title: WNV-M2011-01_WT_CN_IFNb_12h_d

source_name: Mouse cortical neuron IFNb 100  IU/mL treated for 12h hours, replicate d

value: d


title: human esophageal squamous cell carcinoma cell line_TE-10

status: Public on Dec 09 2014

type: RNA

city: Shimotsuke

first: Toshiro

last: Niki

state: Tochigi

address: 3311-1 Yakushiji

department: Department of Integrative Pathology

country: Japan

institute: Jichi Medical University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133 plus2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using 3000 7G

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

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA

growth_protocol: Cells were cultured in RPMI(cancer cell) or DMEM(fibroblast) supplemented with 10% FBS, antibiotics, and glutamine at 37°C in a humidified atmosphere with 5% CO2.

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

treatment_protocol: No specific treatments were done.

tag: cell line

tag: cell type

value: squamous cell carcinoma


title: human esophageal squamous cell carcinoma cell line_TE-15


title: DUC_3031

city: Nantes

first: Richard

last: Danger

address: 30 Boulevard Jean Monnet

country: France

institute: CHU Nantes - INSERM- Nantes Universite

description:
DUC_3031_13292_2_4

This Sample represents one channel of a dual-channel array.

hyb_protocol: cRNA samples were hybridized to an Agilent Technologies Human Gene Expression 8x60K Microarray during 17 hours at 65°C in a rotating hybridization oven (Agilent Technologies). The hybridization slides were washed, stabilized, dried, and immediately scanned.

scan_protocol: Scanned with an Agilent Technologies Microarray Scanner using default parameters (protocol GE2_107_Sep09 and Grid: 028004_D_F_20110325). Each sample represents one channel of a dual-channel array.

data_processing: Data extraction of median feature intensity without background subtraction was peformed with Feature Extraction software v10.7.1.1 (gMedianSignal or rMedianSignal column) (Agilent Technologies). In order to remove systemic signal intensity bias between each array, median feature intensity were normalized with the function lowess (Locally weighted scatterplot smoothing) method, and then spots with half of the samples exhibiting signal less than the mean of all median signals were removed (threshold: 90.83). 30,146 spots were kept out of 58,717.

source_name: Whole blood sample, CF

label_protocol: The cRNA labeling was performed according to Protocol from Agilent Technologies Inc. (Santa Clara, CA) using the Agilent Quick Amp Labeling Kit (Agilent Technologies, Palo Alto, CA) following the two-colour manufacturer's protocol. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted from whole blood using the PAXgeneTM Blood RNA System Kit (PreAnalytix, CA, USA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop ND-1000 spectrophotometer, and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Blood was collected in a PAXgene® tube, incubated at room temperature for 4h for RNA stabilization and then stored at -80°C.

tag: disease state

value: cystic fibrosis (CF)

tag: tissue

value: whole blood

tag: gender

value: female


title: FOAM_10041_V0

description:
FOAM_10041_V0_13297_1_3

This Sample represents one channel of a dual-channel array.

source_name: Whole blood sample, PAH

value: pulmonary arterial hypertension (PAH)

value: male


title: COG_8019

description:
COG_8019_13296_2_3

This Sample represents one channel of a dual-channel array.


title: human esophageal squamous cell carcinoma cell line_TE-11


title: DEA_5010

description:
DEA_5010_13292_2_1

This Sample represents one channel of a dual-channel array.


title: CAS_3030_V0

description:
CAS_3030_V0_13292_2_2

This Sample represents one channel of a dual-channel array.


title: CTL_AN13295_ba41-42-22_6.3

type: SRA

city: Los Angeles

first: Neelroop

last: Parikshak

state: California

address: 695 Charles E. Young Dr. South

country: USA

institute: UCLA

description: Total RNA (rRNA depleted)

library_source: transcriptomic

data_processing:
Aligned to the Human reference genome assembly GRCh37.73 using Tophat2 {v2.0.9, Trapnell:2012gg} as follows:  tophat -o outputfolder -g 10 -p 8 -r 99 --no-novel-juncs -G GRCh37.73.gtf hg19bowtieindex pairedread1.fastq pairedread2.fastq  Aligned reads were sorted and reads mapped to different chromosomes were removed from the BAM file using samtools v0.1.19.
Quantification of gene expression levels with HTSeq (v.0.6.1) with a union exon model as follows:  python -m HTSeq.scripts.count --stranded=no --mode=union --type=exon --quiet inputfile.sam --GTF GRCh37.73.gtf >> outputfolder
Calculated FPKM values from count level data as follows: datFPM <- sweep(log2(datExpr + 1), 2, log2(apply(datExpr,2,sum)/10^6))  keep <- apply(datFPM>1,1,sum)>(0.80*ncol(datFPM)) ## Keep those with > 1 FPM in 80% of samples                                         datExpr <- datFPM[keep,]. Adjusted expression values were calculated by running the following linear model: lm.out <- lm(thisExpr ~ diagnosis + age + sex + RIN + brainbank + seqStatPC1 + seqStatPC2); where seqStatPC1 and seqStatPC2 are calculated from the first two principal components from the 15 sequencing quality metrics. Followed by: thisExpr.reg <- coef[1] + coef[2]*regvars[,"diagnosis"] + lm.out$residuals; where coef[1] and coef[2] are the intercept and the coefficient corresponding to diagnosis, respectively.
Genome_build: hg19
Supplementary_files_format_and_content: Count-level data generated by HTSeq; adjusted FPKM values generated in R as described in the data processing step

source_name: Post-mortem brain tissue

extract_protocol:
Approximately 100mg of tissue across the cortical region of interest was isolated from each sample for up to two RNA extractions using the miRNeasy kit (Qiagen). The best RNA extraction based on RIN was used for RNA-seq.
Ribosomal RNA was depleted from 2ug total RNA with the Ribo-Zero Gold kit (Epicentre). Remaining RNA was then size selected with AMPure XP beads (Beckman Coulter) and resuspended in 8.5 ul of Illumina resuspension buffer and an additional 8.5 ul of 2x EPF buffer. Subsequent steps followed the Illumina TruSeq protocol (starting at page 84 of the sample prep v2 guide, no changes). After this protocol was followed, libraries were quantified with the Quant-iT PicoGreen assay (Life Technologies) and validated on an Agilent 2200 TapeStation system. Libraries were pooled to multiplex 24 samples per lane using Illumina barcodes, and each pool was sequenced six times on a HiSeq2000/2500 instrument using high output mode with standard chemistry and protocols for 50bp paired end reads. Most libraries were sequenced across two sequencing cores at UCLA. Read quality was similar across both core facilities, and reads across six lanes for each sample were pooled after demultiplexing (with Casava v1.8) for downstream analysis.

tag: brainid

tag: regionid

tag: diagnosis

value: CTL

tag: age

tag: Sex

value: M

tag: rin

tag: brainbank

value: ATP

tag: pmi


title: CTL_AN08677_ba41-42-22_8

description: Total RNA (rRNA depleted)


title: CTL_UMB4842_ba41-42-22_8.1

description: Total RNA (rRNA depleted)

value: NICHD

tag: primarycauseofdeath

value: Airway obstruction


title: human esophageal squamous cell carcinoma cell line_TE-8


title: BOSA_10009_V0

description:
BOSA_10009_V0_13297_1_4

This Sample represents one channel of a dual-channel array.


title: human esophageal squamous cell carcinoma cell line_TE-9


title: WNV-M2011-01_WT_CN_IFNb_12h_a

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

description: Gene expression after 12 hours in IFNb treated neurons

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B).

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and RMA Bioconductor packages.

organism: Mus musculus

source_name: Mouse cortical neuron IFNb 100  IU/mL treated for 12h hours, replicate a

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

growth_protocol: Cortical neurons and granule cell neurons were generated from embryonic day 15 (E15) mouse embryos and 6-day-old neonatal mice, respectively. Cells were seeded onto poly-D-lysine/laminin-coated plates and cultured in serum-free Neurobasal/B27 medium (Invitrogen). The purity of neuron cultures (>95%) was determined after staining with anti-MAP-2 (Sigma), anti-glial fibrillary acidic protein (Dako), and anti-CD11b (BD Biosciences) antibodies.

extract_protocol: Total RNA was isolated according to the manufacturer’s protocol with an RNeasy kit (Qiagen)

treatment_protocol: IFN-β treatment or virus infection was performed on neurons cultured for 3 to 4 days. The cultures were incubated for 24 hours at 37 ºC in a humidified incubator with 5% CO2.

value: Cortical neuron

tag: treatment

value: IFNb

tag: timepoint (hours)

tag: replicate

value: a

tag: strain


title: CTL_AN12137_ba41-42-22_6.4

description: Total RNA (rRNA depleted)

value: Asphyxia


title: CTL_AN19760_ba41-42-22_6.1

description: Total RNA (rRNA depleted)

value: Unknown


title: BOC_3027

description:
BOC_3027_13295_1_2

This Sample represents one channel of a dual-channel array.


title: CTL_AN14757_ba41-42-22_8

description: Total RNA (rRNA depleted)

value: Heart Attack


title: WNV-M2011-01_WT_CN_IFNb_12h_c

source_name: Mouse cortical neuron IFNb 100  IU/mL treated for 12h hours, replicate e

tag: cell type

value: c


title: FOAM_1031

description:
FOAM_1031_13295_1_4

This Sample represents one channel of a dual-channel array.

tag: disease state

value: cystic fibrosis (CF)


title: CTL_AN10833_ba41-42-22_1.8

description: Total RNA (rRNA depleted)


title: DAV_6005_V0

description:
DAV_6005_V0_13296_1_3

This Sample represents one channel of a dual-channel array.

tag: tissue

value: whole blood


title: CTL_UMB4590_ba41-42-22_8.3

description: Total RNA (rRNA depleted)

value: Cardiac Arrest

tag: secondarycauseofdeath

value: Dilated Cardiomyopathy; Morbid Obesity


title: CTL_AN07444_ba41-42-22_8.2

description: Total RNA (rRNA depleted)

tag: brainid

value: Hanging


title: ABA_3055

description:
ABA_3055_13292_1_2

This Sample represents one channel of a dual-channel array.

tag: gender

value: male


title: human esophageal squamous cell carcinoma cell line_TE-6

tag: cell line

value: squamous cell carcinoma


title: BOL_3053

description:
BOL_3053_13292_1_4

This Sample represents one channel of a dual-channel array.

value: female


title: ASD_AN09714_ba41-42-22_7.2

description: Total RNA (rRNA depleted)

tag: regionid

tag: diagnosis

value: ASD

tag: age

value: M

value: ATP

value: Pancreatic Cancer


title: human esophageal squamous cell carcinoma cell line_TE-5


title: human esophageal squamous cell carcinoma cell line_TE-1


title: ASD_AN08043_ba41-42-22_7.8

description: Total RNA (rRNA depleted)

tag: Sex

value: F

tag: rin

tag: brainbank


title: ASD_AN03632_ba41-42-22_8.1

description: Total RNA (rRNA depleted)

tag: pmi

tag: primarycauseofdeath

value: Cancer

value: Colorectal spread through abdomen


title: human esophageal squamous cell carcinoma cell line_TTN

value: TTN


title: ASD_AN01971_ba41-42-22_2.9

description: Total RNA (rRNA depleted)

value: Aspiration

value: Pneumonitis


title: human esophageal squamous cell carcinoma cell line_TE-4


title: human esophageal squamous cell carcinoma cell line_TT

value: TT


title: human esophageal squamous cell carcinoma cell line_KYSE270


title: human esophageal squamous cell carcinoma cell line_KYSE180


title: ASD_AN12457_ba41-42-22_6

description: Total RNA (rRNA depleted)

value: Seizure Disorder


title: ASD_AN08166_ba41-42-22_6.4

description: Total RNA (rRNA depleted)

value: Seizure Suspected


title: human esophageal squamous cell carcinoma cell line_KYSE70


title: human esophageal squamous cell carcinoma cell line_KYSE50


title: MNX1

city: Illkirch/Strasbourg

first: Wolfgang

last: Raffelsberger

address: 1 rue Laurent Fries

department: DBGS

institute: IGBMC

description: VCaP xenograft replicate 1

hyb_protocol: Following fragmentation, cRNA was hybridized on Affymetrix 430.2 mouse GeneChips and the arrays were washed and stained in the Affymetrix Fluidics Station 450 according to the andard Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2007, Affymetrix).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 7G scanner

data_processing: We used a special cdf-mask to extract only signal-intensity values specific for mouse transcripts. Human-mouse cross-hybridizing probe-sets that were masked/excluded are shown with 'null' as intensity values. Probe masking is implemented by modifying the cdf environment in BioConductor and standard RMA signal estimation was subsequently applied to the truncated probe sets. CEL files were quantile normalized as part of the standard RMA signal estimation procedure. Procedure based on Naef et al, NAR 2005, PMID: 16030348.

