title: Breast Cancer Sample 156

city: Monterrey

first: Hugo

last: Gomez

state: Nuevo Leon

address: Garza Sada

department: Bioinformatics

country: Mexico

institute: ITESM

description: One color per patient

hyb_protocol: 0.825 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) and 0.825 ug of Cy5-labelled cRNA (specific activity >6.0 pmol C53/ug cRNA) were fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent hybridization buffer 2x Gex was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the GenePix Scanner 4000B (Molecular DEVICES) using two color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100% and Red and Red PMT is set to 100% ).

data_processing: The scanned images were analyzed with Gene Pix Software (Molecular DEVICES) using default parameters (Two color protocol and Grid: 014850_D_20110325) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Sample Tumor of Breast Cancer

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.5 μL at 25ng/μL of RNA using the Two-Color Low RNA Input (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was obtained using the  RNeasy Mini Kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. The protocol includes differential tissue lysis with buffers and a tissue grinder, followed by purification using the kit columns. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Experion Automated Electrophoresis (BioRad,Technopark, Kerala, India).

treatment_protocol: Freshly obtained sample and preserved in RNA Later (Thermo Fisher Scientific). The sample was refrigerated all night at 4ºC. In the next day the RNA Later (Thermo Fisher Scientific) was removed, and the sample was putted into refrigerator at -80ºC by indeterminate time.

tag: tissue

value: Tumor Sample of Breast Cancer

value: Female

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Infiltrating ductal adenocarcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

value: Pos

tag: her2 immunohistochemestry

value: Neg

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

tag: personal pathological hystory

value: Hypertension

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Left

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

value: Poor

tag: final surgery date

value: Paclitaxel

value: Cyclophosphamide

value: Adriamicin

tag: radiotherapy

value: No

tag: date at relapse

tag: place to metastasis

tag: date at death


title: Breast Cancer Sample 113

status: Public on Dec 04 2015

type: RNA

description: One color per patient

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Invasive ductal carcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

value: Sister Pancreatic Cancer

tag: personal pathological hystory

value: Partial

value: Doxorubicin


title: Breast Cancer Sample 157

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

value: Sister GBM and Breast Cancer

value: Knee Surgery

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Right

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

tag: final surgery date

tag: radiotherapy

tag: date at relapse

tag: place to metastasis

tag: date at death


title: Breast Cancer Sample 144

description: One color per patient

tag: tissue

value: Tumor Sample of Breast Cancer

tag: gender

value: Female

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Infiltrating ductal adenocarcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

tag: personal pathological hystory


title: Breast Cancer Sample 162

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

value: Pos

value: Neg

value: Sister Breast Cancer, Brother Prostate Cancer

value: Venous insuficiency

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

tag: final surgery date

tag: radiotherapy

tag: date at relapse

tag: place to metastasis

tag: date at death


title: HT-29 control, biological rep3

city: Sydney

first: Susan

last: Corley

state: NSW

address: D26, Kensignton Campus

department: Biotechnology & Biomolecular Sciences

country: Australia

institute: UNSW

description: Gene expression data from HT-29 cells cultured in medium

hyb_protocol: 10 ug fragmented, biotin labelled aRNA was hybridised to Human Primeview Arrays for 16 hours at 45°C at 60rpm using an Affymetrix hybridization oven. The arrays were washed according to manufacturers instructions on an Affymetrix FS450 fluidics station.

scan_protocol: Arrays were scanned on an Affymetrix Scanner GC3000 7G.

data_processing: The data were analysed using Partek Genomic Solutions (6.13.1224).  RMA background correction was employed with quantile normalisation.

label: biotin

source_name: HT-29 cells

label_protocol: Starting material consisting of 100 ng of total RNA  was amplified using Affymetrix GeneAtlas 3' IVT Express Kit.

growth_protocol: HT-29 cells were seeded in 6-well plates and cultured for approximately 2 weeks unitl 80-90% confluent.

extract_protocol: RNA was isolated from HT-29 cells with TRIzol Total RNA Isolation reagent (Invitrogen).

treatment_protocol: HT-29 cells were treated with 100ng/ml TNF-a in the presence or absence of polymeric formula for 5 hours.

tag: cell line

value: HT-29 cells


title: HT-29 treated with TNF-a and PF, biologial rep1

description: Gene expression data from HT-29 cells treated with TNF-a and polymeric formula


title: Athal_PNM_3dpi_R3

city: Regensburg

first: Urs

last: Lahrmann

address: Am Biopark 9

department: Project Group Personalized Tumor Therapy

country: Germany

institute: Fraunhofer ITEM

description: A. thaliana plants were pre-grown for 14 days prior to mock treatment

hyb_protocol: Hybridization and washing was performed according to Agilent's One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling protocol (version 6.5).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 2um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (gProcessedSignal).

organism: Arabidopsis thaliana

source_name: A. thaliana grown on 1/10 PNM, 3 days post mock treatment, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA according to Agilent's One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling protocol (version 6.5) followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop-1000 Spectrophotometer (Agilent)

growth_protocol: Piriformospora indica Sav. Verma, Aj. Varma, Rexer, G. Kost & P. Franken (DSM11827, Deutsche Sammlung von Mikroorganismen und Zellkulturen, DSMZ, Braunschweig, Germany) cultures were propagated at 28°C in liquid complete medium (CM) (Pham et al., 2004) supplemented with 2% glucose and 130 rpm shaking or on solid medium supplemented with 1.5% agar. S. vermifera cultures were propagated at 25°C in liquid MYP medium (0.7% w/v malt extract; 0.1% w/v peptone; 0.05% w/v yeast extract) and 120 rpm shaling or on solid medium supplemented with 1.5% agar. For microarray experiments P. indica and S. vermifera were cultivated on 1/10 PNM-agar plates (Basiewicz et al., 2011) for 3 days. Arabidopsis thaliana seeds (Ecotype Columbia-0) were incubated for 5 min in 70 % ethanol, surface sterilized for 5 min with 6 % sodium hypochlorite and washed 6 times for 5 min in sterile water. After stratification for 3 days at 4°C in the dark on 1/10 PNM medium, Arabidopsis seedlings were grown for 14 days under sterile conditions in a phytochamber (Vötsch, Balingen-Frommern, Germany) at long day conditions (day: 16 h, 23°C (350 µmol/m-2s-1); night: 8 h, 18°C; 60% humidity).

extract_protocol: Arabidopsis root material was harvested in liquid nitrogen 3, 7 and 14 dpi. For each time point roots from 45 to 60 plants were pooled. S. vermifera hyphae grown on plate were thoroughly scratched from the agar surface with a sterile scalpel 3 dpi and immediately frozen in liquid nitrogen. All experiments were performed in 3 independent biological replications. Total RNA from 200 mg grounded material was extracted with TRIzol (Invitrogen, Karlsruhe, Germany) following the manufacturer's instructions. Amount and quality of the extracted RNA was estimated by NanoDrop-1000 Spectrophotometer (Agilent) and by a 2100 Bioanalyzer (Agilent, Santa Clara, USA).

