title: MDAMB231

first: Kornelia

last: Polyak

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software

label: Cy5 and Cy3

source_name: breast cancer cell line

label_protocol: Standard Illumina Protocol

extract_protocol: standard procedure

value: breast cancer

tag: subtype

value: Basal-like cells


title: PAXGene blood healthy person H5 t0

status: Public on Jun 16 2014

type: RNA

city: Saarbrücken

first: Christina

last: Backes

address: Campus, Building E 2.1

department: Chair for Clinical Bioinformatics

country: Germany

institute: Saarland University

description:
miRNA profiling
PAXGene blood healthy person H5 t0
H5 PAX t0

hyb_protocol: Hybridizations were performed in Agilent SureHyb chambers for 20 hours at 55C and washed according to manufacturer's instructions.

scan_protocol: Array-chips were scanned in a high resolution microarray scanner from Agilent Technologies using Scan Control 8.5.1 software, 3 microns resolution in double path mode.

data_processing: Signal intensity values were extracted from the raw data file using feature extraction software (Agilent Technologies). The gTotalProbeSignals were summed up to calculate the total expression value for each miRNA per sample. Quantile normalization was applied to normalize expression values across the arrays using the preprocessCore package of the programming language R. After that we log2-transformed the expression values.

molecule: total RNA

organism: Homo sapiens

source_name: whole blood

label_protocol: Total RNA samples were labelled using the Agilent miRNA Complete Labelling and Hybridization Kit

extract_protocol: Total RNA including small RNAs was isolated using miRNeasy Micro Kit (Qiagen) according to manufacturer’s instructions.

tag: individual

tag: disease

value: healthy

tag: gender

value: male

tag: age

tag: cell type

value: whole blood

tag: time


title: A375-Vector Rep2

status: Public on Jun 17 2014

city: Boston

first: Markus

middle: Hermann

last: Frank

state: Massachusetts

address: 300 Longwood Avenue

department: Medicine

country: USA

institute: Boston Children's Hospital

hyb_protocol: Refer to Dana Farber Cancer Institute Microarray Core

label: biotin

source_name: Melanoma cell-line, A375, control

extract_protocol: Qiagen miniprep kit with additional 15min on-column DNaseI digestion

