title: BR_FNA_M801

source_name: Sample ID -- 801, fine-needle aspiration, breast cancer cells

tag: age

tag: race

value: white

tag: tbefore

tag: nbefore

tag: bmngrd

tag: er

tag: her2 status

tag: her2 ihc

value: TFEC

value: Taxol x  12 FEC x  4


title: BR_FNA_M795

status: Public on Feb 04 2010

type: RNA

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

country: China

institute: Fudan University

description:
MAQC_Distribution_Status: MAQC_V -- Validation
Please see the GSE20194_MDACC_Sample_Info.xls file on the GSE20194 Series record for additional information on the Sample characteristics

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Sample ID -- 795, fine-needle aspiration, breast cancer cells

label_protocol: biotin labeling

extract_protocol: RNA was extracted from FNA samples using the RNAeasy Kit (Qiagen, Valencia, CA). The amount and quality of RNA were assessed with DU-640 UV Spectrophotometer (Beckman Coulter, Fullerton, CA), and they were considered adequate for further analysis if the optical density 260/280 ratio was ≥1.8 and the total RNA yield was ≥ 1μg.

treatment_protocol: Patients received pretreatment fine-needle aspiration (FNA) of the primary breast tumor or ipsilateral axillary metastasis before starting chemotherapy as part of an ongoing pharmacogenomic marker discovery program. The aspiration was performed using a 23- or 25-gauge needle. Cells from two to three passes were collected in vials containing 1 mL RNA later solution (Ambion, Austin, TX) and stored at -80°C. FNA samples on average contain 80% neoplastic cells and contain little or no stromal cells or normal breast epithelium.

tag: tissue

value: breast cancer cells

value: P

value: RD

value: N

tag: her2 fish

tag: histology

value: IDC

tag: treatment code

value: TFAC

tag: treatments comments

value: Taxol x  12 FAC x  4


title: BR_FNA_M784

source_name: Sample ID -- 784, fine-needle aspiration, breast cancer cells

value: Taxol x 12 FAC x  6


title: BR_FNA_M767

source_name: Sample ID -- 767, fine-needle aspiration, breast cancer cells

value: pCR

value: Taxol x 12  FAC x 4


title: BR_FNA_M774

source_name: Sample ID -- 774, fine-needle aspiration, breast cancer cells

value: Taxol x   12 FEC x  4


title: BR_FNA_M782

source_name: Sample ID -- 782, fine-needle aspiration, breast cancer cells

value: ILC

value: Tamoxifen x 2 weeks  Taxol x 12 FAC x 4


title: BR_FNA_M781

source_name: Sample ID -- 781, fine-needle aspiration, breast cancer cells

value: Taxol x 12 FEC x  4


title: BR_FNA_M728

source_name: Sample ID -- 728, fine-needle aspiration, breast cancer cells

value: black

value: FAC x 4 Taxol x 12


title: BR_FNA_M744

source_name: Sample ID -- 744, fine-needle aspiration, breast cancer cells

value: white

value: Taxol x 12 FAC x 4


title: BR_FNA_M734

source_name: Sample ID -- 734, fine-needle aspiration, breast cancer cells

value: breast cancer cells

value: P

value: TFEC

value: Taxol x 12 FEC x 4


title: BR_FNA_M765

source_name: Sample ID -- 765, fine-needle aspiration, breast cancer cells

value: RD

value: N

value: IDC

value: TFAC


title: BR_FNA_M746

source_name: Sample ID -- 746, fine-needle aspiration, breast cancer cells


title: BR_FNA_M723

source_name: Sample ID -- 723, fine-needle aspiration, breast cancer cells

value: hispanic


title: BR_FNA_M753

source_name: Sample ID -- 753, fine-needle aspiration, breast cancer cells


title: BR_FNA_M709

source_name: Sample ID -- 709, fine-needle aspiration, breast cancer cells

value: pCR


title: BR_FNA_M732

source_name: Sample ID -- 732, fine-needle aspiration, breast cancer cells


title: BR_FNA_M717

source_name: Sample ID -- 717, fine-needle aspiration, breast cancer cells

value: asian

value: FEC x 5 (d/t NC) switch to Taxol x 10 (Pt missed two doses)


title: BR_FNA_M714

source_name: Sample ID -- 714, fine-needle aspiration, breast cancer cells

value: Taxol x 4 FEC x 4


title: BR_FNA_M718

source_name: Sample ID -- 718, fine-needle aspiration, breast cancer cells


title: BR_FNA_M685

source_name: Sample ID -- 685, fine-needle aspiration, breast cancer cells

value: Taxol x 12  FEC x4


title: BR_FNA_M695

source_name: Sample ID -- 695, fine-needle aspiration, breast cancer cells

value: FAC x 4 Taxol x 12


title: BR_FNA_M696

source_name: Sample ID -- 696, fine-needle aspiration, breast cancer cells

value: black

value: Taxol x12 FAC x4


title: BR_FNA_M725

source_name: Sample ID -- 725, fine-needle aspiration, breast cancer cells

value: breast cancer cells

value: white

value: FECT

value: FEC x 6 (P.D “new supra & infraclavicular Ln”)Taxol x 12


title: BR_FNA_M675

source_name: Sample ID -- 675, fine-needle aspiration, breast cancer cells

value: RD

value: Taxol x 12 FAC x4


title: BR_FNA_M690

source_name: Sample ID -- 690, fine-needle aspiration, breast cancer cells

value: P

value: N

value: IDC

value: TFEC

value: Taxol x 12 FEC x4


title: BR_FNA_M710

source_name: Sample ID -- 710, fine-needle aspiration, breast cancer cells

value: ILC/IDC

value: Taxol x 12 FEC x 4


title: BR_FNA_M693

source_name: Sample ID -- 693, fine-needle aspiration, breast cancer cells

value: IDC/ILC

value: TFAC

value: FAC x 4 Taxol x12


title: BR_FNA_M692

source_name: Sample ID -- 692, fine-needle aspiration, breast cancer cells

value: pCR

value: Taxol x 12 FEC x  4


title: BR_FNA_M679

source_name: Sample ID -- 679, fine-needle aspiration, breast cancer cells

value: breast cancer cells

value: white

value: FAC x 4 Taxol x 12


title: BR_FNA_M682

source_name: Sample ID -- 682, fine-needle aspiration, breast cancer cells

value: RD

value: Taxol x 10 (D/T severe low ANC) FEC x4


title: BR_FNA_M683

source_name: Sample ID -- 683, fine-needle aspiration, breast cancer cells

value: P

value: Taxol x 12 FAC x4


title: BR_FNA_M681

source_name: Sample ID -- 681, fine-needle aspiration, breast cancer cells

value: hispanic

value: N

value: IDC


title: BR_FNA_M673

source_name: Sample ID -- 673, fine-needle aspiration, breast cancer cells

value: TFEC

value: Taxol x 11 ( one dose missed & no repleced) FEC x 4


title: BR_FNA_M669

source_name: Sample ID -- 669, fine-needle aspiration, breast cancer cells

value: asian

value: Taxol x 12 FAC x 4


title: BR_FNA_M668

source_name: Sample ID -- 668, fine-needle aspiration, breast cancer cells

value: TFAC


title: BR_FNA_M666

source_name: Sample ID -- 666, fine-needle aspiration, breast cancer cells


title: BR_FNA_M670

source_name: Sample ID -- 670, fine-needle aspiration, breast cancer cells

value: Taxol x 12 FEC x 4


title: BR_FNA_M662

source_name: Sample ID -- 662, fine-needle aspiration, breast cancer cells


title: BR_FNA_M658

source_name: Sample ID -- 658, fine-needle aspiration, breast cancer cells

value: pCR

value: Taxol x 12   FAC x 4


title: BR_FNA_M652

source_name: Sample ID -- 652, fine-needle aspiration, breast cancer cells

value: breast cancer cells

value: white

value: IDC/ILC

value: FAC x 4 Taxol x12 (Abraxene)


title: BR_FNA_M665

source_name: Sample ID -- 665, fine-needle aspiration, breast cancer cells


title: BR_FNA_M671

source_name: Sample ID -- 671, fine-needle aspiration, breast cancer cells

value: P

value: RD


title: BR_FNA_M659

source_name: Sample ID -- 659, fine-needle aspiration, breast cancer cells

value: Taxol x 10 (D/T  N.C swith to) FAC x 4


title: BR_FNA_M651

source_name: Sample ID -- 651, fine-needle aspiration, breast cancer cells

value: N

value: Taxol x 9 (d/t severe parestesias)    FACx 2 (d/t Cholecystiitis + Sx)


title: BR_FNA_M661

source_name: Sample ID -- 661, fine-needle aspiration, breast cancer cells

value: IDC

value: Taxol x 12 FAC x 2 (D/T severe allergic reaction)


title: BR_FNA_M657

source_name: Sample ID -- 657, fine-needle aspiration, breast cancer cells

value: hispanic


title: BR_FNA_M647

source_name: Sample ID -- 647, fine-needle aspiration, breast cancer cells

value: Taxol x 12 FAC x 4


title: BR_FNA_M642

source_name: Sample ID -- 642, fine-needle aspiration, breast cancer cells

value: TFEC

value: FEC x 4  Taxol x 12


title: BR_FNA_M619

source_name: Sample ID -- 619, fine-needle aspiration, breast cancer cells

value: FACT+XRT/X

value: FAC x 6 Taxol  x 12 /  XRT+ Xeloda (as a neo-adj setting)


title: BR_FNA_M626

source_name: Sample ID -- 626, fine-needle aspiration, breast cancer cells

value: breast cancer cells

value: Taxol x 12  FEC x 4


title: BR_FNA_M643

source_name: Sample ID -- 643, fine-needle aspiration, breast cancer cells

value: white

value: Taxol x 12 FEC x 4


title: BR_FNA_M610

source_name: Sample ID -- 610, fine-needle aspiration, breast cancer cells

value: P

value: IDC/LDC

value: TFAC

value: Taxol x 12  FAC x 4


title: BR_FNA_M599

source_name: Sample ID -- 599, fine-needle aspiration, breast cancer cells

value: RD

value: N


title: BR_FNA_M564

source_name: Sample ID -- 564, fine-needle aspiration, breast cancer cells

value: IDC


title: BR_FNA_M571

source_name: Sample ID -- 571, fine-needle aspiration, breast cancer cells

value: black

value: pCR

value: FACT

value: FAC x 4 Taxol x 12


title: BR_FNA_M607

source_name: Sample ID -- 607, fine-needle aspiration, breast cancer cells

value: TFEC


title: BR_FNA_M583

source_name: Sample ID -- 583, fine-needle aspiration, breast cancer cells

value: Taxol x 12  FAC x 6


title: BR_FNA_M566

source_name: Sample ID -- 566, fine-needle aspiration, breast cancer cells

value: breast cancer cells

value: Taxol x  12  FAC x 4


title: BR_FNA_M559

source_name: Sample ID -- 559, fine-needle aspiration, breast cancer cells

value: white


title: BR_FNA_M576

source_name: Sample ID -- 576, fine-needle aspiration, breast cancer cells

value: Taxol x 12 FAC x 4


title: BR_FNA_M617

source_name: Sample ID -- 617, fine-needle aspiration, breast cancer cells

value: Taxol x 12  FEC x 4


title: BR_FNA_M578

source_name: Sample ID -- 578, fine-needle aspiration, breast cancer cells

value: P


title: BR_FNA_M557

source_name: Sample ID -- 557, fine-needle aspiration, breast cancer cells

value: TFAC

value: Taxol x12 FAC x 4


title: BR_FNA_M612

source_name: Sample ID -- 612, fine-needle aspiration, breast cancer cells

value: RD

value: Taxol x 12   FAC x 2  ( d/t CVC infection )


