title: CD16+

source_name: neutrophils CD16+

extract_protocol: Total RNA was isolated from each cell population (2x105 cells) of each donor using a modification of the guanidinium isothiocyanate procedure and ultracentrifugation on cesium chloride gradient. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 bioanalyzer. RNAs originating from 12 donors were pooled in order to obtain at least 2 ug per sample.

treatment_protocol: Neutrophils (CD16+) were isolated from the peripheral blood of 12 healthy donors using magnetic cell-sorting procedures. Briefly, the peripheral blood was subjected to centrifugation on a Ficoll-Hypaque gradient. CD16+ cells were isolated by positive selection from the pellet using CD16 MicroBeads (Miltenyi Biotech, Auburn, CA, USA).

tag: CD16+ from peripheral blood.


title: 04-20L-rep1

status: Public on Jan 31 2008

type: RNA

city: Chicago

first: Pan

last: Du

state: IL

address: 676 N ST Clair St, 1200#

country: USA

institute: Northwestern University

description:
04-20L a
African American with glaucoma

hyb_protocol: Purified biotin-labeled cRNA was fragmented before the hybridization. Hybridization of the labeled cRNA to Human Genome U133A 2.0 and U95 chips (Affymetrix, Santa Clara, CA) was carried out by using Genechip Instrument System (Affymetrix) at the Genechip Core Facility of Washington University (Saint Louis, MO).

scan_protocol: The arrays were washed and stained with streptavidin-phycoerythrin (Molecular Probes, Eugene, OR) followed by scanning on an Agilent GeneArray Scanner G2500A (Agilent Technologies, Palo Alto, CA), and then scanned by an Affymetrix Genearray Scanner.

data_processing: RMA normalized using affy Bioconductor package

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human optic nerve head astrocytes, glaucoma

label_protocol: cRNA was synthesized from 2-5 µg purified RNA by using Superscript Choice system (Gibco BRL Life Technologies, Gaithersburg, MD ) and  T7-(dT)24 primer (GENSET, La Jolla, CA). Using Bioassay High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY), in vitro transcription was carried out by using the cleaned double-stranded cDNA as a template in the presence of biotinylated UTP and CTP.

growth_protocol: Four explants from each lamina cribrosa were dissected and placed into 25-cm2 Primaria tissue culture flasks and maintained in DMEM-F12 supplemented with 10% FBS and antibiotics.Cells were kept in a 37oC, 5% CO2 incubator. After 2-4 weeks, primary cultures were purified by using modified immunopanning procedure described by Mi and Barres (1999). Purified cells were expanded after characterization by immunostaining for astrocyte markers GFAP and NCAM as described (Yang and Hernandez, 2003). Second passage cell cultures were stored in RPMI 1640 with 10% DMSO in liquid nitrogen until use.

extract_protocol: Total RNA was extracted using Qiagen RNeasy mini kits (Qiagen, Valencia, CA). RNA was then purified and quantified by measuring absorbance at 260 nm. Quality and intactness of the RNA was assessed by capillary electrophoresis analysis using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

tag: African American, male, age 67, glaucoma


title: 04-24R-rep2

description:
04-24R b
African American with glaucoma

tag: African American, female, age 53, glaucoma


title: 05-16L-rep1

description:
05-16L a
African American with glaucoma

tag: African American, female, age 56, glaucoma


title: 05-16L-rep2

description:
05-16L b
African American with glaucoma


title: 04-2L-rep1

description:
04-2L
Caucasian American

source_name: Human optic nerve head astrocytes, normal

tag: Caucasian American, male, age 65, normal


title: 03-13L-rep1

description:
03-13L
Caucasian American

tag: Caucasian American, female, age 72, normal


title: 99-6L-rep1

description:
99-6L
Caucasian American

tag: Caucasian American, male, age 42, normal


title: 03-11R-rep1

description:
03-11R
Caucasian American

tag: Caucasian American, female, age 68, normal


title: LC46R-rep1

description:
LC46R
Caucasian American

tag: Caucasian American, male, age 46, normal


title: 99-9R-rep1

description:
99-9R
Caucasian American

tag: Caucasian American, female, age 46, normal


title: transduced with eGFP (937)

status: Public on Mar 05 2008

city: Auckland

first: Cris

last: Print

address: Grafton Campus, Park Rd

country: New Zealand

institute: Auckland University

description: Gene expression data from HUVEC cultured in different conditions or differently genetically modified

hyb_protocol: After fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 dgrees C to the geneChips, which were then washed and stained according to standard Affymetrix protocols.

scan_protocol: Scanned with GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. The data were then normalised by chips using he loess method in R.

source_name: transduced with eGFP

label_protocol: Biotinylated cRNAs were prepared from 5 micrograms total RNA according to the standard Affymetrix protocol.

growth_protocol: Genetically-modified HUVEC grown on a variety of substrates and in a variety of geometries were comared.

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

treatment_protocol: Cultured cells were overlayed with approximately 10x their mass of Trizol then disrupted with a cell scraper.

tag: human umbilical vein endotelial cells (HUVEC)

tag: cultured on plastic in 2D, transduced with eGFP


title: 2-10R-rep1

description: Caucasian American with glaucoma

tag: Caucasian American, female, age 80, glaucoma


title: 04-1L-rep1

description: Caucasian American with glaucoma

tag: Caucasian American, female, age 79, glaucoma


title: 04-5A-rep1

description: Caucasian American with glaucoma

tag: Caucasian American, female, age 72, glaucoma


title: 00-7R-rep1

description: Caucasian American with glaucoma

tag: Caucasian American, male, age 83, glaucoma


title: DU78: Breast tumors from women with early stage breast cancer

status: Public on Jan 16 2008

city: Durham

first: Carey

middle: K.

last: Anders

state: NC

address: 101 Science Drive

department: Institute for Genome Sciences and Policy

institute: Duke University

description:
mRNA Expression values from tumors arising in women with early stage breast cancer
Submitters do not have approval to publish the .CEL files

