title: T cells_empty virus transduced_stimulated_6 hours_rep2

city: Chicago

first: yuanyuan

last: zha

state: IL

department: Department of Pathology

institute: University of Chicago

description:
CD4 T cell clones transfected with empty virus then washed and expanded then stimulated for 6 hours and evaluated
exp2_EV 6; EV 6-2

hyb_protocol: After cleanup of cRNA with Genechip sample cleanup module, 20 µg of cRNA was fragmented in fragmentation buffer for 35 min at 94°C.  The fragmented cRNA (12 µg) was hybridized to Affymetrix MG 430 2.0 expression arrays for 16 h at 45°C and 60 rpm in an affymetrix hybridization oven 640.  Arrays were washed and stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution in an Affymetrix Fluidics Station 450 according to the Affymetrix GeneChip protocol.

scan_protocol: Arrays were washed and stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution in an Affymetrix Fluidics Station 450 according to the Affymetrix GeneChip protocol.  The arrays were scanned using the Affymetrix Gene Chip Scanner 3000 7G. CEL intensity files  generated by Gene Chip Operating Software v. 1.4 (MicroArray Suite 5.0) were used to extract and analyze data using dChip software (Harvard).

data_processing:
Array normalization and expression value calculation were performed uisng dchip_2020_01 (v.1.0.0.1).  Each analysis was done in duplicate utilizing different primary material treated with equivalent experimental conditions.  Arrays were normalized at the probe cell level by the invariant set normalization method to allow for comparison of expression values computed using the model-based method.
Measurement accuracy evaluated by standard error was used to compute 90% confidence intervals of fold changes in two sample and two-group comparisons (ie: EV to Cre comparison done twice and compared for consistency).  Increased or decreased expression of genes by more than 2-fold (lower confidence bound) are presented ['fold_change_data.txt' on Series records].

source_name: T cells_empty virus_stimulated 6hrs

label_protocol: Total RNA was processed to cDNA synthesis, cRNA synthesis, fragmentation, and hybridization to expression arrays according to Genechip Expression analysis technical manual (Affymetrix, Inc).  Briefly, 2 ug of total RNA was used to synthesize double-stranded cDNA using the Genechip Expression 3´ -Amplification one cycle cDNA Synthesis kit (Affymetrix).  First strand cDNA synthesis was primed with a oligo(dT)24 primer that contains T7 promoter sequences.  From the cDNA purified by Genechip sample cleanup module (Affymetrix), biotin-labeled antisense RNA (cRNA) was synthesized using Genechip Expression 3´ amplification IVT labeling kit (Affymetrix).

growth_protocol: For adenoviral transduction, peripheral CAR Tg x PTENflox/flox T cells (total, CD4+, or CD8+) were isolated from splenocytes by negative selection with MACS antibody cocktails and magnetic beads (Miltenyi Biotec).  Transduced CAR Tg x PTENflox/flox Th1 clones were rested overnight and then passaged under normal conditions, and 9 days later clones were harvested for experiments.

extract_protocol: Total RNA was isolated by TRIzol reagent protocol (Invitrogen), followed by RNeasy Mini column purification (QIAGEN) according to manufacturer's instructions.  RNA integrity was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies).  The concentration/purity was determined using a NanoDrop 1000 (Thermo Scientific).  All RNA samples used for hybridization had an OD260/280 and OD260/230 ratio >1.8 and RIN (RNA Integrity Number) > 8.0.

treatment_protocol: T cells were activated with beads (Dynal) coated overnight at 4 degrees with anti-CD3 (145-2C11) at 1 microg/ml and anti-CD28 (PV1) at 1 microg/ml.  For stimulation, T cells were incubated with the antibody-coated beads in 24 well plates at 1x10 6 cells/well in 1 ml for 6 hours at 37°C at a 5:1 bead to T cell ratio.

tag: strain background

tag: genotype/variation

value: CAR Tg x PTENflox/flox

tag: cell type

value: peripheral CD4 T cells

tag: transduced with

value: adeno-EV (empty virus) at x100 MOI for 1h

tag: stimulated with

value: anti-CD3/anti-CD28 mAb-coated beads for 6hrs


title: T cells_Cre virus transduced_stimulated_6 hours_rep2

status: Public on Feb 01 2013

type: RNA

country: USA

description:
CD4 T cell clones transfected with Cre virus then washed and expanded then stimulated for 6 hours then evaluated
exp2_Cre6; Cre 6-2

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: T cells_Cre virus_stimulated 6hrs

value: adeno-Cre at x100 MOI for 1h


title: T cells_Cre virus transduced_stimulated_6 hours_rep1

description:
CD4 T cell clones transfected with Cre virus then washed and expanded then stimulated for 6 hours then evaluated
exp1_Cre6; Cre6-1


title: Glioma-EORTC26951 A1372_14.CEL

city: Rotterdam

first: Pim

last: French

address: Dr Molewaterplein 50

department: Neurology

country: Netherlands

institute: Erasmus MC

description: Abbreviations: IGS: intrinsic glioma subtype; Trt: treatment; SS: survival in years; C: classical; P: proneural; M: mesenchymal; N:neural

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA

organism: Homo sapiens

source_name: Glioma, clinical trial RT v RT+PCV

label_protocol: cDNA synthesis and cRNA labeling was done using the alternative protocol for one-cycle cDNA synthesis.Biotin-labeled cRNA was generated using the ENZO Highyield RNA transcript labeling kit (ENZO Life Sciences, Inc., Farmingdale, NY). Affymetrix (Santa Clara, CA)

extract_protocol: Trizol

tag: tissue

value: glioma

tag: sample

tag: igs

tag: tcga classification

value: C

tag: tissue type

value: FFPE

tag: 1p19q loh

value: no loss

tag: egfr

value: wt

tag: mgmt

value: meth

tag: trt

value: RT

tag: ss (y)

tag: event

value: alive

tag: age

tag: Sex

value: F

tag: original diagnosis

value: AOD

tag: review diagnosis

tag: experiment

value: pt 1


title: Forskolin rep1

city: Berlin

first: Ilya

last: Chuykin

address: Robert-Rossle str 10

department: Molecular Biology of Peptide Hormones

country: Germany

institute: Max-Delbruck Center for Molecular Medicine

description: ILC--10-Forskolin-070610-RatGe-St1-0.CEL

hyb_protocol: labelled ssDNA was hybridized with Hybridization Wash and Stain kit (Affymetrix).

scan_protocol: Gene Chip Scanner 7G, command console software AGCC

data_processing: Arrays have been quantile-normalize with respect to the probe GC content using the RMA algorithm (GC contend adjustment, RMA background correction and mean probe set summarization) using Partek Genomic Suite (v.6.3). After normalization the arrays have been checked for outlier using the principal component analysis using a correlation dispersion matrix and normalized Eigenvector scaling. Differential expression of summarized gene level expression was calculated using the Partek ANOVA statistic followed by a FDR multiple testing correction. Differences between individual pairs ofconditions have been calculated using the LSD post hoc test.

organism: Rattus norvegicus

source_name: Rat XEN cells cultured 1 day with Forskolin

label_protocol: ssDNA was labelled usind WT terminal labeling kit (Affymetrix)

extract_protocol: total RNA were extracted by RNA mini kit (Qiagen), residual genomic DNA was removed by DNAse I treatment (Qiagen).

