title: Ca9-22_HG-U133_Plus_2_rep1

description: Cells were maintained in α-Minimal Essential Medium (Wako, Tokyo, Japan) containing 10% fetal bovine serum (Japan Bio Serum, Tokyo, Japan) and 1% penicillin-streptomycin (Wako) at 37°C in an atmosphere containing 5% CO2.

tag: genotype

value: original (wild type)

tag: cell line


title: Patient 0105, hepatic tissue

status: Public on Aug 21 2016

type: RNA

city: shanghai

first: Mingjie

last: Wang

address: 197 Ruijin Er Road

country: China

institute: Ruijin Hospital,Shanghai Jiaotong University,School of Medicine

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0105, Scheuer score: G1S2

hyb_protocol: After fragmentation, 10 ug of RNA were hybridized for 16 hr at 45C on HG U133 Plus 2.0 array. Chips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: All raw data were manipulated in R version 3.1.3. Background adjusted and normalizaed using R package affy utilizing the RMA algorithm, missing values were evaluate using package impute, and batch effects were removed using package sva

molecule: total RNA

organism: Homo sapiens

source_name: Hepatic tissue from chronic hepatitis B patients 0105

extract_protocol: Total RNA extracted using Trizol following the manufacture's instructions.

tag: tissue

value: Hepatic tissue

tag: gender

value: Female

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: Patient 0104, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0104, Scheuer score: G1S3

source_name: Hepatic tissue from chronic hepatitis B patients 0104

value: Male


title: Patient 0108, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0108, Scheuer score: G1S1

source_name: Hepatic tissue from chronic hepatitis B patients 0108


title: CU6

city: Lund

first: Lao

middle: H

last: Saal

address: Scheelevägen 2, MV404B2

department: Department of Oncology and Pathology

country: Sweden

institute: Lund University

description: breast tumor

hyb_protocol: According to manufacturer (Agilent) specifications.

scan_protocol: According to manufacturer (Agilent) specifications, microarrays were scanned on an Agilent Microarray Scanner.

data_processing: The raw data was loaded into BioArray Software Environment (BASE) for processing. Background-corrected intensities (ch1: 'gMeanSignal' - 'gBGMedianSignal'; ch2: 'rMeanSignal' - 'rBGMedianSignal') were filtered for values with A>0.5 (A=log10(channel1 * channel2) / 2) and the data normalized using the Lowess algorithm.

source_name: Breast tumor CU6

extract_protocol: QIAGEN RNAeasy

tag: er

value: ER positive

tag: pr

value: PR positive

tag: her2 status

value: HER2 negative

tag: ki67 ihc

value: Ki67 high

tag: spf status

tag: ln status

value: LNode positive

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

value: PTEN ihc positive

tag: pten mutant

value: PTEN wildtype

tag: egfr ihc

value: EGFR ihc negative

tag: inpp4b mrna

value: INPP4B low

tag: pik3ca mutant

value: PIK3CA wildtype

tag: pik3ca aa

value: CK5 14 negative

tag: tp53 mutant

value: TP53 wildtype

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu normal

tag: hu basal

tag: hu her2

tag: hu best correlation

tag: hu subtype best

value: LumA

tag: ptensig good

tag: ptensig poor

tag: ptensig score

tag: ptensig class abs0.2

value: unclassified

source_name: Stratagene Universal Human Reference RNA

tag: sample type


title: CU69

description: breast tumor

source_name: Breast tumor CU69

label_protocol: According to manufacturer (Agilent) specifications.

tag: er

tag: pr

tag: her2 status

tag: ki67 ihc

tag: spf status

tag: ln status

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

tag: pten mutant

value: PTEN mutant

tag: egfr ihc

tag: inpp4b mrna

value: PIK3CA mutant

value: TP53 mutant

value: Basal

value: PTEN good

value: Stratagene Universal Human Reference RNA


title: CU62

description: breast tumor

source_name: Breast tumor CU62

value: ER positive

value: PR positive

value: HER2 negative

value: Ki67 low

value: LNode negative

value: INPP4B high

tag: pik3ca mutant

tag: pik3ca aa

tag: tp53 mutant

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu normal

tag: hu basal

tag: hu her2

tag: hu best correlation

tag: hu subtype best

tag: ptensig good

tag: ptensig poor

value: PTEN poor


title: CU67

description: breast tumor

source_name: Breast tumor CU67

tag: er

value: ER negative

tag: pr

value: PR negative

tag: her2 status

tag: ki67 ihc

tag: spf status

tag: ln status

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

value: PTEN ihc positive

value: PTEN wildtype

value: EGFR ihc positive

value: PIK3CA wildtype

value: CK5 14 negative

tag: ptensig score

tag: ptensig class abs0.2

tag: sample type


title: CU71

description: breast tumor

source_name: Breast tumor CU71

value: PTEN ihc negative

tag: pten mutant

tag: egfr ihc

value: EGFR ihc negative

tag: inpp4b mrna

value: INPP4B low

tag: pik3ca mutant

tag: pik3ca aa

value: CK5 14 positive

tag: tp53 mutant

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu normal

tag: hu basal

tag: hu her2

tag: hu best correlation

value: Normal


title: Patient 0102, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0102, Scheuer score: G1S1

source_name: Hepatic tissue from chronic hepatitis B patients 0102

tag: tissue

value: Hepatic tissue

tag: gender

value: Male

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: CU73

description: breast tumor

source_name: Breast tumor CU73

tag: er

tag: pr

value: PR positive

tag: her2 status

value: HER2 negative

tag: ki67 ihc

value: Ki67 high

tag: spf status

tag: ln status

value: LNode positive

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

tag: pten mutant

tag: egfr ihc

tag: inpp4b mrna

value: TP53 mutant

tag: hu subtype best

value: Basal

tag: ptensig good

tag: ptensig poor

tag: ptensig score

tag: ptensig class abs0.2

tag: sample type

value: Stratagene Universal Human Reference RNA


title: KLF10 knockout Replicate 1 of 3

status: Public on Aug 22 2016

city: Chiayi

first: Weng

middle: Ching

last: Chieh

address: No.168, Sec. 1, University Rd., Minhsiung

department: Department of Biomedical Sciences

country: Taiwan

institute: National Chung Cheng University

description: Biological replicate 1 of 3. Pdx-1Cre LSL-KrasG12D P53L/L compared with Pdx-1CreLSL-KrasG12D KLF10L/L P53L/L.

hyb_protocol: 0.3 μg of Cy-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to a Agilent SurePrint G3 Mouse GE 8×60K Microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3 and 625 nm for Cy5.

data_processing: Scanned images are analyzed by Feature extraction 10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature, substantially normalized the data by rank-consistency-filtering LOWESS method.

organism: Mus musculus

source_name: Pdx1-Cre LSL-KrasG12D P53L/L Cell Line

label_protocol: 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 or Cy5 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.

growth_protocol: Mouse primary PDAC cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum, nonessential amino acids, 100 units/ml penicillin and 100 μg/ml streptomycin at 37 °C in a 5% CO2 incubator.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: strain

tag: cell type

value: Pancreatic ductal adenocarcinoma

tag: genotype/variation

value: KLF10 wild type

source_name: Pdx-1Cre LSL-KrasG12D KLF10L/L P53L/L Cell Line

value: KLF10 knockout


title: Patient 0103, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0103, Scheuer score: G1S1

source_name: Hepatic tissue from chronic hepatitis B patients 0103

tag: tissue

tag: gender

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: Patient 0101, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0101, Scheuer score: G0S0

source_name: Hepatic tissue from chronic hepatitis B patients 0101

value: Female


title: CU619

description: breast tumor

source_name: Breast tumor CU619

tag: er

value: ER positive

tag: pr

tag: her2 status

value: HER2 positive

tag: ki67 ihc

value: Ki67 low

tag: spf status

tag: ln status

value: LNode negative

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

value: PTEN ihc positive

tag: pten mutant

value: PTEN wildtype

tag: egfr ihc

value: EGFR ihc negative

tag: pik3ca mutant

value: PIK3CA wildtype

tag: pik3ca aa

value: CK5 14 negative

tag: tp53 mutant

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu normal

tag: hu basal

tag: hu her2

tag: hu best correlation

value: unclassified


title: CU617

description: breast tumor

source_name: Breast tumor CU617

tag: er

tag: pr

value: PR positive

tag: her2 status

value: HER2 negative

tag: ki67 ihc

tag: spf status

tag: ln status

tag: inpp4b mrna

value: INPP4B low

value: TP53 wildtype

tag: hu subtype best

value: LumA

tag: ptensig good

tag: ptensig poor

tag: ptensig score

tag: ptensig class abs0.2

value: PTEN poor

tag: sample type


title: CU606

description: breast tumor

source_name: Breast tumor CU606

value: ER negative

value: PR negative

value: Ki67 high

value: LNode positive

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

tag: pten mutant

tag: egfr ihc

tag: pik3ca mutant

tag: pik3ca aa

tag: tp53 mutant

value: TP53 mutant

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu normal

value: Stratagene Universal Human Reference RNA


title: CU605

description: breast tumor

source_name: Breast tumor CU605

tag: er

tag: pr

tag: her2 status

tag: ki67 ihc

tag: spf status

tag: ln status

value: PTEN ihc negative

value: PTEN wildtype

value: EGFR ihc positive

tag: inpp4b mrna

value: INPP4B high

value: PIK3CA mutant

value: CK5 14 positive

tag: hu basal

tag: hu her2

tag: hu best correlation

tag: hu subtype best

value: Basal

tag: ptensig good

tag: ptensig poor


title: Patient 0099, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0099, Scheuer score: G2S2

source_name: Hepatic tissue from chronic hepatitis B patients 0099

tag: tissue

value: Hepatic tissue

tag: gender

value: Female

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: CU600

description: breast tumor

source_name: Breast tumor CU600

tag: er

value: ER positive

tag: pr

tag: her2 status

value: HER2 negative

value: Ki67 low

value: LNode negative

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

tag: pten mutant

tag: egfr ihc

tag: pik3ca mutant

value: PIK3CA wildtype

tag: pik3ca aa

tag: tp53 mutant

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu normal

tag: ptensig score

tag: ptensig class abs0.2

tag: sample type


title: Patient 0097, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0097, Scheuer score: G0S0

source_name: Hepatic tissue from chronic hepatitis B patients 0097

tag: tissue

tag: gender

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: Patient 0100, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0100, Scheuer score: G0S0

source_name: Hepatic tissue from chronic hepatitis B patients 0100

value: Male


title: CU614

description: breast tumor

source_name: Breast tumor CU614

tag: er

tag: pr

value: PR positive

tag: her2 status

tag: ki67 ihc

value: Ki67 high

tag: spf status

tag: ln status

value: LNode positive

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

value: PTEN ihc positive

tag: pten mutant

tag: egfr ihc

value: EGFR ihc negative

tag: inpp4b mrna

value: CK5 14 negative

value: TP53 wildtype

tag: hu basal

tag: hu her2

tag: hu best correlation

tag: hu subtype best

value: LumA

tag: ptensig good

tag: ptensig poor

value: unclassified

source_name: Stratagene Universal Human Reference RNA


title: CU603

description: breast tumor

source_name: Breast tumor CU603

tag: er

tag: pr

tag: her2 status

value: PTEN wildtype

value: INPP4B low

tag: pik3ca mutant

tag: pik3ca aa

tag: tp53 mutant

value: TP53 mutant

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu normal

value: LumB

tag: ptensig score

tag: ptensig class abs0.2

value: PTEN poor

tag: sample type

value: Stratagene Universal Human Reference RNA


title: Patient 0098, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0098, Scheuer score: G0S0

