title: LNCaP-JMJD5, plus DHT

description:
Affymetrix microarray gene expression profiling data
LNCaP_JMJD5_DHT

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Affymetrix Genechip Human Genome U133 Plus 2 aarays using Affymetrix hybridization kit materials. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using protocol  FS450_0001

data_processing: Data were processed using GeneSpring GX 12.0 software (Agilent Technologies).  Probe intensity values (CEL files) were background-corrected, summarized, and normalized using the Robust Multi-array Average (RMA) algorithm ((Irizarry et al., 2003).

source_name: LNCaP-JMJD5 cells cultured in DHT-supplemented medium

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, Rev3, Affymetrix).

growth_protocol: LNCaP-vector and LNCaP-JMJD5 cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (Omega Scientific, Tarzana, CA), 2 mM L-glutamine, and 100 U/ml penicillin-100 μg/ml streptomycin at 37°C in a humidified environment of 5% CO2 in air

extract_protocol: RNA was isolated by lysis of the treated cell cultures (i.e., in 10-cm dishes) in 5 ml TRIzol Reagent (Life Technologies) and processing according to the manufacturer's standard protocol.

treatment_protocol: LNCaP-vector and LNCaP-JMJD5 cells were seeded into 10-cm tissue culture dishes and cultured in complete medium (RPMI 1640, 10% FBS, L-Glutamine, Pen-Strep) until cultures were 70% confluent.  At this point, the medium was removed and the cultures were washed twice with 1X phosphate-buffered saline.  Treatments were initied by adding fresh androgen deprivation (AD medium) or testosterone-supplemented medium (T medium).  AD medium was RPMI 1640 medium (without phenol red) supplemented with 10% charcoal/dextran-treated fetal bovine serum (CDT-FBS; Omega Scientific), L-Glu, and P-S.  T medium was AD medium supplemented with 1nm 5a-DHT.  Cells were treated under each condition for 3 days.

value: LNCaP human prostate carcinoma

tag: genotype/variation

value: stable expression of wild-type JMJD5

tag: growth protocol

value: +DHT (androgen supplementation)


title: T-ALL_1508

status: Public on Apr 30 2015

type: RNA

city: Paris

first: Andre

last: Bortolini Silveira

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description: Diagnostic T-ALL sample

hyb_protocol: Samples were hybridized on the GeneChip Human Gene 1.0 ST Arrays (Affymetrix, Inc.), according to the manufacturer's instructions. Arrays were washed and stained with the GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned with the GeneChip Scanner 3000, according to the manufacturer's instructions.

data_processing: Arrays were normalized and expression values were obtained with the default transcript level iterPLIER algorithm of the Affymetrix Expression Console software.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Bone marrow mononuclear cells obtained from patient with newly diagnosed T-ALL

label_protocol: Samples were processed with the WT Expression Kit (Ambion, Inc., Austin, TX, USA) and GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Inc., Santa Clara, CA, USA), according to the manufacturer's instructions.

growth_protocol: Mononuclear cells were ficoll-isolated from diagnostic bone marrow samples of T-ALL patients.

extract_protocol: RNA was extracted with the Illustra RNAspin Mini RNA Isolation Kit (GE Healthcare, Little Chalfont, UK), according to the manufacturer's instructions.

treatment_protocol: Five million primary T-ALL cells were preserved in 150 µL of thiocyanate solution at -70ºC until use.

tag: cell type

value: Bone marrow mononuclear cells

tag: il7r mutational status

value: Wild type

tag: age (years)

tag: gender

value: Male

tag: wbc at diagnosis (cells/mm3)

tag: induction failure

value: Remission

tag: relapse

value: Relapse


title: T-ALL_1169

description: Diagnostic T-ALL sample

value: Female


title: T-ALL_1693

description: Diagnostic T-ALL sample

value: No Relapse


title: T-ALL_1647

description: Diagnostic T-ALL sample


title: T-ALL_0826

description: Diagnostic T-ALL sample


title: T-ALL_0958

description: Diagnostic T-ALL sample

value: Induction failure


title: T-ALL_1235

description: Diagnostic T-ALL sample


title: T-ALL_1004

description: Diagnostic T-ALL sample


title: LNCaP-JMJD5, minus DHT

status: Public on May 01 2015

city: Sacramento

first: Clifford

middle: G.

last: Tepper

state: CA

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

country: USA

institute: UC Davis School of Medicine

description:
Affymetrix microarray gene expression profiling data
LNCaP_JMJD5

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

source_name: LNCaP-JMJD5 cells cultured in androgen-deprivation medium

tag: cell line

value: -DHT (androgen deprivation)


title: Diabetic Foot Skin 01 gene expression profile

city: Miami

first: Horacio

middle: Adrian

last: Ramirez

state: Florida

address: 1600 NW10th Avenue RMSB room 2029A

department: Dermatology

institute: University of Miami

description: DFS 01

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing:
The data were analyzed with Affymetrix transcriptome analysis software using Affymetrix default analysis settings and global scaling as normalization method.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.3.1.187

source_name: Diabetic Foot skin

label_protocol: standard Affymetrix protocol

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

tag: tissue

value: non-ulcerated non-neuropathic diabetic foot skin (DFS)


title: scrambled shRNA_1

city: Vienna

first: Robin

last: Ristl

address: Spitalgasse 23

country: Austria

institute: Medical University Vienna

hyb_protocol: Affymetrix, according to manufacturers protocols (Affymetrix, Santa Clara, CA, USA, https://www.affymetrix.com)

scan_protocol: Affymetrix 3000, Software Command Console

data_processing: Statistical analyses were performed with R-Bioconductor. Data was normalized using R-Bioconductor function RMA.

source_name: MEC-1 cell line

label_protocol: Affymetrix WT labeling kit (Biotin)

growth_protocol: RPMI 10%FCS, no phenol red, no antibiotics

extract_protocol: Trizol (Invitrogen) and subsequent RNeasy mini kit (Qiagen)

treatment_protocol: lentiviral shRNA transfection

value: scrambled shRNA


title: Diabetic Foot Skin 02 gene expression profile

description: DFS 02


title: T-ALL_1231

description: Diagnostic T-ALL sample


title: T-ALL_1727

description: Diagnostic T-ALL sample


title: T-ALL_1006

description: Diagnostic T-ALL sample


title: LNCaP-vector, minus DHT

description:
Affymetrix microarray gene expression profiling data
LNCaP_Control

source_name: LNCaP-vector cells cultured in androgen-deprivation medium

value: control


title: LNCaP-vector, plus DHT

description:
Affymetrix microarray gene expression profiling data
LNCaP_Control_DHT

source_name: LNCaP-vector cells cultured in DHT-supplemented medium


title: UGT2B17 knock down shRNA _2

value: UGT2B17 knock down


title: UGT2B17 knock down shRNA _3


title: UGT2B17 knock down shRNA _1


title: PrimaryTALL_15_AS605240

description: Primary T-ALL cells treated with AS605240 for 6h

data_processing: Arrays were normalized and expression values were obtained with the default transcript level iterPLIER algorithm of the Affymetrix Expression Console software (1.3.1.187).

source_name: BMMN cells from patient with newly diagnosed T-ALL_AS605240

label_protocol: Samples were processed with the GeneChip WT cDNA Synthesis and Amplification Kit (Affymetrix, Inc., Santa Clara, CA, USA), according to the manufacturer's instructions.

growth_protocol: Primary cells were washed in RPMI-1640 medium twice and viable cells were isolated with the Dead Cell Removal Kit (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany).

treatment_protocol: Viable cells were cultured with 20 µM of AS605240 or vehicle for 6h in AIM-V medium supplemented with glutamine 2 mM, FBS 10%, penicillin 20 U.I./mL and streptomycin 20 µg/mL at 37°C and 5% CO2, and washed once with ice cold PBS by centrifugation.

value: female

value: Primary T-ALL cells

tag: treated with


title: PrimaryTALL_15_Control

description: Primary T-ALL cells treated with vehicle for 6h

source_name: BMMN cells from patient with newly diagnosed T-ALL_control

value: vehicle for 6h


title: PrimaryTALL_14_AS605240

value: male


title: PrimaryTALL_13_AS605240


title: T-ALL_0591

description: Diagnostic T-ALL sample

value: Bone marrow mononuclear cells


title: PrimaryTALL_11_AS605240


title: T-ALL_0433

description: Diagnostic T-ALL sample

value: Wild type


title: PrimaryTALL_11_Control


title: T-ALL_0388

description: Diagnostic T-ALL sample

value: Male


title: T-ALL_0364

description: Diagnostic T-ALL sample

value: Remission


title: PrimaryTALL_13_Control


title: PrimaryTALL_12_AS605240


title: PrimaryTALL_08_Control


title: PrimaryTALL_14_Control


title: PrimaryTALL_10_Control


title: T-ALL_0444

description: Diagnostic T-ALL sample

value: Relapse


title: PrimaryTALL_10_AS605240


title: PrimaryTALL_06_AS605240


title: PrimaryTALL_09_Control


title: PrimaryTALL_06_Control


title: PrimaryTALL_09_AS605240


title: PrimaryTALL_07_Control


title: PrimaryTALL_04_AS605240


title: PrimaryTALL_08_AS605240


title: PrimaryTALL_12_Control


title: PrimaryTALL_05_AS605240


title: PrimaryTALL_05_Control


title: PrimaryTALL_03_Control


title: PrimaryTALL_07_AS605240


title: PrimaryTALL_03_AS605240


title: PrimaryTALL_01_AS605240


title: PrimaryTALL_04_Control


title: PrimaryTALL_02_AS605240


title: T-ALL_0906

description: Diagnostic T-ALL sample

tag: notch1 mutational status

tag: pten mutational status


title: T-ALL_0887

description: Diagnostic T-ALL sample

value: Mutant


title: T-ALL_0874

description: Diagnostic T-ALL sample

value: No Relapse


title: PrimaryTALL_01_Control


title: T-ALL_0704

description: Diagnostic T-ALL sample


title: T-ALL_0768

description: Diagnostic T-ALL sample


title: T-ALL_0932

description: Diagnostic T-ALL sample

value: Induction failure


title: T-ALL_0660

description: Diagnostic T-ALL sample


title: T-ALL_0974

description: Diagnostic T-ALL sample


title: T-ALL_0860

description: Diagnostic T-ALL sample


title: T-ALL_0808

description: Diagnostic T-ALL sample

value: Female


title: T-ALL_0436

description: Diagnostic T-ALL sample


title: T-ALL_0595

description: Diagnostic T-ALL sample


title: T-ALL_0657

description: Diagnostic T-ALL sample


title: T-ALL_0341

description: Diagnostic T-ALL sample


title: T-ALL_0306

description: Diagnostic T-ALL sample


title: T-ALL_0228

description: Diagnostic T-ALL sample


title: T-ALL_0370

description: Diagnostic T-ALL sample


title: CG13624_KO_male_4d_rep1

city: Heidelberg

first: Aurelio

middle: A

last: Teleman

address: Im Neuenheimer Feld 580

country: Germany

institute: German Cancer Research Center (DKFZ)

description: REPTOR = CG13624

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Drosophila (V2) Gene Expression Microarrays for 17 hours at 65ºC 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 (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1-v1_91 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.

