title: Test4_3A

city: Namur

first: Sophie

last: Depiereux

state: Namur

address: Rue de Bruxelles, 61

country: Belgium

institute: University of Namur

description: Gene expression after 76 days of exposure to 10μg EE2/L in rainbow trout fry testis, sample 1 in tank 3

hyb_protocol: The samples were hybridised on the microarray slides with incubation at 65°C for 17 hours in a hybridisation chamber (Agilent).

scan_protocol: The slides were scanned and pre-processed (signal background corrections) using Agilent’s High-Resolution C Scanner

data_processing: The data analyses were performed using the R statistical software version 2.15.3. available on the R-Project repository (http://cran.r-project.org) and a set of packages available in the Bioconductor repository (http://www.bioconductor.org). Brief descriptions of the analyses are provided below. Detailed scripts are presented in supplementary files. The expression values of the one-color microarray were first submitted to quantile-quantile normalisation using the normalize.quantile function in the preprocessCore package.

organism: Oncorhynchus mykiss

source_name: Testis, 76 days, 10μg EE2/L, replicate 5

label_protocol: Labeled cDNA (using Cyanine-3) was synthesised, purified, quantified and prepared for hybridisation following the Agilent protocol

extract_protocol: Total RNA was extracted from the gonads (n=6; 2 pools of 10 pairs of gonads per tank, 3 tanks per condition) using TRIzol reagent (Invitrogen, Life Technologies Europe B.V., Ghent, Belgium) as described previously (Baron 2005). The total RNA concentration was determined using an ISOGEN NanoDrop 2000c spectrophotometer (Wilmington, Delaware, USA) and RNA quality was controlled on a Bioanalyzer 2100 (Agilent). Only samples with a RIN (RNA Integrity Number) >8 were kept for further analysis.

treatment_protocol: All-male rainbow trout (Oncorhynchus mykiss) fry were exposed from the onset of first feeding [Day 0 = D0 at 60 days post-fertilisation (dpf) to 136 dpf] to 5 nominal concentrations of 17a-ethynylestradiol (purity ³ 98%, Sigma-Aldrich, Germany): 0 (solvent control), 0.01 µg/L, 0.1 µg/L, 1 µg/L and 10 µg/L, with 3 tanks per condition. The actual EE2 concentrations were measured in each tank at 6 time points using the Quantitative Ethynylestradiol Enzyme Immunoassay (EIA) Kit (Marloie, Belgium) according to the manufacturer’s instructions. Mean concentrations of EE2 ± SD were 0.08 ± 0.06 µg/l; 1.62 ± 1.74 µg/l and 9.88 ± 5.06 µg/l. The 0.01 µg/l EE2 concentration was under the detection limit (set at 0.02 µg/l). At the end of the exposure time, the gonads were collected from all fish, immediately frozen in liquid nitrogen and stored at -80°C until RNA extraction. Gonads from 10 fish were pooled to reach enough material for further analyses.

tag: gender

value: Male

value: Testis

tag: age

value: 136 dpf


title: Test4_2B

status: Public on Jun 25 2015

type: RNA

department: Biology

description: Gene expression after 76 days of exposure to 10μg EE2/L in rainbow trout fry testis, sample 2 in tank 2

molecule: total RNA

source_name: Testis, 76 days, 10μg EE2/L, replicate 4

tag: tissue


title: parafilm embedded tissue_normal adjacent_patient9

city: Stony Brook

first: Yuanhao

last: Zhang

address: AMS Department,Stony Brook University

department: Applied Mathematics and Statistics

country: USA

institute: Stony Brook University

hyb_protocol: The tissue RNAs (100 ηg) were labeled using the Agilent miRNA Complete Labeling and Hybridization Kit (Agilent Technologies) and used to probe and hybridized with Agilent Human Microarray Kit V3, 8 x 15K arrays, based on Sanger miRbase release 12.0 (G4470C, Agilent Technologies, Foster City, California).The hybridization was performed at 55o C for 20 h in an Agilent Hybridization Oven according to the manufacturer’s protocol.

scan_protocol: Hybridized microarrays were scanned with a DNA microarray scanner (Agilent G2565BA)

data_processing: Features were extracted using the Agilent Feature Extraction (AFE) image analysis tool (version A.10.7.3.1) with default protocols and settings . The raw probe level data were imported into GeneSpring 12.5GX and the miRNA signal was normalized using the default setting: threshold raw signal to 1.0, percent shift to 90th percentile as the normalization algorithm and no baseline transformation.

organism: Homo sapiens

extract_protocol: For each SBU FFPE sample, total RNA was isolated from three 10 µm thick tissue sections using a miRNeasy FFPE extraction kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol. For each WU frozen samples, total RNA was extracted by Trizol followed by lithium precipitation (Invitrogen, Carlsbad, CA) according to the manufacturer’s protocol at the Siteman Cancer Center Tissue Procurement Facility.  Total RNA quantity and quality was determined using a Nanodrop 2000C (Thermo Scientific, Waltham, MA).

value: Colon Cancer Normal Adjacent

tag: race

value: Caucasian

tag: data source

value: SBU


title: M74_60DAH_2010

city: Beaucouzé

first: Mathilde

last: ORSEL

address: 42, rue Georges Morel

country: France

institute: IRHS

hyb_protocol: The hybridization performed on a NimbleGen Hybridization System 4 (mix mode B) at 42° overnigth. Afterwards, the slide were washed, dried, and scanned.

scan_protocol: Slides were scanned at 532 and 635nm at 2 μm resolution and high sensitivity with a Roche-NimbleGen MS200. Pair-data files were extracted from the scanned images using DEVA 1.2.1 software (Roche).

data_processing: Statistical analyses were performed using R version 2.14.1 (R Development Core Team, 2011) and the package LIMMA 3.10.1 (Smyth G.K., 2005) from the Bioconductor project. Data were normalized by the lowess method from LIMMA.

organism: Malus domestica

source_name: Apple 'M74' fruit flesh, 2 months of cold storage, 2010

label_protocol: 200ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse-transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1.5mmol of Cyanine-3 (Cy3) or Cyanine-5 (Cy5) (Interchim, France), then purified with NucleoSpin Gel and PCR Clean-up column kits (Macherey-Nagel, GmbH & Co. KG, Germany). Purified labeled cDNA were quantified using NanoDrop ND-1000 (Nanodrop Technologies, DE, USA). Labelled samples were combined as 30 pmol for each dye and co-hybridized.

growth_protocol: Fruits were harvested at INRA, Angers (Experimental unit of Bois L'Abbé-La Rétuziére).

extract_protocol: Derived from the apple tissues RNA extraction method (Gasic et al., 2004) and pine tree RNA isolation method (Chang et al., 1993)

treatment_protocol: Cold storage at 1°C, after harvest.

tag: organ

value: Fruit

tag: tissus

value: Parenchyma

tag: genetic background

value: Hybrid M74

tag: genotype

value: Wild-type

tag: tissus developmental stage

value: Harvested at optimum maturity

tag: treatment

value: Cold storage for 60 days after harvest


title: parafilm embedded tissue_tumor_patient9

source_name: parafilm embedded tissue_tumor_patient9

label_protocol: The tissue RNAs (100 ηg) were labeled using the Agilent miRNA Complete Labeling and Hybridization Kit (Agilent Technologies)

value: Colon Cancer Tumor


title: Test3_3B

description: Gene expression after 76 days of exposure to 1μg EE2/L in rainbow trout fry testis, sample 2 in tank 3

source_name: Testis, 76 days, 1μg EE2/L, replicate 6


title: M20_60DAH_2009

source_name: Apple 'M20' fruit flesh, 2 months of cold storage, 2009

value: Hybrid M20


title: M74_60DAH_2009

source_name: Apple 'M74' fruit flesh, 2 months of cold storage, 2009


title: Test4_1A

description: Gene expression after 76 days of exposure to 10μg EE2/L in rainbow trout fry testis, sample 1 in tank 1

source_name: Testis, 76 days, 10μg EE2/L, replicate 1


title: parafilm embedded tissue_normal adjacent_patient8


title: Test4_2A

description: Gene expression after 76 days of exposure to 10μg EE2/L in rainbow trout fry testis, sample 1 in tank 2

source_name: Testis, 76 days, 10μg EE2/L, replicate 3


title: Test4_1B

description: Gene expression after 76 days of exposure to 10μg EE2/L in rainbow trout fry testis, sample 2 in tank 1

source_name: Testis, 76 days, 10μg EE2/L, replicate 2


title: Test3_3A

description: Gene expression after 76 days of exposure to 1μg EE2/L in rainbow trout fry testis, sample 1 in tank31

source_name: Testis, 76 days, 1μg EE2/L, replicate 5


title: parafilm embedded tissue_tumor_patient8

source_name: parafilm embedded tissue_tumor_patient8


title: Test4_3B

description: Gene expression after 76 days of exposure to 10μg EE2/L in rainbow trout fry testis, sample 2 in tank 3

source_name: Testis, 76 days, 10μg EE2/L, replicate 6


title: M74_120DAH_2009

source_name: Apple 'M74' fruit flesh, 4 months of cold storage, 2009

value: Cold storage for 120 days after harvest


title: M20_Harvest_2009

source_name: Apple 'M20' fruit flesh, at harvest, 2009


title: Test3_2B

description: Gene expression after 76 days of exposure to 1μg EE2/L in rainbow trout fry testis, sample 2 in tank 2

source_name: Testis, 76 days, 1μg EE2/L, replicate 4


title: M20_Harvest_2010

source_name: Apple 'M20' fruit flesh, at harvest, 2010


title: Test3_2A

description: Gene expression after 76 days of exposure to 1μg EE2/L in rainbow trout fry testis, sample 1 in tank 2

source_name: Testis, 76 days, 1μg EE2/L, replicate 3


title: parafilm embedded tissue_normal adjacent_patient7

value: African American


title: M74_100DAF_2010

source_name: Apple 'M74' fruit flesh, 100 days after flowering, 2010

value: Fruit development


title: M74_Harvest_2009

source_name: Apple 'M74' fruit flesh, at harvest, 2009


title: parafilm embedded tissue_tumor_patient7

source_name: parafilm embedded tissue_tumor_patient7


title: M20_100DAF_2010

source_name: Apple 'M20' fruit flesh, 100 days after flowering, 2010


title: M20_60DAH_2010

source_name: Apple 'M20' fruit flesh, 2 months of cold storage, 2010


title: M20_100DAF_2009

source_name: Apple 'M20' fruit flesh, 100 days after flowering, 2009


title: parafilm embedded tissue_normal adjacent_patient6


title: M74_Harvest_2010

source_name: Apple 'M74' fruit flesh, at harvest, 2010


title: parafilm embedded tissue_tumor_patient6

source_name: parafilm embedded tissue_tumor_patient6


title: parafilm embedded tissue_normal adjacent_patient5


title: parafilm embedded tissue_tumor_patient5

source_name: parafilm embedded tissue_tumor_patient5


title: parafilm embedded tissue_normal adjacent_patient4


title: Test2_3B

description: Gene expression after 76 days of exposure to 0.1μg EE2/L in rainbow trout fry testis, sample 2 in tank 3

source_name: Testis, 76 days, 0.1μg EE2/L, replicate 6

value: Male


title: Test2_2A

description: Gene expression after 76 days of exposure to 0.1μg EE2/L in rainbow trout fry testis, sample 1 in tank 2

source_name: Testis, 76 days, 0.1μg EE2/L, replicate 3

value: Testis


title: M49_120DAH_2010

source_name: Apple 'M49' fruit flesh, 4 months of cold storage, 2010

value: Hybrid M49


title: M74_100DAF_2009

source_name: Apple 'M74' fruit flesh, 100 days after flowering, 2009


title: parafilm embedded tissue_tumor_patient4

source_name: parafilm embedded tissue_tumor_patient4


title: Test2_1A

description: Gene expression after 76 days of exposure to 0.1μg EE2/L in rainbow trout fry testis, sample 1 in tank 1

source_name: Testis, 76 days, 0.1μg EE2/L, replicate 1

value: 136 dpf


title: Test1_2B

description: Gene expression after 76 days of exposure to 0.01μg EE2/L in rainbow trout fry testis, sample 2 in tank 2

