title: KO-BL, rep 1

description: Gene expression data from stem cells

source_name: p63 KO bladder epithelial stem cell culture

value: bladder

value: bladder epithelial stem cell culture

value: p63 knockout


title: 79_Cy3_6_Cy5

status: Public on Oct 01 2015

type: RNA

city: East Lansing

first: Timothy

last: Zacharewski

state: Michigan

address: 603 Wilson Road

department: BMB

country: USA

institute: Michigan State University

description: C57BL/6 mouse jejunum - animal 79 (30µ/kg TCDD) vs. animal 6 (0µg/kg TCDD)

hyb_protocol: Hybridization was performed according the the Agilent manual G4140-90040 v. 5.7.

scan_protocol: Immediately after washing, microarrays were scanned using a GenePix 4000B microarray scanner (Molecular Devices, Union City, CA) at 532 nm and 635 nm with a scan resolution of 5 um.

data_processing:
Feature signal intensities and flagged features were determined using GenePix Pro 6.0 (Molecular Devices, Union City, CA).
Signal intensities normalized using a semi-parametric approach (Eckel, J. E., Gennings, C., Therneau, T. M., Burgoon, L. D., Boverhof, D. R. and Zacharewski, T. R. (2005). Bioinformatics 21(7), 1078-83.). These normalized signal intensities were then analyzed using an empirical Bayes analysis (Eckel, J. E., Gennings, C., Chinchilli, V. M., Burgoon, L. D., and Zacharewski, T. R., 2004. J Biopharm Stat 14, 647-670.) resulting in a final dataset with blank values where n ≤ 2 for a probe at each time-point.

molecule: total RNA

organism: Mus musculus

source_name: Mouse jejunal epithelium, dosed every 4 days for 28 days with TCDD

label_protocol: Cy3 and Cy5 labeling was performed according to the Agilent manual G4140-90040 v. 5.7.

extract_protocol: Jejunal epithelium were homogenized in TRIzol (Invitrogen, Carlsbad, CA) using a mixer mill 300 tissue homogenizer (Retsch, Germany). Total RNA was isolated according to manufacturers instructions and resuspended in RNA storage solution (Ambion Inc., Austin, TX). RNA was quantified spectrophotometrically (A260) and purity was assessed using the A260/A280 ratio and visual inspection on a denaturing gel.

treatment_protocol: Female C57BL/6 mice were gavaged daily with sesame oil vehicle, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 ug/kg TCDD every  4 days for 28 days.

tag: strain

tag: tissue

value: Jejunal epithelium

tag: gender

value: Female

tag: treatment

value: TCDD

tag: replicate

tag: dose

value: ug/kg

value: Vehicle

tag: dose unit


title: 130JT-PT_39

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:
TUMORS3: 98_primaryTumors_18224.txt
Genotyping on DNA extracted from a primary tumor

hyb_protocol: standard 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: DNA extracted from primary tumor

label_protocol: standard 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).

value: female

tag: age at cancer diagnosis

tag: tumor grade

value: Luminal B, HER2+

tag: tumor focality

value: unifocal

value: primary tumor


title: 138BM-S-PT_42

value: Luminal B, HER2-


title: 129EB-PT_38

value: multifocal


title: UPN727 cells, AIDA PL17 at 1 month

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 serum collected from patient PL17 1 month into treatment

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 (5 arrays per patient, at baseline, 1, 3, 6, and 9 months into treatment, 235 arrays in total).  The statistical significance of differential gene expression and false discovery rates (FDR) were derived through ANOVA as a statistic analysis method in Partek GS.

source_name: UPN727 cells stimulated with AIDA_PL17_M1 serum

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

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

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 Anakinra 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: 1 month into treatment


title: 6_Cy3_79_Cy5

description: C57BL/6 mouse jejunum - animal 6 (0µ/kg TCDD) vs. animal 79 (30µg/kg TCDD)


title: 098WC-PT_36


title: UPN727 cells, AIDA PL18 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL18 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL18_M3 serum

value: 3 month into treatment


title: Hi-Myc castrate rep1

city: New York

first: Yu

last: Chen

state: NY

address: 1275 York Ave, Box 20

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was log2 transformed and quantile normalized using Partek Genomics suite

source_name: Mouse Prostate, Castration 3 days prior

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Hi-Myc transgenic mice were fed ad lib

extract_protocol: Tissue was ground in Trizol using tissue grinder and then purified using Qiagen RNAEasy column

treatment_protocol: Mice underwent surgical castration or drug treat via oral gavage

value: Hi-Myc

tag: tissue type

value: prostate tumor


title: 095ESZ-PT_35


title: UPN727 cells, AIDA PL18 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL18 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL18_M1 serum


title: 100AW-PT_37


title: UPN727 cells, AIDA PL16 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL16 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL16_M6 serum

value: 6 month into treatment


title: Hi-Myc castrate rep2

description: replicate 2


title: 089SD-PT-TU_34

value: Triple negative


title: 086AFT-PT_33


title: 71_Cy3_6_Cy5

description: C57BL/6 mouse jejunum - animal 71 (10µ/kg TCDD) vs. animal 6 (0µg/kg TCDD)

value: Jejunal epithelium

value: Female


title: UPN727 cells, AIDA PL16 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL16 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL16_M3 serum


title: Hi-Myc rep1

description: replicate 1

source_name: Mouse Prostate, Vehicle x 3 days


title: 62_Cy3_6_Cy5

description: C57BL/6 mouse jejunum - animal 62 (3µ/kg TCDD) vs. animal 6 (0µg/kg TCDD)

value: TCDD

value: ug/kg


title: UPN727 cells, AIDA PL16 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL16 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL16_M1 serum


title: UPN727 cells, AIDA PL16 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL16 at baseline

source_name: UPN727 cells stimulated with AIDA_PL16_BL serum

value: at baseline


title: 6_Cy3_62_Cy5

description: C57BL/6 mouse jejunum - animal 6 (0µ/kg TCDD) vs. animal 62 (3µg/kg TCDD)

value: Vehicle


title: 6_Cy3_71_Cy5

description: C57BL/6 mouse jejunum - animal 6 (0µ/kg TCDD) vs. animal 71 (10µg/kg TCDD)


title: 6_Cy3_54_Cy5

description: C57BL/6 mouse jejunum - animal 6 (0µ/kg TCDD) vs. animal 54 (1µg/kg TCDD)


title: UPN727 cells, AIDA PL15 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL15 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL15_M9 serum

value: 9 month into treatment


title: UPN727 cells, AIDA PL15 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL15 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL15_M6 serum


title: 54_Cy3_6_Cy5

description: C57BL/6 mouse jejunum - animal 54 (1µ/kg TCDD) vs. animal 6 (0µg/kg TCDD)


title: UPN727 cells, AIDA PL15 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL15 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL15_M1 serum


title: UPN727 cells, AIDA PL15 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL15 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL15_M3 serum


title: UPN727 cells, AIDA PL15 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL15 at baseline

source_name: UPN727 cells stimulated with AIDA_PL15_BL serum


title: 38_Cy3_6_Cy5

description: C57BL/6 mouse jejunum - animal 38 (0.1µ/kg TCDD) vs. animal 6 (0µg/kg TCDD)


title: 077EP-PT_29

description:
TUMORS3: 98_primaryTumors_18224.txt
Genotyping on DNA extracted from a primary tumor

value: female

value: Luminal B, HER2+

value: unifocal

value: primary tumor


title: 47_Cy3_6_Cy5

description: C57BL/6 mouse jejunum - animal 47 (0.3µ/kg TCDD) vs. animal 6 (0µg/kg TCDD)


title: 6_Cy3_47_Cy5

description: C57BL/6 mouse jejunum - animal 6 (0µ/kg TCDD) vs. animal 47 (0.3µg/kg TCDD)


title: 085AS-PT_32

value: Luminal B, HER2-


title: UPN727 cells, AIDA PL14 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL14 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL14_M6 serum

value: UPN727 cells


title: UPN727 cells, AIDA PL14 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL14 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL14_M9 serum


title: 075JS-PT_28

source_name: DNA extracted from primary tumor

value: multifocal


title: 071ZB-PT_27


title: 081BS-PT_31


title: UPN727 cells, AIDA PL14 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL14 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL14_M1 serum

value: 1 month into treatment


title: UPN727 cells, AIDA PL14 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL14 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL14_M3 serum

value: 3 month into treatment


title: 078AW-PT_30


title: 070ZNK-PT_26

value: Triple negative


title: 30_Cy3_6_Cy5

description: C57BL/6 mouse jejunum - animal 30 (0.03µ/kg TCDD) vs. animal 6 (0µg/kg TCDD)

source_name: Mouse jejunal epithelium, dosed every 4 days for 28 days with TCDD

value: Jejunal epithelium


title: 065AS-PT_25


title: 062BI-PT_23

value: Luminal A


title: 061AS-PT_22


title: 054MJ-PT_21


title: 063JB-PT_24


title: 053KS-PT_20

value: DCIS HG

value: DCIS multifocal


title: 049ASZ-PT_19


title: 043WB-PT_18


title: 22_Cy3_6_Cy5

description: C57BL/6 mouse jejunum - animal 22 (0.01µ/kg TCDD) vs. animal 6 (0µg/kg TCDD)

value: Female

value: TCDD

value: ug/kg


title: UPN727 cells, AIDA PL13 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL13 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL13_M9 serum

