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status: Public on Feb 04 2012

type: RNA

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

description: Gene expression data from Breast primary carcinoma

hyb_protocol: Illumina expression beadarray hybridization

scan_protocol: Ilumina array scanning

data_processing: Variance Stabilization Tranformation and Robust Spline Normalization as suggested in the BioConductor Lumi package. The normlized data were than corrected from the population effect as detailed in the manuscript.

molecule: total RNA

organism: Homo sapiens

source_name: Breast Cancer Carcinoma

label_protocol: Hybridization of Oligo Microarrays with ULS-CY Dye labeled amplified RNA, using the TECAN HS4800 Hybridization Station.

extract_protocol: RNA Isolation with TRIZOL® Reagent (Cell pellets(A), tissues(A) or cell culture dishes(B) (A)RNA isolation from cell pellets or tissues

treatment_protocol: Samples are individually processed (RNA isolation, followed by DNAse treatment and amplification) and equal quantities of each sample are combined to create a pool of amplified RNA.

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value: DCIS high grade

tag: prolifbyge

tag: subtypebyge


title: 429

value: French

value: no ChT

value: no HT

tag: histshape

value: stellate

tag: histtype

value: ductal

tag: histgrade

value: EEI

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

tag: dcis

tag: dcisgrade

value: DCIS intermed grade

tag: lcis

tag: lvi

tag: prbyge

tag: herbyge


title: 287

tag: origin

tag: age

tag: lr

tag: pt

tag: surgicalmargin

value: marg-

tag: surgivalmargininv

tag: surgicalmargindcis

tag: pn

tag: rtboost

tag: rttotaldose

tag: ct

value: ChT

tag: ht

value: lobular

value: EEIII

value: No DCIS inside

value: No DCIS outside

value: No DCIS

value: LCIS present

value: No LVI

tag: lviquant

tag: erbyge

value: LUMB


title: 312

value: French

value: MargInv-

value: MargDCIS-

value: pN-

value: boost

tag: histshape

value: sharply demarcated

tag: histtype

tag: histgrade

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

value: DCIS inside

tag: dcisoutside

tag: dcis

value: DCIS

tag: dcisgrade

value: DCIS high grade

tag: lcis

value: No LCIS

tag: lvi

value: 2-5 LVI

tag: prolifbyge

tag: subtypebyge

value: TNP


title: 433

tag: origin

tag: age

tag: lr

tag: pt

tag: surgicalmargin

value: marg-

tag: surgivalmargininv

tag: surgicalmargindcis

tag: pn

value: pN+

tag: rtboost

tag: rttotaldose

tag: ct

value: ChT

tag: ht

value: no HT

value: ductal

value: EEIII

value: No DCIS inside

value: No DCIS outside

tag: prbyge

tag: herbyge


title: 305

value: French

value: MargInv-

value: MargDCIS-

tag: histshape

value: stellate

tag: histtype

tag: histgrade

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

tag: dcis

tag: dcisgrade

value: DCIS intermed grade

tag: lcis

tag: lvi

value: LVI present

tag: lviquant

value: 1 LVI

tag: erbyge

value: LUMB


title: 422

tag: origin

tag: age

tag: lr

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

tag: surgicalmargindcis

tag: pn

tag: rtboost

value: no boost

tag: rttotaldose

tag: ct

tag: ht

value: sharply demarcated

value: DCIS inside

value: DCIS outside

value: DCIS

value: DCIS high grade

value: No LCIS

value: 2-5 LVI

tag: prolifbyge

tag: subtypebyge

value: TNP


title: 328

value: French

value: marg-

value: pN+

value: boost

value: ChT

value: HT

tag: histshape

tag: histtype

value: ductal

tag: histgrade

value: EEIII

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

tag: dcis

tag: dcisgrade

tag: lcis

tag: lvi

tag: prbyge

tag: herbyge

value: LUMHER


title: 435

tag: origin

tag: age

tag: lr

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

value: MargInv-

tag: surgicalmargindcis

value: MargDCIS-

tag: pn

value: pN-

tag: rtboost

tag: rttotaldose

tag: ct

value: no ChT

tag: ht

value: no HT

value: stellate

value: No DCIS inside

value: DCIS intermed grade

tag: lviquant

value: >5 LVI

tag: erbyge

value: LUMB


title: 319

value: French

value: marg-

value: no boost

tag: histshape

tag: histtype

value: lobular

tag: histgrade

value: EEI

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

value: No DCIS outside

tag: dcis

value: No DCIS

tag: dcisgrade

tag: lcis

value: LCIS present

tag: lvi

value: No LVI

tag: prolifbyge

tag: subtypebyge

value: LUMA


title: 324

tag: origin

tag: age

tag: lr

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

value: MargInv-

tag: surgicalmargindcis

value: MargDCIS-

tag: pn

value: pN+

tag: rtboost

value: boost

tag: rttotaldose

tag: ct

value: ChT

tag: ht

value: ductal

value: DCIS outside

value: DCIS

value: No LCIS

value: 2-5 LVI

tag: prbyge

tag: herbyge


title: 317

value: French

value: marg+

value: no HT

tag: histshape

value: stellate

tag: histtype

tag: histgrade

value: EEIII

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

tag: dcis

tag: dcisgrade

value: DCIS high grade

tag: lcis

tag: lvi

tag: lviquant

tag: erbyge

value: LUMHER


title: 330

tag: origin

tag: age

tag: lr

tag: pt

tag: surgicalmargin

value: marg-

tag: surgivalmargininv

value: MargInv-

tag: surgicalmargindcis

tag: pn

tag: rtboost

tag: rttotaldose

tag: ct

tag: ht

value: EEII

value: >5 LVI

tag: prolifbyge

tag: subtypebyge


title: 113

value: Dutch

value: MargInv+

value: pN+

value: boost

value: ChT

value: HT

tag: histshape

tag: histtype

tag: histgrade

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

tag: dcis

tag: dcisgrade

tag: lcis

tag: lvi

value: No LVI

tag: prbyge

tag: herbyge


title: 159

tag: origin

tag: age

tag: lr

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

tag: surgicalmargindcis

tag: pn

value: pN-

tag: rtboost

value: no boost

tag: rttotaldose

tag: ct

value: no ChT

tag: ht

value: sharply demarcated

value: ductal

value: EEI

value: No DCIS inside

value: DCIS

value: DCIS intermed grade

value: No LCIS

tag: lviquant

tag: erbyge

value: LUMA


title: 299

value: French

value: marg-

value: MargInv-

value: MargDCIS-

value: no HT

tag: histshape

value: stellate

tag: histtype

value: other type

tag: histgrade

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

value: DCIS inside

tag: dcisoutside

value: No DCIS outside

tag: dcis

tag: dcisgrade

value: DCIS low grade

tag: lcis

tag: lvi

tag: prolifbyge

tag: subtypebyge


title: 172

tag: origin

value: Dutch

tag: age

tag: lr

tag: pt

tag: surgicalmargin

value: marg+

tag: surgivalmargininv

value: MargInv+

tag: surgicalmargindcis

tag: pn

value: pN-

tag: rtboost

value: boost

tag: rttotaldose

tag: ct

value: no ChT

tag: ht

value: ductal

value: No LVI

tag: prbyge

tag: herbyge


title: 338

value: French

value: marg-

value: pN+

value: no boost

value: HT

tag: histshape

tag: histtype

tag: histgrade

value: EEII

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

tag: dcis

value: DCIS

tag: dcisgrade

value: DCIS high grade

tag: lcis

value: No LCIS

tag: lvi

tag: lviquant

tag: erbyge

value: LUMA


title: 238

tag: origin

tag: age

tag: lr

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

value: MargInv-

tag: surgicalmargindcis

value: MargDCIS-

tag: pn

tag: rtboost

tag: rttotaldose

tag: ct

value: ChT

tag: ht

value: no HT

value: stellate

value: DCIS inside

value: DCIS outside

value: DCIS intermed grade

value: LVI present

value: 1 LVI

tag: prolifbyge

tag: subtypebyge


title: 190

value: Dutch

value: marg-

value: pN+

value: boost

tag: histshape

tag: histtype

value: ductal

tag: histgrade

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

value: No DCIS inside

tag: dcisoutside

value: No DCIS outside

tag: dcis

value: No DCIS

tag: dcisgrade

tag: lcis

tag: lvi

value: No LVI

tag: prbyge

tag: herbyge


title: 331

tag: origin

value: French

tag: age

tag: lr

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

value: MargInv-

tag: surgicalmargindcis

value: MargDCIS-

tag: pn

tag: rtboost

tag: rttotaldose

tag: ct

value: ChT

tag: ht

value: sharply demarcated

value: EEIII

value: DCIS

value: DCIS high grade

value: No LCIS

tag: lviquant

tag: erbyge

value: TNP


title: 323

value: marg-

value: pN+

value: HT

tag: histshape

value: stellate

tag: histtype

tag: histgrade

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

tag: dcis

tag: dcisgrade

tag: lcis

tag: lvi

value: 2-5 LVI

tag: prolifbyge

tag: subtypebyge

value: LUMB


title: 336

tag: origin

tag: age

tag: lr

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

tag: surgicalmargindcis

tag: pn

value: pN-

tag: rtboost

value: no boost

tag: rttotaldose

tag: ct

value: no ChT

tag: ht

value: no HT

value: lobular

value: EEI

value: No DCIS inside

value: No DCIS outside

value: No DCIS

value: LCIS present

value: No LVI

tag: prbyge

tag: herbyge


title: 416

value: French

value: marg-

value: MargInv-

value: MargDCIS-

tag: histshape

tag: histtype

value: ductal

tag: histgrade

value: EEII

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

value: DCIS inside

tag: dcisoutside

value: DCIS outside

tag: dcis

value: DCIS

tag: dcisgrade

value: DCIS high grade

tag: lcis

value: No LCIS

tag: lvi

tag: lviquant

tag: erbyge


title: 185

tag: origin

value: Dutch

tag: age

tag: lr

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

tag: surgicalmargindcis

tag: pn

value: pN-

tag: rtboost

value: boost

tag: rttotaldose

tag: ct

value: no ChT

tag: ht

value: no HT

value: sharply demarcated

value: other type

value: DCIS intermed grade

tag: prolifbyge

tag: subtypebyge

value: LUMB


title: 239

value: French

value: marg-

value: MargInv-

value: MargDCIS-

value: pN+

value: no boost

value: ChT

tag: histshape

value: multinodular

tag: histtype

tag: histgrade

value: EEI

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

tag: dcis

tag: dcisgrade

tag: lcis

tag: lvi

value: No LVI

tag: prbyge

tag: herbyge

value: LUMA


title: 320

tag: origin

tag: age

tag: lr

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

tag: surgicalmargindcis

tag: pn

value: pN-

tag: rtboost

value: boost

tag: rttotaldose

tag: ct

value: no ChT

tag: ht

value: stellate

value: ductal

value: EEII

value: DCIS

value: No LCIS

value: LVI present

tag: lviquant

value: 1 LVI

tag: erbyge


title: 308

value: French

value: marg-

value: MargInv-

value: MargDCIS-

value: no HT

tag: histshape

tag: histtype

value: lobular

tag: histgrade

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

value: No DCIS inside

tag: dcisoutside

value: No DCIS outside

tag: dcis

value: No DCIS

tag: dcisgrade

tag: lcis

value: LCIS present

tag: lvi

tag: prolifbyge

tag: subtypebyge


title: 434

tag: origin

tag: age

tag: lr

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

tag: surgicalmargindcis

tag: pn

value: pN-

tag: rtboost

value: boost

tag: rttotaldose

tag: ct

value: no ChT

tag: ht

value: stellate

value: EEI

value: DCIS outside

value: DCIS intermed grade

value: No LVI

tag: prbyge

tag: herbyge

value: LUMA


title: 241

value: French