source_name: Testis, 76 days, 0.01μg EE2/L, replicate 4


title: parafilm embedded tissue_normal adjacent_patient2

value: Colon Cancer Normal Adjacent

value: Caucasian


title: M49_Harvest_2010

source_name: Apple 'M49' fruit flesh, at harvest, 2010

value: Fruit


title: parafilm embedded tissue_tumor_patient3

source_name: parafilm embedded tissue_tumor_patient3

value: SBU


title: M49_60DAH_2010

source_name: Apple 'M49' fruit flesh, 2 months of cold storage, 2010

value: Parenchyma


title: Test2_1B

description: Gene expression after 76 days of exposure to 0.1μg EE2/L in rainbow trout fry testis, sample 2 in tank 1

source_name: Testis, 76 days, 0.1μg EE2/L, replicate 2


title: Test3_1A

description: Gene expression after 76 days of exposure to 1μg EE2/L in rainbow trout fry testis, sample 1 in tank 1

source_name: Testis, 76 days, 1μg EE2/L, replicate 1


title: Test1_3B

description: Gene expression after 76 days of exposure to 0.01μg EE2/L in rainbow trout fry testis, sample 2 in tank 3

source_name: Testis, 76 days, 0.01μg EE2/L, replicate 6


title: parafilm embedded tissue_normal adjacent_patient3


title: Test1_3A

description: Gene expression after 76 days of exposure to 0.01μg EE2/L in rainbow trout fry testis, sample 1 in tank 3

source_name: Testis, 76 days, 0.01μg EE2/L, replicate 5


title: M40_120DAH_2010

source_name: Apple 'M40' fruit flesh, 4 months of cold storage, 2010

value: Hybrid M40

value: Wild-type


title: Test2_3A

description: Gene expression after 76 days of exposure to 0.1μg EE2/L in rainbow trout fry testis, sample 1 in tank 3

source_name: Testis, 76 days, 0.1μg EE2/L, replicate 5


title: M49_100DAF_2010

source_name: Apple 'M49' fruit flesh, 100 days after flowering, 2010


title: parafilm embedded tissue_tumor_patient2

source_name: parafilm embedded tissue_tumor_patient2


title: M40_100DAF_2010

source_name: Apple 'M40' fruit flesh, 100 days after flowering, 2010


title: Test1_2A

description: Gene expression after 76 days of exposure to 0.01μg EE2/L in rainbow trout fry testis, sample 1 in tank 2

source_name: Testis, 76 days, 0.01μg EE2/L, replicate 3


title: M40_60DAH_2010

source_name: Apple 'M40' fruit flesh, 2 months of cold storage, 2010

value: Harvested at optimum maturity

value: Cold storage for 60 days after harvest


title: Test1_1B

description: Gene expression after 76 days of exposure to 0.01μg EE2/L in rainbow trout fry testis, sample 2 in tank 1

source_name: Testis, 76 days, 0.01μg EE2/L, replicate 2


title: Test1_1A

description: Gene expression after 76 days of exposure to 0.01μg EE2/L in rainbow trout fry testis, sample 1 in tank 1

source_name: Testis, 76 days, 0.01μg EE2/L, replicate 1


title: Control3B

description: Gene expression after 76 days of exposure to 0μg EE2/L in rainbow trout fry testis, sample 2 in tank 3

source_name: Testis, 76 days, 0μg EE2/L, replicate 6


title: M40_Harvest_2010

source_name: Apple 'M40' fruit flesh, at harvest, 2010


title: M40_120DAH_2009

source_name: Apple 'M40' fruit flesh, 4 months of cold storage, 2009


title: parafilm embedded tissue_tumor_patient1

source_name: parafilm embedded tissue_tumor_patient1

value: Colon Cancer Tumor


title: M49_120DAH_2009

source_name: Apple 'M49' fruit flesh, 4 months of cold storage, 2009

value: Cold storage for 120 days after harvest


title: Wild Type, sample 2 , replicate 2

type: protein

city: St. Peter

first: Sanjive

last: Qazi

state: MN

address: 800 west College Av

institute: Gustavus Adolphus College

hyb_protocol: The biotinylated proteins (~80 µg) were mixed with 6 ml of coupling solution (Full Moon Biosystems, Inc.) and then added over the array slide for a 2 hour incubation at room temperature while shaking. The array was then washed with 30 ml of 1x Wash Solution (Full Moon Biosystems, Inc.) for 10 minutes for a total of three times and then rinsed ten times with Milli-Q water before detection of bound biotinylated proteins using Cy3-conjugated streptavidin..  Subsequently, the array slide was incubated in Cy3-Streptavidin solution for 30 minutes in the dark while shaking.  Next, the slide was washed with 1X Wash buffer and rinsed with Milli-Q water as before. The slide was then dried with compressed nitrogen and scanned using Axon GenePix 4000 scanner and the images were analyzed with GenePix Pro 6.0 (Molecular Devices, Sunnyvale, CA).

scan_protocol: Axon GenePix 4000 scanner

data_processing: The fluorescence signal  of each antibody was obtained from the fluorescence intensity of this antibody spot after subtraction of the blank signal (spot in the absence of antibody). Two technical replicates were performed for each sample.  Median signal intensity for each spot was extracted from array images and the average intensity for each antibody reaction with the protein was determined for replicate spots.  Data were normalized utilizing the median intensity values for the 1318 antibodies on each array  (Normalized data = Average Signal Intensity of Replicate Spots / Median Signal).

label: biotin

molecule: protein

organism: Mus musculus

source_name: Splenocytes

label_protocol: In brief, the cell lysates were biotinylated for two hours at room temperature using the Biotin reagent in the antibody array assay kit (Full Moon BioSystems, Inc.).  The array slide was blocked with blocking solution for 30 min at room temperature on an orbital shaker and then rinsed ten times with Milli-Q grade water.

growth_protocol: Pronuclear microinjection of the human CD22DE12 transgene, founder generation, genotyping analysis of tail DNA, were performed under a service contract at the UC Davis Mouse Biology Program using standard methods. The 5.3-kb [promoter – CD22E12 cDNA - poly A] fragment of the pEµ-SR-CD22E12 transgene construct was microinjected into the pronuclei of freshly fertilized oocytes from C57BL/6J mice. Injected oocytes were transferred to day 0.5 postcoitus (dpc) pseudopregnant CD-1/Crl females to generate CD22ΔE12-Tg mice. Founders were mated to C57BL/6 J mice obtained from Jackson Laboratories; CD-1/Crl mice were obtained from Charles River laboratories. All mouse procedures were carried out in accordance with the Institutional Animal Care and Use Committee at the University of California, Davis (IACUC #15723). Tg founder mice were identified by PCR analysis of genomic tail DNA.   Tg male mice were crossed to age-matched wildtype female C57BL/6 mice to produce transgenic lines and pups were screened for the presence of the transgene by PCR analysis of tail-extracted DNA.  DNA was extracted from approximately 3 mm tail snips using Qiagen DNEasy blood and tissue kit according to manufacturer’s protocol.

extract_protocol: Cells were washed with ice cold 1X PBS.  On addition of Lysis Beads and Extraction Buffer, the sample underwent 2 rounds of rigorous mixing and  vortexing for 30 seconds following incubation  on ice for 10 minutes.  Following centrifugation of the mixture at 10,000 x g for 20 minutes at 4°C the supernatant was transferred to a clean tube.  Spin columns were used to change the buffer in the supernatant  to Labeling Buffer.

treatment_protocol: Eµ-Myc Tg male founders (B6.Cg-Tg[IgHMyc]22Bri/J, hemizygous for Tg[IhHMyc]22Br, JAXEAST:AX12) were obtained from the Jackson Laboratory ( Bar Harbor, Maine). These mice were bred to wildtype female C57BL/6J mice to establish a colony of Eµ-Myc transgenic mice.  For genotyping of Myc-transgenic mice, DNA was extracted from approximately 3 mm tail snips using Qiagen DNEasy blood and tissue kit following manufactures instructions.  DNA was then screened for the Myc transgene via TaqMan® qPCR via the relative Ct method multiplexed with the following oligos:  Transgenic target primers/probe include a forward primer ATGTGCGCGGAACCCCTATT, reverse primer GGGCGACACGGAAATGTTG, probe 6Fam- ACATTCAAATATGTATCCGCTCATGAGACA-NFQ and were quantified next to endogenous reference primers/probe including a forward primer GTCATCAAGTGAGAAAGACATCCT, reverse primer CATCATGAATTTTGATAAGCCCATT, a TaqMan probe CTCCTGGCTGCCTGGCTGGC with a 5’ VIC label (4,7,2′-trichloro-7′-phenyl-6-carboxyfluorescein) as fluorescence reporter and a 3’ TAMRA label (6-carboxytetramethylrhodamine) as quencher. Briefly, 2 µL of each DNA sample was tested in a total reaction volume of 10 µL utilizing Qiagen QuantiTect PCR kit with ROX chemistry.  384 plates were processed on an AB7900HT with the following cycles: 95°C for 15 min and then 40 cycles of 95°C for 30 s, 60°C for 1 min.  Each DNA sample ΔCt was compared against the ΔCt of a transgenic mutant animal as well as a transgenic negative (wildtype) DNA sample using AB RQ Manager 1.2.1 software. Likewise,  commercial BCR-ABL Tg [B6.Cg-Tg(BCR/ABL)623Hkp/J] mice were also obtained from the Jackson Laboratory. The BCR-ABL Tg mice contain the truncated murine metallothionein-1 promoter driving the expression of the 190-kDa BCR-ABL fusion protein characteristic of the t(9;22) BPL. These mice were bred to wildtype female C57BL/6J mice to establish a colony of BCR-ABL transgenic mice. Pups were screened for the presence of the BCR-ABL transgene by PCR analysis of tail DNA with a BCR-ABL Tg forward primer AGAGATCAAACACCCTAACCT and a BCR-ABL Tg reverse primer CCAAAGCCATACTCCAAATGC for an expected BCR-ABL- Tg amplicon of 417-bp. Both transgenic mouse lines develop fatal BPL.

tag: background strain

value: wild type


title: Wild Type, sample 2 , replicate 1


title: Control1A

description: Gene expression after 76 days of exposure to 0μg EE2/L in rainbow trout fry testis, sample 1 in tank 1

source_name: Testis, 76 days, 0μg EE2/L, replicate 1


title: Wild Type, sample 1 , replicate 1


title: Wild Type, sample 1 , replicate 2


title: Control3A

description: Gene expression after 76 days of exposure to 0μg EE2/L in rainbow trout fry testis, sample 1 in tank 3

source_name: Testis, 76 days, 0μg EE2/L, replicate 5


title: Control1B

description: Gene expression after 76 days of exposure to 0μg EE2/L in rainbow trout fry testis, sample 2 in tank 1

source_name: Testis, 76 days, 0μg EE2/L, replicate 2


title: MYC transgenic, sample 2, biological replicate 2

source_name: Leukemia cells

value: Eµ-Myc Tg male founders (B6.Cg-Tg[IgHMyc]22Bri/J, hemizygous for Tg[IhHMyc]22Br, JAXEAST:AX12)


title: Control2B

description: Gene expression after 76 days of exposure to 0μg EE2/L in rainbow trout fry testis, sample 2 in tank 2

source_name: Testis, 76 days, 0μg EE2/L, replicate 4

value: Male


title: Control2A

description: Gene expression after 76 days of exposure to 0μg EE2/L in rainbow trout fry testis, sample 1 in tank 2

source_name: Testis, 76 days, 0μg EE2/L, replicate 3

value: Testis


title: MYC transgenic, sample 2, biological replicate 1


title: Test2_2B

description: Gene expression after 76 days of exposure to 0.1μg EE2/L in rainbow trout fry testis, sample 2 in tank 2

source_name: Testis, 76 days, 0.1μg EE2/L, replicate 4


title: phr123 triple mutant under -P condition repeat2

city: Hangzhou

first: Guo

last: meina

address: 866 Yu Hang Tang Road

country: China

institute: Zhejiang University

description: Gene expression data from phr123 mutant under -P condition

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the affymetrix Genechip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Oryza sativa

source_name: phr123 triple mutant under -P condition

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (GeneChip® 3’ IVT Express Kit User Manual, 2008, Affymetrix).

growth_protocol: Hydroponic experiments were conducted using rice culture solution with NaH2PO4 (0 Î¼M Pi). Nutrient solution was adjusted to pH 5.5 using 1 M NaOH and replaced every 2 days. Experiments were carried out in a greenhouse with a 12 h day (30º)/12 h night (22º) photoperiod, 200 Î¼mol m-2 s-1 photon density, and 60% humidity.