value: 9 month into treatment


title: UPN727 cells, AIDA PL13 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL13 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL13_M6 serum

value: 6 month into treatment


title: UPN727 cells, AIDA PL13 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL13 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL13_M3 serum


title: 6_Cy3_38_Cy5

description: C57BL/6 mouse jejunum - animal 6 (0µ/kg TCDD) vs. animal 38 (0.1µg/kg TCDD)

value: Vehicle


title: 6_Cy3_30_Cy5

description: C57BL/6 mouse jejunum - animal 6 (0µ/kg TCDD) vs. animal 30 (0.03µg/kg TCDD)


title: 78_Cy3_4_Cy5

description: C57BL/6 mouse jejunum - animal 78 (30µ/kg TCDD) vs. animal 4 (0µg/kg TCDD)


title: 4_Cy3_78_Cy5

description: C57BL/6 mouse jejunum - animal 4 (0µ/kg TCDD) vs. animal 78 (30µg/kg TCDD)


title: UPN727 cells, AIDA PL13 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL13 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL13_M1 serum


title: 6_Cy3_22_Cy5

description: C57BL/6 mouse jejunum - animal 6 (0µ/kg TCDD) vs. animal 22 (0.01µg/kg TCDD)


title: UPN727 cells, AIDA PL12 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL12 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL12_M9 serum


title: UPN727 cells, AIDA PL13 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL13 at baseline

source_name: UPN727 cells stimulated with AIDA_PL13_BL serum

value: at baseline


title: UPN727 cells, AIDA PL14 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL14 at baseline

source_name: UPN727 cells stimulated with AIDA_PL14_BL serum


title: 026MS-PT_16

description:
TUMORS3: 98_primaryTumors_18224.txt
Genotyping on DNA extracted from a primary tumor

value: female

value: unifocal

value: primary tumor


title: 70_Cy3_4_Cy5

description: C57BL/6 mouse jejunum - animal 70 (10µ/kg TCDD) vs. animal 4 (0µg/kg TCDD)


title: 60_Cy3_4_Cy5

description: C57BL/6 mouse jejunum - animal 60 (3µ/kg TCDD) vs. animal 4 (0µg/kg TCDD)


title: 4_Cy3_70_Cy5

description: C57BL/6 mouse jejunum - animal 4 (0µ/kg TCDD) vs. animal 70 (10µg/kg TCDD)


title: 025JT-PT_15

value: Luminal B, HER2-


title: UPN727 cells, AIDA PL12 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL12 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL12_M1 serum

value: UPN727 cells

value: 1 month into treatment


title: UPN727 cells, AIDA PL12 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL12 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL12_M3 serum

value: 3 month into treatment


title: 4_Cy3_60_Cy5

description: C57BL/6 mouse jejunum - animal 4 (0µ/kg TCDD) vs. animal 60 (3µg/kg TCDD)

value: Jejunal epithelium


title: UPN727 cells, AIDA PL12 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL12 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL12_M6 serum


title: 52_Cy3_4_Cy5

description: C57BL/6 mouse jejunum - animal 52 (1µ/kg TCDD) vs. animal 4 (0µg/kg TCDD)


title: 4_Cy3_52_Cy5

description: C57BL/6 mouse jejunum - animal 4 (0µ/kg TCDD) vs. animal 52 (1µg/kg TCDD)


title: UPN727 cells, AIDA PL12 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL12 at baseline

source_name: UPN727 cells stimulated with AIDA_PL12_BL serum


title: 44_Cy3_4_Cy5

description: C57BL/6 mouse jejunum - animal 44 (0.3µ/kg TCDD) vs. animal 4 (0µg/kg TCDD)


title: 36_Cy3_4_Cy5

description: C57BL/6 mouse jejunum - animal 36 (0.1µ/kg TCDD) vs. animal 4 (0µg/kg TCDD)


title: 4_Cy3_44_Cy5

description: C57BL/6 mouse jejunum - animal 4 (0µ/kg TCDD) vs. animal 44 (0.3µg/kg TCDD)


title: 037MC-PT_17

value: Luminal A


title: 024MZ-PT_14


title: 017KM-PT_12


title: 021MB-PT_13

value: Luminal B, HER2+


title: UPN727 cells, AIDA PL11 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL11 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL11_M9 serum


title: 013WS-PT_10

value: multifocal


title: 016JS-PT_11

value: Triple negative


title: 012MC-PT_9


title: 011BM-PT_8


title: 006MK-PT_7


title: ZL152-BL_85

description:
CONTROLS3: 78_controls_GPL18224.txt
Control experiment, DNA genotyping on DNA extracted from whole blood

source_name: DNA extracted from whole blood

value: whole blood


title: UV023-BL_84


title: 76_Cy3_2_Cy5

description: C57BL/6 mouse jejunum - animal 76 (30µ/kg TCDD) vs. animal 2 (0µg/kg TCDD)

value: Female

value: TCDD

value: ug/kg


title: UPN727 cells, AIDA PL11 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL11 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL11_M3 serum


title: 28_Cy3_4_Cy5

description: C57BL/6 mouse jejunum - animal 28 (0.03µ/kg TCDD) vs. animal 4 (0µg/kg TCDD)

value: Vehicle


title: TP169-BL_83

value: female


title: UPN727 cells, AIDA PL10 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL10 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL10_M9 serum_OL

value: 9 month into treatment


title: 4_Cy3_20_Cy5

description: C57BL/6 mouse jejunum - animal 4 (0µ/kg TCDD) vs. animal 20 (0.01µg/kg TCDD)


title: 4_Cy3_28_Cy5

description: C57BL/6 mouse jejunum - animal 4 (0µ/kg TCDD) vs. animal 28 (0.03µg/kg TCDD)


title: SK056-BL_82


title: 68_Cy3_2_Cy5

description: C57BL/6 mouse jejunum - animal 68 (10µ/kg TCDD) vs. animal 2 (0µg/kg TCDD)


title: 2_Cy3_76_Cy5

description: C57BL/6 mouse jejunum - animal 2 (0µ/kg TCDD) vs. animal 76 (30µg/kg TCDD)


title: 20_Cy3_4_Cy5

description: C57BL/6 mouse jejunum - animal 20 (0.01µ/kg TCDD) vs. animal 4 (0µg/kg TCDD)


title: UPN727 cells, AIDA PL09 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL09 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL09_M9 serum


title: UPN727 cells, AIDA PL09 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL09 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL09_M6 serum

value: 6 month into treatment


title: UPN727 cells, AIDA PL09 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL09 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL09_M3 serum


title: UPN727 cells, AIDA PL11 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL11 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL11_M1 serum


title: UPN727 cells, AIDA PL10 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL10 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL10_M6 serum


title: UPN727 cells, AIDA PL11 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL11 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL11_M6 serum


title: UPN727 cells, AIDA PL11 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL11 at baseline

source_name: UPN727 cells stimulated with AIDA_PL11_BL serum

value: at baseline


title: 2_Cy3_58_Cy5

description: C57BL/6 mouse jejunum - animal 2 (0µ/kg TCDD) vs. animal 58 (3µg/kg TCDD)

source_name: Mouse jejunal epithelium, dosed every 4 days for 28 days with TCDD


title: 2_Cy3_68_Cy5

description: C57BL/6 mouse jejunum - animal 2 (0µ/kg TCDD) vs. animal 68 (10µg/kg TCDD)


title: UPN727 cells, AIDA PL10 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL10 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL10_M1 serum

value: UPN727 cells


title: 4_Cy3_36_Cy5

description: C57BL/6 mouse jejunum - animal 4 (0µ/kg TCDD) vs. animal 36 (0.1µg/kg TCDD)


title: UPN727 cells, AIDA PL10 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL10 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL10_M3 serum


title: UPN727 cells, AIDA PL10 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL10 at baseline

source_name: UPN727 cells stimulated with AIDA_PL10_BL serum


title: 58_Cy3_2_Cy5

description: C57BL/6 mouse jejunum - animal 58 (3µ/kg TCDD) vs. animal 2 (0µg/kg TCDD)


title: MW158-BL_80

description:
CONTROLS3: 78_controls_GPL18224.txt
Control experiment, DNA genotyping on DNA extracted from whole blood

value: Luminal B, HER2-

value: unifocal


title: UPN727 cells, AIDA PL09 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL09 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL09_M1 serum

value: 1 month into treatment


title: MS168-BL_79


title: MN036-SK_78

description:
CONTROLS3: 78_controls_GPL18224.txt
Control experiment, DNA genotyping on DNA extracted from skin biopsy

source_name: DNA extracted from skin biopsy

value: skin biopsy


title: SD164-BL_81


title: ML012-SK_77

value: Luminal A


title: UPN727 cells, AIDA PL09 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL09 at baseline

source_name: UPN727 cells stimulated with AIDA_PL09_BL serum


title: UPN727 cells, AIDA PL08 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL08 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL08_M9 serum


title: MH047-BL_76

source_name: DNA extracted from whole blood

value: Luminal B, HER2+


title: 2_Cy3_49_Cy5

description: C57BL/6 mouse jejunum - animal 2 (0µ/kg TCDD) vs. animal 49 (1µg/kg TCDD)

value: Jejunal epithelium


title: UPN727 cells, AIDA PL08 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL08 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL08_M6 serum


title: 49_Cy3_2_Cy5

description: C57BL/6 mouse jejunum - animal 49 (1µ/kg TCDD) vs. animal 2 (0µg/kg TCDD)


