title: wild type, rep2

status: Public on Jan 31 2013

type: RNA

city: Cleveland

first: Zhuoming

last: Liu

state: OH

address: 2103 Cornell Road

country: USA

institute: Case Western Reserve University

description: miRNA expression from bone marrow neutrophils of female mice at the age of 10 weeks

hyb_protocol: Affymetrix standard procedure

scan_protocol: Affymetrix standard procedure

data_processing:
RMA-DABG signal intensity calculation expressed in log2 scale.  We sorted out Mus musculus transcripts out of the 131 organisms covered by the miRNA 2.0 array.
program-name = Expression Console
program-version = 1.2.0.20

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: wild type bone marrow neutrophils

label_protocol: One microgram of total RNA was labeled using the Flash Tag Biotin HSR kit (Genisphere)

extract_protocol: Total RNAs containing miRNAs were isolated using mirVana PARIS kit (Life Technology)

treatment_protocol: Bone marrow from tibia and femur were flushed with cold HBSS buffer without calcium and magnesium. The red blood cells were lysed by ACK lysis buffer at room temperature for 5 minutes. The remaining cells were separated by discontinuous density gradient centrifugation in Percoll. The cells enriched at the interface between 81% and 62% Percoll were recovered for miRNA precipitation.

tag: strain

tag: tissue

value: bone marrow neutrophil

tag: gender

value: female

tag: age

value: 10 weeks


title: lcn2 knockout, rep2

source_name: lcn2 knockout bone marrow neutrophils


title: wild type, rep1


title: lcn2 knockout, rep1


title: iPS-NHDF-6 [SNP]

type: genomic

city: Oxford

first: Sally

middle: A

last: Cowley

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

description: SAMPLE 4

hyb_protocol: Standard Illumina hybridisation protocol

scan_protocol: Standard Illumina scanning protocol for BeadChip Arrays

data_processing: The scanned data files were processed by GenomeStudio Genotyping module (v1.9), using the cluster file HumanCytoSNP-12v2-1_H.egt provided by Illumina. Raw data was also uploaded to KaryoStudio (Illumina) for generation of karyotype reports (see publication).

label: biotin (C+G) and dinitrophenyl (A+T)

molecule: genomic DNA

organism: Homo sapiens

source_name: adult normal human dermal fibroblast-derived induced pluripotent stem cell line

label_protocol: Standard Illumina labelling protocol

extract_protocol: genomic DNA was extracted using QIAGEN DNeasy blood and tissue kit

treatment_protocol: untreated cell samples; Fibroblasts grown in ADMEM + 10% FCS; iPSc lines all grown in mTeSR-1 medium + ES-qualified matrigel prior to harvest

tag: culture medium

value: mTeSR-1 + matrigel


title: AU1286202/NA18507

city: Seattle

first: Megan

middle: Y

last: Dennis

state: WA

address: 3720 15th Ave NE

department: Department of Genome Sciences

institute: University of Washington

hyb_protocol: The hybridization protocol was performed per Agilent protocols (http://www.chem.agilent.com/Library/usermanuals/Public/G4410-90020_CGH_ULS_Protocol_v.3.1.pdf) with 10 ug of labelled test sample and 10 ug of labelled reference sample

scan_protocol: The scan protocol was performed using the Agilent Scanner per Agilent protocols (http://www.chem.agilent.com/Library/usermanuals/Public/G4410-90020_CGH_ULS_Protocol_v.3.1.pdf).

data_processing: The data were processed using the Agilent Feature Extraction software 10.5.1.1 using program defaults (http://www.chem.agilent.com/Library/usermanuals/Public/G4410-90020_CGH_ULS_Protocol_v.3.1.pdf)

source_name: whole blood DNA

label_protocol: 250 ng of genomic DNA (unsonicated) was labeled by Klenow using random priming with Cy3/Cy5 nonamers (for test and reference samples, respectively) using Nimblegen labelling kit but with the following changes: reagents were scaled to the smaller amount of input DNA and with DNA labeling occurring overnight.

extract_protocol: unsonicated genomic DNA

value: whole blood

tag: family status

value: mother

tag: ndar guid

tag: cohort

value: AGRE autism

source_name: lymphoblast cell line DNA

tag: cell line


title: iPS-NHDF-2 [SNP]

description: SAMPLE 3


title: NHDF [SNP]

description: SAMPLE 1

source_name: adult normal human dermal fibroblasts

value: ADMEM + 10% FCS


title: AU1228201/NA12878

value: male

value: father


title: AU2157201/NA12878


title: AU1286201/NA12878


title: AU070701/NA18507


title: iPS-NHDF-1 [SNP]

