title: 400R.wt_rep3

source_name: Root of Arabidopsis thaliana plant exposed to 400 ppm [CO2]. Rep 3


title: Rs631_6h_10μM_B11

status: Public on Jul 01 2017

type: RNA

city: Research Triangle Park

first: Patrick

middle: D

last: McMullen

state: North Carolina

address: 6 Davis Drive, P.O. Box 12137

country: USA

institute: The Hamner Institutes for Health Sciences

hyb_protocol: GeneTitan according to manufacturer’s protocol

scan_protocol: Affymetrix GeneTitan

data_processing: Analysis of gene expression data was performed using Partek software (Partek Inc., St. Louis, MO) utlising GC-RMA normalisation. Arrays with average log2 expression value above 0.06 of median log2 expression values across all arrays were excluded for further analyses. A 1-way ANOVA with interactions was performed to compare gene expression between the treated and control cells. Probability values were adjusted for multiple comparisons using a false discovery rate of 5%.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: Cultured primary hepatocytes exposed to GW7647

label_protocol: RNA samples were prepared for microarray hybridization using the GeneAtlas™ 3’ IVT Express Kit according to manufacturer’s protocol (Applied Biosystems, Carlsbad, CA). Briefly, total RNA was reverse transcribed to synthesize first-strand cDNA. The cDNA was then converted into a double-stranded DNA template for transcription. Amplified cRNA (aRNA) was transcribed in vitro, with incorporation of a biotin-congugated nucleotide. The aRNA was then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate, and samples were fragmented to prepare the biotin-labeled aRNA samples for hybridization onto Affymetrix® GeneChip

growth_protocol: Cells were plated on Rat Collagen IV-coated plates and Geltrex was added for a final concentration of 0.25 mg/ml approximately 6 hours after plating. Cells were maintained at 37˚C in a hμMidified 5% CO2 atmosphere in William E medium supplemented with cell maintenance cocktail B (Invitrogen).

extract_protocol: Total RNA was collected from the treated cells using the Qiaxtractor and the Qiagen VX reagent pack according to the manufacturer’s protocol (Qiagen, Valencia, CA). A DNase 1 incubation was performed on all samples to remove any possible contamination of the RNA samples with cellular DNA

treatment_protocol: GW7647 was obtained from Tocris (Bristol, UK)

tag: biological replicate

tag: exposure time

tag: agent

tag: concentration


title: 800L.NR mutant_rep1

city: pamplona

first: Ivan

last: Jáuregui Mosquera

state: Navarra

address: Campus de Arrosadia, s/n,  Dpto. Ciencias del Medio Natural

country: Spain

institute: Universidad Pública de Navarra

description: Gene expression after 5 weeks CO2 tratment. Sample collected 4h from the beginning of the light period

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 mL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 mL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the microarrays. They were incubated in SureHyb microarray hybridization chambers with gasket slides (Agilent Technologies) at 65ºC for 17 h in an rotary oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 10 s with acetonitrile and 30 s in Agilent's stabilization and drying solution, then air dried.

scan_protocol: Hybridized slides were scanned at 5 μm resolution and their signal intensities were detected by a GenePix 4100A microarray scanner (Molecular devices, Sunnyvale, CA, USA).

data_processing: Normalization and differential expression analysis of the data was done using limma R package (Smyth 2004). Normalization was carried out using quantile method and Bayes statistics were applied to determine the differential expression between the comparisons. Statistical significance was corrected for multiple testing using the Benjamini-Hochberg procedure. For this study, the significant difference in gene expression was Q value < 0.05 and log2 fold change > 0.5.

organism: Arabidopsis thaliana

source_name: Leaf of Arabidopsis thaliana NR mutant plant exposed to 800 ppm [CO2]. Rep 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by    NucleoSpin® Gel and PCR Clean-up column purification (Macherey-Nagel, Düren, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Arabidopsis thaliana, Columbia 0 ecotype (col 0) and Arabidopsis thaliana NR mutant (NR double mutant G′4-3, nia1- 1/nia2-5) plants grown under hydroponic conditions.

extract_protocol: Total RNA was isolated according to Liao et al.(2004).

tag: tissue

value: leaf

tag: ecotype

tag: genotype

value: NR double mutant G′4-3, nia1- 1/nia2-5


title: Rs632_6h_0.01μM_B05


title: 800L.wt_rep13

source_name: Leaf of Arabidopsis thaliana plant exposed to 800 ppm [CO2]. Rep 3

value: wild type


title: Rs632_6h_0.1μM_C07


title: Rs631_6h_0μM_B07


title: 400R.wt_rep2

source_name: Root of Arabidopsis thaliana plant exposed to 400 ppm [CO2]. Rep 2

value: root


title: 400R.wt_rep1

source_name: Root of Arabidopsis thaliana plant exposed to 400 ppm [CO2]. Rep 1


title: 800L.NR mutant_rep2

source_name: Leaf of Arabidopsis thaliana NR mutant plant exposed to 800 ppm [CO2]. Rep 2


title: Rs631_6h_0.001μM_D05


title: Rs631_6h_0.1μM_B09


title: 400L.NR mutant_rep2

source_name: Leaf of Arabidopsis thaliana NR mutant plant exposed to 400 ppm [CO2]. Rep 1


title: Rs628_6h_1μM_D08


title: 400L.wt_rep2

source_name: Leaf of Arabidopsis thaliana plant exposed to 400 ppm [CO2]. Rep 2


title: Rs631_6h_1μM_E08


title: 800L.wt_rep1

source_name: Leaf of Arabidopsis thaliana plant exposed to 800 ppm [CO2]. Rep 1


title: 400L.wt_rep1

source_name: Leaf of Arabidopsis thaliana plant exposed to 400 ppm [CO2]. Rep 1


title: Rs631_6h_0.01μM_A03


title: Rs627_6h_0μM_G04


title: 800L.NR mutant_rep3

source_name: Leaf of Arabidopsis thaliana NR mutant plant exposed to 800 ppm [CO2]. Rep 3


title: Rs627_6h_10μM_B05


title: 400L.NR mutant_rep1


title: Rs628_6h_0.01μM_C11


title: 400L.NR mutant_rep3


title: 400L.wt_rep3

source_name: Leaf of Arabidopsis thaliana plant exposed to 400 ppm [CO2]. Rep 3


title: 800L.wt_rep2

source_name: Leaf of Arabidopsis thaliana plant exposed to 800 ppm [CO2]. Rep 2


title: Rs628_6h_0μM_E07


title: Rs627_6h_0.1μM_F09


title: Rs632_2h_0.01μM_C07


title: Patient 7

city: Tokyo

first: Rei

last: Ogawa

address: 1-1-5, Sendagi, Bunkyo-ku

department: Department of Plastic, Reconstructive and Aesthetic Surgery

country: Japan

institute: Nippon Medical School

description: Biological replicate 7 of 7

hyb_protocol: Hybridization was performed according to the Agilent 60-mer oligo microarray processing protocol using the Gene Expression Hybridization kit (Agilent Technologies). Briefly, 825 ng of the corresponding Cy3- and Cy5-labeled fragmented cRNA were combined and hybridized overnight (17 hours, 65 °C) to Agilent 4x44K Whole Human Genome Oligo Microarray using Agilent’s recommended hybridization chamber and oven. Finally, the microarray was washed once with the Agilent Gene Expression Wash Buffer 1 for 1 minute at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37°C) for 1 minute. The last washing step was performed with acetonitrile.

scan_protocol: Fluorescence signals of the hybridized microarray were detected using a DNA microarray scanner (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES;  v.9.1) was used to read out and process the microarray image files.

