title: Barrett's esophagus stem cells from patient 6, rep2

source_name: Barrett's esophagus stem cells_patient 6

value: patient 6


title: 144BW-VB1_1038

status: Public on Oct 01 2015

type: genomic

city: Uppsala

first: Chiara

last: Rasi

state: Sweden

address: Husargatan 3

department: Department of Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

description:
uninvolved margin in the immediate vicinity of the mammilla
144BW-VB1

hyb_protocol: starndard protocol

scan_protocol: The majority of genotyping experiments were conducted at the SNP&SEQ Technology Platform in Uppsala by using four similar in SNP-density Illumina platforms (Human 660W-Quad, Human1M-Duo, HumanOmniExpress and HumanOmniExpressExome beadchips), according to the recommendations of the manufacturer.

data_processing:
The genotyping data was normalized and analyzed using Nexus Copy Number 7 (Biodiscovery). Copy number and allelic imbalances calls were made by using the SNP-FASST segmentation algorithm with the following settings: Significance Threshold: 5.0E-9; Max Contiguous Probe Spacing 500-1000; Min. number of probes per segment: 10; Homozygous Frequency Threshold: 0.85; Homozygous Value Threshold: 0.95; and Heterozygous Imbalance Threshold: 0.46. All the other parameters were left default. Data included in this GEO project was generated using the utility  “convert .ivg to .txt” from Nexus 7.
Log R Ratio and B Allele frequency values are reported for each probe from the four different platforms used in the study.

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: breast tissue from mastectomy, taken outside the site of primary tumor(s)

label_protocol: starndard protocol

extract_protocol: The tissues were stored at -70 degrees C prior to DNA extraction. The solid tissues were homogenized with a Tissuerupter (Qiagen). Proteinase K and Sarcosine was then added and the sample was incubated at 50oC over-night. The samples were transferred to PhaseLock Gel tubes and the DNA was purified with phenol/chloroform extraction. Due to very rich content of fat in UMs, phenol/chloroform extraction was repeated 6 times for all UMs, and 3 times for PTs and control samples from skin. The purified DNA was precipitated with sodium acetate, pH 5.4 and 95% ethanol. The DNA precipitate was dried before dissolving in water. Control samples of blood were extracted with QIAmp DNA Blood Maxi Kit (Qiagen).

tag: gender

value: female

tag: age at cancer diagnosis (yrs)

tag: tumor grade

value: Luminal B, HER2-

tag: tumor focality

value: multifocal??? (1 mm)


title: 144BW-UM-IU_1037

description:
uninvolved margin of breast carcinoma
144BW-UM-IU


title: 3111

type: RNA

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

hyb_protocol: Samples were hybridized on dual color Agilent's custom MCF-7 Microarray (Agilent, Diegem, Belgium; GEO accession number GPL8637).

scan_protocol: After washing, the slides were scanned with a microarray scanner (Agilent) and images were processed using Feature Extraction Software version 8.5 (Agilent).

data_processing: The Agilent processed signal values (i.e., feature gProcessedSignal from Agilent Feature Extraction v8.5.1.1) were used for the data analysis. Base 2 log-ratios (Cy5/Cy3) were computed and averaged over the duplicate spots. Control probes were removed prior to analysis.

molecule: total RNA

label_protocol: From 1 µg of cellular RNA, poly-A RNA was reversed transcribed using a poly dT-T7 primer. The resulting cDNA was immediately used for one round of amplification by T7 in vitro transcription reaction in the presence of Cyanine 5-CTP (LRILAK, Agilent). The amplified and labeled RNA probes were purified separately with RNeasy purification columns (Qiagen, Belgium). Probes were verified for amplification yield and incorporation efficiency by measuring the RNA concentration at 280 nm and Cy5 incorporation at 650 nm using a Nanodrop spectrophotometer.

extract_protocol: RNA was extracted using the RNeasy mini kit from Qiagen, according to the manufacturer's protocol.

treatment_protocol: MCF-7 cells were seeded in T-25 Nunc culture flasks at a density of 300,000 cells per flask. After 72h steroid-deprivation, cells were exposed for 1h, 4h, or 48h at a high or low concentration. The highest concentration represents the highest non-cytotoxic or highest soluble concentration. Non-cytotoxic concentrations were derived from AlamarBlue viability assays (Nociari et al. 1998).

tag: cell line

value: MCF-7 human breast carcinoma cell line (ECACC No. 86012803)

tag: compound

value: Thyroid hormone

tag: concentration

tag: exposure

label_protocol: From 1 µg of cellular RNA, poly-A RNA was reversed transcribed using a poly dT-T7 primer. The resulting cDNA was immediately used for one round of amplification by T7 in vitro transcription reaction in the presence of Cyanine 3-CTP (LRILAK, Agilent) The amplified and labeled RNA probes were purified separately with RNeasy purification columns (Qiagen, Belgium). Probes were verified for amplification yield and incorporation efficiency by measuring the RNA concentration at 280 nm and Cy3 incorporation at 550 nm using a Nanodrop spectrophotometer.

value: solvent control


title: 3110

value: 2,3,7,8 Tetrachloro-dibenzo-p-dioxin


title: 145MJ-UM-EL_1040

description:
uninvolved margin of breast carcinoma
145MJ-UM-EL

value: Luminal A

value: unifocal


title: Barrett's esophagus stem cells from patient 6, rep1

city: Houston

first: Frank

last: McKeon

state: TX

address: 3455 Cullen Blvd

department: Biology and Biochemistry

country: USA

institute: University of Houston

hyb_protocol: GeneChip® Hybridization, Wash, and Stain Kit (affymetrix)

data_processing:
Expression console, Partek Genome Suite 6.6
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

label: Biotin

label_protocol: Encore® Biotin Module (Nugen)

extract_protocol: PicoPure® RNA Isolation Kit (Life Technologies)

tag: patient id

tag: cell type

value: Barett's esophagus stem cells

tag: sample type

value: Cultured stem cells


title: 144BW-UM-IL_1036

description:
uninvolved margin of breast carcinoma
144BW-UM-IL


title: 144BW-UM-EU_1035

description:
uninvolved margin of breast carcinoma
144BW-UM-EU


title: GFP2, Biological rep2

city: Pars

first: Renaud

last: Dentin

address: 24 rue du Faubourg Saint Jacques

department: Endocrinology, Metabolism and Diabetes

country: France

institute: INSERM U1016

description: Liver gene expression data from fed GFP expressing mice

hyb_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® Mouse Gene 1.0 ST (Affymetrix) at 45°C for 17 hours.  After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix).

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix)

data_processing: the data were RMA normalized  and  analysed with Partek Genomic Suit

organism: Mus musculus

source_name: Liver specific GFP overexpressing mice 2

label_protocol: After validation of the RNA quality with Bioanalyzer 2100 (using Agilent RNA6000 nano chip kit), 50 ng of total RNA is reverse transcribed following the Ovation PicoSL WTA System (Nugen). Briefly, the resulting double strand cDNA is used for amplification based on SPIA technology. After purification according to Nugen protocol, 5ug of single strand DNA is used for generation of Sens Target DNA using Ovation Exon Module kit (Nugen). 2.5ug of Sens Target DNA are fragmented and biotin labelled using Encore Biotin Module kit (Nugen)

growth_protocol: The GFP or Phf2 (5.108 pfu / mice) were overexpressed in the liver of 8 weeks old C57BL/6J mice through adenoviral gene delivery (tail vein injection).

extract_protocol: Total RNA were extracted using the SV RNA extraction systeme from Progema according to the manufacturer's instructions.

treatment_protocol: Mice were studied in fed state 3 weeks after the adenovirus injection.

tag: strain

value: male

tag: age

value: 8 weeks

tag: tissue

value: Liver

tag: genotype/variation

value: GFP overexpressing


title: 3 het brain 5 weeks total

city: Milan

first: Daniela

last: Brina

address: Via Sforza 35

country: Italy

institute: INGM

description: Gene expression data from mouse brain

hyb_protocol: Hybridization was performed using the GeneChip® Hybridization, Wash and Stain Kit. It contains mix for target dilution, DMSO at a final concentration of 7% and pre-mixed biotin-labelled control oligo B2 and bioB, bioC, bioD and cre controls (Affymetrix cat #900299) at a final concentration of 50 pM, 1.5 pM, 5 pM, 25 pM and 100 pM, respectively. Targets were diluted in hybridization buffer at a concentration of 25 ng/ul and denatured at 99 °C for 5 minutes incubated at 45 °C for 5 minutes  and centrifuged at maximum speed for 1 minute prior to introduction into the GeneChip® cartridge. A single GeneChip® MOUSE Gene 1.0 ST was then hybridized with each biotin-labeled sense target.   Hybridizations were performed for 16 h at 45 °C in a rotisserie oven.

scan_protocol: GeneChip arrays were scanned using an Affymetrix GeneChip® Scanner3000 7G using default parameters

data_processing: Affymetrix GeneChip® Command Console software (AGCC) was used to acquire GeneChip® images and generate .DAT and .CEL files, which were used for subsequent analysis with proprietary software. Partek Genomics Suite v 6.4 was used for analysis of microarray data. Data are represented as RMA values.

source_name: mouse brain

label_protocol: Biotinylated cRNA were prepared from 150 ng total RNA according to the Ambion® WT Expression Kit (Ambion, Austin, TX). The fragmentation and labeling steps were performed using the Affymetrix GeneChip® WT Teminal Labeling Kit (Affymetrix, Santa Clara, CA). All steps of the labeling protocol were performed as suggested by Affymetrix.

growth_protocol: White adipose tissue and brain from eIF6 heterozygotes and wild-type 5 weeks old mice.

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

treatment_protocol: Five-weeks old mice were sacrified by cervical dislocation, fat and brain were quicly removed, placed in ice-cold Trizol solution (GibcoBRL) and quicly frozen in N2 liquid.

value: brain

value: eIF6 heterozygotes


title: 1 het brain 5 weeks total

description: Gene expression data from mouse brain


title: 144BW-UM-EL_1034

description:
uninvolved margin of breast carcinoma
144BW-UM-EL

value: female


title: Barrett's esophagus stem cells from patient 5, rep2

scan_protocol: GeneChip® Hybridization, Wash, and Stain Kit (affymetrix)

source_name: Barrett's esophagus stem cells_patient 5

value: patient 5


title: 143DMG-VB2_1033

description:
uninvolved margin in the immediate vicinity of the mammilla
143DMG-VB2

value: Luminal B, HER2-


title: 3107

value: MCF-7 human breast carcinoma cell line (ECACC No. 86012803)

value: kepone


title: Barrett's esophagus stem cells from patient 5, rep1


title: 3108

source_name: Ref MCF7


title: Barrett's esophagus stem cells from patient 4, rep1

source_name: Barrett's esophagus stem cells_patient 4

value: patient 4


title: 2 het brain 5 weeks total

description: Gene expression data from mouse brain


title: 143DMG-VB1_1032

description:
uninvolved margin in the immediate vicinity of the mammilla
143DMG-VB1


title: Barrett's esophagus stem cells from patient 4, rep2


title: 143DMG-UM-IU_1031

description:
uninvolved margin of breast carcinoma
143DMG-UM-IU


title: 3105


title: 3106


title: Barrett's esophagus stem cells from patient 3, rep2

source_name: Barrett's esophagus stem cells_patient 3

value: patient 3


title: 143DMG-UM-IL_1030

description:
uninvolved margin of breast carcinoma
143DMG-UM-IL


title: 3104


title: 3109

value: 2,3,7,8 Tetrachloro-dibenzo-p-dioxin


title: 3103

value: solvent control


title: 1 wt brain 5 weeks total

description: Gene expression data from mouse brain

value: wild type


title: 2 wt brain 5 weeks total

description: Gene expression data from mouse brain


title: 3 het fat 5 weeks total

description: Gene expression data from mouse perigonadal white adipose tissue

source_name: mouse perigonadal white adipose tissue

value: white adipose tissue


title: Barrett's esophagus stem cells from patient 3, rep1

value: Barett's esophagus stem cells

value: Cultured stem cells


title: Barrett's esophagus stem cells from patient 2, rep2

source_name: Barrett's esophagus stem cells_patient 2

value: patient 2


title: 3 wt brain 5 weeks total

description: Gene expression data from mouse brain


title: Barrett's esophagus stem cells from patient 2, rep1


title: 143DMG-UM-EU_1029

description:
uninvolved margin of breast carcinoma
143DMG-UM-EU

value: unifocal


title: 143DMG-UM-EL_1028

description:
uninvolved margin of breast carcinoma
143DMG-UM-EL


title: 142AK-VB2_1025

description:
uninvolved margin in the immediate vicinity of the mammilla
142AK-VB2

value: Luminal B, HER2+


title: 3 wt fat 5 weeks total


title: 3102


title: Barrett's esophagus stem cells from patient 1, rep2

source_name: Barrett's esophagus stem cells_patient 1

value: patient 1


title: 2 wt fat 5 weeks total


title: 142AK-VB1_1024

description:
uninvolved margin in the immediate vicinity of the mammilla
142AK-VB1

value: female


title: Barrett's esophagus stem cells from patient 1, rep1


title: 3101

value: Lindane


title: 142AK-UM-IU_1023

description:
uninvolved margin of breast carcinoma
142AK-UM-IU


title: 3100

value: Dicyclohexylphthalate


title: 3099

value: MCF-7 human breast carcinoma cell line (ECACC No. 86012803)

value: Kepone


title: 142AK-UM-IL_1022

description:
uninvolved margin of breast carcinoma
142AK-UM-IL


title: 142AK-UM-EU_1021

description:
uninvolved margin of breast carcinoma
142AK-UM-EU


title: 3098


title: 1 wt fat 5 weeks total


title: 2 het fat 5 weeks total

value: eIF6 heterozygotes


title: Pancreas_Normal_Sample 10

city: Royal Oak

first: Bryan

last: Thibodeau

state: MI

address: 3811 West 13 Mile Road

department: BioBank

institute: Beaumont Research Institute

description:
Pancreas_Normal_AX0665
Gene expression data from normal pancreas tissue adjacent to untreated PDAC

hyb_protocol: Hybridization to Affymetrix Human Exon 1.0 ST Arrays as well as washing and staining (with GeneChip® Fluidics Station 450, Affymetrix) were performed following manufacturer protocols.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000.

