title: snord50b

city: Stanford

first: Paul

last: Khavari

address: 269 Campus Drive

institute: Stanford University

description: Value is intensity fold over background

hyb_protocol: For hybridization ProtoArray Human Protein Microarray v5.0 (Invitrogen, cat# PAH052520) was used. Prior to hybridization, each microarray was equilibrated first to 40C overnight and then to 250C at least for 15 minutes. The microarray slide was assembled in Gentel SIMplex 16 Multi-Array System device (Gentel biosciences, cat# 4-1007) with custom modifications including modified bottom gasket and the top spacers (Additional file 1). The bottom gasket was cut out from silicone slab as a rectangular seal with the following dimensions in mm: outer 65L x 25W x 4H, inner 59L x 20W x 4H. Top spacers were cut out from polycarbonate piece as a rectangular shape with the following dimensions in mm: Upper spacer 5L x 22W x 1H, lower spacer 12L x 22W x 1H. First, microarray slide was placed inside Gentel SIMplex 16 Multi-Array device bottom holder piece, next the silicone gasket was carefully placed on the top of the slide and the device top piece held in place with tightening screws. The slide surface was blocked in 0.7 mL blocking buffer BL: 40 mM Tris-HCl (pH 8.0), 1% BSA (w/v) (globulin free, Sigma, cat# A7638), 100 μg/ml Yeast tRNA, 20 μg/mL heparin and 1 mM DTT for 1 hour at room T0C with gentle agitation. After completion of the blocking step, 10 pmol Cy5 labeled RNA was added to 0.7 mL binding buffer BB: 40 mM Tris-HCl (pH 8.0), 150 mM sodium chloride, 0.5 mM magnesium acetate, 10 μg/ml Yeast tRNA, 10 μg/mL heparin, 1 mM DTT, 0.01% Igepal CA-630, 5% glycerol, 0.2 units/μl RNAseOUT. The blocking buffer was replaced with binding buffer containing labeled RNA and microarray slides incubated in the dark at 250C for 1 hour with gentle agitation. Following RNA hybridization binding buffer was removed and washing steps were implemented using 3 times exchange of 0.75 mL WB buffer: 40 mM Tris-HCl (pH 8.0), 150 mM sodium chloride, 0.5 mM magnesium acetate, 10 μg/ml Yeast tRNA, 10 μg/mL heparin, 1 mM DTT, 0.01% Igipal 40, 5% Glycerol, 0.2 units/μl RNAseOUT for at least 5 minutes each. Finally, the microarray slide was washed in 0.75 mL washing buffer WBF: 40 mM Tris-HCl (pH 8.0), 150 mM sodium chloride, 0.5 mM Magnesium acetate, 10 μg/ml Yeast tRNA, 10 μg/mL heparin, 1 mM DTT, at least 3 times for 5 minutes each. After the last wash, the WBF buffer was removed partially in order to prevent the slide from drying prematurely and slide holder device disassembled immediately. The hybridized microarray slide was placed in ArrayIt microarray high-speed centrifuge and the residual WBF buffer removed via a 30 seconds. Dry slide was scanned at 635 nm (Cy5) using GenePix 4000B Microarray scanner (Molecular Devices) immediately after or at least within 2 hours of the completion of the hybridization.

scan_protocol: Dry slide was scanned at 635 nm (Cy5) using GenePix 4000B Microarray scanner (Molecular Devices) immediately after or at least within 2 hours of the completion of the hybridization. The intensity of the 635 nm wavelength signal at each spotted protein location was determined with GenePix Pro 6.1 software (Molecular Devices)

data_processing: To quantify RNA-protein interactions, the intensity of 635 nm signal (F635) was divided by the local background intensity (B635) at each of the duplicate spots for a given protein

source_name: In vitro transcribed RNA

label_protocol: RNA labeling for microarray hybridizations was performed using Label IT μArray Cy5 labeling kit (Mirus). We first carefully optimized the labeling procedure in order to achieve between 1 to 3 Cy5 dyes covalently attached to RNAs used. This was accomplished via the following modifications from the original manufacturers protocol: the total reaction volume was kept at 25 μl, the ratio of RNA:Label IT Cy5 reagent at 10:1 (w:v) and reaction time not more then 30 minutes at 370C. Briefly, 5 μg RNA in water was mixed with 5 μl Label IT Cy5, diluted 1 to 10 in water to obtain a final volume of 25 μl and incubated 30 minutes at 370C. The reaction was stopped by addition 2.5 μl of 10x STOP buffer (Mirus). The volume was increased to 100 μl with water, supplemented with glycogen (Invitrogen) to final concentration of 0.2 μg/μl, mixed and RNA ethanol precipitated in the presence of 0.5 M NaCl at -20oC for at least 1 hour. The labeled RNA was extensively washed in 70% ethanol, dried and resuspended in 16 μl water. RNA labeling density was evaluated using NanoDrop 1000 spectrophotometer (Thermo Scientific) and visualized using denaturing agarose gel-electrophoreses

growth_protocol: N/A.  RNA used was in vitro transcribed

extract_protocol: N/A.  RNA used was in vitro transcribed

treatment_protocol: N/A.  RNA used was in vitro transcribed

tag: sample type

value: In vitro transcribed snord50b RNA


title: RGE01-Y2-33511

status: Public on Nov 23 2015

type: RNA

city: Los Angeles

first: Steve

last: Cole

state: CA

address: 11-934 Factor Bldg, UCLA

department: Medicine

country: USA

institute: UCLA School of Medicine

description:
raw data file column name: 9224522097_G.AVG_Signal
Illumina Human HT-12 BeadArray

hyb_protocol: Illumina cRNA hybridization protocol for gene expression profiling (carried out by UCLA Neuroscience Genomics Core).

scan_protocol: Standard Illumina scan protocol for gene expression profiling (carried out by UCLA Neuroscience Genomics Core).

data_processing: Raw probe intensity values and quantile-normalized gene expression values were generated by Illumina GenomeStudio software using Gene Expression module 1.1.1.  All available data are provided, with no additional filtering.

label: biotin

molecule: total RNA

organism: Macaca mulatta

source_name: PBMC

label_protocol: Ambion TotalPrep RNA amplification with biotin labeling for gene expression profiling (carried out by UCLA Neuroscience Genomics Core).

extract_protocol: Primary peripheral blood mononuclear cells were isolated and total RNA was extracted using Qiagen RNEasy.

tag: pid

tag: psi

value: HighPSI

tag: age


title: Whole_Blood_LTBI_2009

city: Aurora

first: Nicholas

last: Walter

state: Colorado

address: 12700 East 19th Avenue

institute: University of Colorado

description: Training

hyb_protocol: Following fragmentation, cRNA were hybridized for 16-18 hours at 48C on GeneChip HuGene 1.1 ST Arrays. GeneChips were washed and stained on the Affymetrix GeneTitan instrument.

scan_protocol: Arrays were scanned using the Affymetrix GeneTitan instrument.

data_processing: Expression data were normalized via Robust Multichip Average, log-transformed and adjusted for batch effect

organism: Homo sapiens

source_name: Whole blood collected in PAXgene tubes from LTBI patient

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA using the Affymetrix GeneChip WT Terminal Labeling Kit.

extract_protocol: Whole blood from US patients was collected in PAXGene tubes according to manufacturer's instructions. Total RNA extraction was performed according to the manufacturer's (Qiagen) instructions.

tag: tissue

value: whole blood

tag: Sex

value: Male

tag: clinical group

value: LTBI

tag: race

value: Asian

tag: birthcountry

value: Bhutan

tag: diabetes

value: no

tag: current smoker

value: yes

tag: bcg

value: unknown


title: RGE01-Y2-32164

description:
raw data file column name: 9224522097_B.AVG_Signal
Illumina Human HT-12 BeadArray

value: ModPSI


title: Activated hepatic stellate cells:L8

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description:
Activated hepatic stellate cells:L8
sAHSC_L8

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000

data_processing: Data processing cel files were normalized with 'rma' function of the Bioconductor package (v2.4)  in R.3.0.1

source_name: CTC's group: AHSC

label_protocol: Standard Affymetrix protocol

extract_protocol: Total RNA was purified from qHSCs, aHSCs and hepatocyte samples using RNeasy MICROKit (QIAGEN GmbH, Hilden, Germany) following a deviation of the standard protocol as recommended by the manufacturer and using 1.5 volumes of 100% ethanol before applying the sample into the column. Total RNA concentration and quality control was assessed using the RNA 6000 pico kit (Agilent, Santa Clara, CA).

tag: cell type

value: Activated hepatic stellate cells


title: Whole_Blood_LTBI_2005

description: Training

value: Female

value: Latino

value: Mexico


title: Quiescent hepatic stellate cells:L11

description:
Quiescent hepatic stellate cells:L11
sQHSC_L11

source_name: CTC's group: QHSC

value: Quiescent hepatic stellate cells


title: snord50a

description: Value is intensity fold over background

value: In vitro transcribed snord50a RNA


title: 0449-046-Y9

description:
raw data file: 9234549012_L.AVG_Signal
Illumina Human HT-12 BeadArray

tag: chronicpsi

tag: female

tag: hispanic

tag: black

tag: married

tag: lnincome

tag: bmi

tag: smoke

tag: alcohol

tag: cesd

tag: pss

tag: socsupp

tag: monocytepct


title: RGE01-Y2-35253

description:
raw data file column name: 9224523020_K.AVG_Signal
Illumina Human HT-12 BeadArray

tag: pid

tag: psi

tag: age


title: Activated hepatic stellate cells:L10

description:
Activated hepatic stellate cells:L10
sAHSC_L10

tag: cell type


title: RGE01-Y2-35991

description:
raw data file column name: 9224523020_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: RGE01-Y2-35945

description:
raw data file column name: 9224522097_A.AVG_Signal
Illumina Human HT-12 BeadArray

value: Missing


title: RGE01-Y2-27993

description:
raw data file column name: 9224522097_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: Whole_Blood_TB_1221

description: Test

source_name: Whole blood collected in PAXgene tubes from TB patient

tag: tissue

tag: Sex

tag: clinical group

value: TB

tag: race

tag: birthcountry

value: USA

tag: diabetes

tag: current smoker

tag: bcg


title: Whole_Blood_LTBI_2003

description: Training

value: whole blood

value: Male

value: Black

value: Ethiopia


title: Whole_Blood_LTBI_2004

description: Training

value: LTBI

value: Other

value: Iraq

value: no


title: MeT5A_crocidolite asbestos_4month_rep2

city: Morgantown

first: Todd

middle: A

last: Stueckle

state: WV

address: 1095 Willowdale Road

department: Health Effects Laboratory Division

institute: National Institute for Occupational Safety and Health

description: Genome expression after 4 month crocidolite asbestos in vitro exposure

hyb_protocol: Microarray hybridization was performed at 65°C for 17 hours on NimbleGen 12x135k Whole Human Genome Oligonucleotide Microarray (HG18) in NimbleGen Hybridization System.

scan_protocol: After being washed in an ozone-free environment, image capture was performed with Axon GenePix 4000B (Molecular Devices) and uploaded into NimbleScan (v2.5), and Cy3 label intensities determined.

data_processing: GenePix data were uploaded into NimbleScan for Cy3 label intensity determination.  Intensities were quantile normalized using Robust Multichip Average method included in NimbleScan. Only genes expressing ≥50.0 normalized intensity in all 18 samples were subjected to further analysis. Gene expression text files were imported into GeneSpring GX (ver. 10.0) for further analysis.

source_name: MeT5A immortalized pleural mesothelial cell, crocidolite asbestos exposed, 4 month exposed (16 passages), replicate 2

label_protocol: cDNA samples were amplified, Cy3-labeled with NimbleGen one-color DNA labeling kit following manufacturer’s protocol. Microarray hybridization was performed at 65°C for 17 hours to NimbleGen whole human genome 12x135K microarrays in NimbleGen Hybridization System.

growth_protocol: Cells were maintained in M199 medium (Life Technologies Inc.) supplemented with 5% fetal bovine serum, 2 mM L-glutamine,100 U/mL penicillin/streptomycin, 1 ug/ml EGF, and 50 ug/mL hydrocortisone.  Cell cultures were held in a humid, 37o C and 5% CO2 cell culture incubator.

extract_protocol: RNA samples from each replicate (total n=18) were collected with TRIzol (Invitrogen) post-exposure using manufacturer’s protocol.  RNA quality was assessed in house using gel electrophoresis and 260/280 nm absorbance ratio.  Samples stored at -80o C were shipped to ArrayStar (Rockville, MD).  At ArrayStar, samples were treated with DNase digestion and analyzed for RNA quality using Nanodrop ND-100 and Bioanalyser 2100.

treatment_protocol: 0.1 mg/mL stock solutions of SWCNT, MWCNT, and crocidolite asbestos were prepared in sterile MilliQ water containing 150 microliters/mL of the lung surfactant Survanta®.  Each stock solution was sonicated for 20 seconds using a small sonication horn and then diluted in fresh culture medium and added to culture plates.  Saline and dispersant only containing medium served as negative passage controls.  Unexposed MeT5A cells (2x105 cells/well) were seeded to 6-well plates in triplicate per treatment (n=18).  After 24 hours, cell cultures were either exposed to 0.02 micrograms/sq. cm of each particle or saline or Survanta-dispersant only for the following 4 months.  Cells were passage matched for a total of 16 passages.  Exposed media was changed every 3 to 4 days while cells were split once every 7 days.