value: marg-

value: MargInv-

value: pN+

value: no boost

value: ChT

tag: histshape

tag: histtype

value: ductal

tag: histgrade

value: EEII

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

tag: dcis

value: DCIS

tag: dcisgrade

tag: lcis

value: No LCIS

tag: lvi

tag: lviquant

tag: erbyge


title: 240

tag: origin

tag: age

tag: lr

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

tag: surgicalmargindcis

tag: pn

tag: rtboost

tag: rttotaldose

tag: ct

tag: ht

value: no HT

value: DCIS inside

tag: prolifbyge

tag: subtypebyge

value: LUMB


title: 418

value: marg+

value: MargDCIS+

value: pN-

value: boost

value: no ChT

tag: histshape

value: sharply demarcated

tag: histtype

tag: histgrade

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

tag: dcis

tag: dcisgrade

value: DCIS high grade

tag: lcis

tag: lvi

tag: prbyge

tag: herbyge


title: 329

tag: origin

value: French

tag: age

tag: lr

tag: pt

tag: surgicalmargin

value: marg-

tag: surgivalmargininv

value: MargInv-

tag: surgicalmargindcis

value: MargDCIS-

tag: pn

tag: rtboost

tag: rttotaldose

tag: ct

tag: ht

value: HT

value: stellate

value: EEIII

value: No DCIS outside

value: DCIS intermed grade

value: LVI present

tag: lviquant

value: 1 LVI

tag: erbyge


title: 242

value: no boost

value: no HT

tag: histshape

tag: histtype

value: other type

tag: histgrade

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

value: No DCIS inside

tag: dcisoutside

tag: dcis

value: No DCIS

tag: dcisgrade

tag: lcis

value: No LCIS

tag: lvi

value: No LVI

tag: prolifbyge

tag: subtypebyge

value: TNP


title: 339

tag: origin

value: French

tag: age

tag: lr

tag: pt

tag: surgicalmargin

value: marg-

tag: surgivalmargininv

value: MargInv-

tag: surgicalmargindcis

tag: pn

value: pN-

tag: rtboost

tag: rttotaldose

tag: ct

value: no ChT

tag: ht

value: sharply demarcated

tag: prbyge

tag: herbyge


title: 302

value: boost

tag: histshape

value: stellate

tag: histtype

value: lobular

tag: histgrade

value: EEI

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

tag: dcis

tag: dcisgrade

tag: lcis

value: LCIS present

tag: lvi

tag: lviquant

tag: erbyge

value: LUMA


title: 439

tag: origin

tag: age

tag: lr

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

tag: surgicalmargindcis

value: MargDCIS-

tag: pn

value: pN+

tag: rtboost

value: no boost

tag: rttotaldose

tag: ct

value: ChT

tag: ht

value: no HT

value: ductal

value: EEIII

value: DCIS inside

value: No DCIS outside

value: DCIS

value: DCIS high grade

value: >5 LVI

tag: prolifbyge

tag: subtypebyge

value: LUMB


title: 181

value: Dutch

value: marg-

value: MargInv-

value: pN-

value: boost

value: no ChT

tag: histshape

value: stellate

tag: histtype

tag: histgrade

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

value: No DCIS inside

tag: dcisoutside

tag: dcis

value: No DCIS

tag: dcisgrade

tag: lcis

value: No LCIS

tag: lvi

value: No LVI

tag: prbyge

tag: herbyge


title: 419

tag: origin

value: French

tag: age

tag: lr

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

tag: surgicalmargindcis

value: MargDCIS-

tag: pn

tag: rtboost

value: no boost

tag: rttotaldose

tag: ct

tag: ht

value: no HT

value: ductal

tag: lviquant

tag: erbyge

value: TNP


title: 432

tag: histshape

value: sharply demarcated

tag: histtype

value: other type

tag: histgrade

value: EEII

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

tag: dcis

value: DCIS

tag: dcisgrade

value: DCIS high grade

tag: lcis

tag: lvi

value: 2-5 LVI

tag: prolifbyge

tag: subtypebyge

value: LUMHER


title: 93

tag: origin

value: Dutch

tag: age

tag: lr

tag: pt

tag: surgicalmargin

value: marg-

tag: surgivalmargininv

value: MargInv-

tag: surgicalmargindcis

tag: pn

value: pN+

tag: rtboost

value: boost

tag: rttotaldose

tag: ct

value: no ChT

tag: ht

value: EEIII

value: No DCIS inside

tag: prbyge

tag: herbyge

value: LUMB


title: 167

value: ChT

value: no HT

tag: histshape

value: stellate

tag: histtype

value: ductal

tag: histgrade

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

tag: dcis

tag: dcisgrade

value: DCIS intermed grade

tag: lcis

value: No LCIS

tag: lvi

value: No LVI

tag: lviquant

tag: erbyge


title: 174

tag: origin

tag: age

tag: lr

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

tag: surgicalmargindcis

tag: pn

value: pN-

tag: rtboost

tag: rttotaldose

tag: ct

tag: ht

value: EEI

value: DCIS inside

value: DCIS outside

value: DCIS

value: DCIS low grade

tag: prolifbyge

tag: subtypebyge

value: LUMA


title: 438

value: French

value: marg-

value: MargInv-

value: MargDCIS-

value: pN+

value: boost

tag: histshape

tag: histtype

tag: histgrade

value: EEIII

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

value: No DCIS outside

tag: dcis

value: No DCIS

tag: dcisgrade

tag: lcis

tag: lvi

value: >5 LVI

tag: prbyge

tag: herbyge

value: TNP


title: 95

tag: origin

value: Dutch

tag: age

tag: lr

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

tag: surgicalmargindcis

tag: pn

value: pN-

tag: rtboost

tag: rttotaldose

tag: ct

value: no ChT

tag: ht

value: no HT

value: stellate

value: ductal

value: EEII

value: No DCIS inside

value: No LCIS

value: No LVI

tag: lviquant

tag: erbyge


title: 337

value: French

value: marg-

value: MargInv-

value: MargDCIS-

value: no boost

tag: histshape

tag: histtype

tag: histgrade

value: EEI

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

tag: dcis

tag: dcisgrade

tag: lcis

tag: lvi

tag: prolifbyge

tag: subtypebyge

value: LUMA


title: 316

tag: origin

tag: age

tag: lr

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

tag: surgicalmargindcis

tag: pn

value: pN+

tag: rtboost

value: boost

tag: rttotaldose

tag: ct

value: ChT

tag: ht

value: EEIII

value: DCIS inside

value: DCIS

value: DCIS high grade

value: LVI present

value: 1 LVI

tag: prbyge

tag: herbyge


title: 318

value: pN-

value: no HT

tag: histshape

value: multinodular

tag: histtype

value: other type

tag: histgrade

value: EEII

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

value: DCIS outside

tag: dcis

tag: dcisgrade

tag: lcis

value: No LCIS

tag: lvi

tag: lviquant

value: 2-5 LVI

tag: erbyge

value: LUMB


title: 96

tag: origin

value: Dutch

tag: age

tag: lr

tag: pt

tag: surgicalmargin

value: marg-

tag: surgivalmargininv

value: MargInv-

tag: surgicalmargindcis

tag: pn

tag: rtboost

value: boost

tag: rttotaldose

tag: ct

value: no ChT

tag: ht

value: stellate

value: ductal

value: No LVI

tag: prolifbyge

tag: subtypebyge

value: TNP


title: 177

value: pN-

value: no HT

tag: histshape

value: sharply demarcated

tag: histtype

tag: histgrade

value: EEIII

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

value: No DCIS inside

tag: dcisoutside

tag: dcis

value: DCIS

tag: dcisgrade

value: DCIS high grade

tag: lcis

tag: lvi

tag: prbyge

tag: herbyge


title: 156

tag: origin

tag: age

tag: lr

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

tag: surgicalmargindcis

tag: pn

tag: rtboost

tag: rttotaldose

tag: ct

tag: ht

value: EEII

value: No LCIS

tag: lviquant

value: 2-5 LVI

tag: erbyge

value: LUMHER


title: 303

value: French

value: marg-

value: MargInv-

value: MargDCIS-

value: no boost

value: ChT

tag: histshape

tag: histtype

tag: histgrade

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

value: No DCIS outside

tag: dcis

value: No DCIS

tag: dcisgrade

tag: lcis

tag: lvi

tag: prolifbyge

tag: subtypebyge


title: 155

tag: origin

value: Dutch

tag: age

tag: lr

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

tag: surgicalmargindcis

tag: pn

value: pN+

tag: rtboost

value: boost

tag: rttotaldose

tag: ct

tag: ht

value: no HT

value: stellate

value: ductal

value: DCIS inside

value: DCIS outside

value: No LVI

tag: prbyge

tag: herbyge

value: LUMB


title: 157

value: marg-

value: no ChT

tag: histshape

tag: histtype

value: lobular

tag: histgrade

value: EEII

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

tag: dcis

value: DCIS

tag: dcisgrade

value: DCIS low grade

tag: lcis

value: No LCIS

tag: lvi

tag: lviquant

tag: erbyge

value: LUMA


title: 322

tag: origin

value: French

tag: age

tag: lr

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

value: MargInv-

tag: surgicalmargindcis

value: MargDCIS-

tag: pn

value: pN-

tag: rtboost

tag: rttotaldose

tag: ct

tag: ht

value: No DCIS outside

value: DCIS intermed grade

tag: prolifbyge

tag: subtypebyge


title: 97

value: Dutch

value: boost

tag: histshape

value: sharply demarcated

tag: histtype

value: ductal

tag: histgrade

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

tag: dcis

tag: dcisgrade

tag: lcis

tag: lvi

tag: prbyge

tag: herbyge


title: 325

tag: origin

tag: age

tag: lr

tag: pt

tag: surgicalmargin

value: marg-

tag: surgivalmargininv

tag: surgicalmargindcis

tag: pn

tag: rtboost

tag: rttotaldose

tag: ct

value: ChT

tag: ht

value: no HT

value: EEIII

value: No DCIS inside

value: No DCIS

value: No LVI

tag: lviquant

tag: erbyge

value: TNP


title: 98

value: MargInv-

value: pN+

tag: histshape

value: stellate

tag: histtype

tag: histgrade

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

tag: dcis

value: DCIS

tag: dcisgrade

value: DCIS high grade

tag: lcis

value: No LCIS

tag: lvi

tag: prolifbyge

tag: subtypebyge

value: LUMHER


title: 321

tag: origin

value: French

tag: age

tag: lr

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

tag: surgicalmargindcis

tag: pn

value: pN-

tag: rtboost

value: boost

tag: rttotaldose

tag: ct

tag: ht

value: sharply demarcated

value: DCIS inside

value: DCIS outside

value: 2-5 LVI

tag: prbyge

tag: herbyge


title: 307

value: marg-

value: MargDCIS-

value: no boost

value: ChT

value: no HT

tag: histshape

tag: histtype

value: ductal

tag: histgrade

value: EEIII

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

tag: dcis

tag: dcisgrade

value: DCIS intermed grade

tag: lcis

tag: lvi

value: LVI present

tag: lviquant

value: 1 LVI

tag: erbyge

value: LUMB


title: 293

tag: origin

value: French

tag: age

tag: lr

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

value: MargInv-

tag: surgicalmargindcis

tag: pn

value: pN-

tag: rtboost

tag: rttotaldose

tag: ct

value: no ChT

tag: ht

value: stellate

value: EEII

value: No DCIS inside

value: No DCIS outside

value: No DCIS

value: No LCIS

value: No LVI

tag: prolifbyge

tag: subtypebyge


title: 296

value: marg-

value: MargDCIS-

value: pN+

value: no boost

value: ChT

value: HT

tag: histshape

tag: histtype

value: ductal

tag: histgrade

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

value: DCIS inside

tag: dcisoutside

tag: dcis

value: DCIS

tag: dcisgrade

tag: lcis

tag: lvi

tag: prbyge

tag: herbyge

value: LUMA


title: 332

tag: origin

value: French

tag: age

tag: lr

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

value: MargInv-

tag: surgicalmargindcis

tag: pn

tag: rtboost