source_name: mouse bone marrow

label_protocol: Biotinylated cRNA was prepared from the total RNA according to the Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2008, Affymetrix)

growth_protocol: Animals were grown until post-natal 8 weeks age. Animals were housed with ad-lib access to food and water.

extract_protocol: RNA was extracted using RNEasy isolation kit for soft tissue (Qiagen).

treatment_protocol: C4-2B, VCaP and Ep156T cells were inoculated in the bone marrow cavity of the left tibia of 8 weeks old male CB17 SCID mice. As control (sham), animals were injected with phosphate-buffered saline (PBS) alone. Mice xenografted with VCaP or Ep156T cells were sacrificed after 6 weeks, those inoculated with C4-2B after 8 weeks. Sham operated and intact animals were sacrificed at both time points.

value: CB17 SCID

value: bone marrow

tag: xenograft

value: VCaP human cells

tag: genotype

value: wt/wt


title: MBS1

description: sham bone replicate 1

tag: strain

value: PBS


title: human esophageal squamous cell carcinoma cell line_KYSE140

tag: cell type

value: squamous cell carcinoma


title: MCX3

description: intact bone replicate 3

tag: tissue


title: MBS2

description: sham bone replicate 2


title: MNX2

description: VCaP xenograft replicate 2


title: MCX2

description: C4-2B4 xenograft replicate 2

value: C4-2B4 human cells


title: human esophageal squamous cell carcinoma cell line_KYSE150


title: human esophageal squamous cell carcinoma cell line_KYSE220


title: human esophageal squamous cell carcinoma cell line_KYSE170


title: MBM3

description: C4-2B4 xenograft replicate 3


title: human esophageal squamous cell carcinoma cell line_KYSE30


title: MBM1

description: intact bone replicate 1


title: ASD_AN08792_ba41-42-22_5.1

description: Total RNA (rRNA depleted)

value: ASD

value: M

value: ATP

value: Gastrointestinal Bleeding

tag: secondarycauseofdeath

value: CP; Seizure Disorder


title: MVX2

description: Ep156T xenograft replicate 2

value: Ep156T human cells


title: ASD_AN01570_ba41-42-22_7.1

description: Total RNA (rRNA depleted)

tag: brainid

value: F

value: SUDEP


title: MBM2

description: intact bone replicate 2


title: MCX1

description: C4-2B4 xenograft replicate 1


title: ASD_AN00493_ba41-42-22_7.3

description: Total RNA (rRNA depleted)

value: Drowning

value: Respiratory Arrest


title: ASD_AN04682_ba41-42-22_8.2

description: Total RNA (rRNA depleted)

value: Asphyxia

value: Hanging


title: ASD_AN02987_ba41-42-22_8.6

description: Total RNA (rRNA depleted)

value: Head Trauma


title: GAL_3014_V1R

description:
GAL_3014_V1R_13292_1_1

This Sample represents one channel of a dual-channel array.

tag: disease state

value: pulmonary arterial hypertension (PAH)

value: whole blood

tag: gender

value: female


title: MVX3

description: VCaP xenograft replicate 3

value: CB17 SCID

value: bone marrow

value: VCaP human cells

value: wt/wt


title: MVX1

description: Ep156T xenograft replicate 1


title: ASD_UMB5278_ba41-42-22_7.8

description: Total RNA (rRNA depleted)

tag: regionid

value: ASD

value: NICHD

value: Associated with seizure disorder


title: RVF_sample 13

status: Public on Dec 08 2014

city: Groningen

first: vincent

last: bloks

department: Pediatrics

country: Netherlands

institute: UMCG

description: Right ventricular wall

hyb_protocol: Hybridisation of 5.5ug labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual

scan_protocol: Washing and staining of the arrays was done on a Affymetrix 450 fluidics stations using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual. Arrays where then scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual

data_processing: The data where normalized using RMA normalisation strategies using the MADMAX analysis pipeline pmid:21778530

label: Biotin

organism: Rattus norvegicus

label_protocol: The Affymetrix GeneChip WT Sense Target Labeling and Control Reagents kit (P/N 900652) was used for the preparation of labelled cDNA from 500ng of total RNA without rRNA reduction

extract_protocol: total RNA

treatment_protocol: RNA was extracted out the right vetricular wall of the heart, Rats where sham operated or subjected to pulmonary atery banding,

value: Wistar

value: Males

tag: bw (body weight)

tag: condition

value: RVF

value: Right ventricular wall


title: RVF_sample 14

description: Right ventricular wall


title: RVF_sample 15

description: Right ventricular wall


title: RVF+_sample 10

description: Right ventricular wall

value: RVF+


title: RVF+_sample 12

description: Right ventricular wall


title: RVF+_sample 11

description: Right ventricular wall


title: RVF+_sample 9

description: Right ventricular wall


title: CON_sample 1

description: Right ventricular wall

value: CON


title: CON_sample 6

description: Right ventricular wall


title: HCC827_methylation

type: genomic

city: Houston

first: Amin

middle: A

last: mOMIN

state: TX

address: 6767 Bertner Ave

department: Clinical cancer prevention

institute: MD anderson cancer center

description: sample

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina scan protocol

data_processing: Illumina BeadStudio software v3.2

label: Cy3 and Cy5

molecule: genomic DNA

source_name: Lung cancer cell line

label_protocol: Standard Illumina protocol

growth_protocol: All cell lines were grown in 10% FBS + RPMI 1640 at 37 C at 5% CO2

extract_protocol: Genomic DNA by phenol-chloroform

treatment_protocol: Bisulfite treatment

tag: cell line

value: Lung cancer cell line HCC827

tag: histology

value: adenocarcinoma

tag: age

tag: Sex

tag: tumor origin

value: primary

tag: emt state

value: Hybrid


title: CON_sample 3

description: Right ventricular wall


title: HCC4011_methylation

description: sample

value: Lung cancer cell line HCC4011

value: male

value: unknown


title: RVF_sample 16

description: Right ventricular wall


title: CON_sample 2

description: Right ventricular wall


title: CON_sample 5

description: Right ventricular wall


title: RVF+_sample 8

description: Right ventricular wall


title: Rat-control-1

city: Harbin

first: Xue

middle: dong

last: bo

state: Heilongjiang

address: 23 Youzheng Street

country: China

institute: The First Affiliated Hospital of Harbin Medical University

description: This sample is of exocrine pancreas AR42J cells

hyb_protocol: Preparation of cRNA from 5 μg of total RNA, hybridizations, washes, and detection were done in accordance with the NimbleGen Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA).

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner.

data_processing: Scanned images (TIFF format) were imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. All gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis. Genes that at least 2 out of 2 samples have values greater than or equal to lower cut-off: 100.0 (“All Targets Value”) were chosen for differentially expressed gene screening. (All these genes can be found from the sheet “All Targets Value” in Gene Expression Profiling Data.xls file).

source_name: Exocrine pancreas AR42J cells

label_protocol: Reverse transcription with by invitrogen Superscript ds-cDNA synthesis kit; ds-cDNA labeling with NimbleGen one-color DNA labeling kit.

growth_protocol: They were cultured in Ham's F12K culture medium containing 10% fetal bovine serum, 100 U/ml penicillin and 100 μg/ml streptomycin in a humidified incubator at 37° C and 5% CO2.

extract_protocol: The cells were collected, and the total RNA was extracted according to the instructions for the Trizol reagent (Invitrogen,Carlsbad, Calif, USA).

treatment_protocol: The cells in the treatment group were stimulated by TLC-S (200 μM/L) for 20 min. The cells in the control group did not receive the treatment.

value: pancreas


title: CON_sample 4

description: Right ventricular wall


title: HCC4006_methylation

description: sample

value: Lung cancer cell line HCC4006


title: HCC4017_methylation

description: sample

value: Lung cancer cell line HCC4017

value: female

value: Epithelial


title: Rat-treatment-1

description: This sample is of exocrine pancreas AR42J cells treated with  taurolithocholic acid 3-sulfate

source_name: Exocrine pancreas AR42J cells treated with taurolithocholic acid 3-sulfate


title: HCC2935_methylation

description: sample

value: Lung cancer cell line HCC2935


title: NCI-H969_methylation

description: sample

value: Lung cancer cell line NCI-H969

value: metastatic


title: HCC4019_methylation

description: sample

value: Lung cancer cell line HCC4019


title: CON_sample 7

description: Right ventricular wall

value: Wistar

value: Males

value: CON

value: Right ventricular wall


title: NCI-H838_methylation

description: sample

value: Lung cancer cell line NCI-H838

value: adenocarcinoma

value: Mesenchymal


title: HCC2279_methylation

description: sample

value: Lung cancer cell line HCC2279

value: unknown

value: Hybrid


title: NCI-H647_methylation

description: sample

value: Lung cancer cell line NCI-H647

value: male


title: NCI-H820_methylation

description: sample

value: Lung cancer cell line NCI-H820

value: Epithelial


title: NCI-H2405_methylation

description: sample

value: Lung cancer cell line NCI-H2405


title: NCI-H2228_methylation

description: sample

value: Lung cancer cell line NCI-H2228

value: female

value: primary


title: NCI-H1792_methylation

description: sample

value: Lung cancer cell line NCI-H1792

value: metastatic


title: NCI-H1944_methylation

description: sample

value: Lung cancer cell line NCI-H1944


title: PC-9_methylation

description: sample

value: Lung cancer cell line PC-9


title: NCI-H1650_methylation

description: sample

value: Lung cancer cell line NCI-H1650

value: adenocarcinoma


title: NCI-H650_methylation

description: sample

value: Lung cancer cell line NCI-H650

value: Mesenchymal


title: NCI-H2009_methylation

description: sample

value: Lung cancer cell line NCI-H2009

value: Hybrid


title: NCI-H1395_methylation

description: sample

value: Lung cancer cell line NCI-H1395


title: NCI-H1437_methylation

description: sample

value: Lung cancer cell line NCI-H1437

value: male


title: NCI-H522_methylation

description: sample

value: Lung cancer cell line NCI-H522


title: fhpR mutant NO #2

city: Bunkyo-ku

first: Hiroyuki

last: Arai

state: Tokyo

address: Yayoi 1-1-1

department: Department of Biotechnology

institute: The University of Tokyo

description: Gene expression data from microaerobically grown P. aeruginosa fhpR mutant after exposure to nitric oxide. It is the second of two biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Target hybridization, staining, and scanning were performed according to the instructions designed for the Pseudomonas aeruginosa genome array by Affymetrix.

scan_protocol: Affymetrix GeneChip Scanner 3000 was used.

data_processing: The Affymetrix GeneChip Operating Software was used for data acquisition and processing.

organism: Pseudomonas aeruginosa

source_name: PDM2665 (fhpR mutant) treated with nitric oxide replicate 2

label_protocol: cDNA synthesized from total RNA was fragmented and labeled using the Enzo BioArray terminal labeling kit.

growth_protocol: P. aeruginosa strains were cultivated microaerobically in 500 ml LB medium in a 1-liter jar fermenter at 37°C with a constant supply of a gas mixture consisting 90% N2 and 2% O2. The gas flux was 0.5 liter/min.

