title: Susceptible rice at 6d after inoculation with Xanthomonas oryzae T-7174R::deltahrcV (Exp2-1)

status: Public on Apr 01 2015

first: Eiichi

last: Minami

address: 2-1-2 Kannondai

institute: National Institute of Agrobiological Sciences

description: Gene expression in the leaf sections of rice at 6d after inoculation with X. oryzae (△hrcV) (Exp2-1)

hyb_protocol: Cy3-labeled cRNA (1650 ng) was fragmented and hybridized at 65°C for 17 haccording to the manufacture's protocol.

scan_protocol: Slides were scanned on an Agilent G2505B DNA microarray scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters to obtain background subtracted.

organism: Oryza sativa

source_name: 8 to 10th leaves

label_protocol: Total RNA (400 ng) was labeled with cy3 using Quick Amp Labeling Kit, One-Color (Agilent).

growth_protocol: Rice plants were grown in a greenhouse for 42 days.

extract_protocol: Leaf segments beneath inoculated site (3 to 5mm in length) were collected and total RNA was extracted by using RNeasy Plant Mini kit (Quiagen, #74904).

treatment_protocol: Xanthomonas oryzae (strains T7174R and its mutant deficient in type III secretion system, △hrcV) was inoculated by clippig method on 8th to 10th leaves.

tag: cultivar

value: Nipponbare

value: 8 to 10th leaves

tag: inoculation

value: Xanthomonas oryzae T-7174R::deltahrcV

tag: time point


title: Ecell-H2LNex

status: Public on Apr 02 2015

type: RNA

city: Tokyo

first: Naoomi

last: Tominaga

address: 5-1-1 Tsukiji, Chuo-ku

country: Japan

institute: National Cancer Center Research institute

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028520) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: total RNA

organism: Macaca fascicularis

label_protocol: Agilent one-color Low RNA Input Linear Amplification Kit labeling protocol

extract_protocol: Total RNA was extracted from cultured cells using the QIAzol reagent and the miRNeasy Mini Kit (Qiagen)

treatment_protocol: mRNA expression in brain endothelial cells was treated with negative control miRNA or miR-181c mimic and or with extracellular vesicles from MDA-MB-231-D3H1, MDA-MB-231-D3H2LN, BMD2a and BMD2b breast cancer cell lines.

tag: tissue

value: brain

tag: cell type

value: endothelial cells

tag: treatment

value: extracellular vesicles from LN breast cancer cell line


title: Susceptible rice at 6d after inoculation with Xanthomonas oryzae T-7174R::deltahrcV (Exp1-3)

city: Tsukuba

description: Gene expression in the leaf sections of rice at 6d after inoculation with X. oryzae (△hrcV) (Exp1-3)


title: Ecell-H1ex

value: extracellular vesicles from H1 breast cancer cell line


title: Susceptible rice at 6d after inoculation with Xanthomonas oryzae T-7174R::deltahrcV (Exp2-2)

description: Gene expression in the leaf sections of rice at 6d after inoculation with X. oryzae (△hrcV) (Exp2-2)


title: Susceptible rice at 6d after inoculation with Xanthomonas oryzae T-7174R::deltahrcV (Exp1-1)

description: Gene expression in the leaf sections of rice at 6d after inoculation with X. oryzae (△hrcV) (Exp1-1)


title: Ecell-PBS

source_name: Ecell-PBS

value: PBS


title: Idiopathic Dilated Cardiomyopathy 2

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

department: Medicine

country: USA

institute: Vanderbilt University

description: IDCC 2

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

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.

label: biotin

organism: Homo sapiens

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: Obtained from patients at autopsy

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

tag: subject status

value: idiopathic dilated cardiomyopathy (IDC)

value: heart right ventricular wall


title: Susceptible rice at 6d after inoculation with Xanthomonas oryzae T-7174R::deltahrcV (Exp1-2)

description: Gene expression in the leaf sections of rice at 6d after inoculation with X. oryzae (△hrcV) (Exp1-2)


title: Susceptible rice at 6d after inoculation with Xanthomonas oryzae T-7174R (Exp2-1)

description: Gene expression in the leaf sections of rice at 6d after inoculation with X. oryzae (WT) (Exp2-1)

value: Xanthomonas oryzae T-7174R


title: Susceptible rice at 6d after inoculation with Xanthomonas oryzae T-7174R (Exp1-2)

description: Gene expression in the leaf sections of rice at 6d after inoculation with X. oryzae (WT) (Exp1-2)


title: Susceptible rice at 6d after inoculation with Xanthomonas oryzae T-7174R (Exp1-3)

description: Gene expression in the leaf sections of rice at 6d after inoculation with X. oryzae (WT) (Exp1-3)


title: Susceptible rice at 6d after treatment with water (Exp2)

description: Gene expression in the leaf sections of rice at 6d after mock-inoculation (Exp2)

value: water


title: Susceptible rice at 6d after inoculation with Xanthomonas oryzae T-7174R (Exp1-1)

description: Gene expression in the leaf sections of rice at 6d after inoculation with X. oryzae (WT) (Exp1-1)


title: Susceptible rice at 4d after inoculation with Xanthomonas oryzae T-7174R::deltahrcV (Exp2-1)

description: Gene expression in the leaf sections of rice at 4d after inoculation with X. oryzae (△hrcV) (Exp2-1)


title: Susceptible rice at 6d after treatment with water (Exp1)

description: Gene expression in the leaf sections of rice at 6d after mock-inoculation (Exp1)


title: Susceptible rice at 6d after inoculation with Xanthomonas oryzae T-7174R (Exp2-2)

description: Gene expression in the leaf sections of rice at 6d after inoculation with X. oryzae (WT) (Exp2-2)


title: Susceptible rice at 4d after inoculation with Xanthomonas oryzae T-7174R::deltahrcV (Exp2-2)

description: Gene expression in the leaf sections of rice at 4d after inoculation with X. oryzae (△hrcV) (Exp2-2)


title: Susceptible rice at 4d after inoculation with Xanthomonas oryzae T-7174R::deltahrcV (Exp1-3)

description: Gene expression in the leaf sections of rice at 4d after inoculation with X. oryzae (△hrcV) (Exp1-3)


title: Susceptible rice at 4d after inoculation with Xanthomonas oryzae T-7174R (Exp2-2)

description: Gene expression in the leaf sections of rice at 4d after inoculation with X. oryzae (WT) (Exp2-2)


title: Susceptible rice at 4d after inoculation with Xanthomonas oryzae T-7174R::deltahrcV (Exp1-2)

description: Gene expression in the leaf sections of rice at 4d after inoculation with X. oryzae (△hrcV) (Exp1-2)


title: Susceptible rice at 4d after inoculation with Xanthomonas oryzae T-7174R::deltahrcV (Exp1-1)

description: Gene expression in the leaf sections of rice at 4d after inoculation with X. oryzae (△hrcV) (Exp1-1)


title: Susceptible rice at 4d after inoculation with Xanthomonas oryzae T-7174R (Exp2-1)

description: Gene expression in the leaf sections of rice at 4d after inoculation with X. oryzae (WT) (Exp2-1)


title: Susceptible rice at 2d after inoculation with Xanthomonas oryzae T-7174R::deltahrcV (Exp1-2)

description: Gene expression in the leaf sections of rice at 2d after inoculation with X. oryzae (△hrcV) (Exp1-2)


city: Malaga

first: Rafael

middle: A

last: Cañas

address: Facultad de Ciencias, Campus de Teatinos

department: Biología Molecular y Bioquímica

country: Spain

institute: Universidad de Málaga

description:
10mM WT vs 50mM WT technical replicate 2 biological replicate 2
10mM_WTvs50mMWT_2b

hyb_protocol: Hybridization and slide washing were performed accoding to the manufacturer´s protocol Low Input Quick Amp Labelling Kit - two colour (Agilent Technologies; cat#5190-2306)

scan_protocol: Scanned using GenePix 4100A scanner with a resolution of 5 µm/pixel. Data were extracted from the scanned images using the GenePix v6.0 software.