organism: Drosophila melanogaster

source_name: REPTOR_KO adults, 4d old, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling kit (Agilent, version 6.6) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA, p/n 74104).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 UV-VIS Spectrophotometer.

growth_protocol: 4d old male adults, growth controlled, synchronized Drosophila melanogaster flies

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

treatment_protocol: All flies were grown on standard laboratory food at 25 degrees in a humidified room

tag: Sex

tag: developmental stage

value: 4d old adults

tag: genotype


title: CG13624_KO_male_4d_rep2

description: REPTOR = CG13624

source_name: REPTOR_KO adults, 4d old, replicate 2


title: T-ALL_1009

description: Diagnostic T-ALL sample


title: T-ALL_0295

description: Diagnostic T-ALL sample


title: T-ALL_0529

description: Diagnostic T-ALL sample


title: wild_type_male_4d_rep1

source_name: w1118 adults, 4d old, replicate 1


title: wild_type_male_4d_rep2

source_name: w1118 adults, 4d old, replicate 2


title: T-ALL_0572

description: Diagnostic T-ALL sample


title: CtrlLarvae_rapa_6h_rep2

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 021791_D_F_20131128) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.  The data were normalized using quantile normalization in R.

source_name: w1118 larvae, 6h rapamycin 200µM, replicate 2

growth_protocol: 48h prewandering, growth controlled, synchronized Drosophila melanogaster Larvae

treatment_protocol: Larvae were fed food containing 200µM rapamycin for 6h or food with EtOH at the same concentration as the rapamycin larave for 6h

value: larva

tag: age

value: 48h prewandering

tag: genotype/variation

tag: agent

value: rapamycin


title: REPTOR_KOLarvae_rapa_6h_rep3

source_name: REPTOR_KO larvae, 6h rapamycin 200µM, replicate 3

value: female

value: REPTOR knockout


title: REPTOR_KOLarvae_rapa_6h_rep2

source_name: REPTOR_KO larvae, 6h rapamycin 200µM, replicate 2


title: T-ALL_0213

description: Diagnostic T-ALL sample

tag: cell type

tag: il7r mutational status


title: PrimaryTALL_02_Control

tag: gender

value: Primary T-ALL cells

value: vehicle for 6h


title: CtrlLarvae_rapa_6h_rep3

source_name: w1118 larvae, 6h rapamycin 200µM, replicate 3

value: control


title: REPTOR_KOLarvae_EtOH_rep1

source_name: REPTOR_KO larvae, 6h EtOH, replicate 1

value: EtOH


title: CtrlLarvae_EtOH_rep3

source_name: w1118 larvae, 6h EtOH, replicate 3


title: REPTOR_KOLarvae_EtOH_rep3

source_name: REPTOR_KO larvae, 6h EtOH, replicate 3


title: CtrlLarvae_rapa_6h_rep1

source_name: w1118 larvae, 6h rapamycin 200µM, replicate 1


title: REPTOR_KOLarvae_EtOH_rep2

source_name: REPTOR_KO larvae, 6h EtOH, replicate 2


title: REPTOR_KOLarvae_rapa_6h_rep1

source_name: REPTOR_KO larvae, 6h rapamycin 200µM, replicate 1


title: S2cells_CG18dsRNA_EtOH_rep2

source_name: S2 cells, CG18619 knockdown, 2h EtOH 1:1000, replicate2

growth_protocol: S2 cells were grown in Schneider's Drosophila medium at 25ºC

treatment_protocol: S2 cells treated for 5d with dsRNA, reseeded at 1/3 density in fresh medium, grown overnight and treated with 20nM rapamycin or EtOH (1:1000) for 2 hours

value: S2 cells

value: REPTOR-BP knockdown


title: S2cells_CG18dsRNA_rapamycin_rep2

source_name: S2 cells, CG18619 knockdown, 2h 20nM rapamycin, replicate2


title: S2cells_CG13dsRNA_rapamycin_rep3

source_name: S2 cells, CG13624 knockdown, 2h 20nM rapamycin, replicate3

value: REPTOR knockdown


title: S2cells_CG18dsRNA_rapamycin_rep1

source_name: S2 cells, CG18619 knockdown, 2h 20nM rapamycin, replicate1


title: S2cells_CG13dsRNA_rapamycin_rep1

source_name: S2 cells, CG13624 knockdown, 2h 20nM rapamycin, replicate1


title: S2cells_CG13dsRNA_EtOH_rep2

source_name: S2 cells, CG13624 knockdown, 2h EtOH 1:1000, replicate2


title: S2cells_CG13dsRNA_rapamycin_rep2

source_name: S2 cells, CG13624 knockdown, 2h 20nM rapamycin, replicate2


title: S2cells_GFPdsRNA_rapamycin_rep1

source_name: S2 cells, GFP knockdown, 2h 20nM rapamycin, replicate1


title: S2cells_CG13dsRNA_EtOH_rep3

source_name: S2 cells, CG13624 knockdown, 2h EtOH 1:1000, replicate3


title: S2cells_GFPdsRNA_EtOH_rep3

source_name: S2 cells, GFP knockdown, 2h EtOH 1:1000, replicate3


title: CtrlLarvae_EtOH_rep1

source_name: w1118 larvae, 6h EtOH, replicate 1


title: S2cells_GFPdsRNA_rapamycin_rep2

source_name: S2 cells, GFP knockdown, 2h 20nM rapamycin, replicate2


title: ALL-SIL_Control

hyb_protocol: Samples were hybridized on the GeneChip Human Genome U133 Plus 2.0 Arrays (Affymetrix, Inc.), according to the manufacturer's instructions. Arrays were washed and stained with the GeneChip Fluidics Station 450.

data_processing: Arrays were normalized and expression values were obtained with the default PLIER (PM-MM) algorithm of the Affymetrix Expression Console software (1.3.1.187).

source_name: T-ALL cell line_vehicle

label_protocol: Samples were processed with the One-Cycle Target Labeling and Control Reagents Kit (Affymetrix, Inc., Santa Clara, CA, USA), according to the manufacturer's instructions.

growth_protocol: Cell lines were cultured in RPMI-1640 medium, fetal bovine serum (FBS) 10%, penicillin 20 U.I./mL and streptomycin 20 µg/mL at 37°C and 5% CO2. Cells were resuspended in fresh medium 12-24h before treatment with AS605240 or vehicle.

extract_protocol: RNA was extracted by the phenol-chloroform method and purified with RNAeasy Mini Kit (Qiagen, Inc., Valencia, CA, USA), according to the manufacturer's instructions.

treatment_protocol: Cell lines were cultured with the respective IC50 concentration of AS605240 or vehicle for 6h, washed with ice cold PBS by centrifugation and resuspended in guanidine thiocyanate solution.

value: ALL-SIL

value: T-cell acute lymphoblastic leukemia (T-ALL) cells


title: P12-ICHIKAWA_AS605240

source_name: T-ALL cell line_AS605240


title: S2cells_GFPdsRNA_EtOH_rep2

source_name: S2 cells, GFP knockdown, 2h EtOH 1:1000, replicate2


title: TALL-1_AS605240


title: HPB-ALL_Control

value: HPB-ALL


title: Molt-4_AS605240


title: P12-ICHIKAWA_Control


title: TALL-1_Control


title: S2cells_GFPdsRNA_rapamycin_rep3

source_name: S2 cells, GFP knockdown, 2h 20nM rapamycin, replicate3


title: Jurkat_Control

value: Jurkat


title: S2cells_GFPdsRNA_EtOH_rep1

source_name: S2 cells, GFP knockdown, 2h EtOH 1:1000, replicate1


title: S2cells_CG13dsRNA_EtOH_rep1

source_name: S2 cells, CG13624 knockdown, 2h EtOH 1:1000, replicate1


title: Jurkat_AS605240


title: Molt-4_Control


title: CCRF-CEM_AS605240

value: CCRF-CEM


title: ALL-SIL_AS605240


title: CCRF-CEM_Control


title: HPB-ALL_AS605240


title: S2cells_CG18dsRNA_EtOH_rep1

source_name: S2 cells, CG18619 knockdown, 2h EtOH 1:1000, replicate1


title: Genomic DNA from PBMCs, 42021

status: Public on Mar 20 2015

type: genomic

city: Tampere

first: Saara

last: Marttila

address: Biokatu 6

department: School of Medicine

country: Finland

institute: University of Tampere

hyb_protocol: Four µl of bisulfite-converted DNA was whole genome amplified, enzymatically fragmented and hybridized to the Infinium HumanMethylation450 BeadChip according to the manufacturer's protocol.

scan_protocol: The BeadChips were scanned with the iScan reader.

data_processing:
GenomeStudio software V2011.1, R version 3.0.2.
Processed average beta values (background correction, normalisation with the dasen method (individually for Infinium I and II chemistries), batch effects corrected with BMIQ method and R package Combat).
Prior to any processing, all unspecific or polymorphic sites (N=76775) were removed based on database information [Chen et al., Epigenetics 2013, 8:203-209]. Samples and target sites of a technically poor quality were filtered out by excluding sites with a  beadcount of <3 in 5% of the samples (N=526) and sites for which 1% of the samples showed a detection p-value >0.05 (N=740).

label: Cy5 and Cy3

molecule: genomic DNA

source_name: PBMCs, young control

label_protocol: Standard Illumina Protocol.

extract_protocol: DNA was extracted from PBMCs with QIAamp DNA Mini kit (Qiagen, CA, USA), following the manufacturer's instructions for spin protocol.