extract_protocol: Total RNA was extracted by a hot-phenol method. After contaminated DNA was eliminated by RQ1 DNase (Promega) treatment, RNA was purified by RNeasy mini columns (Qiagen).

treatment_protocol: The culture was mixed with 2 volumes of RNAprotect Bacterial Reagent (Qiagen) before RNA purification.

tag: genotype

value: fhpR mutant

tag: agent

value: nitric oxide


title: NCI-H1299_methylation

description: sample

value: Lung cancer cell line NCI-H1299


title: NCI-H2122_methylation

description: sample

value: Lung cancer cell line NCI-H2122

value: female


title: NCI-H1993_methylation

description: sample

value: Lung cancer cell line NCI-H1993

value: metastatic


title: NCI-H1975_methylation

description: sample

value: Lung cancer cell line NCI-H1975

value: primary


title: NCI-H2030_methylation

description: sample

value: Lung cancer cell line NCI-H2030

value: adenocarcinoma


title: NCI-H23_methylation

description: sample

value: Lung cancer cell line NCI-H23

value: Mesenchymal


title: fhpR mutant NO #1

description: Gene expression data from microaerobically grown P. aeruginosa fhpR mutant after exposure to nitric oxide. It is the first of two biological replicates used in this experiment, each from separate cultures.

source_name: PDM2665 (fhpR mutant) treated with nitric oxide replicate 1


title: fhpR mutant untreated #2

description: Gene expression data from microaerobically grown P. aeruginosa fhpR mutant before exposure to nitric oxide. It is the second of two biological replicates used in this experiment, each from separate cultures.

source_name: PDM2665 (fhpR mutant) untreated replicate 2

value: untreated


title: NCI-H1373_methylation

description: sample

value: Lung cancer cell line NCI-H1373

value: unknown

value: Hybrid


title: NCI-H1355_methylation

description: sample

value: Lung cancer cell line NCI-H1355

value: male


title: NCI-H1693_methylation

description: sample

value: Lung cancer cell line NCI-H1693


title: NCI-H1573_methylation

description: sample

value: Lung cancer cell line NCI-H1573

value: Epithelial


title: DFC1024_methylation

description: sample

value: Lung cancer cell line DFC1024

value: female


title: NCI-H1568_methylation

description: sample

value: Lung cancer cell line NCI-H1568

value: metastatic


title: DFC1032_methylation

description: sample

value: Lung cancer cell line DFC1032


title: anr mutant expressing DNR NO #2

description: Gene expression data from microaerobically grown P. aeruginosa anr mutant expressing DNR after exposure to nitric oxide. It is the second of two biological replicates used in this experiment, each from separate cultures.

source_name: RManrEXdnr (anr mutant expressing DNR) treated with nitric oxide replicate 2

value: anr mutant expressing DNR

value: nitric oxide


title: anr mutant expressing DNR NO #1

description: Gene expression data from microaerobically grown P. aeruginosa anr mutant expressing DNR after exposure to nitric oxide. It is the first of two biological replicates used in this experiment, each from separate cultures.

source_name: RManrEXdnr (anr mutant expressing DNR) treated with nitric oxide replicate 1


title: fhpR mutant untreated #1

description: Gene expression data from microaerobically grown P. aeruginosa fhpR mutant before exposure to nitric oxide. It is the first of two biological replicates used in this experiment, each from separate cultures.

source_name: PDM2665 (fhpR mutant) untreated replicate 1

value: fhpR mutant


title: dnr mutant NO #2

description: Gene expression data from microaerobically grown P. aeruginosa dnr mutant after exposure to nitric oxide. It is the second of two biological replicates used in this experiment, each from separate cultures.

source_name: RMdnr (dnr mutant) treated with nitric oxide replicate 2

value: dnr mutant


title: dnr mutant NO #1

description: Gene expression data from microaerobically grown P. aeruginosa dnr mutant after exposure to nitric oxide. It is the first of two biological replicates used in this experiment, each from separate cultures.

source_name: RMdnr (dnr mutant) treated with nitric oxide replicate 1


title: dnr mutant untreated #2

description: Gene expression data from microaerobically grown P. aeruginosa dnr mutant before exposure to nitric oxide. It is the second of two biological replicates used in this experiment, each from separate cultures.

source_name: RMdnr (dnr mutant) untreated replicate 2

value: untreated


title: anr mutant untreated #1

description: Gene expression data from microaerobically grown P. aeruginosa anr mutant before exposure to nitric oxide. It is the first of two biological replicates used in this experiment, each from separate cultures.

source_name: RManr (anr mutant) untreated replicate 1

value: anr mutant


title: dnr mutant untreated #1

description: Gene expression data from microaerobically grown P. aeruginosa dnr mutant before exposure to nitric oxide. It is the first of two biological replicates used in this experiment, each from separate cultures.

source_name: RMdnr (dnr mutant) untreated replicate 1


title: anr mutant NO #1

description: Gene expression data from microaerobically grown P. aeruginosa anr mutant after exposure to nitric oxide. It is the first of two biological replicates used in this experiment, each from separate cultures.

source_name: RManr (anr mutant) treated with nitric oxide replicate 1


title: anr mutant expressing DNR untreated #1

description: Gene expression data from microaerobically grown P. aeruginosa anr mutant expressing DNR before exposure to nitric oxide. It is the first of two biological replicates used in this experiment, each from separate cultures.

source_name: RManrEXdnr (anr mutant expressing DNR) untreated replicate 1


title: anr mutant expressing DNR untreated #2

description: Gene expression data from microaerobically grown P. aeruginosa anr mutant expressing DNR before exposure to nitric oxide. It is the second of two biological replicates used in this experiment, each from separate cultures.

source_name: RManrEXdnr (anr mutant expressing DNR) untreated replicate 2


title: PAO1ut untreated #2

description: Gene expression data from microaerobically grown P. aeruginosa PAO1ut before exposure to nitric oxide. It is the second of two biological replicates used in this experiment, each from separate cultures.

source_name: PAO1ut (wild type) untreated replicate 2

value: wild type


title: PAO1ut untreated #1

description: Gene expression data from microaerobically grown P. aeruginosa PAO1ut before exposure to nitric oxide. It is the first of two biological replicates used in this experiment, each from separate cultures.

source_name: PAO1ut (wild type) untreated replicate 1


title: PAO1ut NO #2

description: Gene expression data from microaerobically grown P. aeruginosa PAO1ut after exposure to nitric oxide. It is the second of two biological replicates used in this experiment, each from separate cultures.

source_name: PAO1ut (wild type) treated with nitric oxide replicate 2


title: PAO1ut NO #1

description: Gene expression data from microaerobically grown P. aeruginosa PAO1ut after exposure to nitric oxide. It is the first of two biological replicates used in this experiment, each from separate cultures.

source_name: PAO1ut (wild type) treated with nitric oxide replicate 1


title: anr mutant NO #2

description: Gene expression data from microaerobically grown P. aeruginosa anr mutant after exposure to nitric oxide. It is the second of two biological replicates used in this experiment, each from separate cultures.

source_name: RManr (anr mutant) treated with nitric oxide replicate 2


title: anr mutant untreated #2

description: Gene expression data from microaerobically grown P. aeruginosa anr mutant before exposure to nitric oxide. It is the second of two biological replicates used in this experiment, each from separate cultures.

source_name: RManr (anr mutant) untreated replicate 2


title: Primary tumor_#2_H_2-2_biological rep7

city: Fukui

first: Shinya

last: Kawabe

address: 23-3 Shimoaizuki, Matsuoka, Eiheiji

department: Department of Biochemistry

institute: University of Fukui

description: Gene expression data from the orthotopic transplantated MES-SA/GFP human uterine sarcoma in KSN nude mouse.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G (Affymetrix) .

data_processing: The image data was scaled to the target intensity by one-step Tukey’s biweight algorithm using GeneChip Operating software (Affymetrix). The data analysis was performed on the Subio platform  (Subio Inc., Tokyo, Japan).

source_name: orthotopic transplanted uterine sarcoma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA (Affymetrix).

extract_protocol: TriPure Isolation of total RNA was performed according to the manufacturer's instructions.

value: uterus; uterine sarcoma

tag: subline

tag: metastatic potential

value: high


title: Primary tumor_#2_H_1-2_biological rep5

tag: tissue


title: Primary tumor_#1_H_2_biological rep3


title: Primary tumor_#1_L_1-2_biological rep2

value: low


title: Primary tumor_#1_L_2-1_biological rep3


title: Primary tumor_#2_L_2-2_biological rep7


title: Primary tumor_#1_L_1-1_biological rep1


title: Primary tumor_#1_L_2-2_biological rep4


title: Primary tumor_#2_H_2-1_biological rep6


title: Primary tumor_#2_L_1_biological rep5


title: Primary tumor_#2_H_1-1_biological rep4


title: Primary tumor_#2_L_2-1_biological rep6


title: Primary tumor_#1_H_1-2_biological rep2


title: Primary tumor_#1_H_1-1_biological rep1


title: qRT-PCR gene expression data of human prostate tissue IGP91

city: Heidelberg

first: Ruprecht

last: Kuner

address: Im Neuenheimer Feld 460

department: Molecular Genetics

country: Germany

institute: German Cancer Research Center and National Center of Tumor Diseases

description:
benign
prostate biopsy preparation: After surgical removal of the prostate, tissue samples were immediately taken with a 6 mm punch biopsy instrument from areas that were suspected to contain tumor foci based on information obtained from the preoperative systematic 10 location biopsies. Each tissue punch biopsy was immediately immersed in RNAlater (Qiagen, Hilden, Germany), stored overnight at ambient temperature and frozen at  - 20 C.
tissue section preparation: Preparation of tissue sections: First, the specimen was thawed at room temperature. To elute most of the RNAlater from the tissue, two subsequent washing steps of 5 min each in 10 ml ice-cold sterile PBS-buffer were performed. After fixation using Tissue-TekVR and thorough freezing in a cryo-microtome, cryo-sections were taken, stained with hematoxylin and eosin (HE) and analyzed by an uropathologist. Tissues were only enrolled into the validation if at least 70% of cells were epithelial prostate tumor cells. Then, 10 - 15 subsequent unstained sections were transferred to a cryo-tube.
tissue diagnosis: Tissue sections were HE stained and analyzed by an uropathologist. Normal prostate tissues were collected from tumor free areas and processed as described. In total 51 tumor and 48 benign tissues from different patients were included into miRNA analysis (no patient matched tissues).

data_processing:
The Ct-values of the TaqMan arrays were analyzed for differential occurrences of miRNAs using the statistical computational environment R (http://www.r-project.org/).
Raw data includes measurements from 768 miRNA assays (671 non-redundant assays) derived from both miRNA Taqman array plates V2 A/B.
Data filtering was done as follow: Ct-values not detected in the measurable range (Ct larger 40) were considered as undetermined. A filtering step was applied, wherein Ct values larger 35 were considered as nonspecific. 246 miRNA assays, for which >70% of all values were nonspecific or undetermined, were excluded from the analysis resulting in 522 miRNA assays for further analysis.
Median normalization was performed within each plate series A and B. A quotient from median was calculated for each sample and charged against each raw Ct value.
Fold Change worksheet reports tumor/benign ratios. Limma analysis was used to identify differentially expressed miRNAs between prostate tumor and benign tissues. Only miRNAs with multiple testing adjusted false discovery rates < 0.05 were considered as significant and presented in the worksheet.

label: FAM dye

source_name: human prostate tissue benign

label_protocol: 100 ng total RNA was reverse transcribed to cDNA by priming with a mixture of looped primers and preamplified according to the manufacturer’s instructions (Megaplex Pools with Preamplification, Applied Biosystems, Foster City, CA). Subsequently, quantitative real-time PCR amplification of miRNAs using low-density Taqman arrays v2.0 was performed using the Applied Biosystems 7900 Sequence Detection System.

extract_protocol: Total RNA including miRNAs was extracted using the All-Prep DNA/RNA Mini kit (Qiagen) according to the manufacturer’s instructions. Tissue sections were homogenized in 1ml RLT Plus buffer using TissueLyser (Qiagen). After DNA separation, 1.5 volumes of 100% ethanol were added to the total RNA and the mixture was purified. Total RNA including miRNA was stored at - 80°C.