data_processing: Normalization and differential expression analysis of the data was done using limma R package (Smyth 2004). Normalization was carried out using quantile method and Bayes statistics were applied to determine the differential expression between the comparisons. Statistical significance was corrected for multiple testing using the Benjamini-Hochberg procedure. Genes were declared as differentially expressed with adjusted p-value < 0.05 and log FC 1

organism: Populus tremula x Populus alba

source_name: 50mM WT leaves

label_protocol: 200 ng of total RNA was used for each sample. Microarray labelling was performed accoding to the manufacturer´s protocol Low Input Quick Amp Labelling Kit - two colour (Agilent Technologies; cat#5190-2306)

growth_protocol: Untransformed (WT) hybrid poplar (Populus tremula x P. alba, clone INRA 7171-B, Institut National de la Recherche Agronomique, INRA) and a transgenic line overexpressing a glutamine synthetase cytosolic pine (GS1a) under the control of cauliflower mosaic virus 35S promoter (CaMV35S) were produced and maintained in vitro as previously described (Fu et al. 2003. Plant Cell Environ. 26:411-418). Rooted shoots of transformed and WT plants were maintained in plant growth chambers with a photoperiod of 16 h light with light intensity of 295 μmol m2 s-1, a constant temperature 24°C and 80% humidity. Plants were cultivated in plastic pots containing a potting mix and vermiculite in proportions 1:1 and watered with distilled water supplemented with macro and micronutrients for optimal growth (Jing et al. 2004. New Phytol. 164:137-145).

extract_protocol: Total RNA extracted as described by Canales el al. (2010) Amino Acids 39:991-1001.

treatment_protocol: After 8 weeks of growth, plants with similar height (approximately 60 cm) were divided by genotype: Untransformed controls and transgenic poplars (24 individuals per genotype) and each group of plants were then subdivided randomly into 2 groups. One of the groups was irrigated with a nutrient solution enriched with 10 mM nitrate. The remaining group of plants was supplied with 50 mM nitrate. The plants were watered with the nutrient solution once a week by flooding, for a total of 4 weeks. At the end of the growing period plants were harvested.

tag: genotype/variation

value: WT (untransformed)

value: leaves

tag: nutrition

value: 50mM Nitrate

source_name: 10mM WT leaves

value: 10mM Nitrate


title: Susceptible rice at 4d after inoculation with Xanthomonas oryzae T-7174R (Exp1-3)

description: Gene expression in the leaf sections of rice at 4d after inoculation with X. oryzae (WT) (Exp1-3)


title: Susceptible rice at 2d after inoculation with Xanthomonas oryzae T-7174R::deltahrcV (Exp1-1)

description: Gene expression in the leaf sections of rice at 2d after inoculation with X. oryzae (△hrcV) (Exp1-1)


title: Susceptible rice at 2d after inoculation with Xanthomonas oryzae T-7174R::deltahrcV (Exp2-1)

description: Gene expression in the leaf sections of rice at 2d after inoculation with X. oryzae (△hrcV) (Exp2-1)


title: Susceptible rice at 2d after inoculation with Xanthomonas oryzae T-7174R::deltahrcV (Exp2-2)

description: Gene expression in the leaf sections of rice at 2d after inoculation with X. oryzae (△hrcV) (Exp2-2)


title: Susceptible rice at 2d after inoculation with Xanthomonas oryzae T-7174R (Exp1-1)

description: Gene expression in the leaf sections of rice at 2d after inoculation with X. oryzae (WT) (Exp1-1)


title: Susceptible rice at 2d after inoculation with Xanthomonas oryzae T-7174R (Exp2-2)

description: Gene expression in the leaf sections of rice at 2d after inoculation with X. oryzae (WT) (Exp2-2)


title: Susceptible rice at 4d after treatment with water (Exp1)

description: Gene expression in the leaf sections of rice at 4d after mock-inoculation (Exp1)


title: Susceptible rice at 2d after inoculation with Xanthomonas oryzae T-7174R::deltahrcV (Exp1-3)

description: Gene expression in the leaf sections of rice at 2d after inoculation with X. oryzae (△hrcV) (Exp1-3)


title: Susceptible rice at 4d after treatment with water (Exp2)

description: Gene expression in the leaf sections of rice at 4d after mock-inoculation (Exp2)


title: Susceptible rice at 2d after inoculation with Xanthomonas oryzae T-7174R (Exp1-2)

description: Gene expression in the leaf sections of rice at 2d after inoculation with X. oryzae (WT) (Exp1-2)


title: Susceptible rice at 4d after inoculation with Xanthomonas oryzae T-7174R (Exp1-1)

description: Gene expression in the leaf sections of rice at 4d after inoculation with X. oryzae (WT) (Exp1-1)


title: Susceptible rice at 2d after inoculation with Xanthomonas oryzae T-7174R (Exp1-3)

description: Gene expression in the leaf sections of rice at 2d after inoculation with X. oryzae (WT) (Exp1-3)


title: Susceptible rice at 4d after inoculation with Xanthomonas oryzae T-7174R (Exp1-2)

description: Gene expression in the leaf sections of rice at 4d after inoculation with X. oryzae (WT) (Exp1-2)


title: Susceptible rice at 2d after treatment with water (Exp2)

description: Gene expression in the leaf sections of rice at 2d after mock-inoculation (Exp2)


title: Susceptible rice at 2d after inoculation with Xanthomonas oryzae T-7174R (Exp2-1)

description: Gene expression in the leaf sections of rice at 2d after inoculation with X. oryzae (WT) (Exp2-1)


title: Susceptible rice at 1d after inoculation with Xanthomonas oryzae T-7174R::deltahrcV (Exp2-1)

description: Gene expression in the leaf sections of rice at 1d after inoculation with X. oryzae (△hrcV) (Exp2-1)


title: Susceptible rice at 2d after treatment with water (Exp1)

description: Gene expression in the leaf sections of rice at 2d after mock-inoculation (Exp1)


title: Susceptible rice at 1d after inoculation with Xanthomonas oryzae T-7174R (Exp2-2)

description: Gene expression in the leaf sections of rice at 1d after inoculation with X. oryzae (WT) (Exp2-2)


title: Susceptible rice at 1d after treatment with water (Exp2)

description: Gene expression in the leaf sections of rice at 1d after mock-inoculation (Exp2)


title: Susceptible rice at 1d after inoculation with Xanthomonas oryzae T-7174R (Exp2-1)