description: SAMPLE 2


title: AU0039202/NA18507


title: AU061801/NA18507


title: AU1802201/NA12878


title: AU084501/NA18507


title: AU1006202/NA18507


title: AU061802/NA12878


title: AU0976202/NA18507


title: AU1228202/NA18507


title: AU1763202/NA18507


title: AU022702/NA12878


title: AU1802202/NA18507


title: AU020701/NA18507


title: AU0039201/NA12878


title: AU1959202/NA18507


title: AU1006201/NA12878


title: AU2554201/NA12878


title: AU020702/NA12878


title: AU2157202/NA18507


title: AU0976201/NA12878


title: AU2554202/NA18507


title: AU084502/NA12878


title: AU1959201/NA12878


title: AU1848202/NA18507


title: AU1848201/NA12878


title: AU1678202/NA18507


title: AU1997201/NA12878


title: AU3068202/NA18507


title: AU026202/NA12878


title: AU1300201/NA12878


title: AU0962202/NA18507


title: AU1512202/NA18507


title: AU1631201/NA12878


title: AU025702/NA12878


title: AU1678201/NA12878


title: AU1997202/NA18507


title: AU1575202/NA18507


title: AU1512201/NA12878


title: AU1631202/NA18507


title: AU1300202/NA18507


title: AU2050202/NA18507


title: AU1400202/NA18507


title: AU2050201/NA12878


title: AU3068201/NA12878


title: AU026201/NA18507


title: AU0962201/NA12878


title: AU1400201/NA12878


title: AU025701/NA18507


title: AU081201/NA18507


title: AU083502/NA12878


title: AU081202/NA12878


title: AU083501/NA18507


title: AU1686202/NA18507


title: AU1575201/NA12878


title: AU1686201/NA12878


title: AU1107201/NA12878


title: AU029302/NA12878


title: AU055002/NA12878


title: CS_0553/NA18507

value: unknown

value: ClinSeq control


title: CS_0516/NA18507


title: CS_0577/NA18507


title: AU055001/NA18507


title: CS_0505/NA18507


title: CS_0564/NA18507


title: CS_0540/NA18507


title: CS_0493/NA18507


title: CS_0528/NA18507


title: CS_0552/NA18507


title: CS_0563/NA18507


title: AU029301/NA18507


title: CS_0576/NA18507


title: CS_0504/NA18507


title: CS_0541/NA18507


title: AU1699202/NA18507


title: CS_0527/NA18507


title: CS_0492/NA18507


title: CS_0515/NA18507


title: CS_0503/NA18507


title: CS_0539/NA18507


title: CS_0575/NA18507


title: CS_0551/NA18507


title: CS_0565/NA18507


title: CS_0574/NA18507


title: CS_0526/NA18507


title: CS_0550/NA18507


title: CS_0491/NA18507


title: CS_0562/NA18507


title: CS_0514/NA18507


title: CS_0538/NA18507


title: CS_0513/NA18507


title: CS_0537/NA18507


title: CS_0489/NA18507


title: CS_0502/NA18507


title: CS_0549/NA18507


title: CS_0525/NA18507


title: CS_0572/NA18507


title: CS_0559/NA18507


title: CS_0512/NA18507


title: CS_0536/NA18507


title: CS_0490/NA18507


title: CS_0524/NA18507


title: CS_0500/NA18507


title: CS_0511/NA18507


title: CS_0571/NA18507


title: CS_0523/NA18507


title: CS_0548/NA18507


title: CS_0546/NA18507


title: CS_0560/NA18507


title: CS_0488/NA18507


title: CS_0510/NA18507


title: CS_0547/NA18507


title: CS_0545/NA18507


title: CS_0558/NA18507


title: CS_0534/NA18507


title: CS_0521/NA18507


title: CS_0569/NA18507


title: CS_0486/NA18507


title: CS_0509/NA18507


title: CS_0533/NA18507


title: CS_0535/NA18507


title: CS_0485/NA18507


title: CS_0570/NA18507


title: CS_0568/NA18507


title: CS_0487/NA18507


title: CS_0544/NA18507


title: CS_0484/NA18507


title: CS_0522/NA18507


title: CS_0556/NA18507


title: CS_0497/NA18507


title: CS_0555/NA18507


title: CS_0508/NA18507


title: CS_0499/NA18507


title: CS_0532/NA18507


title: CS_0520/NA18507


title: CS_0554/NA18507


title: CS_0543/NA18507


title: CS_0567/NA18507


title: CS_0496/NA18507


title: CS_0566/NA18507


title: CS_0507/NA18507


title: CS_0483/NA18507


title: CS_0519/NA18507


title: CS_0530/NA18507


title: CS_0557/NA18507


title: CS_0542/NA18507


title: CS_0494/NA18507


title: CS_0495/NA18507


title: CS_0518/NA18507


title: CS_0481/NA18507


title: CS_0409/NA18507


title: CS_0469/NA18507


title: CS_0457/NA18507


title: CS_0445/NA18507


title: CS_0506/NA18507


title: CS_0531/NA18507


title: CS_0397/NA18507


title: CS_0480/NA18507


title: CS_0421/NA18507


title: CS_0482/NA18507


title: CS_0456/NA18507


title: CS_0433/NA18507


title: CS_0468/NA18507


title: CS_0396/NA18507


title: CS_0408/NA18507


title: CS_0467/NA18507


title: CS_0479/NA18507


title: CS_0443/NA18507


title: CS_0432/NA18507


title: CS_0431/NA18507


title: CS_0455/NA18507


title: CS_0444/NA18507


title: CS_0419/NA18507


title: CS_0478/NA18507


title: CS_0407/NA18507


title: CS_0395/NA18507


title: CS_0466/NA18507


title: CS_0406/NA18507


title: CS_0465/NA18507


title: CS_0429/NA18507


title: CS_0441/NA18507


title: CS_0430/NA18507


title: CS_0464/NA18507


title: CS_0453/NA18507


title: CS_0476/NA18507


title: CS_0405/NA18507


title: CS_0418/NA18507


title: CS_0454/NA18507


title: CS_0420/NA18507


title: CS_0417/NA18507


title: CS_0442/NA18507


title: CS_0475/NA18507


title: CS_0451/NA18507


title: CS_0416/NA18507


title: CS_0394/NA18507


title: CS_0452/NA18507


title: CS_0392/NA18507


title: CS_0439/NA18507


title: CS_0440/NA18507


title: CS_0427/NA18507


title: CS_0393/NA18507


title: CS_0404/NA18507


title: CS_0463/NA18507


title: CS_0415/NA18507


title: CS_0391/NA18507


title: CS_0477/NA18507


title: CS_0428/NA18507


title: CS_0403/NA18507


title: CS_0474/NA18507


title: CS_0402/NA18507


title: CS_0414/NA18507


title: CS_0389/NA18507


title: CS_0425/NA18507


title: CS_0401/NA18507


title: CS_0473/NA18507


title: CS_0472/NA18507


title: CS_0438/NA18507


title: CS_0424/NA18507


title: CS_0462/NA18507


title: CS_0412/NA18507


title: CS_0436/NA18507


title: CS_0448/NA18507


title: CS_0437/NA18507


title: CS_0435/NA18507


title: CS_0423/NA18507


title: CS_0459/NA18507


title: CS_0399/NA18507


title: CS_0390/NA18507


title: CS_0471/NA18507


title: CS_0460/NA18507


title: CS_0400/NA18507


title: CS_0388/NA18507


title: CS_0470/NA18507


title: CS_0387/NA18507


title: CS_0411/NA18507


title: CS_0434/NA18507


title: CS_0450/NA18507


title: CS_0426/NA18507


title: CS_0461/NA18507


title: CS_0446/NA18507


title: CS_0422/NA18507


title: CS_0410/NA18507


title: CS_0361/NA18507


title: CS_0373/NA18507


title: CS_0447/NA18507


title: CS_0349/NA18507


title: CS_0337/NA18507


title: Normal lung_31645

city: Koto-ku

first: Yuichi

last: Ishikawa

state: Tokyo

address: 3-8-31 Ariake

country: Japan

institute: Cancer Insitute

hyb_protocol: 100 ng of Cy3-labelled RNA was fragmented at 100°C for 5 minutes in a reaction volume of 45 ul containing 2x Agilent Hi-RPM Hybridization Buffer and 10x Agilent Gene Expression Blocking Agent following the manufacturers instructions. The mixture was hybridized to Agilent Human miRNA Microarray (G4471A) for 20 hours at 55°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 5 minutes at room temperature with Gene Expression Wash Buffer 1 (Agilent) and 5 minutes with 37°C Gene Expression Wash buffer 2 (Agilent). A microarray dried while withdrawing from GE wash buffer 2 taking for 5 to 10 seconds.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565BA) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green. High Green PMT and Low Green PMT are set to 100% and 5%, respectively).

data_processing: The scanned images were quantified with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters (protocol miRNA-v1_95_May07 and Grid: 021827_D_20081121) to obtain background subtracted and gTotalGeneSignal. Next, the data was processed with GeneSpring GX10 software (Agilent).  Raw data of intensities <1.0 were transformed to 1.0. Then, all raw data were log2 transformed. Then, signal intensties of each sample were normalized to its 75%tile intensity by using GeneSpring normalization option. Finally, features whose raw intensities <5.0 in all samples were excluded.

source_name: frozen block

label_protocol: 100 ng of RNA was labeled by Cyanine-3 (Cy3) using the miRNA Labelling and Hybridization kit (Agilent) according to the manufacturer's instructions.

extract_protocol: RNA was prepared using the mirVana miRNA Isolation kit (Applied Biosystems, Foster City, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: sample type

value: frozen block

value: Male

value: Normal lung

tag: prognosis


title: CS_0325/NA18507


title: CS_0324/NA18507


title: Normal lung_31167


title: CS_0313/NA18507


title: CS_0372/NA18507


title: CS_0385/NA18507


title: CS_0384/NA18507


title: Normal lung_31757


title: CS_0386/NA18507


title: CS_0348/NA18507


title: Normal lung_9962


title: CS_0301/NA18507


title: Normal lung_9481

value: Female


title: CS_0336/NA18507


title: CS_0312/NA18507


title: CS_0449/NA18507


title: CS_0371/NA18507


title: CS_0458/NA18507


title: Normal lung_5200


title: CS_0335/NA18507


title: CS_0347/NA18507


title: CS_0360/NA18507


title: Normal lung_31715


title: Adenocarcinoma_2361

value: Adenocarcinoma


title: Adenocarcinoma_2071


title: Adenocarcinoma_2326


title: Normal lung_5009


title: Squamous cell carcinoma_1509

value: Squamous cell carcinoma


title: Squamous cell carcinoma_1601


title: Squamous cell carcinoma_1196


title: CS_0311/NA18507


title: Squamous cell carcinoma_1438


title: Adenocarcinoma_2435


title: CS_0300/NA18507


title: Large cell neuroendocrine cancer_5883

value: Large cell neuroendocrine cancer

value: Dead by aother cause


title: Squamous cell carcinoma_779


title: Large cell neuroendocrine cancer_11157

value: Alive


title: Large cell neuroendocrine cancer_11152


title: CS_0299/NA18507

value: whole blood


title: Large cell neuroendocrine cancer_6042


title: CS_0398/NA18507


title: Large cell neuroendocrine cancer_22327


title: CS_0370/NA18507


title: CS_0323/NA18507


title: CS_0334/NA18507


title: Large cell neuroendocrine cancer_18944


title: CS_0322/NA18507


title: CS_0382/NA18507


title: Large cell neuroendocrine cancer_26692

value: Dead by cancer


title: Large cell neuroendocrine cancer_19359


title: CS_0383/NA18507


title: Small-cell lung cancer_23213

value: Small-cell lung cancer


title: CS_0346/NA18507


title: CS_0345/NA18507


title: Small-cell lung cancer_23037


title: CS_0359/NA18507


title: CS_0369/NA18507


title: CS_0310/NA18507


title: Small-cell lung cancer_19596


title: Large cell neuroendocrine cancer_23294


title: Small-cell lung cancer_28888


title: Small-cell lung cancer_27562


title: CS_0357/NA18507


title: CS_0297/NA18507


title: Large cell neuroendocrine cancer_25563


title: CS_0380/NA18507


title: CS_0309/NA18507


title: CS_0368/NA18507


title: CS_0333/NA18507


title: Small-cell lung cancer_27204


title: Small-cell lung cancer_26689


title: CS_0356/NA18507


title: CS_0321/NA18507


title: Small-cell lung cancer_25232


title: CS_0296/NA18507


title: CS_0358/NA18507


title: CS_0298/NA18507


title: Small-cell lung cancer_17989


title: Small-cell lung cancer_22002


title: CS_0332/NA18507


title: Small-cell lung cancer_24810


title: Large cell neuroendocrine cancer_23643


title: CS_0320/NA18507


title: Small-cell lung cancer_12822


title: CS_0308/NA18507


title: CS_0381/NA18507


title: CS_0379/NA18507


title: Small-cell lung cancer_11044


title: Small-cell lung cancer_8526


title: CS_0344/NA18507


title: CS_0355/NA18507


title: Small-cell lung cancer_12004


title: Small-cell lung cancer_8289


title: Small-cell lung cancer_6221


title: CS_0367/NA18507


title: Small-cell lung cancer_6086


title: Small-cell lung cancer_6013


title: Small-cell lung cancer_5395


title: Small-cell lung cancer_4567


title: CS_0343/NA18507


title: Small-cell lung cancer_4271


title: Small-cell lung cancer_3170


title: CS_0307/NA18507


title: CS_0331/NA18507


title: Small-cell lung cancer_2942


title: CS_0295/NA18507


title: Small-cell lung cancer_3424


title: CS_0354/NA18507


title: Small-cell lung cancer_2760


title: Small-cell lung cancer_7853


title: CS_0378/NA18507


title: CS_0306/NA18507


title: Small-cell lung cancer_2230


title: Small-cell lung cancer_2212


title: Small-cell lung cancer_3105


title: Small-cell lung cancer_545


title: CS_0330/NA18507


title: Small-cell lung cancer_431


title: CS_0318/NA18507


title: CS_0342/NA18507


title: CS_0377/NA18507


title: Small-cell lung cancer_409


title: CS_0341/NA18507


title: CS_0365/NA18507


title: CS_0329/NA18507


title: Small-cell lung cancer_140


title: CS_0294/NA18507


title: Small-cell lung cancer_2425


title: CS_0319/NA18507


title: CS_0305/NA18507


title: CS_0353/NA18507


title: CS_0364/NA18507


title: CS_0293/NA18507


title: CS_0317/NA18507


title: WT (glucose) vs. xprGdelta (glucose) Rep 3

city: Armidale

first: Margaret

middle: E.

last: Katz

state: NSW

address: McClymont Building

department: Molecular and Cellular Biology

country: Australia

institute: University of New England

hyb_protocol: TIGR protocol (Hasseman et a. 2006, ftp.jcvi.org/pub/data/PFGRC/MAIN/pdf_files/protocols/M008.pdf) was used for hybridisation.

scan_protocol: The hybridized slides were scanned immediately at 10 µm resolution in Axon 4200AL scanner (Molecular Devices, Union City, CA). The intensity values for the two channels for each spot were acquired by automatic photomultiplier tube gains to obtain the highest intensity with 0.05% saturated pixels. The resulting images were analysed by measuring the fluorescence of all features on the slides using the GenePix Pro 6.1 software (Molecular Devices, Union City, CA). The median fluorescence intensity of these pixels within each feature was taken as the intensity value for the feature.

data_processing: Quality control measures, pre-processing and analyses were performed using the statistical computing language R (R Development Core Team 2011) and Bioconductor (Gentleman et al. 2004). All microarray images and quality control measurements were within recommended limits (Gondro and van der Werf 2008). The quality of the arrays was assessed through standard quality control measures: pseudo-images of the arrays (to detect spatial effects), MA (M is the intensity ratio and A is the average intensity) scatter plots of the arrays versus a pseudo-median reference chip, and other summary statistics including histogram and boxplots of raw log intensities, signal-to-noise ratios on both channels, boxplots of plates and print tips, boxplots of normalized log ratios, among others. Transcription intensities in adjusted log2 were estimated after within array normalization using maximum likelihood (Irizarry et al. 2003) followed by between array variance stabilization (Huber et al. 2002). Briefly, the data was adjusted by an affine transformation and then all slides were log2 transformed to stabilize the variance. Prior to testing for differential expression, the data were filtered to remove control (n=1,000 from A. thaliana) and empty spots (n=1,430) and spots flagged as bad in over 90% of the slides (n=4,754), thus leaving 9,104 unique features to be tested.

label: Alexa Fluor 555

organism: Aspergillus nidulans

source_name: xprG+ (glucose)

label_protocol: cDNAs labelled with Alexa Fluor 555 and Alexa Fluor 647 were prepared from mRNA using the SuperScript Plus Indirect cDNA Labeling System (Invitrogen).

growth_protocol: Mycelia were harvested after growing in Aspergillus nidulans minimal medium containing 1% glucose for 24 hours.

extract_protocol: Total RNA was prepared using a procedure developed by Reinert et al. (1981).  PolyATtract® mRNA Isolation System IV  (Promega Corp, ) used to prepare mRNA.  mRNA treated with Turbo DNA-free Kit (Ambion).

treatment_protocol: Mycelia were washed and transferred to Aspergillus nidulans minimal medium containing 1% glucose or carbon-free medium for 16 hours.