organism: Homo sapiens

source_name: Patient 7_keloid

label_protocol: Total RNA (1 mg) was amplified by a low RNA input fluorescent linear amp kit (Agilent Technologies) and labeled with cyanin(Cy)3 and Cy5 for control and keloid samples, respectively (CyDye; PerkinElmer, Boston, MA), during the in vitro transcription process, according to the manufacturer’s protocol.Briefly, 825 ng of the corresponding Cy3- and Cy5-labeled fragmented cRNA were combined and hybridized overnight (17 hours, 65 °C) to Agilent 4x44K Whole Human Genome Oligo Microarray using Agilent’s recommended hybridization chamber and oven.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: This part of the study was approved by the ethical committee at Nippon Medical School, Tokyo, Japan (No.22-11-143). Seven patients with keloids (aged 21-60 years), undergoing surgical treatment were recruited. Informed consent was obtained from all subjects. Once the tissue was harvested, the specimens were immediately frozen in liquid nitrogen and stored at -80°C prior to analysis. During surgery, 5 mm squares were marked on a peripheral redness area of severe pain, considered as a strong inflammatory area and on an adjacent normal skin area that should be resected and discarded as “dog ear” for aesthetic reason, showing no inflammatory change by the naked eye, as a control.

value: keloid lesion

source_name: Patient 7_normal

value: normal skin


title: Rs632_2h_0.1μM_G12


title: Rs627_6h_1μM_B03


title: Patient 5

description: Biological replicate 5 of 7

source_name: Patient 5_keloid

source_name: Patient 5_normal


title: Patient 6

description: Biological replicate 6 of 7

source_name: Patient 6_keloid

source_name: Patient 6_normal


title: Rs632_2h_10μM_G05

source_name: Cultured primary hepatocytes exposed to GW7647


title: Rs627_6h_0.001μM_E09


title: Rs632_2h_0μM_D04


title: Rs632_2h_1μM_B01


title: Patient 2

description: Biological replicate 2 of 7

source_name: Patient 2_keloid

source_name: Patient 2_normal


title: Patient 1

description: Biological replicate 1 of 7

source_name: Patient 1_keloid

source_name: Patient 1_normal


title: con_replicate 5

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description:
8784129079_F
replicate 5

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization in Partek Genomic Suite

organism: Mus musculus

source_name: Bone marrow-derived macrophages

label_protocol: Biotinylated cRNA were prepared with the TargetAmpTM Nano-gTM Biotin-aRNA Labeling Kit

extract_protocol: Total RNA from all cell samples was isolated using TRIzol Reagent (Invitrogen).

tag: treatment

value: untreated

tag: strain

tag: age

value: 10-15 months

value: Bone marrow

tag: cell type

value: Bone marrow-derived macrophages (BMDMs)


title: CD_replicate 5

description:
9020366075_F
replicate 5

value: 6 h HPβCD

value: 2-5 months


title: CD-cc_replicate 5

description:
9020366075_C
replicate 5

value: CC + 6h HPβCD


title: Rs631_2h_10μM_A06


title: Rs632_2h_0.001μM_C03_2


title: con_replicate 4

description:
8784129079_E
replicate 4


title: Patient 3

description: Biological replicate 3 of 7

source_name: Patient 3_keloid

source_name: Patient 3_normal


title: Patient 4

description: Biological replicate 4 of 7

source_name: Patient 4_keloid

source_name: Patient 4_normal


title: Rs628_2h_10μM_A05_2


title: CD_replicate 4

description:
8784129079_D
replicate 4


title: CD_replicate 3

description:
8784129079_B
replicate 3


title: Rs631_2h_1μM_H10


title: Rs631_2h_0.001μM_F08


title: Rs631_2h_0.1μM_C07


title: Rs631_2h_0μM_A11


title: Rs631_2h_0.01μM_D11


title: cc_replicate 5

description:
8784129079_C
replicate 5

value: CC


title: CD_replicate 2

description:
8784129079_A
replicate 2


title: Rs628_2h_1μM_H04


title: Rs628_2h_0.1μM_A02


title: Rs627_2h_10μM_B04


title: cc_replicate 2

description:
8615616013_F
replicate 2


title: CD_replicate 1

description:
8762536007_B
replicate 1


title: con_replicate 3

description:
8762536031_D
replicate 3


title: Rs627_2h_0μM_F07


title: Rs627_2h_0.1μM_B02


title: Rs627_2h_0.001μM_C05


title: con_replicate 1

description:
8615616013_D
replicate 1


title: In-Vivo_10mg/kg_7

source_name: adult male Sprague Dawley SD:CD rat liver

growth_protocol: Forty nine adult male Sprague Dawley SD:CD rats (~200 g) were obtained from Charles Rivers Laboratories.  All animals were delivered to an AAALAC accredited animal facility located at The Hamner Institutes, which is operated by trained animal care personnel employed by Mispro Biotech Services Corporation.  Animals were kept in a humidity- and temperature-controlled, HEPA-filtered, mass air-displacement room.  The room was maintained on a 12 h light-dark cycle at approximately 19–25 °C with a relative humidity of approximately 40-60%. Rodent diet NIH-07 feed (Zeigler Brothers Inc., Gardners, PA) and reverse osmosis water were provided ad libitum.  These studies were approved by the Mispro Biotech Services’ Animal Care and Use Committee.

extract_protocol: Total RNA was collected from samples using the Qiaxtractor and the Qiagen VX reagent pack according to the manufacturer’s protocol (Qiagen, Valencia, CA). A DNase 1 incubation was performed on all samples to remove any possible contamination of the RNA samples with cellular DNA

treatment_protocol: The rats were administered vehicle or GW7647 at 0.1, 1 or 10 mg/kg (n=10/dose) by oral gavage daily for 4 days. Twenty-four hours after the final dose, rats were euthanized by isoflurane anesthesia followed by exsanguination.  Livers were excised from animal, section into 0.5 cm cubes and placed in RNA later solution or snap frozen in liquid nitrogen.

value: adult

tag: gender

value: male

value: Sprague Dawley SD:CD

tag: dose (mg/kg/d)


title: cc_replicate 4

description:
8762536007_F
replicate 4


title: CD-cc_replicate 4

description:
8762536031_F
replicate 4


title: cc_replicate 1

description:
8615616013_E
replicate 1


title: Rs627_2h_0.01μM_H08


title: In-Vivo_10mg/kg_6


title: In-Vivo_10mg/kg_8


title: In-Vivo_10mg/kg_4


title: CD-cc_replicate 1

description:
8615616013_A
replicate 1


title: cc_replicate 3

description:
8762536005_C
replicate 3


title: In-Vivo_10mg/kg_2


title: In-Vivo_10mg/kg_5


title: CD-cc_replicate 2

description:
8615616013_B
replicate 2


title: In-Vivo_1mg/kg_10


title: In-Vivo_10mg/kg_3


title: In-Vivo_10mg/kg_1


title: In-Vivo_10mg/kg_10


title: In-Vivo_10mg/kg_9


title: con_replicate 2

description:
8762536005_F
replicate 2


title: CD-cc_replicate 3

description:
8615616013_C
replicate 3


title: In-Vivo_1mg/kg_1


title: In-Vivo_1mg/kg_5


title: In-Vivo_1mg/kg_6


title: In-Vivo_1mg/kg_2


title: In-Vivo_1mg/kg_7


title: In-Vivo_0mg/kg_10


title: In-Vivo_1mg/kg_3


title: In-Vivo_1mg/kg_8


title: In-Vivo_0mg/kg_9


title: In-Vivo_0mg/kg_8


title: In-Vivo_0mg/kg_6


title: In-Vivo_0mg/kg_4


title: In-Vivo_1mg/kg_4


title: In-Vivo_0mg/kg_1


title: In-Vivo_0mg/kg_2


title: In-Vivo_0mg/kg_5


title: In-Vivo_0.1mg/kg_10


title: In-Vivo_0mg/kg_7


title: In-Vivo_0.1mg/kg_7


title: In-Vivo_0.1mg/kg_3


title: In-Vivo_0.1mg/kg_6


title: In-Vivo_1mg/kg_9


title: In-Vivo_0.1mg/kg_4


title: In-Vivo_0.1mg/kg_8


title: In-Vivo_0.1mg/kg_9


title: Huh7 cells with HBeAg, biological rep2

city: New Delhi

first: Perumal

last: Vivekanandan

state: Delhi

address: Kusuma School of Biological Sciences, IIT Delhi, Hauz Khas, New Delhi-110016

department: Kusuma School of biological Sciences, IIT Delhi

country: India

institute: Indian Institute of technology Delhi

hyb_protocol: Hybridization was done for 16 hours at 45°C and 60 rpm using Affymetrix Hybridization Oven

scan_protocol: The gene chips were scanned using Affymetrix Gene chip scanner 3000 7G.