data_processing:
The CEL files containing the raw intensity data from the Affymetrix GeneChip arrays were imported into Partek Genomics Suite and normalized using the robust multichip average with a guanine-cytosine content background correction, quantile normalization, log2-transformation, and median polish probeset summarization. Exons were then summarized to genes using the average of the probesets.
probe group file: HuEx-1_0-st-v2

source_name: Adjacent normal pancreas_untreated

label_protocol: Using the Ambion® WT Expression Kit (Affymetrix, Santa Clara, CA), total RNA was used to generate purified sense cDNA ready for fragmentation and labeling. Fragmentation and terminal labeling was done according to manufacturer’s protocols using the GeneChip® WT Terminal Labeling and Controls Kit.

extract_protocol: Tissue was homogenized with the gentleMACS Dissociator using gentleMACS M Tubes (Miltenyi Biotec Inc., Auburn, CA) prior to total RNA isolation using the Omega Total RNA Isolation Kit (Omega Bio-Tek 400, Norcross, GA). Following the manufacturer’s protocol, total RNA was purified using spin cartridge technology, quantified (Nanodrop 8000, Thermo Scientific), and stored at -80°C. RNA integrity was determined by Bioanalyzer analysis (Agilent, Santa Clara, CA) just prior to processing for expression microarray analysis.

treatment_protocol: Patients undergoing pancreatic resection at William Beaumont Hospital (Royal Oak, MI) were consented prior to surgery with local IRB oversight. Samples were collected at time of surgery and stored at -80°C according to CAP (College of American Pathologist)-accredited standard operating procedures. Disease pathology of frozen samples was validated with hematoxylin and eosin stained tissue sections from adjacently collected formalin fixed paraffin embedded tissue.

value: normal pancreas

tag: treatment


title: Pancreas_Normal_Sample 9

description:
Pancreas_Normal_AX0573
Gene expression data from normal pancreas tissue adjacent to untreated PDAC


title: 3097


title: Pancreas_Normal_Sample 8

description:
Pancreas_Normal_AX0537
Gene expression data from normal pancreas tissue adjacent to untreated PDAC


title: 1 het liver 3 weeks polysomal

description: polysomal RNA

data_processing: Affymetrix GeneChip® Command Console software (AGCC) was used to acquire GeneChip® images and generate .DAT and .CEL files, which were used for subsequent analysis with proprietary software.

source_name: liver

label_protocol: Double stranded cDNA synthesis and related cRNA was performed with GeneChip® WT cDNA Synthesis and Amplification Kit starting from 200 ng of total RNA. With the same kit was synthesized the sense strand cDNA before to be fragmented and labeled with Affymetrix GeneChip® WT Teminal Labeling Kit (Affymetrix, Santa Clara, CA). All steps of the labeling protocol were performed as suggested by Affymetrix (GeneChip® WT Sense Target Labeling Assay manual).

growth_protocol: Liver from eIF6 heterozygotes or wild-type 3 weeks old mice.

extract_protocol: Liver homogeneate were loaded on 15-50% sucrose cushion and ultracentrifuged at 39000 rpm for 3 hours and 30 minutes. Absorbance of RNA were read at 254 nm and 1 ml fractions were collected. Fifty microliters of liver homogeneate was considered as total RNA. Fractions correspondant to polysomes were pooled and considered polysomal RNA.Trizol extraction of total RNA and polysomal RNA was performed according to the manufacturer's instructions.

treatment_protocol: Three-weeks old mice were sacrified by cervical dislocation, liver were quicly removed, placed in ice-cold Trizol solution (GibcoBRL) and quicly frozen in N2 liquid.

value: liver

tag: genotype

value: eIF6 heterozygote


title: 142AK-UM-EL_1020

description:
uninvolved margin of breast carcinoma
142AK-UM-EL

tag: gender


title: 3096

value: Dimethyl-benz(a)anthracene


title: 2 het liver 3 weeks polysomal

description: polysomal RNA


title: Pancreas_Normal_Sample 6

description:
Pancreas_Normal_AX0235
Gene expression data from normal pancreas tissue adjacent to untreated PDAC


title: 1 het liver 3 weeks total

description: total RNA


title: 141BB-VB1_1016

description:
uninvolved margin in the immediate vicinity of the mammilla
141BB-VB1

tag: age at cancer diagnosis (yrs)

value: Luminal B, HER2-


title: 3093

value: solvent control


title: 141BB-UM-IL_1014

description:
uninvolved margin of breast carcinoma
141BB-UM-IL


title: 141BB-UM-EU_1013

description:
uninvolved margin of breast carcinoma
141BB-UM-EU


title: 3095

value: Thyroid hormone


title: 3092


title: Pancreas_Normal_Sample 5

description:
Pancreas_Normal_AX0162
Gene expression data from normal pancreas tissue adjacent to untreated PDAC


title: 141BB-VB2_1017

description:
uninvolved margin in the immediate vicinity of the mammilla
141BB-VB2


title: Pancreas_Normal_Sample 4

description:
Pancreas_Normal_AX0064
Gene expression data from normal pancreas tissue adjacent to untreated PDAC


title: 3094


title: Pancreas_Normal_Sample 7

description:
Pancreas_Normal_AX0380
Gene expression data from normal pancreas tissue adjacent to untreated PDAC


title: 1 wt liver 3 weeks polysomal

description: polysomal RNA

value: wild type


title: 3089

value: 2,3,7,8 Tetrachloro-dibenzo-p-dioxin


title: 2 het liver 3 weeks total

description: total RNA


title: 141BB-UM-EL_1012

description:
uninvolved margin of breast carcinoma
141BB-UM-EL

value: unifocal


title: Pancreas_Normal_Sample 2

description:
Pancreas_Normal_AX0047
Gene expression data from normal pancreas tissue adjacent to untreated PDAC


title: 309


title: 3 wt liver 3 weeks total

description: total RNA


title: Pancreas_Normal_Sample 1

description:
Pancreas_Normal_AX0001
Gene expression data from normal pancreas tissue adjacent to untreated PDAC


title: 2 wt liver 3 weeks total

description: total RNA


title: 141BB-UM-IU_1015

description:
uninvolved margin of breast carcinoma
141BB-UM-IU


title: 1 wt liver 3 weeks total

description: total RNA


title: PDAC_Surgery Only_Sample 10

description:
PDAC_Surgery Only_AX2351
Gene expression data from untreated PDAC

value: pancreatic ductal adenocarcinoma


title: PDAC_Surgery Only_Sample 9

description:
PDAC_Surgery Only_AX1898
Gene expression data from untreated PDAC


title: 2 wt liver 3 weeks polysomal

description: polysomal RNA


title: Endometrial Biopsy-Endometrial Stromal Fibroblast [ETB125-+Late]

city: San Francisco

first: Linda

middle: C.

last: Giudice

state: CA

address: 499 Illinois St., Sixth Floor

department: Center for Reproductive Health at Mission Bay

institute: UC San Francisco

hyb_protocol: Microarrays were hybridized, washed, stained, and scanned according to the protocol described in the WT sense target labeling assay manual from Affymetrix (version 4; FS450_0007).

scan_protocol: Microarrays were hybridized, washed, stained, and scanned according to the protocol described in WT Sense Target Labeling Assay Manual from Affymetrix (Version 4; FS450_0007) at the UCSF Gladstone Genomics Core Facility.

data_processing: GeneSpringGX 12.0, Microarray Technology: Affymetrix.ExonExprChip.HuGene-1_0-st-v1, Summarization Algorithm: ExonRMA16, Normalization: Quantile, Baseline Transformation: median of all samples

source_name: Endometrium

label_protocol: RNA was reverse transcribed/amplified into cDNA using the NuGEN FFPE kit, and sense-strand cDNA targets were created using the NuGEN WT-Ovation Exon Module, followed by fragmentation and labeling using NuGEN Encore Biotin Module for hybridization to Affymetrix Human Gene 1.0 ST arrays.

growth_protocol: eMSC and eSF from control and endometriosis samples were cultured in parallel at clonal densities (Figure 1) for 2-8 weeks in in serum-containing fibroblast growth medium (SCM: 75% phenol red-free Dulbecco's Modified Eagle's Medium (DMEM)/25% MCDB-105 supplemented with 10% charcoal-striped fetal bovine serum (FBS) and 5 µg/ml insulin) differentiation medium   and selected for early (2-3 weeks, eMSCEarly, eSFEarly) and late (4-8 weeks, eMSCLate, eSFLate) cultures, depending on colony size, morphology, and time in culture.

extract_protocol: FACS analyzed sorted cell populations were subject to RNA isolation and purification, with DNAse treatment, using Pico Pure RNA Isolation Kit

tag: disease

value: No Endometriosis

tag: fresh tissue sample/time in culture

value: 4-8 Weeks in Culture

value: Endometrial Stromal Fibroblast


title: Pancreas_Normal_Sample 3

description:
Pancreas_Normal_AX0063
Gene expression data from normal pancreas tissue adjacent to untreated PDAC


title: Endometrial Biopsy-Endometrial Stromal Fibroblast [ETB128-+Late]


title: 3441

tag: cell line

value: MCF-7 human breast carcinoma cell line (ECACC No. 86012803)


title: 140MF-VB2_1009

description:
uninvolved margin in the immediate vicinity of the mammilla
140MF-VB2

value: female

value: Triple negative

tag: tumor focality


title: Endometrial Biopsy-Endometrial Stromal Fibroblast [ETB99-+Late]


title: Endometrial Biopsy-Endometrial Stromal Fibroblast [ETB109-+Late]


title: 3087

tag: compound

tag: concentration


title: 3090

value: Kepone

tag: exposure


title: 140MF-UM-IU_1007

description:
uninvolved margin of breast carcinoma
140MF-UM-IU


title: 140MF-UM-IL_1006

description:
uninvolved margin of breast carcinoma
140MF-UM-IL


title: 140MF-UM-EU_1005

description:
uninvolved margin of breast carcinoma
140MF-UM-EU


title: 140MF-UM-EL_1004

description:
uninvolved margin of breast carcinoma
140MF-UM-EL


title: 3086


title: 3085

value: Lindane


title: 139MD-VB2_1003

description:
uninvolved margin in the immediate vicinity of the mammilla
139MD-VB2

tag: tumor grade


title: Endometrial Biopsy-Endometrial Stromal Fibroblast [UC249-+Late]

tag: cell type


title: 140MF-VB1_1008

description:
uninvolved margin in the immediate vicinity of the mammilla
140MF-VB1


title: PDAC_Surgery Only_Sample 8

description:
PDAC_Surgery Only_AX1649
Gene expression data from untreated PDAC


title: 3084


title: PDAC_Surgery Only_Sample 6

description:
PDAC_Surgery Only_AX1249
Gene expression data from untreated PDAC


title: PDAC_Surgery Only_Sample 5

description:
PDAC_Surgery Only_AX1017
Gene expression data from untreated PDAC


title: PDAC_Surgery Only_Sample 7

description:
PDAC_Surgery Only_AX1606
Gene expression data from untreated PDAC


title: 139MD-VB1_1002

description:
uninvolved margin in the immediate vicinity of the mammilla
139MD-VB1