source_name: Hepatic tissue from chronic hepatitis B patients 0098

tag: tissue

value: Hepatic tissue

tag: gender

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: Patient 0089, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0089, Scheuer score: G1S0

source_name: Hepatic tissue from chronic hepatitis B patients 0089

value: Male


title: CU591

description: breast tumor

source_name: Breast tumor CU591

tag: er

value: ER positive

tag: pr

value: PR positive

tag: her2 status

value: HER2 negative

tag: ki67 ihc

tag: spf status

tag: ln status

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

value: PTEN ihc negative

tag: pten mutant

tag: egfr ihc

tag: inpp4b mrna

value: PIK3CA wildtype

tag: hu basal

tag: hu her2

tag: hu best correlation

tag: hu subtype best

tag: ptensig good

tag: ptensig poor


title: Patient 0094, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0094, Scheuer score: G2S2

source_name: Hepatic tissue from chronic hepatitis B patients 0094

tag: tissue

tag: gender

value: Female

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: CU597

description: breast tumor

source_name: Breast tumor CU597

tag: er

tag: pr

tag: her2 status

tag: ki67 ihc

value: Ki67 high

tag: spf status

tag: ln status

value: LNode positive

tag: grade

tag: tumor size

tag: age at dx

value: PTEN ihc positive

value: EGFR ihc negative

tag: pik3ca mutant

tag: pik3ca aa

value: CK5 14 negative

tag: tp53 mutant

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu normal

tag: ptensig score

tag: ptensig class abs0.2

tag: sample type


title: CU601

description: breast tumor

source_name: Breast tumor CU601

tag: er

tag: pr

tag: her2 status

value: HER2 positive

value: Ki67 low

value: LNode negative

tag: pten ihc

tag: pten mutant

value: PTEN wildtype

tag: egfr ihc

tag: inpp4b mrna

value: INPP4B low

value: TP53 wildtype

tag: hu basal

tag: hu her2

tag: hu best correlation

tag: hu subtype best

tag: ptensig good

tag: ptensig poor


title: CU604

description: breast tumor

source_name: Breast tumor CU604

value: ER positive

tag: ki67 ihc

tag: spf status

tag: ln status

tag: grade

tag: tumor size

tag: age at dx

tag: pik3ca mutant

value: PIK3CA mutant

tag: pik3ca aa

tag: tp53 mutant

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu normal

value: LumA

value: unclassified

value: Stratagene Universal Human Reference RNA


title: CU587

description: breast tumor

source_name: Breast tumor CU587

tag: er

tag: pr

value: PR positive

tag: her2 status

value: HER2 negative

tag: pten ihc

tag: pten mutant

tag: egfr ihc

tag: inpp4b mrna

value: PIK3CA wildtype

tag: hu basal

tag: hu her2

tag: hu best correlation

tag: ptensig score

tag: ptensig class abs0.2

value: PTEN good

tag: sample type


title: CU595

description: breast tumor

source_name: Breast tumor CU595

value: ER negative

value: PR negative

tag: ki67 ihc

tag: spf status

tag: ln status

tag: grade

tag: tumor size

tag: age at dx

value: PTEN ihc negative

value: PTEN mutant

value: EGFR ihc positive

tag: pik3ca mutant

tag: pik3ca aa

value: CK5 14 positive

tag: tp53 mutant

value: TP53 mutant

tag: stathmin ihc score

tag: hu subtype best

value: Basal

tag: ptensig good

tag: ptensig poor

value: PTEN poor


title: Patient 0093, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0093, Scheuer score: G0S0

source_name: Hepatic tissue from chronic hepatitis B patients 0093

tag: tissue

value: Hepatic tissue

tag: gender

value: Male

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: CU583

description: breast tumor

source_name: Breast tumor CU583

tag: er

tag: pr

tag: her2 status

value: HER2 positive

tag: ki67 ihc

tag: spf status

tag: ln status

tag: pten ihc

value: PTEN ihc positive

tag: pten mutant

value: PTEN wildtype

tag: egfr ihc

tag: inpp4b mrna

value: INPP4B low

value: PIK3CA mutant

value: TP53 wildtype

tag: hu lumb

tag: hu luma

tag: hu normal

tag: hu basal

tag: hu her2

tag: hu best correlation

tag: ptensig score

tag: ptensig class abs0.2

tag: sample type


title: Patient 0090, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0090, Scheuer score: G0S0

source_name: Hepatic tissue from chronic hepatitis B patients 0090

tag: tissue

tag: gender

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: Patient 0087, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0087, Scheuer score: G1S0

source_name: Hepatic tissue from chronic hepatitis B patients 0087


title: CU582

description: breast tumor

source_name: Breast tumor CU582

tag: er

value: ER positive

tag: pr

value: PR positive

tag: her2 status

tag: ki67 ihc

value: Ki67 high

tag: spf status

tag: ln status

value: LNode positive

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

tag: pten mutant

tag: egfr ihc

value: EGFR ihc negative

tag: pik3ca mutant

value: PIK3CA wildtype

tag: pik3ca aa

value: CK5 14 negative

tag: tp53 mutant

tag: stathmin ihc score

tag: hu subtype best

value: LumB

tag: ptensig good

tag: ptensig poor

value: Stratagene Universal Human Reference RNA


title: CU602

description: breast tumor

source_name: Breast tumor CU602

tag: er

value: ER negative

tag: pr

value: PR negative

tag: her2 status

value: HER2 negative

value: Ki67 low

value: LNode negative

value: PTEN ihc negative

value: EGFR ihc positive

tag: inpp4b mrna

value: INPP4B high

value: TP53 mutant

tag: hu lumb

tag: hu luma

tag: hu normal

tag: hu basal

tag: hu her2

tag: hu best correlation

value: Basal

tag: ptensig score

tag: ptensig class abs0.2

value: PTEN poor

tag: sample type


title: Patient 0096, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0096, Scheuer score: G4S2

source_name: Hepatic tissue from chronic hepatitis B patients 0096

tag: tissue

value: Hepatic tissue

tag: gender

value: Male

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: Patient 0088, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0088, Scheuer score: G2S2

source_name: Hepatic tissue from chronic hepatitis B patients 0088

value: Female


title: Patient 0095, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0095, Scheuer score: G0S1

source_name: Hepatic tissue from chronic hepatitis B patients 0095


title: Patient 0092, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0092, Scheuer score: G0S0

source_name: Hepatic tissue from chronic hepatitis B patients 0092


title: Patient 0091, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0091, Scheuer score: G0S1

source_name: Hepatic tissue from chronic hepatitis B patients 0091


title: CU581

description: breast tumor

source_name: Breast tumor CU581

tag: er

value: ER positive

tag: pr

tag: her2 status

tag: ki67 ihc

tag: spf status

tag: ln status

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

value: PTEN ihc positive

tag: pten mutant

value: PTEN wildtype

tag: egfr ihc

value: EGFR ihc negative

value: INPP4B low

tag: pik3ca mutant

value: PIK3CA wildtype

tag: pik3ca aa

value: CK5 14 negative

tag: tp53 mutant

value: TP53 wildtype

tag: stathmin ihc score

tag: hu subtype best

value: Normal

tag: ptensig good

tag: ptensig poor

value: PTEN good

source_name: Stratagene Universal Human Reference RNA


title: Patient 0086, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0086, Scheuer score: G4S4

source_name: Hepatic tissue from chronic hepatitis B patients 0086

tag: tissue

tag: gender

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: pp3_Control_0h_h

city: Zurich

first: Christian

middle: Andreas

last: Schaer

address: Raemistrasse 100

country: Switzerland

institute: University Hospital Zurich

description: Wild type embryonal fibroblasts (MEF) (=pp3)

hyb_protocol: After purification of amplified cRNA according to the QIAgen RNeasy purification protocol (QIAGEN) 825 ng of Cy3 and Cy5 labeled cRNA were competitively hybridized for 17 hours at 65° C in a hybridization oven (Agilent G2545A) set to 10 rpm in GEx Hybridization buffer HI-RPM according to the manufacturer's protocol (Agilent’s Two-Color Microarray-Based Gene Expression Analysis). Washing was performed according to the recommended protocol including the Stabilization and Drying Solution step.

scan_protocol: Array slides were XDR scanned at 5 mcm resolution on a Agilent Microarray High-Resolution C Scanner (G2505C) with 100% PMT and 10% for lower intensity.

data_processing:
Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software Version 10.7.3.1. Spot values were normalized using the default linear-lowess normalization. To identify differentially expressed features, calculated log10 ratio values (Cy5/Cy3) were imported into JMP Genomics 5.1 without further normalization and the built-in Basic Expression Workflow (ANOVA, LSMeans Differences) was performed.
We don't provide a Matrix Table as we imported the calculated and lowess-normalized log10 ratios of the Feature Extraction result text files directly into JMP Genomis 5.1 and performed the statistical analysis without further normalization.

label_protocol: Fluorescently labeled cRNA was generated from 500 ng total RNA with the Quick Amp Labeling Kit (Agilent) according to Agilent’s Two-Color Microarray-Based Gene Expression Analysis Protocol Version 5.7, March 2008 (Agilent publication number G4140-90050). In short, total RNA was reverse transcripted to cDNA using T7 Promotor Primer and MMLV-RT. Then cDNA was converted to cRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP.

extract_protocol: After washing and lysing the cells with Buffer RLT, total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Basel, Switzerland) according to the manufacturer’s instructions, including an on-column DNA digestion step (RNase-Free DNase Set; QIAGEN). To ensure that only high quality RNA (RIN >7.0) was used for gene expression analysis, each RNA sample was checked on a RNA Nanochip with a Bioanalyzer 2100 (Agilent Technologies, Basel, Switzerland). RNA was quantified spectrophotometrically with a NanoDrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).