treatment_protocol: For inoculation of Arabidopsis roots with P. indica or S. vermifera, plants of roughly the same size were first transferred to square petri dishes containing 1/10 PNM. Arabidopsis roots were inoculated directly with either 500.000 P. indica spores per 20 seedlings or 2 plugs S. vermifera mycellium per plant root or mock treated with tween water (0.002% TWEEN20).

tag: tissue

value: root

tag: age


title: Breast Cancer Sample 158

description: One color per patient

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

tag: histological grade

tag: estrogen receptor immunohistochemestry

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

value: Progresive

value: Paclitaxel

value: Cyclophosphamide

value: Adriamicin

value: No


title: HT-29 treated with TNF-a and PF, biologial rep3

tag: cell line


title: Breast Cancer Sample 112

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

tag: histological grade

tag: estrogen receptor immunohistochemestry

tag: breast affected

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

tag: final surgery date

value: Doxorubicin

tag: radiotherapy

tag: date at relapse

tag: place to metastasis

tag: date at death


title: Breast Cancer Sample 48

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

value: Invasive ductal carcinoma

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

value: Left

value: Partial


title: Breast Cancer Sample 41

description: One color per patient

tag: tissue

value: Tumor Sample of Breast Cancer

tag: gender

value: Female

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: diagnosis

value: Poorly differentiated invasive ductal carcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

value: Absent

tag: breast affected

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

value: Poor

tag: final surgery date

tag: radiotherapy

value: Yes

tag: date at relapse

tag: place to metastasis

tag: date at death


title: Breast Cancer Sample 91

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

value: Pos

tag: her2 immunohistochemestry

value: Neg

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

value: Sister Liver Cancer

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

value: Right


title: Breast Cancer Sample 33

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: diagnosis

tag: histological grade

tag: estrogen receptor immunohistochemestry

value: Mother Endometrial Cancer

value: Hypertension

tag: breast affected

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

value: Progresive

tag: final surgery date

value: Cyclophosphamide

tag: radiotherapy

tag: date at relapse

tag: place to metastasis

tag: date at death


title: Breast Cancer Sample 21

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

value: Invasive ductal carcinoma

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

value: Liver Cancer

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

value: Complete

value: Paclitaxel


title: Breast Cancer Sample 39

description: One color per patient

tag: tissue

value: Tumor Sample of Breast Cancer

tag: gender

value: Female

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: diagnosis

value: Invasive ductal carcinoma, carcinoma in situ associated with comedo necrosis

tag: histological grade

tag: estrogen receptor immunohistochemestry

value: Hypertension and Rheumatoid Artritis

tag: breast affected

value: Both

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

tag: final surgery date

value: Trastuzumab

tag: radiotherapy

value: No

tag: date at relapse

tag: place to metastasis

tag: date at death


title: Breast Cancer Sample 34

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

value: Infiltrating ductal carcinoma high

value: Pos

tag: her2 immunohistochemestry

value: Neg

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

value: Absent

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

value: Diabetes and Heart Disease

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

value: Poor

value: Doxorubicin


title: pSS_high_P95

type: genomic

city: Uppsala

first: Juliana

last: Imgenberg-Kreuz

address: Husargatan 3

department: Medical Sciences

country: Sweden

institute: Uppsala University

description: SAMPLE 47

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 Beadchip using standard Illumina protocol

scan_protocol: Fluorescence signals were measured using the iScan instrument (Illumina)

data_processing: Analyses were performed using the Minfi software package for R

label: Biotin

molecule: genomic DNA

source_name: whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from whole bood samples using the QIAamp DNA Blood Mini Kit (Qiagen)

tag: gender

value: M

tag: age

tag: tissue

value: blood


title: pSS_high_P94

description: SAMPLE 44

value: F


title: pSS_high_P86

description: SAMPLE 48


title: HT-29 control, biological rep1

tag: cell line

value: HT-29 cells


title: pSS_high_P91

description: SAMPLE 43


title: Breast Cancer Sample 12

description: One color per patient

value: Tumor Sample of Breast Cancer

value: Female

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Infiltrating ductal carcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

value: Father Lung Cancer

value: Dyslipidemia

tag: breast affected

value: Right

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

value: Partial

tag: final surgery date

value: Tamoxifen

value: Adriamicin

tag: radiotherapy

tag: date at relapse

tag: place to metastasis

tag: date at death


title: pSS_low_P68

description: SAMPLE 42

tag: gender

tag: age

tag: tissue


title: pSS_high_P75

description: SAMPLE 46


title: Breast Cancer Sample 10

description: One color per patient

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: High grade invasive ductal carcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

value: Neg

tag: her2 immunohistochemestry

value: Pos

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

value: Absent

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

value: Left

value: Trastuzumab

value: Yes


title: pSS_high_P126

description: SAMPLE 31

tag: gender

value: M

tag: age

tag: tissue

value: blood


title: pSS_low_P128

description: SAMPLE 45

value: F


title: Breast Cancer Sample 5

description: One color per patient

value: Tumor Sample of Breast Cancer

value: Female

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Moderately differentiated infiltrating ductal adenocarcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

tag: her2 immunohistochemestry

tag: her2 fish

tag: breast affected

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

value: Complete

tag: final surgery date

value: Paclitaxel

value: Epirrubicin

value: Cyclophosphamide

tag: radiotherapy

tag: date at relapse

tag: place to metastasis

tag: date at death


title: pSS_low_P115

description: SAMPLE 37

tag: gender

tag: age

tag: tissue


title: pSS_high_P93

description: SAMPLE 26


title: pSS_high_P120

description: SAMPLE 41


title: pSS_low_P79

description: SAMPLE 36


title: pSS_low_P131

description: SAMPLE 38


title: Breast Cancer Sample 2

description: One color per patient

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Invasive ductal adenocarcinoma high nuclear grade

tag: histological grade

tag: estrogen receptor immunohistochemestry

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

value: Father Lung Cancer

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

value: Right


title: YMD692+BUL1 Q146K c2

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

country: USA

institute: University of Washington

description: MD323-C11 vs FY4. Disome 5 backcross to BUL1 SNP

hyb_protocol: reference URL : http://dunham.gs.washington.edu/UWAgilentDNA.pdf

scan_protocol: Pixel Size : 5 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : 10.5.1.1
Datafile type : Agilent result file

organism: Saccharomyces cerevisiae

extract_protocol:
Extracted molecule : Genomic DNA
Extraction method : Hoffman-Winston prep http://dunham.gs.washington.edu/UWyeastDNAprep.pdf

