title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 49

source_name: Comparative experiment (#3-1) of Fe strain (Fe nitrogenase only strain)


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 38

status: Public on Nov 10 2005

type: RNA

city: Seattle

first: Yasuhiro

last: Oda

state: WA

address: Box 357242, 1705 N.E. Pacific Street, HSB K-354

department: Department of Microbiology

country: USA

institute: University of Washington

description: The software package lcDNA was used for data normalization and assessment of the statistical confidence intervals of gene expression. Duplicate calibration experiments and three comparative experiments using RNA from three separately grown cultures (three biological replicates) with duplicate slides for each (10 slides in total) were used to generate each data set.

data_processing: Images (Cy3 and Cy5) were captured as TIFF files and were analyzed with the image processing software ImaGene version 5.6 (BioDiscovery, Inc., El Segundo, CA).

molecule: total RNA

organism: Rhodopseudomonas palustris

source_name: Comparative experiment (#2-2) of V strain (V nitrogenase only strain)

tag: RNA from V strain grown under N2-fixing conditions (+V)

tag: RNA from V strain grown under non-N2-fixing conditions (+V)


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 36

source_name: Comparative experiment (#1-2) of V strain (V nitrogenase only strain)


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 46

source_name: Comparative experiment (#1-2) of Fe strain (Fe nitrogenase only strain)

tag: RNA from Fe strain grown under non-N2-fixing conditions

tag: RNA from Fe strain grown under N2-fixing conditions


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 41

source_name: Calibration experiment (#1-1) of Fe strain (Fe nitrogenase only strain)

tag: Mixed RNA from Fe strain grown under N2-fixing and non-N2-fixing conditions


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 44

source_name: Calibration experiment (#2-2) of Fe strain (Fe nitrogenase only strain)


title: palisading 1

status: Public on Nov 11 2005

city: Charlestown

first: Shumin

last: Dong

state: MA

department: Pathology and Neurosurgical services

institute: Massachusetts General Hospital

description: specific tumor cell type-pseudopalisading cells in human glioblastoma, case 1

organism: Homo sapiens

source_name: human glioblastoma


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 42

source_name: Calibration experiment (#1-2) of Fe strain (Fe nitrogenase only strain)


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 39

source_name: Comparative experiment (#3-1) of V strain (V nitrogenase only strain)


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 37

source_name: Comparative experiment (#2-1) of V strain (V nitrogenase only strain)


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 47

source_name: Comparative experiment (#2-1) of Fe strain (Fe nitrogenase only strain)


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 35

source_name: Comparative experiment (#1-1) of V strain (V nitrogenase only strain)


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 33

source_name: Calibration experiment (#2-1) of V strain (V nitrogenase only strain)

tag: Mixed RNA from V strain grown under N2-fixing (+V) and non-N2-fixing conditions (+V)


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 34

source_name: Calibration experiment (#2-2) of V strain (V nitrogenase only strain)


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 32

source_name: Calibration experiment (#1-2) of V strain (V nitrogenase only strain)


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 28

source_name: Comparative experiment (#2-2) of Mo strain (Mo nitrogenase only strain)

tag: RNA from Mo strain grown under N2-fixing conditions

tag: RNA from Mo strain grown under non-N2-fixing conditions


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 31

source_name: Calibration experiment (#1-1) of V strain (V nitrogenase only strain)


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 29

source_name: Comparative experiment (#3-1) of Mo strain (Mo nitrogenase only strain)


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 30

source_name: Comparative experiment (#3-2) of Mo strain (Mo nitrogenase only strain)


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 27

source_name: Comparative experiment (#2-1) of Mo strain (Mo nitrogenase only strain)


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 26

source_name: Comparative experiment (#1-2) of Mo strain (Mo nitrogenase only strain)


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 25

source_name: Comparative experiment (#1-1) of Mo strain (Mo nitrogenase only strain)


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 22

source_name: Calibration experiment (#1-2) of Mo strain (Mo nitrogenase only strain)

tag: Mixed RNA from Mo strain grown under N2-fixing and non-N2-fixing conditions


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 24

source_name: Calibration experiment (#2-2) of Mo strain (Mo nitrogenase only strain)


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 21

source_name: Calibration experiment (#1-1) of Mo strain (Mo nitrogenase only strain)


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 23

source_name: Calibration experiment (#2-1) of Mo strain (Mo nitrogenase only strain)


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 18

source_name: Comparative experiment (#2-2) of wild-type (+V)

tag: RNA from wild-type strain grown under N2-fixing conditions (+V)

tag: RNA from wild-type strain grown under non-N2-fixing conditions (+V)


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 20

source_name: Comparative experiment (#3-2) of wild-type (+V)


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 7

source_name: Comparative experiment (#2-1) of wild-type

tag: RNA from wild-type strain grown under non-N2-fixing conditions

tag: RNA from wild-type strain grown under N2-fixing conditions


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 9

source_name: Comparative experiment (#3-1) of wild-type


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 10

source_name: Comparative experiment (#3-2) of wild-type


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 19

source_name: Comparative experiment (#3-1) of wild-type (+V)


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 11

source_name: Calibration experiment (#1-1) of wild-type (+V)

tag: Mixed RNA from wild-type strain grown under N2-fixing (+V) and non-N2-fixing conditions (+V)


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 12

source_name: Calibration experiment (#1-2) of wild-type (+V)


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 8

source_name: Comparative experiment (#2-2) of wild-type


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 17

source_name: Comparative experiment (#2-1) of wild-type (+V)


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 6

source_name: Comparative experiment (#1-2) of wild-type


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 4

source_name: Calibration experiment (#2-2) of wild-type

tag: Mixed RNA from wild-type strain grown under N2-fixing and non-N2-fixing conditions


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 3

source_name: Calibration experiment (#2-1) of wild-type


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 15

source_name: Comparative experiment (#1-1) of wild-type (+V)


title: cDNA array - Cancer pathway finder (Superarray) of EM-G3 cells

status: Public on Nov 08 2005

city: Prague 2

first: Zdenek

last: Kleibl

address: U nemocnice 5

department: Dept. of Biochemistry and Experimental Oncology

country: Czech Republic

institute: First Faculty of Medicine, Charles University in Prague

description: The aim was to scan expression profile of the newly developed human breast cancer cell line. The 3 independent experiments performed with the same results.

scan_protocol: According to manufacturer (www.superarray.com). - Array membranes were developed on X-OMAT (Kodak film) for 16h

data_processing: Autoradiogram scaned to TIFF / Quantitation performed using ScanAnalyze 2.05 and GEArray Analyzer/ Data normalized to PPIA

source_name: Human breast cancer cell line EM-G3

growth_protocol: H-MEM supplemented with non-essential amino acids, 0.5 mg/ml hydrocortisone, 5 mg/ml insulin, 10-10 M cholera toxin, 5 ng/ml epidermal growth factor (EGF), 10% bovine and 2% fetal bovine serum

treatment_protocol: without treatment

tag: EM-G3 cell line in  passage 197


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 16

source_name: Comparative experiment (#1-2) of wild-type (+V)


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 5

source_name: Comparative experiment (#1-1) of wild-type


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 2

source_name: Calibration experiment (#1-2) of wild-type


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 14

source_name: Calibration experiment (#2-2) of wild-type (+V)


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 1

source_name: Calibration experiment (#1-1) of wild-type


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 13

source_name: Calibration experiment (#2-1) of wild-type (+V)


title: R-MDA-MB-231

status: Public on Nov 07 2005

city: Durham

first: Joseph

middle: R.

last: Nevins

state: NC

address: 2133 CIEMAS, 101 Science Dr.

department: IGSP

institute: Duke University

description: Microarray analysis of breast cancer cell lines

data_processing: Affymetrix Microarray Suite version 5.0

label: biotin

source_name: RNA from growing cell lines

tag: breast cancer cell line


title: I-BT-549


title: S-MDA-MB-453


title: E-CAMA-1


title: D-HS578T


title: Q-MDA-MB-435S


title: J-SK-BR-3


title: O-HCC1428


title: P-HCC38


title: RAS-9

description: RNA was extracted from human mammary epithelial cells expressing oncogenes (or GFP control)


title: F-MDA-MB-361


title: M-HCC1143


title: A-BT-20

description: Microarray analysis of breast cancer cell lines.


title: RAS-3

source_name: mammary epithelial cells expressing oncogenes (or GFP control)


title: E2F3-8

tag: mammary epithelial cells expressing oncogenes (or GFP control)