tag: cell line

value: non-pigmented melanoma


title: HCC2157

type: genomic

state: MA

molecule: genomic DNA


title: CD3 fraction healthy person H3 t2

description:
miRNA profiling
CD3 fraction healthy person H3 t2
H3 CD3 t2

source_name: CD3 cells

value: CD3 cells


title: MCF7

value: Luminal cells


title: T47D


title: CD3 fraction healthy person H3 t1

description:
miRNA profiling
CD3 fraction healthy person H3 t1
H3 CD3 t1


title: CD19 fraction healthy person H3 t0

description:
miRNA profiling
CD19 fraction healthy person H3 t0
H3 CD19+ t0

source_name: CD19 cells

value: CD19 cells


title: CD19 fraction healthy person H3 t2

description:
miRNA profiling
CD19 fraction healthy person H3 t2
H3 CD19 t2


title: CD15 fraction healthy person H3 t0

description:
miRNA profiling
CD15 fraction healthy person H3 t0
H3 CD15+ t0

source_name: CD15 cells

value: CD15 cells


title: CD15 fraction healthy person H3 t1

description:
miRNA profiling
CD15 fraction healthy person H3 t1
H3 CD15 t1


title: CD15 fraction healthy person H3 t2

description:
miRNA profiling
CD15 fraction healthy person H3 t2
H3 CD15 t2


title: CD19 fraction healthy person H3 t1

description:
miRNA profiling
CD19 fraction healthy person H3 t1
H3 CD19 t1


title: CD56 fraction healthy person H3 t2

description:
miRNA profiling
CD56 fraction healthy person H3 t2
H3 CD56 t2

source_name: CD56 cells

value: CD56 cells


title: CD3 fraction healthy person H3 t0

description:
miRNA profiling
CD3 fraction healthy person H3 t0
H3 CD3+ t0


title: CD19 fraction healthy person H2 t0

description:
miRNA profiling
CD19 fraction healthy person H2 t0
H2 CD19+ t0

value: female


title: CD14 fraction healthy person H2 t0

description:
miRNA profiling
CD14 fraction healthy person H2 t0
H2 CD14+ t0

source_name: CD14 cells

value: CD14 cells


title: CD56 fraction healthy person H2 t0

description:
miRNA profiling
CD56 fraction healthy person H2 t0
H2 CD56+ t0


title: CD3 fraction healthy person H2 t0

description:
miRNA profiling
CD3 fraction healthy person H2 t0
H2 CD3+ t0


title: PAXGene blood healthy person H1 t1

description:
miRNA profiling
PAXGene blood healthy person H1 t1
H1 PAX t1


title: CD14 fraction healthy person H3 t1

description:
miRNA profiling
CD14 fraction healthy person H3 t1
H3 CD14 t1


title: CD14 fraction healthy person H3 t2

description:
miRNA profiling
CD14 fraction healthy person H3 t2
H3 CD14 t2


title: PAXGene blood healthy person H2 t0

description:
miRNA profiling
PAXGene blood healthy person H2 t0
H2 PAX t0


title: CD14 fraction healthy person H3 t0

description:
miRNA profiling
CD14 fraction healthy person H3 t0
H3 CD14+ t0


title: PAXGene blood healthy person H1 t2

description:
miRNA profiling
PAXGene blood healthy person H1 t2
H1 PAX t2


title: Exosomes healthy person H1 t2

description:
miRNA profiling
Exosomes healthy person H1 t2
H1 Exos t2

source_name: Exosomes

value: Exosomes


title: CD56 fraction healthy person H1 t0

description:
miRNA profiling
CD56 fraction healthy person H1 t0
H1 CD56+ t0


title: CD56 fraction healthy person H1 t1

description:
miRNA profiling
CD56 fraction healthy person H1 t1
H1 CD56 t1


title: CD3 fraction healthy person H1 t0

description:
miRNA profiling
CD3 fraction healthy person H1 t0
H1 CD3+ t0


title: CD56 fraction healthy person H1 t2

description:
miRNA profiling
CD56 fraction healthy person H1 t2
H1 CD56 t2


title: CD3 fraction healthy person H1 t1

description:
miRNA profiling
CD3 fraction healthy person H1 t1
H1 CD3 t1


title: CD3 fraction healthy person H1 t2

description:
miRNA profiling
CD3 fraction healthy person H1 t2
H1 CD3 t2


title: CD15 fraction healthy person H2 t0

description:
miRNA profiling
CD15 fraction healthy person H2 t0
H2 CD15+ t0


title: Exosomes healthy person H1 t1

description:
miRNA profiling
Exosomes healthy person H1 t1
H1 Exos t1


title: CD19 fraction healthy person H1 t1

description:
miRNA profiling
CD19 fraction healthy person H1 t1
H1 CD19 t1


title: CD19 fraction healthy person H1 t0

description:
miRNA profiling
CD19 fraction healthy person H1 t0
H1 CD19+ t0


title: CD19 fraction healthy person H1 t2

description:
miRNA profiling
CD19 fraction healthy person H1 t2
H1 CD19 t2


title: CD15 fraction healthy person H1 t0

description:
miRNA profiling
CD15 fraction healthy person H1 t0
H1 CD15+ t0


title: CD15 fraction healthy person H1 t2

description:
miRNA profiling
CD15 fraction healthy person H1 t2
H1 CD15 t2


title: CD14 fraction healthy person H1 t0

description:
miRNA profiling
CD14 fraction healthy person H1 t0
H1 CD14+ t0


title: CD15 fraction healthy person H1 t1

description:
miRNA profiling
CD15 fraction healthy person H1 t1
H1 CD15 t1


title: CD14 fraction healthy person H1 t2

description:
miRNA profiling
CD14 fraction healthy person H1 t2
H1 CD14 t2


title: CD14 fraction healthy person H1 t1

description:
miRNA profiling
CD14 fraction healthy person H1 t1
H1 CD14 t1


title: 28 dpc_crush - left optic nerve

city: Fort Worth

first: Tasneem

middle: Putliwala

last: Sharma

state: Texas

address: 3500 Camp Bowie Blvd

department: Cell Biology and Anatomy- Visual Sciences

institute: UNTHSC

description: gene expression data from optic nerve following ONC

hyb_protocol: Biotin-labeled cDNA was mixed with Affymetrix eukaryotic hybridization buffer, placed onto Affymetrix Mouse Gene 1.0 ST arrays, and incubated at 45º C for 18 h with 60 rpm rotation in an Affymetrix Model 640 Genechip Hybridization Oven.  Following hybridization, the arrays were washed, stained with streptavidin-phycoerythrin, and the signal was amplified with an anti-streptavidin antibody using the Affymetrix Model 450 Fluidics Station.

scan_protocol: Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade

data_processing: Data were collected using the using the GeneChip operating software (GCOS) v1.4 with Affymetrix default analysis settings and global scaling as normalization method

organism: Mus musculus

source_name: Optic nerves harvested at 28 dpc

label_protocol: Biotinylated cDNA were prepared using NuGen FL-Ovation cDNA Biotin Module according to manufacturers protocol.

growth_protocol: BALB/cJ mice aged 2-4 months were utilized for all the experiments and were obtained from the Jackson Laboratories.

extract_protocol: ON samples were collected in 1ml of TRIzol and homogenized using 5mm steel beads in the TissueLyser LT for five minutes at 50 oscillations/second. For phase separation 50μl of BAN Phase Separation Reagent was added to the homogenized samples, and samples were centrifuged at 14,000rpm for 15 minutes. The upper aqueous phase was transferred to an RNeasy mini column and processed according to the manufacturer's protocol. Total RNA was pooled from each group (experimental or control group at each time point) and 50ng of RNA from pool was converted to cDNA

treatment_protocol: The ON of the left eye was crushed 0.5mm posterior from the globe for 4 seconds using the Nickell’s technique. For the microarray studies, five mice were used per time-point. After the ON tissues were harvested samples were all pooled for each experimental (left, n=5) and control eye (right, n=5) group and sent for microarray analysis

tag: strain

value: BALB/cJ

tag: stress

value: ONC of left eye

tag: tissue

value: left optic nerve

tag: timepoint

value: 28 dpc


title: RafGOFNotchIC_3

city: Worcester

first: Thomas

middle: C

last: Greenough

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

description: Raf GOF and Notch IC (intracellular domain) overexpression female fly midgut

hyb_protocol: Affymetrix Eukaryotic Target Hybridization protocol (GeneChip Expression Analysis Technical Manual)

scan_protocol: Affymetrix GeneChip Scanner 3000 with GCOS software according to manufacturer's protocol (GeneChip Expression Analysis Technical Manual)

data_processing: Probset signal normalization with RMA, GeneSpring 7.30, GENECLUSTER 2.0

label: Biotin

organism: Drosophila melanogaster

source_name: Intestine

label_protocol: GeneChip 3'IVT Express Kit Ambion

extract_protocol: Trisol extraction

tag: genotype

value: RAF GOF Notch IC overexpression

value: midgut


title: RafGOFNotchDN_1

description: Raf GOF and Notch DN (dominant negative) overexpression female fly midgut

value: RAF GOF Notch DN


title: µ0.04 rep3 10 min

city: Toulouse

first: Muriel

last: Cocaign-Bousquet

address: 135 avenue de Rangueil

department: UMR5504 INSA/CNRS - UMR792 INSA/INRA

country: France

institute: Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés

hyb_protocol: see Redon et al. 2005. Role of mRNA stability during genome-wide adaptation of Lactococcus lactis to carbon starvation. J Biol Chem 280(43):36380-385

data_processing: Raw data were processed to access mRNA concentrations and were normalized to the mean intensity of the reference membrane (before rifampicin addition) for each batch. mRNA half-lives (t1/2) were calculated from the degradation rate constant (k), which corresponds to the slope of mRNA concentration logarithm as a function of time with the relation t1/2=ln(2)/k

organism: Lactococcus lactis

source_name: batch 0.04 h-1 repet3 10min

growth_protocol: cultures were performed in chemically defined medium with low Branched-Chain Amino Acid concentrations. Chemostat cultures (growth rates of 0.51 and 0.11h-1) were isoleucine limited whereas isoleucine starvation occured progressively in batch cultures (grawth rates of 0.8, 0.38 and 0.04 h-1).

treatment_protocol: At T=0 rifampicin was added into the culture at a final concentration of 500 µg.mL-1 so as to block transcription, mRNA levels were followed during the next 20 minutes

tag: treatment

value: µ0.04 rifampicin

value: 10 min


title: RafGOF_3

description: Raf GOF (gain of function) overexpression female fly midgut

value: RAF GOF


title: RafGOFNotchDN_2


title: RafGOFNotchIC_1


title: PAXGene blood healthy person H1 t0

description:
miRNA profiling
PAXGene blood healthy person H1 t0
H1 PAX t0

value: healthy

value: whole blood


title: µ0.04 rep2 12.67 min

scan_protocol: see Redon et al. 2005. Role of mRNA stability during genome-wide adaptation of Lactococcus lactis to carbon starvation. J Biol Chem 280(43):36380-385

source_name: batch 0.04 h-1 repet2 12.67min


title: RafGOF_4


title: RafGOFNotchIC_2


title: RafGOFNotchDN_4


title: RafGOFNotchDN_3


title: µ0.04 rep2 4.67 min

source_name: batch 0.04 h-1 repet2 4.67min

label_protocol: see Redon et al. 2005. Role of mRNA stability during genome-wide adaptation of Lactococcus lactis to carbon starvation. J Biol Chem 280(43):36380-385


title: µ0.04 rep1 8 min

source_name: batch 0.04 h-1 repet1 8min

extract_protocol: see Redon et al. 2005. Role of mRNA stability during genome-wide adaptation of Lactococcus lactis to carbon starvation. J Biol Chem 280(43):36380-385