title: BR_FNA_M549

source_name: Sample ID -- 549, fine-needle aspiration, breast cancer cells

value: hispanic

value: N

value: IDC/ILC

value: Taxol x 12 FEC x4


title: BR_FNA_M513

source_name: Sample ID -- 513, fine-needle aspiration, breast cancer cells

value: black

value: pCR

value: IDC

value: FAC x 4(d/t N.C) Taxol x 6 (d/t severe Fatigue) (FAC resistance & pCR at the end)


title: BR_FNA_M507

source_name: Sample ID -- 507, fine-needle aspiration, breast cancer cells

value: breast cancer cells

value: FAC x 4 Taxol x 12


title: BR_FNA_M531

source_name: Sample ID -- 531, fine-needle aspiration, breast cancer cells

value: white

value: Taxol x 12 FAC x 4


title: BR_FNA_M486

source_name: Sample ID -- 486, fine-needle aspiration, breast cancer cells

value: P

value: TFEC

value: Taxol x 12 FEC x 4


title: BR_FNA_M556

source_name: Sample ID -- 556, fine-needle aspiration, breast cancer cells

value: RD

value: TFAC/HT

value: Taxol x 13 FAC x 3(d/t cardiotox)   Anastrozole  x 3 Moths


title: BR_FNA_M433

source_name: Sample ID -- 433, fine-needle aspiration, breast cancer cells

value: hispanic

value: N

value: Taxol x12 FEC x 4


title: BR_FNA_M443

source_name: Sample ID -- 443, fine-needle aspiration, breast cancer cells


title: BR_FNA_M558

source_name: Sample ID -- 558, fine-needle aspiration, breast cancer cells

value: TFAC


title: BR_FNA_M417

source_name: Sample ID -- 417, fine-needle aspiration, breast cancer cells

value: ILC


title: BR_FNA_M425

source_name: Sample ID -- 425, fine-needle aspiration, breast cancer cells

value: IDC


title: BR_FNA_M423

source_name: Sample ID -- 423, fine-needle aspiration, breast cancer cells

value: black


title: BR_FNA_M431

source_name: Sample ID -- 431, fine-needle aspiration, breast cancer cells

value: breast cancer cells

value: IDC/ILC


title: BR_FNA_M411

source_name: Sample ID -- 411, fine-needle aspiration, breast cancer cells

value: asian

value: Taxol x 12 FAC x 6


title: BR_FNA_M430

source_name: Sample ID -- 430, fine-needle aspiration, breast cancer cells

value: Taxol x 12 FAC x 4


title: BR_FNA_M545

source_name: Sample ID -- 545, fine-needle aspiration, breast cancer cells


title: BR_FNA_M396

source_name: Sample ID -- 396, fine-needle aspiration, breast cancer cells

value: P

value: TFEC


title: BR_FNA_M385

source_name: Sample ID -- 385, fine-needle aspiration, breast cancer cells

value: white

value: RD

value: FEC x 3 ( d/t N.C)Taxol x 12


title: BR_FNA_M365

source_name: Sample ID -- 365, fine-needle aspiration, breast cancer cells


title: BR_FNA_M502

source_name: Sample ID -- 502, fine-needle aspiration, breast cancer cells

value: FECT

value: FEC x 3 (N.C) Taxol x 12


title: BR_FNA_M382

source_name: Sample ID -- 382, fine-needle aspiration, breast cancer cells

value: N

value: pCR


title: BR_FNA_M360

source_name: Sample ID -- 360, fine-needle aspiration, breast cancer cells

value: ILC

value: Taxol x 12 FEC x 4


title: BR_FNA_M363

source_name: Sample ID -- 363, fine-needle aspiration, breast cancer cells

value: IDC


title: BR_FNA_M345

source_name: Sample ID -- 345, fine-needle aspiration, breast cancer cells

value: breast cancer cells

value: black

value: TFAC

value: Taxol x 9 (P.D)  FAC x 8 (P.D) - No Sx


title: BR_FNA_M339

source_name: Sample ID -- 339, fine-needle aspiration, breast cancer cells

value: IDC, medullary features

value: Taxol x 12 FAC x 4


title: BR_FNA_M294

source_name: Sample ID -- 294, fine-needle aspiration, breast cancer cells

value: P


title: BR_FNA_M332

source_name: Sample ID -- 332, fine-needle aspiration, breast cancer cells

value: white

value: Taxol x 6 (d/t P.D)   FAC x 4


title: BR_FNA_M319

source_name: Sample ID -- 319, fine-needle aspiration, breast cancer cells

value: RD


title: BR_FNA_US097

description:
MAQC_Distribution_Status: MAQC_Q -- Not used
Please see the GSE20194_MDACC_Sample_Info.xls file on the GSE20194 Series record for additional information on the Sample characteristics

source_name: Sample ID -- US097, fine-needle aspiration, breast cancer cells

value: TXFAC


title: BR_FNA_M302R1

description:
MAQC_Distribution_Status: MDA_R -- Not used
Please see the GSE20194_MDACC_Sample_Info.xls file on the GSE20194 Series record for additional information on the Sample characteristics

source_name: Sample ID -- 302, fine-needle aspiration, breast cancer cells

value: mixed

value: Taxol 80 mg/m2 x12 , FEC X4


title: BR_FNA_M233R1

source_name: Sample ID -- 233, fine-needle aspiration, breast cancer cells

value: N

value: IDC/DCIS

value: 00-005:Taxol 80 mg/m2.q weekly x 12, FAC X 4


title: BR_FNA_M281

source_name: Sample ID -- 281, fine-needle aspiration, breast cancer cells

value: IDC

value: TFEC

value: Taxol q.3 week x 4 FEC  x 4


title: BR_FNA_US092

source_name: Sample ID -- US092, fine-needle aspiration, breast cancer cells

value: breast cancer cells

value: ILC


title: BR_FNA_M314

source_name: Sample ID -- 314, fine-needle aspiration, breast cancer cells

value: black

value: TFAC

value: FAC x 3 (no response) Taxol x 8 (no response)


title: BR_FNA_M283

source_name: Sample ID -- 283, fine-needle aspiration, breast cancer cells

value: white

value: P

value: Taxol  x 12  FAC  x 4


title: BR_FNA_M340

source_name: Sample ID -- 340, fine-needle aspiration, breast cancer cells

value: hispanic

value: RD

value: FAC x 6 Taxol x 12


title: BR_FNA_M263

source_name: Sample ID -- 263, fine-needle aspiration, breast cancer cells

value: N

value: Taxol x 12 FAC x 4


title: BR_FNA_M286R1

source_name: Sample ID -- 286, fine-needle aspiration, breast cancer cells

value: Taxol 80 mg/m2 x12 , FEC X4


title: BR_FNA_M195

source_name: Sample ID -- 195, fine-needle aspiration, breast cancer cells

value: IDC

value: FAC x 4 Taxol x 12


title: BR_FNA_M355

source_name: Sample ID -- 355, fine-needle aspiration, breast cancer cells


title: BR_FNA_M232

source_name: Sample ID -- 232, fine-needle aspiration, breast cancer cells

value: pCR

value: Taxol q.3 week x 4 FAC x 4


title: BR_FNA_US002

source_name: Sample ID -- US002, fine-needle aspiration, breast cancer cells

value: breast cancer cells

value: TXFAC


title: BR_FNA_US134

source_name: Sample ID -- US134, fine-needle aspiration, breast cancer cells


title: BR_FNA_US031

source_name: Sample ID -- US031, fine-needle aspiration, breast cancer cells


title: BR_FNA_PERU55

source_name: Sample ID -- PERU55, fine-needle aspiration, breast cancer cells

value: FAC

value: FAC x 6


title: BR_FNA_US123

source_name: Sample ID -- US123, fine-needle aspiration, breast cancer cells


title: BR_FNA_US147

source_name: Sample ID -- US147, fine-needle aspiration, breast cancer cells


title: BR_FNA_US125

source_name: Sample ID -- US125, fine-needle aspiration, breast cancer cells


title: BR_FNA_M713

source_name: Sample ID -- 713, fine-needle aspiration, breast cancer cells

value: white

value: FEC

value: FEC x 4


title: BR_FNA_M434

description:
MAQC_Distribution_Status: MAQC_T -- Training
Please see the GSE20194_MDACC_Sample_Info.xls file on the GSE20194 Series record for additional information on the Sample characteristics

source_name: Sample ID -- 434, fine-needle aspiration, breast cancer cells

value: P

value: TFAC

value: PACLITAXEL x 12, FEC x 4


title: BR_FNA_US129

source_name: Sample ID -- US129, fine-needle aspiration, breast cancer cells

value: N


title: BR_FNA_US120

source_name: Sample ID -- US120, fine-needle aspiration, breast cancer cells

value: RD


title: BR_FNA_M334

source_name: Sample ID -- 334, fine-needle aspiration, breast cancer cells

value: PACLITAXEL x 12, FAC x 4


title: BR_FNA_M341

source_name: Sample ID -- 341, fine-needle aspiration, breast cancer cells

value: ND

value: IDC


title: BR_FNA_M469

source_name: Sample ID -- 469, fine-needle aspiration, breast cancer cells

value: PACLITAXEL x 12, FAC x 6


title: BR_FNA_M484

source_name: Sample ID -- 484, fine-needle aspiration, breast cancer cells

value: NEG

value: PACLITAXEL x 11, FAC x 4


title: BR_FNA_PERU09

source_name: Sample ID -- PERU-9, fine-needle aspiration, breast cancer cells

value: breast cancer cells

value: hispanic

value: 12 pACLITAXEL + 4FAC


title: BR_FNA_M525

source_name: Sample ID -- 525, fine-needle aspiration, breast cancer cells

value: white

value: PACLITAXEL x (12), FAC x ( 4)


title: BR_FNA_M129

source_name: Sample ID -- 129, fine-needle aspiration, breast cancer cells

value: IDC+DCIS

value: Taxol q 3wk (225mg/m2) x 4, FAC x4


title: BR_FNA_PERU01

source_name: Sample ID -- PERU-1, fine-needle aspiration, breast cancer cells

value: P

value: TFAC

value: 12 PACLITAXEL+ 4 FAC


title: BR_FNA_PERU12-14

source_name: Sample ID -- PERU-12-14, fine-needle aspiration, breast cancer cells

value: RD

value: N

value: 12 PACLITAXEL + 4FAC


title: BR_FNA_M497

source_name: Sample ID -- 497, fine-needle aspiration, breast cancer cells

value: IDC

value: PACLITAXEL x 12, FEC x 4


title: BR_FNA_M506

source_name: Sample ID -- 506, fine-needle aspiration, breast cancer cells

value: ND

value: PACLITAXEL x 8 , FEC x 4


title: BR_FNA_PERU08

source_name: Sample ID -- PERU08, fine-needle aspiration, breast cancer cells

value: breast cancer cells

value: FAC

value: FAC x 6


title: BR_FNA_M146

source_name: Sample ID -- 146, fine-needle aspiration, breast cancer cells

value: white

value: pCR

value: Taxol (80 mg q weekly) x12, FAC


title: BR_FNA_M421

source_name: Sample ID -- 421, fine-needle aspiration, breast cancer cells

value: NEG

value: PACLITAXEL x 12, FAC x 4


title: BR_FNA_M141

source_name: Sample ID -- 141, fine-needle aspiration, breast cancer cells

value: hispanic

value: P

value: TFAC

value: FAC, X 4, TAXOL X 4


title: BR_FNA_M503

source_name: Sample ID -- 503, fine-needle aspiration, breast cancer cells

value: N

value: RD


title: BR_FNA_M384

source_name: Sample ID -- 384, fine-needle aspiration, breast cancer cells

value: IDC

value: PACLITAXEL x 12, FEC x 4


title: BR_FNA_M373

source_name: Sample ID -- 373, fine-needle aspiration, breast cancer cells


title: BR_FNA_M343

source_name: Sample ID -- 343, fine-needle aspiration, breast cancer cells

value: asian


title: BR_FNA_PERU11

source_name: Sample ID -- PERU-11, fine-needle aspiration, breast cancer cells

value: breast cancer cells

value: ND

value: 12 PACLITAXEL + 4FAC


title: BR_FNA_M482

source_name: Sample ID -- 482, fine-needle aspiration, breast cancer cells


title: BR_FNA_PERU07

source_name: Sample ID -- PERU-7, fine-needle aspiration, breast cancer cells


title: BR_FNA_M356

source_name: Sample ID -- 356, fine-needle aspiration, breast cancer cells

value: white


title: BR_FNA_M357

source_name: Sample ID -- 357, fine-needle aspiration, breast cancer cells


title: BR_FNA_M485

source_name: Sample ID -- 485, fine-needle aspiration, breast cancer cells

value: pCR

value: PACLITAXEL x 11, FAC x 4


title: BR_FNA_M107

source_name: Sample ID -- 107, fine-needle aspiration, breast cancer cells

value: black

value: IDC+DCIS

value: Taxol q wk (150mg/m2) x12, Fac x5


title: BR_FNA_M315

source_name: Sample ID -- 315, fine-needle aspiration, breast cancer cells

value: P

value: IDC+ILC

value: PACLITAXEL x 7 , FAC x 4


title: BR_FNA_M399

source_name: Sample ID -- 399, fine-needle aspiration, breast cancer cells

value: N

value: IDC + DCIS

value: TFAC

value: PACLITAXEL x 12, FAC x 4


title: BR_FNA_M367

source_name: Sample ID -- 367, fine-needle aspiration, breast cancer cells


title: BR_FNA_M534

source_name: Sample ID -- 534, fine-needle aspiration, breast cancer cells

value: RD

value: IDC

value: FEC x 4 , PACLITAXELx (12 )