title: ME029-BL_75

value: multifocal

value: whole blood


title: 42_Cy3_2_Cy5

description: C57BL/6 mouse jejunum - animal 42 (0.3µ/kg TCDD) vs. animal 2 (0µg/kg TCDD)

value: Female

value: TCDD


title: MD006-SK_73


title: MD052-BL_74


title: 2_Cy3_42_Cy5

description: C57BL/6 mouse jejunum - animal 2 (0µ/kg TCDD) vs. animal 42 (0.3µg/kg TCDD)

value: Vehicle

value: ug/kg


title: MB032-SK_72

value: female


title: UPN727 cells, AIDA PL08 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL08 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL08_M3 serum

value: 3 month into treatment


title: MA018-SK_71


title: UPN727 cells, AIDA PL08 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL08 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL08_M1 serum


title: LH045-SK_70


title: LF042-BL_69


title: 34_Cy3_2_Cy5

description: C57BL/6 mouse jejunum - animal 34 (0.1µ/kg TCDD) vs. animal 2 (0µg/kg TCDD)


title: KS150-BL_68


title: 2_Cy3_34_Cy5

description: C57BL/6 mouse jejunum - animal 2 (0µ/kg TCDD) vs. animal 34 (0.1µg/kg TCDD)


title: 26_Cy3_2_Cy5

description: C57BL/6 mouse jejunum - animal 26 (0.03µ/kg TCDD) vs. animal 2 (0µg/kg TCDD)


title: KM159-BL_67


title: UPN727 cells, AIDA PL07 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL07 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL07_M6 serum

value: 6 month into treatment


title: UPN727 cells, AIDA PL07 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL07 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL07_M3 serum

value: UPN727 cells


title: UPN727 cells, AIDA PL08 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL08 at baseline

source_name: UPN727 cells stimulated with AIDA_PL08_BL serum

value: at baseline


title: UPN727 cells, AIDA PL07 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL07 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL07_M9 serum

value: 9 month into treatment


title: UPN727 cells, AIDA PL07 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL07 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL07_M1 serum

value: 1 month into treatment


title: 2_Cy3_18_Cy5

description: C57BL/6 mouse jejunum - animal 2 (0µ/kg TCDD) vs. animal 18 (0.01µg/kg TCDD)

source_name: Mouse jejunal epithelium, dosed every 4 days for 28 days with TCDD


title: KK151-BL_66

description:
CONTROLS3: 78_controls_GPL18224.txt
Control experiment, DNA genotyping on DNA extracted from whole blood

value: unifocal


title: 18_Cy3_2_Cy5

description: C57BL/6 mouse jejunum - animal 18 (0.01µ/kg TCDD) vs. animal 2 (0µg/kg TCDD)


title: SJW/AOM tumor 2

city: bethesda

first: yan

last: cai

state: maryland

address: 9000 rockville pike

department: NCI

institute: NIH

hyb_protocol: Blocking buffer and Hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: mages were quantified using Agilent Feature Extraction Software. Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

source_name: Tumor area of mouse small intestine with SJW diet and AOM injection

label_protocol: cDNA was generated with SuperScript® Indirect cDNA Labeling Core kit (Invitrogen) and labeled with Cy3/Cy5-mono reactive dye pack (GE healthcare), and the labeled cDNA was purified with Qiagen kit (#28004)

extract_protocol: Total RNA extracted using Trizol from liver and purified with QIAGEN kit (#74104) following manufacturer's instructions.

treatment_protocol: Collected tissues from fresh small intestines

value: SJW diet and AOM injection

value: Male

value: Tumor area of mouse small intestine

source_name: Ambion Mouse Assorted Total RNA

value: Swiss Webster

value: brain, embryo (10–12 days), heart, kidney, liver, lung, ovary, spleen, testicle, and thymus


title: SJW/AOM tumor 1


title: UPN727 cells, AIDA PL07 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL07 at baseline

source_name: UPN727 cells stimulated with AIDA_PL07_BL serum


title: SJW/AOM tumor 3


title: 2_Cy3_26_Cy5

description: C57BL/6 mouse jejunum - animal 2 (0µ/kg TCDD) vs. animal 26 (0.03µg/kg TCDD)

value: Jejunal epithelium

value: Female


title: Con/AOM tumor 3

source_name: Tumor area of mouse small intestine with control diet and AOM injection

value: control diet and AOM injection


title: UPN727 cells, AIDA PL06 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL06 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL06_M1 serum


title: UPN727 cells, AIDA PL06 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL06 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL06_M3 serum


title: IP008-SK_64

description:
CONTROLS3: 78_controls_GPL18224.txt
Control experiment, DNA genotyping on DNA extracted from skin biopsy

source_name: DNA extracted from skin biopsy

value: Luminal A

value: multifocal

value: skin biopsy


title: Con/AOM tumor 2


title: UPN727 cells, AIDA PL06 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL06 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL06_M6 serum

value: 6 month into treatment


title: Con/AOM tumor 1


title: UPN727 cells, AIDA PL06 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL06 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL06_M9 serum_OL

value: UPN727 cells


title: HZK162-BL_63

source_name: DNA extracted from whole blood

value: female

value: Luminal B, HER2-

value: whole blood


title: SJW/AOM non-tumor 3

source_name: Non-tumor area of mouse small intestine with SJW diet and AOM injection

value: Non-tumor area of mouse small intestine


title: GS166-BL_62

value: Triple negative

value: unifocal


title: GS011-SK_61


title: UPN727 cells, AIDA PL06 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL06 at baseline

source_name: UPN727 cells stimulated with AIDA_PL06_BL serum

value: at baseline


title: GGB040-SK_60


title: GC147-SK_59


title: JP149-BL_65


title: EW155-BL_58


title: SJW/AOM non-tumor 2

value: SJW diet and AOM injection

value: Male

value: Swiss Webster


title: EJ001-BL_57


title: EG163-BL_56

value: multifocal???


title: UPN727 cells, AIDA PL05 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL05 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL05_M3 serum

value: 3 month into treatment


title: UPN727 cells, AIDA PL05 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL05 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL05_M6 serum


title: UPN727 cells, AIDA PL05 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL05 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL05_M9 serum

value: 9 month into treatment


title: SJW/Sal non-tumor 2

source_name: Non-tumor area of mouse small intestine with SJW diet and saline injection

value: SJW diet and saline injection

value: brain, embryo (10–12 days), heart, kidney, liver, lung, ovary, spleen, testicle, and thymus


title: UPN727 cells, AIDA PL04 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL04 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL04_M6 serum

value: 6 month into treatment


title: UPN727 cells, AIDA PL05 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL05 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL05_M1 serum

value: UPN727 cells

value: 1 month into treatment


title: Con/AOM non-tumor 3

source_name: Non-tumor area of mouse small intestine with control diet and AOM injection

value: control diet and AOM injection

source_name: Ambion Mouse Assorted Total RNA


title: Con/Sal non-tumor 3

source_name: Non-tumor area of mouse small intestine with control diet and saline injection

value: control diet and saline injection


title: SJW/AOM non-tumor 1

value: Non-tumor area of mouse small intestine


title: UPN727 cells, AIDA PL05 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL05 at baseline

source_name: UPN727 cells stimulated with AIDA_PL05_BL serum


title: UPN727 cells, AIDA PL04 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL04 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL04_M9 serum


title: BK008-SK_55

source_name: DNA extracted from skin biopsy

value: female

value: Luminal B, HER2+

value: skin biopsy


title: BD038-SK_54

value: Luminal A

value: multifocal


title: SJW/Sal non-tumor 1

value: Male

value: Swiss Webster


title: AW020-BL_53

description:
CONTROLS3: 78_controls_GPL18224.txt
Control experiment, DNA genotyping on DNA extracted from whole blood

value: whole blood


title: SJW/Sal non-tumor 3


title: Con/AOM non-tumor 1


title: Con/AOM non-tumor 2


title: AH028-BL_52

value: Luminal B, HER2-


title: Con/Sal non-tumor 1


title: Con/Sal non-tumor 2


title: AE031-SK_51


title: UPN727 cells, AIDA PL04 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL04 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL04_M3 serum

value: 3 month into treatment


title: UPN727 cells, AIDA PL04 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL04 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL04_M1 serum


title: UPN727 cells, AIDA PL03 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL03 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL03_M3 serum


title: UPN727 cells, AIDA PL03 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL03 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL03_M6 serum


title: 143DMG-SK_49

value: unifocal


title: 142AK-SK_48


title: 141BB-SK_47


title: ACV037-SK_50


title: 139MD-SK_46


title: 138BM-S-SK_45


title: 130JT-SK_42


title: UPN727 cells, AIDA PL03 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL03 at baseline

source_name: UPN727 cells stimulated with AIDA_PL03_BL serum

value: at baseline


title: UPN727 cells, AIDA PL03 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL03 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL03_M1 serum

value: UPN727 cells


title: 131SD-SK_43

description:
CONTROLS3: 78_controls_GPL18224.txt
Control experiment, DNA genotyping on DNA extracted from skin biopsy


title: 129EB-SK_41


title: UPN727 cells, AIDA PL04 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL04 at baseline

source_name: UPN727 cells stimulated with AIDA_PL04_BL serum


title: 133ML-SK_44


title: 099OLZ-SK_39

value: Triple negative


title: 100AW-BL_40

source_name: DNA extracted from whole blood


title: 095ESZ-BL_37


title: UPN727 cells, AIDA PL02 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL02 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL02_M3 serum