value: 8 min


title: µ0.04 rep2 0 min

source_name: batch 0.04 h-1 repet2 0min

value: 0 min


title: µ0.04 rep2 8.67 min

source_name: batch 0.04 h-1 repet2 8.67min


title: µ0.04 rep1 12 min

source_name: batch 0.04 h-1 repet1 12min

value: 12 min


title: µ0.04 rep3 6.67 min

source_name: batch 0.04 h-1 repet3 6.67min


title: µ0.04 rep3 3.33 min

source_name: batch 0.04 h-1 repet3 3.33min


title: µ0.04 rep3 0 min

source_name: batch 0.04 h-1 repet3 0min


title: µ0.04 rep1 4 min

source_name: batch 0.04 h-1 repet1 4min

value: 4 min


title: RafGOFNotchIC_4

value: female


title: µ0.04 rep1 0 min

source_name: batch 0.04 h-1 repet1 0min


title: wildtype_4

description: Wild type female fly midgut

value: WT


title: wildtype_3

description: Wild type female fly midgut


title: RafGOF_1


title: wildtype_2

description: Wild type female fly midgut


title: RafGOF_2


title: µ0.38 rep3 0 min

source_name: batch 0.38 h-1 repet3 0min

value: µ0.38 rifampicin


title: µ0.38 rep2 11.33 min

source_name: batch 0.38 h-1 repet2 11.33min


title: µ0.38 rep3 5.33 min

source_name: batch 0.38 h-1 repet3 5.33min


title: µ0.38 rep3 8.67 min

source_name: batch 0.38 h-1 repet3 8.67min


title: µ0.38 rep2 7.33 min

source_name: batch 0.38 h-1 repet2 7.33min


title: µ0.38 rep1 12 min

source_name: batch 0.38 h-1 repet1 12min


title: µ0.38 rep1 8 min

source_name: batch 0.38 h-1 repet1 8min


title: µ0.38 rep2 3.33 min

source_name: batch 0.38 h-1 repet2 3.33min


title: µ0.38 rep2 0 min

source_name: batch 0.38 h-1 repet2 0min


title: µ0.38 rep3 2.67 min

source_name: batch 0.38 h-1 repet3 2.67min


title: µ0.38 rep1 4.17 min

source_name: batch 0.38 h-1 repet1 4.17min


title: wildtype_1

description: Wild type female fly midgut

source_name: Intestine


title: µ0.38 rep1 0 min

source_name: batch 0.38 h-1 repet1 0min


title: µ0.8 rep6 7.66 min

source_name: batch 0.8 h-1 repet6 7.66min

value: µ0.8 rifampicin


title: µ0.8 rep6 3.66 min

source_name: batch 0.8 h-1 repet6 3.66min


title: µ0.8 rep6 1.33 min

source_name: batch 0.8 h-1 repet6 1.33min


title: Jun KD, PGC1a OV, biol. rep. 2

city: Basel

first: Christoph

last: Handschin

address: Spitalstrasse 41

country: Switzerland

institute: Biozentrum, University of Basel

hyb_protocol: 3 µg of fragmented cRNA were hybridized for 17 hr at 45°C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Fluidics Station 450 (Affymetrix) under FS450_0002 protocol, using the Hybridization Wash and Stain Kit (Affymetrix)

scan_protocol: The GeneChips were scanned with an Affymetrix GeneChip Scanner 3000 7G

data_processing: Raw probe intensities were corrected for background and unspecific binding using the Bioconductor package “affy”. Probes were classified as expressed or non-expressed by using the “Mclust” R package and, after removal of non-expressed probes, the intensity values were quantile normalized across all samples. Using mapping of the probes to the UCSC collection of mouse mRNAs, probes were then associated to a comprehensive collection of mouse promoters available from the SwissRegulon database (Pachkov et al., 2013). The log2 expression level of a given promoter was calculated as the weighted average of the expression levels of all probes associated to it.

source_name: C2C12 cells with Jun KD, PGC1a OV

label_protocol: Biotinylated cDNA were prepared according to the WT Expression Kit (Ambion) followed by the  WT Terminal Labeling and Hybridization Labeling Kit (Affymetrix) from 270ng total RNA

growth_protocol: C2C12 cells were grown to 90% confluence in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 Units/ml penicillin and 100ug/ml streptomycin. The differentiation to myotubes was induced by changing the medium to DMEM supplemented with 2% horse serum for 72h.

extract_protocol: The RNA was extracted using Trizol® and according to the Trizol® Reagent RNA extraction protocol.

treatment_protocol: The siRNAs for the individual knockdown of the following genes were purchased from Dharmacon (Fisher Scientific) and used to transfect myotubes: Fos, Jun, Atf3 and the non-targeting siRNA pool (control). The transfection was performed using the siRNAs at a final concentration of 50nM and DharmaFECT1 transfection reagent  according to the Thermo Scientific DharmaFECT Transfection Reagents siRNA Transfection Protocol. 24h after the transfection with siRNAs for Fos, Jun and Atf3 knockdown, the cells were cultivated in the presence of the PGC-1alpha expressing adenovirus for 48h. The control transfection cells (previously transfected with the non-targeting siRNA pool) were cultivated in the presence of either GFP or PGC-1alpha adenovirus.

tag: differentiation stage

value: C2C12 myotubes

tag: phenotype

value: PGC-1alpha over-expression

value: Jun siRNA


title: Fos KD, PGC1a OV, biol. rep. 2

source_name: C2C12 cells with Fos KD, PGC1a OV

value: Fos siRNA


title: Ctrl KD, PGC1a OV, biol. rep. 2

source_name: C2C12 cells with Ctrl KD, PGC1a OV

value: non-targeting siRNA


title: 546778A09 - mpk6_mock_bio2 vs mpk6_flg_bio2

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: Analysis of flg22-induced transcriptional changes in mpk3, mpk4 and mpk6 mutants.

hyb_protocol: mpk6_flg_bio2 Cy5 / mpk6_mock_bio2 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: Mapix, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Arabidopsis thaliana

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: whole plant - 0,5xMS(sigma6899),0.5g/L MES,pH 5.7, 0.5g/l Agar TypeE. Hygrometry:45%, temperature:22°C, light:6h-22h.

treatment_protocol: Name:flg22_treatment - compound based treatment - biotic stress,flg22:quantity 1uM time 30min . Plants were grown on solid media for 13 days,then submerged with liquid 0.5x MS for 24h.Flg22 was finally added to the liquid MS, plates were agitated for homogeneisation for a few secondes and samples freezed in liquid nitrogen after 30min treatment.

tag: harvest date

value: whole plant

treatment_protocol: Name:mock_treatment - compound based treatment - biotic stress,h2o:time 30min . Plants were grown on solid media for 13 days,then submerged with liquid 0.5x MS for 24h.Wwas finally added to the liquid MS, plates were agitated for homogeneisation for a few secondes and samples freezed in liquid nitrogen after 30min treatment.

value: mock


title: 546778A12 - mpk6_flg_bio3 vs mpk6_mock_bio3

hyb_protocol: mpk6_mock_bio3 Cy5 / mpk6_flg_bio3 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.