value: immortalized pleural mesothelial cells


title: Whole_Blood_LTBI_2007

description: Training

value: Female

value: Asian

value: Bhutan


title: Whole_Blood_TB_1225

description: Training

value: Latino


title: MeT5A_dispersed multiwall carbon nanotube_4month_rep3

description: Genome expression after 4 month dispersed multi wall carbon nanotube in vitro exposure

source_name: MeT5A immortalized pleural mesothelial cell, dispersed multi wall carbon nanotube, 4 month exposed (16 passages), replicate 3


title: Activated hepatic stellate cells:L11

description:
Activated hepatic stellate cells:L11
sAHSC_L11

value: Activated hepatic stellate cells


title: Activated hepatic stellate cells:L4

description:
Activated hepatic stellate cells:L4
sAHSC_L4


title: Whole_Blood_TB_1227

description: Test

value: Mexico

value: yes


title: MeT5A_crocidolite asbestos_4month_rep1

source_name: MeT5A immortalized pleural mesothelial cell, crocidolite asbestos exposed, 4 month exposed (16 passages), replicate 1


title: RGE01-Y2-35949

description:
raw data file column name: 9224523020_J.AVG_Signal
Illumina Human HT-12 BeadArray

value: HighPSI


title: Whole_Blood_LTBI_2000

description: Test

value: whole blood

value: Philippines


title: RGE01-Y2-36684

description:
raw data file column name: 9224523020_I.AVG_Signal
Illumina Human HT-12 BeadArray

value: Missing


title: MeT5A_dispersed multiwall carbon nanotube_4month_rep2

source_name: MeT5A immortalized pleural mesothelial cell, dispersed multi wall carbon nanotube, 4 month exposed (16 passages), replicate 2


title: MeT5A_crocidolite asbestos_4month_rep3

source_name: MeT5A immortalized pleural mesothelial cell, crocidolite asbestos exposed, 4 month exposed (16 passages), replicate 3


title: liver sinusoidal endothelial cells:L10

description:
liver sinusoidal endothelial cells:L10
sLSEC_L10

source_name: CTC's group: LSEC

value: liver sinusoidal endothelial cells


title: RGE01-Y2-34849

description:
raw data file column name: 9224523020_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: Whole_Blood_TB_1220

description: Training

value: TB

value: USA


title: Whole_Blood_TB_1214

description: Training

value: Male


title: MeT5A_dispersed single wall carbon nanotube_4month_rep2

description: Genome expression after 4 month dispersed single wall carbon nanotube in vitro exposure

source_name: MeT5A immortalized pleural mesothelial cell, dispersed single wall carbon nanotube, 4 month exposed (16 passages), replicate 2


title: RGE01-Y2-35652

description:
raw data file column name: 9224523020_F.AVG_Signal
Illumina Human HT-12 BeadArray

value: LowPSI


title: RGE01-Y2-30633

description:
raw data file column name: 9224523020_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: Whole_Blood_TB_1219

description: Training

value: no


title: MeT5A_dispersed multiwall carbon nanotube_4month_rep1

source_name: MeT5A immortalized pleural mesothelial cell, dispersed multi wall carbon nanotube, 4 month exposed (16 passages), replicate 1

value: immortalized pleural mesothelial cells


title: Whole_Blood_TB_1213

description: Training


title: RGE01-Y2-35634

description:
raw data file column name: 9224523020_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: Whole_Blood_TB_1211

description: Training


title: MeT5A_dispersant_4month_rep3

description: Genome expression after 4 month dispersant-only in vitro exposure

source_name: MeT5A immortalized pleural mesothelial cell, dispersant only, 4 month exposed (16 passages), replicate 3


title: MeT5A_dispersed single wall carbon nanotube_4month_rep1

source_name: MeT5A immortalized pleural mesothelial cell, dispersed single wall carbon nanotube, 4 month exposed (16 passages), replicate 1


title: MeT5A_dispersed single wall carbon nanotube_4month_rep3

source_name: MeT5A immortalized pleural mesothelial cell, dispersed single wall carbon nanotube, 4 month exposed (16 passages), replicate 3


title: Whole_Blood_TB_1216

description: Training


title: RGE01-Y2-37313

description:
raw data file column name: 9224523020_C.AVG_Signal
Illumina Human HT-12 BeadArray

value: ModPSI


title: MeT5A_saline_4month_rep3

description: Genome expression after 4 month saline-only in vitro exposure

source_name: MeT5A immortalized pleural mesothelial cell, saline only, 4 month exposed (16 passages), replicate 3


title: MeT5A_dispersant_4month_rep1

source_name: MeT5A immortalized pleural mesothelial cell, dispersant only, 4 month exposed (16 passages), replicate 1


title: MeT5A_dispersant_4month_rep2

source_name: MeT5A immortalized pleural mesothelial cell, dispersant only, 4 month exposed (16 passages), replicate 2


title: RGE01-Y2-36600

description:
raw data file column name: 9224523020_A.AVG_Signal
Illumina Human HT-12 BeadArray

source_name: PBMC


title: Whole_Blood_TB_1207

description: Test

value: Female


title: RGE01-Y2-37018

description:
raw data file column name: 9224523065_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: RGE01-Y2-34027

description:
raw data file column name: 9224523065_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: Whole_Blood_TB_1206

description: Training

value: Latino


title: Whole_Blood_TB_1209

description: Training


title: Whole_Blood_TB_1200

description: Test

value: mexico


title: Whole_Blood_TB_1204

description: Test

value: Mexico


title: RGE01-Y2-33709

description:
raw data file column name: 9224523065_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: DKO BMMC with 100ng/ml LPS, biological rep2

city: Ithaca

first: Weishan

last: Huang

state: New York

address: C5 121, Cornell U.

department: Microbiology & Immunology

institute: Cornell University

description:
Gene expression in WT BMMCs, in response to 100ng/ml LPS for 1 hour
DKOLPS2

hyb_protocol: 1650ng per sample of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 11ul 25x Agilent fragmentation buffer and 2.2 ul 10x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized 100ul to Agilent Whole Mouse Genome Microarray Kit, 4x44K (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Red & Green and both the Red and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using parameters (protocol GE1-105_DEC8 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.  Data were further analyzed in GeneSpring, version 12.0. GAPDH-normalized probe values (WT non- treated average set as 1) were converted into gene expression values  with Quantile normalization for further analysis. WT PBS control average values were set as basal level 1. The GAPDH-normalized probe signal intensities are available in the sample tables and on the series record in the file:  Probe-level_analysis_with_annotation.txt. The gene-level analysis is available on the series record in the file: Gene-level_analysis_quantile-normalized.txt.

organism: Mus musculus

source_name: ItkBtk double knockout BMMC, LPS, 1 hour, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the One-Color Low RNA Input QuickAmp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy Plus column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Bone marrow cells were isolated from 8-week old females. Individualized bone marrow cells were cultured in complete DMEM supplemented with 10ng/ml IL-3 and 50ng SCF. BMMCs that are 5 weeks in culture with > 96% FceRIa+c-Kit+ were used in experiments.

extract_protocol: Cells were subjected to total RNA extraction using RNeasy Plus Mini Kit with removal of gDNA following the manufacturer's instruction (Qiagen, cat: 74134). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: WT and DKO BMMCs were factor starved in complete DMEM without IL-3/SCF for 12 hours, and treated with PBS or LPS (100ng/ml) for 1 hour.

tag: genotype

value: ItkBtk double knockout

tag: strain

value: Bone marrow

value: bone marrow-derived mast cells (BMMC)

tag: gender

value: female

value: 8 weeks bone marrow, 5 weeks BMMC


title: RGE01-Y2-36305

description:
raw data file column name: 9224523065_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: DKO BMMC with 100ng/ml LPS, biological rep1

description:
Gene expression in WT BMMCs, in response to 100ng/ml LPS for 1 hour
DKOLPS1

source_name: ItkBtk double knockout BMMC, LPS, 1 hour, replicate 1


title: RGE01-Y2-36422

description:
raw data file column name: 9224523065_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: MeT5A_saline_4month_rep2

source_name: MeT5A immortalized pleural mesothelial cell, saline only, 4 month exposed (16 passages), replicate 2


title: Btk-/- BMMC with 100ng/ml LPS, biological rep2

description:
Gene expression in WT BMMCs, in response to 100ng/ml LPS for 1 hour
BtkLPS2

source_name: Btk-/- BMMC, LPS, 1 hour, replicate 2

value: Btk-/-


title: RGE01-Y2-35577

description:
raw data file column name: 9224523065_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: RGE01-Y2-37345

description:
raw data file column name: 9224523065_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: RGE01-Y2-37098

description:
raw data file column name: 9224523065_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: Whole_Blood_TB_1103

description: Training

source_name: Whole blood collected in PAXgene tubes from TB patient

value: whole blood

value: TB

value: yes


title: RGE01-Y2-34847

description:
raw data file column name: 9224523065_H.AVG_Signal
Illumina Human HT-12 BeadArray

value: LowPSI


title: MeT5A_saline_4month_rep1

source_name: MeT5A immortalized pleural mesothelial cell, saline only, 4 month exposed (16 passages), replicate 1


title: Btk-/- BMMC with 100ng/ml LPS, biological rep1

description:
Gene expression in WT BMMCs, in response to 100ng/ml LPS for 1 hour
BtkLPS1

source_name: Btk-/- BMMC, LPS, 1 hour, replicate 1


title: Whole_Blood_TB_1035

description: Test

value: USA

value: no


title: DKO BMMC with 100ng/ml LPS, biological rep3

description:
Gene expression in WT BMMCs, in response to 100ng/ml LPS for 1 hour
DKOLPS3

source_name: ItkBtk double knockout BMMC, LPS, 1 hour, replicate 3


title: Btk-/- BMMC with 100ng/ml LPS, biological rep3

description:
Gene expression in WT BMMCs, in response to 100ng/ml LPS for 1 hour
BtkLPS3

source_name: Btk-/- BMMC, LPS, 1 hour, replicate 3


title: Whole_Blood_TB_1104

description: Test

value: Male

value: White


title: RGE01-Y2-36543

description:
raw data file column name: 9224523065_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: Itk-/- BMMC with 100ng/ml LPS, biological rep3

description:
Gene expression in WT BMMCs, in response to 100ng/ml LPS for 1 hour
ItkLPS3

source_name: Itk-/- BMMC, LPS, 1 hour, replicate 3

value: Itk-/-


title: Whole_Blood_TB_1101

description: Training

value: Female

value: Latino


title: Itk-/- BMMC with 100ng/ml LPS, biological rep2

description:
Gene expression in WT BMMCs, in response to 100ng/ml LPS for 1 hour
ItkLPS2

source_name: Itk-/- BMMC, LPS, 1 hour, replicate 2


title: Whole_Blood_TB_1102

description: Training


title: Whole_Blood_TB_1033

description: Training

value: Asian

value: Nepal

value: unknown


title: Whole_Blood_TB_1032

description: Training


title: RGE01-Y2-35537

description:
raw data file column name: 9224523065_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: RGE01-Y2-34880

description:
raw data file column name: 9224523065_B.AVG_Signal
Illumina Human HT-12 BeadArray

value: HighPSI


title: RGE01-Y2-37379

description:
raw data file column name: 9234549030_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: WT BMMC with 100ng/ml LPS, biological rep3

description:
Gene expression in WT BMMCs, in response to 100ng/ml LPS for 1 hour
WTLPS3

source_name: WT BMMC, LPS, 1 hour, replicate 3

value: wildtype

value: Bone marrow

value: bone marrow-derived mast cells (BMMC)

value: female

value: 8 weeks bone marrow, 5 weeks BMMC


title: RGE01-Y2-36653

description:
raw data file column name: 9224523020_B.AVG_Signal
Illumina Human HT-12 BeadArray

value: LowPSI


title: Whole_Blood_TB_1030

description: Test

value: whole blood

value: TB


title: WT BMMC with 100ng/ml LPS, biological rep2

description:
Gene expression in WT BMMCs, in response to 100ng/ml LPS for 1 hour
WTLPS2

source_name: WT BMMC, LPS, 1 hour, replicate 2


title: Whole_Blood_TB_1020

description: Training

value: Male

value: Indonesia

value: no


title: Itk-/- BMMC with 100ng/ml LPS, biological rep1

description:
Gene expression in WT BMMCs, in response to 100ng/ml LPS for 1 hour
ItkLPS1

source_name: Itk-/- BMMC, LPS, 1 hour, replicate 1

value: Itk-/-


title: RGE01-Y2-37289

description:
raw data file column name: 9234549030_K.AVG_Signal
Illumina Human HT-12 BeadArray

value: ModPSI


title: DKO BMMC with PBS as control, biological rep3

description:
Gene expression in WT BMMCs, basal level
DKO3

source_name: ItkBtk double knockout BMMC, PBS, 1 hour, replicate 3

value: ItkBtk double knockout


title: WT BMMC with 100ng/ml LPS, biological rep1

description:
Gene expression in WT BMMCs, in response to 100ng/ml LPS for 1 hour
WTLPS1

source_name: WT BMMC, LPS, 1 hour, replicate 1


title: Whole_Blood_TB_1019

description: Training

value: Female

value: Latino

value: Mexico

value: yes


title: DKO BMMC with PBS as control, biological rep1

description:
Gene expression in WT BMMCs, basal level
DKO1

source_name: ItkBtk double knockout BMMC, PBS, 1 hour, replicate 1

value: Bone marrow


title: Whole_Blood_TB_1017

description: Training

value: USA


title: Btk-/- BMMC with PBS as control, biological rep3

description:
Gene expression in WT BMMCs, basal level
Btk3

source_name: Btk-/- BMMC, PBS, 1 hour, replicate 3

value: Btk-/-

value: bone marrow-derived mast cells (BMMC)

value: female


title: RGE01-Y2-30840

description:
raw data file column name: 9234549030_J.AVG_Signal
Illumina Human HT-12 BeadArray

source_name: PBMC


title: RGE01-Y2-34177

description:
raw data file column name: 9234549030_E.AVG_Signal
Illumina Human HT-12 BeadArray

value: HighPSI


title: RGE01-Y2-36175

description:
raw data file column name: 9234549030_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: Whole_Blood_TB_1018