value: boost

tag: rttotaldose

tag: ct

tag: ht

value: sharply demarcated

value: EEIII

value: DCIS high grade

tag: lviquant

value: >5 LVI

tag: erbyge

value: LUMHER


title: 334

value: marg-

value: MargDCIS-

value: no HT

tag: histshape

value: stellate

tag: histtype

tag: histgrade

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

value: No DCIS outside

tag: dcis

tag: dcisgrade

tag: lcis

value: No LCIS

tag: lvi

value: No LVI

tag: prolifbyge

tag: subtypebyge

value: LUMB


title: 292

tag: origin

tag: age

tag: lr

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

tag: surgicalmargindcis

tag: pn

value: pN-

tag: rtboost

tag: rttotaldose

tag: ct

value: no ChT

tag: ht

value: ductal

value: EEII

value: DCIS

value: DCIS intermed grade

tag: prbyge

tag: herbyge

value: LUMA


title: 298

value: French

value: boost

value: ChT

tag: histshape

value: sharply demarcated

tag: histtype

tag: histgrade

value: EEIII

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

value: No DCIS inside

tag: dcisoutside

value: DCIS outside

tag: dcis

tag: dcisgrade

value: DCIS high grade

tag: lcis

tag: lvi

tag: lviquant

tag: erbyge

value: TNP


title: 335

tag: origin

tag: age

tag: lr

tag: pt

tag: surgicalmargin

value: marg+

tag: surgivalmargininv

value: MargInv+

tag: surgicalmargindcis

value: MargDCIS-

tag: pn

value: pN+

tag: rtboost

value: no boost

tag: rttotaldose

tag: ct

tag: ht

value: no HT

value: stellate

value: No DCIS outside

value: No DCIS

value: No LCIS

value: No LVI

tag: prolifbyge

tag: subtypebyge


title: 304

value: French

value: marg-

value: MargInv-

value: boost

value: ChT

tag: histshape

tag: histtype

value: ductal

tag: histgrade

value: EEII

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

tag: dcis

value: DCIS

tag: dcisgrade

value: DCIS intermed grade

tag: lcis

tag: lvi

value: LVI present

value: 1 LVI

tag: prbyge

tag: herbyge

value: LUMA


title: 83

tag: origin

value: Dutch

tag: age

tag: lr

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

tag: surgicalmargindcis

tag: pn

value: pN-

tag: rtboost

tag: rttotaldose

tag: ct

value: no ChT

tag: ht

value: no HT

value: sharply demarcated

value: EEIII

value: No DCIS inside

value: DCIS high grade

tag: lviquant

tag: erbyge

value: LUMB


title: 309

value: French

value: marg-

value: MargInv-

value: boost

tag: histshape

tag: histtype

tag: histgrade

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

tag: dcis

tag: dcisgrade

tag: lcis

value: No LCIS

tag: lvi

value: No LVI

tag: prolifbyge

tag: subtypebyge


title: 300

tag: origin

tag: age

tag: lr

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

tag: surgicalmargindcis

value: MargDCIS-

tag: pn

tag: rtboost

tag: rttotaldose

tag: ct

tag: ht

value: HT

value: stellate

value: ductal

value: EEII

value: DCIS inside

value: DCIS

value: DCIS intermed grade

tag: prbyge

tag: herbyge


title: 77

value: Dutch

value: marg+

value: MargInv+

value: no ChT

value: no HT

tag: histshape

tag: histtype

tag: histgrade

value: EEIII

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

value: DCIS outside

tag: dcis

tag: dcisgrade

tag: lcis

tag: lvi

tag: lviquant

tag: erbyge

value: LUMHER


title: 80

tag: origin

tag: age

tag: lr

tag: pt

tag: surgicalmargin

value: marg-

tag: surgivalmargininv

value: MargInv-

tag: surgicalmargindcis

tag: pn

value: pN+

tag: rtboost

value: boost

tag: rttotaldose

tag: ct

value: ChT

tag: ht

value: No LCIS

value: No LVI

tag: prolifbyge

tag: subtypebyge

value: LUMA


title: 94

value: pN-

tag: histshape

value: stellate

tag: histtype

value: ductal

tag: histgrade

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

value: No DCIS inside

tag: dcisoutside

value: No DCIS outside

tag: dcis

value: No DCIS

tag: dcisgrade

tag: lcis

tag: lvi

tag: prbyge

tag: herbyge

value: LUMB


title: 35

tag: origin

value: Dutch

tag: age

tag: lr

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

tag: surgicalmargindcis

tag: pn

tag: rtboost

value: no boost

tag: rttotaldose

tag: ct

tag: ht

value: no HT

value: EEIII

value: DCIS outside

value: DCIS

value: DCIS high grade

tag: lviquant

tag: erbyge


title: 37

value: marg-

value: MargInv-

value: no ChT

tag: histshape

tag: histtype

tag: histgrade

value: EEII

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

value: DCIS inside

tag: dcisoutside

tag: dcis

tag: dcisgrade

value: DCIS intermed grade

tag: lcis

value: No LCIS

tag: lvi

tag: prolifbyge

tag: subtypebyge


title: 314

tag: origin

value: French

tag: age

tag: lr

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

tag: surgicalmargindcis

value: MargDCIS-

tag: pn

value: pN+

tag: rtboost

value: boost

tag: rttotaldose

tag: ct

value: ChT

tag: ht

value: HT

value: stellate

value: other type

value: No DCIS outside

value: 2-5 LVI

tag: prbyge

tag: herbyge

value: LUMHER


title: 40

value: Dutch

value: marg-

value: MargInv-

value: pN-

value: no HT

tag: histshape

tag: histtype

value: ductal

tag: histgrade

value: EEI

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

value: DCIS outside

tag: dcis

value: DCIS

tag: dcisgrade

value: DCIS high grade

tag: lcis

tag: lvi

value: No LVI

tag: lviquant

tag: erbyge

value: LUMA


title: 34

tag: origin

tag: age

tag: lr

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

tag: surgicalmargindcis

tag: pn

value: pN+

tag: rtboost

value: boost

tag: rttotaldose

tag: ct

value: ChT

tag: ht

value: sharply demarcated

value: EEIII

value: No DCIS inside

value: No LCIS

tag: prolifbyge

tag: subtypebyge

value: TNP


title: 79

value: Dutch

value: marg-

value: MargInv-

value: pN-

value: no ChT

tag: histshape

value: stellate

tag: histtype

tag: histgrade

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

tag: dcis

tag: dcisgrade

tag: lcis

tag: lvi

tag: prbyge

tag: herbyge


title: 82

tag: origin

tag: age

tag: lr

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

tag: surgicalmargindcis

tag: pn

tag: rtboost

tag: rttotaldose

tag: ct

tag: ht

value: no HT

value: ductal

value: No DCIS outside

value: No DCIS

value: LCIS present

tag: lviquant

value: >5 LVI

tag: erbyge


title: 313

value: French

value: MargDCIS-

value: pN+

value: boost

value: ChT

tag: histshape

tag: histtype

tag: histgrade

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

tag: dcis

tag: dcisgrade

tag: lcis

tag: lvi

value: No LVI

tag: prolifbyge

tag: subtypebyge


title: 41

tag: origin

value: Dutch

tag: age

tag: lr

tag: pt

tag: surgicalmargin

value: marg-

tag: surgivalmargininv

tag: surgicalmargindcis

tag: pn

tag: rtboost

tag: rttotaldose

tag: ct

tag: ht

value: EEIII

value: DCIS outside

value: DCIS

value: DCIS high grade

value: No LCIS

tag: prbyge

tag: herbyge

value: TNP


title: 78

value: MargInv-

value: pN-

value: no ChT

value: no HT

tag: histshape

value: stellate

tag: histtype

value: ductal

tag: histgrade

value: EEI

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

value: No DCIS inside

tag: dcisoutside

value: No DCIS outside

tag: dcis

value: No DCIS

tag: dcisgrade

tag: lcis

tag: lvi

tag: lviquant

tag: erbyge

value: LUMA


title: 36

tag: origin

value: Dutch

tag: age

tag: lr

tag: pt

tag: surgicalmargin

value: marg-

tag: surgivalmargininv

tag: surgicalmargindcis

tag: pn

value: pN+

tag: rtboost

value: boost

tag: rttotaldose

tag: ct

value: ChT

tag: ht

value: EEII

value: DCIS intermed grade

value: No LVI

tag: prolifbyge

tag: subtypebyge

value: LUMB


title: 33

value: MargInv-

value: pN-

value: no ChT

value: no HT

tag: histshape

tag: histtype

tag: histgrade

value: EEIII

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

value: DCIS inside

tag: dcisoutside

value: DCIS outside

tag: dcis

value: DCIS

tag: dcisgrade

value: DCIS high grade

tag: lcis

value: No LCIS

tag: lvi

tag: prbyge

tag: herbyge


title: 92

tag: origin

value: Dutch

tag: age

tag: lr

tag: pt

tag: surgicalmargin

value: marg+

tag: surgivalmargininv

value: MargInv+

tag: surgicalmargindcis

tag: pn

tag: rtboost

tag: rttotaldose

tag: ct

tag: ht

value: ductal

tag: lviquant

tag: erbyge


title: 30

value: marg-

value: boost

tag: histshape

value: sharply demarcated

tag: histtype

tag: histgrade

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

value: No DCIS inside

tag: dcisoutside

value: No DCIS outside

tag: dcis

value: No DCIS

tag: dcisgrade

tag: lcis

tag: lvi

value: >5 LVI

tag: prolifbyge

tag: subtypebyge

value: LUMA


title: 29

tag: origin

tag: age

tag: lr

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

value: MargInv-

tag: surgicalmargindcis

tag: pn

value: pN-

tag: rtboost

tag: rttotaldose

tag: ct

value: no ChT

tag: ht

value: no HT

value: EEIII

value: 2-5 LVI

tag: prbyge

tag: herbyge

value: TNP


title: 91

value: Dutch

value: pN+

tag: histshape

tag: histtype

tag: histgrade

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

tag: dcis

value: DCIS

tag: dcisgrade

value: DCIS high grade

tag: lcis

value: No LCIS

tag: lvi

tag: lviquant

tag: erbyge

value: LUMHER


title: 90

tag: origin

tag: age

tag: lr

tag: pt

tag: surgicalmargin

value: marg-

tag: surgivalmargininv

tag: surgicalmargindcis

tag: pn

tag: rtboost

value: boost

tag: rttotaldose

tag: ct

tag: ht

value: stellate

value: ductal

value: EEII

value: DCIS inside

value: DCIS outside

value: DCIS intermed grade

value: No LVI

tag: prolifbyge

tag: subtypebyge


title: 26

value: marg+

value: MargInv-

value: MargDCIS-

value: no ChT

value: no HT

tag: histshape

tag: histtype

tag: histgrade

value: EEIII

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

tag: dcis

tag: dcisgrade

tag: lcis

tag: lvi

value: >5 LVI

tag: prbyge

tag: herbyge

value: LUMA


title: CR diet MKO 7

city: Boston

first: Marcia

middle: C

last: Haigis

state: MA

address: 77 Ave Louis Pasteur

country: USA

institute: Harvard Medical School

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse Genome Array Mouse430_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Raw data were processed using the dChip algorithm in GenePattern. All further data analysis was performed using GenePattern modules.

label: biotin

organism: Mus musculus

source_name: TA/EDL muscle, CR diet, MKO genotype

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Individually-housed littermate FLOX and MKO mice were used for all experiments.

extract_protocol: Trizol extraction of total RNA was performed according to manufacturer instructions (Invitrogen). RNA was cleaned using RNeasy MiniKit from Qiagen.

treatment_protocol: Mice were fed AIN-93M diet (BioServe, NJ) ad libitum for at least 10 days until baseline food intake was determined. Mice were randomly divided into control (C) or calorie restricted (CR) groups. Control mice were fed 90% and CR mice were fed 80% of their ad libitum food intake. After one week, CR mice were switched to AIN-93M 40% CR diet and fed 60% of their ad libitum intake until sacrifice approximately 11 weeks later.