growth_protocol: whole plant - 0,5xMS(sigma6899),0.5g/L MES,pH 5.7, 0.5g/l Agar TypeE. Hygrometry:45%, Temperature:22°C, light:6h-22h.


title: µ0.8 rep5 7 min

source_name: batch 0.8 h-1 repet5 7min

value: 7 min


title: µ0.8 rep6 0 min

source_name: batch 0.8 h-1 repet6 0min


title: 546778A07 - mpk6_mock_bio1 vs mpk6_flg_bio1

hyb_protocol: mpk6_flg_bio1 Cy5 / mpk6_mock_bio1 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: µ0.8 rep5 0.66 min

source_name: batch 0.8 h-1 repet5 0.66min


title: µ0.8 rep5 3.33 min

source_name: batch 0.8 h-1 repet5 3.33min


title: 546778A06 - mpk6_mock_bio3 vs col_mock_bio3

hyb_protocol: col_mock_bio3 Cy5 / mpk6_mock_bio3 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.

value: col (wild type)


title: Ctrl KD, GFP OV, biol. rep. 2

source_name: C2C12 cells with Ctrl KD, GFP OV

value: GFP over-expression


title: 546778A10 - mpk6_flg_bio2 vs mpk6_mock_bio2

hyb_protocol: mpk6_mock_bio2 Cy5 / mpk6_flg_bio2 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: Atf3 KD, PGC1a OV, biol. rep. 2

source_name: C2C12 cells with Atf3 KD, PGC1a OV

value: Atf3 siRNA


title: µ0.8 rep5 0 min

source_name: batch 0.8 h-1 repet5 0min

value: 0 min


title: 546778A05 - col_mock_bio3 vs mpk6_mock_bio3

hyb_protocol: mpk6_mock_bio3 Cy5 / col_mock_bio3 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: 546778A03 - col_mock_bio2 vs mpk6_mock_bio2

hyb_protocol: mpk6_mock_bio2 Cy5 / col_mock_bio2 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: 546778A04 - mpk6_mock_bio2 vs col_mock_bio2

hyb_protocol: col_mock_bio2 Cy5 / mpk6_mock_bio2 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: 546778A11 - mpk6_mock_bio3 vs mpk6_flg_bio3

hyb_protocol: mpk6_flg_bio3 Cy5 / mpk6_mock_bio3 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: 546778A08 - mpk6_flg_bio1 vs mpk6_mock_bio1

hyb_protocol: mpk6_mock_bio1 Cy5 / mpk6_flg_bio1 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: 546740A12 - mpk4_mock_bio3 vs col_mock_bio3

hyb_protocol: col_mock_bio3 Cy5 / mpk4_mock_bio3 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: 546778A02 - mpk6_mock_bio1 vs col_mock_bio1

hyb_protocol: col_mock_bio1 Cy5 / mpk6_mock_bio1 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: 546778A01 - col_mock_bio1 vs mpk6_mock_bio1

hyb_protocol: mpk6_mock_bio1 Cy5 / col_mock_bio1 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: 546740A10 - mpk4_mock_bio2 vs col_mock_bio2

hyb_protocol: col_mock_bio2 Cy5 / mpk4_mock_bio2 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: 546740A11 - col_mock_bio3 vs mpk4_mock_bio3

hyb_protocol: mpk4_mock_bio3 Cy5 / col_mock_bio3 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: 546740A09 - col_mock_bio2 vs mpk4_mock_bio2

hyb_protocol: mpk4_mock_bio2 Cy5 / col_mock_bio2 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: Ctrl KD, GFP OV, biol. rep. 1

hyb_protocol: 3 µg of fragmented cRNA were hybridized for 17 hr at 45°C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Fluidics Station 450 (Affymetrix) under FS450_0002 protocol, using the Hybridization Wash and Stain Kit (Affymetrix)


title: PGC1a OV, biol. rep. 2

source_name: C2C12 cells with PGC1a OV

label_protocol: Biotinylated cDNA were prepared according to the WT Expression Kit (Ambion) followed by the  WT Terminal Labeling and Hybridization Labeling Kit (Affymetrix) from 200ng total RNA

treatment_protocol: The myotubes were grown in the presence of either GFP control adenovirus (condition 1) or PGC-1alpha expressing adenovirus (condition 2) for 48h.


title: Atf3 KD, PGC1a OV, biol. rep. 1


title: Ctrl KD, PGC1a OV, biol. rep. 1


title: Fos KD, PGC1a OV, biol. rep. 1


title: PGC1a OV, biol. rep. 3


title: GFP OV, biol. rep. 3

source_name: C2C12 cells with GFP OV


title: PGC1a OV, biol. rep. 1


title: GFP OV, biol. rep. 2


title: µ0.8 rep4 0 min

hyb_protocol: see Redon et al. 2005. Role of mRNA stability during genome-wide adaptation of Lactococcus lactis to carbon starvation. J Biol Chem 280(43):36380-385

source_name: batch 0.8 h-1 repet4 0min


title: µ0.8 rep4 8.33 min

source_name: batch 0.8 h-1 repet4 8.33min


title: µ0.8 rep4 1 min

source_name: batch 0.8 h-1 repet4 1min

value: 1 min


title: GFP OV, biol. rep. 1


title: µ0.8 rep3 5 min

source_name: batch 0.8 h-1 repet3 5min

value: 5 min


title: µ0.8 rep4 4 min

source_name: batch 0.8 h-1 repet4 4min

value: 4 min


title: µ0.8 rep3 3 min

source_name: batch 0.8 h-1 repet3 3min

value: 3 min


title: 546740A07 - col_mock_bio1 vs mpk4_mock_bio1

hyb_protocol: mpk4_mock_bio1 Cy5 / col_mock_bio1 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: µ0.8 rep3 1.083 min

source_name: batch 0.8 h-1 repet3 1.083min

value: µ0.8 rifampicin


title: 546740A06 - col_flg_bio3 vs col_mock_bio3

hyb_protocol: col_mock_bio3 Cy5 / col_flg_bio3 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.

extract_protocol: col_flg_bio3:100mg. (Qiagen_RNeasy.pdf)


title: µ0.8 rep3 0 min

source_name: batch 0.8 h-1 repet3 0min


title: µ0.8 rep2 6.33 min

source_name: batch 0.8 h-1 repet2 6.33min


title: 546740A08 - mpk4_mock_bio1 vs col_mock_bio1

hyb_protocol: col_mock_bio1 Cy5 / mpk4_mock_bio1 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: 546740A04 - col_flg_bio2 vs col_mock_bio2

hyb_protocol: col_mock_bio2 Cy5 / col_flg_bio2 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.

extract_protocol: col_flg_bio2:100mg. (Qiagen_RNeasy.pdf)


title: 546740A02 - col_flg_bio1 vs col_mock_bio1

hyb_protocol: col_mock_bio1 Cy5 / col_flg_bio1 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.