description: Gene expression in the leaf sections of rice at 1d after inoculation with X. oryzae (WT) (Exp2-1)


title: Susceptible rice at 1d after inoculation with Xanthomonas oryzae T-7174R (Exp1-3)

description: Gene expression in the leaf sections of rice at 1d after inoculation with X. oryzae (WT) (Exp1-3)


title: Susceptible rice at 1d after treatment with water (Exp1)

description: Gene expression in the leaf sections of rice at 1d after mock-inoculation (Exp1)


title: Susceptible rice at 1d after inoculation with Xanthomonas oryzae T-7174R::deltahrcV (Exp1-1)

description: Gene expression in the leaf sections of rice at 1d after inoculation with X. oryzae (△hrcV) (Exp1-1)


title: Susceptible rice at 1d after inoculation with Xanthomonas oryzae T-7174R::deltahrcV (Exp2-2)

description: Gene expression in the leaf sections of rice at 1d after inoculation with X. oryzae (△hrcV) (Exp2-2)


title: Susceptible rice at 1d after inoculation with Xanthomonas oryzae T-7174R::deltahrcV (Exp1-3)

description: Gene expression in the leaf sections of rice at 1d after inoculation with X. oryzae (△hrcV) (Exp1-3)


title: Susceptible rice at 1d after inoculation with Xanthomonas oryzae T-7174R::deltahrcV (Exp1-2)

description: Gene expression in the leaf sections of rice at 1d after inoculation with X. oryzae (△hrcV) (Exp1-2)


title: Susceptible rice at 1d after inoculation with Xanthomonas oryzae T-7174R (Exp1-1)

description: Gene expression in the leaf sections of rice at 1d after inoculation with X. oryzae (WT) (Exp1-1)


title: Susceptible rice at 12h after inoculation with Xanthomonas oryzae T-7174R::deltahrcV (Exp1-2)

description: Gene expression in the leaf sections of rice at 12h after inoculation with X. oryzae (△hrcV) (Exp1-2)


title: Susceptible rice at 12h after inoculation with Xanthomonas oryzae T-7174R::deltahrcV (Exp1-3)

description: Gene expression in the leaf sections of rice at 12h after inoculation with X. oryzae (△hrcV) (Exp1-3)


title: Susceptible rice at 12h after inoculation with Xanthomonas oryzae T-7174R::deltahrcV (Exp1-1)

description: Gene expression in the leaf sections of rice at 12h after inoculation with X. oryzae (△hrcV) (Exp1-1)


title: Susceptible rice at 12h after inoculation with Xanthomonas oryzae T-7174R (Exp2-2)

description: Gene expression in the leaf sections of rice at 12h after inoculation with X. oryzae (WT) (Exp2-2)


title: Susceptible rice at 12h after inoculation with Xanthomonas oryzae T-7174R::deltahrcV (Exp2-2)

description: Gene expression in the leaf sections of rice at 12h after inoculation with X. oryzae (△hrcV) (Exp2-2)


title: Susceptible rice at 1d after inoculation with Xanthomonas oryzae T-7174R (Exp1-2)

description: Gene expression in the leaf sections of rice at 1d after inoculation with X. oryzae (WT) (Exp1-2)


title: Susceptible rice at 12h after inoculation with Xanthomonas oryzae T-7174R (Exp2-1)

description: Gene expression in the leaf sections of rice at 12h after inoculation with X. oryzae (WT) (Exp2-1)


title: Susceptible rice at 12h after inoculation with Xanthomonas oryzae T-7174R::deltahrcV (Exp2-1)

description: Gene expression in the leaf sections of rice at 12h after inoculation with X. oryzae (△hrcV) (Exp2-1)


title: Susceptible rice at 12h after inoculation with Xanthomonas oryzae T-7174R (Exp1-2)

description: Gene expression in the leaf sections of rice at 12h after inoculation with X. oryzae (WT) (Exp1-2)


title: Susceptible rice at 12h after inoculation with Xanthomonas oryzae T-7174R (Exp1-1)

description: Gene expression in the leaf sections of rice at 12h after inoculation with X. oryzae (WT) (Exp1-1)


title: Susceptible rice at 12h after treatment with water (Exp2)

description: Gene expression in the leaf sections of rice at 12h after mock-inoculation (Exp2)


title: Susceptible rice at 6h after inoculation with Xanthomonas oryzae T-7174R::deltahrcV (Exp2-1)

description: Gene expression in the leaf sections of rice at 6h after inoculation with X. oryzae (△hrcV) (Exp2-1)


title: Susceptible rice at 6h after inoculation with Xanthomonas oryzae T-7174R::deltahrcV (Exp2-2)

description: Gene expression in the leaf sections of rice at 6h after inoculation with X. oryzae (△hrcV) (Exp2-2)


title: Susceptible rice at 6h after inoculation with Xanthomonas oryzae T-7174R::deltahrcV (Exp1-1)

description: Gene expression in the leaf sections of rice at 6h after inoculation with X. oryzae (△hrcV) (Exp1-1)


title: Susceptible rice at 12h after inoculation with Xanthomonas oryzae T-7174R (Exp1-3)

description: Gene expression in the leaf sections of rice at 12h after inoculation with X. oryzae (WT) (Exp1-3)


title: Susceptible rice at 6h after inoculation with Xanthomonas oryzae T-7174R::deltahrcV (Exp1-2)

description: Gene expression in the leaf sections of rice at 6h after inoculation with X. oryzae (△hrcV) (Exp1-2)


title: Susceptible rice at 6h after treatment with water (Exp2)

description: Gene expression in the leaf sections of rice at 6h after mock-inoculation (Exp2)


title: Susceptible rice at 6h after inoculation with Xanthomonas oryzae T-7174R (Exp2-2)

description: Gene expression in the leaf sections of rice at 6h after inoculation with X. oryzae (WT) (Exp2-2)


title: Susceptible rice at 12h after treatment with water (Exp1)

description: Gene expression in the leaf sections of rice at 12h after mock-inoculation (Exp1)


title: Susceptible rice at 6h after treatment with water (Exp1)

description: Gene expression in the leaf sections of rice at 6h after mock-inoculation (Exp1)


title: Susceptible rice at 6h after inoculation with Xanthomonas oryzae T-7174R (Exp1-2)

description: Gene expression in the leaf sections of rice at 6h after inoculation with X. oryzae (WT) (Exp1-2)


title: Susceptible rice at 3h after inoculation with Xanthomonas oryzae T-7174R::deltahrcV (Exp2-2)

description: Gene expression in the leaf sections of rice at 3h after inoculation with X. oryzae (△hrcV) (Exp2-2)


title: Susceptible rice at 3h after inoculation with Xanthomonas oryzae T-7174R::deltahrcV (Exp1-3)

description: Gene expression in the leaf sections of rice at 3h after inoculation with X. oryzae (△hrcV) (Exp1-3)


title: Susceptible rice at 6h after inoculation with Xanthomonas oryzae T-7174R (Exp1-3)

description: Gene expression in the leaf sections of rice at 6h after inoculation with X. oryzae (WT) (Exp1-3)


title: Susceptible rice at 3h after inoculation with Xanthomonas oryzae T-7174R::deltahrcV (Exp1-1)

description: Gene expression in the leaf sections of rice at 3h after inoculation with X. oryzae (△hrcV) (Exp1-1)