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

treatment_protocol: Fourteen days plants growth under hydroponic +P condition (200 µM) were treated with –P (no phosphate) for another 7 days, shoot of plants from 3 biological repeats were sampled for Affymetrix microarray analysis.

value: Leaf

value: phr123 triple mutant

value: -P condition


title: M49_60DAH_2009

source_name: Apple 'M49' fruit flesh, 2 months of cold storage, 2009

value: Hybrid M49


title: Wildtype Nipponbare under -P condition repeat3

description: Gene expression data from WT under -P condition

source_name: Wildtype Nipponbare under -P condition

value: Wildtype Nipponbare


title: phr123 triple mutant under -P condition repeat3


title: phr3 mutant under -P condition repeat3

description: Gene expression data from phr3 mutant under -P condition

source_name: phr3 mutant under -P condition

value: phr3 mutant


title: Wildtype Nipponbare under -P condition repeat1


title: M49_Harvest_2009

source_name: Apple 'M49' fruit flesh, at harvest, 2009

value: Fruit

value: Parenchyma


title: Wildtype Nipponbare under -P condition repeat2


title: M40_Harvest_2009

source_name: Apple 'M40' fruit flesh, at harvest, 2009

value: Hybrid M40

value: Wild-type


title: phr3 mutant under -P condition repeat2


title: M40_100DAF_2009

source_name: Apple 'M40' fruit flesh, 100 days after flowering, 2009

value: Fruit development


title: phr123 triple mutant under -P condition repeat1


title: MYC transgenic, sample 1, biological replicate 2


title: Test3_1B

description: Gene expression after 76 days of exposure to 1μg EE2/L in rainbow trout fry testis, sample 2 in tank 1

source_name: Testis, 76 days, 1μg EE2/L, replicate 2

value: 136 dpf


title: phr1 mutant under -P condition repeat3

description: Gene expression data from phr1 mutant under -P condition

source_name: phr1 mutant under -P condition

value: phr1 mutant


title: M40_60DAH_2009

source_name: Apple 'M40' fruit flesh, 2 months of cold storage, 2009

value: Harvested at optimum maturity

value: Cold storage for 60 days after harvest


title: phr3 mutant under -P condition repeat1


title: M49_100DAF_2009

source_name: Apple 'M49' fruit flesh, 100 days after flowering, 2009


title: phr1 mutant under -P condition repeat2


title: MYC transgenic, sample 1, biological replicate 1

value: Eµ-Myc Tg male founders (B6.Cg-Tg[IgHMyc]22Bri/J, hemizygous for Tg[IhHMyc]22Br, JAXEAST:AX12)


title: CD22DE12 transgenic, sample 2, biological replicate 1

value: pEµ-SR-CD22E12 transgene in C57BL/6J mice


title: CD22DE12 transgenic, sample 1, biological replicate 2


title: CD22DE12 transgenic, sample 2, biological replicate 2


title: BCR-ABL transgenic, sample 2,  biological replicate 1

value: commercial BCR-ABL Tg [B6.Cg-Tg(BCR/ABL)623Hkp/J] mice


title: CD22DE12 transgenic, sample 1, biological replicate 1


title: BCR-ABL transgenic, sample 1,  biological replicate 1


title: BCR-ABL transgenic, sample 2,  biological replicate 2


title: Lung_Live_Control_Rep9

city: Pyeongchang

first: Joonghoon

last: Park

state: Kangwon

address: Pyeongchang daero 1447

department: International Agricultural Technology

country: South Korea

institute: Seoul National University

description:
Biological replicate 9 of 10, control, one-month
UM_CTR_47-2_Lu_Cy3

hyb_protocol: Sample cDNA resolved in hybridization buffer (50% Formamide, 10X SSC, 0.2% SDS) was applied to microarrays, and then enclosed in Corning hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Microarrays were scanned on GenePix 4000B microarray scanner (Molecular Devices, Union City, CA), and signal intensities were extracted by GenePix Pro 6.0 (Molecular Device).

data_processing: GeneSpring 6.1 (Agilent Techologies, Palo Alto, CA) was used for background subtraction and LOWESS normalization.

organism: Sus scrofa

label_protocol: Aminoallyl-linked cDNA was generated from 10 mcg of the reference and extracted total RNA by reverse transcription, followed by labeling with Cy3 or Cy5.

growth_protocol: Frozen lung tissues of cloned piglets by SCNT and of age-matched controls by conventional breeding were provided by Dr. Randall Prather of the University of Missouri-Columbia.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen, Carlsbad, CA) and treated with DNase I (Invitrogen) to remove any possible genomic DNA contamination.

treatment_protocol: Seven clones that died shortly after birth were designated as the “deceased” group, and five one-month old clones as the “live” group.  Each cloned group was age-matched with five controls from conventional reproduction.

tag: maternal lineage

value: Duroc

value: One-month

tag: status

value: alive

tag: sample group

value: age-matched control group

value: lung

source_name: Reference RNA

tag: sample type

value: Pooled RNA from brain, kidney, liver, and lung of male and female control piglets

tag: Sex

value: Both


title: BCR-ABL transgenic, sample 1,  biological replicate 2


title: Lung_Live_Control_Rep10

description:
Biological replicate 10 of 10, control, one-month
UM_CTR_47-2_Lu_Cy5


title: soleus-cKO-5

city: Tucson

first: Henk

middle: L

last: Granzier

state: AZ

address: 1656 E Mabel St.

institute: University of Arizona

description: nebulin-deficient soleus

hyb_protocol: Samples were hybridized at 45C 17hours using the Affymetrix GeneChip Hybridization Buffers in with the Affymetrix Hyb Oven 645 and Fluidics Station 450.

scan_protocol: The Affymetrix Scanner 3000 7G was used to scan the GeneChips using Affymetrix GeneChip Console.

data_processing: Affymetrix Expression Console used RMA default settings and MoGene-1_0-st-v1.na34.mm10.transcript.csv annotation file.  Affymetrix Transcript Analysis Console was used with One-Way Between-Subject ANOVA (Unpaired) and default filter criteria: Fold Change (linear) < -2 or Fold Change (linear) > 2 and ANOVA p-value (Condition pair) < 0.05.

source_name: soleus muscle

label_protocol: Samples were biotin-labelled using the Affymetrix GeneChip WT Plus reagant per manufacturer's protocol.

growth_protocol: Mice are on a mixed C57BL/6J and 1219S6/SvEvTac background.  Mice are grown in a pathogen-free barrier facility with 12hr light:12hr dark cycle and are provided water and Teklad Global Rodent Diet (2919) ad libitum.

extract_protocol: Tissues were stored in Invitrogen RNAlater following manufacturer's protocol.  Total RNA was isolated using Qiagen RNeasy fibrous tissue kit following the manufacturer's protocol.

treatment_protocol: Mice are homozygous for the conditional nebulin allele and are hemizygous for the muscle-specific MCK-Cre transgene (cKO) or lack the MCK-Cre transgene (Control).

value: soleus

value: nebulin KO

value: male

value: 42 days old


title: soleus-cKO-6

description: nebulin-deficient soleus

value: 40 days old


title: soleus-cKO-4

description: nebulin-deficient soleus

value: 41 days old


title: soleus-cKO-2

description: nebulin-deficient soleus


title: soleus-cKO-3

description: nebulin-deficient soleus


title: soleus-cKO-1

description: nebulin-deficient soleus


title: Lung_Live_Control_Rep7

description:
Biological replicate 7 of 10, control, one-month
UM_CTR_42-8_Lu_Cy3


title: Lung_Live_Control_Rep6

description:
Biological replicate 6 of 10, control, one-month
UM_CTR_42-12_Lu_Cy5


title: phr1 mutant under -P condition repeat1

value: Leaf

value: phr1 mutant

value: -P condition


title: soleus-control-3

description: normal soleus

value: control


title: Lung_Live_Control_Rep8

description:
Biological replicate 8 of 10, control, one-month
UM_CTR_42-8_Lu_Cy5

value: Duroc


title: soleus-control-6

description: normal soleus


title: soleus-control-5

description: normal soleus


title: soleus-control-2

description: normal soleus


title: OCI-AML3 leukemic cell line treated with OTX replicate 2

city: Paris

first: Marc

last: Delord

address: Hopital Saint-Louis, 1 avenue Claude Vellefaux

department: Recherche clinique

institute: Centre hospitalier de Versailles

description:
OCI-AML3 cell line treated with OTX replicate 2
OCI_OTX2

hyb_protocol: Incubeted with rotation at 60 RPM for 16 hours at 45C

scan_protocol: Scanned with the Affymetrix® GeneChip Scanner 3000 7G using the Command Console software (Affymetrix®)

data_processing: Analysed using the Affymetrix® rma-sketch routine.

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix manual target preparation for genechip ®  whole transcript expression array.

extract_protocol: ARN were extrated using a promega extractor according to manufacturer protocol

treatment_protocol: 500 nM OTX or 500 nM JQ1 or DMSO 0.1% or nothing

tag: drug

value: OTX

tag: cell line


title: Lung_Live_Control_Rep4

description:
Biological replicate 4 of 10, control, one-month
UM_CTR_42-7_Lu_Cy5

tag: age

value: One-month

value: alive

tag: tissue


title: Lung_Live_Control_Rep5

description:
Biological replicate 5 of 10, control, one-month
UM_CTR_42-12_Lu_Cy3

value: age-matched control group

value: lung


title: OCI-AML3 leukemic cell line treated with OTX replicate 3

description:
OCI-AML3 cell line treated with OTX replicate 3
OCI_OTX3


title: soleus-control-4

description: normal soleus


title: Lung_Live_Control_Rep3

description:
Biological replicate 3 of 10, control, one-month
UM_CTR_42-7_Lu_Cy3

value: Pooled RNA from brain, kidney, liver, and lung of male and female control piglets

value: Both


title: soleus-control-1

description: normal soleus

value: soleus


title: quad-cKO-6

description: nebulin-deficient quadriceps

source_name: quadriceps muscle

value: quadriceps

value: nebulin KO

value: male


title: OCI-AML3 leukemic cell line treated with JQ1 replicate 1

description:
OCI-AML3 cell line treated with JQ1 replicate 1
OCI_JQ1_1


title: parafilm embedded tissue_normal adjacent_patient1

value: Colon Cancer Normal Adjacent

tag: race

value: Caucasian

tag: data source

value: SBU


title: OCI-AML3 leukemic cell line treated with DMSO replicate 2

description:
OCI-AML3 cell line treated with DMSO replicate 2
OCI_DMSO2

value: DMSO


title: OCI-AML3 leukemic cell line treated with OTX replicate 1

description:
OCI-AML3 cell line treated with OTX replicate 1
OCI_OTX1


title: OCI-AML3 leukemic cell line treated with DMSO replicate 3

description:
OCI-AML3 cell line treated with DMSO replicate 3
OCI_DMSO3


title: Lung_Live_Control_Rep2

description:
Biological replicate 2 of 10, control, one-month
UM_CTR_42-11_Lu_Cy5


title: Lung_Live_Control_Rep1

description:
Biological replicate 1 of 10, control, one-month
UM_CTR_42-11_Lu_Cy3


title: Lung_Live_Clone_Rep10

description:
Biological replicate 10 of 10, clone, one-month
UM_CL_45-1_Lu_Cy5

value: Large White

value: cloned group


title: quad-cKO-5

description: nebulin-deficient quadriceps

value: 42 days old


title: quad-cKO-4

description: nebulin-deficient quadriceps

value: 40 days old


title: quad-cKO-3

description: nebulin-deficient quadriceps

value: 41 days old


title: NOMO-1 leukemic cell line treated with OTX replicate 1

description:
NOMO-1 cell line treated with OTX replicate 1
NOMO_OTX1

value: OTX


title: Lung_Live_Clone_Rep9

description:
Biological replicate 9 of 10, clone, one-month
UM_CL_45-1_Lu_Cy3

value: One-month

value: alive

value: lung


title: OCI-AML3 leukemic cell line treated with DMSO replicate 1

description:
OCI-AML3 cell line treated with DMSO replicate 1
OCI_DMSO1


title: quad-cKO-2

description: nebulin-deficient quadriceps


title: NOMO-1 leukemic cell line treated with OTX replicate 2

description:
NOMO-1 cell line treated with OTX replicate 2
NOMO_OTX2


title: quad-control-5

description: normal quadriceps

value: control


title: quad-control-6

description: normal quadriceps

value: quadriceps


title: Lung_Live_Clone_Rep5

description:
Biological replicate 5 of 10, clone, one-month
UM_CL_44-1_Lu_Cy3

value: Duroc

value: Pooled RNA from brain, kidney, liver, and lung of male and female control piglets