title: PDAC_Surgery Only_Sample 4

description:
PDAC_Surgery Only_AX0808
Gene expression data from untreated PDAC


title: PDAC_Surgery Only_Sample 3

description:
PDAC_Surgery Only_AX0739
Gene expression data from untreated PDAC


title: 139MD-UM-IU_1001

description:
uninvolved margin of breast carcinoma
139MD-UM-IU


title: 3080

value: Dicyclohexylphthalate


title: Endometrial Biopsy-Endometrial Stromal Fibroblast [LA22-+_Late]

value: Endometriosis


title: PDAC_Surgery Only_Sample 1

description:
PDAC_Surgery Only_AX0001
Gene expression data from untreated PDAC


title: Endometrial Biopsy-Endometrial Stromal Fibroblast [LA55-+_Late]


title: 3082


title: 3083


title: Endometrial Biopsy-Endometrial Mesenchymal Stem Cell [ETB125++Late]

value: Endometrial Mesenchymal Stem Cell


title: Endometrial Biopsy-Endometrial Stromal Fibroblast [LA34-+_Late]


title: PDAC_Surgery Only_Sample 2

description:
PDAC_Surgery Only_AX0235
Gene expression data from untreated PDAC


title: Endometrial Biopsy-Endometrial Mesenchymal Stem Cell [ETB128++Late]


title: 139MD-UM-IL_1000

description:
uninvolved margin of breast carcinoma
139MD-UM-IL

value: Luminal B, HER2-


title: Endometrial Biopsy-Endometrial Mesenchymal Stem Cell [UC249++Late]


title: Endometrial Biopsy-Endometrial Mesenchymal Stem Cell [ETB109++Late]


title: 139MD-UM-EU_999

description:
uninvolved margin of breast carcinoma
139MD-UM-EU


title: PDAC_Neoadjuvant_Sample 6

description:
PDAC_Neoadjuvant_AX1587
Gene expression data from PDAC treated with neoadjuvant chemoradiation

source_name: PDAC_treated with chemoradiation

value: neoadjuvant chemoradiation


title: 3081


title: PDAC_Neoadjuvant_Sample 5

description:
PDAC_Neoadjuvant_AX1380
Gene expression data from PDAC treated with neoadjuvant chemoradiation


title: 3079

value: Dimethyl-benz(a)anthracene


title: 139MD-UM-EL_998

description:
uninvolved margin of breast carcinoma
139MD-UM-EL


title: 3077

value: solvent control

value: thyroid hormone


title: Endometrial Biopsy-Endometrial Mesenchymal Stem Cell [ETB99++Late]


title: PDAC_Neoadjuvant_Sample 4

description:
PDAC_Neoadjuvant_AX1260
Gene expression data from PDAC treated with neoadjuvant chemoradiation

value: pancreatic ductal adenocarcinoma


title: Endometrial Biopsy-Endometrial Mesenchymal Stem Cell [LA22++_Late]


title: PDAC_Neoadjuvant_Sample 3

description:
PDAC_Neoadjuvant_AX0907
Gene expression data from PDAC treated with neoadjuvant chemoradiation


title: 138BM-S-VB2_995

description:
uninvolved margin in the immediate vicinity of the mammilla
138BM-S-VB2

value: unifocal


title: 3076


title: 138BM-S-UM-IU_993

description:
uninvolved margin of breast carcinoma
138BM-S-UM-IU


title: 138BM-S-VB1_994

description:
uninvolved margin in the immediate vicinity of the mammilla
138BM-S-VB1


title: 3075


title: Endometrial Biopsy-Endometrial Mesenchymal Stem Cell [LA55++_Late]

value: 4-8 Weeks in Culture


title: 3078


title: 3074


title: 138BM-S-UM-IL_992

description:
uninvolved margin of breast carcinoma
138BM-S-UM-IL


title: 138BM-S-UM-EU_991

description:
uninvolved margin of breast carcinoma
138BM-S-UM-EU


title: PDAC_Neoadjuvant_Sample 2

description:
PDAC_Neoadjuvant_AX0721
Gene expression data from PDAC treated with neoadjuvant chemoradiation


title: 138BM-S-UM-EL_990

description:
uninvolved margin of breast carcinoma
138BM-S-UM-EL


title: PDAC_Neoadjuvant_Sample 1

description:
PDAC_Neoadjuvant_AX0640
Gene expression data from PDAC treated with neoadjuvant chemoradiation


title: 137WK-VB1_986

description:
uninvolved margin in the immediate vicinity of the mammilla
137WK-VB1

value: Luminal A


title: Endometrial Biopsy-Endometrial Mesenchymal Stem Cell [LA34++_Late]


title: 137WK-VB2_987

description:
uninvolved margin in the immediate vicinity of the mammilla
137WK-VB2


title: Endometrial Biopsy-Endometrial Stromal Fibroblast [ETB128-+Early]

value: No Endometriosis

value: 2-3 Weeks in Culture

value: Endometrial Stromal Fibroblast


title: 137WK-UM_985

description:
uninvolved margin of breast carcinoma
137WK-UM

value: female


title: Esophagus stem cell-2

hyb_protocol: GeneChip® Hybridization, Wash, and Stain Kit

scan_protocol: GeneChip® Scanner 3000 7G

data_processing:
Expression console and Partek genomic suites
Probe group file: HuEx-1_0-st-v2.r2.pgf
Meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: Cloned esophagus stem cells

label_protocol: WT Pico RNA Amplification System V2 and Encore Biotin Module (NuGEN Technologies, CA, USA).

growth_protocol: Stem cells are cultured on 3T3 feeder layer and total RNA is extracted by Picopure RNA isolation kit from  a single colony.

extract_protocol: PicoPure® RNA Isolation Kit

tag: disease state

value: control

value: esophagus stem cell


title: Esophagus stem cell-3


title: 3072

value: MCF-7 human breast carcinoma cell line (ECACC No. 86012803)

value: Testosterone


title: Esophagus stem cell-1


title: 3073

value: Tetrabromobisphenol A


title: Endometrial Biopsy-Endometrial Stromal Fibroblast [ETB116-+Early]

tag: age


title: 3070


title: Barrett’s esophagus stem cell-6

source_name: Cloned Barrett’s esophagus stem cells

value: Barrett’s esophagus


title: 3071


title: Endometrial Biopsy-Endometrial Stromal Fibroblast [LA22-+_Early]

value: Endometriosis


title: Endometrial Biopsy-Endometrial Stromal Fibroblast [ETB109-+Early]


title: 3067

value: Atrazine


title: Endometrial Biopsy-Endometrial Stromal Fibroblast [LA55-+_Early]


title: Endometrial Biopsy-Endometrial Stromal Fibroblast [ETB125-+Early]


title: Barrett’s esophagus stem cell-3


title: Endometrial Biopsy-Endometrial Stromal Fibroblast [LA34-+_Early]


title: 136BS-VB2_984

description:
uninvolved margin in the immediate vicinity of the mammilla
136BS-VB2


title: Barrett’s esophagus stem cell-4


title: Barrett’s esophagus stem cell-5


title: Endometrial Biopsy-Endometrial Mesenchymal Stem Cell [ETB128++Early]

value: Endometrial Mesenchymal Stem Cell


title: Barrett’s esophagus stem cell-2


title: 3069


title: Endometrial Biopsy-Endometrial Mesenchymal Stem Cell [ETB116++Early]


title: 136BS-VB1_983

description:
uninvolved margin in the immediate vicinity of the mammilla
136BS-VB1


title: Endometrial Biopsy-Endometrial Mesenchymal Stem Cell [ETB109++Early]


title: 136BS-UM-IU_982

description:
uninvolved margin of breast carcinoma
136BS-UM-IU


title: Endometrial Biopsy-Endometrial Mesenchymal Stem Cell [ETB99++Early]


title: 3068


title: Barrett’s esophagus stem cell-1


title: 136BS-UM-EU_980

description:
uninvolved margin of breast carcinoma
136BS-UM-EU


title: 136BS-UM-IL_981

description:
uninvolved margin of breast carcinoma
136BS-UM-IL


title: 3066

value: Diethylhexylphthalate


title: 136BS-UM-EL_979

description:
uninvolved margin of breast carcinoma
136BS-UM-EL

value: unifocal


title: PBMC-Control-28

city: London

first: Robert

middle: Daniel

last: Petty

address: Charterhouse Square

department: Haemato-oncology

country: United Kingdom

institute: Barts Cancer Institute, Queen Mary, University of London

description:
C292
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt

hyb_protocol: Standard Ambion mirVana bioarray hybridization protocol

scan_protocol: Array slides were scanned using a Genetic Microsystems GMS 418 scanner with a laser intensity of 95%, at multiple gain settings to avoid saturation of array spots. Intensity values were generated using Imagene V5.5 (BioDiscovery, USA) using automatic segmentation

data_processing: Un-background corrected median intensity values were corrected using Microarray valuation imp (MAVI) Pro 2.6.0 software (MWG biotech AG Ebersburg, Germany), which conducts a linear regression analysis on three gain scans of an array image to impute the values at the periphery of detection. Data was then normalized by averaging duplicate probe values and  then filtering data to discard any data within 2 standard deviations of the mean of the empty control spots then median scaling, setting the median of each array to 100 and log transformed (base10), adapted from Shingara J et al 2005.

source_name: Peripheral blood

label_protocol: miRNA were tailed with amine residues (mirVana™ miRNA Labelling Kit, Ambion) and labelled with Cy5 as recommended by the manufacturer

extract_protocol: PBMCs were isolated in vaccutainer CPT Cell Preparation tubes with Sodium Citrate (BD biosciences, NJ, USA) from 16ml of blood. RNA was extracted by Trizol and enriched for the small RNA fraction (<40nt) using the Ambion Flash-PAGE system

value: Control

tag: Sex

value: Female

value: PBMC


title: 3065


title: 3064


title: PBMC-Control-29

description:
C293
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: PBMC-Control-27

description:
C291
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: 135LS-VB2_978

description:
uninvolved margin in the immediate vicinity of the mammilla
135LS-VB2

source_name: breast tissue from mastectomy, taken outside the site of primary tumor(s)

value: Luminal B, HER2+


title: PBMC-Control-25

description:
C289
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: 3063


title: Endometrial Biopsy-Endometrial Mesenchymal Stem Cell [LA34++_Early]

value: 2-3 Weeks in Culture


title: Endometrial Biopsy-Endometrial Mesenchymal Stem Cell [LA22++_Early]


title: Endometrial Biopsy-Endometrial Mesenchymal Stem Cell [UC249++Early]

value: No Endometriosis


title: 135LS-VB1_977

description:
uninvolved margin in the immediate vicinity of the mammilla
135LS-VB1

value: female


title: 3061

value: solvent control


title: PBMC-Control-26

description:
C290
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: 3060

value: MCF-7 human breast carcinoma cell line (ECACC No. 86012803)

value: Genistein


title: Endometrial Biopsy-Endometrial Mesenchymal Stem Cell [LA55++_Early]


title: 3059


title: Endometrial Biopsy-Endometrial Stromal Fibroblast [UC-209-+]

value: Fresh Tissue Sample

value: Endometrial Stromal Fibroblast


title: 135LS-UM-IU_976

description:
uninvolved margin of breast carcinoma
135LS-UM-IU


title: Endometrial Biopsy-Endometrial Stromal Fibroblast [ETB125-+FACS]


title: PBMC-Control-23

description:
C287
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: 3058


title: 3062


title: 135LS-UM-IL_975

description:
uninvolved margin of breast carcinoma
135LS-UM-IL


title: 135LS-UM-EU_974

description:
uninvolved margin of breast carcinoma
135LS-UM-EU


title: PBMC-Control-22

description:
C286
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: 135LS-UM-EL_973

description:
uninvolved margin of breast carcinoma
135LS-UM-EL


title: PBMC-Control-24

description:
C288
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: 3057

value: Tetrabromobisphenol A


title: 134GJ-VB1_971

description:
uninvolved margin in the immediate vicinity of the mammilla
134GJ-VB1

value: Luminal A


title: PBMC-Control-21

description:
C285
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: 134GJ-VB2_972

description:
uninvolved margin in the immediate vicinity of the mammilla
134GJ-VB2


title: Endometrial Biopsy-Endometrial Stromal Fibroblast [FS08-+]

value: Endometriosis


title: 134GJ-UM-IU_970

description:
uninvolved margin of breast carcinoma
134GJ-UM-IU


title: Endometrial Biopsy-Endometrial Stromal Fibroblast [FACS ETB99-+]


title: PBMC-Control-19

description:
C281
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: PBMC-Control-20

description:
C284
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: PBMC-Control-18

description:
C280
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: PBMC-Control-17