value: human prostate tissue benign


title: qRT-PCR gene expression data of human prostate tissue IGP89


title: qRT-PCR gene expression data of human prostate tissue IGP87


title: qRT-PCR gene expression data of human prostate tissue IGP86


title: qRT-PCR gene expression data of human prostate tissue IGP92


title: TC1A9_IFN_3

city: Prague

first: Milan

last: Reinis

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR, v. v. i.

hyb_protocol: Standard Illumina hybridization protocol (6-Sample BeadChip with IntelliHyb Seal)

scan_protocol: Standard Illumina scanning protocol

data_processing: Quantile normalisation (limma package), Log2 transformation. Probes were filtered to be present (detection p-value<0,01) in at least one sample when creating comparisons.

label: biotin (Cy3)

label_protocol: Standard Illumina labeling protocol (TotalPrep RNA Ampliﬁcation Kit)

growth_protocol: TC-1/A9 cells were maintained in RPMI 1640 medium supplemented with 10% FCS, 2 mM L-glutamine and antibiotics, cultured at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol: Rneasy Mini Kit Quiagen

treatment_protocol: Cells were cultured in fresh medium for 24 h, after which the medium was removed and the cells were grown in medium containing IFNγ (50 U/ml, R&D Systems, Minneapolis, USA ) for additional 24h.

tag: strain background

tag: cell type

value: tumour cells cultured in vitro.

tag: treated with

value: 50 U/ml IFNγ


title: qRT-PCR gene expression data of human prostate tissue IGP90


title: qRT-PCR gene expression data of human prostate tissue IGP84


title: qRT-PCR gene expression data of human prostate tissue IGP88


title: TC1A9_IFN_2


title: qRT-PCR gene expression data of human prostate tissue IGP83

description:
tumor
prostate biopsy preparation: After surgical removal of the prostate, tissue samples were immediately taken with a 6 mm punch biopsy instrument from areas that were suspected to contain tumor foci based on information obtained from the preoperative systematic 10 location biopsies. Each tissue punch biopsy was immediately immersed in RNAlater (Qiagen, Hilden, Germany), stored overnight at ambient temperature and frozen at  - 20 C.
tissue section preparation: Preparation of tissue sections: First, the specimen was thawed at room temperature. To elute most of the RNAlater from the tissue, two subsequent washing steps of 5 min each in 10 ml ice-cold sterile PBS-buffer were performed. After fixation using Tissue-TekVR and thorough freezing in a cryo-microtome, cryo-sections were taken, stained with hematoxylin and eosin (HE) and analyzed by an uropathologist. Tissues were only enrolled into the validation if at least 70% of cells were epithelial prostate tumor cells. Then, 10 - 15 subsequent unstained sections were transferred to a cryo-tube.
tissue diagnosis: Tissue sections were HE stained and analyzed by an uropathologist. Normal prostate tissues were collected from tumor free areas and processed as described. In total 51 tumor and 48 benign tissues from different patients were included into miRNA analysis (no patient matched tissues).

source_name: human prostate tissue tumor

value: human prostate tissue tumor


title: TC1A9_untreated_1

value: none (control)


title: qRT-PCR gene expression data of human prostate tissue IGP81


title: qRT-PCR gene expression data of human prostate tissue IGP82


title: TC1A9_IFN_1


title: qRT-PCR gene expression data of human prostate tissue IGP80


title: qRT-PCR gene expression data of human prostate tissue IGP79


title: TC1A9_untreated_2


title: qRT-PCR gene expression data of human prostate tissue IGP78


title: qRT-PCR gene expression data of human prostate tissue IGP76


title: NCI-H3255_methylation

description: sample

source_name: Lung cancer cell line

value: Lung cancer cell line NCI-H3255

value: adenocarcinoma

value: female

value: unknown

value: Epithelial


title: TC1A9_untreated_3


title: qRT-PCR gene expression data of human prostate tissue IGP75


title: qRT-PCR gene expression data of human prostate tissue IGP64


title: qRT-PCR gene expression data of human prostate tissue IGP62


title: qRT-PCR gene expression data of human prostate tissue IGP61


title: qRT-PCR gene expression data of human prostate tissue IGP60


title: qRT-PCR gene expression data of human prostate tissue IGP59


title: qRT-PCR gene expression data of human prostate tissue IGP55


title: qRT-PCR gene expression data of human prostate tissue IGP57


title: qRT-PCR gene expression data of human prostate tissue IGP54


title: qRT-PCR gene expression data of human prostate tissue IGP53


title: qRT-PCR gene expression data of human prostate tissue IGP52


title: qRT-PCR gene expression data of human prostate tissue IGP51


title: qRT-PCR gene expression data of human prostate tissue IGP63


title: qRT-PCR gene expression data of human prostate tissue IGP47


title: qRT-PCR gene expression data of human prostate tissue IGP48


title: qRT-PCR gene expression data of human prostate tissue IGP49


title: qRT-PCR gene expression data of human prostate tissue IGP45


title: qRT-PCR gene expression data of human prostate tissue IGP43


title: qRT-PCR gene expression data of human prostate tissue IGP42


title: qRT-PCR gene expression data of human prostate tissue IGP44


title: qRT-PCR gene expression data of human prostate tissue IGP40


title: qRT-PCR gene expression data of human prostate tissue IGP41


title: qRT-PCR gene expression data of human prostate tissue IGP39


title: qRT-PCR gene expression data of human prostate tissue IGP37


title: qRT-PCR gene expression data of human prostate tissue IGP38


title: qRT-PCR gene expression data of human prostate tissue IGP36


title: qRT-PCR gene expression data of human prostate tissue IGP35


title: WT1 post-exercise

city: Montréal

first: Vincent

last: Giguère

state: QC

address: 1160 Pine Ave West, McIntyre Bldg Room 710

department: Goodman Cancer Centre

country: Canada

institute: McGill University

description: WT gastrocnemius post-exercise, biological rep1

hyb_protocol: Hybridization of cRNA was performed according to standard Affymetrix guidelines and the cRNA was stained with streptavidin phycoerythrin.

scan_protocol: The arrays were scanned using a GeneArray Scanner at exciation wavelength 488nm.

data_processing: Microarray probe intensities were RMA normalized using Transcriptome Analysis Console (TAC) software and differential gene expression was subsequently performed using Expression Console software.

source_name: Gastrocnemius muscle, pre-exercise

label_protocol: Total RNA is reverse transcribed into cDNA and in vitro transcription is performed to generate biotin-labeled cRNA for subsequent hybridization.

extract_protocol: Total RNA was extracted from mouse gastrocnemius muscle using an RNeasy Fibrous Tissue Kit (Qiagen).

tag: strain

value: FVB

tag: gender

value: male

tag: genotype/variation

value: Wild type

value: gastrocnemius muscle


title: ERRa KO3 pre-exercise

description: ERRa-null gastrocnemius pre-exercise, biological rep3

source_name: Gastrocnemius muscle, 2 h post exhaustive treadmill running

value: ERRa-null


title: ERRa KO2 post-exercise

description: ERRa-null gastrocnemius post-exercise, biological rep2


title: qRT-PCR gene expression data of human prostate tissue IGP33


title: qRT-PCR gene expression data of human prostate tissue IGP34


title: WT3 post-exercise

description: WT gastrocnemius post-exercise, biological rep3


title: qRT-PCR gene expression data of human prostate tissue IGP32


title: WT2 post-exercise

description: WT gastrocnemius post-exercise, biological rep2


title: WT3 pre-exercise

description: WT gastrocnemius pre-exercise, biological rep3


title: ERRa KO3 post-exercise

description: ERRa-null gastrocnemius post-exercise, biological rep3


title: ERRa KO2 pre-exercise

description: ERRa-null gastrocnemius pre-exercise, biological rep2


title: qRT-PCR gene expression data of human prostate tissue IGP30


title: qRT-PCR gene expression data of human prostate tissue IGP29


title: qRT-PCR gene expression data of human prostate tissue IGP31


title: qRT-PCR gene expression data of human prostate tissue IGP26


title: qRT-PCR gene expression data of human prostate tissue IGP25


title: qRT-PCR gene expression data of human prostate tissue IGP27


title: qRT-PCR gene expression data of human prostate tissue IGP23


title: qRT-PCR gene expression data of human prostate tissue IGP185


title: qRT-PCR gene expression data of human prostate tissue IGP184


title: qRT-PCR gene expression data of human prostate tissue IGP21


title: qRT-PCR gene expression data of human prostate tissue IGP183


title: ERRa KO1 post-exercise

description: ERRa-null gastrocnemius post-exercise, biological rep1


title: ERRa KO1 pre-exercise

description: ERRa-null gastrocnemius pre-exercise, biological rep1


title: qRT-PCR gene expression data of human prostate tissue IGP28


title: qRT-PCR gene expression data of human prostate tissue IGP182


title: qRT-PCR gene expression data of human prostate tissue IGP181


title: WT1 pre-exercise

description: WT gastrocnemius pre-exercise, biological rep1


title: qRT-PCR gene expression data of human prostate tissue IGP190


title: qRT-PCR gene expression data of human prostate tissue IGP180


title: qRT-PCR gene expression data of human prostate tissue IGP18


title: qRT-PCR gene expression data of human prostate tissue IGP179


title: qRT-PCR gene expression data of human prostate tissue IGP178


title: TC1A9_DAC_2

treatment_protocol: Cells were cultured in fresh medium for 24 h, after which the medium was removed and the cells were grown in medium containing 3 μM 5-2´-deoxyazacytidine (DAC) for the 48h (medium was replaced with fresh one with inhibitor after 24h) and for the additional 24 h in the presence of 30 ng/ml Trichostatin A (TSA).

tag: cell line

value: 3 μM 5-2´-deoxyazacytidine (DAC) and 30 ng/ml Trichostatin A (TSA)


title: RVP3_DAC_2

growth_protocol: RVP3 cells were cultured in RPMI 1640 medium supplemented with 10% FCS, 2 mM L-glutamine and antibiotics, cultured at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol: Rneasy Mini Kit Qiagen

value: tumour cells cultured in vitro


title: TC1A9_CTL_2


title: qRT-PCR gene expression data of human prostate tissue IGP175

value: human prostate tissue benign


title: qRT-PCR gene expression data of human prostate tissue IGP176


title: RVP3_DAC_3


title: TC1A9_CTL_3

value: tumour cells cultured in vitro.


title: qRT-PCR gene expression data of human prostate tissue IGP174


title: TC1A9_CTL_1


title: RVP3_CTL_2


title: qRT-PCR gene expression data of human prostate tissue IGP177


title: RVP3_DAC_1


title: TC1A9_DAC_1


title: IB_tissue

city: Minneapolis

first: Jong-Hyuk

last: Kim

state: MN

address: 425 East River Rd.

department: Dept of Veterinary Clinical Science

institute: University of Minnesota

description: gene expression in canine hemangiosarcoma tissue

hyb_protocol: Hybridized to Agilent canine 4 x 44,000 feature gene chips according to Agilent’s Protocol Version 6

scan_protocol: Read using an Agilent High Resolution G2500C scanner (Agilent, Santa Clara, CA, USA)

data_processing:
Agilent quality control algorithms in Expressionist Refiner Module (v. 7.5; Genedata, Basel, Switzerland,) were used to confirm that data from each chip met the manufacturer’s standards for quality control and quality assurance. Of 45,220 features on each array, 35,676 that had annotation to known genes were used for analysis.
Annotated probe signal levels were quantile-normalized and summarized using the GeneChip-Robust Multichip Averaging algorithm in the Expressionist Analyst Module (v. 7.1)

label: Cyanine-3 (Cy3)

organism: Canis lupus familiaris

source_name: canine hemangiosarcoma tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500 ng RNA using the One-Color using Agilent’s Microarray One-Color Quick Amp Labeling kit

growth_protocol: Primary tumor cells or cryopreserved cultured cells. Snap Frozen primary tissue used for 24 samples .