data_processing: The data was analyzed using GeneSpring software; RMA normalization

source_name: Huh7 cells with HBeAg

label_protocol: Biotinlyated RNAs were prepared according to genechip 3' IVT  Express kit.

growth_protocol: Huh-7 cells were maintained in DMEM supplemented with 10% FBS, 5000U/ml Penicillin and 5000μg/ml Streptomycin at 37°C with 5% carbon-dioxide.

extract_protocol: Total RNA was isolated using Trizol as per the manufacturer's instructions.

treatment_protocol: Huh-7 cells were transfected with HBeAg-expression vector and total RNA was harvested post 48 hours transfection.

tag: cell line

value: human hepatocellular carcinoma cell line

tag: transfected with

value: control vector


title: In-Vivo_0mg/kg_3


title: THP-1-AzaPan-Biological replicate-5

city: Wilmington

first: Sonali

middle: P

last: Barwe

state: DE

address: 1701 Rockland Road

institute: Alfred I. duPont Hospital for Children

description: Gene expression data from 3 uM azacytidine + 5 nm panobinostat treated, 48 h, biological replicate 5, THP-1

hyb_protocol: Labeled RNA samples were hybridized to GeneChip Human Gene 2.0 ST Array overnight in a Hybridization oven 645.

scan_protocol: Stained arrays were scanned on GeneChip scanner 3000 7G system.

data_processing:
The array images were processed and quality accessed using Affymetrix GeneChip Command Console Software (AGCC) and Affymetrix Expression Console Software following manufacturer's instructions.
RMA

source_name: THP-1 cells

label_protocol: Biotinylated and amplified DNA targets were generated from 100 ng RNA using the GeneChip WT Plus Reagent Kit following manufacturer's protocol.

growth_protocol: see above under characteristics : growth conditions

extract_protocol: Total RNA was isolated using Trizol Reagent (Invitrogen, ThermoFisher Scientific, Waltham, MA) following manufacturer's protocol.

treatment_protocol: Azacytidine and panobinostat solubiilzed in DMSO were diluted in respective culture medium at indicated concentrations, either alone or in combination. Cells were incubated with the indicated agents for 48 h in an incubator at 37C with 5% carbon-di-oxide before harvesting.

tag: growth conditions

value: RPMI with 10% FBS


title: Huh7 cells with HBeAg, biological rep1


title: In-Vivo_0.1mg/kg_2


title: Huh7 cells control, biological rep1

description: wild type1_(PrimeView).as.rma-Signal

source_name: Huh7 cells control

value: HBeAg-expression vector


title: Huh7 cells control, biological rep2

description: wild type2_(PrimeView).as.rma-Signal


title: THP-1-AzaPan-Biological replicate-3

description: Gene expression data from 3 uM azacytidine + 5 nm panobinostat treated, 48 h, biological replicate 3, THP-1


title: In-Vivo_0.1mg/kg_5


title: In-Vivo_0.1mg/kg_1


title: THP-1-Pan-Biological replicate-3

description: Gene expression data from 5 nm panobinostat treated, 48 h, biological replicate 3, THP-1


title: THP-1-Pan-Biological replicate-2

description: Gene expression data from 5 nm panobinostat treated, 48 h, biological replicate 2, THP-1


title: THP-1-AzaPan-Biological replicate-4

description: Gene expression data from 3 uM azacytidine + 5 nm panobinostat treated, 48 h, biological replicate 4, THP-1


title: THP-1-Pan-Biological replicate-5

description: Gene expression data from 5 nm panobinostat treated, 48 h, biological replicate 5, THP-1


title: THP-1-AzaPan-Biological replicate-2

description: Gene expression data from 3 uM azacytidine + 5 nm panobinostat treated, 48 h, biological replicate 2, THP-1


title: THP-1-Aza-Biological replicate-5

description: Gene expression data from 3 uM azacytidine treated, 48 h, biological replicate 5, THP-1


title: THP-1-Pan-Biological replicate-4

description: Gene expression data from 5 nm panobinostat treated, 48 h, biological replicate 4, THP-1


title: THP-1-AzaPan-Biological replicate-1

description: Gene expression data from 3 uM azacytidine + 5 nm panobinostat treated, 48 h, biological replicate 1, THP-1


title: THP-1-Aza-Biological replicate-4

description: Gene expression data from 3 uM azacytidine treated, 48 h, biological replicate 4, THP-1


title: THP-1-Pan-Biological replicate-1

description: Gene expression data from 5 nm panobinostat treated, 48 h, biological replicate 1, THP-1


title: THP-1-Aza-Biological replicate-1

description: Gene expression data from 3 uM azacytidine treated, 48 h, biological replicate 1, THP-1


title: invasive Cottus replicate 7

type: genomic

city: Ploen

first: Stefan

last: Dennenmoser

address: August-Thienemann Str. 2

department: Evolutionary Genetics

institute: Max-Planck Institute for Evolutionary Biology

hyb_protocol: see “direct method” as outlined in the Agilent protocol “Agilent Oligonucleotide Array-based CGH for genomic DNA analysis” (version 7.3, March 2014, Agilent Technologies).

scan_protocol: Agilent type C scanner

data_processing: Signal intensity values were extracted using the Agilent Feature Extraction software version 10.7.3.1.; Data were cleared for outlier values; calibrated for probe responsiveness (following Pozhitkov et al. (2014) and normalized (LOESS-normalization without background correction).

molecule: genomic DNA

organism: Cottus

source_name: DNA extraction from blood

extract_protocol: genomic DNA extracted from blood samples, using the 5 prime ArchivePure DNA Tissue kit (5 PRIME, Hamburg, Germany) or the Qiagen Blood and Tissue kit.

tag: species

value: Cottus sp. invasive

value: blood

organism: Cottus perifretum

source_name: common reference individual

tag: population

value: Larse Beek


title: THP-1-Aza-Biological replicate-2

description: Gene expression data from 3 uM azacytidine treated, 48 h, biological replicate 2, THP-1


title: THP-1-Aza-Biological replicate-3

description: Gene expression data from 3 uM azacytidine treated, 48 h, biological replicate 3, THP-1


title: THP-1-Control-Biological replicate-3

description: Gene expression data from vehicle treated, 48 h, biological replicate 3, THP-1


title: THP-1-Control-Biological replicate-5

description: Gene expression data from vehicle treated, 48 h, biological replicate 5, THP-1


title: C.rhenanus replicate 7

organism: Cottus rhenanus

label_protocol: see “direct method” as outlined in the Agilent protocol “Agilent Oligonucleotide Array-based CGH for genomic DNA analysis” (version 7.3, March 2014, Agilent Technologies).