tag: strain

value: Fisher

tag: cell type

value: Rat XEN cells

tag: treated with

value: 10 μM Forskolin


title: T cells_empty virus transduced_stimulated_6 hours_rep1

description:
CD4 T cell clones transfected with empty virus then washed and expanded then stimulated for 6 hours and evaluated
exp1_Ev6; Ev6-1

tag: strain background

tag: genotype/variation

value: CAR Tg x PTENflox/flox

value: peripheral CD4 T cells

tag: transduced with

value: adeno-EV (empty virus) at x100 MOI for 1h

tag: stimulated with


title: Forskolin rep2

description: ILC--11-Forskolin-070610-RatGe-St1-0.CEL


title: Glioma-EORTC26951 A1372_13.CEL

tag: tissue

value: glioma

tag: sample

tag: igs

tag: tcga classification

tag: tissue type

tag: idhmut

value: mut

tag: 1p19q loh

tag: egfr

value: deceased

value: M


title: Glioma-EORTC26951 A1372_09.CEL

value: C

value: FFPE

value: no loss

value: wt

tag: mgmt

tag: trt

tag: ss (y)

tag: event

tag: age

tag: Sex

tag: original diagnosis

value: AOA

tag: review diagnosis

value: LGG


title: Glioma-EORTC26951 A1372_06.CEL

value: FF

value: amp

value: meth

value: RT/PCV

tag: experiment

value: pt 1


title: Glioma-EORTC26951 A1372_12.CEL

tag: tissue

value: AOD


title: Glioma-EORTC26951 A1372_05.CEL

tag: sample

value: RT


title: Glioma-EORTC26951 A1372_10.CEL

value: glioma

tag: igs

value: LOH

value: alive

value: F


title: Glioma-EORTC26951 A1372_08.CEL

tag: tcga classification

value: C

value: mut

value: M


title: Forskolin rep3

tag: strain

value: Fisher

tag: cell type

value: Rat XEN cells

tag: treated with

value: 10 μM Forskolin


title: Glioma-EORTC26951 A1372_02.CEL

tag: tissue type

value: FFPE

tag: idhmut

value: wt

tag: 1p19q loh

value: no loss

tag: egfr

value: deceased


title: Glioma-EORTC26951 A1372_03.CEL

value: amp

tag: mgmt

value: meth

tag: trt

value: RT/PCV

tag: ss (y)

tag: event

value: pt 1


title: CHIR_Forskolin rep3

description: ILC--09-CHIR_Forskolin-070610-RatGe-St1-0.CEL

source_name: Rat XEN cells cultured 1 day with inhibitor of GSK3 kinase and 1 day with inhibitor of GSK3 kinase and Forskolin

value: 3 μM CHIR99021 and 10μM Forskolin (Sigma)


title: Glioma-EORTC26951 A1372_04.CEL

value: glioma

value: unmeth

value: RT

tag: age

tag: Sex

tag: original diagnosis

value: AOA

tag: review diagnosis


title: CHIR_Forskolin rep2

description: ILC--08-CHIR_Forskolin-070610-RatGe-St1-0.CEL


title: Glioma-EORTC26951 A1372_07.CEL

tag: tissue

tag: sample

tag: igs

value: M

value: GBM/AA

tag: experiment


title: Glioma-EORTC26951 A1372_11.CEL

tag: tcga classification

value: C


title: E2A-deficient DN2 replicate 3

first: Barbara

last: Kee

address: 924 East 57th Street

department: Pathology

hyb_protocol: Following fragmentation, 10 microg of cRNA was hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Chips were scanned using an Affymetrix GeneChip Scanner 3000. Chip target intensity was arbitrarily scaled to 100 before rendering CHP files.

data_processing: Expression values were calculated by RMA express (http://rmaexpress.bmbolstad.com/) using background adjustment and quantile normalization.

source_name: Sorted DN2 cells from fetal thymus

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix; Small Sample Labelling Protocol v.2, with the exception that the second round of in vitro transcription (IVT) was performed using Affymetrix GeneChip Expression 3 amplification kit.

extract_protocol: Cells were directly sorted into buffer RLT and RNA prepared using RNeasy Micro (Qiagen) according to manufacturer's instructions.

tag: genetic background

value: FVB

tag: cell type

tag: genotype

value: E2A deficient


title: 353051-1

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description:
balb pbs 7j-3
Date:2009/05/15

hyb_protocol: Agilent : 20000.0 ng at 53 degree_C during 24 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Interslide norm. : quantile, Intraslide norm. : none, Background norm. : none, Software used : onechannelgui --> VALUE data obtained from average signal.

source_name: balb pbs 7j-3

label_protocol: Invitrogen - Ulysis

extract_protocol: Chomzynski

tag: agent

value: PBS

tag: time point

value: lung

tag: strain

value: BALB/c


title: E2A-deficient DN2 replicate 2


title: E2A-deficient DN2 replicate 1


title: CHIR_Forskolin rep1

description: ILC--07-CHIR_Forskolin-070610-RatGe-St1-0.CEL

value: Fisher

value: Rat XEN cells

tag: treated with


title: CHIR rep3

source_name: Rat XEN cells cultured 2 days with inhibitor of GSK3 kinase

value: 3 μM CHIR99021 (Axon Medchem)


title: DN2 replicate 1

value: wild type


title: CHIR rep2


title: DN2 replicate 2


title: Control rep3

source_name: Rat XEN cells cultured without treatments


title: CHIR rep1


title: TGF beta1 treated for 96h #3

city: Birmingham

first: Gang

last: Liu

state: Alabama

address: 901 19TH ST S

department: Medicine

institute: University of Alabama at Birmingham

description:
Biological replicate 3 of 3. MRC-5 cells, TGF beta1 treated for 96h.
'1_Exiqon*.txt' and '0_Exiqon*.txt' represent the raw data for Hy3 and Hy5, respectively.

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA Array version 5th Generation (Exiqon, Denmark), which contains capture probes targeting all miRNAs for human, mouse or rat registered in the miRBASE version 15.0 at the Sanger Institute. The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria)

scan_protocol: 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. 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 8.0 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.

source_name: human lung fibroblasts MRC-5 cells

label_protocol: 1000 ng total RNA from sample and reference was labelled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer

growth_protocol: MEM containing 10% FBS, 37 degree and 5% CO2

extract_protocol: Total RNA extracted using Qiagen RNAeasy kit following manufacturer's instructions

treatment_protocol: After overnight serum starvation, cells were treat with TGF beta1 for 48 h or 96 h

tag: cell line

value: lung fibroblasts MRC-5

value: TGF beta1

tag: time

source_name: common reference (pooled total RNA from human lung fibroblasts MRC-5 cells that were untreated, treated with TGF beta1 for 48 and 96h)

tag: sample type

value: common reference (pooled total RNA of equal amount of the 9 samples)


title: HC-D-Healthy Control

city: Gainesville

first: Ashay

middle: Dilip

last: Bhatwadekar

state: FL

address: 1600 SW Archer Road

department: Pharmacology and Therapeutics

institute: University of Florida

hyb_protocol: Hybridizations were performed using standard Affymetrix protocol for 18 hrs at 45C

scan_protocol: Posthybridization washing and staining was performed by the Affymetrix FS450 fluidics station using manufacturer recommended protocols.  Arrays were scanned using a GeneChip Scanner 3000 7G

data_processing: Intensity Data was aligned and normalized by RMA using Rosetta Resolver

source_name: Peripheral blood CD34+ cells

label_protocol: NuGEN 50 ng input Ribo-SPIA amplification with biotin end labeling per manufactures recommendations.

growth_protocol: Fresh CD34+ cells were isolated from peripheral blood

extract_protocol: Total RNA from CD34 cells was extracted using Trizol followed by AffyNugen amplification, and the cDNA was probed to Human RSTA Affymetrix 2.0 chip. 1-5ng of total RNA was added to the initial reaction mix together with 250ng of pBR322 (Invitrogen). After the first round of IVT, the plasmid carrier was removed with DNase1 treatment and the product was purified using Qiagen MinElute Kit.