description:
C279
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: 3055

value: Testosterone


title: 3056


title: 3054


title: Endometrial Biopsy-Endometrial Stromal Fibroblast [ETB109-+FACS]


title: PBMC-Control-16

description:
C277
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: Endometrial Biopsy-Endometrial Stromal Fibroblast [LA22-+]


title: 3052

value: Atrazine


title: Endometrial Biopsy-Endometrial Stromal Fibroblast [LA34-+_FACS]


title: 134GJ-UM-IL_969

description:
uninvolved margin of breast carcinoma
134GJ-UM-IL

value: unifocal


title: 134GJ-UM-EU_968

description:
uninvolved margin of breast carcinoma
134GJ-UM-EU


title: 3053


title: Endometrial Biopsy-Endometrial Stromal Fibroblast [LA07-+]


title: 3051

value: Diethylhexylphthalate


title: PBMC-Control-15

description:
C275
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt

value: Control

value: Female

value: PBMC


title: Endometrial Biopsy-Endometrial Mesenchymal Stem Cell [ETB61 ++]

value: No Endometriosis

value: Endometrial Mesenchymal Stem Cell


title: Endometrial Biopsy-Endometrial Stromal Fibroblast [LA55-+_FACS]


title: 134GJ-UM-EL_967

description:
uninvolved margin of breast carcinoma
134GJ-UM-EL

value: female


title: PBMC-Control-14

description:
C274
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: 3050

value: MCF-7 human breast carcinoma cell line (ECACC No. 86012803)


title: 133ML-VB2_966

description:
uninvolved margin in the immediate vicinity of the mammilla
133ML-VB2

value: Luminal B, HER2-


title: 3049


title: 133ML-VB1_965

description:
uninvolved margin in the immediate vicinity of the mammilla
133ML-VB1


title: Endometrial Biopsy-Endometrial Mesenchymal Stem Cell [ETB100++]

value: Fresh Tissue Sample


title: Endometrial Biopsy-Endometrial Mesenchymal Stem Cell [ETB128++FACS]


title: 133ML-UM-IU_964

description:
uninvolved margin of breast carcinoma
133ML-UM-IU


title: 3048


title: Endometrial Biopsy-Endometrial Mesenchymal Stem Cell [ETB116++FACS]


title: PBMC-Control-11

description:
C270
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: 133ML-UM-IL_963

description:
uninvolved margin of breast carcinoma
133ML-UM-IL


title: 3047

value: solvent control


title: 133ML-UM-EU_962

description:
uninvolved margin of breast carcinoma
133ML-UM-EU


title: PBMC-Control-10

description:
C269
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: PBMC-Control-9

description:
C268
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt

value: Male


title: 133ML-UM-EL_961

description:
uninvolved margin of breast carcinoma
133ML-UM-EL


title: 3046


title: Endometrial Biopsy-Endometrial Mesenchymal Stem Cell [FS08++]


title: 132EM-VB2_958

description:
uninvolved margin in the immediate vicinity of the mammilla
132EM-VB2


title: PBMC-Control-8

description:
C267
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: 3044


title: Endometrial Biopsy-Endometrial Mesenchymal Stem Cell [LA07++]


title: Endometrial Biopsy-Endometrial Mesenchymal Stem Cell [ST185++]


title: 132EM-VB1_957

description:
uninvolved margin in the immediate vicinity of the mammilla
132EM-VB1


title: 3045


title: 132EM-UM-IL_955

description:
uninvolved margin of breast carcinoma
132EM-UM-IL


title: PBMC-Control-5

description:
C262
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: PBMC-Control-13

description:
C273
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: PBMC-Control-6

description:
C263
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: PBMC-Control-12

description:
C272
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: PBMC-Control-4

description:
C260
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: PBMC-Control-3

description:
C259
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: 3041

value: Bisphenol A


title: 3040


title: 3042

value: p,p'-DDT


title: PBMC-Control-7

description:
C265
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: 3039


title: 131SD-VB2_953

description:
uninvolved margin in the immediate vicinity of the mammilla
131SD-VB2

value: Luminal A


title: 131SD-UM-IU_951

description:
uninvolved margin of breast carcinoma
131SD-UM-IU


title: 131SD-VB1_952

description:
uninvolved margin in the immediate vicinity of the mammilla
131SD-VB1


title: Age control D18CM

city: San Sebastián

first: David

last: Otaegui

state: Guipuzcoa

address: Paseo Dr begiristain s/n

department: Neurosciences

country: Spain

institute: Biodonostia Research institute

hyb_protocol: GeneChip Fluidics Station 450 (Affymetrix, Santa Clara, California, USA)

scan_protocol: GeneChip 7G Scanner (Affymetrix, Santa Clara, California, USA)

data_processing: EC, BRB arrays tools and Bioconductor

source_name: Blood

label_protocol: WT Expression Kit (Life Technologies, Carlsbad, California, USA) and the GeneChip Hybridization Wash and Stain kit (Affymetrix, Santa Clara, California, USA)

extract_protocol: LeucoLOCKTM Total RNA Isolation System (Life Technologies, Carlsbad, California, USA) with the alternative protocol to recover Total RNA

value: leukocyte


title: Age control D6_CM_2


title: Age control D1CV


title: 3043


title: PBMC-Control-2

description:
C255
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: 132EM-UM-IU_956

description:
uninvolved margin of breast carcinoma
132EM-UM-IU

value: unifocal


title: 3038


title: Endometrial Biopsy-Endometrial Mesenchymal Stem Cell [UC152 ++]

value: Endometriosis


title: PBMC-Control-1

description:
C253
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt

value: Control


title: Endometrial Biopsy-Endometrial Mesenchymal Stem Cell [ETB65 ++]


title: 3037

value: Methoxychlor


title: 131SD-UM-IL_950

description:
uninvolved margin of breast carcinoma
131SD-UM-IL


title: Endometrial Biopsy-Endometrial Mesenchymal Stem Cell [LA55++_FACS]


title: Age control D10CV


title: 130JT-VB2_944

description:
uninvolved margin in the immediate vicinity of the mammilla
130JT-VB2

value: Luminal B, HER2+


title: 3035

value: Benzo(a)pyrene


title: Age control 11-504CM


title: PBMC-CFS/ME-Patient_14

description:
P113
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt

value: CFS/ME

value: Female

value: PBMC


title: PBMC-CFS/ME-Patient_13

description:
P112
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: 130JT-UM-IU_942

description:
uninvolved margin of breast carcinoma
130JT-UM-IU

value: female


title: PBMC-CFS/ME-Patient_12

description:
P111
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: PBMC-CFS/ME-Patient_11

description:
P110
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: 130JT-UM-IL_941

description:
uninvolved margin of breast carcinoma
130JT-UM-IL


title: Age control 11-460CM_2


title: 3032

value: MCF-7 human breast carcinoma cell line (ECACC No. 86012803)

value: Toxaphene


title: 3440


title: Age control 11-502CM


title: PBMC-CFS/ME-Patient_10

description:
P109
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: 130JT-UM-EU_940

description:
uninvolved margin of breast carcinoma
130JT-UM-EU


title: Age control 10-321CM


title: 3036


title: 3031

value: Nonylphenol


title: Age control D17CM


title: 3030


title: PBMC-CFS/ME-Patient_15

description:
P114
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: 131SD-UM-EL_947

description:
uninvolved margin of breast carcinoma
131SD-UM-EL


title: Age control 09-902CV


title: 130JT-UM-EL_939

description:
uninvolved margin of breast carcinoma
130JT-UM-EL


title: Age control 09-901CV


title: PBMC-CFS/ME-Patient_9

description:
P108
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: 130JT-VB1_943

description:
uninvolved margin in the immediate vicinity of the mammilla
130JT-VB1


title: Age control 09-900CV


title: 3029


title: Age control 09-899CV


title: PBMC-CFS/ME-Patient_8

description:
P107
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt

value: Male


title: 3033


title: 3028

value: solvent control


title: 129EB-VB2_936

description:
uninvolved margin in the immediate vicinity of the mammilla
129EB-VB2

value: Luminal B, HER2-

value: multifocal


title: PBMC-CFS/ME-Patient_7

description:
P106
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: Age control 09-883CV

value: leukocyte


title: 129EB-VB1_934

description:
uninvolved margin in the immediate vicinity of the mammilla
129EB-VB1


title: 129EB-UM-IU_933

description:
uninvolved margin of breast carcinoma
129EB-UM-IU


title: 129EB-UM-IL_932

description:
uninvolved margin of breast carcinoma
129EB-UM-IL


title: PBMC-CFS/ME-Patient_6

description:
P105
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: PBMC-CFS/ME-Patient_4

description:
P103
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: 2991


title: 129EB-UM-EL_929

description:
uninvolved margin of breast carcinoma
129EB-UM-EL


title: Age control 09-880CV


title: PBMC-CFS/ME-Patient_5

description:
P104
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: 128WS-VB2_926

description:
uninvolved margin in the immediate vicinity of the mammilla
128WS-VB2

value: unifocal


title: Age control 09-708CM_2


title: 128WS-VB1_925

description:
uninvolved margin in the immediate vicinity of the mammilla
128WS-VB1


title: PBMC-CFS/ME-Patient_3

description:
P102
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: 2989

value: Bisphenol A

value: Genistein


title: 2987


title: PBMC-CFS/ME-Patient_2

description:
P101
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: Age control 09-171CM


title: Age control 09-1203CM


title: PBMC-CFS/ME-Patient_1

description:
P100
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt


title: 128WS-UM-IU_924

description:
uninvolved margin of breast carcinoma
128WS-UM-IU

value: Luminal B, HER2+


title: Age control 08-759CV


title: Age control 09-221CV


title: 2990


title: 2986

value: Methoxychlor


title: Age control 08-650CM


title: 2985

value: Benzo(a)pyrene


title: 128WS-UM-IL_923

description:
uninvolved margin of breast carcinoma
128WS-UM-IL


title: Age control 08-659CM


title: 2984


title: 2988


title: 128WS-UM-EU_922

description:
uninvolved margin of breast carcinoma
128WS-UM-EU


title: 2983


title: 128WS-UM-EL_921

description:
uninvolved margin of breast carcinoma
128WS-UM-EL


title: Age control 08-647CV


title: GFP-positive cells from twi-GAL4 UAS-2EGFP embryos, rep 2

city: Bethesda

first: Shaad

middle: M.

last: Ahmad

state: MD

address: Building 10, Room 7N311, 10 Center Drive MSC 1654

department: Systems Biology Center

institute: National Heart Lung and Blood Institute

description: FACS-sorted GFP positive cells from single cell suspensions of stage 11/early stage 12 embryos with twi-GAL4 and UAS-2EGFP insertions that target GFP fluorescence to Twist expressing mesodermal cells

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: The data were analyzed with the Bioconductor affy package, using the rma command with default settings, and log2 transformed.

organism: Drosophila melanogaster

source_name: FACS-sorted Drosophila cells

label_protocol: Approximately 2-5 µg of total RNA was processed to produce biotinylated cRNA targets

growth_protocol: Embryos were aged to stage 11-early stage 12 at 25°C.