title: BR_FNA_M524

source_name: Sample ID -- 524, fine-needle aspiration, breast cancer cells

value: breast cancer cells

value: hispanic

value: PACLITAXEL x (12), FAC x ( 4)


title: BR_FNA_M442

source_name: Sample ID -- 442, fine-needle aspiration, breast cancer cells

value: white

value: pCR


title: BR_FNA_M353

source_name: Sample ID -- 353, fine-needle aspiration, breast cancer cells

value: NEG


title: BR_FNA_M120

source_name: Sample ID -- 120, fine-needle aspiration, breast cancer cells

value: asian

value: Taxol q 3wk (225mg/m2) x4, FAC x4


title: BR_FNA_M447

source_name: Sample ID -- 447, fine-needle aspiration, breast cancer cells

value: black

value: P

value: ND

value: PACLITAXEL x 12, FEC x 4


title: BR_FNA_M523

source_name: Sample ID -- 523, fine-needle aspiration, breast cancer cells

value: N

value: TFAC

value: PACLITAXEL x (12 ), FAC x (4 )


title: BR_FNA_PERU14-16

source_name: Sample ID -- PERU-14-16, fine-needle aspiration, breast cancer cells

value: RD

value: IDC

value: 12 PACLITAXEL +4FAC


title: BR_FNA_M145

source_name: Sample ID -- 145, fine-needle aspiration, breast cancer cells

value: breast cancer cells

value: hispanic

value: IDC+DCIS

value: Taxol (150 mg q weekly) x12, FAC x4


title: BR_FNA_M323

source_name: Sample ID -- 323, fine-needle aspiration, breast cancer cells

value: PACLITAXEL x12 FACx 3


title: BR_FNA_M387R1

source_name: Sample ID -- 387, fine-needle aspiration, breast cancer cells

value: white

value: PACLITAXEL x 12, FAC x 4


title: BR_FNA_M371

source_name: Sample ID -- 371, fine-needle aspiration, breast cancer cells

value: pCR

value: TH/FAC

value: Taxol/Herceptin+FAC:updated from(PACLITAXEL x 12, FEC x 4)


title: BR_FNA_M330R1

source_name: Sample ID -- 330, fine-needle aspiration, breast cancer cells

value: P

value: PACLITAXEL x ( ), FEC x ( )


title: BR_FNA_M386R1

source_name: Sample ID -- 386, fine-needle aspiration, breast cancer cells

value: N

value: ND

value: TFAC

value: PACLITAXEL x 12, FEC x 4


title: BR_FNA_M331R1

source_name: Sample ID -- 331, fine-needle aspiration, breast cancer cells

value: IDC


title: BR_FNA_M316R1

source_name: Sample ID -- 316, fine-needle aspiration, breast cancer cells

value: breast cancer cells

value: IDC + DCIS

value: TH/FEC

value: Taxol/FEC+Herceptin:updated from(PACLITAXEL x 12, FEC x 4)


title: BR_FNA_M322R1

source_name: Sample ID -- 322, fine-needle aspiration, breast cancer cells

value: RD

value: IDC+ILC


title: BR_FNA_M333R1

source_name: Sample ID -- 333, fine-needle aspiration, breast cancer cells

value: white


title: BR_FNA_M375R1

source_name: Sample ID -- 375, fine-needle aspiration, breast cancer cells


title: BR_FNA_M331

value: hispanic

value: pCR

value: PACLITAXEL x 12, FAC x 4


title: BR_FNA_M316

value: P


title: BR_FNA_M302

source_name: Sample ID -- 302, fine-needle aspiration, breast cancer cells

value: mixed

value: Taxol 80 mg/m2 x12 , FEC X4


title: BR_FNA_M333

value: N

value: ND


title: BR_FNA_M295

source_name: Sample ID -- 295, fine-needle aspiration, breast cancer cells

value: TFAC

value: Taxol 80 mg/m2 x12 , FAC X4


title: BR_FNA_M322

value: breast cancer cells


title: BR_FNA_M371R1

value: IDC

value: TH/FAC

value: Taxol/Herceptin+FAC:updated from(PACLITAXEL x 12, FEC x 4)


title: BR_FNA_M402R1

source_name: Sample ID -- 402, fine-needle aspiration, breast cancer cells


title: BR_FNA_M330

value: RD

value: PACLITAXEL x ( ), FEC x ( )


title: BR_FNA_M261

source_name: Sample ID -- 261, fine-needle aspiration, breast cancer cells

value: white

value: IDC/DCIS

value: Taxol 80 mg/m2 x12, FEC X 4


title: BR_FNA_M375

value: PACLITAXEL x 12, FEC x 4


title: BR_FNA_M282

source_name: Sample ID -- 282, fine-needle aspiration, breast cancer cells

value: P

value: IC/DCIS


title: BR_FNA_M387

value: PACLITAXEL x 12, FAC x 4


title: BR_FNA_M386

value: N


title: BR_FNA_ML20

source_name: Sample ID -- L20, fine-needle aspiration, breast cancer cells

value: black

value: pCR

value: NEG


title: BR_FNA_M304

source_name: Sample ID -- 304, fine-needle aspiration, breast cancer cells

value: breast cancer cells

value: TFAC

value: Taxol 80 mg/m2 x12 , FEC X4


title: BR_FNA_M402

value: ND

value: IDC


title: BR_FNA_M463

source_name: Sample ID -- 463, fine-needle aspiration, breast cancer cells

value: hispanic

value: RD


title: BR_FNA_PERU53

source_name: Sample ID -- PERU53, fine-needle aspiration, breast cancer cells

value: FAC

value: FAC x 6


title: BR_FNA_M297

source_name: Sample ID -- 297, fine-needle aspiration, breast cancer cells

value: Taxol 80 mg/m2 x12 , FAC X6


title: BR_FNA_M309

source_name: Sample ID -- 309, fine-needle aspiration, breast cancer cells

value: white

value: P


title: BR_FNA_M286

source_name: Sample ID -- 286, fine-needle aspiration, breast cancer cells


title: BR_FNA_M287

source_name: Sample ID -- 287, fine-needle aspiration, breast cancer cells

value: FEC X3, Taxol 80 mg/m2 x12


title: BR_FNA_M270

source_name: Sample ID -- 270, fine-needle aspiration, breast cancer cells

value: N


title: BR_FNA_M231

source_name: Sample ID -- 231, fine-needle aspiration, breast cancer cells


title: BR_FNA_M251

source_name: Sample ID -- 251, fine-needle aspiration, breast cancer cells

value: IDC/DCIS

value: Taxol 80mg/m2. q weekly x 12, FAC X 4


title: BR_FNA_M247

source_name: Sample ID -- 247, fine-needle aspiration, breast cancer cells

value: Taxol 80mg/m2.q weekly x 12, FAC X 4


title: BR_FNA_M260

source_name: Sample ID -- 260, fine-needle aspiration, breast cancer cells

value: breast cancer cells

value: IDC/ILC

value: Taxol 100mg/m2 x 12, FAC X 4


title: BR_FNA_M270R1

value: TFAC

value: Taxol 80 mg/m2 x12 , FEC X4


title: BR_FNA_M259

source_name: Sample ID -- 259, fine-needle aspiration, breast cancer cells

value: IDC

value: Taxol 80 mg/m2 x12, FAC X 4


title: BR_FNA_M310

source_name: Sample ID -- 310, fine-needle aspiration, breast cancer cells

value: RD

value: Taxol 80 mg/m2 x12 , FAC X4


title: BR_FNA_M234

source_name: Sample ID -- 234, fine-needle aspiration, breast cancer cells

value: IDC/ILC/LCIS

value: 00-005:Taxol 100mg/m2.q weekly x10, FAC X 4.