description: Training

value: whole blood

value: TB

value: Black

value: Somalia


title: Whole_Blood_TB_1027

description: Training

value: Other

value: Tonga

value: no


title: DKO BMMC with PBS as control, biological rep2

description:
Gene expression in WT BMMCs, basal level
DKO2

source_name: ItkBtk double knockout BMMC, PBS, 1 hour, replicate 2

value: ItkBtk double knockout

value: 8 weeks bone marrow, 5 weeks BMMC


title: RGE01-Y2-35550

description:
raw data file column name: 9234549030_F.AVG_Signal
Illumina Human HT-12 BeadArray

value: LowPSI


title: RGE01-Y2-30592

description:
raw data file column name: 9234549030_H.AVG_Signal
Illumina Human HT-12 BeadArray

value: ModPSI


title: Btk-/- BMMC with PBS as control, biological rep2

description:
Gene expression in WT BMMCs, basal level
Btk2

source_name: Btk-/- BMMC, PBS, 1 hour, replicate 2

value: Bone marrow


title: RGE01-Y2-33235

description:
raw data file column name: 9234549030_I.AVG_Signal
Illumina Human HT-12 BeadArray

value: Missing


title: Whole_Blood_TB_1013

description: Test

source_name: Whole blood collected in PAXgene tubes from TB patient

value: Male

value: Asian

value: Burma

value: yes


title: Whole_Blood_TB_1010

description: Training

value: whole blood

value: China

value: unknown


title: Btk-/- BMMC with PBS as control, biological rep1

description:
Gene expression in WT BMMCs, basal level
Btk1

source_name: Btk-/- BMMC, PBS, 1 hour, replicate 1

value: Btk-/-

value: bone marrow-derived mast cells (BMMC)

value: female


title: Whole_Blood_TB_1215

description: Training

value: TB

value: Latino

value: Mexico

value: no


title: RGE01-Y2-37244

description:
raw data file column name: 9224523020_D.AVG_Signal
Illumina Human HT-12 BeadArray

value: LowPSI


title: RGE01-Y2-36273

description:
raw data file column name: 9234549030_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: Whole_Blood_TB_1006

description: Training


title: Whole_Blood_TB_1009

description: Training

value: Korea


title: Whole_Blood_TB_1105

description: Test


title: RGE01-Y2-33064

description:
raw data file column name: 9234549030_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: RGE01-Y2-34043

description:
raw data file column name: 9234549030_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: RGE01-Y2-32287

description:
raw data file column name: 9234549030_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: Whole_Blood_TB_1003

description: Test

value: Female

value: White

value: USA


title: Itk-/- BMMC with PBS as control, biological rep3

description:
Gene expression in WT BMMCs, basal level
Itk3

source_name: Itk-/- BMMC, PBS, 1 hour, replicate 3

value: Itk-/-

value: Bone marrow

value: 8 weeks bone marrow, 5 weeks BMMC


title: WT BMMC with PBS as control, biological rep3

description:
Gene expression in WT BMMCs, basal level
WT3

source_name: WT BMMC, PBS, 1 hour, replicate 3

value: wildtype


title: mouse_retinal pigment epithelium_3

city: Amsterdam

first: Anna

last: Bennis

address: Meibergdreef 9

department: Clinical Genetics

country: Netherlands

institute: Amsterdam Medical Centre Amsterdam

description: Sample name: RPE 3

hyb_protocol: Labeled RNA of interest (CH, RPE or PR) and labeled common reference sample together according to the protocol provided by Agilent (hybridization protocol is described in ”Two-color microarray based gene expression analysis (low input quick amp labeling) protocol”.

scan_protocol: Scanned on an Agilent scanner, protocol GE2-v5_95_Feb07

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and linear lowess dye normalization. This resulted amongst others in normalized log ratios (test/reference) data that can be find in the Agilent Feature Extraction files. Further data processing was done in R (version 2.14.0 for Windows, R Development Core Team, 2009), with package Limma. We read in the raw data (RG <-read.maimage). Next we normalized within arrays (method 'loess', resulating in MA) and subsequently we normalized the red signals between arrays to make it possible to compare the red channels (method q, resulting in MA.s).

source_name: retinal pigment epithelium, laser dissected

label_protocol: aRNA samples were labeled with a Cy5 fluorescent probe (Cy5 mono-reactive dye pack, GE Healthcare UK, Little Chalfont, Buckinghamshire, UK). In short, aRNA was coupled to Cy5 (dissolved in DMSO) in 0.5 M NaHCO3 (pH 9.0) for one hour. Free dyes were quenched by the addition of 4 M hydroxylamine and removed by filtration over a Chroma Spin-30 column (DEPC-H20 Columns, Clontech Laboratories) with glycogen as a carrier. Cy3-labeled common reference sample.

extract_protocol: Total RNA was isolated using RNeasy Micro Kit (Qiagen Benelux, Venlo, The Netherlands). Subsequently, the mRNA component was amplified with Amino Allyl MessageAmp II aRNA Amplification kit (#1753, Ambion Applied Biosystems Europe B.V.).

value: 6mnths(+/- 2wks)

value: retinal pigment epithelium

source_name: choroid/RPE (common reference)

value: choroid/RPE


title: mouse_photoreceptors_1

description: Sample name: PR 1

source_name: photoreceptors, laser dissected

value: photoreceptors


title: Itk-/- BMMC with PBS as control, biological rep2

description:
Gene expression in WT BMMCs, basal level
Itk2

source_name: Itk-/- BMMC, PBS, 1 hour, replicate 2

value: bone marrow-derived mast cells (BMMC)

value: female


title: Itk-/- BMMC with PBS as control, biological rep1

description:
Gene expression in WT BMMCs, basal level
Itk1

source_name: Itk-/- BMMC, PBS, 1 hour, replicate 1


title: WT BMMC with PBS as control, biological rep1

description:
Gene expression in WT BMMCs, basal level
WT1

source_name: WT BMMC, PBS, 1 hour, replicate 1


title: mouse_photoreceptors_3

description: Sample name: PR 3


title: mouse_choroid_3

description: Sample name: CH 3

source_name: choroid, laser dissected

value: choroid


title: WT BMMC with PBS as control, biological rep2

description:
Gene expression in WT BMMCs, basal level
WT2

source_name: WT BMMC, PBS, 1 hour, replicate 2


title: MCF7 r1

city: Milan

first: Maurizio

last: Callari

address: Via Amadeo, 42

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

description: MCF7 replicate 1

hyb_protocol: One μg of the biotinylated cRNA sample was mixed with the Hyb E1 hybridization buffer containing 37.5% (w/w) formamide and then hybridised at 58 °C overnight to the Illumina BeadChips HumanRef-8 V3

scan_protocol: Array chips were scanned with the Illumina BeadArray Reader

data_processing: log2 transformation and Robust Spline Normalization

source_name: breast cancer cell line

label_protocol: 800 ng of total RNA were reverse transcribed, labelled with biotin and amplified overnight using the Illumina RNA TotalPrep Amplification kit (Ambion, Austin, TX) according to manufacturer’s protocol.

extract_protocol: Cell pellets (~106 cells) were immediately put on ice, homogenized in 1 mL of TRIzol® Reagent (Invitrogen, Life technologies, Foster City, CA, USA) and lysates were stored at -80 °C for not more than 2 weeks. Total RNA was extracted following the manufacturer instructions. Contaminating DNA was digested using the Ambion® (Austin, TX, USA) recombinant DNase I and RNA samples were purified using the RNeasy MinElute Cleanup Kit (Qiagen, Germantown, Maryland, USA).

tag: cell line

tag: cell line type

value: parental


title: Whole_Blood_TB_1004

description: Training

value: whole blood

value: Male

value: TB

value: Black

value: Ethiopia

value: yes

value: no


title: mouse_retinal pigment epithelium_2

description: Sample name: RPE 2

value: Female


title: MCF7 r3

description: MCF7 replicate 3


title: MCFS r3

description: MCFS replicate 3

value: MCFS

value: tumor promoting mammospheres


title: MCF7 r2

description: MCF7 replicate 2


title: mouse_photoreceptors_2

description: Sample name: PR 2

value: 6mnths(+/- 2wks)


title: MCFS r2

description: MCFS replicate 2


title: mouse_choroid_2

description: Sample name: CH 2

value: choroid/RPE


title: mouse_retinal pigment epithelium_1

description: Sample name: RPE 1

value: retinal pigment epithelium


title: mouse_choroid_1

description: Sample name: CH 1


title: CAD Patient_CODE17 - EAT

status: Public on Nov 22 2015

city: Bari

first: Antonio

last: Moschetta

address: Via Orazio Flacco, 65

institute: IRCCS Ospedale Oncologico di Bari

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization (background was not subtracted) with Illumina Genome Studio Software; items with detection p values >0.001 or AVG Signal <700 in more than 1 group were excluded. Data were analyzed with non parametric analysis plus False Discovery Rate, FDR.

source_name: EAT

label_protocol: Standard Illumina Protocol

extract_protocol: Total RNA was extracted using the Qiagen miRNeay Kit, following manufacturer's instructions. Quality control was performed with Biorad Experion.

tag: disease state

value: coronary artery disease

value: Epicardial Adipose


title: CAD Patient_CODE18 - SAT

source_name: SAT

value: Subcutaneous Adipose


title: CAD Patient_CODE18 - EAT


title: CAD Patient_CODE16 - SAT


title: CAD Patient_CODE11 - SAT


title: CAD Patient_CODE14 - SAT


title: CAD Patient_CODE17 - SAT


title: CAD Patient_CODE14 - EAT


title: CAD Patient_CODE16 - EAT


title: MCFS r1

description: MCFS replicate 1


title: CAD Patient_CODE20 - EAT


title: CAD Patient_CODE21 - EAT


title: CAD Patient_CODE20 - SAT


title: CAD Patient_CODE23 - EAT


title: CAD Patient_CODE19 - EAT


title: CAD Patient_CODE21 - SAT


title: CAD Patient_CODE40 - EAT


title: CAD Patient_CODE27 - SAT


title: CAD Patient_CODE23 - SAT


title: CAD Patient_CODE45 - EAT


title: CAD Patient_CODE38 - EAT


title: CAD Patient_CODE19 - SAT


title: CAD Patient_CODE27 - EAT


title: CAD Patient_CODE40 - SAT


title: CAD Patient_CODE45 - SAT


title: CAD Patient_CODE38 - SAT


title: CTRL Patient_CODE24 - SAT

value: control


title: CTRL Patient_CODE28 - SAT


title: CTRL Patient_CODE28 - EAT


title: CTRL Patient_CODE24 - EAT


title: CAD Patient_CODE11 - SAT

data_processing: The data were normalised using quantile normalization (background was not subtracted) with Illumina Genome Studio Software; items with detection p values >0.001 or AVG Signal <100 in more than 1 group were excluded. Data were analyzed with non parametric analysis plus False Discovery Rate, FDR.


title: CTRL Patient_CODE32 - EAT


title: CAD Patient_CODE11 - EAT


title: CAD Patient_CODE14 - EAT


title: CTRL Patient_CODE37 - EAT


title: CTRL Patient_CODE43 - EAT


title: CTRL Patient_CODE44 - SAT


title: CAD Patient_CODE16 - EAT


title: CTRL Patient_CODE34 - SAT

description: replicate 1


title: CTRL Patient_CODE32 - SAT


title: CTRL Patient_CODE34 - EAT


title: CTRL Patient_CODE42 - EAT


title: CTRL Patient_CODE43 - SAT


title: CTRL Patient_CODE44 - EAT


title: CAD Patient_CODE14 - SAT


title: CTRL Patient_CODE37 - SAT


title: CTRL Patient_CODE42 - SAT


title: CTRL Patient_CODE46 - EAT


title: CAD Patient_CODE18 - EAT


title: CAD Patient_CODE16 - SAT


title: CAD Patient_CODE19 - SAT


title: CAD Patient_CODE17 - SAT


title: CAD Patient_CODE17 - EAT


title: CAD Patient_CODE11 - EAT


title: CAD Patient_CODE21 - EAT


title: CAD Patient_CODE18 - SAT


title: CAD Patient_CODE27 - SAT


title: CAD Patient_CODE20 - EAT


title: CAD Patient_CODE20 - SAT


title: CAD Patient_CODE21 - SAT


title: CAD Patient_CODE23 - EAT


title: CAD Patient_CODE27 - EAT


title: CAD Patient_CODE19 - EAT


title: CTRL Patient_CODE46 - SAT


title: CTRL Patient_CODE6 - SAT


title: CTRL Patient_CODE6 - EAT


title: CAD Patient_CODE38 - EAT


title: CAD Patient_CODE40 - EAT


title: CAD Patient_CODE38 - SAT


title: CAD Patient_CODE45 - EAT


title: VMM39 - IFNgamma Treated - mAdbID:125499

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

description: mAdb experiment ID: 125499

hyb_protocol: Affymetrix Hybridization Protocol Other: Fragmented single-stranded sense DNA were hybridized to the Human GeneChip 2.0 ST array and stained on a Genechip Fluidics Station 450 (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

scan_protocol: Scanning Protocol Other: Arrays were scanned on a GeneChip Scanner 3000-7G (Affymetrix).

data_processing:
Data Processing Protocol
Calculation Method: Data were analyzed using Expression Console and Transcriptome Analysis Console Software (St. Louis, MO). After Robust Multichip Average normalization, differentially expressed genes were identified by anova test with a significance cut off p<0.05 and fold change >2 fold.

source_name: VMM39 - IFNgamma Treated

label_protocol:
Affymetrix Labeling Protocol
Other: RNA was amplified using the Ambion WT expression kit (Life Technologies, Carlsbad, CA). Fragmented single-stranded sense DNA were terminally labeled with biotin according to the manufacturer's protocol.

extract_protocol:
Sample Extraction Protocol
Other: Cells were lysed using QIAzol Lysis Reagent (Qiagen, Hilden, Germany) and RNA was extracted according to the manufacturer's protocol.

treatment_protocol:
Treatment type: small molecule
Agent: IFNgamma
Treatment dose: 1000 IU/mL
Treatment time: overnight
Treatment temperature: 37 C
In-vitro treatment: Melanoma cell lines were seeded into 6-well plates at 1x10(6) cells/well in RPMI and individually stimulated in media with rh-IFNgamma (1000 IU/mL; PeproTech) overnight at 37C.