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

value: FACS-sorted GFP positive cells

tag: genotype/variation

value: twi-GAL4 UAS-2EGFP


title: 127ZR-VB1_919

description:
uninvolved margin in the immediate vicinity of the mammilla
127ZR-VB1

value: female


title: 2981

value: MCF-7 human breast carcinoma cell line (ECACC No. 86012803)


title: GFP-positive cells from twi-GAL4 UAS-2EGFP embryos, rep 1

value: cell suspensions of stage 11/early stage 12 embryos


title: Age control 07-515


title: Age control 08-584CV


title: GFP-positive cells from twi-GAL4 Df(3R)Exel6157/UAS-2EGFP Df(3R)Exel6157 embryos, rep 3

description: FACS-sorted GFP positive cells from single cell suspensions of stage 11/early stage 12 embryos which are homozygous for the jumu null deficiency Df(3R)Exel6157 and possess both twi-GAL4 and UAS-2EGFP insertions that target GFP fluorescence to Twist expressing mesodermal cells


title: GFP-positive cells from twi-GAL4 UAS-2EGFP embryos, rep 3


title: 127ZR-UM-IU_918

description:
uninvolved margin of breast carcinoma
127ZR-UM-IU


title: 127ZR-UM-IL_917

description:
uninvolved margin of breast carcinoma
127ZR-UM-IL


title: 2980

value: Nonylphenol, 10µM


title: 127ZR-UM-EU_916

description:
uninvolved margin of breast carcinoma
127ZR-UM-EU


title: Age control 07-445


title: GFP-positive cells from twi-GAL4 Df(3R)Exel6157/UAS-2EGFP Df(3R)Exel6157 embryos, rep 2


title: 2982


title: 127ZR-VB2_920

description:
uninvolved margin in the immediate vicinity of the mammilla
127ZR-VB2


title: Age control 07-514


title: GFP-positive cells from Df(1)CHES-1-like1; twi-GAL4 UAS-2EGFP embryos, rep 3

description: FACS-sorted GFP positive cells from single cell suspensions of stage 11/early stage 12 embryos which are homozygous for the CHES-1-like null mutation Df(1)CHES-1-like1 and possess both twi-GAL4 and UAS-2EGFP insertions that target GFP fluorescence to Twist expressing mesodermal cells

value: Df(1)CHES-1-like1; twi-GAL4 UAS-2EGFP


title: Age control 07-437


title: 126AS-VB2_915

description:
uninvolved margin in the immediate vicinity of the mammilla
126AS-VB2


title: Age control 08-588CM


title: 2977

value: Toxaphene

value: Nonylphenol


title: 2978

value: solvent control


title: GFP-positive cells from Df(1)CHES-1-like1; twi-GAL4 UAS-2EGFP embryos, rep 1


title: GFP-positive cells from twi-GAL4 Df(3R)Exel6157/UAS-2EGFP Df(3R)Exel6157 embryos, rep 1


title: GFP-positive cells from Df(1)CHES-1-like1; twi-GAL4 UAS-2EGFP embryos, rep 2


title: 3439


title: Age control 07-424

value: leukocyte


title: Age control 07-422


title: 126AS-VB1_914

description:
uninvolved margin in the immediate vicinity of the mammilla
126AS-VB1

value: unifocal


title: 2975

value: p,p'-DDT


title: 126AS-UM-IU_913

description:
uninvolved margin of breast carcinoma
126AS-UM-IU


title: 2974


title: 2973


title: 126AS-UM-EL_911

description:
uninvolved margin of breast carcinoma
126AS-UM-EL


title: Age control 07-414


title: Age control 07-420


title: 2976


title: 125KL-VB2_910

description:
uninvolved margin in the immediate vicinity of the mammilla
125KL-VB2

value: Luminal B, HER2-


title: armGFP, nmoP1 eye imaginal discs, biological rep3

city: Burjassot

first: Veronica

last: Munoz-Soriano

state: Valencia

address: C/ Dr. Moliner, 50

department: Genetics

institute: University of Valencia

description:
Gene expression data from armGFP, nmoP1 third instar larvae eye imaginal discs
NP_D

hyb_protocol: Hybridization was performed following Affymetrix protocol, chips were washed and stained using Fluidics protocol midiEuk2v3_450 on an Affymetrix GeneChip Fluidics Station 450

scan_protocol: Affymetrix scanner GeneChip 3000 7G was used to read the arrays

data_processing: Pre-processing of data was performed using the rma function of the affy package and differential expression analysis using the limma package, both from Bioconductor (www.bioconductor.com)

source_name: armGFP, nmoP1 eye imaginal discs

label_protocol: labeling was performed according to standard Affymetrix protocol

growth_protocol: Flies were allowed to lay eggs for 6-12 h. These developed at 25C until third intar larvae.

extract_protocol: Total RNA was extracted with the mirVANATM miRNA isolaton kit (Ambion#AM1260) following manufacturer’s instructions.

treatment_protocol: Approximately 500 eye imaginal discs were dissected in cold PBS, then sedimented by microcentrifugation. PBS was completely removed and discs were stored at -80C.

tag: developmental stage

value: third instar larvae (at 25°C)

value: armGFP_nmoP1 mutant

tag: tissue

value: eye imaginal disc


title: armGFP, nmoP1 eye imaginal discs, biological rep2

description:
Gene expression data from armGFP, nmoP1 third instar larvae eye imaginal discs
NP_B


title: Age control 07-413


title: 2972

source_name: Ref MCF7


title: armGFP, nmoP1 eye imaginal discs, biological rep1

description:
Gene expression data from armGFP, nmoP1 third instar larvae eye imaginal discs
NP_A


title: 125KL-VB1_909

description:
uninvolved margin in the immediate vicinity of the mammilla
125KL-VB1

tag: gender


title: 2302

value: Endosulfan


title: 125KL-UM-IU_908

description:
uninvolved margin of breast carcinoma
125KL-UM-IU

tag: age at cancer diagnosis (yrs)


title: Age control 07-404


title: 2013


title: armGFP eye imaginal discs, biological rep2

description:
Gene expression data from armGFP third instar larvae eye imaginal discs
NP_F

source_name: armGFP eye imaginal discs

value: armGFP_wild type control


title: 126AS-UM-EU_912

description:
uninvolved margin of breast carcinoma
126AS-UM-EU

value: female


title: 125KL-UM-IL_907

description:
uninvolved margin of breast carcinoma
125KL-UM-IL


title: 125KL-UM-EU_906

description:
uninvolved margin of breast carcinoma
125KL-UM-EU


title: 125KL-UM-EL_905

description:
uninvolved margin of breast carcinoma
125KL-UM-EL


title: 2011

value: MCF-7 human breast carcinoma cell line (ECACC No. 86012803)


title: 124AA-VB2_904

description:
uninvolved margin in the immediate vicinity of the mammilla
124AA-VB2

value: multifocal


title: 2012


title: 124AA-VB1_903

description:
uninvolved margin in the immediate vicinity of the mammilla
124AA-VB1


title: 2008


title: Age control 07-356


title: 2010


title: Age control 07-087


title: 124AA-UM-IU_902

description:
uninvolved margin of breast carcinoma
124AA-UM-IU


title: 2007


title: armGFP eye imaginal discs, biological rep1

description:
Gene expression data from armGFP third instar larvae eye imaginal discs
NP_E


title: 2301


title: armGFP eye imaginal discs, biological rep3

description:
Gene expression data from armGFP third instar larvae eye imaginal discs
NP_G


title: Age control 07-151


title: tumor_B14

city: Wuhan

first: Juncheng

last: Wei

address: Jiefang Dadao 1095

department: Department of Obstetrics and Gynecology

country: China

institute: Huazhong University of Science and Technology

description: Gene expression data from invasive primary breast carcinoma tissues

hyb_protocol: The biotin-labeled cRNA (15µg) was mixed with 6µl of 59 fragmentation buffer and adjusted to a final volume of 30 µl. The fragmented cRNA was hybridized at 45℃ for 16 h onto a human genome U133 Plus 2.0 array in a 300µl hybridization reaction containing 0.05 nM control oligonucleotide, 1× eukaryotic hybridization controls (bioB, bioC, bioD, cre), 0.1 mg/ml herring sperm DNA, 0.5 mg/ml BSA, and 1× hybridization buffer. After hybridization, the arrays were washed with 2× SSC with 0.05% SDS at room temperature for 2 min, 1× SSC at room temperature for 2 min, and three times with 0.2× SSC at 50℃ for 1 min.

scan_protocol: The arrays with hybridization probes were scanned with the Affymetrix® GeneChip Scanner 3000.

data_processing: The scanned images data were analyzed using GeneChip Expression Analysis Software and Microsoft Access.

label_protocol: The resulting dsDNA was extracted as previously described,and was now ready for biotinylation. The second in vitro transcription (IVT) reaction was performed to produce biotin-labeled cRNA from the dsDNA.

growth_protocol: Normal breast tissues and invasive primary breast carcinoma tissues were obtained from patients undergoing surgery.

extract_protocol: Total RNA from the captured LECs was isolated using RNAqueous_-Micro Kit (Ambion, USA), according to manufacturer’s instructions for LCM-derived small samples. Owing to the small starting amounts of total RNA (10–100 ng), two rounds of cDNA synthesis and in vitro transcription (IVT) amplification were performed in order to produce sufficient amounts of labeled antisense RNA (aRNA) targets for microarray analysis.

treatment_protocol: After the fresh tissues were cut into several pieces (approximately 1.0 ×1.0 × 0.5 cm3) and fixed immediately in RNALater solution in the operating room, the fixed samples were preserved at -80℃.

value: breast

value: lymphatic endothelium

tag: diagnosis

value: primary breast carcinoma


title: 124AA-UM-IL_901

description:
uninvolved margin of breast carcinoma
124AA-UM-IL


title: Age control 07-402


title: Age control 07-038


title: normal_N4

description:
Gene expression data from normal breast tissues
CEL file for this sample was lost.

source_name: Normal breast tissues

value: normal


title: Age control 06-271


title: Age control 06-243


title: 2005

value: solvent control


title: 124AA-UM-EU_900

description:
uninvolved margin of breast carcinoma
124AA-UM-EU


title: tumor_BL1

description:
Gene expression data from invasive primary breast carcinoma tissues
CEL file for this sample was lost.


title: 2004

value: thyroid hormone

value: Kepone


title: Age control 07-037

value: leukocyte


title: 124AA-UM-EL_899

description:
uninvolved margin of breast carcinoma
124AA-UM-EL


title: 2006


title: Teff cells co-cultured with Treg.X3-R6-_rep2

city: Cambridge

first: Scott

last: Davis

state: MA

address: 200 Technology Square, Suite 602

department: Tempero DPU

institute: GSK

description: Gene expression data from Treg subset with indicated cell surface phenotype on the sample name

hyb_protocol: The labeled fragmented DNA was hybridized to the Gene Arrays 1.0ST for 16-18 hours in GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm).  The hybridized samples were washed and stained using Affymetrix fluidics station 450.

scan_protocol: Microarrays were immediately scanned using Affymetrix GeneArray Scanner 3000 7G Plus

data_processing: Samples were RMA normalized using Affymetrix Power Tools (gcbg background correction, quantile normalization, median polish) on the annotated set of probesets. Unannotated probesets were removed prior to normalization (see supplemental *.mps file)

source_name: Human effector CD4 T cells co-cultured with Treg subsets from peripheral blood

label_protocol: 100 ng of total RNA was amplified and labeled with Ambion® WT Expression Kit Protocol (Life Technologies) and GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix).

growth_protocol: Buffy coat from human peripheral blood was processed through RosetteSe Human CD4+ T Cell Enrichment Cocktail, followed by antibody staining and washing.

extract_protocol: Total RNA was extracted with Qiagen RNeasy mini columns according to the manufacturer's instructions.

treatment_protocol: Isolated Teff cells were labeled with CFSE, followed by incubation with Tregs and dendritic cells in the in vitro suppression assay. CFSE-positive cells were sorted after 18 hours.

tag: sample type

value: Sorted Human effector CD4 T cells activated and  co-cultured with Treg subsets for 18 h

value: effector CD4 T cells

tag: treatment


title: UPN727 cells, ulcerative colitis (UC)  plasma patients 13

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description: Gene expression data from UPN727 cells stimulated with ulcerative colitis (UC) plasma

hyb_protocol: The GeneChip Human Genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

data_processing: Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log intensity/ratios.  The statistical significance of differential gene expression and false discovery rates (FDR) were derived through ANOVA function in Partek GS.

source_name: UPN727 cells stimulated with UC13 Plasma

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: Commercial cryopreserved PBMCs of healthy Caucasian male donor UPN727 were thawed and washed per the manufacturer’s protocol (Cellular Technology Ltd., Shaker Heights, OH).

extract_protocol: Total RNA was extracted and amplified using an Affymetrix express cDNA synthesis kit (Affymetrix, Santa Clara, CA).

treatment_protocol: Gene expression was accomplished by culturing PBMCs at 37°C in 5% CO2 with 40% of Crohn’s disease (CD), ulcerative colitis (UC), and unrelated healthy control (uHC) plasma cultured.  Cultures were prepared in a Costar 24-well plate (Corning) using 500,000 cells/well and in RPMI 1640 medium supplemented with 100U/ml penicillin and 100ug/ml streptomycin in a total of 500 µl.  After culture (9 hours optimal for cryopreserved PBMCs) total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies).