title: E2F3-10


title: N-HCC1806


title: RAS-7


title: RAS-5


title: RAS-8


title: B-BT-474


title: RAS-10


title: RAS-6


title: G-MDA-MB-157


title: E2F3-9


title: RAS-1


title: H-BT-483


title: RAS-4


title: C-MCF7


title: RAS-2


title: M810

description: frozen tissue of ovarian tumors

source_name: ovarian tumors

tag: frozen tissue of ovarian tumors


title: M5668

description: frozen tissue of ovarian tumors


title: E2F3-7


title: M6199

description: frozen tissue of ovarian tumors


title: E2F3-6


title: M806

description: frozen tissue of ovarian tumors


title: E2F3-5


title: M5775

description: frozen tissue of ovarian tumors


title: M3484

description: frozen tissue of ovarian tumors


title: M3514

description: frozen tissue of ovarian tumors


title: M4161

description: frozen tissue of ovarian tumors


title: M444

description: frozen tissue of ovarian tumors


title: E2F3-3


title: M359

description: frozen tissue of ovarian tumors


title: M503

description: frozen tissue of ovarian tumors


title: M485

description: frozen tissue of ovarian tumors


title: E2F3-1


title: Bcat-5


title: Bcat-7


title: Bcat-1


title: BCAT-8


title: Bcat-2


title: M4171

description: frozen tissue of ovarian tumors


title: M3627

description: frozen tissue of ovarian tumors


title: M337

description: frozen tissue of ovarian tumors


title: BCAT-9


title: Bcat-3


title: Bcat-4


title: E2F3-2


title: Bcat-6


title: M3035

description: frozen tissue of ovarian tumors


title: M3142

description: frozen tissue of ovarian tumors


title: M2729

description: frozen tissue of ovarian tumors


title: M2070

description: frozen tissue of ovarian tumors


title: Src-7


title: Src-1


title: Src-3


title: Src-6


title: M2807

description: frozen tissue of ovarian tumors


title: M2097

description: frozen tissue of ovarian tumors


title: M2437

description: frozen tissue of ovarian tumors


title: Myc-10


title: M17 0

description: frozen tissue of ovarian tumors


title: Myc-9


title: M2515

description: frozen tissue of ovarian tumors


title: M1572

description: frozen tissue of ovarian tumors


title: M1891

description: frozen tissue of ovarian tumors


title: M1777

description: frozen tissue of ovarian tumors


title: M1390

description: frozen tissue of ovarian tumors


title: M2184

description: frozen tissue of ovarian tumors


title: Myc-8


title: Src-4


title: Myc-7


title: Myc-6


title: Src-5


title: M1503

description: frozen tissue of ovarian tumors


title: Myc-4


title: Myc-5


title: Myc-3


title: Src-2


title: M1241

description: frozen tissue of ovarian tumors


title: Myc-2


title: M1054

description: frozen tissue of ovarian tumors


title: D2792

description: frozen tissue of ovarian tumors


title: M1055

description: frozen tissue of ovarian tumors


title: D2775

description: frozen tissue of ovarian tumors


title: M120

description: frozen tissue of ovarian tumors


title: D2736

description: frozen tissue of ovarian tumors


title: Myc-1


title: D2733

description: frozen tissue of ovarian tumors


title: D2791

description: frozen tissue of ovarian tumors


title: D2732

description: frozen tissue of ovarian tumors


title: GFP-9


title: D2749

description: frozen tissue of ovarian tumors


title: GFP-5


title: GFP-8


title: GFP-10


title: D2776

description: frozen tissue of ovarian tumors


title: GFP-4


title: GFP-7


title: GFP-1


title: GFP-6


title: GFP-2


title: M1025

description: frozen tissue of ovarian tumors


title: D2738

description: frozen tissue of ovarian tumors


title: D2726

description: frozen tissue of ovarian tumors


title: D2734

description: frozen tissue of ovarian tumors


title: D2700

description: frozen tissue of ovarian tumors


title: D2711

description: frozen tissue of ovarian tumors


title: GFP-3


title: D2727

description: frozen tissue of ovarian tumors


title: D2691

description: frozen tissue of ovarian tumors


title: D2668

description: frozen tissue of ovarian tumors


title: D2651

description: frozen tissue of ovarian tumors


title: D2679

description: frozen tissue of ovarian tumors


title: D2648

description: frozen tissue of ovarian tumors


title: D2612

description: frozen tissue of ovarian tumors


title: D2610

description: frozen tissue of ovarian tumors


title: D2603

description: frozen tissue of ovarian tumors


title: D2611

description: frozen tissue of ovarian tumors


title: D2640

description: frozen tissue of ovarian tumors


title: D2622

description: frozen tissue of ovarian tumors


title: D2578

description: frozen tissue of ovarian tumors


title: D2689

description: frozen tissue of ovarian tumors


title: D2581

description: frozen tissue of ovarian tumors


title: D2629

description: frozen tissue of ovarian tumors


title: D2557

description: frozen tissue of ovarian tumors


title: D2576

description: frozen tissue of ovarian tumors


title: D2572

description: frozen tissue of ovarian tumors


title: D2528

description: frozen tissue of ovarian tumors


title: D2560

description: frozen tissue of ovarian tumors


title: D2559

description: frozen tissue of ovarian tumors


title: D2575

description: frozen tissue of ovarian tumors


title: D2433

description: frozen tissue of ovarian tumors


title: D2332

description: frozen tissue of ovarian tumors


title: D2421

description: frozen tissue of ovarian tumors


title: D2443

description: frozen tissue of ovarian tumors


title: D2432

description: frozen tissue of ovarian tumors


title: D2480

description: frozen tissue of ovarian tumors


title: D2358

description: frozen tissue of ovarian tumors


title: D2342

description: frozen tissue of ovarian tumors


title: D2287

description: frozen tissue of ovarian tumors


title: D2208

description: frozen tissue of ovarian tumors


title: D2251

description: frozen tissue of ovarian tumors


title: D2247

description: frozen tissue of ovarian tumors


title: D1805

description: frozen tissue of ovarian tumors


title: D2098

description: frozen tissue of ovarian tumors


title: D2159

description: frozen tissue of ovarian tumors


title: 3090

description: frozen tissue of ovarian tumors


title: D1837

description: frozen tissue of ovarian tumors


title: D1462

description: frozen tissue of ovarian tumors


title: D2171

description: frozen tissue of ovarian tumors


title: 3107

description: frozen tissue of ovarian tumors


title: 2673_b

description: frozen tissue of ovarian tumors


title: 3250

description: frozen tissue of ovarian tumors


title: 1447

description: frozen tissue of ovarian tumors


title: D2147

description: frozen tissue of ovarian tumors


title: 2895

description: frozen tissue of ovarian tumors


title: 2981

description: frozen tissue of ovarian tumors


title: 3018

description: frozen tissue of ovarian tumors


title: 2739_b

description: frozen tissue of ovarian tumors


title: 1024_a

description: frozen tissue of ovarian tumors


title: 2505_a

description: frozen tissue of ovarian tumors


title: 2802

description: frozen tissue of ovarian tumors


title: 2542

description: frozen tissue of ovarian tumors


title: 2479_b

description: frozen tissue of ovarian tumors


title: 2424_b

description: frozen tissue of ovarian tumors


title: 2479_a

description: frozen tissue of ovarian tumors


title: 2476

description: frozen tissue of ovarian tumors


title: 2046

description: frozen tissue of ovarian tumors


title: 2063_a

description: frozen tissue of ovarian tumors


title: 1552

description: frozen tissue of ovarian tumors


title: 3102

description: frozen tissue of ovarian tumors


title: 1877_b

description: frozen tissue of ovarian tumors


title: 2198

description: frozen tissue of ovarian tumors


title: 2424_a

description: frozen tissue of ovarian tumors


title: 2849

description: frozen tissue of ovarian tumors


title: 2573

description: frozen tissue of ovarian tumors


title: 1913

description: frozen tissue of ovarian tumors


title: 2063_b

description: frozen tissue of ovarian tumors


title: 1024_b

description: frozen tissue of ovarian tumors


title: 1578

description: frozen tissue of ovarian tumors


title: Rb knockout mouse tumor(replicate6)

description: frozen tissue of primary tumors

organism: Mus musculus

source_name: frozen tissue from mouse tumor

tag: Rb knockout mouse tumor(replicate6)


title: Rb knockout mouse tumor(replicate5)

description: frozen tissue of primary tumors

tag: Rb knockout mouse tumor(replicate5)


title: 1877_a

description: frozen tissue of ovarian tumors


title: 2064

description: frozen tissue of ovarian tumors


title: 2673_a

description: frozen tissue of ovarian tumors


title: 1929

description: frozen tissue of ovarian tumors


title: Rb knockout mouse tumor(replicate2)

description: frozen tissue of primary tumors

tag: Rb knockout mouse tumor(replicate2)


title: 1590

description: frozen tissue of ovarian tumors


title: 1504

description: frozen tissue of ovarian tumors


title: 3142

description: frozen tissue of ovarian tumors


title: 2324

description: frozen tissue of ovarian tumors


title: 1774

description: frozen tissue of ovarian tumors


title: 1665

description: frozen tissue of ovarian tumors


title: Rb knockout mouse tumor (replicate1)

description: frozen tissue of primary tumors

tag: Rb knockout mouse tumor (replicate1)


title: 1623

description: frozen tissue of ovarian tumors


title: Rb knockout mouse tumor(replicate3)

description: frozen tissue of primary tumors

tag: Rb knockout mouse tumor(replicate3)


title: 2967

description: frozen tissue of ovarian tumors


title: 1674

description: frozen tissue of ovarian tumors


title: 2999

description: frozen tissue of ovarian tumors


title: 2739_a

description: frozen tissue of ovarian tumors


title: 1858

description: frozen tissue of ovarian tumors


title: 2465

description: frozen tissue of ovarian tumors


title: 2422

description: frozen tissue of ovarian tumors


title: 2505_b

description: frozen tissue of ovarian tumors


title: Rb knockout mouse tumor(replicate4)

description: frozen tissue of primary tumors

tag: Rb knockout mouse tumor(replicate4)


title: 1675

description: frozen tissue of ovarian tumors


title: Mouse transgenic tumor driven by Ras(replicate3) expression

description: frozen tissue of primary tumors


title: 98-771

description: frozen tissue of primary lung tumors

source_name: frozen tissue of primary lung tumor

value: Cell type:A; Surv(months):68.33333333; STATUS(0=alive, 1=dead):0


title: 1615

description: frozen tissue of ovarian tumors


title: Mouse transgenic tumor driven by Myc (replicate5) expression

description: frozen tissue of primary tumors


title: Mouse transgenic tumor driven by Ras(replicate2) expression

description: frozen tissue of primary tumors


title: Mouse transgenic tumor driven by Ras(replicate1) expression

description: frozen tissue of primary tumors


title: 0.08

description: frozen tissue of ovarian tumors


title: 2204

description: frozen tissue of ovarian tumors


title: 2075

description: frozen tissue of ovarian tumors


title: Mouse transgenic tumor driven by Myc (replicate4) expression

description: frozen tissue of primary tumors


title: 1834

description: frozen tissue of ovarian tumors


title: 860

description: frozen tissue of ovarian tumors


title: Mouse transgenic tumor driven by Myc (replicate1) expression

description: frozen tissue of primary tumors


title: 2419

description: frozen tissue of ovarian tumors


title: Mouse transgenic tumor driven by Myc (replicate3) expression

description: frozen tissue of primary tumors


title: Mouse transgenic tumor driven by Myc (replicate2) expression

description: frozen tissue of primary tumors


title: 872

description: frozen tissue of ovarian tumors


title: 1846

description: frozen tissue of ovarian tumors


title: Wild type tissue(replicate7)

description: frozen tissue

source_name: frozen tissue from normal mouse

tag: Wild type tissue(replicate7)


title: Wild type tissue(replicate6)

description: frozen tissue

tag: Wild type tissue(replicate6)


title: Wild type tissue(replicate5)

description: frozen tissue

tag: Wild type tissue(replicate5)


title: 1451

description: frozen tissue of ovarian tumors


title: Rb knockout mouse tumor(replicate5) B

description: frozen tissue of primary tumors


title: 1526

description: frozen tissue of ovarian tumors


title: Mouse transgenic tumor driven by Ras(replicate3) B expression

description: frozen tissue of primary tumors

tag: Mouse transgenic tumor driven by Ras(replicate3) expression


title: Mouse transgenic tumor driven by Ras(replicate2) B expression

description: frozen tissue of primary tumors

tag: Mouse transgenic tumor driven by Ras(replicate2) expression


title: Rb knockout mouse tumor(replicate6) B

description: frozen tissue of primary tumors


title: Wild type tissue(replicate4)

description: frozen tissue

tag: Wild type tissue(replicate4)


title: Rb knockout mouse tumor(replicate2) B

description: frozen tissue of primary tumors


title: Rb knockout mouse tumor(replicate4) B

description: frozen tissue of primary tumors


title: 922

description: frozen tissue of ovarian tumors


title: 1784

description: frozen tissue of ovarian tumors


title: Rb knockout mouse tumor(replicate3) B

description: frozen tissue of primary tumors


title: Rb knockout mouse tumor (replicate1) B

description: frozen tissue of primary tumors


title: Mouse transgenic tumor driven by Myc (replicate5) B expression

description: frozen tissue of primary tumors

tag: Mouse transgenic tumor driven by Myc (replicate5) expression


title: Wild type tissue(replicate3)

description: frozen tissue

tag: Wild type tissue(replicate3)


title: Mouse transgenic tumor driven by HER2 (replicate 7) expression

description: frozen tissue of primary tumors


title: Wild type tissue(replicate1)

description: frozen tissue

tag: Wild type tissue(replicate1)


title: Mouse transgenic tumor driven by Myc (replicate3) B expression

description: frozen tissue of primary tumors

tag: Mouse transgenic tumor driven by Myc (replicate3) expression


title: Mouse transgenic tumor driven by Myc (replicate2) B expression

description: frozen tissue of primary tumors

tag: Mouse transgenic tumor driven by Myc (replicate2) expression


title: Mouse transgenic tumor driven by Ras(replicate1) B expression

description: frozen tissue of primary tumors

tag: Mouse transgenic tumor driven by Ras(replicate1) expression


title: Mouse transgenic tumor driven by Myc (replicate1) B expression

description: frozen tissue of primary tumors

tag: Mouse transgenic tumor driven by Myc (replicate1) expression


title: Wild type tissue(replicate7) B

description: frozen tissue


title: Wild type tissue(replicate2)

description: frozen tissue

tag: Wild type tissue(replicate2)