value: MH2 (biA1; niiA4)

tag: growth medium

value: 1% glucose

label: Alexa Fluor 647

source_name: xprGdelta (glucose)

value: MK422 (biA1; xprG::argB)


title: WT (carbon-free) vs. xprGdelta (carbon-free) Rep 3

source_name: xprGdelta (carbon-free)

value: carbon-free

source_name: xprG+ (carbon-free)


title: WT (glucose) vs. WT (carbon-free) Rep 3


title: CS_0376/NA18507

value: unknown

value: ClinSeq control


title: xprGdelta (glucose) vs. xprGdelta (carbon-free) Rep 3


title: WT (glucose) vs. xprGdelta (glucose) Rep 1


title: WT (glucose) vs. xprGdelta (glucose) Rep 2


title: CS_0340/NA18507


title: xprGdelta (glucose) vs. xprGdelta (carbon-free) Rep 2


title: CS_0328/NA18507


title: WT (carbon-free) vs. xprGdelta (carbon-free) Rep 2


title: WT (carbon-free) vs. xprGdelta (carbon-free) Rep 1


title: xprGdelta (glucose) vs. xprGdelta (carbon-free) Rep 1


title: CS_0316/NA18507


title: CS_0375/NA18507


title: WT (glucose) vs. WT (carbon-free) Rep 1


title: CS_0363/NA18507


title: CS_0292/NA18507


title: WTvsWTmitomycinC CDML replicate 3

city: Louvain-La-Neuve

first: Pascal

last: Hols

address: Place Croix du Sud 5

department: Institut des Sciences de la Vie

country: Belgium

institute: Université catholique de louvain

description: Biological replicate 1 of  2, dye swap

hyb_protocol: Hybridization of the labeled cDNA (0.3 microg per sample) were added to hybridization buffer (Agilent In Situ Hybridization Kit Plus)  and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially according to Agilent instructions.

scan_protocol: Scanned on an Agilent Scanner G2565B Images were quantified using Agilent Feature Extraction Software (version 9.1).

data_processing: Agilent Feature Extraction Software (v 9.1) was used for background subtraction and LOWESS normalization.

organism: Streptococcus thermophilus

source_name: LMD-9WTmitomycinC CDML OD 0.4

label_protocol:
First strand cDNA was synthetized from 10 microg RNA. Synthesized cDNA were purified and labeled with Alexa Fluor 555 and Alexa Fluor 647. Experiments were carried out according to instructions of the Superscript Plus Indirect cDNA Labeling system (Invitrogen).
The quality of the labeled cDNA and its concentration were respectively measured with the 2100 Bioanalyser (Agilent Technologies, Santa Clara, CA) and ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE).

growth_protocol: Strains LMD-9 WT without or with mitomycin C 0.08 microg/ml were grown at 37°C during 16h in M17 medium supplemented with lactose 1% (M17L), washed twice (5,000 x g, 9 min, room temperature) in one volume of CDM medium supplemented with lactose 1% (CDML) and resuspended in one volume of CDML. Cultures were then 30-fold diluted in CDML. When cells reached the mid-log phase (OD600 of 0.4), 25-ml aliquots were collected for total RNA extraction.

extract_protocol: Cells were harvested by centrifugation (7,000 x g for 4 min) and mechanically broken with 0.18-mm-diameter glass beads in a Braun Homogenizer (three 1-min periods of homogenization with 1-min intervals on ice). Total RNA was extracted using the High Pure RNA isolation kit (ROCHE, Basel, Switzerland)

tag: isolate

value: clone 1

tag: treatment

value: with mitomycin C 0.08 microg/ml

source_name: LMD-9WT CDML OD 0.4


title: WT (glucose) vs. WT (carbon-free) Rep 2


title: WTvsWTmitomycinC CDML replicate 2

description: Biological replicate 2 of  2

value: clone 2


title: CS_0304/NA18507


title: CS_0303/NA18507


title: CS_0374/NA18507


title: CS_0351/NA18507


title: CS_0352/NA18507


title: WTvsWTmitomycinC CDML replicate 1

description: Biological replicate 1 of  2


title: CS_0291/NA18507


title: WTvsKOhdiR CDML replicate 2

description: Biological replicate 2 of  2

source_name: KOhdiR CDML OD 0.4

growth_protocol: Strains LMD-9 WT and CB0082 were grown at 37°C during 16h in M17 medium supplemented with lactose 1% (M17L), washed twice (5,000 x g, 9 min, room temperature) in one volume of CDM medium supplemented with lactose 1% (CDML) and resuspended in one volume of CDML. Cultures were then 30-fold diluted in CDML. When cells reached the mid-log phase (OD600 of 0.4), 25-ml aliquots were collected for total RNA extraction.


title: CS_0327/NA18507


title: CS_0315/NA18507


title: CS_0362/NA18507


title: FFPE_normal prostate specimen_623

city: Detroit

first: Aliccia

middle: B

last: Bollig-Fischer

state: MI

address: 4100 John R, HWCRC rm 815

institute: Karmanos Cancer Inst., Wayne State University

hyb_protocol: hybridization was done according to manufacturer's instructions

scan_protocol: Arrays were scanned using Illumina's BeadArray Reader  Arrays were scanned using Illumina's BeadArray Reader

data_processing: Data were exported from Illumina’s Bead Studio software after performing the needed quality control checks and ddata were quantile normalized using the 'qn' function in the SRMA package in R.

source_name: normal (matched) prostate

label_protocol: cy3 labeling was done according to manufacturer's instructions

extract_protocol: 10 micron sections were deparaffinized and total RNA was isolated using the High Pure RNA Paraffin kit (Roche, Indianapolis, IN)

treatment_protocol: Formalin-fixed paraffin-embedded (FFPE) normal prostate specimens