tag: tissue

value: TA/EDL muscles

tag: diet

value: CR diet

tag: genotype

value: MKO


title: 61

tag: origin

value: Dutch

tag: age

tag: lr

tag: pt

tag: surgicalmargin

value: marg-

tag: surgivalmargininv

tag: surgicalmargindcis

tag: pn

value: pN+

tag: rtboost

value: boost

tag: rttotaldose

tag: ct

value: ChT

tag: ht

tag: histshape

value: ductal

value: DCIS

value: DCIS high grade

value: No LCIS

tag: lviquant

tag: erbyge

tag: prolifbyge

tag: subtypebyge


title: 89

tag: origin

value: marg+

value: MargInv-

value: MargDCIS-

value: pN-

value: no ChT

value: stellate

tag: histtype

value: other type

tag: histgrade

value: EEII

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

value: No DCIS inside

tag: dcisoutside

value: No DCIS outside

tag: dcis

value: No DCIS

tag: dcisgrade

tag: lcis

value: LCIS present

tag: lvi

value: No LVI

tag: prbyge

tag: herbyge

value: LUMHER


title: CR diet MKO 6

tag: tissue

value: TA/EDL muscles

tag: diet

value: CR diet

tag: genotype

value: MKO


title: 88

tag: origin

value: Dutch

tag: age

tag: lr

tag: pt

tag: surgicalmargin

value: marg+

tag: surgivalmargininv

value: MargInv+

tag: surgicalmargindcis

tag: pn

tag: rtboost

value: boost

tag: rttotaldose

tag: ct

tag: ht

value: no HT

tag: histshape

value: ductal

tag: lviquant

tag: erbyge

tag: prolifbyge

tag: subtypebyge

value: LUMB


title: CR diet MKO 5

tag: tissue

tag: diet

tag: genotype


title: 58

tag: origin

tag: age

tag: lr

tag: pt

value: pN+

value: ChT

value: stellate

tag: histtype

tag: histgrade

value: EEIII

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

tag: dcis

tag: dcisgrade

tag: lcis

value: No LCIS

tag: lvi

tag: prbyge

tag: herbyge


title: CR diet MKO 3

tag: tissue

tag: diet

tag: genotype


title: 84

tag: origin

tag: age

tag: lr

tag: pt

tag: surgicalmargin

value: marg-

tag: surgivalmargininv

value: MargInv-

tag: surgicalmargindcis

tag: pn

value: pN-

tag: rtboost

tag: rttotaldose

tag: ct

value: no ChT

tag: ht

tag: histshape

value: other type

value: EEII

value: No DCIS outside

tag: lviquant

tag: erbyge

tag: prolifbyge

tag: subtypebyge

value: LUMA


title: CR diet MKO 2

tag: tissue

value: TA/EDL muscles

tag: diet

value: CR diet

tag: genotype

value: MKO


title: 327

tag: origin

value: French

tag: age

tag: lr

tag: pt

value: MargDCIS-

value: boost

value: HT

tag: histtype

value: ductal

tag: histgrade

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

value: DCIS inside

tag: dcisoutside

value: DCIS outside

tag: dcis

value: DCIS

tag: dcisgrade

value: DCIS high grade

tag: lcis

tag: lvi

value: >5 LVI

tag: prbyge

tag: herbyge

value: LUMHER


title: 44

tag: origin

value: Dutch

tag: surgicalmargin

tag: surgivalmargininv

tag: surgicalmargindcis

tag: pn

value: pN-

tag: rtboost

tag: rttotaldose

tag: ct

value: no ChT

tag: ht

value: no HT

tag: histshape

value: stellate

value: other type

value: EEII

value: No DCIS inside

value: No DCIS

value: LCIS present

value: No LVI

tag: lviquant

tag: erbyge

tag: prolifbyge

tag: subtypebyge


title: CR diet FLOX 5

source_name: TA/EDL muscle, CR diet, FLOX genotype

tag: tissue

value: TA/EDL muscles

tag: diet

value: CR diet

tag: genotype

value: FLOX


title: 43

tag: origin

tag: age

tag: lr

tag: pt

value: marg-

value: MargInv-

value: pN+

value: boost

value: ChT

tag: histtype

value: ductal

tag: histgrade

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

value: No DCIS outside

tag: dcis

tag: dcisgrade

tag: lcis

value: No LCIS

tag: lvi

tag: prbyge

tag: herbyge


title: 42

tag: origin

value: Dutch

tag: surgicalmargin

tag: surgivalmargininv

tag: surgicalmargindcis

tag: pn

tag: rtboost

tag: rttotaldose

tag: ct

tag: ht

value: no HT

tag: histshape

value: stellate

value: EEIII

value: DCIS

value: DCIS high grade

tag: lviquant

tag: erbyge

tag: prolifbyge

tag: subtypebyge


title: CR diet MKO 4

tag: tissue

value: TA/EDL muscles

tag: diet

tag: genotype

value: MKO


title: CR diet MKO 1

value: CR diet


title: CR diet FLOX 6

value: FLOX


title: 75

tag: origin

tag: age

tag: lr

tag: pt

value: marg+

value: MargInv-

value: MargDCIS-

value: no ChT

tag: histtype

tag: histgrade

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

value: No DCIS inside

tag: dcisoutside

tag: dcis

tag: dcisgrade

tag: lcis

tag: lvi

value: No LVI

tag: prbyge

tag: herbyge

value: LUMB


title: CR diet FLOX 3

tag: tissue

tag: diet

tag: genotype


title: 62

tag: origin

value: Dutch

tag: age

tag: lr

tag: pt

tag: surgicalmargin

value: marg-

tag: surgivalmargininv

tag: surgicalmargindcis

tag: pn

value: pN-

tag: rtboost

value: no boost

tag: rttotaldose

tag: ct

tag: ht

tag: histshape

value: ductal

value: EEI

value: DCIS low grade

value: No LCIS

tag: lviquant

tag: erbyge

tag: prolifbyge

tag: subtypebyge

value: LUMA


title: 73

tag: origin

value: pN+

value: boost

value: ChT

value: no HT

value: stellate

tag: histtype

tag: histgrade

value: EEIII

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

value: No DCIS outside

tag: dcis

value: No DCIS

tag: dcisgrade

tag: lcis

tag: lvi

value: >5 LVI

tag: prbyge

tag: herbyge


title: 72

value: Dutch

tag: age

tag: lr

tag: pt

tag: surgicalmargin

value: marg-

tag: surgivalmargininv

value: MargInv-

tag: surgicalmargindcis

tag: pn

tag: rtboost

tag: rttotaldose

tag: ct

value: no ChT

tag: ht

tag: histshape

value: sharply demarcated

value: No DCIS inside

value: DCIS outside

value: DCIS

value: DCIS high grade

value: No LVI

tag: lviquant

tag: erbyge

value: LUMHER


title: 8

tag: origin

value: pN+

value: boost

value: no HT

tag: histtype

value: ductal

tag: histgrade

value: EEI

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

tag: dcis

tag: dcisgrade

value: DCIS low grade

tag: lcis

value: No LCIS

tag: lvi

tag: prolifbyge

tag: subtypebyge

value: LUMA


title: CR diet FLOX 4

tag: tissue

value: TA/EDL muscles

tag: diet

value: CR diet

tag: genotype

value: FLOX


title: 69

tag: origin

value: Dutch

tag: age

tag: lr

tag: pt

tag: surgicalmargin

value: marg-

tag: surgivalmargininv

value: MargInv-

tag: surgicalmargindcis

tag: pn

value: pN-

tag: rtboost

value: no boost

tag: rttotaldose

tag: ct

value: no ChT

tag: ht

tag: histshape

value: EEII

value: DCIS intermed grade

tag: lviquant

tag: erbyge

tag: prbyge

tag: herbyge

value: LUMB


title: Control diet MKO 6

source_name: TA/EDL muscle, control diet, MKO genotype

tag: tissue

tag: diet

value: control diet

tag: genotype

value: MKO


title: Control diet MKO 7


title: 64

tag: origin

tag: age

tag: lr

tag: pt

value: boost

value: no HT

value: stellate

tag: histtype

value: ductal

tag: histgrade

value: EEI

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

value: DCIS inside

tag: dcisoutside

tag: dcis

value: DCIS

tag: dcisgrade

tag: lcis

tag: lvi

value: No LVI

tag: prolifbyge

tag: subtypebyge


title: Control diet MKO 3

tag: tissue

value: TA/EDL muscles

tag: diet

tag: genotype


title: 7

tag: origin

value: Dutch

tag: age