title: Susceptible rice at 6h after inoculation with Xanthomonas oryzae T-7174R::deltahrcV (Exp1-3)

description: Gene expression in the leaf sections of rice at 6h after inoculation with X. oryzae (△hrcV) (Exp1-3)


title: Susceptible rice at 3h after inoculation with Xanthomonas oryzae T-7174R::deltahrcV (Exp2-1)

description: Gene expression in the leaf sections of rice at 3h after inoculation with X. oryzae (△hrcV) (Exp2-1)


title: Susceptible rice at 6h after inoculation with Xanthomonas oryzae T-7174R (Exp2-1)

description: Gene expression in the leaf sections of rice at 6h after inoculation with X. oryzae (WT) (Exp2-1)


title: Susceptible rice at 3h after inoculation with Xanthomonas oryzae T-7174R::deltahrcV (Exp1-2)

description: Gene expression in the leaf sections of rice at 3h after inoculation with X. oryzae (△hrcV) (Exp1-2)


title: Susceptible rice at 6h after inoculation with Xanthomonas oryzae T-7174R (Exp1-1)

description: Gene expression in the leaf sections of rice at 6h after inoculation with X. oryzae (WT) (Exp1-1)


title: Susceptible rice at 3h after inoculation with Xanthomonas oryzae T-7174R (Exp1-3)

description: Gene expression in the leaf sections of rice at 3h after inoculation with X. oryzae (WT) (Exp1-3)


title: Susceptible rice at 3h after inoculation with Xanthomonas oryzae T-7174R (Exp2-1)

description: Gene expression in the leaf sections of rice at 3h after inoculation with X. oryzae (WT) (Exp2-1)


title: Susceptible rice at 3h after treatment with water (Exp2)

description: Gene expression in the leaf sections of rice at 3h after mock-inoculation (Exp2)


title: Susceptible rice at 3h after inoculation with Xanthomonas oryzae T-7174R (Exp2-2)

description: Gene expression in the leaf sections of rice at 3h after inoculation with X. oryzae (WT) (Exp2-2)


title: WR_Pia-Exp3-S3dH2O

description:
Susceptible rice at 3 days after treatment with H2O (Exp3)
Gene expression in the fourth leaves of rice (pia) at 3 days after treatment with water

growth_protocol: Rice seeds were germinated for 5 to 6 days and grown on steel mesh in plant box under 14 h light (28°C) / 10 h dark (24°C) for 2 days. After inoculation, crown roots were harvested at 1,2,3, and 5 dpi.

extract_protocol: RNeasy Plant Mini kit (Quiagen, #74904) was used.

treatment_protocol: Roots were soaked in the conidial suspension for 30 sec and incubated in fresh media until harvest.

value: Crown root

tag: blast resistance transgene

value: pia

tag: blast resistance phenotype

value: Susceptible

tag: inoculant


title: WR_Pia-Exp3-S1dH2O

description:
Susceptible rice at 1 day after treatment with H2O (Exp3)
Gene expression in the fourth leaves of rice (pia) at 1 day after treatment with water

value: Nipponbare


title: Susceptible rice at 3h after inoculation with Xanthomonas oryzae T-7174R (Exp1-2)

description: Gene expression in the leaf sections of rice at 3h after inoculation with X. oryzae (WT) (Exp1-2)

value: 8 to 10th leaves


title: Susceptible rice at 3h after inoculation with Xanthomonas oryzae T-7174R (Exp1-1)

description: Gene expression in the leaf sections of rice at 3h after inoculation with X. oryzae (WT) (Exp1-1)


title: WR_Pia-Exp3-S3d15B

description:
Susceptible rice at 3 days after inoculation with rice blast fungus P91-15B (Exp3)
Gene expression in the fourth leaves of rice (pia) at 3 days after inoculation with virulent line of rice blast fungus

value: virulent line of rice blast fungus


title: WR_Pia-Exp3-S5dH2O

description:
Susceptible rice at 5 days after treatment with H2O (Exp3)
Gene expression in the fourth leaves of rice (pia) at 5 days after treatment with water


title: WR_Pia-Exp2-S2dH2O

description:
Susceptible rice at 2 days after treatment with H2O (Exp2)
Gene expression in the fourth leaves of rice (pia) at 2 days after treatment with water


title: WR_Pia-Exp2-R3dH2O

description:
Resistant rice at 3 days after treatment with H2O (Exp2)
Gene expression in the fourth leaves of rice (Pia) at 3 days after treatment with water

value: Pia

value: Resistant


title: WR_Pia-Exp3-S5d15B

description:
Susceptible rice at 5 days after inoculation with rice blast fungus P91-15B (Exp3)
Gene expression in the fourth leaves of rice (pia) at 5 days after inoculation with virulent line of rice blast fungus


title: WR_Pia-Exp3-S2dH2O

description:
Susceptible rice at 2 days after treatment with H2O (Exp3)
Gene expression in the fourth leaves of rice (pia) at 2 days after treatment with water


title: WR_Pia-Exp3-S1d15B

description:
Susceptible rice at 1 day after inoculation with rice blast fungus P91-15B (Exp3)
Gene expression in the fourth leaves of rice (pia) at 1 day after inoculation with virulent line of rice blast fungus


title: WR_Pia-Exp2-S5dH2O

description:
Susceptible rice at 5 days after treatment with H2O (Exp2)
Gene expression in the fourth leaves of rice (pia) at 5 days after treatment with water


title: WR_Pia-Exp3-R2d15B

description:
Resistant rice at 2 days after inoculation with rice blast fungus P91-15B (Exp3)
Gene expression in the fourth leaves of rice (Pia) at 2 days after inoculation with avirulent line of rice blast fungus

value: avirulent line of rice blast fungus


title: WR_Pia-Exp3-R3d15B

description:
Resistant rice at 3 days after inoculation with rice blast fungus P91-15B (Exp3)
Gene expression in the fourth leaves of rice (Pia) at 3 days after inoculation with avirulent line of rice blast fungus


title: WR_Pia-Exp2-S2d15B

description:
Susceptible rice at 2 days after inoculation with rice blast fungus P91-15B (Exp2)
Gene expression in the fourth leaves of rice (pia) at 2 days after inoculation with virulent line of rice blast fungus


title: WR_Pia-Exp2-R5dH2O

description:
Resistant rice at 5 days after treatment with H2O (Exp2)
Gene expression in the fourth leaves of rice (Pia) at 5 days after treatment with water


title: WR_Pia-Exp3-R1dH2O

description:
Resistant rice at 1 day after treatment with H2O (Exp3)
Gene expression in the fourth leaves of rice (Pia) at 1 day after treatment with water


title: WR_Pia-Exp3-S2d15B

description:
Susceptible rice at 2 days after inoculation with rice blast fungus P91-15B (Exp3)
Gene expression in the fourth leaves of rice (pia) at 2 days after inoculation with virulent line of rice blast fungus


title: Susceptible rice at 3h after treatment with water (Exp1)

description: Gene expression in the leaf sections of rice at 3h after mock-inoculation (Exp1)


title: WR_Pia-Exp2-S1d15B

description:
Susceptible rice at 1 day after inoculation with rice blast fungus P91-15B (Exp2)
Gene expression in the fourth leaves of rice (pia) at 1 day after inoculation with virulent line of rice blast fungus