tag: cell line

tag: treatment

value: no treatment

tag: incubation time

tag: cell type

tag: genotype

value: wild type


title: Patient 0085, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0085, Scheuer score: G2S1

source_name: Hepatic tissue from chronic hepatitis B patients 0085


title: Patient 0084, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0084, Scheuer score: G0S1

source_name: Hepatic tissue from chronic hepatitis B patients 0084


title: CU52

description: breast tumor

source_name: Breast tumor CU52

tag: er

tag: pr

value: PR positive

tag: her2 status

value: HER2 negative

tag: ki67 ihc

value: Ki67 high

tag: spf status

tag: ln status

value: LNode positive

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

tag: pten mutant

tag: egfr ihc

tag: inpp4b mrna

value: INPP4B high

tag: pik3ca mutant

value: PIK3CA mutant

tag: pik3ca aa

tag: hu lumb

tag: hu luma

tag: hu normal

tag: hu basal

tag: hu her2

tag: hu best correlation

value: LumA

tag: ptensig score

tag: ptensig class abs0.2

tag: sample type

value: Stratagene Universal Human Reference RNA


title: pp3_Control_0h_e

tag: cell line

tag: treatment

tag: incubation time

tag: cell type

value: Wild type embryonal fibroblasts (MEF) (=pp3)

tag: genotype


title: CU56

description: breast tumor

source_name: Breast tumor CU56

tag: er

value: ER negative

tag: pr

tag: her2 status

tag: ki67 ihc

tag: spf status

tag: ln status

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

value: PTEN ihc negative

tag: pten mutant

value: PTEN wildtype

tag: egfr ihc

value: EGFR ihc negative

tag: inpp4b mrna

tag: tp53 mutant

value: TP53 mutant

tag: stathmin ihc score

tag: hu subtype best

value: Basal

tag: ptensig good

tag: ptensig poor

value: PTEN poor


title: CU580

description: breast tumor

source_name: Breast tumor CU580

tag: er

value: ER positive

tag: pr

value: HER2 positive

value: Ki67 low

value: LNode negative

value: PTEN ihc positive

value: INPP4B low

tag: pik3ca mutant

value: PIK3CA wildtype

tag: pik3ca aa

value: CK5 14 negative

tag: hu lumb

tag: hu luma

tag: hu normal

tag: hu basal

tag: hu her2

tag: hu best correlation

tag: ptensig score

tag: ptensig class abs0.2

tag: sample type


title: CU476

description: breast tumor

source_name: Breast tumor CU476

value: PR positive

tag: her2 status

value: HER2 negative

tag: ki67 ihc

value: Ki67 high

tag: spf status

tag: ln status

value: LNode positive

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

tag: pten mutant

tag: egfr ihc

tag: inpp4b mrna

value: INPP4B high

tag: tp53 mutant

value: TP53 wildtype

tag: stathmin ihc score

value: LumA

value: PTEN good

value: Stratagene Universal Human Reference RNA


title: pp3_Control_0h_f

tag: cell line

tag: treatment

value: no treatment

tag: incubation time

tag: cell type

value: Wild type embryonal fibroblasts (MEF) (=pp3)

tag: genotype

value: wild type


title: CU558

description: breast tumor

source_name: Breast tumor CU558

tag: er

value: ER positive

tag: pr

tag: her2 status

tag: ki67 ihc

value: PTEN wildtype

value: EGFR ihc negative

tag: pik3ca mutant

tag: pik3ca aa

tag: hu lumb

tag: hu luma

tag: hu normal

tag: hu basal

tag: hu her2

tag: hu best correlation

tag: hu subtype best

value: LumB

tag: ptensig good

tag: ptensig poor

tag: ptensig score

tag: ptensig class abs0.2

value: PTEN poor

tag: sample type


title: pp3_Control_0h_g

tag: cell line

tag: treatment

tag: incubation time

tag: cell type

tag: genotype


title: CU47

description: breast tumor

source_name: Breast tumor CU47

tag: er

tag: pr

value: PR positive

tag: her2 status

value: HER2 positive

tag: ki67 ihc

value: Ki67 low

tag: spf status

tag: ln status

value: LNode negative

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

value: PTEN ihc positive

tag: pten mutant

tag: egfr ihc

tag: inpp4b mrna

tag: pik3ca mutant

value: PIK3CA wildtype

tag: pik3ca aa

value: CK5 14 positive

tag: tp53 mutant

tag: stathmin ihc score

tag: hu lumb


title: CU478

description: breast tumor

source_name: Breast tumor CU478

tag: er

tag: pr

value: HER2 negative

value: INPP4B low

value: CK5 14 negative

value: TP53 mutant

tag: hu luma

tag: hu normal

tag: hu basal

tag: hu her2

tag: hu best correlation

tag: hu subtype best

tag: ptensig good

tag: ptensig poor

tag: ptensig score

tag: ptensig class abs0.2

value: unclassified

tag: sample type


title: Patient 0083, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0083, Scheuer score: G3S3

source_name: Hepatic tissue from chronic hepatitis B patients 0083

tag: tissue

value: Hepatic tissue

tag: gender

value: Male

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: CU472

description: breast tumor

source_name: Breast tumor CU472

tag: er

value: ER positive

tag: pr

tag: her2 status

tag: ki67 ihc

value: Ki67 high

tag: spf status

tag: ln status

value: LNode positive

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

tag: pten mutant

value: PTEN wildtype

tag: egfr ihc

value: EGFR ihc negative

tag: inpp4b mrna

tag: pik3ca mutant

tag: pik3ca aa

tag: tp53 mutant

value: TP53 wildtype

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

value: LumA

value: PTEN good

value: Stratagene Universal Human Reference RNA


title: CU482

description: breast tumor

source_name: Breast tumor CU482

tag: er

tag: pr

value: PR negative

tag: her2 status

value: PTEN ihc positive

value: PIK3CA wildtype

tag: hu normal

tag: hu basal

tag: hu her2

tag: hu best correlation

tag: hu subtype best

value: LumB

tag: ptensig good

tag: ptensig poor

tag: ptensig score

tag: ptensig class abs0.2

value: PTEN poor

tag: sample type


title: CU485

description: breast tumor

source_name: Breast tumor CU485

value: PR positive

value: HER2 negative

tag: ki67 ihc

value: Ki67 low

tag: spf status

tag: ln status

value: LNode negative

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

tag: pten mutant

tag: egfr ihc

tag: inpp4b mrna

value: INPP4B low

tag: pik3ca mutant

tag: pik3ca aa

tag: tp53 mutant


title: Patient 0082, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0082, Scheuer score: G3S3

source_name: Hepatic tissue from chronic hepatitis B patients 0082

tag: tissue

value: Hepatic tissue

tag: gender

value: Male

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: Patient 0081, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0081, Scheuer score: G3S3

source_name: Hepatic tissue from chronic hepatitis B patients 0081


title: pp3_Bortezomib_8h_d

tag: cell line

tag: treatment

value: no treatment

tag: incubation time

tag: cell type

value: Wild type embryonal fibroblasts (MEF) (=pp3)

tag: genotype

value: wild type

value: 100nM Bortezomib


title: pp3_Bortezomib_8h_a


title: CU552

description: breast tumor

source_name: Breast tumor CU552

tag: er

value: ER positive

tag: pr

tag: her2 status

tag: ki67 ihc

value: Ki67 high

tag: spf status

tag: ln status

value: LNode positive

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

tag: pten mutant

value: PTEN wildtype

value: EGFR ihc negative

value: CK5 14 negative

value: TP53 wildtype

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu normal

tag: hu basal

tag: hu her2

tag: hu best correlation

tag: hu subtype best

value: Normal

tag: ptensig good

tag: ptensig poor

tag: ptensig score

tag: ptensig class abs0.2

value: PTEN good

source_name: Stratagene Universal Human Reference RNA

tag: sample type


title: Patient 0080, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0080, Scheuer score: G3S3

source_name: Hepatic tissue from chronic hepatitis B patients 0080

tag: tissue

tag: gender

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: pp3_Bortezomib_8h_b

tag: cell line

tag: treatment

tag: incubation time

tag: cell type

tag: genotype


title: pp3_Bortezomib_8h_c


title: CU475

description: breast tumor

source_name: Breast tumor CU475

tag: er

value: ER negative

tag: pr

value: PR negative

tag: her2 status

value: HER2 positive

tag: ki67 ihc

tag: spf status

tag: ln status

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

value: PTEN ihc positive

tag: pten mutant

tag: egfr ihc

tag: inpp4b mrna

tag: pik3ca mutant

value: PIK3CA mutant

tag: pik3ca aa

tag: tp53 mutant

value: TP53 mutant

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu normal

tag: hu basal

tag: hu her2

tag: hu best correlation

tag: hu subtype best

value: unclassified

value: Stratagene Universal Human Reference RNA


title: CU477

description: breast tumor

source_name: Breast tumor CU477

tag: er

value: ER positive

tag: pr

value: PR positive

tag: her2 status

value: HER2 negative

tag: ki67 ihc

value: Ki67 low

tag: spf status

tag: ln status

value: LNode negative

tag: grade

tag: tumor size

value: INPP4B high

value: PIK3CA wildtype

value: LumA

tag: ptensig good

tag: ptensig poor

tag: ptensig score

tag: ptensig class abs0.2

tag: sample type


title: CU54

description: breast tumor

source_name: Breast tumor CU54

value: Ki67 high

value: LNode positive

tag: age at dx

tag: pten ihc

tag: pten mutant

value: PTEN wildtype

tag: egfr ihc

value: EGFR ihc negative

tag: inpp4b mrna

value: INPP4B low

tag: pik3ca mutant

tag: pik3ca aa

value: CK5 14 negative

tag: tp53 mutant

value: TP53 wildtype

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu normal

tag: hu basal

value: PTEN good


title: pp3_Control_0h_d

description: Wild type Mouse embryonal fibroblasts (MEF) (=pp3)

tag: hmox

value: positive

tag: treatment

value: no treatment

tag: incubation time

tag: cell type

tag: genotype

value: Wild type


title: pp3_Control_0h_a

value: Wild type Mouse embryonal fibroblasts (MEF) (=pp3)


title: CU432

description: breast tumor

source_name: Breast tumor CU432

tag: er

value: ER positive

tag: pr

value: PR negative

tag: her2 status

value: HER2 negative

tag: ki67 ihc

tag: spf status

tag: ln status

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

value: PTEN ihc negative

value: TP53 mutant

tag: hu her2

tag: hu best correlation

tag: hu subtype best

value: LumB

tag: ptensig good

tag: ptensig poor

tag: ptensig score

tag: ptensig class abs0.2

value: unclassified

tag: sample type

value: Stratagene Universal Human Reference RNA


title: CU417

description: breast tumor

source_name: Breast tumor CU417

tag: er

value: ER negative

tag: pr

value: Ki67 high

value: LNode positive

value: PTEN ihc positive

tag: pten mutant

value: PTEN wildtype

tag: egfr ihc

value: EGFR ihc positive

tag: inpp4b mrna

tag: pik3ca mutant

value: PIK3CA mutant

tag: pik3ca aa

value: CK5 14 positive

tag: tp53 mutant

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu normal

tag: hu basal

value: Basal

value: PTEN poor


title: CU447

description: breast tumor

source_name: Breast tumor CU447

value: PR negative

tag: her2 status

tag: ki67 ihc

value: Ki67 low

tag: spf status

tag: ln status

value: LNode negative

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

value: EGFR ihc negative

value: INPP4B high

value: PIK3CA wildtype

value: TP53 wildtype

tag: hu her2

tag: hu best correlation

tag: hu subtype best

tag: ptensig good

tag: ptensig poor

value: PTEN good


title: CU415

description: breast tumor

source_name: Breast tumor CU415

tag: er

value: ER positive

tag: pr

value: PR positive

value: HER2 negative

value: Ki67 high

tag: pten mutant

tag: egfr ihc

tag: inpp4b mrna

value: INPP4B low

tag: pik3ca mutant

tag: pik3ca aa

value: CK5 14 negative

tag: tp53 mutant

tag: stathmin ihc score

tag: hu lumb

value: Normal

tag: ptensig score

tag: ptensig class abs0.2

tag: sample type

value: Stratagene Universal Human Reference RNA


title: Patient 0078, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0078, Scheuer score: G1S1

source_name: Hepatic tissue from chronic hepatitis B patients 0078

tag: tissue

value: Hepatic tissue

tag: gender

value: Female

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: pp3_10mcM_8h_a

tag: hmox

value: positive

tag: treatment

value: no treatment

tag: incubation time

tag: cell type

value: Wild type Mouse embryonal fibroblasts (MEF) (=pp3)

tag: genotype

value: Wild type

value: 10mcM heme


title: Patient 0079, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0079, Scheuer score: G1S0

