tag: p53 ihc


title: Blood_15mg silica, 1 week post-exposure_rep8

source_name: 15mg/m3 silica, 1 week post-exposure rat 72 blood

tag: strain

tag: gender

tag: age

tag: treatment

value: 15mg silica

tag: time


title: Blood_15mg silica, 0 week post-exposure_rep7

source_name: 15mg/m3 silica, 0 week post-exposure rat 87 blood

tag: tissue

value: 0 week post-exposure


title: ECRG4 set: BC53

value: ILC

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)


title: ECRG4 set: BC63

tag: age at diagnosis

tag: histology


title: Blood_15mg silica, 0 week post-exposure_rep5

source_name: 15mg/m3 silica, 0 week post-exposure rat 85 blood


title: D17-1B-WT

tag: background strain

tag: tissue type

tag: experiment


title: ECRG4 set: BC51

tag: pt

tag: pn

tag: sbr grade

tag: er ihc

tag: molecular subtype

value: Normal


title: Blood_0mg silica, 0 week post-exposure_rep2 (control for 1mg silica)

source_name: 0mg/m3 silica, 0 week post-exposure rat 138 blood (control for 1mg/m3 silica)

tag: strain

tag: gender

tag: age


title: Blood_15mg silica, 2 week post-exposure_rep8

source_name: 15mg/m3 silica, 2 week post-exposure rat 56 blood

tag: tissue

tag: treatment

tag: time

value: 2 week post-exposure


title: ECRG4 set: BC46

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)


title: D7-1C-WT

source_name: Day 7, whole tissue

tag: background strain

tag: tissue type

value: Whole tissue sections of ip oil granulomata

tag: experiment

value: study 2


title: Blood_1mg silica, 0 week post-exposure_rep3

source_name: 1mg/m3 silica, 0 week post-exposure rat 131 blood

value: 3 mo

value: 1mg silica


title: D7-3A-WT


title: ECRG4 set: BC49

tag: age at diagnosis

tag: histology

value: IDC

tag: pt

tag: pn

tag: sbr grade

value: Basal


title: ECRG4 set: BC48

tag: er ihc

tag: molecular subtype


title: ECRG4 set: BC50

tag: tissue


title: Blood_15mg silica, 8 week post-exposure_rep5

source_name: 15mg/m3 silica, 8 week post-exposure rat 21 blood

tag: strain

tag: gender

tag: age

value: blood

tag: treatment

tag: time

value: 8 week post-exposure


title: ECRG4 set: BC43

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)

value: LuminalA

value: breast cancer tumor


title: Blood_15mg silica, 16 week post-exposure_rep4

source_name: 15mg/m3 silica, 16 week post-exposure rat 4 blood

value: CDF Fisher 344

value: male

value: 16 week post-exposure


title: ECRG4 set: BC45

source_name: human breast cancer tumors

tag: age at diagnosis

tag: histology

value: LuminalB


title: D7-2A-WT

tag: background strain

tag: tissue type

tag: experiment


title: D105-3C-T_1

description: Gene expression data from LMD nascent tumor cells

source_name: Day 105, LMD

value: Laser-captured nascent plasma cell tumor cells from ip oil granulomata


title: D105-3C-T_4


title: Blood_2mg silica, 0 week post-exposure_rep8

source_name: 2mg/m3 silica, 0 week post-exposure rat 104 blood

value: 2mg silica

value: 0 week post-exposure


title: ECRG4 set: BC47

value: ILC

tag: pt

tag: pn

tag: sbr grade

tag: er ihc

tag: molecular subtype

value: Normal


title: ECRG4 set: BC42

tag: tissue


title: ECRG4 set: BC82


title: ECRG4 set: BC44


title: ECRG4 set: BC41


title: D105-2B-T_2

value: study 2


title: Blood_1mg silica, 0 week post-exposure_rep4

source_name: 1mg/m3 silica, 0 week post-exposure rat 132 blood

tag: strain

tag: gender

tag: age

value: 3 mo

tag: treatment

value: 1mg silica

tag: time


title: ECRG4 set: BC40

value: IDC

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)