extract_protocol: RNA was isolated using the TriPure Isolation Reagent (Roche Applied Science, Indianapolis, IN, USA) and the RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. Samples determined to be suitable for analysis based on RNA quality (ratio of absorbance at 260 nm over 280 nm between 1.95 and 2.1 and Bioanalyzer RNA Integrity Number > 6.1)

tag: tissue/cell line

value: Tissue

tag: breed

value: Golden Retriever

tag: origin

value: Spleen

tag: il-8 group (high vs low) defined by il-8 median value

value: high


title: RVP3_CTL_3

value: none (control)


title: qRT-PCR gene expression data of human prostate tissue IGP173


title: RVP3_CTL_1


title: TCH_tissue

value: Heart


title: NP_tissue

value: Liver

value: low


title: SAL_tissue


title: qRT-PCR gene expression data of human prostate tissue IGP17


title: qRT-PCR gene expression data of human prostate tissue IGP16


title: GM_tissue

value: Portuguese Water Dog


title: qRT-PCR gene expression data of human prostate tissue IGP144


title: JSP_tissue


title: SAS_tissue


title: qRT-PCR gene expression data of human prostate tissue IGP143


title: RG_tissue

value: German Shepherd


title: qRT-PCR gene expression data of human prostate tissue IGP85


title: FH_tissue


title: SH_tissue


title: qRT-PCR gene expression data of human prostate tissue IGP142


title: qRT-PCR gene expression data of human prostate tissue IGP145


title: JLI_tissue


title: qRT-PCR gene expression data of human prostate tissue IGP141


title: MH_tissue


title: SJ_tissue


title: TS_tissue


title: PA_tissue


title: RC_tissue


title: JLU_tissue

value: Lung


title: TCL_tissue


title: CS_tissue

value: Border Collie


title: MK_tissue

value: Bernese Mtn Dog


title: Lupus PBMCs, non-treated, 19

city: Ann Arbor

first: Celine

middle: C

last: Berthier

state: MI

address: 1150 W. Medical Center Dr, MSRB2

institute: University of Michigan

description:
Lupus_19
Gene expression data from lupus PBMCs not incubated with Pioglitazone.

hyb_protocol: Biotin-labeled cDNA was fragmented and hybridized to Affymetrix Human U133 Plus 2.0 GeneChip arrays (Santa Clara, CA) according to the manufacturer's protocol.

scan_protocol: GeneChip arrays were scanned by GeneChip Scanner 3000 7G according to the Affymetrix Expression Analysis Technical Manual.

data_processing: The data were analyzed using the GenePattern pipeline: RMA method and Human Entrez Gene custom CDF annotation version 10 were used for the normalization.

source_name: PBMCs from lupus human, not incubated with Pioglitazone

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

growth_protocol: Freshly isolated PBMCs were cultured in RPMI/10% FBS in the presence or absence of 1µM pioglitazone (Sigma-Aldrich, St. Louis, MO, USA) for various timepoints. For microarray studies, PBMCs were cultured with pioglitazone for 6 h, harvested and RNA isolated.

extract_protocol: Total RNA was isolated with TriPure (Roche). For microarray analysis, RNA was further purified and concentrated using an RNeasy kit (Qiagen).

treatment_protocol: Cells were incubated in the presence or absence of Pioglitazone for 6 hours prior to RNA harvesting.

tag: disease status

value: systemic lupus erythematosus

value: PBMCs

tag: treatment


title: Lupus PBMCs, Pioglitazone-treated, 20

description:
Lupus_Pio_20
Gene expression data from lupus PBMCs incubated with Pioglitazone.

source_name: PBMCs from lupus human, incubated with Pioglitazone

value: Pioglitazone


title: qRT-PCR gene expression data of human prostate tissue IGP139

value: human prostate tissue benign


title: OH_tissue

value: Tissue


title: Lupus PBMCs, non-treated, 15

description:
Lupus_15
Gene expression data from lupus PBMCs not incubated with Pioglitazone.


title: AH_tissue


title: qRT-PCR gene expression data of human prostate tissue IGP140

description:
benign
prostate biopsy preparation: After surgical removal of the prostate, tissue samples were immediately taken with a 6 mm punch biopsy instrument from areas that were suspected to contain tumor foci based on information obtained from the preoperative systematic 10 location biopsies. Each tissue punch biopsy was immediately immersed in RNAlater (Qiagen, Hilden, Germany), stored overnight at ambient temperature and frozen at  - 20 C.
tissue section preparation: Preparation of tissue sections: First, the specimen was thawed at room temperature. To elute most of the RNAlater from the tissue, two subsequent washing steps of 5 min each in 10 ml ice-cold sterile PBS-buffer were performed. After fixation using Tissue-TekVR and thorough freezing in a cryo-microtome, cryo-sections were taken, stained with hematoxylin and eosin (HE) and analyzed by an uropathologist. Tissues were only enrolled into the validation if at least 70% of cells were epithelial prostate tumor cells. Then, 10 - 15 subsequent unstained sections were transferred to a cryo-tube.
tissue diagnosis: Tissue sections were HE stained and analyzed by an uropathologist. Normal prostate tissues were collected from tumor free areas and processed as described. In total 51 tumor and 48 benign tissues from different patients were included into miRNA analysis (no patient matched tissues).


title: Lupus PBMCs, Pioglitazone-treated, 14

description:
Lupus_Pio_14
Gene expression data from lupus PBMCs incubated with Pioglitazone.


title: EFS_cell

description: gene expression in canine hemangiosarcoma cell line

source_name: canine hemangiosarcoma cell line

value: Cell Line

value: Golden Retriever

value: Brain


title: FH-2_cell

value: Spleen

value: high


title: Lupus PBMCs, Pioglitazone-treated, 16

description:
Lupus_Pio_16
Gene expression data from lupus PBMCs incubated with Pioglitazone.


title: qRT-PCR gene expression data of human prostate tissue IGP138


title: qRT-PCR gene expression data of human prostate tissue IGP137


title: AW_tissue


title: CB_tissue

value: Keeshond


title: Lupus PBMCs, non-treated, 13

description:
Lupus_13
Gene expression data from lupus PBMCs not incubated with Pioglitazone.


title: EFB_cell

value: low


title: qRT-PCR gene expression data of human prostate tissue IGP126


title: qRT-PCR gene expression data of human prostate tissue IGP127


title: qRT-PCR gene expression data of human prostate tissue IGP124


title: JHE-2_cell

value: Heart


title: JHE-1_cell


title: Lupus PBMCs, Pioglitazone-treated, 12

description:
Lupus_Pio_12
Gene expression data from lupus PBMCs incubated with Pioglitazone.


title: Lupus PBMCs, non-treated, 11

description:
Lupus_11
Gene expression data from lupus PBMCs not incubated with Pioglitazone.


title: qRT-PCR gene expression data of human prostate tissue IGP123


title: SB_cell

value: German Shepherd

value: Cutaneous


title: FH-1_cell


title: GM_cell

value: Portuguese Water Dog


title: qRT-PCR gene expression data of human prostate tissue IGP122


title: JLI_cell

value: Liver


title: SH_cell


title: Healthy control PBMCs, Pioglitazone-treated, 8

description:
Ctrl_Pio_8
Gene expression data from healthy control PBMCs incubated with Pioglitazone.

source_name: Control PBMCs from healthy human, incubated with Pioglitazone

value: healthy


title: qRT-PCR gene expression data of human prostate tissue IGP119


title: DD1_cell

value: GR Mix


title: Healthy control PBMCs, non-treated, 9

description:
Ctrl_9
Gene expression data from healthy control PBMCs not incubated with Pioglitazone.

source_name: Control PBMCs from healthy human, not incubated with Pioglitazone

value: PBMCs


title: Healthy control PBMCs, non-treated, 7

description:
Ctrl_7
Gene expression data from healthy control PBMCs not incubated with Pioglitazone.


title: Healthy control PBMCs, Pioglitazone-treated, 6

description:
Ctrl_Pio_6
Gene expression data from healthy control PBMCs incubated with Pioglitazone.

value: Pioglitazone


title: Healthy control PBMCs, Pioglitazone-treated, 10

description:
Ctrl_Pio_10
Gene expression data from healthy control PBMCs incubated with Pioglitazone.


title: JLU_cell

value: Lung


title: qRT-PCR gene expression data of human prostate tissue IGP118

description:
tumor
prostate biopsy preparation: After surgical removal of the prostate, tissue samples were immediately taken with a 6 mm punch biopsy instrument from areas that were suspected to contain tumor foci based on information obtained from the preoperative systematic 10 location biopsies. Each tissue punch biopsy was immediately immersed in RNAlater (Qiagen, Hilden, Germany), stored overnight at ambient temperature and frozen at  - 20 C.
tissue section preparation: Preparation of tissue sections: First, the specimen was thawed at room temperature. To elute most of the RNAlater from the tissue, two subsequent washing steps of 5 min each in 10 ml ice-cold sterile PBS-buffer were performed. After fixation using Tissue-TekVR and thorough freezing in a cryo-microtome, cryo-sections were taken, stained with hematoxylin and eosin (HE) and analyzed by an uropathologist. Tissues were only enrolled into the validation if at least 70% of cells were epithelial prostate tumor cells. Then, 10 - 15 subsequent unstained sections were transferred to a cryo-tube.
tissue diagnosis: Tissue sections were HE stained and analyzed by an uropathologist. Normal prostate tissues were collected from tumor free areas and processed as described. In total 51 tumor and 48 benign tissues from different patients were included into miRNA analysis (no patient matched tissues).

value: human prostate tissue tumor


title: qRT-PCR gene expression data of human prostate tissue IGP117


title: Healthy control PBMCs, Pioglitazone-treated, 4

description:
Ctrl_Pio_4
Gene expression data from healthy control PBMCs incubated with Pioglitazone.


title: HCCIS_2_low_risk [06_HCC_7T_low]

city: Regensburg

first: Stefan

last: Brunner

address: Franz-Josef-Strauss-Allee 11

institute: Univeritaetsklinikum Regensburg

hyb_protocol: Following fragmentation, 12 μg of cRNA were hybridized for 16 h at 45°C on GeneChip PrimeView Human GE Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChip Arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with RMA within Affymetrix Expression Console 1.1.1 using quantile normalization.

label_protocol: Biotinylated cRNA was prepared from 250 ng totalRNA according to the  Affymetrix GeneChip 3’ IVT Express Kit manual (Rev. 6)

extract_protocol: RNA was isolated from fresh tumor tissue of HCCs using the RNeasy Mini Kit (No. 74104, Qiagen, Venlo, Netherlands).

tag: disease

value: hepatocellular carcinoma (HCC)

tag: patient id

value: patient 7

tag: hcc risk group

value: HCCIS 2 low risk group

tag: local cd8 il-33 expression level

value: CD8 IL-33 high


title: HCCIS_2_low_risk [07_HCC_8T_low]

value: patient 8


title: Cerebral cortex_E16.5_n=2

city: Tokyo

first: Shinobu

last: Hirai

address: Setagaya Kamikitazawa 2-1-6

institute: Tokyo Metropolitan Institute of Medical Science

hyb_protocol: The labeled and fragmented aRNAs  (mixture of Cy3 and Cy5) was hybridized onto microarray slide for 16 hours at 60゜C. Slides were washed in 4xSSC+0.1% SDS, 2xSSC+0.1% SSC, 2xSSC, and 1xSSC.And dry by centrifuge.

scan_protocol: Fluorescent array images were scanned for both Cy3 and Cy5 with a ScanArray HT (PerkinElmer, Boston, MA) and signal values were calculated using DNASIS Array (Hitachi Software Engineering, Tokyo, Japan).

data_processing: This data were analyzed by DNASIS array software(Hitachi Software Engineering), which converted the signal intensity of each spot into text format. Log2-ratios of the median subtracted background intensity levels were analyzed. The log ratios of all spots on the DNA microarray were normalized by the method of global ratio median normalization.