title: WR_Pia-Exp2-S3dH2O

description:
Susceptible rice at 3 days after treatment with H2O (Exp2)
Gene expression in the fourth leaves of rice (pia) at 3 days after treatment with water


title: WR_Pia-Exp3-R5dH2O

description:
Resistant rice at 5 days after treatment with H2O (Exp3)
Gene expression in the fourth leaves of rice (Pia) at 5 days after treatment with water


title: WR_Pia-Exp3-R2dH2O

description:
Resistant rice at 2 days after treatment with H2O (Exp3)
Gene expression in the fourth leaves of rice (Pia) at 2 days after treatment with water


title: WR_Pia-Exp2-S1dH2O

description:
Susceptible rice at 1 day after treatment with H2O (Exp2)
Gene expression in the fourth leaves of rice (pia) at 1 day after treatment with water


title: WR_Pia-Exp2-S5d15B

description:
Susceptible rice at 5 days after inoculation with rice blast fungus P91-15B (Exp2)
Gene expression in the fourth leaves of rice (pia) at 5 days after inoculation with virulent line of rice blast fungus


title: WR_Pia-Exp3-R3dH2O

description:
Resistant rice at 3 days after treatment with H2O (Exp3)
Gene expression in the fourth leaves of rice (Pia) at 3 days after treatment with water


title: WR_Pia-Exp3-R1d15B

description:
Resistant rice at 1 day after inoculation with rice blast fungus P91-15B (Exp3)
Gene expression in the fourth leaves of rice (Pia) at 1 day after inoculation with avirulent line of rice blast fungus


title: WR_Pia-Exp3-R5d15B

description:
Resistant rice at 5 days after inoculation with rice blast fungus P91-15B (Exp3)
Gene expression in the fourth leaves of rice (Pia) at 5 days after inoculation with avirulent line of rice blast fungus


title: WR_Pia-Exp2-S3d15B

description:
Susceptible rice at 3 days after inoculation with rice blast fungus P91-15B (Exp2)
Gene expression in the fourth leaves of rice (pia) at 3 days after inoculation with virulent line of rice blast fungus


title: WR_Pia-Exp2-R2dH2O

description:
Resistant rice at 2 days after treatment with H2O (Exp2)
Gene expression in the fourth leaves of rice (Pia) at 2 days after treatment with water


title: WR_Pia-Exp2-R1dH2O

description:
Resistant rice at 1 day after treatment with H2O (Exp2)
Gene expression in the fourth leaves of rice (Pia) at 1 day after treatment with water


title: WR_Pia-Exp2-R5d15B

description:
Resistant rice at 5 days after inoculation with rice blast fungus P91-15B (Exp2)
Gene expression in the fourth leaves of rice (Pia) at 5 days after inoculation with avirulent line of rice blast fungus


title: WR_Pia-Exp2-R3d15B

description:
Resistant rice at 3 days after inoculation with rice blast fungus P91-15B (Exp2)
Gene expression in the fourth leaves of rice (Pia) at 3 days after inoculation with avirulent line of rice blast fungus


title: WR_Pia-Exp2-R1d15B

description:
Resistant rice at 1 day after inoculation with rice blast fungus P91-15B (Exp2)
Gene expression in the fourth leaves of rice (Pia) at 1 day after inoculation with avirulent line of rice blast fungus


title: WR_Pia-Exp1-R5dH2O

description:
Resistant rice at 5 days after treatment with H2O (Exp1)
Gene expression in the fourth leaves of rice (Pia) at 5 days after treatment with water


title: WR_Pia-Exp1-S2dH2O

description:
Susceptible rice at 2 days after treatment with H2O (Exp1)
Gene expression in the fourth leaves of rice (pia) at 2 days after treatment with water


title: WR_Pia-Exp1-S5dH2O

description:
Susceptible rice at 5 days after treatment with H2O (Exp1)
Gene expression in the fourth leaves of rice (pia) at 5 days after treatment with water


title: WR_Pia-Exp1-R3d15B

description:
Resistant rice at 3 days after inoculation with rice blast fungus P91-15B (Exp1)
Gene expression in the fourth leaves of rice (Pia) at 3 days after inoculation with avirulent line of rice blast fungus


title: WR_Pia-Exp1-S1d15B

description:
Susceptible rice at 1 day after inoculation with rice blast fungus P91-15B (Exp1)
Gene expression in the fourth leaves of rice (pia) at 1 day after inoculation with virulent line of rice blast fungus


title: WL_Pish-Exp3-S5dH2O

description:
Susceptible rice at 5 days after treatment with H2O (Exp3)
Gene expression in the fourth leaves of rice (pish) at 5 days after treatment with water

growth_protocol: Rice seedlings at 4.5 leaf stage were grown in a chamber under 14 h light (28C) and 10 h dark (24C).

treatment_protocol: Conidia suspension of rice blast fungus (1 × 106/mL) was sprayed on the fourth leaves of rice plants, which was harvested at 1, 2, 3, and 5 days after inoculation.

value: Fourth leaves

value: pish


title: WR_Pia-Exp1-S5d15B

description:
Susceptible rice at 5 days after inoculation with rice blast fungus P91-15B (Exp1)
Gene expression in the fourth leaves of rice (pia) at 5 days after inoculation with virulent line of rice blast fungus


title: WR_Pia-Exp1-R5d15B

description:
Resistant rice at 5 days after inoculation with rice blast fungus P91-15B (Exp1)
Gene expression in the fourth leaves of rice (Pia) at 5 days after inoculation with avirulent line of rice blast fungus


title: WR_Pia-Exp1-S1dH2O

description:
Susceptible rice at 1 day after treatment with H2O (Exp1)
Gene expression in the fourth leaves of rice (pia) at 1 day after treatment with water


title: WR_Pia-Exp1-R1d15B

description:
Resistant rice at 1 day after inoculation with rice blast fungus P91-15B (Exp1)
Gene expression in the fourth leaves of rice (Pia) at 1 day after inoculation with avirulent line of rice blast fungus


title: WR_Pia-Exp2-R2d15B

description:
Resistant rice at 2 days after inoculation with rice blast fungus P91-15B (Exp2)
Gene expression in the fourth leaves of rice (Pia) at 2 days after inoculation with avirulent line of rice blast fungus


title: WR_Pia-Exp1-S2d15B

description:
Susceptible rice at 2 days after inoculation with rice blast fungus P91-15B (Exp1)
Gene expression in the fourth leaves of rice (pia) at 2 days after inoculation with virulent line of rice blast fungus


title: WL_Pish-Exp3-S2dH2O

description:
Susceptible rice at 2 days after treatment with H2O (Exp3)
Gene expression in the fourth leaves of rice (pish) at 2 days after treatment with water


title: WL_Pish-Exp3-S5d77

description:
Susceptible rice at 5 days after inoculation with rice blast fungus Kyu77-07A (Exp3)
Gene expression in the fourth leaves of rice (pish) at 5 days after inoculation with virulent line of rice blast fungus


title: WL_Pish-Exp3-S3d77

description:
Susceptible rice at 3 days after inoculation with rice blast fungus Kyu77-07A (Exp3)
Gene expression in the fourth leaves of rice (pish) at 3 days after inoculation with virulent line of rice blast fungus