value: Both


title: Lung_Live_Clone_Rep4

description:
Biological replicate 4 of 10, clone, one-month
UM_CL_43-3_Lu_Cy5


title: NOMO-1 leukemic cell line treated with OTX replicate 3

description:
NOMO-1 cell line treated with OTX replicate 3
NOMO_OTX3


title: NOMO-1 leukemic cell line treated with JQ1 replicate 3

description:
NOMO-1 cell line treated with JQ1 replicate 3
NOMO_JQ1_3


title: Lung_Live_Clone_Rep3

description:
Biological replicate 3 of 10, clone, one-month
UM_CL_43-3_Lu_Cy3


title: quad-control-4

description: normal quadriceps

value: male


title: quad-control-2

description: normal quadriceps


title: quad-cKO-1

description: nebulin-deficient quadriceps

value: nebulin KO


title: NOMO-1 leukemic cell line treated with JQ1 replicate 2

description:
NOMO-1 cell line treated with JQ1 replicate 2
NOMO_JQ1_2


title: Lung_Live_Clone_Rep8

description:
Biological replicate 8 of 10, clone, one-month
UM_CL_43-2_Lu_Cy5


title: NOMO-1 leukemic cell line treated with JQ1 replicate 1

description:
NOMO-1 cell line treated with JQ1 replicate 1
NOMO_JQ1_1


title: NOMO-1 leukemic cell line treated with DMSO replicate 3

description:
NOMO-1 cell line treated with DMSO replicate 3
NOMO_DMSO3

value: DMSO


title: Lung_Live_Clone_Rep6

description:
Biological replicate 6 of 10, clone, one-month
UM_CL_44-1_Lu_Cy5


title: NOMO-1 leukemic cell line treated with DMSO replicate 2

description:
NOMO-1 cell line treated with DMSO replicate 2
NOMO_DMSO2


title: quad-control-3

description: normal quadriceps


title: Lung_Live_Clone_Rep7

description:
Biological replicate 7 of 10, clone, one-month
UM_CL_43-2_Lu_Cy3

value: Large White


title: quad-control-1

description: normal quadriceps


title: NOMO-1 leukemic cell line treated with DMSO replicate 1

description:
NOMO-1 cell line treated with DMSO replicate 1
NOMO_DMSO1


title: KG1A leukemic cell line treated with OTX replicate 3

description:
KG1A cell line treated with OTX replicate 3
KG1a_OTX3


title: Lung_Deceased_Clone_Rep14

description:
Biological replicate 14 of 14, clone, neonatal
PPL_CL_635-2_Lu_Cy5

value: Neonatal

value: deceased

value: cloned group


title: Lung_Live_Clone_Rep1

description:
Biological replicate 1 of 10, clone, one-month
UM_CL_43-1_Lu_Cy3


title: Lung_Deceased_Clone_Rep11

description:
Biological replicate 11 of 14, clone, neonatal
PPL_CL_635-1_Lu_Cy3


title: KG1A leukemic cell line treated with OTX replicate 2

description:
KG1A cell line treated with OTX replicate 2
KG1a_OTX2


title: Wild Type splenocyte 2

hyb_protocol: Following fragmentation, 45 ug of cRNA were hybridized on Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChip Scanner 3000 7G.

data_processing: PM signal values for probesets were extracted utilizing raw CEL files matched with probe identifiers obtained from a CDF file supplied by Mark Robinson on 2008-08-28 (MoGene-1_0-st-v1,r3.cdf) implemented by Aroma Affymetrix statistical packages ran in R-studio environment (Version 0.97.551, R-studio Inc., running with R 3.01).  The PM signals were quantified using Robust Multiarray Analysis in a 3 step process including RMA background correction, quantile normalization, and summarization by a log additive model of probes in a probeset across  these samples (RmaPlm method adapted in Aroma Affymetrix).  All expression values were log2 scaled.

source_name: Splenocytes

label_protocol: WholeTranscript (WT) Sense Target Labeling andControl Reagents,

extract_protocol: Total cellular RNA was extracted from homogenized lysate samples of leukemia cells using the Qiagen RNeasy Plus Mini Kit (Cat No 74134) (Qiagen, Santa Clarita, CA). In order to minimize the genomic DNA contamination in the RNA samples, the homogenized lysate samples were first run through a DNA binding spin column prior to steps of RNA binding, washing and elution. Total RNA (45L/ sample) was obtained with a concentration range of 60-200ng/L and an absorbance ratio (A260/A280) ranging from 1.9-2.1. RNA quality as judged by the integrity of the 28S and 18S ribosomal RNA was determined by an Agilent 2100 Bioanalyzer to ensure it was acceptable for subsequent microarray analysis.

value: wild type


title: KG1A leukemic cell line treated with OTX replicate 1

description:
KG1A cell line treated with OTX replicate 1
KG1a_OTX1

value: OTX


title: Lung_Deceased_Clone_Rep13

description:
Biological replicate 13 of 14, clone, neonatal
PPL_CL_635-2_Lu_Cy3


title: Wild Type splenocyte 1


title: Lung_Deceased_Clone_Rep7

description:
Biological replicate 7 of 14, clone, neonatal
PPL_CL_642-1_Lu_Cy3


title: KG1A leukemic cell line treated with JQ1 replicate 3

description:
KG1A cell line treated with JQ1 replicate 3
KG1A_JQ1_3


title: Lung_Live_Clone_Rep2

description:
Biological replicate 2 of 10, clone, one-month
UM_CL_43-1_Lu_Cy5

value: One-month


title: Lung_Deceased_Clone_Rep8

description:
Biological replicate 8 of 14, clone, neonatal
PPL_CL_642-1_Lu_Cy5


title: CD22DE12 transgenic biological replicate 2

source_name: Leukemia cells

value: pEµ-SR-CD22E12 transgene in C57BL/6J mice


title: Lung_Deceased_Clone_Rep12

description:
Biological replicate 12 of 14, clone, neonatal
PPL_CL_635-1_Lu_Cy5

value: lung


title: KG1A leukemic cell line treated with JQ1 replicate 1

description:
KG1A cell line treated with JQ1 replicate 1
KG1A_JQ1_1


title: Wild Type splenocyte 3


title: Lung_Deceased_Clone_Rep5

description:
Biological replicate 5 of 14, clone, neonatal
PPL_CL_629-1_Lu_Cy3


title: Lung_Deceased_Clone_Rep10

description:
Biological replicate 10 of 14, clone, neonatal
PPL_CL_671-5_Lu_Cy5


title: Lung_Deceased_Clone_Rep9

description:
Biological replicate 9 of 14, clone, neonatal
PPL_CL_671-5_Lu_Cy3


title: K562 leukemic cell line treated with OTX replicate 3

description:
K562 cell line treated with OTX replicate 3
K562_OTX3


title: KG1A leukemic cell line treated with JQ1 replicate 2

description:
KG1A cell line treated with JQ1 replicate 2
KG1A_JQ1_2


title: KG1A leukemic cell line treated with DMSO replicate 3

description:
KG1A cell line treated with DMSO replicate 3
KG1a_DMSO3


title: MYC transgenic biological replicate 2

value: Eµ-Myc Tg male founders (B6.Cg-Tg[IgHMyc]22Bri/J, hemizygous for Tg[IhHMyc]22Br, JAXEAST:AX12)


title: Lung_Deceased_Clone_Rep6

description:
Biological replicate 6 of 14, clone, neonatal
PPL_CL_629-1_Lu_Cy5


title: BCR-ABL transgenic  biological replicate 1

value: commercial BCR-ABL Tg [B6.Cg-Tg(BCR/ABL)623Hkp/J] mice


title: KG1A leukemic cell line treated with DMSO replicate 2

description:
KG1A cell line treated with DMSO replicate 2
KG1a_DMSO2


title: BCR-ABL transgenic  biological replicate 2


title: Lung_Deceased_Clone_Rep4

description:
Biological replicate 4 of 14, clone, neonatal
PPL_CL_637-1_Lu_Cy5


title: KG1A leukemic cell line treated with DMSO replicate 1

description:
KG1A cell line treated with DMSO replicate 1
KG1a_DMSO1


title: Lung_Deceased_Clone_Rep2

description:
Biological replicate 2 of 14, clone, neonatal
PPL_CL_628-1_Lu_Cy5


title: Lung_Deceased_Clone_Rep3

description:
Biological replicate 3 of 14, clone, neonatal
PPL_CL_637-1_Lu_Cy3


title: K562 leukemic cell line treated with OTX replicate 2

description:
K562 cell line treated with OTX replicate 2
K562_OTX2


title: Wild Type splenocyte 4


title: MYC transgenic biological replicate 1


title: Lung_Deceased_Control_Rep10

description:
Biological replicate 10 of 10, control, neonatal
PPL_CTR_263-5_Lu_Cy5

value: age-matched control group


title: CD22DE12 transgenic biological replicate 1


title: Lung_Deceased_Clone_Rep1

description:
Biological replicate 1 of 14, clone, neonatal
PPL_CL_628-1_Lu_Cy3

value: Pooled RNA from brain, kidney, liver, and lung of male and female control piglets


title: Lung_Deceased_Control_Rep7

description:
Biological replicate 7 of 10, control, neonatal
PPL_CTR_263-4_Lu_Cy3

value: Both


title: K562 leukemic cell line treated with JQ1 replicate 2

description:
K562 cell line treated with JQ1 replicate 2
K562_JQ1_2


title: Lung_Deceased_Control_Rep9

description:
Biological replicate 9 of 10, control, neonatal
PPL_CTR_263-5_Lu_Cy3


title: K562 leukemic cell line treated with JQ1 replicate 1

description:
K562 cell line treated with JQ1 replicate 1
K562_JQ1_1


title: Lung_Deceased_Control_Rep8

description:
Biological replicate 8 of 10, control, neonatal
PPL_CTR_263-4_Lu_Cy5


title: Lung_Deceased_Control_Rep6

description:
Biological replicate 6 of 10, control, neonatal
PPL_CTR_263-3_Lu_Cy5


title: Lung_Deceased_Control_Rep3

description:
Biological replicate 3 of 10, control, neonatal
PPL_CTR_263-2_Lu_Cy3


title: K562 leukemic cell line treated with OTX replicate 1

description:
K562 cell line treated with OTX replicate 1
K562_OTX1


title: K562 leukemic cell line treated with DMSO replicate 1

description:
K562 cell line treated with DMSO replicate 1
k562_DMSO1


title: Lung_Deceased_Control_Rep4

description:
Biological replicate 4 of 10, control, neonatal
PPL_CTR_263-2_Lu_Cy5


title: Lung_Deceased_Control_Rep1

description:
Biological replicate 1 of 10, control, neonatal
PPL_CTR_263-1_Lu_Cy3


title: HL60 leukemic cell line treated with OTX replicate 2

description:
HL60 cell line treated with OTX replicate 2
HL60_OTX2


title: K562 leukemic cell line treated with DMSO replicate 2

description:
K562 cell line treated with DMSO replicate 2
k562_DMSO2


title: HL60 leukemic cell line treated with OTX replicate 3

description:
HL60 cell line treated with OTX replicate 3
HL60_OTX3


title: HL60 leukemic cell line treated with OTX replicate 1

description:
HL60 cell line treated with OTX replicate 1
HL60_OTX1


title: HL60 leukemic cell line treated with JQ1 replicate 1

description:
HL60 cell line treated with JQ1 replicate 1
HL60_JQ1_1


title: HL60 leukemic cell line treated with DMSO replicate 3

description:
HL60 cell line treated with DMSO replicate 3
HL60_DMSO3


title: Lung_Deceased_Control_Rep2

description:
Biological replicate 2 of 10, control, neonatal
PPL_CTR_263-1_Lu_Cy5


title: HL60 leukemic cell line treated with JQ1 replicate 2

description:
HL60 cell line treated with JQ1 replicate 2
HL60_JQ1_2


title: HL60 leukemic cell line treated with JQ1 replicate 3

description:
HL60 cell line treated with JQ1 replicate 3
HL60_JQ1_3


title: HUVEC hypoxia [array]

city: Hannover

first: Jan

last: Fiedler

address: Carl-Neuberg-Str. 1

department: Institute of Molecular and Translational Therapeutic Strategies (IMTTS), IFB-Tx

country: Germany

institute: Hannover Medical School

description: HUVECs cultured under hypoxic condition for 24 h

hyb_protocol: Labeled cRNA was hybridized to  Ncode™ Human Non-coding RNA Microarray (Invitrogen) microarrays for 17h at 65°C and scanned using the Agilent DNA Microarray Scanner.