title: BR_FNA_M257

source_name: Sample ID -- 257, fine-needle aspiration, breast cancer cells

value: white

value: P

value: Taxol 100 mg/m2 x 12, FAC X 4


title: BR_FNA_M247R1

value: N

value: IDC/DCIS


title: BR_FNA_M256R1

source_name: Sample ID -- 256, fine-needle aspiration, breast cancer cells

value: Taxol 100mg/m2.q.weekly x 12,


title: BR_FNA_M266R1

source_name: Sample ID -- 266, fine-needle aspiration, breast cancer cells

value: breast cancer cells

value: asian

value: Taxol 80mg/m2 x 12, FAC X 4


title: BR_FNA_M255

source_name: Sample ID -- 255, fine-needle aspiration, breast cancer cells

value: IDC/ILC/DCIS

value: TFAC

value: Taxol 80mg/m2.q.weekly x12, FAC X 4


title: BR_FNA_M245R1

source_name: Sample ID -- 245, fine-needle aspiration, breast cancer cells

value: TH/FAC

value: Taxol 100mg/m2.q weekly x 12, Trastuzumab, FAC X 4


title: BR_FNA_M235

source_name: Sample ID -- 235, fine-needle aspiration, breast cancer cells

value: black

value: RD

value: IDC

value: 99-146:Taxol 225mg/m2 q.3 week x 4, FAC x4


title: BR_FNA_M231R1

value: white

value: P


title: BR_FNA_M301

source_name: Sample ID -- 301, fine-needle aspiration, breast cancer cells

value: N

value: pCR

value: IDC/anaplastic

value: Taxol 80 mg/m2 x12 , FAC X4


title: BR_FNA_M235R1

value: breast cancer cells


title: BR_FNA_M257R1

value: Taxol 100 mg/m2 x 12, FAC X 4


title: BR_FNA_M238

source_name: Sample ID -- 238, fine-needle aspiration, breast cancer cells

value: asian

value: IDC/DCIS

value: 99-146:Taxol weekly x 12, FACX 4


title: BR_FNA_M256

value: TFAC

value: Taxol 100mg/m2.q.weekly x 12,


title: BR_FNA_M280R1

source_name: Sample ID -- 280, fine-needle aspiration, breast cancer cells

value: Taxol 80 mg/m2 x12 , FEC X4


title: BR_FNA_M264R1

source_name: Sample ID -- 264, fine-needle aspiration, breast cancer cells

value: black

value: RD

value: Taxol 80 mg/m2 x12, FAC X 4


title: BR_FNA_M280

value: white

value: IDC


title: BR_FNA_M245

value: P

value: TH/FAC

value: Taxol 100mg/m2.q weekly x 12, Trastuzumab, FAC X 4


title: BR_FNA_M238R1

value: pCR


title: BR_FNA_M266

value: breast cancer cells

value: N

value: Taxol 80mg/m2 x 12, FAC X 4


title: BR_FNA_M230

source_name: Sample ID -- 230, fine-needle aspiration, breast cancer cells

value: Taxol 80 mg/m2.q weekly x 12, FEC X 4


title: BR_FNA_M239

source_name: Sample ID -- 239, fine-needle aspiration, breast cancer cells

value: FAC X 4, Taxol weekly x 12


title: BR_FNA_M236R1

source_name: Sample ID -- 236, fine-needle aspiration, breast cancer cells

value: TFAC

value: 00-005:Taxol weekly x 12,FAC X 5


title: BR_FNA_M258R1

source_name: Sample ID -- 258, fine-needle aspiration, breast cancer cells

value: Taxol 100mg/m2 x 12Herceptin, FAC X 6


title: BR_FNA_M237

source_name: Sample ID -- 237, fine-needle aspiration, breast cancer cells

value: hispanic

value: IDC/DCIS

value: 99-146:Taxol weeklyx 12, FAC x 4


title: BR_FNA_M258

value: white

value: RD


title: BR_FNA_M237R1

value: P


title: BR_FNA_M117

source_name: Sample ID -- 117, fine-needle aspiration, breast cancer cells

value: IDC


title: BR_FNA_M133

source_name: Sample ID -- 133, fine-needle aspiration, breast cancer cells


title: BR_FNA_M205

source_name: Sample ID -- 205, fine-needle aspiration, breast cancer cells

value: Taxol 80mg/m2 weekly x 12, FAC x 4


title: BR_FNA_M181

source_name: Sample ID -- 181, fine-needle aspiration, breast cancer cells

value: ILC

value: Taxol 80 mg/m2 weekly x12, FACx 3


title: BR_FNA_M123

source_name: Sample ID -- 123, fine-needle aspiration, breast cancer cells

value: breast cancer cells

value: pCR

value: N

value: ILC/IDC


title: BR_FNA_M246R1

source_name: Sample ID -- 246, fine-needle aspiration, breast cancer cells

value: TFAC

value: Taxol 80mg/m2.q weekly x 12, FAC X 4


title: BR_FNA_M230R1

value: Taxol 80 mg/m2.q weekly x 12, FEC X 4


title: BR_FNA_M211

source_name: Sample ID -- 211, fine-needle aspiration, breast cancer cells


title: BR_FNA_M179

source_name: Sample ID -- 179, fine-needle aspiration, breast cancer cells

value: Taxol 80 mg/m2 weekly x12, FAC x4


title: BR_FNA_M189

source_name: Sample ID -- 189, fine-needle aspiration, breast cancer cells

value: IMC


title: BR_FNA_M182

source_name: Sample ID -- 182, fine-needle aspiration, breast cancer cells

value: hispanic

value: IDC/DCIS

value: Taxol 80 mg/m2 weekly / FAC x4


title: BR_FNA_M239R1

value: white

value: P

value: FAC X 4, Taxol weekly x 12


title: BR_FNA_M139

source_name: Sample ID -- 139, fine-needle aspiration, breast cancer cells

value: RD

value: IDC


title: BR_FNA_M135

source_name: Sample ID -- 135, fine-needle aspiration, breast cancer cells

value: breast cancer cells


title: BR_FNA_M246


title: BR_FNA_M108

source_name: Sample ID -- 108, fine-needle aspiration, breast cancer cells


title: BR_FNA_M106

source_name: Sample ID -- 106, fine-needle aspiration, breast cancer cells


title: BR_FNA_M236

source_name: Sample ID -- 236, fine-needle aspiration, breast cancer cells

value: 00-005:Taxol weekly x 12,FAC X 5


title: BR_FNA_M217

source_name: Sample ID -- 217, fine-needle aspiration, breast cancer cells

value: N

value: Taxol 80 weekly x 12, FAC x4


title: BR_FNA_M126

source_name: Sample ID -- 126, fine-needle aspiration, breast cancer cells

value: TFAC

value: Taxol q3wk (225mg/m2) x 4, NO FAC


title: BR_FNA_M216

source_name: Sample ID -- 216, fine-needle aspiration, breast cancer cells

value: Taxol 80 weekly x12 , FAC x 6


title: BR_FNA_M136

source_name: Sample ID -- 136, fine-needle aspiration, breast cancer cells

value: pCR


title: BR_FNA_M233

source_name: Sample ID -- 233, fine-needle aspiration, breast cancer cells

value: 00-005:Taxol 80 mg/m2.q weekly x 12, FAC X 4


title: BR_FNA_M206

source_name: Sample ID -- 206, fine-needle aspiration, breast cancer cells

value: Taxol 80mg/m2 weekly x 12, FAC x 4


title: BR_FNA_M226

source_name: Sample ID -- 226, fine-needle aspiration, breast cancer cells

value: Taxol 80 weekly X 12, FAC X 6


title: BR_FNA_M188

source_name: Sample ID -- 188, fine-needle aspiration, breast cancer cells

value: black

value: Taxol 80 mg/m2 weekly x12, FAC x4


title: BR_FNA_M121

source_name: Sample ID -- 121, fine-needle aspiration, breast cancer cells

value: white


title: BR_FNA_M177

source_name: Sample ID -- 177, fine-needle aspiration, breast cancer cells

value: P


title: BR_FNA_M128

source_name: Sample ID -- 128, fine-needle aspiration, breast cancer cells

value: RD

value: ILC/IDC


title: BR_FNA_M158

source_name: Sample ID -- 158, fine-needle aspiration, breast cancer cells

value: breast cancer cells

value: asian

value: IDC

value: Taxol 100mg/2 q wk x 12, FAC x4


title: BR_FNA_M199

source_name: Sample ID -- 199, fine-needle aspiration, breast cancer cells

value: N

value: TFAC

value: Taxol 100 g/m2 weekly x 12, FAC x 4


title: BR_FNA_M159

source_name: Sample ID -- 159, fine-needle aspiration, breast cancer cells

value: pCR


title: BR_FNA_M156

source_name: Sample ID -- 156, fine-needle aspiration, breast cancer cells


title: BR_FNA_M161

source_name: Sample ID -- 161, fine-needle aspiration, breast cancer cells

value: IDC/DCIS

value: Taxol (100mg/m2 weekly) x12, FAC x4


title: BR_FNA_M228

source_name: Sample ID -- 228, fine-needle aspiration, breast cancer cells

value: Taxol 100 weekly X 12, FAC X 6


title: BR_FNA_M153

source_name: Sample ID -- 153, fine-needle aspiration, breast cancer cells

value: 98-240 Taxol (150 mg q weekly) x12, FAC x4


title: BR_FNA_M155

source_name: Sample ID -- 155, fine-needle aspiration, breast cancer cells

value: 98-240 Taxol (225 mg q 3 wk) x 4, FAX x4


title: BR_FNA_M116

source_name: Sample ID -- 116, fine-needle aspiration, breast cancer cells

value: hispanic

value: IDC/IBC

value: Taxol q wk (80mg/m2) x 12, No FAC!


title: BR_FNA_M165

source_name: Sample ID -- 165, fine-needle aspiration, breast cancer cells

value: black

value: P

value: RD

value: Taxol 225 mg/m2 x4, FAC x4


title: BR_FNA_M180

source_name: Sample ID -- 180, fine-needle aspiration, breast cancer cells

value: breast cancer cells

value: white

value: Taxol 80 mg/m2 weekly x12 FAC x4


title: BR_FNA_M215

source_name: Sample ID -- 215, fine-needle aspiration, breast cancer cells

value: N

value: IDC

value: TFAC

value: Taxol 80 weekly x 12, FAC x4


title: BR_FNA_M201

source_name: Sample ID -- 201, fine-needle aspiration, breast cancer cells

value: Taxol 80mg/m2 weekly x 12, FAC x 4


title: BR_FNA_M111

source_name: Sample ID -- 111, fine-needle aspiration, breast cancer cells

value: pCR


title: BR_FNA_M186

source_name: Sample ID -- 186, fine-needle aspiration, breast cancer cells

value: Taxol 80 mg/m2 weekly x12, FAC x4


title: BR_FNA_M154

source_name: Sample ID -- 154, fine-needle aspiration, breast cancer cells

value: Tonly

value: Taxol 80 mg/m2 weekly off study for PD


title: BR_FNA_M220

source_name: Sample ID -- 220, fine-needle aspiration, breast cancer cells

value: Taxol 80 weekly x 11, FACx4


title: BR_FNA_M212

source_name: Sample ID -- 212, fine-needle aspiration, breast cancer cells

value: asian

value: Taxol 225 x 4, FEC x 4


title: BR_FNA_M113

source_name: Sample ID -- 113, fine-needle aspiration, breast cancer cells

value: black

value: RD


title: BR_FNA_M130

source_name: Sample ID -- 130, fine-needle aspiration, breast cancer cells

value: breast cancer cells

value: P


title: BR_FNA_M227

source_name: Sample ID -- 227, fine-needle aspiration, breast cancer cells

value: white

value: Taxol 100 weekly X 12, FAC X 6


title: BR_FNA_M157

source_name: Sample ID -- 157, fine-needle aspiration, breast cancer cells

value: N

value: IDC

value: 98-240 Taxol (80mg/m2 q wk), FAC x4


title: BR_FNA_M196

source_name: Sample ID -- 196, fine-needle aspiration, breast cancer cells

value: IMC/IDC

value: TFAC

value: Taxol 80 mg/m2 weekly x12, FAC


title: BR_FNA_M214

source_name: Sample ID -- 214, fine-needle aspiration, breast cancer cells

value: Taxol 80 weekly x 12, FAC x4


title: BR_FNA_M176

source_name: Sample ID -- 176, fine-needle aspiration, breast cancer cells

value: mixed

value: Taxol 80 mg/m2 weekly x12, FAC x1


title: BR_FNA_M264

source_name: Sample ID -- 264, fine-needle aspiration, breast cancer cells

value: Taxol 80 mg/m2 x12, FAC X 4


title: XXX_5927

status: Public on Jan 26 2010

city: Toronto

first: Benjamin

last: Haibe-Kains

state: Ontario

address: 610 University Avenue

department: Princess Margaret Research

country: Canada

institute: Princess Margaret Cancer Centre

description: Please see the GSE16446_TOP_README.txt supplementary file on the Series record for a definition of the clinical characteristics

hyb_protocol: standard Affymetrix procedures.

scan_protocol: standard Affymetrix procedures.

data_processing: RMA Bioconductor (default parameters) and log2 transformation.

label_protocol: Approximately 1 microgram of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Isolation of RNA was performed using the Trizol method (Invitrogen) according to the manufacturers instructions and was purified using RNeasy mini-columns (Qiagen, Valencia, CA). The quality of the RNA obtained from each tumour sample was assessed based on the RNA profile generated by the bioanalyzer (Agilent Inc)olation of RNA was performed using the Trizol method (Invitrogen) according to the manufacturers instructions and was purified using RNeasy mini-columns (Qiagen, Valencia, CA). The quality of the RNA obtained from each tumour sample was assessed based on the RNA profile generated by the bioanalyzer (Agilent Inc).