treatment_protocol: No treatment

value: Peripheral blood CD34+

tag: age

tag: disease state

value: healthy


title: Control rep2


title: DN2 replicate 3


title: HC-E-Healthy Control


title: Glioma-EORTC26951 A1372_01.CEL

tag: tissue

value: glioma

tag: tissue type

value: FFPE

tag: idhmut

value: wt

tag: 1p19q loh

value: no loss

tag: egfr

tag: mgmt

value: unmeth

tag: trt

value: RT/PCV

tag: ss (y)

tag: event

value: deceased

tag: Sex

value: M

tag: original diagnosis

value: AOA

tag: review diagnosis

value: AOD

value: pt 1


title: TGF beta1 treated for 96h #1

description:
Biological replicate 1 of 3. MRC-5 cells, TGF beta1 treated for 96h.
'1_Exiqon*.txt' and '0_Exiqon*.txt' represent the raw data for Hy3 and Hy5, respectively.

tag: cell line

tag: agent


title: TGF beta1 treated for 96h #2

description:
Biological replicate 2 of 3. MRC-5 cells, TGF beta1 treated for 96h.
'1_Exiqon*.txt' and '0_Exiqon*.txt' represent the raw data for Hy3 and Hy5, respectively.

tag: time

tag: sample type


title: HC-B-Healthy Control

tag: cell type

tag: age

tag: disease state


title: HC-A-Healthy Control


title: Control rep1

tag: strain

value: Fisher

value: Rat XEN cells


title: TGF beta1 treated for 48h #3

description:
Biological replicate 3 of 3. MRC-5 cells, TGF beta1 treated for 48h.
'1_Exiqon*.txt' and '0_Exiqon*.txt' represent the raw data for Hy3 and Hy5, respectively.

value: lung fibroblasts MRC-5

value: TGF beta1


title: TGF beta1 treated for 48h #2

description:
Biological replicate 2 of 3. MRC-5 cells, TGF beta1 treated for 48h.
'1_Exiqon*.txt' and '0_Exiqon*.txt' represent the raw data for Hy3 and Hy5, respectively.

value: common reference (pooled total RNA of equal amount of the 9 samples)


title: IR-C-Long standing diabetes with no complications

value: Peripheral blood CD34+

value: diabetes with no complications


title: T_SHG006-Mouse430_2, Ly6G-DC3

city: Toledo

first: Hironori

last: Matsushima

state: OH

address: 3000 Arlington Avenue Mail Stop 1021

department: Medical Microbiology and Immunology

institute: University of Toledo College of Medicine

description:
T_SHG006-Mouse430_2
Gene expression data of sorted Ly6G-DC from BM cultures.

hyb_protocol: Labeled cRNA (15.0 ug) was fragmented by ion-mediated hydrolysis and hybridized for 16hr at 45oC to Affymetrix Mouse Genome 430 2.0 short oligomer arrays, which detect approximately 44,000 mouse transcripts representing over 34,000 well-characterized mouse genes (Affymetrix, Santa Clara, CA). Arrays were washed and stained using a Fluidics Station 450 (Affymetrix) according to the manufacturer’s recommended procedures. The arrays were stained with phycoerythrein-conjugated streptavidin (Invitrogen, Carlsbad, CA).

scan_protocol: The fluorescence intensities were determined using a GCS 3000 7G high-resolution confocal laser scanner and AGCC software (Affymetrix).

data_processing: The scanned images were analyzed using Expression Console v2.0 software (Affymetrix). Quality control metrics for cRNA integrity, sample loading, and variations in staining were determined after background correction and signal summarization by MAS 5.0 statistical algorithms resident in GCOS and standardization of each array by global scaling the average of the fluorescent intensities of all genes on an array to a constant mean target intensity (TGT) of 250.

source_name: bone marrow, Ly6G- DC

label_protocol: RNA was processed and labeled according to standard RT-IVT methods. First- and-second strand cDNA were synthesized from 200 ng of total RNA using oligo-dT24-T7 (5’-GGC CAG TGA ATT GTA ATA CGA CTC ACT ATA GGG AGG CGG-3’) as primer and cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription for 16hr at 37oC, using the 3’ IVT Express cDNA/cRNA Synthesis and Labeling Kit (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions.

growth_protocol: Crude bone marrow cells were propagated from C57BL/6 mice. The cells were cultured at 37C in the presence of 10 ng/ml GM-CSF to generate CD11c+ DC populations. On day 6, CD11c+/MHC II+/Ly6G+ DC and CD11c+/MHC II+/Ly6G- DC were simultaneously sorted from the same cultures by FACSAria.

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

tag: tissue

value: bone marrow

value: CD11c+/MHC II+/Ly6G- dendritic cells


title: TGF beta1 treated for 48h #1

description:
Biological replicate 1 of 3. MRC-5 cells, TGF beta1 treated for 48h.
'1_Exiqon*.txt' and '0_Exiqon*.txt' represent the raw data for Hy3 and Hy5, respectively.


title: T_SHG007-Mouse430_2, Ly6G+DC3

description:
T_SHG007-Mouse430_2
Gene expression data of sorted Ly6G+DC from BM cultures.

source_name: bone marrow, Ly6G+ DC

value: CD11c+/MHC II+/Ly6G+ dendritic cells


title: T_SHG004-Mouse430_2, Ly6G-DC2

description:
T_SHG004-Mouse430_2
Gene expression data of sorted Ly6G-DC from BM cultures.


title: GN-A-Long standing diabetes with microvascular disease

value: diabetes with microvascular disease


title: GN-D-Long standing diabetes with microvascular disease


title: No treated control #3

description:
Biological replicate 3 of 3. MRC-5 cells, untreated.
'1_Exiqon*.txt' and '0_Exiqon*.txt' represent the raw data for Hy3 and Hy5, respectively.

value: untreated

value: control


title: GN-B-Long standing diabetes with microvascular disease


title: T_SHG003-Mouse430_2, Ly6G+DC2

description:
T_SHG003-Mouse430_2
Gene expression data of sorted Ly6G+DC from BM cultures.


title: No treated control #2

description:
Biological replicate 2 of 3. MRC-5 cells, untreated.
'1_Exiqon*.txt' and '0_Exiqon*.txt' represent the raw data for Hy3 and Hy5, respectively.


title: T_SHG002-Mouse430_2_2, Ly6G-DC1

description:
T_SHG002-Mouse430_2_2
Gene expression data of sorted Ly6G-DC from BM cultures.


title: T_SHG001-Mouse430_2_2, Ly6G+DC1

description:
T_SHG001-Mouse430_2_2
Gene expression data of sorted Ly6G+DC from BM cultures.


title: HC-C-Healthy Control

value: healthy


title: MM14

type: genomic

city: Liverpool

first: Sarah

last: Lake

address: 6th Floor, Duncan Building, Daulby Street

department: Molecular and Clinical Cancer Medicine

country: United Kingdom

institute: University of Liverpool

description: Genome-wide Human SNP 6.0 array

hyb_protocol: Hybridised to Affymetrix SNP 6.0 arrays according to manufacturers protocol

scan_protocol: Arrays were scanned using the Affymetrix GeneChip 3000 7G Scanner with the GeneChip Command Console software.

data_processing:
SNP genotypes and confidence scores were generated by fitting two-dimensional Gaussian functions to the SNP data using a customised Expectation-Maximisation algorithm (Birdseed, Affymetrix). Subsequent data analysis was performed using the Partek Genomics Suite of software (Partek Inc, St Louis, USA). In the absence of DNA from matched normal tissues, the 794 sample HapMap baseline, available from Partek, was used. Copy number variation (CNV) and loss of heterozygosity (LOH) workflows were used to determine CNVs and LOH. Cross-platform normalisations were performed to adjust for local GC content and remove “GC-waves” (based on the regression model approach of Diskin et al.)[26] The binary logarithm was generated for all data and used in genomic segmentation (p=0.00001).
CHP files generated using Affymetrix Genotyping Console software. Copy number data generated in Partek Genomics Suite,  adjustment was made for local GC content and the log2 value of data generated prior to Genomic Segmentation P value 0.00001.