tag: race

value: White

tag: gleason's grade


title: WTvsKOhdiR CDML replicate 3

description: Biological replicate 1 of  2, dye swap


title: FFPE_normal prostate specimen_625


title: CS_0350/NA18507


title: CS_0339/NA18507


title: FFPE_normal prostate specimen_622


title: FFPE_normal prostate specimen_621

value: Black


title: FFPE_normal prostate specimen_616


title: FFPE_normal prostate specimen_614


title: CS_0314/NA18507


title: WTvsKOhdiR CDML replicate 1

description: Biological replicate 1 of  2


title: FFPE_normal prostate specimen_612


title: CS_0326/NA18507


title: CS_0290/NA18507


title: CS_0302/NA18507


title: FFPE_normal prostate specimen_611


title: CS_0265/NA18507


title: FFPE_normal prostate specimen_610


title: FFPE_normal prostate specimen_606


title: FFPE_normal prostate specimen_600


title: FFPE_normal prostate specimen_599


title: CS_0338/NA18507


title: CS_0277/NA18507


title: CS_0289/NA18507


title: FFPE_normal prostate specimen_594


title: FFPE_normal prostate specimen_597


title: FFPE_normal prostate specimen_591


title: CS_0253/NA18507


title: CS_0205/NA18507


title: FFPE_normal prostate specimen_577


title: CS_0241/NA18507


title: FFPE_normal prostate specimen_576


title: CS_0288/NA18507


title: FFPE_normal prostate specimen_572


title: FFPE_normal prostate specimen_609


title: FFPE_normal prostate specimen_569


title: CS_0229/NA18507


title: FFPE_normal prostate specimen_564


title: CS_0264/NA18507


title: FFPE_normal prostate specimen_560


title: CS_0240/NA18507


title: CS_0216/NA18507


title: CS_0228/NA18507


title: FFPE_normal prostate specimen_589


title: CS_0275/NA18507


title: CS_0204/NA18507


title: FFPE_normal prostate specimen_555


title: CS_0252/NA18507


title: CS_0263/NA18507


title: FFPE_normal prostate specimen_545


title: FFPE_normal prostate specimen_539


title: FFPE_normal prostate specimen_537


title: FFPE_normal prostate specimen_536


title: CS_0215/NA18507


title: FFPE_normal prostate specimen_532


title: CS_0251/NA18507


title: CS_0239/NA18507


title: FFPE_normal prostate specimen_525


title: FFPE_normal prostate specimen_526


title: CS_0227/NA18507


title: CS_0203/NA18507


title: FFPE_normal prostate specimen_552


title: CS_0274/NA18507


title: CS_0262/NA18507


title: CS_0202/NA18507


title: FFPE_normal prostate specimen_523


title: CS_0217/NA18507


title: FFPE_normal prostate specimen_518


title: FFPE_normal prostate specimen_517


title: CS_0286/NA18507


title: FFPE_normal prostate specimen_510


title: FFPE_normal prostate specimen_513


title: FFPE_normal prostate specimen_509


title: CS_0226/NA18507


title: CS_0287/NA18507


title: CS_0238/NA18507


title: CS_0250/NA18507


title: FFPE_normal prostate specimen_503


title: FFPE_normal prostate specimen_493


title: FFPE_normal prostate specimen_488


title: FFPE_normal prostate specimen_490


title: CS_0261/NA18507


title: FFPE_normal prostate specimen_484


title: FFPE_normal prostate specimen_485


title: FFPE_normal prostate specimen_478


title: FFPE_normal prostate specimen_475


title: FFPE_normal prostate specimen_474


title: CS_0249/NA18507


title: CS_0273/NA18507


title: CS_0201/NA18507


title: FFPE_normal prostate specimen_473


title: CS_0225/NA18507


title: CS_0260/NA18507


title: CS_0214/NA18507


title: CS_0237/NA18507


title: FFPE_normal prostate specimen_467


title: FFPE_normal prostate specimen_466


title: CS_0283/NA18507


title: CS_0213/NA18507


title: FFPE_normal prostate specimen_465


title: CS_0236/NA18507


title: FFPE_normal prostate specimen_460


title: CS_0272/NA18507


title: FFPE_normal prostate specimen_459


title: CS_0224/NA18507


title: CS_0212/NA18507


title: CS_0271/NA18507


title: CS_0247/NA18507


title: CS_0248/NA18507


title: CS_0223/NA18507


title: FFPE_normal prostate specimen_456


title: FFPE_normal prostate specimen_498


title: FFPE_normal prostate specimen_452


title: CS_0285/NA18507


title: CS_0200/NA18507


title: FFPE_normal prostate specimen_447


title: FFPE_normal prostate specimen_449


title: FFPE_normal prostate specimen_445


title: CS_0235/NA18507


title: FFPE_normal prostate specimen_438


title: FFPE_normal prostate specimen_436


title: FFPE_normal prostate specimen_424


title: FFPE_normal prostate specimen_423


title: CS_0211/NA18507


title: FFPE_normal prostate specimen_421


title: CS_0270/NA18507


title: CS_0259/NA18507


title: FFPE_normal prostate specimen_414


title: FFPE_normal prostate specimen_401


title: CS_0222/NA18507


title: FFPE_normal prostate specimen_407


title: CS_0281/NA18507


title: FFPE_normal prostate specimen_399


title: FFPE_normal prostate specimen_392


title: FFPE_normal prostate specimen_388


title: CS_0269/NA18507


title: CS_0234/NA18507


title: CS_0258/NA18507


title: CS_0246/NA18507


title: FFPE_normal prostate specimen_412


title: FFPE_normal prostate specimen_381


title: FFPE_normal prostate specimen_379


title: CS_0210/NA18507


title: CS_0198/NA18507


title: FFPE_normal prostate specimen_376


title: FFPE_normal prostate specimen_386


title: FFPE_normal prostate specimen_373


title: FFPE_normal prostate specimen_375


title: CS_0245/NA18507


title: CS_0257/NA18507


title: FFPE_normal prostate specimen_364


title: FFPE_normal prostate specimen_362


title: CS_0209/NA18507


title: CS_0197/NA18507


title: FFPE_normal prostate specimen_365


title: CS_0233/NA18507


title: CS_0232/NA18507


title: FFPE_normal prostate specimen_348


title: CS_0279/NA18507


title: CS_0208/NA18507


title: CS_0284/NA18507


title: FFPE_normal prostate specimen_326


title: FFPE_normal prostate specimen_329


title: CS_0244/NA18507


title: FFPE_normal prostate specimen_324


title: FFPE_normal prostate specimen_355


title: CS_0220/NA18507


title: CS_0268/NA18507


title: CS_0267/NA18507


title: FFPE_normal prostate specimen_323


title: CS_0219/NA18507


title: CS_0196/NA18507


title: CS_0255/NA18507


title: FFPE_normal prostate specimen_319


title: CS_0256/NA18507


title: FFPE_normal prostate specimen_317


title: FFPE_normal prostate specimen_314


title: FFPE_normal prostate specimen_318


title: FFPE_normal prostate specimen_311


title: FFPE_normal prostate specimen_307


title: FFPE_normal prostate specimen_305


title: CS_0207/NA18507


title: CS_0221/NA18507


title: CS_0243/NA18507


title: FFPE_normal prostate specimen_300


title: CS_0195/NA18507


title: FFPE_normal prostate specimen_303


title: CS_0266/NA18507


title: CS_0254/NA18507


title: FFPE_normal prostate specimen_290


title: CS_0278/NA18507


title: FFPE_normal prostate specimen_272


title: FFPE_normal prostate specimen_287


title: CS_0230/NA18507


title: CS_0231/NA18507


title: FFPE_normal prostate specimen_271


title: FFPE_normal prostate specimen_270


title: FFPE_normal prostate specimen_268


title: FFPE_normal prostate specimen_263


title: AU0780301/NA12878

value: male

value: proband

value: AGRE autism


title: CS_0218/NA18507

value: whole blood


title: CS_0206/NA18507


title: FFPE_normal prostate specimen_262


title: CS_0280/NA18507


title: FFPE_normal prostate specimen_253


title: AU056203/NA12878


title: AU078703/NA18507

value: female


title: FFPE_normal prostate specimen_250


title: AU1911301/NA12878


title: FFPE_normal prostate specimen_235


title: CS_0242/NA18507


title: AU023504/NA12878


title: FFPE_normal prostate specimen_220


title: AU1156301/NA12878


title: FFPE_normal prostate specimen_217


title: FFPE_normal prostate specimen_230


title: AU0883301/NA12878


title: AU1019301/NA12878


title: FFPE_normal prostate specimen_215


title: AU0911301/NA12878


title: FFPE_normal prostate specimen_293


title: AU1056301/NA12878


title: FFPE_normal prostate specimen_213


title: FFPE_normal prostate specimen_209


title: CS_0194/NA18507


title: FFPE_normal prostate specimen_203


title: AU078304/NA12878


title: AU0921302/NA12878


title: FFPE_normal prostate specimen_195


title: AU031104/NA12878


title: AU082505/NA12878


title: AU2690301/NA12878


title: FFPE_normal prostate specimen_187


title: FFPE_normal prostate specimen_211


title: FFPE_normal prostate specimen_183


title: AU006804/NA18507


title: AU021005/NA12878


title: AU056705/NA12878


title: FFPE_normal prostate specimen_182


title: FFPE_normal prostate specimen_181


title: AU2275301/NA12878


title: AU2185302/NA12878


title: FFPE_normal prostate specimen_174


title: AU2691301/NA12878


title: AU0948302/NA12878


title: FFPE_normal prostate specimen_177


title: AU0931306/NA12878


title: FFPE_normal prostate specimen_166


title: AU2487302/NA12878


title: FFPE_normal prostate specimen_185


title: FFPE_normal prostate specimen_172


title: AU2831301/NA12878


title: FFPE_normal prostate specimen_202


title: AU025506/NA18507


title: FFPE_normal prostate specimen_145


title: FFPE_normal prostate specimen_132


title: FFPE_normal prostate specimen_130


title: FFPE_normal prostate specimen_160


title: FFPE_normal prostate specimen_119


title: AU2830302/NA12878


title: AU2054302/NA18507


title: FFPE_normal prostate specimen_118


title: FFPE_normal prostate specimen_120


title: AU075603/NA12878


title: AU2814301/NA18507


title: AU2460302/NA12878


title: AU0946302/NA12878


title: FFPE_normal prostate specimen_100


title: FFPE_normal prostate specimen_117


title: AU1929301/NA12878


title: FFPE_normal prostate specimen_93


title: AU045304/NA12878


title: FFPE_normal prostate specimen_113


title: AU2554301/NA18507


title: AU1428305/NA18507


title: FFPE_normal prostate specimen_103


title: AU066103/NA12878


title: FFPE_normal prostate specimen_116


title: FFPE_normal prostate specimen_89


title: FFPE_normal prostate specimen_92


title: FFPE_normal prostate specimen_87


title: AU0947302/NA12878


title: AU034904/NA12878


title: AU2863302/NA18507


title: FFPE_normal prostate specimen_84


title: FFPE_normal prostate specimen_75


title: AU0972301/NA12878


title: FFPE_normal prostate specimen_65


title: AU0549301/NA12878


title: FFPE_normal prostate specimen_62


title: FFPE_normal prostate specimen_60


title: AU1092302/NA12878


title: FFPE_normal prostate specimen_57


title: AU2689306/NA12878


title: FFPE_normal prostate specimen_72


title: FFPE_normal prostate specimen_45


title: AU077205/NA18507


title: AU0782302/NA12878


title: FFPE_normal prostate specimen_38


title: FFPE_normal prostate specimen_41


title: AU2182302/NA12878


title: FFPE_normal prostate specimen_31


title: AU086803/NA12878


title: AU079104/NA12878


title: AU075210/NA12878


title: FFPE_normal prostate specimen_29


title: FFPE_normal prostate specimen_28


title: FFPE_normal prostate specimen_27


title: FFPE_normal prostate specimen_26


title: FFPE_normal prostate specimen_23


title: AU079403/NA18507


title: FFPE_normal prostate specimen_16


title: AU1959302/NA12878


title: AU1212301/NA18507


title: FFPE_normal prostate specimen_4


title: AU1687303/NA12878


title: AU016504/NA12878


title: FFPE_normal prostate specimen_3


title: AU023005/NA12878


title: AU019303/NA12878


title: AU1329301/NA12878


title: FFPE_normal prostate specimen_18


title: AU1094301/NA12878


title: AU021204/NA12878


title: FFPE_prostate tumor specimen_638

data_processing: Data were exported from Illumina’s Bead Studio software after performing the needed quality control checks and data were quantile normalized using the 'qn' function in the SRMA package in R.

source_name: prostate tumor

treatment_protocol: Formalin-fixed paraffin-embedded (FFPE) prostate cancer specimens