tag: agebin

tag: t

tag: n

tag: grade

tag: topoihc

value: YES

tag: pcr


title: XXX_3099


title: XXX_4405


title: XXX_6519


title: XXX_3438


title: XXX_4270


title: XXX_2621


title: XXX_7173


title: XXX_7634


title: XXX_9517


title: XXX_5783

value: NO


title: XXX_1536


title: XXX_3736


title: XXX_9280


title: XXX_5490


title: XXX_2944


title: XXX_8844


title: XXX_5328


title: XXX_6151


title: XXX_1753


title: XXX_8884


title: XXX_453


title: XXX_9576


title: XXX_8740


title: XXX_1767


title: XXX_4682


title: XXX_7195


title: XXX_8103


title: XXX_8999


title: XXX_4938


title: XXX_6852


title: XXX_845


title: XXX_5751


title: XXX_6471


title: XXX_1786


title: XXX_7500


title: XXX_1312


title: XXX_5706


title: XXX_2165


title: XXX_9677


title: XXX_5704


title: XXX_2090


title: XXX_123


title: XXX_9994


title: XXX_3041


title: XXX_1674


title: XXX_3714


title: XXX_6839


title: XXX_5396


title: XXX_2744


title: XXX_1157


title: XXX_6975


title: XXX_4511


title: XXX_3374


title: XXX_9762


title: XXX_4082


title: XXX_9064


title: XXX_1366


title: XXX_3414


title: XXX_5180


title: XXX_9049


title: XXX_5920


title: XXX_9386


title: XXX_1109


title: XXX_5437


title: XXX_4864


title: XXX_6116


title: XXX_3864


title: XXX_682


title: XXX_494


title: XXX_5150


title: XXX_933


title: XXX_8960


title: XXX_3276


title: XXX_8675


title: XXX_4291


title: XXX_2733


title: XXX_9665


title: XXX_1277


title: XXX_220


title: XXX_2337


title: XXX_6181


title: XXX_2976


title: XXX_9263


title: XXX_8319


title: XXX_6951


title: XXX_7752


title: XXX_7469


title: XXX_6276


title: XXX_7713


title: XXX_2012


title: XXX_1003


title: XXX_5622


title: XXX_8238


title: XXX_9516


title: XXX_6754


title: XXX_4917


title: XXX_8950


title: XXX_989


title: XXX_8342


title: XXX_6198


title: XXX_1763


title: XXX_534


title: XXX_1391


title: XXX_4617


title: XXX_193


title: XXX_9171


title: XXX_9927


title: XXX_6787


title: XXX_6759


title: XXX_8739


title: XXX_2325


title: XXX_3731


title: XXX_4984


title: XXX_6772


title: XXX_9434


title: XXX_8660


title: tumor breast tissue AR2005110814

status: Public on Jan 05 2010

city: Manhattan

first: Ross

last: Levine

state: NY

address: RRL

country: USA

institute: MSKCC

description: affymetrix u133plus expression for tumor breast tissue

hyb_protocol: Standard Affymetrix procedure

scan_protocol: Standard Affymetrix procedure

data_processing: The 115 arrays were log-transformed and normalized using dChip invariant method and PM-MM difference method for backgroud subtraction (Ref: Li, Wong et al.).  Invariable genes were removed by correlation filtering using dChip software (p-value < 0.05).

source_name: tumor breast tissue

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

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

value: breast tumor tissue

tag: tumor recurrence (36mo)

value: no

tag: patientid

tag: age

tag: histology type

value: Ductal

tag: grade (modified, bloom, richardson)

value: III

value: pos

tag: pr

tag: tumor size (cm)

tag: lymph nodes

value: positive

tag: adjuvant chemotherapy

value: Unknown

tag: chemo class

tag: hormonal rx

value: unknown

tag: time of followup (mo)

tag: distant recurrence free survival (mo)

tag: distant recur (yn)


title: tumor breast tissue AR2004031231

tag: tissue

value: yes

tag: er

value: pos-low

value: neg

value: AC x 4

value: Anthracycline-based

value: Tam

value: N


title: tumor breast tissue AR2005110816

value: Lobular

value: II

value: negative

value: Y


title: tumor breast tissue AR2005110811

value: breast tumor tissue

value: no

value: Ductal


title: tumor breast tissue AR2005110817

value: III

value: pos


title: tumor breast tissue AR2004031232

value: Mixed

value: positive

value: AC-taxol/Herceptin

value: Trastuzumab


title: tumor breast tissue AR2005110807

value: neg


title: XXX_2024

tag: agebin

tag: t

tag: n

tag: grade

tag: topoihc

value: NO

tag: pcr


title: tumor breast tissue AR2005110813

tag: tumor recurrence (36mo)

tag: patientid

tag: age

tag: histology type

tag: grade (modified, bloom, richardson)

tag: pr

value: AC-taxol

value: Anthracycline-based


title: tumor breast tissue AR2005110808

tag: tumor size (cm)

tag: lymph nodes

tag: adjuvant chemotherapy

tag: chemo class

tag: hormonal rx

value: Tam

tag: time of followup (mo)

value: N


title: tumor breast tissue AR2005110809

tag: tissue

tag: er

value: AC-taxotere

value: unknown

tag: distant recurrence free survival (mo)

tag: distant recur (yn)


title: tumor breast tissue AR2004031219

value: breast tumor tissue

value: Lobular

value: II


title: tumor breast tissue AR2004031211

value: no

value: III


title: XXX_993

tag: agebin

tag: t

tag: n

tag: grade

tag: topoihc

value: YES

tag: pcr


title: tumor breast tissue AR2004031222

tag: tumor recurrence (36mo)

tag: patientid

tag: age

tag: histology type

value: Ductal

tag: grade (modified, bloom, richardson)

value: pos

tag: pr

value: CAF


title: tumor breast tissue AR2004031210

value: neg

tag: tumor size (cm)

tag: lymph nodes

value: positive

tag: adjuvant chemotherapy

value: CMF

tag: chemo class

value: Other

tag: hormonal rx

tag: time of followup (mo)


title: tumor breast tissue AR2004031221

tag: tissue

tag: er

value: Arimidex

tag: distant recurrence free survival (mo)

tag: distant recur (yn)


title: tumor breast tissue AR2004031223

value: AC-taxol/Herceptin

value: Trastuzumab

value: Tam

value: N


title: tumor breast tissue AR2004031208

value: breast tumor tissue

value: Mixed

value: I


title: tumor breast tissue AR2004031209

value: no

value: II

value: Anthracycline-based


title: XXX_6767

tag: agebin

tag: t

tag: n

tag: grade

tag: topoihc

value: YES

tag: pcr


title: tumor breast tissue AR2004021293

tag: tumor recurrence (36mo)

tag: patientid

tag: age

tag: histology type

value: Ductal

tag: grade (modified, bloom, richardson)

value: pos

tag: pr

value: negative


title: tumor breast tissue AR2004021295

value: neg

tag: tumor size (cm)

tag: lymph nodes

tag: adjuvant chemotherapy

value: AC-taxol

tag: chemo class

tag: hormonal rx

tag: time of followup (mo)


title: tumor breast tissue AR2004021294

tag: tissue

value: Lobular

tag: er

tag: distant recurrence free survival (mo)

tag: distant recur (yn)


title: tumor breast tissue AR2004021296

value: pos-low

value: low pos (2+)


title: tumor breast tissue AR2004031204

value: III

value: positive


title: tumor breast tissue AR2004021292

value: breast tumor tissue

value: Tam

value: N


title: tumor breast tissue AR2004021297

value: no

value: Mixed

value: I


title: tumor breast tissue AR2004031202

value: AC x 4

value: Anthracycline-based

value: Arimidex


title: tumor breast tissue AR2004021281

value: yes

value: Ductal

value: pos

value: Y


title: tumor breast tissue AR2004021290

value: pos-low

value: neg

value: negative


title: tumor breast tissue AR2004021291


title: tumor breast tissue AR2004021288

value: Lobular


title: tumor breast tissue AR2004021274

value: breast tumor tissue

value: III

value: positive

value: AC-taxol


title: tumor breast tissue AR2004021271

value: no

value: Tam

value: N


title: tumor breast tissue AR2004021279

value: II

value: Anthracycline-based


title: tumor breast tissue AR2004021263

value: AC x 4


title: tumor breast tissue AR2004021289

value: Mixed

value: I


title: tumor breast tissue AR2004021273

value: Ductal

value: pos


title: tumor breast tissue AR2004021254


title: tumor breast tissue AR2004021277

value: pos-low

value: Unknown


title: tumor breast tissue AR2004021147

value: neg


title: tumor breast tissue AR2004021286

value: breast tumor tissue

value: Lobular


title: tumor breast tissue AR2004021267

value: III

value: negative


title: tumor breast tissue AR2004021278

value: no


title: tumor breast tissue AR2004021144

value: positive

value: AC-taxol

value: Tam


title: tumor breast tissue AR2004021253

value: Anthracycline-based

value: N


title: tumor breast tissue AR2004021145

value: low pos (2+)

value: AC x 4


title: tumor breast tissue AR2004021272

value: yes

value: Mixed

value: Y


title: tumor breast tissue AR2004021275

value: Ductal

value: I

value: pos


title: tumor breast tissue AR2004021141

value: breast tumor tissue


title: tumor breast tissue AR2004021252

value: neg


title: tumor breast tissue AR2004021139

value: Lobular

value: II

value: negative


title: tumor breast tissue AR2004021276

value: no

value: positive

value: AC-taxol


title: tumor breast tissue AR2004021255

value: III

value: Anthracycline-based

value: N


title: tumor breast tissue AR2004021265

value: pos-low

value: AC x 4

value: Tam


title: tumor breast tissue AR2004021143

value: Ductal


title: tumor breast tissue AR2004021257

value: yes

value: Y


title: tumor breast tissue AR2004021285

value: breast tumor tissue

value: pos

value: CMF

value: Other


title: tumor breast tissue AR2004021132

value: neg

value: negative

value: Unknown

value: unknown


title: tumor breast tissue AR2004021137

value: Lobular

value: III

value: positive

value: AC x 2, Taxol


title: tumor breast tissue AR2004021129

value: no

value: I

value: AC-taxol

value: Anthracycline-based

value: N


title: tumor breast tissue AR2004021133

value: breast tumor tissue

value: Ductal

value: AC x 4


title: tumor breast tissue AR2004021138


title: tumor breast tissue AR2004021121

value: yes

value: Y


title: tumor breast tissue AR2004021130

value: pos

value: low pos (2+)