molecule: genomic DNA

source_name: Uveal melanoma, monosomy chr 3, metastasising

label_protocol: Affymetrix Genome-Wide Human SNP Nsp/Sty 6.0 Assay following the manufacturers protocol with the exception of doubling the number of PCR reactions to compensate for using FFPE material.

extract_protocol: Qiagen DNeasy blood and tissue kit following FFPE protocol. Final purification using GenElute (Sigma) following the manaufacturer's protocol.

value: Uveal melanoma

tag: genotype

value: monosomy chr 3

tag: metastasis status

value: metastasising


title: IR-A-Long standing diabetes with no complications


title: MM15

description: Genome-wide Human SNP 6.0 array


title: No treated control #1

description:
Biological replicate 1 of 3. MRC-5 cells, untreated.
'1_Exiqon*.txt' and '0_Exiqon*.txt' represent the raw data for Hy3 and Hy5, respectively.


title: 252800510941-1

description: siControl exp#2

hyb_protocol: cRNA Agilent

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Feature extraction software. Interslide quantile normalization performed using the Limma package available from Bioconductor (http://www.bioconductor.org).

source_name: siControl exp#2

label_protocol: Agilent - Low RNA input QuickAmp

extract_protocol: miRNeasy Qiagen

tag: amount

tag: rin

value: C2C12 myoblastic cell line

tag: genotype/variation


title: MM10

description: Genome-wide Human SNP 6.0 array


title: 14269127 - N138 BR2 vs Col0 BR2

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

description: What are the structural and regulator genes regulated by MYB52 transcription factor?

hyb_protocol: Col0 BR2 Cy5 / N138 BR2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

source_name: Col0 BR2

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: stem - Media=soil hygrometry=70% Temperature=22°C/20°C Light=8h/24h

extract_protocol: Col0 BR2:12ug. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

value: wildtype

tag: ecotype

value: columbia

tag: developmental stage (boyes et al. plant cell 2001)

value: atmyb52 mutant


title: MM12

description: Genome-wide Human SNP 6.0 array


title: 252800510940-7

description: siControl exp#1

source_name: siControl exp#1


title: MM11

description: Genome-wide Human SNP 6.0 array


title: GN-E-Long standing diabetes with microvascular disease


title: 14269126 - Col0 BR2 vs N138 BR2

hyb_protocol: N138 BR2 Cy5 / Col0 BR2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: IR-D-Long standing diabetes with no complications (4.3ng 1st Round AMP)


title: 252800510941-2

description: siFxr1 exp#2

source_name: siFxr1 exp#2


title: MM13

description: Genome-wide Human SNP 6.0 array


title: GN-C-Long standing diabetes with microvascular disease


title: 14269125 - N138 BR1 vs Col0 BR1

hyb_protocol: Col0 BR1 Cy5 / N138 BR1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 BR1

extract_protocol: Col0 BR1:12ug. (Qiagen_RNeasy.pdf)


title: MM16

description: Genome-wide Human SNP 6.0 array


title: IR-E-Long standing diabetes with no complications (1.75ng 1st Round AMP)


title: 252800510958-5

description: C57 PBS-1

hyb_protocol: Agilent : 600.0 ng at 65 degree_C during 17 hours

data_processing: Feature extraction data processing (version 10.7.3.1)

source_name: C57 PBS-1

label_protocol:
Agilent - Low RNA input QuickAmp
amplification protocol: cRNA Agilent

value: PBS

value: lung

tag: amount in (µg)

tag: rin number


title: 252800510940-8

description: siFxr1 exp#1

source_name: siFxr1 exp#1

tag: cell line


title: MM8

description: Genome-wide Human SNP 6.0 array


title: MM7

description: Genome-wide Human SNP 6.0 array


title: 14269123 - Col0 BR1 vs N138 BR1

hyb_protocol: N138 BR1 Cy5 / Col0 BR1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14286679 - 9 days Repet3 vs 10 days Repet3

description: CDKs are major regulators of the mitotic as well as the meiotic cell cycle. In comparison with the mitotic cell cycle much less is known about the regulation of meiosis, especially in plants. One of the reasons for this is the very low abundance and the difficult accessibility of cell undergoing meiosis. We have developed a system to enrich for meiocytes. This will be the material with which we will search for CDK substrates in a biochemical approach. To first get an overview about the meiotic genes expressed in this system, we want to perform here a time series at four time points after the induction that leads to the synchronized development of meiocytes. The in the microarray identified genes, will then set the frame for the upcoming biochemical experiments.

hyb_protocol: 10 days Repet3 Cy5 / 9 days Repet3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 10 days Repet3

growth_protocol: aerial - Media=soil hygrometry=? Temperature=day 20/ night 18 Light=16 hours light/ 8 hours dark

extract_protocol: Kit AMBION MessageAmp aRNA Amplification #1750

treatment_protocol: Name:Dexamethasone 10days - time course study - compound addition,dexamethasone:quantity 10uM time 10day . One large drop of the dexamethasone solution was placed on the contral region of rosette plants. 10 uM Dexamethasone, 0,1% EtOH, 0,015% Silwet L77

value: landsberg erecta

value: mutant ( at1g69120 (ap1))

source_name: 9 days Repet3

treatment_protocol: Name:Dexamethasone 9days - time course study - compound addition,dexamethasone:quantity 10uM time 9day . One large drop of the dexamethasone solution was placed on the contral region of rosette plants. 10 uM Dexamethasone, 0,1% EtOH, 0,015% Silwet L77


title: 14286680 - 10 days Repet3 vs 9 days Repet3

hyb_protocol: 9 days Repet3 Cy5 / 10 days Repet3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 252800510958-7

description: C57 PBS-5

source_name: C57 PBS-5

tag: agent


title: MM6

description: Genome-wide Human SNP 6.0 array


title: 14286678 - 10 days Repet2 vs 9 days Repet2

hyb_protocol: 9 days Repet2 Cy5 / 10 days Repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 9 days Repet2

source_name: 10 days Repet2


title: MM5

description: Genome-wide Human SNP 6.0 array


title: 252800510941-5

description: C57 PBS-2

source_name: C57 PBS-2


title: 252800510958-8

description: C57 PBS-4

source_name: C57 PBS-4


title: MM2

description: Genome-wide Human SNP 6.0 array


title: MM4

description: Genome-wide Human SNP 6.0 array


title: MM3

description: Genome-wide Human SNP 6.0 array


title: 14286675 - 10 days Repet1 vs 9 days Repet1

hyb_protocol: 9 days Repet1 Cy5 / 10 days Repet1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 9 days Repet1

source_name: 10 days Repet1


title: 14286677 - 9 days Repet2 vs 10 days Repet2

hyb_protocol: 10 days Repet2 Cy5 / 9 days Repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14286674 - 9 days Repet1 vs 10 days Repet1

hyb_protocol: 10 days Repet1 Cy5 / 9 days Repet1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: MM1

description: Genome-wide Human SNP 6.0 array

source_name: Uveal melanoma, monosomy chr 3, metastasising


title: MS17

description: Genome-wide Human SNP 6.0 array

source_name: Uveal melanoma, monosomy chr 3, long-term survival

value: non-metastasising


title: MS16

description: Genome-wide Human SNP 6.0 array


title: 252800510941-6

description: C57 PBS-3

source_name: C57 PBS-3


title: 252800510941-7

description: C57 Bleo-2

source_name: C57 Bleo-2

value: bleomycin


title: 14286671 - 9 days Repet2 vs 8 days Repet2

hyb_protocol: 8 days Repet2 Cy5 / 9 days Repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 8 days Repet2

treatment_protocol: Name:Dexamethasone 8days - time course study - compound addition,dexamethasone:quantity 10uM time 8day . One large drop of the dexamethasone solution was placed on the contral region of rosette plants. 10 uM Dexamethasone, 0,1% EtOH, 0,015% Silwet L77


title: 252800510958-1

description: C57 Bleo-1

source_name: C57 Bleo-1


title: MM9

description: Genome-wide Human SNP 6.0 array


title: 14286672 - 8 days Repet3 vs 9 days Repet3

hyb_protocol: 9 days Repet3 Cy5 / 8 days Repet3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 8 days Repet3


title: 14286670 - 8 days Repet2 vs 9 days Repet2

hyb_protocol: 9 days Repet2 Cy5 / 8 days Repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Δrny_32min

city: Oklahoma City

first: Jens

last: Kreth

address: 940 Stanton L. Young Blvd

department: Microbiology & Immunology

institute: University of Oklahoma Health Sciences Center

hyb_protocol: Following fragmentation, 2 μl of cDNA were hybridized for 16 hr at 47℃ on GeneChip S. pyogenes Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using a laser scanner 7G (Affymetrix)

data_processing: Data were analyzed with Gene Chip Operating Software version 1.4 (GCOS 1.4) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Streptococcus pyogenes

source_name: Δrny_32 min after rifampicin addition

label_protocol: Biotinylated cDNA was prepared according to the standard Affymetrix protocol.