title: Mouse transgenic tumor driven by HER2 (replicate 6) expression

description: frozen tissue of primary tumors


title: Mouse transgenic tumor driven by HER2 (replicate 5) expression

description: frozen tissue of primary tumors


title: Wild type tissue(replicate3) B

description: frozen tissue


title: Mouse transgenic tumor driven by Myc (replicate4) B expression

description: frozen tissue of primary tumors

tag: Mouse transgenic tumor driven by Myc (replicate4) expression


title: Wild type tissue(replicate2) B

description: frozen tissue


title: Wild type tissue(replicate6) B

description: frozen tissue


title: Wild type tissue(replicate5) B

description: frozen tissue


title: Wild type tissue(replicate4) B

description: frozen tissue


title: Mouse transgenic tumor driven by HER2 (replicate 7) B expression

description: frozen tissue of primary tumors

tag: Mouse transgenic tumor driven by HER2 (replicate 7) expression


title: Mouse transgenic tumor driven by HER2 (replicate 2) expression

description: frozen tissue of primary tumors


title: Mouse transgenic tumor driven by HER2 (replicate 1) B expression

description: frozen tissue of primary tumors

tag: Mouse transgenic tumor driven by HER2 (replicate 1) expression


title: Mouse transgenic tumor driven by HER2 (replicate 1) expression

description: frozen tissue of primary tumors


title: Mouse transgenic tumor driven by HER2 (replicate 6) B expression

description: frozen tissue of primary tumors

tag: Mouse transgenic tumor driven by HER2 (replicate 6) expression


title: Mouse transgenic tumor driven by HER2 (replicate 3) B expression

description: frozen tissue of primary tumors

tag: Mouse transgenic tumor driven by HER2 (replicate 3) expression


title: Mouse transgenic tumor driven by HER2 (replicate 4) B expression

description: frozen tissue of primary tumors

tag: Mouse transgenic tumor driven by HER2 (replicate 4) expression


title: Mouse transgenic tumor driven by HER2 (replicate 5) B expression

description: frozen tissue of primary tumors

tag: Mouse transgenic tumor driven by HER2 (replicate 5) expression


title: Mouse transgenic tumor driven by HER2 (replicate 4) expression

description: frozen tissue of primary tumors


title: Mouse transgenic tumor driven by HER2 (replicate 2) B expression

description: frozen tissue of primary tumors

tag: Mouse transgenic tumor driven by HER2 (replicate 2) expression


title: Mouse transgenic tumor driven by HER2 (replicate 3) expression

description: frozen tissue of primary tumors


title: Wild type tissue(replicate1) B

description: frozen tissue


title: 1-11 Mu11KsubB_48hr TCL

status: Public on Nov 05 2005

city: Stanford

first: Lawrence

last: Steinman

state: CA

address: 279 Campus Drive, Rm B002

department: Neurology and Neurological Sciences

institute: Stanford University School of Medicine

description: Double stranded cDNA was generated from total RNA extracted from MBP Ac 11-11 activated purified CD4+ T cells.  Biotinylated cRNA was manufactured by in vitro transcription and hybridized to the Affymetrix genechip murine Mu11k set according to the manufacturer’s protocols.

data_processing: Affymetrix MAS4.0

label: biotinylated CTP and UTP

source_name: MBP Ac1-11 CD4+ TCL 48hr

tag: Strain

value: B10.PL MBP Ac1-11 TCR Transgenic

tag: Gender

value: female

tag: Tissue

value: Spleen and lymph node

tag: Cell type

value: CD4+ T cell purified


title: 1-11Mu11ksubA_48hrTCL

value: B10.PL MBP Ac1-11 TCR transgenics

value: Female

value: spleen and lymph node


title: OI/II+N, ghA23scan1.gpr

status: Public on Nov 03 2005

city: Canberra

first: Andrew

last: Spriggs

state: ACT

address: GPO Box 1600

department: Bioinformatics Group

country: Australia

institute: CSIRO Plant Industry

description:
Comparisons of DP16 0 dpa ovule outer integument to inner integument and nucellus
Biological Replicate: 2, Technical Replicate: 1, Dye Swapped: true

data_processing: Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.

organism: Gossypium hirsutum

source_name: inner integument and nucellus

tag: inner integument and nucellus, Biological Repl

value: 2, Technical repl:1

source_name: outer integument

tag: outer integument, Biological Repl


title: fl/Xu-142, ghA64scan1.gpr

description:
0 dpa ovule comparisons
Biological Replicate: 1, Technical Replicate: 2, Dye Swapped: true

tag: Xu-142, Biological Repl

value: 1, Technical repl:2

source_name: fl

tag: fl, Biological Repl


title: OI/II+N, ghA15scan1.gpr

description:
Comparisons of DP16 0 dpa ovule outer integument to inner integument and nucellus
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: false

value: 1, Technical repl:1


title: fl/Xu-142, ghA63scan1.gpr

description:
0 dpa ovule comparisons
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: false


title: fl/Xu-142, ghA65scan1.gpr

description:
0 dpa ovule comparisons
Biological Replicate: 2, Technical Replicate: 1, Dye Swapped: false


title: OI/II+N, ghA16scan1.gpr

description:
Comparisons of DP16 0 dpa ovule outer integument to inner integument and nucellus
Biological Replicate: 1, Technical Replicate: 2, Dye Swapped: true


title: SL1-7-1/DP16, ghA49scan1.gpr

description:
0 dpa ovule comparisons
Biological Replicate: 3, Technical Replicate: 1, Dye Swapped: false

tag: SL 1-7-1, Biological Repl

value: 3, Technical repl:1

tag: DP16, Biological Repl


title: 5B/DP16, ghA40scan1.gpr

tag: 5B, Biological Repl


title: 5B/DP16, ghA54scan1.gpr

description:
0 dpa ovule comparisons
Biological Replicate: 2, Technical Replicate: 2, Dye Swapped: false

value: 2, Technical repl:2


title: 53/DP16, ghA44scan1.gpr

description:
0 dpa ovule comparisons
Biological Replicate: 2, Technical Replicate: 2, Dye Swapped: true

tag: 53, Biological Repl


title: 53/DP16, ghA35scan1.gpr


title: SL1-7-1/DP16, ghA47scan1.gpr


title: fl/Xu-142, ghA66scan1.gpr


title: 53/DP16, ghA36scan1.gpr


title: SL1-7-1/DP16, ghA38scan1.gpr


title: SL1-7-1/DP16, ghA48scan1.gpr


title: 5B/DP16, ghA53scan1.gpr

description:
0 dpa ovule comparisons
Biological Replicate: 2, Technical Replicate: 1, Dye Swapped: true


title: OI/II+N, ghA24scan1.gpr

description:
Comparisons of DP16 0 dpa ovule outer integument to inner integument and nucellus
Biological Replicate: 2, Technical Replicate: 2, Dye Swapped: false


title: 5B/DP16, ghA39scan1.gpr


title: 1A/DP16, ghA52scan1.gpr

description:
0 dpa ovule comparisons
Biological Replicate: 4, Technical Replicate: 2, Dye Swapped: true

value: 4, Technical repl:2

tag: 1A, Biological Repl


title: 53/DP16, ghA43scan1.gpr


title: 1A/DP16, ghA33scan1.gpr


title: SL1-7-1/DP16, ghA50scan1.gpr

description:
0 dpa ovule comparisons
Biological Replicate: 3, Technical Replicate: 2, Dye Swapped: true

value: 3, Technical repl:2


title: 1A/DP16, ghA51scan1.gpr

description:
0 dpa ovule comparisons
Biological Replicate: 4, Technical Replicate: 1, Dye Swapped: false

value: 4, Technical repl:1


title: SL1-7-1/DP16, ghA37scan1.gpr


title: 1A/DP16, ghA41scan1.gpr


title: 1A/DP16, ghA45scan1.gpr


title: 1A/DP16, ghA34scan1.gpr


title: 1A/DP16, ghA46scan1.gpr


title: 1A/DP16, ghA42scan1.gpr


title: 4A/DP16, ghA19scan1.gpr

tag: 4A, Biological Repl


title: 4A/DP16, ghA13scan1.gpr


title: 4A/DP16, ghA05scan1.gpr

description:
0 dpa ovule comparisons
Biological Replicate: 1, Technical Replicate: 4, Dye Swapped: true

value: 1, Technical repl:4


title: 4A/DP16, ghA04scan1.gpr

description:
0 dpa ovule comparisons
Biological Replicate: 1, Technical Replicate: 3, Dye Swapped: false

value: 1, Technical repl:3


title: Gene Expression effects from dyssynchrony in left ventricle of mouse heart - biological replicate3

city: Germantown

first: Will

last: Ferguson

state: MD

department: Integrated Biology Solutions

institute: Agilent Technologies

description: A hyb of 2 samples isolated from the left ventricle of the heart

data_processing: Agilent Feature Extraction v7.5

source_name: 5S -Septal Wall

tag: RNA from septal wall

source_name: 5L - Lateral Wall

tag: RNA from lateral wall


title: 4A/DP16, ghA03scan1.gpr


title: 4A/DP16, ghA14scan1.gpr


title: DP16 2dpa/0dpa, ghA58scan1.gpr

description:
DP16 ovules of 2 dpa compared to 0 dpa
Biological Replicate: 1, Technical Replicate: 2, Dye Swapped: true

source_name: DP16 0 dpa ovules

tag: DP16 0 dpa ovules, Biological Repl

source_name: DP16 2 dpa ovules

tag: DP16 2 dpa ovules, Biological Repl


title: DP16 2dpa/0dpa, ghA60scan1.gpr

description:
DP16 ovules of 2 dpa compared to 0 dpa
Biological Replicate: 2, Technical Replicate: 1, Dye Swapped: false


title: 4A/DP16, ghA20scan1.gpr


title: DP16 -2dpa/0dpa, ghA17scan1.gpr

description:
DP16 ovules of -2 dpa compared to 0 dpa.
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: false

source_name: DP16 -2 dpa ovules

tag: DP16 -2 dpa ovules, Biological Repl


title: DP16 -2dpa/0dpa, ghA32scan1.gpr

description:
DP16 ovules of -2 dpa compared to 0 dpa.
Biological Replicate: 2, Technical Replicate: 2, Dye Swapped: true


title: Gene Expression effects from dyssynchrony in left ventricle of mouse heart - biological replicate3 -dye flip

hyb_protocol: this is a dye flip

source_name: 5L -Lateral Wall

source_name: 5S - Septal Wall


title: DP16 -4dpa/0dpa, ghA30scan1.gpr

description:
DP16 ovules of -4 dpa compared to 0 dpa
Biological Replicate: 2, Technical Replicate: 2, Dye Swapped: true

source_name: DP16 -4 dpa ovules

tag: DP16 -4 dpa ovules, Biological Repl


title: DP16 -4dpa/0dpa, ghA27scan1.gpr

description:
DP16 ovules of -4 dpa compared to 0 dpa
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: false


title: DP16 2dpa/0dpa, ghA57scan1.gpr

description:
DP16 ovules of 2 dpa compared to 0 dpa
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: false


title: DP16 2dpa/0dpa, ghA61scan1.gpr

description:
DP16 ovules of 2 dpa compared to 0 dpa
Biological Replicate: 2, Technical Replicate: 2, Dye Swapped: true


title: DP16 0 DPA/DP16 0DPA, ghA59scan1.gpr

description:
DP16 0 dpa ovule self comparisons
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: false

source_name: DP16 0 dpa ovule

tag: DP16 0 dpa ovule, Biological Repl


title: DP16 -2dpa/0dpa, ghA18scan1.gpr

description:
DP16 ovules of -2 dpa compared to 0 dpa.
Biological Replicate: 1, Technical Replicate: 2, Dye Swapped: true


title: DP16 0 DPA/DP16 0DPA, ghA67scan3.gpr

description:
DP16 0 dpa ovule self comparisons
Biological Replicate: 3, Technical Replicate: 1, Dye Swapped: false


title: 4A/DP16, ghA01scan2n.gpr

description:
0 dpa ovule comparisons
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: false


title: DP16 -4dpa/0dpa, ghA28scan1.gpr

description:
DP16 ovules of -4 dpa compared to 0 dpa
Biological Replicate: 1, Technical Replicate: 2, Dye Swapped: true


title: DP16 -2dpa/0dpa, ghA31scan1.gpr

description:
DP16 ovules of -2 dpa compared to 0 dpa.
Biological Replicate: 2, Technical Replicate: 1, Dye Swapped: false


title: Gene Expression effects from dyssynchrony in left ventricle of mouse heart - biological replicate2 - dye flip

source_name: 4L -Lateral Wall

source_name: 4S - Septal Wall


title: DP16 0 DPA/DP16 0DPA, ghA62scan2.gpr

description:
DP16 0 dpa ovule self comparisons
Biological Replicate: 2, Technical Replicate: 1, Dye Swapped: false


title: DP16 -4dpa/0dpa, ghA29scan1.gpr

description:
DP16 ovules of -4 dpa compared to 0 dpa
Biological Replicate: 2, Technical Replicate: 1, Dye Swapped: false


title: Gene Expression effects from dyssynchrony in left ventricle of mouse heart - biological replicate - dye flip

description: A hyb of 2 samples isolated from the left ventricle of the heart

source_name: 3L -Lateral Wall

source_name: 3S - Septal Wall


title: CHX +/- Comparison, ghA06scan1.gpr

description:
Cycloheximide treatment of cotton ovules
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: false

source_name: CHX +

tag: CHX +, Biological Repl

source_name: CHX -

tag: CHX -, Biological Repl


title: Gene Expression effects from dyssynchrony - pooled control

source_name: PNS

tag: pooled control RNA

source_name: PNL


title: CHX +/- Comparison, ghA07scan1.gpr

description:
Cycloheximide treatment of cotton ovules
Biological Replicate: 1, Technical Replicate: 2, Dye Swapped: true


title: Gene Expression effects from dyssynchrony in left ventricle of mouse heart - biological replicate 2

source_name: 4S -Septal Wall

source_name: 4L - Lateral Wall


title: GM12891_rep1

status: Public on Oct 27 2005

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

description: Sample description = RNA was extracted from lymphoblastoid cells of the CEPH individuals from the International HapMap Project.  The cells were grown at a density of 5 x 105 cells/ ml in RPMI 1640 with 15% FBS, 1% penicillin-streptomycin, 2mM L-glutamine at 37°C in a humidified 5% CO2 chamber.  RNA samples were processed and hybridized onto the Affymetrix Human Focus Arrays according to the manufacturer’s suggestion.  Arrays were scanned and analyzed using MAS 5.0 software (Affymetrix).  Expression intensity was sclaed to 500 and log2 transformed.