source_name: Hepatic tissue from chronic hepatitis B patients 0079

value: Male


title: CU419

description: breast tumor

source_name: Breast tumor CU419

tag: er

value: ER negative

tag: pr

value: PR negative

tag: her2 status

tag: ki67 ihc

value: Ki67 low

tag: spf status

tag: ln status

value: LNode negative

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

value: PTEN ihc positive

tag: pten mutant

value: PTEN wildtype

tag: egfr ihc

value: EGFR ihc negative

tag: inpp4b mrna

tag: pik3ca mutant

value: PIK3CA wildtype

tag: pik3ca aa

tag: tp53 mutant

value: TP53 wildtype

tag: hu luma

tag: hu normal

tag: hu basal

tag: hu her2

tag: hu best correlation

tag: hu subtype best

value: LumA

tag: ptensig good

tag: ptensig poor

value: PTEN good


title: Patient 0074, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0074, Scheuer score: G2S2

source_name: Hepatic tissue from chronic hepatitis B patients 0074

tag: tissue

value: Hepatic tissue

tag: gender

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: Patient 0072, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0072, Scheuer score: G2S1

source_name: Hepatic tissue from chronic hepatitis B patients 0072


title: pp3_Control_0h_b

tag: hmox

value: positive

tag: treatment

value: no treatment

tag: incubation time

tag: cell type

tag: genotype


title: pp3_10mcM_8h_d

value: Wild type Mouse embryonal fibroblasts (MEF) (=pp3)

value: Wild type


title: CU430

description: breast tumor

source_name: Breast tumor CU430

tag: er

value: ER positive

tag: pr

tag: her2 status

value: HER2 negative

tag: ki67 ihc

tag: spf status

tag: ln status

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

tag: pten mutant

tag: egfr ihc

tag: inpp4b mrna

value: INPP4B high

tag: pik3ca mutant

tag: pik3ca aa

value: CK5 14 negative

tag: tp53 mutant

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu normal

tag: hu basal

tag: ptensig score

tag: ptensig class abs0.2

tag: sample type

value: Stratagene Universal Human Reference RNA


title: CU424

description: breast tumor

source_name: Breast tumor CU424

tag: er

tag: pr

value: PR negative

tag: her2 status

tag: ki67 ihc

value: Ki67 low

tag: spf status

tag: ln status

value: LNode negative

tag: grade

tag: tumor size

value: PTEN ihc positive

value: INPP4B low

value: PIK3CA mutant

tag: hu her2

tag: hu best correlation

tag: hu subtype best

tag: ptensig good

tag: ptensig poor


title: CU462

description: breast tumor

source_name: Breast tumor CU462

value: PR positive

tag: age at dx

tag: pten ihc

tag: pten mutant

value: PTEN wildtype

tag: egfr ihc

value: EGFR ihc negative

tag: inpp4b mrna

tag: pik3ca mutant

value: PIK3CA wildtype

tag: pik3ca aa

tag: tp53 mutant

value: TP53 wildtype

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu normal

tag: hu basal

value: LumA

value: PTEN good


title: CU455

description: breast tumor

source_name: Breast tumor CU455

tag: er

value: ER positive

tag: pr

tag: her2 status

value: HER2 negative

tag: ki67 ihc

tag: spf status

tag: ln status

tag: grade

tag: tumor size

value: TP53 mutant

tag: hu her2

tag: hu best correlation

value: Normal

tag: ptensig score

tag: ptensig class abs0.2

source_name: Stratagene Universal Human Reference RNA

tag: sample type


title: pp3_Control_0h_c

tag: hmox

value: positive

tag: treatment

value: no treatment

tag: incubation time

tag: cell type

value: Wild type Mouse embryonal fibroblasts (MEF) (=pp3)

tag: genotype

value: Wild type


title: CU42

description: breast tumor

source_name: Breast tumor CU42

tag: er

value: ER negative

tag: pr

value: PR negative

tag: age at dx

tag: pten ihc

value: PTEN ihc positive

tag: pten mutant

tag: egfr ihc

value: EGFR ihc positive

tag: inpp4b mrna

value: INPP4B low

tag: pik3ca mutant

tag: pik3ca aa

value: CK5 14 positive

tag: tp53 mutant

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu normal

tag: hu basal

tag: hu subtype best

value: Basal

tag: ptensig good

tag: ptensig poor

value: PTEN poor

value: Stratagene Universal Human Reference RNA


title: pp3_10mcM_8h_c

tag: hmox

tag: treatment

tag: incubation time

tag: cell type

tag: genotype

value: 10mcM heme


title: Patient 0077, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0077, Scheuer score: G2S1

source_name: Hepatic tissue from chronic hepatitis B patients 0077

tag: tissue

value: Hepatic tissue

tag: gender

value: Male

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: CU406

description: breast tumor

source_name: Breast tumor CU406

tag: er

tag: pr

tag: her2 status

value: HER2 negative

tag: ki67 ihc

value: Ki67 high

tag: spf status

tag: ln status

value: LNode positive

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

value: PTEN ihc negative

tag: pten mutant

value: PTEN wildtype

tag: egfr ihc

tag: inpp4b mrna

tag: pik3ca mutant

value: PIK3CA wildtype

tag: pik3ca aa

value: CK5 14 negative

tag: tp53 mutant

value: TP53 mutant

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu her2

tag: hu best correlation

tag: ptensig score

tag: ptensig class abs0.2

value: PTEN good

tag: sample type


title: Patient 0073, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0073, Scheuer score: G1S1

source_name: Hepatic tissue from chronic hepatitis B patients 0073

tag: tissue

tag: gender

value: Female

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: CU411

description: breast tumor

source_name: Breast tumor CU411

tag: er

value: ER positive

tag: pr

value: PR positive

tag: her2 status

tag: ki67 ihc

value: Ki67 low

tag: spf status

tag: ln status

value: LNode negative

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

value: PTEN ihc positive

tag: pten mutant

tag: egfr ihc

value: EGFR ihc negative

tag: inpp4b mrna

value: INPP4B low

tag: pik3ca mutant

value: PIK3CA mutant

tag: hu normal

tag: hu basal

tag: hu subtype best

value: LumA

tag: ptensig good

tag: ptensig poor


title: Patient 0075, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0075, Scheuer score: G3S3

source_name: Hepatic tissue from chronic hepatitis B patients 0075

tag: tissue

value: Hepatic tissue

tag: gender

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: CU463

description: breast tumor

source_name: Breast tumor CU463

tag: er

value: ER negative

tag: pr

value: PR negative

tag: her2 status

value: HER2 positive

tag: ki67 ihc

value: Ki67 high

tag: spf status

tag: ln status

value: LNode positive

tag: grade

tag: tumor size

tag: age at dx

value: EGFR ihc positive

tag: pik3ca aa

value: CK5 14 positive

tag: tp53 mutant

value: TP53 wildtype

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu her2

tag: hu best correlation

value: Basal

tag: ptensig score

tag: ptensig class abs0.2

value: PTEN poor

tag: sample type

value: Stratagene Universal Human Reference RNA


title: Patient 0076, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0076, Scheuer score: G1S1

source_name: Hepatic tissue from chronic hepatitis B patients 0076

tag: tissue

tag: gender

value: Male

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: CU405

description: breast tumor

source_name: Breast tumor CU405

tag: er

value: ER positive

tag: pr

value: PR positive

tag: her2 status

value: HER2 negative

tag: ki67 ihc

value: Ki67 low

tag: spf status

tag: ln status

value: LNode negative

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

value: PTEN ihc positive

tag: pten mutant

value: PTEN wildtype

tag: egfr ihc

value: EGFR ihc negative

tag: inpp4b mrna

tag: pik3ca mutant

value: PIK3CA wildtype

value: CK5 14 negative

tag: hu normal

tag: hu basal

tag: hu subtype best

tag: ptensig good

tag: ptensig poor

value: PTEN good


title: CU412

description: breast tumor

source_name: Breast tumor CU412

tag: er

tag: pr

value: PR negative

tag: her2 status

value: INPP4B low

tag: pik3ca aa

tag: tp53 mutant

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu her2

tag: hu best correlation

value: LumB

tag: ptensig score

tag: ptensig class abs0.2

tag: sample type


title: CU404

description: breast tumor

source_name: Breast tumor CU404

value: ER negative

tag: ki67 ihc

tag: spf status

tag: ln status

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

value: PTEN ihc negative

tag: pten mutant

tag: egfr ihc

tag: inpp4b mrna

tag: pik3ca mutant

value: TP53 wildtype

tag: hu normal

tag: hu basal

value: Basal

value: PTEN poor


title: pp3_10mcM_4h_c

tag: hmox

value: positive

tag: treatment

value: no treatment

tag: incubation time

tag: cell type

value: Wild type Mouse embryonal fibroblasts (MEF) (=pp3)

tag: genotype

value: Wild type

value: 10mcM heme


title: CU375

description: breast tumor

source_name: Breast tumor CU375

tag: er

value: ER positive

tag: pr

value: PR positive

tag: her2 status

value: HER2 negative

tag: ki67 ihc

value: Ki67 low

tag: spf status

value: LNode negative

value: PTEN ihc positive

value: PTEN wildtype

value: EGFR ihc negative

value: PIK3CA mutant

tag: pik3ca aa

tag: tp53 mutant

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu her2

tag: hu best correlation

tag: hu subtype best

value: LumA

tag: ptensig good

tag: ptensig poor

tag: ptensig score

tag: ptensig class abs0.2

value: unclassified

tag: sample type

value: Stratagene Universal Human Reference RNA


title: CU372

description: breast tumor

source_name: Breast tumor CU372

tag: er

tag: pr

tag: ln status

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

tag: pten mutant

tag: egfr ihc

tag: inpp4b mrna

value: INPP4B low

tag: pik3ca mutant

value: CK5 14 negative

value: TP53 wildtype

tag: hu normal

tag: hu basal

value: Normal

value: PTEN good


title: pp3_10mcM_4h_b

tag: hmox

value: positive

tag: treatment

value: no treatment

tag: incubation time

tag: cell type

value: Wild type Mouse embryonal fibroblasts (MEF) (=pp3)

tag: genotype

value: Wild type

value: 10mcM heme


title: CU363

description: breast tumor

source_name: Breast tumor CU363

tag: er

value: ER positive

tag: pr

value: PR positive

tag: her2 status

value: HER2 positive

tag: ki67 ihc

value: Ki67 high

tag: spf status

value: LNode positive

value: INPP4B high

tag: pik3ca aa

tag: tp53 mutant

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu her2

tag: hu best correlation

tag: hu subtype best

tag: ptensig good

tag: ptensig poor

tag: ptensig score

tag: ptensig class abs0.2

tag: sample type


title: CU374

description: breast tumor

source_name: Breast tumor CU374

tag: er

tag: pr

value: HER2 negative

value: Ki67 low

tag: ln status

value: LNode negative

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

value: PTEN ihc positive

tag: pten mutant

value: PTEN wildtype

tag: egfr ihc

value: EGFR ihc negative

tag: inpp4b mrna

tag: pik3ca mutant

value: PIK3CA wildtype

tag: hu normal

tag: hu basal

value: Stratagene Universal Human Reference RNA


title: pp3_10mcM_8h_b

tag: hmox

value: positive

tag: treatment

value: no treatment

tag: incubation time

tag: cell type

value: Wild type Mouse embryonal fibroblasts (MEF) (=pp3)

tag: genotype


title: pp3_10mcM_1h_c

value: Wild type

value: 10mcM heme


title: Patient 0070, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0070, Scheuer score: G1S2