value: Basal


title: D105-2B-T_1

tag: background strain

tag: tissue type

tag: experiment


title: ECRG4 set: BC52

tag: age at diagnosis

tag: histology

tag: pt

tag: pn

tag: sbr grade


title: D105-1C-T_2


title: ECRG4 set: BC39

tag: er ihc

tag: molecular subtype

tag: tissue


title: ECRG4 set: BC35


title: Blood_2mg silica, 0 week post-exposure_rep3

source_name: 2mg/m3 silica, 0 week post-exposure rat 99 blood

tag: strain

tag: gender

tag: age

value: blood

tag: treatment

tag: time


title: ECRG4 set: BC37

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)

value: LuminalA


title: ECRG4 set: BC36

tag: age at diagnosis

tag: histology

value: TUB

value: breast cancer tumor


title: ECRG4 set: BC38

tag: pt

tag: pn


title: Blood_15mg silica, 4 week post-exposure_rep5

source_name: 15mg/m3 silica, 4 week post-exposure rat 37 blood

value: CDF Fisher 344

value: male

value: 15mg silica

value: 4 week post-exposure


title: D49-3B-T_2

source_name: Day 49, LMD

tag: background strain

tag: tissue type

value: Laser-captured nascent plasma cell tumor cells from ip oil granulomata

tag: experiment


title: ECRG4 set: BC34

tag: sbr grade

tag: er ihc

tag: molecular subtype

tag: tissue


title: ECRG4 set: BC33


title: Blood_0mg silica, 16week post-exposure_rep4

source_name: 0mg/m3 silica, 16 week post-exposure rat 12 blood

tag: strain

tag: gender

tag: age

tag: treatment

value: 0mg silica

tag: time

value: 16week post-exposure


title: Blood_15mg silica, 8 week post-exposure_rep7

source_name: 15mg/m3 silica, 8 week post-exposure rat 23 blood

value: 8 week post-exposure


title: LO28_BMM_4hrs_repB

city: Chicago

first: Jess

last: Leber

state: IL

address: 920 E. 58th Street CLSC 615

department: Microbiology

institute: The University of Chicago

description:
WT LO28 LM in BMM  B
Biological replicate 2 of 2.

hyb_protocol: Applied to spotted arrays in binding buffer containing HEPES, SSC, tRNA, and SDS at 63 °C for 48 hours (see Leber et al., PloS Pathogens, 2008 (PMID 18193943) for more detail).

scan_protocol: Images were scanned on a Molecular Devices GenePix 4100B scanner using GenePix Pro software.

data_processing: Background-subtracted data obtained from log2 of processed Red signal/processed Green signal using GenePix Pro software.

organism: Listeria monocytogenes

source_name: WT LO28 LM grown in BMM

label_protocol: 5 ug amplified RNA was reacted with Cy dye for 60 min, and purified using Zymo clean and concentrate columns (see Leber et al., PloS Pathogens, 2008 (PMID 18193943) for more detail).

growth_protocol: WT C57BL6 mouse bone marrow-derived macrophages (BMM), 37 °C, 4 hours post-infection.

extract_protocol: Trizol with silica beads in MP FastPrep.

tag: genotype

value: wild-type

tag: host

value: mouse bone marrow-derived macrophages

tag: time post-infection

value: 4 hours

source_name: Pooled reference total RNA from all 4 samples used in this experiment

tag: sample type

value: reference


title: LO28_BMM_4hrs_repA

description:
WT LO28 LM in BMM  A
Biological replicate 1 of 2.


title: D49-3B-T_1

value: study 2


title: ECRG4 set: BC32

tag: age at diagnosis

tag: histology

value: IDC

tag: pt

tag: pn

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)

value: LuminalB