tag: lr

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

tag: surgicalmargindcis

tag: pn

value: pN-

tag: rtboost

tag: rttotaldose

tag: ct

tag: ht

tag: histshape

value: EEIII

value: DCIS high grade

value: No LCIS

tag: lviquant

value: >5 LVI

tag: erbyge

tag: prbyge

tag: herbyge


title: 6

tag: origin

value: marg-

value: MargInv-

value: no ChT

tag: histtype

tag: histgrade

value: EEII

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

value: No DCIS inside

tag: dcisoutside

value: No DCIS outside

tag: dcis

value: No DCIS

tag: dcisgrade

tag: lcis

tag: lvi

tag: prolifbyge

tag: subtypebyge

value: LUMA


title: CR diet FLOX 1

tag: tissue

tag: diet

value: CR diet

tag: genotype

value: FLOX


title: Control diet MKO 5

value: TA/EDL muscles

value: control diet

value: MKO


title: 1

tag: origin

value: Dutch

tag: age

tag: lr

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

tag: surgicalmargindcis

tag: pn

value: pN-

tag: rtboost

value: boost

tag: rttotaldose

tag: ct

tag: ht

value: no HT

tag: histshape

value: sharply demarcated

value: ductal

value: EEIII

value: No LVI

tag: lviquant

tag: erbyge

tag: prbyge

tag: herbyge

value: TNP


title: 21

tag: origin

value: marg-

value: MargInv-

value: pN+

value: ChT

value: stellate

tag: histtype

tag: histgrade

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

value: No DCIS inside

tag: dcisoutside

tag: dcis

value: DCIS

tag: dcisgrade

value: DCIS high grade

tag: lcis

value: No LCIS

tag: lvi

value: 2-5 LVI

tag: prolifbyge

tag: subtypebyge


title: 4

value: Dutch

tag: age

tag: lr

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

tag: surgicalmargindcis

tag: pn

tag: rtboost

value: boost

tag: rttotaldose

tag: ct

tag: ht

tag: histshape

value: EEII

value: DCIS intermed grade

tag: lviquant

tag: erbyge

value: LUMA


title: 5

tag: origin

value: no HT

tag: histtype

value: ductal

tag: histgrade

value: EEI

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

tag: dcis

tag: dcisgrade

value: DCIS low grade

tag: lcis

tag: lvi

value: No LVI

tag: prbyge

tag: herbyge


title: 24

tag: age

tag: lr

tag: pt

tag: surgicalmargin

value: marg-

tag: surgivalmargininv

value: MargInv-

tag: surgicalmargindcis

tag: pn

value: pN+

tag: rtboost

tag: rttotaldose

tag: ct

value: ChT

tag: ht

tag: histshape

value: EEIII

tag: prolifbyge

tag: subtypebyge

value: TNP


title: 20

tag: origin

value: sharply demarcated

tag: histtype

tag: histgrade

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

value: No DCIS inside

tag: dcisoutside

value: No DCIS outside

tag: dcis

value: No DCIS

tag: dcisgrade

tag: lcis

value: No LCIS

tag: lvi

tag: lviquant

value: >5 LVI

tag: erbyge


title: Control diet MKO 1

tag: tissue

value: TA/EDL muscles

tag: diet

value: control diet

tag: genotype

value: MKO


title: Control diet MKO 2


title: Control diet MKO 4


title: 18

tag: origin

value: Dutch

tag: age

tag: lr

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

tag: surgicalmargindcis

tag: pn

value: pN-

tag: rtboost

value: no boost

tag: rttotaldose

tag: ct

value: no ChT

tag: ht

value: no HT

tag: histshape

value: ductal

tag: prbyge

tag: herbyge

tag: prolifbyge

tag: subtypebyge

value: LUMA


title: 16

tag: origin

value: marg-

value: MargInv-

value: boost

tag: histtype

tag: histgrade

value: EEIII

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

tag: dcis

tag: dcisgrade

tag: lcis

tag: lvi

tag: lviquant

value: 2-5 LVI

tag: erbyge

value: LUMHER


title: 19

tag: age

tag: lr

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

tag: surgicalmargindcis

tag: pn

value: pN+

tag: rtboost

tag: rttotaldose

tag: ct

value: ChT

tag: ht

tag: histshape

value: stellate

value: No DCIS inside

value: No DCIS outside

value: No DCIS

value: No LCIS

value: No LVI

tag: prbyge

tag: herbyge

value: TNP


title: 17

tag: origin

value: Dutch

value: marg+

value: MargDCIS-

value: HT

tag: histtype

value: ductal

tag: histgrade

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

tag: dcis

tag: dcisgrade

tag: lcis

tag: lvi

tag: prolifbyge

tag: subtypebyge


title: CR diet FLOX 2

tag: tissue

value: TA/EDL muscles

tag: diet

value: CR diet

tag: genotype

value: FLOX


title: 15

tag: origin

tag: age

tag: lr

tag: pt

tag: surgicalmargin

value: marg-

tag: surgivalmargininv

value: MargInv-

tag: surgicalmargindcis

tag: pn

value: pN-

tag: rtboost

value: boost

tag: rttotaldose

tag: ct

value: no ChT

tag: ht

value: no HT

tag: histshape

value: sharply demarcated

value: EEIII

tag: lviquant

tag: erbyge

tag: prbyge

tag: herbyge


title: 14

tag: origin

value: pN+

value: ChT

tag: histtype

tag: histgrade

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

tag: dcis

value: DCIS

tag: dcisgrade

value: DCIS high grade

tag: lcis

value: No LCIS

tag: lvi

tag: prolifbyge

tag: subtypebyge

value: TNP


title: Saos2 p63-53O-24 h

city: Sapporo

first: Yasushi

last: Sasaki

address: S-1, W-17, Chuo-ku

department: Cancer Research Institute

country: Japan

institute: Sapporo Medical University

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: MAS 5.0

source_name: Saos2 osteosarcoma cells infected with p63-53O expressing adenovirus for 24 h

label_protocol: Affymetrix standard protocol

extract_protocol: Trizol

tag: cell line

tag: transfection

value: p63-53O expressing adenovirus


title: 13

value: Dutch

tag: age

tag: lr

tag: pt

tag: surgicalmargin

value: marg+

tag: surgivalmargininv

value: MargInv+

tag: surgicalmargindcis

tag: pn

tag: rtboost

tag: rttotaldose

tag: ct

tag: ht

tag: histshape

value: stellate

value: ductal

value: EEII

value: DCIS intermed grade

value: No LVI

tag: lviquant

tag: erbyge

tag: prbyge

tag: herbyge

value: LUMA


title: Saos2 TAp63 gamma-24 h

source_name: Saos2 osteosarcoma cells infected with TAp63gamma expressing adenovirus for 24 h

tag: cell line

tag: transfection

value: TAp63gamma expressing adenovirus


title: 10

tag: origin

tag: age

tag: lr

value: marg-

value: MargInv-

value: pN-

value: boost

value: no ChT

value: no HT

tag: histtype

tag: histgrade

value: EEI

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

tag: dcisoutside

tag: dcis

tag: dcisgrade

value: DCIS low grade

tag: lcis

tag: lvi

value: 2-5 LVI

tag: prolifbyge

tag: subtypebyge


title: 11

value: Dutch

tag: pt

tag: surgicalmargin

tag: surgivalmargininv

tag: surgicalmargindcis

tag: pn

value: pN+

tag: rtboost

tag: rttotaldose

tag: ct

value: ChT

tag: ht

tag: histshape

value: No DCIS inside

value: No DCIS outside

value: No DCIS

value: No LCIS

tag: lviquant

tag: erbyge

tag: prbyge

tag: herbyge


title: Control diet FLOX 4

source_name: TA/EDL muscle, control diet, FLOX genotype

tag: tissue

value: TA/EDL muscles

tag: diet

value: control diet

tag: genotype

value: FLOX


title: Control diet FLOX 5


title: DLL4 day3_mouse2

city: Amsterdam

first: Derk

last: Amsen

address: Meibergdreef 9

country: Netherlands

institute: AMC

hyb_protocol: Whole Genome Expression with IntelliHyb Seal.