tag: strain name

value: wt

value: chr 5 disome + BUL1 Q146K c2


title: Breast Cancer Sample 1

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

tag: histological grade

tag: estrogen receptor immunohistochemestry

value: Pos

value: Neg

value: Absent

value: Paternal Grandmother Breast Cancer

tag: breast affected

value: Left

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

value: Progresive

tag: final surgery date

tag: radiotherapy

value: No

tag: date at relapse

tag: place to metastasis

tag: date at death


title: pSS_high_P69

description: SAMPLE 29

tag: gender

value: F

tag: age

tag: tissue

value: blood


title: pSS_low_P130

description: SAMPLE 35


title: pSS_low_P127

description: SAMPLE 39


title: pSS_low_P88

description: SAMPLE 40

value: M


title: pSS_high_P121

description: SAMPLE 32


title: pSS_low_P101

description: SAMPLE 24


title: pSS_high_P84

description: SAMPLE 23


title: YMD671+BUL1 Q146K c1

description: MD322-A5 vs FY4. bul1Q146K, MD322-A5 vs FY4

label_protocol: reference URL : http://dunham.gs.washington.edu/UWAgilentDNA.pdf

tag: strain name


title: pSS_low_P139

description: SAMPLE 34


title: pSS_low_P65

description: SAMPLE 33


title: pSS_low_P140

description: SAMPLE 28


title: pSS_low_P96

description: SAMPLE 30


title: pSS_high_P67

description: SAMPLE 27


title: Breast Cancer Sample 153

description: One color per patient

value: Tumor Sample of Breast Cancer

value: Female

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Infiltrating ductal adenocarcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

tag: personal pathological hystory

value: Hypertension and Diabetes

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Poor

value: Paclitaxel

value: Adriamicin


title: Breast Cancer Sample 143

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Carcinoma in situ associated with comedo necrosis

tag: histological grade

tag: estrogen receptor immunohistochemestry

value: Pos

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

tag: final surgery date

value: Cyclophosphamide

value: Trastuzumab

tag: radiotherapy

tag: date at relapse

tag: place to metastasis

tag: date at death


title: pSS_low_P72

description: SAMPLE 18

tag: gender

tag: age

tag: tissue


title: pSS_low_P63

description: SAMPLE 22


title: chr 11 disome + BUL1Δ c1

description: YMD686, Disome 11, BUL1::NatMX4, clonal, YGO1137 vs FY4

tag: strain name

value: wt

value: chr 11 disome + bul1 c1


title: w303 + BUL1 Q146K c2

description: MD322-C8 vs FY4. bul1Q146K


title: chr 9 disome + BUL1Δ c1

description: YMD676, Disome 9, BUL1::NatMX4, clonal, YGO1136 vs FY4

value: chr 9 disome + bul1 c1


title: pSS_low_P83

description: SAMPLE 19

value: F


title: Breast Cancer Sample 142

description: One color per patient

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Moderately differentiated infiltrating ductal adenocarcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

value: Neg

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

tag: personal pathological hystory

value: 3 C sections

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Right

value: Partial

value: Doxorubicin

value: No


title: Breast Cancer Sample 145

description: One color per patient

tag: tissue

value: Tumor Sample of Breast Cancer

tag: gender

value: Female

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Poorly differentiated ductal adenocarcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

value: C section

value: Left

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

value: Complete

tag: final surgery date

value: Epirubicin

value: Paclitaxel

tag: radiotherapy

tag: date at relapse

tag: place to metastasis

tag: date at death


title: Breast Cancer Sample 134

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Cyclophosphamide


title: w303 + BUL1Δ c2

description: A8, W303, mat a, YMD671, BUL1::NatMX4, clonal, YGO1139 vs FY4

tag: strain name

value: wt


title: chr 5 disome + BUL1Δ c2

description: C4, YMD692, Disome 5, BUL1::NatMX4, clonal, YGO1141 vs FY4

value: chr 5 disome + bul1 c2


title: Breast Cancer Sample 141

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

tag: histological grade

tag: estrogen receptor immunohistochemestry

value: Pos

value: Neg

tag: her2 immunohistochemestry

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

tag: final surgery date

value: Adriamicin

value: Trastuzumab

tag: radiotherapy

value: Yes

tag: date at relapse

tag: place to metastasis

tag: date at death


title: chr 8 disome + BUL1Δ c1

description: D2, YMD685, Disome 8, BUL1::NatMX4, clonal, YGO1142 vs FY4

tag: strain name

value: chr 8 disome + bul1 c1


title: pSS_low_P135

description: SAMPLE 21

tag: gender

value: F

tag: age

tag: tissue

value: blood


title: Breast Cancer Sample 133

description: One color per patient

value: Tumor Sample of Breast Cancer

value: Female

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Moderately differentiated invasive ductal carcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Poor


title: Breast Cancer Sample 129

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Ductal carcinoma in situ comedonicus type

tag: histological grade

tag: estrogen receptor immunohistochemestry

value: Mother and Sister Ovarian Cancer

value: Both

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

value: Partial

tag: final surgery date

value: Taxol

tag: radiotherapy

value: No

tag: date at relapse

tag: place to metastasis

tag: date at death


title: chr 5 disome + BUL1Δ c1

description: C1, YMD692, Disome 5, BUL1::NatMX4, clonal, YGO1140 vs FY4

tag: strain name

value: wt

value: chr 5 disome + bul1 c1


title: pSS_high_P106

description: SAMPLE 25

tag: gender

value: M

tag: age

tag: tissue


title: YMD285 x YMD2566 zygote 3 segregant 10A

description: MD309-B5 vs FY4. Disome 5 segregant

scan_protocol: Pixel Size : 5 Scan Date : 2013-11-23 Scan Time : 10:29:10 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

value: YMD285 x YMD2566 zygote 3 segregant 10A


title: pSS_high_P85

description: SAMPLE 20


title: pSS_high_P97

description: SAMPLE 16


title: pSS_high_P132

description: SAMPLE 12


title: pSS_low_P137

description: SAMPLE 14


title: pSS_high_P114

description: SAMPLE 10


title: pSS_high_P60

description: SAMPLE 15


title: Breast Cancer Sample 141

description: One color per patient

hyb_protocol: Once the sample is labeled, it is dried in a Speed Vacuum Concentrator at 55ºC for 3.5 hours.The resuspension of the samples is as follows: Add 18μL of nuclease free water. Add 4.5μL of GE Blocking Agent 10x. Add 22.5μL of Hi-RPM Hybridization Buffer 2x. Agitate in vortex and heat at 100ºC for 5 minutes. Spin the samples and place them on ice. The hybridization process was made by putting 22.5μL of each sample into the array, instead the 45μL of the one color protocol. Next, put the labeled samples into the Gasket Slide. The process was the following. To hybridize the sample in the Gasket Slide. Put the Gasket Slide into the SureHyb Chamber. Add 45μL of the samples to the corresponding array (G4470B). Put the 8x15K array and close the SureHyb Chamber. Hybridize at 53ºC for 20 hours at 10RPM.

scan_protocol: Slides were scanned immediately after washing on the GenePix Scanner 4000B (Molecular DEVICES) using two color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100% and Red and Red PMT is set to 100% ).

data_processing: The scanned images were analyzed with Gene Pix Software (Molecular DEVICES) using default parameters (Two color protocol and Grid:019118_D_20121224) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 2 μL at 100ng/μL of RNA using the One-Color RNA  (Agilent, Palo Alto, CA) according to the manufacturer's instructions and employing the Cy5-pCp (Jena BioScience) following the publication of Wang et al. PMID:17105992.