tag: age group

value: young control

value: peripheral blood mononuclear cells

tag: ratio of cd4+/cd8+ cells

tag: percentage of cd14+ cells

tag: percentage of cd4+cd28- cells

tag: percentage of cd8+cd28- cells

tag: maternal age at death

tag: paternal age at death


title: CtrlLarvae_EtOH_rep2

source_name: w1118 larvae, 6h EtOH, replicate 2

value: larva

value: 48h prewandering


title: Genomic DNA from PBMCs, 42025

value: female


title: Genomic DNA from PBMCs, 42030


title: Genomic DNA from PBMCs, 81136

source_name: PBMCs, nonagenarian

value: nonagenarian


title: Genomic DNA from PBMCs, 42037


title: Genomic DNA from PBMCs, 42029

value: male


title: Genomic DNA from PBMCs, 42034


title: Genomic DNA from PBMCs, 81084


title: Genomic DNA from PBMCs, 42017


title: Genomic DNA from PBMCs, 42009


title: Genomic DNA from PBMCs, 42022


title: Genomic DNA from PBMCs, 42035


title: Genomic DNA from PBMCs, 81018


title: Genomic DNA from PBMCs, 42007


title: Genomic DNA from PBMCs, 42023


title: Genomic DNA from PBMCs, 42005


title: Genomic DNA from PBMCs, 81059


title: Genomic DNA from PBMCs, 42016


title: Genomic DNA from PBMCs, 42036


title: Genomic DNA from PBMCs, 81074


title: Genomic DNA from PBMCs, 42020


title: Genomic DNA from PBMCs, 42018


title: Genomic DNA from PBMCs, 42019


title: Genomic DNA from PBMCs, 81019


title: Genomic DNA from PBMCs, 42028


title: Genomic DNA from PBMCs, 81064


title: Genomic DNA from PBMCs, 42038


title: Genomic DNA from PBMCs, 28895


title: Genomic DNA from PBMCs, 81012


title: Genomic DNA from PBMCs, 42008


title: Genomic DNA from PBMCs, 28897


title: Genomic DNA from PBMCs, 28807


title: Genomic DNA from PBMCs, 28812


title: Genomic DNA from PBMCs, 28803


title: Genomic DNA from PBMCs, 28861


title: Genomic DNA from PBMCs, 28716


title: Genomic DNA from PBMCs, 28706


title: Genomic DNA from PBMCs, 28657


title: Genomic DNA from PBMCs, 28647


title: Genomic DNA from PBMCs, 28623


title: Genomic DNA from PBMCs, 28760


title: Genomic DNA from PBMCs, 28798


title: Genomic DNA from PBMCs, 28782


title: Genomic DNA from PBMCs, 28736


title: Genomic DNA from PBMCs, 28655


title: Genomic DNA from PBMCs, 28735


title: Genomic DNA from PBMCs, 28720


title: Genomic DNA from PBMCs, 28667


title: Genomic DNA from PBMCs, 28630


title: Genomic DNA from PBMCs, 28698


title: Genomic DNA from PBMCs, 28614


title: Genomic DNA from PBMCs, 28615


title: Genomic DNA from PBMCs, 28726


title: Genomic DNA from PBMCs, 28816


title: Genomic DNA from PBMCs, 28629


title: Genomic DNA from PBMCs, 28649


title: Genomic DNA from PBMCs, 28600


title: Genomic DNA from PBMCs, 28603


title: Genomic DNA from PBMCs, 28664


title: Genomic DNA from PBMCs, 28472


title: Genomic DNA from PBMCs, 28575


title: Genomic DNA from PBMCs, 28612


title: Genomic DNA from PBMCs, 28346


title: Genomic DNA from PBMCs, 28498


title: Genomic DNA from PBMCs, 28588


title: Genomic DNA from PBMCs, 28395


title: Genomic DNA from PBMCs, 28448


title: Genomic DNA from PBMCs, 28501


title: Genomic DNA from PBMCs, 28453


title: Genomic DNA from PBMCs, 28438


title: Genomic DNA from PBMCs, 28298


title: Genomic DNA from PBMCs, 28341


title: Genomic DNA from PBMCs, 28358


title: Genomic DNA from PBMCs, 28401


title: Genomic DNA from PBMCs, 28393


title: Genomic DNA from PBMCs, 28330


title: Genomic DNA from PBMCs, 28290


title: Genomic DNA from PBMCs, 28319


title: Genomic DNA from PBMCs, 28303


title: Genomic DNA from PBMCs, 28406


title: Genomic DNA from PBMCs, 28376


title: Genomic DNA from PBMCs, 28291


title: Genomic DNA from PBMCs, 28288


title: Genomic DNA from PBMCs, 28247


title: Genomic DNA from PBMCs, 28286


title: Genomic DNA from PBMCs, 28269


title: Genomic DNA from PBMCs, 28289


title: Genomic DNA from PBMCs, 28198


title: Genomic DNA from PBMCs, 28202


title: Genomic DNA from PBMCs, 28204


title: Genomic DNA from PBMCs, 28232


title: Genomic DNA from PBMCs, 28591


title: Genomic DNA from PBMCs, 28183


title: Genomic DNA from PBMCs, 28189


title: Genomic DNA from PBMCs, 28175


title: Genomic DNA from PBMCs, 28140


title: Genomic DNA from PBMCs, 28188


title: Genomic DNA from PBMCs, 28456


title: Genomic DNA from PBMCs, 28179


title: Genomic DNA from PBMCs, 28131


title: Genomic DNA from PBMCs, 28035


title: Genomic DNA from PBMCs, 28015


title: Genomic DNA from PBMCs, 28778


title: Genomic DNA from PBMCs, 28119


title: Genomic DNA from PBMCs, 28806


title: Genomic DNA from PBMCs, 28123


title: Genomic DNA from PBMCs, 28020


title: Genomic DNA from PBMCs, 28073


title: Genomic DNA from PBMCs, 28663


title: Genomic DNA from PBMCs, 28752


title: Genomic DNA from PBMCs, 28592


title: Genomic DNA from PBMCs, 28675


title: Genomic DNA from PBMCs, 28058


title: Genomic DNA from PBMCs, 28611


title: Genomic DNA from PBMCs, 28583


title: Genomic DNA from PBMCs, 28704


title: Genomic DNA from PBMCs, 28042


title: Genomic DNA from PBMCs, 28582


title: Genomic DNA from PBMCs, 28148


title: Genomic DNA from PBMCs, 28581


title: Genomic DNA from PBMCs, 28502


title: Genomic DNA from PBMCs, 28559


title: Primary Melanoma_118

status: Public on Feb 01 2015

city: New York

first: Eva

last: Hernando-Monge

state: NY

address: 550 1st Ave. Smilow 305

institute: NYU Langone Medical Center

description: 1_Exiqon is Cy3

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA microRNA array (6th gen - hsa, mmu & rno) (Exiqon, Denmark), which contains capture probes targeting all miRNAs for human, mouse or rat registered in the miRBASE version 16.0 at the Sanger Institute. The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria). After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes.

scan_protocol: The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 9.0 software (BioDiscovery, Inc., USA).

data_processing: The quantified signals were background corrected (Normexp with offset value 10 – Ritchie et al., 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.  Spots were flagged as follows: 0 - no flag, spot OK; 1 - manual flagging; 2 - empty spot; 3 - poor spot; 4 - negative spot; 5 - empty spot (manual); poor spot (manual); negative spot (manual).  Spots flagged 1 or higher were removed from consideration.  Capture probes for which both Hy3 and Hy5 values were less than 1.5x the median signal intensity for a given slide were excluded from further analysis.  Excluded capture probes are indicated byt the acronym' NA' in the expression matrix.  For each spot, a log base 2 ratio (Hy3/Hy5) was calculated, and the median log-ratio of four replicate spots per array was selected as representative of relative miRNA expression for a given sample.  Median log-ratios were used for all subsequent analyses.

label: Cy3 (Hy3)

source_name: Cutaneous primary melanoma

label_protocol: 300 ng total RNA from sample and reference was labelled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA microRNA Hi-Power Labelling Kit, Hy3/Hy5 (Exiqon, Denmark) following the procedure described by the manufacturer.

extract_protocol: RNA was extracted using Qiagen miRNeasy FFPE kits following the manufacturer's recommended protocol.  RNA quantity and quality was assessed by Nanodrop and Agilent 2100 Bioanalyzer.

treatment_protocol: After surgical excision, primary melanomas were fixed in formalin and embedded in parrafin by NYU Langone's clinical pathology lab.  5uM  FFPE sections were affixed to Leica PEN membrane slides.  3 tp 10 sections were used for RNA extraction from each patient case.  A consecutive section was stained by H&E and tumor area was marked by an attending pathologist.  Tumor was macro-dissected from sections under a dissecting microscope and transferred to microfuge tubes prior to RNA extraction.  RNA extraction was performed within 4 days of tissue section to reduce air-related RNA degradation

tag: identifier

value: M

tag: primary tumor thickness (mm)

tag: mitotic index

value: Many

tag: ulceration status

value: Present

tag: histotype

value: Nodular

tag: anatomical site of primary tumor

value: Axial

tag: Stage

value: IIB

tag: recurrence

value: Y

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

value: DV

tag: brain as isolated 1st site of recurrence

value: N

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)

tag: follow-up time (months)

tag: last status

value: Died, With Melanoma

tag: Cause of death

value: Melanoma

label: Cy5 (Hy5)

source_name: Common Reference

tag: material

value: Equal mixture of all samples


title: Primary Melanoma_119

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

value: F

tag: age

tag: primary tumor thickness (mm)

tag: mitotic index

value: Superficial Spreading

value: Extremity

value: Alive, No Melanoma


title: Primary Melanoma_116

description: 1_Exiqon is Cy3

tag: ulceration status

tag: histotype

tag: anatomical site of primary tumor

tag: Stage

tag: recurrence


title: Primary Melanoma_117

description: 1_Exiqon is Cy3

value: Few

value: Absent

value: IIIA

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

tag: brain as isolated 1st site of recurrence

tag: b-met


title: Genomic DNA from PBMCs, 28032

tag: age group

value: nonagenarian

tag: Sex

value: female

tag: cell type

value: peripheral blood mononuclear cells

tag: ratio of cd4+/cd8+ cells

tag: percentage of cd14+ cells

tag: percentage of cd4+cd28- cells

tag: percentage of cd8+cd28- cells

tag: maternal age at death

tag: paternal age at death


title: Primary Melanoma_115

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

value: M

tag: age

tag: primary tumor thickness (mm)

tag: mitotic index

value: Many

tag: ulceration status

value: Present

tag: histotype

value: Nodular

tag: anatomical site of primary tumor

value: Axial

value: IIC

tag: time to b-met (days)

tag: follow-up time (days)

tag: follow-up time (months)

tag: last status

tag: Cause of death

tag: material


title: Primary Melanoma_114

description: 1_Exiqon is Cy3

value: Desmoplastic

tag: Stage

value: IIB

tag: recurrence

value: N

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

tag: brain as isolated 1st site of recurrence

tag: b-met

value: Equal mixture of all samples


title: Primary Melanoma_105

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

value: F

tag: age

tag: primary tumor thickness (mm)

tag: mitotic index

value: Acral Lentiginous

value: Extremity

value: IIIB

value: Y

value: LR

value: Alive, With Melanoma


title: Primary Melanoma_104

description: 1_Exiqon is Cy3

value: M

tag: ulceration status

tag: histotype

tag: anatomical site of primary tumor

value: IIA

tag: time to b-met (days)

tag: follow-up time (days)