value: Cottus rhenanus


title: C.rhenanus replicate 6


title: AML-193-AzaPan-Biological replicate-5

description: Gene expression data from 5 uM azacytidine + 5 nM panobinostat treated, 48 h, biological replicate 5, AML-193

source_name: AML-193 cells

value: IMDM with 5% FBS, 0.5 ng/ml insulin, 5 ng/ml transferrin receptor and 5 ng/ml GM-CSF


title: THP-1-Control-Biological replicate-2

description: Gene expression data from vehicle treated, 48 h, biological replicate 2, THP-1


title: invasive Cottus replicate 8


title: invasive Cottus replicate 5


title: invasive Cottus replicate 6


title: AML-193-AzaPan-Biological replicate-3

description: Gene expression data from 5 uM azacytidine + 5 nM panobinostat treated, 48 h, biological replicate 3, AML-193


title: THP-1-Control-Biological replicate-4

description: Gene expression data from vehicle treated, 48 h, biological replicate 4, THP-1


title: AML-193-AzaPan-Biological replicate-4

description: Gene expression data from 5 uM azacytidine + 5 nM panobinostat treated, 48 h, biological replicate 4, AML-193


title: C.perifretum replicate 8

value: Cottus perifretum


title: THP-1-Control-Biological replicate-1

description: Gene expression data from vehicle treated, 48 h, biological replicate 1, THP-1


title: AML-193-AzaPan-Biological replicate-2

description: Gene expression data from 5 uM azacytidine + 5 nM panobinostat treated, 48 h, biological replicate 2, AML-193


title: C.perifretum replicate 7


title: C.perifretum replicate 6


title: invasive Cottus replicate 4


title: AML-193-AzaPan-Biological replicate-1

description: Gene expression data from 5 uM azacytidine + 5 nM panobinostat treated, 48 h, biological replicate 1, AML-193


title: GNEM reanalysis-2 254

first: Satoru

last: Noguchi

address: 4-1-1, Ogawahigashi, Kodaira

department: Neuromuscular Research

institute: National Institute of Neuroscience, NCNP

description: GNE myopathy model

hyb_protocol: The microarrays were hybridized with 10 microgram of biotin-labeled aRNA samples by using Codelink controls and buffer kit (Applied Microarrays cat#320001)

scan_protocol: The arrays were  scanned  with An arrayscanner  GenePIx  4400A (Molecular Devices, LLC)

data_processing: The raw image data were annalyzed  to quantify the spot intensities with Codelink Expression annalysis software v5.0 (Applied Microarryas)

source_name: Triceps bracii

label_protocol: 1 microgram of total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) and then second-strand cDNA was synthesized with E.coli DNA polymerase I. After purification of RNA using a Quiagen QIAquick purification kit, cRNA was produced by invitrotranscription with Biotin 11-UTPusing Message AMP II Biotin enhanced kit (Life Technologies cat# AM1791)

extract_protocol: In average, 600um-thick cryostat sections were prepared for the extraction of total RNA from frozen triceps muscles

value: Gne-/- mutGNE Tg


title: GNEM reanalysis-2 257

description: GNE myopathy model


title: invasive Cottus replicate 3


title: GNEM reanalysis-2 258

description: GNE myopathy model


title: C.perifretum replicate 5


title: AML-193-Pan-Biological replicate-5

description: Gene expression data from 5 nM panobinostat treated, 48 h, biological replicate 5, AML-193


title: GNEM reanalysis-2 260

description: GNE myopathy model


title: C.perifretum replicate 4


title: AML-193-Pan-Biological replicate-4

description: Gene expression data from 5 nM panobinostat treated, 48 h, biological replicate 4, AML-193


title: GNEM reanalysis-2 253

description: GNE myopathy model


title: invasive Cottus replicate 2


title: GNEM reanalysis-2 251

description: GNE myopathy model


title: AML-193-Pan-Biological replicate-2

description: Gene expression data from 5 nM panobinostat treated, 48 h, biological replicate 2, AML-193


title: AML-193-Pan-Biological replicate-1

description: Gene expression data from 5 nM panobinostat treated, 48 h, biological replicate 1, AML-193


title: AML-193-Pan-Biological replicate-3

description: Gene expression data from 5 nM panobinostat treated, 48 h, biological replicate 3, AML-193


title: AML-193-Aza-Biological replicate-4

description: Gene expression data from 5 uM azacytidine treated, 48 h, biological replicate 4, AML-193


title: GNEM reanalysis-2 252

description: GNE myopathy model


title: AML-193-Aza-Biological replicate-5

description: Gene expression data from 5 uM azacytidine treated, 48 h, biological replicate 5, AML-193


title: GNEM 283

description: GNE myopathy model

value: Treatment with 1% N-acetylcysteine in drink water for 34 weeks


title: C.perifretum replicate 3


title: GNEM 280

description: GNE myopathy model

value: Treatment with 1% N-acetylcysteine in drink water for 33 weeks


title: C.rhenanus replicate 4


title: AML-193-Aza-Biological replicate-3

description: Gene expression data from 5 uM azacytidine treated, 48 h, biological replicate 3, AML-193


title: GNEM 284

description: GNE myopathy model

value: Treatment with 1% N-acetylcysteine in drink water for 35 weeks


title: GNEM 279

description: GNE myopathy model

value: Treatment with 1% N-acetylcysteine in drink water for 32 weeks


title: GNEM 277

description: GNE myopathy model

value: Treatment with 1% N-acetylcysteine in drink water for 31 weeks


title: C.perifretum replicate 2


title: C.rhenanus replicate 5


title: AML-193-Aza-Biological replicate-1

description: Gene expression data from 5 uM azacytidine treated, 48 h, biological replicate 1, AML-193


title: GNEM reanalysis 263

description: GNE myopathy model


title: GNEM 276

description: GNE myopathy model

value: Treatment with 1% N-acetylcysteine in drink water for 30 weeks


title: C.rhenanus replicate 3


title: AML-193-Control-Biological replicate-5

description: Gene expression data from vehicle treated, 48 h, biological replicate 5, AML-193


title: C.perifretum replicate 1


title: invasive Cottus replicate 1


title: AML-193-Aza-Biological replicate-2

description: Gene expression data from 5 uM azacytidine treated, 48 h, biological replicate 2, AML-193


title: C.rhenanus replicate 1


title: C.rhenanus replicate 2


title: GNEM reanalysis 262

description: GNE myopathy model


title: GNEM reanalysis 260

description: GNE myopathy model


title: AML-193-Control-Biological replicate-3

description: Gene expression data from vehicle treated, 48 h, biological replicate 3, AML-193


title: GNEM reanalysis 257

description: GNE myopathy model


title: AML-193-Control-Biological replicate-4

description: Gene expression data from vehicle treated, 48 h, biological replicate 4, AML-193


title: GNEM reanalysis 254

description: GNE myopathy model


title: AML-193-Control-Biological replicate-1

description: Gene expression data from vehicle treated, 48 h, biological replicate 1, AML-193


title: AML-193-Control-Biological replicate-2

description: Gene expression data from vehicle treated, 48 h, biological replicate 2, AML-193


title: MV4;11-AzaPan-Biological replicate-5

description: Gene expression data from 0.5 uM azacytidine + 1.5 nM panobinostat treated, 48 h, biological replicate 5, MV4;11

source_name: MV4;11 cells

value: IMDM with 10% FBS


title: MV4;11-AzaPan-Biological replicate-2

description: Gene expression data from 0.5 uM azacytidine + 1.5 nM panobinostat treated, 48 h, biological replicate 2, MV4;11


title: GNEM reanalysis 252

description: GNE myopathy model


title: GNEM reanalysis 251

description: GNE myopathy model


title: MV4;11-AzaPan-Biological replicate-4

description: Gene expression data from 0.5 uM azacytidine + 1.5 nM panobinostat treated, 48 h, biological replicate 4, MV4;11


title: MV4;11-AzaPan-Biological replicate-3

description: Gene expression data from 0.5 uM azacytidine + 1.5 nM panobinostat treated, 48 h, biological replicate 3, MV4;11


title: GNEM reanalysis 253

description: GNE myopathy model


title: GNEM reanalysis 258

description: GNE myopathy model


title: GNEM 294

description: GNE myopathy model

value: Treatment with 0.1% N-acetylcysteine in drink water for 35 weeks


title: MV4;11-Pan-Biological replicate-4

description: Gene expression data from 1.5 nM panobinostat treated, 48 h, biological replicate 4, MV4;11


title: sdhA_FA_I

city: Tainan

first: Jenn-Wei

last: Chen

address: No.1, University Road

country: Taiwan

institute: National Cheng Kung University

hyb_protocol: 0.6 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent SurePrint G3 Custom GE 8x60K 078966 (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: Microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing:
GeneSpring GX v.13.1
The values below 0.01 were set to 0.01. The log2 ratio of the intensity of signal channel to that of control channel was calculated and was then normalized to each slide’s median intensity ratio. The default interpretation mode was set to‘log of ratio’. Each time point was then tested separately for statistical differences using ANOVA at 5% confidence level, in conjunction with Benjamini-Hochberg multiple testing correction.