source_name: Hepatic tissue from chronic hepatitis B patients 0070

tag: tissue

value: Hepatic tissue

tag: gender

value: Female

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: CU361

description: breast tumor

source_name: Breast tumor CU361

tag: er

value: ER positive

tag: pr

value: PR positive

tag: her2 status

tag: ki67 ihc

tag: spf status

tag: ln status

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

tag: pten mutant

value: INPP4B low

value: PIK3CA mutant

tag: pik3ca aa

value: CK5 14 negative

tag: tp53 mutant

value: TP53 wildtype

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu her2

tag: hu best correlation

tag: hu subtype best

value: LumA

tag: ptensig good

tag: ptensig poor

tag: ptensig score

tag: ptensig class abs0.2

value: PTEN good

source_name: Stratagene Universal Human Reference RNA

tag: sample type


title: CU234

description: breast tumor

source_name: Breast tumor CU234

tag: er

value: ER negative

tag: pr

value: PR negative

tag: her2 status

value: HER2 positive

tag: ki67 ihc

value: Ki67 high

tag: spf status

tag: ln status

value: LNode positive

tag: grade

tag: tumor size

value: PTEN wildtype

tag: egfr ihc

value: EGFR ihc negative

tag: inpp4b mrna

tag: pik3ca mutant

value: PIK3CA wildtype

tag: hu normal

tag: hu basal

value: Normal


title: pp3_10mcM_1h_d

tag: hmox

value: positive

tag: treatment

value: no treatment

tag: incubation time

tag: cell type

value: Wild type Mouse embryonal fibroblasts (MEF) (=pp3)

tag: genotype

value: Wild type

value: 10mcM heme


title: pp3_10mcM_4h_a


title: pp3_10mcM_4h_d


title: CU355

description: breast tumor

source_name: Breast tumor CU355

tag: er

value: ER positive

tag: pr

value: HER2 negative

value: Ki67 low

value: LNode negative

tag: age at dx

tag: pten ihc

value: PTEN ihc positive

tag: pten mutant

value: INPP4B low

tag: pik3ca aa

value: CK5 14 negative

tag: tp53 mutant

value: TP53 wildtype

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu her2

tag: hu best correlation

tag: hu subtype best

tag: ptensig good

tag: ptensig poor

tag: ptensig score

tag: ptensig class abs0.2

tag: sample type

value: Stratagene Universal Human Reference RNA


title: CU232

description: breast tumor

source_name: Breast tumor CU232

tag: er

tag: pr

value: PR positive

tag: her2 status

tag: ki67 ihc

tag: spf status

tag: ln status

tag: grade

tag: tumor size

value: PTEN wildtype

tag: egfr ihc

value: EGFR ihc negative

tag: inpp4b mrna

tag: pik3ca mutant

tag: hu normal

tag: hu basal

value: LumA

value: unclassified


title: CU233

description: breast tumor

source_name: Breast tumor CU233

value: ER negative

value: PR negative

tag: age at dx

tag: pten ihc

tag: pten mutant

value: EGFR ihc positive

value: INPP4B high

value: PIK3CA wildtype

tag: pik3ca aa

value: CK5 14 positive

tag: tp53 mutant

value: TP53 mutant

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu her2

tag: hu best correlation

tag: hu subtype best

value: Basal

tag: ptensig good

tag: ptensig poor

value: PTEN poor


title: Patient 0068, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0068, Scheuer score: G2S3

source_name: Hepatic tissue from chronic hepatitis B patients 0068

tag: tissue

value: Hepatic tissue

tag: gender

value: Female

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: Patient 0069, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0069, Scheuer score: G0S0

source_name: Hepatic tissue from chronic hepatitis B patients 0069


title: CU228

description: breast tumor

source_name: Breast tumor CU228

tag: er

value: ER positive

tag: pr

tag: her2 status

value: HER2 negative

tag: ki67 ihc

value: Ki67 high

tag: spf status

tag: ln status

value: LNode positive

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

value: PTEN ihc negative

tag: pten mutant

tag: egfr ihc

tag: inpp4b mrna

value: INPP4B low

tag: pik3ca mutant

value: CK5 14 negative

value: TP53 wildtype

tag: hu normal

tag: hu basal

tag: ptensig score

tag: ptensig class abs0.2

value: PTEN good

tag: sample type

value: Stratagene Universal Human Reference RNA


title: CU369

description: breast tumor

source_name: Breast tumor CU369

tag: er

tag: pr

value: PR positive

tag: her2 status

value: PTEN ihc positive

value: PTEN wildtype

value: EGFR ihc negative

value: PIK3CA wildtype

tag: pik3ca aa

tag: tp53 mutant

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu her2

tag: hu best correlation

tag: hu subtype best

value: LumB

tag: ptensig good

tag: ptensig poor


title: CU32

description: breast tumor

source_name: Breast tumor CU32

value: PR negative

tag: ki67 ihc

tag: spf status

tag: ln status

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

tag: pten mutant

tag: egfr ihc

value: EGFR ihc positive

tag: inpp4b mrna

tag: pik3ca mutant

value: CK5 14 positive

value: TP53 mutant

tag: hu normal

tag: hu basal

value: Basal

value: PTEN poor


title: Patient 0071, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0071, Scheuer score: G0S1

source_name: Hepatic tissue from chronic hepatitis B patients 0071

tag: tissue

value: Hepatic tissue

tag: gender

value: Male

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: Patient 0066, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0066, Scheuer score: G2S2

source_name: Hepatic tissue from chronic hepatitis B patients 0066


title: Patient 0067, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0067, Scheuer score: G2S2

source_name: Hepatic tissue from chronic hepatitis B patients 0067


title: CU230

description: breast tumor

source_name: Breast tumor CU230

tag: er

value: ER positive

tag: pr

tag: her2 status

value: HER2 negative

tag: ki67 ihc

value: Ki67 low

tag: spf status

tag: ln status

value: LNode negative

value: INPP4B low

tag: pik3ca aa

value: CK5 14 negative

tag: tp53 mutant

value: TP53 wildtype

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu her2

tag: hu best correlation

tag: hu subtype best

value: LumA

tag: ptensig good

tag: ptensig poor

tag: ptensig score

tag: ptensig class abs0.2

tag: sample type


title: Patient 0065, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0065, Scheuer score: G0S0

source_name: Hepatic tissue from chronic hepatitis B patients 0065

tag: tissue

tag: gender

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: CU229

description: breast tumor

source_name: Breast tumor CU229

tag: er

tag: pr

value: PR positive

tag: her2 status

tag: ki67 ihc

tag: spf status

tag: ln status

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

value: PTEN ihc positive

tag: pten mutant

value: PTEN wildtype

tag: egfr ihc

value: EGFR ihc negative

tag: inpp4b mrna

tag: pik3ca mutant

value: PIK3CA mutant

tag: pik3ca aa

tag: tp53 mutant

tag: stathmin ihc score

tag: hu normal

tag: hu basal

value: LumB

value: unclassified

value: Stratagene Universal Human Reference RNA


title: pp3_10mcM_1h_b

tag: hmox

value: positive

tag: treatment

value: no treatment

tag: incubation time

tag: cell type

value: Wild type Mouse embryonal fibroblasts (MEF) (=pp3)

tag: genotype

value: Wild type

value: 10mcM heme


title: pp3_10mcM_1h_a


title: mm_Control_0h_d

description: HMOX knocked out Mouse embryonal fibroblasts (MEF) from embryo 1 (=mm)

source_name: mm

value: negative

value: HMOX knocked out


title: CU227

description: breast tumor

source_name: Breast tumor CU227

tag: er

value: ER positive

tag: pr

tag: her2 status

value: HER2 negative

tag: ki67 ihc

value: Ki67 high

tag: spf status

tag: ln status

value: LNode positive

tag: grade

tag: tumor size

value: INPP4B low

value: CK5 14 negative

value: TP53 wildtype

tag: hu lumb

tag: hu luma

tag: hu her2

tag: hu best correlation

tag: hu subtype best

tag: ptensig good

tag: ptensig poor

tag: ptensig score

tag: ptensig class abs0.2

value: PTEN good

source_name: Stratagene Universal Human Reference RNA

tag: sample type


title: Patient 0064, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0064, Scheuer score: G0S0

source_name: Hepatic tissue from chronic hepatitis B patients 0064

tag: tissue

value: Hepatic tissue

tag: gender

value: Male

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: mm_Control_0h_c

tag: hmox

tag: treatment

tag: incubation time

tag: cell type

value: HMOX knocked out Mouse embryonal fibroblasts (MEF) from embryo 1 (=mm)

tag: genotype


title: CU219

description: breast tumor

source_name: Breast tumor CU219

tag: er

value: ER negative

tag: pr

value: PR positive

tag: her2 status

value: HER2 positive

tag: ki67 ihc

tag: spf status

tag: ln status

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

value: PTEN ihc positive

tag: pten mutant

value: PTEN wildtype

tag: egfr ihc

value: EGFR ihc positive

tag: inpp4b mrna

value: INPP4B high

tag: pik3ca mutant

value: PIK3CA wildtype

tag: pik3ca aa

tag: tp53 mutant

value: TP53 mutant

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu normal

tag: hu basal

tag: hu her2

tag: hu best correlation

tag: hu subtype best

value: Stratagene Universal Human Reference RNA


title: CU156

description: breast tumor

source_name: Breast tumor CU156

tag: er

tag: pr

value: PR negative

tag: her2 status

value: HER2 negative

tag: ki67 ihc

value: Ki67 high

tag: spf status

tag: ln status

value: LNode positive

tag: grade

tag: tumor size

value: INPP4B low

value: Basal

tag: ptensig good

tag: ptensig poor

tag: ptensig score

tag: ptensig class abs0.2

tag: sample type


title: CU210

description: breast tumor

source_name: Breast tumor CU210

value: ER positive

tag: age at dx

tag: pten ihc

value: PTEN ihc negative

tag: pten mutant

tag: egfr ihc

tag: inpp4b mrna

tag: pik3ca mutant

tag: pik3ca aa

value: CK5 14 negative

tag: tp53 mutant

value: TP53 wildtype

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu normal

tag: hu basal

value: Normal

value: PTEN good


title: CU207

description: breast tumor

source_name: Breast tumor CU207

tag: er

value: ER negative

tag: pr

tag: her2 status

tag: ki67 ihc

value: Ki67 low

tag: spf status

tag: ln status

value: LNode negative

tag: grade

tag: tumor size

value: PTEN wildtype

value: EGFR ihc positive

value: CK5 14 positive

tag: hu her2

tag: hu best correlation

tag: hu subtype best

tag: ptensig good

tag: ptensig poor

value: PTEN poor


title: Patient 0062, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0062, Scheuer score: G3S2

source_name: Hepatic tissue from chronic hepatitis B patients 0062

tag: tissue

value: Hepatic tissue

tag: gender

value: Male

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: Patient 0060, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0060, Scheuer score: G1S0

source_name: Hepatic tissue from chronic hepatitis B patients 0060


title: CU160

description: breast tumor

source_name: Breast tumor CU160

tag: er

tag: pr

value: PR positive

tag: her2 status

value: HER2 negative

tag: age at dx

tag: pten ihc

value: PTEN ihc positive

tag: pten mutant

tag: egfr ihc

tag: inpp4b mrna

value: INPP4B high

tag: pik3ca mutant

value: PIK3CA wildtype

tag: pik3ca aa

tag: tp53 mutant

value: TP53 mutant

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu normal

tag: hu basal

tag: ptensig score

tag: ptensig class abs0.2

tag: sample type

value: Stratagene Universal Human Reference RNA


title: Patient 0061, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0061, Scheuer score: G3S3