scan_protocol: Standard Illumina scanning protocol using the Illumina HiScan.

data_processing: Array data were extracted using Illumina's GenomeStudio software. Normalization and statistical analyses were carried out using Bioconductor packages in the statistical software package R. We performed normexp-by-control background correction, quantile normalization and log2 transformation on the Illumina sample and control probe profiles using the limma package. Probes that were not expressed (detection p-value < 0.05) on any of the arrays were filtered out. The arrayQualityMetrics package was used to ensure that the microarray data was of good quality. The normalized intensities of technical replicate arrays were averaged. Differential expression between the DLL4-Fc activated and control-Ig samples was assessed via a paired moderated t-test using the limma package.

source_name: naive CD4+ T cells, Delta4-Ig, day 3

label_protocol: Total RNA samples were amplified and biotinylated using the Ambion Illumina TotalPrep RNA Amplification Kit.

growth_protocol: Cells were grown in IMDM with 10% FCS, 2mM GlutaMAX (Invitrogen), 100 U/ml penicillin (Invitrogen), 100 μg/ml streptomycin (Invitrogen) and 50μM β-Mercaptoethanol.

extract_protocol: RNA was extracted using Trizol followed by purification with RNeasy columns.

treatment_protocol: Mouse CD62L+CD44-CD25-DX5-CD4+ T cells were stimulated with plate-bound anti-CD3e (10ug/ml), soluble anti-CD28 (1ug/ml) in the presence of plate-bound Delta4-Ig or control Ig (each at 5ug/ml).

tag: strain

value: inguinal, axillary and brachial lymph nodes and spleen

tag: cell type

value: naive CD4+ T cells

tag: stimulus

tag: timepoint

value: day 3

tag: mouse


title: Control diet FLOX 2


title: DLL4_day3_mouse1 (technical replicate)


title: DLL4_day3_mouse1


title: Control diet FLOX 3


title: C-Ig_day3_mouse2

source_name: naive CD4+ T cells, control, day 3

value: control Ig


title: C-Ig_day3_mouse1 (technical replicate)


title: IS-tAPX-19-23, biological replicate 1

city: Matsue

first: Takanori

last: Maruta

address: 1060 Nishikawatsu

institute: Shimane University

description: Biological replicate 1 of 2. Estrogen-treated IS-tAPX-19-23 leaves.

hyb_protocol: The labeled probes were hybridized to an Agilent Arabidopsis 3 Oligo Microarray (Agilent Technologies).

scan_protocol: Agilent Technologies Scanner G2505B US22502551

data_processing: Feature extraction software (GeneSpring, Agilent Technologies) was used.

organism: Arabidopsis thaliana

source_name: Leaves of IS-tAPX-19-23

label_protocol: Total RNA was used to produce Cy3-labeled cRNA probe. We used only Cy3, and didn't use Cy5 for labeling.

growth_protocol: The IS-GUS (control) and IS-tAPX plants were grown for 17 days under continuous light (100 µmol photons/m2/s).

extract_protocol: Total RNA was isolated using Sepasol-RNA I (Nakarai Tesque, Kyoto, Japan) from the control and IS-tAPX plants, and purified using an RNeasy Plant Mini Kit (Qiagen, Valencia, CA).

treatment_protocol: Seventeen-day-old IS-GUS and IS-tAPX plants were sprayed with 100 µM estrogen.  At 2 days after the treatment, the leaves were harvested.

value: rosette leaves

tag: cultivar


title: Control diet FLOX 1


title: IS-GUS-2-17, biological replicate 2

description: Biological replicate 2 of 2. Estrogen-treated IS-GUS-2-17 leaves.

source_name: Leaves of IS-GUS-2-17


title: DLL4_day1_mouse1

source_name: naive CD4+ T cells, Delta4-Ig, day 1

value: day 1


title: TCDD_1.0_363

status: Public on Feb 03 2012

city: Midland

first: Craig

last: Rowlands

state: MI

address: 1803 Bldg Washington Street

department: Toxicology & Environmental Research & Consulting

institute: The Dow Chemical Company

hyb_protocol: On each microarray, 1.65 ug of labeled cRNA was hybridized for 17 hours and subsequently washed per the Agilent protocol.

scan_protocol: Microarrays were scanned using the Agilent dual laser DNA microarray scanner, model G2565AA, with 5 µm resolution. The extended dynamic range option was used.

data_processing: Scanned images were processed with Agilent Feature Extraction software. Within Genespring, the data for each microarray were normalized to the median signal intensity of the microarray. Data were then log2 transformed.

organism: Rattus norvegicus

source_name: primary hepatocytes treated for 24h

label_protocol: For each sample, Alexa555-labeled cRNAs was generated from 500 ng of total RNA using the Epicentre TargetAMP 1-Round Aminoallyl-cRNA Amplification Kit per the vendor’s protocol (Epicentre Biotechnologies, Madison, WI). The Aminoallyl-cRNA was then purified using Qiagen RNeasy Mini Elute Kit.

growth_protocol: Primary cultures of rat hepatocytes were obtained from five individual 10-week-old female Sprague-Dawley rats.  Each individual rat was treated as a biological replicate.  Preplating cell viability, determined by trypan blue exclusion, ranged from 90 to 94% in rat hepatocytes. Following isolation, hepatocytes were resuspended in DMEM containing 5% fetal calf serum, insulin (4 ng/ml), and dexamethasone (1 nM).   The hepatocytes were then added to 24-well BioCoat (BD Biosciences) plates coated with collagen type 1 substratum and allowed to attach for 3–6 h at 37°C in a humidified chamber with 95% relative humidity and 5% CO2.  After attachment, the culture plates were swirled and the medium containing debris and unattached cells was aspirated.  Fresh, ice-cold, serum-free DMEM/Ham’s F12 medium containing 50 nM dexamethasone, 6.25 ng/ml insulin, 6.25 ng/ml transferrin, 6.25 ng/ml selenium (ITS+), and 0.25 mg/ml Matrigel was added to the culture plate and immediately returned to the humidified chamber. Serum-free medium was used since serum can significantly reduce the cellular uptake of TCDD. Medium was kept in the dark prior to use and was not changed during the incubation periods.

extract_protocol: Cells (24-well format) were washed with one volume of HBSS, lysed by addition of 0.35 ml of ABI Nucleic Acid Lysis Solution (Applied Biosystems, Foster City, CA), and frozen at -70 C.  Lysates were thawed and total RNA was isolated from each sample using an ABI 6100 Prepstation according to the manufacturer’s protocol.

treatment_protocol: Stock solutions of TCDD (100 µM) were diluted in DMSO and added to culture media (DMEM-Ham’s F12) to a final DMSO concentration of 0.1% .  The hepatocyte cultures were exposed for 24 h to the DMSO vehicle (0.1%) or one of the following TCDD concentrations: 0.00001, 0.0001, 0.001, 0.003, 0.01, 0.03, 0.1, 0.3, 1, 10, 100 nM. Cell viability was examined at the 24 h time point in the vehicle control hepatocytes and hepatocytes treated with 100 nM TCDD.  Viability was assessed by morphological appearance, LDH leakage (CytoTox-ONE, Promega, Madison, WI), ATP levels (CellTiterGlo, Promega), and phase contrast microscopy (LeCluyse et al., 2000; Meunier et al., 2000).  Cell viability end points did not demonstrate treatment-related cytotoxicity.

value: Sprague-Dawley

tag: gender

value: female

tag: age

value: primary hepatocytes

tag: treatment

value: TCDD

tag: dose

tag: tcdd sample


title: IS-tAPX-19-23, biological replicate 2

description: Biological replicate 2 of 2. Estrogen-treated IS-tAPX-19-23 leaves.


title: TCDD_0.03_363


title: C-Ig day1_mouse1

source_name: naive CD4+ T cells, control, day 1


title: C-Ig_day3_mouse1


title: TCDD_10.0_363


title: TCDD_0.1_363


title: TCDD_100.0_363


title: TCDD_0.003_363


title: TCDD_100.0_361


title: IS-GUS-2-17, biological replicate 1

description: Biological replicate 1 of 2. Estrogen-treated IS-GUS-2-17 leaves.


title: TCDD_10.0_361


title: TCDD_0.001_363


title: TCDD_1.0_361


title: 71

tag: origin

value: Dutch

tag: lr

tag: pt

tag: surgicalmargin

value: marg-

tag: surgivalmargininv

value: MargInv-

tag: surgicalmargindcis

tag: pn

value: pN+

tag: rtboost

value: boost

tag: rttotaldose

tag: ct

value: ChT

tag: ht

value: no HT

tag: histshape

value: stellate

tag: histtype

value: ductal

tag: histgrade

value: EEIII

tag: tubuleformation

tag: polymorphism

tag: mitoticindex

tag: dcisinside

value: No DCIS inside

tag: dcisoutside

tag: dcis

tag: dcisgrade

tag: lcis

tag: lvi

value: No LVI

tag: lviquant

tag: erbyge

tag: prolifbyge

tag: subtypebyge

value: LUMA


title: TCDD_0.03_361

tag: strain

value: Sprague-Dawley

tag: gender

tag: age

tag: tissue

tag: treatment

tag: dose

tag: tcdd sample


title: TCDD_0.001_361

value: female


title: TCDD_0.1_361

value: primary hepatocytes


title: TCDD_0.0001_363

value: TCDD


title: TCDD_0.01_361


title: TCDD_0.0001_361


title: TCDD_0.01_363


title: TCDD_0.3_363


title: TCDD_1.0_302


title: TCDD_0.3_361


title: TCDD_100.0_302


title: TCDD_0.3_302


title: Control diet FLOX 6

value: TA/EDL muscles

tag: diet

value: control diet

tag: genotype

value: FLOX


title: TCDD_0.003_361


title: TCDD_0.01_302


title: TCDD_0.001_302


title: TCDD_0.0001_302


title: TCDD_0.1_302


title: TCDD_0.00001_361


title: TCDD_100.0_293


title: TCDD_0.003_302


title: TCDD_10.0_302


title: TCDD_0.00001_302


title: TCDD_0.03_302


title: TCDD_0.1_293


title: TCDD_10.0_293


title: TCDD_0.001_293


title: TCDD_0.00001_363


title: TCDD_0.03_293


title: TCDD_0.003_293


title: TCDD_0.01_293-2


title: TCDD_0.01_293-1


title: TCDD_0.00001_293


title: TCDD_0.0001_293


title: TCDD_100.0_277


title: TCDD_0.3_277


title: TCDD_10.0_277


title: TCDD_1.0_293


title: TCDD_1.0_277


title: TCDD_0.01_277


title: TCDD_0.1_277


title: TCDD_0.03_277


title: TCDD_0.003_277


title: TCDD_0.00001_277


title: male breast cancer 21

city: Lund

first: Ida

last: Johansson

address: Department of Oncology Clinical Sciences Lund University BMC C13

department: Oncology

country: Sweden

institute: Lund University

description: replicate 21

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with BASE2 Combat adjusted one the hybridization batches