source_name: Lymphoblastoid cell line

tag: Coriell cell line repository identifier


title: GM12892_rep1


title: GM12057_rep1


title: CHX +/- Comparison, ghA76scan1.gpr

description:
Cycloheximide treatment of cotton ovules
Biological Replicate: 3, Technical Replicate: 1, Dye Swapped: false


title: Gene Expression effects from dyssynchrony in left ventricle of mouse heart - biological replicate

source_name: 3S -Septal Wall

source_name: 3L - Lateral Wall


title: GM12004_rep1


title: Gene Expression effects from dyssynchrony - pooled control - dye flip

description: Total RNA was extracted with TRIzol reagent from LV segments, and septal and lateral isolates from the 4 dyssynchronous mice were kept separate. RNA from the synchronous mice were pooled into a control septal and lateral sample.  Functional genomic analysis was conducted on these 10 RNA samples with fluorophore reversal, such that each sample was assayed on two different microarrays.  Corresponding septal and lateral samples from the same heart were paired on the same microarray to enhance signal/noise for assessing relative gene expression.

hyb_protocol: This is a dye flip

tag: pooled control


title: GM12003_rep1


title: GM12005_rep1


title: GM12717_rep1


title: Gene Expression effects from dyssynchrony in left ventricle of mouse heart between septal and lateral walls

source_name: 1S -Septal Wall

source_name: 1L - Lateral Wall


title: GM11839_rep1


title: GM11830_rep1


title: GM11832_rep1


title: GM12056_rep1


title: GM12234_rep1


title: GM11831_rep1


title: GM12006_rep1


title: CHX +/- Comparison, ghA75scan1.gpr

description:
Cycloheximide treatment of cotton ovules
Biological Replicate: 2, Technical Replicate: 2, Dye Swapped: true


title: Gene Expression effects from dyssynchrony in left ventricle of mouse heart between lateral and septal walls

source_name: 1L -Lateral Wall

source_name: 1S- Septal Wall


title: GM11829_rep1


title: CHX +/- Comparison, ghA77scan1.gpr

description:
Cycloheximide treatment of cotton ovules
Biological Replicate: 3, Technical Replicate: 2, Dye Swapped: true


title: CHX +/- Comparison, ghA74scan1.gpr

description:
Cycloheximide treatment of cotton ovules
Biological Replicate: 2, Technical Replicate: 1, Dye Swapped: false


title: GM12716_rep1


title: Patient sample ST140, Sarcoma, NOS

status: Public on Oct 11 2005

city: Bethesda

first: Sean

last: Davis

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

description:
Diagnosis: Sarcoma, NOS
Keywords = sarcoma, cDNA, Sarcoma, NOS

source_name: Sarcoma, NOS

source_name: Pooled sarcoma cell lines


title: Patient sample ST380, Malignant Fibrous Histiocytoma

description:
Diagnosis: Malignant Fibrous Histiocytoma
Keywords = sarcoma, cDNA, Malignant Fibrous Histiocytoma

source_name: Malignant Fibrous Histiocytoma


title: Patient sample ST302, Liposarcoma

description:
Diagnosis: Liposarcoma
Keywords = sarcoma, cDNA, Liposarcoma

source_name: Liposarcoma


title: Patient sample ST169, Malignant Fibrous Histiocytoma


title: Patient sample ST146, Sarcoma, NOS


title: Patient sample ST114, Malignant Fibrous Histiocytoma


title: Patient sample ST134, Gastrointestinal Stromal Tumor

description:
Diagnosis: Gastrointestinal Stromal Tumor
Keywords = sarcoma, cDNA, Gastrointestinal Stromal Tumor

source_name: Gastrointestinal Stromal Tumor


title: Patient sample ST281, Dermatofibrosarcoma

description:
Diagnosis: Dermatofibrosarcoma
Keywords = sarcoma, cDNA, Dermatofibrosarcoma

source_name: Dermatofibrosarcoma


title: Patient sample ST84, Malignant Fibrous Histiocytoma


title: Patient sample ST233, Gastrointestinal Stromal Tumor


title: Patient sample ST395, Malignant Fibrous Histiocytoma


title: Patient sample ST305, Malignant Fibrous Histiocytoma


title: Patient sample ST401, Ewing Sarcoma

description:
Diagnosis: Ewing Sarcoma
Keywords = sarcoma, cDNA, Ewing Sarcoma

source_name: Ewing Sarcoma


title: Patient sample ST248, Liposarcoma


title: Patient sample ST70, Fibrosarcoma

description:
Diagnosis: Fibrosarcoma
Keywords = sarcoma, cDNA, Fibrosarcoma

source_name: Fibrosarcoma


title: Patient sample ST429, Synovial Cell Sarcoma

description:
Diagnosis: Synovial Cell Sarcoma
Keywords = sarcoma, cDNA, Synovial Cell Sarcoma

source_name: Synovial Cell Sarcoma


title: Patient sample ST353, Liposarcoma


title: Patient sample ST1, Malignant Fibrous Histiocytoma


title: Patient sample ST322, Rhabdomyosarcoma

description:
Diagnosis: Rhabdomyosarcoma
Keywords = sarcoma, cDNA, Rhabdomyosarcoma

source_name: Rhabdomyosarcoma


title: Patient sample ST412, Rhabdomyosarcoma


title: Patient sample ST44, Fibrosarcoma


title: Patient sample ST273, Clear Cell Sarcoma

description:
Diagnosis: Clear Cell Sarcoma
Keywords = sarcoma, cDNA, Clear Cell Sarcoma

source_name: Clear Cell Sarcoma


title: Patient sample ST432, Synovial Cell Sarcoma


title: Patient sample ST411, Ewing Sarcoma


title: Patient sample ST405, Ewing Sarcoma


title: Patient sample ST64, Leiomyosarcoma

description:
Diagnosis: Leiomyosarcoma
Keywords = sarcoma, cDNA, Leiomyosarcoma

source_name: Leiomyosarcoma


title: Patient sample ST87, Malignant Fibrous Histiocytoma


title: Patient sample ST366, Liposarcoma


title: Patient sample ST423, Synovial Cell Sarcoma


title: Patient sample ST253, Liposarcoma


title: Patient sample ST271, Dermatofibrosarcoma


title: Patient sample ST62, Leiomyosarcoma


title: Patient sample ST341, Leiomyosarcoma


title: Patient sample ST231, Malignant Fibrous Histiocytoma


title: Patient sample ST219, Sarcoma, NOS


title: Patient sample ST42, Liposarcoma


title: Patient sample ST90, Malignant Fibrous Histiocytoma


title: Patient sample ST351, Liposarcoma


title: Patient sample ST420, Ewing Sarcoma


title: Patient sample ST69, Malignant Fibrous Histiocytoma


title: Patient sample ST347, Sarcoma, NOS


title: Patient sample ST393, Malignant Fibrous Histiocytoma


title: Patient sample ST81, Schwannoma

description:
Diagnosis: Schwannoma
Keywords = sarcoma, cDNA, Schwannoma

source_name: Schwannoma


title: Patient sample ST79, Schwannoma


title: Patient sample ST229, Malignant Fibrous Histiocytoma


title: Patient sample ST226, Gastrointestinal Stromal Tumor


title: Patient sample ST427, Synovial Cell Sarcoma


title: Patient sample ST102, Liposarcoma


title: Patient sample ST425, Synovial Cell Sarcoma


title: Patient sample ST400, Ewing Sarcoma


title: Patient sample ST373, Malignant Fibrous Histiocytoma


title: Patient sample ST294, Liposarcoma


title: Patient sample ST336, Liposarcoma


title: Patient sample ST215, Sarcoma, NOS


title: Patient sample ST348, Liposarcoma


title: Patient sample ST310, Sarcoma, NOS


title: Patient sample ST415, Rhabdomyosarcoma


title: Patient sample ST48, Liposarcoma


title: Patient sample ST175, Malignant Fibrous Histiocytoma


title: Patient sample ST88, Malignant Fibrous Histiocytoma


title: Patient sample ST284, Leiomyosarcoma


title: Patient sample ST118, Schwannoma


title: Patient sample ST343, Liposarcoma


title: Patient sample ST133, Sarcoma, NOS


title: Patient sample ST274, Leiomyosarcoma


title: Patient sample ST369, Liposarcoma


title: Patient sample ST291, Osteosarcoma

description:
Diagnosis: Osteosarcoma
Keywords = sarcoma, cDNA, Osteosarcoma

source_name: Osteosarcoma


title: Patient sample ST406, Ewing Sarcoma


title: Patient sample ST338, Malignant Hemangiopericytoma

description:
Diagnosis: Malignant Hemangiopericytoma
Keywords = sarcoma, cDNA, Malignant Hemangiopericytoma

source_name: Malignant Hemangiopericytoma


title: Patient sample ST52, Malignant Fibrous Histiocytoma


title: Patient sample ST150, Malignant Hemangiopericytoma


title: Patient sample ST417, Ewing Sarcoma


title: Patient sample ST397, Malignant Fibrous Histiocytoma


title: Patient sample ST247, Liposarcoma


title: Patient sample ST279, Dermatofibrosarcoma


title: Patient sample ST243, Liposarcoma


title: Patient sample ST153, Fibrosarcoma


title: Patient sample ST166, Leiomyosarcoma


title: Patient sample ST103, Leiomyosarcoma


title: Patient sample ST240, Fibrosarcoma


title: Patient sample ST357, Liposarcoma


title: Patient sample ST65, Synovial Cell Sarcoma


title: Patient sample ST419, Ewing Sarcoma


title: Patient sample ST312, Leiomyosarcoma


title: Patient sample ST433, Synovial Cell Sarcoma


title: Patient sample ST430, Synovial Cell Sarcoma


title: Patient sample ST317, Malignant Peripheral Nerve Sheath Tumor

description:
Diagnosis: Malignant Peripheral Nerve Sheath Tumor
Keywords = sarcoma, cDNA, Malignant Peripheral Nerve Sheath Tumor