scan_protocol: GE1_107_Sep09 (Read Only)

data_processing: Expression values were calculated by the software package Feature Extraction 10.7.3.1 (Agilent Technologies; Waldbronn, Germany) and further processed with GeneSpring Software (Agilent)

source_name: Cell culture of HUVEC

label_protocol: Quality and integrity of the total RNA was controlled on an Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany). 100ng of total RNA were applied for Cy3-labelling reaction using the one color Quick Amp Low Input Labeling protocol (Agilent Technologies; Waldbronn, Germany).

growth_protocol: Human Umbilical Vein Endothelial Cells (HUVECs) were purchased from Lonza and cultured in EBM-2 (Lonza) supplemented with hEGF, hydrocortisone, VEGF, hFGF-B, R3-IGF-1, ascorbic acid, gentamicin/amphotericin-B and 10% FBS under standard cell culture conditions (37°C, 5% CO2).

extract_protocol: miRNeasy Kit Qiagen

treatment_protocol: 24 h of normoxia or hypoxia (0.1-0.2%O2)

value: HUVEC


title: Lung_Deceased_Control_Rep5

description:
Biological replicate 5 of 10, control, neonatal
PPL_CTR_263-3_Lu_Cy3


title: K562 leukemic cell line treated with DMSO replicate 3

description:
K562 cell line treated with DMSO replicate 3
k562_DMSO3


title: HEK293T_KO_REP4

status: Public on Jun 24 2015

city: Edegem

first: Ken

last: Op de Beeck

address: Universiteitsplein 1

institute: University Of Antwerp

description: replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were quantile normalized in limma 3.24.4 for R

label_protocol: Biotinylated cRNA were prepared with the Illumina Totalprep RNA amplification kit (Life technologies)

growth_protocol: The microarray experiments in human cell lines were performed using Human Embryonic Kidney 293T cells (HEK293T). HEK293T cells were subcultured in 60 mm dishes at a density of 2 × 106 cells in Dulbecco’s modified Eagle’s medium containing 4500 mg/L glucose supplemented with 10% (v/v) fetal calf serum, 100 U/ml penicillin, 100 μg/ml streptomycin, and 2 mM L-glutamine.

extract_protocol: An RNeasy mini kit was used for RNA extraction from transfected HEK293T cells (Qiagen, Hilden, Germany) at different time-points. For the microarray experiment, RNA was extracted 12h post-transfection.

treatment_protocol: Overnight cultures were transfected with either  wtDFNA5 or mutDFNA5 using lipofectamine. Six hours post transfection, cells were harvested using Triple-x reagent for RNA extraction.

tag: cell type

value: human embryonic kidney cells

tag: transfected with

value: mutant DFNA5


title: HEK293T_KO_REP3

description: replicate 3


title: hES

city: Qingdao

first: zhenyu

last: wang

address: No. 5. Yanerdao Road

institute: Shandong Eye Institute

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 1 out of 3 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis.

source_name: human embryonic stem cell line H1

label_protocol: Total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: The human ESC line H1 were cultured and passaged in standard embryonic stem cell medium at 37°C with 5% CO2. The RA_SB were cultured in defined keratinocyte serum-free mediumin at 37°C with 5% CO2 after differentiation. The epithelial_cell were cultured in DMEM/F12 mediumin at 37°C with 5% CO2 after digested from limbus.

extract_protocol: The total RNA was extracted by TRIzol after harvesting cells.

value: human embryonic stem cell line


title: HEK293T_KO_REP2

description: replicate 2


title: HEK293T_KO_REP1

description: replicate 1


title: HEK293T_WT_REP4

description: replicate 4

value: wild type DFNA5


title: epithelial_cell

source_name: the primary human limbal stem cells

tag: source cell line/subject

value: male, aged 25~45

value: limbal of eye

value: primary human limbal stem cells


title: HEK293T_WT_REP2

description: replicate 2


title: HL60 leukemic cell line treated with DMSO replicate 1

description:
HL60 cell line treated with DMSO replicate 1
HL60_DMSO1

value: DMSO


title: HEK293T_WT_REP5

description: replicate 5


title: HUVEC normoxia [array]

description: HUVECs cultured under normoxic condition for 24 h


title: HEK293T_KO_REP5

description: replicate 5


title: RA_SB

source_name: the corneal epithelial-like cells derived from hES by differentiation


title: HEK293T_WT_REP3

description: replicate 3


title: GW_301 Head and neck squamous cell carcinoma Illumina HT12v4

city: Leipzig

first: Maciej

last: Rosolowski

address: Härtelstr. 16-18

institute: Institute for Medical Informatics, Statistics and Epidemiology (IMISE)

hyb_protocol: 750 ng of cRNA were hybridized to Human HT12 v4 Expression BeadChips (Illumina, San Diego, CA, USA)

scan_protocol: and scanned on the Illumina HiScan instrument according to the manufacturer’s specifications

data_processing: Raw data of all 47,323 probes was extracted by Illumina GenomeStudio without additional background correction. Data was further processed within R / Bioconductor. Expression values were log2-transformed and normalized using RSN. Batch effects of expression BeadChips were corrected using ComBat. Two criteria were used to remove arrays of low quality. First, the number of detected features with P<0.01 on an array was required to be within 3 interquartile ranges from the median of all arrays. 9 samples did not pass this criterion. Second, the Mahalanobis distance of several quality characteristics was computed for each array. These quality characteristics included signals from perfect-match and miss-match control probes, control probes present at different concentrations, mean of negative control probes, mean of house-keeping genes, number of expressed genes, mean signal strength of biotin-control-probes, and Euclidean distances of expression values. Thereby, Euclidean distances of expression values of each sample were based on their distances to the center, which was defined as the average of all samples after removing 10% samples farthest away from the center. The Mahalanobis distances of 4 arrays were more than 3 interquartile ranges away from the median of all arrays and were therefore excluded. Overall, of the assayed 300 samples 13 samples were excluded for quality reasons. Features detected by Illumina GenomeStudio with P<0.05 in less than 1% of the samples were excluded resulting in 31,347 features. Additionally, 17 feature were removed as their expression levels were still found to be significantly associated after Bonferroni-correction with batches of BeadChips. Finally, the preprocessing resulted in 31,330 features.  There were 12 paired measurements in the data including 10 pairs of samples taken from the same patients at short intervals, 1 pair of a primary and relapse tumor and 1 pair of biopsies from a first and second relapse. To remove the duplicates, the array with more detected features at P<0.01 was selected from each pair. Among the remaining 275 samples, 3 were taken from lymph node metastases and 2 were cell lines and 270 (included here) were tumor samples.

label_protocol: Before microarray analysis RNA integrity and concentration was examined on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) using the RNA 6.000 LabChip Kit (Agilent Technologies) according to the manufacturer’s instructions. Of the available 307 tumor samples 298 samples fulfilled criteria of good RNA-quality and together with 2 additional tumor cell lines were selected for further analysis conducted at the microarray core facility of the Interdisciplinary Center for Clinical Research Leipzig (Faculty of Medicine, University of Leipzig). 250 ng RNA per sample were ethanol precipitated with GlycoBlue (Invitrogen) as carrier and dissolved at a concentration of 100 – 150 ng/µl prior to probe synthesis using the TargetAmp™-Nano Labeling Kit for Illumina Expression BeadChip (Epicentre Biotechnologies, Madison, WI, USA).

extract_protocol: Biopsy samples of HNSCC taken during panendoscopy or definitive surgery. They were immediately transfered into TRIzol™ (Invitrogen, Darmstadt, Germany) and then stored at -80°C until mechanical disintegration of the frozen sample for 80 sec at 4000 rpm in a Peqlab MiniLys (Peqlab, Erlangen, Germany) followed by isolation of DNA, RNA, and protein according to the method of Chomczynski (1) as specified in the standard TRIzol® protocol provided by the manufacturer (Invitrogen). The aqueous phase was used for RNA preparation by use of the Ambion Pure Link™ RNA Mini Kit (Life technologies, Carlsbad) including the on-column DNase I digestion (Qiagen, Hilden, Germany) according the manufacturer’s instructions. After ethanol precipitation of the interphase, DNA was resolved in water and used without further cleanup. Quantity and quality of DNA and RNA were determined by measuring optical density (OD) at λ1=260 nm and λ2=280 nm using the Take3 plate (BioTek, Bad Friedrichshall, Germany) in the Synergy2 spectrophotometer (BioTek), and a quotient of (OD1/OD2)>1.8 and >1.95 were regarded as sufficient quality of DNA and RNA, respectively.