source_name: male breast cancer

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: size [mm]

tag: er

value: positive

tag: pr

tag: year of diagnosis

tag: hybridization batch

tag: extraction date

tag: pathology department

value: male

value: breast cancer tumor


title: male breast cancer 18

description: replicate 18

tag: nottingham histological grade (nhg)


title: male breast cancer 24 rep2

description: replicate 24


title: male breast cancer 26

description: replicate 26


title: male breast cancer 22

description: replicate 22


title: TCDD_0.0001_277

tag: strain


title: TCDD_0.001_277

tag: gender


title: male breast cancer 20

description: replicate 20

tag: age


title: male breast cancer 28

description: replicate 28

value: negative

tag: tissue


title: male breast cancer 19

description: replicate 19


title: male breast cancer 27

description: replicate 27


title: male breast cancer 23 rep2

description: replicate 23


title: (+Cd/C)WS_2w rep1

city: Miyagi

first: Yasuhiro

last: Ishimaru

address: 6-3 Aramakiaza-aoba, Aoba-ku, Sendai

institute: Tohoku University

hyb_protocol: Cy3-labelled cRNA and Cy5-labelled cRNA (825ng each) were mixed, fragmented and hybridized with the rice 4x44K microarray RAP-DB (G2519F#15241) for 17 hours at 65°C using the Agilent Gene Expression Hybridization kit.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using two color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended processed signal intensities.detrended processed signal intensities.

organism: Oryza sativa Japonica Group

source_name: WT grown under control conditions

label_protocol: Labeled cRNA was prepared from 400 ng RNA using the Low RNA Input Linear Amplification/Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Rice plant grown in hydroponic solution for 4 weeks under control condition.

extract_protocol: RNA was prepared using RNeasy Plant Mini kit (Qiagen) following the manufacturer's recommendations. The protocol includes an on-column DNase digestion. RNA was quantified using a NanoDrop ND-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: cultivar

value: Tsukinohikari

value: day 42

value: Shoot

source_name: WT grown under +Cd conditions

value: day 35


title: (+Cd/C)WS_2w rep3


title: (+Cd/C)WR_2w rep4

value: Root


title: (+Cd/C)WS_2w rep2


title: (+Cd/C)WR_2w rep3


title: (+Cd/C)WR_2w rep1


title: (+Cd/C)WS_2w rep4


title: male breast cancer 25

description: replicate 25


title: (+Cd/C)WR_2w rep2


title: male breast cancer 23 rep1

description: replicate 23


title: male breast cancer 66

description: replicate 66


title: KS/WS-rep6

source_name: OsNRAMP5 RNAi plant

value: day 28

source_name: WT


title: KS/WS-rep5


title: KS/WS-rep2


title: KS/WS-rep1


title: KS/WS-rep4


title: male breast cancer 24 rep1

description: replicate 24


title: iR/WR-rep6


title: male breast cancer 65

description: replicate 65


title: iR/WR-rep3


title: male breast cancer 64

description: replicate 64


title: HFHQ 3d_2.0_rep3

city: London

first: Stephen

last: Sturzenbaum

address: 150 Stamford Street

department: Analytical, Environmental and Forensic Sciences

country: United Kingdom

institute: King's College London

description: Standard affymetrix recommended quality control parameters were used during entire experiment.

hyb_protocol: 10 μg of Biotin end labeled aRNA (amplified RNA) was fragmented and hybridized to the Affymetrix C. elegans GeneChips as recommended by Affymetrix. The quality & quantity of the aRNA probe preparation was assessed before hybridization using an Agilent 2100 bioanalyzer & Nanodrop-1000 spectrophotometer, receptively.

scan_protocol: Affymetrix GeneChip® Command Console (AGCC) software was used for the control of array washing (GeneChip Fluidics Station-450), data acquisition (Scanner 3000-7G) as well as for the preliminary data analysis.

data_processing: Pre-processing of DNA microarray raw data included probe-specific background correction, summarisation of probe set values, and normalisation using the GCRMA algorithm with CARMAweb 1.4, an R- and Bioconductor-based web service for microarray data analysis (Rainer et al., 2006) (https://carmaweb.genome.tugraz.at/carma/). Then, the data were initially filtered for missing values and then subjected to a CLEAR-test that combines differential expression and variability using the GEPAS software (Herrero et al., 2003) (http://www.gepas.org). For selection of differentially expressed genes (DEGs), an unpaired t-test was performed followed by a significance analysis of microarray (SAM) test including a calculation that estimates the false discovery rate (FDR). FDR was set to a non-stringent level of <12.5%, mainly to guard from an increase of type II error (Swain et al., 2010). DEGs exceeding a fold change of 1.25 were further analyzed with respect to their functional clustering. This analysis was conducted using the functional annotation clustering tool of the Database for Annotation, Visualization and Integrated Discovery (DAVID) (Huang et al., 2007) (http://david.abcc.ncifcrf.gov/). This tool identifies annotation categories including, e.g., gene ontology (GO) terms and bio-pathways that are significantly enriched within the gene list, followed by a multiple sample correction (Benjamini and Hochberg, 1995). The resultant annotation clusters were ranked according to the statistical significance of cluster enrichment.

organism: Caenorhabditis elegans

source_name: HF_HQ 3d_2.0_rep3

label_protocol: 200 ng of total RNA was subjected to aRNA amplification and Biotin labeling as described in the MessageAmpTM Premier RNA Amplification Kit (Ambion) for microarray analysis. aRNA cleanup was achieved using magnetic beads (Ambion).

growth_protocol: C. elegans (GE24, pha-1(e2123) were chunked onto control plates (no HF) and treatment plates (0.2 and 2.0 mM HF and HF-HQ dissolved organic carbon (DOC), respectively) and incubated at 15 °C for five days. Then, a synchronous culture was generated by filtering worms through a 10 µm membrane (SM 16510/11, Sartorius, Germany), a pore size that retains all but first stage juveniles (L1). For each individual experiment, 15,000 larvae were distributed to three freshly prepared plates (Ø = 94 mm) and cultivated at 25 °C to the young adult stage (3 days) or an older adult stage (11 days). Nematodes were fed every third day by replenishing the bacterial suspension and supplemented with a fresh preparation of humic substances (0, 0.2 and 2.0 mM, respectively). Following the respective exposures, nematodes were harvested by rinsing off with M9 buffer, rewashed twice, frozen in liquid nitrogen and stored at -80°C until use. Each condition was cultivated in triplicate.

extract_protocol: Total RNA was isolated using an innuSPEED Tissue RNA Kit (AnalytikJena, Jena, Germany), which included a homogenization step with a SpeedMill (AnalytikJena, Jena, Germany) and the removal of genomic DNA through an initial spin filter column step. The RNA quality and quantity was analysed both spectroscopically (NanoDrop1000, ThermoScientific, UK) and by means of an Agilent’s Bioanalyser 2100 equipped with a RNA 6000 Nano kit (Agilent Technologies, Santa Clara, CA, USA). All RNA-samples showed no signs of degradation as indicated by Agilent’s RNA integrity numbers of 9 or 10.

value: larvae (L4)

value: whole animal

tag: genotype/variation

tag: treatment

value: 2.0 mM Huminfeed-Hydroquinone

tag: harvest date

value: 3 days


title: HFHQ 3d_2.0_rep2

source_name: HF_HQ 3d_2.0_rep2

treatment_protocol: C. elegans (GE24, pha-1(e2123) were chunked onto control plates (no HF) and treatment plates (0.2 and 2.0 mM HF and HF-HQ dissolved organic carbon (DOC), respectively) and incubated at 15 °C for five days. Then, a synchronous culture was generated by filtering worms through a 10 µm membrane (SM 16510/11, Sartorius, Germany), a pore size that retains all but first stage juveniles (L1). For each individual experiment, 15,000 larvae were distributed to three freshly prepared plates (Ø = 94 mm) and cultivated at 25 °C to the young adult stage (3 days) or an older adult stage (11 days). Nematodes were fed every third day by replenishing the bacterial suspension and supplemented with a fresh preparation of humic substances (0, 0.2 and 2.0 mM, respectively). Following the respective exposures, nematodes were harvested by rinsing off with M9 buffer, rewashed twice, frozen in liquid nitrogen and stored at -80°C until use. Each condition was cultivated in triplicate.