value: Alive, No Melanoma


title: Primary Melanoma_109

description: 1_Exiqon is Cy3

value: Moderate

value: Present

value: Nodular

tag: Stage

tag: follow-up time (months)

tag: last status

value: Died, No Melanoma

tag: Cause of death

tag: material


title: Primary Melanoma_108

description: 1_Exiqon is Cy3

value: Many

value: IIB

tag: recurrence

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

value: RLN , RS

tag: brain as isolated 1st site of recurrence

value: Died, With Melanoma

value: Melanoma


title: Genomic DNA from PBMCs, 28489

tag: age group

value: nonagenarian

tag: Sex

value: male

tag: cell type

value: peripheral blood mononuclear cells

tag: ratio of cd4+/cd8+ cells

tag: percentage of cd14+ cells

tag: percentage of cd4+cd28- cells

tag: percentage of cd8+cd28- cells

tag: maternal age at death

tag: paternal age at death


title: Genomic DNA from PBMCs, 28544


title: Primary Melanoma_106

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: age

tag: primary tumor thickness (mm)

tag: mitotic index

tag: ulceration status

tag: histotype

tag: anatomical site of primary tumor

value: Axial

tag: Stage

value: Y

value: RLN ,RS

value: N

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)

tag: follow-up time (months)

tag: last status

value: Equal mixture of all samples


title: Genomic DNA from PBMCs, 28306

tag: age group

tag: Sex

tag: cell type

tag: ratio of cd4+/cd8+ cells

tag: percentage of cd14+ cells

tag: percentage of cd4+cd28- cells

tag: percentage of cd8+cd28- cells


title: Primary Melanoma_113

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

value: M

tag: age

tag: primary tumor thickness (mm)

tag: mitotic index

value: Absent

value: Superficial Spreading

value: IB

tag: recurrence

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

value: DV

tag: brain as isolated 1st site of recurrence

tag: Cause of death

tag: material


title: Primary Melanoma_112

description: 1_Exiqon is Cy3

value: Many

tag: ulceration status

tag: histotype

tag: anatomical site of primary tumor

tag: Stage

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)

tag: follow-up time (months)

tag: last status

value: Alive, With Melanoma


title: Genomic DNA from PBMCs, 28399

tag: age group

tag: Sex

tag: cell type

tag: ratio of cd4+/cd8+ cells

tag: percentage of cd14+ cells

tag: percentage of cd4+cd28- cells

tag: percentage of cd8+cd28- cells

tag: maternal age at death

tag: paternal age at death


title: Genomic DNA from PBMCs, 28381


title: Primary Melanoma_110

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

value: F

tag: age

tag: primary tumor thickness (mm)

tag: mitotic index

tag: ulceration status

value: Present

tag: histotype

value: Nodular

value: IIIC

tag: recurrence

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

value: RLN

tag: brain as isolated 1st site of recurrence

value: Died, With Melanoma

tag: Cause of death

tag: material


title: Genomic DNA from PBMCs, 28284

tag: age group

value: nonagenarian

tag: Sex

value: male

tag: cell type

value: peripheral blood mononuclear cells

tag: ratio of cd4+/cd8+ cells

tag: percentage of cd14+ cells

tag: percentage of cd4+cd28- cells

tag: percentage of cd8+cd28- cells


title: Genomic DNA from PBMCs, 28301

tag: maternal age at death

tag: paternal age at death


title: Genomic DNA from PBMCs, 28191


title: Genomic DNA from PBMCs, 28165


title: Primary Melanoma_103

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: age

tag: primary tumor thickness (mm)

tag: mitotic index

tag: ulceration status

tag: histotype

tag: anatomical site of primary tumor

value: Axial

tag: Stage

value: IIA

value: N

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)

tag: follow-up time (months)

tag: last status

value: Alive, No Melanoma

value: Equal mixture of all samples


title: Primary Melanoma_102

description: 1_Exiqon is Cy3

value: M

value: Absent

value: Superficial Spreading

value: IIIA

tag: recurrence

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

tag: brain as isolated 1st site of recurrence

tag: Cause of death

tag: material


title: Primary Melanoma_111

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: age

tag: primary tumor thickness (mm)

tag: mitotic index

value: Many

value: Present

value: IIC

value: Y


title: Genomic DNA from PBMCs, 28172

tag: age group

tag: Sex

tag: cell type

tag: maternal age at death

tag: paternal age at death


title: Primary Melanoma_100

description: 1_Exiqon is Cy3

value: Few

tag: ulceration status

tag: histotype

value: Nodular

tag: anatomical site of primary tumor

tag: Stage

tag: recurrence

value: DV

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)

tag: follow-up time (months)

tag: last status

value: Alive, With Melanoma


title: Primary Melanoma_099

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

value: F

tag: age

tag: primary tumor thickness (mm)

value: Moderate

value: Axial

value: IIIB

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

tag: brain as isolated 1st site of recurrence

value: Died, With Melanoma

tag: Cause of death

value: Melanoma

tag: material


title: Genomic DNA from PBMCs, 28200

tag: age group

value: nonagenarian

tag: Sex

value: male

tag: cell type

value: peripheral blood mononuclear cells

tag: ratio of cd4+/cd8+ cells

tag: percentage of cd14+ cells

tag: percentage of cd4+cd28- cells

tag: percentage of cd8+cd28- cells

tag: maternal age at death

tag: paternal age at death


title: Primary Melanoma_101

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: age

tag: mitotic index

value: Many

tag: ulceration status

value: Absent

tag: histotype

value: Superficial Spreading

tag: anatomical site of primary tumor

value: Extremity

tag: Stage

value: IB

tag: recurrence

value: N

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)

tag: follow-up time (months)

tag: last status

value: Alive, No Melanoma

value: Equal mixture of all samples


title: Primary Melanoma_096

description: 1_Exiqon is Cy3

value: M

tag: primary tumor thickness (mm)

value: Present

value: Nodular

value: IV

value: Y

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

value: DV

tag: brain as isolated 1st site of recurrence

tag: Cause of death

tag: material


title: Primary Melanoma_097

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

value: F

tag: age

tag: mitotic index

tag: ulceration status

value: IIB


title: Primary Melanoma_098

description: 1_Exiqon is Cy3

value: Few

tag: histotype

tag: anatomical site of primary tumor

value: Axial

tag: Stage

value: IIIB

tag: recurrence

tag: b-met


title: Genomic DNA from PBMCs, 28272

tag: age group

value: nonagenarian

tag: Sex

value: male

tag: cell type

value: peripheral blood mononuclear cells

tag: ratio of cd4+/cd8+ cells

tag: percentage of cd14+ cells

tag: percentage of cd4+cd28- cells

tag: percentage of cd8+cd28- cells

tag: maternal age at death

tag: paternal age at death


title: Primary Melanoma_094

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: age

tag: primary tumor thickness (mm)

value: Moderate

value: Absent

value: Superficial Spreading

value: IIA

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

tag: brain as isolated 1st site of recurrence

value: N

tag: time to b-met (days)

tag: follow-up time (days)

tag: follow-up time (months)

tag: last status

tag: Cause of death

tag: material


title: Genomic DNA from PBMCs, 28048

tag: age group

tag: Sex

tag: cell type

tag: ratio of cd4+/cd8+ cells

tag: percentage of cd14+ cells

tag: percentage of cd4+cd28- cells

tag: percentage of cd8+cd28- cells


title: Genomic DNA from PBMCs, 28396

tag: maternal age at death

tag: paternal age at death


title: Primary Melanoma_092

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: age

tag: primary tumor thickness (mm)

tag: mitotic index

tag: ulceration status

value: Present

tag: histotype

value: Acral Lentiginous

tag: anatomical site of primary tumor

tag: Stage

tag: recurrence

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

value: RS

tag: b-met

value: Alive, No Melanoma

value: Equal mixture of all samples


title: Primary Melanoma_107

description: 1_Exiqon is Cy3

value: F

value: Many

value: Nodular

value: Y

value: DV

tag: brain as isolated 1st site of recurrence

tag: time to b-met (days)

tag: follow-up time (days)

tag: follow-up time (months)

tag: last status

value: Died, With Melanoma

tag: Cause of death

value: Melanoma

tag: material


title: Primary Melanoma_093

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: age

tag: primary tumor thickness (mm)

tag: mitotic index

value: Axial

value: IIIC

value: Melanom


title: Primary Melanoma_091

description: 1_Exiqon is Cy3

value: M

value: Few

tag: ulceration status

value: Absent

tag: histotype

value: Superficial Spreading

tag: anatomical site of primary tumor

tag: Stage

value: IB

tag: recurrence

value: Died, No Melanoma

value: Other


title: Primary Melanoma_090

description: 1_Exiqon is Cy3

value: Moderate

value: IIA

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

tag: brain as isolated 1st site of recurrence

value: N

tag: b-met

value: Equal mixture of all samples


title: Primary Melanoma_089

description: 1_Exiqon is Cy3

value: Nodular

value: Extremity

value: Y

value: DV

tag: time to b-met (days)

tag: follow-up time (days)

tag: follow-up time (months)

tag: last status

tag: Cause of death


title: Genomic DNA from PBMCs, 28242

tag: age group

value: nonagenarian

tag: Sex

value: male

tag: cell type

value: peripheral blood mononuclear cells

tag: ratio of cd4+/cd8+ cells

tag: percentage of cd14+ cells

tag: percentage of cd4+cd28- cells

tag: percentage of cd8+cd28- cells

tag: maternal age at death

tag: paternal age at death


title: Primary Melanoma_088

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

value: M

tag: age

tag: primary tumor thickness (mm)

tag: mitotic index

value: Few

tag: ulceration status

tag: histotype

tag: anatomical site of primary tumor

value: Axial

tag: Stage

value: IIB

tag: recurrence

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

value: Alive, No Melanoma

tag: material


title: Genomic DNA from PBMCs, 28258

tag: age group

tag: Sex

tag: cell type

tag: ratio of cd4+/cd8+ cells

tag: percentage of cd14+ cells

tag: percentage of cd4+cd28- cells

tag: percentage of cd8+cd28- cells


title: Genomic DNA from PBMCs, 28277

tag: maternal age at death

tag: paternal age at death


title: Primary Melanoma_087

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: age

tag: primary tumor thickness (mm)

tag: mitotic index

tag: ulceration status

value: Present

tag: histotype

value: Acral Lentiginous

value: RS

tag: brain as isolated 1st site of recurrence

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)

tag: follow-up time (months)

tag: last status

value: Alive, With Melanoma

tag: Cause of death


title: Primary Melanoma_086

description: 1_Exiqon is Cy3

value: F

value: Absent

tag: anatomical site of primary tumor

tag: Stage

value: IB

tag: recurrence

value: N

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

tag: material

value: Equal mixture of all samples


title: Primary Melanoma_085

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: age

tag: primary tumor thickness (mm)