source_name: Malignant Peripheral Nerve Sheath Tumor


title: Patient sample ST404, Ewing Sarcoma


title: Patient sample ST413, Rhabdomyosarcoma


title: Patient sample ST375, Malignant Fibrous Histiocytoma


title: Patient sample ST121, Synovial Cell Sarcoma


title: Patient sample ST354, Liposarcoma


title: Patient sample ST361, Liposarcoma


title: Patient sample ST377, Malignant Fibrous Histiocytoma


title: Patient sample ST424, Synovial Cell Sarcoma


title: Patient sample ST295, Synovial Cell Sarcoma


title: Patient sample ST138, Liposarcoma


title: Patient sample ST212, Malignant Hemangiopericytoma


title: Patient sample ST113, Malignant Fibrous Histiocytoma


title: Patient sample ST21, Dermatofibrosarcoma


title: Patient sample ST187, Liposarcoma


title: Patient sample ST266, Leiomyosarcoma


title: Patient sample ST408, Ewing Sarcoma


title: Patient sample ST428, Synovial Cell Sarcoma


title: Patient sample ST407, Ewing Sarcoma


title: Patient sample ST155, Malignant Fibrous Histiocytoma


title: Patient sample ST116, Malignant Peripheral Nerve Sheath Tumor


title: Patient sample ST422, Ewing Sarcoma


title: Patient sample ST402, Ewing Sarcoma


title: Patient sample ST287, Osteosarcoma


title: Patient sample ST160, Sarcoma, NOS


title: Patient sample ST163, Liposarcoma


title: Patient sample ST350, Liposarcoma


title: Patient sample ST68, Leiomyosarcoma


title: Patient sample ST234, Malignant Peripheral Nerve Sheath Tumor


title: Patient sample ST426, Synovial Cell Sarcoma


title: Patient sample ST141, Gastrointestinal Stromal Tumor


title: Patient sample ST232, Synovial Cell Sarcoma


title: Patient sample ST333, Ewing Sarcoma


title: Patient sample ST421, Ewing Sarcoma


title: Patient sample ST272, Malignant Hemangiopericytoma


title: Patient sample ST416, Rhabdomyosarcoma


title: Patient sample ST339, Leiomyosarcoma


title: Patient sample ST390, Malignant Fibrous Histiocytoma


title: Patient sample ST5, Malignant Fibrous Histiocytoma


title: Patient sample ST275, Leiomyosarcoma


title: Patient sample ST289, Osteosarcoma


title: Patient sample ST214, Malignant Hemangiopericytoma


title: Patient sample ST178, Liposarcoma


title: Patient sample ST342, Liposarcoma


title: Patient sample ST246, Liposarcoma


title: Patient sample ST355, Liposarcoma


title: Patient sample ST242, Osteosarcoma


title: Patient sample ST346, Liposarcoma


title: Patient sample ST403, Ewing Sarcoma


title: Patient sample ST290, Malignant Peripheral Nerve Sheath Tumor


title: Patient sample ST431, Synovial Cell Sarcoma


title: Patient sample ST409, Ewing Sarcoma


title: Patient sample ST147, Mullerian

description:
Diagnosis: Mullerian
Keywords = sarcoma, cDNA, Mullerian

source_name: Mullerian


title: Patient sample ST285, Osteosarcoma


title: Patient sample ST196, Leiomyosarcoma


title: Patient sample ST217, Fibrosarcoma


title: Patient sample ST105, Mullerian


title: Patient sample ST13, Leiomyosarcoma


title: Patient sample ST161, Liposarcoma


title: Patient sample ST283, Chondrosarcoma

description:
Diagnosis: Chondrosarcoma
Keywords = sarcoma, cDNA, Chondrosarcoma

source_name: Chondrosarcoma


title: Patient sample ST89, Leiomyosarcoma

source_name: Pooled sarcoma cell lines


title: Patient sample ST230, Gastrointestinal Stromal Tumor


title: Patient sample ST337, Synovial Cell Sarcoma


title: Patient sample ST165, Malignant Fibrous Histiocytoma

source_name: Malignant Fibrous Histiocytoma


title: Patient sample ST71, Malignant Fibrous Histiocytoma


title: Patient sample ST225, Leiomyosarcoma


title: Patient sample ST345, Liposarcoma

source_name: Liposarcoma


title: Patient sample ST85, Malignant Fibrous Histiocytoma


title: Patient sample ST221, Fibrosarcoma


title: Patient sample ST418, Ewing Sarcoma


title: Patient sample ST132, Alveolar Soft Part Sarcoma

description:
Diagnosis: Alveolar Soft Part Sarcoma
Keywords = sarcoma, cDNA, Alveolar Soft Part Sarcoma

source_name: Alveolar Soft Part Sarcoma


title: Patient sample ST16, Leiomyosarcoma


title: Patient sample ST110, Malignant Fibrous Histiocytoma

description:
Diagnosis: Malignant Fibrous Histiocytoma
Keywords = sarcoma, cDNA, Malignant Fibrous Histiocytoma


title: Patient sample ST293, Malignant Peripheral Nerve Sheath Tumor


title: Patient sample ST309, Malignant Fibrous Histiocytoma


title: Patient sample ST367, Liposarcoma

description:
Diagnosis: Liposarcoma
Keywords = sarcoma, cDNA, Liposarcoma


title: Patient sample ST398, Malignant Fibrous Histiocytoma


title: Patient sample ST32, Liposarcoma


title: Patient sample ST6, Malignant Fibrous Histiocytoma


title: Patient sample ST410, Ewing Sarcoma


title: Patient sample ST37, Liposarcoma


title: Patient sample ST130, Sarcoma, NOS

description:
Diagnosis: Sarcoma, NOS
Keywords = sarcoma, cDNA, Sarcoma, NOS

source_name: Sarcoma, NOS


title: Patient sample ST278, Fibrosarcoma


title: Patient sample ST168, Malignant Fibrous Histiocytoma


title: Patient sample ST414, Rhabdomyosarcoma


title: Patient sample ST18, Dermatofibrosarcoma

description:
Diagnosis: Dermatofibrosarcoma
Keywords = sarcoma, cDNA, Dermatofibrosarcoma

source_name: Dermatofibrosarcoma


title: Xba-SR

status: Public on Jul 02 2005

type: genomic

city: Boston

first: William

last: Sellers

address: 44 Binney Street

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: leukemia cell line

molecule: genomic DNA


title: Xba-UO-31

description: renal cancer cell line


title: UO-31

description: renal cancer cell line


title: CAKI-1

description: renal cancer cell line


title: Patient sample ST2, Malignant Fibrous Histiocytoma


title: ACHN

description: renal cancer cell line


title: SN12C

description: renal cancer cell line


title: Xba-SN12C

description: renal cancer cell line


title: Xba-MOLT-4

description: leukemia cell line


title: Xba-TK-10

description: renal cancer cell line


title: TK-10

description: renal cancer cell line


title: 786-O

description: renal cancer cell line


title: Xba-ACHN

description: renal cancer cell line


title: Xba-A498

description: renal cancer cell line


title: Xba-CAKI-1

description: renal cancer cell line


title: Xba-786-O

description: renal cancer cell line


title: PC-3

description: prostate cancer cell line


title: DU-145

description: prostate cancer cell line


title: OVCAR-8

description: ovarian cancer cell line


title: SK-OV-3

description: ovarian cancer cell line


title: Xba-DU-145

description: prostate cancer cell line


title: OVCAR-5

description: ovarian cancer cell line


title: Xba-PC-3

description: prostate cancer cell line


title: Xba-OVCAR-8

description: ovarian cancer cell line


title: Xba-OVCAR-4

description: ovarian cancer cell line


title: Xba-OVCAR-5

description: ovarian cancer cell line


title: OVCAR-4

description: ovarian cancer cell line


title: Xba-OVCAR-3

description: ovarian cancer cell line


title: IGROV1

description: ovarian cancer cell line


title: A498

description: renal cancer cell line


title: NCI-H226

description: non-small cell lung cancer cell line


title: Xba-NCI-H460

description: non-small cell lung cancer cell line


title: NCI-H522

description: non-small cell lung cancer cell line


title: Xba-SK-OV-3

description: ovarian cancer cell line


title: Xba-NCI-H522

description: non-small cell lung cancer cell line


title: NCI-H322M

description: non-small cell lung cancer cell line


title: Xba-NCI-H322M

description: non-small cell lung cancer cell line


title: HOP-62

description: non-small cell lung cancer cell line


title: HOP-92

description: non-small cell lung cancer cell line


title: Xba-NCI-H23

description: non-small cell lung cancer cell line


title: NCI-H23

description: non-small cell lung cancer cell line


title: Xba-HOP-92

description: non-small cell lung cancer cell line


title: Xba-IGROV1

description: ovarian cancer cell line


title: EKVX

description: non-small cell lung cancer cell line


title: Xba-EKVX

description: non-small cell lung cancer cell line


title: Xba-NCI-H226

description: non-small cell lung cancer cell line


title: A549 ATCC

description: non-small cell lung cancer cell line


title: OVCAR-3

description: ovarian cancer cell line


title: UACC-257

description: melanoma cell line


title: SK-MEL-5

description: melanoma cell line


title: NCI-H460

description: non-small cell lung cancer cell line


title: Xba-HOP-62

description: non-small cell lung cancer cell line


title: Xba-A549 ATCC

description: non-small cell lung cancer cell line


title: Xba-UACC-62

description: melanoma cell line


title: Xba-UACC-257

description: melanoma cell line


title: UACC-62

description: melanoma cell line


title: Xba-SK-MEL-5

description: melanoma cell line


title: Xba-SK-MEL-2

description: melanoma cell line


title: SK-MEL-2

description: melanoma cell line


title: SK-MEL-28

description: melanoma cell line


title: MDA-MB435

description: melanoma cell line


title: Xba-MDA-MB435

description: melanoma cell line


title: Xba-MALME-3M

description: melanoma cell line


title: SR

description: leukemia cell line


title: MALME-3M

description: melanoma cell line


title: Xba-LOX IMVI

description: melanoma cell line


title: RPMI-8226

description: leukemia cell line


title: Xba-M 14

description: melanoma cell line


title: LOX IMVI

description: melanoma cell line


title: SW-620

description: colon cancer cell line


title: MOLT-4

description: leukemia cell line


title: Xba-CCRF-CEM

description: leukemia cell line


title: Xba-K-562

description: leukemia cell line


title: KM12

description: colon cancer cell line


title: K-562

description: leukemia cell line


title: Xba-HL-60

description: leukemia cell line


title: HL-60

description: leukemia cell line


title: Xba-NCI-ADR-RES

description: leukemia cell line


title: Xba-KM12

description: colon cancer cell line


title: CCRF-CEM

description: leukemia cell line


title: Xba-SW-620

description: colon cancer cell line


title: Xba-HT29

description: colon cancer cell line


title: M 14

description: melanoma cell line


title: Xba-HCT-15

description: colon cancer cell line


title: Xba-RPMI-8226

description: leukemia cell line


title: Xba-SK-MEL-28

description: melanoma cell line


title: HT29

description: colon cancer cell line


title: Xba-COLO 205

description: colon cancer cell line


title: Xba-HCC-2998

description: colon cancer cell line


title: Xba-HCT-116

description: colon cancer cell line


title: NCI-ADR-RES

description: leukemia cell line


title: Xba-T47D

description: breast cancer cell line


title: T47D

description: breast cancer cell line


title: Xba-MDA-MB-231

description: breast cancer cell line


title: Xba-MCF7

description: breast cancer cell line


title: Xba-SF-295

description: CNS cancer cell line


title: Xba-SNB-19

description: CNS cancer cell line


title: SF-539

description: CNS cancer cell line


title: SNB-75

description: CNS cancer cell line


title: U251

description: CNS cancer cell line


title: Xba-BT-549

description: breast cancer cell line


title: Xba-HS 578T

description: breast cancer cell line


title: SF-295

description: CNS cancer cell line


title: Xba-U251

description: CNS cancer cell line


title: HCC-2998

description: colon cancer cell line


title: Xba-SF-539

description: CNS cancer cell line


title: SF-268

description: CNS cancer cell line


title: SNB-19

description: CNS cancer cell line


title: Xba-SNB-75

description: CNS cancer cell line


title: Xba-SF-268

description: CNS cancer cell line


title: BT-549

description: breast cancer cell line


title: RB

description: normal diploid control


title: MDA-MB-231

description: breast cancer cell line


title: Xba-GP

description: normal diploid control


title: Xba-JG16

description: normal diploid control


title: Xba-AffyControl4

description: normal diploid control


title: MCF7

description: breast cancer cell line


title: Xba-RB

description: normal diploid control


title: JG16

description: normal diploid control


title: COLO 205

description: colon cancer cell line


title: AffyControl5

description: normal diploid control


title: HCT-15

description: colon cancer cell line


title: GP

description: normal diploid control


title: Xba-AffyControl5

description: normal diploid control


title: Xba-RefDNA

description: normal diploid control


title: AffyControl4

description: normal diploid control


title: HS 578T

description: breast cancer cell line


title: hif-1 2N vs. hif-1 2H

status: Public on Jun 25 2005

first: Min

last: Jiang

institute: Stanford University

description: Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-03/27036.gif; format: GIF