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Breast

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

tag: Tumor

tag: EA_Designation = 78

tag: %_Tumor = 60

tag: Race = White

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Not Graded / Unknown

tag: Path_T = 2

tag: Path_Stg = 2A

tag: Tumor_Size_(cm) = 4

tag: Regional_Nodes_Examined = 30

tag: ER = Borderline,Undetermined

tag: PR = Negative/Normal

tag: Type_of_Surgery = MRM

tag: Margins = negative

tag: LVI = absent

tag: EIC = present

tag: Age_at_Dx = 65

tag: Recurrence = 1

tag: TYPE_1st_Recur = Distant

tag: 1st_Distant_Site_Recur = Bone

tag: 2nd_Distant_Site_Recur = None

tag: 3rd_Distant_Site_Recur = None

tag: XRT = No

tag: Type_1st_XRT = None

tag: Chemotherapy = No

tag: Type_1st_Chemo = None

tag: Hormone_Tx = No


title: DU86: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 86

tag: %_Tumor = 50

tag: Race = White

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Poorly Diff

tag: Path_T = 1C

tag: Path_N = 1B

tag: Path_Stg = 2A

tag: Tumor_Size_(cm) = 2

tag: Regional_Nodes_Positive = 1

tag: Regional_Nodes_Examined = 24

tag: ER = Negative/Normal

tag: Nuclear_Grade = 2

tag: EIC = absent

tag: Age_at_Dx = 74

tag: TYPE_1st_Recur = None

tag: 1st_Distant_Site_Recur = None

tag: Hormone_Tx = Yes


title: DU83: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 83

tag: %_Tumor = 60

tag: Path_T = 1B

tag: Path_N = 2

tag: Path_Stg = 3A

tag: Tumor_Size_(cm) = 0.8

tag: Regional_Nodes_Positive = 2

tag: Regional_Nodes_Examined = 9

tag: ER = Positive/elevated

tag: PR = Positive/elevated

tag: Type_of_Surgery = MRM

tag: Margins = negative

tag: LVI = present

tag: Age_at_Dx = 67

tag: 2nd_Distant_Site_Recur = None

tag: 3rd_Distant_Site_Recur = None

tag: XRT = No

tag: Type_1st_XRT = None

tag: Chemotherapy = No

tag: Type_1st_Chemo = None


title: DU85: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 85

tag: %_Tumor = 70

tag: Race = White

tag: Histo_Desc = Paget Disease & Infiltrating Duct Carcinoma

tag: Histo_Grade = Poorly Diff

tag: Path_T = 1C

tag: Path_N = 1B

tag: Path_Stg = 2A

tag: Tumor_Size_(cm) = 2

tag: Regional_Nodes_Positive = 1

tag: Regional_Nodes_Examined = 11

tag: PR = Negative/Normal

tag: Nuclear_Grade = 3

tag: Age_at_Dx = 65

tag: TYPE_1st_Recur = None

tag: 1st_Distant_Site_Recur = None

tag: XRT = Yes

tag: Type_1st_XRT = Beam

tag: Chemotherapy = Yes

tag: Type_1st_Chemo = 1

tag: = CAF

tag: Hormone_Tx = Yes


title: DU87: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 87

tag: %_Tumor = 90

tag: Race = White

tag: Histo_Desc = Carcinoma, NOS

tag: Histo_Grade = Poorly Diff

tag: Path_T = 1C

tag: Path_N = 2

tag: Path_M = 1

tag: Path_Stg = 4

tag: Tumor_Size_(cm) = 1.5

tag: Regional_Nodes_Positive = 42

tag: Regional_Nodes_Examined = 42

tag: ER = Negative/Normal

tag: Type_of_Surgery = None

tag: Age_at_Dx = 59

tag: Recurrence = na

tag: TYPE_1st_Recur = Never Disease Free

tag: 2nd_Distant_Site_Recur = None

tag: 3rd_Distant_Site_Recur = None

tag: XRT = No

tag: Type_1st_XRT = None

tag: Hormone_Tx = No


title: DU79: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 79

tag: %_Tumor = 70

tag: Race = White

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Poorly Diff

tag: Path_T = 2

tag: Path_N = 1B

tag: Path_Stg = 2B

tag: Tumor_Size_(cm) = 2

tag: Regional_Nodes_Positive = 2

tag: Regional_Nodes_Examined = 26

tag: PR = Borderline,Undetermined

tag: Type_of_Surgery = MRM

tag: Margins = negative

tag: Nuclear_Grade = 3

tag: LVI = absent

tag: EIC = present

tag: Age_at_Dx = 39

tag: TYPE_1st_Recur = None

tag: 1st_Distant_Site_Recur = None

tag: Chemotherapy = Yes

tag: Type_1st_Chemo = 1

tag: = CAF


title: 00-6R-rep1

description: Caucasian American with glaucoma

tag: Caucasian American, female, age 56, glaucoma


title: DU82: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 82

tag: %_Tumor = 50

tag: Race = Black

tag: Histo_Desc = Infiltrating Duct & Lobualar Carcinoma

tag: Histo_Grade = Poorly Diff

tag: Path_T = 1C

tag: Path_N = 2

tag: Path_Stg = 3A

tag: ER = Positive/elevated

tag: PR = Positive/elevated

tag: Type_of_Surgery = Partial Mastectomy

tag: Margins = positive

tag: LVI = present

tag: Multicentric_Tumor = yes

tag: Age_at_Dx = 40

tag: 2nd_Distant_Site_Recur = None

tag: 3rd_Distant_Site_Recur = None

tag: XRT = No

tag: Type_1st_XRT = None

tag: Type_1st_Chemo = 3

tag: = ACT

tag: Hormone_Tx = No


title: DU80: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 80

tag: %_Tumor = 60

tag: Race = White

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Moderately Diff

tag: Path_T = 2

tag: Path_Stg = 2A

tag: Tumor_Size_(cm) = 2.5

tag: Regional_Nodes_Examined = 11

tag: Type_of_Surgery = MRM

tag: Margins = negative

tag: Nuclear_Grade = 2

tag: EIC = present

tag: Age_at_Dx = 67

tag: TYPE_1st_Recur = None

tag: 1st_Distant_Site_Recur = None

tag: Chemotherapy = No

tag: Type_1st_Chemo = None

tag: Hormone_Tx = Yes


title: DU90: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 90

tag: %_Tumor = 60

tag: Race = White

tag: Histo_Grade = Poorly Diff

tag: Path_T = 1C

tag: Path_N = 1B

tag: Tumor_Size_(cm) = 2

tag: Regional_Nodes_Positive = 19

tag: Regional_Nodes_Examined = 24

tag: ER = Negative/Normal

tag: PR = Negative/Normal

tag: Nuclear_Grade = 3

tag: LVI = absent

tag: EIC = absent

tag: Age_at_Dx = 49

tag: 2nd_Distant_Site_Recur = None

tag: 3rd_Distant_Site_Recur = None

tag: XRT = Yes

tag: Type_1st_XRT = Beam

tag: Chemotherapy = Yes

tag: Type_1st_Chemo = 1

tag: Hormone_Tx = No


title: 00-7L-rep1

description: Caucasian American with glaucoma

tag: Caucasian American, male, age 83, glaucoma


title: DU89: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 89

tag: %_Tumor = 60

tag: Race = Am Indian

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Moderately Diff

tag: Path_T = 1C

tag: Path_N = 1B

tag: Path_Stg = 2A

tag: Tumor_Size_(cm) = 2

tag: Regional_Nodes_Positive = 3

tag: Regional_Nodes_Examined = 16

tag: Type_of_Surgery = Partial Mastectomy

tag: Margins = negative

tag: Nuclear_Grade = 2

tag: Age_at_Dx = 63

tag: TYPE_1st_Recur = Local

tag: 1st_Distant_Site_Recur = None

tag: XRT = No

tag: Type_1st_XRT = None

tag: = AC


title: DU81: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 81

tag: %_Tumor = 60

tag: Race = White

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Poorly Diff

tag: Path_T = 2

tag: Path_Stg = 2B

tag: Tumor_Size_(cm) = 2.5

tag: Regional_Nodes_Examined = 32

tag: ER = Negative/Normal

tag: PR = Negative/Normal

tag: Type_of_Surgery = MRM

tag: Nuclear_Grade = 3

tag: LVI = present

tag: Age_at_Dx = 57

tag: TYPE_1st_Recur = None

tag: 2nd_Distant_Site_Recur = None

tag: 3rd_Distant_Site_Recur = None

tag: Chemotherapy = Yes

tag: Type_1st_Chemo = 3

tag: Hormone_Tx = No


title: 02-1R-rep1

description: Caucasian American with glaucoma

tag: Caucasian American, male, age 69, glaucoma


title: DU88: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 88

tag: %_Tumor = 60

tag: Race = Black

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Moderately Diff

tag: Path_T = 1C

tag: Path_N = 1B

tag: Path_Stg = 2A

tag: Tumor_Size_(cm) = 1.8

tag: Regional_Nodes_Positive = 6

tag: Regional_Nodes_Examined = 17

tag: ER = Positive/elevated

tag: PR = Positive/elevated

tag: Margins = positive

tag: Nuclear_Grade = 2

tag: EIC = present

tag: Age_at_Dx = 51

tag: Recurrence = 1

tag: TYPE_1st_Recur = Distant

tag: 1st_Distant_Site_Recur = Bone

tag: 2nd_Distant_Site_Recur = Lung

tag: XRT = No

tag: Type_1st_XRT = None

tag: Type_1st_Chemo = 1


title: DU75: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 75

tag: %_Tumor = 80

tag: Race = White

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Moderately Diff

tag: Path_T = 2

tag: Path_Stg = 2A

tag: Tumor_Size_(cm) = 2

tag: Regional_Nodes_Examined = 15

tag: PR = Unknown if Done

tag: Type_of_Surgery = MRM

tag: Margins = negative

tag: LVI = absent

tag: EIC = absent

tag: TYPE_1st_Recur = None

tag: 1st_Distant_Site_Recur = None

tag: 2nd_Distant_Site_Recur = None

tag: 3rd_Distant_Site_Recur = None

tag: Chemotherapy = Yes

tag: Hormone_Tx = Yes


title: DU74: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 74

tag: %_Tumor = 80

tag: Race = White

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Poorly Diff

tag: Tumor_Size_(cm) = 4

tag: Regional_Nodes_Examined = 17

tag: ER = Negative/Normal

tag: PR = Negative/Normal

tag: Nuclear_Grade = 3

tag: LVI = present

tag: Age_at_Dx = 60

tag: Recurrence = 1

tag: TYPE_1st_Recur = Distant

tag: 1st_Distant_Site_Recur = Lung

tag: 2nd_Distant_Site_Recur = Distant Lymph Nodes

tag: XRT = No

tag: Type_1st_XRT = None

tag: Chemotherapy = No

tag: Type_1st_Chemo = None

tag: Hormone_Tx = No


title: DU76: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 76

tag: %_Tumor = 50

tag: Race = White

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Moderately Diff

tag: Path_T = 2

tag: Path_N = 1B

tag: Path_Stg = 2B

tag: Tumor_Size_(cm) = 2.3

tag: Regional_Nodes_Positive = 4

tag: Regional_Nodes_Examined = 13

tag: PR = Positive/elevated

tag: Type_of_Surgery = MRM

tag: Margins = negative

tag: Nuclear_Grade = 2

tag: EIC = present

tag: Age_at_Dx = 49

tag: TYPE_1st_Recur = None

tag: 1st_Distant_Site_Recur = None

tag: 2nd_Distant_Site_Recur = None

tag: 3rd_Distant_Site_Recur = None

tag: Chemotherapy = Yes

tag: Type_1st_Chemo = 1

tag: = AC


title: DU69: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 69

tag: %_Tumor = 60

tag: Race = White

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Poorly Diff

tag: Path_T = 2

tag: Path_Stg = 2A

tag: Tumor_Size_(cm) = 3.5

tag: Regional_Nodes_Examined = 14

tag: ER = Positive/elevated

tag: PR = Negative/Normal

tag: Nuclear_Grade = 3

tag: Age_at_Dx = 60

tag: XRT = No

tag: Type_1st_XRT = None

tag: Hormone_Tx = Yes


title: DU73: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 73

tag: Path_N = 1A

tag: Path_Stg = 2B

tag: Tumor_Size_(cm) = 2.6

tag: Regional_Nodes_Positive = 1

tag: Regional_Nodes_Examined = 13

tag: PR = Positive/elevated

tag: Type_of_Surgery = MRM

tag: Margins = negative

tag: LVI = present

tag: EIC = absent

tag: Age_at_Dx = 56

tag: Recurrence = 1

tag: TYPE_1st_Recur = Distant

tag: 1st_Distant_Site_Recur = Liver

tag: 2nd_Distant_Site_Recur = None

tag: 3rd_Distant_Site_Recur = None

tag: Chemotherapy = No

tag: Type_1st_Chemo = None

tag: Hormone_Tx = No


title: DU67: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 67

tag: %_Tumor = 90

tag: Race = White

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Poorly Diff

tag: Path_T = 2

tag: Path_N = 1B

tag: Path_Stg = 2B

tag: Tumor_Size_(cm) = 3

tag: Regional_Nodes_Positive = 7

tag: Regional_Nodes_Examined = 12

tag: ER = Positive/elevated

tag: LVI = absent

tag: Age_at_Dx = 68

tag: TYPE_1st_Recur = None

tag: 1st_Distant_Site_Recur = None

tag: XRT = No

tag: Type_1st_XRT = None

tag: Chemotherapy = Yes

tag: Type_1st_Chemo = 1


title: DU71: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 71

tag: %_Tumor = 60

tag: Race = White

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Moderately Diff

tag: Regional_Nodes_Positive = 1

tag: Regional_Nodes_Examined = 20

tag: PR = Positive/elevated

tag: Type_of_Surgery = MRM

tag: Margins = negative

tag: Nuclear_Grade = 2

tag: EIC = absent

tag: Age_at_Dx = 42

tag: 2nd_Distant_Site_Recur = None

tag: 3rd_Distant_Site_Recur = None

tag: Hormone_Tx = Yes


title: DU65: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 65

tag: %_Tumor = 70

tag: Histo_Desc = Atypical medullary carcinoma

tag: Path_T = 2

tag: Path_N = 1

tag: Path_Stg = 2B

tag: Tumor_Size_(cm) = 3

tag: Regional_Nodes_Positive = 4

tag: Regional_Nodes_Examined = 22

tag: ER = Unknown if Done

tag: PR = Unknown if Done

tag: LVI = absent

tag: Age_at_Dx = 34

tag: TYPE_1st_Recur = None

tag: 1st_Distant_Site_Recur = None

tag: XRT = No

tag: Type_1st_XRT = None

tag: Chemotherapy = Yes

tag: Type_1st_Chemo = 1

tag: = CAF

tag: Hormone_Tx = No


title: DU68: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 68

tag: %_Tumor = 50

tag: Race = White

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Poorly Diff

tag: Path_T = 2

tag: Path_Stg = 2A

tag: Tumor_Size_(cm) = 3.5

tag: Regional_Nodes_Examined = 8

tag: ER = Negative/Normal

tag: PR = Positive/elevated

tag: Type_of_Surgery = MRM

tag: Margins = negative

tag: Nuclear_Grade = 3

tag: EIC = absent

tag: Age_at_Dx = 50

tag: Recurrence = 1

tag: TYPE_1st_Recur = Distant

tag: 1st_Distant_Site_Recur = Bone

tag: 2nd_Distant_Site_Recur = None

tag: 3rd_Distant_Site_Recur = None

tag: Chemotherapy = No