title: FFPE_prostate tumor specimen_637


title: AU2372301/NA12878


title: FFPE_prostate tumor specimen_635


title: FFPE_prostate tumor specimen_636


title: AU1292302/NA12878


title: AU052103/NA12878


title: FFPE_prostate tumor specimen_634


title: AU1298301/NA12878


title: AU1351301/NA12878


title: AU1081301/NA12878


title: AU053503/NA12878


title: FFPE_normal prostate specimen_15


title: AU028503/NA18507


title: FFPE_prostate tumor specimen_639


title: AU3068301/NA12878


title: AU1073301/NA12878


title: FFPE_prostate tumor specimen_629


title: AU1520301/NA12878


title: AU0871302/NA12878


title: AU1232302/NA18507


title: FFPE_prostate tumor specimen_632


title: AU046503/NA12878


title: FFPE_prostate tumor specimen_631


title: FFPE_prostate tumor specimen_633


title: FFPE_prostate tumor specimen_630


title: AU1848302/NA18507


title: FFPE_prostate tumor specimen_627


title: FFPE_prostate tumor specimen_626


title: AU002503/NA12878


title: AU012305/NA18507


title: AU2835301/NA12878


title: FFPE_prostate tumor specimen_624


title: FFPE_prostate tumor specimen_625


title: FFPE_prostate tumor specimen_623


title: AU028703/NA12878


title: FFPE_prostate tumor specimen_622


title: FFPE_prostate tumor specimen_621


title: FFPE_prostate tumor specimen_618


title: FFPE_prostate tumor specimen_628


title: AU0971302/NA18507


title: FFPE_prostate tumor specimen_617


title: AU1147301/NA12878


title: FFPE_prostate tumor specimen_620


title: AU1779301/NA12878


title: AU1448301/NA12878


title: AU0540302/NA18507


title: AU1496302/NA12878


title: FFPE_prostate tumor specimen_614


title: AU1679303/NA12878


title: FFPE_prostate tumor specimen_612


title: FFPE_prostate tumor specimen_619


title: FFPE_prostate tumor specimen_611


title: AU081403/NA12878


title: FFPE_prostate tumor specimen_615


title: AU1575302/NA12878


title: AU0993301/NA12878


title: FFPE_prostate tumor specimen_610


title: FFPE_prostate tumor specimen_616


title: AU0974302/NA12878


title: AU0962303/NA12878


title: AU3106303/NA12878


title: FFPE_prostate tumor specimen_613


title: AU1243301/NA12878


title: FFPE_prostate tumor specimen_608


title: AU0922301/NA12878


title: AU048303/NA12878


title: FFPE_prostate tumor specimen_607


title: AU031204/NA18507


title: FFPE_prostate tumor specimen_606


title: FFPE_prostate tumor specimen_605


title: AU023604/NA18507


title: AU061104/NA12878


title: FFPE_prostate tumor specimen_604


title: FFPE_prostate tumor specimen_603


title: AU078804/NA12878


title: FFPE_prostate tumor specimen_609


title: FFPE_prostate tumor specimen_602


title: FFPE_prostate tumor specimen_601


title: FFPE_prostate tumor specimen_600


title: AU008403/NA12878


title: FFPE_prostate tumor specimen_599


title: AU1394302/NA12878


title: AU065604/NA12878


title: FFPE_prostate tumor specimen_596


title: FFPE_prostate tumor specimen_598


title: FFPE_prostate tumor specimen_597


title: FFPE_prostate tumor specimen_594


title: AU048204/NA12878


title: AU024703/NA12878


title: AU0995301/NA12878


title: FFPE_prostate tumor specimen_593


title: FFPE_prostate tumor specimen_592


title: FFPE_prostate tumor specimen_595


title: FFPE_prostate tumor specimen_590


title: FFPE_prostate tumor specimen_589


title: AU019904/NA12878


title: FFPE_prostate tumor specimen_588


title: AU010803/NA12878


title: FFPE_prostate tumor specimen_587


title: AU024003/NA12878


title: AU016204/NA18507


title: FFPE_prostate tumor specimen_591


title: AU004104/NA18507


title: AU004304/NA12878


title: AU080803/NA12878


title: FFPE_prostate tumor specimen_586


title: AU1207301/NA18507


title: FFPE_prostate tumor specimen_583


title: AU080203/NA12878


title: AU1165302/NA12878


title: AU0983301/NA12878


title: FFPE_prostate tumor specimen_582


title: FFPE_prostate tumor specimen_584


title: AU1887301/NA18507


title: AU1625301/NA18507


title: AU1692301/NA12878


title: AU0907301/NA18507


title: FFPE_prostate tumor specimen_577


title: AU1871301/NA12878


title: FFPE_prostate tumor specimen_580


title: FFPE_prostate tumor specimen_578


title: FFPE_prostate tumor specimen_579


title: AU3006301/NA18507


title: FFPE_prostate tumor specimen_581


title: AU2882301/NA12878


title: FFPE_prostate tumor specimen_576


title: FFPE_prostate tumor specimen_585


title: AU1454302/NA12878


title: AU3187302/NA12878


title: AU1414302/NA12878


title: AU1533301/NA18507


title: FFPE_prostate tumor specimen_575


title: AU2004302/NA12878


title: AU1631301/NA12878


title: AU066404/NA12878


title: FFPE_prostate tumor specimen_572


title: FFPE_prostate tumor specimen_571


title: FFPE_prostate tumor specimen_570


title: FFPE_prostate tumor specimen_573


title: FFPE_prostate tumor specimen_574


title: FFPE_prostate tumor specimen_569


title: AU015703/NA12878


title: FFPE_prostate tumor specimen_568


title: FFPE_prostate tumor specimen_567


title: FFPE_prostate tumor specimen_566


title: AU1753302/NA12878


title: FFPE_prostate tumor specimen_565


title: AU1335301/NA12878


title: FFPE_prostate tumor specimen_563


title: FFPE_prostate tumor specimen_562


title: FFPE_prostate tumor specimen_561


title: AU079303/NA12878


title: FFPE_prostate tumor specimen_564


title: FFPE_prostate tumor specimen_560


title: AU065304/NA18507


title: FFPE_prostate tumor specimen_559


title: AU069603/NA12878


title: AU026203/NA12878


title: FFPE_prostate tumor specimen_558


title: AU0675302/NA12878


title: AU1830302/NA12878


title: AU1265303/NA12878


title: FFPE_prostate tumor specimen_554


title: AU1678301/NA12878


title: FFPE_prostate tumor specimen_553


title: AU1644303/NA18507


title: AU1412301/NA12878


title: AU1522303/NA12878


title: AU1525303/NA12878


title: FFPE_prostate tumor specimen_555


title: AU1731302/NA12878


title: FFPE_prostate tumor specimen_556


title: AU1497302/NA12878


title: AU1565302/NA12878


title: AU000704/NA18507


title: FFPE_prostate tumor specimen_551


title: AU1849303/NA12878


title: AU056503/NA12878


title: AU012204/NA12878


title: FFPE_prostate tumor specimen_549


title: FFPE_prostate tumor specimen_552


title: FFPE_prostate tumor specimen_550


title: FFPE_prostate tumor specimen_557


title: AU005303/NA12878


title: FFPE_prostate tumor specimen_548


title: FFPE_prostate tumor specimen_547


title: AU0316301/NA18507


title: FFPE_prostate tumor specimen_546


title: AU000504/NA12878


title: AU062603/NA12878


title: AU0263302/NA12878


title: FFPE_prostate tumor specimen_545


title: FFPE_prostate tumor specimen_544


title: FFPE_prostate tumor specimen_543


title: AU1374302/NA12878


title: AU030804/NA12878


title: FFPE_prostate tumor specimen_542


title: AU022704/NA12878


title: FFPE_prostate tumor specimen_541


title: AU1469302/NA12878


title: AU1470303/NA12878


title: FFPE_prostate tumor specimen_540


title: FFPE_prostate tumor specimen_539


title: FFPE_prostate tumor specimen_537


title: FFPE_prostate tumor specimen_536


title: FFPE_prostate tumor specimen_535


title: AU063004/NA18507


title: FFPE_prostate tumor specimen_534


title: FFPE_prostate tumor specimen_533


title: FFPE_prostate tumor specimen_532


title: AU011103/NA12878


title: FFPE_prostate tumor specimen_538


title: FFPE_prostate tumor specimen_531


title: FFPE_prostate tumor specimen_530


title: AU2479301/NA18507


title: FFPE_prostate tumor specimen_528


title: AU2909303/NA12878


title: AU1536304/NA12878


title: AU2811301/NA18507


title: AU2580301/NA12878


title: AU2643302/NA12878


title: FFPE_prostate tumor specimen_526


title: AU2157301/NA18507


title: FFPE_prostate tumor specimen_527


title: AU2290301/NA12878


title: AU2908301/NA18507


title: FFPE_prostate tumor specimen_529


title: AU2921303/NA12878


title: AU1888301/NA12878


title: AU2681301/NA12878


title: AU1756302/NA12878


title: AU1664302/NA12878


title: FFPE_prostate tumor specimen_523


title: AU2065301/NA18507


title: AU2135301/NA12878


title: AU2950302/NA18507


title: FFPE_prostate tumor specimen_525


title: AU2282302/NA12878


title: FFPE_prostate tumor specimen_521


title: AU1763301/NA18507


title: FFPE_prostate tumor specimen_519


title: AU2525302/NA12878


title: AU1300302/NA18507


title: AU2332301/NA12878


title: FFPE_prostate tumor specimen_520


title: AU2482301/NA12878


title: FFPE_prostate tumor specimen_518


title: FFPE_prostate tumor specimen_517


title: AU2557302/NA12878


title: FFPE_prostate tumor specimen_515


title: FFPE_prostate tumor specimen_516


title: FFPE_prostate tumor specimen_513


title: FFPE_prostate tumor specimen_512


title: AU2842302/NA12878


title: FFPE_prostate tumor specimen_511


title: AU1209302/NA12878


title: FFPE_prostate tumor specimen_524


title: AU071803/NA18507


title: FFPE_prostate tumor specimen_510


title: FFPE_prostate tumor specimen_506


title: FFPE_prostate tumor specimen_509


title: FFPE_prostate tumor specimen_514


title: AU1196301/NA12878


title: FFPE_prostate tumor specimen_522


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title: FFPE_prostate tumor specimen_174