value: tumor

value: Melanoma cells

value: Melanoma


title: CTRL Patient_CODE24 - EAT


title: CTRL Patient_CODE28 - EAT


title: DM13 - IFNgamma Treated - mAdbID:125480

description: mAdb experiment ID: 125480

source_name: DM13 - IFNgamma Treated


title: CAD Patient_CODE45 - SAT


title: CTRL Patient_CODE28 - SAT


title: CTRL Patient_CODE24 - SAT


title: VMM39 - MALP-2 Treated - mAdbID:125497

description: mAdb experiment ID: 125497

source_name: VMM39 - MALP-2 Treated

treatment_protocol:
Agent: MALP-2
Treatment dose: 100 ng/mL
Treatment time: overnight
Treatment temperature: 37 C
In-vitro treatment: Melanoma cell lines were seeded into 6-well plates at 1x10(6) cells/well in RPMI and individually stimulated with TLR2/6 agonist, MALP-2 (100 ng/mL; Imgenex), and Ionomycin (1 mg/mL; Sigma-Aldrich, St. Louis, MO) overnight at 37C.


title: DM13 - MALP-2 and IFNgamma Treated - mAdbID:125481

description: mAdb experiment ID: 125481

source_name: DM13 - MALP-2 and IFNgamma Treated

treatment_protocol:
Agent: MALP-2; IFNgamma
Treatment dose: MALP-2 (1000 ng/mL); IFNgamma (1000 IU/mL)
Treatment time: overnight
Treatment temperature: 37 C
In-vitro treatment: Melanoma cell lines were seeded into 6-well plates at 1x10(6) cells/well in RPMI and individually stimulated with TLR2/6 agonist, MALP-2 (100 ng/mL; Imgenex), and Ionomycin (1 mg/mL; Sigma-Aldrich, St. Louis, MO) overnight at 37C. Stimulation was performed in the presence of rh-IFNgamma (1000 IU/mL; PeproTech).


title: DM13 - FSL-1 and IFNgamma Treated - mAdbID:125482

description: mAdb experiment ID: 125482

source_name: DM13 - FSL-1 and IFNgamma Treated

treatment_protocol:
Agent: FSL-1; IFNgamma
Treatment dose: FSL-1 (5 ug/mL); IFNgamma (1000 IU/mL)
Treatment time: overnight
Treatment temperature: 37 C
In-vitro treatment: Melanoma cell lines were seeded into 6-well plates at 1x10(6) cells/well in RPMI and individually stimulated with TLR2/6 agonist, FSL-1 (5 ug/mL; InvivoGen, San Diego, CA), and Ionomycin (1 mg/mL; Sigma-Aldrich, St. Louis, MO) overnight at 37C. Stimulation was performed in the presence of rh-IFNgamma (1000 IU/mL; PeproTech).


title: CAD Patient_CODE40 - SAT


title: VMM39 - FSL-1 Treated - mAdbID:125498

description: mAdb experiment ID: 125498

source_name: VMM39 - FSL-1 Treated

treatment_protocol:
Agent: FSL-1
Treatment dose: 5 ug/mL
Treatment time: overnight
Treatment temperature: 37 C
In-vitro treatment: Melanoma cell lines were seeded into 6-well plates at 1x10(6) cells/well in RPMI and individually stimulated with TLR2/6 agonist, FSL-1 (5 ug/mL; InvivoGen, San Diego, CA), and Ionomycin (1 mg/mL; Sigma-Aldrich, St. Louis, MO) overnight at 37C.


title: DM13 - FSL-1 Treated - mAdbID:125479

description: mAdb experiment ID: 125479

source_name: DM13 - FSL-1 Treated


title: VMM39 - FSL-1 and IFNgamma Treated - mAdbID:125501

description: mAdb experiment ID: 125501

source_name: VMM39 - FSL-1 and IFNgamma Treated


title: VMM39 - Media Treated - mAdbID:125496

description: mAdb experiment ID: 125496

source_name: VMM39 - Media Treated

treatment_protocol:
Treatment time: overnight
Treatment temperature: 37 C
In-vitro treatment: Melanoma cell lines were seeded into 6-well plates at 1x10(6) cells/well in RPMI overnight at 37C.


title: CTRL Patient_CODE37 - EAT


title: CTRL Patient_CODE34 - EAT


title: VMM39 - MALP-2 and IFNgamma Treated - mAdbID:125500

description: mAdb experiment ID: 125500

source_name: VMM39 - MALP-2 and IFNgamma Treated


title: DM13 - MALP-2 Treated - mAdbID:125478

description: mAdb experiment ID: 125478

source_name: DM13 - MALP-2 Treated


title: DM93 - FSL-1 and IFNgamma Treated - mAdbID:125476

description: mAdb experiment ID: 125476

source_name: DM93 - FSL-1 and IFNgamma Treated


title: CTRL Patient_CODE34 - SAT


title: CTRL Patient_CODE32 - EAT


title: CTRL Patient_CODE37 - SAT


title: CTRL Patient_CODE32 - SAT


title: CTRL Patient_CODE42 - SAT


title: DM13 - Media Treated - mAdbID:125477

description: mAdb experiment ID: 125477

source_name: DM13 - Media Treated


title: DM93 - IFNgamma Treated - mAdbID:125474

description: mAdb experiment ID: 125474

source_name: DM93 - IFNgamma Treated


title: DM93 - FSL-1 Treated - mAdbID:125473

description: mAdb experiment ID: 125473

source_name: DM93 - FSL-1 Treated


title: DM93 - Media Treated - mAdbID:125471

description: mAdb experiment ID: 125471

source_name: DM93 - Media Treated


title: CTRL Patient_CODE42 - EAT

source_name: EAT


title: VMM1 - FSL-1 and IFNgamma Treated - mAdbID:125470

description: mAdb experiment ID: 125470

source_name: VMM1 - FSL-1 and IFNgamma Treated


title: DM93 - MALP-2 and IFNgamma Treated - mAdbID:125475

description: mAdb experiment ID: 125475

source_name: DM93 - MALP-2 and IFNgamma Treated


title: CTRL Patient_CODE46 - SAT

source_name: SAT


title: VMM1 - FSL-1 Treated - mAdbID:125467

description: mAdb experiment ID: 125467

source_name: VMM1 - FSL-1 Treated


title: B. animalis sbsp. lactis CECT 8145_SL117

city: Paterna

first: Patricia

last: Martorell

state: Valencia

address: Catedrático Agustín Escardino Benlloch, 9, Building 2

department: Agrifood Biotechnology

institute: Biópolis SL

hyb_protocol: Hybridization was performed as described by the manufacturer (Affymetrix, SantaClara, CA). The complementary RNA hybridization cocktail was incubated overnight at 45C while rotating in a hybridization oven. After 16 h of hybridization, the cocktail was removed and the arrays were washed and stained in an Affymetrix GeneChip Fluidics Station 450, according to the Affymetrix-recommended protocol

scan_protocol: Arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G (Affymetrix, Santa Clara, CA, USA).

data_processing: GeneChip Operating Software supplied by Affymetrix was used to perform gene expression analysis. Four samples of control fed conditions and four samples of treated conditions were statistically analysed. Raw data obtained from Affymetrix arrays were background corrected using RMA methodology. Intensity signal was standardized across arrays via quantile normalization algorithm. The difference between treated samples and controls was statistically tested using limma moderate t-statistic. Aiming to control the false disocvery rate, p-values were corrected for multiple testing using Benjamini and Hochberg method

organism: Caenorhabditis elegans

source_name: N2_B animalis_young adult

label_protocol: Gene expression analysis was performed according to the Affymetrix-recommended protocol using Affymetrix C.Elegans Genome Array. GeneChips containing probes for over 22,500 transcripts. Total RNA (300 ng per sample) was biotin- labeled using the Affymetrix GeneChip 3' IVT express protocol

growth_protocol: C. elegans was cultured in Nematode Growth Medium (NGM) as estándar diet. Nematodes were age-synchronized by isolating eggs from gravid adults. Embryos were incubated in the corresponding agar plates at 20ºC for 3 days (until reach young adult stage)

extract_protocol: Worms from each fed condition (NGM or strain CECT 8145) were collected with M9 buffer and disrupted by sonication (3 pulses at 10W, 20s/pulse). RNA was isolated with a comercial kit (RNAsy Kit, Qiagen)

treatment_protocol: Treated nematodes were cultured in NGM plates supplemented with a lawn of the strain B. animalis sbsp. lactis CECT 8145 and incubated at 20ºC from egg to young adult stage.

tag: genotype/variation

value: wild type

tag: culture media

value: NGM supplemented with B. animalis

tag: bacterial strain

value: Bifidobacterium animalis sbsp. lactis CECT 8145

tag: developmental stage

value: young adult stage


title: DM93 - MALP-2 Treated - mAdbID:125472

description: mAdb experiment ID: 125472

source_name: DM93 - MALP-2 Treated

tag: tissue

tag: cell type


title: CTRL Patient_CODE6 - EAT

tag: age


title: B. animalis sbsp. lactis CECT 8145_SL113


title: CTRL Patient_CODE43 - EAT


title: B. animalis sbsp. lactis CECT 8145_SL119


title: VMM1 - MALP-2 Treated - mAdbID:125466

description: mAdb experiment ID: 125466

source_name: VMM1 - MALP-2 Treated


title: B. animalis sbsp. lactis CECT 8145_SL115


title: VMM1 - MALP-2 and IFNgamma Treated - mAdbID:125469

description: mAdb experiment ID: 125469

source_name: VMM1 - MALP-2 and IFNgamma Treated


title: VMM1 - Media Treated - mAdbID:125465

description: mAdb experiment ID: 125465

source_name: VMM1 - Media Treated


title: CTRL Patient_CODE46 - EAT


title: NGM_SL118

source_name: N2_NGM control_young adult

value: Control; Nematode Growth medium (NGM)


title: NGM_SL116


title: VMM1 - IFNgamma Treated - mAdbID:125468

description: mAdb experiment ID: 125468

source_name: VMM1 - IFNgamma Treated


title: NGM_SL112


title: CAD Patient_CODE23 - SAT


title: NGM_SL114


title: CTRL Patient_CODE6 - SAT


title: CTRL Patient_CODE43 - SAT


title: CTRL Patient_CODE44 - SAT


title: Macaque brain tissue BV injected, biological rep6

status: Public on Nov 21 2015

city: Singapore

first: Timothy

middle: Weixin

last: Kwang

address: 46 Kim Yan Road, The Herencia #01-14/15

country: Singapore

institute: Tessa Therapeutics Pte. Ltd.

description:
Macaque3 brain tissue 2 expt.
Gene expression data from brain tissue around site injected with BV-HSVtk.

hyb_protocol: Hybridization mixes with 15 μg of fragmented cRNA were prepared according to the standard protocol from Affymetrix GeneChip Hybridization, Wash and Stain kit. 200µl of clarified hybridization cocktail (15 µg of labeled cRNA) was hybridized onto arrays for 16 h at 45 °C. Arrays were washed and stained with streptavidin-phycoerythrin in Affymetrix GeneChip Fluidics Station 450 using recommended reagents from Affymetrix Hybridization, Wash and Stain kit.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were acquired with GCOS v 1.4.0.036, scaling and normalization factors were set to user-defined values of 1. The statistical expression algorithm was used for analysis.

organism: Macaca fascicularis

source_name: Macaque 3 left hemisphere brain tissue injected with BV-HSVtk

label_protocol: 5μg of purified RNA was used to prepare labeled cRNA using Affymetrix One Cycle Target Labeling and Control reagents and Kreactech RNA ampULSE amplification labeling kit.

extract_protocol: Total RNA was isolated from brain tissue using Trizol according to the manufacturer's instructions and cleaned up using Qiagen RNeasy Mini column.

treatment_protocol: 3 adult male cynomolgus macaques weighing approximately 3-4 kg were administered with baculovirus BV-HSVtk purified by membrane chromatography + high-speed centrifugation (MC+HS) as 4 separate intrastriatal microinjections into the left hemisphere (anteroposterior: 0.0 mm and +3.0 mm to the bi-lateral commissural line targeting the center of caudate and putamen) - 1E8 viral particles in 10 μl per injection site. Corresponding coordinates on right hemisphere were injected with mock virus preparation. Mock virus preparation refers to Sf9 culture medium containing no baculovirus subjected to purification by MC+HS. Brain samples weighing around 100 mg were collected 2 days after virus inoculation and placed in Trizol.

value: brain

value: adult

tag: Sex

value: male

tag: treatment

value: BV-HSVtk

tag: animal id


title: CTRL Patient_CODE44 - EAT


title: Macaque brain tissue mock control, biological rep3

description:
Macaque2 brain tissue 1 ctrl.
Gene expression data from brain tissue around site injected with mock supernatant.

source_name: Macaque 2 right hemisphere brain tissue injected with mock supernatant

value: mock


title: Macaque brain tissue mock control, biological rep2

description:
Macaque1 brain tissue 2 ctrl.
Gene expression data from brain tissue around site injected with mock supernatant.

source_name: Macaque 1 right hemisphere brain tissue injected with mock supernatant


title: Macaque brain tissue BV injected, biological rep4

description:
Macaque2 brain tissue 2 expt.
Gene expression data from brain tissue around site injected with BV-HSVtk.

source_name: Macaque 2 left hemisphere brain tissue injected with BV-HSVtk


title: Macaque brain tissue mock control, biological rep4

description:
Macaque2 brain tissue 2 ctrl.
Gene expression data from brain tissue around site injected with mock supernatant.


title: Macaque brain tissue BV injected, biological rep3

description:
Macaque2 brain tissue 1 expt.
Gene expression data from brain tissue around site injected with BV-HSVtk.


title: Macaque brain tissue BV injected, biological rep2

description:
Macaque1 brain tissue 2 expt.
Gene expression data from brain tissue around site injected with BV-HSVtk.