tag: Type_1st_Chemo = None

tag: Hormone_Tx = Yes


title: DU66: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 66

tag: %_Tumor = 80

tag: Race = White

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Poorly Diff

tag: Path_T = 2

tag: Path_N = 1B

tag: Path_Stg = 2B

tag: Tumor_Size_(cm) = 5

tag: Regional_Nodes_Positive = 1

tag: Regional_Nodes_Examined = 12

tag: PR = Negative/Normal

tag: LVI = present

tag: Age_at_Dx = 49

tag: XRT = No

tag: Type_1st_XRT = None

tag: Chemotherapy = Yes

tag: Type_1st_Chemo = 1

tag: Hormone_Tx = No


title: DU72: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 72

tag: %_Tumor = 70

tag: Race = White

tag: Histo_Grade = Moderately Diff

tag: Tumor_Size_(cm) = 3.5

tag: Regional_Nodes_Positive = 4

tag: Regional_Nodes_Examined = 23

tag: ER = Negative/Normal

tag: PR = Positive/elevated

tag: Type_of_Surgery = MRM

tag: Margins = negative

tag: Nuclear_Grade = 2

tag: LVI = absent

tag: EIC = present

tag: Age_at_Dx = 53

tag: Recurrence = 1

tag: TYPE_1st_Recur = Distant

tag: 1st_Distant_Site_Recur = Pleura

tag: 2nd_Distant_Site_Recur = None

tag: 3rd_Distant_Site_Recur = None

tag: = CAF


title: DU64: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 64

tag: %_Tumor = 80

tag: Race = White

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Poorly Diff

tag: Path_T = 2

tag: Path_Stg = 2A

tag: Tumor_Size_(cm) = 4.5

tag: Regional_Nodes_Examined = 29

tag: ER = Positive/elevated

tag: Nuclear_Grade = 3

tag: EIC = absent

tag: Age_at_Dx = 33

tag: TYPE_1st_Recur = None

tag: 1st_Distant_Site_Recur = None

tag: XRT = No

tag: Type_1st_XRT = None

tag: Chemotherapy = Yes

tag: Type_1st_Chemo = 3

tag: = CMF

tag: Hormone_Tx = Yes


title: DU59: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 59

tag: %_Tumor = 90

tag: Race = Black

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Poorly Diff

tag: Tumor_Size_(cm) = 3.6

tag: Regional_Nodes_Examined = 17

tag: PR = Positive/elevated

tag: Type_of_Surgery = Partial Mastectomy

tag: Margins = positive

tag: Nuclear_Grade = 2

tag: LVI = absent

tag: Age_at_Dx = 62

tag: 2nd_Distant_Site_Recur = None

tag: 3rd_Distant_Site_Recur = None

tag: XRT = Yes

tag: Type_1st_XRT = Beam

tag: Chemotherapy = No

tag: Type_1st_Chemo = None


title: DU58: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 58

tag: %_Tumor = 60

tag: Race = White

tag: Histo_Desc = Infiltrating Duct & Lobualar Carcinoma

tag: Histo_Grade = Moderately Diff

tag: Path_T = 2

tag: Path_Stg = 2A

tag: Tumor_Size_(cm) = 3.5

tag: Regional_Nodes_Examined = 11

tag: ER = Positive/elevated

tag: Nuclear_Grade = 1

tag: LVI = present

tag: EIC = absent

tag: Age_at_Dx = 52

tag: TYPE_1st_Recur = None

tag: 1st_Distant_Site_Recur = None

tag: XRT = No

tag: Type_1st_XRT = None

tag: Hormone_Tx = No


title: DU51: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 51

tag: %_Tumor = 70

tag: Race = White

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Poorly Diff

tag: Path_N = 1B

tag: Path_Stg = 2B

tag: Tumor_Size_(cm) = 2.5

tag: Regional_Nodes_Positive = 11

tag: Regional_Nodes_Examined = 18

tag: PR = Positive/elevated

tag: Type_of_Surgery = MRM

tag: Margins = negative

tag: Nuclear_Grade = 3

tag: Age_at_Dx = 46

tag: DFS = 92

tag: 2nd_Distant_Site_Recur = None

tag: 3rd_Distant_Site_Recur = None

tag: XRT = Yes

tag: Type_1st_XRT = Beam

tag: Chemotherapy = Yes

tag: Type_1st_Chemo = 3

tag: = ACMF

tag: Hormone_Tx = Yes


title: DU61: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 61

tag: %_Tumor = 60

tag: Race = Black

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Poorly Diff

tag: Path_T = 2

tag: Path_N = 1B

tag: Path_Stg = 2B

tag: Tumor_Size_(cm) = 4.5

tag: Regional_Nodes_Positive = 1

tag: Regional_Nodes_Examined = 12

tag: ER = Negative/Normal

tag: PR = Negative/Normal

tag: LVI = absent

tag: EIC = absent

tag: Age_at_Dx = 77

tag: Recurrence = 1

tag: TYPE_1st_Recur = Distant

tag: 1st_Distant_Site_Recur = Bone

tag: XRT = No

tag: Type_1st_XRT = None

tag: Chemotherapy = No

tag: Type_1st_Chemo = None

tag: Hormone_Tx = No


title: DU56: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 56

tag: %_Tumor = 60

tag: Race = White

tag: Histo_Desc = Lobular carcinoma, NOS

tag: Histo_Grade = Not Graded / Unknown

tag: Path_T = 2

tag: Path_Stg = 2A

tag: Tumor_Size_(cm) = 2.5

tag: Regional_Nodes_Examined = 8

tag: ER = Positive/elevated

tag: PR = Positive/elevated

tag: Type_of_Surgery = MRM

tag: Margins = positive

tag: Nuclear_Grade = 2

tag: Age_at_Dx = 46

tag: Recurrence = na

tag: TYPE_1st_Recur = Never Disease Free

tag: 1st_Distant_Site_Recur = None

tag: 2nd_Distant_Site_Recur = None

tag: 3rd_Distant_Site_Recur = None

tag: Chemotherapy = Yes

tag: Type_1st_Chemo = 3

tag: Hormone_Tx = Yes


title: DU55: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 55

tag: %_Tumor = 70

tag: Race = White

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Poorly Diff

tag: Path_T = 2

tag: Path_Stg = 2A

tag: Tumor_Size_(cm) = 4.3

tag: Regional_Nodes_Examined = 11

tag: Type_of_Surgery = Partial Mastectomy

tag: Margins = negative

tag: Nuclear_Grade = 3

tag: LVI = present

tag: EIC = absent

tag: Age_at_Dx = 42

tag: TYPE_1st_Recur = None

tag: XRT = Yes

tag: Type_1st_XRT = Beam

tag: = AC


title: DU52: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 52

tag: %_Tumor = 60

tag: Race = Black

tag: Histo_Grade = Moderately Diff

tag: Path_N = 1B

tag: Path_Stg = 2B

tag: Tumor_Size_(cm) = 3

tag: Regional_Nodes_Positive = 3

tag: Regional_Nodes_Examined = 23

tag: ER = Negative/Normal

tag: PR = Negative/Normal

tag: Margins = positive

tag: LVI = absent

tag: Age_at_Dx = 53

tag: Recurrence = 1

tag: TYPE_1st_Recur = Distant

tag: 1st_Distant_Site_Recur = CNS

tag: 2nd_Distant_Site_Recur = Other, generalized, Unknown Site

tag: 3rd_Distant_Site_Recur = None

tag: Chemotherapy = Yes

tag: Type_1st_Chemo = 3

tag: = CAF

tag: Hormone_Tx = No


title: DU50: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 50

tag: %_Tumor = 80

tag: Race = White

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Poorly Diff

tag: Path_T = 2

tag: Path_N = 1B

tag: Path_Stg = 2B

tag: Tumor_Size_(cm) = 2.9

tag: Regional_Nodes_Positive = 9

tag: Regional_Nodes_Examined = 35

tag: ER = Borderline,Undetermined

tag: Type_of_Surgery = MRM

tag: Margins = negative

tag: Nuclear_Grade = 3

tag: LVI = present

tag: EIC = present

tag: TYPE_1st_Recur = None

tag: 1st_Distant_Site_Recur = None

tag: 2nd_Distant_Site_Recur = None

tag: XRT = No

tag: Type_1st_XRT = None

tag: Chemotherapy = No

tag: Type_1st_Chemo = None


title: DU53: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 53

tag: %_Tumor = 60

tag: Race = White

tag: Histo_Desc = Lobular carcinoma, NOS

tag: Histo_Grade = Not Graded / Unknown

tag: Path_T = 2

tag: Path_Stg = 2A

tag: Tumor_Size_(cm) = 4.5

tag: Regional_Nodes_Examined = 17

tag: ER = Positive/elevated

tag: PR = Negative/Normal

tag: LVI = absent

tag: EIC = absent

tag: Age_at_Dx = 42

tag: 3rd_Distant_Site_Recur = None

tag: Hormone_Tx = No


title: DU47: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 47

tag: %_Tumor = 80

tag: Race = Black

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Undifferentiated

tag: Path_N = 1B

tag: Path_Stg = 2B

tag: Tumor_Size_(cm) = 3.6

tag: Regional_Nodes_Positive = 1

tag: Regional_Nodes_Examined = 24

tag: ER = Negative/Normal

tag: Type_of_Surgery = MRM

tag: Margins = negative

tag: Nuclear_Grade = 3

tag: LVI = present

tag: Age_at_Dx = 52

tag: TYPE_1st_Recur = None

tag: 1st_Distant_Site_Recur = None

tag: 2nd_Distant_Site_Recur = None

tag: XRT = Yes

tag: Type_1st_XRT = Beam

tag: Chemotherapy = Yes

tag: Type_1st_Chemo = 3

tag: = ACT


title: DU49: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 49

tag: %_Tumor = 70

tag: Race = Black

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Poorly Diff

tag: Path_T = 2

tag: Path_Stg = 2A

tag: Tumor_Size_(cm) = 4.2

tag: Regional_Nodes_Examined = 15

tag: PR = Negative/Normal

tag: LVI = absent

tag: EIC = absent

tag: Age_at_Dx = 82

tag: Recurrence = 1

tag: TYPE_1st_Recur = DIstant

tag: 1st_Distant_Site_Recur = Lung

tag: 3rd_Distant_Site_Recur = None

tag: XRT = No

tag: Type_1st_XRT = None

tag: Chemotherapy = No

tag: Type_1st_Chemo = None

tag: Hormone_Tx = No


title: DU43: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 43

tag: %_Tumor = 60

tag: Race = White

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Poorly Diff

tag: Path_T = 2

tag: Tumor_Size_(cm) = 5

tag: Regional_Nodes_Examined = 23

tag: ER = Positive/elevated

tag: PR = Positive/elevated

tag: Type_of_Surgery = MRM

tag: Margins = negative

tag: Nuclear_Grade = 2

tag: LVI = present

tag: EIC = present

tag: Age_at_Dx = 49

tag: TYPE_1st_Recur = None

tag: 1st_Distant_Site_Recur = None

tag: 2nd_Distant_Site_Recur = None

tag: Chemotherapy = Yes

tag: Type_1st_Chemo = 3

tag: = AC


title: DU44: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 44

tag: %_Tumor = 60

tag: Race = White

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Undifferentiated

tag: Path_T = 2

tag: Path_Stg = 2A

tag: Tumor_Size_(cm) = 3.3

tag: Regional_Nodes_Examined = 6

tag: ER = Negative/Normal

tag: PR = Negative/Normal

tag: Nuclear_Grade = 3

tag: LVI = absent

tag: EIC = absent

tag: Age_at_Dx = 60

tag: DFS = 54

tag: 3rd_Distant_Site_Recur = None

tag: XRT = No

tag: Type_1st_XRT = None

tag: Hormone_Tx = No


title: DU41: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 41

tag: %_Tumor = 60

tag: Race = White

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Poorly Diff

tag: Path_N = 1B

tag: Path_Stg = 2B

tag: Tumor_Size_(cm) = 2.5

tag: Regional_Nodes_Positive = 4

tag: Regional_Nodes_Examined = 26

tag: Type_of_Surgery = MRM

tag: Margins = negative

tag: LVI = present

tag: TYPE_1st_Recur = None

tag: 1st_Distant_Site_Recur = None

tag: 2nd_Distant_Site_Recur = None

tag: XRT = Yes

tag: Type_1st_XRT = Beam

tag: Chemotherapy = Yes

tag: Type_1st_Chemo = 3

tag: = ACT


title: DU42: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 42

tag: %_Tumor = 70

tag: Race = Black

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Moderately Diff

tag: Path_T = 2

tag: Path_Stg = 2A

tag: Tumor_Size_(cm) = 3.5

tag: Regional_Nodes_Examined = 14

tag: ER = Negative/Normal

tag: PR = Negative/Normal

tag: Nuclear_Grade = 2

tag: LVI = absent

tag: EIC = absent

tag: Age_at_Dx = 49

tag: 3rd_Distant_Site_Recur = None

tag: XRT = No

tag: Type_1st_XRT = None

tag: = AC

tag: Hormone_Tx = No


title: DU38: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 38

tag: %_Tumor = 70

tag: Race = White

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Poorly Diff

tag: Path_T = 1C

tag: Path_Stg = 1

tag: Tumor_Size_(cm) = 1.9

tag: Regional_Nodes_Examined = 18

tag: ER = Positive/elevated

tag: PR = Borderline,Undetermined

tag: Type_of_Surgery = Partial Mastectomy

tag: Margins = positive

tag: LVI = present

tag: Age_at_Dx = 56

tag: TYPE_1st_Recur = None

tag: 1st_Distant_Site_Recur = None

tag: 2nd_Distant_Site_Recur = None

tag: Chemotherapy = Yes

tag: Type_1st_Chemo = 3


title: DU31: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 31

tag: %_Tumor = 50

tag: Race = White

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Path_N = 1B

tag: Path_Stg = 2A

tag: Tumor_Size_(cm) = 1.6

tag: Regional_Nodes_Positive = 1

tag: Regional_Nodes_Examined = 12

tag: PR = Positive/elevated

tag: Nuclear_Grade = 2

tag: LVI = absent

tag: EIC = absent

tag: Multicentric_Tumor = yes

tag: Age_at_Dx = 47

tag: 3rd_Distant_Site_Recur = None

tag: XRT = No

tag: Type_1st_XRT = None

tag: = CMF

tag: Hormone_Tx = No


title: DU40: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 40

tag: %_Tumor = 60

tag: Race = Black

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Poorly Diff

tag: Path_T = 2

tag: Tumor_Size_(cm) = 2.5

tag: Regional_Nodes_Examined = 18

tag: ER = Positive/elevated

tag: Type_of_Surgery = MRM

tag: Margins = negative

tag: Age_at_Dx = 65

tag: TYPE_1st_Recur = None

tag: 1st_Distant_Site_Recur = None

tag: 2nd_Distant_Site_Recur = None

tag: Chemotherapy = No

tag: Type_1st_Chemo = None

tag: Hormone_Tx = Yes


title: DU35: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 35

tag: %_Tumor = 60

tag: Race = White

tag: Histo_Desc = Infiltrating Duct & Lobualar Carcinoma

tag: Histo_Grade = Moderately Diff

tag: Path_T = 1C

tag: Path_Stg = 1

tag: Tumor_Size_(cm) = 1.6

tag: Regional_Nodes_Examined = 16

tag: PR = Positive/elevated

tag: Nuclear_Grade = 3

tag: LVI = absent

tag: EIC = absent

tag: Age_at_Dx = 58

tag: 3rd_Distant_Site_Recur = None