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

organism: Caenorhabditis elegans

source_name: hif-1 2H

tag: hif-1 2H

source_name: hif-1 2N

tag: hif-1 2N


title: c97 colonII

status: Public on May 07 2005

city: Pamplona

first: Raquel

last: Malumbres

state: Navarra

address: Avenida Pio XII 55

department: Hemato-Oncology

country: Spain

institute: University of Navarra/ Clínica Universidad de Navarra

description:
Female patient, 58 years old, T3N0M0 stage, tumor size below 5 cm of diameter, located in left colon. Followed five years, with recurrence.
High quality total RNA was isolated from the frozen tissues disrupted using an Ultra Turrax T25 homogenizer. Extraction of total RNA was performed with Trizol total RNA isolation reagent (Gibco BRL, Life Technologies, Gaitherburg, MD, USA) according to the manufacturer´s instructions. All the RNAs used in this study were cleaned up with RNeasy Mini Kit (Quiagen, Valencia, CA) and were exhaustively treated with RNase-free DNAse I (Quiagen) to remove residual DNA. The concentration was quantified using RiboGreen Quantification kit (Molecular Probes, Leiden, The Netherlands) and RNA was adjusted to 1microg/microl. Quality control of RNA was performed by electrophoresis and ethidium bromide staining on a 2% agarose gel.
The corresponding cDNA probes were prepared using the Micromax system (NEN, Perkin Elmer, Boston, MA) according to the manufacturer´s protocol. Briefly, 2 microg of RNA were labeled with Fluorescein-12-dCTP and reversely transcribed for 1h at 42ºC. Subsequently, the labeled cDNA was purified by precipitation with 3M acetate (pH 5.2) and isopropanol in order to eliminate the unincorporated nucleotides. After two washes with 70% ethanol, the labeled cDNA was dried and resuspended in 50 microl of GlassHyb Hybridization Solution (Clontech, Palo Alto, CA). The labeled cDNA was then pre-heated to 50ºC and hybridized to Human 19K Oligo Array slides (60 mers) (Center for Applied Genomics, University of Medicine of New Jersey). These slides were previously prehybridized by incubation at 42 ºC for 45 min in a solution consisting of 25% formamide, 5x SSC, 0.1% SDS, then rinsed in water and isopropanol and dried before hybridization.
After hybridization at 48 ºC for 16 hours in a slide cassette (Telechem, Sunnyvale, CA), slides were washed sequentially in a series of solutions of increasing stringency: 0.5xSSC, 0.01% SDS (5 minutes, room temperature); 0.06xSSC, 0.01% SDS (5 minutes, room temperature) and 0.06xSSC (2 minutes, room temperature). Immediately after washing, the presence of fluorescein labeled cDNAs on the microarray was detected using a fluorescent anti-fluorescein antibody conjugate and TSA detection (Micromax) according to the manufacturer´s protocol with appropriate modifications.
The GMS 418 scanner (Genetic Microsystems, Woburn, MA), a confocal scanning instrument containing 2 laser sources and high-resolution photo multiplier tubes (10 micron resolution), was used for scanning the hybridized microarrays. After image acquisition, the scanned images were imported into ImaGene 4.1 software (BioDiscovery, Marina del Re, CA) to quantify the signal intensities. Data from spots not recognized by the ImaGene analysis software were excluded from further considerations (empty, poor and negative spots). We also removed data from spots visually identified as flawed (< 15% in all arrays). Only the spots with flag value equal to 0 were included in the analysis.

Keywords = colon cancer stage II
Keywords = recurrent

source_name: Frozen primary colorectal tumor, Dukes´stage B, patient with subsequent recurrence


title: c95 colonII

description:
Male patient, 72 years old, T2N0M0 stage, tumor size below 5 cm of diameter, located in colon-sigma. Followed five years, with recurrence.
High quality total RNA was isolated from the frozen tissues disrupted using an Ultra Turrax T25 homogenizer. Extraction of total RNA was performed with Trizol total RNA isolation reagent (Gibco BRL, Life Technologies, Gaitherburg, MD, USA) according to the manufacturer´s instructions. All the RNAs used in this study were cleaned up with RNeasy Mini Kit (Quiagen, Valencia, CA) and were exhaustively treated with RNase-free DNAse I (Quiagen) to remove residual DNA. The concentration was quantified using RiboGreen Quantification kit (Molecular Probes, Leiden, The Netherlands) and RNA was adjusted to 1microg/microl. Quality control of RNA was performed by electrophoresis and ethidium bromide staining on a 2% agarose gel.
The corresponding cDNA probes were prepared using the Micromax system (NEN, Perkin Elmer, Boston, MA) according to the manufacturer´s protocol. Briefly, 2 microg of RNA were labeled with Fluorescein-12-dCTP and reversely transcribed for 1h at 42ºC. Subsequently, the labeled cDNA was purified by precipitation with 3M acetate (pH 5.2) and isopropanol in order to eliminate the unincorporated nucleotides. After two washes with 70% ethanol, the labeled cDNA was dried and resuspended in 50 microl of GlassHyb Hybridization Solution (Clontech, Palo Alto, CA). The labeled cDNA was then pre-heated to 50ºC and hybridized to Human 19K Oligo Array slides (60 mers) (Center for Applied Genomics, University of Medicine of New Jersey). These slides were previously prehybridized by incubation at 42 ºC for 45 min in a solution consisting of 25% formamide, 5x SSC, 0.1% SDS, then rinsed in water and isopropanol and dried before hybridization.
After hybridization at 48 ºC for 16 hours in a slide cassette (Telechem, Sunnyvale, CA), slides were washed sequentially in a series of solutions of increasing stringency: 0.5xSSC, 0.01% SDS (5 minutes, room temperature); 0.06xSSC, 0.01% SDS (5 minutes, room temperature) and 0.06xSSC (2 minutes, room temperature). Immediately after washing, the presence of fluorescein labeled cDNAs on the microarray was detected using a fluorescent anti-fluorescein antibody conjugate and TSA detection (Micromax) according to the manufacturer´s protocol with appropriate modifications.
The GMS 418 scanner (Genetic Microsystems, Woburn, MA), a confocal scanning instrument containing 2 laser sources and high-resolution photo multiplier tubes (10 micron resolution), was used for scanning the hybridized microarrays. After image acquisition, the scanned images were imported into ImaGene 4.1 software (BioDiscovery, Marina del Re, CA) to quantify the signal intensities. Data from spots not recognized by the ImaGene analysis software were excluded from further considerations (empty, poor and negative spots). We also removed data from spots visually identified as flawed (< 15% in all arrays). Only the spots with flag value equal to 0 were included in the analysis.

Keywords = colon cancer stage II
Keywords = recurrent


title: hif-1 3N vs. hif-1 3H

description: Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-03/27038.gif; format: GIF

source_name: hif-1 3H

tag: hif-1 3H

source_name: hif-1 3N

tag: hif-1 3N


title: c78 colonII

description:
Male patient, 81 years old, T3N0M0 stage, tumor size below 5 cm of diameter, located in colon-sigma. Followed five years, without recurrence.
High quality total RNA was isolated from the frozen tissues disrupted using an Ultra Turrax T25 homogenizer. Extraction of total RNA was performed with Trizol total RNA isolation reagent (Gibco BRL, Life Technologies, Gaitherburg, MD, USA) according to the manufacturer´s instructions. All the RNAs used in this study were cleaned up with RNeasy Mini Kit (Quiagen, Valencia, CA) and were exhaustively treated with RNase-free DNAse I (Quiagen) to remove residual DNA. The concentration was quantified using RiboGreen Quantification kit (Molecular Probes, Leiden, The Netherlands) and RNA was adjusted to 1microg/microl. Quality control of RNA was performed by electrophoresis and ethidium bromide staining on a 2% agarose gel.
The corresponding cDNA probes were prepared using the Micromax system (NEN, Perkin Elmer, Boston, MA) according to the manufacturer´s protocol. Briefly, 2 microg of RNA were labeled with Fluorescein-12-dCTP and reversely transcribed for 1h at 42ºC. Subsequently, the labeled cDNA was purified by precipitation with 3M acetate (pH 5.2) and isopropanol in order to eliminate the unincorporated nucleotides. After two washes with 70% ethanol, the labeled cDNA was dried and resuspended in 50 microl of GlassHyb Hybridization Solution (Clontech, Palo Alto, CA). The labeled cDNA was then pre-heated to 50ºC and hybridized to Human 19K Oligo Array slides (60 mers) (Center for Applied Genomics, University of Medicine of New Jersey). These slides were previously prehybridized by incubation at 42 ºC for 45 min in a solution consisting of 25% formamide, 5x SSC, 0.1% SDS, then rinsed in water and isopropanol and dried before hybridization.
After hybridization at 48 ºC for 16 hours in a slide cassette (Telechem, Sunnyvale, CA), slides were washed sequentially in a series of solutions of increasing stringency: 0.5xSSC, 0.01% SDS (5 minutes, room temperature); 0.06xSSC, 0.01% SDS (5 minutes, room temperature) and 0.06xSSC (2 minutes, room temperature). Immediately after washing, the presence of fluorescein labeled cDNAs on the microarray was detected using a fluorescent anti-fluorescein antibody conjugate and TSA detection (Micromax) according to the manufacturer´s protocol with appropriate modifications.
The GMS 418 scanner (Genetic Microsystems, Woburn, MA), a confocal scanning instrument containing 2 laser sources and high-resolution photo multiplier tubes (10 micron resolution), was used for scanning the hybridized microarrays. After image acquisition, the scanned images were imported into ImaGene 4.1 software (BioDiscovery, Marina del Re, CA) to quantify the signal intensities. Data from spots not recognized by the ImaGene analysis software were excluded from further considerations (empty, poor and negative spots). We also removed data from spots visually identified as flawed (< 15% in all arrays). Only the spots with flag value equal to 0 were included in the analysis.