growth_protocol: Cells were grown aerobically in C-medium (0.5% proteose peptone #3, 1.5% yeast extract, 10 mM K2SO4, 0.4 mM MgSO4, 17 mM NaCl)

extract_protocol: Cells were lysed using beat-beater. Extraction of total RNA was performed using TRIzol reagent (Invitrogen) according to the manufacturers protocol.

treatment_protocol: Cells were grown to the late exponential phase (OD600 = 0.5-0.55). Rifampicin and glucose were added to the culture at final concentrations of 1 μg/ml and 0.5%(wt/vol). Samples were collected before (t = 0 min) and after (t = 0.5, 1, 2, 4, 8, 16, 32 min) rifampicin addition.

tag: strain background

value: Δrny

tag: sample collection

value: 32 min after rifampicin addition


title: 252800510941-8

description: C57 Bleo-3

source_name: C57 Bleo-3


title: MS12

description: Genome-wide Human SNP 6.0 array

hyb_protocol: Hybridised to Affymetrix SNP 6.0 arrays according to manufacturers protocol


title: 252800510958-2

description: C57 Bleo-4

source_name: C57 Bleo-4


title: Δrny_16min

source_name: Δrny_16 min after rifampicin addition

value: 16 min after rifampicin addition


title: 252800510958-3

description: C57 Bleo-5

source_name: C57 Bleo-5


title: 14286673 - 9 days Repet3 vs 8 days Repet3

hyb_protocol: 8 days Repet3 Cy5 / 9 days Repet3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 9 days Repet3


title: MS11

description: Genome-wide Human SNP 6.0 array


title: MS13

description: Genome-wide Human SNP 6.0 array


title: MS14

description: Genome-wide Human SNP 6.0 array


title: Δrny_8min

source_name: Δrny_8 min after rifampicin addition

value: 8 min after rifampicin addition


title: 14286668 - 9 days Repet1 vs 8 days Repet1

hyb_protocol: 8 days Repet1 Cy5 / 9 days Repet1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 8 days Repet1


title: 14286667 - 8 days Repet3 vs 2 days Repet3

hyb_protocol: 2 days Repet3 Cy5 / 8 days Repet3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 2 days Repet3

treatment_protocol: Name:Dexamethasone 2days - time course study - compound addition,dexamethasone:quantity 10uM time 2day . One large drop of the dexamethasone solution was placed on the contral region of rosette plants. 10 uM Dexamethasone, 0,1% EtOH, 0,015% Silwet L77


title: MS15

description: Genome-wide Human SNP 6.0 array

value: Uveal melanoma


title: Δrny_4min

source_name: Δrny_4 min after rifampicin addition

value: 4 min after rifampicin addition


title: 14286669 - 8 days Repet1 vs 9 days Repet1

hyb_protocol: 9 days Repet1 Cy5 / 8 days Repet1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 9 days Repet1


title: Δrny_2min

source_name: Δrny_2 min after rifampicin addition

value: 2 min after rifampicin addition


title: 14286666 - 2 days Repet3 vs 8 days Repet3

hyb_protocol: 8 days Repet3 Cy5 / 2 days Repet3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: MS10

description: Genome-wide Human SNP 6.0 array

source_name: Uveal melanoma, monosomy chr 3, long-term survival

value: monosomy chr 3


title: Δrny_1min

source_name: Δrny_1 min after rifampicin addition

value: 1 min after rifampicin addition


title: MS8

description: Genome-wide Human SNP 6.0 array


title: Δrny_0.5min

source_name: Δrny_0.5 min after rifampicin addition

value: 0.5 min after rifampicin addition


title: 14286665 - 8 days Repet2 vs 2 days Repet2

hyb_protocol: 2 days Repet2 Cy5 / 8 days Repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 2 days Repet2

source_name: 8 days Repet2


title: MS9

description: Genome-wide Human SNP 6.0 array


title: 14286664 - 2 days Repet2 vs 8 days Repet2

hyb_protocol: 8 days Repet2 Cy5 / 2 days Repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Δrny_0min

source_name: Δrny_before rifampicin addition

value: before rifampicin addition


title: WT_32min

source_name: WT_32 min after rifampicin addition

value: wild type


title: 14286662 - 11 days Repet3 vs 10 days Repet3

hyb_protocol: 10 days Repet3 Cy5 / 11 days Repet3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 10 days Repet3

source_name: 11 days Repet3

treatment_protocol: Name:Dexamethasone 11days - time course study - compound addition,dexamethasone:quantity 10uM time 11day . One large drop of the dexamethasone solution was placed on the contral region of rosette plants. 10 uM Dexamethasone, 0,1% EtOH, 0,015% Silwet L77


title: 14286661 - 10 days Repet3 vs 11 days Repet3

hyb_protocol: 11 days Repet3 Cy5 / 10 days Repet3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14286660 - 11 days Repet2 vs 10 days Repet2

hyb_protocol: 10 days Repet2 Cy5 / 11 days Repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 10 days Repet2

source_name: 11 days Repet2


title: WT_16min

source_name: WT_16 min after rifampicin addition


title: MS7

description: Genome-wide Human SNP 6.0 array


title: WT_8min

source_name: WT_8 min after rifampicin addition


title: MS6

description: Genome-wide Human SNP 6.0 array


title: 14286659 - 10 days Repet2 vs 11 days Repet2

hyb_protocol: 11 days Repet2 Cy5 / 10 days Repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: WT_4min

source_name: WT_4 min after rifampicin addition


title: MS3

description: Genome-wide Human SNP 6.0 array


title: WT_2min

source_name: WT_2 min after rifampicin addition


title: 14286658 - 11 days Repet1 vs 10 days Repet1

hyb_protocol: 10 days Repet1 Cy5 / 11 days Repet1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 10 days Repet1

source_name: 11 days Repet1


title: WT_1min

source_name: WT_1 min after rifampicin addition


title: MS5

description: Genome-wide Human SNP 6.0 array

source_name: Uveal melanoma, monosomy chr 3, long-term survival


title: 14286663 - 8 days Repet1 vs 2 days Repet1

hyb_protocol: 2 days Repet1 Cy5 / 8 days Repet1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 2 days Repet1

source_name: 8 days Repet1


title: MS1

description: Genome-wide Human SNP 6.0 array


title: 14163000 - 2 days Repet1 vs 8 days Repet1

hyb_protocol: 8 days Repet1 Cy5 / 2 days Repet1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: WT_0min

source_name: WT_before rifampicin addition


title: WT_0.5min

source_name: WT_0.5 min after rifampicin addition


title: Δrny_LE2

source_name: Δrny_late exponential phase

tag: growth stage

value: late exponential phase


title: Glioma-EORTC26951 182 275.CEL

description: Abbreviations: IGS: intrinsic glioma subtype; Trt: treatment; SS: survival in years; C: classical; P: proneural; M: mesenchymal; N:neural