tag: XRT = No

tag: Type_1st_XRT = None


title: DU39: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 39

tag: %_Tumor = 70

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Poorly Diff

tag: Regional_Nodes_Examined = 15

tag: ER = Negative/Normal

tag: PR = Negative/Normal

tag: Type_of_Surgery = Partial Mastectomy

tag: Margins = negative

tag: Age_at_Dx = 46

tag: TYPE_1st_Recur = None

tag: 1st_Distant_Site_Recur = None

tag: 2nd_Distant_Site_Recur = None

tag: XRT = Yes

tag: Type_1st_XRT = Beam

tag: Chemotherapy = Yes

tag: Type_1st_Chemo = 3

tag: = AT

tag: Hormone_Tx = No


title: DU36: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 36

tag: %_Tumor = 70

tag: Race = White

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Path_T = 1B

tag: Path_Stg = 1

tag: Tumor_Size_(cm) = 1

tag: Regional_Nodes_Examined = 12

tag: Margins = positive

tag: Nuclear_Grade = 3

tag: LVI = present

tag: EIC = present

tag: Multicentric_Tumor = yes

tag: Age_at_Dx = 62

tag: DFS = 50

tag: 3rd_Distant_Site_Recur = None

tag: Chemotherapy = No

tag: Type_1st_Chemo = None


title: DU24: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 24

tag: %_Tumor = 70

tag: Histo_Grade = Poorly Diff

tag: Path_T = 1C

tag: Tumor_Size_(cm) = 1.7

tag: Regional_Nodes_Examined = 23

tag: ER = Positive/elevated

tag: PR = Positive/elevated

tag: Type_of_Surgery = Partial Mastectomy

tag: Margins = negative

tag: EIC = absent

tag: Age_at_Dx = 52

tag: TYPE_1st_Recur = None

tag: 1st_Distant_Site_Recur = None

tag: 2nd_Distant_Site_Recur = None

tag: XRT = Yes

tag: Type_1st_XRT = Beam

tag: Hormone_Tx = Yes


title: DU28: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 28

tag: %_Tumor = 50

tag: Race = White

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Moderately Diff

tag: Path_Stg = 1

tag: Tumor_Size_(cm) = 1.5

tag: Regional_Nodes_Examined = 2

tag: PR = Negative/Normal

tag: Nuclear_Grade = 2

tag: LVI = absent

tag: Age_at_Dx = 58

tag: 3rd_Distant_Site_Recur = None

tag: Chemotherapy = No

tag: Type_1st_Chemo = None


title: DU26: Breast tumors from women with early stage breast cancer

tag: EA_Designation = 26

tag: %_Tumor = 60

tag: Race = Black

tag: Path_T = 1C

tag: Tumor_Size_(cm) = 2

tag: Regional_Nodes_Examined = 9

tag: ER = Positive/elevated

tag: PR = Positive/elevated

tag: Type_of_Surgery = MRM

tag: Margins = negative

tag: EIC = absent

tag: Age_at_Dx = 60

tag: TYPE_1st_Recur = None

tag: 1st_Distant_Site_Recur = None

tag: 2nd_Distant_Site_Recur = None

tag: XRT = No

tag: Type_1st_XRT = None

tag: Hormone_Tx = Yes


title: DU27: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 27

tag: %_Tumor = 70

tag: Race = White

tag: Histo_Desc = Infiltrating Duct & Lobualar Carcinoma

tag: Histo_Grade = Poorly Diff

tag: Path_Stg = 1

tag: Tumor_Size_(cm) = 1.9

tag: Regional_Nodes_Examined = 8

tag: Nuclear_Grade = 2

tag: LVI = absent

tag: Age_at_Dx = 81

tag: 3rd_Distant_Site_Recur = None

tag: Chemotherapy = No

tag: Type_1st_Chemo = None


title: DU32: Breast tumors from women with early stage breast cancer

tag: EA_Designation = 32

tag: %_Tumor = 50

tag: Histo_Desc = Papillary Carcinoma, NOS

tag: Histo_Grade = Moderately Diff

tag: Path_T = 1C

tag: Tumor_Size_(cm) = 2

tag: Regional_Nodes_Examined = 26

tag: ER = Positive/elevated

tag: PR = Positive/elevated

tag: Type_of_Surgery = Partial Mastectomy

tag: Margins = positive

tag: Nuclear_Grade = 3

tag: EIC = absent

tag: Multicentric_Tumor = yes

tag: Age_at_Dx = 44

tag: TYPE_1st_Recur = None

tag: 1st_Distant_Site_Recur = None

tag: 2nd_Distant_Site_Recur = None

tag: XRT = No

tag: Type_1st_XRT = None


title: DU25: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 25

tag: %_Tumor = 70

tag: Race = White

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Poorly Diff

tag: Path_Stg = 1

tag: Tumor_Size_(cm) = 1.5

tag: Regional_Nodes_Examined = 9

tag: Type_of_Surgery = MRM

tag: Margins = negative

tag: Nuclear_Grade = 2

tag: LVI = absent

tag: Age_at_Dx = 48

tag: 3rd_Distant_Site_Recur = None

tag: Chemotherapy = Yes

tag: Type_1st_Chemo = 3

tag: = CMF

tag: Hormone_Tx = No


title: DU33: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 33

tag: %_Tumor = 60

tag: Path_T = 1C

tag: Tumor_Size_(cm) = 2

tag: Regional_Nodes_Examined = 19

tag: ER = Positive/elevated

tag: PR = Negative/Normal

tag: Nuclear_Grade = 3

tag: EIC = absent

tag: Age_at_Dx = 41

tag: TYPE_1st_Recur = None

tag: 1st_Distant_Site_Recur = None

tag: 2nd_Distant_Site_Recur = None

tag: XRT = No

tag: Type_1st_XRT = None


title: DU30: Breast tumors from women with early stage breast cancer

tag: EA_Designation = 30

tag: Race = Black

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Poorly Diff

tag: Path_Stg = 1

tag: Regional_Nodes_Examined = 25

tag: Type_of_Surgery = Partial Mastectomy

tag: Margins = negative

tag: Nuclear_Grade = 2

tag: LVI = absent

tag: Multicentric_Tumor = yes

tag: Age_at_Dx = 61

tag: DFS = 71

tag: 3rd_Distant_Site_Recur = None

tag: XRT = Yes

tag: Type_1st_XRT = Beam

tag: Chemotherapy = No

tag: Type_1st_Chemo = None

tag: Hormone_Tx = Yes


title: DU34: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 34

tag: %_Tumor = 80

tag: Race = White

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Moderately Diff

tag: Path_T = 1C

tag: Path_N = 1B

tag: Path_Stg = 2A

tag: Tumor_Size_(cm) = 1.6

tag: Regional_Nodes_Positive = 1

tag: Regional_Nodes_Examined = 12

tag: ER = Positive/elevated

tag: PR = Positive/elevated

tag: Type_of_Surgery = MRM

tag: LVI = present

tag: EIC = absent

tag: Age_at_Dx = 81

tag: TYPE_1st_Recur = None

tag: 1st_Distant_Site_Recur = None

tag: 2nd_Distant_Site_Recur = None

tag: XRT = No

tag: Type_1st_XRT = None

tag: Hormone_Tx = No


title: DU37: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 37

tag: %_Tumor = 60

tag: Race = White

tag: Histo_Desc = Mucinous Adenocarcinoma

tag: Histo_Grade = Not Graded / Unknown

tag: Path_T = 1C

tag: Path_Stg = 1

tag: Tumor_Size_(cm) = 1.8

tag: Regional_Nodes_Examined = 28

tag: ER = Negative/Normal

tag: PR = Negative/Normal

tag: Margins = negative

tag: LVI = absent

tag: Age_at_Dx = 65

tag: 3rd_Distant_Site_Recur = None

tag: Chemotherapy = No

tag: Type_1st_Chemo = None


title: DU23: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 23

tag: Race = Black

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Poorly Diff

tag: Path_T = 1B

tag: Tumor_Size_(cm) = 1

tag: Regional_Nodes_Examined = 36

tag: ER = Positive/elevated

tag: PR = Borderline,Undetermined

tag: Type_of_Surgery = MRM

tag: Nuclear_Grade = 3

tag: EIC = present

tag: Age_at_Dx = 38

tag: TYPE_1st_Recur = None

tag: 1st_Distant_Site_Recur = None

tag: 2nd_Distant_Site_Recur = None

tag: XRT = No

tag: Type_1st_XRT = None

tag: Hormone_Tx = No


title: DU21: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 21

tag: %_Tumor = 70

tag: Race = Asian

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Path_T = 1C

tag: Path_Stg = 1

tag: Tumor_Size_(cm) = 1.5

tag: Regional_Nodes_Examined = 15

tag: PR = Positive/elevated

tag: Margins = negative

tag: LVI = absent

tag: EIC = absent

tag: Age_at_Dx = 47

tag: 3rd_Distant_Site_Recur = None

tag: Chemotherapy = Yes

tag: Type_1st_Chemo = 3

tag: Hormone_Tx = Yes


title: DU20: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 20

tag: %_Tumor = 50

tag: Race = White

tag: Histo_Grade = Moderately Diff

tag: Regional_Nodes_Examined = 32

tag: ER = Negative/Normal

tag: PR = Negative/Normal

tag: Type_of_Surgery = MRM

tag: Nuclear_Grade = 2

tag: EIC = present

tag: Age_at_Dx = 50

tag: TYPE_1st_Recur = None

tag: 1st_Distant_Site_Recur = None

tag: 2nd_Distant_Site_Recur = None

tag: XRT = No

tag: Type_1st_XRT = None

tag: Chemotherapy = No

tag: Type_1st_Chemo = None


title: DU15: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 15

tag: %_Tumor = 80

tag: Histo_Desc = Lobular carcinoma, NOS

tag: Histo_Grade = Well Diff

tag: Path_T = 1C

tag: Path_Stg = 1

tag: Tumor_Size_(cm) = 1.5

tag: Regional_Nodes_Examined = 19

tag: ER = Positive/elevated

tag: Margins = negative

tag: Nuclear_Grade = 1

tag: LVI = absent

tag: EIC = absent

tag: Age_at_Dx = 69

tag: 3rd_Distant_Site_Recur = None

tag: Hormone_Tx = Yes


title: DU19: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 19

tag: %_Tumor = 60

tag: Race = White

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Poorly Diff

tag: Path_N = 1A

tag: Path_Stg = 2A

tag: Regional_Nodes_Positive = 1

tag: Regional_Nodes_Examined = 28

tag: PR = Positive/elevated

tag: Type_of_Surgery = MRM

tag: Nuclear_Grade = 3

tag: Age_at_Dx = 67

tag: TYPE_1st_Recur = None

tag: 1st_Distant_Site_Recur = None

tag: 2nd_Distant_Site_Recur = None

tag: XRT = No

tag: Type_1st_XRT = None

tag: Chemotherapy = No

tag: Type_1st_Chemo = None


title: DU13: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 13

tag: %_Tumor = 50

tag: Race = Black

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Moderately Diff

tag: Path_T = 1C

tag: Path_Stg = 1

tag: Tumor_Size_(cm) = 1.5

tag: Regional_Nodes_Examined = 16

tag: ER = Borderline,Undetermined

tag: Margins = negative

tag: Nuclear_Grade = 2

tag: LVI = absent

tag: EIC = absent

tag: Age_at_Dx = 60

tag: 3rd_Distant_Site_Recur = None

tag: XRT = Yes

tag: Type_1st_XRT = Beam

tag: Hormone_Tx = Yes


title: DU11: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 11

tag: %_Tumor = 80

tag: Race = White

tag: Path_N = 1B

tag: Path_Stg = 2A

tag: Tumor_Size_(cm) = 1.7

tag: Regional_Nodes_Positive = 2

tag: ER = Positive/elevated

tag: PR = Positive/elevated

tag: Type_of_Surgery = MRM

tag: Nuclear_Grade = 3

tag: LVI = present

tag: Age_at_Dx = 74

tag: TYPE_1st_Recur = None

tag: 1st_Distant_Site_Recur = None

tag: 2nd_Distant_Site_Recur = None

tag: XRT = No

tag: Type_1st_XRT = None

tag: Chemotherapy = No

tag: Type_1st_Chemo = None


title: DU14: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 14

tag: %_Tumor = 70

tag: Race = White

tag: Histo_Desc = Mucinous Adenocarcinoma

tag: Histo_Grade = Not Graded / Unknown

tag: Path_T = 1B

tag: Path_Stg = 1

tag: Tumor_Size_(cm) = 0.8

tag: Regional_Nodes_Examined = 17

tag: Margins = negative

tag: LVI = absent

tag: Age_at_Dx = 68

tag: 3rd_Distant_Site_Recur = None

tag: Hormone_Tx = Yes


title: DU22: Breast tumors from women with early stage breast cancer

tag: EA_Designation = 22

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Poorly Diff

tag: Regional_Nodes_Examined = 13

tag: ER = Positive/elevated

tag: PR = Positive/elevated

tag: Type_of_Surgery = MRM

tag: Nuclear_Grade = 2

tag: EIC = absent

tag: Age_at_Dx = 45

tag: TYPE_1st_Recur = None

tag: 1st_Distant_Site_Recur = None

tag: 2nd_Distant_Site_Recur = None

tag: XRT = No

tag: Type_1st_XRT = None

tag: Chemotherapy = No

tag: Hormone_Tx = No


title: DU10: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 10

tag: %_Tumor = 80

tag: Race = White

tag: Path_T = 1C

tag: Path_Stg = 1

tag: Tumor_Size_(cm) = 2

tag: Regional_Nodes_Examined = 18

tag: Margins = negative

tag: LVI = present

tag: Age_at_Dx = 65

tag: Recurrence = 1

tag: TYPE_1st_Recur = Distant

tag: 1st_Distant_Site_Recur = Bone

tag: 3rd_Distant_Site_Recur = None

tag: Type_1st_Chemo = None


title: DU16: Breast tumors from women with early stage breast cancer

tag: EA_Designation = 16

tag: %_Tumor = 50

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Poorly Diff

tag: Tumor_Size_(cm) = 1.8

tag: Regional_Nodes_Examined = 19

tag: ER = Positive/elevated

tag: PR = Positive/elevated

tag: Type_of_Surgery = MRM

tag: Nuclear_Grade = 2

tag: LVI = absent

tag: EIC = absent

tag: Age_at_Dx = 61

tag: 1st_Distant_Site_Recur = Distant Lymph Nodes

tag: 2nd_Distant_Site_Recur = Lung

tag: XRT = No

tag: Type_1st_XRT = None

tag: Chemotherapy = No

tag: Hormone_Tx = Yes


title: DU6: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 6

tag: %_Tumor = 90

tag: Race = White

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Path_T = 1C

tag: Path_N = 1B

tag: Path_Stg = 2A

tag: Tumor_Size_(cm) = 1.5

tag: Regional_Nodes_Positive = 2

tag: Regional_Nodes_Examined = 27

tag: Margins = negative

tag: Age_at_Dx = 47

tag: Recurrence = 1

tag: TYPE_1st_Recur = Distant

tag: 2nd_Distant_Site_Recur = None

tag: 3rd_Distant_Site_Recur = None

tag: Chemotherapy = Yes

tag: Type_1st_Chemo = 1

tag: = CAF


title: DU12: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 12

tag: %_Tumor = 60

tag: Race = White

tag: Histo_Grade = Poorly Diff

tag: Path_T = 2

tag: Tumor_Size_(cm) = 4

tag: Regional_Nodes_Examined = 18

tag: ER = Positive/elevated

tag: PR = Negative/Normal

tag: Type_of_Surgery = MRM