title: UPN727 cells, AIDA PL03 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL03 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL03_M9 serum

value: 9 month into treatment


title: 089SD-BL_36


title: UPN727 cells, AIDA PL01 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL01 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL01_M6 serum

value: 6 month into treatment


title: UPN727 cells, AIDA PL02 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL02 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL02_M6 serum


title: UPN727 cells, AIDA PL01 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL01 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL01_M1 serum

value: 1 month into treatment


title: UPN727 cells, AIDA PL01 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL01 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL01_M3 serum


title: 086AFT-BL_35

value: female


title: UPN727 cells, AIDA PL02 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL02 at baseline

source_name: UPN727 cells stimulated with AIDA_PL02_BL serum


title: UPN727 cells, AIDA PL02 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL02 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL02_M1 serum


title: UPN727 cells, AIDA PL01 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL01 at baseline

source_name: UPN727 cells stimulated with AIDA_PL01_BL serum


title: UPN727 cells, AIDA PL01 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL01 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL01_M9 serum


title: 085AS-BL_34

description:
CONTROLS3: 78_controls_GPL18224.txt
Control experiment, DNA genotyping on DNA extracted from whole blood


title: 098WC-BL_38


title: UPN727 cells, AIDA AK22 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK22 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK22_M6 serum


title: UPN727 cells, AIDA AK22 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK22 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK22_M3 serum


title: Hippocampal homogenates at 4month, biological rep2

city: Edinburgh

first: Barry

middle: W

last: McColl

address: 49 Little France Crescent

department: Centre for Discovery Brain Sciences

country: United Kingdom

institute: University of Edinburgh

description: Gene expression data from hippocampal homogenates of 4 month old mice

hyb_protocol: Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C to the Affymetrix HT_MG-430_PM-16 plate array in the Gene Titan using the Affymetrix standard protocols.

scan_protocol: GeneChips were scanned using the Gene Titan Multi-channel  instrument from Affymetrix.

data_processing: The data were analyzed with Affymetric Expression Console built-in Robust Multiarray Averaging (RMA) method using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Hippocampal homogenates at 4 month of age

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: C57BL/6J mice maintained under standard conditions.

extract_protocol: Rneasy Plus Micro Kit (isolated microglia) and Rneasy Midi Kit (regional homogenates) extraction of total RNA was performed according to the manufacturer's instructions.

value: brain

tag: genotype

tag: age


title: UPN727 cells, AIDA AK22 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK22 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK22_M1 serum


title: UPN727 cells, AIDA AK22 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK22 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK22_M9 serum


title: UPN727 cells, AIDA PL02 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient PL02 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_PL02_M9 serum


title: Cerebellar homogenates at 4month, biological rep2

description: Gene expression data from cerebellar homogenates of 4 month old mice

source_name: Cerebellar homogenates at 4 month of age


title: 081BS-BL_33

source_name: DNA extracted from whole blood


title: Hippocampal homogenates at 4month, biological rep1


title: UPN727 cells, AIDA AK22 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK22 at baseline

source_name: UPN727 cells stimulated with AIDA_AK22_BL serum


title: Cortical homogenates at 4month, biological rep1

description: Gene expression data from cortical homogenates of 4 month old mice

source_name: Cortical homogenates at 4 month of age


title: 078AW-BL_32

value: Luminal B, HER2+


title: Striatal homogenates at 4month, biological rep2

description: Gene expression data from striatal homogenates of 4 month old mice

source_name: Striatal homogenates at 4 month of age


title: Striatal homogenates at 4month, biological rep1


title: UPN727 cells, AIDA AK21 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK21 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK21_M6 serum


title: Cortical homogenates at 4month, biological rep2


title: 077EP-BL_31


title: UPN727 cells, AIDA AK21 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK21 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK21_M3 serum


title: 071ZB-BL_29


title: 075JS-BL_30


title: 070ZNK-BL_28


title: 065AS-BL_27


title: 062BI-BL_25

value: Luminal A


title: UPN727 cells, AIDA AK21 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK21 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK21_M9 serum


title: 061AS-BL_24


title: UPN727 cells, AIDA AK21 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK21 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK21_M1 serum


title: UPN727 cells, AIDA AK20 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK20 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK20_M6 serum


title: UPN727 cells, AIDA AK20 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK20 at baseline

source_name: UPN727 cells stimulated with AIDA_AK20_BL serum


title: UPN727 cells, AIDA AK20 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK20 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK20_M9 serum


title: Striatal microglia at 4month, biological rep3

description: Gene expression data from striatal microglia of 4 month old mice

source_name: Microglia extracted from striatum at 4 month of age


title: Hippocampal microglia at 4month, biological rep1

description: Gene expression data from hippocampal microglia of 4 month old mice

source_name: Microglia extracted from hippocampus at 4 month of age


title: 053KS-BL_22

description:
CONTROLS3: 78_controls_GPL18224.txt
Control experiment, DNA genotyping on DNA extracted from whole blood

value: DCIS HG

value: DCIS multifocal


title: UPN727 cells, AIDA AK20 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK20 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK20_M3 serum


title: Hippocampal microglia at 4month, biological rep4


title: UPN727 cells, AIDA AK19 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK19 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK19_M3 serum


title: 054MJ-BL_23


title: 063JB-BL_26

value: multifocal


title: Hippocampal microglia at 4month, biological rep3


title: UPN727 cells, AIDA AK21 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK21 at baseline

source_name: UPN727 cells stimulated with AIDA_AK21_BL serum


title: Hippocampal microglia at 4month, biological rep2


title: Striatal microglia at 4month, biological rep4


title: Cortical microglia at 4month, biological rep3

description: Gene expression data from cortical microglia of 4 month old mice

source_name: Microglia extracted from cortex at 4 month of age


title: Striatal microglia at 4month, biological rep1


title: Striatal microglia at 4month, biological rep2


title: 049ASZ-BL_21

source_name: DNA extracted from whole blood

value: whole blood


title: UPN727 cells, AIDA AK19 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK19 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK19_M6 serum


title: UPN727 cells, AIDA AK20 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK20 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK20_M1 serum


title: Cerebellar homogenates at 4month, biological rep1

description: Gene expression data from cerebellar homogenates of 4 month old mice

source_name: Cerebellar homogenates at 4 month of age


title: Cortical microglia at 4month, biological rep4


title: 044JD-BL_20

value: Luminal B, HER2-


title: 043WB-BL_19


title: 026MS-BL_17


title: 024MZ-BL_15


title: 025JT-BL_16


title: 021MB-BL_14


title: 016JS-BL_12


title: 017KM-SK_13

description:
CONTROLS3: 78_controls_GPL18224.txt
Control experiment, DNA genotyping on DNA extracted from skin biopsy

source_name: DNA extracted from skin biopsy

value: skin biopsy


title: UPN727 cells, AIDA AK19 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK19 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK19_M9 serum


title: 013WS-BL_11


title: 012MC-BL_10

value: unifocal


title: Cortical microglia at 4month, biological rep1


title: Cortical microglia at 4month, biological rep2


title: UPN727 cells, AIDA AK19 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK19 at baseline

source_name: UPN727 cells stimulated with AIDA_AK19_BL serum

value: at baseline


title: 037MC-BL_18


title: UPN727 cells, AIDA AK19 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK19 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK19_M1 serum

value: UPN727 cells


title: UPN727 cells, AIDA AK18 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK18 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK18_M3 serum

value: 3 month into treatment


title: Cerebellar microglia at 4month, biological rep3

description: Gene expression data from cerebellar microglia of 4 month old mice

source_name: Microglia extracted from cerebellum at 4 month of age


title: UPN727 cells, AIDA AK17 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK17 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK17_M9 serum

value: 9 month into treatment


title: UPN727 cells, AIDA AK18 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK18 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK18_M1 serum


title: UPN727 cells, AIDA AK18 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK18 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK18_M6 serum

value: 6 month into treatment


title: UPN727 cells, AIDA AK18 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK18 at baseline

source_name: UPN727 cells stimulated with AIDA_AK18_BL serum


title: UPN727 cells, AIDA AK17 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK17 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK17_M1 serum

value: 1 month into treatment


title: UPN727 cells, AIDA AK17 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK17 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK17_M3 serum


title: Cerebellar microglia at 4month, biological rep4


title: UPN727 cells, AIDA AK16 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK16 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK16_M9 serum


title: UPN727 cells, AIDA AK18 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK18 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK18_M9 serum


title: Cerebellar microglia at 4month, biological rep1


title: 011BM-BL_9

description:
CONTROLS3: 78_controls_GPL18224.txt
Control experiment, DNA genotyping on DNA extracted from whole blood

source_name: DNA extracted from whole blood

value: female


title: UPN727 cells, AIDA AK17 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK17 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK17_M6 serum


title: Cerebellar microglia at 4month, biological rep2

value: brain


title: UPN727 cells, AIDA AK17 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK17 at baseline

source_name: UPN727 cells stimulated with AIDA_AK17_BL serum


title: UPN727 cells, AIDA AK16 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK16 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK16_M6 serum


title: 006MK-SK_8

description:
CONTROLS3: 78_controls_GPL18224.txt
Control experiment, DNA genotyping on DNA extracted from skin biopsy

source_name: DNA extracted from skin biopsy


title: ZL152-VB2-M_1709

description:
uninvolved margin in the immediate vicinity of the mammilla
ZL152-VB2-M