tag: ID

tag: gender

value: F

tag: smoking

value: No

tag: packyears

tag: alcohol

value: no

value: Secondary

value: IVB

value: multi

value: Negative

value: DNA-

tag: os

value: FALSE

tag: pfs

value: TRUE

value: Atypical IR 1


title: GW_302 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: Yes

value: Primary

value: Cavum Oris

value: II

tag: treatment

value: mono

value: Basal 4

value: Disruptive


title: HEK293T_WT_REP1

description: replicate 1

value: human embryonic kidney cells

value: wild type DFNA5


title: GW_306 Head and neck squamous cell carcinoma Illumina HT12v4

value: Secondary

value: Oropharynx

value: I


title: GW_307 Head and neck squamous cell carcinoma Illumina HT12v4

value: No

value: multi

value: Negative

value: DNA-


title: GW_303 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: Larynx

value: FALSE

value: WT


title: GW_300 Head and neck squamous cell carcinoma Illumina HT12v4

value: no

value: Primary

value: IVB

value: Atypical IR 1


title: GW_305 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: IVA


title: GW_299 Head and neck squamous cell carcinoma Illumina HT12v4

value: F

value: mono

value: Basal 4

value: Non-disruptive


title: GW_298 Head and neck squamous cell carcinoma Illumina HT12v4

value: Cavum Oris

value: TRUE

value: Mesenchymal 3


title: HL60 leukemic cell line treated with DMSO replicate 2

description:
HL60 cell line treated with DMSO replicate 2
HL60_DMSO2

tag: drug

value: DMSO


title: GW_295 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: Oropharynx

value: multi

value: DNA+RNA-

value: Disruptive


title: GW_296 Head and neck squamous cell carcinoma Illumina HT12v4

value: Primary

value: Hypopharynx

value: Negative

value: DNA-

value: FALSE

value: Classical 2

value: WT


title: GW_297 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: III

value: mono

value: Atypical IR 1


title: GW_294 Head and neck squamous cell carcinoma Illumina HT12v4

value: No

value: IVA

value: DNA+RNA+


title: GW_290 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: TRUE


title: GW_288 Head and neck squamous cell carcinoma Illumina HT12v4

value: F

value: Oropharynx

value: multi

value: Basal 4


title: GW_289 Head and neck squamous cell carcinoma Illumina HT12v4

value: Primary

value: Cavum Oris

value: Negative

value: DNA-


title: GW_293 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: Larynx

value: II

value: FALSE

value: Classical 2


title: GW_292 Head and neck squamous cell carcinoma Illumina HT12v4

value: IVA

value: Other HPV

value: Mesenchymal 3


title: GW_286 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: I

value: palliative


title: GW_284 Head and neck squamous cell carcinoma Illumina HT12v4

value: Oropharynx

value: multi

value: TRUE


title: GW_282 Head and neck squamous cell carcinoma Illumina HT12v4

value: Primary

value: Basal 4


title: GW_283 Head and neck squamous cell carcinoma Illumina HT12v4

value: Cavum Oris

value: DNA+RNA-


title: GW_285 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: mono

value: DNA+RNA+

value: WT


title: GW_275 Head and neck squamous cell carcinoma Illumina HT12v4

value: no

value: IVA

value: Negative

value: DNA-

value: Atypical IR 1


title: GW_280 Head and neck squamous cell carcinoma Illumina HT12v4

value: M


title: GW_281 Head and neck squamous cell carcinoma Illumina HT12v4

value: FALSE


title: GW_272 Head and neck squamous cell carcinoma Illumina HT12v4

value: F

value: Relapse

value: Hypopharynx

value: multi

value: Mesenchymal 3


title: GW_287 Head and neck squamous cell carcinoma Illumina HT12v4

value: No

value: Primary

value: Oropharynx

value: III


title: HEK293T_KO_REP6

description: replicate 6

tag: cell line

value: human embryonic kidney cells

value: mutant DFNA5


title: GW_263 Head and neck squamous cell carcinoma Illumina HT12v4

tag: age

value: Yes

value: Secondary

value: Cavum Oris

value: IVA

value: WT


title: GW_266 Head and neck squamous cell carcinoma Illumina HT12v4

value: no

value: Larynx

value: Negative

value: DNA-

value: FALSE

value: TRUE

value: Basal 4


title: GW_265 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: IVC

value: mono


title: GW_269 Head and neck squamous cell carcinoma Illumina HT12v4

value: F

value: No

value: Relapse

value: III

value: multi


title: GW_257 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: Secondary

value: Hypopharynx

value: Classical 2


title: GW_262 Head and neck squamous cell carcinoma Illumina HT12v4

value: Larynx

value: IVA

value: Negative

value: Disruptive


title: GW_268 Head and neck squamous cell carcinoma Illumina HT12v4

value: Cavum Oris

value: DNA-

value: FALSE

value: TRUE

value: Basal 4


title: GW_258 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: mono

value: Atypical IR 1

value: Non-disruptive


title: GW_256 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: I

value: multi

value: WT


title: GW_250 Head and neck squamous cell carcinoma Illumina HT12v4

value: Primary

value: Larynx

value: II

value: Classical 2


title: GW_251 Head and neck squamous cell carcinoma Illumina HT12v4

value: Hypopharynx

value: IVA

value: DNA+RNA-

value: Mesenchymal 3


title: GW_249 Head and neck squamous cell carcinoma Illumina HT12v4

value: F

value: No

value: Cavum Oris

value: palliative

value: Negative

value: DNA-

value: FALSE


title: GW_253 Head and neck squamous cell carcinoma Illumina HT12v4

value: multi

value: Other HPV

value: TRUE


title: GW_271 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: Yes

value: Secondary

value: Larynx

value: mono


title: GW_247 Head and neck squamous cell carcinoma Illumina HT12v4

value: Primary

value: IVA


title: GW_255 Head and neck squamous cell carcinoma Illumina HT12v4

value: no

value: Relapse

value: Hypopharynx

value: II

value: Atypical IR 1

value: Non-disruptive


title: GW_244 Head and neck squamous cell carcinoma Illumina HT12v4

value: F

value: Cavum Oris

value: Negative

value: DNA-

value: FALSE

value: Mesenchymal 3

value: WT


title: GW_243 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: Yes

value: Oropharynx

value: DNA+RNA+


title: GW_246 Head and neck squamous cell carcinoma Illumina HT12v4

value: Primary

value: IVC

value: multi

value: TRUE

value: Basal 4


title: GW_241 Head and neck squamous cell carcinoma Illumina HT12v4

value: II

value: DNA+RNA-

value: Non-disruptive


title: GW_233 Head and neck squamous cell carcinoma Illumina HT12v4

value: IVA

value: Negative


title: GW_242 Head and neck squamous cell carcinoma Illumina HT12v4

value: mono

value: FALSE


title: GW_248 Head and neck squamous cell carcinoma Illumina HT12v4

value: No

value: Atypical IR 1


title: GW_235 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: Yes

value: Cavum Oris

value: DNA-

value: Disruptive


title: GW_229 Head and neck squamous cell carcinoma Illumina HT12v4

value: F

value: Primary

value: multi

value: Mesenchymal 3

value: WT


title: GW_230 Head and neck squamous cell carcinoma Illumina HT12v4

value: Oropharynx

value: DNA+RNA+


title: GW_238 Head and neck squamous cell carcinoma Illumina HT12v4

value: III


title: GW_245 Head and neck squamous cell carcinoma Illumina HT12v4

value: IVA

value: mono

value: Negative

value: TRUE


title: GW_239 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: Non-disruptive


title: GW_234 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: Cavum Oris


title: GW_226 Head and neck squamous cell carcinoma Illumina HT12v4

value: I

value: DNA-

value: FALSE

value: Basal 4


title: GW_237 Head and neck squamous cell carcinoma Illumina HT12v4

value: no

value: Primary

value: IVB


title: GW_227 Head and neck squamous cell carcinoma Illumina HT12v4

value: F

value: No

value: Disruptive


title: GW_225 Head and neck squamous cell carcinoma Illumina HT12v4

value: III

value: multi

value: Classical 2

value: WT


title: GW_224 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: IVA

value: DNA+RNA+

value: Atypical IR 1


title: GW_231 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: Cavum Oris

value: Negative

value: DNA-

value: Mesenchymal 3

value: Non-disruptive


title: GW_228 Head and neck squamous cell carcinoma Illumina HT12v4

value: Primary

value: Oropharynx

value: IVB

value: mono

value: TRUE


title: GW_240 Head and neck squamous cell carcinoma Illumina HT12v4

value: multi


title: GW_220 Head and neck squamous cell carcinoma Illumina HT12v4

value: WT


title: GW_219 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: no

value: II

value: FALSE

value: Basal 4


title: GW_222 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: Cavum Oris

value: IVA

value: Disruptive


title: GW_223 Head and neck squamous cell carcinoma Illumina HT12v4

value: Negative

value: DNA-


title: GW_216 Head and neck squamous cell carcinoma Illumina HT12v4

value: Primary

value: Oropharynx

value: Other HPV

value: Atypical IR 1


title: GW_211 Head and neck squamous cell carcinoma Illumina HT12v4

value: F

value: mono

value: TRUE

value: Mesenchymal 3


title: GW_218 Head and neck squamous cell carcinoma Illumina HT12v4

value: No

value: I

value: DNA+RNA-

value: WT


title: GW_206 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: Yes

value: Cavum Oris

value: multi


title: GW_207 Head and neck squamous cell carcinoma Illumina HT12v4

value: IVB

value: Negative

value: DNA-

value: Disruptive


title: GW_210 Head and neck squamous cell carcinoma Illumina HT12v4

value: Primary

value: Oropharynx

value: II

value: FALSE

value: Basal 4


title: GW_202 Head and neck squamous cell carcinoma Illumina HT12v4

value: IVA

value: mono

value: TRUE


title: GW_214 Head and neck squamous cell carcinoma Illumina HT12v4

value: DNA+RNA+

value: Atypical IR 1

value: WT


title: GW_205 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: No

value: no

value: Cavum Oris


title: GW_203 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: multi

value: DNA+RNA-

value: Non-disruptive


title: GW_201 Head and neck squamous cell carcinoma Illumina HT12v4

value: Primary

value: Oropharynx

value: Negative

value: DNA-

value: Mesenchymal 3

value: Disruptive


title: GW_193 Head and neck squamous cell carcinoma Illumina HT12v4

value: Larynx

value: IVA

value: FALSE

value: Basal 4


title: GW_215 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: DNA+RNA+

value: Atypical IR 1

value: WT


title: GW_200 Head and neck squamous cell carcinoma Illumina HT12v4

value: F

value: Yes

value: Cavum Oris

value: IVC

value: multi

value: TRUE


title: GW_192 Head and neck squamous cell carcinoma Illumina HT12v4

value: Primary

value: Hypopharynx

value: III

value: Negative

value: DNA-

value: Classical 2

value: Non-disruptive


title: GW_217 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: No

value: Oropharynx

value: IVA

value: FALSE


title: GW_212 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: DNA+RNA+

value: Atypical IR 1

value: WT


title: GW_204 Head and neck squamous cell carcinoma Illumina HT12v4

value: Cavum Oris

value: multi

value: Mesenchymal 3


title: GW_198 Head and neck squamous cell carcinoma Illumina HT12v4

value: Primary

value: Basal 4

value: Disruptive


title: GW_191 Head and neck squamous cell carcinoma Illumina HT12v4

value: Larynx

value: I

value: mono

value: DNA+RNA-


title: GW_209 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: Negative

value: DNA-


title: GW_197 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: IVA

value: TRUE


title: GW_196 Head and neck squamous cell carcinoma Illumina HT12v4

value: Hypopharynx

value: IVB


title: GW_189 Head and neck squamous cell carcinoma Illumina HT12v4

value: multi

value: Non-disruptive


title: GW_199 Head and neck squamous cell carcinoma Illumina HT12v4

value: Primary

value: FALSE

value: Mesenchymal 3

value: WT


title: GW_186 Head and neck squamous cell carcinoma Illumina HT12v4

value: Larynx

value: Basal 4


title: GW_188 Head and neck squamous cell carcinoma Illumina HT12v4

value: mono

value: Disruptive


title: GW_190 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: No

value: Negative

value: Atypical IR 1


title: GW_187 Head and neck squamous cell carcinoma Illumina HT12v4

value: Cavum Oris

value: II

value: DNA-


title: GW_183 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: I

value: TRUE


title: GW_185 Head and neck squamous cell carcinoma Illumina HT12v4

value: Primary

value: FALSE


title: GW_184 Head and neck squamous cell carcinoma Illumina HT12v4

value: IVA

value: multi

value: Mesenchymal 3


title: GW_182 Head and neck squamous cell carcinoma Illumina HT12v4

value: WT


title: GW_180 Head and neck squamous cell carcinoma Illumina HT12v4

value: Oropharynx

value: Basal 4


title: GW_173 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: Larynx

value: III

value: Disruptive


title: GW_177 Head and neck squamous cell carcinoma Illumina HT12v4

value: Negative

value: Atypical IR 1


title: GW_171 Head and neck squamous cell carcinoma Illumina HT12v4

value: F

value: Yes

value: DNA-

value: Classical 2


title: GW_178 Head and neck squamous cell carcinoma Illumina HT12v4

value: Primary

value: Hypopharynx

value: FALSE


title: GW_179 Head and neck squamous cell carcinoma Illumina HT12v4

value: IVA

value: multi


title: GW_172 Head and neck squamous cell carcinoma Illumina HT12v4

value: Cavum Oris

value: I

value: mono

value: TRUE

value: WT


title: GW_181 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: Basal 4

value: Disruptive


title: GW_174 Head and neck squamous cell carcinoma Illumina HT12v4

value: F

value: No

value: no

value: III

value: Negative


title: GW_170 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: Primary

value: Oropharynx

value: DNA+RNA+

value: Mesenchymal 3


title: GW_168 Head and neck squamous cell carcinoma Illumina HT12v4

value: Larynx

value: II

value: DNA-

value: FALSE


title: GW_166 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: mono

value: DNA+RNA-

value: TRUE

value: Atypical IR 1


title: GW_236 Head and neck squamous cell carcinoma Illumina HT12v4

value: Cavum Oris

value: I

value: Basal 4

value: Non-disruptive


title: GW_169 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: Primary

value: Hypopharynx

value: III

value: Negative

value: WT


title: GW_159 Head and neck squamous cell carcinoma Illumina HT12v4

value: No

value: IVA

value: multi

value: DNA-

value: Mesenchymal 3

value: Disruptive


title: GW_165 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: FALSE


title: GW_167 Head and neck squamous cell carcinoma Illumina HT12v4

value: Oropharynx

value: II

value: mono


title: GW_156 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: Cavum Oris

value: Basal 4


title: GW_163 Head and neck squamous cell carcinoma Illumina HT12v4

value: F

value: Primary

value: I

value: TRUE


title: GW_160 Head and neck squamous cell carcinoma Illumina HT12v4

value: no

value: Larynx

value: IVA

value: Negative

value: Classical 2

value: WT


title: GW_157 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: Hypopharynx

value: multi

value: DNA-

value: FALSE

value: Atypical IR 1

value: Disruptive


title: GW_164 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: Mesenchymal 3