tag: Nuclear_Grade = 3

tag: LVI = absent

tag: EIC = present

tag: Age_at_Dx = 39

tag: TYPE_1st_Recur = None

tag: 1st_Distant_Site_Recur = None

tag: XRT = No

tag: Type_1st_XRT = None

tag: = CMF

tag: Hormone_Tx = Yes


title: DU7: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 7

tag: %_Tumor = 60

tag: Race = White

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Poorly Diff

tag: Path_Stg = 2A

tag: Tumor_Size_(cm) = 2

tag: Regional_Nodes_Examined = 23

tag: ER = Negative/Normal

tag: Margins = negative

tag: Age_at_Dx = 56

tag: 2nd_Distant_Site_Recur = None

tag: 3rd_Distant_Site_Recur = None

tag: Chemotherapy = Yes

tag: Type_1st_Chemo = 1

tag: = MF

tag: Hormone_Tx = No


title: DU4: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 4

tag: %_Tumor = 50

tag: Race = Black

tag: Histo_Grade = Moderately Diff

tag: Path_T = 1B

tag: Path_Stg = 1

tag: Tumor_Size_(cm) = 0.7

tag: Regional_Nodes_Examined = 15

tag: ER = Positive/elevated

tag: PR = Negative/Normal

tag: Type_of_Surgery = MRM

tag: LVI = absent

tag: EIC = present

tag: Age_at_Dx = 62

tag: TYPE_1st_Recur = None

tag: 1st_Distant_Site_Recur = None

tag: XRT = No

tag: Type_1st_XRT = None

tag: Chemotherapy = No

tag: Type_1st_Chemo = None

tag: Hormone_Tx = Yes


title: DU18: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 18

tag: %_Tumor = 60

tag: Race = Black

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Poorly Diff

tag: Path_T = 1C

tag: Tumor_Size_(cm) = 1.8

tag: ER = Negative/Normal

tag: Type_of_Surgery = Partial Mastectomy

tag: Margins = negative

tag: Nuclear_Grade = 3

tag: LVI = present

tag: EIC = absent

tag: Age_at_Dx = 50

tag: 2nd_Distant_Site_Recur = None

tag: 3rd_Distant_Site_Recur = None

tag: XRT = Yes

tag: Type_1st_XRT = Beam

tag: Chemotherapy = Yes

tag: Type_1st_Chemo = 3

tag: = MF, Lecovorin

tag: Hormone_Tx = No


title: DU8: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 8

tag: %_Tumor = 50

tag: Race = White

tag: Histo_Desc = Infiltrating Duct & Lobualar Carcinoma

tag: Histo_Grade = Not Graded / Unknown

tag: Path_T = 1C

tag: Path_Stg = 1

tag: Tumor_Size_(cm) = 1.5

tag: Regional_Nodes_Examined = 12

tag: PR = Positive/elevated

tag: Type_of_Surgery = MRM

tag: Age_at_Dx = 42

tag: TYPE_1st_Recur = None

tag: 1st_Distant_Site_Recur = None

tag: XRT = No

tag: Type_1st_XRT = None

tag: Chemotherapy = No

tag: Type_1st_Chemo = None

tag: Hormone_Tx = Yes


title: DU17: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 17

tag: %_Tumor = 70

tag: Race = White

tag: Histo_Desc = Lobular carcinoma, NOS

tag: Regional_Nodes_Examined = 13

tag: ER = Positive/elevated

tag: PR = Negative/Normal

tag: Type_of_Surgery = Partial Mastectomy

tag: Margins = positive

tag: LVI = present

tag: Age_at_Dx = 43

tag: 2nd_Distant_Site_Recur = None

tag: 3rd_Distant_Site_Recur = None

tag: XRT = Yes

tag: Type_1st_XRT = Beam

tag: Chemotherapy = Yes

tag: Type_1st_Chemo = 1

tag: = MF


title: DU3: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 3

tag: %_Tumor = 70

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Poorly Diff

tag: Path_T = 1B

tag: Path_N = 1B

tag: Path_Stg = 2A

tag: Tumor_Size_(cm) = 1

tag: Regional_Nodes_Positive = 11

tag: Regional_Nodes_Examined = 27

tag: Type_of_Surgery = MRM

tag: EIC = present

tag: Age_at_Dx = 39

tag: TYPE_1st_Recur = None

tag: 1st_Distant_Site_Recur = None

tag: XRT = No

tag: Type_1st_XRT = None

tag: = CMFVP-A

tag: Hormone_Tx = Yes


title: DU2: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 2

tag: %_Tumor = 60

tag: Race = White

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Path_T = 1C

tag: Path_M = X

tag: Path_Stg = 99

tag: Tumor_Size_(cm) = 1.6

tag: Regional_Nodes_Positive = 6

tag: Regional_Nodes_Examined = 23

tag: ER = Positive/elevated

tag: PR = Positive/elevated

tag: Nuclear_Grade = 2

tag: Age_at_Dx = 65

tag: Recurrence = 1

tag: TYPE_1st_Recur = Distant

tag: 1st_Distant_Site_Recur = Other, generalized, Unknown Site

tag: 2nd_Distant_Site_Recur = None

tag: 3rd_Distant_Site_Recur = None

tag: Chemotherapy = No

tag: Type_1st_Chemo = None


title: DU9: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 9

tag: %_Tumor = 80

tag: Race = White

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Poorly Diff

tag: Path_T = 1C

tag: Path_N = 1B

tag: Path_Stg = 2A

tag: Tumor_Size_(cm) = 1.2

tag: Regional_Nodes_Positive = 1

tag: Regional_Nodes_Examined = 11

tag: ER = Negative/Normal

tag: PR = Negative/Normal

tag: Type_of_Surgery = MRM

tag: Margins = negative

tag: Age_at_Dx = 74

tag: TYPE_1st_Recur = None

tag: 1st_Distant_Site_Recur = None

tag: XRT = No

tag: Type_1st_XRT = None

tag: Hormone_Tx = No


title: DU1: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 1

tag: %_Tumor = 80

tag: Race = White

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Histo_Grade = Poorly Diff

tag: Path_T = 1A

tag: Path_Stg = 1

tag: Tumor_Size_(cm) = 1.6

tag: Regional_Nodes_Examined = 12

tag: ER = Positive/elevated

tag: PR = Positive/elevated

tag: Nuclear_Grade = 2

tag: LVI = absent

tag: EIC = absent

tag: Age_at_Dx = 67

tag: 2nd_Distant_Site_Recur = None

tag: 3rd_Distant_Site_Recur = None

tag: Chemotherapy = No

tag: Type_1st_Chemo = None

tag: Hormone_Tx = Yes


title: DU5: Breast tumors from women with early stage breast cancer

tag: Tumor

tag: EA_Designation = 5

tag: %_Tumor = 50

tag: Race = Asian

tag: Histo_Desc = Ductal Carcinoma, NOS

tag: Tumor_Size_(cm) = 0.2

tag: ER = Negative/Normal

tag: PR = Negative/Normal

tag: Type_of_Surgery = MRM

tag: Margins = negative

tag: Nuclear_Grade = 3

tag: EIC = present

tag: Age_at_Dx = 39

tag: TYPE_1st_Recur = None

tag: 1st_Distant_Site_Recur = None

tag: XRT = No

tag: Type_1st_XRT = None

tag: Chemotherapy = Yes

tag: Type_1st_Chemo = 1

tag: Hormone_Tx = No


title: PCNSL biopsy (PCNSL28)

status: Public on Dec 16 2007

city: Cologne

first: Manuel

last: Montesinos-Rongen

state: NRW

address: Kerpenerstr. 62

department: Institute for Neuropathology

country: Germany

institute: University Hospital Cologne

description: PCNSL biopsy. The frozen tissue was homogeneized in Trizol reagent and RNA was purified following manufacturer instructions. Targets were produced starting from 6 ug of total RNA following standard Affymetrix protocol.

data_processing: obtained by using GCOS1.2

label: Biotin

source_name: PCNSL biopsy

tag: Primary CNS lymphoma (PCNSL) biopsy.


title: PCNSL biopsy (PCNSL27)

hyb_protocol: Targets were produced starting from 6 ug of total RNA following standard Affymetrix protocol.

extract_protocol: The frozen tissue was homogeneized in Trizol reagent and RNA was purified following manufacturer instructions.


title: epithelial; pair 2

status: Public on Jan 03 2008

city: Richmond

first: Latasha

middle: C

last: Redmond

state: VA

address: 401 College Street

department: Human Genetics

institute: Virginia Commonwealth University

description: Gene expression data from pair 2 E9.5 yolk sac epithelial cells

hyb_protocol: Fifteen μg of labeled erythroid or epithelial cRNA was fragmented and 10 μg was hybridized to Affymetrix GeneChip Mouse Genome 430A 2.0 arrays for 18 hours (Affymetrix Inc.).  The 8 microarrays were washed and stained with streptavidin–phycoerythrin as described  (Redmond et al., Blood Cells Molecules and  Diseases 2006, 37:27).

scan_protocol: Image analysis was performed on the E9.5 yolk sac data set using the GeneChip Operating System version 1.4 (GCOS1.1, Affymetrix Inc.).  The image of the scanned array was stored as a DAT file using the Affymetrix software.

data_processing: Quality control parameters such as scaling factors used to normalize the chips, average background and noise were analyzed and similar, thus making all comparisons valid.  The raw intensities for each probe set were stored in electronic formats by the GCOS software.  Scaling factors used to normalize the chips to a target value (TGT), and in this study, the TGT was set at 100. Probe set expression summaries were calculated with the Microarray Suite version 5.0 (MAS5) algorithm. MAS5 expression summaries were obtained using the mas5 function in the affy package in R/Bioconductor. Significance score (S-score) method was used to compare 4 sets of paired GeneChips to determine significant changes in gene expression between erythroid and epithelial cells. A paired set consisted of an erythroid and epithelial GeneChip, for which the two different cell types were isolated from the same yolk sacs.  It uses an error-based model to determine the variances for probe pair signals and follows a normal standard distribution. S-score values were obtained using the SScore function in the sscore package in Bioconductor.  Probe sets with absolute values of the S-score greater or equal to 2.00 were considered to correspond to significant differences between the two types of samples.  P-values were calculated from S-score values and were combined using Fisher’s procedure for combining p-values.

organism: Mus musculus

source_name: Pair 2-Mus musculus E9.5 yolk sac epithelial cells

label_protocol: Ten to 39 ng of erythroid or epithelial RNA was used to generate double stranded cDNA with the T7-oligo (dT) primer according to the Affymetrix GeneChip Two cycle target labeling protocol (Affymetrix Inc., Santa Clara, CA, USA).  Labeled cRNA yield and purity was determined as described (Redmond et al., 2006).

growth_protocol: Timed-pregnant FVB/N mice were anesthetized and sacrificed. E9.5 yolk sacs were dissected from the embryo and cryoprotected in PBS with 20% sucrose.

extract_protocol: Total RNA was isolated from 4 different pairs of erythroid and epithelial cells using reagents from the (ToTALLY RNA isolation kit; Ambion Inc., Austin, TX, USA) and quality assessment by capillary electrophoresis were performed as previously described (Redmond et al., Blood Cells Molecules and  Diseases 2006, 37:27).

treatment_protocol: E9.5 yolk sacs tissues were rinsed once in 1:1 20% sucrose PBS:Optimal Cutting Temperature freezing media (OCT, Tissue-Tek), then OCT alone and frozen.  Eight micron E9.5 sections were stained with the LCM frozen section staining kit (Molecular Devices, Mountain View, CA, USA) and used for laser capture dissection experiments. Using the PixCell II Laser Capture Microdissection System (Arcturus Bioscience), approximately 1 E9.5 yolk sac erythroid cell was collected for every 2 to 3 laser pulses, and 1 epithelial cell was collected per pulse on LCM HS Capsure caps. Epithelial cells were collected from the same microscope slides immediately following procurement of the erythroid cells, and were used as the non-erythroid control.  Approximately 12 to 50 microscope slides, using 2 to 4 yolk sacs from 2 different litters were used per biological replicate.

tag: FVB/N embryonic day 9.5


title: PCNSL biopsy (PCNSL22)

scan_protocol: Targets were produced starting from 6 ug of total RNA following standard Affymetrix protocol.


title: PCNSL biopsy (PCNSL26)

label_protocol: Targets were produced starting from 6 ug of total RNA following standard Affymetrix protocol.


title: PCNSL biopsy (PCNSL24)


title: epithelial; pair 1

description: Gene expression data from pair 1 E9.5 yolk sac epithelial cells

source_name: Pair 1-Mus musculus E9.5 yolk sac epithelial cells


title: PCNSL biopsy (PCNSL11)


title: PCNSL biopsy (PCNSL17)


title: PCNSL biopsy (PCNSL14)


title: PCNSL biopsy (PCNSL16)


title: PCNSL biopsy (PCNSL25)


title: PCNSL biopsy (PCNSL09)

tag: Primary CNS lymphoma (PCNSL) biopsy


title: PCNSL biopsy (PCNSL20)


title: PCNSL biopsy (PCNSL10)


title: PCNSL biopsy (PCNSL07)


title: PCNSL biopsy (PCNSL21)


title: epithelial; pair 4

description: Gene expression data from pair 4 E9.5 yolk sac epithelial cells

source_name: Pair 4-Mus musculus E9.5 yolk sac epithelial cells


title: PCNSL biopsy (PCNSL05)


title: PCNSL biopsy (PCNSL03)


title: PCNSL biopsy (PCNSL06)


title: Suprachiasmatic Nucleus after 30-min Light pulse rep3

status: Public on Oct 31 2007

city: Kent

first: Eric

middle: M

last: Mintz

state: OH

address: Cunningham Hall

department: Biological Sciences

institute: Kent State University

description: Gene Expression data from the suprachiasmatic nucleus of an animal euthanized 1.5 hours after lights off.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on a GeneChip Mouse 430A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned using the Affymetrix Scanner 3000

data_processing: The data were analyzed with GeneChip Operating Systtem 1.1 using the MAS 5.0 algorithm, using Affymetrix default analysis settings and global scaling as normalization method, using the default normalization target setting of 500.