hyb_protocol: Hybridization was performed according to the Affymetrix (Santa Clara, CA) Labelling Assay manual

scan_protocol: Genechip scanner 3000 7G

source_name: Glioma, clinical trial RT v RT+PCV

label_protocol: labelling was performed according to the Affymetrix (Santa Clara, CA) Labelling Assay manual

extract_protocol: Qiagen Rneasy

value: glioma

tag: sample

tag: igs

tag: tcga classification

value: P

tag: tissue type

value: FF

tag: cimp

value: CIMP+

tag: idhmut

value: mut

tag: 1p19q loh

value: LOH

tag: egfr

value: wt

tag: trt

value: RT

tag: ss (y)

tag: event

value: deceased

tag: age

tag: Sex

value: F

tag: original diagnosis

value: AOD

tag: review diagnosis

value: LGG

tag: experiment

value: pt 2


title: Glioma-EORTC26951 84 670.CEL

tag: tissue

value: C

value: CIMP-

value: no loss

value: amp

value: RT/PCV

value: AOA


title: 14286657 - 10 days Repet1 vs 11 days Repet1

hyb_protocol: 11 days Repet1 Cy5 / 10 days Repet1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: ecotype

value: landsberg erecta

tag: genotype

value: mutant ( at1g69120 (ap1))

tag: developmental stage (boyes et al. plant cell 2001)


title: Δrny_LE1

hyb_protocol: Following fragmentation, 2 μl of cDNA were hybridized for 16 hr at 47℃ on GeneChip S. pyogenes Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

tag: strain background

tag: genotype/variation

value: Δrny

tag: growth stage

value: late exponential phase


title: Glioma-EORTC26951 41 662.CEL

value: glioma

tag: sample

tag: igs

tag: tcga classification

value: P

tag: tissue type

value: FF

tag: idhmut

value: wt

tag: 1p19q loh

tag: mgmt

value: unmeth


title: DM15

description: Genome-wide Human SNP 6.0 array

hyb_protocol: Hybridised to Affymetrix SNP 6.0 arrays according to manufacturers protocol

source_name: Uveal melanoma, disomy chr 3, metastasising

value: Uveal melanoma

value: disomy chr 3

tag: metastasis status

value: metastasising


title: WT_LE2

source_name: WT_late exponential phase

value: wild type


title: MS2

description: Genome-wide Human SNP 6.0 array

value: monosomy chr 3

value: non-metastasising


title: Glioma-EORTC26951 33 568.CEL

value: mut

value: no loss

tag: egfr

value: meth

tag: trt

value: RT/PCV

tag: ss (y)

tag: event

value: alive

tag: age

tag: Sex

value: F

tag: original diagnosis

tag: review diagnosis

value: pt 2


title: Glioma-EORTC26951 48 490.CEL

tag: tissue

value: glioma

value: P

value: RT

value: deceased

value: M

value: AOA

tag: experiment


title: Glioma-EORTC26951 50 271.CEL

tag: sample

tag: igs

value: C

value: FF

value: wt

value: amp

value: AOD


title: WT_LE1

tag: strain background

tag: genotype/variation

value: wild type

tag: growth stage

value: late exponential phase


title: Solvent control, replicate 2

city: Doha

first: Tanwir

last: Habib

address: Al Luqta Street

country: Qatar

institute: Weill Cornell Medicine Qatar

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array 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), 1 minute with 37°C GE Wash buffer 2 (Agilent), 30 seconds with Acetonitrile, and dried with Agilent Stabilization and Drying Solution.

scan_protocol: Slides were scanned immediately after washing on a GenePix 4200AL scanner at PMT gain level 420 using default setting (Scan resolution 5um, One channel-Green, Laser power 100%).

data_processing: The scanned images were analyzed with GenePix Pro 6.1  (Molecular Devices, Sunnyvale, CA) using default parameters and Agilient-provided GEML grid file 023710_D_F_20090417.xml to obtain signal intensities.  GeneSpring GX (Agilent Technologies) was used to normalize data by quantile normalizaton and baseline transformation to the median of all samples.  Statistical analysis was also performed in GeneSpring utilizing data from all microarray probes and consisted of one-way ANOVA to test for significant differential expression of microarray targets.

organism: Daphnia magna

source_name: Whole daphnia (20 daphnia/replicate)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.4 ug 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, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: U.S. EPA. 1996. OPPTS 850.1300 Daphnid Chronic Toxicity Test

tag: agent

value: Solvent control


title: MS4

description: Genome-wide Human SNP 6.0 array

value: Uveal melanoma

tag: genotype

value: monosomy chr 3

tag: metastasis status

value: non-metastasising


title: DM11

description: Genome-wide Human SNP 6.0 array

value: disomy chr 3

value: metastasising


title: DM10

description: Genome-wide Human SNP 6.0 array


title: DM13

description: Genome-wide Human SNP 6.0 array


title: Solvent control, replicate 1

treatment_protocol: U.S. EPA. 1996. OPPTS 850.1300 Daphnid Chronic Toxicity Test


title: Glioma-EORTC26951 31 270.CEL

value: glioma

tag: tcga classification

value: P

tag: tissue type

tag: cimp

value: CIMP+

tag: idhmut

value: mut

tag: 1p19q loh

value: LOH

tag: egfr

tag: mgmt

value: meth

tag: trt

value: RT/PCV

value: F

value: pt 2


title: male T1KO#65versus male T2KO#16 Replicate 1

city: Cambridge

first: Inmaculada

last: Barrasa

state: MA

address: Nine Cambridge Center

institute: Whitehead Institute

hyb_protocol: Agilent V2 Mouse 4x44k expression arrays were hybridized and washed according to manufacturer's instructions

scan_protocol: Agilent DNA microarray scanner was used following manufaturer's instructions

data_processing: Data were normalized within array by loess normalization and between arrays by quantile normalization of average intensities (“Aquantile”) using Bioconductor. Probes for the same gene were summarized by mean and technical replicas were combined by average

source_name: male Tet1 ESC

label_protocol: Cy3 and Cy5-labeled cRNA was prepared using the Low Input Quick Amp labeling kit (Agilent) starting with 200ng of total RNA

growth_protocol: Mouse embryonic stem cells were cultured on gamma irridiated feeders in LIF contianing medium.

extract_protocol: RNA was extracted using Qiagen RNAeasy Kit

treatment_protocol: Feeders were separated by preplating on gelatin coated platesprior to mRNA extraction.

tag: background strain

tag: gender

value: male

value: Tet1 knockout

source_name: male Tet2 ESC

value: Tet2 knockout


title: male T1KO#65versus male T2KO#16 Replicate 2


title: DM7

description: Genome-wide Human SNP 6.0 array

tag: tissue

value: Uveal melanoma


title: Solvent control, replicate 4

value: Solvent control


title: CantonS, larvalCNS-stimulated-biorep3

city: Denver

first: Scott

middle: A

last: Barbee

state: CO

address: 2190 E. ILIFF Ave.

department: Biological Sciences

institute: University of Denver

data_processing: In the Matrix normalized sheet the  deltaCt values for three biological replicates (each the average of three technical replicates) was calculated based on the formula Ct_Target - Ct_HKG where HKG is the internal U1 snRNA control. In the fold changed sheet, fold change was calculated using the formula 2^-deltadeltaCt, where -deltadeltaCt = -[deltaCttest -deltaCtcontrol]. deltaCttest = the deltaCt values calculated for stimulated samples on the Matrix normalized sheet. deltaCtcontrol = the global control deltaCt values (or a single deltaCt value calculated from the average of three mock stimulated biological replicates).

label: SYBR Green

organism: Drosophila melanogaster

source_name: CantonS, larvalCNS-stimulated-biorep3-techrep1 to techrep3

label_protocol: Three technical replicates of three biological replicate were then amplified using miScript SYBR Green PCR Kit (Qiagen).

growth_protocol: Flies were grown on standard Bloomington media at 25°C.