source_name: Macaque 1 left hemisphere brain tissue injected with BV-HSVtk


title: Macaque brain tissue mock control, biological rep6

description:
Macaque3 brain tissue 2 ctrl.
Gene expression data from brain tissue around site injected with mock supernatant.

source_name: Macaque 3 right hemisphere brain tissue injected with mock supernatant


title: Macaque brain tissue mock control, biological rep5

description:
Macaque3 brain tissue 1 ctrl.
Gene expression data from brain tissue around site injected with mock supernatant.


title: parental cells (SH-SY5Y), biological replicate 2

city: Boston

first: David

last: Debruyne

address: 450 Brookline avenue

institute: Dana-Farber Cancer Institute

description:
gene expression data from parental sensitive cells
SH-SY5Y_2
10_SH-SY5Y_2.rma-Signal

hyb_protocol: Hybridization, washing and staining were done using the GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix, Santa Clara, CA, USA) on GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, CA, USA) in the Affymetric Fluidics Station 450.

scan_protocol: The arrays were scanned on GeneChip Scanner 3000 7G.

data_processing:
The data were analyzed with Expression Console software using RMA algorithm (log transformed and quantile normalized).
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.3.1.187

source_name: SH-SY5Y control_sensitive to TAE684

label_protocol: Target preparation was done using the 3' IVT Express Kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol: Cells were grown in RPMI-1640 media supplemented with 10% FBS and 1% Penicillin/Streptomycin.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer's instructions.

treatment_protocol: Whereas the parental sensitive SH-SY5Y cells were maintained in media only, the resistant SY5Y-TR1 cells were maintained in media with TAE684 at a concentration of 1uM.

value: neuroblastoma cell line bearing ALKF1174L mutation

tag: tae684 sensitivity

value: parental TAE684-sensitive cells


title: resistant cells (SY5Y-TR1), biological replicate 1

description:
gene expression data from TAE684-resistant cells
SY5Y-TR1_A
12_SY5Y-TR1_A.rma-Signal

source_name: SY5Y-TR1_resistant to TAE684

value: TAE684-resistant cells


title: Macaque brain tissue BV injected, biological rep5

description:
Macaque3 brain tissue 1 expt.
Gene expression data from brain tissue around site injected with BV-HSVtk.


title: resistant cells (SY5Y-TR1), biological replicate 2

description:
gene expression data from TAE684-resistant cells
SY5Y-TR1_B
13_SY5Y-TR1_B.rma-Signal


title: patient 096_cancer_expression

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 2-1-1 Hongo

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

description: Gene expression profile of surgically resected material

hyb_protocol: Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.

source_name: surgically resected material

label_protocol: cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).

treatment_protocol: Gene expression profiles for 125 cancer tissues from colorectal cancer patients were used.

tag: metastasis

value: distant metastasis

value: colorectal cancer, LCM


title: parental cells (SH-SY5Y), biological replicate 3

description:
gene expression data from parental sensitive cells
SH-SY5Y_3
11_SH-SY5Y_3.rma-Signal


title: Macaque brain tissue BV injected, biological rep1

description:
Macaque1 brain tissue 1 expt.
Gene expression data from brain tissue around site injected with BV-HSVtk.


title: resistant cells (SY5Y-TR1), biological replicate 3

description:
gene expression data from TAE684-resistant cells
SY5Y-TR1_C
14_SY5Y-TR1_C.rma-Signal


title: patient 095_cancer_expression


title: patient 097_cancer_expression


title: parental cells (SH-SY5Y), biological replicate 1

description:
gene expression data from parental sensitive cells
SH-SY5Y_1
9_SH-SY5Y_1.rma-Signal


title: patient 099_cancer_expression


title: patient 089_cancer_expression


title: patient 094_cancer_expression


title: patient 083_cancer_expression


title: patient 072_cancer_expression


title: patient 070_cancer_expression


title: patient 065_cancer_expression


title: patient 055_cancer_expression


title: patient 078_cancer_expression


title: patient 053_cancer_expression


title: patient 048_cancer_expression


title: patient 086_cancer_expression


title: patient 088_cancer_expression


title: patient 057_cancer_expression


title: patient 098_cancer_expression


title: patient 061_cancer_expression


title: patient 068_cancer_expression


title: patient 052_cancer_expression


title: patient 073_cancer_expression


title: patient 046_cancer_expression


title: patient 036_cancer_expression


title: patient 031_cancer_expression


title: patient 030_cancer_expression


title: patient 034_cancer_expression


title: patient 041_cancer_expression


title: patient 044_cancer_expression


title: patient 028_cancer_expression


title: patient 063_cancer_expression


title: patient 045_cancer_expression


title: patient 033_cancer_expression


title: patient 026_cancer_expression


title: patient 023_cancer_expression


title: patient 234_cancer_expression


title: patient 241_cancer_expression


title: patient 244_cancer_expression


title: Macaque brain tissue mock control, biological rep1

description:
Macaque1 brain tissue 1 ctrl.
Gene expression data from brain tissue around site injected with mock supernatant.


title: patient 235_cancer_expression


title: patient 243_cancer_expression


title: patient 219_cancer_expression


title: patient 242_cancer_expression


title: patient 230_cancer_expression


title: patient 226_cancer_expression


title: patient 025_cancer_expression


title: patient 217_cancer_expression


title: patient 223_cancer_expression


title: patient 229_cancer_expression


title: patient 240_cancer_expression


title: patient 220_cancer_expression


title: patient 214_cancer_expression


title: patient 227_cancer_expression


title: patient 211_cancer_expression


title: patient 222_cancer_expression


title: patient 213_cancer_expression


title: patient 215_cancer_expression


title: patient 082_cancer_expression


title: patient 231_cancer_expression


title: patient 204_cancer_expression


title: patient 210_cancer_expression


title: patient 207_cancer_expression


title: patient 188_cancer_expression


title: patient 196_cancer_expression


title: patient 191_cancer_expression


title: patient 201_cancer_expression


title: patient 202_cancer_expression


title: patient 187_cancer_expression


title: patient 194_cancer_expression


title: patient 184_cancer_expression


title: patient 209_cancer_expression


title: patient 203_cancer_expression


title: patient 195_cancer_expression


title: patient 190_cancer_expression


title: patient 197_cancer_expression


title: patient 180_cancer_expression


title: patient 017_cancer_expression


title: patient 200_cancer_expression


title: patient 181_cancer_expression


title: patient 178_cancer_expression


title: patient 173_cancer_expression


title: patient 175_cancer_expression


title: patient 179_cancer_expression


title: laird-00098: TCGA-02-0104-01A-01D-0297-05

type: genomic

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

hyb_protocol: See mage-tab files linked to series entry for additional details

molecule: genomic DNA

source_name: Brain

tag: diseasestate

value: GLIOBLASTOMA MULTIFORME

tag: organismpart

value: Brain

tag: individual

tag: pathologic status

tag: histologic diagnosis

value: NOT SPECIFIED

tag: tissue anatomic site


title: laird-00098: TCGA-06-0165-01A-01D-0242-05

scan_protocol: See mage-tab files linked to series entry for additional details


title: laird-00098: TCGA-02-0015-01A-01D-0297-05

data_processing: See mage-tab files linked to series entry for additional details


title: laird-00098: TCGA-06-0156-01A-02D-0242-05

label_protocol: See mage-tab files linked to series entry for additional details

value: GLIOBLASTOMA

value: OCCIPITAL LOBE


title: laird-00098: TCGA-06-0156-01A-03D-0242-05

extract_protocol: See mage-tab files linked to series entry for additional details