extract_protocol: col_flg_bio1:100mg. (Qiagen_RNeasy.pdf)


title: 546740A05 - col_mock_bio3 vs col_flg_bio3

hyb_protocol: col_flg_bio3 Cy5 / col_mock_bio3 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: 546740A03 - col_mock_bio2 vs col_flg_bio2

hyb_protocol: col_flg_bio2 Cy5 / col_mock_bio2 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: µ0.8 rep2 1.33 min

source_name: batch 0.8 h-1 repet2 1.33min


title: µ0.8 rep2 4 min

source_name: batch 0.8 h-1 repet2 4min


title: 546739A09 - col_mock_bio2 vs mpk3_mock_bio2

hyb_protocol: mpk3_mock_bio2 Cy5 / col_mock_bio2 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: Carbo Day4 (413R)

city: St Andrews

first: Antonis

last: Koussounadis

address: Sir Harold Mitchell Building

department: Biology

country: United Kingdom

institute: University of St Andrews

description: Sample name: 413R

hyb_protocol: standard Illumina

scan_protocol: standard Illumina

data_processing: background correction, VS, RSN using Bioconductor package lumi (Du et al., 2008)

source_name: HOX424 Carbo Day4

label_protocol: Illumina TotalPrep RNA Amplification Kit (Ambion) according to manufacturers’ standard procedure

extract_protocol: Qiagen miRNeasy Mini kit and TissueRaptor following manufacturer's instructions

tag: disease state

value: Ovarian cancer

tag: xenograft from ovarian cancer model

tag: agent

value: Carbo


title: 546739A11 - col_mock_bio3 vs mpk3_mock_bio3

hyb_protocol: mpk3_mock_bio3 Cy5 / col_mock_bio3 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: SUM159

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

source_name: breast cancer cell line

value: breast cancer

tag: subtype

value: Basal-like cells


title: 546739A12 - mpk3_mock_bio3 vs col_mock_bio3

hyb_protocol: col_mock_bio3 Cy5 / mpk3_mock_bio3 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: CarboTax Day7 (411R)

description: Sample name: 411R

source_name: HOX424 CarboTax Day7

value: CarboTax


title: µ0.8 rep2 0 min

source_name: batch 0.8 h-1 repet2 0min


title: CarboTax Day7 (412L)

description: Sample name: 412L


title: CarboTax Day1 (64L)

description: Sample name: 64L

source_name: HOX424 CarboTax Day1


title: CarboTax Day1 (64R)

description: Sample name: 64R


title: CarboTax Day1 (383R)

description: Sample name: 383R


title: µ0.8 rep1 7.66 min

source_name: batch 0.8 h-1 repet1 7.66min


title: CarboTax Day7 (411L)

description: Sample name: 411L


title: 546739A10 - mpk3_mock_bio2 vs col_mock_bio2

hyb_protocol: col_mock_bio2 Cy5 / mpk3_mock_bio2 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.

value: whole plant


title: CarboTax Day7 (412R)

description: Sample name: 412R


title: Carbo Day4 (66L)

description: Sample name: 66L


title: 546740A01 - col_mock_bio1 vs col_flg_bio1

hyb_protocol: col_flg_bio1 Cy5 / col_mock_bio1 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.

value: mock


title: 546694A12 - mpk3_flg_bio3 vs mpk3_mock_bio3

hyb_protocol: mpk3_mock_bio3 Cy5 / mpk3_flg_bio3 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: Carbo Day7 (416L)

description: Sample name: 416L

source_name: HOX424 Carbo Day7


title: Carbo Day4 (413L)

description: Sample name: 413L


title: Control Day1 (392L)

description: Sample name: 392L

source_name: HOX424 Control Day1

value: Control


title: µ0.8 rep1 4.33 min

source_name: batch 0.8 h-1 repet1 4.33min


title: CarboTax Day1 (383L)

description: Sample name: 383L


title: µ0.8 rep1 2 min

source_name: batch 0.8 h-1 repet1 2min

value: 2 min


title: µ0.8 rep1 0 min

source_name: batch 0.8 h-1 repet1 0min


title: µ0.1 rep4 15 min

source_name: chemostat 0.1 h-1 repet4 15min

value: µ0.1 rifampicin

value: 15 min


title: Carbo Day7 (417L)

description: Sample name: 417L


title: 546694A11 - mpk3_mock_bio3 vs mpk3_flg_bio3

hyb_protocol: mpk3_flg_bio3 Cy5 / mpk3_mock_bio3 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: Control Day1 (393L)

description: Sample name: 393L


title: Carbo Day7 (419L)

description: Sample name: 419L


title: Control Day14 (457L)

description: Sample name: 457L

source_name: HOX424 Control Day14


title: Control Day1 (394L)

description: Sample name: 394L


title: Control Day14 (441L)

description: Sample name: 441L


title: 546694A10 - mpk3_flg_bio2 vs mpk3_mock_bio2

hyb_protocol: mpk3_mock_bio2 Cy5 / mpk3_flg_bio2 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: µ0.1 rep4 3 min

hyb_protocol: see Redon et al. 2005. Role of mRNA stability during genome-wide adaptation of Lactococcus lactis to carbon starvation. J Biol Chem 280(43):36380-385

source_name: chemostat 0.1 h-1 repet4 3min


title: 546694A09 - mpk3_mock_bio2 vs mpk3_flg_bio2

hyb_protocol: mpk3_flg_bio2 Cy5 / mpk3_mock_bio2 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: µ0.1 rep4 7 min

source_name: chemostat 0.1 h-1 repet4 7min

value: 7 min


title: Carbo Day7 (417R)

description: Sample name: 417R


title: Jun KD, PGC1a OV, biol. rep. 1

hyb_protocol: 3 µg of fragmented cRNA were hybridized for 17 hr at 45°C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Fluidics Station 450 (Affymetrix) under FS450_0002 protocol, using the Hybridization Wash and Stain Kit (Affymetrix)

source_name: C2C12 cells with Jun KD, PGC1a OV

value: C2C12 myotubes

value: PGC-1alpha over-expression

value: Jun siRNA


title: Control Day7 (418L)

description: Sample name: 418L

source_name: HOX424 Control Day7


title: CarboTax Day2 (423L)

description: Sample name: 423L

source_name: HOX424 CarboTax Day2


title: Carbo Day1 (396L)

description: Sample name: 396L

source_name: HOX424 Carbo Day1


title: Carbo Day14 (454L)

description: Sample name: 454L

source_name: HOX424 Carbo Day14


title: 546694A07 - mpk3_mock_bio1 vs mpk3_flg_bio1

hyb_protocol: mpk3_flg_bio1 Cy5 / mpk3_mock_bio1 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: Carbo Day1 (397L)

description: Sample name: 397L


title: Carbo Day14 (453R)

description: Sample name: 453R


title: 546694A05 - mpk4_mock_bio3 vs mpk4_flg_bio3

hyb_protocol: mpk4_flg_bio3 Cy5 / mpk4_mock_bio3 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: µ0.1 rep4 0 min

source_name: chemostat 0.1 h-1 repet4 0min

value: 0 min


title: Control Day14 (440L)

description: Sample name: 440L


title: CarboTax Day2 (421L)