title: WR_Pia-Exp1-S3dH2O

description:
Susceptible rice at 3 days after treatment with H2O (Exp1)
Gene expression in the fourth leaves of rice (pia) at 3 days after treatment with water


title: WR_Pia-Exp1-S3d15B

description:
Susceptible rice at 3 days after inoculation with rice blast fungus P91-15B (Exp1)
Gene expression in the fourth leaves of rice (pia) at 3 days after inoculation with virulent line of rice blast fungus


title: WR_Pia-Exp1-R2dH2O

description:
Resistant rice at 2 days after treatment with H2O (Exp1)
Gene expression in the fourth leaves of rice (Pia) at 2 days after treatment with water


title: WR_Pia-Exp1-R1dH2O

description:
Resistant rice at 1 day after treatment with H2O (Exp1)
Gene expression in the fourth leaves of rice (Pia) at 1 day after treatment with water


title: WR_Pia-Exp1-R2d15B

description:
Resistant rice at 2 days after inoculation with rice blast fungus P91-15B (Exp1)
Gene expression in the fourth leaves of rice (Pia) at 2 days after inoculation with avirulent line of rice blast fungus


title: WL_Pish-Exp3-S2d77

description:
Susceptible rice at 2 days after inoculation with rice blast fungus Kyu77-07A (Exp3)
Gene expression in the fourth leaves of rice (pish) at 2 days after inoculation with virulent line of rice blast fungus


title: WL_Pish-Exp3-S1dH2O

description:
Susceptible rice at 1 day after treatment with H2O (Exp3)
Gene expression in the fourth leaves of rice (pish) at 1 day after treatment with water


title: WR_Pia-Exp1-R3dH2O

description:
Resistant rice at 3 days after treatment with H2O (Exp1)
Gene expression in the fourth leaves of rice (Pia) at 3 days after treatment with water


title: WL_Pish-Exp3-S1d77

description:
Susceptible rice at 1 day after inoculation with rice blast fungus Kyu77-07A (Exp3)
Gene expression in the fourth leaves of rice (pish) at 1 day after inoculation with virulent line of rice blast fungus


title: WL_Pish-Exp3-R5dH2O

description:
Resistant rice at 5 days after treatment with H2O (Exp3)
Gene expression in the fourth leaves of rice (Pish) at 5 days after treatment with water

value: Pish


title: WL_Pish-Exp3-S3dH2O

description:
Susceptible rice at 3 days after treatment with H2O (Exp3)
Gene expression in the fourth leaves of rice (pish) at 3 days after treatment with water

value: water


title: WL_Pish-Exp3-R5d77

description:
Resistant rice at 5 days after inoculation with rice blast fungus Kyu77-07A (Exp3)
Gene expression in the fourth leaves of rice (Pish) at 5 days after inoculation with avirulent line of rice blast fungus


title: WL_Pish-Exp2-S3dH2O

description:
Susceptible rice at 3 days after treatment with H2O (Exp2)
Gene expression in the fourth leaves of rice (pish) at 3 days after treatment with water


title: WL_Pish-Exp2-S5dH2O

description:
Susceptible rice at 5 days after treatment with H2O (Exp2)
Gene expression in the fourth leaves of rice (pish) at 5 days after treatment with water


title: WL_Pish-Exp3-R3dH2O

description:
Resistant rice at 3 days after treatment with H2O (Exp3)
Gene expression in the fourth leaves of rice (Pish) at 3 days after treatment with water


title: WL_Pish-Exp3-R1d77

description:
Resistant rice at 1 day after inoculation with rice blast fungus Kyu77-07A (Exp3)
Gene expression in the fourth leaves of rice (Pish) at 1 day after inoculation with avirulent line of rice blast fungus


title: WL_Pish-Exp2-S3d77

description:
Susceptible rice at 3 days after inoculation with rice blast fungus Kyu77-07A (Exp2)
Gene expression in the fourth leaves of rice (pish) at 3 days after inoculation with virulent line of rice blast fungus


title: WL_Pish-Exp2-S1dH2O

description:
Susceptible rice at 1 day after treatment with H2O (Exp2)
Gene expression in the fourth leaves of rice (pish) at 1 day after treatment with water


title: WL_Pish-Exp2-S2dH2O

description:
Susceptible rice at 2 days after treatment with H2O (Exp2)
Gene expression in the fourth leaves of rice (pish) at 2 days after treatment with water


title: WL_Pish-Exp3-R3d77

description:
Resistant rice at 3 days after inoculation with rice blast fungus Kyu77-07A (Exp3)
Gene expression in the fourth leaves of rice (Pish) at 3 days after inoculation with avirulent line of rice blast fungus


title: WL_Pish-Exp2-R5d77

description:
Resistant rice at 5 days after inoculation with rice blast fungus Kyu77-07A (Exp2)
Gene expression in the fourth leaves of rice (Pish) at 5 days after inoculation with avirulent line of rice blast fungus


title: WL_Pish-Exp2-R5dH2O

description:
Resistant rice at 5 days after treatment with H2O (Exp2)
Gene expression in the fourth leaves of rice (Pish) at 5 days after treatment with water


title: WL_Pish-Exp3-R1dH2O

description:
Resistant rice at 1 day after treatment with H2O (Exp3)
Gene expression in the fourth leaves of rice (Pish) at 1 day after treatment with water


title: WL_Pish-Exp2-S5d77

description:
Susceptible rice at 5 days after inoculation with rice blast fungus Kyu77-07A (Exp2)
Gene expression in the fourth leaves of rice (pish) at 5 days after inoculation with virulent line of rice blast fungus


title: WL_Pish-Exp2-R2dH2O

description:
Resistant rice at 2 days after treatment with H2O (Exp2)
Gene expression in the fourth leaves of rice (Pish) at 2 days after treatment with water


title: WL_Pish-Exp2-R3d77

description:
Resistant rice at 3 days after inoculation with rice blast fungus Kyu77-07A (Exp2)
Gene expression in the fourth leaves of rice (Pish) at 3 days after inoculation with avirulent line of rice blast fungus


title: WL_Pish-Exp2-R1d77

description:
Resistant rice at 1 day after inoculation with rice blast fungus Kyu77-07A (Exp2)
Gene expression in the fourth leaves of rice (Pish) at 1 day after inoculation with avirulent line of rice blast fungus


title: WL_Pish-Exp3-R2d77

description:
Resistant rice at 2 days after inoculation with rice blast fungus Kyu77-07A (Exp3)
Gene expression in the fourth leaves of rice (Pish) at 2 days after inoculation with avirulent line of rice blast fungus


title: WL_Pish-Exp2-S2d77

description:
Susceptible rice at 2 days after inoculation with rice blast fungus Kyu77-07A (Exp2)
Gene expression in the fourth leaves of rice (pish) at 2 days after inoculation with virulent line of rice blast fungus


title: WL_Pish-Exp2-S1d77

description:
Susceptible rice at 1 day after inoculation with rice blast fungus Kyu77-07A (Exp2)
Gene expression in the fourth leaves of rice (pish) at 1 day after inoculation with virulent line of rice blast fungus


title: WL_Pish-Exp2-R2d77

description:
Resistant rice at 2 days after inoculation with rice blast fungus Kyu77-07A (Exp2)
Gene expression in the fourth leaves of rice (Pish) at 2 days after inoculation with avirulent line of rice blast fungus