organism: Escherichia coli O157:H7

source_name: O157:H7 EDL933 sdhA in LB with FA

label_protocol: 0.2 μg of total RNA was amplified by a Agilent Low Input Quick-Amp WT Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.

growth_protocol: The overnight cultures of bacteria in LB broth were refreshed with the ratio of 1:100 into fresh LB broth, and incubated at 30℃ with continuous shaking until the absorbance at 590 nm reached 0.5 to 0.6.

extract_protocol: Bacterial RNA was purified with Qiagen RNeasy mini kit, and the samples with RNA Integrity Number (RIN) >9 were used for labeling

treatment_protocol: with/without 2.5 mM Fumaric acid

tag: strain background

tag: genotype/variation

value: sdhA deletion mutant

tag: culture media

value: LB with 2.5 mM Fumaric acid


title: GNEM 293

description: GNE myopathy model

value: Treatment with 0.1% N-acetylcysteine in drink water for 34 weeks


title: sdhA_FA_II


title: MV4;11-Pan-Biological replicate-5

description: Gene expression data from 1.5 nM panobinostat treated, 48 h, biological replicate 5, MV4;11


title: GNEM 290

description: GNE myopathy model

value: Treatment with 0.1% N-acetylcysteine in drink water for 33 weeks


title: MV4;11-AzaPan-Biological replicate-1

description: Gene expression data from 0.5 uM azacytidine + 1.5 nM panobinostat treated, 48 h, biological replicate 1, MV4;11


title: sdhA_FA_III


title: sdhA_LB_II

source_name: O157:H7 EDL933 sdhA in LB

value: LB


title: GNEM 288

description: GNE myopathy model

value: Treatment with 0.1% N-acetylcysteine in drink water for 31 weeks


title: sdhA_LB_I


title: MV4;11-Pan-Biological replicate-2

description: Gene expression data from 1.5 nM panobinostat treated, 48 h, biological replicate 2, MV4;11


title: GNEM 287

description: GNE myopathy model

value: Treatment with 0.1% N-acetylcysteine in drink water for 30 weeks


title: GNEM 289

description: GNE myopathy model

value: Treatment with 0.1% N-acetylcysteine in drink water for 32 weeks


title: sdhA_LB_III


title: MV4;11-Pan-Biological replicate-1

description: Gene expression data from 1.5 nM panobinostat treated, 48 h, biological replicate 1, MV4;11


title: EDL933_LB_II

source_name: O157:H7 EDL933 in LB

value: wild type


title: MV4;11-Pan-Biological replicate-3

description: Gene expression data from 1.5 nM panobinostat treated, 48 h, biological replicate 3, MV4;11


title: EDL933_LB_I


title: GNEM 260

description: GNE myopathy model

value: Gne-/- mutGNE Tg


title: MV4;11-Aza-Biological replicate-4

description: Gene expression data from 0.5 uM azacytidine treated, 48 h, biological replicate 4, MV4;11


title: MV4;11-Aza-Biological replicate-3

description: Gene expression data from 0.5 uM azacytidine treated, 48 h, biological replicate 3, MV4;11


title: MV4;11-Aza-Biological replicate-5

description: Gene expression data from 0.5 uM azacytidine treated, 48 h, biological replicate 5, MV4;11


title: GNEM 262

description: GNE myopathy model


title: MV4;11-Aza-Biological replicate-1

description: Gene expression data from 0.5 uM azacytidine treated, 48 h, biological replicate 1, MV4;11


title: MV4;11-Aza-Biological replicate-2

description: Gene expression data from 0.5 uM azacytidine treated, 48 h, biological replicate 2, MV4;11


title: GNEM 254

description: GNE myopathy model


title: GNEM 263

description: GNE myopathy model


title: GNEM 257

description: GNE myopathy model


title: Littermate 261

description: Control littermate

value: Gne+/- mutGNE Tg


title: MV4;11-Control-Biological replicate-4

description: Gene expression data from vehicle treated, 48 h, biological replicate 4, MV4;11


title: GNEM 251

description: GNE myopathy model


title: GNEM 258

description: GNE myopathy model


title: MV4;11-Control-Biological replicate-5

description: Gene expression data from vehicle treated, 48 h, biological replicate 5, MV4;11


title: Littermate 264

description: Control littermate


title: MV4;11-Control-Biological replicate-1

description: Gene expression data from vehicle treated, 48 h, biological replicate 1, MV4;11


title: MV4;11-Control-Biological replicate-3

description: Gene expression data from vehicle treated, 48 h, biological replicate 3, MV4;11


title: MV4;11-Control-Biological replicate-2

description: Gene expression data from vehicle treated, 48 h, biological replicate 2, MV4;11


title: GNEM reanalysis-2 262

description: GNE myopathy model


title: GNEM 253

description: GNE myopathy model


title: GNEM reanalysis-2 263

description: GNE myopathy model


title: Littermate 255

description: Control littermate


title: Sample_1600ng_Cy5

description:
raw data file:
US84303580_256762410001_S01_CGH_107_Sep09_2_4.txt

data_processing: Signal intensity values were extracted using the Agilent Feature Extraction software version 10.7.3.1.; For each probe, signal intensities were averaged over two probe replicates

source_name: DNA extraction from C. perifretum blood

value: Cottus perifretum

tag: tissue

value: blood


title: Sample_200ng_Cy5

description:
raw data file:
US84303580_256762410001_S01_CGH_107_Sep09_1_4.txt


title: Sample_400ng_Cy5

description:
raw data file:
US84303580_256762410001_S01_CGH_107_Sep09_2_1.txt


title: Sample_800ng_Cy5

description:
raw data file:
US84303580_256762410001_S01_CGH_107_Sep09_2_2.txt


title: GNEM 252

description: GNE myopathy model


title: Sample_1200ng_Cy5

description:
raw data file:
US84303580_256762410001_S01_CGH_107_Sep09_2_3.txt


title: Sample_50ng_Cy5

description:
raw data file:
US84303580_256762410001_S01_CGH_107_Sep09_1_2.txt


title: Sample_25ng_Cy5

description:
raw data file:
US84303580_256762410001_S01_CGH_107_Sep09_1_1.txt


title: Sample_100ng_Cy5

description:
raw data file:
US84303580_256762410001_S01_CGH_107_Sep09_1_3.txt


title: Sample_800ng_Cy3

source_name: DNA extraction from C. rhenanus blood

value: Cottus rhenanus


title: Plasma_Repressor_3

city: Vienna

first: Georg

last: Mair

address: Veterinaerplatz 1

country: Austria

institute: University for Veterinary Medicine Vienna

description: RMA dedection values derived from the Affymetrix Expression Console software (Affymetrix, Santa Clara, USA)

hyb_protocol: Samples were hybridized for 16 hours at 48 °C on the Affymetrix GeneChip miRNA 3.0 Array (Affymetrix, Santa Clara, USA) using the Affymetrix Hybridization, Wash and Stain Kit (Affymetrix, Santa Clara, USA)  (Performed by Aros Applied Biotechnology (Aros, Aarhus, Denmark))

scan_protocol: Array scanning was performed according to the SOP at Aros Applied Biotechnology (Aros, Aarhus, Denmark)

data_processing: Raw data was processed with the Affymetrix Gene Expression Console for background correction and normalization using default settings.

source_name: healthy male; repressor

label_protocol: Labeling was performed with the FlashTag Biotin HSR RNA Labeling Kit (Affymetrix, Santa Clara, USA) according to the manufacturer´s protocol. (Performed by Aros Applied Biotechnology (Aros, Aarhus, Denmark))

extract_protocol: Total RNA was isolated using the miRNeasy Serum/Plasma Kit (Qiagen, Hilden, Germany) via  the QIAcube liquid handling system (Qiagen, Hilden, Germany)) according to the manufacturer´s protocol for total RNA extraction.

treatment_protocol: EDTA blood samples were centrifuged at 3500 rpm for 15 minutes. 150 µl of the supernatant were mixed with 700µl Qiazol Lysis Reagent (Qiagen, Hilden, Germany) and stored at -80 °C until further processing. Prior to the RNA isolation the plasma/QIAzol mixtures were pooled to gain three biological-technical replicates for each coping mode.