extract_protocol: Total RNA was extracted using the miRNeasy RNA Isolation kit (Qiagen) yielding ~150 ng of total RNA per CNS. RNA was eluted with 40 ul of RNAse free water (Ambion), flash frozen, and stored at -80°C.

treatment_protocol: The stimulated group was subjected to 5x high K+ spaced depolarization. The mock stimulated group was subjected to 5x normal K+ (also referred to as 0x high K+)

tag: developmental stage

value: third instar larvae

value: Ventral ganglia + optic lobes (- eye imaginal discs)

tag: treatment

value: synaptic stimulation

tag: strain

value: Canton S


title: DM12

description: Genome-wide Human SNP 6.0 array

value: disomy chr 3

value: metastasising


title: CantonS, larvalCNS-stimulated-biorep2

source_name: CantonS, larvalCNS-stimulated-biorep2-techrep1 to techrep3


title: DM8

description: Genome-wide Human SNP 6.0 array


title: DM9

description: Genome-wide Human SNP 6.0 array


title: male T1KO#99 Replicate 2

source_name: male ESC,not included in differential expression analysis due to false genotype


title: Solvent control, replicate 3

tag: agent


title: male T1KO#99 Replicate 1

tag: genotype


title: Glioma-EORTC26951 290 223.CEL

value: glioma

tag: sample

tag: igs

value: M

value: FF

value: CIMP-

value: wt

value: no loss

value: RT

tag: ss (y)

tag: event

value: deceased

tag: age

tag: Sex

tag: original diagnosis

value: AOD

tag: review diagnosis

tag: experiment


title: CantonS, larvalCNS-stimulated-biorep1

source_name: CantonS, larvalCNS-stimulated-biorep1-techrep1 to techrep3


title: DM6

description: Genome-wide Human SNP 6.0 array

value: Uveal melanoma

tag: metastasis status


title: Solvent control, replicate 6

value: Solvent control


title: DM14

description: Genome-wide Human SNP 6.0 array


title: Glioma-EORTC26951 259 214.CEL

tag: tcga classification

value: P

tag: tissue type

tag: cimp

value: CIMP+

tag: idhmut

value: mut

tag: 1p19q loh

tag: egfr

tag: mgmt

value: unmeth

tag: trt

value: RT/PCV

value: AOA

value: pt 2


title: female DKO#59 versus female WT#94 Replicate 2

source_name: female WT ESC

tag: background strain

tag: gender

value: female

tag: genotype

value: wildtype

source_name: female Tet1 Tet2 DKO ESC

value: Tet1/Tet2 double knockout


title: Solvent control, replicate 5

tag: agent


title: CantonS, larvalCNS-unstimulated-biorep3

source_name: CantonS, larvalCNS-unstimulated-biorep3-techrep1 to techrep3

tag: developmental stage

value: third instar larvae

tag: tissue

value: Ventral ganglia + optic lobes (- eye imaginal discs)

tag: treatment

value: unstimulated

tag: strain

value: Canton S


title: Glioma-EORTC26951 305 190.CEL

value: glioma

tag: sample

tag: igs

value: FF

value: no loss

value: RT

tag: ss (y)

tag: event

value: deceased

tag: age

tag: Sex

value: M

tag: original diagnosis

tag: experiment


title: 1.85mg/L TNT, replicate 2

value: 1.85mg/L TNT


title: female DKO#59 versus female WT#94 Replicate 1


title: CantonS, larvalCNS-unstimulated-biorep2

source_name: CantonS, larvalCNS-unstimulated-biorep2-techrep1 to techrep3


title: Glioma-EORTC26951 58 259.CEL

tag: tcga classification

value: P

tag: tissue type

tag: cimp

value: CIMP+

tag: idhmut

value: mut

tag: 1p19q loh

value: LOH

tag: egfr

value: wt

tag: mgmt

value: meth

tag: trt

value: AOD

tag: review diagnosis


title: DM1

description: Genome-wide Human SNP 6.0 array

tag: tissue

value: Uveal melanoma

tag: genotype

value: disomy chr 3

tag: metastasis status

value: metastasising


title: CantonS, larvalCNS-unstimulated-biorep1

source_name: CantonS, larvalCNS-unstimulated-biorep1-techrep1 to techrep3

tag: developmental stage

value: third instar larvae

value: Ventral ganglia + optic lobes (- eye imaginal discs)

tag: treatment

value: unstimulated

tag: strain

value: Canton S


title: 1.85mg/L TNT, replicate 4

tag: agent


title: female DKO#60 versus female WT#7 Replicate 1

tag: background strain

tag: gender

value: female

value: wildtype

value: Tet1/Tet2 double knockout


title: Glioma-EORTC26951 113 188.CEL

value: glioma

tag: sample

tag: igs

tag: tcga classification

value: P

tag: tissue type

value: FF

value: no loss

value: RT/PCV

tag: ss (y)

tag: event

value: deceased

tag: age

tag: Sex

value: M

tag: original diagnosis

value: AOA

tag: experiment

value: pt 2


title: Glioma-EORTC26951 57 189.CEL

tag: tissue

tag: cimp

value: CIMP+

tag: 1p19q loh

value: LOH

tag: egfr

value: wt

tag: mgmt

value: meth

tag: trt

value: alive

value: AOD

tag: review diagnosis


title: male DKO#51 versus male WT#6 Replicate 2

source_name: male WT ESC

tag: background strain

tag: gender

value: male

tag: genotype

value: wildtype

source_name: male Tet1 Tet2 DKO ESC


title: 1.85mg/L TNT, replicate 3

tag: agent

value: 1.85mg/L TNT


title: DS9

description: Genome-wide Human SNP 6.0 array

source_name: Uveal melanoma, disomy chr 3, long-term survival

value: Uveal melanoma

value: disomy chr 3

tag: metastasis status

value: non-metastasising


title: larvalCNS-chr2un-rep1

description: raw files 0_ are Hy3 and1_ are Hy5

hyb_protocol: The Hy3-labeled samples and a Hy5-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNA array version 11.0 Other Species (Exiqon, Denmark), which contains capture probes targeting all miRNAs for all other species than human, mouse or rat registered in the miRBASE version 14.0 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 8.0 software (BioDiscovery, Inc., USA).

source_name: larvalCNS, ChR2, unstimulated

label_protocol: Total RNA from sample and reference was labelled with Hy3 and Hy5  fluorescent label, respectively, using the miRCURY™ LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer.

growth_protocol: The white genotype was grown on standard Bloomington media at 25°C. ChR2-expressing genotypes were grown on standard Bloomington food supplemented with 100mM all-trans retinal at 25°C.

extract_protocol: Total RNA was extracted using the miRCURY RNA Isolation kit (Exiqon) yielding ~125 ng of total RNA per CNS. RNA was eluted with 40 ul of RNAse free water (Ambion), flash frozen, and stored at -80°C.

treatment_protocol: The chr2-stim group was subjected to 5x spaced light stimulation. The chr2-un group was subjected to 0x mock stimulation.