source_name: Suprachiasmatic Nucleus, captured at end of 30-minute light pulse

label_protocol: Following the 2nd round of linear amplification, the total amount of cDNA was biotinylated according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix).  15 ug of labeled cRNA was fragmented, then 10 ug was hybridized to Affymetrix 430A 2.0 Genechips according to standard Affymetrix protocols (Expression Analysis Technical Manual, 2004, Affymetix)

growth_protocol: Adult male C57BL/6 mice were individually housed in a 14:10 light/dark cycle in their experimental room and cage for at least two weeks prior to the experiment.

extract_protocol: The pooled samples were purified using an RNA purification kit (Picopure from Molecular Devices) including a DNase treatment.  A 1 µl aliquot of each sample was removed and processed on an Agilent Bioanalyzer 2100 using the Agilent Lab-on-a-Chip Picochip RNA kit.  Only samples with RNA integrity numbers about 6.8 were processed further.  RNA was stored at -70?C until ready to proceed.  1 ng of total RNA was then processed through two rounds of linear amplification using Riboamp HS amplification kits (Molecular Devices).

treatment_protocol: They were then exposed to a 30 minute light pulse (2400lux) or a dark pulse (sham) starting one hour after lights off (Zeitgeber time (ZT) 13).  Immediately after treatment, mice were euthanized via cervical dislocation.  Dark pulse mice were euthanized under dim red light, and both light and dark pulse animals’ eyes were dissected out immediately to avoid excess exposure to light.  The mice were then decapitated and the brains were quickly removed and frozen in isopentane cooled in dry ice.  Brains were stored at -70?C until ready for further processing.  Brains were cut into 12 µm thick sections on a cryostat and directly mounted onto glass slides.  Sections were stained using a quick protocol to allow for visual identification of the suprachiasmatic nucleus.  First the sections were fixed in a 75% EtOH solution for 30 seconds, rinsed in water to remove excess EtOH from the slide, and then immersed in Hematoxylin for 90 seconds.  Slides were then washed in molecular biology grade water.  The slides then were taken through an alcohol dehydration series of 75%, 95% and 100% EtOH for 30 seconds each, followed by immersion in xylenes for 5 minutes.  The slides were removed from the xylene, and once the remaining xylenes had evaporated the slides were placed into a laser capture microscope (Arcturus) and the SCN was identified and captured into CapSure® HS LCM Caps (Molecular Devices).  For microarrays and validation of microarrays by quantitative real-time PCR (qRT-PCR), 6 consecutive SCN sections were captured from each mouse.  Samples from three mice were then pooled together within the same treatment, so in total there were 18 SCN sections pooled together.

tag: Strain

value: C57BL/6; Gender:Male; Age:2-4 months


title: WGACON-71 (sample found to have AD-like pathology removed from AJHG report)

status: Public on Nov 04 2007

city: Miami

first: Amanda

last: Myers

state: FL

address: 1600 NW 10th Ave

department: Psychiatry and Behavioral Sciences

institute: Miller School of Medicine, University of Miami

description: Human Cortex from neurologically normal control, Caucasian, male.

hyb_protocol: RNA: Illumina Whole Genome Gene Expression Rev. F (Illumina Doc #11763837)

scan_protocol: RNA: Illumina Beadstation

data_processing: RNA: Beadstudio software v 1.5.0.34, rank invariant normalization to extract, log10 transformation before analysis

source_name: neuropathologically normal frozen temporal cortex

label_protocol: RNA: per ambion manual for cat #IL1791, biotinylated cRNA created from in vitro translation targeting poly A tail, cy3 used to image RNA signal

extract_protocol: total RNA (Qiagen Rneasy Lipid Tissue cat #cat 74804, Qiagen Rnase free dnase set- cat # 79254)


title: PCNSL biopsy (PCNSL04)


title: Suprachiasmatic Nucleus after 30-min Light pulse rep2


title: WGACON-108 ((included Nat genet report, not included AJHG report-male reported, gender appears ambiguous on PLINK test)

hyb_protocol: RNA: Illumina Whole Genome Gene Expression Rev. F (Illumina Doc #11763837);DNA: Allele Specific Hybridization, Affymetrix Mapping 500K Assay Manual (Affymetrix P/N 701930 Rev. 3)

scan_protocol: RNA: Illumina Beadstation; DNA: Genechip Scanner 3000

label_protocol: RNA: per ambion manual for cat #IL1791, biotinylated cRNA created from in vitro translation targeting poly A tail, cy3 used to image RNA signal DNA: biotin labeled as per Affymetrix protocol for cat # 900753/900754

extract_protocol: total RNA (Qiagen Rneasy Lipid Tissue cat #cat 74804, Qiagen Rnase free dnase set- cat # 79254), genomic DNA (Qiagen Dneasy kit cat # 69504)


title: Suprachiasmatic Nucleus after 30-min dark pulse rep1

source_name: Suprachiasmatic Nucleus, captured at end of 30-minute sham light pulse


title: Jnk1 Adv-shRNA 5

status: Public on Oct 02 2007

city: Abbott Park

first: Paul

last: Jung

address: 100 Abbott Park Road

department: Gene Expression Analysis

institute: Abbott Laboratories

description: Jnk1 Adv-shRNA treated liver from C57BL/6J DIO mice.

scan_protocol: Scan protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 3000

data_processing: Rosetta Resolver 6.0

label_protocol: Enzo Biochem

extract_protocol: Total RNA was isolated from pulverized liver tissues using Qiagen RNeasy 96 Universal Tissue 8000 Kit.

tag: Male C57BL/6J mice (Jackson Laboratories) were housed on a 12-hour light-dark cycle and were allowed free access to water and standard laboratory chow or high fat diet (Research Diet D12450Bi, D12492i) for 22-24 weeks. Adenoviruses were purified and diluted in saline solution, and 2E11 viral particles were delivered into the animals by a single tail-vein injection on day zero. Animals were fed ad libitum and were sacrificed at day 5 after adenovirus injection.


title: WGACON-212 (included Nat genet report, not included AJHG report-male reported, gender appears ambiguous on PLINK test)

source_name: neuropathologically normal frozen frontal cortex


title: Suprachiasmatic Nucleus after 30-min Light pulse rep1


title: Jnk1 Adv-shRNA 4

source_name: Jnk1 Adv-shRNA treated liver from C57BL/6J DIO mice.


title: PCNSL biopsy (PCNSL18)


title: Jnk1 Adv-shRNA 3


title: WGACON-78 (sample found to have AD-like pathology removed from AJHG report)


title: Suprachiasmatic Nucleus after 30-min dark pulse rep3


title: Suprachiasmatic Nucleus after 30-min dark pulse rep2


title: WGACON-105 ((included Nat genet report, not included AJHG report-female reported, gender appears male on PLINK test)

description: Human Cortex from neurologically normal control, Caucasian, female.


title: GFP Adv-shRNA 2

description: GFP Adv-shRNA treated liver from C57BL/6J DIO mice.


title: fibroblasts_OA_patient118

status: Public on Aug 30 2007

city: Dresden

first: Andreas

last: Beyer

address: Tatzberg. 47/49

institute: BIOTEC

description: see publication for details

hyb_protocol: Hybridization and washing of gene chips was performed according to the supplier’s instructions (http://www.affymetrix.com).

scan_protocol: Microarrays were analyzed by laser scanning (Hewlett-Packard Gene Scanner).

data_processing: Background-corrected signal intensities were determined using the MAS 5.0 software (Affymetrix).

source_name: Synovial fibroblasts, osteoarthritis patient no. 118.

label_protocol: RNA probes were labeled according to the supplier’s instructions (Affymetrix, Santa Clara, CA, USA).

growth_protocol: The tissue samples were minced, digested with trypsin/collagenase P, and the resulting single cell suspension cultured for 7 days. Non-adherent cells were removed by medium exchange. SFB were then negatively purified using Dynabeads® M-450 CD14 and subsequently cultured over 2 passages in DMEM containing 100 μg/ml gentamycin, 100 μg/ml penicillin/streptomycin, 20 mM HEPES and 10% fetal calf serum (FCS, all from PAA Laboratories, Cölbe, Germany).

extract_protocol: At the end of the 2nd passage, the SFB were starved with medium containing 1% fetal calf serum (FCS) for 72 h, to minimize stimulating effects by serum components. After washing with PBS, the cells were lysed with RLT buffer (Qiagen, Hilden, Germany) and frozen at -70°C. Total RNA was isolated using the RNeasy Kit (Qiagen) according to the supplier’s recommendation.

treatment_protocol: Synovial tissue was obtained from open joint replacement surgery or arthroscopic synovectomy at the Clinic of Orthopedics, Waldkrankenhaus “Rudolf Elle” (Eisenberg, Germany). Patients with RA or OA (n = 6 each for gene expression analysis and further patients for validation experiments) were classified according to the ACR criteria.

tag: male, 72 yrs, treatment with NSAIDs.


title: GFP Adv-shRNA 1

source_name: GFP Adv-shRNA treated liver from C57BL/6J DIO mice.


title: Jnk1 Adv-shRNA 2


title: GFP Adv-shRNA 5


title: Jnk1 Adv-shRNA 1


title: fibroblasts_OA_patient115

description: see publication for details

source_name: Synovial fibroblasts, osteoarthritis patient no. 115.

tag: female, 56 yrs, treatment with NSAIDs.


title: GFP Adv-shRNA 3


title: DIO Vehicle 2

description: Vehicle treated liver from C57BL/6J DIO mice.

tag: Male C57BL/6J mice (Jackson Laboratories) were housed on a 12-hour light-dark cycle and were allowed free access to water and standard laboratory chow or high fat diet (Research Diet D12450Bi, D12492i) for 22-24 weeks. Animals were fed ad libitum and were sacrificed at day 5 after injection.


title: DIO Vehicle 3

source_name: Vehicle treated liver from C57BL/6J DIO mice.


title: DIO Vehicle 5


title: DIO Vehicle 4


title: fibroblasts_OA_patient102

description: see publication for details

source_name: Synovial fibroblasts, osteoarthritis patient no. 102.

tag: female, 73 yrs, treatment with NSAIDs.


title: fibroblasts_RA_patient87

description: see publication for details

source_name: Synovial fibroblasts, rheumatoid arthritis patient no. 87

tag: female, 65 yrs, treatment with NSAIDs.


title: fibroblasts_OA_patient77

description: see publication for details

source_name: Synovial fibroblasts, osteoarthritis patient no. 77.

tag: female, 66 yrs, no concurrent treatment.


title: DIO Vehicle 1


title: fibroblasts_RA_patient108

description: see publication for details

source_name: Synovial fibroblasts, rheumatoid arthritis patient no 108.

tag: female, 72 yrs, treatment with NSAIDs & steroids.


title: fibroblasts_OA_patient90

description: see publication for details

source_name: Synovial fibroblasts, osteoarthritis patient no. 90.

tag: female, 61 yrs, no concurrent treatment.


title: fibroblasts_OA_patient81

description: see publication for details

source_name: Synovial fibroblasts, osteoarthritis patient no. 81.

tag: female, 56 yrs, no concurrent treatment.


title: fibroblasts_RA_patient74

description: see publication for details

source_name: Synovial fibroblasts, rheumatoid arthritis patient no. 74.

tag: female, 71 yrs, treatment with NSAIDs.


title: fibroblasts_RA_patient73

description: see publication for details

source_name: Synovial fibroblasts, rheumatoid arthritis patient no. 73.

tag: male, 68 yrs, treatment with MTX.


title: fibroblasts_RA_patient96

description: see publication for details

source_name: Synovial fibroblasts, rheumatoid arthritis patient 96.

treatment_protocol: Synovial tissue was obtained from open joint replacement surgery or arthroscopic synovectomy at the Clinic of Orthopedics, Waldkrankenhaus “Rudolf  Elle” (Eisenberg, Germany). Patients with RA or OA (n = 6 each for gene expression analysis and further patients for validation experiments) were classified according to the ACR criteria.

tag: male, 67 yrs, treatment with NSAIDs.


title: 547T1 || K-ras Lkb1 L/- || primary lung tumor || Ad

status: Public on Aug 28 2007

city: boston

first: kwok-kin

last: wong

state: MA

address: 44 binney street

department: medical oncology

institute: dana farber cancer institute

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: RMA

label_protocol: Affymetrix standard protocol

extract_protocol: Affymetrix standard protocol

tag: 547-T1 Tumor N LSL-Kras , Lkb1L/- Adenocarcinoma


title: 540T2 || K-ras Lkb1 L/- || primary lung tumor || Sq

tag: 540-T2 Tumor T2 LSL-Kras, Lkb1L/- Squamous carcinoma


title: KBHU

city: Duarte

first: Xiyong

last: Liu

state: CA

address: 1500 E Duarte Rd

department: Medical Oncology & Therapeutic Research

institute: City of Hope

description: total RNA was extracted from KBHU cells. Hybridization and scan was performed in USC Microarray co-facilty

data_processing: GCOS and Genespring

label: KBHU

source_name: Hydroxyurea drug resistant KB clone

tag: KBHU was selected from KB cells step- wise exposed to Hydroxyurea.