source_name: RP58 KO mouse cerebral cortex

label_protocol: Total RNA was amplified, and 5-(3-aminoallyl)-UTP was incorporated to it using AminoAllyl aRNA amplification Kit (SIGMA Aldrich Japan, Tokyo, Japan). The amino allyl aRNA was further labeled by coupling reaction with NHS ester fluorescent dye, Cy5.

extract_protocol: Two independent cortices were mixed and homogenized in Trizol and purified with RNeasy mini kit ( Qiagen).

value: RP58 KO mouse

tag: tissue

value: cerebral cortex

tag: developmental stage

source_name: Wild type mouse cerebral cortex

label_protocol: Total RNA was amplified, and 5-(3-aminoallyl)-UTP was incorporated to it using AminoAllyl aRNA amplification Kit (SIGMA Aldrich Japan, Tokyo, Japan). The amino allyl aRNA was further labeled by coupling reaction with NHS ester fluorescent dye, Cy3.

value: Wild type mouse


title: qRT-PCR gene expression data of human prostate tissue IGP116


title: qRT-PCR gene expression data of human prostate tissue IGP120

value: human prostate tissue benign


title: Healthy control PBMCs, non-treated, 5

description:
Ctrl_5
Gene expression data from healthy control PBMCs not incubated with Pioglitazone.

tag: cell type


title: HCCIS_2_low_risk [08_HCC_13T_low]

value: patient 13


title: Healthy control PBMCs, non-treated, 3

description:
Ctrl_3
Gene expression data from healthy control PBMCs not incubated with Pioglitazone.


title: qRT-PCR gene expression data of human prostate tissue IGP115


title: Healthy control PBMCs, Pioglitazone-treated, 2

description:
Ctrl_Pio_2
Gene expression data from healthy control PBMCs incubated with Pioglitazone.


title: TC1A9_DAC_3

tag: strain background

value: tumour cells cultured in vitro.

tag: treated with

value: 3 μM 5-2´-deoxyazacytidine (DAC) and 30 ng/ml Trichostatin A (TSA)


title: qRT-PCR gene expression data of human prostate tissue IGP113


title: WT2 pre-exercise

description: WT gastrocnemius pre-exercise, biological rep2

tag: strain

value: FVB

tag: gender

value: male

tag: genotype/variation

value: Wild type

value: gastrocnemius muscle


title: qRT-PCR gene expression data of human prostate tissue IGP105

value: human prostate tissue tumor


title: qRT-PCR gene expression data of human prostate tissue IGP110


title: qRT-PCR gene expression data of human prostate tissue IGP104

description:
benign
prostate biopsy preparation: After surgical removal of the prostate, tissue samples were immediately taken with a 6 mm punch biopsy instrument from areas that were suspected to contain tumor foci based on information obtained from the preoperative systematic 10 location biopsies. Each tissue punch biopsy was immediately immersed in RNAlater (Qiagen, Hilden, Germany), stored overnight at ambient temperature and frozen at  - 20 C.
tissue section preparation: Preparation of tissue sections: First, the specimen was thawed at room temperature. To elute most of the RNAlater from the tissue, two subsequent washing steps of 5 min each in 10 ml ice-cold sterile PBS-buffer were performed. After fixation using Tissue-TekVR and thorough freezing in a cryo-microtome, cryo-sections were taken, stained with hematoxylin and eosin (HE) and analyzed by an uropathologist. Tissues were only enrolled into the validation if at least 70% of cells were epithelial prostate tumor cells. Then, 10 - 15 subsequent unstained sections were transferred to a cryo-tube.
tissue diagnosis: Tissue sections were HE stained and analyzed by an uropathologist. Normal prostate tissues were collected from tumor free areas and processed as described. In total 51 tumor and 48 benign tissues from different patients were included into miRNA analysis (no patient matched tissues).


title: HCCIS_2_low_risk [05_HCC_3T_low]

value: hepatocellular carcinoma (HCC)

value: patient 3


title: qRT-PCR gene expression data of human prostate tissue IGP103


title: qRT-PCR gene expression data of human prostate tissue IGP102


title: HCCIS_0_high_risk [02_HCC_5T_high]

value: patient 5

value: HCCIS 0 high risk group

value: CD8 IL-33 low


title: qRT-PCR gene expression data of human prostate tissue IGP111


title: HCCIS_0_high_risk [01_HCC_4T_high]

value: patient 4


title: Healthy control PBMCs, non-treated, 1

description:
Ctrl_1
Gene expression data from healthy control PBMCs not incubated with Pioglitazone.

value: healthy

value: PBMCs


title: HCCIS_0_high_risk [04_HCC_12T_high]

value: patient 12


title: Origin-3

city: Columbus

first: Sandya

last: Liyanarachchi

state: OH

address: Rm 830, 460, W 12th Avenue

department: Human Genetics

institute: OSU

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalized using cubic-spline normalization with Illumina Bead Studio software

source_name: Wt NSC-3

label_protocol: cDNA was prepared with the Invitrogen SuperScript III kit

growth_protocol: Neurosphere culture condition, containing EGF and FGF

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN Lipid RNeasy kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: No treatment

value: C57/129/CBA mix

tag: age

value: adult

value: SVZ neurospheres


title: TF-pMSCVpuro-GNB1K89E-no Cytokine withdrawl-replicate 2

status: Public on Dec 07 2014

city: Boston

first: Andrew

last: Lane

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

hyb_protocol: Following fragmentation, cRNA was hybridized overnight according to the Affymetrix protocol.

scan_protocol: GCS3000 (Affymetrix)

data_processing: The raw cel files were converted into probeset-specific expression values using Affymetrix RMA summarization method using Brainarray cdf annotations (hugene10st_Hs_ENSG.cdf, version 16) with the ExpressionFileCreator module (version 11.14) embedded in the GenePattern environment (Reich et al., 2006).

label_protocol: cRNA was biotinylated according to the standard Affymetrix protocol.

growth_protocol: Total RNA was extracted in biological triplicates using Trizol from stably transfected TF-1 cells (empty vector control vs. K89E) with or without 12 hour cytokine starvation.

extract_protocol: Cells were homogenized in Trizol and RNA was extracted according to standard protocols.

tag: cell line

tag: transduced with

tag: time point

value: 12 after maintained in GM-CSF

tag: cytokine withdrawl

value: no


title: Tumor-1

source_name: Mut6 glioma-1

value: glioma neurospheres


title: TF-pMSCVpuro-GNB1K89E-no Cytokine withdrawl-replicate 1


title: TF-pMSCVpuro-no Cytokine withdrawl-replicate 3

source_name: TF-pMSCVpuro-no Cytokine withdrawl

value: pMSCV-puro empty vector


title: Origin-2

source_name: Wt NSC-2


title: TF-pMSCVpuro-GNB1K89E-no Cytokine withdrawl-replicate 3


title: TF-pMSCVpuro-no Cytokine withdrawl-replicate 2


title: HCCIS_0_high_risk [03_HCC_10T_high]

tag: disease

value: patient 10


title: Tumor-3

source_name: Mut6 glioma-3


title: Origin-1

source_name: Wt NSC-1


title: TF-pMSCVpuro-GNB1K89E-Cytokine withdrawl-replicate 2

value: 12 hrs after GM-CSF withdrawal

value: yes


title: TF-pMSCVpuro-GNB1K89E-Cytokine withdrawl-replicate 3


title: TF-pMSCVpuro-GNB1K89E-Cytokine withdrawl-replicate 1


title: Tumor-2

source_name: Mut6 glioma-2


title: TF-pMSCVpuro-Cytokine withdrawl-replicate 3

source_name: TF-pMSCVpuro-Cytokine withdrawl


title: TF-pMSCVpuro-Cytokine withdrawl-replicate 2


title: TF-pMSCVpuro-no Cytokine withdrawl-replicate 1


title: Endometrium_histology_10A

status: Public on Dec 06 2014

city: Chicago

first: Gulum

last: Kosova

address: 920 E 58th Street

institute: University of Chicago

data_processing: 19,591probes were filtered out because they did not meet the following quality control  (QC) criteria: 1) map uniquely to the HG19 genome using BWA (and there were no secondary  hits with 1 mismatch), 2) overlap an Ensembl gene (release 65) on the same strand, 3) do not  encompass any SNPs included in HapMap CEU with QC+ designation. For the remaining probes, data was log2 transformed and normalized with quantile normalization using the Bioconductor package lumi in the R statistical environment.

source_name: human endometrium

label_protocol: standard Illumina protocol

growth_protocol: Endometrial biopsies were collected during midsecretory phase

extract_protocol: RNA was extracted using Trizol reagent, followed by Qiagen Rneasy mini kit for clean up in accordance with the recommended protocol provided by Qiagen. RNA quality control was performed with Agilent Bioanalyzer.

treatment_protocol: Biopsy samples were frozen immediately and stored in -80C until RNA extraction

value: endometrium

value: Female

tag: classification

value: out-of-phase histology

tag: bmi

tag: microarraychip

value: D

tag: season of biopsy collection

value: f

tag: extraction order

value: A


title: Endometrium_cyclinE_1B

tag: tissue

value: abnormal high cyclin E

value: w

value: B


title: Endometrium_histology_10B

value: E


title: Endometrium_histology_8A

value: H

value: sp


title: Endometrium_histology_5B

value: su


title: Endometrium_histology_8B

value: F


title: Endometrium_histology_7A

value: G


title: Endometrium_histology_7B


title: Endometrium_cyclinE_1A


title: Endometrium_histology_5A


title: Endometrium_histology_3A

value: C


title: Endometrium_histology_6B


title: Endometrium_histology_4B


title: Endometrium_histology_2B


title: Endometrium_histology_6A


title: Endometrium_histology_9A


title: Endometrium_histology_4A


title: Endometrium_histology_2A


title: Endometrium_histology_3B


title: Endometrium_histology_1A


title: Endometrium_histology_1B


title: 3368C

city: Singapore

first: Ahmad Nazri

last: Mohamed Naim

address: 60 Biopolis Street, Genome, #02-01

department: Infectious disease

country: Singapore

institute: Genome institute of Singapore

data_processing: All datasets were normalized by using R (http://www.bioconductor.org). The raw data was log10 transformed before Z score transformation was performed [10]. The Z score was calculated for each sample by subtracting the overall mean gene intensity from the raw intensity signal for each gene. After that, this data was divided by the standard deviation of all of the measured intensities

source_name: Human whole blood

label_protocol: Biotinylated cRNA were pared with the Illumina TotalP RNA Amplification Kit for Illumina arrays

extract_protocol: Total RNA was extracted from whole blood drawn in pax-gene vacutainer tubes by PAX-gene RNA kit (Qiagen). Quality control was performed with NanoDrop 1000 instrument