description: Sample name: 421L


title: 546694A08 - mpk3_flg_bio1 vs mpk3_mock_bio1

hyb_protocol: mpk3_mock_bio1 Cy5 / mpk3_flg_bio1 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: µ0.1 rep3 15 min

source_name: chemostat 0.1 h-1 repet3 15min


title: 546694A06 - mpk4_flg_bio3 vs mpk4_mock_bio3

hyb_protocol: mpk4_mock_bio3 Cy5 / mpk4_flg_bio3 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: µ0.1 rep3 3 min

source_name: chemostat 0.1 h-1 repet3 3min

value: 3 min


title: µ0.1 rep3 7 min

source_name: chemostat 0.1 h-1 repet3 7min


title: µ0.1 rep3 0 min

source_name: chemostat 0.1 h-1 repet3 0min


title: Carbo Day1 (396R)

description: Sample name: 396R

value: Ovarian cancer


title: µ0.1 rep2 18 min

source_name: chemostat 0.1 h-1 repet2 8min

value: 18 min


title: Carbo Day2 (409R)

description: Sample name: 409R

source_name: HOX424 Carbo Day2

value: Carbo


title: Carbo Day14 (455R)

description: Sample name: 455R


title: µ0.1 rep2 8 min

source_name: chemostat 0.1 h-1 repet2 4min

value: 8 min


title: µ0.1 rep2 4 min

source_name: chemostat 0.1 h-1 repet2 2min

value: 4 min


title: Control Day7 (388L)

description: Sample name: 388L


title: 546694A04 - mpk4_flg_bio2 vs mpk4_mock_bio2

hyb_protocol: mpk4_mock_bio2 Cy5 / mpk4_flg_bio2 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.

value: whole plant


title: Carbo Day1 (408R)

description: Sample name: 408R

hyb_protocol: standard Illumina


title: 546694A03 - mpk4_mock_bio2 vs mpk4_flg_bio2

hyb_protocol: mpk4_flg_bio2 Cy5 / mpk4_mock_bio2 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.

value: mock


title: Carbo Day14 (439R)

description: Sample name: 439R


title: 546694A02 - mpk4_flg_bio1 vs mpk4_mock_bio1

hyb_protocol: mpk4_mock_bio1 Cy5 / mpk4_flg_bio1 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: Control Day7 (420R)

description: Sample name: 420R

value: Control


title: 546694A01 - mpk4_mock_bio1 vs mpk4_flg_bio1

hyb_protocol: mpk4_flg_bio1 Cy5 / mpk4_mock_bio1 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: Carbo Day2 (65R)

description: Sample name: 65R


title: 546628A12 - mpk3_mock_bio1 vs col_mock_bio1

hyb_protocol: col_mock_bio1 Cy5 / mpk3_mock_bio1 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.

value: col (wild type)


title: Control Day0 (395L)

description: Sample name: 395L

source_name: HOX424 Control Day0


title: µ0.1 rep2 0 min

source_name: chemostat 0.1 h-1 repet2 0min

value: µ0.1 rifampicin


title: CarboTax Day4 (428L)

description: Sample name: 428L

source_name: HOX424 CarboTax Day4

value: CarboTax


title: 546628A11 - col_mock_bio1 vs mpk3_mock_bio1

hyb_protocol: mpk3_mock_bio1 Cy5 / col_mock_bio1 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: CarboTax Day4 (426L)

description: Sample name: 426L


title: µ0.1 rep1 18 min

source_name: chemostat 0.1 h-1 repet1 8min


title: Control Day0 (451R)

description: Sample name: 451R


title: Control Day0 (425L)

description: Sample name: 425L


title: Carbo Day2 (410L)

description: Sample name: 410L


title: CarboTax Day4 (428R)

description: Sample name: 428R


title: Intratumoral heterogeneity of colorectal cancers, patient 5, biopsy 1, metastasis

city: Seoul

first: Tae-Min

last: Kim

address: Seocho-Gu, Banpo-Dong

department: Dept of Medical Informatics

country: South Korea

institute: The Catholic University of Korea, College of Medicine

description:
Patient 5, metastatic biopsy #1
CRC5-M1

hyb_protocol: Standard Agilent protocol

scan_protocol: Scanned on an Agilent Technologies Scanner G2505C Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and normalization.

source_name: Tumor

label_protocol: DNA labelling and hybridization was performed according to the manufacturer's instruction

extract_protocol: Genomic DNA was extracted using phenol-chloroform extraction method.  The purity and quantity of the DNA was estimated using Nanodrop spectrophotometer.

value: Metastatic colorectal cancer (liver)

tag: individual

value: Patient 5

source_name: Matched normal

value: Matched normal (adjacent)


title: CarboTax Day4 (426R)

description: Sample name: 426R


title: µ0.1 rep1 0 min

source_name: chemostat 0.1 h-1 repet1 0min


title: Carbo Day2 (409L)

description: Sample name: 409L


title: µ0.1 rep1 4 min

source_name: chemostat 0.1 h-1 repet1 2min


title: Intratumoral heterogeneity of colorectal cancers, patient 5, biopsy 2, metastasis

description:
Patient 5, metastatic biopsy #2
CRC5-M2


title: Intratumoral heterogeneity of colorectal cancers, patient 5, biopsy 2, primary

description:
Patient 5, primary biopsy #2
CRC5-P2

value: Primary colorectal cancer


title: µ0.1 rep1 8 min

source_name: chemostat 0.1 h-1 repet1 4min


title: CarboTax Day14 (385R)

description: Sample name: 385R

source_name: HOX424 CarboTax Day14


title: CarboTax Day14 (385L)

description: Sample name: 385L


title: CarboTax Day4 (345R)

description: Sample name: 345R

source_name: OV1002 CarboTax Day4


title: Carbo Day2 (72L)

description: Sample name: 72L

source_name: OV1002 Carbo Day2


title: µ0.51 rep4 15 min

source_name: chemostat 0.51 h-1 repet4 15min

value: µ0.51 rifampicin

value: 15 min


title: µ0.51 rep4 7 min

source_name: chemostat 0.51 h-1 repet4 7min

value: 7 min


title: Intratumoral heterogeneity of colorectal cancers, patient 4, biopsy 3, metastasis

description:
Patient 4, metastatic biopsy #3
CRC4-M3

value: Patient 4


title: Intratumoral heterogeneity of colorectal cancers, patient 4, biopsy 4, metastasis

description:
Patient 4, metastatic biopsy #4
CRC4-M4


title: Carbo Day2 (352L)

description: Sample name: 352L

value: Ovarian cancer

value: Carbo


title: µ0.51 rep4 3 min

source_name: chemostat 0.51 h-1 repet4 3min

value: 3 min


title: CarboTax Day4 (340R)

description: Sample name: 340R


title: Intratumoral heterogeneity of colorectal cancers, patient 5, biopsy 1, primary

description:
Patient 5, primary biopsy #1
CRC5-P1


title: Intratumoral heterogeneity of colorectal cancers, patient 4, biopsy 2, metastasis

description:
Patient 4, metastatic biopsy #2
CRC4-M2


title: CarboTax Day14 (384L)