title: laird-00098: TCGA-06-0156-01A-01D-0242-05


title: laird-00098: TCGA-02-0106-01A-01D-0287-05


title: patient 169_cancer_expression


title: laird-00098: TCGA-02-0046-01A-01D-0186-05

value: TEMPORAL LOBE


title: patient 164_cancer_expression


title: laird-00098: TCGA-08-0349-01A-01D-0314-05

value: OVERLAPPING LESION OF BRAIN


title: patient 171_cancer_expression


title: patient 174_cancer_expression


title: laird-00098: TCGA-02-0060-01A-01D-0186-05


title: patient 155_cancer_expression


title: laird-00098: TCGA-06-0182-01A-01D-0287-05


title: patient 162_cancer_expression


title: patient 168_cancer_expression


title: patient 144_cancer_expression


title: patient 146_cancer_expression


title: patient 156_cancer_expression


title: patient 158_cancer_expression


title: patient 142_cancer_expression


title: patient 141_cancer_expression


title: patient 157_cancer_expression


title: patient 140_cancer_expression


title: patient 150_cancer_expression


title: laird-00098: TCGA-06-0402-01A-01D-0287-05


title: patient 143_cancer_expression


title: patient 148_cancer_expression


title: laird-00098: TCGA-08-0511-01A-01D-0287-05


title: laird-00098: TCGA-08-0389-01A-01D-0297-05


title: patient 139_cancer_expression


title: patient 15,_cancer_expression


title: laird-00098: TCGA-06-0744-01A-01D-0337-05


title: laird-00098: TCGA-08-0516-01A-01D-0287-05

value: PARIETAL LOBE


title: laird-00098: TCGA-02-0324-01A-01D-0279-05


title: laird-00098: TCGA-08-0360-01A-01D-0297-05


title: laird-00098: TCGA-02-0014-01A-01D-0186-05


title: laird-00098: TCGA-06-0214-01A-02D-0242-05

value: FRONTAL LOBE


title: laird-00098: TCGA-02-0271-01A-01D-0287-05


title: patient 147_cancer_expression


title: patient 027_cancer_expression


title: laird-00098: TCGA-02-0258-01A-01D-0279-05


title: patient 136_cancer_expression


title: laird-00098: TCGA-06-0188-01A-01D-0242-05


title: laird-00098: TCGA-06-0743-01A-01D-0337-05


title: laird-00098: TCGA-02-0033-01A-01D-0186-05


title: patient 133_cancer_expression


title: laird-00098: TCGA-02-0079-01A-01D-0314-05


title: laird-00098: TCGA-02-0054-01A-01D-0186-05


title: patient 123_cancer_expression


title: patient 135_cancer_expression


title: patient 125_cancer_expression


title: patient 127_cancer_expression


title: patient 124_cancer_expression


title: patient 129_cancer_expression


title: laird-00098: TCGA-06-0158-01A-01D-0242-05


title: patient 110_cancer_expression


title: patient 117_cancer_expression


title: patient 108_cancer_expression


title: laird-00098: TCGA-02-0057-01A-01D-0186-05


title: patient 221_cancer_expression


title: laird-00098: TCGA-08-0344-01A-01D-0297-05


title: patient 130_cancer_expression


title: patient 106_cancer_expression


title: laird-00224: TCGA-13-0758-01A-01D-0359-05

source_name: Primary solid_tumor

value: Serous Cystadenocarcinoma

value: Ovary

tag: diseasestaging

value: IV

value: FEMALE

tag: clinical diagnosis

tag: external id

tag: tumorgrading


title: patient 109_cancer_expression

tag: tissue


title: patient 116_cancer_expression


title: patient 101_cancer_expression


title: laird-00224: TCGA-24-2298-01A-01D-0708-05

value: IIIC

tag: age


title: patient 008_cancer_expression


title: laird-00224: TCGA-57-1582-01A-01D-0536-05

tag: Sex


title: laird-00098: TCGA-06-0141-01A-01D-0218-05


title: laird-00098: TCGA-02-0086-01A-01D-0199-05


title: laird-00098: TCGA-06-0190-01A-01D-0242-05


title: laird-00224: TCGA-61-2094-01A-01D-0667-05


title: laird-00224: TCGA-13-0900-01B-01D-0460-05


title: laird-00098: TCGA-08-0392-01A-01D-0297-05


title: laird-00098: TCGA-02-0111-01A-01D-0287-05


title: patient 103_cancer_expression


title: laird-00098: TCGA-02-0059-01A-01D-0297-05


title: patient 102_cancer_expression


title: laird-00224: TCGA-24-1474-01A-01D-0501-05


title: laird-00224: TCGA-13-1405-01A-01D-0460-05


title: laird-00098: TCGA-08-0514-01A-01D-0287-05


title: laird-00098: TCGA-15-0742-01A-01D-0337-05


title: laird-00224: TCGA-29-1781-01A-01D-0563-05


title: laird-00224: TCGA-09-1669-01A-01D-0536-05

value: IIIA


title: laird-00224: TCGA-25-1625-01A-01D-0536-05


title: laird-00098: TCGA-02-0026-01B-01D-0297-05


title: laird-00224: TCGA-24-2254-01A-01D-0667-05


title: laird-00224: TCGA-23-1021-01B-01D-0432-05


title: laird-00098: TCGA-02-0055-01A-01D-0186-05


title: laird-00224: TCGA-13-1487-01A-01D-0475-05

value: GX


title: laird-00098: TCGA-02-0116-01A-01D-0199-05


title: laird-00224: TCGA-25-2390-01A-01D-0708-05


title: laird-00098: TCGA-02-0037-01A-01D-0186-05


title: laird-00224: TCGA-61-1725-01A-01D-0581-05


title: laird-00098: TCGA-02-0075-01A-01D-0199-05


title: laird-00098: TCGA-08-0346-01A-01D-0297-05


title: laird-00224: TCGA-04-1652-01A-01D-0581-05


title: laird-00098: TCGA-02-0269-01B-01D-0287-05


title: laird-00224: TCGA-09-1666-01A-01D-0536-05


title: laird-00224: TCGA-24-2288-01A-01D-0708-05


title: laird-00098: TCGA-02-0084-01A-01D-0314-05


title: laird-00098: TCGA-08-0354-01A-01D-0297-05


title: laird-00098: TCGA-06-0129-01A-01D-0218-05


title: laird-00224: TCGA-04-1655-01A-01D-0563-05

value: IIIB


title: laird-00224: TCGA-61-2012-01A-01D-0667-05

value: IIC


title: laird-00098: TCGA-06-0154-01A-03D-0242-05

value: GLIOBLASTOMA MULTIFORME

value: Brain


title: laird-00098: TCGA-06-0143-01A-01D-0218-05


title: laird-00224: TCGA-24-1549-01A-01D-0501-05

value: NOT SPECIFIED


title: laird-00098: TCGA-02-0432-01A-02D-0287-05


title: laird-00224: TCGA-24-1436-01A-01D-0475-05


title: laird-00224: TCGA-23-1809-01A-01D-0563-05


title: laird-00098: TCGA-06-0154-01A-02D-0242-05


title: laird-00224: TCGA-29-1768-01A-01D-0563-05


title: laird-00224: TCGA-04-1350-01A-01D-0460-05


title: laird-00098: TCGA-06-0139-01A-01D-0218-05


title: laird-00098: TCGA-02-0339-01A-01D-0287-05


title: laird-00098: TCGA-12-0769-01A-01D-0337-05


title: laird-00098: TCGA-06-0210-01A-01D-0242-05


title: laird-00224: TCGA-31-1955-01A-01D-0652-05


title: laird-00098: TCGA-06-0210-01B-01D-0242-05


title: laird-00224: TCGA-13-0723-01A-02D-0359-05


title: laird-00224: TCGA-09-1667-01C-01D-0536-05


title: laird-00098: TCGA-08-0521-01A-01D-0287-05


title: laird-00224: TCGA-24-1416-01A-01D-0475-05


title: laird-00098: TCGA-08-0353-01A-01D-0297-05


title: laird-00098: TCGA-06-0176-01A-02D-0242-05


title: laird-00224: TCGA-23-1029-01B-01D-0581-05


title: laird-00224: TCGA-13-0893-01B-01D-0460-05


title: laird-00098: TCGA-06-0176-01A-03D-0242-05


title: laird-00224: TCGA-23-1117-01A-02D-0432-05


title: laird-00098: TCGA-12-0707-01A-01D-0337-05


title: laird-00098: TCGA-06-0169-01A-01D-0218-05


title: laird-00098: TCGA-12-0620-01A-01D-0314-05


title: laird-00224: TCGA-13-0899-01A-01D-0402-05


title: laird-00224: TCGA-25-2391-01A-01D-0708-05


title: laird-00224: TCGA-36-1580-01A-01D-0536-05


title: laird-00098: TCGA-12-0691-01A-01D-0337-05


title: laird-00098: TCGA-06-0157-01A-01D-0242-05

value: CEREBRUM


title: laird-00224: TCGA-09-2053-01C-01D-0667-05


title: laird-00098: TCGA-08-0375-01A-01D-0297-05


title: laird-00098: TCGA-06-0151-01A-01D-0242-05


title: laird-00224: TCGA-13-0751-01A-01D-0359-05


title: laird-00098: TCGA-02-0333-01A-02D-0287-05


title: laird-00098: TCGA-08-0352-01A-01D-0314-05


title: laird-00224: TCGA-61-2017-01A-01D-0667-05


title: laird-00224: TCGA-24-2281-01A-01D-0708-05

value: IIA


title: laird-00098: TCGA-06-0138-01A-02D-0242-05

value: TEMPORAL LOBE


title: laird-00098: TCGA-06-0750-01A-01D-0337-05


title: laird-00224: TCGA-25-1312-01A-01D-0460-05


title: laird-00224: TCGA-24-1843-01A-01D-0581-05


title: laird-00098: TCGA-08-0386-01A-01D-0314-05


title: laird-00224: TCGA-24-1616-01A-01D-0501-05


title: laird-00224: TCGA-13-0803-01A-01D-0359-05


title: laird-00098: TCGA-06-0138-01A-01D-0242-05


title: laird-00224: TCGA-61-1724-01A-01D-0652-05


title: laird-00098: TCGA-06-0121-01A-04D-0218-05


title: laird-00224: TCGA-24-1930-01A-01D-0652-05


title: laird-00098: TCGA-02-0034-01A-01D-0186-05


title: laird-00098: TCGA-02-0281-01A-01D-0287-05


title: laird-00224: TCGA-13-1497-01A-01D-0475-05


title: laird-00224: TCGA-24-1544-01A-01D-0536-05


title: laird-00098: TCGA-02-0446-01A-01D-0287-05


title: laird-00224: TCGA-13-1489-01A-01D-0475-05


title: laird-00098: TCGA-02-0325-01A-01D-0279-05


title: laird-00224: TCGA-23-1111-01A-01D-0581-05


title: laird-00224: TCGA-24-1560-01A-01D-0536-05


title: laird-00098: TCGA-02-0080-01A-01D-0199-05


title: laird-00224: TCGA-13-1489-02A-01D-0807-05

source_name: Recurrent Solid Tumor


title: laird-00098: TCGA-02-0039-01A-01D-0297-05


title: laird-00224: TCGA-24-2027-01A-01D-0652-05


title: laird-00098: TCGA-06-0412-01A-01D-0287-05


title: laird-00224: TCGA-13-0757-01A-01D-0359-05


title: laird-00224: TCGA-25-1314-01A-01D-0460-05


title: laird-00098: TCGA-06-0213-01A-01D-0242-05

value: PARIETAL LOBE


title: laird-00098: TCGA-08-0510-01A-01D-0287-05

value: FRONTAL LOBE


title: laird-00098: TCGA-06-0219-01A-01D-0242-05

value: OVERLAPPING LESION OF BRAIN


title: laird-00224: TCGA-13-1409-01A-01D-0460-05

value: Serous Cystadenocarcinoma

value: Ovary


title: laird-00098: TCGA-02-0326-01A-01D-0287-05


title: laird-00224: TCGA-24-1923-01A-01D-0652-05

value: FEMALE


title: laird-00098: TCGA-02-0102-01A-01D-0199-05


title: laird-00098: TCGA-02-0071-01A-01D-0199-05


title: laird-00098: TCGA-02-0024-01B-01D-0186-05


title: laird-00098: TCGA-02-0070-01A-01D-0297-05


title: laird-00224: TCGA-13-1403-01A-01D-0460-05

value: IIIC


title: laird-00098: TCGA-06-0166-01A-01D-0242-05


title: laird-00224: TCGA-24-0981-01A-01D-0432-05


title: laird-00224: TCGA-24-2030-01A-01D-0667-05


title: laird-00098: TCGA-06-0747-01A-01D-0337-05


title: laird-00224: TCGA-24-1562-01A-01D-0501-05


title: laird-00224: TCGA-25-1318-01A-01D-0460-05


title: laird-00098: TCGA-06-0178-01A-01D-0242-05


title: laird-00224: TCGA-13-0801-01A-01D-0359-05


title: laird-00098: TCGA-12-0703-01A-02D-0337-05


title: laird-00224: TCGA-29-1783-01A-01D-0563-05


title: laird-00098: TCGA-06-0686-01A-01D-0337-05


title: laird-00224: TCGA-30-1880-01A-01D-0652-05


title: laird-00224: TCGA-13-0883-01A-02D-0402-05


title: laird-00224: TCGA-13-2060-01A-01D-0708-05

value: IV


title: laird-00098: TCGA-08-0525-01A-01D-0287-05

value: ANAPLASTIC ASTROCYTOMA


title: laird-00098: TCGA-02-0011-01B-01D-0186-05


title: laird-00224: TCGA-24-2036-01A-01D-0667-05

value: IIIA


title: laird-00224: TCGA-61-1738-01A-01D-0581-05


title: laird-00098: TCGA-07-0227-20A-01D-0287-05


title: laird-00224: TCGA-24-1428-01A-01D-0475-05


title: laird-00224: TCGA-24-0975-01B-02D-0432-05


title: laird-00098: TCGA-08-0373-01A-01D-0314-05


title: laird-00224: TCGA-13-0897-01A-01D-0402-05


title: laird-00098: TCGA-06-0648-01A-01D-0314-05


title: laird-00098: TCGA-07-0227-20A-01D-0314-05


title: laird-00098: TCGA-07-0227-20A-01D-0337-05


title: laird-00224: TCGA-13-0793-01A-01D-0359-05


title: laird-00224: TCGA-24-2261-01A-01D-0667-05


title: laird-00098: TCGA-07-0227-20A-01D-0242-05


title: laird-00098: TCGA-02-0266-01A-01D-0279-05


title: laird-00224: TCGA-09-1659-01B-01D-0536-05


title: laird-00098: TCGA-06-0160-01A-01D-0242-05

value: NON-MALIGNANT

value: NO HISTOLOGY AVAILABLE


title: laird-00098: TCGA-06-0644-01A-02D-0314-05

value: GLIOBLASTOMA MULTIFORME

value: Brain


title: laird-00224: TCGA-61-1722-01A-01D-0581-05

value: IB

value: NOT SPECIFIED


title: laird-00098: TCGA-06-0397-01A-01D-0287-05

value: MALIGNANT


title: laird-00224: TCGA-61-2008-02A-01D-0807-05

value: IIC


title: laird-00098: TCGA-06-0149-01A-05D-0287-05

value: TEMPORAL LOBE


title: laird-00224: TCGA-61-2018-01A-01D-0667-05

value: IC


title: laird-00224: TCGA-25-1871-01A-01D-0652-05