tag: responder cell line

tag: diagnosis of plasma donor

value: ulcerative colitis (UC)


title: 2278

tag: cell line

tag: compound

tag: concentration


title: 2002

value: Thyroid hormone

tag: exposure


title: 123HS-VB2_898

description:
uninvolved margin in the immediate vicinity of the mammilla
123HS-VB2

label_protocol: starndard protocol

tag: tumor grade

value: Luminal B, HER2-

tag: tumor focality

value: unifocal


title: UPN727 cells, ulcerative colitis (UC)  plasma patients 14

source_name: UPN727 cells stimulated with UC14 Plasma


title: Teff cells co-cultured with Treg.X3-R6-_rep1

tag: cell type

value: activated and  co-cultured with Treg subsets for 18 h


title: UPN727 cells, ulcerative colitis (UC)  plasma patients 15

source_name: UPN727 cells stimulated with UC15 Plasma


title: UPN727 cells, ulcerative colitis (UC)  plasma patients 12

source_name: UPN727 cells stimulated with UC12 Plasma


title: 123HS-VB1_897

description:
uninvolved margin in the immediate vicinity of the mammilla
123HS-VB1

value: female


title: UPN727 cells, ulcerative colitis (UC)  plasma patients 11

source_name: UPN727 cells stimulated with UC11 Plasma


title: 123HS-UM-IU_896

description:
uninvolved margin of breast carcinoma
123HS-UM-IU


title: 2001

label_protocol: From 1 µg of cellular RNA, poly-A RNA was reversed transcribed using a poly dT-T7 primer. The resulting cDNA was immediately used for one round of amplification by T7 in vitro transcription reaction in the presence of Cyanine 5-CTP (LRILAK, Agilent). The amplified and labeled RNA probes were purified separately with RNeasy purification columns (Qiagen, Belgium). Probes were verified for amplification yield and incorporation efficiency by measuring the RNA concentration at 280 nm and Cy5 incorporation at 650 nm using a Nanodrop spectrophotometer.

value: MCF-7 human breast carcinoma cell line (ECACC No. 86012803)

value: 2,3,7,8 Tetrachloro-dibenzo-p-dioxin


title: 123HS-UM-IL_895

description:
uninvolved margin of breast carcinoma
123HS-UM-IL


title: Teff cells co-cultured with Treg.X3-R6+_rep1


title: UPN727 cells, ulcerative colitis (UC)  plasma patients 09

source_name: UPN727 cells stimulated with UC09 Plasma


title: UPN727 cells, ulcerative colitis (UC)  plasma patients 10

source_name: UPN727 cells stimulated with UC10 Plasma


title: 1999

label_protocol: From 1 µg of cellular RNA, poly-A RNA was reversed transcribed using a poly dT-T7 primer. The resulting cDNA was immediately used for one round of amplification by T7 in vitro transcription reaction in the presence of Cyanine 3-CTP (LRILAK, Agilent) The amplified and labeled RNA probes were purified separately with RNeasy purification columns (Qiagen, Belgium). Probes were verified for amplification yield and incorporation efficiency by measuring the RNA concentration at 280 nm and Cy3 incorporation at 550 nm using a Nanodrop spectrophotometer.


title: Teff cells co-cultured with Treg.X3+R6+_rep2


title: 099OLZ-VB_reRun_887

description:
uninvolved margin in the immediate vicinity of the mammilla
099OLZ-VB_2

value: Triple negative


title: 1998

value: Dimethyl-benz(a)anthracene


title: Teff cells co-cultured with Treg.X3+R6+_rep1


title: 1997


title: Teff cells co-cultured with Treg.CD39-CD26-_rep2


title: Teff cells co-cultured with Treg.X3-R6+_rep2


title: 2000


title: UPN727 cells, ulcerative colitis (UC)  plasma patients 06

source_name: UPN727 cells stimulated with UC06 Plasma


title: UPN727 cells, ulcerative colitis (UC)  plasma patients 08

source_name: UPN727 cells stimulated with UC08 Plasma


title: Teff cells co-cultured with Treg.CD39-CD26-_rep1


title: 1996


title: UPN727 cells, ulcerative colitis (UC)  plasma patients 07

source_name: UPN727 cells stimulated with UC07 Plasma


title: 099OLZ-UM-IU_886

description:
uninvolved margin of breast carcinoma
099OLZ-UM-IU

source_name: breast tissue from mastectomy, taken outside the site of primary tumor(s)


title: UPN727 cells, ulcerative colitis (UC)  plasma patients 05

source_name: UPN727 cells stimulated with UC05 Plasma


title: UPN727 cells, ulcerative colitis (UC)  plasma patients 04

source_name: UPN727 cells stimulated with UC04 Plasma


title: Teff cells co-cultured with Treg.CD39+CD26-_rep2


title: Teff cells co-cultured with Treg.CD39+CD26-_rep1


title: Teff cells co-cultured with Treg.CD39+CD26+_rep2


title: UPN727 cells, ulcerative colitis (UC)  plasma patients 02

source_name: UPN727 cells stimulated with UC02 Plasma


title: UPN727 cells, ulcerative colitis (UC)  plasma patients 03

source_name: UPN727 cells stimulated with UC03 Plasma


title: 123HS-UM-EU_894

description:
uninvolved margin of breast carcinoma
123HS-UM-EU


title: 123HS-UM-EL_893

description:
uninvolved margin of breast carcinoma
123HS-UM-EL


title: UPN727 cells, ulcerative colitis (UC)  plasma patients 01

source_name: UPN727 cells stimulated with UC01 Plasma


title: Teff cells co-cultured with Treg.CD39+CD26+_rep1

source_name: Human effector CD4 T cells co-cultured with Treg subsets from peripheral blood


title: 099OLZ-UM-IL_885

description:
uninvolved margin of breast carcinoma
099OLZ-UM-IL


title: 1993

value: Lindane


title: 099OLZ-UM-EL_883

description:
uninvolved margin of breast carcinoma
099OLZ-UM-EL


title: 1995

value: Dicyclohexylphthalate


title: 099OLZ-UM-EU_884

description:
uninvolved margin of breast carcinoma
099OLZ-UM-EU


title: UPN727 cells, Crohn’s disease (CD)  plasma patients 22

description: Gene expression data from UPN727 cells stimulated with Crohn’s disease (CD)  plasma

source_name: UPN727 cells stimulated with CD22 Plasma

value: Crohn’s disease (CD)


title: 098WC-VB_882

description:
uninvolved margin in the immediate vicinity of the mammilla
098WC-VB


title: 2242

source_name: Ref MCF7


title: 1991


title: 098WC-UM-IL_880

description:
uninvolved margin of breast carcinoma
098WC-UM-IL


title: Teff cells co-cultured with Treg.ICOS-_rep1


title: 098WC-UM-IU_881

description:
uninvolved margin of breast carcinoma
098WC-UM-IU


title: 1990

value: solvent control


title: 1994


title: Teff cells co-cultured with Treg.ICOS+_rep1

description: Gene expression data from Treg subset with indicated cell surface phenotype on the sample name


title: 098WC-UM-EU_879

description:
uninvolved margin of breast carcinoma
098WC-UM-EU


title: UPN727 cells, Crohn’s disease (CD)  plasma patients 20

source_name: UPN727 cells stimulated with CD20 Plasma


title: UPN727 cells, Crohn’s disease (CD)  plasma patients 21

source_name: UPN727 cells stimulated with CD21 Plasma


title: Teff cells co-cultured with Treg.ICOS+_rep2


title: 2299


title: 2240


title: 098WC-UM-EL_878

description:
uninvolved margin of breast carcinoma
098WC-UM-EL


title: Teff cells co-cultured with Treg.DR+_rep2


title: UPN727 cells, Crohn’s disease (CD)  plasma patients 19

source_name: UPN727 cells stimulated with CD19 Plasma


title: Teff cells co-cultured with Treg.CLA-_rep2


title: 1987

value: Diethylhexylphthalate


title: UPN727 cells, Crohn’s disease (CD)  plasma patients 17

source_name: UPN727 cells stimulated with CD17 Plasma


title: 1986

value: Testosterone


title: UPN727 cells, Crohn’s disease (CD)  plasma patients 16

source_name: UPN727 cells stimulated with CD16 Plasma


title: Teff cells co-cultured with Treg.DR+_rep1

value: Sorted Human effector CD4 T cells activated and  co-cultured with Treg subsets for 18 h

value: effector CD4 T cells


title: 082HM-VB_862

description:
uninvolved margin in the immediate vicinity of the mammilla
082HM-VB


title: Teff cells co-cultured with Treg.CLA-_rep1


title: UPN727 cells, Crohn’s disease (CD)  plasma patients 18

source_name: UPN727 cells stimulated with CD18 Plasma


title: UPN727 cells, Crohn’s disease (CD)  plasma patients 15

source_name: UPN727 cells stimulated with CD15 Plasma


title: 2239


title: UPN727 cells, Crohn’s disease (CD)  plasma patients 14

source_name: UPN727 cells stimulated with CD14 Plasma


title: 082HM-UM-IU_861

description:
uninvolved margin of breast carcinoma
082HM-UM-IU

source_name: breast tissue from mastectomy, taken outside the site of primary tumor(s)


title: 082HM-UM-EU_860

description:
uninvolved margin of breast carcinoma
082HM-UM-EU


title: 1985


title: 082HM-UM-EL_859

description:
uninvolved margin of breast carcinoma
082HM-UM-EL


title: 089SD-VB-U3_871

description:
uninvolved margin in the immediate vicinity of the mammilla
089SD-VB-U3


title: Teff cells co-cultured with Treg.mem_rep1


title: 2238

value: Tetrabromobisphenol A


title: Teff cells co-cultured with Treg.naive_rep1


title: UPN727 cells, Crohn’s disease (CD)  plasma patients 13

source_name: UPN727 cells stimulated with CD13 Plasma


title: 078AW-VB_856

description:
uninvolved margin in the immediate vicinity of the mammilla
078AW-VB

value: Luminal B, HER2+


title: UPN727 cells, Crohn’s disease (CD)  plasma patients 12

source_name: UPN727 cells stimulated with CD12 Plasma


title: 2276


title: Teff cells co-cultured with Treg.naive_rep2


title: 2237

value: Atrazine


title: Teff cells co-cultured with Treg.ICOS-_rep2

value: activated and  co-cultured with Treg subsets for 18 h


title: UPN727 cells, Crohn’s disease (CD)  plasma patients 11

source_name: UPN727 cells stimulated with CD11 Plasma


title: Teff cells co-cultured with Treg.mem_rep2


title: Teff cells activated_rep2

value: Sorted Human effector CD4 T cells activated for 18 h

value: activated for 18 h


title: Teff cells activated_rep1


title: UPN727 cells, Crohn’s disease (CD)  plasma patients 09

source_name: UPN727 cells stimulated with CD09 Plasma


title: UPN727 cells, Crohn’s disease (CD)  plasma patients 10

source_name: UPN727 cells stimulated with CD10 Plasma


title: 2236

value: MCF-7 human breast carcinoma cell line (ECACC No. 86012803)


title: 078AW-UM-IL_854

description:
uninvolved margin of breast carcinoma
078AW-UM-IL

value: female

value: unifocal


title: 078AW-UM-EU_853

description:
uninvolved margin of breast carcinoma
078AW-UM-EU


title: 078AW-UM-EL_851

description:
uninvolved margin of breast carcinoma
078AW-UM-EL


title: 1980


title: 075JS-VB_846

description:
uninvolved margin in the immediate vicinity of the mammilla
075JS-VB

value: Luminal B, HER2-

value: multifocal


title: 078AW-UM-IU_855

description:
uninvolved margin of breast carcinoma
078AW-UM-IU


title: 075JS-UM-IU_845

description:
uninvolved margin of breast carcinoma
075JS-UM-IU


title: 075JS-UM-IL_844

description:
uninvolved margin of breast carcinoma
075JS-UM-IL


title: 1976


title: 1978


title: Teff cells unstimulated_rep2

source_name: Human effector CD4 T cells co-cultured with Treg subsets from peripheral blood

value: Sorted Human effector CD4 T cells resting

value: resting


title: 075JS-UM-EU_843

description:
uninvolved margin of breast carcinoma
075JS-UM-EU


title: Treg.CD45RO+_d1.rep3

description: Gene expression data from Treg subset with indicated cell surface phenotype on the sample name

source_name: Human Treg subsets from peripheral blood

growth_protocol: All the samples are sorted ex vivo cells from human peripheral blood.

treatment_protocol: Buffy coat from human peripheral blood was processed through RosetteSe Human CD4+ T Cell Enrichment Cocktail, followed by antibody staining and washing.