value: Tam


title: tumor breast tissue AR2004021135

value: neg


title: tumor breast tissue AR2004021131

value: II

value: negative


title: tumor breast tissue AR2004021123

value: pos-low

value: positive


title: tumor breast tissue AR2004021134

value: no

value: Lobular

value: I


title: tumor breast tissue AR2004021125

value: III

value: Anthracycline-based

value: N


title: tumor breast tissue AR2004021122

value: breast tumor tissue

value: Ductal

value: AC x 4


title: tumor breast tissue AR2004021117

value: AC-taxotere


title: tumor breast tissue AR2004021118

value: pos


title: tumor breast tissue AR2004021115

value: Tam


title: tumor breast tissue AR2004021112

value: Mixed

value: neg


title: tumor breast tissue AR2004021107

value: II

value: negative


title: tumor breast tissue AR2004021108


title: tumor breast tissue AR2004021113


title: tumor breast tissue AR2004021111


title: tumor breast tissue AR2004021124

value: positive

value: AC-taxol


title: tumor breast tissue AR2004021126

value: no


title: tumor breast tissue AR2004021104

value: pos-low


title: tumor breast tissue AR2004021114


title: tumor breast tissue AR2004021101

value: Lobular

value: I


title: tumor breast tissue AR2004021102

value: III

value: Unknown

value: unknown

value: N


title: tumor breast tissue AR2004021110

value: breast tumor tissue

value: Ductal

value: AC x 4

value: Anthracycline-based


title: tumor breast tissue AR2004020640

value: neg

value: AC-taxotere


title: tumor breast tissue AR2004020632

value: negative


title: tumor breast tissue AR2004020635


title: tumor breast tissue AR2004020642

value: pos

value: positive

value: Tam


title: tumor breast tissue AR2004020628

value: no

value: AC-taxol


title: tumor breast tissue AR2004020633


title: tumor breast tissue AR2004020618

value: II


title: tumor breast tissue AR2004020639

value: III

value: CAF


title: tumor breast tissue AR2004020611


title: tumor breast tissue AR2004020610


title: tumor breast tissue AR2004020634

value: yes

value: Y


title: tumor breast tissue AR2004020615

value: breast tumor tissue

value: N


title: tumor breast tissue AR2004020622

value: Ductal

value: Unknown


title: tumor breast tissue AR2004020631

value: neg

value: AC x 4

value: Anthracycline-based


title: tumor breast tissue AR2004020636


title: tumor breast tissue AR2004020623

value: negative


title: tumor breast tissue AR2004020621

value: Epirubicin, Cytoxan, Xeloda


title: tumor breast tissue AR2004020612

value: positive


title: tumor breast tissue AR2004020629

value: no


title: tumor breast tissue AR2004020624


title: tumor breast tissue AR2004020609

value: AC-taxol


title: tumor breast tissue AR2004020625


title: tumor breast tissue AR2004020619


title: tumor breast tissue AR2004020626

value: AC-taxol/Herceptin

value: Trastuzumab


title: tumor breast tissue AR2004021105

value: Mixed

value: II

value: pos

value: CMF

value: Other

value: Tam


title: tumor breast tissue AR2004020608

value: breast tumor tissue

value: Ductal

value: III

value: N


title: tumor breast tissue AR2004020607

value: yes

value: neg

value: Anthracycline-based

value: Y


title: tumor breast tissue AR2004020606

value: no

value: negative

value: AC x 4


title: tumor breast tissue AR2004020603

value: positive

value: AC-taxol


title: tumor breast tissue AR2004020604


title: pt26.or

status: Public on Oct 30 2009

city: Seattle

first: Larissa

last: Korde

state: WA

address: 825 Eastlake Ave, E G30630

department: Division of Medical Oncology

institute: University of Washington

hyb_protocol: Hybridization cocktails from each fragmentation reaction were prepared according to the Affymetrix GeneChip® protocol.

scan_protocol: The hybridization cocktail was applied to the Affymetrix HU-U133 Plus 2.0 GeneChip® Arrays, processed on the Affymetrix® Fluidics Station 400 then analyzed on the Agilent GeneArray Scanner with Affymetrix Microarray Suite version 5.0.0.032 software.

data_processing: Probe-level data were normalized and gene expression summaries were computed for each probe set using Robust Multichip Analysis (RMA).  Statistical analyses were performed using BRB Array Tools version 3.4.1.  All gene expression summary intensities (gene summaries) below 50 were thresholded to the value of 50 and genes showing variability significantly smaller than the median gene variability (variance-based screening criteria) were screened out (P<.01, based on chi-square test as implemented in BRB Array Tools (6)).   Samples were clustered using agglomerative hierarchical clustering and using the mean-centered 24,224 genes passing the variance-based screening, with centered correlation as distance metric and average linkage as linkage function.

label_protocol: Double-stranded cDNA was synthesized from this preparation using the GeneChip® Expression 3’–Amplification Two-Cycle cDNA Synthesis Kit according to the protocol for Affymetrix GeneChip® Eukaryotic Target Preparation.  The resulting double stranded cDNA was purified using the GeneChip® Sample Cleanup Module (Qiagen). Synthesis of Biotin-Labeled cRNA was obtained by in vitro transcription of the purified template cDNA using the GeneChip® Expression 3’ Amplification Reagents for IVT Labeling (Affymetrix). The cRNA target was purified by using the GeneChip® Sample Cleanup Module (Qiagen). A 1:10 dilution was made with 1ul of the purified IVT reaction product and then run on the Agilent Technologies 2100 Bioanalyzer (Bio Sizing  Software version A.02.01., Agilent Technologies) to determine sample quality and the Nanodrop ®  for quantitation. The cRNA was then adjusted according to the Affymetrix protocol prior to fragmentation using the GeneChip® Sample Cleanup Module (Qiagen). One microliter was removed from the fragmentation reaction and checked on the Agilent Technologies 2100 Bioanalyzer (Bio Sizing Software version A.02.01., Agilent Technologies) to confirm proper fragmentation prior to hybridization.

extract_protocol: Total RNA was extracted from frozen tissues using TRIzol® Reagent (Life Technologies, Inc.) according to the standard protocol. The quantity and quality of the RNA was determined by the Agilent Technologies 2100 Bioanalyzer (Bio Sizing Software version A.02.01., Agilent Technologies) and the quantity determined with the Nanodrop ®  (Nanodrop Technologies).  Samples containing high-quality total RNA with ratios between 1.8 and 2.1 were purified with the RNeasy Mini Kit (Qiagen) or the RNeasy Micro Kit (Qiagen), dependent on sample size. An “on column” digest was performed as part of this purification step using the RNase-Free DNase Set (Qiagen).

tag: tissue type

value: breast tumor biopsies

tag: upin

tag: time point

value: or

tag: include in paired

tag: include in bl

tag: response category

value: NR

tag: er original

value: pos

tag: her2 summary


title: pt27.c2

value: R

tag: pr


title: pt29.or


title: pt27.bl

value: bl


title: pt29.c2


title: tumor breast tissue AR2004021103

value: breast tumor tissue

tag: tumor recurrence (36mo)

tag: patientid

tag: age

tag: histology type

value: Ductal

tag: grade (modified, bloom, richardson)

value: I

value: low pos (2+)

tag: tumor size (cm)

tag: lymph nodes

tag: adjuvant chemotherapy

value: Tam


title: pt29.bl

tag: tissue type

value: Y

value: neg


title: pt28.bl

tag: upin

value: N


title: pt30.c2

tag: time point


title: pt23.c2

tag: include in paired


title: pt28.or

tag: include in bl


title: pt24.bl

tag: response category


title: pt22.or

tag: er original


title: pt25.c2

tag: her2 summary


title: pt21.bl

tag: pr


title: pt26.c2


title: pt30.or


title: pt20.c2


title: pt20.bl


title: HB131

status: Public on Dec 16 2009

city: Bordeaux

first: Richard

last: Iggo

address: 229 cours de l'Argonne

department: Bergonie Cancer Institute

country: France

institute: University of Bordeaux

description: Series of 161 tumours

data_processing: RMA

source_name: Human Breast Tumor

label_protocol: Standard Affymetrix procedure

extract_protocol: Qiagen RNeasy Mini Kit

tag: pCR - pathological complete response


title: pt24.or


title: pt26.bl


title: pt25.bl


title: pt12.or

value: focally pos


title: pt23.or


title: pt19.bl


title: pt19.c2


title: pt20.or


title: pt18.or


title: pt22.c2


title: pt19.or


title: pt13.bl


title: pt17.or


title: pt16.or


title: pt13.c2


title: pt14.c2


title: pt18.c2


title: pt13.or


title: pt18.bl


title: pt15.c2


title: pt12.c2


title: pt12.bl


title: pt10.or


title: pt17.bl


title: pt8.c2


title: pt15.or


title: pt17.c2


title: pt7.or


title: pt15.bl


title: pt14.bl


title: pt7.bl


title: pt11.or


title: pt8.or


title: pt16.bl


title: pt8.bl


title: pt6.bl


title: pt4.bl


title: pt5.or


title: pt3.or


title: pt6.c2


title: BIG1_98_X52

status: Public on Jul 09 2009

description:
samplename: unique (anonymous) id for the patient
Case.control: case = 0, control = 1
Cluster.ID: cluster ID
GGI: raw values of the Gene expression Grade Index
size
age: age in years
Post.menopausal.status: before chemotherapy = 1, after chemotherapy = 2
ER.PgR: ER+/PgR+ = 1, ER+/PgR- = 2
Adj.neoadj.chemotherapy.received: no = 0, yes = 1
grade: tumor grade
Local.Therapy: BCS/RT = 1, BCS/no RT = 2, Mx/RT = 3
node: node negative = 0, node positive = 1
Treatment: Letrozol = 0, Tamoxifen = 1
t.rfs.months: disease-free survival in months
HER2.status: negative = 0, positive = 1
size: tumor size <= 2cm = 1, tumor size > 2cm = 2