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Poorly differentiated ductal adenocarcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

value: Pos

value: Neg

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Left

value: Adriamicin

value: Cyclophosphamide

value: Paclitaxel

value: Trastuzumab

value: Yes


title: pSS_high_P100

description: SAMPLE 11

tag: gender

value: F

tag: age

tag: tissue

value: blood


title: pSS_low_P90

description: SAMPLE 8


title: pSS_low_P110

description: SAMPLE 17


title: pSS_low_P113

description: SAMPLE 13


title: pSS_high_P122

description: SAMPLE 6


title: pSS_high_P124

description: SAMPLE 5


title: YMD285 x YMD2566 zygote 1 segregant 8D

description: MD308-H4, second run. Disome 5 segregant

scan_protocol: Pixel Size : 5 Scan Date : 2013-11-24 Scan Time : 10:01:19 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

tag: strain name

source_name: MD308-H4, second run

value: YMD285 x YMD2566 zygote 1 segregant 8D


title: Breast Cancer Sample 109

description: One color per patient

value: Tumor Sample of Breast Cancer

value: Female

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Poorly differentiated invasive ductal carcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

value: Mother Breast Cancer

value: Hypertension

value: Right

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

value: Poor

tag: final surgery date

tag: radiotherapy

tag: date at relapse

tag: place to metastasis

value: Lung

tag: date at death


title: Breast Cancer Sample 137

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Moderately differentiated invasive ductal carcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

value: Pos

value: Neg

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Left

value: Progresive

value: No


title: Breast Cancer Sample 125

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

value: Ocular Surgery

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

tag: final surgery date

tag: radiotherapy

tag: date at relapse

tag: place to metastasis

tag: date at death


title: Breast Cancer Sample 106

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Undifferentiated carcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Complete

value: Adriamicin

value: Cyclophosphamide

value: Trastuzumab

value: Yes


title: pSS_low_P87

description: SAMPLE 9

tag: gender

value: F

tag: age

tag: tissue

value: blood


title: pSS_high_P125

description: SAMPLE 4


title: Breast Cancer Sample 147

description: One color per patient

value: Tumor Sample of Breast Cancer

value: Female

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Infiltrating ductal adenocarcinoma

tag: histological grade

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

value: Hysterechtomy

value: Right

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

value: Poor

tag: final surgery date

value: Epirubicin

value: Paclitaxel

tag: radiotherapy

tag: date at relapse

tag: place to metastasis

tag: date at death


title: Breast Cancer Sample 107

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Poorly differentiated invasive ductal carcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

value: Pos

value: Neg

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Left

value: Taxol

value: Adramicin

value: No


title: Breast Cancer Sample 142

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

value: Moderately differentiated infiltrating ductal adenocarcinoma

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

value: 3 C sections

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

value: Partial

tag: final surgery date

value: Doxorubicin

value: Cyclophosphamide

tag: radiotherapy

tag: date at relapse

tag: place to metastasis


title: YMD285 x YMD2566 zygote 3 segregant 9C

description: MD309-A7 vs FY4. Disome 5 segregant

tag: strain name

value: wt

value: YMD285 x YMD2566 zygote 3 segregant 9C


title: Breast Cancer Sample 97

description: One color per patient

tag: tissue

value: Tumor Sample of Breast Cancer

tag: gender

value: Female

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

tag: histological grade

tag: estrogen receptor immunohistochemestry

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

value: Sister Brain Cancer

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Right

value: Yes

tag: date at death


title: Breast Cancer Sample 107

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

value: Poorly differentiated invasive ductal carcinoma

value: Pos

tag: her2 immunohistochemestry

value: Neg

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

value: Poor

tag: final surgery date

tag: radiotherapy

tag: date at relapse

tag: place to metastasis


title: w303 + BUL1Δ c1

description: A2, W303, mat a, YMD671, BUL1::NatMX4, clonal, YGO1138 vs FY4

tag: strain name


title: Breast Cancer Sample 162

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Infiltrating ductal adenocarcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

value: Sister Breast Cancer, Brother Prostate Cancer

tag: personal pathological hystory

value: Venous insuficiency

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Left

value: Paclitaxel

value: Adriamicin

tag: date at death


title: pSS_high_P129

description: SAMPLE 7

tag: gender

value: F

tag: age

tag: tissue

value: blood


title: Breast Cancer Sample 93

description: One color per patient

value: Tumor Sample of Breast Cancer

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Moderately differentiated invasive ductal carcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

value: Diabetes

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

value: Progresive

tag: final surgery date

value: Cyclophosphamide

value: Taxol

tag: radiotherapy

value: No

tag: date at relapse

tag: place to metastasis

value: Lung


title: Breast Cancer Sample 56

description: One color per patient

tag: tissue

tag: gender

value: Female

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Invasive ductal carcinoma

tag: histological grade

value: Pos

value: Neg

tag: e-cadherina ihc

tag: t

tag: n

tag: m

value: x

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

tag: personal pathological hystory

value: Hypertension and Diabetes

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Right

value: Yes

tag: date at death


title: pSS_high_P112

description: SAMPLE 3

tag: gender

value: F

tag: age

tag: tissue

value: blood


title: Breast Cancer Sample 113

description: One color per patient

value: Tumor Sample of Breast Cancer

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

tag: histological grade

tag: estrogen receptor immunohistochemestry

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

value: Sister Pancreatic Cancer

value: Left

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

value: Partial

tag: final surgery date

value: Paclitaxel

value: Doxorubicin

tag: radiotherapy

tag: date at relapse

tag: place to metastasis


title: YMD285 x YMD2566 zygote 3 segregant 5C

description: MD309-E3 vs FY4. Disome 5 segregant

tag: strain name

value: wt

value: YMD285 x YMD2566 zygote 3 segregant 5C


title: Breast Cancer Sample 88

description: One color per patient

tag: tissue

tag: gender

value: Female

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Invasive ductal carcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Poor

value: Cyclophosphamide

tag: date at death


title: pSS_low_P136

description: SAMPLE 2

tag: gender

tag: age

tag: tissue


title: Breast Cancer Sample 157

description: One color per patient

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Infiltrating ductal adenocarcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

value: Pos

value: Neg

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

value: Sister GBM and Breast Cancer

value: Knee Surgery

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

tag: final surgery date

value: Adriamicin

tag: radiotherapy

value: No

tag: date at relapse

tag: place to metastasis


title: YMD285 x YMD2566 zygote 2 segregant 3A

description: MD308-D5 vs FY4. Disome 5 segregant

scan_protocol: Pixel Size : 5 Scan Date : 2013-11-23 Scan Time : 10:21:15 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