value: Serous Cystadenocarcinoma


title: laird-00224: TCGA-13-0800-01A-01D-0359-05

value: Ovary


title: laird-00098: TCGA-08-0351-01A-01D-0297-05

value: OVERLAPPING LESION OF BRAIN


title: laird-00098: TCGA-02-0027-01A-01D-0186-05

value: FRONTAL LOBE


title: laird-00224: TCGA-13-1482-01A-01D-0475-05

value: IV

value: FEMALE


title: laird-00224: TCGA-13-0727-01A-01D-0359-05

value: IIIC


title: laird-00098: TCGA-06-0145-01A-05D-0218-05

value: BRAIN, NOS


title: laird-00098: TCGA-06-0145-01A-01D-0218-05


title: laird-00224: TCGA-29-1784-01A-02D-0563-05


title: patient 006_cancer_expression

value: distant metastasis

value: colorectal cancer, LCM


title: laird-00098: TCGA-06-0145-01A-04D-0218-05

value: GLIOBLASTOMA MULTIFORME

value: Brain


title: laird-00098: TCGA-06-0145-01A-03D-0218-05


title: laird-00224: TCGA-57-1585-01A-01D-0536-05

value: NOT SPECIFIED


title: laird-00224: TCGA-29-1771-01A-01D-0563-05


title: laird-00224: TCGA-04-1651-01A-01D-0581-05


title: laird-00224: TCGA-29-1764-01A-01D-0563-05


title: laird-00098: TCGA-06-0649-01B-01D-0337-05


title: laird-00224: TCGA-25-2399-01A-01D-0708-05


title: laird-00098: TCGA-02-0006-01B-01D-0186-05

value: MALIGNANT


title: laird-00224: TCGA-61-2008-01A-02D-0667-05

value: IIC


title: laird-00098: TCGA-06-0145-01A-06D-0218-05


title: laird-00224: TCGA-13-0760-01A-01D-0359-05


title: laird-00098: TCGA-12-0616-01A-01D-0314-05

value: TEMPORAL LOBE


title: laird-00098: TCGA-12-0773-01A-01D-0337-05


title: laird-00098: TCGA-06-0164-01A-01D-0287-05

value: OCCIPITAL LOBE


title: laird-00224: TCGA-25-1328-01A-01D-0460-05

value: Serous Cystadenocarcinoma


title: laird-00098: TCGA-12-0657-01A-01D-0337-05


title: laird-00098: TCGA-06-0133-01A-02D-0218-05


title: laird-00224: TCGA-13-1504-01A-01D-0475-05

value: Ovary


title: laird-00224: TCGA-24-1850-01A-01D-0581-05


title: laird-00098: TCGA-06-0145-01A-02D-0218-05


title: laird-00224: TCGA-09-0366-01A-01D-0359-05


title: laird-00224: TCGA-20-1684-01A-01D-0563-05


title: laird-00224: TCGA-13-0886-01A-01D-0402-05


title: laird-00098: TCGA-06-0208-01A-01D-0242-05


title: laird-00098: TCGA-06-0208-01B-01D-0242-05


title: laird-00224: TCGA-04-1335-01A-01D-0432-05

value: IB


title: laird-00098: TCGA-06-0140-01A-01D-0218-05


title: laird-00224: TCGA-31-1950-01A-01D-0652-05


title: laird-00224: TCGA-04-1517-01A-01D-0536-05


title: laird-00224: TCGA-04-1514-01A-01D-0501-05

value: IIIA


title: laird-00098: TCGA-06-0126-01A-01D-0218-05

value: FRONTAL LOBE


title: laird-00224: TCGA-09-1662-01A-01D-0536-05

value: IV

value: FEMALE


title: laird-00224: TCGA-23-2072-01A-01D-0667-05


title: laird-00098: TCGA-08-0518-01A-01D-0287-05


title: laird-00098: TCGA-08-0359-01A-01D-0297-05


title: laird-00224: TCGA-09-1673-01A-01D-0563-05


title: laird-00098: TCGA-02-0422-01A-01D-0287-05


title: laird-00098: TCGA-06-0167-01A-01D-0242-05


title: laird-00224: TCGA-13-1507-01A-01D-0475-05

value: IIIC


title: laird-00224: TCGA-09-2043-01A-01D-0708-05

value: IC


title: laird-00224: TCGA-24-1928-01A-01D-0652-05


title: laird-00224: TCGA-24-1466-01A-01D-0475-05


title: laird-00098: TCGA-06-0147-01A-01D-0218-05

value: PARIETAL LOBE


title: laird-00224: TCGA-13-1485-01A-02D-0475-05


title: laird-00098: TCGA-06-0122-01A-01D-0218-05

value: GLIOBLASTOMA MULTIFORME

value: OVERLAPPING LESION OF BRAIN


title: laird-00098: TCGA-12-0775-01A-01D-0337-05

value: Brain

value: NOT SPECIFIED


title: laird-00224: TCGA-24-1467-01A-01D-0475-05


title: laird-00098: TCGA-06-0187-01A-01D-0242-05

value: MALIGNANT


title: laird-00098: TCGA-06-0174-01A-01D-0242-05


title: laird-00224: TCGA-23-1114-01B-01D-0563-05


title: laird-00098: TCGA-02-0025-01A-01D-0297-05


title: laird-00098: TCGA-02-0285-01A-01D-0287-05


title: laird-00098: TCGA-06-0147-01A-02D-0242-05


title: laird-00224: TCGA-61-1737-01A-01D-0581-05


title: laird-00098: TCGA-02-0337-01A-01D-0287-05


title: laird-00098: TCGA-02-0051-01A-01D-0297-05


title: laird-00224: TCGA-09-2050-01A-01D-0708-05

value: IIA


title: laird-00224: TCGA-25-1870-01A-01D-0652-05


title: laird-00224: TCGA-13-0791-01A-01D-0359-05


title: laird-00098: TCGA-08-0245-01A-01D-0297-05

value: OCCIPITAL LOBE


title: laird-00098: TCGA-06-0194-01A-01D-0287-05

value: TEMPORAL LOBE


title: laird-00224: TCGA-13-0791-02A-01D-0807-05

value: Serous Cystadenocarcinoma

value: Ovary


title: laird-00098: TCGA-12-0656-01A-03D-0337-05


title: laird-00098: TCGA-02-0003-01A-01D-0186-05


title: laird-00224: TCGA-13-1407-01A-01D-0460-05


title: laird-00224: TCGA-24-1846-01A-01D-0581-05


title: laird-00098: TCGA-06-0168-01A-02D-0242-05


title: laird-00098: TCGA-12-0654-01B-01D-0337-05


title: laird-00224: TCGA-13-0799-01A-01D-0359-05


title: laird-00098: TCGA-06-0148-01A-03D-0242-05


title: laird-00224: TCGA-24-2280-01A-01D-0708-05


title: laird-00098: TCGA-06-0148-01A-05D-0242-05


title: laird-00224: TCGA-04-1648-01A-01D-0581-05


title: laird-00224: TCGA-13-0765-01A-01D-0359-05


title: laird-00098: TCGA-06-0148-01A-04D-0242-05


title: laird-00098: TCGA-06-0148-01A-01D-0218-05


title: laird-00224: TCGA-24-1842-01A-01D-0581-05


title: laird-00224: TCGA-24-1464-01A-01D-0475-05


title: laird-00098: TCGA-02-0099-01A-01D-0199-05


title: laird-00224: TCGA-61-1907-01A-01D-0581-05


title: laird-00098: TCGA-02-0048-01A-01D-0297-05


title: laird-00224: TCGA-61-2097-01A-02D-0667-05

value: IIC


title: laird-00224: TCGA-24-0980-01A-01D-0402-05


title: laird-00098: TCGA-06-0125-01A-01D-0218-05


title: laird-00224: TCGA-23-2077-01A-01D-0667-05


title: laird-00224: TCGA-24-1435-01A-01D-0475-05


title: laird-00224: TCGA-24-1550-01A-01D-0501-05


title: laird-00098: TCGA-06-0142-01A-01D-0218-05


title: laird-00098: TCGA-06-0168-01A-01D-0242-05


title: laird-00224: TCGA-23-2081-01A-01D-0667-05


title: laird-00098: TCGA-02-0321-01A-01D-0287-05


title: laird-00224: TCGA-23-1123-01A-01D-0432-05


title: laird-00098: TCGA-06-0173-01A-01D-0242-05


title: laird-00098: TCGA-08-0350-01A-01D-0297-05


title: laird-00224: TCGA-36-1570-01A-01D-0536-05


title: laird-00098: TCGA-06-0209-01A-01D-0242-05


title: laird-00224: TCGA-13-1484-01A-01D-0475-05


title: laird-00224: TCGA-24-1425-01A-02D-0501-05


title: laird-00098: TCGA-12-0653-01B-01D-0337-05


title: laird-00224: TCGA-24-2033-01A-01D-0667-05


title: laird-00098: TCGA-02-0289-01A-01D-0287-05


title: laird-00224: TCGA-25-1627-01A-01D-0536-05


title: laird-00098: TCGA-08-0348-01A-01D-0297-05


title: laird-00098: TCGA-02-0107-01A-01D-0199-05


title: laird-00224: TCGA-13-1483-01A-01D-0475-05


title: laird-00224: TCGA-30-1867-01A-01D-0652-05

value: GX


title: laird-00098: TCGA-02-0089-01A-01D-0199-05


title: laird-00098: TCGA-02-0016-01A-01D-0297-05


title: laird-00224: TCGA-24-1844-01A-01D-0581-05


title: laird-00098: TCGA-06-0394-01A-01D-0287-05


title: laird-00098: TCGA-06-0171-01A-02D-0242-05


title: laird-00224: TCGA-61-1998-01A-01D-0667-05


title: laird-00224: TCGA-13-0720-01A-01D-0359-05


title: laird-00098: TCGA-06-0185-01A-01D-0242-05


title: laird-00224: TCGA-23-2084-01A-02D-0667-05

value: IV


title: laird-00098: TCGA-12-0692-01A-01D-0337-05


title: laird-00224: TCGA-13-1817-02A-01D-0807-05

value: FEMALE


title: laird-00098: TCGA-06-0119-01A-08D-0218-05


title: laird-00098: TCGA-02-0332-01A-01D-0279-05


title: laird-00098: TCGA-02-0115-01A-01D-0199-05


title: laird-00098: TCGA-08-0512-01A-01D-0287-05

value: FRONTAL LOBE


title: laird-00224: TCGA-13-1817-01A-01D-0807-05

value: IIIC


title: laird-00098: TCGA-02-0085-01A-01D-0199-05


title: laird-00224: TCGA-25-1635-01A-01D-0536-05


title: laird-00224: TCGA-25-1628-01A-01D-0536-05


title: laird-00098: TCGA-02-0074-01A-01D-0199-05

value: PARIETAL LOBE


title: laird-00098: TCGA-06-0240-01A-03D-0242-05

value: GLIOBLASTOMA MULTIFORME


title: laird-00224: TCGA-29-1776-01A-01D-0581-05


title: laird-00224: TCGA-25-1319-01A-01D-0460-05


title: laird-00098: TCGA-12-0618-01A-01D-0314-05


title: laird-00098: TCGA-06-0177-01A-01D-0279-05


title: laird-00098: TCGA-06-0413-01A-01D-0287-05


title: laird-00224: TCGA-24-1427-01A-01D-0475-05


title: laird-00224: TCGA-29-2428-01A-01D-0708-05


title: laird-00098: TCGA-02-0113-01A-01D-0199-05


title: laird-00224: TCGA-13-0792-01A-01D-0359-05


title: laird-00224: TCGA-10-0926-01A-01D-0402-05


title: laird-00224: TCGA-13-1499-01A-01D-0475-05


title: laird-00098: TCGA-08-0509-01A-01D-0287-05


title: laird-00224: TCGA-13-0764-01A-03D-0359-05


title: laird-00224: TCGA-61-1913-01A-01D-0581-05

value: IIIB


title: laird-00098: TCGA-06-0152-01A-02D-0314-05

value: Brain

value: OVERLAPPING LESION OF BRAIN


title: laird-00098: TCGA-06-0221-01A-01D-0242-05

value: MALIGNANT


title: laird-00098: TCGA-06-0414-01A-01D-0287-05


title: laird-00224: TCGA-59-2348-01A-01D-0708-05

value: NOT SPECIFIED


title: laird-00098: TCGA-06-0189-01A-01D-0242-05


title: laird-00098: TCGA-12-0780-01A-01D-0337-05


title: laird-00224: TCGA-24-0968-01A-01D-0432-05


title: laird-00224: TCGA-09-0365-01A-02D-0359-05


title: laird-00098: TCGA-08-0356-01A-01D-0297-05


title: laird-00224: TCGA-24-1470-01A-01D-0501-05


title: laird-00098: TCGA-08-0380-01A-01D-0297-05


title: laird-00224: TCGA-24-1105-01A-01D-0432-05


title: laird-00098: TCGA-12-0615-01A-01D-0314-05


title: laird-00224: TCGA-24-1434-01A-01D-0475-05


title: laird-00224: TCGA-24-1419-01A-01D-0475-05


title: laird-00224: TCGA-13-1501-01A-01D-0475-05


title: laird-00098: TCGA-02-0038-01A-01D-0186-05


title: laird-00224: TCGA-04-1654-01A-02D-0652-05


title: laird-00098: TCGA-06-0238-01A-02D-0314-05


title: laird-00098: TCGA-02-0028-01A-01D-0186-05


title: laird-00224: TCGA-13-0724-01A-01D-0359-05


title: laird-00224: TCGA-61-2088-01A-01D-0667-05


title: laird-00224: TCGA-61-2003-01A-01D-0667-05


title: laird-00098: TCGA-02-0001-01C-01D-0186-05

value: BRAIN, NOS


title: laird-00224: TCGA-29-2427-01A-01D-0708-05


title: laird-00098: TCGA-02-0043-01A-01D-0186-05


title: laird-00098: TCGA-08-0347-01A-01D-0297-05

value: TEMPORAL LOBE


title: laird-00224: TCGA-24-1413-01A-01D-0460-05

value: Serous Cystadenocarcinoma


title: laird-00098: TCGA-06-0159-01A-01D-0242-05


title: laird-00098: TCGA-06-0192-01B-01D-0337-05


title: laird-00098: TCGA-02-0338-01A-01D-0287-05


title: laird-00224: TCGA-13-0905-01B-01D-0460-05

value: Ovary


title: laird-00098: TCGA-02-0330-01A-01D-0287-05


title: laird-00098: TCGA-02-0047-01A-01D-0186-05


title: laird-00224: TCGA-61-2111-01A-01D-0667-05


title: laird-00098: TCGA-08-0529-01A-02D-0287-05


title: laird-00224: TCGA-04-1371-01A-01D-0460-05


title: laird-00098: TCGA-02-0430-01A-01D-0287-05


title: laird-00224: TCGA-24-2289-01A-01D-0708-05


title: laird-00224: TCGA-61-2110-01A-01D-0667-05


title: laird-00098: TCGA-02-0317-01A-01D-0287-05


title: laird-00224: TCGA-36-1578-01A-01D-0536-05


title: laird-00098: TCGA-02-0451-01A-01D-0287-05


title: laird-00098: TCGA-06-0184-01A-01D-0242-05


title: laird-00224: TCGA-24-2019-01A-02D-0667-05


title: laird-00098: TCGA-06-0127-01A-01D-0315-05


title: laird-00098: TCGA-02-0069-01A-01D-0199-05


title: laird-00224: TCGA-23-1118-01A-01D-0432-05


title: laird-00224: TCGA-24-1567-01A-01D-0536-05


title: laird-00224: TCGA-13-0795-01A-01D-0359-05


title: laird-00224: TCGA-30-1714-01A-02D-0563-05


title: laird-00098: TCGA-02-0260-01A-03D-0287-05


title: laird-00224: TCGA-23-1032-01A-02D-0432-05


title: laird-00098: TCGA-02-0023-01B-01D-0297-05


title: laird-00098: TCGA-08-0357-01A-01D-0297-05


title: laird-00224: TCGA-24-0982-01A-01D-0432-05


title: laird-00098: TCGA-02-0068-01A-01D-0297-05


title: laird-00098: TCGA-08-0246-01A-01D-0297-05


title: laird-00224: TCGA-24-1563-01A-01D-0501-05