value: Blood plasma

value: male

tag: mci coping strategy

value: Repressor

tag: cognitive avoidance score

tag: vigilance score

tag: pooled/standalone

value: Pool of two samples (1:1)

tag: plasma sample (20 samples; a to t)

value: F/I

tag: ng total rna to label


title: Sample_1200ng_Cy3


title: Sample_400ng_Cy3


title: Plasma_Sensitizer_1

source_name: healthy male; sensitizer

tag: gender

value: Sensitizer

value: Pool of three samples (1:1:1)

value: M/N/O


title: Sample_1600ng_Cy3


title: Plasma_Non-defensive_3

source_name: healthy male; non-defensive

value: Non defensive

value: Standalone

value: D


title: Plasma_High-anxious_3

source_name: healthy male; high-anxious

value: High anxious

value: Pool of two samples (2:1)

value: L/K


title: Plasma_Non-defensive_2

value: C


title: Plasma_Sensitizer_2

value: P/Q/R


title: Plasma_Repressor_1

value: E/F


title: Plasma_High-anxious_2

value: Blood plasma

value: J/K


title: Plasma_Sensitizer_3

value: male

value: S/T


title: Plasma_Non-defensive_1

value: Pool of two samples (1:1)

value: A/B


title: Sample_50ng_Cy3

value: Cottus rhenanus

value: blood


title: C.rhenanus replicate 8

value: Larse Beek


title: Sample_25ng_Cy3


title: Sample_200ng_Cy3


title: Plasma_High-anxious_1

value: Standalone

value: J


title: Plasma_Repressor_2

value: Repressor

value: G/H


title: CRC0574-A-1

status: Public on Jun 19 2017

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

country: Italy

institute: Candiolo Cancer Institute, University of Torino

data_processing: Data were normalized by Bioconductor (3.0) lumi pipeline with loess normalization

label: biotin-SA Cy3

source_name: LM CRC PDX sample

label_protocol: Synthesis of cDNA and biotinylated cRNA were performed using the Illumina Total-Prep RNA Amplification Kit (Ambion, Austin, TX, USA, cat. no. IL1791), according to the manufacturer’s protocol, for which hybridization was carried out on Illumina HumanHT-12 V3 arrays

growth_protocol: Tumor were collected upon surgical resection and stored in liquid nitrogen

extract_protocol: RNA was extracted using the Trizol Plus purification Kit (Invitrogen, Frederick, MD, USA, cat. no.12183555), according to the manufacturer’s protocol. Quantification and quality analysis of RNA was performed on a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA).

treatment_protocol: Cryostatic section of the frozen specimens were cut for RNA extraction

value: LM CRC PDX

tag: cris class

value: CRISC

tag: cris distance to template

tag: cris bh.fdr

tag: sampling region

value: A


title: Sample_100ng_Cy3

tag: species


title: CRC0394-A-2


title: CRC0264-B-1

value: B


title: CRC0327-A-1


title: CRC0394-A-1

value: CRISD


title: CRC0261-A-1

value: CRISA


title: CRC0327-B-1


title: CRC0264-A-1


title: CRC0574-A-2


title: CRC0261-A-2


title: CRC0080-B-1


title: CRC0202-A-1

value: CRISB


title: CRC0080-A-1


title: CRC0254-B-1


title: CRC0078-A-1


title: CRC0081-B-1


title: CRC0254-A-1


title: CRC0179-A-1


title: CRC0104-B-1


title: H3K27me3_primaryspermatocytes_rep2

status: Public on May 02 2017

city: Cambridge

first: Rob

last: White

address: Downing Street

department: Physiology, Development and Neuroscience

country: United Kingdom

institute: University of Cambridge

hyb_protocol: 34 µg labelled ChIP DNA and 34 µg labelled input DNA were combined and hybridised, using the NimbleGen Hybridisation Kit, onto Nimblegen ChIP-chip 2.1M Whole-Genome Tiling Arrays (using the NimbleGen hybridisation station at 42°C, mix mode B, for 20 hr). Post-hybridisation washes were performed according to the NimbleGen Wash Buffer Kit instructions.

scan_protocol: Arrays were scanned on an Axon 4000B scanner according to the manufacturer's instructions.

data_processing:
The scanned images were processed using NimbleScan software to generate raw data (*.pair.gz) files for each channel. Loess spatial correction was performed using the NimbleScan software, and an in-house R script was used to generate normalized log2 ChIP/input ratio (*.sgr) files; for each array the median intensity per channel was scaled to 500 then quantile normalisation was performed across all channels. The normalized ratio scores for both arrays were averaged then smoothed by computing the mean score per 1 kb tiling window (*. bedgraph file).
Normalised primary spermatocyte H3K27me3 euchromatin oligo scores were binned at 1 kb resolution taking the mean score per bin. A HMM using normal distribution was fitted for two states using the RHmm R package for each chromosome. This divided the data into D (depleted in H3K27me3,  H3K27me3_HMM_D_state.bed.gz) and E (enriched in H3K27me3, H3K27me3_HMM_E_state.bed.gz) bins. Adjacent bins with the same HMM state were then combined into regions. Gaps in the genome for which there were no oligo probes were closed if the same state was present on both sides.

organism: Drosophila melanogaster

source_name: anti-H3K27me3 ChIP DNA from FACS-sorted primary spermatocytes

label_protocol: For each of the ChIP and input samples, 2 μg of amplified DNA was labelled using the BioPrime DNA Labeling Kit (Invitrogen) in the presence of Cy3- or Cy5-dCTP (GE Healthcare) according to the manufacturer's instructions. The DNA was quantified using a Nanodrop spectrophotometer.

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

extract_protocol: Sorted cells were spun down in a swing-out rotor at 4,000 g for 15 min at 4°C, transferred to a thin-walled 0.5 ml microfuge tube (Axygen PCR-05-C), re-spun down and resuspended in 130 µl Lysis Buffer (17 mM Tris.HCl (pH 8), 3.4 mM EDTA.Na2, 0.34% SDS) containing protease inhibitors (Sigma-Aldrich P8340), and sonicated for 5 cycles at high setting using a Diagenode Bioruptor (1 cycle is 30 s ON and 30 s OFF). After sonication, the sample was centrifuged at 16,000 g for 15 min at 4°C, the chromatin-containing supernatant transferred to a fresh microfuge tube, and 70 µl RIPA buffer (36.7 mM Tris.HCl (pH 8), 2.5 mM EDTA.Na2, 0.01% SDS, 2.46% Triton X-100, 374 mM NaCl) containing protease inhibitors added to the chromatin sample. The ChIP reaction, washes and DNA purification were performed as in Dahl and Collas (2008 Nucleic Acids Res 36: e15, 2008 Nat Protoc 3: 1032–1045). In brief, magnetic beads were coated with 2.4 µg of rabbit anti-H3K27me3 antibody (Millipore 07-449), and incubated overnight in a volume of 100 µl with chromatin from ~100,000 YFP+ sorted events. Beads were washed, chromatin eluted, RNA and proteins digested, and the DNA then purified by phenol/chloroform extraction and ethanol precipitation using linear acrylamide as carrier and resuspended in 10 µl PCR grade water. Approximately 5 µl of chromatin was retained as input and purified alongside the ChIP sample. ChIP and input DNA were amplified using the GenomePlex Single Cell Whole Genome Amplification Kit (Sigma-Aldrich WGA4) following the manufacturer's instructions from the library preparation stage. Approximately 150 pg of DNA was used for amplification. Samples were amplified for 22 cycles, and amplified DNA was purified using the QIAquick PCR Purification Kit (Qiagen).