source_name: Hepatic tissue from chronic hepatitis B patients 0061

tag: tissue

tag: gender

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: CU159

description: breast tumor

source_name: Breast tumor CU159

tag: er

value: ER positive

tag: pr

tag: her2 status

tag: ki67 ihc

tag: spf status

tag: ln status

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

tag: pten mutant

tag: egfr ihc

value: EGFR ihc negative

tag: inpp4b mrna

value: INPP4B low

tag: pik3ca mutant

value: CK5 14 negative

value: TP53 wildtype

tag: hu her2

tag: hu best correlation

tag: hu subtype best

value: LumA

tag: ptensig good

tag: ptensig poor

value: PTEN good


title: Patient 0063, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0063, Scheuer score: G0S2

source_name: Hepatic tissue from chronic hepatitis B patients 0063

tag: tissue

tag: gender

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: CU151

description: breast tumor

source_name: Breast tumor CU151

tag: er

tag: pr

tag: her2 status

value: HER2 positive

tag: ki67 ihc

value: Ki67 low

tag: spf status

tag: ln status

value: LNode negative

tag: grade

tag: tumor size

tag: age at dx

value: PTEN wildtype

tag: pik3ca aa

tag: tp53 mutant

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu normal

tag: hu basal

value: Basal

tag: ptensig score

tag: ptensig class abs0.2

value: unclassified

tag: sample type


title: CU150

description: breast tumor

source_name: Breast tumor CU150

tag: er

tag: pr

value: PR positive

tag: her2 status

value: HER2 negative

value: Ki67 high

value: LNode positive

tag: pten ihc

value: PTEN ihc positive

tag: pten mutant

tag: egfr ihc

tag: inpp4b mrna

tag: pik3ca mutant

value: PIK3CA mutant

tag: hu her2

tag: hu best correlation

tag: hu subtype best

tag: ptensig good

tag: ptensig poor


title: CU158

description: breast tumor

source_name: Breast tumor CU158

value: ER positive

tag: ki67 ihc

tag: spf status

tag: ln status

tag: grade

tag: tumor size

tag: age at dx

value: INPP4B low

tag: pik3ca aa

tag: tp53 mutant

value: TP53 mutant

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu normal

tag: hu basal

value: PTEN poor

value: Stratagene Universal Human Reference RNA


title: Patient 0058, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0058, Scheuer score: G3S1

source_name: Hepatic tissue from chronic hepatitis B patients 0058

tag: tissue

value: Hepatic tissue

tag: gender

value: Male

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: mm_Control_0h_b

source_name: mm

tag: hmox

value: negative

tag: treatment

value: no treatment

tag: incubation time

tag: cell type

value: HMOX knocked out Mouse embryonal fibroblasts (MEF) from embryo 1 (=mm)

tag: genotype

value: HMOX knocked out


title: CU133

description: breast tumor

source_name: Breast tumor CU133

tag: er

tag: pr

value: PR positive

tag: her2 status

tag: ki67 ihc

tag: spf status

tag: ln status

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

tag: pten mutant

value: PTEN wildtype

tag: egfr ihc

value: EGFR ihc negative

tag: inpp4b mrna

tag: pik3ca mutant

tag: pik3ca aa

value: CK5 14 negative

tag: tp53 mutant

value: TP53 wildtype

tag: hu her2

tag: hu best correlation

tag: hu subtype best

value: LumB

tag: ptensig good

tag: ptensig poor

tag: ptensig score

tag: ptensig class abs0.2

source_name: Stratagene Universal Human Reference RNA

tag: sample type


title: mm_Control_0h_a

tag: hmox

tag: treatment

tag: incubation time

tag: cell type

tag: genotype


title: CU153

description: breast tumor

source_name: Breast tumor CU153

tag: er

value: ER negative

tag: pr

tag: her2 status

value: HER2 negative

tag: ki67 ihc

value: Ki67 high

tag: spf status

tag: ln status

value: LNode positive

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

value: PTEN ihc positive

tag: pten mutant

tag: egfr ihc

tag: inpp4b mrna

value: PIK3CA mutant

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu normal

tag: hu basal

value: Normal

value: PTEN good


title: CU147

description: breast tumor

source_name: Breast tumor CU147

tag: er

tag: pr

value: PR negative

value: PTEN ihc negative

value: EGFR ihc positive

value: INPP4B high

tag: pik3ca mutant

value: PIK3CA wildtype

tag: pik3ca aa

value: CK5 14 positive

tag: tp53 mutant

tag: hu her2

tag: hu best correlation

tag: hu subtype best

value: Basal

tag: ptensig good

tag: ptensig poor

tag: ptensig score

tag: ptensig class abs0.2

value: PTEN poor

tag: sample type

value: Stratagene Universal Human Reference RNA


title: CU144

description: breast tumor

source_name: Breast tumor CU144

value: ER positive

value: PR positive

tag: her2 status

tag: ki67 ihc

value: Ki67 low

tag: spf status

tag: ln status

value: LNode negative

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

tag: pten mutant

value: PTEN wildtype

tag: egfr ihc

value: EGFR ihc negative

tag: inpp4b mrna

value: INPP4B low

value: TP53 wildtype

tag: stathmin ihc score

tag: hu lumb

value: LumA


title: CU137

description: breast tumor

source_name: Breast tumor CU137

tag: er

tag: pr

value: HER2 negative

value: PTEN ihc positive

tag: pik3ca mutant

tag: pik3ca aa

value: CK5 14 negative

tag: tp53 mutant

tag: hu luma

tag: hu normal

tag: hu basal

tag: hu her2

tag: hu best correlation

tag: hu subtype best

value: LumB

tag: ptensig good

tag: ptensig poor


title: Patient 0059, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0059, Scheuer score: G1S0

source_name: Hepatic tissue from chronic hepatitis B patients 0059

tag: tissue

value: Hepatic tissue

tag: gender

value: Male

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: mm_10mcM_8h_b

tag: hmox

value: negative

tag: treatment

value: no treatment

tag: incubation time

tag: cell type

value: HMOX knocked out Mouse embryonal fibroblasts (MEF) from embryo 1 (=mm)

tag: genotype

value: HMOX knocked out

value: 10mcM heme


title: mm_10mcM_8h_c


title: Patient 0057, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0057, Scheuer score: G3S2

source_name: Hepatic tissue from chronic hepatitis B patients 0057

value: Female


title: mm_10mcM_8h_d


title: CU123

description: breast tumor

source_name: Breast tumor CU123

tag: er

value: ER positive

tag: pr

value: PR positive

tag: her2 status

tag: ki67 ihc

value: Ki67 low

tag: spf status

tag: ln status

value: LNode negative

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

tag: pten mutant

value: PTEN wildtype

tag: egfr ihc

tag: inpp4b mrna

tag: pik3ca mutant

value: PIK3CA mutant

tag: pik3ca aa

tag: tp53 mutant

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu normal

tag: hu basal

tag: ptensig score

tag: ptensig class abs0.2

value: PTEN good

tag: sample type

value: Stratagene Universal Human Reference RNA


title: CU11

description: breast tumor

source_name: Breast tumor CU11

tag: er

value: ER negative

tag: pr

value: PR negative

tag: her2 status

value: HER2 negative

tag: ki67 ihc

value: Ki67 high

tag: spf status

tag: ln status

value: LNode positive

tag: grade

tag: tumor size

value: PTEN ihc negative

value: PTEN mutant

value: EGFR ihc positive

value: INPP4B low

value: PIK3CA wildtype

value: CK5 14 positive

value: TP53 mutant

tag: hu her2

tag: hu best correlation

tag: hu subtype best

value: Basal

tag: ptensig good

tag: ptensig poor

value: PTEN poor


title: CU106

description: breast tumor

source_name: Breast tumor CU106

value: ER positive

value: PR positive

tag: age at dx

tag: pten ihc

value: PTEN ihc positive

tag: pten mutant

value: PTEN wildtype

tag: egfr ihc

value: EGFR ihc negative

tag: inpp4b mrna

tag: pik3ca mutant

tag: pik3ca aa

value: CK5 14 negative

tag: tp53 mutant

value: TP53 wildtype

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu normal

tag: hu basal

value: LumB


title: CU103

description: breast tumor

source_name: Breast tumor CU103

tag: er

tag: pr

tag: her2 status

value: HER2 negative

tag: ki67 ihc

value: Ki67 high

tag: spf status

tag: ln status

value: LNode positive

tag: grade

tag: tumor size

tag: hu her2

tag: hu best correlation

value: LumA

tag: ptensig score

tag: ptensig class abs0.2

value: unclassified

tag: sample type

value: Stratagene Universal Human Reference RNA


title: Patient 0054, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0054, Scheuer score: G0S4

source_name: Hepatic tissue from chronic hepatitis B patients 0054

tag: tissue

value: Hepatic tissue

tag: gender

value: Male

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: mm_10mcM_4h_d

tag: hmox

value: negative

tag: treatment

value: no treatment

tag: incubation time

tag: cell type

value: HMOX knocked out Mouse embryonal fibroblasts (MEF) from embryo 1 (=mm)

tag: genotype

value: HMOX knocked out

value: 10mcM heme


title: CU114

description: breast tumor

source_name: Breast tumor CU114

tag: er

value: ER positive

tag: pr

value: PR positive

tag: her2 status

tag: ki67 ihc

tag: spf status

tag: ln status

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

value: PTEN ihc positive

tag: pten mutant

value: PTEN wildtype

tag: egfr ihc

value: EGFR ihc negative

tag: inpp4b mrna

value: INPP4B low

tag: pik3ca mutant

value: PIK3CA wildtype

tag: pik3ca aa

tag: tp53 mutant

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu normal

tag: hu basal

tag: hu subtype best

tag: ptensig good

tag: ptensig poor


title: Patient 0055, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0055, Scheuer score: G0S0

source_name: Hepatic tissue from chronic hepatitis B patients 0055

tag: tissue

tag: gender

value: Female

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: mm_10mcM_4h_b

tag: hmox

tag: treatment

tag: incubation time

tag: cell type

tag: genotype


title: CU132

description: breast tumor

source_name: Breast tumor CU132

tag: er

tag: pr

value: PR negative

tag: her2 status

value: HER2 negative

tag: ki67 ihc

value: Ki67 low

tag: spf status

tag: ln status

value: LNode negative

tag: grade

tag: tumor size

tag: age at dx

tag: pten ihc

tag: pten mutant

tag: egfr ihc

tag: inpp4b mrna

tag: pik3ca mutant

value: PIK3CA mutant

tag: pik3ca aa

value: CK5 14 negative

tag: tp53 mutant

value: TP53 mutant

tag: stathmin ihc score

tag: hu lumb

tag: hu luma

tag: hu her2

tag: hu best correlation

value: LumB

tag: ptensig score

tag: ptensig class abs0.2

value: PTEN poor

tag: sample type


title: mm_10mcM_4h_c

source_name: mm

tag: hmox

value: negative

tag: treatment

value: no treatment

tag: incubation time

tag: cell type

value: HMOX knocked out Mouse embryonal fibroblasts (MEF) from embryo 1 (=mm)

tag: genotype

value: HMOX knocked out

value: 10mcM heme


title: Patient 0056, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0056, Scheuer score: G2S2

source_name: Hepatic tissue from chronic hepatitis B patients 0056

tag: tissue

value: Hepatic tissue

tag: gender

value: Male

tag: age

tag: batch

tag: scheuer score g

tag: scheuer score s


title: mm_10mcM_4h_a


title: Patient 0053, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0053, Scheuer score: G3S4