title: KBwt

description: total RNA was extracted from KB cell. The hybridization and scan were performed in University of South California Microarray co-facility

label: KBwt

source_name: KB parental cell

tag: human cancer cell line KB


title: 392T2 || K-ras Lkb1 L/+ || primary lung tumor || Ad

tag: 392-T2 Tumor P2 LSL-Kras, Lkb1L/+ Adenocarcinoma


source_name: 452T1 || K-ras Lkb1 L/- || primary lung tumor || Ad-sq (mixed); different tumor from 452T2 in the same mouse

tag: 452-T1 Tumor R2 LSL-Kras, Lkb1L/- Adenosquamous carcinoma


source_name: 452T2 || K-ras Lkb1 L/- || primary lung tumor || Ad-sq (mixed) different tumor from 452T1 in the same mouse

tag: 452-T2 Tumor R1 LSL-Kras, Lkb1L/- Adenosquamous carcinoma


title: fibroblasts_RA_patient88

description: see publication for details

source_name: Synovial fibroblasts, rheumatoid arthritis patient 88.

tag: female, 62 yrs, treatment with NSAIDs.


title: 592T1 || K-ras Lkb1 L/L|| primary lung tumor || Ad

tag: 592-T1 Tumor O1 LSL-Kras, Lkb1L/L Adenocarcinoma


title: 861T1 || K-ras LKB1 L/L || primary lung tumor || Ad

tag: 861-T1 Tumor Q LSL-Kras, Lkb1L/L Adenocarcinoma


title: 459T1 || K-ras Lkb1 L/- || primary lung tumor || Ad

tag: 459-T1 Tumor M LSL-Kras , Lkb1L/- Adenocarcinoma


title: 392T1 || K-ras Lkb1 L/+ || primary lung tumor || Ad

tag: 392-T1 Tumor P1 LSL-Kras, Lkb1L/+ Adenocarcinoma


title: 113-T1 || K-ras Lkb1 L/- || primary lung tumor || Sq

tag: 113-T1 Tumor S LSL-Kras, Lkb1L/- Squamous carcinoma


title: 592T2 || K-ras Lkb1 L/L || primary lung tumor || Ad

tag: 592-T2 Tumor O2 LSL-Kras, Lkb1L/L Adenocarcinoma


title: 592-M || K-ras LKB L/L  || Met || Ad

source_name: 592-M || K-ras LKB L/L  || Met || Ad

tag: 592-M Tumor O3 LSL-Kras, Lkb1L/L Adenocarcinoma,metastasis


title: 500T1 || K-ras p53L/L || primary lung tumor || Ad

tag: 500-T1 Tumor D LSL-Kras, p53L/L Adenocarcinoma


title: 91T1 || K-ras p16Ink4a-/- || primary lung tumor || Ad

tag: 91-T1 Tumor F LSL-Kras, p16Ink4a-/- Adenocarcinoma


title: 268T1 ||  Kras || primary lung tumor || Ad

tag: 268-T1 Tumor I LSL-Kras Adenocarcinoma


title: 186T1 || K-ras p53L/L || primary lung tumor || Ad

tag: 186-T1 Tumor C LSL-Kras, p53L/L Adenocarcinoma


title: 197T1 || K-ras p53L/L || primary lung tumor || Ad

tag: 197-T1 Tumor E LSL-Kras, p53L/L Adenocarcinoma


title: 196T1 || K-ras p53L/L || primary lung tumor || Ad

tag: 196-T1 Tumor B LSL-Kras, p53L/L Adenocarcinoma


title: 405 ||  Kras || primary lung tumor || Ad

source_name: 405 ||  Kras || primary lung tumor || Ad

tag: 405 Tumor A LSL-Kras Adenocarcinoma


title: 498(1)T1 || K-ras p53L/L || primary lung tumor || Ad

tag: 498 (1)-T1 Tumor H LSL-Kras, p53L/L Adenocarcinoma


title: 287 ||  Kras || primary lung tumor || Ad

source_name: 287 ||  Kras || primary lung tumor || Ad

tag: 287 Tumor L LSL-Kras Adenocarcinoma


title: 14T1 || K-ras p16Ink4a-/- || primary lung tumor || Ad

tag: 14-T1 Tumor G LSL-Kras, p16Ink4a-/- Adenocarcinoma


title: G9a-K165A

status: Public on Aug 14 2007

city: New York

first: Agnes

last: Viale

state: NY

address: 1275 York Avenue

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

description: Transcription profiling involves H3 methyltransferase G9a-deleted MEFs reconstituted with empty vector (delta), wild type FLAG-G9a (WT), FLAG-G9a K165A (K165A) or FLAG-G9a H1093K catalytic mutant (H1093K).

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Affymetrix GS3000 scanner - 5um scanning

data_processing:
OVerall intensity of the image was targeted to 500
Probe set intensity was extracted by GCOS 1.4

source_name: Mouse embryonic fibroblast

label_protocol: Affymetrix standard one round RT-IVT labeling.

extract_protocol: Trizol /RNAeasy cleaning

tag: G9a-deleted MEFs reconstituted with FLAG-G9a K165A (K165A)


title: 498(2)-T1 ||  Kras || primary lung tumor || Ad

tag: 498 (2)-T1 Tumor J LSL-Kras Adenocarcinoma


title: 484 ||  Kras || primary lung tumor || Ad

source_name: 484 ||  Kras || primary lung tumor || Ad

tag: 484 Tumor K LSL-Kras Adenocarcinoma


title: G9a-H1093K

source_name: mouse embryonic fibroblast

tag: G9a-deleted MEFs reconstituted with FLAG-G9a H1093K catalytic mutant (H1093K).


title: G9a-H1093K_2


title: G9a-deleted_2

tag: G9a-deleted MEFs


title: G9a-K165A_2


title: G9a-deleted


title: Non-inner ear tissues pooled from E11 to E15, replicate1

city: Saint Louis

first: Samin

middle: A

last: Sajan

state: MO

address: 4566 Scott Avenue

institute: Washington University Medical School

description: Pool of 4 non-inner ear tissue samples at E11, E11.5, E12, E15; 2 at E13, E13.5; 3 at E14, E14.5; 5 at E12.5

hyb_protocol: Fragmentation of cRNA was carried out following the standard Affymetrix procedure, and 10ug of fragmented cRNA from each sample was hybridized to the MOE 430A_2 gene chips for 16-18 hours at 45oC.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: The data were normalized and modeled using the PM/MM model in DNA Chip (dChip) program, June 2, 2005 version. All expression values below 10 were designated a default of 10. The Presence/Absence calls used were those generated by the Affymetrix MAS5 software.

source_name: Mouse non-inner ear tissue from E11 to E15

label_protocol: To synthesize biotin-labeled target (cRNA) for hybridization to Affymetrix arrays, 22ul of the purified cDNA were used as template in in-vitro transcription reactions using the BioArray HighYield RNA Transcript Labeling Kit (ENZO Life Sciences, NY). Besides the template cDNA, all other components were added following the instructions provided by the manufacturer, and reactions were incubated at 37oC for 10 hours on the PCR machine mentioned above under 'extract protocol'. Labeled cRNA was purified using an RNA purification kit (Qiagen) following the manufacturer’s instructions and eluted in 50ul of water.

extract_protocol: Inner ear dissections    Timed pregnant CBA/J mice (Jackson Laboratory) were euthanized by placing in a chamber with CO2. While euthanasia was carried out by considering the morning of vaginal plug observation to be 0.5 days post-conception, the gestational stage of each embryo in a litter was determined individually by the number of somites (from E9 to E11) and various other developmental features such as the extent of digit and limb development, appearance of hair follicles and so on (beyond E11), as described by M.H. Kaufman in The Atlas of Mouse Development, revised edition, 1998, Academic Press, San Diego, CA. Embryos were removed and immediately placed in Hank’s Balanced Salt Solution (HBSS) supplemented with L-Glutamine on ice. All subsequent dissections were carried out in ice-cold Dulbecco’s calcium and magnesium-free phosphate buffered saline (PBS) solution. Whole inner ears, containing both inner ear (IE) and non-inner ear (NIE) tissues, were removed from embryos under a dissecting microscope (Nikon SMZ645, Boyce Scientific Inc) and transferred in 3-5mg/mL dispase (Gibco) in PBS on ice for either 8-10 minutes (gestational stages E9-E10.5) or 20-25 minutes (E11-E15) to facilitate the separation of IE epithelium from the surrounding NIE tissue. After incubation in dispase, the tissue was transferred to a 35mm glass bottom culture dish with a 10mm microwell (MatTek Corporation, MA) containing ice-cold PBS. IE epithelium was then micro-dissected under a stereo microscope (Nikon SMZ1500, Boyce Scientific Inc) using Dumostar 5 forceps (Biomedical Research Instruments) and immediately placed in TRIZOL (Invitrogen). For each gestational stage, two biological replicates were obtained, i.e., two pools of tissues of identical stage from different litters. From E9-E10, IE epithelia from 5-8 embryos were pooled per stage per replicate. From E10.5-E12, the ventral cochlear region and the dorsal vestibular region (without the endolymphatic duct) were separated and pooled separately for each stage, again from 5-8 embryos per stage per tissue-type per replicate. For stages E12.5-E15, the cochleae and the saccules were separately pooled, whereas the utricles and the ampullae of the three semi-circular canals were combined and pooled together (without the endolymphatic duct and canals) from 3-6 embryos per stage per tissue-type per replicate. The NIE tissue was also obtained from each stage and pooled followingly. From stage E9, the NIE tissue was obtained from 4-5 embryos per replicate. From E9.5-E10.5, the NIE tissue was obtained from 2-7 embryos per stage per replicate and then pooled together. From E11-E15, NIE tissue was obtained from 2-3 embryos per stage per replicate and then pooled. Hence, a total of 29 samples of IE and 3 of N-IE were obtained, each in duplicate, from 13 distinct developmental stages.    Total RNA isolation, cDNA synthesis and amplification     Total RNA was isolated from TRIZOL by following manufacturer’s instructions (Invitrogen) and resuspended in either 7-10ul (for stages E9-E10.5) or 15-20ul (for stages E11-E15) of distilled and deionized water (VWR). PolyA RNA was then amplified from at least one-fifth to one-half of total RNA using micro-cDNA methods described elsewhere [Hawkins RD et al. (2003) Human Molecular Genetics 12, 1261-1272] with the following modifications. Total RNA was denatured at 65oC in a 5ul volume in water for 5 minutes on a PCR machine (GeneAmp PCR system 9700, Applied Biosystems) and immediately added to an equal volume of oligo-(dT)24-coated paramagnetic beads (Dynal) in binding buffer. After 20 minutes at room remperature with periodic mixing, the supernatant was removed and beads washed twice with 50ul of wash buffer and once with 1X reverse transcriptase buffer (Invitrogen). All non-room temperature incubations were carried on the PCR machine mentioned above. The sequence of the 5’ SMART primer (referred to here as the Not1-SP6-3G primer) used was 5’-GCGGCCGCTATT TAGGTGACACTATAGAAGAGGG-3’ (synthesis by Invitrogen, PAGE-purified). Following cDNA synthesis, beads were washed twice with 50ul of water and once with 50ul of 1X Not1 digestion buffer (Invitrogen) prior to Not1 digestion at 37oC for 20 minutes in a 10ul reaction volume containing 15 units of enzyme in 1X digestion buffer. Post-digestion, beads were washed thrice with 50ul of water and subjected to 4 rounds of PCR cycles using the SP6 and T7-(T)24-VN primers whose sequences were 5’-ATTTAGGTGACACTATAGAA-3’ (synthesis by Invitrogen) and 5’-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG(T)24VN-3’ (synthesis by IDT, PAGE-purified), respectively. The PCR was carried out in a 50ul volume and included, in addition to the beads, 0.2mM dNTP mix, 0.02uM of each of the two primers, and 1X Advantage 2 Taq polymerase mix (BD Biosciences) in 1X Advantage 2 PCR buffer (40mM tricine-KOH pH 8.7, 15mM potassium acetate, 3.5mM magnesium acetate, 3.75ug/ml BSA, 0.005% tween-20, and 0.005% nonidet-P40). Cycle settings included an initial denaturation at 95oC for 2 minutes, then 95oC for 15 seconds, 42oC for 15 seconds, 68oC for 6 minutes, and an extra 4-minute elongation at 68oC for the last cycle. After this PCR, the supernatant was transferred to a new PCR tube to which was added a 50ul-mixture of 0.2mM dNTP mix, 0.2uM of the Not1-SP6-3G and T7-(T)24-VN primers each, and 1X Advantage 2 Taq polymerase mix in 1X Advantage 2 PCR buffer to obtain a total of 100ul reaction volume. This was subjected to additional 8 rounds of PCR cycles following the same settings as above except that primer annealing was carried out at 60oC. The resulting amplified cDNA was purified using a PCR purification kit (Qiagen) following the manufacturer’s instructions and eluted in 40ul of elution buffer.