tag: strain name

value: YMD285 x YMD2566 zygote 2 segregant 3A


title: Breast Cancer Sample 57

description: One color per patient

tag: tissue

value: Tumor Sample of Breast Cancer

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Poorly differentiated infiltrating ductal carcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Both

value: Complete

value: Lung

tag: date at death


title: Breast Cancer Sample 156

description: One color per patient

tag: tissue

tag: gender

value: Female

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

value: Hypertension

value: Left

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

tag: final surgery date

value: Paclitaxel

tag: radiotherapy

tag: date at relapse

tag: place to metastasis


title: YMD285 x YMD2566 zygote 2 segregant 7A

description: MD308-H5 vs FY4, second run. Disome 5 segregant

tag: strain name

value: wt

source_name: MD308-H5, second run

value: YMD285 x YMD2566 zygote 2 segregant 7A


title: YMD285 x YMD2566 zygote 1 segregant 5D

description: MD308-E4 vs FY4, second run. Disome 5 segregant

source_name: MD308-E4, second run

value: YMD285 x YMD2566 zygote 1 segregant 5D


title: Breast Cancer Sample 153

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Infiltrating ductal adenocarcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

value: Neg

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

tag: personal pathological hystory

value: Hypertension and Diabetes

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Right

value: Poor

value: Cyclophosphamide

tag: date at death


title: Breast Cancer Sample 147

description: One color per patient

tag: tissue

value: Tumor Sample of Breast Cancer

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

value: Hysterechtomy

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

tag: final surgery date

value: Epirubicin

value: Trastuzumab

tag: radiotherapy

value: No

tag: date at relapse

tag: place to metastasis


title: YMD285 x YMD2566 zygote 3 segregant 1C

description: MD309-A3 vs FY4. DIsome 5 segregant

tag: strain name

value: YMD285 x YMD2566 zygote 3 segregant 1C


title: YMD285 x YMD2566 zygote 1 segregant 4A

description: MD308-D1 vs FY4. Disome 5 segregant

value: YMD285 x YMD2566 zygote 1 segregant 4A


title: YMD285 x YMD2566 zygote 1 segregant 7C

description: MD308-G3 vs FY4, second run. Disome 5 segregant

source_name: MD308-G3, second run

value: YMD285 x YMD2566 zygote 1 segregant 7C


title: Breast Cancer Sample 51

description: One color per patient

tag: tissue

tag: gender

value: Female

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Poorly differentiated invasive ductal carcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

value: Father Laringeal Cancer

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Partial

value: Adriamicin

value: Taxol

value: Yes

tag: date at death


title: Breast Cancer Sample 56

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

value: Invasive ductal carcinoma

value: Pos

tag: her2 immunohistochemestry

value: Neg

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

value: x

value: Hypertension and Diabetes

value: Right

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

value: Progresive

tag: final surgery date

value: Paclitaxel

tag: radiotherapy

tag: date at relapse

tag: place to metastasis


title: Breast Cancer Sample 47

description: One color per patient

tag: tissue

value: Tumor Sample of Breast Cancer

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: diagnosis

tag: histological grade

tag: estrogen receptor immunohistochemestry

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

value: Father Pancreas Cancer. Maternal Aunt Breast Cancer. Father Aunts Ovarian Cancer. Cousin Breast Cancer

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Left

value: Cyclophosphamide

tag: date at death


title: pSS_low_P70

description: SAMPLE 1

tag: gender

value: F

tag: age

tag: tissue

value: blood


title: Breast Cancer Sample 144

description: One color per patient

value: Female

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Infiltrating ductal adenocarcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

value: Hypertension

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

value: Poor

tag: final surgery date

value: Adriamicin

tag: radiotherapy

value: No

tag: date at relapse

tag: place to metastasis


title: Breast Cancer Sample 48

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Invasive ductal carcinoma

tag: histological grade

value: Pos

value: Neg

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Partial

value: Doxorubicin

tag: date at death


title: Breast Cancer Sample 143

description: One color per patient

tag: tissue

value: Tumor Sample of Breast Cancer

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

value: Carcinoma in situ associated with comedo necrosis

tag: estrogen receptor immunohistochemestry

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

tag: final surgery date

value: Trastuzumab

tag: radiotherapy

tag: date at relapse

tag: place to metastasis


title: Breast Cancer Sample 145

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Poorly differentiated ductal adenocarcinoma

tag: histological grade

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

tag: personal pathological hystory

value: C section

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Left

value: Complete

value: Epirubicin

value: Cyclophosphamide

value: Paclitaxel

tag: date at death


title: YMD285 x YMD2566 zygote 1 segregant 3B

description: MD308-C2 vs FY4. Disome 5 segregant

tag: strain name

value: wt

value: YMD285 x YMD2566 zygote 1 segregant 3B


title: Breast Cancer Sample 52

description: One color per patient

tag: tissue

tag: gender

value: Female

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

value: Invasive ductal adenocarcinoma

tag: estrogen receptor immunohistochemestry

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

value: x

value: Fater Liver Cancer

value: Hypothyroidism

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

value: Poor

tag: final surgery date

value: Adriamicin

tag: radiotherapy

value: Yes

tag: date at relapse

tag: place to metastasis


title: Breast Cancer Sample 36

description: One color per patient

tag: tissue

value: Tumor Sample of Breast Cancer

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Poorly differentiated invasive ductal carcinoma

tag: histological grade

value: Pos

value: Neg

value: Absent

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Right

value: Partial

value: Trastuzumab

value: Taxol

tag: date at death


title: Breast Cancer Sample 112

description: One color per patient

tag: tissue

tag: gender

value: Female

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

value: Infiltrating ductal adenocarcinoma

tag: estrogen receptor immunohistochemestry

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

value: Progresive

tag: final surgery date

value: Paclitaxel

value: Doxorubicin

value: Cyclophosphamide

tag: radiotherapy

value: No

tag: date at relapse

tag: place to metastasis


title: Breast Cancer Sample 33

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

tag: histological grade

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

value: Mother Endometrial Cancer

tag: personal pathological hystory

value: Hypertension

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Left

value: Adriamicin

value: Yes

tag: date at death


title: Breast Cancer Sample 36

description: One color per patient

tag: tissue

value: Tumor Sample of Breast Cancer

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

value: Poorly differentiated invasive ductal carcinoma

tag: estrogen receptor immunohistochemestry

value: Pos

value: Neg

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

value: Absent

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

tag: final surgery date

tag: radiotherapy

tag: date at relapse

tag: place to metastasis


title: Breast Cancer Sample 109

description: One color per patient

tag: tissue

tag: gender

value: Female

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

tag: histological grade

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

value: Mother Breast Cancer

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Right

value: Poor

value: Lung

tag: date at death


title: Breast Cancer Sample 35

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: estrogen receptor immunohistochemestry