tag: phase

value: Convalescent

tag: phenotype

value: Severe

tag: doi

tag: aneurysm

value: Normal

tag: ivig

value: Resistant

tag: Sex

value: Whole Blood


title: 3366C

value: Moderate

value: Responsive


title: 3406A

value: Acute


title: 3363C


title: 3368A


title: 3403C

value: Dilated


title: 3386A

value: Aneurysm


title: 3405C


title: 3363A


title: 3402C


title: 3365C


title: 3365A


title: 3400C


title: 3366A


title: 3397C


title: 3402A


title: 3397A


title: 3403A


title: 3395C


title: 3400A


title: 3405A


title: 3244C


title: 3251C


title: 3251A


title: 3244A


title: 3240C


title: 3236A


title: 3240A


title: 3390C

value: OFI


title: TF-pMSCVpuro-Cytokine withdrawl-replicate 1

tag: cell line

value: pMSCV-puro empty vector

value: 12 hrs after GM-CSF withdrawal

value: yes


title: 3392C


title: 3389A


title: 3390A


title: 3394A


title: 3235C


title: 3235A


title: 3389C


title: 3272A


title: 3236C


title: 3219A


title: 3220A


title: 3394C


title: 3246A


title: 3393A


title: 3208A


title: 3262A


title: 3393C


title: 3237C


title: 3227A


title: 3237A


title: 3258A


title: Endometrium_histology_9B

value: endometrium

tag: gender

value: Female

value: out-of-phase histology

tag: age

value: F

value: f

value: B


title: 3204A


title: 3170A


title: 3190A

value: Normal


title: 3192A

value: Whole Blood


title: 3443C

value: Convalescent


title: 3392A

value: Resistant


title: 3202A

value: Acute

value: Responsive


title: 3147A

value: Dilated


title: 3189A

value: OFI


title: 3211A


title: 3174A


title: 3150A


title: 3175A

value: Aneurysm


title: 3065C


title: 3177A


title: 3446C


title: 3205A


title: 3141A


title: 3443A


title: 3442C


title: 3162A


title: 3067A


title: 3012C


title: 3012A


title: 3442A


title: 3004A


title: 3006C


title: 3006A


title: 3395A


title: 3180A


title: 3421A


title: 3204C


title: 3007C


title: 3005C


title: 3054A


title: 3440A


title: 3189C


title: 3430C


title: 3192C


title: 3205C


title: 3004C


title: 3005A


title: 3007A


title: 3440C


title: 3162C


title: 3446A


title: 3191C


title: 3177C


title: 3262C


title: 3147C


title: 3272C


title: 3327C


title: 3258C


title: 3334C


title: 3109C


title: 3332A


title: 3326C


title: 3330C


title: 3246C


title: 3100C


title: 3334A


title: 3102C


title: 3106C


title: 3106A


title: 3100A


title: 3330A


title: 3327A


title: 3096C


title: 3102A


title: 3098C


title: 3109A


title: 3123C


title: 3326A


title: 3123A


title: 3332C


title: 3096A


title: 3098A


title: 3118A


title: 3121C


title: 3115C


title: 3020C


title: 3019C


title: 3121A


title: 3115A


title: 3191A


title: 3013A


title: 3013C


title: 3026A


title: 3119C


title: 3110A


title: 3016A


title: 3119A


title: 3014A


title: 3019A


title: 3014C


title: 3020A


title: 3016C


title: 3110C


title: 3360C


title: 3362A


title: 3361C


title: 3360A


title: 3356C


title: 3362C


title: 3361A


title: 3355C


title: 3355A


title: 3304C


title: 3356A


title: 3304A


title: 3301A


title: 3297C


title: 3297A


title: 3296C


title: 3296A


title: 3293C


title: 3291C


title: 3291A


title: 3290C


title: 3293A


title: 3294A


title: 3301C


title: 3284A


title: 3284C


title: 3288C


title: 3287A


title: 3294C


title: 3290A


title: 3295C


title: 3288A


title: 3063A


title: 3287C


title: 3295A


title: 3059A


title: 3064A


title: 3118C


title: 3063C


title: 3059C


title: 3064C


title: 3058C


title: 3182A


title: 3049C


title: 3054C


title: 3058A


title: 3164C

value: Mild


title: 3127C


title: 3157C


title: 3164A


title: 3182C


title: 3172A


title: 3035A


title: 3172C


title: 3157A


title: 3149C


title: 3035C


title: 3127A


title: 3140A


title: 3145C


title: 3028C


title: 3149A


title: 3145A


title: 3034C


title: 3029C


title: 3033A


title: 3029A


title: 3143C


title: 3033C


title: 3133A


title: 3034A


title: 3037A


title: 3143A


title: 3133C


title: 3263C


title: 3270A


title: 3267C


title: 3270C


title: 3279C


title: 3279A


title: 3278C


title: 3278A


title: 3283A


title: 3266A


title: 3266C


title: 3283C


title: 3261A


title: 3202C


title: 3256A


title: 3261C


title: 3259A


title: 3255C


title: 3026C


title: 3211C


title: 3267A


title: 3220C


title: 3253C


title: 3140C


title: 3028A


title: 3253A


title: 3263A


title: 3259C


title: 3227C


title: 3255A


title: 3256C


title: 3175C


title: 3046A


title: 3047A


title: 3049A


title: 3170C


title: 3038C


title: 3174C


title: 3430A


title: 3038A


title: 3040A


title: 3423C


title: 3180C


title: 3411C


title: 3043A


title: 3150C


title: 3421C


title: 3043C


title: 3411A


title: 3047C


title: 3141C


title: 3190C


title: 3046C


title: 3423A


title: 3410A


title: 3410C


title: 3407C


title: 3407A


title: 3228C


title: 3406C


title: 3225C


title: 3225A


title: 3228A


title: 3040C


title: 3316C


title: 3200A


title: 3214A


title: 3184C


title: 3316A


title: 3188C


title: 3314C


title: 3214C


title: 3310C


title: 3314A


title: 3306A


title: 3313A


title: 3313C


title: 3308A


title: 3184A


title: 3073C


title: 3306C


title: 3188A


title: 3074C


title: 3200C


title: 3073A


title: 3074A


title: 3072C


title: 3310A


title: 3067C


title: 3308C


title: 3068A


title: 3068C


title: 3072A


title: 3065A


title: 3089A


title: 3089C


title: ovarian cancer surgical sample C285

city: Gliwice

first: Katarzyna

middle: Marta

last: Lisowska

address: ul. Wybrzeże Armii Krajowej 15

department: Center for Translational Research  and Molecular Biology of Cancer

country: Poland

institute: MSC Memorial Cancer Center and Institute of Oncology, Gliwice Branch

description: gene expression data from clearcell ovarian cancer

hyb_protocol: 16 ug of fragmented cRNA were hybridized for 16 hr at 45ͦC on HG U133 Plus 2.0 Gene Chip oligonucleotide arrays (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)

data_processing:
acquired by GCOS 1.2 software (Affymetrix); preprocessed by Robust Multiarray Analysis (RMA, Bioconductor)
The data were analyzed with Bioconductor and rma package with default normalization parameters settings

source_name: frozen surgical sample of clearcell ovarian cancer; p53-mutated

label_protocol: Total RNA (8 ug) was used for synthesis of double stranded cDNA according to manufacturer's instructions. Biotinylated cRNA was synthesized with the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics).

extract_protocol: Total RNA was isolated using Rneasy Mini Kit (Qiagen) according to the manufacturer's instructions.

tag: clinical sample

value: surgical tumor sample

tag: histophatological type of tumor

value: clearcell ovarian ca.

tag: adjuwant chemotherapy

tag: brca1 mutation

value: no mutation

tag: somatic tp53 mutation

value: mutation

tag: tp53 accumulation in cancer cells (assesed by immunohistochemistry)

value: accumulation

tag: tumor grade (g1 - well differentiated; g2 - moderately differentiated; g3 - poorly differentiated; g4 - undifferentiated)

tag: residual tumor size (r0 < 1 cm;  1 < r1 < 5 cm; r2 > 5cm)

tag: clinical status post 1st line chemotherapy (cr - complete response; pr - partial response; sd - stable disease; p - progression)

tag: platinium sensitivity (resistant

value: DFS<180 days; moderately sensitive:180>DFS>732; highly sensitive:DFS>732 days):NA

tag: dfs - disease-free survival [days]

tag: os - overall survival [days]

tag: clinical status at last follow-up (awd - alive with disease; dod - dead from disease; ned - no evidence of disease)


title: ovarian cancer surgical sample C304


title: ovarian cancer surgical sample C208

source_name: frozen surgical sample of clearcell ovarian cancer

value: no accumulation


title: ovarian cancer surgical sample C199


title: 3082C

tag: phase

tag: phenotype

tag: doi

tag: aneurysm

tag: ivig

tag: Sex

tag: tissue


title: 3095A

value: Normal


title: ovarian cancer surgical sample C339

tag: clinical sample

tag: histophatological type of tumor

tag: adjuwant chemotherapy

tag: brca1 mutation


title: 3082A

value: Whole Blood


title: 3078C

value: Convalescent


title: 3084C


title: 3350A

value: Resistant


title: 3081A

value: Acute


title: 3350C


title: 3081C

value: Responsive


title: ovarian cancer surgical sample C365

tag: somatic tp53 mutation

tag: tp53 accumulation in cancer cells (assesed by immunohistochemistry)

tag: tumor grade (g1 - well differentiated; g2 - moderately differentiated; g3 - poorly differentiated; g4 - undifferentiated)

tag: residual tumor size (r0 < 1 cm;  1 < r1 < 5 cm; r2 > 5cm)


title: ovarian cancer surgical sample C456

tag: clinical status post 1st line chemotherapy (cr - complete response; pr - partial response; sd - stable disease; p - progression)

tag: platinium sensitivity (resistant

tag: dfs - disease-free survival [days]

tag: os - overall survival [days]


title: 3084A

tag: phase

tag: phenotype

tag: doi

value: Dilated


title: 3095C

tag: aneurysm

tag: ivig

tag: Sex


title: ovarian cancer surgical sample C445

tag: clinical sample

tag: histophatological type of tumor

tag: clinical status at last follow-up (awd - alive with disease; dod - dead from disease; ned - no evidence of disease)


title: ovarian cancer surgical sample C94

tag: adjuwant chemotherapy

tag: brca1 mutation

tag: somatic tp53 mutation


title: ovarian cancer surgical sample E169

description: gene expression data from endometrioid ovarian cancer

source_name: frozen surgical sample of endometrioid ovarian cancer

value: endometrioid ovarian ca.

tag: tp53 accumulation in cancer cells (assesed by immunohistochemistry)

tag: tumor grade (g1 - well differentiated; g2 - moderately differentiated; g3 - poorly differentiated; g4 - undifferentiated)

tag: residual tumor size (r0 < 1 cm;  1 < r1 < 5 cm; r2 > 5cm)


title: ovarian cancer surgical sample E165

description: gene expression data from undifferentiated ovarian cancer

source_name: frozen surgical sample of undifferentiated ovarian cancer; p53-mutated

value: undifferentiated ovarian ca.

tag: clinical status post 1st line chemotherapy (cr - complete response; pr - partial response; sd - stable disease; p - progression)

tag: platinium sensitivity (resistant

tag: dfs - disease-free survival [days]


title: 3343C

tag: phase

tag: phenotype

value: Mild

value: Aneurysm

tag: tissue


title: 3345C

tag: doi

tag: aneurysm

tag: ivig


title: ovarian cancer surgical sample E159

tag: clinical sample

value: surgical tumor sample

tag: histophatological type of tumor

tag: os - overall survival [days]


title: 3037C

tag: Sex


title: 3345A


title: 3078A


title: ovarian cancer surgical sample E188BT

tag: adjuwant chemotherapy

tag: brca1 mutation

value: no mutation

tag: somatic tp53 mutation

tag: clinical status at last follow-up (awd - alive with disease; dod - dead from disease; ned - no evidence of disease)


title: ovarian cancer surgical sample E188CA

tag: tp53 accumulation in cancer cells (assesed by immunohistochemistry)

tag: tumor grade (g1 - well differentiated; g2 - moderately differentiated; g3 - poorly differentiated; g4 - undifferentiated)

tag: residual tumor size (r0 < 1 cm;  1 < r1 < 5 cm; r2 > 5cm)

tag: clinical status post 1st line chemotherapy (cr - complete response; pr - partial response; sd - stable disease; p - progression)


title: ovarian cancer surgical sample E309

source_name: frozen surgical sample of endometrioid ovarian cancer; BRCA1-mutated

tag: platinium sensitivity (resistant

tag: dfs - disease-free survival [days]


title: 3208C

tag: phase

tag: phenotype

tag: doi

tag: tissue


title: 3343A

tag: aneurysm

tag: ivig


title: 3341C

tag: Sex


title: 3219C


title: ovarian cancer surgical sample E179

source_name: frozen surgical sample of endometrioid ovarian cancer; p53-mutated

tag: clinical sample

tag: histophatological type of tumor

tag: adjuwant chemotherapy

value: mutation

tag: os - overall survival [days]


title: 3339A


title: ovarian cancer surgical sample E254

tag: brca1 mutation

tag: somatic tp53 mutation

tag: tp53 accumulation in cancer cells (assesed by immunohistochemistry)

value: accumulation

tag: clinical status at last follow-up (awd - alive with disease; dod - dead from disease; ned - no evidence of disease)


title: 3341A


title: ovarian cancer surgical sample E428

tag: tumor grade (g1 - well differentiated; g2 - moderately differentiated; g3 - poorly differentiated; g4 - undifferentiated)

tag: residual tumor size (r0 < 1 cm;  1 < r1 < 5 cm; r2 > 5cm)

tag: clinical status post 1st line chemotherapy (cr - complete response; pr - partial response; sd - stable disease; p - progression)

tag: platinium sensitivity (resistant

value: DFS<180 days; moderately sensitive:180>DFS>732; highly sensitive:DFS>732 days):NA


title: ovarian cancer surgical sample E436

tag: dfs - disease-free survival [days]


title: 3339C

tag: phase

tag: phenotype

tag: doi

tag: tissue


title: ovarian cancer surgical sample E444

tag: clinical sample

value: no accumulation


title: ovarian cancer surgical sample X376

description: gene expression data from serous ovarian cancer

source_name: frozen surgical sample of serous ovarian cancer; BRCA1-mutated

tag: histophatological type of tumor

value: serous ovarian ca.