tag: treatment

value: unstimulated

value: UAS-ChR2 x C380-Gal4

tag: developmental stage

value: third instar larvae

value: Ventral ganglia + optic lobes (- eye imaginal discs)

source_name: common reference pool

value: common reference pool


title: Glioma-EORTC26951 147 187.CEL

source_name: Glioma, clinical trial RT v RT+PCV

value: glioma

tag: sample

tag: igs

tag: tcga classification

value: C

tag: tissue type

value: FF

value: CIMP-

value: no loss

value: amp

value: RT

tag: ss (y)

tag: event

value: deceased

tag: age

tag: Sex

value: M

value: AOA

value: pt 2


title: 1.85mg/L TNT, replicate 1

source_name: Whole daphnia (20 daphnia/replicate)

value: 1.85mg/L TNT


title: 1.85mg/L TNT, replicate 5


title: Glioma-EORTC26951 66 186.CEL

tag: tissue

tag: 1p19q loh

tag: trt

value: F

tag: original diagnosis

tag: experiment


title: Glioma-EORTC26951 301 229.CEL

value: P

tag: cimp

value: CIMP+

tag: idhmut

value: mut

value: LOH

value: RT/PCV

value: alive

value: AOD

tag: review diagnosis


title: male DKO#61 versus male WT#92 Replicate 1

tag: background strain

tag: gender

value: male

tag: genotype

value: wildtype

value: Tet1/Tet2 double knockout


title: DS6

description: Genome-wide Human SNP 6.0 array

value: Uveal melanoma

value: disomy chr 3

tag: metastasis status

value: non-metastasising


title: larvalCNS-chr2stim-rep1

description: raw files 0_ are Hy3 and1_ are Hy5

source_name: larvalCNS, ChR2, stimulated

tag: treatment

value: synaptic stimulation

value: UAS-ChR2 x C380-Gal4

tag: developmental stage

value: third instar larvae

value: Ventral ganglia + optic lobes (- eye imaginal discs)

value: common reference pool


title: larvalCNS-white-rep1

description: raw files 0_ are Hy3 and1_ are Hy5

source_name: larvalCNS, white, unstimulated

value: unstimulated


title: DM3

description: Genome-wide Human SNP 6.0 array

source_name: Uveal melanoma, disomy chr 3, metastasising

value: metastasising


title: male DKO#51 versus male WT#6 Replicate 1


title: DM4

description: Genome-wide Human SNP 6.0 array


title: Glioma-EORTC26951 275 185.CEL

value: glioma

tag: sample

tag: igs

tag: tcga classification

value: P

tag: tissue type

value: FF

value: LOH

tag: ss (y)

tag: event

value: M

value: pt 2


title: DS5

description: Genome-wide Human SNP 6.0 array

tag: tissue


title: 0.12mg/L TNT, replicate 1

tag: agent

value: 0.12mg/L TNT


title: High fat/high fructose diet (HFD) 9083

city: Portland

first: Alina

last: Maloyan

state: OR

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health and Science University

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.  Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].  A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.  t-Test is performed between “control” and “test” sample groups. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.  All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

organism: Papio hamadryas

source_name: left ventricle

label_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started from 4 to 8 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent Cy3 dye staining.

growth_protocol: Baboon females were fed either a regular or a high fat/high fructose diet before and during the pregnancy, At the day 165 of gestation, c-section was performed and fetal heart were collected for microarray analysis

extract_protocol: Total RNA was isolated from fetal hearts

treatment_protocol: Two dietary regimen: regualar or high fat/high fructose diet

value: male

value: heart left ventricle

value: maternal high fat/high fructose diet

tag: age

value: 165 d of gestation


title: High fat/high fructose diet (HFD) 9047


title: DS7

description: Genome-wide Human SNP 6.0 array

value: Uveal melanoma

value: disomy chr 3

value: non-metastasising


title: Glioma-EORTC26951 125 150.CEL

value: N

tag: cimp

value: CIMP-

tag: idhmut

value: wt

tag: 1p19q loh

value: no loss

tag: egfr

tag: mgmt

value: unmeth

tag: trt

value: RT/PCV

value: deceased

tag: Sex

tag: original diagnosis

value: AOD

tag: experiment


title: Glioma-EORTC26951 117 162.CEL

value: glioma

tag: sample

tag: igs

value: C

value: FF

value: amp

value: meth

value: RT

value: F

value: AOA

tag: review diagnosis

value: pt 2


title: 0.12mg/L TNT, replicate 4

value: 0.12mg/L TNT


title: DS8

description: Genome-wide Human SNP 6.0 array

value: Uveal melanoma

tag: genotype

value: disomy chr 3

tag: metastasis status

value: non-metastasising


title: regular diet (RD) 8015

tag: gender

value: male

tag: tissue

value: heart left ventricle

tag: treatment

value: maternal regular diet

value: 165 d of gestation


title: DS3

description: Genome-wide Human SNP 6.0 array


title: DM5

description: Genome-wide Human SNP 6.0 array

value: metastasising


title: High fat/high fructose diet (HFD) 9126

value: female

value: maternal high fat/high fructose diet

tag: age


title: High fat/high fructose diet (HFD) 9045


title: Glioma-EORTC26951 54 144.CEL

value: glioma

tag: tcga classification

value: P

tag: tissue type

value: FF

tag: cimp

value: CIMP+

tag: idhmut

value: mut

value: LOH

value: wt

value: RT/PCV

tag: ss (y)

tag: event

value: alive

value: M

value: AOD


title: High fat/high fructose diet (HFD) 9081

value: heart left ventricle


title: Glioma-EORTC26951 17 084.CEL

tag: trt

value: deceased

tag: Sex

value: F

tag: original diagnosis

value: pt 2


title: Glioma-EORTC26951 32 141.cel

tag: sample

tag: igs

value: C

tag: 1p19q loh

value: no loss

tag: egfr

value: amp

tag: mgmt

value: unmeth

value: RT

tag: experiment


title: 0.12mg/L TNT, replicate 5

tag: agent

value: 0.12mg/L TNT


title: regular diet (RD) 8013

tag: gender

value: male

tag: tissue

tag: treatment

value: maternal regular diet

tag: age

value: 165 d of gestation


title: Glioma-EORTC26951 262 113.CEL

value: glioma

tag: tcga classification

tag: tissue type

value: FF

tag: idhmut

value: mut

value: wt

value: meth

value: RT/PCV

value: AOA

tag: review diagnosis


title: 0.12mg/L TNT, replicate 6


title: 0.12mg/L TNT, replicate 3


title: Glioma-EORTC26951 27 083.CEL

tag: cimp

value: CIMP-

tag: trt

tag: ss (y)

tag: event

value: deceased

tag: Sex

value: F

value: AOD

value: pt 2


title: 0.004mg/L TNT, replicate 2

value: 0.004mg/L TNT


title: DS4

description: Genome-wide Human SNP 6.0 array

value: Uveal melanoma

tag: genotype

value: disomy chr 3

tag: metastasis status

value: non-metastasising


title: DM2

description: Genome-wide Human SNP 6.0 array

value: metastasising


title: regular diet (RD) 8005

value: male

value: heart left ventricle

value: maternal regular diet

value: 165 d of gestation


title: DS10

description: Genome-wide Human SNP 6.0 array


title: regular diet (RD) 8007

value: female


title: regular diet (RD) 8003


title: Glioma-EORTC26951 242 082.CEL

value: glioma

tag: sample

tag: igs

value: P

value: FF

value: CIMP+

tag: 1p19q loh

value: no loss

tag: egfr

value: wt

tag: mgmt

value: meth

value: RT/PCV

value: M

tag: original diagnosis

tag: experiment


title: 1.85mg/L TNT, replicate 6

tag: agent

value: 1.85mg/L TNT


title: 0.004mg/L TNT, replicate 4

value: 0.004mg/L TNT


title: regular diet (RD) 8001

tag: gender

tag: tissue

tag: treatment

tag: age


title: 0.004mg/L TNT, replicate 1


title: Glioma-EORTC26951 13 020.CEL

tag: tcga classification

tag: tissue type

tag: idhmut

value: LOH

tag: trt

tag: ss (y)

value: deceased

value: AOD

tag: review diagnosis

value: pt 2


title: DS1

description: Genome-wide Human SNP 6.0 array

value: Uveal melanoma

tag: genotype

value: disomy chr 3

tag: metastasis status

value: non-metastasising


title: 0.004mg/L TNT, replicate 6


title: 0.004mg/L TNT, replicate 5


title: 0.004mg/L TNT, replicate 3


title: Glioma-EORTC26951 326 021.CEL

value: glioma

tag: sample

tag: igs

value: P

tag: cimp

value: mut

tag: 1p19q loh

tag: egfr

tag: event

tag: Sex

value: GBM/AA