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

tag: final surgery date

value: Paclitaxel

value: Doxorubicin

value: Cyclophosphamide

tag: radiotherapy

tag: date at relapse

tag: place to metastasis


title: chr 5 disome evolved clone 2

description: YMD285 vs FY4

scan_protocol: Pixel Size : 5 Scan Date : 2013-07-21 Scan Time : 13:00:59 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

tag: strain name

value: wt

value: chr 5 disome evolved clone 2


title: Breast Cancer Sample 19

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Poorly differentiated invasive ductal adenocarcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

value: Hypertension

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Left

value: No

tag: date at death


title: Breast Cancer Sample 14

description: One color per patient

tag: tissue

value: Tumor Sample of Breast Cancer

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

value: Infiltrating ductal adenocarcinoma

tag: her2 immunohistochemestry

value: Pos

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

value: Partial

tag: final surgery date

value: Trastazumab

tag: radiotherapy

value: Yes

tag: date at relapse

tag: place to metastasis


title: Breast Cancer Sample 2

description: One color per patient

tag: tissue

tag: gender

value: Female

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: diagnosis

value: Invasive ductal adenocarcinoma high nuclear grade

tag: histological grade

tag: estrogen receptor immunohistochemestry

value: Neg

value: Absent

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

value: Father Lung Cancer

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Right

value: Complete

value: Trastuzumab

tag: date at death


title: chr 5 disome

description: YMD692 vs FY4

tag: strain name

value: wt

value: chr 5 disome


title: Breast Cancer Sample 29

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Right Breast Ductal carcinoma in situ Left Breast infiltrating ductal adenocarcinoma poorly differentiated

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

value: Both

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

value: Poor

tag: final surgery date

value: Paclitaxel

value: Doxorubicin

value: Cyclophosphamide

tag: radiotherapy

value: No

tag: date at relapse

tag: place to metastasis


title: Breast Cancer Sample 25

description: One color per patient

tag: tissue

value: Tumor Sample of Breast Cancer

tag: gender

value: Female

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

value: Invasive ductal carcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

value: Liver Cancer

tag: personal pathological hystory

tag: tabaquism

value: Pos

tag: age at menarche

tag: birads

tag: breast affected

value: Left

value: Adriamicin

value: Yes

tag: date at death


title: Breast Cancer Sample 18

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: diagnosis

value: Poorly differentiated infiltrating ductal adenocarcinoma

tag: her2 immunohistochemestry

value: Neg

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

value: Absent

value: Apendicitis

value: Right

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

value: Progresive

tag: final surgery date

tag: radiotherapy

tag: date at relapse

tag: place to metastasis


title: Breast Cancer Sample 31

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

value: Infiltrating lobular carcinoma high nuclear grade

tag: histological grade

tag: estrogen receptor immunohistochemestry

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

value: Nev

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Partial

tag: date at death


title: Breast Cancer Sample 37

description: One color per patient

tag: tissue

value: Tumor Sample of Breast Cancer

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: diagnosis

value: High nuclear grade ductal carcinoma associated with carcinoma in situ

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

value: Hypertension and Diabetes

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

value: Poor

tag: final surgery date

value: Cyclophosphamide

tag: radiotherapy

tag: date at relapse

tag: place to metastasis

value: Liver


title: YMD285 x YMD2566 zygote 2 segregant 10A

description: MD308-C9 vs FY4. Disome 5 segregant

tag: strain name

value: wt

value: YMD285 x YMD2566 zygote 2 segregant 10A


title: Breast Cancer Sample 1

description: One color per patient

tag: tissue

tag: gender

value: Female

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Moderately differentiated infiltrating ductal adenocarcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

value: Pos

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

value: Paternal Grandmother Breast Cancer

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Left

value: Paclitaxel

value: No

tag: date at death


title: Breast Cancer Sample 31

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

value: Infiltrating lobular carcinoma high nuclear grade

value: Neg

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

value: Absent

value: Nev

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

tag: final surgery date

value: Adriamicin

tag: radiotherapy

value: Yes

tag: date at relapse

tag: place to metastasis


title: Breast Cancer Sample 16

description: One color per patient

tag: tissue

value: Tumor Sample of Breast Cancer

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: diagnosis

value: Poorly differentiated invasive carcinoma with chondroid metaplasia

tag: histological grade

tag: estrogen receptor immunohistochemestry

value: POs

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

value: Diabetes

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Right

value: Progresive

tag: date at death


title: Breast Cancer Sample 13

description: One color per patient

tag: tissue

tag: gender

value: Female

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

value: Infiltrating ductal carcinoma high

tag: her2 immunohistochemestry

value: Pos

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

value: Mother Breast Cancer

value: Rheumatoid Arthritis

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

value: Poor

tag: final surgery date

value: Trastazumab

tag: radiotherapy

tag: date at relapse

tag: place to metastasis


title: Breast Cancer Sample 13

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: diagnosis

tag: histological grade

tag: estrogen receptor immunohistochemestry

value: Neg

value: Absent

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Paclitaxel

tag: date at death


title: Breast Cancer Sample 35

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

value: Poorly differentiated invasive ductal carcinoma

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

tag: final surgery date

value: Doxorubicin

value: Cyclophosphamide

tag: radiotherapy

value: Yes

tag: date at relapse

tag: place to metastasis


title: Breast Cancer Sample 11

description: One color per patient

tag: tissue

value: Tumor Sample of Breast Cancer

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: diagnosis

value: Poorly differentiated ductal adenocarcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

tag: date at death


title: Breast Cancer Sample 47

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

value: Invasive ductal carcinoma

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

value: Father Pancreas Cancer. Maternal Aunt Breast Cancer. Father Aunts Ovarian Cancer. Cousin Breast Cancer

value: Left

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

value: Partial

tag: final surgery date

value: Adriamicin

value: Taxol

tag: radiotherapy

tag: date at relapse

tag: place to metastasis


title: Breast Cancer Sample 125

description: One color per patient

tag: tissue

tag: gender

value: Female

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: diagnosis

value: Moderately differentiated invasive ductal carcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

tag: personal pathological hystory

value: Ocular Surgery

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Right

value: Poor

tag: date at death


title: Breast Cancer Sample 14

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

value: Infiltrating ductal adenocarcinoma

value: Neg

tag: her2 immunohistochemestry

value: Pos

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

value: Absent

value: Hypertension

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

tag: final surgery date

value: Paclitaxel

value: Trastazumab

tag: radiotherapy

tag: date at relapse

tag: place to metastasis


title: Breast Cancer Sample 93

description: One color per patient

tag: tissue

value: Tumor Sample of Breast Cancer

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: diagnosis

tag: histological grade

tag: estrogen receptor immunohistochemestry

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

value: Diabetes

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Progresive

value: Cyclophosphamide

value: No

value: Lung

tag: date at death


title: Breast Cancer Sample 9

description: One color per patient

tag: tissue

tag: gender

value: Female

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

value: High grade invasive ductal carcinoma

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

value: Maternal Aunt Breast Cancer

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

value: Partial

tag: final surgery date

value: Doxorubicin

tag: radiotherapy

value: Yes

tag: date at relapse

tag: place to metastasis


title: Breast Cancer Sample 18

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: diagnosis

value: Poorly differentiated infiltrating ductal adenocarcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