title: iR/WR-rep5


title: iR/WR-rep2


title: male breast cancer 62

description: replicate 62


title: male breast cancer 63

description: replicate 63


title: iR/WR-rep4


title: KS/WS-rep3


title: iR/WR-rep1


title: male breast cancer 2

description: replicate 2


title: male breast cancer 61

description: replicate 61


title: TCDD_10.0_579

growth_protocol: Primary cultures of human hepatocytes were prepared from remnants of normal resected liver tissue from five women ages 44–77 years. The choice of only females was made based on the use of female rats in the two-year cancer bioassay (NTP 2006).  Each donor was fully consented under an institutional review board application approved by the individual institutions where liver resection surgery was conducted.  The resected liver tissue was determined to be disease free by a board-certified pathologist.  Four of the five human donors did not consume alcohol and all were free of hepatitis and HIV.  The research on the human samples was carried out in accordance with the principles of the current version of the Helsinki Declaration.  Each individual human was treated as a biological replicate.  Preplating cell viability, determined by trypan blue exclusion, ranged from 82 to 93% in human hepatocytes.  Following isolation, hepatocytes were resuspended in DMEM containing 5% fetal calf serum, insulin (4 ng/ml), and dexamethasone (1 nM).   The hepatocytes were then added to 24-well BioCoat (BD Biosciences) plates coated with collagen type 1 substratum and allowed to attach for 3–6 h at 37°C in a humidified chamber with 95% relative humidity and 5% CO2.  After attachment, the culture plates were swirled and the medium containing debris and unattached cells was aspirated.  Fresh, ice-cold, serum-free DMEM/Ham’s F12 medium containing 50 nM dexamethasone, 6.25 ng/ml insulin, 6.25 ng/ml transferrin, 6.25 ng/ml selenium (ITS+), and 0.25 mg/ml Matrigel was added to the culture plate and immediately returned to the humidified chamber. Serum-free medium was used since serum can significantly reduce the cellular uptake of TCDD. Medium was kept in the dark prior to use and was not changed during the incubation periods.

value: primary hepatocytes

tag: sample

value: TCDD

tag: tcdd dose


title: TCDD_0.1_579


title: HFHQ 3d_0.2_rep3

source_name: HF_HQ 3d_0.2_rep3

value: 0.2 mM Huminfeed-Hydroquinone


title: HFHQ 3d control_rep1

source_name: HF_HQ 3d control_rep1


title: male breast cancer 60

description: replicate 60

tag: size [mm]

tag: er

value: positive


title: male breast cancer 46

description: replicate 46

tag: pr

tag: year of diagnosis

value: male


title: HFHQ 3d_0.2_rep1

source_name: HF_HQ 3d_0.2_rep1


title: HFHQ 3d_2.0_rep1

source_name: HF_HQ 3d_2.0_rep1


title: HFHQ 3d_0.2_rep2

source_name: HF_HQ 3d_0.2_rep2


title: male breast cancer 59

description: replicate 59

tag: hybridization batch

tag: extraction date

value: breast cancer tumor


title: male breast cancer 44

description: replicate 44

tag: pathology department


title: TCDD_100.0_579


title: TCDD_1.0_579


title: male breast cancer 45

description: replicate 45


title: TCDD_0.03_579


title: HFHQ 3d control_rep3

source_name: HF_HQ 3d control_rep3

tag: strain


title: HFHQ 3d control_rep2

source_name: HF_HQ 3d control_rep2


title: TCDD_0.3_579


title: HF 11d_2.0_rep2

value: 2.0 mM HuminFeed

value: 11 days


title: HF 11d_2.0_rep1


title: male breast cancer 58

description: replicate 58

tag: gender


title: TCDD_0.01_579


title: male breast cancer 57

description: replicate 57

tag: age


title: TCDD_0.001_579

tag: tissue


title: HF 11d_0.2_rep3

value: 0.2 mM HuminFeed


title: TCDD_0.003_579


title: HF 11d_2.0_rep3


title: TCDD_0.0001_579


title: male breast cancer 56

description: replicate 56


title: TCDD_0.00001_579


title: male breast cancer 55

description: replicate 55


title: HF 11d_0.2_rep1


title: HF 11d control_rep3

source_name: HF 11d control_rep3


title: TCDD_10.0_572

source_name: primary hepatocytes treated for 24h


title: DMSO_0.0_579

value: DMSO


title: male breast cancer 53

description: replicate 53


title: TCDD_100.0_572


title: male breast cancer 54

description: replicate 54


title: HF 11d control_rep2

source_name: HF 11d control_rep2


title: HF 11d_0.2_rep2


title: male breast cancer 41

description: replicate 41

source_name: male breast cancer


title: TCDD_1.0_572


title: HF 3d_2.0_rep2


title: HF 11d control_rep1

source_name: HF 11d control_rep1


title: TCDD_0.3_572


title: male breast cancer 52

description: replicate 52

value: negative


title: male breast cancer 43

description: replicate 43


title: HF 3d_2.0_rep1


title: HF 3d_0.2_rep3


title: male breast cancer 42 rep1

description: replicate 42


title: male breast cancer 8

description: replicate 8

tag: nottingham histological grade (nhg)


title: HF 3d_2.0_rep3

tag: genotype/variation


title: TCDD_0.01_572

tag: treatment


title: male breast cancer 42 rep2

description: replicate 42


title: TCDD_0.003_572


title: TCDD_0.03_572


title: TCDD_0.1_572


title: male breast cancer 17 rep2

description: replicate 17


title: HF 3d_0.2_rep2

tag: harvest date


title: HF 3d_0.2_rep1


title: TCDD_0.001_572

tag: sample


title: TCDD_0.0001_572

tag: tcdd dose


title: male breast cancer 51

description: replicate 51

tag: size [mm]


title: HF 3d control_rep3

source_name: HF 3d control_rep3


title: TA300_rep2

data_processing: Pre-processing of raw microarray data included probe-specific background correction, summation of probe set values, and normalization using the GCRMA algorithm with CARMAweb 1.4, an R- and Bioconductor-based web service for microarray data analysis (https://carmaweb.genome.tugraz.at/carma) (Rainer et al., 2006). The quality of normalization was assessed by box plot and MA-graph analyses. Differences between treatments were visualized by Principal Component Analysis (PCA) plotting with MeV (MultiExperiment Viewer, http://www.tm4.org/mev) (Saeed et al., 2003). Data was initially filtered for missing values and then subjected to a CLEAR-test that combines differential expression and variability using the GEPAS web server at http://www.gepas.org (Joaquín et al., 2008). An unpaired t-test was followed by a Significance Analysis of Microarray (SAM) testing including a calculation that estimates the False Discovery Rate (FDR). The FDR was set to a non-stringent level of <12.5%. Differentially Expressed Genes (DEGs) showing a fold change of at least 1.25 were analyzed for their molecular functions, biological processes, and cellular components using the software packages GoMiner (Zeeberg et al., 2005) and DAVID (http://david.abcc.ncifcrf.gov/).

growth_protocol: N2 wild type C. elegans were maintained on nematode growth medium (NGM) plates using Escherichia coli OP50 as food. Untreated nematodes (the P0 generation) were chunked onto control and treatment plates (50, 100, and 200 µM Quercetin; 100, 200, and 300 µM Tannic Acid) and incubated at 20°C for 4 days. A synchronous culture was generated through egg preparation with sodium hypochlorite. Hatched L1s were rotated over night (20 rpm) and subsequently transferred to plates containing the respective doses of Quercetin or Tannic Acid. Worms were grown to the young (pre-reproductive) adult stage, harvested by rinsing off with M9 buffer, shock frozen in liquid nitrogen and stored at -80°C.

extract_protocol: RNA was isolated following the standard procedures as defined by the Trizol protocol (Invitrogen) but modified to include a homogenization step with 0.5 mm glass beads to maximize cell breakage. The resultant RNA was further processed by means of a RNeasy purification followed by DNase digestion (Qiagen). All samples were stored at -80°C until further use.

value: N2 (Bristol)

value: wild type

value: 300 µM Tannic acid


title: male breast cancer 15

description: replicate 15

tag: er


title: male breast cancer 17 rep1

description: replicate 17

tag: pr


title: HF 3d control_rep2

source_name: HF 3d control_rep2

value: larvae (L4)

value: whole animal


title: DMSO_0.0_572


title: TCDD_10.0_497


title: male breast cancer 50

description: replicate 50

tag: year of diagnosis


title: HF 3d control_rep1

source_name: HF 3d control_rep1

value: 3 days


title: TCDD_0.00001_572

value: primary hepatocytes


title: male breast cancer 16

description: replicate 16

tag: hybridization batch


title: TA300_rep3

treatment_protocol: N2 wild type C. elegans were maintained on nematode growth medium (NGM) plates using Escherichia coli OP50 as food. Untreated nematodes (the P0 generation) were chunked onto control and treatment plates (50, 100, and 200 µM Quercetin; 100, 200, and 300 µM Tannic Acid) and incubated at 20°C for 4 days. A synchronous culture was generated through egg preparation with sodium hypochlorite. Hatched L1s were rotated over night (20 rpm) and subsequently transferred to plates containing the respective doses of Quercetin or Tannic Acid. Worms were grown to the young (pre-reproductive) adult stage, harvested by rinsing off with M9 buffer, shock frozen in liquid nitrogen and stored at -80°C.


title: TCDD_1.0_497

value: TCDD


title: male breast cancer 6

description: replicate 6

tag: extraction date


title: TCDD_100.0_497


title: TA200_rep2

value: 200 µM Tannic acid


title: male breast cancer 38 rep2

description: replicate 38

value: positive

tag: pathology department


title: TCDD_0.1_497


title: male breast cancer 5

description: replicate 5

value: male


title: TA300_rep1

tag: strain


title: TA200_rep1


title: TCDD_0.03_497


title: male breast cancer 7 rep2

description: replicate 7

tag: gender

value: breast cancer tumor


title: TCDD_0.003_497


title: TA200_rep3

tag: age


title: male breast cancer 4

description: replicate 4

tag: tissue


title: male breast cancer 37

description: replicate 37

tag: nottingham histological grade (nhg)


title: TCDD_0.3_497


title: TCDD_0.00001_497


title: male breast cancer 7 rep1

description: replicate 7


title: male breast cancer 38 rep1

description: replicate 38


title: male breast cancer 14

description: replicate 14


title: TCDD_0.001_497


title: TCDD_0.01_497


title: TCDD_0.0001_497


title: TA Control_rep2

source_name: TA Control_rep2

tag: genotype/variation


title: TA100_rep3

tag: treatment

value: 100 µM Tannic acid


title: TA100_rep2


title: TA Control_rep3

source_name: TA Control_rep3


title: TA100_rep1


title: TA Control_rep1

source_name: TA Control_rep1


title: male breast cancer 13 rep2

description: replicate 13


title: TCDD_100.0_489


title: TCDD_10.0_489


title: male breast cancer 36

description: replicate 36


title: DMSO_0.0_497


title: male breast cancer 11

description: replicate 11


title: male breast cancer 48 rep2

description: replicate 48


title: Q200_rep3

value: 200 µM Quercetin


title: Q200_rep2


title: TCDD_1.0_489


title: male breast cancer 10

description: replicate 10


title: Q100_rep1

value: 100 µM Quercetin


title: Q100_rep2