tag: mitotic index

value: Nodular

value: Extremity


title: Primary Melanoma_083

description: 1_Exiqon is Cy3

value: Moderate

tag: ulceration status

tag: histotype

value: IIIB

tag: brain as isolated 1st site of recurrence

tag: b-met

tag: time to b-met (days)


title: Primary Melanoma_082

description: 1_Exiqon is Cy3

value: M

value: Desmoplastic

tag: anatomical site of primary tumor

value: IIC

value: Y

tag: follow-up time (days)

tag: follow-up time (months)

tag: last status

value: Died, With Melanoma

tag: Cause of death

value: Melanoma


title: Genomic DNA from PBMCs, 28028

tag: age group

value: nonagenarian

tag: Sex

value: male

tag: cell type

value: peripheral blood mononuclear cells

tag: ratio of cd4+/cd8+ cells

tag: percentage of cd14+ cells

tag: percentage of cd4+cd28- cells

tag: percentage of cd8+cd28- cells

tag: maternal age at death

tag: paternal age at death


title: Primary Melanoma_080

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: age

tag: primary tumor thickness (mm)

tag: mitotic index

value: Few

tag: ulceration status

value: Absent

tag: histotype

tag: Stage

tag: recurrence

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

value: RS

tag: brain as isolated 1st site of recurrence

value: Alive, No Melanoma

tag: material


title: Genomic DNA from PBMCs, 28542

tag: age group

tag: Sex

tag: cell type

tag: ratio of cd4+/cd8+ cells

tag: percentage of cd14+ cells

tag: percentage of cd4+cd28- cells

tag: percentage of cd8+cd28- cells


title: Primary Melanoma_081

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: age

tag: primary tumor thickness (mm)

tag: mitotic index

value: Nodular

tag: anatomical site of primary tumor

value: Axial

value: IIA

value: N

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)

tag: follow-up time (months)

tag: last status

value: Died, No Melanoma

tag: Cause of death

value: Other

value: Equal mixture of all samples


title: Primary Melanoma_084

description: 1_Exiqon is Cy3

value: F

tag: ulceration status

value: Present

tag: histotype

value: Superficial Spreading

value: Extremity

tag: Stage

tag: recurrence

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

tag: brain as isolated 1st site of recurrence

tag: material


title: Primary Melanoma_079

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

value: M

tag: age

tag: primary tumor thickness (mm)

tag: mitotic index

value: IIIA


title: Primary Melanoma_078

description: 1_Exiqon is Cy3

value: Many

tag: anatomical site of primary tumor

value: IIIC

value: Y

value: DV

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)

tag: follow-up time (months)

value: Died, With Melanoma

value: Melanoma


title: Primary Melanoma_077

description: 1_Exiqon is Cy3

value: Few

tag: ulceration status

value: Absent

tag: histotype

tag: Stage

value: IB

tag: last status

value: Alive, No Melanoma

tag: Cause of death


title: Primary Melanoma_076

description: 1_Exiqon is Cy3

value: Axial

tag: recurrence

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

value: RS

tag: brain as isolated 1st site of recurrence

value: N

value: Equal mixture of all samples


title: Primary Melanoma_075

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

value: F

tag: age

tag: primary tumor thickness (mm)

value: Moderate

value: Present

value: Nodular

value: Extremity

value: IIC

value: DS

tag: material


title: Primary Melanoma_073

description: 1_Exiqon is Cy3

tag: mitotic index

value: Superficial Spreading

tag: anatomical site of primary tumor

value: IIB

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)


title: Genomic DNA from PBMCs, 28487

tag: age group

value: nonagenarian

tag: Sex

value: male

tag: cell type

value: peripheral blood mononuclear cells

tag: ratio of cd4+/cd8+ cells

tag: percentage of cd14+ cells

tag: percentage of cd4+cd28- cells

tag: percentage of cd8+cd28- cells

tag: maternal age at death

tag: paternal age at death


title: Primary Melanoma_070

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

value: M

tag: age

tag: ulceration status

tag: histotype

tag: Stage

tag: recurrence

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

tag: brain as isolated 1st site of recurrence

tag: follow-up time (months)

tag: last status

value: Died, No Melanoma

tag: Cause of death

value: Other


title: Primary Melanoma_072

description: 1_Exiqon is Cy3

tag: primary tumor thickness (mm)

tag: mitotic index

value: Absent

tag: anatomical site of primary tumor

value: Axial

value: IA

value: N

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)

value: Alive, No Melanoma

tag: material


title: Primary Melanoma_069

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

value: F

tag: age

value: Few

tag: ulceration status

tag: histotype

value: IB

value: Equal mixture of all samples


title: Primary Melanoma_071

description: 1_Exiqon is Cy3

value: Superficial Spreading

tag: Stage

tag: recurrence

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: site of 1st recurrence


title: Primary Melanoma_066

description: 1_Exiqon is Cy3

tag: primary tumor thickness (mm)

value: Present

value: Nodular

value: Extremity

value: IIB

tag: brain as isolated 1st site of recurrence

tag: follow-up time (months)

tag: last status

tag: Cause of death


title: Primary Melanoma_067

description: 1_Exiqon is Cy3

tag: mitotic index

tag: anatomical site of primary tumor

value: Y

value: RLN

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)

value: Died, Melanoma Status Unknown

value: Unknown


title: Primary Melanoma_068

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

value: M

tag: age

tag: ulceration status

value: Axial

value: LR

value: Died, With Melanoma

value: Melanoma

tag: material


title: Primary Melanoma_074

description: 1_Exiqon is Cy3

value: Absent

tag: histotype

tag: Stage

value: IIIA

tag: recurrence

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

value: DV

value: N


title: Primary Melanoma_065

description: 1_Exiqon is Cy3

value: F

tag: primary tumor thickness (mm)

value: Few

value: Acral Lentiginous

tag: site of 1st recurrence

value: RS

tag: brain as isolated 1st site of recurrence

tag: follow-up time (months)

tag: last status

value: Equal mixture of all samples


title: Primary Melanoma_064

description: 1_Exiqon is Cy3

tag: mitotic index

value: Many

value: Present

value: Superficial Spreading

tag: anatomical site of primary tumor

value: IIA

value: Y

value: RLN

tag: b-met

tag: time to b-met (days)

value: Alive, With Melanoma

tag: Cause of death


title: Primary Melanoma_062

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

value: M

tag: age

tag: ulceration status

value: Nodular

value: Extremity

value: IIIB

tag: follow-up time (days)

value: Died, With Melanoma

value: Melanoma


title: Primary Melanoma_063

description: 1_Exiqon is Cy3

tag: histotype

value: Axial

tag: Stage

tag: recurrence

value: N

tag: time to 1st recurrence (days)

value: Alive, No Melanoma

tag: material


title: Primary Melanoma_058

description: 1_Exiqon is Cy3

value: F

tag: primary tumor thickness (mm)

value: Few

value: IIB

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

tag: brain as isolated 1st site of recurrence

tag: follow-up time (months)

value: Died, No Melanoma

value: Other

value: Equal mixture of all samples


title: Primary Melanoma_057

description: 1_Exiqon is Cy3

tag: mitotic index

value: Absent

value: Superficial Spreading

tag: anatomical site of primary tumor

value: IIA

value: Y

value: DS

tag: b-met

tag: time to b-met (days)

tag: last status


title: Primary Melanoma_059

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

value: M

tag: age

tag: ulceration status

value: Present

tag: Cause of death


title: Primary Melanoma_060

description: 1_Exiqon is Cy3

tag: histotype

value: Nodular

tag: Stage

tag: recurrence

tag: time to 1st recurrence (days)

tag: follow-up time (days)


title: Primary Melanoma_061

description: 1_Exiqon is Cy3

tag: primary tumor thickness (mm)

value: Many

value: Axial

value: IIIB

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

value: RS

tag: brain as isolated 1st site of recurrence

value: Died, With Melanoma

value: Melanoma

tag: material


title: Primary Melanoma_056

description: 1_Exiqon is Cy3

tag: mitotic index

value: Moderate

tag: anatomical site of primary tumor

value: IIIC

value: N

tag: b-met

tag: time to b-met (days)

tag: follow-up time (months)


title: Primary Melanoma_053

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: age

value: Few

tag: ulceration status

value: Absent

value: IIIA

value: DV

tag: last status

value: Equal mixture of all samples


title: Primary Melanoma_055

description: 1_Exiqon is Cy3

value: F

tag: histotype

value: Acral Lentiginous

value: Extremity

tag: Stage

value: IB

tag: recurrence

value: Y

tag: time to 1st recurrence (days)

tag: Cause of death


title: Primary Melanoma_054

description: 1_Exiqon is Cy3

tag: primary tumor thickness (mm)

value: Superficial Spreading

value: IA

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

tag: brain as isolated 1st site of recurrence

tag: follow-up time (days)

value: Alive, No Melanoma


title: Primary Melanoma_050

description: 1_Exiqon is Cy3

tag: mitotic index

value: Many

value: Present

value: Nodular

tag: anatomical site of primary tumor

value: IIC

tag: b-met

tag: time to b-met (days)

tag: material


title: Primary Melanoma_052

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: age

value: Few

tag: ulceration status

value: N

tag: follow-up time (months)


title: Primary Melanoma_051

description: 1_Exiqon is Cy3

value: M

value: Absent

tag: histotype

value: Axial

tag: Stage

value: IIIA

tag: recurrence

tag: time to 1st recurrence (days)

tag: last status

value: Died, With Melanoma

value: Melanoma


title: Primary Melanoma_049

description: 1_Exiqon is Cy3

tag: primary tumor thickness (mm)

value: Extremity

value: IIIB

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

value: DS

tag: brain as isolated 1st site of recurrence

tag: Cause of death

value: Equal mixture of all samples


title: Primary Melanoma_048

description: 1_Exiqon is Cy3

value: F

tag: mitotic index

value: Moderate

value: Acral Lentiginous

tag: anatomical site of primary tumor

value: Y

value: RS

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)


title: Primary Melanoma_042

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: age

value: Few

tag: ulceration status

value: Present

value: Superficial Spreading

value: DV

tag: material


title: Primary Melanoma_043

description: 1_Exiqon is Cy3

value: M

tag: histotype

value: Axial

tag: Stage

value: IIA

tag: recurrence

value: N

tag: time to 1st recurrence (days)

tag: follow-up time (months)

value: Alive, No Melanoma


title: Primary Melanoma_045

description: 1_Exiqon is Cy3

tag: primary tumor thickness (mm)

value: Many

value: Absent

value: Nodular

value: Extremity

value: IIIB

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

tag: brain as isolated 1st site of recurrence

tag: last status

value: Died, No Melanoma

value: Other


title: Primary Melanoma_038

description: 1_Exiqon is Cy3

tag: mitotic index

tag: anatomical site of primary tumor

tag: b-met

tag: time to b-met (days)