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

label_protocol: starndard protocol

tag: age at cancer diagnosis (yrs)

value: Luminal B, HER2+


title: RH117A3_2_6

description:
TUMORS2: 2_primaryTumors_GPL13135.txt
Genotyping on DNA extracted from a primary tumor

source_name: DNA extracted from primary tumor

value: primary tumor


title: ZL152-UM-IU_1707

description:
uninvolved margin of breast carcinoma
ZL152-UM-IU


title: ZL152-VB1-M_1708

description:
uninvolved margin in the immediate vicinity of the mammilla
ZL152-VB1-M


title: KS141A3_2_5

value: Triple negative


title: ZL152-UM-IL2_1706

description:
uninvolved margin of breast carcinoma
ZL152-UM-IL2


title: ZL152-UM-IL1_1705

description:
uninvolved margin of breast carcinoma
ZL152-UM-IL1


title: RH117K_june2012_583

description:
uninvolved margin of breast carcinoma
RH117K_2


title: ZL152-UM-IL_1704

description:
uninvolved margin of breast carcinoma
ZL152-UM-IL


title: UPN727 cells, AIDA AK15 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK15 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK15_M9 serum


title: RH117B_june2012_581

description:
uninvolved margin of breast carcinoma
RH117B_2


title: UPN727 cells, AIDA AK16 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK16 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK16_M3 serum


title: UPN727 cells, AIDA AK16 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK16 at baseline

source_name: UPN727 cells stimulated with AIDA_AK16_BL serum


title: UPN727 cells, AIDA AK16 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK16 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK16_M1 serum


title: ML012-UM98_509

description:
uninvolved margin of breast carcinoma
ML012-UM98

value: Luminal A


title: UPN727 cells, AIDA AK15 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK15 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK15_M6 serum


title: ML012-UM99_copy_511

description:
uninvolved margin of breast carcinoma
ML012-UM99_2

value: multifocal


title: UPN727 cells, AIDA AK15 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK15 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK15_M3 serum


title: ZL152-UM-EU2_1703

description:
uninvolved margin of breast carcinoma
ZL152-UM-EU2


title: ML012-UM2_508

description:
uninvolved margin of breast carcinoma
ML012-UM2


title: ZL152-UM-EU1_1702

description:
uninvolved margin of breast carcinoma
ZL152-UM-EU1


title: ZL152-UM-EU_1701

description:
uninvolved margin of breast carcinoma
ZL152-UM-EU


title: ZL152-UM-EL2_1700

description:
uninvolved margin of breast carcinoma
ZL152-UM-EL2


title: ML012-UM1_507

description:
uninvolved margin of breast carcinoma
ML012-UM1


title: KS141K_2_7

description:
CONTROLS2: 2_controls_GPL13135.txt
Control experiment, DNA genotyping on DNA extracted from whole blood

value: whole blood


title: ZL152-UM-EL1_1699

description:
uninvolved margin of breast carcinoma
ZL152-UM-EL1


title: KS141B_june2012_455

description:
uninvolved margin of breast carcinoma
KS141B_2


title: 023GC-SK_6

description:
CONTROLS2: 2_controls_GPL13135.txt
Control experiment, DNA genotyping on DNA extracted from skin biopsy

value: mulifocal


title: ZL152-UM-EL_1698

description:
uninvolved margin of breast carcinoma
ZL152-UM-EL


title: IP008-UM3_405

description:
uninvolved margin of breast carcinoma
IP008-UM3


title: WK007-UM99_1695

description:
uninvolved margin of breast carcinoma
WK007-UM99

value: Luminal B, HER2-


title: IP008-UM2_june2012_404

description:
uninvolved margin of breast carcinoma
IP008-UM2_2


title: UPN727 cells, AIDA AK14 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK14 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK14_M3 serum


title: UPN727 cells, AIDA AK14 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK14 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK14_M6 serum


title: UPN727 cells, AIDA AK14 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK14 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK14_M9 serum


title: WK007-UM1_1694

description:
uninvolved margin of breast carcinoma
WK007-UM1

value: unifocal


title: IP008-UM1_402

description:
uninvolved margin of breast carcinoma
IP008-UM1


title: UPN727 cells, AIDA AK14 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK14 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK14_M1 serum


title: UV023-UM5_copy_1690

description:
uninvolved margin of breast carcinoma
UV023-UM5_2


title: HS006-UM1_393

description:
uninvolved margin of breast carcinoma
HS006-UM1


title: UPN727 cells, AIDA AK15 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK15 at baseline

source_name: UPN727 cells stimulated with AIDA_AK15_BL serum

value: at baseline


title: UV023-UM98_1691

description:
uninvolved margin of breast carcinoma
UV023-UM98


title: GS011-UM98_387

description:
uninvolved margin of breast carcinoma
GS011-UM98


title: UV023-UM3_1687

description:
uninvolved margin of breast carcinoma
UV023-UM3


title: UV023-UM4_1688

description:
uninvolved margin of breast carcinoma
UV023-UM4


title: UPN727 cells, AIDA AK13 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK13 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK13_M9 serum

value: UPN727 cells


title: UPN727 cells, AIDA AK13 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK13 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK13_M6 serum


title: UPN727 cells, AIDA AK15 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK15 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK15_M1 serum


title: UV023-UM2_1686

description:
uninvolved margin of breast carcinoma
UV023-UM2


title: UPN727 cells, AIDA AK13 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK13 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK13_M1 serum


title: GS011-UM1_385

description:
uninvolved margin of breast carcinoma
GS011-UM1

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


title: UPN727 cells, AIDA AK12 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK12 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK12_M9 serum


title: UPN727 cells, AIDA AK13 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK13 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK13_M3 serum

value: 3 month into treatment


title: UPN727 cells, AIDA AK13 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK13 at baseline

source_name: UPN727 cells stimulated with AIDA_AK13_BL serum


title: GS011-UM99_388

description:
uninvolved margin of breast carcinoma
GS011-UM99


title: 101ZM-VB_271

description:
uninvolved margin in the immediate vicinity of the mammilla
101ZM-VB


title: UV023-UM1_1685

description:
uninvolved margin of breast carcinoma
UV023-UM1


title: GS011-UM2_386

description:
uninvolved margin of breast carcinoma
GS011-UM2


title: 101ZM-UM-IL_269

description:
uninvolved margin of breast carcinoma
101ZM-UM-IL


title: UBM043-UM99_1680

description:
uninvolved margin of breast carcinoma
UBM043-UM99


title: 101ZM-UM-IU_270

description:
uninvolved margin of breast carcinoma
101ZM-UM-IU


title: UBM043-UM2_1678

description:
uninvolved margin of breast carcinoma
UBM043-UM2


title: 101ZM-UM-EU_268

description:
uninvolved margin of breast carcinoma
101ZM-UM-EU


title: UPN727 cells, AIDA AK14 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK14 at baseline

source_name: UPN727 cells stimulated with AIDA_AK14_BL serum


title: 101ZM-UM-EL_267

description:
uninvolved margin of breast carcinoma
101ZM-UM-EL


title: TP169-VB1-M_1673

description:
uninvolved margin in the immediate vicinity of the mammilla
TP169-VB1-M


title: TP169-VB2-M_1674

description:
uninvolved margin in the immediate vicinity of the mammilla
TP169-VB2-M


title: TP169-UM-IU2_1672

description:
uninvolved margin of breast carcinoma
TP169-UM-IU2


title: UPN727 cells, AIDA AK12 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK12 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK12_M6 serum


title: 100AW-VB_266

description:
uninvolved margin in the immediate vicinity of the mammilla
100AW-VB


title: UPN727 cells, AIDA AK11 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK11 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK11_M9 serum

value: 9 month into treatment


title: UPN727 cells, AIDA AK12 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK12 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK12_M3 serum


title: UPN727 cells, AIDA AK12 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK12 at baseline

source_name: UPN727 cells stimulated with AIDA_AK12_BL serum


title: UPN727 cells, AIDA AK11 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK11 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK11_M6 serum

value: 6 month into treatment


title: UPN727 cells, AIDA AK12 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK12 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK12_M1 serum

value: 1 month into treatment


title: UPN727 cells, AIDA AK11 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK11 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK11_M3 serum


title: UBM043-UM98_1679

description:
uninvolved margin of breast carcinoma
UBM043-UM98

value: female


title: 100AW-UM-IU_265

description:
uninvolved margin of breast carcinoma
100AW-UM-IU


title: TP169-UM-IU_1670

description:
uninvolved margin of breast carcinoma
TP169-UM-IU


title: 100AW-UM-IL_264

description:
uninvolved margin of breast carcinoma
100AW-UM-IL


title: UBM043-UM1_1677

description:
uninvolved margin of breast carcinoma
UBM043-UM1


title: 097MM-VB_261

description:
uninvolved margin in the immediate vicinity of the mammilla
097MM-VB


title: TP169-UM-IL2_1669

description:
uninvolved margin of breast carcinoma
TP169-UM-IL2


title: TP169-UM-IU1_1671

description:
uninvolved margin of breast carcinoma
TP169-UM-IU1


title: 100AW-UM-EU_263

description:
uninvolved margin of breast carcinoma
100AW-UM-EU


title: UPN727 cells, AIDA AK11 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK11 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK11_M1 serum


title: UPN727 cells, AIDA AK10 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK10 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK10_M9 serum