title: FFPE_prostate tumor specimen_175


title: AU2312302/NA12878


title: AU1437301/NA12878


title: FFPE_prostate tumor specimen_172


title: FFPE_prostate tumor specimen_173


title: FFPE_prostate tumor specimen_171


title: AU1185301/NA12878


title: FFPE_prostate tumor specimen_170


title: AU0884301/NA12878


title: AU073805/NA12878


title: AU2581302/NA12878


title: FFPE_prostate tumor specimen_169


title: FFPE_prostate tumor specimen_168


title: FFPE_prostate tumor specimen_167


title: AU2481301/NA12878


title: FFPE_prostate tumor specimen_182


title: AU1362301/NA12878


title: FFPE_prostate tumor specimen_165


title: FFPE_prostate tumor specimen_184


title: AU1512301/NA12878


title: FFPE_prostate tumor specimen_164


title: AU1402301/NA18507


title: AU012704/NA12878


title: AU0914301/NA18507


title: AU1638301/NA12878


title: AU0452303/NA12878


title: FFPE_prostate tumor specimen_162


title: AU1727303/NA12878


title: AU1835302/NA12878


title: FFPE_prostate tumor specimen_178


title: FFPE_prostate tumor specimen_161


title: AU2050301/NA12878


title: FFPE_prostate tumor specimen_159


title: FFPE_prostate tumor specimen_158


title: AU1739302/NA12878


title: FFPE_prostate tumor specimen_163


title: AU1885302/NA12878


title: FFPE_prostate tumor specimen_157


title: FFPE_prostate tumor specimen_156


title: AU1365301/NA12878


title: FFPE_prostate tumor specimen_155


title: FFPE_prostate tumor specimen_154


title: FFPE_prostate tumor specimen_152


title: FFPE_prostate tumor specimen_151


title: FFPE_prostate tumor specimen_150


title: AU1371302/NA12878


title: FFPE_prostate tumor specimen_153


title: AU1967303/NA12878


title: AU1765302/NA12878


title: AU2094301/NA12878


title: FFPE_prostate tumor specimen_149


title: AU1732302/NA12878


title: AU2071301/NA12878


title: FFPE_prostate tumor specimen_148


title: FFPE_prostate tumor specimen_160


title: FFPE_prostate tumor specimen_166


title: FFPE_prostate tumor specimen_146


title: AU2081301/NA12878


title: AU1686301/NA12878


title: AU1067302/NA12878


title: FFPE_prostate tumor specimen_145


title: FFPE_prostate tumor specimen_147


title: FFPE_prostate tumor specimen_144


title: AU020103/NA12878


title: FFPE_prostate tumor specimen_143


title: AU026705/NA12878


title: FFPE_prostate tumor specimen_141


title: AU2112302/NA12878


title: AU1858301/NA18507


title: AU072203/NA12878


title: FFPE_prostate tumor specimen_140


title: FFPE_prostate tumor specimen_139


title: FFPE_prostate tumor specimen_142


title: FFPE_prostate tumor specimen_138


title: AU2025303/NA12878


title: AU1924302/NA12878


title: AU2146302/NA12878


title: FFPE_prostate tumor specimen_137


title: AU2076301/NA12878


title: AU1563301/NA12878


title: FFPE_prostate tumor specimen_136


title: AU1673301/NA12878


title: FFPE_prostate tumor specimen_135


title: AU0975301/NA12878


title: FFPE_prostate tumor specimen_134


title: FFPE_prostate tumor specimen_133


title: FFPE_prostate tumor specimen_132


title: AU1699302/NA18507


title: FFPE_prostate tumor specimen_131


title: AU1230301/NA12878


title: AU1813301/NA12878


title: FFPE_prostate tumor specimen_129


title: FFPE_prostate tumor specimen_128


title: FFPE_prostate tumor specimen_130


title: AU1923302/NA12878


title: FFPE_prostate tumor specimen_127


title: AU1942302/NA12878


title: FFPE_prostate tumor specimen_126


title: FFPE_prostate tumor specimen_125


title: AU1718301/NA12878


title: FFPE_prostate tumor specimen_124


title: FFPE_prostate tumor specimen_122


title: FFPE_prostate tumor specimen_123


title: FFPE_prostate tumor specimen_121


title: FFPE_prostate tumor specimen_120


title: 150-14694/NA12878

tag: cell type

value: lymphoblast cell line

value: NIMH control


title: 150-13643/NA12878


title: AU1996301/NA12878


title: FFPE_prostate tumor specimen_118


title: AU1952305/NA12878


title: 150-14599/NA18507


title: 150-13943/NA12878


title: AU1744301/NA12878


title: AU1453302/NA12878


title: 150-14161/NA12878


title: 150-14256/NA12878


title: 150-14758/NA18507


title: FFPE_prostate tumor specimen_116


title: AU1582302/NA12878


title: FFPE_prostate tumor specimen_117


title: 150-14022/NA18507


title: 150-14722/NA18507


title: 150-14389/NA18507


title: 150-13805/NA12878


title: FFPE_prostate tumor specimen_114


title: FFPE_prostate tumor specimen_113


title: AU1997301/NA12878


title: 150-13759/NA18507


title: FFPE_prostate tumor specimen_119


title: 150-15248/NA18507


title: FFPE_prostate tumor specimen_112


title: 150-15337/NA18507


title: FFPE_prostate tumor specimen_115


title: FFPE_prostate tumor specimen_111


title: FFPE_prostate tumor specimen_110


title: 150-13787/NA12878


title: 150-13656/NA18507


title: FFPE_prostate tumor specimen_108


title: FFPE_prostate tumor specimen_107


title: FFPE_prostate tumor specimen_109


title: FFPE_prostate tumor specimen_106


title: 150-14823/NA12878


title: FFPE_prostate tumor specimen_105


title: FFPE_prostate tumor specimen_104


title: FFPE_prostate tumor specimen_102


title: FFPE_prostate tumor specimen_103


title: FFPE_prostate tumor specimen_101


title: FFPE_prostate tumor specimen_100


title: 150-14759/NA12878


title: FFPE_prostate tumor specimen_99


title: 150-14087/NA18507


title: FFPE_prostate tumor specimen_98


title: 150-14911/NA18507


title: 150-13696/NA12878


title: FFPE_prostate tumor specimen_97


title: 150-14957/NA18507


title: FFPE_prostate tumor specimen_96


title: 150-15341/NA18507


title: FFPE_prostate tumor specimen_94


title: 150-14747/NA12878


title: FFPE_prostate tumor specimen_93


title: 150-15113/NA12878


title: FFPE_prostate tumor specimen_95


title: Leaf-Cvi-High_light-rep3

city: Kongens Lyngby

first: Simon

last: Rasmussen

address: Kemitorvet, Building 208

department: Department of Systems Biology

country: Denmark

institute: Technical University of Denmark

hyb_protocol: 4 ug of the labelled products were loaded onto microarrays, hybridized overnight, and washed in the NimbleGen Wash Buffer Kit following the NimbleGen protocol.

scan_protocol: Scanning was performed on a Roche 2-microns scanner and the images analyzed with the NimbleScan software.

data_processing: Data was imported into R (R Core Team, 2012) using the oligo (Carvalho and Irizarry, 2010) and pdInfoBuilder packages (Falcon, 2012) using the AgilentAT6 build. Normalization was performed using quantiles (Bolstad et al., 2003) and expression indexes calculated using RMA (Irizarry et al., 2003).

organism: Arabidopsis thaliana

label_protocol: Reverse transcription of messenger RNA was performed from total RNA using a double stranded cDNA synthesis kit (Superscript, Invitrogen) and labelled with Cy3 using NimbleGen Gene Expression protocol.

growth_protocol: Three week-old plants were subjected to stress treatments for three hours in triplicate, at environmentally controlled chambers (RISØ DTU National Laboratory, Roskilde, Denmark). To reduce effects of circadium rhythmicity, treatments were performed 5 hours after chamber dawn.

extract_protocol: Total RNA samples were extracted using RiboPure kit (Ambion, Austin, TX, USA).

treatment_protocol: Combinations of high-light (800 µm photons m-2s-1), cold (10°C), heat (38°C), high salinity (100 mM NaCl), and foliar spray application of a bacterial elicitor (20 µM flagellin peptide flg22). For the Cold+HL treatment, heat from 3 sodium lamps was displaced by circulating fans and a plexiglass shield and ambient plant temperature maintained by ice trays and monitored at 10°C  with an infrared thermometer (ThermaTwin TN408LC).

tag: ecotype

value: Cvi

value: 3 week-old

tag: stress type

tag: stress treatment

value: 800 µm photons m-2s-1 for 3hrs

value: leaves


title: FFPE_prostate tumor specimen_92

tag: age


title: AU1784302/NA18507

tag: tissue

tag: gender


title: Leaf-An1-Salt+Heat-rep3

value: Salt+Heat

value: 100 mM NaCl + 38C for 3hrs


title: 150-14956/NA18507

tag: family status

tag: ndar guid


title: 150-14872/NA18507

tag: cohort

tag: cell line


title: 150-15122/NA18507


title: Leaf-Col-Cold-rep3

source_name: Leaf-Col-Cold

value: Col

value: Cold

value: 10C for 3hrs


title: 150-14897/NA18507


title: 150-15126/NA12878


title: 150-15147/NA12878


title: Leaf-Eri-Heat-rep3

source_name: Leaf-Eri-Heat

value: Eri

value: Heat

value: 38C for 3hrs


title: 150-14822/NA12878

value: male


title: 150-15058/NA12878


title: FFPE_prostate tumor specimen_90

value: White


title: 150-14944/NA18507

value: female


title: FFPE_prostate tumor specimen_91


title: FFPE_prostate tumor specimen_89

value: Black


title: Leaf-Sha-Cold-rep3

source_name: Leaf-Sha-Cold

value: Sha


title: Leaf-Kond-Heat-rep3

source_name: Leaf-Kond-Heat

value: Kond


title: Leaf-Ler-Salt-rep3

source_name: Leaf-Ler-Salt

value: Ler

value: 3 week-old

value: Salt

value: 100 mM NaCl for 3hrs


title: Leaf-Cvi-Salt-rep3

source_name: Leaf-Cvi-Salt

value: Cvi

value: leaves


title: 150-15028/NA18507

source_name: lymphoblast cell line DNA

value: lymphoblast cell line

value: NIMH control


title: 150-14848/NA18507


title: Leaf-Ler-High_light-rep3

value: 800 µm photons m-2s-1 for 3hrs


title: 150-15073/NA12878


title: FFPE_prostate tumor specimen_88


title: 150-15036/NA18507


title: 150-10545/NA18507


title: 150-15060/NA12878


title: Leaf-Kond-Salt+Heat-rep3

source_name: Leaf-Kond-Salt+Heat

value: Salt+Heat

value: 100 mM NaCl + 38C for 3hrs


title: 150-15085/NA18507


title: Leaf-Col-FLG-rep3

source_name: Leaf-Col-FLG

value: Col

value: FLG

value: foliar spray:20 µM flagellin peptide flg22


title: 150-10532/NA12878

value: male


title: FFPE_prostate tumor specimen_87

value: White


title: FFPE_prostate tumor specimen_86


title: 150-11093/NA18507

value: female


title: 150-14686/NA12878


title: FFPE_prostate tumor specimen_85


title: FFPE_prostate tumor specimen_84


title: Leaf-Col-Heat+FLG+Silwet-rep3

source_name: Leaf-Col-Heat+FLG+Silwet

value: Heat+FLG+Silwet

value: 38C for 3hrs + foliar spray:20 µM flagellin peptide flg22


title: 150-15151/NA18507


title: FFPE_prostate tumor specimen_83

value: Black


title: Leaf-C24-Cold-rep3

value: 3 week-old

value: Cold

value: 10C for 3hrs


title: Leaf-Kyo2-Heat-rep3

value: Heat

value: 38C for 3hrs

value: leaves


title: Leaf-Eri-Ctrl-rep3

source_name: Leaf-Eri-Ctrl

value: Eri

value: control plants


title: Leaf-Ler-Cold+FLG+Silwet-rep3

source_name: Leaf-Ler-Cold+FLG+Silwet

value: Ler

value: Cold+FLG+Silwet

value: 10C 3hrs + 20 µM flagellin peptide flg22 spray


title: 150-14986/NA12878

value: lymphoblast cell line

value: male

value: NIMH control


title: FFPE_prostate tumor specimen_82

value: White


title: FFPE_prostate tumor specimen_81


title: Leaf-Kas1-Ctrl-rep3


title: Leaf-Ler-Ctrl+Silwet-rep3

source_name: Leaf-Ler-Ctrl+Silwet

value: control plants+Silwet

value: silwet detergent used for flagellin application


title: Leaf-Ler-Heat+Silwet-rep3

source_name: Leaf-Ler-Heat+Silwet

value: 3 week-old

value: Heat+Silwet

value: 38C for 3hrs + silwet detergent used for flagellin application


title: Leaf-Col-High_light-rep3

value: Col

value: 800 µm photons m-2s-1 for 3hrs


title: Leaf-Kas1-Heat-rep3

value: Heat

value: 38C for 3hrs

value: leaves


title: Leaf-Sha-High_light-rep3

value: Sha


title: Leaf-An1-Cold-rep3

value: Cold

value: 10C for 3hrs


title: FFPE_prostate tumor specimen_80


title: FFPE_prostate tumor specimen_79


title: Leaf-Kyo2-Ctrl-rep3

value: control plants


title: Leaf-Sha-Salt-rep3

source_name: Leaf-Sha-Salt

value: Salt

value: 100 mM NaCl for 3hrs


title: 150-14297/NA12878

value: lymphoblast cell line

value: male

value: NIMH control


title: 150-14970/NA18507

value: female


title: Leaf-Kond-High_light-rep3

value: Kond

value: 3 week-old


title: Leaf-Eri-Salt-rep3

source_name: Leaf-Eri-Salt

value: Eri


title: Leaf-Col-Cold+FLG+Silwet-rep3

source_name: Leaf-Col-Cold+FLG+Silwet

value: Col

value: Cold+FLG+Silwet

value: 10C 3hrs + 20 µM flagellin peptide flg22 spray


title: Leaf-Ler-Cold+High_light-rep3

value: Ler

value: 10C for 3hrs + heat from 3 sodium lamps was displaced by circulating fans and a plexiglass shield and ambient plant temperature maintained by ice trays and monitored at 10°C

value: leaves


title: FFPE_prostate tumor specimen_77

source_name: prostate tumor

value: White


title: Leaf-Sha-Heat-rep3

source_name: Leaf-Sha-Heat

value: Sha

value: Heat

value: 38C for 3hrs


title: 150-15116/NA12878

value: lymphoblast cell line


title: FFPE_prostate tumor specimen_76

value: Black


title: Leaf-Cvi-Salt+Heat-rep3

source_name: Leaf-Cvi-Salt+Heat

value: Cvi

value: Salt+Heat

value: 100 mM NaCl + 38C for 3hrs


title: Leaf-Kyo2-Cold-rep3

value: 3 week-old

value: Cold

value: 10C for 3hrs


title: Leaf-Col-Ctrl-rep3

source_name: Leaf-Col-Ctrl

value: Col

value: control plants


title: 150-13939/NA18507

value: female

value: NIMH control


title: FFPE_prostate tumor specimen_75


title: 150-14958/NA12878

value: male


title: Leaf-Ler-Salt+High_light-rep3

value: Ler

value: 100 mM NaCl + 800 µm photons m-2s-1 for 3hrs

value: leaves


title: 150-15021/NA12878


title: Leaf-Col-Cold+High_light-rep3

value: 10C for 3hrs + heat from 3 sodium lamps was displaced by circulating fans and a plexiglass shield and ambient plant temperature maintained by ice trays and monitored at 10°C