Keywords = colon cancer stage II
Keywords = non-recurrent

source_name: Frozen primary colorectal tumor, Dukes´stage B, patient without subsequent recurrence


title: wt 3N vs. wt 3H

description: Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-03/27035.gif; format: GIF

source_name: wt 3H

tag: wt 3H

source_name: wt 3N

tag: wt 3N


title: c96 colonII

description:
Male patient, 60 years old, T2N0M0 stage, tumor size below 5 cm of diameter, located in right colon. Followed five years, with recurrence.
High quality total RNA was isolated from the frozen tissues disrupted using an Ultra Turrax T25 homogenizer. Extraction of total RNA was performed with Trizol total RNA isolation reagent (Gibco BRL, Life Technologies, Gaitherburg, MD, USA) according to the manufacturer´s instructions. All the RNAs used in this study were cleaned up with RNeasy Mini Kit (Quiagen, Valencia, CA) and were exhaustively treated with RNase-free DNAse I (Quiagen) to remove residual DNA. The concentration was quantified using RiboGreen Quantification kit (Molecular Probes, Leiden, The Netherlands) and RNA was adjusted to 1microg/microl. Quality control of RNA was performed by electrophoresis and ethidium bromide staining on a 2% agarose gel.
The corresponding cDNA probes were prepared using the Micromax system (NEN, Perkin Elmer, Boston, MA) according to the manufacturer´s protocol. Briefly, 2 microg of RNA were labeled with Fluorescein-12-dCTP and reversely transcribed for 1h at 42ºC. Subsequently, the labeled cDNA was purified by precipitation with 3M acetate (pH 5.2) and isopropanol in order to eliminate the unincorporated nucleotides. After two washes with 70% ethanol, the labeled cDNA was dried and resuspended in 50 microl of GlassHyb Hybridization Solution (Clontech, Palo Alto, CA). The labeled cDNA was then pre-heated to 50ºC and hybridized to Human 19K Oligo Array slides (60 mers) (Center for Applied Genomics, University of Medicine of New Jersey). These slides were previously prehybridized by incubation at 42 ºC for 45 min in a solution consisting of 25% formamide, 5x SSC, 0.1% SDS, then rinsed in water and isopropanol and dried before hybridization.
After hybridization at 48 ºC for 16 hours in a slide cassette (Telechem, Sunnyvale, CA), slides were washed sequentially in a series of solutions of increasing stringency: 0.5xSSC, 0.01% SDS (5 minutes, room temperature); 0.06xSSC, 0.01% SDS (5 minutes, room temperature) and 0.06xSSC (2 minutes, room temperature). Immediately after washing, the presence of fluorescein labeled cDNAs on the microarray was detected using a fluorescent anti-fluorescein antibody conjugate and TSA detection (Micromax) according to the manufacturer´s protocol with appropriate modifications.
The GMS 418 scanner (Genetic Microsystems, Woburn, MA), a confocal scanning instrument containing 2 laser sources and high-resolution photo multiplier tubes (10 micron resolution), was used for scanning the hybridized microarrays. After image acquisition, the scanned images were imported into ImaGene 4.1 software (BioDiscovery, Marina del Re, CA) to quantify the signal intensities. Data from spots not recognized by the ImaGene analysis software were excluded from further considerations (empty, poor and negative spots). We also removed data from spots visually identified as flawed (< 15% in all arrays). Only the spots with flag value equal to 0 were included in the analysis.

Keywords = colon cancer stage II
Keywords = recurrent


title: wt 2N vs. wt 2H

description: Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-03/27034.gif; format: GIF

source_name: wt 2H

tag: wt 2H

source_name: wt 2N

tag: wt 2N


title: c80 colonII

description:
Male patient, 67 years old, T2N0M0 stage, tumor size below 5 cm of diameter, located in right colon. Followed five years, without recurrence.
High quality total RNA was isolated from the frozen tissues disrupted using an Ultra Turrax T25 homogenizer. Extraction of total RNA was performed with Trizol total RNA isolation reagent (Gibco BRL, Life Technologies, Gaitherburg, MD, USA) according to the manufacturer´s instructions. All the RNAs used in this study were cleaned up with RNeasy Mini Kit (Quiagen, Valencia, CA) and were exhaustively treated with RNase-free DNAse I (Quiagen) to remove residual DNA. The concentration was quantified using RiboGreen Quantification kit (Molecular Probes, Leiden, The Netherlands) and RNA was adjusted to 1microg/microl. Quality control of RNA was performed by electrophoresis and ethidium bromide staining on a 2% agarose gel.
The corresponding cDNA probes were prepared using the Micromax system (NEN, Perkin Elmer, Boston, MA) according to the manufacturer´s protocol. Briefly, 2 microg of RNA were labeled with Fluorescein-12-dCTP and reversely transcribed for 1h at 42ºC. Subsequently, the labeled cDNA was purified by precipitation with 3M acetate (pH 5.2) and isopropanol in order to eliminate the unincorporated nucleotides. After two washes with 70% ethanol, the labeled cDNA was dried and resuspended in 50 microl of GlassHyb Hybridization Solution (Clontech, Palo Alto, CA). The labeled cDNA was then pre-heated to 50ºC and hybridized to Human 19K Oligo Array slides (60 mers) (Center for Applied Genomics, University of Medicine of New Jersey). These slides were previously prehybridized by incubation at 42 ºC for 45 min in a solution consisting of 25% formamide, 5x SSC, 0.1% SDS, then rinsed in water and isopropanol and dried before hybridization.
After hybridization at 48 ºC for 16 hours in a slide cassette (Telechem, Sunnyvale, CA), slides were washed sequentially in a series of solutions of increasing stringency: 0.5xSSC, 0.01% SDS (5 minutes, room temperature); 0.06xSSC, 0.01% SDS (5 minutes, room temperature) and 0.06xSSC (2 minutes, room temperature). Immediately after washing, the presence of fluorescein labeled cDNAs on the microarray was detected using a fluorescent anti-fluorescein antibody conjugate and TSA detection (Micromax) according to the manufacturer´s protocol with appropriate modifications.
The GMS 418 scanner (Genetic Microsystems, Woburn, MA), a confocal scanning instrument containing 2 laser sources and high-resolution photo multiplier tubes (10 micron resolution), was used for scanning the hybridized microarrays. After image acquisition, the scanned images were imported into ImaGene 4.1 software (BioDiscovery, Marina del Re, CA) to quantify the signal intensities. Data from spots not recognized by the ImaGene analysis software were excluded from further considerations (empty, poor and negative spots). We also removed data from spots visually identified as flawed (< 15% in all arrays). Only the spots with flag value equal to 0 were included in the analysis.

Keywords = colon cancer stage II
Keywords = non-recurrent


title: hif-1 1N vs. hif-1 1H

description: Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-03/27033.gif; format: GIF

source_name: hif-1 1H

tag: hif-1 1H

source_name: hif-1 1N

tag: hif-1 1N


title: c70 colonII

description:
Female patient, 69 years old, T3N0M0 stage, tumor size over 5 cm of diameter, located in right colon. Followed five years, without recurrence.
High quality total RNA was isolated from the frozen tissues disrupted using an Ultra Turrax T25 homogenizer. Extraction of total RNA was performed with Trizol total RNA isolation reagent (Gibco BRL, Life Technologies, Gaitherburg, MD, USA) according to the manufacturer´s instructions. All the RNAs used in this study were cleaned up with RNeasy Mini Kit (Quiagen, Valencia, CA) and were exhaustively treated with RNase-free DNAse I (Quiagen) to remove residual DNA. The concentration was quantified using RiboGreen Quantification kit (Molecular Probes, Leiden, The Netherlands) and RNA was adjusted to 1microg/microl. Quality control of RNA was performed by electrophoresis and ethidium bromide staining on a 2% agarose gel.
The corresponding cDNA probes were prepared using the Micromax system (NEN, Perkin Elmer, Boston, MA) according to the manufacturer´s protocol. Briefly, 2 microg of RNA were labeled with Fluorescein-12-dCTP and reversely transcribed for 1h at 42ºC. Subsequently, the labeled cDNA was purified by precipitation with 3M acetate (pH 5.2) and isopropanol in order to eliminate the unincorporated nucleotides. After two washes with 70% ethanol, the labeled cDNA was dried and resuspended in 50 microl of GlassHyb Hybridization Solution (Clontech, Palo Alto, CA). The labeled cDNA was then pre-heated to 50ºC and hybridized to Human 19K Oligo Array slides (60 mers) (Center for Applied Genomics, University of Medicine of New Jersey). These slides were previously prehybridized by incubation at 42 ºC for 45 min in a solution consisting of 25% formamide, 5x SSC, 0.1% SDS, then rinsed in water and isopropanol and dried before hybridization.
After hybridization at 48 ºC for 16 hours in a slide cassette (Telechem, Sunnyvale, CA), slides were washed sequentially in a series of solutions of increasing stringency: 0.5xSSC, 0.01% SDS (5 minutes, room temperature); 0.06xSSC, 0.01% SDS (5 minutes, room temperature) and 0.06xSSC (2 minutes, room temperature). Immediately after washing, the presence of fluorescein labeled cDNAs on the microarray was detected using a fluorescent anti-fluorescein antibody conjugate and TSA detection (Micromax) according to the manufacturer´s protocol with appropriate modifications.
The GMS 418 scanner (Genetic Microsystems, Woburn, MA), a confocal scanning instrument containing 2 laser sources and high-resolution photo multiplier tubes (10 micron resolution), was used for scanning the hybridized microarrays. After image acquisition, the scanned images were imported into ImaGene 4.1 software (BioDiscovery, Marina del Re, CA) to quantify the signal intensities. Data from spots not recognized by the ImaGene analysis software were excluded from further considerations (empty, poor and negative spots). We also removed data from spots visually identified as flawed (< 15% in all arrays). Only the spots with flag value equal to 0 were included in the analysis.

Keywords = colon cancer stage II
Keywords = non-recurrent


title: vhl-1 3N vs. vhl-1 3H

description: Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-03/27042.gif; format: GIF

source_name: vhl-1 3H

tag: vhl-1 3H

source_name: vhl-1 3N

tag: vhl-1 3N


title: HCT-116

description: colon cancer cell line


title: c75 colonII

description:
Male patient, 67 years old, T2N0M0 stage, tumor size below 5 cm of diameter, located in colon-sigma. Followed five years, without recurrence.
High quality total RNA was isolated from the frozen tissues disrupted using an Ultra Turrax T25 homogenizer. Extraction of total RNA was performed with Trizol total RNA isolation reagent (Gibco BRL, Life Technologies, Gaitherburg, MD, USA) according to the manufacturer´s instructions. All the RNAs used in this study were cleaned up with RNeasy Mini Kit (Quiagen, Valencia, CA) and were exhaustively treated with RNase-free DNAse I (Quiagen) to remove residual DNA. The concentration was quantified using RiboGreen Quantification kit (Molecular Probes, Leiden, The Netherlands) and RNA was adjusted to 1microg/microl. Quality control of RNA was performed by electrophoresis and ethidium bromide staining on a 2% agarose gel.
The corresponding cDNA probes were prepared using the Micromax system (NEN, Perkin Elmer, Boston, MA) according to the manufacturer´s protocol. Briefly, 2 microg of RNA were labeled with Fluorescein-12-dCTP and reversely transcribed for 1h at 42ºC. Subsequently, the labeled cDNA was purified by precipitation with 3M acetate (pH 5.2) and isopropanol in order to eliminate the unincorporated nucleotides. After two washes with 70% ethanol, the labeled cDNA was dried and resuspended in 50 microl of GlassHyb Hybridization Solution (Clontech, Palo Alto, CA). The labeled cDNA was then pre-heated to 50ºC and hybridized to Human 19K Oligo Array slides (60 mers) (Center for Applied Genomics, University of Medicine of New Jersey). These slides were previously prehybridized by incubation at 42 ºC for 45 min in a solution consisting of 25% formamide, 5x SSC, 0.1% SDS, then rinsed in water and isopropanol and dried before hybridization.
After hybridization at 48 ºC for 16 hours in a slide cassette (Telechem, Sunnyvale, CA), slides were washed sequentially in a series of solutions of increasing stringency: 0.5xSSC, 0.01% SDS (5 minutes, room temperature); 0.06xSSC, 0.01% SDS (5 minutes, room temperature) and 0.06xSSC (2 minutes, room temperature). Immediately after washing, the presence of fluorescein labeled cDNAs on the microarray was detected using a fluorescent anti-fluorescein antibody conjugate and TSA detection (Micromax) according to the manufacturer´s protocol with appropriate modifications.
The GMS 418 scanner (Genetic Microsystems, Woburn, MA), a confocal scanning instrument containing 2 laser sources and high-resolution photo multiplier tubes (10 micron resolution), was used for scanning the hybridized microarrays. After image acquisition, the scanned images were imported into ImaGene 4.1 software (BioDiscovery, Marina del Re, CA) to quantify the signal intensities. Data from spots not recognized by the ImaGene analysis software were excluded from further considerations (empty, poor and negative spots). We also removed data from spots visually identified as flawed (< 15% in all arrays). Only the spots with flag value equal to 0 were included in the analysis.