title: TP169-UM-IL_1667

description:
uninvolved margin of breast carcinoma
TP169-UM-IL


title: UPN727 cells, AIDA AK10 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK10 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK10_M6 serum


title: UPN727 cells, AIDA AK11 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK11 at baseline

source_name: UPN727 cells stimulated with AIDA_AK11_BL serum


title: TP169-UM-EU2_1666

description:
uninvolved margin of breast carcinoma
TP169-UM-EU2


title: 100AW-UM-EL_262

description:
uninvolved margin of breast carcinoma
100AW-UM-EL


title: C1_p53null_jnk2null

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software

data_processing: Data for both channels were Lowess-normalized and then the log(2) ratio was taken

source_name: Whole Mouse Reference RNA

extract_protocol: Total RNA isolated using Qiagen RNeasy Kit

tag: reference

value: common reference RNA sample for these experiments consisted of total RNA harvested from equal numbers of C57Bl6/J and 129 male and female Day1 pups

extract_protocol: Total RNA isolated using Qiagen Rneasy Kit

value: cell line

tag: genotype/variation

value: Trp53ko, Jnk2ko

tag: cell line origin

value: BALB/c


title: TP169-UM-IL1_1668

description:
uninvolved margin of breast carcinoma
TP169-UM-IL1

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

tag: gender


title: Strain_p53-/- jnk1+/+ jnk2+/+_7656_Van_Den_Berg

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125

value: mammary tumor

tag: strain


title: Strain_p53-/- jnk1+/+ jnk2+/+_3931_Van_Den_Berg


title: TP169-UM-EU1_1665

description:
uninvolved margin of breast carcinoma
TP169-UM-EU1


title: C2_MT_jnk2_Add_Back

value: Trp53ko, Jnk2ko (JNK2 added back using a GFP-JNK2 expression plasmid)

value: PyMT (MT) mammary tumor mouse model


title: UPN727 cells, AIDA AK10 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK10 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK10_M3 serum


title: C2_MT_jnk2null


title: 097MM-UM-IL_258

description:
uninvolved margin of breast carcinoma
097MM-UM-IL

value: Luminal A


title: Strain_p53-/- jnk1+/+ jnk2+/+_3930_Van_Den_Berg


title: Strain_p53-/- jnk1+/+ jnk2+/+_173_Van_Den_Berg


title: C1_p53null_jnk2_Add_Back


title: Strain_p53-/- jnk1+/+ jnk2+/+_3933_Van_Den_Berg


title: UPN727 cells, AIDA AK10 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK10 at baseline

source_name: UPN727 cells stimulated with AIDA_AK10_BL serum


title: UPN727 cells, AIDA AK9 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK09 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK09_M6 serum


title: 096MSZ-UM-IU_255

description:
uninvolved margin of breast carcinoma
096MSZ-UM-IU

value: Luminal B, HER2-


title: 097MM-UM-EU_257

description:
uninvolved margin of breast carcinoma
097MM-UM-EU

value: unifocal


title: TP169-UM-EL_1663

description:
uninvolved margin of breast carcinoma
TP169-UM-EL


title: UPN727 cells, AIDA AK10 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK10 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK10_M1 serum


title: 096MSZ-UM-IL_254

description:
uninvolved margin of breast carcinoma
096MSZ-UM-IL


title: Strain_p53-/- jnk1+/+ jnk2-/-_9012_Van_Den_Berg


title: 097MM-UM-IU_259

description:
uninvolved margin of breast carcinoma
097MM-UM-IU


title: Strain_p53-/- jnk1+/+ jnk2+/+_3929_Van_Den_Berg


title: UPN727 cells, AIDA AK9 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK09 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK09_M1 serum


title: 096MSZ-VB_256

description:
uninvolved margin in the immediate vicinity of the mammilla
096MSZ-VB


title: 096MSZ-UM-EU_253

description:
uninvolved margin of breast carcinoma
096MSZ-UM-EU


title: SW030-UM3_1658

description:
uninvolved margin of breast carcinoma
SW030-UM3

value: multifocal


title: UPN727 cells, AIDA AK9 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK09 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK09_M9 serum

value: UPN727 cells


title: experiment 3: Ezh2 post-rescue condition, replicate 2

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

hyb_protocol: Affymetrix GeneChip Mouse Exon 1.0 ST Array were hybridized with 4,7 µg of labelled DNA according Affymetrix protocols, for 17h at 45°C and 60rpm

scan_protocol: An Affymetrix GCS3000 7G scanner was used to scan microarrays, following mouse exon array requirements and specifications

data_processing: Raw data were normalized with the RMA method available in the Bioconductor R package oligo and the pd.mogene.1.1.st.v1 annotation package. For rescue experiments, given the observed batch bias between the first and second replicates, the data were then batch-corrected using a linear model (limma R package).

source_name: C2 iMEFs

label_protocol: 100 ng of total RNA was used to prepare biotinilated DNA, according Affymetrix recomandations (http://media.affymetrix.com/support/downloads/manuals/wt_expressionkit_manual.pdf). Whole transcript targets were produced using the Ambion WT kit and the Affymetrix kit (The Affymetrix GeneChip WT Terminal Labeling Kit) to fragment and labelled DNA.

growth_protocol: Sample 1 to 4: mES cells grown in DMEM medium supplemented with 15% FCS, 100 mM non essential amino acids, 0.1 mM 2-mercaptoethanol, 1 mM L-Glutamine and 103 U/ul leukemia inhibitory factor (LIF).Sample 5 to 24: iMEF cells grown in DMEM medium supplemented with 10% FCS, 100 mM non essential amino acids, 1 mM L-Glutamine.

treatment_protocol: Cells were treated with vehicle (EtOH) or Tamoxifen.

tag: cell type

value: iMEFs

value: Ezh2 post-rescue


title: Strain_p53-/- jnk1+/+ jnk2-/-_8967_Van_Den_Berg


title: Strain_p53-/- jnk1+/+ jnk2-/-_7970_Van_Den_Berg


title: TP169-UM-EU_1664

description:
uninvolved margin of breast carcinoma
TP169-UM-EU


title: Strain_p53-/- jnk1+/+ jnk2-/-_8979_Van_Den_Berg


title: experiment 3: Ezh2 pre-rescue condition, replicate 2

value: Ezh2 pre-rescue


title: experiment 3: Ezh2 post-rescue condition, replicate 1


title: UPN727 cells, AIDA AK9 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK09 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK09_M3 serum

value: 3 month into treatment


title: SW030-UM2_1657

description:
uninvolved margin of breast carcinoma
SW030-UM2

value: female


title: SK056-UM99_1653

description:
uninvolved margin of breast carcinoma
SK056-UM99

value: Triple negative


title: SW030-UM99_1660

description:
uninvolved margin of breast carcinoma
SW030-UM99


title: 095ESZ-UM-IL_249

description:
uninvolved margin of breast carcinoma
095ESZ-UM-IL


title: 096MSZ-UM-EL_252

description:
uninvolved margin of breast carcinoma
096MSZ-UM-EL


title: Strain_p53-/- jnk1+/+ jnk2-/-_8970_Van_Den_Berg

value: common reference RNA sample for these experiments consisted of total RNA harvested from equal numbers of C57Bl6/J and 129 male and female Day1 pups


title: SW030-UM98_1659

description:
uninvolved margin of breast carcinoma
SW030-UM98


title: 095ESZ-VB_251

description:
uninvolved margin in the immediate vicinity of the mammilla
095ESZ-VB


title: Strain_p53-/- jnk1+/+ jnk2-/-_9003_Van_Den_Berg

value: Trp53ko, Jnk2ko


title: Strain_p53-/- jnk1+/+ jnk2-/-_8971_Van_Den_Berg

value: BALB/c


title: 095ESZ-UM-IU_250

description:
uninvolved margin of breast carcinoma
095ESZ-UM-IU


title: SK056-UM4_1651

description:
uninvolved margin of breast carcinoma
SK056-UM4


title: 094MSZ-UM-IL_245

description:
uninvolved margin of breast carcinoma
094MSZ-UM-IL


title: 094MSZ-UM-EU_244

description:
uninvolved margin of breast carcinoma
094MSZ-UM-EU


title: 095ESZ-UM-EU_248

description:
uninvolved margin of breast carcinoma
095ESZ-UM-EU


title: UPN727 cells, AIDA AK9 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK09 at baseline

source_name: UPN727 cells stimulated with AIDA_AK09_BL serum

value: at baseline


title: UPN727 cells, AIDA AK08 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK08 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK08_M9 serum

value: 9 month into treatment


title: UPN727 cells, AIDA AK08 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK08 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK08_M6 serum

value: 6 month into treatment


title: SK056-UM3_1650

description:
uninvolved margin of breast carcinoma
SK056-UM3


title: 095ESZ-UM-EL_247

description:
uninvolved margin of breast carcinoma
095ESZ-UM-EL


title: experiment 3: Ezh2 pre-rescue condition, replicate 1


title: UPN727 cells, AIDA AK08 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK08 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK08_M3 serum


title: UPN727 cells, AIDA AK08 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK08 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK08_M1 serum

value: 1 month into treatment


title: UPN727 cells, AIDA AK07 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK07 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK07_M9 serum


title: UPN727 cells, AIDA AK08 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK08 at baseline

source_name: UPN727 cells stimulated with AIDA_AK08_BL serum


title: experiment 3: Ezh1 pre-rescue condition, replicate 1

value: Ezh1 pre-rescue


title: SD164-VB1-M_1642

description:
uninvolved margin in the immediate vicinity of the mammilla
SD164-VB1-M