title: Leaf-Eri-High_light-rep3

value: Eri

value: 800 µm photons m-2s-1 for 3hrs


title: FFPE_prostate tumor specimen_74

value: Black


title: Leaf-Col-Heat-rep3

source_name: Leaf-Col-Heat

value: Heat

value: 38C for 3hrs


title: 150-15075/NA18507

value: lymphoblast cell line


title: Leaf-Ler-Cold+Silwet-rep3

source_name: Leaf-Ler-Cold+Silwet

value: 3 week-old

value: Cold+Silwet

value: 10C for 3hrs + silwet detergent used for flagellin application


title: 150-14878/NA18507

source_name: lymphoblast cell line DNA


title: FFPE_prostate tumor specimen_73

value: White


title: 150-15088/NA12878


title: Leaf-Kond-Salt-rep3

source_name: Leaf-Kond-Salt

value: Kond

value: Salt

value: 100 mM NaCl for 3hrs


title: FFPE_prostate tumor specimen_72


title: 150-15012/NA12878

value: male

value: NIMH control


title: Leaf-Kas1-Cold-rep3

value: Cold

value: 10C for 3hrs

value: leaves


title: FFPE_prostate tumor specimen_71


title: FFPE_prostate tumor specimen_70


title: 150-15104/NA18507

value: female


title: 150-14924/NA12878


title: Leaf-Cvi-Cold-rep3

source_name: Leaf-Cvi-Cold

value: Cvi


title: Leaf-An1-Heat-rep3

value: Heat


title: FFPE_prostate tumor specimen_69


title: Leaf-Ler-Salt+Heat-rep3

source_name: Leaf-Ler-Salt+Heat

value: Ler

value: Salt+Heat

value: 100 mM NaCl + 38C for 3hrs


title: Leaf-Sha-Ctrl-rep3

source_name: Leaf-Sha-Ctrl

value: Sha

value: 3 week-old

value: control plants


title: Leaf-Col-Salt-rep3

source_name: Leaf-Col-Salt

value: Col


title: Leaf-Kas1-High_light-rep3

value: 800 µm photons m-2s-1 for 3hrs


title: FFPE_prostate tumor specimen_78

value: Black


title: Leaf-C24-Ctrl-rep3


title: Leaf-Col-Salt+High_light-rep3

value: 100 mM NaCl + 800 µm photons m-2s-1 for 3hrs


title: Leaf-Kyo2-Salt-rep3

value: Salt

value: 100 mM NaCl for 3hrs


title: 150-14921/NA12878

value: lymphoblast cell line

value: male

value: NIMH control


title: 150-12989/NA18507

value: female


title: 150-15123/NA12878


title: 150-15112/NA12878


title: 150-15130/NA18507


title: FFPE_prostate tumor specimen_65

value: White


title: Leaf-Ler-Heat+FLG+Silwet-rep3

source_name: Leaf-Ler-Heat+FLG+Silwet

value: Ler

value: Heat+FLG+Silwet

value: 38C for 3hrs + foliar spray:20 µM flagellin peptide flg22

value: leaves


title: FFPE_prostate tumor specimen_67


title: FFPE_prostate tumor specimen_66


title: FFPE_prostate tumor specimen_68


title: Leaf-Sha-Salt+Heat-rep3

source_name: Leaf-Sha-Salt+Heat

value: Sha

value: 3 week-old

value: Salt+Heat

value: 100 mM NaCl + 38C for 3hrs


title: 150-15117/NA12878


title: FFPE_prostate tumor specimen_64


title: 150-14936/NA12878


title: Leaf-C24-Heat-rep3

value: Heat

value: 38C for 3hrs


title: Leaf-Col-Heat+High_light-rep3

value: Col

value: 38C for 3hrs + 800 µm photons m-2s-1


title: Leaf-Kas1-Salt-rep3

value: Salt

value: 100 mM NaCl for 3hrs


title: Leaf-Kyo2-High_light-rep3

value: 800 µm photons m-2s-1 for 3hrs


title: Leaf-Ler-Cold-rep3

source_name: Leaf-Ler-Cold

value: Cold

value: 10C for 3hrs


title: Leaf-An1-Ctrl-rep3

value: control plants


title: FFPE_prostate tumor specimen_63

value: Black


title: Leaf-Ler-FLG-rep3

source_name: Leaf-Ler-FLG

value: Ler

value: FLG

value: foliar spray:20 µM flagellin peptide flg22


title: 150-15048/NA18507

value: lymphoblast cell line

value: female

value: NIMH control


title: Leaf-Col-Cold+Silwet-rep3

source_name: Leaf-Col-Cold+Silwet

value: 3 week-old

value: Cold+Silwet

value: 10C for 3hrs + silwet detergent used for flagellin application

value: leaves


title: Leaf-Col-Salt+Heat-rep3

source_name: Leaf-Col-Salt+Heat

value: Col

value: Salt+Heat

value: 100 mM NaCl + 38C for 3hrs


title: FFPE_prostate tumor specimen_61

source_name: prostate tumor


title: FFPE_prostate tumor specimen_62


title: Leaf-Kas1-High_light-rep2

value: 800 µm photons m-2s-1 for 3hrs


title: 150-10210/NA12878

value: male


title: FFPE_prostate tumor specimen_60

value: White


title: Leaf-An1-Heat-rep2

value: Heat

value: 38C for 3hrs


title: Leaf-Kyo2-Salt-rep2

value: Salt

value: 100 mM NaCl for 3hrs


title: Leaf-Cvi-Cold-rep2

value: Cvi

value: Cold

value: 10C for 3hrs


title: 150-14368/NA18507

value: lymphoblast cell line

value: female

value: NIMH control


title: FFPE_prostate tumor specimen_59


title: Leaf-Kyo2-High_light-rep2

value: 3 week-old

value: leaves


title: Leaf-Ler-Heat+FLG+Silwet-rep2

value: Ler

value: Heat+FLG+Silwet

value: 38C for 3hrs + foliar spray:20 µM flagellin peptide flg22


title: Leaf-Col-Heat+High_light-rep2

value: Col

value: 38C for 3hrs + 800 µm photons m-2s-1


title: FFPE_prostate tumor specimen_58

value: Black


title: FFPE_prostate tumor specimen_57

value: White


title: Leaf-Ler-Cold-rep2


title: Leaf-Sha-Salt+Heat-rep2

value: Sha

value: Salt+Heat

value: 100 mM NaCl + 38C for 3hrs


title: Leaf-Kas1-Salt-rep2

value: Salt

value: 100 mM NaCl for 3hrs


title: Leaf-C24-Heat-rep2

value: Heat

value: 38C for 3hrs


title: FFPE_prostate tumor specimen_56


title: Leaf-An1-Ctrl-rep2

value: control plants


title: Leaf-Col-Cold+Silwet-rep2

value: 3 week-old

value: Cold+Silwet

value: 10C for 3hrs + silwet detergent used for flagellin application


title: 150-13797/NA12878

value: lymphoblast cell line

value: male

value: NIMH control


title: FFPE_prostate tumor specimen_55


title: Leaf-Col-Salt+Heat-rep2

value: Col

value: leaves


title: Leaf-Ler-FLG-rep2

value: Ler

value: FLG

value: foliar spray:20 µM flagellin peptide flg22


title: 150-13937/NA18507

value: female


title: 150-14706/NA12878


title: Leaf-Sha-Cold-rep2

source_name: Leaf-Sha-Cold

value: Sha

value: Cold

value: 10C for 3hrs


title: 150-11613/NA12878


title: FFPE_prostate tumor specimen_54

value: White


title: 150-12633/NA12878


title: Leaf-C24-Ctrl-rep2

value: control plants


title: FFPE_prostate tumor specimen_53


title: Leaf-Cvi-Salt-rep2

source_name: Leaf-Cvi-Salt

value: Cvi

value: 3 week-old

value: Salt

value: 100 mM NaCl for 3hrs


title: 150-14499/NA12878

value: lymphoblast cell line

value: male


title: Leaf-Eri-Ctrl-rep2

source_name: Leaf-Eri-Ctrl

value: Eri


title: Leaf-Col-Heat+FLG+Silwet-rep2

source_name: Leaf-Col-Heat+FLG+Silwet

value: Col

value: Heat+FLG+Silwet

value: 38C for 3hrs + foliar spray:20 µM flagellin peptide flg22

value: leaves


title: Leaf-Kond-Heat-rep2

source_name: Leaf-Kond-Heat

value: Kond

value: Heat

value: 38C for 3hrs


title: Leaf-Ler-Cold+FLG+Silwet-rep2

source_name: Leaf-Ler-Cold+FLG+Silwet

value: Ler

value: Cold+FLG+Silwet

value: 10C 3hrs + 20 µM flagellin peptide flg22 spray


title: 150-13812/NA18507

source_name: lymphoblast cell line DNA

value: female

value: NIMH control


title: Leaf-Cvi-High_light-rep2

value: Cvi

value: 3 week-old

value: 800 µm photons m-2s-1 for 3hrs


title: 150-11620/NA12878

value: lymphoblast cell line

value: male


title: 150-12384/NA12878


title: FFPE_prostate tumor specimen_52

value: Black


title: FFPE_prostate tumor specimen_51


title: FFPE_prostate tumor specimen_50


title: FFPE_prostate tumor specimen_49

value: White


title: Leaf-An1-Salt+Heat-rep2

value: Salt+Heat

value: 100 mM NaCl + 38C for 3hrs


title: Leaf-Ler-Salt-rep2

source_name: Leaf-Ler-Salt

value: Salt

value: 100 mM NaCl for 3hrs

value: leaves


title: Leaf-Ler-High_light-rep2

value: Ler


title: FFPE_prostate tumor specimen_48


title: 150-13652/NA18507


title: Leaf-Kond-Ctrl-rep2

source_name: Leaf-Kond-Ctrl

value: Kond

value: control plants


title: Leaf-Kas1-Heat-rep2

value: Heat

value: 38C for 3hrs


title: 150-12352/NA12878

value: NIMH control


title: Leaf-Eri-Heat-rep2

source_name: Leaf-Eri-Heat

value: Eri

value: 3 week-old


title: Leaf-An1-Cold-rep2

value: Cold

value: 10C for 3hrs


title: 150-10675/NA12878

value: lymphoblast cell line

value: male


title: Leaf-Sha-Salt-rep2

source_name: Leaf-Sha-Salt

value: Sha


title: 150-12609/NA12878


title: FFPE_prostate tumor specimen_47

value: White


title: Leaf-Kond-Salt+Heat-rep2

source_name: Leaf-Kond-Salt+Heat

value: Salt+Heat

value: 100 mM NaCl + 38C for 3hrs


title: Leaf-Kyo2-Ctrl-rep2

value: leaves


title: FFPE_prostate tumor specimen_45


title: FFPE_prostate tumor specimen_44


title: Leaf-Sha-High_light-rep2

value: 800 µm photons m-2s-1 for 3hrs


title: 150-10931/NA12878


title: Leaf-Col-Cold+FLG+Silwet-rep2

source_name: Leaf-Col-Cold+FLG+Silwet

value: Col

value: Cold+FLG+Silwet

value: 10C 3hrs + 20 µM flagellin peptide flg22 spray


title: FFPE_prostate tumor specimen_43

value: Black


title: Leaf-Kyo2-Heat-rep2

value: Heat

value: 38C for 3hrs


title: Leaf-Ler-Cold+High_light-rep2

value: Ler

value: 3 week-old

value: 10C for 3hrs + heat from 3 sodium lamps was displaced by circulating fans and a plexiglass shield and ambient plant temperature maintained by ice trays and monitored at 10°C