description: Sample name: 384L


title: Carbo Day2 (376R)

description: Sample name: 376R


title: CarboTax Day4 (359R)

description: Sample name: 359R


title: µ0.51 rep3 7 min

source_name: chemostat 0.51 h-1 repet3 7min


title: µ0.51 rep3 15 min

source_name: chemostat 0.51 h-1 repet3 15min


title: Carbo Day2 (355R)

description: Sample name: 355R


title: CarboTax Day4 (314R)

description: Sample name: 314R


title: CarboTax Day14 (384R)

description: Sample name: 384R


title: µ0.51 rep4 0 min

source_name: chemostat 0.51 h-1 repet4 0min

value: 0 min


title: Intratumoral heterogeneity of colorectal cancers, patient 4, biopsy 1, metastasis

description:
Patient 4, metastatic biopsy #1
CRC4-M1


title: Carbo Day7 (320R)

description: Sample name: 320R

source_name: OV1002 Carbo Day7


title: CarboTax Day1 (377L)

description: Sample name: 377L

source_name: OV1002 CarboTax Day1


title: Intratumoral heterogeneity of colorectal cancers, patient 4, biopsy 2, primary

description:
Patient 4, primary biopsy #2
CRC4-P2


title: µ0.51 rep3 3 min

source_name: chemostat 0.51 h-1 repet3 3min


title: CarboTax Day1 (341L)

description: Sample name: 341L


title: Carbo Day7 (374L)

description: Sample name: 374L


title: Intratumoral heterogeneity of colorectal cancers, patient 4, biopsy 1, primary

description:
Patient 4, primary biopsy #1
CRC4-P1

source_name: Tumor


title: Control Day14 (460L)

description: Sample name: 460L

source_name: OV1002 Control Day14


title: µ0.51 rep3 0 min

source_name: chemostat 0.51 h-1 repet3 0min


title: Intratumoral heterogeneity of colorectal cancers, patient 3, biopsy 5, metastasis

description:
Patient 3, metastatic biopsy #5
CRC3-M5

value: Patient 3

source_name: Matched normal


title: Intratumoral heterogeneity of colorectal cancers, patient 3, biopsy 6, metastasis

description:
Patient 3, metastatic biopsy #6
CRC3-M6


title: CarboTax Day1 (339R)

description: Sample name: 339R


title: Carbo Day7 (368L)

description: Sample name: 368L


title: Intratumoral heterogeneity of colorectal cancers, patient 3, biopsy 4, metastasis

description:
Patient 3, metastatic biopsy #4
CRC3-M4


title: µ0.51 rep2 8 min

source_name: chemostat 0.51 h-1 repet2 8min

value: 8 min


title: µ0.51 rep2 2 min

source_name: chemostat 0.51 h-1 repet2 2min

value: 2 min


title: Intratumoral heterogeneity of colorectal cancers, patient 3, biopsy 3, metastasis

description:
Patient 3, metastatic biopsy #3
CRC3-M3


title: µ0.51 rep2 0 min

source_name: chemostat 0.51 h-1 repet2 0min


title: Control Day14 (360L)

description: Sample name: 360L

value: Control


title: Carbo Day7 (311R)

description: Sample name: 311R


title: CarboTax Day1 (347R)

description: Sample name: 347R

value: CarboTax


title: µ0.51 rep2 4 min

source_name: chemostat 0.51 h-1 repet2 4min

value: 4 min


title: Control Day14 (329L)

description: Sample name: 329L


title: µ0.51 rep1 8 min

source_name: chemostat 0.51 h-1 repet1 8min


title: CarboTax Day14 (324R)

description: Sample name: 324R

source_name: OV1002 CarboTax Day14


title: Intratumoral heterogeneity of colorectal cancers, patient 3, biopsy 1, metastasis

description:
Patient 3, metastatic biopsy #1
CRC3-M1

value: Metastatic colorectal cancer (liver)


title: µ0.51 rep1 4 min

source_name: chemostat 0.51 h-1 repet1 4min


title: Intratumoral heterogeneity of colorectal cancers, patient 3, biopsy 2, metastasis

description:
Patient 3, metastatic biopsy #2
CRC3-M2

value: Matched normal (adjacent)


title: Intratumoral heterogeneity of colorectal cancers, patient 3, biopsy 5, primary

description:
Patient 3, primary biopsy #5
CRC3-P5

value: Primary colorectal cancer


title: Carbo Day4 (71L)

description: Sample name: 71L

source_name: OV1002 Carbo Day4


title: Control Day1 (357R)

description: Sample name: 357R

source_name: OV1002 Control Day1


title: µ0.51 rep1 2 min

source_name: chemostat 0.51 h-1 repet1 2min

value: µ0.51 rifampicin


title: CarboTax Day7 (465L)

description: Sample name: 465L

source_name: OV1002 CarboTax Day7


title: Carbo Day4 (336R)

description: Sample name: 336R


title: Intratumoral heterogeneity of colorectal cancers, patient 3, biopsy 4, primary

description:
Patient 3, primary biopsy #4
CRC3-P4


title: Carbo Day1 (332L)

description: Sample name: 332L

source_name: OV1002 Carbo Day1


title: Control Day1 (380R)

description: Sample name: 380R


title: CarboTax Day14 (346L)

description: Sample name: 346L


title: Intratumoral heterogeneity of colorectal cancers, patient 3, biopsy 3, primary

description:
Patient 3, primary biopsy #3
CRC3-P3


title: Control Day1 (328R)

description: Sample name: 328R


title: Intratumoral heterogeneity of colorectal cancers, patient 3, biopsy 1, primary

description:
Patient 3, primary biopsy #1
CRC3-P1


title: Carbo Day4 (358L)

description: Sample name: 358L


title: Carbo Day4 (379R)

description: Sample name: 379R


title: Intratumoral heterogeneity of colorectal cancers, patient 3, biopsy 2, primary

description:
Patient 3, primary biopsy #2
CRC3-P2


title: CarboTax Day14 (324L)

description: Sample name: 324L


title: µ0.51 rep1 0 min

source_name: chemostat 0.51 h-1 repet1 0min


title: Control Day7 (335R)

description: Sample name: 335R

source_name: OV1002 Control Day7


title: CarboTax Day7 (343L)

description: Sample name: 343L


title: Intratumoral heterogeneity of colorectal cancers, patient 2, biopsy 2, metastasis

description:
Patient 2, metastatic biopsy #2
CRC2-M2

source_name: Tumor

value: Patient 2


title: CarboTax Day14 (350L)

description: Sample name: 350L


title: Control Day7 (313R)

description: Sample name: 313R


title: Carbo Day1 (370L)

description: Sample name: 370L


title: CarboTax Day7 (338L)

description: Sample name: 338L


title: CarboTax Day7 (304R)

description: Sample name: 304R


title: Carbo Day1 (75L)

description: Sample name: 75L


title: Control Day0 (356L)

description: Sample name: 356L

source_name: OV1002 Control Day0


title: Intratumoral heterogeneity of colorectal cancers, patient 2, biopsy 1, metastasis