title: laird-00224: TCGA-04-1348-01A-01D-0460-05


title: laird-00224: TCGA-29-1692-01B-01D-0807-05


title: laird-00098: TCGA-08-0531-01A-01D-0287-05


title: laird-00224: TCGA-23-1031-01A-01D-0432-05


title: laird-00224: TCGA-29-1692-02A-01D-0807-05


title: laird-00098: TCGA-02-0058-01A-01D-0186-05


title: laird-00098: TCGA-06-0749-01A-01D-0337-05


title: laird-00224: TCGA-30-1859-01A-01D-0652-05


title: laird-00098: TCGA-02-0064-01A-01D-0199-05


title: laird-00224: TCGA-61-2016-01A-01D-0667-05


title: laird-00098: TCGA-12-0662-01A-01D-0337-05


title: laird-00098: TCGA-06-0175-01A-01D-0287-05


title: laird-00098: TCGA-02-0009-01A-01D-0186-05


title: laird-00098: TCGA-02-0456-01A-01D-0287-05


title: laird-00224: TCGA-25-1320-01A-01D-0460-05


title: laird-00098: TCGA-02-0010-01A-01D-0186-05


title: laird-00224: TCGA-04-1646-01A-01D-0581-05


title: laird-00224: TCGA-30-1860-01A-01D-0652-05


title: laird-00224: TCGA-23-1119-01A-02D-0432-05


title: laird-00224: TCGA-25-1324-01A-01D-0460-05


title: laird-00098: TCGA-08-0522-01A-01D-0287-05


title: laird-00098: TCGA-02-0004-01A-01D-0297-05


title: laird-00224: TCGA-25-1317-01A-01D-0460-05


title: laird-00098: TCGA-06-0745-01A-01D-0337-05


title: laird-00098: TCGA-08-0358-01A-01D-0314-05


title: laird-00224: TCGA-24-1920-01A-01D-0652-05


title: laird-00224: TCGA-57-1994-01A-01D-0652-05


title: laird-00098: TCGA-02-0440-01A-01D-0287-05


title: laird-00098: TCGA-06-0241-01A-02D-0242-05


title: laird-00224: TCGA-36-1574-01A-01D-0536-05


title: laird-00224: TCGA-31-1956-01A-01D-0652-05


title: laird-00224: TCGA-09-2051-01A-01D-0708-05


title: laird-00224: TCGA-29-1707-01A-01D-0563-05

value: IIC


title: laird-00098: TCGA-02-0002-01A-01D-0186-05


title: laird-00224: TCGA-13-1479-01A-01D-0475-05


title: laird-00098: TCGA-12-0772-01A-01D-0337-05


title: laird-00098: TCGA-06-0128-01A-01D-0218-05

value: OCCIPITAL LOBE


title: laird-00224: TCGA-29-1707-02A-01D-0807-05


title: laird-00224: TCGA-24-1927-01A-01D-0652-05


title: laird-00098: TCGA-06-0206-01A-01D-0242-05


title: laird-00224: TCGA-29-1688-01A-01D-0563-05


title: laird-00098: TCGA-12-0619-01A-01D-0314-05


title: laird-00224: TCGA-29-1698-01A-01D-0563-05


title: laird-00098: TCGA-06-0197-01A-02D-0242-05


title: laird-00098: TCGA-06-0146-01A-01D-0287-05


title: laird-00224: TCGA-61-1734-01B-01D-0667-05

value: IC


title: laird-00224: TCGA-13-1511-01A-01D-0475-05

value: IV

value: FEMALE


title: laird-00098: TCGA-08-0244-01A-01D-0297-05


title: laird-00224: TCGA-10-0928-01A-02D-0402-05

value: IIIC


title: laird-00098: TCGA-06-0410-01A-01D-0287-05

value: FRONTAL LOBE


title: laird-00224: TCGA-29-1702-01A-01D-0563-05


title: laird-00224: TCGA-61-1743-01A-01D-0652-05


title: laird-00098: TCGA-06-0124-01A-01D-0218-05

value: GLIOBLASTOMA MULTIFORME


title: laird-00098: TCGA-06-0162-01A-01D-0287-05


title: laird-00098: TCGA-12-0688-01A-02D-0337-05


title: laird-00224: TCGA-29-1711-01A-01D-0563-05


title: laird-00224: TCGA-09-2055-01B-01D-0708-05


title: laird-00098: TCGA-08-0345-01A-01D-0314-05

value: PARIETAL LOBE


title: laird-00098: TCGA-12-0778-01A-01D-0337-05

value: Brain


title: laird-00224: TCGA-09-1664-01A-01D-0581-05


title: laird-00098: TCGA-08-0520-01A-01D-0287-05


title: laird-00224: TCGA-59-2350-01A-01D-0708-05


title: laird-00224: TCGA-04-1342-01A-01D-0432-05


title: laird-00098: TCGA-08-0517-01A-01D-0287-05


title: laird-00098: TCGA-06-0211-01B-01D-0242-05

value: OVERLAPPING LESION OF BRAIN


title: laird-00098: TCGA-06-0211-01A-01D-0242-05

value: MALIGNANT


title: laird-00224: TCGA-13-0920-01A-01D-0402-05

value: NOT SPECIFIED


title: laird-00098: TCGA-02-0052-01A-01D-0186-05


title: laird-00098: TCGA-06-0646-01A-01D-0314-05


title: laird-00224: TCGA-61-2095-01A-01D-0667-05


title: laird-00224: TCGA-61-2095-02A-01D-0807-05


title: laird-00224: TCGA-04-1341-01A-01D-0432-05


title: laird-00224: TCGA-29-2414-01A-02D-0708-05


title: laird-00098: TCGA-02-0007-01A-01D-0186-05


title: laird-00224: TCGA-29-2414-02A-01D-0807-05


title: laird-00224: TCGA-23-1030-01A-02D-0432-05


title: laird-00098: TCGA-02-0021-01A-01D-0186-05


title: laird-00098: TCGA-02-0439-01A-01D-0287-05


title: laird-00224: TCGA-29-1785-01A-01D-0563-05


title: laird-00224: TCGA-23-1116-01A-01D-0432-05


title: laird-00098: TCGA-06-0179-01A-02D-0287-05


title: laird-00098: TCGA-06-0645-01A-01D-0314-05


title: laird-00098: TCGA-06-0137-01A-02D-0218-05


title: laird-00098: TCGA-06-0237-01A-02D-0242-05


title: laird-00224: TCGA-13-1819-02A-01D-0807-05


title: laird-00224: TCGA-13-1819-01A-01D-0807-05


title: laird-00098: TCGA-06-0130-01A-01D-0218-05


title: laird-00098: TCGA-06-0137-01A-03D-0218-05


title: laird-00224: TCGA-29-1693-01A-01D-0563-05


title: laird-00098: TCGA-06-0137-01B-02D-0218-05


title: laird-00098: TCGA-08-0524-01A-01D-0287-05


title: laird-00224: TCGA-24-1845-01A-01D-0581-05


title: laird-00098: TCGA-02-0114-01A-01D-0199-05


title: laird-00224: TCGA-61-2087-01A-01D-0667-05


title: laird-00224: TCGA-24-2029-01A-01D-0652-05


title: laird-00224: TCGA-13-1408-01A-01D-0460-05


title: laird-00098: TCGA-06-0132-01A-02D-0242-05


title: laird-00098: TCGA-06-0409-01A-02D-0287-05


title: laird-00098: TCGA-02-0083-01A-01D-0199-05


title: laird-00224: TCGA-61-2113-01A-01D-0667-05


title: laird-00224: TCGA-24-1924-01A-01D-0652-05


title: laird-00224: TCGA-31-1946-01A-01D-0652-05


title: laird-00098: TCGA-06-0195-01B-01D-0242-05


title: laird-00224: TCGA-13-1505-01A-01D-0475-05


title: laird-00098: TCGA-06-0216-01A-01D-0242-05


title: laird-00224: TCGA-61-1911-01A-01D-0581-05

value: IIA


title: laird-00224: TCGA-24-0979-01A-01D-0432-05


title: laird-00098: TCGA-06-0137-01A-01D-0218-05


title: laird-00098: TCGA-06-0216-01B-01D-0337-05


title: laird-00098: TCGA-02-0087-01A-01D-0287-05


title: laird-00098: TCGA-06-0150-01A-01D-0242-05


title: laird-00224: TCGA-23-1023-01A-03D-0432-05


title: laird-00098: TCGA-12-0776-01A-01D-0337-05


title: laird-00224: TCGA-61-1904-01A-01D-0581-05


title: laird-00224: TCGA-24-1552-01A-01D-0501-05


title: laird-00051: Brain_TCGA-06-0412

value: TEMPORAL LOBE


title: laird-00051: Brain_TCGA-08-0359


title: laird-00051: Brain_TCGA-06-0128


title: laird-00224: TCGA-04-1367-01A-01D-0460-05

value: Serous Cystadenocarcinoma


title: laird-00224: TCGA-20-0996-01A-03D-0432-05

value: Ovary


title: laird-00051: Brain_TCGA-06-0138


title: laird-00224: TCGA-10-0936-01A-01D-0402-05


title: laird-00098: TCGA-02-0290-01A-01D-0287-05


title: laird-00224: TCGA-25-1877-01A-01D-0652-05


title: laird-00051: Brain_TCGA-08-0246


title: laird-00051: Brain_TCGA-06-0209


title: laird-00224: TCGA-13-1410-01A-01D-0460-05

value: GX


title: laird-00051: Brain_TCGA-02-0034


title: laird-00224: TCGA-24-2023-01A-01D-0652-05

value: IIIA


title: laird-00051: Brain_TCGA-06-0139


title: laird-00224: TCGA-24-1471-01A-01D-0501-05


title: laird-00224: TCGA-13-0884-01B-01D-0460-05


title: laird-00224: TCGA-23-1023-01R-01D-0807-05


title: laird-00051: Brain_TCGA-02-0058


title: laird-00224: TCGA-23-1024-01A-02D-0432-05


title: laird-00051: Brain_TCGA-08-0354


title: laird-00051: Brain_TCGA-06-0173


title: laird-00224: TCGA-25-1322-01A-01D-0460-05


title: laird-00224: TCGA-25-1631-01A-01D-0536-05


title: laird-00224: TCGA-13-0714-01A-01D-0359-05


title: laird-00051: Brain_TCGA-02-0107


title: laird-00051: Brain_TCGA-06-0213


title: laird-00224: TCGA-13-1498-01A-01D-0475-05


title: laird-00224: TCGA-24-1565-01A-01D-0501-05


title: laird-00224: TCGA-04-1536-01A-01D-0536-05


title: laird-00051: Brain_TCGA-08-0514


title: laird-00051: Brain_TCGA-06-0187


title: laird-00224: TCGA-24-1545-01A-01D-0536-05


title: laird-00224: TCGA-13-1411-01A-01D-0460-05


title: laird-00051: Brain_TCGA-06-0190


title: laird-00224: TCGA-59-2349-01A-01D-0708-05

value: IA


title: laird-00051: Brain_TCGA-06-0154


title: laird-00051: Brain_TCGA-06-0157

value: CEREBRUM


title: laird-00224: TCGA-23-1027-01A-02D-0432-05

value: FEMALE


title: laird-00224: TCGA-61-1733-01A-01D-0581-05

value: IIIC


title: laird-00051: Brain_TCGA-08-0358


title: laird-00224: TCGA-59-2363-01A-01D-0708-05


title: laird-00051: Brain_TCGA-02-0021


title: laird-00051: Brain_TCGA-02-0338


title: laird-00224: TCGA-04-1638-01A-01D-0581-05

value: IV


title: laird-00224: TCGA-30-1892-01A-01D-0652-05


title: laird-00051: Brain_TCGA-12-0619

value: GLIOBLASTOMA MULTIFORME


title: laird-00051: Brain_TCGA-02-0281


title: laird-00224: TCGA-61-1740-01A-01D-0581-05


title: laird-00051: Brain_TCGA-08-0512

value: FRONTAL LOBE


title: laird-00051: Brain_TCGA-06-0174

value: Brain


title: laird-00224: TCGA-61-2096-01A-01D-0667-05

value: IC


title: laird-00224: TCGA-29-1775-01A-01D-0581-05


title: laird-00051: Brain_TCGA-06-0149

value: MALIGNANT


title: laird-00224: TCGA-25-1623-01A-01D-0536-05

value: NOT SPECIFIED


title: laird-00051: Brain_TCGA-02-0289


title: laird-00051: Brain_TCGA-02-0326


title: laird-00051: Brain_TCGA-06-0140


title: laird-00224: TCGA-61-2092-01A-01D-0667-05


title: laird-00051: Brain_TCGA-06-0216


title: laird-00224: TCGA-13-0885-01A-02D-0402-05


title: laird-00224: TCGA-61-1914-01A-01D-0581-05


title: laird-00051: Brain_TCGA-06-0648


title: laird-00224: TCGA-25-2404-01A-01D-0708-05


title: laird-00051: Brain_TCGA-02-0102


title: laird-00051: Brain_TCGA-08-0524

value: OVERLAPPING LESION OF BRAIN


title: laird-00224: TCGA-04-1361-01A-01D-0460-05

value: IIIB


title: laird-00224: TCGA-29-1766-01A-01D-0563-05

value: Serous Cystadenocarcinoma

value: PERITONEUM (OVARY)


title: laird-00224: TCGA-29-1777-01A-01D-0581-05

value: Ovary


title: laird-00051: Brain_TCGA-02-0038


title: laird-00051: Brain_TCGA-06-0219


title: laird-00051: Brain_TCGA-08-0531

value: PARIETAL LOBE


title: laird-00224: TCGA-61-2109-01A-01D-0667-05


title: laird-00051: Brain_TCGA-06-0240


title: laird-00224: TCGA-29-1774-01A-01D-0581-05


title: laird-00224: TCGA-10-0938-01A-02D-0402-05


title: laird-00224: TCGA-61-1721-01A-01D-0652-05


title: laird-00051: Brain_TCGA-08-0389

value: TEMPORAL LOBE


title: laird-00051: Brain_TCGA-08-0347


title: laird-00224: TCGA-10-0930-01A-02D-0402-05


title: laird-00051: Brain_TCGA-06-0644


title: laird-00224: TCGA-29-1770-01A-01D-0563-05


title: laird-00224: TCGA-29-1770-02A-01D-0807-05


title: laird-00224: TCGA-24-2293-01A-01D-0708-05

value: OMENTUM


title: laird-00051: Brain_TCGA-02-0324


title: laird-00224: TCGA-31-1953-01A-01D-0652-05

value: FEMALE


title: laird-00224: TCGA-04-1530-01A-02D-0501-05

value: IIIC


title: laird-00051: Brain_TCGA-06-0397


title: laird-00051: Brain_TCGA-06-0146


title: laird-00224: TCGA-09-2056-01B-01D-0667-05


title: laird-00224: TCGA-09-0369-01A-01D-0359-05


title: laird-00051: Brain_TCGA-02-0271


title: laird-00051: Brain_TCGA-02-0332


title: laird-00051: Brain_TCGA-02-0266


title: laird-00224: TCGA-13-0887-01A-01D-0402-05


title: laird-00051: Brain_TCGA-02-0432


title: laird-00051: Brain_TCGA-02-0079


title: laird-00051: Brain_TCGA-02-0064


title: laird-00224: TCGA-57-1992-01A-01D-0652-05


title: laird-00224: TCGA-29-1691-01A-01D-0563-05


title: laird-00224: TCGA-13-0891-01A-01D-0402-05

value: IV


title: laird-00224: TCGA-13-1509-01A-01D-0475-05


title: laird-00051: Brain_TCGA-06-0179

value: GLIOBLASTOMA MULTIFORME


title: laird-00051: Brain_TCGA-08-0522


title: laird-00051: Brain_TCGA-08-0511


title: laird-00051: Brain_TCGA-08-0516


title: laird-00224: TCGA-30-1861-01A-01D-0652-05


title: laird-00051: Brain_TCGA-06-0162


title: laird-00051: Brain_TCGA-02-0054


title: laird-00051: Brain_TCGA-02-0074


title: laird-00224: TCGA-09-2044-01B-01D-0708-05

value: IIB


title: laird-00051: Brain_TCGA-06-0165

value: Brain