title: Leaf-C24-Cold-rep2

value: Cold

value: 10C for 3hrs


title: Leaf-Col-Salt-rep2

source_name: Leaf-Col-Salt

value: Salt

value: 100 mM NaCl for 3hrs


title: 150-11102/NA12878

value: lymphoblast cell line

value: male

value: NIMH control


title: 150-11037/NA12878


title: 150-11172/NA12878


title: Leaf-Col-FLG-rep2

source_name: Leaf-Col-FLG

value: FLG

value: foliar spray:20 µM flagellin peptide flg22

value: leaves


title: 150-14369/NA12878


title: Leaf-Ler-Ctrl+Silwet-rep2

source_name: Leaf-Ler-Ctrl+Silwet

value: control plants+Silwet

value: silwet detergent used for flagellin application


title: FFPE_prostate tumor specimen_42

source_name: prostate tumor

value: Black


title: 150-14983/NA12878


title: 150-10807/NA12878


title: Leaf-Kas1-Ctrl-rep2

value: control plants


title: 150-15218/NA12878


title: FFPE_prostate tumor specimen_39


title: FFPE_prostate tumor specimen_40


title: FFPE_prostate tumor specimen_41

value: White


title: Leaf-Ler-Heat+Silwet-rep2

source_name: Leaf-Ler-Heat+Silwet

value: Ler

value: 3 week-old

value: Heat+Silwet

value: 38C for 3hrs + silwet detergent used for flagellin application


title: FFPE_prostate tumor specimen_46


title: Leaf-Col-High_light-rep2

value: Col

value: 800 µm photons m-2s-1 for 3hrs


title: 150-14852/NA12878

value: lymphoblast cell line


title: FFPE_prostate tumor specimen_38


title: Leaf-An1-Salt-rep2

value: Salt

value: 100 mM NaCl for 3hrs


title: Leaf-Cvi-Ctrl-rep2

source_name: Leaf-Cvi-Ctrl

value: Cvi


title: Leaf-Kas1-Salt+Heat-rep2

value: Salt+Heat

value: 100 mM NaCl + 38C for 3hrs


title: FFPE_prostate tumor specimen_37


title: Leaf-Col-Cold+High_light-rep2

value: 10C for 3hrs + heat from 3 sodium lamps was displaced by circulating fans and a plexiglass shield and ambient plant temperature maintained by ice trays and monitored at 10°C

value: leaves


title: Leaf-Ler-Salt+High_light-rep2

value: 100 mM NaCl + 800 µm photons m-2s-1 for 3hrs


title: 150-14763/NA12878

value: male

value: NIMH control


title: FFPE_prostate tumor specimen_36

value: White


title: Leaf-Kond-Cold-rep2

source_name: Leaf-Kond-Cold

value: Kond

value: 3 week-old

value: Cold

value: 10C for 3hrs


title: Leaf-Cvi-Heat-rep2

source_name: Leaf-Cvi-Heat

value: Heat

value: 38C for 3hrs


title: Leaf-Eri-Cold-rep2

source_name: Leaf-Eri-Cold

value: Eri


title: 150-15205/NA12878

value: lymphoblast cell line


title: FFPE_prostate tumor specimen_35

value: Black


title: Leaf-C24-Salt-rep2

value: Salt

value: 100 mM NaCl for 3hrs


title: Leaf-Ler-Ctrl-rep2

source_name: Leaf-Ler-Ctrl

value: Ler

value: control plants


title: Leaf-C24-High_light-rep2

value: 800 µm photons m-2s-1 for 3hrs

value: leaves


title: Leaf-Col-Ctrl+Silwet-rep2

source_name: Leaf-Col-Ctrl+Silwet

value: Col

value: control plants+Silwet

value: silwet detergent used for flagellin application


title: Leaf-Col-Heat+Silwet-rep2

source_name: Leaf-Col-Heat+Silwet

value: 3 week-old

value: Heat+Silwet

value: 38C for 3hrs + silwet detergent used for flagellin application


title: Leaf-An1-High_light-rep2


title: FFPE_prostate tumor specimen_34

value: White


title: FFPE_prostate tumor specimen_33


title: 150-15097/NA12878

source_name: lymphoblast cell line DNA

value: male

value: NIMH control


title: Leaf-Ler-Heat-rep2

source_name: Leaf-Ler-Heat

value: Heat

value: 38C for 3hrs


title: 150-14483/NA18507

value: lymphoblast cell line

value: female


title: Leaf-Kond-Salt-rep2

source_name: Leaf-Kond-Salt

value: Kond

value: Salt

value: 100 mM NaCl for 3hrs


title: FFPE_prostate tumor specimen_32


title: Leaf-Kas1-Cold-rep2

value: Cold

value: 10C for 3hrs

value: leaves


title: 150-14984/NA12878


title: Leaf-Sha-Ctrl-rep2

source_name: Leaf-Sha-Ctrl

value: Sha

value: control plants


title: FFPE_prostate tumor specimen_31


title: FFPE_prostate tumor specimen_30


title: Leaf-Sha-Heat-rep2

source_name: Leaf-Sha-Heat

value: 3 week-old


title: 150-14845/NA12878


title: 150-15200/NA12878


title: Leaf-Kond-High_light-rep2

value: 800 µm photons m-2s-1 for 3hrs


title: Leaf-Ler-Salt+Heat-rep2

source_name: Leaf-Ler-Salt+Heat

value: Ler

value: Salt+Heat

value: 100 mM NaCl + 38C for 3hrs


title: Leaf-Col-Salt+High_light-rep2

value: Col

value: 100 mM NaCl + 800 µm photons m-2s-1 for 3hrs


title: Leaf-Kyo2-Cold-rep2


title: FFPE_prostate tumor specimen_29

value: White


title: Leaf-Ler-Heat+High_light-rep2

value: 38C for 3hrs + 800 µm photons m-2s-1


title: FFPE_prostate tumor specimen_28

value: Black


title: Leaf-Eri-Salt-rep2

source_name: Leaf-Eri-Salt

value: Eri

value: Salt


title: 150-15241/NA12878

value: lymphoblast cell line

value: male

value: NIMH control


title: Leaf-Cvi-Salt+Heat-rep2

source_name: Leaf-Cvi-Salt+Heat

value: Cvi

value: leaves


title: Leaf-Col-Ctrl-rep2

source_name: Leaf-Col-Ctrl

value: 3 week-old

value: control plants


title: Leaf-Eri-High_light-rep2

value: 800 µm photons m-2s-1 for 3hrs


title: FFPE_prostate tumor specimen_27

source_name: prostate tumor


title: 150-15252/NA12878


title: FFPE_prostate tumor specimen_26


title: 150-15237/NA12878


title: FFPE_prostate tumor specimen_25


title: 150-15107/NA12878


title: Leaf-Kond-Salt-rep1

value: Kond

value: 100 mM NaCl for 3hrs


title: Leaf-Ler-Cold+Silwet-rep2

source_name: Leaf-Ler-Cold+Silwet

value: Ler

value: Cold+Silwet

value: 10C for 3hrs + silwet detergent used for flagellin application


title: Leaf-Sha-Ctrl-rep1

value: Sha


title: FFPE_prostate tumor specimen_24

value: Black


title: FFPE_prostate tumor specimen_23

value: White


title: Leaf-Kas1-Cold-rep1

value: Cold

value: 10C for 3hrs


title: Leaf-Sha-Heat-rep1

value: Heat

value: 38C for 3hrs


title: Leaf-Col-Heat-rep2

source_name: Leaf-Col-Heat

value: Col


title: 150-15039/NA12878

value: lymphoblast cell line

value: male

value: NIMH control


title: Leaf-Col-Salt+High_light-rep1

value: 3 week-old

value: 100 mM NaCl + 800 µm photons m-2s-1 for 3hrs

value: leaves


title: Leaf-Ler-Salt+Heat-rep1

value: Ler

value: Salt+Heat

value: 100 mM NaCl + 38C for 3hrs


title: 150-15216/NA12878


title: 150-14998/NA12878


title: 150-14919/NA12878


title: Leaf-Eri-Salt-rep1

value: Eri

value: Salt

value: 100 mM NaCl for 3hrs


title: 150-14929/NA12878


title: Leaf-Kyo2-Cold-rep1

value: Cold


title: Leaf-Kond-High_light-rep1

value: Kond

value: 800 µm photons m-2s-1 for 3hrs


title: FFPE_prostate tumor specimen_20

value: White


title: Leaf-Col-Ctrl-rep1

value: Col

value: control plants


title: 150-14821/NA12878

value: lymphoblast cell line

value: male


title: Leaf-Eri-High_light-rep1

value: 3 week-old


title: FFPE_prostate tumor specimen_21

value: Black


title: 150-14772/NA12878

value: NIMH control


title: Leaf-Cvi-Salt+Heat-rep1

value: Cvi

value: leaves


title: FFPE_prostate tumor specimen_22


title: Leaf-Kas1-Salt-rep1


title: Leaf-Col-Heat-rep1

value: Heat

value: 38C for 3hrs


title: Leaf-Ler-Cold+Silwet-rep1

value: Ler

value: Cold+Silwet

value: 10C for 3hrs + silwet detergent used for flagellin application


title: FFPE_prostate tumor specimen_19


title: 150-14730/NA12878


title: 150-15201/NA12878


title: FFPE_prostate tumor specimen_18


title: FFPE_prostate tumor specimen_16


title: FFPE_prostate tumor specimen_17


title: Leaf-Kas1-High_light-rep1


title: 150-14587/NA12878


title: Leaf-Col-Salt+Heat-rep1

source_name: Leaf-Col-Salt+Heat

value: Salt+Heat

value: 100 mM NaCl + 38C for 3hrs


title: Leaf-Cvi-Cold-rep1

source_name: Leaf-Cvi-Cold

value: Cold

value: 10C for 3hrs


title: Leaf-Kyo2-Salt-rep1

value: Salt

value: 100 mM NaCl for 3hrs


title: Leaf-An1-Ctrl-rep1

value: control plants


title: Leaf-An1-Heat-rep1

value: 3 week-old


title: Leaf-Ler-FLG-rep1

source_name: Leaf-Ler-FLG

value: FLG

value: foliar spray:20 µM flagellin peptide flg22


title: 150-10107/NA12878

value: lymphoblast cell line

value: male

value: NIMH control


title: FFPE_prostate tumor specimen_14

value: White


title: FFPE_prostate tumor specimen_15

value: Black