Keywords = colon cancer stage II
Keywords = non-recurrent


title: c77 colonII

description:
Female patient, 66 years old, T3N0M0 stage, tumor size below 5 cm of diameter, located in colon-sigma. Followed five years, without recurrence.
High quality total RNA was isolated from the frozen tissues disrupted using an Ultra Turrax T25 homogenizer. Extraction of total RNA was performed with Trizol total RNA isolation reagent (Gibco BRL, Life Technologies, Gaitherburg, MD, USA) according to the manufacturer´s instructions. All the RNAs used in this study were cleaned up with RNeasy Mini Kit (Quiagen, Valencia, CA) and were exhaustively treated with RNase-free DNAse I (Quiagen) to remove residual DNA. The concentration was quantified using RiboGreen Quantification kit (Molecular Probes, Leiden, The Netherlands) and RNA was adjusted to 1microg/microl. Quality control of RNA was performed by electrophoresis and ethidium bromide staining on a 2% agarose gel.
The corresponding cDNA probes were prepared using the Micromax system (NEN, Perkin Elmer, Boston, MA) according to the manufacturer´s protocol. Briefly, 2 microg of RNA were labeled with Fluorescein-12-dCTP and reversely transcribed for 1h at 42ºC. Subsequently, the labeled cDNA was purified by precipitation with 3M acetate (pH 5.2) and isopropanol in order to eliminate the unincorporated nucleotides. After two washes with 70% ethanol, the labeled cDNA was dried and resuspended in 50 microl of GlassHyb Hybridization Solution (Clontech, Palo Alto, CA). The labeled cDNA was then pre-heated to 50ºC and hybridized to Human 19K Oligo Array slides (60 mers) (Center for Applied Genomics, University of Medicine of New Jersey). These slides were previously prehybridized by incubation at 42 ºC for 45 min in a solution consisting of 25% formamide, 5x SSC, 0.1% SDS, then rinsed in water and isopropanol and dried before hybridization.
After hybridization at 48 ºC for 16 hours in a slide cassette (Telechem, Sunnyvale, CA), slides were washed sequentially in a series of solutions of increasing stringency: 0.5xSSC, 0.01% SDS (5 minutes, room temperature); 0.06xSSC, 0.01% SDS (5 minutes, room temperature) and 0.06xSSC (2 minutes, room temperature). Immediately after washing, the presence of fluorescein labeled cDNAs on the microarray was detected using a fluorescent anti-fluorescein antibody conjugate and TSA detection (Micromax) according to the manufacturer´s protocol with appropriate modifications.
The GMS 418 scanner (Genetic Microsystems, Woburn, MA), a confocal scanning instrument containing 2 laser sources and high-resolution photo multiplier tubes (10 micron resolution), was used for scanning the hybridized microarrays. After image acquisition, the scanned images were imported into ImaGene 4.1 software (BioDiscovery, Marina del Re, CA) to quantify the signal intensities. Data from spots not recognized by the ImaGene analysis software were excluded from further considerations (empty, poor and negative spots). We also removed data from spots visually identified as flawed (< 15% in all arrays). Only the spots with flag value equal to 0 were included in the analysis.

Keywords = colon cancer stage II
Keywords = non-recurrent


title: c52 colonII

description:
Male patient, 78 years old, T3N0M0 stage, tumor size below 5 cm of diameter, located in right colon. Followed five years, without recurrence.
High quality total RNA was isolated from the frozen tissues disrupted using an Ultra Turrax T25 homogenizer. Extraction of total RNA was performed with Trizol total RNA isolation reagent (Gibco BRL, Life Technologies, Gaitherburg, MD, USA) according to the manufacturer´s instructions. All the RNAs used in this study were cleaned up with RNeasy Mini Kit (Quiagen, Valencia, CA) and were exhaustively treated with RNase-free DNAse I (Quiagen) to remove residual DNA. The concentration was quantified using RiboGreen Quantification kit (Molecular Probes, Leiden, The Netherlands) and RNA was adjusted to 1microg/microl. Quality control of RNA was performed by electrophoresis and ethidium bromide staining on a 2% agarose gel.
The corresponding cDNA probes were prepared using the Micromax system (NEN, Perkin Elmer, Boston, MA) according to the manufacturer´s protocol. Briefly, 2 microg of RNA were labeled with Fluorescein-12-dCTP and reversely transcribed for 1h at 42ºC. Subsequently, the labeled cDNA was purified by precipitation with 3M acetate (pH 5.2) and isopropanol in order to eliminate the unincorporated nucleotides. After two washes with 70% ethanol, the labeled cDNA was dried and resuspended in 50 microl of GlassHyb Hybridization Solution (Clontech, Palo Alto, CA). The labeled cDNA was then pre-heated to 50ºC and hybridized to Human 19K Oligo Array slides (60 mers) (Center for Applied Genomics, University of Medicine of New Jersey). These slides were previously prehybridized by incubation at 42 ºC for 45 min in a solution consisting of 25% formamide, 5x SSC, 0.1% SDS, then rinsed in water and isopropanol and dried before hybridization.
After hybridization at 48 ºC for 16 hours in a slide cassette (Telechem, Sunnyvale, CA), slides were washed sequentially in a series of solutions of increasing stringency: 0.5xSSC, 0.01% SDS (5 minutes, room temperature); 0.06xSSC, 0.01% SDS (5 minutes, room temperature) and 0.06xSSC (2 minutes, room temperature). Immediately after washing, the presence of fluorescein labeled cDNAs on the microarray was detected using a fluorescent anti-fluorescein antibody conjugate and TSA detection (Micromax) according to the manufacturer´s protocol with appropriate modifications.
The GMS 418 scanner (Genetic Microsystems, Woburn, MA), a confocal scanning instrument containing 2 laser sources and high-resolution photo multiplier tubes (10 micron resolution), was used for scanning the hybridized microarrays. After image acquisition, the scanned images were imported into ImaGene 4.1 software (BioDiscovery, Marina del Re, CA) to quantify the signal intensities. Data from spots not recognized by the ImaGene analysis software were excluded from further considerations (empty, poor and negative spots). We also removed data from spots visually identified as flawed (< 15% in all arrays). Only the spots with flag value equal to 0 were included in the analysis.

Keywords = colon cancer stage II
Keywords = non-recurrent


title: vhl-1 2N vs. vhl-1 2H

description: Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-03/27041.gif; format: GIF

source_name: vhl-1 2H

tag: vhl-1 2H

source_name: vhl-1 2N

tag: vhl-1 2N


title: c25 colonII

description:
Male patient, 72 years old, T3N0M0 stage, tumor size below 5 cm of diameter, located in colon-sigma. Followed five years, with recurrence.
High quality total RNA was isolated from the frozen tissues disrupted using an Ultra Turrax T25 homogenizer. Extraction of total RNA was performed with Trizol total RNA isolation reagent (Gibco BRL, Life Technologies, Gaitherburg, MD, USA) according to the manufacturer´s instructions. All the RNAs used in this study were cleaned up with RNeasy Mini Kit (Quiagen, Valencia, CA) and were exhaustively treated with RNase-free DNAse I (Quiagen) to remove residual DNA. The concentration was quantified using RiboGreen Quantification kit (Molecular Probes, Leiden, The Netherlands) and RNA was adjusted to 1microg/microl. Quality control of RNA was performed by electrophoresis and ethidium bromide staining on a 2% agarose gel.
The corresponding cDNA probes were prepared using the Micromax system (NEN, Perkin Elmer, Boston, MA) according to the manufacturer´s protocol. Briefly, 2 microg of RNA were labeled with Fluorescein-12-dCTP and reversely transcribed for 1h at 42ºC. Subsequently, the labeled cDNA was purified by precipitation with 3M acetate (pH 5.2) and isopropanol in order to eliminate the unincorporated nucleotides. After two washes with 70% ethanol, the labeled cDNA was dried and resuspended in 50 microl of GlassHyb Hybridization Solution (Clontech, Palo Alto, CA). The labeled cDNA was then pre-heated to 50ºC and hybridized to Human 19K Oligo Array slides (60 mers) (Center for Applied Genomics, University of Medicine of New Jersey). These slides were previously prehybridized by incubation at 42 ºC for 45 min in a solution consisting of 25% formamide, 5x SSC, 0.1% SDS, then rinsed in water and isopropanol and dried before hybridization.
After hybridization at 48 ºC for 16 hours in a slide cassette (Telechem, Sunnyvale, CA), slides were washed sequentially in a series of solutions of increasing stringency: 0.5xSSC, 0.01% SDS (5 minutes, room temperature); 0.06xSSC, 0.01% SDS (5 minutes, room temperature) and 0.06xSSC (2 minutes, room temperature). Immediately after washing, the presence of fluorescein labeled cDNAs on the microarray was detected using a fluorescent anti-fluorescein antibody conjugate and TSA detection (Micromax) according to the manufacturer´s protocol with appropriate modifications.
The GMS 418 scanner (Genetic Microsystems, Woburn, MA), a confocal scanning instrument containing 2 laser sources and high-resolution photo multiplier tubes (10 micron resolution), was used for scanning the hybridized microarrays. After image acquisition, the scanned images were imported into ImaGene 4.1 software (BioDiscovery, Marina del Re, CA) to quantify the signal intensities. Data from spots not recognized by the ImaGene analysis software were excluded from further considerations (empty, poor and negative spots). We also removed data from spots visually identified as flawed (< 15% in all arrays). Only the spots with flag value equal to 0 were included in the analysis.

Keywords = colon cancer stage II
Keywords = recurrent


title: c94 colonII

description:
Female patient, 48 years old, T2N0M0 stage, tumor size below 5 cm of diameter, located in colon-sigma. Followed five years, without recurrence.
High quality total RNA was isolated from the frozen tissues disrupted using an Ultra Turrax T25 homogenizer. Extraction of total RNA was performed with Trizol total RNA isolation reagent (Gibco BRL, Life Technologies, Gaitherburg, MD, USA) according to the manufacturer´s instructions. All the RNAs used in this study were cleaned up with RNeasy Mini Kit (Quiagen, Valencia, CA) and were exhaustively treated with RNase-free DNAse I (Quiagen) to remove residual DNA. The concentration was quantified using RiboGreen Quantification kit (Molecular Probes, Leiden, The Netherlands) and RNA was adjusted to 1microg/microl. Quality control of RNA was performed by electrophoresis and ethidium bromide staining on a 2% agarose gel.
The corresponding cDNA probes were prepared using the Micromax system (NEN, Perkin Elmer, Boston, MA) according to the manufacturer´s protocol. Briefly, 2 microg of RNA were labeled with Fluorescein-12-dCTP and reversely transcribed for 1h at 42ºC. Subsequently, the labeled cDNA was purified by precipitation with 3M acetate (pH 5.2) and isopropanol in order to eliminate the unincorporated nucleotides. After two washes with 70% ethanol, the labeled cDNA was dried and resuspended in 50 microl of GlassHyb Hybridization Solution (Clontech, Palo Alto, CA). The labeled cDNA was then pre-heated to 50ºC and hybridized to Human 19K Oligo Array slides (60 mers) (Center for Applied Genomics, University of Medicine of New Jersey). These slides were previously prehybridized by incubation at 42 ºC for 45 min in a solution consisting of 25% formamide, 5x SSC, 0.1% SDS, then rinsed in water and isopropanol and dried before hybridization.
After hybridization at 48 ºC for 16 hours in a slide cassette (Telechem, Sunnyvale, CA), slides were washed sequentially in a series of solutions of increasing stringency: 0.5xSSC, 0.01% SDS (5 minutes, room temperature); 0.06xSSC, 0.01% SDS (5 minutes, room temperature) and 0.06xSSC (2 minutes, room temperature). Immediately after washing, the presence of fluorescein labeled cDNAs on the microarray was detected using a fluorescent anti-fluorescein antibody conjugate and TSA detection (Micromax) according to the manufacturer´s protocol with appropriate modifications.
The GMS 418 scanner (Genetic Microsystems, Woburn, MA), a confocal scanning instrument containing 2 laser sources and high-resolution photo multiplier tubes (10 micron resolution), was used for scanning the hybridized microarrays. After image acquisition, the scanned images were imported into ImaGene 4.1 software (BioDiscovery, Marina del Re, CA) to quantify the signal intensities. Data from spots not recognized by the ImaGene analysis software were excluded from further considerations (empty, poor and negative spots). We also removed data from spots visually identified as flawed (< 15% in all arrays). Only the spots with flag value equal to 0 were included in the analysis.

Keywords = colon cancer stage II
Keywords = non-recurrent