title: GW_158 Head and neck squamous cell carcinoma Illumina HT12v4

value: Primary

value: Cavum Oris

value: I

value: mono

value: Non-disruptive


title: GW_144 Head and neck squamous cell carcinoma Illumina HT12v4

value: Larynx

value: II

value: Negative


title: GW_153 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: No

value: IVA

value: TRUE

value: Basal 4


title: GW_149 Head and neck squamous cell carcinoma Illumina HT12v4

value: Oropharynx

value: Other HPV


title: GW_154 Head and neck squamous cell carcinoma Illumina HT12v4

value: IVC

value: DNA-

value: Atypical IR 1

value: WT


title: GW_147 Head and neck squamous cell carcinoma Illumina HT12v4

value: F

value: Primary

value: multi

value: DNA+RNA-


title: GW_150 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: Cavum Oris

value: II

value: Classical 2


title: GW_151 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: III

value: mono

value: FALSE

value: Disruptive


title: GW_155 Head and neck squamous cell carcinoma Illumina HT12v4

value: Hypopharynx

value: IVA

value: Negative

value: TRUE

value: Mesenchymal 3


title: GW_142 Head and neck squamous cell carcinoma Illumina HT12v4

value: Primary

value: Larynx

value: DNA-

value: WT


title: GW_143 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: multi

value: Atypical IR 1


title: GW_140 Head and neck squamous cell carcinoma Illumina HT12v4

value: M


title: GW_152 Head and neck squamous cell carcinoma Illumina HT12v4

value: Cavum Oris

value: II

value: DNA+RNA+


title: GW_148 Head and neck squamous cell carcinoma Illumina HT12v4

value: FALSE

value: Non-disruptive


title: GW_146 Head and neck squamous cell carcinoma Illumina HT12v4

value: I

value: mono


title: GW_137 Head and neck squamous cell carcinoma Illumina HT12v4

value: Hypopharynx

value: III

value: Negative


title: GW_136 Head and neck squamous cell carcinoma Illumina HT12v4

value: No

value: Primary

value: IVA

value: TRUE

value: Disruptive


title: GW_138 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: multi

value: DNA-

value: Mesenchymal 3

value: WT


title: GW_134 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: Larynx

value: II

value: FALSE


title: GW_135 Head and neck squamous cell carcinoma Illumina HT12v4

value: I

value: mono

value: Classical 2


title: GW_130 Head and neck squamous cell carcinoma Illumina HT12v4

value: No

value: IVC

value: Negative


title: GW_133 Head and neck squamous cell carcinoma Illumina HT12v4

value: Primary

value: IVB

value: TRUE


title: GW_128 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: III

value: multi

value: Basal 4


title: GW_139 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: DNA-

value: WT


title: GW_141 Head and neck squamous cell carcinoma Illumina HT12v4

value: Larynx

value: FALSE


title: GW_131 Head and neck squamous cell carcinoma Illumina HT12v4

value: Cavum Oris

value: IVA

value: Mesenchymal 3

value: Disruptive


title: GW_145 Head and neck squamous cell carcinoma Illumina HT12v4

value: mono

value: Negative


title: GW_124 Head and neck squamous cell carcinoma Illumina HT12v4

value: Primary

value: I


title: GW_175 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: Hypopharynx

value: TRUE

value: Atypical IR 1


title: GW_122 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: II

value: multi

value: Non-disruptive


title: GW_126 Head and neck squamous cell carcinoma Illumina HT12v4

value: DNA-

value: FALSE

value: WT


title: GW_116 Head and neck squamous cell carcinoma Illumina HT12v4

value: Larynx

value: IVA

value: Basal 4


title: GW_117 Head and neck squamous cell carcinoma Illumina HT12v4

value: mono

value: Negative

value: Mesenchymal 3


title: GW_120 Head and neck squamous cell carcinoma Illumina HT12v4

value: F

value: No

value: Primary


title: GW_221 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: Oropharynx

value: TRUE

value: Classical 2


title: GW_119 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: Hypopharynx

value: III

value: multi

value: Atypical IR 1


title: GW_118 Head and neck squamous cell carcinoma Illumina HT12v4

value: IVA

value: DNA-

value: FALSE

value: Disruptive


title: GW_109 Head and neck squamous cell carcinoma Illumina HT12v4

value: Cavum Oris

value: Negative

value: Mesenchymal 3

value: WT


title: GW_127 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: Primary

value: Basal 4


title: GW_125 Head and neck squamous cell carcinoma Illumina HT12v4

value: F

value: No

value: no

value: Larynx

value: DNA+RNA-

value: Classical 2


title: GW_106 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: Hypopharynx

value: IVC

value: multi

value: TRUE

value: Atypical IR 1


title: GW_129 Head and neck squamous cell carcinoma Illumina HT12v4

value: IVA

value: DNA+RNA+

value: FALSE


title: GW_110 Head and neck squamous cell carcinoma Illumina HT12v4

value: Primary

value: Oropharynx

value: WT


title: GW_108 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: II

value: mono

value: Negative

value: DNA-


title: GW_096 Head and neck squamous cell carcinoma Illumina HT12v4

value: F

value: III


title: GW_112 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: Cavum Oris

value: Basal 4

value: Non-disruptive


title: GW_111 Head and neck squamous cell carcinoma Illumina HT12v4

value: Larynx

value: IVA

value: multi

value: Classical 2


title: GW_107 Head and neck squamous cell carcinoma Illumina HT12v4

value: Primary

value: Oropharynx

value: I

value: FALSE

value: TRUE

value: Disruptive


title: GW_102 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: Hypopharynx

value: Negative

value: DNA-


title: GW_103 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: No

value: II

value: mono

value: Mesenchymal 3


title: GW_104 Head and neck squamous cell carcinoma Illumina HT12v4

value: WT


title: GW_105 Head and neck squamous cell carcinoma Illumina HT12v4

value: Larynx

value: III

value: multi

value: Basal 4

value: Non-disruptive


title: GW_101 Head and neck squamous cell carcinoma Illumina HT12v4

value: no

value: Secondary

value: TRUE

value: Classical 2


title: GW_115 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: Primary

value: IVA

value: Negative

value: FALSE

value: Atypical IR 1


title: GW_113 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: DNA-


title: GW_095 Head and neck squamous cell carcinoma Illumina HT12v4

value: F

value: No

value: Oropharynx

value: II

value: mono

value: DNA+RNA+


title: GW_097 Head and neck squamous cell carcinoma Illumina HT12v4

value: III

value: multi

value: Basal 4


title: GW_094 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: Other HPV

value: TRUE

value: WT


title: GW_091 Head and neck squamous cell carcinoma Illumina HT12v4

value: Primary

value: IVA

value: Negative

value: Mesenchymal 3

value: Disruptive


title: GW_088 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: no

value: FALSE

value: Atypical IR 1


title: PML/RARa Late Promyelocytes replicate 4

city: San Francisco

first: Scott

last: Kogan

state: CA

address: 513 Parnassus, S-561, Box 0451

department: Laboratory Medicine

institute: UCSF

description: Gene Expression after  bone marrow harvest and double sorting of populations by flow cytometry (no culture, reflects in vivo settings)

hyb_protocol: Hybridizations were performed for 14 hrs, according to the manufacturers protocol.

scan_protocol: Arrays were scanned using the Agilent microarray scanner and raw signal intensities were extracted with Feature Extraction 10.1 software, using median feature pixel intensity.

data_processing: The dataset was quantile normalized (ref: Bolstad et al, 2003) without background subtraction. Differential expression analysis using moderated t statistic with Benjamini–Hochberg false discovery rate (adjusted P value) correction was performed using the limma R/Bioconductor package.

source_name: Bone Marrow PML/RARa transgenic

label_protocol: RNA was amplified (2 rounds) and labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol. Labeled cRNA was assessed using the Nanodrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 labeled target were hybridized to Agilent whole genome mouse 4x44K arrays, which included 14 UCSF custom probes.

extract_protocol:
Bone Marrow was harvested. Following gradient centrifugation (Histopaque 1119) and ckit-enrichment, the cell suspension was stained to isolate the populations by flow cytometry. After two rounds of sorting, cells were sorted into Trizol. Following phenol/chloroform extraction, RNA was purified on PicoPure columns (Life technologies #KIT0204). Quality was assessed on the Bioanalyzer.
Sample preparation, labeling, and array hybridizations were performed according to standard protocols from the UCSF Shared Microarray Core Facilities and Agilent Technologies (http://www.arrays.ucsf.edu and http://www.agilent.com)

value: mix male:female (1:1)

value: 3 weeks 5 days

tag: strain

value: FVB/n

tag: genotype/variation

value: MRP8-PML/RARa transgenic

tag: Stage

value: late promyelocyte


title: GW_086 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: Larynx

value: mono

value: DNA-


title: PML/RARa Late Promyelocytes replicate 2


title: GW_089 Head and neck squamous cell carcinoma Illumina HT12v4

value: Primary

value: Oropharynx

value: IVA

value: multi

value: TRUE

value: Basal 4


title: GW_083 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: No

value: IVB

value: Negative

value: FALSE

value: Classical 2

value: WT


title: GW_093 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: III


title: PML/RARa Late Promyelocytes replicate 1

value: mix male:female (1:1)

value: 3 weeks 5 days

value: FVB/n

value: MRP8-PML/RARa transgenic

value: early promyelocyte


title: GW_123 Head and neck squamous cell carcinoma Illumina HT12v4

value: Primary

value: Hypopharynx

value: multi

value: DNA-

value: Disruptive


title: GW_087 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: no

value: TRUE

value: Mesenchymal 3


title: GW_082 Head and neck squamous cell carcinoma Illumina HT12v4

value: Cavum Oris

value: IVA

value: Negative

value: FALSE

value: Basal 4

value: WT


title: GW_092 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: Oropharynx

value: Atypical IR 1

value: Non-disruptive


title: GW_080 Head and neck squamous cell carcinoma Illumina HT12v4

value: Primary

value: multi


title: GW_076 Head and neck squamous cell carcinoma Illumina HT12v4

value: II

value: mono

value: DNA-


title: GW_079 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: TRUE


title: PML/RARa Early Promyelocytes replicate 2

value: mix male:female (1:1)

value: 3 weeks 5 days

value: FVB/n

value: MRP8-PML/RARa transgenic

value: early promyelocyte


title: GW_078 Head and neck squamous cell carcinoma Illumina HT12v4

value: F

value: no

value: Cavum Oris

value: IVA

value: Negative


title: GW_081 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: Primary

value: Oropharynx

value: Atypical IR 1

value: Non-disruptive


title: PML/RARa GMP replicate 3

value: GMP


title: PML/RARa Early Promyelocytes replicate 1


title: GW_084 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: multi

value: DNA-

value: TRUE

value: Mesenchymal 3

value: WT


title: GW_085 Head and neck squamous cell carcinoma Illumina HT12v4

value: FALSE

value: Basal 4


title: GW_074 Head and neck squamous cell carcinoma Illumina HT12v4

value: No

value: no

value: Cavum Oris

value: palliative


title: PML/RARa Early Promyelocytes replicate 3

value: mix male:female (1:1)

value: 3 weeks 5 days

value: FVB/n

value: MRP8-PML/RARa transgenic

value: early promyelocyte


title: PML/RARa Late Promyelocytes replicate 3

value: late promyelocyte


title: GW_075 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: Yes

value: Primary

value: Oropharynx

value: IVA

value: multi

value: Negative

value: Disruptive


title: PML/RARa GMP replicate 4

value: GMP


title: GW_073 Head and neck squamous cell carcinoma Illumina HT12v4

value: DNA-

value: FALSE

value: Mesenchymal 3

value: WT


title: GW_071 Head and neck squamous cell carcinoma Illumina HT12v4

value: F

value: Atypical IR 1


title: GW_068 Head and neck squamous cell carcinoma Illumina HT12v4

value: TRUE

value: Basal 4


title: Wt Early Promyelocytes replicate 4

source_name: Bone Marrow Wild Type

value: mix male:female (1:1)