title: WL_Pish-Exp1-S3dH2O

description:
Susceptible rice at 3 days after treatment with H2O (Exp1)
Gene expression in the fourth leaves of rice (pish) at 3 days after treatment with water


title: WL_Pish-Exp1-S1dH2O

description:
Susceptible rice at 1 day after treatment with H2O (Exp1)
Gene expression in the fourth leaves of rice (pish) at 1 day after treatment with water


title: WL_Pish-Exp1-S5d77

description:
Susceptible rice at 5 days after inoculation with rice blast fungus Kyu77-07A (Exp1)
Gene expression in the fourth leaves of rice (pish) at 5 days after inoculation with virulent line of rice blast fungus


title: WL_Pish-Exp2-R1dH2O

description:
Resistant rice at 1 day after treatment with H2O (Exp2)
Gene expression in the fourth leaves of rice (Pish) at 1 day after treatment with water


title: WL_Pish-Exp2-R3dH2O

description:
Resistant rice at 3 days after treatment with H2O (Exp2)
Gene expression in the fourth leaves of rice (Pish) at 3 days after treatment with water


title: WL_Pish-Exp1-S5dH2O

description:
Susceptible rice at 5 days after treatment with H2O (Exp1)
Gene expression in the fourth leaves of rice (pish) at 5 days after treatment with water


title: WL_Pish-Exp1-S2dH2O

description:
Susceptible rice at 2 days after treatment with H2O (Exp1)
Gene expression in the fourth leaves of rice (pish) at 2 days after treatment with water


title: WL_Pish-Exp1-S3d77

description:
Susceptible rice at 3 days after inoculation with rice blast fungus Kyu77-07A (Exp1)
Gene expression in the fourth leaves of rice (pish) at 3 days after inoculation with virulent line of rice blast fungus


title: WL_Pish-Exp1-R5dH2O

description:
Resistant rice at 5 days after treatment with H2O (Exp1)
Gene expression in the fourth leaves of rice (Pish) at 5 days after treatment with water


title: WL_Pish-Exp1-S2d77

description:
Susceptible rice at 2 days after inoculation with rice blast fungus Kyu77-07A (Exp1)
Gene expression in the fourth leaves of rice (pish) at 2 days after inoculation with virulent line of rice blast fungus


title: WL_Pish-Exp1-R3dH2O

description:
Resistant rice at 3 days after treatment with H2O (Exp1)
Gene expression in the fourth leaves of rice (Pish) at 3 days after treatment with water


title: WL_Pish-Exp1-R2dH2O

description:
Resistant rice at 2 days after treatment with H2O (Exp1)
Gene expression in the fourth leaves of rice (Pish) at 2 days after treatment with water


title: WL_Pish-Exp1-R3d77

description:
Resistant rice at 3 days after inoculation with rice blast fungus Kyu77-07A (Exp1)
Gene expression in the fourth leaves of rice (Pish) at 3 days after inoculation with avirulent line of rice blast fungus


title: WL_Pish-Exp1-R1dH2O

description:
Resistant rice at 1 day after treatment with H2O (Exp1)
Gene expression in the fourth leaves of rice (Pish) at 1 day after treatment with water


title: WL_Pish-Exp1-S1d77

description:
Susceptible rice at 1 day after inoculation with rice blast fungus Kyu77-07A (Exp1)
Gene expression in the fourth leaves of rice (pish) at 1 day after inoculation with virulent line of rice blast fungus


title: WL_Pia-Exp3-S5dH2O

description:
Susceptible rice at 5 days after treatment with H2O (Exp3)
Gene expression in the fourth leaves of rice (pia) at 5 days after treatment with water


title: WL_Pish-Exp1-R1d77

description:
Resistant rice at 1 day after inoculation with rice blast fungus Kyu77-07A (Exp1)
Gene expression in the fourth leaves of rice (Pish) at 1 day after inoculation with avirulent line of rice blast fungus


title: WL_Pia-Exp3-S1dH2O

description:
Susceptible rice at 1 day after treatment with H2O (Exp3)
Gene expression in the fourth leaves of rice (pia) at 1 day after treatment with water


title: WL_Pia-Exp3-S3dH2O

description:
Susceptible rice at 3 days after treatment with H2O (Exp3)
Gene expression in the fourth leaves of rice (pia) at 3 days after treatment with water


title: WL_Pia-Exp3-S3d15B

description:
Susceptible rice at 3 days after inoculation with rice blast fungus P91-15B (Exp3)
Gene expression in the fourth leaves of rice (pia) at 3 days after inoculation with virulent line of rice blast fungus


title: WL_Pish-Exp1-R5d77

description:
Resistant rice at 5 days after inoculation with rice blast fungus Kyu77-07A (Exp1)
Gene expression in the fourth leaves of rice (Pish) at 5 days after inoculation with avirulent line of rice blast fungus


title: WL_Pia-Exp3-S5d15B

description:
Susceptible rice at 5 days after inoculation with rice blast fungus P91-15B (Exp3)
Gene expression in the fourth leaves of rice (pia) at 5 days after inoculation with virulent line of rice blast fungus


title: WL_Pia-Exp3-S1d15B

description:
Susceptible rice at 1 day after inoculation with rice blast fungus P91-15B (Exp3)
Gene expression in the fourth leaves of rice (pia) at 1 day after inoculation with virulent line of rice blast fungus


title: WL_Pia-Exp3-R1dH2O

description:
Resistant rice at 1 day after treatment with H2O (Exp3)
Gene expression in the fourth leaves of rice (Pia) at 1 day after treatment with water


title: WL_Pish-Exp1-R2d77

description:
Resistant rice at 2 days after inoculation with rice blast fungus Kyu77-07A (Exp1)
Gene expression in the fourth leaves of rice (Pish) at 2 days after inoculation with avirulent line of rice blast fungus


title: WL_Pia-Exp3-R5dH2O

description:
Resistant rice at 5 days after treatment with H2O (Exp3)
Gene expression in the fourth leaves of rice (Pia) at 5 days after treatment with water


title: WL_Pia-Exp2-S5dH2O

description:
Susceptible rice at 5 days after treatment with H2O (Exp2)
Gene expression in the fourth leaves of rice (pia) at 5 days after treatment with water


title: WL_Pia-Exp3-R3d15B

description:
Resistant rice at 3 days after inoculation with rice blast fungus P91-15B (Exp3)
Gene expression in the fourth leaves of rice (Pia) at 3 days after inoculation with avirulent line of rice blast fungus


title: WL_Pia-Exp3-R5d15B

description:
Resistant rice at 5 days after inoculation with rice blast fungus P91-15B (Exp3)
Gene expression in the fourth leaves of rice (Pia) at 5 days after inoculation with avirulent line of rice blast fungus


title: WL_Pia-Exp3-S2dH2O

description:
Susceptible rice at 2 days after treatment with H2O (Exp3)
Gene expression in the fourth leaves of rice (pia) at 2 days after treatment with water


title: WL_Pia-Exp2-S2d15B

description:
Susceptible rice at 2 days after inoculation with rice blast fungus P91-15B (Exp2)
Gene expression in the fourth leaves of rice (pia) at 2 days after inoculation with virulent line of rice blast fungus