treatment_protocol: Testes from homozygous flies of the YFP-tagged protein-trap line CPTI-2406 (Ryder et al. 2009. Bioinformatics 25: 548-549; http://www.flyprot.org) were used to purify primary spermatocytes. Testes were dissected in ice-cold Schneider's medium (supplemented with 10% fetal calf serum) and incubated with collagenase (5 mg/ml, Sigma-Aldrich C8051) plus protease inhibitors (Sigma-Aldrich P8340) in medium for 5 min at room temperature. After washing in medium, cells were extracted by gently pipetting for 5 min, using a P200 tip (Rainin RT-200F; with 1.5 mm of the tip cut off to increase the diameter of the opening), in 100 µl medium; and fixed by adding an equal volume of 2% formaldehyde (Sigma-Aldrich F8775) in PBS, mixing thoroughly, and incubating for 10 min at 23°C in an Eppendorf Thermomixer at 700 rpm. Fixation was stopped by adding 400 µl ice-cold medium and placing the sample on ice. The sample was spun down in a swing-out rotor at 1,000 g for 5 min at 4°C, and the pellet snap frozen in liquid N2 and stored at −80°C. A total of 1,000 testes were dissected for each ChIP-array replicate. Testes were dissected in batches of 100, and for each batch, the time lapsing from the start of dissection till fixation was approximately 1 hr. For cell sorting, aliquots of extracted cells stored at −80°C were thawed, combined in PBS/0.01% Triton X-100 and 50 µm filtered (Partec 04-004-2327). Cells were sorted using a 100 µm nozzle on a MoFlo FACS machine (Beckman Coulter) equipped with a 488 nm argon laser (100 mW). Cells were sorted into a microfuge tube containing 700 µl PBS/0.01% Triton X-100. Events were triggered on forward scatter and YFP+ events were sorted. Data was acquired and analysed using Summit software (Beckman Coulter).

tag: fly stock

value: YFP-tagged protein-trap line CPTI-2406

tag: age

value: 1- to 3-day-old adults

value: sorted primary spermatocytes

tag: chip antibody

source_name: Input DNA from FACS-sorted primary spermatocytes


title: CRC0059-A-1


title: H3K27me3_primaryspermatocytes_rep1


title: CRC0059-B-1


title: CRC0179-B-1


title: CRC0078-B-1


title: CRC0059-B-3


title: CRC0202-B-1


title: CRC0081-A-1


title: CRC0151-A-1

value: CRISE


title: CRC0030-B-1


title: CRC0059-B-2


title: CRC0104-A-1


title: CRC0030-A-1


title: root_amino acid_1

status: Public on Apr 26 2017

city: Verona

first: Anita

last: Zamboni

address: Strada Le Grazie, 15

department: Biotechnology

institute: University of Verona

hyb_protocol: 1.65 µg of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom Array 4x44K (GPL22578) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent G2565CA Mycroarray Scanner System (Agilent) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 3 µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (GE1_105_Dec08 and Grid: 076115_D_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Zea mays

source_name: 4-day-old maize seedling, 3 days of treatment with amino acids

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Maize seeds (P0423 Hybrid, Pioneer Italia S.p.a) were soaked in water for 24 h and germinated in the dark. After 72 h, the seedlings were transferred to plastic pots containing 0.05 mM CaSO4 and grown for 24 h under a 16/8h light/dark regime at 22-26 °C, 40-50% relative humidity,  125 μE m-2s-1 light intensity.

extract_protocol: Total RNA was isolated using the SpectrumTM Plant Total RNA kit (Sigma-Aldrich).

treatment_protocol: Seedlings were then grown in a diluted nutrient solution (Pinton et al. 1999) supplemented with either protein hydrolysates (SICIT2000 Spa) (0.1 mlL-1 ) or inorganic nitrogen (NH4H2PO4) or a mixture of amino acids mimicking the amino acids content of the protein hydrolysates, keeping  the total N constant (11.3 mgL-1) in the three treatments. After 3 days, roots were collected to obtain three independent biological replicates (each composed of 24 seedlings).

tag: seed product

value: P0423 Hybrid, Pioneer Italia S.p.a

value: 4-day-old maize seedlings

tag: treated with

value: mixture of amino acids (mimicking the amino acids content of the protein hydrolysates) for 3 days

value: root


title: root_amino acid_2

tag: tissue


title: root_amino acid_3


title: root_inorganic nitrogen_2

source_name: 4-day-old maize seedling, 3 days of treatment with inorganic nitrogen

value: inorganic nitrogen (NH4H2PO4) for 3 days


title: root_protein hydrolysate_1

source_name: 4-day-old maize seedling, 3 days of treatment with protein hydrolysates

value: protein hydrolysates (SICIT2000 Spa) for 3 days


title: root_protein hydrolysate_3


title: root_protein hydrolysate_2


title: root_inorganic nitrogen_1


title: root_inorganic nitrogen_3


title: NSCLC_sample_84A

status: Public on Aug 31 2016

city: Uppsala

last: Micke

address: Rudbeck laboratory

country: Sweden

institute: Uppsala University

description:
Hybridized to 250K_Nsp
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)

hyb_protocol: Array experiments were performed according to the standard protocols for Affymetrix GeneChip® Mapping 250K Nsp I arrays (Gene Chip Mapping 500K Assay Manual, P/N 701930 Rev2., Affymetrix Inc., Santa Clara, CA, U.S.A. ). The arrays were then washed using Affymetrix fluidics stations.

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000 7G.

data_processing:
The array image was acquired using Affymetrix GeneChip® Operating Software.
Copy number values for individual SNPs were extracted and converted from CEL files using R package aroma.affymetrix v2.11.1.
The copy number values were calculated as 2*(sample chip effect/median reference chip effect). On X chromosome the information on the sex was used to assess plausible copy number estimates (men:  sample chip effect/median male reference chip effect, women: 2*sample chip effect/median female reference chip effect). No segmentation perfermormed yet.
As reference data set 90 publicly available HapMap samples were used ((CEU), The International HapMap Consortium. The International HapMap Project. Nature 426, 789-796 (2003)).

label: Biotin

source_name: NSCLC tissue fresh frozen

growth_protocol: human cancer tissue

extract_protocol: DNA were extracted from 2 to 10 frozen tissue sections (10  mm) using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany).

value: non-small cell lung cancer

tag: dead

tag: survival

tag: who performance status

tag: stadium

tag: smoking

tag: Sex

value: male

tag: histology

value: Squamous cell carcinoma

tag: cell line

value: crude cancer tissue


title: NSCLC_sample_98A

description:
Hybridized to 250K_Nsp
GSM707473
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)

label_protocol: Array experiments were performed according to the standard protocols for Affymetrix GeneChip® Mapping 250K Nsp I arrays (Gene Chip Mapping 500K Assay Manual, P/N 701930 Rev2., Affymetrix Inc., Santa Clara, CA, U.S.A. ).


title: NSCLC_sample_61A

description:
Hybridized to 250K_Nsp
GSM707472
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)

value: Adenocarcinoma


title: NSCLC_sample_81A

description:
Hybridized to 250K_Nsp
GSM707548
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_62A

value: female


title: NSCLC_sample_96A


title: NSCLC_sample_68A


title: NSCLC_sample_79A


title: NSCLC_sample_80 A


title: NSCLC_sample_8A


title: NSCLC_sample_7A


title: NSCLC_sample_59A


title: NSCLC_sample_93A


title: NSCLC_sample_92A


title: NSCLC_sample_74A


title: NSCLC_sample_58A


title: NSCLC_sample_66A


title: NSCLC_sample_88A

description:
Hybridized to 250K_Nsp
GSM707552
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_75A


title: NSCLC_sample_55 B


title: NSCLC_sample_52A


title: NSCLC_sample_43A


title: NSCLC_sample_5A


title: NSCLC_sample_64B


title: NSCLC_sample_6A

description:
Hybridized to 250K_Nsp
GSM707546
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_76A

value: Large cell carcinoma


title: NSCLC_sample_56A


title: NSCLC_sample_78A


title: NSCLC_sample_48A

description:
Hybridized to 250K_Nsp
GSM707544
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_375A

description:
Hybridized to 250K_Nsp
GSM707471
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_370A

description:
Hybridized to 250K_Nsp
GSM707538
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_41A


title: NSCLC_sample_373B

description:
Hybridized to 250K_Nsp
GSM707539
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_361A