tag: sample name

tag: case control 0- case, 1 - control

value: CNT

tag: ggi

tag: post menopausal status

tag: er pgr

tag: adj neoadj chemotherapy received

tag: grade

tag: local therapy

tag: node

tag: treatment

tag: t rfs months

tag: her2 status

tag: size

tag: tissue

value: primary breast tumor


title: BIG1_98_X47

tag: age


title: BIG1_98_X42


title: BIG1_98_X50


title: BIG1_98_X44


title: BIG1_98_X55


title: pt3.bl

tag: tissue type

value: breast tumor biopsies

tag: upin

tag: time point

tag: include in paired

tag: include in bl

tag: response category

tag: er original

tag: pr

tag: her2 summary


title: pt6.or

value: or


title: BIG1_98_X49

tag: sample name

tag: case control 0- case, 1 - control

tag: ggi

tag: post menopausal status

tag: er pgr

tag: adj neoadj chemotherapy received

tag: grade

tag: local therapy


title: BIG1_98_X54

tag: age

tag: node

tag: treatment

tag: t rfs months

tag: her2 status

tag: size

tag: tissue


title: BIG1_98_X45


title: pt1.c2

tag: tissue type

tag: upin

tag: time point

tag: include in paired

tag: include in bl

tag: response category

tag: er original

tag: pr


title: BIG1_98_X40

tag: sample name

tag: case control 0- case, 1 - control

tag: ggi

tag: post menopausal status

tag: er pgr

tag: adj neoadj chemotherapy received

tag: grade


title: BIG1_98_X38

tag: age

tag: local therapy

tag: node

tag: treatment

tag: t rfs months

tag: her2 status

tag: size


title: BIG1_98_X43

tag: tissue


title: BIG1_98_X39


title: BIG1_98_X48


title: BIG1_98_X53


title: BIG1_98_X41


title: BIG1_98_X35


title: BIG1_98_X51


title: BIG1_98_X46


title: BIG1_98_X36


title: BIG1_98_X37


title: BIG1_98_X34


title: BIG1_98_X33


title: BIG1_98_X29


title: BIG1_98_X26


title: BIG1_98_X27


title: BIG1_98_X24


title: BIG1_98_X11


title: BIG1_98_X22


title: BIG1_98_X32


title: BIG1_98_X30


title: BIG1_98_X28


title: BIG1_98_X31


title: BIG1_98_X25


title: BIG1_98_X20


title: BIG1_98_X9


title: BIG1_98_X19


title: BIG1_98_X16


title: BIG1_98_X13


title: BIG1_98_X14


title: BIG1_98_X17


title: BIG1_98_X23


title: BIG1_98_X8


title: BIG1_98_X21


title: BIG1_98_X7


title: BIG1_98_X3


title: BIG1_98_X15


title: BIG1_98_X12


title: BIG1_98_X5


title: BIG1_98_X18


title: BIG1_98_X4


title: BIG1_98_X6


title: BIG1_98_X10


title: BIG1_98_X2


title: HB84

status: Public on Dec 19 2008

city: Lausanne

first: Mauro

last: Delorenzi

address: Génopode Building, Quartier Sorge

country: Switzerland

institute: Swiss Institute of Bioinformatics

description: Series of 102 tumours

label_protocol: standard Affymetrix procedure

tag: Label

value: npCR

tag: Estrogen Receptor

value: En

tag: Progesterone Receptor

value: Pn

tag: Size

tag: Node


title: HB80

description: Series of 102 tumours

value: pCR


title: HB100

description: Series of 102 tumours

value: T-

value: N-


title: HB96

description: Series of 102 tumours


title: HB81

description: Series of 102 tumours


title: HB92

description: Series of 102 tumours


title: HB94

description: Series of 102 tumours


title: HB101

description: Series of 102 tumours


title: HB102

description: Series of 102 tumours


title: HB90

description: Series of 102 tumours


title: HB87

description: Series of 102 tumours


title: HB83

description: Series of 102 tumours


title: HB88

description: Series of 102 tumours


title: HB98

description: Series of 102 tumours


title: HB95

description: Series of 102 tumours


title: HB77

description: Series of 102 tumours


title: HB78

description: Series of 102 tumours


title: HB99

description: Series of 102 tumours


title: HB97

description: Series of 102 tumours


title: HB79

description: Series of 102 tumours


title: HB85

description: Series of 102 tumours


title: HB76

description: Series of 102 tumours


title: HB75

description: Series of 102 tumours


title: HB93

description: Series of 102 tumours


title: HB82

description: Series of 102 tumours


title: HB86

description: Series of 102 tumours


title: HB72

description: Series of 102 tumours

value: Ep


title: BIG1_98_X1

tag: sample name

tag: case control 0- case, 1 - control

tag: ggi

tag: post menopausal status


title: HB89

description: Series of 102 tumours


title: HB74

description: Series of 102 tumours


title: HB71

description: Series of 102 tumours


title: HB73

description: Series of 102 tumours


title: HB67

description: Series of 102 tumours


title: HB68

description: Series of 102 tumours


title: HB63

description: Series of 102 tumours


title: HB60

description: Series of 102 tumours


title: HB70

description: Series of 102 tumours

value: Pp


title: HB65

description: Series of 102 tumours


title: HB58

description: Series of 102 tumours


title: HB61

description: Series of 102 tumours


title: HB55

description: Series of 102 tumours


title: HB66

description: Series of 102 tumours


title: HB62

description: Series of 102 tumours


title: HB69

description: Series of 102 tumours


title: HB64

description: Series of 102 tumours


title: HB49

description: Series of 102 tumours


title: HB47

description: Series of 102 tumours


title: HB56

description: Series of 102 tumours


title: HB91

description: Series of 102 tumours


title: HB44

description: Series of 102 tumours


title: HB52

description: Series of 102 tumours


title: HB59

description: Series of 102 tumours


title: HB48

description: Series of 102 tumours


title: HB46

description: Series of 102 tumours


title: HB50

description: Series of 102 tumours


title: HB45

description: Series of 102 tumours


title: HB43

description: Series of 102 tumours


title: HB54

description: Series of 102 tumours


title: HB51

description: Series of 102 tumours


title: HB53

description: Series of 102 tumours


title: HB57

description: Series of 102 tumours


title: HB39

description: Series of 102 tumours


title: HB41

description: Series of 102 tumours


title: HB38

description: Series of 102 tumours


title: HB33

description: Series of 102 tumours


title: HB31

description: Series of 102 tumours


title: HB36

description: Series of 102 tumours


title: HB32

description: Series of 102 tumours


title: HB37

description: Series of 102 tumours


title: HB27

description: Series of 102 tumours


title: HB28

description: Series of 102 tumours


title: HB29

description: Series of 102 tumours


title: HB42

description: Series of 102 tumours


title: HB30

description: Series of 102 tumours


title: HB35

description: Series of 102 tumours


title: HB13

description: Series of 102 tumours


title: HB22

description: Series of 102 tumours


title: HB16

description: Series of 102 tumours


title: HB26

description: Series of 102 tumours


title: HB23

description: Series of 102 tumours

value: P-


title: HB20

description: Series of 102 tumours


title: HB15

description: Series of 102 tumours


title: HB19

description: Series of 102 tumours


title: HB18

description: Series of 102 tumours


title: HB21

description: Series of 102 tumours


title: HB24

description: Series of 102 tumours


title: HB17

description: Series of 102 tumours


title: HB25

description: Series of 102 tumours


title: HB14

description: Series of 102 tumours


title: HB12

description: Series of 102 tumours


title: HB10

description: Series of 102 tumours


title: Mammary Gland: 88.1 hours of estrus cycle

status: Public on Aug 04 2008

city: Oklahoma City

first: Michael

middle: C.

last: Rudolph

state: OK

address: 975 NE 10th St. BRC North rm 364

department: Biochemistry and Physiology

institute: OUHSC

description: Gene expression data from mammary glands of non parous rats

hyb_protocol: Hybridization protocol according to affymetrix. Following fragmentation  15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mu74Av2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scan protocol according to affymetrix on GeneChip Scanner 3000

data_processing: samples were evaluated for quality control parameters using Gene Chip Operating System from Affymetrix.  CEL files were then imported into GeneSpring (Agilent Technologies) and processed using their native GC-RMA algorithem.

organism: Rattus norvegicus

label_protocol: all samples were biotin labeled using the ENZO labeling kit and protocol according to affymetrix parameters beginning from 2ug of total RNA converted to cDNA

growth_protocol: Sprague Dawley rats were housed at the University of Colorado vivarium on a standard laboratory chow diet

extract_protocol: the fourth mammary glands on mice were excised and the lymph nodes were removed  samples were stored in RNA Later from Qiagen according to manufacturers instructions. Total RNA was isolated using RNA easy from qiagen according to their protocol  and total RNA was examined for purity using a nanodrop and for integrity using agilent bioanalyzer.