value: Luminal B, HER2-

value: unifocal


title: SK056-UM2_1649

description:
uninvolved margin of breast carcinoma
SK056-UM2

value: multifocal


title: experiment 3: control replicate 2

value: iMEFs

value: Ezh2 WT


title: 094MSZ-VB_246

description:
uninvolved margin in the immediate vicinity of the mammilla
094MSZ-VB


title: experiment 3: Ezh2 -/-, replicate 2


title: SK056-UM1_1648

description:
uninvolved margin of breast carcinoma
SK056-UM1


title: SD164-VB2-M_1643

description:
uninvolved margin in the immediate vicinity of the mammilla
SD164-VB2-M


title: experiment 2: TAM-treated day 32 replicate 2

value: clone C2 32 days after Tamoxifen


title: experiment 3: Ezh1 pre-rescue condition, replicate 2


title: experiment 3: Ezh2 -/-, replicate 1


title: UPN727 cells, AIDA AK07 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK07 at baseline

source_name: UPN727 cells stimulated with AIDA_AK07_BL serum

value: UPN727 cells


title: UPN727 cells, AIDA AK07 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK07 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK07_M1 serum


title: UPN727 cells, AIDA AK07 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK07 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK07_M6 serum


title: experiment 2: TAM-treated day 32 replicate 1


title: SD164-UM-IU2-2_1641

description:
uninvolved margin of breast carcinoma
SD164-UM-IU2-2

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

value: female


title: 093AZ-UM-EL_239

description:
uninvolved margin of breast carcinoma
093AZ-UM-EL

value: Luminal B, HER2+


title: SD164-UM-IU2-1_1640

description:
uninvolved margin of breast carcinoma
SD164-UM-IU2-1


title: 093AZ-VB_242

description:
uninvolved margin in the immediate vicinity of the mammilla
093AZ-VB


title: 093AZ-UM-IU_241

description:
uninvolved margin of breast carcinoma
093AZ-UM-IU


title: Strain_p53-/- jnk1+/+ jnk2-/-_7968_Van_Den_Berg

source_name: Whole Mouse Reference RNA

value: common reference RNA sample for these experiments consisted of total RNA harvested from equal numbers of C57Bl6/J and 129 male and female Day1 pups

value: mammary tumor


title: 094MSZ-UM-EL_243

description:
uninvolved margin of breast carcinoma
094MSZ-UM-EL


title: experiment 3: control replicate 1


title: UPN727 cells, AIDA AK06 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK06 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK06_M9 serum


title: SD164-UM-IU_1639

description:
uninvolved margin of breast carcinoma
SD164-UM-IU


title: UPN727 cells, AIDA AK07 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK07 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK07_M3 serum

value: 3 month into treatment


title: SD164-UM-EU1_1636

description:
uninvolved margin of breast carcinoma
SD164-UM-EU1


title: 092SP-VB_238

description:
uninvolved margin in the immediate vicinity of the mammilla
092SP-VB


title: SD164-UM-EU2_1637

description:
uninvolved margin of breast carcinoma
SD164-UM-EU2


title: 092SP-UM-IU_237

description:
uninvolved margin of breast carcinoma
092SP-UM-IU


title: 093AZ-UM-EU_240

description:
uninvolved margin of breast carcinoma
093AZ-UM-EU


title: SD164-UM-EL1_1724

description:
uninvolved margin of breast carcinoma
SD164-UM-EL1


title: SD164-UM-EL2_1725

description:
uninvolved margin of breast carcinoma
SD164-UM-EL2


title: experiment 2: TAM-treated day 18 replicate 1

value: clone C2 18 days after Tamoxifen


title: experiment 2: TAM-treated day 5 replicate 1

value: clone C2 5 days after Tamoxifen


title: SD164-UM-IL_1638

description:
uninvolved margin of breast carcinoma
SD164-UM-IL


title: experiment 2: TAM-treated day 5 replicate 2


title: UPN727 cells, AIDA AK06 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK06 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK06_M3 serum


title: experiment 2: TAM-treated day 18 replicate 2

source_name: C2 iMEFs


title: SD164-UM-EU_1635

description:
uninvolved margin of breast carcinoma
SD164-UM-EU


title: 092SP-UM-EU_235

description:
uninvolved margin of breast carcinoma
092SP-UM-EU


title: 092SP-UM-IL_236

description:
uninvolved margin of breast carcinoma
092SP-UM-IL


title: experiment 2: vehicle-treated replicate 2

value: clone C2 vehicle-treated


title: SD164-UM-EL_1634

description:
uninvolved margin of breast carcinoma
SD164-UM-EL


title: UPN727 cells, AIDA AK06 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK06 at baseline

source_name: UPN727 cells stimulated with AIDA_AK06_BL serum

value: at baseline


title: UPN727 cells, AIDA AK06 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK06 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK06_M6 serum

value: 6 month into treatment


title: RK010-UM99_1631

description:
uninvolved margin of breast carcinoma
RK010-UM99


title: 092SP-UM-EL_234

description:
uninvolved margin of breast carcinoma
092SP-UM-EL

value: Luminal B, HER2-


title: experiment 2: vehicle-treated replicate 1


title: UPN727 cells, AIDA AK06 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK06 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK06_M1 serum

value: 1 month into treatment


title: UPN727 cells, AIDA AK05 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK05 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK05_M9 serum

value: 9 month into treatment


title: SecondaryLung_1

city: Nashville

first: Pengcheng

last: Lu

state: TN

address: 2200 Pierce Avenue

institute: Vanderbilt University

description: Secondary Lung M195-specific CD8+ T cells replicate #1

hyb_protocol: The Affymetrix GeneChip Mouse Gene 1.1 ST 16-array plate consists of 16 single Gene 1.1 ST arrays arranged into the standard 96 well plate format. Array hybridization, washing and scanning were performed on a GeneTitan Instrument according to the manufacturer’s recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument.

data_processing: Microarray data were processed using the oligo package implementation of rma in R software.

label: Biotin

source_name: Lung M195-specific CD8+ T cells sorted from lungs of HMPV-infected mice at day 7 post-challenge following intranasal immunization 14 days prior with M195 peptide-loaded bone marrow-derived DCs

label_protocol: The FL-Ovation cDNA Biotin Molecule V2 (NuGen) was used to fragment and label single-stranded cDNA targets for subsequent hybridization.

extract_protocol: Total RNA was isolated from sorted naive, spleen, lung, and secondary lung M195-specific CD8+ T cells using an RNeasy kit (QIAGEN) according to the manufacturer's instructions. On-column DNase digestion was performed and eluted RNA was quantified and checked for integrity using an Agilent 2100 Bioanalyzer. RNA was judged as suitable only if samples showed intact bands of 18S and 28S ribosomal RNA subunits, displayed no chromosomal peaks or RNA degradation products, and had a RNA integrity number (RIN) above 8.0.

treatment_protocol: sort protocol: HMPV (pathogenic clinical strain TN/94-49, genotype A2) was grown and titered in LLC-MK2 cells.  Mice were anesthetized with ketamine-xylazine and infected intranasally with 1x106 PFU of HMPV. Lymphocytes were isolated from spleens and lungs of infected animals. To obtain sufficient quantities of primary epitope-specific CD8+ T cells, on day 7 after HMPV infection the spleens and lungs from three mice were pooled together after processing. Samples were stained, sorted, and RNA purified on separate days in independent experiments. Cells were processed in ice-cold R10 media containing 10nM dasatinib to prevent activation and TCR signaling. Splenocytes were depleted of B cells by incubation on goat anti-mouse IgG and IgM coated (100μg/mL) T-75 flasks at 106 cells/mL for 1hr at 37C. Both lung and spleen cells were stained for viability, CD19, CD8, and M195-tetramers (both PE- and APC-conjugated). Surface/tetramer staining was performed for 1 hour at RT in PBS containing 1% FBS and 50nM dasatinib. Splenocytes were also stained for CD44 and CD62L to obtain control naïve cells. Dual-tetramer positive CD8+ T cells were sorted using a BD FACSAria III. Samples were maintained at 4C for the entirety of the sort and purity was 97–99% for all populations.

tag: strain background

value: 8-12 weeks

value: B6-Kb0Db0,B7.2 transgenic (B7tg) mice

tag: infected with

value: human metapneumovirus (HMPV)

tag: tissue

value: lung

value: Secondary Lung CD8+ T cells


title: 091MB-UM-IL_232

description:
uninvolved margin of breast carcinoma
091MB-UM-IL

value: female

tag: tumor grade

tag: tumor focality

value: unifocal


title: RK010-UM1_1630

description:
uninvolved margin of breast carcinoma
RK010-UM1

value: Luminal B, HER2+


title: 091MB-UM-EU_231

description:
uninvolved margin of breast carcinoma
091MB-UM-EU


title: UPN727 cells, AIDA AK05 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK05 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK05_M3 serum

tag: responder cells

value: UPN727 cells

tag: patient

value: 3 month into treatment


title: SecondaryLung_2

description: Secondary Lung M195-specific CD8+ T cells replicate #2


title: Lung_4

description: Lung M195-specific CD8+ T cells replicate #4

source_name: Lung M195-specific CD8+ T cells sorted from lungs of HMPV-infected mice at day 7 post-infection.