tag: Cause of death

value: Equal mixture of all samples


title: Primary Melanoma_041

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: age

tag: ulceration status

value: IIIC

value: Y

tag: follow-up time (days)


title: Primary Melanoma_044

description: 1_Exiqon is Cy3

value: F

value: Moderate

value: Present

tag: histotype

value: Acral Lentiginous

tag: Stage

tag: recurrence

tag: time to 1st recurrence (days)

value: DLN

value: Died, With Melanoma

value: Melanoma

tag: material


title: Primary Melanoma_039

description: 1_Exiqon is Cy3

value: M

tag: primary tumor thickness (mm)

value: Many

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

value: RS

tag: brain as isolated 1st site of recurrence

value: N

tag: follow-up time (months)

value: Alive, No Melanoma


title: Primary Melanoma_040

description: 1_Exiqon is Cy3

tag: mitotic index

value: Absent

tag: anatomical site of primary tumor

value: Axial

value: IIB

tag: b-met

tag: time to b-met (days)

tag: last status


title: Primary Melanoma_037

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: age

tag: ulceration status

value: Superficial Spreading

value: IB

value: DV

tag: Cause of death

value: Equal mixture of all samples


title: Primary Melanoma_046

description: 1_Exiqon is Cy3

value: F

value: Few

tag: histotype

value: Extremity

tag: Stage

tag: recurrence

tag: time to 1st recurrence (days)

tag: follow-up time (days)


title: Primary Melanoma_035

description: 1_Exiqon is Cy3

tag: primary tumor thickness (mm)

value: Desmoplastic

value: Y

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

tag: brain as isolated 1st site of recurrence

tag: material


title: Primary Melanoma_034

description: 1_Exiqon is Cy3

value: M

tag: mitotic index

value: Present

value: Nodular

tag: anatomical site of primary tumor

value: IIIC

tag: b-met

tag: time to b-met (days)

tag: follow-up time (months)

value: Died, With Melanoma

value: Melanoma


title: Primary Melanoma_047

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: age

value: Moderate

tag: ulceration status

value: Absent

value: N

tag: last status

value: Alive, No Melanoma


title: Primary Melanoma_036

description: 1_Exiqon is Cy3

value: Many

tag: histotype

value: Axial

tag: Stage

value: IIIB

tag: recurrence

tag: time to 1st recurrence (days)

value: DV

tag: Cause of death


title: Primary Melanoma_030

description: 1_Exiqon is Cy3

tag: primary tumor thickness (mm)

value: Superficial Spreading

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

value: LR

tag: brain as isolated 1st site of recurrence

tag: follow-up time (days)

value: Equal mixture of all samples


title: Primary Melanoma_031

description: 1_Exiqon is Cy3

value: M

tag: mitotic index

tag: anatomical site of primary tumor

value: IIC

tag: b-met

tag: time to b-met (days)

value: Died, No Melanoma

value: Natural Causes

tag: material


title: Primary Melanoma_033

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: age

value: Few

tag: ulceration status

value: IIIA

tag: follow-up time (months)


title: Primary Melanoma_028

description: 1_Exiqon is Cy3

value: Present

tag: histotype

value: Nodular

tag: Stage

value: IV

tag: recurrence

value: Y

tag: time to 1st recurrence (days)

value: DS

tag: last status

value: Died, With Melanoma

value: Melanoma


title: Primary Melanoma_027

description: 1_Exiqon is Cy3

value: F

tag: primary tumor thickness (mm)

value: Many

value: Extremity

value: N

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

tag: brain as isolated 1st site of recurrence

value: Alive, No Melanoma

tag: Cause of death


title: Primary Melanoma_095

description: 1_Exiqon is Cy3

tag: mitotic index

value: Absent

value: Acral Lentiginous

tag: anatomical site of primary tumor

value: IB

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)

value: Equal mixture of all samples


title: Primary Melanoma_021

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

value: M

tag: age

tag: ulceration status

value: IIIC

tag: material


title: Primary Melanoma_025

description: 1_Exiqon is Cy3

value: Present

tag: histotype

value: Superficial Spreading

value: Axial

tag: Stage

value: IIIB

tag: recurrence

tag: time to 1st recurrence (days)

value: RLN , RS

tag: follow-up time (months)


title: Primary Melanoma_024

description: 1_Exiqon is Cy3

tag: primary tumor thickness (mm)

value: Moderate

value: Desmoplastic

value: IIA

value: Y

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

value: RLN

tag: brain as isolated 1st site of recurrence

tag: last status


title: Primary Melanoma_022

description: 1_Exiqon is Cy3

tag: mitotic index

value: Few

tag: anatomical site of primary tumor

value: RS

value: N

tag: b-met

tag: time to b-met (days)

value: Alive, No Melanoma

tag: Cause of death


title: Primary Melanoma_020

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: age

tag: ulceration status

value: Absent

value: IIB

value: LR

tag: follow-up time (days)

value: Equal mixture of all samples


title: Primary Melanoma_019

description: 1_Exiqon is Cy3

value: F

tag: histotype

value: Superficial Spreading

tag: Stage

value: IA

tag: recurrence

tag: time to 1st recurrence (days)

value: DV

value: Died, With Melanoma

value: Melanoma

tag: material


title: Primary Melanoma_017

description: 1_Exiqon is Cy3

tag: primary tumor thickness (mm)

value: Present

value: Nodular

value: Axial

value: IIIB

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

tag: brain as isolated 1st site of recurrence

tag: follow-up time (months)


title: Primary Melanoma_018

description: 1_Exiqon is Cy3

value: M

tag: mitotic index

value: Many

tag: anatomical site of primary tumor

tag: b-met

tag: time to b-met (days)

tag: last status

value: Died, No Melanoma

value: Old Age


title: Primary Melanoma_016

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: age

tag: ulceration status

value: Extremity

value: IIB

value: Y

value: RLN , RS

value: N

tag: Cause of death


title: Primary Melanoma_015

description: 1_Exiqon is Cy3

value: Few

tag: histotype

value: Acral Lentiginous

tag: Stage

value: IIC

tag: recurrence

tag: time to 1st recurrence (days)

tag: follow-up time (days)

value: Equal mixture of all samples


title: Primary Melanoma_029

description: 1_Exiqon is Cy3

tag: primary tumor thickness (mm)

value: Moderate

value: Present

value: IIIC

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

value: DV

tag: brain as isolated 1st site of recurrence

value: Died, With Melanoma

value: Melanoma

tag: material


title: Primary Melanoma_012

description: 1_Exiqon is Cy3

value: M

tag: mitotic index

value: Absent

tag: anatomical site of primary tumor

value: IB

value: RLN

tag: b-met

tag: time to b-met (days)

tag: follow-up time (months)


title: Primary Melanoma_011

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: age

tag: ulceration status

value: Nodular

value: Axial

value: Y

value: DS

tag: last status


title: Primary Melanoma_010

description: 1_Exiqon is Cy3

value: Many

tag: histotype

tag: Stage

tag: recurrence

tag: time to 1st recurrence (days)

value: N

tag: Cause of death


title: Primary Melanoma_026

description: 1_Exiqon is Cy3

value: F

tag: primary tumor thickness (mm)

value: Few

value: Acral Lentiginous

value: Extremity

value: IIA

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

value: RLN , RS

tag: brain as isolated 1st site of recurrence

tag: follow-up time (days)

value: Equal mixture of all samples


title: Primary Melanoma_009

description: 1_Exiqon is Cy3

tag: mitotic index

value: Moderate

tag: anatomical site of primary tumor

value: IIIA

tag: b-met

tag: time to b-met (days)

value: Alive, No Melanoma

tag: material


title: Primary Melanoma_007

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

value: M

tag: age

tag: ulceration status

value: Absent

value: DV

tag: follow-up time (months)

value: Died, With Melanoma

value: Melanoma


title: Primary Melanoma_023

description: 1_Exiqon is Cy3

value: Many

tag: histotype

value: Nodular

tag: Stage

value: IIB

tag: recurrence

tag: time to 1st recurrence (days)

tag: last status


title: Primary Melanoma_006

description: 1_Exiqon is Cy3

tag: primary tumor thickness (mm)

value: Few

value: Desmoplastic

value: Y

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

value: RLN ,RS

tag: brain as isolated 1st site of recurrence

value: N

tag: Cause of death


title: Primary Melanoma_005

description: 1_Exiqon is Cy3

tag: mitotic index

tag: anatomical site of primary tumor

value: Axial

value: DS

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)

value: Died, No Melanoma

value: Prostate Cancer

value: Equal mixture of all samples


title: Patient tumor samples

status: Public on Jan 27 2015

type: SRA

city: Salt Lake City

first: Mumtahena

last: Rahman

state: UT

address: 20 South 2030 East, Rm 420

department: Biomedical Informatics

institute: University of Utah

description:
Please note that the samples were sequenced using Illumina Genome Analyzer or Illumina HiSeq 2000 (https://wiki.nci.nih.gov/display/TCGA/RNASeq+Version+2).
7706 tumor samples data [release date: 1/27/2015], 9264 tumor samples data [release date: 6/1/2015]

library_source: transcriptomic

data_processing:
Alignment and quantification with R open source package "Rsubread" v 1.14.2
FPKM normalization with R open source packages edgeR and limma
TPM normalization from the FPKM values.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Tab delimited text files containing integer based raw gene counts for 9264 tumor samples in TCGA_24.Illumina.tumor_Rsubread_FeatureCounts.txt, FPKM values in TCGA_24.Illumina.tumor_Rsubread_FPKM.txt and TPM values in PANCAN24.Illumina.tumor_Rsubread_TPM.txt. Tab delimited txt file containing all 548 clinical variables for 9264 samples in TCGA_24_548_Clinical_Variables_9264_Samples.txt. In addition, Tab delimited text file containing integer based raw gene counts, FPKM and TPM values for 741 normal samples in TCGA_24.Illumina.normal_Rsubread_FeatureCounts.txt, TCGA_24.Illumina.normal_Rsubread_FPKM.txt and TCGA_24.Illumina.normal_Rsubread_TPM.txt respectively.

source_name: All 7706 or 9264 samples have been combined to create the processed matrix files

extract_protocol: Please refer to TCGA Genome Characterization Center extraction and library contruction protocol.