treatment_protocol: no treatments


title: HB05

description: Series of 102 tumours


title: Mammary Gland: 65.6 hours of estrus cycle


title: Mammary Gland: 86.3 hours of estrus cycle


title: HB11

description: Series of 102 tumours


title: Mammary Gland: 64.2 hours of estrus cycle


title: HB08

description: Series of 102 tumours


title: Mammary Gland: 85.3 hours of estrus cycle


title: Mammary Gland: 57 hours of estrus cycle

source_name: Mammary Gland: 57 hours of estrus cycle


title: HB09

description: Series of 102 tumours


title: Mammary Gland: 82.5 hours of estrus cycle


title: Mammary Gland: 67.1 hours of estrus cycle


title: Mammary Gland: 80.9 hours of estrus cycle


title: Mammary Gland: 62.5 hours of estrus cycle


title: Mammary Gland: 79.3 hours of estrus cycle


title: HB06

description: Series of 102 tumours


title: HB03

description: Series of 102 tumours


title: Mammary Gland: 59.8 hours of estrus cycle


title: Mammary Gland: 43 hours of estrus cycle

source_name: Mammary Gland: 43 hours of estrus cycle


title: Mammary Gland: 58 hours of estrus cycle

source_name: Mammary Gland: 58 hours of estrus cycle


title: Mammary Gland: 61.3 hours of estrus cycle


title: HB04

description: Series of 102 tumours


title: HB01

description: Series of 102 tumours


title: Mammary Gland: 83.9 hours of estrus cycle


title: HB40

description: Series of 102 tumours


title: HB02

description: Series of 102 tumours


title: Mammary Gland: 41.6 hours of estrus cycle


title: Mammary Gland: 37.1 hours of estrus cycle


title: Mammary Gland: 32.8 hours of estrus cycle


title: Mammary Gland: 38.3 hours of estrus cycle


title: Mammary Gland: 17.6 hours of estrus cycle


title: Mammary Gland: 7 hours of estrus cycle

source_name: Mammary Gland: 7 hours of estrus cycle


title: HB34

description: Series of 102 tumours


title: Mammary Gland: 16 hours of estrus cycle

source_name: Mammary Gland: 16 hours of estrus cycle


title: Mammary Gland: 34.5 hours of estrus cycle


title: Mammary Gland: 31.6 hours of estrus cycle


title: Mammary Gland: 13.2 hours of estrus cycle


title: Mammary Gland: 13 hours of estrus cycle

source_name: Mammary Gland: 13 hours of estrus cycle


title: Mammary Gland: 35.5 hours of estrus cycle


title: Mammary Gland: 14.6 hours of estrus cycle


title: Mammary Gland: 40 hours of estrus cycle

source_name: Mammary Gland: 40 hours of estrus cycle


title: Mammary Gland: 10 hours of estrus cycle

source_name: Mammary Gland: 10 hours of estrus cycle


title: HB161

status: Public on Nov 23 2007

address: 155 Boveresses

institute: ISREC

description: Series of 161 tumours

tag: pCR - pathological complete response


title: HB158

description: Series of 161 tumours

tag: npCR - no pathological complete response


title: Mammary Gland: 7.5 hours of estrus cycle


title: HB156

description: Series of 161 tumours


title: HB153

description: Series of 161 tumours


title: HB152

description: Series of 161 tumours


title: HB162

description: Series of 161 tumours


title: HB151

description: Series of 161 tumours


title: HB155

description: Series of 161 tumours


title: HB154

description: Series of 161 tumours


title: HB157

description: Series of 161 tumours


title: HB160

description: Series of 161 tumours


title: HB150

description: Series of 161 tumours


title: HB159

description: Series of 161 tumours


title: HB142

description: Series of 161 tumours


title: HB138

description: Series of 161 tumours


title: HB144

description: Series of 161 tumours


title: HB140

description: Series of 161 tumours


title: HB146

description: Series of 161 tumours


title: HB141

description: Series of 161 tumours


title: HB139

description: Series of 161 tumours


title: HB07

description: Series of 102 tumours


title: HB135

description: Series of 161 tumours


title: HB148

description: Series of 161 tumours


title: HB134

description: Series of 161 tumours


title: HB149

description: Series of 161 tumours


title: HB145

description: Series of 161 tumours


title: HB129

description: Series of 161 tumours


title: HB147

description: Series of 161 tumours


title: HB120

description: Series of 161 tumours


title: HB137

description: Series of 161 tumours


title: HB124

description: Series of 161 tumours


title: HB128

description: Series of 161 tumours


title: HB127

description: Series of 161 tumours


title: HB122

description: Series of 161 tumours


title: HB133

description: Series of 161 tumours


title: HB125

description: Series of 161 tumours


title: HB119

description: Series of 161 tumours


title: HB132

description: Series of 161 tumours


title: HB126

description: Series of 161 tumours


title: HB123

description: Series of 161 tumours


title: HB121

description: Series of 161 tumours


title: HB118

description: Series of 161 tumours


title: HB111

description: Series of 161 tumours


title: HB143

description: Series of 161 tumours


title: HB114

description: Series of 161 tumours


title: HB136

description: Series of 161 tumours


title: HB103

description: Series of 161 tumours


title: HB108

description: Series of 161 tumours


title: HB112

description: Series of 161 tumours


title: HB115

description: Series of 161 tumours


title: HB109

description: Series of 161 tumours


title: HB116

description: Series of 161 tumours


title: HB100bis

description: Series of 161 tumours


title: HB110

description: Series of 161 tumours


title: HB97bis

description: Series of 161 tumours


title: HB104

description: Series of 161 tumours


title: HB94bis

description: Series of 161 tumours


title: HB113

description: Series of 161 tumours


title: HB101bis

description: Series of 161 tumours


title: HB106

description: Series of 161 tumours


title: HB92bis

description: Series of 161 tumours


title: HB95bis

description: Series of 161 tumours


title: HB93bis

description: Series of 161 tumours


title: HB99bis

description: Series of 161 tumours


title: HB107

description: Series of 161 tumours


title: HB98bis

description: Series of 161 tumours


title: HB102bis

description: Series of 161 tumours


title: HB105

description: Series of 161 tumours


title: HB91bis

description: Series of 161 tumours


title: HB117

description: Series of 161 tumours


title: HB96bis

description: Series of 161 tumours


title: HB90bis

description: Series of 161 tumours


title: HB84bis

description: Series of 161 tumours


title: HB81bis

description: Series of 161 tumours


title: HB80bis

description: Series of 161 tumours


title: HB87bis

description: Series of 161 tumours


title: HB83bis

description: Series of 161 tumours


title: HB82bis

description: Series of 161 tumours


title: HB88bis

description: Series of 161 tumours


title: HB86bis

description: Series of 161 tumours


title: HB85bis

description: Series of 161 tumours


title: HB74bis

description: Series of 161 tumours


title: HB71bis

description: Series of 161 tumours


title: HB75bis

description: Series of 161 tumours


title: HB68bis

description: Series of 161 tumours


title: HB73bis

description: Series of 161 tumours


title: HB79bis

description: Series of 161 tumours


title: HB77bis

description: Series of 161 tumours


title: HB66bis

description: Series of 161 tumours


title: HB64bis

description: Series of 161 tumours


title: HB76bis

description: Series of 161 tumours


title: HB65bis

description: Series of 161 tumours


title: HB78bis

description: Series of 161 tumours


title: HB69bis

description: Series of 161 tumours


title: HB72bis

description: Series of 161 tumours


title: HB70bis

description: Series of 161 tumours


title: HB61bis

description: Series of 161 tumours


title: HB67bis

description: Series of 161 tumours


title: HB62bis

description: Series of 161 tumours


title: HB63bis

description: Series of 161 tumours


title: HB53bis

description: Series of 161 tumours


title: HB52bis

description: Series of 161 tumours


title: HB48bis

description: Series of 161 tumours


title: HB47bis

description: Series of 161 tumours


title: HB49bis

description: Series of 161 tumours


title: HB59bis

description: Series of 161 tumours


title: HB50bis

description: Series of 161 tumours


title: HB44bis

description: Series of 161 tumours


title: HB54bis

description: Series of 161 tumours


title: HB56bis

description: Series of 161 tumours


title: HB58bis

description: Series of 161 tumours


title: HB51bis

description: Series of 161 tumours


title: HB42bis

description: Series of 161 tumours


title: HB60bis

description: Series of 161 tumours


title: HB89bis

description: Series of 161 tumours


title: HB33bis

description: Series of 161 tumours


title: HB37bis

description: Series of 161 tumours


title: HB35bis

description: Series of 161 tumours


title: HB55bis

description: Series of 161 tumours


title: HB32bis

description: Series of 161 tumours


title: HB38bis

description: Series of 161 tumours


title: HB41bis

description: Series of 161 tumours


title: HB34bis

description: Series of 161 tumours


title: HB45bis

description: Series of 161 tumours


title: HB36bis

description: Series of 161 tumours


title: HB57bis

description: Series of 161 tumours


title: HB46bis

description: Series of 161 tumours


title: HB40bis

description: Series of 161 tumours


title: HB43bis

description: Series of 161 tumours


title: HB39bis

description: Series of 161 tumours


title: HB08bis

description: Series of 161 tumours


title: HB20bis

description: Series of 161 tumours


title: HB27bis

description: Series of 161 tumours


title: HB29bis

description: Series of 161 tumours


title: HB16bis

description: Series of 161 tumours


title: HB14bis

description: Series of 161 tumours


title: HB09bis

description: Series of 161 tumours


title: HB21bis

description: Series of 161 tumours


title: HB23bis

description: Series of 161 tumours


title: HB19bis

description: Series of 161 tumours


title: HB24bis

description: Series of 161 tumours


title: HB25bis

description: Series of 161 tumours


title: HB26bis

description: Series of 161 tumours


title: HB22bis

description: Series of 161 tumours


title: HB15bis

description: Series of 161 tumours


title: HB10bis

description: Series of 161 tumours


title: HB13bis

description: Series of 161 tumours


title: HB30bis

description: Series of 161 tumours


title: HB04bis

description: Series of 161 tumours


title: HB12bis

description: Series of 161 tumours


title: HB17bis

description: Series of 161 tumours


title: HB11bis

description: Series of 161 tumours


title: HB28bis

description: Series of 161 tumours


title: HB31bis

description: Series of 161 tumours


title: HB02bis

description: Series of 161 tumours


title: HB05bis

description: Series of 161 tumours


title: HB18bis

description: Series of 161 tumours


title: HB07bis

description: Series of 161 tumours


title: HB06bis

description: Series of 161 tumours


title: HB03bis

description: Series of 161 tumours


title: HB01bis

description: Series of 161 tumours


title: Mammary Gland @  Invo2, biological rep2

status: Public on Jun 21 2007

description: Gene expression data from mammary glands of involuting mice

hyb_protocol: Hybridization protocol according to affymetrix. Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mu74Av2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: Samples were evaluated for quality control parameters using Gene Chip Operating System from Affymetrix. CEL files were then imported into GeneSpring (Agilent Technologies) and processed using their native GC-RMA algorithm.

organism: Mus musculus

source_name: Mammary Gland @  Invo2, biological rep2

growth_protocol: mice were grown at the University of Colorado vivarium on a standard laboratory chow diet

extract_protocol: the fourth mammary glands on mice were excised and the lymph nodes were removed, samples were stored in RNA Later from Qiagen according to manufacturers instructions. Total RNA was isolated using RNA easy from qiagen according to their protocol, and total RNA was examined for purity using a nanodrop and for integrity using agilent bioanalyzer.


title: Mammary Gland @ Invo2, biological rep1

source_name: Mammary Gland @ Invo2, biological rep1


title: Mammary Gland @  Lac2, biological rep3

description: Gene expression data from mammary glands of lactating mice

source_name: Mammary Gland @  Lac2, biological rep3


title: Mammary Gland @  Invo2, biological rep3

source_name: Mammary Gland @  Invo2, biological rep3


title: Mammary Gland @ Lac2, biological rep1

source_name: Mammary Gland @ Lac2, biological rep1


title: Mammary Gland @  Invo2, biological rep4

source_name: Mammary Gland @  Invo2, biological rep4


title: Mammary Gland @  Lac1, biological rep2

source_name: Mammary Gland @  Lac1, biological rep2


title: Mammary Gland @  Lac2, biological rep4

source_name: Mammary Gland @  Lac2, biological rep4


title: Mammary Gland @  Lac9, biological rep3

source_name: Mammary Gland @  Lac9, biological rep3


title: Mammary Gland @ Lac9, biological rep1

source_name: Mammary Gland @ Lac9, biological rep1


title: Mammary Gland @  Lac9, biological rep4

source_name: Mammary Gland @  Lac9, biological rep4


title: Mammary Gland @  Lac2, biological rep2

source_name: Mammary Gland @  Lac2, biological rep2


title: Mammary Gland @  Lac1, biological rep4

source_name: Mammary Gland @  Lac1, biological rep4


title: Mammary Gland @ Preg19, biological rep4

description: Gene expression data from mammary glands of pregnant mice

source_name: Mammary Gland @ Preg19, biological rep4


title: Mammary Gland @ Preg19, biological rep2

source_name: Mammary Gland @ Preg19, biological rep2


title: Mammary Gland @ Lac1, biological rep1

source_name: Mammary Gland @ Lac1, biological rep1


title: Mammary Gland @ Preg19, biological rep3

source_name: Mammary Gland @ Preg19, biological rep3


title: Mammary Gland @ Preg17, biological rep1

source_name: Mammary Gland @ Preg17, biological rep1


title: Mammary Gland @  Lac1, biological rep3

source_name: Mammary Gland @  Lac1, biological rep3


title: Mammary Gland @  Lac9, biological rep2

source_name: Mammary Gland @  Lac9, biological rep2


title: Mammary Gland @ Preg17, biological rep3

source_name: Mammary Gland @ Preg17, biological rep3


title: Mammary Gland @ Preg19, biological rep1

source_name: Mammary Gland @ Preg19, biological rep1


title: Mammary Gland @ Preg12, biological rep4

source_name: Mammary Gland @ Preg12, biological rep4


title: Mammary Gland @ Preg12, biological rep1

source_name: Mammary Gland @ Preg12, biological rep1


title: Mammary Gland @ Preg17, biological rep2

source_name: Mammary Gland @ Preg17, biological rep2


title: Mammary Gland @ Preg12, biological rep2

source_name: Mammary Gland @ Preg12, biological rep2


title: Mammary Gland @ Preg17, biological rep4

source_name: Mammary Gland @ Preg17, biological rep4


title: Mammary Gland @ Preg7, biological rep4

source_name: Mammary Gland @ Preg7, biological rep4


title: Mammary Gland @ Preg12, biological rep3

source_name: Mammary Gland @ Preg12, biological rep3


title: Mammary Gland @ Preg7, biological rep3

source_name: Mammary Gland @ Preg7, biological rep3


title: MamGland normal dietary fat replicate1 PD12

status: Public on Feb 10 2006

description: Wildtype FVB mouse mammary tissue, normal dietary fat

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: GeneSpring version 7.2 GC-RMA processing

label: ENZO biotin labeled

source_name: Mammary Gland

label_protocol: Approximately 5 micrograms of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Excised tissue was stored in RNALater and then polytron homogenized and lysed as individual samples in RLT buffer (Qiagen).Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: Wild type, Pregnant Day 12 whole mammary gland less Lymph node


title: MamGland normal dietary fat replicate1 PD17

tag: Wild type, Pregnant Day 17 whole mammary gland less Lymph node


title: MamGland normal dietary fat replicate1 LD9

tag: Wild type, Lactation Day 9 whole mammary gland less Lymph node


title: MamGland normal dietary fat replicate2 PD17


title: MamGland normal dietary fat replicate2 LD9


title: MamGland normal dietary fat replicate2 PD12


title: Mammary Gland @ Preg1, biological rep3

source_name: Mammary Gland @ Preg1, biological rep3


title: Liver 8% dietary fat replicate2

description: Wildtype FVB mouse liver tissue, 8% dietary fat

source_name: Liver

tag: Wild type, Lactation Day 10 whole Liver tissue, same animal as mammary sample


title: Mammary Gland @ Preg1, biological rep4

source_name: Mammary Gland @ Preg1, biological rep4


title: Mammary Gland @ Preg3, biological rep1

source_name: Mammary Gland @ Preg3, biological rep1


title: MamGland normal dietary fat replicate3 LD1

tag: Wild type, Laction Day 1 whole mammary gland less Lymph node


title: Mammary Gland @ Preg7, biological rep1

source_name: Mammary Gland @ Preg7, biological rep1


title: MamGland normal dietary fat replicate4 PD17


title: Mammary Gland @ Preg3, biological rep2

source_name: Mammary Gland @ Preg3, biological rep2


title: Mammary Gland @ Preg7, biological rep2

source_name: Mammary Gland @ Preg7, biological rep2


title: MamGland normal dietary fat replicate4 LD1


title: MamGland normal dietary fat replicate4 LD9


title: MamGland normal dietary fat replicate3 LD9


title: MamGland normal dietary fat replicate4 LD2

tag: Wild type, Lactation Day 2 whole mammary gland less Lymph node


title: MamGland normal dietary fat replicate3 PD12


title: Liver 8% dietary fat replicate3


title: MamGland normal dietary fat replicate4 PD12


title: Mammary Gland @ Preg3, biological rep4

source_name: Mammary Gland @ Preg3, biological rep4


title: MamGland normal dietary fat replicate3 PD17


title: Liver 8% dietary fat replicate1


title: Mammary Gland @ Preg1, biological rep2

source_name: Mammary Gland @ Preg1, biological rep2


title: Mammary Gland @ Preg3, biological rep3

source_name: Mammary Gland @ Preg3, biological rep3


title: Mammary Gland @ Preg1, biological rep1

source_name: Mammary Gland @ Preg1, biological rep1


title: MamGland normal dietary fat replicate2 LD1


title: MamGland normal dietary fat replicate1 LD1


title: MamGland normal dietary fat replicate2 LD2


title: MamGland normal dietary fat replicate3 LD2


title: MamGland 16% dietary fat replicate2

description: Wildtype FVB mouse mammary tissue, 40% dietary fat

tag: Wild type, Lactation Day 10 whole mammary gland less Lymph node


title: MamGland normal dietary fat replicate1 LD2


title: MamGland 8% dietary fat replicate3


title: MamGland 40% dietary fat replicate1

description: Wildtype FVB mouse mammary tissue, 40% dietary fat, Lactation Day 10


title: MamGland 8% dietary fat replicate1


title: MamGland 8% dietary fat replicate2


title: MamGland 16% dietary fat replicate3


title: MamGland 40% dietary fat replicate2


title: MamGland 16% dietary fat replicate1


title: MamGland 40% dietary fat replicate3