value: Pos

value: Neg

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

tag: personal pathological hystory

value: Apendicitis

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Right

tag: date at death


title: Breast Cancer Sample 91

description: One color per patient

tag: tissue

value: Tumor Sample of Breast Cancer

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

value: Poorly differentiated invasive ductal carcinoma

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

value: Sister Liver Cancer

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

value: Poor

tag: final surgery date

value: Paclitaxel

tag: radiotherapy

tag: date at relapse

tag: place to metastasis


title: Breast Cancer Sample 158

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: diagnosis

value: Infiltrating ductal adenocarcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Progresive

value: Cyclophosphamide

value: Adriamicin

value: No

tag: date at death


title: Breast Cancer Sample 34

description: One color per patient

tag: tissue

tag: gender

value: Female

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

value: Infiltrating ductal carcinoma high

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

value: Absent

value: Diabetes and Heart Disease

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

tag: final surgery date

value: Doxorubicin

tag: radiotherapy

tag: date at relapse

tag: place to metastasis


title: Breast Cancer Sample 5

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: diagnosis

value: Moderately differentiated infiltrating ductal adenocarcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

value: Pos

value: Neg

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Complete

value: Epirrubicin

value: Yes

tag: date at death


title: 38C_HET

city: New York

first: Riccardo

last: Dalla-Favera

state: NY

address: 1130 St Nicholas Avenue

institute: Columbia University

description: Gene expression data from murine FOXO1+/-, splenic germinal center B cells (1 single animal)

hyb_protocol: 3.75 micrograms of fragmented, Biotin-labeled amplified cDNA was hybridized using the Affymetrix HWS kit, Standard Array (49 Format), using NuGEN's Encore Biotin kit instructions. Samples were hybridized for 16 hours. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: Affymetrix GeneChip Scanner 3000 7G, connected to Command Console software

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.

organism: Mus musculus

source_name: Spleen, SRBC immunized mouse, 12 days post-immunization

label_protocol: cDNA was generated using the NuGen Ovation Amplification System V2, starting from 25 ng of total RNA (RIN>9),  following manufacturer's instructions. Amplified SPIA cDNA was isolated using QiaGen MinElute kit. Biotinylation and fragmentation were performed using NuGen's Encore Biotin Module, following the manufacturer's instructions.

growth_protocol: 10 wk -old mice were immunized with two rounds of injection of sheep red blood cells (SRBC) (at day 0 and day 5), and Germinal center B cells isolated from spleens at Day 12.

extract_protocol: RNA extraction was performed using the RNA XS isolation kit (Macherey-Nagel), as per manufacturer's instructions. Linear polyacrylamide (5 micrograms) as used as  carrier.

treatment_protocol: Germinal center B cells were isolated from B-cell enriched fractions (Mouse B cell isolation kit, Miltenyi), using Fluorescence Activated Cell Sorting, based on the expression of specific surface markers (B220hi, PNAhi, CD95hi), and collected in PBS+0.5% BSA+2% FBS. Cells were pelleted and resuspended in RA1 buffer (+ TCEP) (Macherey-Nagel), and stored at -80C until RNA isolation.

tag: tissue

value: FACS-sorted GC B cells (B220hi, CD95hi, PNAhi)

tag: age

value: 10 wk

tag: genotype

value: FOXO1f/+, Cg1-Cre


title: Breast Cancer Sample 16

description: One color per patient

value: Tumor Sample of Breast Cancer

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Poorly differentiated invasive carcinoma with chondroid metaplasia

tag: histological grade

tag: estrogen receptor immunohistochemestry

value: POs

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

value: Diabetes

value: Right

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

value: Progresive

tag: final surgery date

value: Paclitaxel

tag: radiotherapy

tag: date at relapse

tag: place to metastasis


title: Breast Cancer Sample 133

description: One color per patient

tag: tissue

tag: gender

value: Female

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Moderately differentiated invasive ductal carcinoma

tag: histological grade

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Left

value: Poor

value: Cyclophosphamide

tag: date at death


title: 37C_HET

tag: tissue

tag: age

tag: genotype


title: Breast Cancer Sample 37

description: One color per patient

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: High nuclear grade ductal carcinoma associated with carcinoma in situ

tag: histological grade

tag: estrogen receptor immunohistochemestry

value: Neg

tag: her2 immunohistochemestry

value: Pos

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

value: Absent

value: Hypertension and Diabetes

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

tag: final surgery date

value: Adriamicin

tag: radiotherapy

tag: date at relapse

tag: place to metastasis

value: Liver


title: Breast Cancer Sample 41

description: One color per patient

tag: tissue

value: Tumor Sample of Breast Cancer

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Poorly differentiated invasive ductal carcinoma

tag: histological grade

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Doxorubicin

value: Yes

tag: date at death


title: Breast Cancer Sample 51

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: estrogen receptor immunohistochemestry

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

value: Father Laringeal Cancer

value: Right

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

value: Partial

tag: final surgery date

value: Taxol

tag: radiotherapy

tag: date at relapse

tag: place to metastasis


title: 7C_KO

description: Gene expression data from murine FOXO1 null, splenic germinal center B cells (1 single animal)

tag: tissue

value: FACS-sorted GC B cells (B220hi, CD95hi, PNAhi)

tag: age

value: 10 wk

tag: genotype

value: FOXO1f/f, Cg1-Cre


title: 12C_HET

value: FOXO1f/+, Cg1-Cre


title: Breast Cancer Sample 21

description: One color per patient

tag: gender

value: Female

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Invasive ductal carcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

value: Pos

tag: her2 immunohistochemestry

value: Neg

tag: her2 fish

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

value: Liver Cancer

tag: personal pathological hystory

value: Hypertension

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Complete

value: Paclitaxel

tag: date at death


title: 34C_WT

description: Gene expression data from murine FOXO1 +/+, splenic germinal center B cells (1 single animal)

tag: tissue

tag: age

tag: genotype

value: FOXO1+/+, Cg1-Cre


title: brm-1 hd2c-3_heat stress_rep3

city: Warsaw

first: Daniel

last: Buszewicz

address: Pawińskiego 5A

department: Institute of Biochemistry and Biophysics

country: Poland

institute: Polish Academy of Sciences

hyb_protocol: Labeled samples were hybridized to the Arabidopsis Gene 1.1 ST Array Strip (Affymetrix, Santa Clara, CA).

scan_protocol: The microarrays were scanned with an Affymetrix GeneAtlas Scanner and the intensity signals for each of the probe sets were written by Affymetrix software into CEL files.