description:
Hybridized to 250K_Nsp
GSM707535
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_38B


title: NSCLC_sample_363A


title: NSCLC_sample_367A

description:
Hybridized to 250K_Nsp
GSM707537
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_87A

description:
Hybridized to 250K_Nsp
GSM707550
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_369A

description:
Hybridized to 250K_Nsp
GSM707470
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_357A

description:
Hybridized to 250K_Nsp
GSM707469
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_341A

description:
Hybridized to 250K_Nsp
GSM707467
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_354A


title: NSCLC_sample_347A

description:
Hybridized to 250K_Nsp
GSM707532
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_350A

description:
Hybridized to 250K_Nsp
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_37A

description:
Hybridized to 250K_Nsp
GSM707540
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_35A

description:
Hybridized to 250K_Nsp
GSM707534
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_359A

description:
Hybridized to 250K_Nsp
GSM707533
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_332Y

description:
Hybridized to 250K_Nsp
GSM707465
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_39A

description:
Hybridized to 250K_Nsp
GSM707542
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_344A

description:
Hybridized to 250K_Nsp
GSM707468
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_36C


title: NSCLC_sample_342A

description:
Hybridized to 250K_Nsp
GSM707531
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_353A


title: NSCLC_sample_336A


title: NSCLC_sample_334A


title: NSCLC_sample_348A


title: NSCLC_sample_338A

description:
Hybridized to 250K_Nsp
GSM707529
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_360A


title: NSCLC_sample_327A


title: NSCLC_sample_331A

description:
Hybridized to 250K_Nsp
GSM707528
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_320A


title: NSCLC_sample_365A

description:
Hybridized to 250K_Nsp
GSM707536
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_319A

description:
Hybridized to 250K_Nsp
GSM707525
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_32A

description:
Hybridized to 250K_Nsp
GSM707526
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_321 A


title: NSCLC_sample_318B


title: NSCLC_sample_317A

description:
Hybridized to 250K_Nsp
GSM707524
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_309A

description:
Hybridized to 250K_Nsp
GSM707521
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_314A

description:
Hybridized to 250K_Nsp
GSM707523
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_312A


title: NSCLC_sample_310A

description:
Hybridized to 250K_Nsp
GSM707522
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_311C

description:
Hybridized to 250K_Nsp
GSM707464
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_302A

description:
Hybridized to 250K_Nsp
GSM707463
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_296A

description:
Hybridized to 250K_Nsp
GSM707516
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_292B

description:
Hybridized to 250K_Nsp
GSM707461
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_284A

description:
Hybridized to 250K_Nsp
GSM707513
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_301A

description:
Hybridized to 250K_Nsp
GSM707462
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_295B

description:
Hybridized to 250K_Nsp
GSM707515
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_300A

description:
Hybridized to 250K_Nsp
GSM707519
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_29A

description:
Hybridized to 250K_Nsp
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_290A


title: NSCLC_sample_299B

description:
Hybridized to 250K_Nsp
GSM707518
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_291A

description:
Hybridized to 250K_Nsp
GSM707460
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_288A

description:
Hybridized to 250K_Nsp
GSM707514
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_285A


title: NSCLC_sample_287A


title: NSCLC_sample_297A

description:
Hybridized to 250K_Nsp
GSM707517
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_28A


title: NSCLC_sample_271A

description:
Hybridized to 250K_Nsp
GSM707509
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_282A

description:
Hybridized to 250K_Nsp
GSM707459
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_276 B


title: NSCLC_sample_275A


title: NSCLC_sample_274A

description:
Hybridized to 250K_Nsp
GSM707458
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_305A

description:
Hybridized to 250K_Nsp
GSM707520
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_272B

description:
Hybridized to 250K_Nsp
GSM707457
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_256A

description:
Hybridized to 250K_Nsp
GSM707506
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_260A

description:
Hybridized to 250K_Nsp
GSM707456
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_244A


title: NSCLC_sample_257A


title: NSCLC_sample_255A

description:
Hybridized to 250K_Nsp
GSM707505
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_27A

description:
Hybridized to 250K_Nsp
GSM707511
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_236A


title: NSCLC_sample_263A


title: NSCLC_sample_241 B


title: NSCLC_sample_243A

description:
Hybridized to 250K_Nsp
GSM707454
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_265A

description:
Hybridized to 250K_Nsp
GSM707508
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_234A

description:
Hybridized to 250K_Nsp
GSM707502
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_226B

description:
Hybridized to 250K_Nsp
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_249A

description:
Hybridized to 250K_Nsp
GSM707455
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_228B

description:
Hybridized to 250K_Nsp
GSM707451
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_223A

description:
Hybridized to 250K_Nsp
GSM707449
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_23A

description:
Hybridized to 250K_Nsp
GSM707453
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_224A

description:
Hybridized to 250K_Nsp
GSM707450
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_235A

description:
Hybridized to 250K_Nsp
GSM707503
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_229A

description:
Hybridized to 250K_Nsp
GSM707501
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_239B


title: NSCLC_sample_278A

description:
Hybridized to 250K_Nsp
GSM707510
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_220A


title: NSCLC_sample_218 A


title: NSCLC_sample_22B

description:
Hybridized to 250K_Nsp
GSM707452
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_215A

description:
Hybridized to 250K_Nsp
GSM707447
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_258A

description:
Hybridized to 250K_Nsp
GSM707507
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_277A


title: NSCLC_sample_212A

description:
Hybridized to 250K_Nsp
GSM707444
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_207A

description:
Hybridized to 250K_Nsp
GSM707500
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_213A

description:
Hybridized to 250K_Nsp
GSM707445
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_209A


title: NSCLC_sample_201A

description:
Hybridized to 250K_Nsp
GSM707441
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_202A

description:
Hybridized to 250K_Nsp
GSM707442
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_217A

description:
Hybridized to 250K_Nsp
GSM707448
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_195B

description:
Hybridized to 250K_Nsp
GSM707495
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_214A

description:
Hybridized to 250K_Nsp
GSM707446
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_196A

description:
Hybridized to 250K_Nsp
GSM707496
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_203B

description:
Hybridized to 250K_Nsp
GSM707443
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_200A

description:
Hybridized to 250K_Nsp
GSM707440
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_204A

description:
Hybridized to 250K_Nsp
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_197B

description:
Hybridized to 250K_Nsp
GSM707499
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_190B


title: NSCLC_sample_184C


title: NSCLC_sample_20A


title: NSCLC_sample_189A

description:
Hybridized to 250K_Nsp
GSM707493
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_178A


title: NSCLC_sample_174A

description:
Hybridized to 250K_Nsp
GSM707436
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_182A


title: NSCLC_sample_187A


title: NSCLC_sample_175B

description:
Hybridized to 250K_Nsp
GSM707492
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_180A


title: NSCLC_sample_169D

description:
Hybridized to 250K_Nsp
GSM707489
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_173A


title: NSCLC_sample_192C

description:
Hybridized to 250K_Nsp
GSM707437
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_254A


title: NSCLC_sample_186B


title: NSCLC_sample_165C

description:
Hybridized to 250K_Nsp
GSM707486
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_164A


title: NSCLC_sample_168B


title: NSCLC_sample_163A


title: NSCLC_sample_171A

description:
Hybridized to 250K_Nsp
GSM707435
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_172C

description:
Hybridized to 250K_Nsp
GSM707490
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_158A

description:
Hybridized to 250K_Nsp
GSM707434
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_149A


title: NSCLC_sample_160A


title: NSCLC_sample_16A


title: NSCLC_sample_156A


title: NSCLC_sample_154A


title: NSCLC_sample_162A

description:
Hybridized to 250K_Nsp
GSM707484
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_139 A


title: NSCLC_sample_150A


title: NSCLC_sample_193B

description:
Hybridized to 250K_Nsp
GSM707438
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_14A

description:
Hybridized to 250K_Nsp
GSM707482
characteristics: dead survival status: alive=0, dead=1
characteristics: survival  survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b)  versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)


title: NSCLC_sample_130A