value: Treg CD45RO+_d1

value: Sorted ex vivo Treg subset


title: Treg.CD45RO+_d1.rep2


title: 1975

source_name: Ref MCF7


title: 2163


title: UPN727 cells, Crohn’s disease (CD)  plasma patients 06

description: Gene expression data from UPN727 cells stimulated with Crohn’s disease (CD)  plasma

source_name: UPN727 cells stimulated with CD06 Plasma

value: Crohn’s disease (CD)


title: Teff cells unstimulated_rep1

value: effector CD4 T cells


title: Treg.CD45RO+_d1.rep1


title: 1979

value: Diethylhexylphthalate

value: Tetrabromobisphenol A


title: UPN727 cells, Crohn’s disease (CD)  plasma patients 05

source_name: UPN727 cells stimulated with CD05 Plasma


title: Treg.CD45RO-_d1.rep3

value: Treg CD45RO-_d1


title: Treg.CD45RO-_d1.rep2


title: Treg.CD45RO-_d1.rep1


title: 2162

value: Methoxychlor


title: UPN727 cells, Crohn’s disease (CD)  plasma patients 07

source_name: UPN727 cells stimulated with CD07 Plasma


title: UPN727 cells, unrelated healthy control (uHC) plasma patients 10

description: Gene expression data from UPN727 cells stimulated with unrelated healthy control (uHC) plasma

source_name: UPN727 cells stimulated with HC10 Plasma

value: healthy


title: UPN727 cells, Crohn’s disease (CD)  plasma patients 04

source_name: UPN727 cells stimulated with CD04 Plasma


title: UPN727 cells, Crohn’s disease (CD)  plasma patients 02

source_name: UPN727 cells stimulated with CD02 Plasma


title: UPN727 cells, Crohn’s disease (CD)  plasma patients 08

source_name: UPN727 cells stimulated with CD08 Plasma


title: UPN727 cells, Crohn’s disease (CD)  plasma patients 03

source_name: UPN727 cells stimulated with CD03 Plasma


title: 074DP-UM-IU_839

description:
uninvolved margin of breast carcinoma
074DP-UM-IU

source_name: breast tissue from mastectomy, taken outside the site of primary tumor(s)


title: Teff.CD45RO+_d1.rep3

source_name: Human Teff subsets from peripheral blood

value: Teff CD45RO+_d1


title: 074DP-UM-EU_837

description:
uninvolved margin of breast carcinoma
074DP-UM-EU


title: 074DP-VB_840

description:
uninvolved margin in the immediate vicinity of the mammilla
074DP-VB


title: 1971

value: MCF-7 human breast carcinoma cell line (ECACC No. 86012803)


title: 1970

value: Genistein


title: 1969

value: Bisphenol A


title: 074DP-UM-EL_836

description:
uninvolved margin of breast carcinoma
074DP-UM-EL

value: female

value: Luminal B, HER2-

value: unifocal


title: UPN727 cells, unrelated healthy control (uHC) plasma patients 09

source_name: UPN727 cells stimulated with HC09 Plasma


title: 1973


title: UPN727 cells, unrelated healthy control (uHC) plasma patients 08

source_name: UPN727 cells stimulated with HC08 Plasma


title: 073TS-VB_835

description:
uninvolved margin in the immediate vicinity of the mammilla
073TS-VB


title: UPN727 cells, Crohn’s disease (CD)  plasma patients 01

source_name: UPN727 cells stimulated with CD01 Plasma


title: 1977

value: solvent control


title: UPN727 cells, unrelated healthy control (uHC) plasma patients 06

source_name: UPN727 cells stimulated with HC06 Plasma


title: Teff.CD45RO-_d1.rep3

value: Teff CD45RO-_d1


title: Teff.CD45RO-_d1.rep2

value: Sorted ex vivo Treg subset


title: 073TS-UM-IU_834

description:
uninvolved margin of breast carcinoma
073TS-UM-IU


title: UPN727 cells, unrelated healthy control (uHC) plasma patients 07

source_name: UPN727 cells stimulated with HC07 Plasma


title: 073TS-UM-IL_833

description:
uninvolved margin of breast carcinoma
073TS-UM-IL


title: UPN727 cells, unrelated healthy control (uHC) plasma patients 05

source_name: UPN727 cells stimulated with HC05 Plasma


title: Teff.CD45RO-_d1.rep1


title: Teff.CD45RO+_d1.rep1


title: 073TS-UM-EU_832

description:
uninvolved margin of breast carcinoma
073TS-UM-EU


title: 1968


title: Teff.CD45RO+_d1.rep2


title: 2160


title: 2161


title: Treg.CD45RO+.Intb7+.CD49d+.rep2

source_name: Human Treg subsets from peripheral blood

value: Treg CD45RO+ Intb7+ CD49d+


title: UPN727 cells, unrelated healthy control (uHC) plasma patients 04

source_name: UPN727 cells stimulated with HC04 Plasma


title: 073TS-UM-EL_831

description:
uninvolved margin of breast carcinoma
073TS-UM-EL


title: UPN727 cells, unrelated healthy control (uHC) plasma patients 03

source_name: UPN727 cells stimulated with HC03 Plasma


title: UPN727 cells, unrelated healthy control (uHC) plasma patients 02

source_name: UPN727 cells stimulated with HC02 Plasma


title: 072KS-VB_830

description:
uninvolved margin in the immediate vicinity of the mammilla
072KS-VB

value: Luminal A


title: 072KS-UM-IU_829

description:
uninvolved margin of breast carcinoma
072KS-UM-IU


title: UPN727 cells, unrelated healthy control (uHC) plasma patients 01

source_name: UPN727 cells stimulated with HC01 Plasma


title: Treg.CD45RO+.Intb7-.CD49d+.rep3

value: Treg CD45RO+ Intb7- CD49d+


title: 072KS-UM-IL_828

description:
uninvolved margin of breast carcinoma
072KS-UM-IL


title: 1963

value: Benzo(a)pyrene


title: Treg.CD45RO+.Intb7-.CD49d+.rep2


title: 072KS-UM-EU_827

description:
uninvolved margin of breast carcinoma
072KS-UM-EU


title: 1965

source_name: Ref MCF7


title: 1964


title: 1962

value: p,p'-DDT


title: 1961


title: 1960

value: Nonylphenol


title: 1959

value: Toxaphene


title: 071ZB-UM-IU_822

description:
uninvolved margin of breast carcinoma
071ZB-UM-IU

value: Triple negative


title: Treg.CD45RO+.Intb7+.CD49d+.rep1

description: Gene expression data from Treg subset with indicated cell surface phenotype on the sample name


title: Treg.CD45RO+.Intb7-.CD49d+.rep1


title: 1958

value: MCF-7 human breast carcinoma cell line (ECACC No. 86012803)


title: Treg.CD45RO+.Intb7-.CD49d-.rep3

value: Treg CD45RO+ Intb7- CD49d-


title: UPN727 cells, TN14 PL20 at 12 month

hyb_protocol: Purified total RNA (~50ng) was amplified using the two-cycle cDNA synthesis kit (Affymetrix  900432) and cRNA was synthesized,  labeled,  fragmented and hybridized to the arrays in accordance to standard Affymetrix protocols (Affymetrix,  Santa Clara,  CA)

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log intensities.  Each sample was independently analyzed (3 arrays per patient, at baseline, 9, and 12 months into treatment, 189 arrays in total).  The statistical significance of differential gene expression and false discovery rates (FDR) were derived through ANalysis Of VAriation (ANOVA) using Partek Genomics Suite 6.5.

source_name: UPN727 cells stimulated with TN14_PL20_M12 serum

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

treatment_protocol: Gene expression was accomplished by culturing PBMCs at 37°C in 5% CO2 with 40% serum from recent-onset (RO) T1D patients that were given Placebo or Canakinumab at their respective time points.  Cultures were prepared in a Costar 24-well plate (Corning) using 500,000 cells/well and in RPMI 1640 medium supplemented with 100U/ml penicillin and 100ug/ml streptomycin in a total of 500 µl.  After culture (9 hours optimal for cryopreserved PBMCs) total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies).

tag: responder cells

value: UPN727 cells

tag: patient

tag: timepoint

value: 12 month into treatment


title: Treg.CD45RO+.Intb7-.CD49d-.rep1


title: 1957


title: Treg.CD45RO+.Intb7-.CD49d-.rep2


title: Treg.CD45RO+.ICOS+.rep3

value: Treg CD45RO+ ICOS+


title: Treg.CD45RO+.ICOS+.rep2


title: UPN727 cells, TN14 PL20 at 9 month

source_name: UPN727 cells stimulated with TN14_PL20_M9 serum

value: 9 month into treatment


title: 072KS-UM-EL_826

description:
uninvolved margin of breast carcinoma
072KS-UM-EL

data_processing:
The genotyping data was normalized and analyzed using Nexus Copy Number 7 (Biodiscovery). Copy number and allelic imbalances calls were made by using the SNP-FASST segmentation algorithm with the following settings: Significance Threshold: 5.0E-9; Max Contiguous Probe Spacing 500-1000; Min. number of probes per segment: 10; Homozygous Frequency Threshold: 0.85; Homozygous Value Threshold: 0.95; and Heterozygous Imbalance Threshold: 0.46. All the other parameters were left default. Data included in this GEO project was generated using the utility  “convert .ivg to .txt” from Nexus 7.
Log R Ratio and B Allele frequency values are reported for each probe from the four different platforms used in the study.

tag: gender

value: female

value: unifocal


title: UPN727 cells, TN14 PL19 at 12 month

source_name: UPN727 cells stimulated with TN14_PL19_M12 serum


title: UPN727 cells, TN14 PL19 at 9 month

source_name: UPN727 cells stimulated with TN14_PL19_M9 serum


title: 1956

data_processing: The Agilent processed signal values (i.e., feature gProcessedSignal from Agilent Feature Extraction v8.5.1.1) were used for the data analysis. Base 2 log-ratios (Cy5/Cy3) were computed and averaged over the duplicate spots. Control probes were removed prior to analysis.

value: solvent control


title: UPN727 cells, TN14 PL19 at baseline

source_name: UPN727 cells stimulated with TN14_PL19_BL serum

value: at baseline


title: UPN727 cells, TN14 PL20 at baseline

source_name: UPN727 cells stimulated with TN14_PL20_BL serum


title: UPN727 cells, TN14 PL18 at 12 month

source_name: UPN727 cells stimulated with TN14_PL18_M12 serum


title: 071ZB-UM-IL_821

description:
uninvolved margin of breast carcinoma
071ZB-UM-IL

source_name: breast tissue from mastectomy, taken outside the site of primary tumor(s)

tag: age at cancer diagnosis (yrs)


title: 071ZB-VB_823

description:
uninvolved margin in the immediate vicinity of the mammilla
071ZB-VB


title: Treg.CD45RO+.ICOS+.rep1

value: Sorted ex vivo Treg subset


title: 071ZB-UM-EL_819

description:
uninvolved margin of breast carcinoma
071ZB-UM-EL


title: 1955


title: 071ZB-UM-EU_820

description:
uninvolved margin of breast carcinoma
071ZB-UM-EU


title: UPN727 cells, TN14 PL18 at 9 month

source_name: UPN727 cells stimulated with TN14_PL18_M9 serum


title: UPN727 cells, TN14 PL18 at baseline

source_name: UPN727 cells stimulated with TN14_PL18_BL serum


title: 070ZNK-VB_816

description:
uninvolved margin in the immediate vicinity of the mammilla
070ZNK-VB


title: 070ZNK-UM-EU_815

description:
uninvolved margin of breast carcinoma
070ZNK-UM-EU


title: 069EKJ-UM-IU_811

description:
uninvolved margin of breast carcinoma
069EKJ-UM-IU

value: Luminal A


title: 069EKJ-VB_812

description:
uninvolved margin in the immediate vicinity of the mammilla
069EKJ-VB


title: Treg.CD45RO+.Intb7+.CD49d+.rep3

value: Treg CD45RO+ Intb7+ CD49d+


title: 1953

value: p,p'-DDT


title: Treg.CD45RO+.ICOS-.rep3

value: Treg CD45RO+ ICOS-


title: UPN727 cells, TN14 PL17 at 12 month

source_name: UPN727 cells stimulated with TN14_PL17_M12 serum


title: 1954

value: Toxaphene


title: 069EKJ-UM-IL_810

description:
uninvolved margin of breast carcinoma
069EKJ-UM-IL


title: Treg.CD45RO+.HLADR+.rep3

source_name: Human Treg subsets from peripheral blood

value: Treg CD45RO+ HLADR+


title: 069EKJ-UM-EU_809

description:
uninvolved margin of breast carcinoma
069EKJ-UM-EU


title: Treg.CD45RO+.ICOS-.rep1


title: Treg.CD45RO+.HLADR+.rep2


title: UPN727 cells, TN14 PL16 at 12 month

source_name: UPN727 cells stimulated with TN14_PL16_M12 serum


title: UPN727 cells, TN14 PL17 at 9 month

source_name: UPN727 cells stimulated with TN14_PL17_M9 serum


title: Treg.CD45RO+.HLADR+.rep1


title: Treg.CD45RO+.ICOS-.rep2


title: 069EKJ-UM-EL_808

description:
uninvolved margin of breast carcinoma
069EKJ-UM-EL


title: mamma_E2+3-MC,rat-2

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45oC on GeneChip Rat Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix Scanner 3000 7G with AGCC software.

data_processing: CEL files were analyzed for quality using Affymetrix Expression Console software, and imported into GeneSpring GX11.5. Data was quantile-normalized using PLIER and baseline transformed to the median of the control samples.