description:
Patient 2, metastatic biopsy #1
CRC2-M1

source_name: Matched normal


title: Intratumoral heterogeneity of colorectal cancers, patient 2, biopsy 5, primary

description:
Patient 2, primary biopsy #5
CRC2-P5


title: CarboTax Day2 (463R)

description: Sample name: 463R

source_name: OV1002 CarboTax Day2


title: Intratumoral heterogeneity of colorectal cancers, patient 2, biopsy 4, primary

description:
Patient 2, primary biopsy #4
CRC2-P4


title: Carbo Day1 (73R)

description: Sample name: 73R


title: Control Day7 (316L)

description: Sample name: 316L


title: Intratumoral heterogeneity of colorectal cancers, patient 2, biopsy 3, primary

description:
Patient 2, primary biopsy #3
CRC2-P3


title: OGD 7h_R1

city: Coimbra

first: Joana

middle: Filipa

last: Fernandes

state: -- Please Select --

address: Rua Larga, Faculdade de Medicina 2º andar, lab 206A Coimbra

department: Life Sciences

country: Portugal

institute: Center for Neuroscience and Cell Biology

description: Gene expression of OGD-stimulated neurons after 7h

hyb_protocol: Hybridizations were carried out following Agilent Technologies instructions for One-Color Microarray-Based Gene Expression Analysis (Agilent Technologies, Santa Clara, CA, USA), using whole-genome Rat GE 4x44K v3 Microarrays.

scan_protocol: Images were obtained using Agilent G2565AA microarray scanner and fluorescence quantization was performed using Agilent Feature Extraction 10.5.1.1 software and GE1_105_Dec08 protocol.

data_processing: The signal intensity was aligned and normalized between microarrays by centering the median of the signal distribution using BRB-ArrayTools v3.8.1.

organism: Rattus norvegicus

source_name: Oxygen and Glucose Deprivation 7h_R1

label_protocol: Equal amounts of RNA extract (200 ng) from each replicate were amplified and Cy-3-labeled using the Low Input Quick Amp Labeling kit (Agilent Technologies)

growth_protocol: The cultures were maintained in Neurobasal medium in a humidified incubator with 5% CO2/95% air, at 37°C, for 14-15 days.

extract_protocol: Total RNA from three rat hippocampal neuronal cultures submitted to control or OGD conditions were collected after 7h and 24h of recovery

treatment_protocol: For the OGD challenge, hippocampal cultures were incubated in a glucose-free saline buffer (in mM: 10 HEPES, 116 NaCl, 5.4 KCl, 0.8 MgSO4, 1 NaH2PO4, 1.8 CaCl2, 25 NaHCO3, 25 sucrose, pH 7.3) in an anaerobic chamber (Forma Anaerobic System, Thermo Fisher Scientific), at 37C, for the indicated times. Control neurons were placed in a similar saline buffer with 25 mM glucose instead of sucrose and kept in an air/CO2 incubator, at 37C, for the same period of time. After the stimulus periods, the saline buffers were replaced by conditioned medium and the cultures returned to the air/CO2 incubator, where they were kept to recover for the indicated times.

tag: strain background

value: Wistar

tag: develpmetal stage

value: E18 rat embryos

value: Primary hippocampal neurons

tag: exposed to

value: Oxygen and Glucose deprivation (OGD)

tag: time point

value: after 7h recovery


title: Intratumoral heterogeneity of colorectal cancers, patient 2, biopsy 1, primary

description:
Patient 2, primary biopsy #1
CRC2-P1


title: Intratumoral heterogeneity of colorectal cancers, patient 2, biopsy 2, primary

description:
Patient 2, primary biopsy #2
CRC2-P2


title: OGD 7h_R3

source_name: Oxygen and Glucose Deprivation 7h_R3


title: Intratumoral heterogeneity of colorectal cancers, patient 1, biopsy 3, metastasis

description:
Patient 1, metastatic biopsy #3
CRC1-M3

value: Patient 1


title: Carbo Day14 (301L)

description: Sample name: 301L

source_name: OV1002 Carbo Day14

value: Ovarian cancer

value: Carbo

tag: time


title: Control Day0 (76L)

description: Sample name: 76L


title: Carbo Day14 (349R)

description: Sample name: 349R


title: Carbo Day14 (378R)

description: Sample name: 378R


title: Intratumoral heterogeneity of colorectal cancers, patient 1, biopsy 2, metastasis

description:
Patient 1, metastatic biopsy #2
CRC1-M2

tag: tissue


title: OGD 24h_R2

description: Gene expression of OGD-stimulated neurons after 24h

source_name: Oxygen and Glucose Deprivation 24h_R2

value: after 24h recovery


title: CarboTax Day2 (366R)

description: Sample name: 366R


title: OGD 7h_R2

source_name: Oxygen and Glucose Deprivation 7h_R2


title: CarboTax Day2 (364L)

description: Sample name: 364L


title: Carbo Day14 (351L)

description: Sample name: 351L


title: PRKO oviduct, biological rep3

city: St Lucia

first: Lisa

last: Akison

state: QLD

address: Sir William MacGregor Building

department: Biomedical Sciences

country: Australia

institute: University of Queensland

description: Gene expression data from oviducts collected from homozygous progesterone receptor mutants (PRKO) at 8h post-hCG

hyb_protocol: Following fragmentation and biotinylation, samples were hybridised at 45C for 16-18 h on Affymetrix Mouse Gene 1.0 ST arrays.  Arrays were washed and then stained using a fluorescently-labelled antibody using the GeneChip® Fluidics Station 450/250.

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

data_processing: Microarray data were analysed using Partek Genomics Suite software (Partek Inc.). Background correction was performed by robust multichip averaging followed by probe affinity adjustment for the variable G-C content of probes. Quantile normalisation was performed to remove systematic variations resulting from array preparation or sample hybridization conditions. A mean probe-set summary was obtained by averaging the intensity values for the multiple probes representing an individual gene.

source_name: Mouse oviduct, PRKO genotype, 8h post-hCG

label_protocol: Biotinylated cRNA were prepared using the GeneChip® Whole-Transcript (WT) cDNA Synthesis and Amplification kit (Affymetrix) according to the manufacturer’s instructions.

growth_protocol: All mice were injected i.p. with 5IU of equine chorionic gonadotropin and 5IU of human chorionic gonadotropin prior to collection of oviducts.  Oviducts were collected at 8h post-hCG.

extract_protocol: Oviducts were homogenised in 1 ml Tri Reagent (Sigma-Aldrich Pty. Ltd.) using a Precellys 24 tissue homogeniser (Sapphire Bioscience).  Total RNA was extracted using a modified Tri Reagent protocol, which included an overnight precipitation step at -20C and the addition of 1 μl Ambion GlycoBlue (15 mg/ml; Applied Biosystems) during precipitation.

value: oviduct

value: PRKO


title: CarboTax Day2 (319L)

description: Sample name: 319L

value: CarboTax


title: Intratumoral heterogeneity of colorectal cancers, patient 1, biopsy 4, primary

description:
Patient 1, primary biopsy #4
CRC1-P4


title: PRKO oviduct, biological rep4