tag: tissue type

value: Tumor


title: Primary Melanoma_004

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

value: M

tag: age

value: Moderate

tag: ulceration status

value: Absent

value: Superficial Spreading

value: Extremity

value: IB

tag: follow-up time (months)

value: Alive, No Melanoma

tag: material


title: Primary Melanoma_014

description: 1_Exiqon is Cy3

value: F

tag: primary tumor thickness (mm)

value: Present

tag: histotype

value: Nodular

tag: Stage

value: IIC

tag: recurrence

tag: time to 1st recurrence (days)

tag: last status

value: Died, Melanoma Status Unknown

value: Unknown


title: Primary Melanoma_013

description: 1_Exiqon is Cy3

tag: mitotic index

value: Many

tag: anatomical site of primary tumor

value: Axial

value: IIIA

value: Y

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

value: RLN

tag: brain as isolated 1st site of recurrence

value: N

value: Died, With Melanoma

tag: Cause of death

value: Melanoma


title: Primary Melanoma_002

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

value: M

value: Absent

value: Superficial Spreading

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)

value: Equal mixture of all samples


title: Primary Melanoma_001

description: 1_Exiqon is Cy3

value: F

tag: age

tag: primary tumor thickness (mm)

value: Moderate

tag: ulceration status

value: Present

value: Extremity

value: IIIB

value: DV

tag: follow-up time (months)

tag: material


title: Primary Melanoma_008

description: 1_Exiqon is Cy3

value: Many

tag: histotype

value: Nodular

tag: Stage

value: IIC

tag: recurrence

tag: time to 1st recurrence (days)

value: RS

tag: last status

value: Died, No Melanoma

value: Adenocarcinoma


title: Primary Melanoma_003

description: 1_Exiqon is Cy3

tag: mitotic index

tag: anatomical site of primary tumor

value: IIB

value: Y

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

value: RLN

tag: brain as isolated 1st site of recurrence

value: N

value: Burns


title: BM-CD138+, diagnosis (MM90)

status: Public on Dec 23 2014

city: Bologna

first: Carolina

last: Terragna

address: Via Massarenti, 9

department: Department of Experimental, Diagnostic and Specialty Medicine - DIMES

country: Italy

institute: Institute of Hematology "L.A.Seràgnoli"

description: BM-CD138+, diagnosis

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on U133 Plus2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Array Scanner 7G

data_processing: The data were analyzed with Partek Genomics Suite 6.6, using RMA as normalization and summarization

source_name: BM-CD138+ cell fraction obtained from newly diagnosed Multiple Myeloma patient

label_protocol: Samples with at least 30ng/uL RNA were labelled for gene expression profiling, using the Affymetrix One-cycle Gene Chip microarray system, according to the standard Affymetrix procedures.

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

treatment_protocol: Pre-treatment plasma cells (PC) were purified from mononuclear bone marrow cells obtained by Ficoll-Hypaque density gradient centrifugation using anti-CD138 micro beads on an AutoMacs Magnetic Cell Separator (MACS system, Miltenyi Biotec, Auburn, CA). CD138+ cell fractions were than stored at -80°C in guanidium thiocyanate, until use.

tag: cell type

tag: disease state

value: multiple myeloma

tag: neuropathy > 2

value: no


title: MCF7colonies_cisplatin_1

status: Public on Jan 30 2015

city: New Haven

first: Kohei

last: Kume

state: CT

address: 300 George St

department: Center of Molecular and Cellular Oncology

institute: Yale University

description: Gene expression in bulk human cancer cell colonies emerged in the presence of cisplatin

hyb_protocol: 600 ng 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 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression 8x60K Microarray Kit (G4851A) 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 (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028004_D_F_20110819) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Breast cancer cell, drug-tolerant colony, 13-days-after dissemination

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy kit (QIAGEN) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: MCF7 cells were diluted to single cell suspensions, and seeded in the presence or absence of 0.8 uM cisplatin at low density (8 cells/cm^2). Colonies were collected 13 days after dissemination.

tag: cell line

tag: gender

value: female

tag: age (years)


title: BM-CD138+, diagnosis (MM97)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM98)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM96)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM94)

description: BM-CD138+, diagnosis


title: MCF7colonies_cisplatin_2


title: BM-CD138+, diagnosis (MM88)

description: BM-CD138+, diagnosis

value: yes


title: BM-CD138+, diagnosis (MM91)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM86)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM83)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM93)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM57)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM72)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM95)

description: BM-CD138+, diagnosis


title: MCF7colonies_untreated_2

description: Gene expression in bulk human cancer cell colonies

source_name: Breast cancer cell, colony, 13-days-after dissemination


title: BM-CD138+, diagnosis (MM59)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM85)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM92)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM89)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM56)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM48)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM50)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM49)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM44)

description: BM-CD138+, diagnosis


title: MCF7colonies_untreated_1

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).


title: BM-CD138+, diagnosis (MM55)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM43)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM40)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM34)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM31)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM42)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM47)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM39)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM41)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM37)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM36)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM32)

description: BM-CD138+, diagnosis


title: Primary Melanoma_032

description: 1_Exiqon is Cy3

tag: identifier

value: F

tag: age

tag: primary tumor thickness (mm)

value: Moderate

tag: ulceration status

value: Present

value: Superficial Spreading

value: Axial

value: IIIB

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)

tag: follow-up time (months)

value: Died, With Melanoma

tag: Cause of death

value: Melanoma

tag: material

value: Equal mixture of all samples


title: BM-CD138+, diagnosis (MM22)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM33)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM30)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM21)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM35)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM38)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM28)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM167)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM20)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM168)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM165)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM162)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM158)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM164)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM19)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM159)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM155)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM161)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM156)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM153)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM15)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM152)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM150)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM148)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM145)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM163)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM166)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM157)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM160)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM144)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM151)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM149)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM136)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM141)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM154)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM143)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM139)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM147)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM140)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM134)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM138)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM146)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM137)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM135)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM130)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM131)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM128)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM133)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM13)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM132)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM126)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM14)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM129)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM124)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM123)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM125)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM121)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM108)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM115)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM107)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM118)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM120)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM119)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM117)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM113)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM105)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM112)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM102)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM08)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM106)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM110)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM111)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM114)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM101)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM104)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM07)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM100)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM103)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM06)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM02)

description: BM-CD138+, diagnosis


title: BM-CD138+, diagnosis (MM05)

description: BM-CD138+, diagnosis


title: CVC d25-1

status: Public on Oct 10 2014

city: Rotterdam

first: Jeroen

last: van de Peppel

address: 's Gravendijkwal 230

country: Netherlands

institute: ErasmusMC

description: Coronary derived Vascular Smooth Muscle Cells cultured in osteogenic differentiation medium, day 25, replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was background subtracted, vst transformation and a quantile normalization was applied. Probes that were detected at least 3 times in the experiments (illumina detection p-value <0.01; independently for MSC and VSMC), were considered to be expressed and further analyzed for differential expression using Limma.

label_protocol: cDNA and Biotinylated cRNA were prepared with the Illumina Totalprep RNA Amplification kit (Ambion)

growth_protocol: DMEM, 20mM HEPES, strep/pen, 1.8 mM CaCl2, 10% FCS

extract_protocol: Total RNA extracted using Trizol (invitrogen)

treatment_protocol: Osteogenic differentiation medium: 5 mM beta-glycerophosphate, 100 nM dexamethasone, 0.1 mM Vitamin C

value: Female

tag: age (y)

tag: source tissue

value: Coronary Artery

value: Coronary derived Vascular Smooth Muscle cells

tag: time

value: day 25

tag: treatment

value: cultured in osteogenic differentiation medium day 25


title: CVC d25-3

description: Coronary derived Vascular Smooth Muscle Cells cultured in osteogenic differentiation medium, day 25, replicate 3

tag: cell type


title: CVC d12-3

description: Coronary derived Vascular Smooth Muscle Cells cultured in osteogenic differentiation medium, day 12, replicate 3

tag: gender

value: day 12

value: cultured in osteogenic differentiation medium day 12


title: CVC d8-3

description: Coronary derived Vascular Smooth Muscle Cells cultured in osteogenic differentiation medium, day 8, replicate 3

value: day 8

value: cultured in osteogenic differentiation medium day 8


title: CVC d12-2

description: Coronary derived Vascular Smooth Muscle Cells cultured in osteogenic differentiation medium, day 12, replicate 2


title: VSMC d0-3

description: Coronary derived Vascular Smooth Muscle Cells cultured undifferentiated day 0, replicate 3

value: day 0

value: undifferentiated day 0


title: CVC d8-1

description: Coronary derived Vascular Smooth Muscle Cells cultured in osteogenic differentiation medium, day 8, replicate 1


title: BM-CD138+, diagnosis (MM142)

description: BM-CD138+, diagnosis

tag: disease state

value: multiple myeloma

tag: neuropathy > 2

value: no


title: Osteoblasts d25-1

description: Bone marrow derived Mesenchymal Stem cells cultured in osteogenic differentiation medium, day 25, replicate 1

value: Male

value: Bone Marrow


title: CVC d8-2

description: Coronary derived Vascular Smooth Muscle Cells cultured in osteogenic differentiation medium, day 8, replicate 2


title: Osteoblasts d12-1

description: Bone marrow derived Mesenchymal Stem cells cultured in osteogenic differentiation medium, day 12, replicate 1


title: CVC d25-2

description: Coronary derived Vascular Smooth Muscle Cells cultured in osteogenic differentiation medium, day 25, replicate 2


title: Osteoblasts d8-2

description: Bone marrow derived Mesenchymal Stem cells cultured in osteogenic differentiation medium, day 8, replicate 2


title: Osteoblasts d8-1

description: Bone marrow derived Mesenchymal Stem cells cultured in osteogenic differentiation medium, day 8, replicate 1


title: Osteoblasts d2-2

description: Bone marrow derived Mesenchymal Stem cells cultured in osteogenic differentiation medium, day 2, replicate 2

value: day 2

value: cultured in osteogenic differentiation medium day 2


title: Osteoblasts d25-2

description: Bone marrow derived Mesenchymal Stem cells cultured in osteogenic differentiation medium, day 25, replicate 2


title: Osteoblasts d8-3

description: Bone marrow derived Mesenchymal Stem cells cultured in osteogenic differentiation medium, day 8, replicate 3


title: Osteoblasts d12-3

description: Bone marrow derived Mesenchymal Stem cells cultured in osteogenic differentiation medium, day 12, replicate 3


title: Osteoblasts d25-3

description: Bone marrow derived Mesenchymal Stem cells cultured in osteogenic differentiation medium, day 25, replicate 3


title: CVC d12-1

description: Coronary derived Vascular Smooth Muscle Cells cultured in osteogenic differentiation medium, day 12, replicate 1

value: Female


title: VSMC d0-4

description: Coronary derived Vascular Smooth Muscle Cells cultured undifferentiated day 0, replicate 4

value: Coronary Artery


title: MSC d0-2

description: Bone marrow derived Mesenchymal Stem cells cultured undifferentiated day 0, replicate 2


title: MSC d0-4

description: Bone marrow derived Mesenchymal Stem cells cultured undifferentiated day 0, replicate 4