data_processing: The CEL files were imported into the Partek Genomic Suite v 6.6 software with the use of RMA (Robust Multiarray Averaging). During this step, background correction was applied based on the global distribution of the PM (perfect match) probe intensities and the affinity for each of the probes (based on their sequences) was calculated. In addition, the probe intensities were quantile normalized (Bolstad et al., 2003), log2 transformed and median polish summarization was applied to each of the probe sets.

source_name: brm-1 hd2c-3_heat stress

label_protocol: Labeled cDNA was prepared using the Affymetrix GeneChip® WT Terminal Labeling Kit (Part no. 900671).

growth_protocol: Arabidopsis plants were grown on soil under long day (16h light / 8h dark) conditions at 22-23°C, with 70% humidity and 120-150 µM m-2 s-1 light intensity.

extract_protocol: RNA was isolated using MagNA Pure Compact Instrument and MagNA Pure Compact RNA Isolation Kit (Roche) according to manufacturer's insturctions.

treatment_protocol: 3-week-old plants were transferred to 38°C for 1 hour.

tag: ecotype background

tag: genotype/variation

value: brm-1 hd2c-3

value: 3 weeks

tag: exposed to

value: 38°C for 1 h; heat stress


title: Breast Cancer Sample 97

description: One color per patient

value: Tumor Sample of Breast Cancer

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Poorly differentiated invasive ductal carcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

tag: e-cadherina ihc

tag: t

tag: n

value: Sister Brain Cancer

value: Right

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

value: Partial

tag: final surgery date

value: Taxol

tag: radiotherapy

value: Yes

tag: date at relapse

tag: place to metastasis


title: 44C_KO

tag: tissue

value: FACS-sorted GC B cells (B220hi, CD95hi, PNAhi)

tag: age

value: 10 wk

tag: genotype

value: FOXO1f/f, Cg1-Cre


title: Breast Cancer Sample 10

description: One color per patient

tag: gender

value: Female

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: High grade invasive ductal carcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

value: Neg

tag: her2 immunohistochemestry

value: Pos

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

value: Absent

tag: e-cadherina ihc

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Left

value: Poor

value: Trastuzumab

tag: date at death


title: 42C_KO

tag: tissue

tag: age

tag: genotype


title: 19C_WT

value: FOXO1+/+, Cg1-Cre


title: 33C_WT


title: PlCH_2

city: Genova

first: Ulrich

last: Pfeffer

address: L. Benzi 10

country: Italy

institute: IRCCS AOU San Martino - IST

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip MG_430.2 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix G3000 scanner

data_processing: Data were pre-processed together with the samples from the datasets GSE2981, GSE27787, GSE43042, GSE6933, GSE47935 using the justRMA package implemented in R-BioConductor

source_name: PlCH cells isolated from peripheral blood of 15 mice by flow cytometry

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 50 ug total RNA

growth_protocol: PlCH cells isolated form peripheral blood by multiparametric flow cytometry

extract_protocol: extraction of total RNA using Qiagen RNAeasy mini kit following the instructions of the provider

tag: strain

tag: gender

value: male and female

tag: developmental stage

value: adult, 7 months

value: peripheral blood, PlCH cells


title: Breast Cancer Sample 129

description: One color per patient

value: Tumor Sample of Breast Cancer

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Ductal carcinoma in situ comedonicus type

tag: histological grade

tag: estrogen receptor immunohistochemestry

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

tag: e-cadherina ihc

tag: t

tag: n

value: Mother and Sister Ovarian Cancer

value: Both

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

value: Partial

tag: final surgery date

value: Adriamicin

value: Cyclophosphamide

value: Taxol

tag: radiotherapy

value: No

tag: date at relapse

tag: place to metastasis


title: PlCH_1

tag: strain

tag: gender

tag: developmental stage

tag: tissue


title: brm-1 hd2c-3_heat stress_rep1

tag: ecotype background

tag: genotype/variation

value: brm-1 hd2c-3

tag: age

value: 3 weeks

tag: exposed to

value: 38°C for 1 h; heat stress


title: brm-1 hd2c-3_heat stress_rep2


title: brm-1_heat stress_rep3

source_name: brm-1_heat stress


title: Breast Cancer Sample 106

description: One color per patient

value: Female

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Undifferentiated carcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

value: Neg

tag: her2 immunohistochemestry

value: Pos

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Left

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

value: Complete

value: Trastuzumab

value: Yes

tag: date at death


title: Breast Cancer Sample 19

description: One color per patient

tag: tissue

value: Tumor Sample of Breast Cancer

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Poorly differentiated invasive ductal adenocarcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

value: Absent

value: Hypertension

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

value: Poor

tag: final surgery date

value: Paclitaxel

tag: radiotherapy

tag: date at relapse

tag: place to metastasis


title: Breast Cancer Sample 137

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

value: Moderately differentiated invasive ductal carcinoma

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

value: Progresive

value: No

tag: date at death


title: Breast Cancer Sample 52

description: One color per patient

tag: tissue

tag: gender

value: Female

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Invasive ductal adenocarcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

value: x

value: Fater Liver Cancer

value: Hypothyroidism

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

tag: final surgery date

value: Adriamicin

value: Cyclophosphamide

tag: radiotherapy

tag: date at relapse

tag: place to metastasis


title: Breast Cancer Sample 9

description: One color per patient

tag: tissue

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

value: High grade invasive ductal carcinoma

value: Neg

tag: e-cadherina ihc

tag: t

tag: n

tag: m

tag: data at diagnosis

tag: age at diagnosis

tag: pathological family history

value: Maternal Aunt Breast Cancer

tag: personal pathological hystory

tag: tabaquism

tag: age at menarche

tag: birads

tag: breast affected

value: Right

tag: initial highest diameter in mm by image

tag: initial clinical size in mm by palpation

tag: final pathology size in mm

value: Partial

value: Doxorubicin

value: Yes

tag: date at death


title: Breast Cancer Sample 88

description: One color per patient

tag: tissue

value: Tumor Sample of Breast Cancer

tag: gender

tag: rna ng/ul

tag: rna 260/280 (nanodrop)

tag: rna 260/230 (nanodrop)

tag: rqi experion

tag: diagnosis

value: Invasive ductal carcinoma

tag: histological grade

tag: estrogen receptor immunohistochemestry

value: Pos

tag: her2 immunohistochemestry

tag: her2 fish

tag: percentage ki67 ihc

tag: p63 ihc

tag: final clinical size in mm by palpation

tag: final number of positive ganglia

tag: final number of resected ganglia

tag: response to treatment

value: Poor

tag: final surgery date

value: Paclitaxel

tag: radiotherapy

tag: date at relapse

tag: place to metastasis


title: brm-1_heat stress_rep2

tag: ecotype background

tag: genotype/variation

tag: age

value: 3 weeks

tag: exposed to

value: 38°C for 1 h; heat stress