title: ovarian cancer surgical sample G204

source_name: frozen surgical sample of serous ovarian cancer, BRCA1-mutated

tag: adjuwant chemotherapy

value: IV


title: ovarian cancer surgical sample G152

source_name: frozen surgical sample of undifferentiated ovarian cancer, BRCA1-mutated

value: IIIC

tag: os - overall survival [days]


title: SSc9

city: Fukuoka

first: Masahiro

last: Ayano

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Medicine and Biosystemic Science

institute: Kyushu University Graduate School of Medical Sciences

description: SAMPLE 14

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using quantile normalization with lumi and preprocess package in R.

source_name: sort-purified effector memory CD8+ T cells, SSc

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification Kit.

extract_protocol: RNA from sort-purified effector memory CD8+ T cells was extracted with Trizol reagent.

tag: disease status

value: systemic sclerosis (SSc)

tag: cell type


title: SSc8

description: SAMPLE 13


title: SSc7

description: SAMPLE 12


title: SSc5

description: SAMPLE 10


title: ovarian cancer surgical sample E602

tag: brca1 mutation

tag: somatic tp53 mutation

tag: tp53 accumulation in cancer cells (assesed by immunohistochemistry)


title: SSc3

description: SAMPLE 8


title: SSc4

description: SAMPLE 9


title: ovarian cancer surgical sample X604

source_name: frozen surgical sample of undifferentiated ovarian cancer; BRCA1-mutated; p53-mutated

tag: tumor grade (g1 - well differentiated; g2 - moderately differentiated; g3 - poorly differentiated; g4 - undifferentiated)

tag: residual tumor size (r0 < 1 cm;  1 < r1 < 5 cm; r2 > 5cm)

tag: clinical status at last follow-up (awd - alive with disease; dod - dead from disease; ned - no evidence of disease)


title: ovarian cancer surgical sample T286

source_name: frozen surgical sample of serous ovarian cancer; p53-mutated

value: taxane/platinum

tag: clinical status post 1st line chemotherapy (cr - complete response; pr - partial response; sd - stable disease; p - progression)

value: CR

tag: platinium sensitivity (resistant

value: DFS<180 days; moderately sensitive:180>DFS>732; highly sensitive:DFS>732 days):highly sensitive

tag: dfs - disease-free survival [days]

value: NED


title: SSc2

description: SAMPLE 7


title: ovarian cancer surgical sample X101


title: ovarian cancer surgical sample P266

value: platinum/cyclophosphamide


title: Endometrium_afterProg_5A

value: endometrium

tag: gender

value: Female

tag: classification

value: improved cyclin E after progesterone treatment

tag: age

tag: bmi

tag: microarraychip

value: C

tag: season of biopsy collection

value: f

tag: extraction order

value: A


title: ovarian cancer surgical sample P112

tag: clinical sample

value: surgical tumor sample

tag: histophatological type of tumor

tag: adjuwant chemotherapy

value: no mutation

value: mutation

value: accumulation

tag: os - overall survival [days]

value: DOD


title: HC2

description: SAMPLE 2

source_name: sort-purified effector memory CD8+ T cells, healthy control

tag: disease status

value: healthy

tag: cell type


title: ovarian cancer surgical sample T322

source_name: frozen surgical sample of serous ovarian cancer; BRCA1-mutated; p53-mutated

value: serous ovarian ca.

value: taxane/platinum

tag: brca1 mutation

tag: somatic tp53 mutation

tag: tp53 accumulation in cancer cells (assesed by immunohistochemistry)

tag: tumor grade (g1 - well differentiated; g2 - moderately differentiated; g3 - poorly differentiated; g4 - undifferentiated)

value: IIB

tag: residual tumor size (r0 < 1 cm;  1 < r1 < 5 cm; r2 > 5cm)

tag: clinical status at last follow-up (awd - alive with disease; dod - dead from disease; ned - no evidence of disease)


title: ovarian cancer surgical sample P50

value: IIIB

tag: clinical status post 1st line chemotherapy (cr - complete response; pr - partial response; sd - stable disease; p - progression)

value: CR

tag: platinium sensitivity (resistant

value: DFS<180 days; moderately sensitive:180>DFS>732; highly sensitive:DFS>732 days):highly sensitive

tag: dfs - disease-free survival [days]


title: Endometrium_beforeProg_5B_techRepl

description: technical replicate of 4.5aB.1

tag: tissue

value: endometrium

tag: gender

value: Female

tag: classification

value: abnormal high cyclin E before progesterone

tag: age

tag: bmi

tag: microarraychip

tag: season of biopsy collection

value: B


title: SSc6

description: SAMPLE 11

tag: disease status

value: systemic sclerosis (SSc)

tag: cell type


title: ovarian cancer surgical sample P278

tag: clinical sample

value: surgical tumor sample

tag: histophatological type of tumor

tag: adjuwant chemotherapy

value: platinum/cyclophosphamide

tag: brca1 mutation

tag: somatic tp53 mutation

value: no accumulation

value: IIIC

tag: os - overall survival [days]


title: Endometrium_afterProg_5B

value: improved cyclin E after progesterone treatment

value: f

tag: extraction order


title: HC4

description: SAMPLE 4

value: healthy


title: ovarian cancer surgical sample T300

value: serous ovarian ca.

value: taxane/platinum

value: mutation

tag: tp53 accumulation in cancer cells (assesed by immunohistochemistry)

value: accumulation

tag: tumor grade (g1 - well differentiated; g2 - moderately differentiated; g3 - poorly differentiated; g4 - undifferentiated)

tag: residual tumor size (r0 < 1 cm;  1 < r1 < 5 cm; r2 > 5cm)

tag: clinical status post 1st line chemotherapy (cr - complete response; pr - partial response; sd - stable disease; p - progression)

tag: platinium sensitivity (resistant

tag: dfs - disease-free survival [days]

tag: clinical status at last follow-up (awd - alive with disease; dod - dead from disease; ned - no evidence of disease)

value: DOD


title: HC3

description: SAMPLE 3


title: HC5

description: SAMPLE 5


title: Endometrium_beforeProg_5B

tag: tissue

value: endometrium

tag: gender

tag: classification

tag: age

tag: bmi

tag: microarraychip

tag: season of biopsy collection


title: ovarian cancer surgical sample T206

tag: clinical sample

tag: histophatological type of tumor

tag: adjuwant chemotherapy

tag: brca1 mutation

value: no mutation

tag: somatic tp53 mutation

value: CR

value: DFS<180 days; moderately sensitive:180>DFS>732; highly sensitive:DFS>732 days):highly sensitive


title: HC1

description: SAMPLE 1

tag: disease status

tag: cell type


title: ovarian cancer surgical sample P37

source_name: frozen surgical sample of serous ovarian cancer

tag: tp53 accumulation in cancer cells (assesed by immunohistochemistry)

tag: tumor grade (g1 - well differentiated; g2 - moderately differentiated; g3 - poorly differentiated; g4 - undifferentiated)

tag: residual tumor size (r0 < 1 cm;  1 < r1 < 5 cm; r2 > 5cm)

tag: clinical status post 1st line chemotherapy (cr - complete response; pr - partial response; sd - stable disease; p - progression)

tag: platinium sensitivity (resistant

tag: os - overall survival [days]


title: ovarian cancer surgical sample T374

tag: dfs - disease-free survival [days]

tag: clinical status at last follow-up (awd - alive with disease; dod - dead from disease; ned - no evidence of disease)


title: SSc1

description: SAMPLE 6

value: systemic sclerosis (SSc)


title: ovarian cancer surgical sample T172

value: surgical tumor sample

value: undifferentiated ovarian ca.

value: IIIA


title: Endometrium_beforeProg_5A

source_name: human endometrium

tag: tissue

tag: gender

value: Female

tag: classification

value: abnormal high cyclin E before progesterone

tag: age

tag: bmi

tag: microarraychip

value: G

tag: extraction order

value: A


title: ovarian cancer surgical sample T314

tag: clinical sample

tag: histophatological type of tumor

value: serous ovarian ca.

tag: adjuwant chemotherapy

tag: brca1 mutation

tag: somatic tp53 mutation

value: IIIC


title: Endometrium_beforeProg_4B

value: F

tag: season of biopsy collection

value: su

value: B


title: ovarian cancer surgical sample P280

value: platinum/cyclophosphamide

value: mutation

tag: tp53 accumulation in cancer cells (assesed by immunohistochemistry)

value: accumulation

tag: tumor grade (g1 - well differentiated; g2 - moderately differentiated; g3 - poorly differentiated; g4 - undifferentiated)

tag: residual tumor size (r0 < 1 cm;  1 < r1 < 5 cm; r2 > 5cm)

tag: clinical status post 1st line chemotherapy (cr - complete response; pr - partial response; sd - stable disease; p - progression)

tag: platinium sensitivity (resistant

value: DFS<180 days; moderately sensitive:180>DFS>732; highly sensitive:DFS>732 days):moderately sensitive

value: DOD


title: Endometrium_afterProg_4B

tag: tissue

value: endometrium

tag: gender

value: corrected cyclin E after progesterone treatment

value: D

value: f


title: ovarian cancer surgical sample T431

value: surgical tumor sample

value: taxane/platinum

value: CR

tag: dfs - disease-free survival [days]

tag: os - overall survival [days]

tag: clinical status at last follow-up (awd - alive with disease; dod - dead from disease; ned - no evidence of disease)


title: Endometrium_afterProg_4A

value: Female

tag: classification

tag: age

tag: bmi

tag: microarraychip

tag: extraction order

value: A


title: ovarian cancer surgical sample T328

tag: clinical sample

tag: histophatological type of tumor

value: serous ovarian ca.

tag: adjuwant chemotherapy

tag: brca1 mutation

tag: somatic tp53 mutation

value: no accumulation

value: IIIA

value: DFS<180 days; moderately sensitive:180>DFS>732; highly sensitive:DFS>732 days):highly sensitive

value: AWD


title: Endometrium_beforeProg_4A

value: abnormal high cyclin E before progesterone

value: H

tag: season of biopsy collection

value: su


title: ovarian cancer surgical sample P270

value: platinum/cyclophosphamide

value: no mutation

tag: tp53 accumulation in cancer cells (assesed by immunohistochemistry)

tag: tumor grade (g1 - well differentiated; g2 - moderately differentiated; g3 - poorly differentiated; g4 - undifferentiated)

value: IIIC

tag: residual tumor size (r0 < 1 cm;  1 < r1 < 5 cm; r2 > 5cm)

tag: clinical status post 1st line chemotherapy (cr - complete response; pr - partial response; sd - stable disease; p - progression)

tag: platinium sensitivity (resistant

value: DFS<180 days; moderately sensitive:180>DFS>732; highly sensitive:DFS>732 days):moderately sensitive


title: Endometrium_afterProg_3A

tag: tissue

value: endometrium

tag: gender

value: corrected cyclin E after progesterone treatment


title: Endometrium_afterProg_3B

tag: classification

tag: age

value: E

value: B