value: 3 weeks 5 days

value: FVB/n

value: wild type

value: early promyelocyte


title: GW_056 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: Yes

value: Primary

value: Cavum Oris

value: II

value: multi


title: GW_062 Head and neck squamous cell carcinoma Illumina HT12v4

value: Oropharynx

value: III

value: Negative

value: DNA-

value: FALSE

value: Non-disruptive


title: GW_067 Head and neck squamous cell carcinoma Illumina HT12v4

value: Basal 4


title: GW_066 Head and neck squamous cell carcinoma Illumina HT12v4

value: I

value: mono

value: TRUE

value: Classical 2


title: GW_061 Head and neck squamous cell carcinoma Illumina HT12v4

value: F

value: No

value: no

value: IVA

value: WT


title: GW_057 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: Yes

value: Primary

value: multi

value: Mesenchymal 3


title: GW_065 Head and neck squamous cell carcinoma Illumina HT12v4

value: Oropharynx

value: Negative

value: DNA-


title: Wt Late Promyelocytes replicate 1

value: mix male:female (1:1)

value: 3 weeks 5 days

value: FVB/n

value: wild type

value: late promyelocyte


title: Wt GMP replicate 4

value: GMP


title: GW_064 Head and neck squamous cell carcinoma Illumina HT12v4

value: No

value: Cavum Oris

value: mono

value: TRUE


title: GW_054 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: Yes

value: IVA

value: WT


title: GW_053 Head and neck squamous cell carcinoma Illumina HT12v4

value: Primary

value: Oropharynx

value: III

value: multi

value: Basal 4


title: GW_063 Head and neck squamous cell carcinoma Illumina HT12v4

value: Negative

value: DNA-

value: FALSE

value: Mesenchymal 3

value: Non-disruptive


title: GW_058 Head and neck squamous cell carcinoma Illumina HT12v4

value: Classical 2

value: Disruptive


title: PML/RARa GMP replicate 1

value: mix male:female (1:1)

value: 3 weeks 5 days

value: FVB/n

value: MRP8-PML/RARa transgenic

value: GMP


title: Wt Early Promyelocytes replicate 1

value: wild type

value: early promyelocyte


title: GW_059 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: Yes

value: Primary

value: Oropharynx

value: IVA

value: mono

value: TRUE


title: Wt Early Promyelocytes replicate 3


title: GW_077 Head and neck squamous cell carcinoma Illumina HT12v4

value: Cavum Oris

value: I

value: Negative

value: DNA-

value: FALSE

value: Basal 4

value: WT


title: Wt Late Promyelocytes replicate 4

value: mix male:female (1:1)

value: 3 weeks 5 days

value: FVB/n

value: late promyelocyte


title: GW_070 Head and neck squamous cell carcinoma Illumina HT12v4

value: F

value: No

value: no

value: multi


title: PML/RARa GMP replicate 2

value: MRP8-PML/RARa transgenic

value: GMP


title: Wt GMP replicate 3

value: wild type


title: GW_060 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: Primary

value: Cavum Oris

value: II

value: mono

value: TRUE

value: Atypical IR 1


title: GW_072 Head and neck squamous cell carcinoma Illumina HT12v4

value: IVA

value: Negative

value: DNA-

value: FALSE

value: Mesenchymal 3

value: WT


title: GW_051 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: Oropharynx


title: GW_045 Head and neck squamous cell carcinoma Illumina HT12v4

value: F

value: multi

value: Other HPV


title: GW_041 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: no

value: Primary

value: IVB

value: DNA+RNA+


title: GW_043 Head and neck squamous cell carcinoma Illumina HT12v4

value: Cavum Oris

value: TRUE

value: Basal 4


title: Wt Late Promyelocytes replicate 2

value: mix male:female (1:1)

value: 3 weeks 5 days

value: FVB/n

value: wild type

value: late promyelocyte


title: GW_040 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: Oropharynx

value: IVA

value: FALSE

value: Atypical IR 1


title: GW_049 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: Larynx

value: multi

value: Negative

value: DNA-

value: WT


title: GW_052 Head and neck squamous cell carcinoma Illumina HT12v4

value: Secondary

value: Hypopharynx

value: III

value: TRUE

value: Mesenchymal 3


title: GW_038 Head and neck squamous cell carcinoma Illumina HT12v4

value: Primary

value: Cavum Oris

value: II

value: DNA+RNA-

value: Classical 2

value: Disruptive


title: GW_039 Head and neck squamous cell carcinoma Illumina HT12v4

value: F

value: No

value: Oropharynx

value: IVA

value: mono

value: FALSE

value: Atypical IR 1


title: GW_033 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: Yes

value: multi

value: DNA+RNA+

value: WT


title: GW_032 Head and neck squamous cell carcinoma Illumina HT12v4

value: Primary

value: TRUE

value: Basal 4


title: GW_026 Head and neck squamous cell carcinoma Illumina HT12v4

value: III


title: GW_042 Head and neck squamous cell carcinoma Illumina HT12v4

value: IVB

value: DNA+RNA-

value: Mesenchymal 3

value: Non-disruptive


title: GW_030 Head and neck squamous cell carcinoma Illumina HT12v4

value: Oropharynx


title: GW_029 Head and neck squamous cell carcinoma Illumina HT12v4

value: No

value: Cavum Oris

value: IVA


title: GW_035 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: no

value: Atypical IR 1


title: GW_031 Head and neck squamous cell carcinoma Illumina HT12v4

value: F

value: Yes

value: multi

value: DNA+RNA+

value: FALSE


title: GW_028 Head and neck squamous cell carcinoma Illumina HT12v4

value: Primary

value: WT


title: GW_034 Head and neck squamous cell carcinoma Illumina HT12v4

value: DNA+RNA-

value: TRUE


title: GW_023 Head and neck squamous cell carcinoma Illumina HT12v4


title: Wt GMP replicate 2

value: mix male:female (1:1)

value: 3 weeks 5 days

value: FVB/n

value: wild type

value: GMP


title: GW_046 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: Oropharynx

value: IVA

value: Negative

value: DNA-


title: GW_044 Head and neck squamous cell carcinoma Illumina HT12v4

value: No

value: mono

value: Other HPV

value: Basal 4


title: GW_047 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: no

value: Primary

value: multi

value: FALSE

value: Atypical IR 1

value: Disruptive


title: GW_027 Head and neck squamous cell carcinoma Illumina HT12v4

value: Cavum Oris

value: DNA+RNA+

value: TRUE

value: WT


title: GW_036 Head and neck squamous cell carcinoma Illumina HT12v4

value: F

value: Oropharynx

value: IVB


title: GW_025 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: DNA+RNA-

value: Classical 2


title: GW_022 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: IVA

value: mono

value: Other HPV

value: Basal 4


title: GW_021 Head and neck squamous cell carcinoma Illumina HT12v4

value: Primary

value: II

value: multi

value: FALSE

value: Atypical IR 1


title: GW_020 Head and neck squamous cell carcinoma Illumina HT12v4

value: IVC

value: TRUE

value: WT


title: MT_PD/WT_PD rep 2 colourflip

hyb_protocol: A mixture of purified and labeled cRNA (Cy3 label: 5 pmol; Cy5 label: 3.5 pmol) was hybridized on Agilent Yeastv2 arrays followed by washing, according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, arrays were scanned using the Agilent DNA MicroArray Scanner and probe signals were quantified using Agilent’s Feature Extractor software (version 10.5.1.1).

data_processing: Analysis of the microarray data was performed using the R package LIMMA (http://www.bioconductor.org) (Gentleman et al., 2004). Fold changes were computed using raw Cy3 and Cy5 intensities values provided by Agilent’s Feature Extractor software (version 10.5.1.1) and loess normalization and background correction were performed to determine the log2-ratios per array. Differential expression was assessed via the moderated t-statistic, described in (Smyth, 2004). To control the false discovery rate, multiple testing correction was performed.

organism: Saccharomyces cerevisiae

source_name: BY4741_mut dfna5_post diauxic shift

label_protocol: Before labeling, RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies). RNA integrity was assessed using a Bioanalyzer 2100 (Agilent). Per sample, an amount of 1 μg of total RNA spiked with 10 viral polyA transcript controls (Agilent, Santa Clara, CA, USA) was converted to double ￼stranded cDNA in a reverse transcription reaction. Subsequently,the samples were converted to antisense cRNA, amplified andlabeled with Cyanine 3-CTP (Cy3) or Cyanine 5-CTP (Cy5) in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent, Santa Clara, CA, USA).

growth_protocol: Yeast strains were grown at 30◦C in selective medium containing 2% glucose (SD-URA). Fifty milliliter yeast cultures, transformed with either wtDFNA5 or mutDFNA5, were harvested in mid-exponential phase (OD600nm = 3.5 − 4.2) and at the post-diauxic shift (OD600nm = 7.4 − 8.4).

extract_protocol: RNA was collected from yeast at mid-exponential phase and just after the post-diauxic shift using RNA pure kit following the manufactures instructions (GenHunter Corporation, Nashville, TN, USA). All steps were performed in duplo at 4◦C to avoid RNA degradation.

treatment_protocol: Fifty milliliter yeast cultures were transformed with either wtDFNA5 or mutDFNA5. Standard transformation techniques were applied for these transformations.

tag: transformed with

value: mut dfna5

tag: growth phase

value: post diauxic shift

source_name: BY4741_wt dfna5_post diauxic shift

value: wt dfna5


title: WT_EXP/MT_EXP rep 2 colourflip

source_name: BY4741_wt dfna5_exponential phase

value: exponential phase

source_name: BY4741_mut dfna5_exponential phase


title: WT_PD/MT_PD rep1


title: MT_EXP/WT_EXP rep1


title: MT_PD/MUT_EXP rep1


title: MUT_EXP/MT_STAT rep 2 colourflip


title: WT_PD/WT_EXP rep2 colourflip


title: GW_016 Head and neck squamous cell carcinoma Illumina HT12v4

value: F

value: Yes

value: Cavum Oris

value: III

value: Negative

value: DNA-

value: Mesenchymal 3


title: GW_015 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: No

value: Primary

value: IVA

value: multi

value: DNA+RNA-


title: Activated Neutrophils (MRL/MpJ), biological replicate 2

city: Lübeck

first: Saleh

middle: M.

last: Ibrahim

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Dermatology

institute: Universität zu Lübeck

description: Neutrophils activated using immune complex

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner 3000.

data_processing: The data was processed using oligo R package. The data was normalized using RMA method.

source_name: Neutrophils

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Neutrophils were derived from bone marrow of MRL/MpJ and C57Bl/6J mice.

extract_protocol: Total RNA was isolated from neutrophils using TRIzol (Invitrogen, Germany). Total RNA was digested with DNase, and cDNA synthesis from 500 ng of RNA was carried out using a SuperScript first-strand synthesis system for RT-PCR (Invitrogen).

treatment_protocol: The derived neutrophils were stimulated from immune complexes (IC) and Phorbol myristate acetate (PMA).

value: MRL/MpJ

tag: sample type


title: Activated Neutrophils (MRL/MpJ), biological replicate 1

value: Neutrophils activated using immune complex


title: GW_037 Head and neck squamous cell carcinoma Illumina HT12v4

tag: ID

value: Oropharynx

value: TRUE

value: Basal 4

value: WT


title: GW_013 Head and neck squamous cell carcinoma Illumina HT12v4

tag: gender

value: Yes

value: Cavum Oris

value: II

value: FALSE


title: GW_017 Head and neck squamous cell carcinoma Illumina HT12v4

value: F

tag: smoking

value: Negative

value: DNA-

value: Classical 2


title: Un-activated Neutrophils (MRL/MpJ), biological replicate 2

description: Neutrophils unactivated

value: Neutrophils unactivated


title: Un-activated Neutrophils (C57Bl/6J), biological replicate 3

description: Neutrophils unactivated


title: Un-activated Neutrophils (C57Bl/6J), biological replicate 2

description: Neutrophils unactivated


title: GW_014 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

tag: packyears

value: Primary

value: IVA

value: multi

value: Mesenchymal 3


title: GW_011 Head and neck squamous cell carcinoma Illumina HT12v4

tag: alcohol

value: Non-disruptive


title: Un-activated Neutrophils (MRL/MpJ), biological replicate 3

description: Neutrophils unactivated

value: MRL/MpJ


title: WT_EXP/WT_PD rep1

value: wt dfna5

value: exponential phase

value: post diauxic shift