organism: Rattus norvegicus

source_name: rat mammary gland, 48 h treatment, E2+3-MC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix WT protocol

treatment_protocol: Rats were treated with vehicle control (DMSO), 17β-Estradiol (E2), 3-Methylcholanthrene (3-MC) or E2+3-MC for 48 h.  Mammary glands were obtained 24 h after the last treatment. 3 biological samples from three rats were analyzed for each treatment group .

tag: tissue

value: mammary gland

tag: strain

value: Lewis


title: mamma_E2+3-MC,rat-3


title: 068AP-VB_807

description:
uninvolved margin in the immediate vicinity of the mammilla
068AP-VB

hyb_protocol: starndard protocol

scan_protocol: The majority of genotyping experiments were conducted at the SNP&SEQ Technology Platform in Uppsala by using four similar in SNP-density Illumina platforms (Human 660W-Quad, Human1M-Duo, HumanOmniExpress and HumanOmniExpressExome beadchips), according to the recommendations of the manufacturer.


title: UPN727 cells, TN14 PL16 at 9 month

source_name: UPN727 cells stimulated with TN14_PL16_M9 serum

value: UPN727 cells


title: mamma_E2+3-MC,rat-1


title: Treg.CD45RO+.HLADR-.rep3

value: Treg CD45RO+ HLADR-

tag: sample type


title: Treg.CD45RO+.HLADR-.rep2


title: UPN727 cells, TN14 PL17 at baseline

source_name: UPN727 cells stimulated with TN14_PL17_BL serum


title: Treg.CD45RO+.HLADR-.rep1


title: UPN727 cells, TN14 PL15 at 12 month

source_name: UPN727 cells stimulated with TN14_PL15_M12 serum

value: 12 month into treatment


title: UPN727 cells, TN14 PL15 at 9 month

source_name: UPN727 cells stimulated with TN14_PL15_M9 serum

value: 9 month into treatment


title: 068AP-UM-IL_805

description:
uninvolved margin of breast carcinoma
068AP-UM-IL

value: female


title: 074DP-UM-IL_838

description:
uninvolved margin of breast carcinoma
074DP-UM-IL

value: Luminal B, HER2-

value: unifocal


title: mamma_3-MC,rat-2

source_name: rat mammary gland, 48 h treatment, 3-MC


title: mamma_3-MC,rat-3


title: 068AP-UM-EU_804

description:
uninvolved margin of breast carcinoma
068AP-UM-EU


title: 068AP-UM-IU_806

description:
uninvolved margin of breast carcinoma
068AP-UM-IU


title: mamma_E2,rat-3

source_name: rat mammary gland, 48 h treatment, E2


title: 068AP-UM-EL_803

description:
uninvolved margin of breast carcinoma
068AP-UM-EL


title: mamma_E2,rat-2


title: UPN727 cells, TN14 PL15 at baseline

source_name: UPN727 cells stimulated with TN14_PL15_BL serum

value: at baseline


title: Treg.CD45RO+.CXCR3+.CCR6+.rep2

description: Gene expression data from Treg subset with indicated cell surface phenotype on the sample name

value: Treg CD45RO+ CXCR3+ CCR6+

value: Sorted ex vivo Treg subset


title: Treg.CD45RO+.CXCR3+.CCR6+.rep1


title: mamma_3-MC,rat-1


title: UPN727 cells, TN14 PL14 at 12 month

source_name: UPN727 cells stimulated with TN14_PL14_M12 serum


title: 067JB-VB_802

description:
uninvolved margin in the immediate vicinity of the mammilla
067JB-VB

value: Luminal A


title: mamma_E2,rat-1


title: Treg.CD45RO+.CXCR3+.CCR6+.rep3


title: UPN727 cells, TN14 PL16 at baseline

source_name: UPN727 cells stimulated with TN14_PL16_BL serum


title: mamma_DMSO,rat-3

source_name: rat mammary gland, 48 h treatment, VEHICLE


title: mamma_DMSO,rat-1


title: 067JB-UM-IU_801

description:
uninvolved margin of breast carcinoma
067JB-UM-IU

source_name: breast tissue from mastectomy, taken outside the site of primary tumor(s)


title: UPN727 cells, TN14 PL13 at 12 month

source_name: UPN727 cells stimulated with TN14_PL13_M12 serum


title: UPN727 cells, TN14 PL14 at 9 month

source_name: UPN727 cells stimulated with TN14_PL14_M9 serum


title: mamma_DMSO,rat-2


title: UPN727 cells, TN14 PL14 at baseline

source_name: UPN727 cells stimulated with TN14_PL14_BL serum


title: 067JB-UM-EU_800

description:
uninvolved margin of breast carcinoma
067JB-UM-EU


title: 067JB-UM-EL_799

description:
uninvolved margin of breast carcinoma
067JB-UM-EL


title: Treg.CD45RO+.CXCR3+.CCR6-.rep2

source_name: Human Treg subsets from peripheral blood

value: Treg CD45RO+ CXCR3+ CCR6-


title: 066JD-VB_798

description:
uninvolved margin in the immediate vicinity of the mammilla
066JD-VB


title: 066JD-UM-IU_797

description:
uninvolved margin of breast carcinoma
066JD-UM-IU


title: Treg.CD45RO+.CXCR3+.CCR6-.rep1


title: 066JD-UM-IL_796

description:
uninvolved margin of breast carcinoma
066JD-UM-IL


title: Treg.CD45RO+.CXCR3+.CCR6-.rep3


title: UPN727 cells, TN14 PL13 at 9 month

source_name: UPN727 cells stimulated with TN14_PL13_M9 serum


title: Treg.CD45RO+.CXCR3-.CCR6+.rep3

value: Treg CD45RO+ CXCR3- CCR6+


title: Treg.CD45RO+.CXCR3-.CCR6+.rep1


title: Treg.CD45RO+.CXCR3-.CCR6-.rep1

value: Treg CD45RO+ CXCR3- CCR6-


title: 066JD-UM-EU_795

description:
uninvolved margin of breast carcinoma
066JD-UM-EU


title: p300kd cardiac myocytes at T8 biological rep 3

city: Miami

first: Sumit

last: Jain

state: Florida

address: 1600 NW 10th Avenue RMSB 6041

department: Molecular and Cellular Pharmacology

institute: University of Miami

description: Cardiac myocytes transfected with anti-p300 siRNA

hyb_protocol: Biotinylated and fragmented cDNA (5.5 ug/samples) was diluted in hybridization buffer along with hybridization controls and control oligo. The mixture was denatured for 5 minutes at 99C and then loaded on to the surface of Affmetrix Rat Gene ST 1.0 GeneChips and hybridized for 16-18 hours at 45C under constant rotation in a Affymetrix Model 640 hybridization oven.

scan_protocol: The Affymetrix 3000 7G Plus Scanner controlled by Affymetrix AGCC software was used for data acquisition.

data_processing: Expression Console Version 1.1 software was used to generate probe set intensities using .CEL files. Specifically the RMA algorithm was used for background adjustment, quantile normalization, and probe set summarization; then untransformed probe set intensities were outputted for presentation and archiving. Log2-transformed probe intensities were outputted for purposes of statistical analysis.

source_name: p300kd neonatal rat cardiac myocytes, DOX 8 hr

label_protocol: Total RNA samples were converted to antisense cRNA and then to sense-strand cDNA using the Ambion (Carlsbad, CA) WT Expression kit. Sense strand cDNA generated was fragmented and biotin labeled using the Affymetrix (Santa Clara, CA) GeneChip® WT Terminal Labeling kit.

growth_protocol: The final myocyte cultures contained >90% cardiac myocytes at 60-70%% confluence; 0.1mmol/L bromodeoxyuridine was included in the medium for the first 4 days after plating to inhibit fibroblast growth. Cells were serum-starved for two days with TIB (MEM supplemented with transferrin, vitamin B12, insulin) before experiments.

extract_protocol: Total RNA was extracted using miRVana RNA isolation kit from AMBION using manufacturer's protocol.

treatment_protocol: Neonatal rat cardiac myocytes were cultured for 2 days in complete MEM media containing 1% BrdU, then transfected with either non-silencing (NS) or p300 (p300kd) siRNA. Following transfection and two additional days in complete medium, cells were cultured for an additional 48 hrs in serum-free TIB media before initiation of experiments.  Cells were then treated with 1 micromolar Doxorubicin (Dox) for either 0 or 8 hrs.

value: Sprague Dawley

value: neonatal rat cardiac myocytes

tag: treatment group

value: p300kd cardiac myocytes 8hr Dox


title: UPN727 cells, TN14 PL13 at baseline

source_name: UPN727 cells stimulated with TN14_PL13_BL serum

value: UPN727 cells


title: p300kd cardiac myocytes at T8 biological rep 2


title: NS cardiac myocytes at T8 biological rep 2

description: Cardiac myocytes transfected with Non-silencing siRNA

source_name: NS neonatal rat cardiac myocytes, DOX 8 hr

value: NS cardiac myocytes 8hr Dox


title: NS cardiac myocytes at T8 biological rep 3


title: UPN727 cells, TN14 PL12 at 12 month

source_name: UPN727 cells stimulated with TN14_PL12_M12 serum

value: 12 month into treatment


title: Treg.CD45RO+.CXCR3-.CCR6+.rep2


title: 066JD-UM-EL_794

description:
uninvolved margin of breast carcinoma
066JD-UM-EL

extract_protocol: The tissues were stored at -70 degrees C prior to DNA extraction. The solid tissues were homogenized with a Tissuerupter (Qiagen). Proteinase K and Sarcosine was then added and the sample was incubated at 50oC over-night. The samples were transferred to PhaseLock Gel tubes and the DNA was purified with phenol/chloroform extraction. Due to very rich content of fat in UMs, phenol/chloroform extraction was repeated 6 times for all UMs, and 3 times for PTs and control samples from skin. The purified DNA was precipitated with sodium acetate, pH 5.4 and 95% ethanol. The DNA precipitate was dried before dissolving in water. Control samples of blood were extracted with QIAmp DNA Blood Maxi Kit (Qiagen).


title: UPN727 cells, TN14 PL11 at 12 month

source_name: UPN727 cells stimulated with TN14_PL11_M12 serum


title: 065AS-VB_793

description:
uninvolved margin in the immediate vicinity of the mammilla
065AS-VB

value: Triple negative


title: UPN727 cells, TN14 PL12 at baseline

source_name: UPN727 cells stimulated with TN14_PL12_BL serum


title: 065AS-UM-IU_792

description:
uninvolved margin of breast carcinoma
065AS-UM-IU

value: female


title: 065AS-UM-IL_791

description:
uninvolved margin of breast carcinoma
065AS-UM-IL


title: Treg.CD45RO+.CLA+.rep3

value: Treg CD45RO+ CLA+


title: Treg.CD45RO+.CXCR3-.CCR6-.rep2


title: Treg.CD45RO+.CLA+.rep2


title: UPN727 cells, TN14 PL12 at 9 month

source_name: UPN727 cells stimulated with TN14_PL12_M9 serum

value: 9 month into treatment


title: UPN727 cells, TN14 PL11 at 9 month

source_name: UPN727 cells stimulated with TN14_PL11_M9 serum


title: NS cardiac myocytes at T8 biological rep 1


title: Treg.CD45RO+.CLA+.rep1


title: Treg.CD45RO+.CLA-.rep3

value: Treg CD45RO+ CLA-


title: SE135A1_133

description:
TUMORS4: 29_primaryTumors_GPL6984.txt
Genotyping on DNA extracted from a primary tumor

hyb_protocol: standard protocol

data_processing:
The genotyping data was normalized and analyzed using Nexus Copy Number 7 (Biodiscovery). Copy number and allelic imbalances calls were made by using the SNP-FASST segmentation algorithm with the following settings: Significance Threshold: 5.0E-9; Max Contiguous Probe Spacing 500-1000; Min. number of probes per segment: 10; Homozygous Frequency Threshold: 0.85; Homozygous Value Threshold: 0.95; and Heterozygous Imbalance Threshold: 0.46. All the other parameters were left default. Data included in this GEO project was generated using the utility “convert .ivg to .txt” from Nexus 7.
Log R Ratio and B Allele frequency values are reported for each probe from the four different platforms used in the study.

source_name: DNA extracted from primary tumor

label_protocol: standard protocol

tag: age at cancer diagnosis

value: Luminal B, HER2-

value: unifocal

value: primary tumor


title: UPN727 cells, TN14 PL11 at baseline

source_name: UPN727 cells stimulated with TN14_PL11_BL serum

value: at baseline


title: p300kd cardiac myocytes at T0 biological rep 3

source_name: p300kd neonatal rat cardiac myocytes, DOX 0 hr

value: p300kd cardiac myocytes 0hr Dox