source_name: Hepatic tissue from chronic hepatitis B patients 0053


title: mm_10mcM_8h_a


title: mm_10mcM_1h_d


title: Patient 0051, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0051, Scheuer score: G1S2

source_name: Hepatic tissue from chronic hepatitis B patients 0051


title: 9664921051_L

city: New Haven

first: Victoria

middle: Elizabeth

last: Clark

state: CT

address: 300 Cedar Street TAC S330

department: Departments of Neurosurgery and Genetics

country: USA

institute: Yale University School of Medicine

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using  normal-exponential convolution model-based background correction and quantile normalization. All the batches is normalized at once after excluding probes with low quality. (Limma R package is used)

label_protocol: not provided

extract_protocol: not provided

value: meningioma

tag: mutation group

tag: primary status

value: Primary

tag: grade

tag: radiation

value: No


title: 9664921052_D


title: 9664921052_C


title: Patient 0052, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0052, Scheuer score: G2S0

source_name: Hepatic tissue from chronic hepatitis B patients 0052

value: Female


title: 9664921052_H


title: Patient 0050, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0050, Scheuer score: G3S3

source_name: Hepatic tissue from chronic hepatitis B patients 0050


title: 9664921052_J


title: mm_10mcM_1h_c


title: 9664921051_K


title: 9664921051_H


title: 9664921051_F


title: 9664921052_L


title: mm_10mcM_1h_a


title: mm_10mcM_1h_b


title: 9664921052_E


title: 9664921052_I


title: 9664921051_G


title: Patient 0048, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0048, Scheuer score: G0S0

source_name: Hepatic tissue from chronic hepatitis B patients 0048


title: 9664921051_B


title: mm3_Control_0h_a

description: HMOX knocked out Mouse embryonal fibroblasts (MEF) from embryo 3 (=mm3)


title: Patient 0049, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0049, Scheuer score: G1S1

source_name: Hepatic tissue from chronic hepatitis B patients 0049


title: 9664921051_A


title: Patient 0047, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0047, Scheuer score: G2S2

source_name: Hepatic tissue from chronic hepatitis B patients 0047


title: 9372962036_I


title: 9372962036_G


title: Patient 0046, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0046, Scheuer score: G0S2

source_name: Hepatic tissue from chronic hepatitis B patients 0046


title: 9372962036_E


title: 9372962036_D

source_name: SUFU

value: SUFU


title: 9372962032_I


title: 9372962032_G


title: 9372962035_D


title: 9372962035_G


title: Patient 0045, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0045, Scheuer score: G2S2

source_name: Hepatic tissue from chronic hepatitis B patients 0045


title: Patient 0043, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0043, Scheuer score: G2S1

source_name: Hepatic tissue from chronic hepatitis B patients 0043


title: 9372962032_F


title: Patient 0044, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0044, Scheuer score: G2S2

source_name: Hepatic tissue from chronic hepatitis B patients 0044


title: mm3_10mcM_1h_c

value: HMOX knocked out Mouse embryonal fibroblasts (MEF) from embryo 3 (=mm3)


title: mm3_10mcM_4h_a


title: mm3_10mcM_4h_b


title: mm3_10mcM_8h_b


title: 9372962032_A


title: 9372962032_B


title: 9372962035_I


title: Patient 0041, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0041, Scheuer score: G2S3

source_name: Hepatic tissue from chronic hepatitis B patients 0041


title: 9372962065_L


title: mm3_10mcM_8h_a


title: mm3_10mcM_8h_c


title: mm3_10mcM_4h_c


title: 9372962035_A


title: Patient 0040, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0040, Scheuer score: G0S1

source_name: Hepatic tissue from chronic hepatitis B patients 0040


title: Patient 0042, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0042, Scheuer score: G3S3

source_name: Hepatic tissue from chronic hepatitis B patients 0042


title: 9372962022_F


title: Patient 0039, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0039, Scheuer score: G3S3

source_name: Hepatic tissue from chronic hepatitis B patients 0039


title: mm3_10mcM_1h_b


title: 9372962013_I


title: mm3_10mcM_1h_a


title: 9372962013_F


title: Patient 0038, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0038, Scheuer score: G0S0

source_name: Hepatic tissue from chronic hepatitis B patients 0038


title: 9372962013_A


title: 9372962008_K


title: 9372962009_I


title: 9372962008_I


title: 9372962008_A


title: Patient 0036, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0036, Scheuer score: G1S1

source_name: Hepatic tissue from chronic hepatitis B patients 0036


title: Patient 0034, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0034, Scheuer score: G2S3

source_name: Hepatic tissue from chronic hepatitis B patients 0034


title: Patient 0037, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0037, Scheuer score: G2S2

source_name: Hepatic tissue from chronic hepatitis B patients 0037


title: 9372962009_B


title: 9372962007_H


title: 9372962013_C


title: 9372962013_G


title: 9372962009_G


title: Patient 0035, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0035, Scheuer score: G0S0

source_name: Hepatic tissue from chronic hepatitis B patients 0035


title: 9372962007_F


title: 9372962007_K


title: 9372962007_G


title: 9372962009_A


title: 9372962007_I


title: Patient 0032, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0032, Scheuer score: G2S0

source_name: Hepatic tissue from chronic hepatitis B patients 0032


title: Patient 0033, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0033, Scheuer score: G4S3

source_name: Hepatic tissue from chronic hepatitis B patients 0033


title: 9256760094_L

value: meninges


title: Patient 0030, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0030, Scheuer score: G2S0

source_name: Hepatic tissue from chronic hepatitis B patients 0030


title: Patient 0031, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0031, Scheuer score: G0S2

source_name: Hepatic tissue from chronic hepatitis B patients 0031


title: 9256760094_K


title: 9256760094_H


title: Patient 0029, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0029, Scheuer score: G1S2

source_name: Hepatic tissue from chronic hepatitis B patients 0029


title: 9256760094_E


title: 9256760094_B


title: Patient 0027, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0027, Scheuer score: G3S4

source_name: Hepatic tissue from chronic hepatitis B patients 0027


title: 9256760094_J


title: 9256760094_I


title: 9256760094_G


title: mm3_Control_0h_b

description: HMOX knocked out Mouse embryonal fibroblasts (MEF) from embryo 3 (=mm3)


title: 9256760085_L


title: 9256760094_D


title: 9256760085_G


title: Patient 0023, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0023, Scheuer score: G1S2

source_name: Hepatic tissue from chronic hepatitis B patients 0023


title: 9256760085_H


title: 9256760085_K


title: Patient 0022, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0022, Scheuer score: G2S2

source_name: Hepatic tissue from chronic hepatitis B patients 0022


title: 9256760085_F


title: 9256760094_A


title: 9256760085_E


title: Patient 0024, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0024, Scheuer score: G0S0

source_name: Hepatic tissue from chronic hepatitis B patients 0024


title: 9256760085_I


title: 9256760085_J


title: 9256760067_L


title: 9256760085_D


title: Patient 0026, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0026, Scheuer score: G2S4

source_name: Hepatic tissue from chronic hepatitis B patients 0026


title: Patient 0021, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0021, Scheuer score: G4S4

source_name: Hepatic tissue from chronic hepatitis B patients 0021


title: 9256760085_A


title: 9256760085_B


title: 9256760067_K


title: Patient 0019, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0019, Scheuer score: G0S0

source_name: Hepatic tissue from chronic hepatitis B patients 0019


title: 9256760067_J


title: 9256760058_I

source_name: SMO L412F

value: SMO L412F


title: Patient 0020, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0020, Scheuer score: G1S2

source_name: Hepatic tissue from chronic hepatitis B patients 0020


title: Patient 0018, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0018, Scheuer score: G0S0

source_name: Hepatic tissue from chronic hepatitis B patients 0018


title: 9256760085_C


title: 9256760058_H


title: Patient 0017, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0017, Scheuer score: G2S2

source_name: Hepatic tissue from chronic hepatitis B patients 0017


title: 9256760058_G


title: Patient 0028, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0028, Scheuer score: G4S4

source_name: Hepatic tissue from chronic hepatitis B patients 0028


title: 7754315089_B


title: Patient 0025, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0025, Scheuer score: G1S3

source_name: Hepatic tissue from chronic hepatitis B patients 0025


title: Patient 0015, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0015, Scheuer score: G2S0

source_name: Hepatic tissue from chronic hepatitis B patients 0015


title: Patient 0014, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0014, Scheuer score: G1S2

source_name: Hepatic tissue from chronic hepatitis B patients 0014


title: 7754315079_F


title: 7754315079_D


title: 9372962022_I


title: 7754315089_G


title: 7754315079_C


title: 9256760058_F


title: Patient 0016, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0016, Scheuer score: G2S3

source_name: Hepatic tissue from chronic hepatitis B patients 0016


title: 7754315062_I


title: Patient 0011, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0011, Scheuer score: G2S2

source_name: Hepatic tissue from chronic hepatitis B patients 0011


title: 7911739007_C


title: 7911739007_E


title: 7754315062_F


title: 7911739007_A


title: Patient 0012, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0012, Scheuer score: G1S1

source_name: Hepatic tissue from chronic hepatitis B patients 0012


title: Patient 0013, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0013, Scheuer score: G3S4

source_name: Hepatic tissue from chronic hepatitis B patients 0013


title: 7911747005_I


title: 9372962022_A


title: 7911739035_C


title: Patient 0008, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0008, Scheuer score: G1S0

source_name: Hepatic tissue from chronic hepatitis B patients 0008


title: 7911739007_G


title: 7911747005_A


title: 7911739004_G


title: 7911747005_E


title: Patient 0009, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0009, Scheuer score: G0S4

source_name: Hepatic tissue from chronic hepatitis B patients 0009


title: 7911739023_L


title: 7911747016_J


title: 7911739023_J


title: 7754315062_H


title: Patient 0007, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0007, Scheuer score: G1S0

source_name: Hepatic tissue from chronic hepatitis B patients 0007


title: Patient 0006, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0006, Scheuer score: G1S0

source_name: Hepatic tissue from chronic hepatitis B patients 0006


title: Patient 0010, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0010, Scheuer score: G0S0

source_name: Hepatic tissue from chronic hepatitis B patients 0010


title: 7911739001_F


title: 7911747016_H


title: 7754315088_I


title: 7911747016_B


title: Patient 0005, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0005, Scheuer score: G2S0

source_name: Hepatic tissue from chronic hepatitis B patients 0005


title: 7911747016_F


title: 7911739001_B


title: Patient 0003, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0003, Scheuer score: G0S0

source_name: Hepatic tissue from chronic hepatitis B patients 0003


title: 7754315086_I

source_name: SUFU


title: 7754315088_B


title: 7754315086_H


title: Patient 0001, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0001, Scheuer score: G0S2

source_name: Hepatic tissue from chronic hepatitis B patients 0001


title: 7754315014_L


title: 7754315014_K


title: Patient 0002, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0002, Scheuer score: G1S2

source_name: Hepatic tissue from chronic hepatitis B patients 0002


title: 7754315014_F


title: 7754315086_E


title: 7754315088_C


title: 7754315014_J


title: 7911739003_E


title: 7911739005_I


title: HMEC-1_trophoblastic debris_21hours_rep3

city: AUCKLAND

first: Larry

last: Chamley

address: 85 Park Road

department: Obstetrics and Gynaecology

country: New Zealand

institute: The University of Auckland

description: After co-culture for the indicated length of time, debris was washed off the culture plate by PBS twice before extracting the RNA

hyb_protocol: Following fragmentation, 10 ug of aRNA were hybridized for 16 hr at 45C on GeneChip PrimeView Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.