tag: Strain

value: CBA/J

tag: Tissue

value: non-inner ear


title: G9a-delta_2

tag: G9a-deleted MEFs reconstituted with empty vector (Delta)


title: Saccule at E14, replicate1

description: Pool of 10 saccules at E14

source_name: Mouse saccule at E14

value: inner ear


title: Saccule at E15, replicate1

description: Pool of 11 saccules at E15

source_name: Mouse saccule at E15


title: Non-inner ear tissue at E9, replicate2

description: Pool of 9 non-inner ear tissue samples at E9

source_name: Mouse non-inner ear tissue at E9


title: Non-inner ear tissues pooled from E9.5 to E10.5, replicate2

description: Pool of 12 non-inner ear tissue samples at E9.5; 6 at E10; 6 at E10.5

source_name: Mouse non-inner ear tissue from E9.5 to E10.5


title: Non-inner ear tissues pooled from E11 to E15, replicate2

description: Pool of 5 non-inner ear tissue samples at E11, E12, E12.5; 4 at E14, E15; 6 at E13; 3 at E11.5, E13.5, E14.5


title: Saccule at E14.5, replicate2

description: Pool of 6 saccules at E14.5

source_name: Mouse saccule at E14.5


title: Saccule at E13.5, replicate2

description: Pool of 7 saccules at E13.5

source_name: Mouse saccule at E13.5


title: Saccule at E14, replicate2

description: Pool of 13 saccules at E14


title: RD_with_PAX3-FKHR-ER_without_4-OHT_rep2

status: Public on Mar 10 2009

city: Philadelphia

first: Frederic

last: Barr

state: PA

address: 422 Curie Blvd

institute: University of Pennsylvania

description: Embryonal Rhabdomyosarcoma cell line transduced with PAX3-FKHR joined to the modified estrogen receptor ligand binding domain

scan_protocol: Standard protocol for Affymetrix GeneChip Human Genome U133A array performed in the Penn Microarray Facility using the Affymetrix GCS 2500 Scanner

data_processing: The scanned .CEL files were analyzed using Affymetrix GCOS software.  The .CHP files were generated using the MAS5 algorithm

source_name: RD cell line transduced with PAX3-FKHR-ER without 4-hydroxy-tamoxifen (4-OHT)

growth_protocol: DMEM with 10% FBS and 1% antibiotics

extract_protocol: Qiagen RNeasy Mini Kit

treatment_protocol: without 4-OHT treatment

tag: cell line

value: Embryonal Rhabdomyosarcoma


title: Non-inner ear tissues pooled from E9.5 to E10.5, replicate1

description: Pool of 3 non-inner ear tissue samples at E9.5; 14 at E10; 4 at E10.5


title: Non-inner ear tissue at E9, replicate1

description: Pool of 8 non-inner ear tissue samples at E9


title: Saccule at E15, replicate2

description: Pool of 11 saccules at E15


title: Saccule at E14.5, replicate1

description: Pool of 6 saccules at E14.5


title: G9a-WT_2

source_name: mouse embroynic fibroblast

tag: G9a-deleted MEFs reconstituted with wild type FLAG-G9a (WT)


title: Saccule at E12.5, replicate2

description: Pool of 7 saccules at E12.5

source_name: Mouse saccule at E12.5


title: Utricle and 3 ampullae at E14.5, replicate1

description: Pool of 7 (1 utricle and 3 ampullae) at E14.5

source_name: Mouse utricle and 3 ampullae at E14.5


title: Saccule at E13, replicate1

description: Pool of 10 saccules at E13

source_name: Mouse saccule at E13


title: G9a-WT

source_name: Mouse Embryonic fibroblast


title: Saccule at E13, replicate2

description: Pool of 10 saccules at E13


title: Saccule at E12.5, replicate1

description: Pool of 12 saccules at E12.5


title: Utricle and 3 ampullae at E13.5, replicate1

description: Pool of 9 (1 utricle and 3 ampullae) at E13.5

source_name: Mouse utricle and 3 ampullae at E13.5


title: Utricle and 3 ampullae at E15, replicate2

description: Pool of 11 (1 utricle and 3 ampullae) at E15

source_name: Mouse utricle and 3 ampullae at E15


title: Utricle and 3 ampullae at E15, replicate1


title: Utricle and 3 ampullae at E13, replicate2

description: Pool of 10 (1 utricle and 3 ampullae) at E13

source_name: Mouse utricle and 3 ampullae at E13


title: Utricle and 3 ampullae at E14, replicate2

description: Pool of 13 (1 utricle and 3 ampullae) at E14

source_name: Mouse utricle and 3 ampullae at E14


title: Utricle and 3 ampullae at E13, replicate1


title: Utricle and 3 ampullae at E12.5, replicate2

description: Pool of 9 (1 utricle and 3 ampullae) at E12.5

source_name: Mouse utricle and 3 ampullae at E12.5


title: Utricle and 3 ampullae at E14, replicate1

description: Pool of 10 (1 utricle and 3 ampullae) at E14


title: G9a-delta

source_name: mouse embryonic fibroblast


title: Utricle and 3 ampullae at E14.5, replicate2

description: Pool of 6 (1 utricle and 3 ampullae) at E14.5


title: Utricle and 3 ampullae at E13.5, replicate2

description: Pool of 8 (1 utricle and 3 ampullae) at E13.5


title: Saccule at E13.5, replicate1

description: Pool of 9 saccules at E13.5


title: Utricle and 3 ampullae at E12.5, replicate1

description: Pool of 13 (1 utricle and 3 ampullae) at E12.5


title: Vestibular organ at E12, replicate1

description: Pool of 15 vestibular tissues at E12

source_name: Mouse vestibular organ at E12


title: Vestibular organ at E11.5, replicate2

description: Pool of 13 vestibular tissues at E11.5

source_name: Mouse vestibular organ at E11.5


title: Vestibular organ at E12, replicate2

description: Pool of 12 vestibular tissues at E12


title: Cochlea at E14, replicate2

description: Pool of 13 cochlear tissues at E14

source_name: Mouse cochlea at E14


title: Cochlea at E15, replicate2

description: Pool of 11 cochlear tissues at E15

source_name: Mouse cochlea at E15


title: Cochlea at E14.5, replicate1

description: Pool of 7 cochlear tissues at E14.5

source_name: Mouse cochlea at E14.5


title: Vestibular organ at E11.5, replicate1

description: Pool of 15 vestibular tissues at E11.5


title: Vestibular organ at E11, replicate2

description: Pool of 17 vestibular tissues at E11

source_name: Mouse vestibular organ at E11


title: Vestibular organ at E10.5, replicate1

description: Pool of 11 vestibular tissues at E10.5

source_name: Mouse vestibular organ at E10.5


title: Vestibular organ at E11, replicate1

description: Pool of 16 vestibular tissues at E11


title: Cochlea at E13.5, replicate1

description: Pool of 9 cochlear tissues at E13.5

source_name: Mouse cochlea at E13.5


title: Cochlea at E13.5, replicate2

description: Pool of 8 cochlear tissues at E13.5


title: Cochlea at E13, replicate2

description: Pool of 10 cochlear tissues at E13

source_name: Mouse cochlea at E13


title: Vestibular organ at E10.5, replicate2

description: Pool of 12 vestibular tissues at E10.5


title: Cochlea at E15, replicate1

description: Pool of 11 cochlear tissues at E15


title: Cochlea at E14.5, replicate2

description: Pool of 6 cochlear tissues at E14.5


title: Cochlea at E13, replicate1

description: Pool of 10 cochlear tissues at E13


title: Cochlea at E12.5, replicate2

description: Pool of 7 cochlear tissues at E12.5

source_name: Mouse cochlea at E12.5


title: Cochlea at E12, replicate2

description: Pool of 9 cochlear tissues at E12

source_name: Mouse cochlea at E12


title: Cochlea at E12.5, replicate1

description: Pool of 12 cochlear tissues at E12.5


title: Chimpanzee dorsolateral prefrontal cortex 6.3 years old, rep8

city: Leipzig

first: Mehmet

last: Somel

address: Deutscher Platz 6

department: Evolutionary Genetics

institute: Max Planck Institute for Evolutionary Anthropology

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 6.3 years old chimpanzee individual

hyb_protocol: Hybridization to Affymetrix HG-U133 Plus 2.0 GeneChip arrays was carried out following standard Affymetrix protocols.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneChip Scanner 3000.

data_processing: Affymetrix microarray image data were collected with Affymetrix GeneChip Operating Software version 1.1 using default parameters. For summarizing the expression data, we used custom chip definition files (Custom CDF, v. 11) based on Ensembl gene annotation rather than Affymetrix annotation (Dai et al., PMID: 16284200). Further, we only accepted probes that perfectly matched both the human, the chimpanzee and the rhesus macaque genomes at a single location (hg18, panTro2, and rheMac2, respectively; see Khaitovich et al., PMID: 16141373), which correspond to 31% of probes on the microarray. Further, we did not include probesets with less than 8 probes in our analysis. The list of exluded probes is supplied as supplement to the CDF file. This list can be used in combination with the removeprobe function in the customCDF package (http://arrayanalysis.mbni.med.umich.edu/MBNIUM.html#CustomCDF) to create CDF environments with masked probes. We used the R Bioconductor 'affy' software package for further data analysis. Signal intensities were calculated with the 'rma' function using default parameters, including quantile normalization and log2 transformation. Detection p-values were calculated with the 'mas5calls' function using default parameters. Note that, for analyses of gene expression changes during postnatal development in humans and chimpanzees only, it is advisable to use CDF files masked for mismatches to the human and chimpanzee genomes, and for analyses involving humans only, to use non-masked CDF files. This is because masking out probes strongly decreases statistical power.

organism: Pan troglodytes

source_name: Dissected chimpanzee post-mortem dorsolateral prefrontal cortex

label_protocol: Biotinylated cRNA were prepared from 1 microg. total RNA following standard Affymetrix protocols.

extract_protocol: Trizol extraction of total RNA from 100 mg of tissue was performed according to the manufacturer's instructions.

treatment_protocol: All human postmortem brain tissue samples were obtained from the NICHD Brain and Tissue Bank for Developmental Disorders (NICHDBB)(Baltimore, MD, USA). All subjects were defined as normal controls by forensic pathologists at the NICHDBB. No subjects with prolonged agonal state were used. Chimpanzee samples were obtained from the Yerkes Primate Center (Atlanta, GA, USA), from the Biomedical Primate Research Centre (Rijswijk, Netherlands) and from the Anthropological Institute of the University of Zurich (Switzerland). The majority of chimpanzees used in this study belonged to the Western chimpanzee population. Rhesus macaque samples were obtained from the German Primate Center (DPZ)(Goettingen, Germany). All non-human primates used in this study suffered sudden deaths for reasons other than their participation in this study and without any relation to the tissue used. The human prefrontal cortex samples were taken from the middle third of the middle frontal gyrus: a cortical region approximately corresponding to Brodmann area 46, and from the equivalent region in the non-human primates. For all samples special care was taken to dissect primarily grey matter (in the order of 90-95% of the total sample). The human caudate nucleus samples were taken from the central part of the nucleus in order to avoid any cross-contamination by adjacent brain structures. See publication for a more detailed description of the samples.

tag: age

value: 2313 days

tag: sex

value: Female

tag: tissue

value: dorsolateral prefrontal cortex of the brain


title: Cochlea at E14, replicate1

description: Pool of 10 cochlear tissues at E14


title: Cochlea at E12, replicate1

description: Pool of 11 cochlear tissues at E12


title: Cochlea at E11.5, replicate1

description: Pool of 13 cochlear tissues at E11.5

source_name: Mouse cochlea at E11.5


title: Otic vesicle at E10, replicate 1

description: Pool of 15 otic vesicles at E10

source_name: Mouse otic vesicle at E10


title: Cochlea at E11, replicate2

description: Pool of 16 cochlear tissues at E11

source_name: Mouse cochlea at E11


title: Cochlea at E10.5, replicate1

description: Pool of 10 cochlear tissues at E10.5

source_name: Mouse cochlea at E10.5


title: Cochlea at E10.5, replicate2

description: Pool of 12 cochlear tissues at E10.5


title: Otic vesicle at E10, replicate 2

description: Pool of 16 otic vesicles at E10


title: Otic vesicle at E9.5, replicate2

description: Pool of 10 otic vesicles at E9.5

source_name: Mouse otic vesicle at E9.5


title: Cochlea at E11, replicate1

description: Pool of 16 cochlear tissues at E11


title: Cochlea at E11.5, replicate2

description: Pool of 13 cochlear tissues at E11.5


title: HMEC_stimulated A3

status: Public on Aug 08 2007

city: Hannover

first: Dorothee

last: Viemann

state: Deutschland

address: Carl-Neuberg-Straße 1

department: Department of Pediatric Pulmonology, Allergy and Neonatology

institute: Hannover Medical School

description: standard culture conditions, treatemnt for 6h with MRP8/MRP14 (200 ?g/ml)

data_processing: MAS 5.0

tag: cell culture


title: Otic placode at E9, replicate1

description: Pool of 14 otic placodes at E9

source_name: Mouse otic placode at E9


title: Otic vesicle at E9.5, replicate1

description: Pool of 12 otic vesicles at E9.5


title: Otic placode at E9, replicate2

description: Pool of 13 otic placodes at E9


title: HMEC_stimulated A4


title: HMEC_stimulated A2


title: HMEC_stimulated A1

description: standard culture conditions, treatemnt for 6h with MRP8/MRP14 (200 µg/ml)


title: HMEC_control A3

description: standard culture conditions, no treatment


title: HMEC_control A4