value: Lung CD8+ T cells


title: 091MB-UM-IU_233

description:
uninvolved margin of breast carcinoma
091MB-UM-IU


title: 090MP-VB_229

description:
uninvolved margin in the immediate vicinity of the mammilla
090MP-VB


title: Lung_3

description: Lung M195-specific CD8+ T cells replicate #3


title: RJ019-UM98_1626

description:
uninvolved margin of breast carcinoma
RJ019-UM98

value: Luminal A

value: multifocal


title: UPN727 cells, AIDA AK05 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK05 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK05_M1 serum

tag: timepoint


title: UPN727 cells, AIDA AK05 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK05 at baseline

source_name: UPN727 cells stimulated with AIDA_AK05_BL serum

value: at baseline


title: 090MP-UM-IU_228

description:
uninvolved margin of breast carcinoma
090MP-UM-IU

value: Luminal B, HER2-


title: UPN727 cells, AIDA AK05 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK05 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK05_M6 serum

value: 6 month into treatment


title: UPN727 cells, AIDA AK04 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK04 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK04_M9 serum

value: 9 month into treatment


title: PD005-UM99_1621

description:
uninvolved margin of breast carcinoma
PD005-UM99

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


title: RJ019-UM3_1625

description:
uninvolved margin of breast carcinoma
RJ019-UM3


title: PD005-UM2_1620

description:
uninvolved margin of breast carcinoma
PD005-UM2


title: Lung_2

description: Lung M195-specific CD8+ T cells replicate #2

value: 8-12 weeks


title: RJ019-UM99_1627

description:
uninvolved margin of breast carcinoma
RJ019-UM99


title: 090MP-UM-IL_227

description:
uninvolved margin of breast carcinoma
090MP-UM-IL


title: PD005-UM1_1619

description:
uninvolved margin of breast carcinoma
PD005-UM1


title: UPN727 cells, AIDA AK04 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK04 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK04_M6 serum


title: 091MB-UM-EL_230

description:
uninvolved margin of breast carcinoma
091MB-UM-EL


title: 090MP-UM-EU_226

description:
uninvolved margin of breast carcinoma
090MP-UM-EU


title: Lung_1

description: Lung M195-specific CD8+ T cells replicate #1

value: B6-Kb0Db0,B7.2 transgenic (B7tg) mice


title: UPN727 cells, AIDA AK04 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK04 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK04_M3 serum


title: Spleen_3

description: Spleen M195-specific CD8+ T cells replicate #3

source_name: Spleen M195-specific CD8+ T cells sorted from spleens of HMPV-infected mice at day 7 post-infection.

value: human metapneumovirus (HMPV)

value: spleen

value: Spleen CD8+ T cells


title: UPN727 cells, AIDA AK04 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK04 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK04_M1 serum

value: 1 month into treatment


title: PA002-UM99_1616

description:
uninvolved margin of breast carcinoma
PA002-UM99

value: female

value: unifocal


title: Spleen_1

description: Spleen M195-specific CD8+ T cells replicate #1


title: Naïve_3

description: Naïve CD44-CD62L+ CD8+ T cells replicate #3

source_name: Naïve CD44-CD62L+ CD8+ T cells sorted from spleens

value: Naïve CD8+ T cells


title: UPN727 cells, AIDA AK04 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK04 at baseline

source_name: UPN727 cells stimulated with AIDA_AK04_BL serum

value: UPN727 cells


title: UPN727 cells, AIDA AK03 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK03 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK03_M6 serum


title: Spleen_2

description: Spleen M195-specific CD8+ T cells replicate #2


title: UPN727 cells, AIDA AK03 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK03 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK03_M3 serum

value: 3 month into treatment


title: 089SD-UM-IU_223

description:
uninvolved margin of breast carcinoma
089SD-UM-IU

value: Triple negative


title: UPN727 cells, AIDA AK03 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK03 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK03_M9 serum


title: 090MP-UM-EL_225

description:
uninvolved margin of breast carcinoma
090MP-UM-EL


title: PA002-UM2_1614

description:
uninvolved margin of breast carcinoma
PA002-UM2


title: UPN727 cells, AIDA AK03 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK03 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK03_M1 serum


title: 089SD-VB_224

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


title: Naïve_2

description: Naïve CD44-CD62L+ CD8+ T cells replicate #2


title: 089SD-UM-EL_220

description:
uninvolved margin of breast carcinoma
089SD-UM-EL


title: NHB053-UM99_1610

description:
uninvolved margin of breast carcinoma
NHB053-UM99

value: Luminal A

value: multifocal


title: PA002-UM98_1615

description:
uninvolved margin of breast carcinoma
PA002-UM98

value: Luminal B, HER2-


title: Strain_p53-/- jnk1+/+ jnk2-/-_7969_Van_Den_Berg

source_name: Whole Mouse Reference RNA

value: common reference RNA sample for these experiments consisted of total RNA harvested from equal numbers of C57Bl6/J and 129 male and female Day1 pups

tag: tissue type

value: mammary tumor

value: Trp53ko, Jnk2ko

value: BALB/c


title: 088AW-VB_219

description:
uninvolved margin in the immediate vicinity of the mammilla
088AW-VB


title: NHB053-UM3_1608

description:
uninvolved margin of breast carcinoma
NHB053-UM3


title: 088AW-UM-IU_218

description:
uninvolved margin of breast carcinoma
088AW-UM-IU


title: 089SD-UM-IL_222

description:
uninvolved margin of breast carcinoma
089SD-UM-IL


title: NHB053-UM2_1607

description:
uninvolved margin of breast carcinoma
NHB053-UM2


title: 089SD-UM-EU_221

description:
uninvolved margin of breast carcinoma
089SD-UM-EU


title: PA002-UM1_1613

description:
uninvolved margin of breast carcinoma
PA002-UM1


title: Naïve_1

description: Naïve CD44-CD62L+ CD8+ T cells replicate #1

tag: age

value: 8-12 weeks

value: B6-Kb0Db0,B7.2 transgenic (B7tg) mice


title: CD630_WT2-Cy3_prdR2-Cy5

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

institute: Institut Pasteur

description: Biological replicate 2 of 2.

hyb_protocol: Samples were applied to microarrays enclosed in Agilent hybridization chambers for 17h at 65°C. After hybridization, slides were washed with Agilent washing buffers.

scan_protocol: Scanned on a GenePix Pro 6 dual-channel laser scanner.

data_processing: R limma package - Function used - Background correction : backgroundCorrect normexp ; Normalization : normalizeWithinArrays loess - Correlation of spot duplicate : duplicateCorrelation - Adjust to linear method : lmFit - Statistical analysis : eBayes, decideTests global BH.

organism: Clostridioides difficile

source_name: strain C630E grown 3.5h in TY with proline (reference)

label_protocol: 10 µg of total RNA and pdN6 primer were heated at 70°C for 5 min, then reversed transcribed at 42°C for 3 h in the presence of 800 U SuperScript III Reverse Transcriptase (Invitrogen), each dATP, dTTP, dGTP, dCTP. cDNA were then incubated with Cy5 or Cy3 dyes 1h at room temperature in the dark.

growth_protocol: C. difficile strain C630E and the prdR mutant were grown in TY supplemented with 30 mM L-proline to an OD600 of 0.5-0.7.

extract_protocol: Total RNA was extracted using the QIAgen RNeasy kit.

value: wild-type

tag: growth condition

value: Ty medium with proline

source_name: prdR mutant grown 4.25h in TY with proline

tag: background

value: prdR mutation


title: CD630_prdR1-Cy3_WT1-Cy5

description: Biological replicate 1 of 2.

tag: genotype/variation


title: UPN727 cells, AIDA AK01 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK01 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK01_M9 serum

value: 9 month into treatment


title: UPN727 cells, AIDA AK03 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK03 at baseline

source_name: UPN727 cells stimulated with AIDA_AK03_BL serum

value: at baseline


title: MCF7 Hotair +E2

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

description: SAMPLE 4

hyb_protocol: The arrays were processed at University of Chicago Genomics Core (Illinois) according to manufacturer’s protocol.

data_processing: The data were processed and normalised using Illumina GenomeStudio

growth_protocol: Cells were maintained in DMEM supplemented with 10% FBS

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. The quantity and quality of the isolated RNAs were determined using ND-1000 Spectrophotometer.

treatment_protocol: Lentiviral infected Ctrl or HOTAIR stable MCF7 cells were deprived for 3 days and then treated with ethanol or 1 nM E2 for 6h, cells were collected for RNA extraction.

tag: cell line

value: HOTAIR

tag: agent

value: 1 nM E2


title: 088AW-UM-EL_215

description:
uninvolved margin of breast carcinoma
088AW-UM-EL

tag: gender

value: female

tag: age at cancer diagnosis (yrs)

value: unifocal


title: UPN727 cells, AIDA AK02 at 9 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK02 9 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK02_M9 serum

value: UPN727 cells


title: NHB053-UM98_1609

description:
uninvolved margin of breast carcinoma
NHB053-UM98

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

value: Luminal A

value: multifocal


title: UPN727 cells, AIDA AK02 at 6 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK02 6 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK02_M6 serum

value: 6 month into treatment


title: UPN727 cells, AIDA AK02 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK02 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK02_M1 serum

value: 1 month into treatment


title: MW158-VB1-M_1601

description:
uninvolved margin in the immediate vicinity of the mammilla
MW158-VB1-M

value: Luminal B, HER2-