data_processing: The statistical software program R was used to analyse the results. The data was pre-processed and normalised using RMA from the R package affy. The package limma was used to check for differential expression, and an empirical Bayes method used to moderate the t-statistic. The Benjamini-Hochberg method was used to adjust the p-values for multiple testing

label: Biotin

source_name: Human microvascular endothelial cells treated with human trophoblstic debris for 21 hours rep3

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA (GeneChip 3’IVT Express Kit, Affymetrix).

growth_protocol: HMEC-1 was grown in MCDB 131 medium supplemented with 10% FBS, 1% L-glutamine and 1% Penicillin/Streptomycin at 37°C until 80% confluent

extract_protocol: Total RNA was extraced and purified by Trizol and PureLink® RNA Mini Kit according to the manufacturer's instructions.

treatment_protocol: Trophoblastic debris was added into the HMEC-1 cells culture at the final concentration of 60ug total protein per Ml for either 2 or 21 hours.

tag: gestation week

value: gestation week smaller than 12 weeks

tag: vesicle size

value: debris diameter larger than 10µm

tag: cell line


title: 7754315086_D


title: 7754315014_A

source_name: SMO L412F


title: 7754315014_C

source_name: SMO W535L

value: SMO W535L


title: 7754315014_G


title: Patient 0004, hepatic tissue

description: Gene expression of hepatic tissue from chronic hepatitis B patients 0004, Scheuer score: G1S2

source_name: Hepatic tissue from chronic hepatitis B patients 0004


title: 7911739003_D


title: 7911739005_J


title: 7754315086_B


title: UBP1b ox heatstress rep. 3

city: Yokohama

first: Akihiro

last: Matsui

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Sustainable Resource Science

country: Japan

institute: RIKEN

hyb_protocol: 600 ng of cRNAs  were hybridized to the microarray (GPL20796) at 65 degree for 17 hours, using Gene Expression Hybridization kit. After hybridization, the microarray was washed with Gene Expression Wash Buffer 1 (Agilent) and Gene Expression Wash Buffer  (Agilent), and then dried immediately by brief centrifugation.

scan_protocol: The microarray was scanned by Agilent DNA Microarray Scanner G2505B and  raw data was extracted using Feature Extraction program ver 9.1.

data_processing: RMA normalization was performed for signals of microarray probes using limma package (Ritchie et al., 2015) on R 2.12.1 program.

organism: Arabidopsis thaliana

source_name: UBP1b ox heatstress

label_protocol: Fluorescent-labeled (Cy3) cRNAs were prepared from 400 ng total RNA from each sample using a Quick Amp labeling kit (Agilent Technologies)

growth_protocol: Seeds of Arabidopsis thaliana (Venus-UBP1b-overexpressing and Venus control, Col-0 ecotype) were grown on MS medium at 22°C under 16-h-light/8-h-dark for 14 days.

extract_protocol: RNA was extracted from at least three biological replicates with the Plant RNA Reagent (Thermo Fisher Scientific) according to the manufacturer’s instructions

treatment_protocol: The heat treatment was performed using 40°C condition. Samples were collected at different time points: 0 h (non-treated) and 1h.

tag: ecotype

tag: genotype/variation

value: UBP1 overexpressing

tag: treatment

value: heat stress


title: HMEC-1_untreated_21hours_rep3

source_name: untreated human microvascular endothelial cells at 21hours rep3

value: no trophoblastic tissue


title: RPMI_GSKJ5_2000_6

city: Oxford

first: Udo

last: Oppermann

state: Oxfordshire

address: Botnar Research Centre, Nuffield Orthopaedic Centre, Windmill Road

department: Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences

country: United Kingdom

institute: University of Oxford

description: SAMPLE 12

hyb_protocol: Stanard Illumina Human_HT12V4

scan_protocol: Standard Illumina Genome Studio

data_processing: Data analyzed using the lumi and Bioconductor packages in R.  Data processed using the lumiExpresso function with all default values.

source_name: RPMI Cell line

label_protocol: Illumina TotalPrep RNA amplification kit

growth_protocol: Standard cell culture procedures - cells in log phase of growth.

extract_protocol: Total RNA extracted using Trizol reagent according to manufacturer's recommendation.  Quantification and quality control using both Nanodrop 1000 and Agilent Bioanalyzer

value: RPMI

tag: dose (nm)

tag: treatment time


title: RPMI_GSKJ4_2000_6

description: SAMPLE 11


title: JJN3_GSKJ5_2000_6

description: SAMPLE 9

source_name: JJN-3 Cell line


title: HMEC-1_untreated_21hours_rep2

source_name: untreated human microvascular endothelial cells at 21hours rep2


title: UBP1b ox heatstress rep. 1


title: UBP1b ox non-stress rep. 3

source_name: UBP1b ox non-stress

value: non-stress


title: RPMI_DMSO_6

description: SAMPLE 10

value: DMSO


title: UBP1b ox heatstress rep. 2


title: UBP1b ox non-stress rep. 1


title: HMEC-1_trophoblastic debris_2hours_rep3

source_name: Human microvascular endothelial cells treated with human trophoblstic debris for 2hours rep3


title: Venus heat stress rep. 3

source_name: Venus heat stress

value: vector control


title: HMEC-1_untreated_2hours_rep3

source_name: untreated human microvascular endothelial cells at 2hours rep3


title: HMEC-1_trophoblastic debris_21hours_rep2

source_name: Human microvascular endothelial cells treated with human trophoblstic debris for 21 hours rep2


title: Venus heat stress rep. 2


title: HMEC-1_untreated_21hours_rep1

source_name: untreated human microvascular endothelial cells at 21hours rep1


title: UBP1b ox non-stress rep. 2


title: JJN3_DMSO_6

description: SAMPLE 7


title: JJN3_Bortez_10_6

description: SAMPLE 6

value: Bortezomib


title: JJN3_GSKJ5_500_24

description: SAMPLE 5


title: JJN3_GSKJ4_2000_6

description: SAMPLE 8


title: HMEC-1_untreated_2hours_rep1

source_name: untreated human microvascular endothelial cells at 2hours rep1


title: HMEC-1_untreated_2hours_rep2

source_name: untreated human microvascular endothelial cells at 2hours rep2


title: Venus non-stress rep. 3

source_name: Venus non-stress


title: HMEC-1_trophoblastic debris_2hours_rep2

source_name: Human microvascular endothelial cells treated with human trophoblstic debris for 2hours rep2


title: Venus heat stress rep. 1


title: HMEC-1_trophoblastic debris_21hours_rep1

source_name: Human microvascular endothelial cells treated with human trophoblstic debris for 21 hours rep1


title: JJN3_GSKJ5_2000_24

description: SAMPLE 4


title: JJN3_GSKJ4_500_24

description: SAMPLE 3


title: Strain BP536 RisA D60N versus BP536 replicate 2

status: Public on Aug 20 2016

city: Lille

first: David

last: Hot

address: 1 rue du professeur Calmette

department: Center for Infection and Immunity of Lille

country: France

institute: Institut Pasteur de Lille

description: BP536 vs BP536 RisA D60N comparison

hyb_protocol: Hybridization was performed in 40% formamide, 5x Denhardt’s solution, 0.1% SDS, 1 mM Sodium pyrophosphate and 5x SSC during 14-16h at 52°C under agitation in rotating oven. Slides were then washed sequentially in 2× SSC/0.2% SDS during 5 min, 0.5× SSC during 10 min, 0.05x SSC during 5 min and 0.01x SSC during 1 min at room temperature before drying.

scan_protocol: Scanned on an Innoscan 700 scanner (Innopsys), images were segmented using Mapix Software (version 3.2.1).

data_processing: For normalization and differential expression analyses the LIMMA package (Linear Models for Microarray Data), running under the statistical language R v2.15.0, was used. Statistically significant regulation was identified using moderated t-statistic with empirical Bayes shrinkage of the standard errors. Because of multiple testing, obtained P-values were corrected using Benjamini & Hochberg method to control false discovery rates.

organism: Bordetella pertussis

source_name: pellet of bacteria

label_protocol: 15 µg of total RNA was reverse transcribed with 400 units of SuperScript III (Invitrogen) in presence of 100µM Cy3-dCTP or Cy5-dCTP (GE) and 300 mM of hexanucleotide random (Roche) during 2 hours à 42°C. The labelled cDNA was then NaOH treated to degrade RNA and purified on Qiaquick PCR purification kit (Qiagen) according to the manufacturer’s instructions.

growth_protocol: Bordetella pertussis strains were first grown on Bordet-Gengou (BG) agar plates and in Stainer-Scholte (SS) liquid medium supplemented with 100 µg/ml streptomycin

extract_protocol: Total RNA extracted using TriReagent (Ambion) following manufacturer's instructions

tag: strain

tag: genotype

value: Wild-type

tag: modulation mg

value: No

value: RisA D60N mutant

tag: modulation


title: Strain BP536 RisA D60N versus BP536 replicate 1, dye-swap

description: BP536 vs BP536 RisA D60N comparison


title: Strain BP536 RisA D60N Mg modulated versus BP536 replicate 2, dye-swap

description: BP536 vs BP536 RisA D60N Mg comparison

value: Yes


title: Strain BP536 RisA D60N versus BP536 replicate 2, dye-swap

description: BP536 vs BP536 RisA D60N comparison


title: Strain BP536 RisA D60N Mg modulated versus BP536 replicate 1

description: BP536 vs BP536 RisA D60N Mg comparison


title: Venus non-stress rep. 1


title: Strain BP536 RisA D60N Mg modulated versus BP536 replicate 1, dye-swap

description: BP536 vs BP536 RisA D60N Mg comparison


title: Strain BP536 RisA D60E Mg modulated versus BP536 replicate 1

description: BP536 vs BP536 RisA D60E Mg comparison

value: RisA D60E mutant


title: Strain BP536 RisA Mg modulated versus BP536 replicate 2, dye-swap

description: BP536 vs BP536 RisA Mg comparison

value: RisA mutant


title: Strain BP536 RisA D60E Mg modulated versus BP536 replicate 2, dye-swap

description: BP536 vs BP536 RisA D60E Mg comparison


title: Strain BP536 RisA D60E Mg modulated versus BP536 replicate 1, dye-swap

description: BP536 vs BP536 RisA D60E Mg comparison


title: Strain BP536 RisA D60N Mg modulated versus BP536 replicate 2

description: BP536 vs BP536 RisA D60N Mg comparison


title: Strain BP536 RisA D60E Mg modulated versus BP536 replicate 2

description: BP536 vs BP536 RisA D60E Mg comparison


title: Strain BP536 RisA D60E versus BP536 replicate 1, dye-swap

description: BP536 vs BP536 RisA D60E comparison


title: Strain BP536 RisA Mg modulated versus BP536 replicate 1

description: BP536 vs BP536 RisA Mg comparison


title: Strain BP536 RisA D60N versus BP536 replicate 1

description: BP536 vs BP536 RisA D60N comparison


title: Strain BP536 RisA D60E versus BP536 replicate 1

description: BP536 vs BP536 RisA D60E comparison


title: Strain BP536 RisA Mg modulated versus BP536 replicate 2

description: BP536 vs BP536 RisA Mg comparison


title: HMEC-1_trophoblastic debris_2hours_rep1

source_name: Human microvascular endothelial cells treated with human trophoblstic debris for 2hours rep1

value: gestation week smaller than 12 weeks


title: Strain BP536 RisA D60E versus BP536 replicate 2, dye-swap

description: BP536 vs BP536 RisA D60E comparison