title: Osteoblasts d2-1

description: Bone marrow derived Mesenchymal Stem cells cultured in osteogenic differentiation medium, day 2, replicate 1


title: VSMC d0-1

description: Coronary derived Vascular Smooth Muscle Cells cultured undifferentiated day 0, replicate 1

value: Coronary derived Vascular Smooth Muscle cells


title: MSC d0-3

description: Bone marrow derived Mesenchymal Stem cells cultured undifferentiated day 0, replicate 3


title: Osteoblasts d2-3

description: Bone marrow derived Mesenchymal Stem cells cultured in osteogenic differentiation medium, day 2, replicate 3


title: CVC d2-2

description: Coronary derived Vascular Smooth Muscle Cells cultured in osteogenic differentiation medium, day 2, replicate 2


title: CVC d2-1

description: Coronary derived Vascular Smooth Muscle Cells cultured in osteogenic differentiation medium, day 2, replicate 1


title: Osteoblasts d12-2

description: Bone marrow derived Mesenchymal Stem cells cultured in osteogenic differentiation medium, day 12, replicate 2


title: CVC d2-3

description: Coronary derived Vascular Smooth Muscle Cells cultured in osteogenic differentiation medium, day 2, replicate 3


title: VSMC d0-2

description: Coronary derived Vascular Smooth Muscle Cells cultured undifferentiated day 0, replicate 2


title: MSC d0-1

description: Bone marrow derived Mesenchymal Stem cells cultured undifferentiated day 0, replicate 1


title: F1 256_UD:0000039 38E-L

status: Public on Aug 13 2014

city: S. Michele a/Adige

first: Giulia

last: Malacarne

state: Trento

address: Via Edmund Mach,1

department: Genomics and Biology of Fruit Crops Department

institute: Edmund Mach Foundation

description: Gene expression data from berry skin at stage UD:0000039 38E-L of a low flavonoid producer

hyb_protocol: Following fragmentation, 10 mg of cRNAs were hybridized on GeneChip® GrapeGena520510F Arrays for 16 hr at 45°C. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G System.

data_processing: Robust Multi-array Analysis (RMA) algorithm was used for background correction, normalization and expression levels summarization (Irizarry et al., 2003). Probesets with significant differential expression (DEPs) between LFPs and HFPs were selected in two steps and under the assumption that the four individuals of the LFPs and HFPs groups can be treated as biological replicates (pseudoreplicates). Step 1: within each group (LFPs and HFPs), the data were analyzed through pairwise comparisons of developmental stages (PV vs. VER, PV vs. MAT and VER vs. MAT). Differential expression analysis was performed with the Bayes t-statistics from LIMMA (Linear Models for Microarray Data), and p-values were corrected for multiple testing using the Benjamini-Hochberg method (Benjamini and Hochberg, 1995). Three lists of DEPs for each group were thus obtained (with a False Discovery Rate (FDR) < 5% and a cut-off of 2-fold change (FC) between each pair of stages). Step 2: the lists of DEPs were then compared between LFPs and HFPs to provide a final list of probesets either exclusively modulated in LFPs or in HFPs, or modulated in both groups but with low correlation (-0.5 > (logFCLFPs - logFCHFPs) pairwise comparison > 0.5).

organism: Vitis vinifera

source_name: F1 256_exocarp_UD:0000039 38E-L_low flavonoid producer

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 4 mg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The population derived from 'Syrah' x 'Pinot Noir' was obtained at Edmund Mach Foundation (FEM, San Michele all'Adige, Italy, 46°18' N, 11°13' E). All the plants were grown at the experimental field "Giaroni" of FEM, grafted on the rootstock Kober 5BB and trained according to the Guyot system. One representative sample for each genotype at each developmental stage was collected in the early morning. To be more representative of the canopy, berries were collected both from a cluster on the shady side and from a cluster on the sunny side. From the second stage (35E-L), the collected berries were dissected into skin, flesh and seeds and then skins were frozen in nitrogen liquid and stored at -80°C till transcriptome analysis.

extract_protocol: Total RNA was extracted from frozen berries using the Spectrum Plant Total RNA Kit  (Sigma Aldrich)

tag: genotype

value: F1 256 (Syrah x Pinot Noir cross)

tag: organism part

tag: developmental stage

tag: metabolic profile

value: low flavonoid producer

tag: growth media

value: field soil


title: F1 16_UD:0000039 38E-L

description: Gene expression data from berry skin at stage UD:0000039 38E-L of a high flavonoid producer

source_name: F1 16_exocarp_UD:0000039 38E-L_high flavonoid producer

value: F1 16 (Syrah x Pinot Noir cross)

value: high flavonoid producer


title: F1 260_UD:0000036 35E-L

description: Gene expression data from berry skin at stage UD:0000036 35E-L of a low flavonoid producer

source_name: F1 260_exocarp_UD:0000036 35E-L_low flavonoid producer

value: F1 260 (Syrah x Pinot Noir cross)


title: F1 223_UD:0000036 35E-L

description: Gene expression data from berry skin at stage UD:0000036 35E-L of a high flavonoid producer

source_name: F1 223_exocarp_UD:0000036 35E-L_high flavonoid producer

value: F1 223 (Syrah x Pinot Noir cross)


title: PN_UD:0000039 38E-L

source_name: PN_exocarp_UD:0000039 38E-L_low flavonoid producer

value: Pinot Noir (clone ENTAV 115)


title: F1 63_UD:0000039 38E-L

source_name: F1 63_exocarp_UD:0000039 38E-L_high flavonoid producer

value: F1 63 (Syrah x Pinot Noir cross)


title: F1 223_UD:0000039 38E-L

source_name: F1 223_exocarp_UD:0000039 38E-L_high flavonoid producer


title: F1 256_UD:0000034 33E-L

description: Gene expression data from whole berry at stage UD:0000034 33E-L of a low flavonoid producer

source_name: F1 256_fruit_UD:0000034 33E-L_low flavonoid producer


title: F1 260_UD:0000039 38E-L

source_name: F1 260_exocarp_UD:0000039 38E-L_low flavonoid producer


title: PN_UD:0000036 35E-L

source_name: PN_exocarp_UD:0000036 35E-L_low flavonoid producer


title: F1 256_UD:0000036 35E-L

source_name: F1 256_exocarp_UD:0000036 35E-L_low flavonoid producer


title: F1 56_UD:0000039 38E-L

source_name: F1 56_exocarp_UD:0000039 38E-L_high flavonoid producer

value: F1 56 (Syrah x Pinot Noir cross)


title: F1 16_UD:0000036 35E-L

source_name: F1 16_exocarp_UD:0000036 35E-L_high flavonoid producer


title: F1 56_UD:0000034 33E-L

description: Gene expression data from whole berry at stage UD:0000034 33E-L of a high flavonoid producer

source_name: F1 56_fruit_ UD:0000034 33E-L_high flavonoid producer


title: F1 223_UD:0000034 33E-L

source_name: F1 223_fruit_UD:0000034 33E-L_high flavonoid producer


title: F1 260_UD:0000034 33E-L

source_name: F1 260_fruit_UD:0000034 33E-L_low flavonoid producer


title: F1 63_UD:0000036 35E-L

source_name: F1 63_exocarp_UD:0000036 35E-L_high flavonoid producer


title: F1 64_UD:0000036 35E-L

source_name: F1 64_exocarp_UD:0000036 35E-L_low flavonoid producer

value: F1 64 (Syrah x Pinot Noir cross)


title: PN_UD:0000034 33E-L

source_name: PN_fruit_UD:0000034 33E-L_low flavonoid producer


title: F1 63_UD:0000034 33E-L

source_name: F1 63_fruit_UD:0000034 33E-L_high flavonoid producer


title: F1 16_UD:0000034 33E-L

source_name: F1 16_fruit_UD:0000034 33E-L _high flavonoid producer


title: F1 56_UD:0000036 35E-L

source_name: F1 56_exocarp_UD:0000036 35E-L_high flavonoid producer


title: 54558302

status: Public on Nov 09 2013

city: Vairao

first: Antonio

last: Muñoz

state: Porto

address: Rua Padre Armando Quintas, 7 (Campus Agrario)

country: Portugal

institute: CIBIO-InBIO (University of Porto)

description: Shoots from Olea europaea taken at 33 months of growth

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

molecule: polyA RNA

organism: Olea europaea

source_name: 33-months c

label_protocol: PolyA RNA was obtained and labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com

growth_protocol: 21 seedlings originating from open pollination of olive cultivar ‘Arbequina’ were grown in a greenhouse in Centro IFAPA “Churriana” Málaga, Spain. At the sixth month the apical shoot was removed and kept for genomic analysis. Any lateral shoot was removed to force the growth along just one axis.

extract_protocol: 1 cm long apical-shoot tips of olive seedlings were taken every three months, starting at the sixth month and frozen in liquid nitrogen. Tissues were homogenized with a mixer mill MM 400 (Retsch). Total RNA was extracted and purified from samples by TRIzol® Reagent (Invitrogen Corporation, Carlsbad, CA, USA) and treated with DNase I RNase free (Roche, Basel, Switzerland). Finally, total RNA was purified with the RNeasy Mini Kit® (Quiagen) and quantified by spectrophotometry with a Take3 Synergy HT spectrophotometer (Bio-Tek) and stored at -80°C until used.

treatment_protocol: Every three months a new (1 cm long) apical-shoot tip was taken, which included the meristem down to two very small young leaves. When the apical-shoot tip is removed the two lateral buds immediately below are activated, one of them is removed, and the other one becomes the new apical-shoot tip. Seedlings reaching 50 nodes or 1 m high were allowed to form a top canopy. From then, the samples were taken from apical shoots of higher branches.

tag: cultivar

value: Arbequina

tag: tissue

value: apical shoot

tag: collection time

value: 33 months


title: F1 64_UD:0000034 33E-L

source_name: F1 64_fruit_UD:0000034 33E-L_low flavonoid producer


title: 54557102

description: Shoots from Olea europaea taken at 21 months of growth

source_name: 21-months a

value: 21 months


title: 54557202

description: Shoots from Olea europaea taken at 6 months of growth

value: 6 months


title: 54556602

description: Shoots from Olea europaea taken at 27 months of growth

source_name: 27-months a

value: 27 months


title: 54557902

source_name: 21-months c


title: 3TG-A-CxF1

status: Public on Sep 16 2013

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: R packages: lumi, genefilter, mpm

organism: Mus musculus

source_name: C57BL/6 Brain Frontal Cortex 356-A-CxF1

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from brain samples using phenol-extraction standard protocol.

tag: strain

value: Brain Frontal Cortex


title: 54556702

description: Shoots from Olea europaea taken at 18 months of growth

source_name: 18-months b

value: 18 months


title: 54556202

description: Shoots from Olea europaea taken at 30 months of growth

value: 30 months