title: WL_Pia-Exp2-S1dH2O

description:
Susceptible rice at 1 day after treatment with H2O (Exp2)
Gene expression in the fourth leaves of rice (pia) at 1 day after treatment with water


title: WL_Pia-Exp2-S3d15B

description:
Susceptible rice at 3 days after inoculation with rice blast fungus P91-15B (Exp2)
Gene expression in the fourth leaves of rice (pia) at 3 days after inoculation with virulent line of rice blast fungus


title: WL_Pia-Exp3-R2dH2O

description:
Resistant rice at 2 days after treatment with H2O (Exp3)
Gene expression in the fourth leaves of rice (Pia) at 2 days after treatment with water


title: WL_Pia-Exp2-S5d15B

description:
Susceptible rice at 5 days after inoculation with rice blast fungus P91-15B (Exp2)
Gene expression in the fourth leaves of rice (pia) at 5 days after inoculation with virulent line of rice blast fungus


title: WL_Pia-Exp3-R1d15B

description:
Resistant rice at 1 day after inoculation with rice blast fungus P91-15B (Exp3)
Gene expression in the fourth leaves of rice (Pia) at 1 day after inoculation with avirulent line of rice blast fungus


title: WL_Pia-Exp3-S2d15B

description:
Susceptible rice at 2 days after inoculation with rice blast fungus P91-15B (Exp3)
Gene expression in the fourth leaves of rice (pia) at 2 days after inoculation with virulent line of rice blast fungus


title: WL_Pia-Exp3-R2d15B

description:
Resistant rice at 2 days after inoculation with rice blast fungus P91-15B (Exp3)
Gene expression in the fourth leaves of rice (Pia) at 2 days after inoculation with avirulent line of rice blast fungus


title: WL_Pia-Exp2-S1d15B

description:
Susceptible rice at 1 day after inoculation with rice blast fungus P91-15B (Exp2)
Gene expression in the fourth leaves of rice (pia) at 1 day after inoculation with virulent line of rice blast fungus


title: WL_Pia-Exp3-R3dH2O

description:
Resistant rice at 3 days after treatment with H2O (Exp3)
Gene expression in the fourth leaves of rice (Pia) at 3 days after treatment with water


title: WL_Pia-Exp2-S2dH2O

description:
Susceptible rice at 2 days after treatment with H2O (Exp2)
Gene expression in the fourth leaves of rice (pia) at 2 days after treatment with water


title: WL_Pia-Exp1-S5dH2O

description:
Susceptible rice at 5 days after treatment with H2O (Exp1)
Gene expression in the fourth leaves of rice (pia) at 5 days after treatment with water


title: WL_Pia-Exp2-R3dH2O

description:
Resistant rice at 3 days after treatment with H2O (Exp2)
Gene expression in the fourth leaves of rice (Pia) at 3 days after treatment with water


title: WL_Pia-Exp2-R3d15B

description:
Resistant rice at 3 days after inoculation with rice blast fungus P91-15B (Exp2)
Gene expression in the fourth leaves of rice (Pia) at 3 days after inoculation with avirulent line of rice blast fungus


title: WL_Pia-Exp2-S3dH2O

description:
Susceptible rice at 3 days after treatment with H2O (Exp2)
Gene expression in the fourth leaves of rice (pia) at 3 days after treatment with water


title: WL_Pia-Exp1-S2dH2O

description:
Susceptible rice at 2 days after treatment with H2O (Exp1)
Gene expression in the fourth leaves of rice (pia) at 2 days after treatment with water


title: WL_Pia-Exp2-R1dH2O

description:
Resistant rice at 1 day after treatment with H2O (Exp2)
Gene expression in the fourth leaves of rice (Pia) at 1 day after treatment with water


title: WL_Pia-Exp1-S1dH2O

description:
Susceptible rice at 1 day after treatment with H2O (Exp1)
Gene expression in the fourth leaves of rice (pia) at 1 day after treatment with water


title: WL_Pia-Exp2-R2dH2O

description:
Resistant rice at 2 days after treatment with H2O (Exp2)
Gene expression in the fourth leaves of rice (Pia) at 2 days after treatment with water


title: WL_Pia-Exp2-R2d15B

description:
Resistant rice at 2 days after inoculation with rice blast fungus P91-15B (Exp2)
Gene expression in the fourth leaves of rice (Pia) at 2 days after inoculation with avirulent line of rice blast fungus


title: WL_Pia-Exp2-R5dH2O

description:
Resistant rice at 5 days after treatment with H2O (Exp2)
Gene expression in the fourth leaves of rice (Pia) at 5 days after treatment with water


title: WL_Pia-Exp2-R5d15B

description:
Resistant rice at 5 days after inoculation with rice blast fungus P91-15B (Exp2)
Gene expression in the fourth leaves of rice (Pia) at 5 days after inoculation with avirulent line of rice blast fungus


title: WL_Pish-Exp3-R2dH2O

description:
Resistant rice at 2 days after treatment with H2O (Exp3)
Gene expression in the fourth leaves of rice (Pish) at 2 days after treatment with water


title: WL_Pia-Exp2-R1d15B

description:
Resistant rice at 1 day after inoculation with rice blast fungus P91-15B (Exp2)
Gene expression in the fourth leaves of rice (Pia) at 1 day after inoculation with avirulent line of rice blast fungus


title: WL_Pia-Exp1-R5dH2O

description:
Resistant rice at 5 days after treatment with H2O (Exp1)
Gene expression in the fourth leaves of rice (Pia) at 5 days after treatment with water


title: WL_Pia-Exp1-S1d15B

description:
Susceptible rice at 1 day after inoculation with rice blast fungus P91-15B (Exp1)
Gene expression in the fourth leaves of rice (pia) at 1 day after inoculation with virulent line of rice blast fungus


title: WL_Pia-Exp1-S3d15B

description:
Susceptible rice at 3 days after inoculation with rice blast fungus P91-15B (Exp1)
Gene expression in the fourth leaves of rice (pia) at 3 days after inoculation with virulent line of rice blast fungus


title: WL_Pia-Exp1-R3dH2O

description:
Resistant rice at 3 days after treatment with H2O (Exp1)
Gene expression in the fourth leaves of rice (Pia) at 3 days after treatment with water


title: WL_Pia-Exp1-R5d15B

description:
Resistant rice at 5 days after inoculation with rice blast fungus P91-15B (Exp1)
Gene expression in the fourth leaves of rice (Pia) at 5 days after inoculation with avirulent line of rice blast fungus


title: WL_Pia-Exp1-S3dH2O

description:
Susceptible rice at 3 days after treatment with H2O (Exp1)
Gene expression in the fourth leaves of rice (pia) at 3 days after treatment with water


title: WL_Pia-Exp1-S2d15B

description:
Susceptible rice at 2 days after inoculation with rice blast fungus P91-15B (Exp1)
Gene expression in the fourth leaves of rice (pia) at 2 days after inoculation with virulent line of rice blast fungus


title: WL_Pia-Exp1-S5d15B

description:
Susceptible rice at 5 days after inoculation with rice blast fungus P91-15B (Exp1)
Gene expression in the fourth leaves of rice (pia) at 5 days after inoculation with virulent line of rice blast fungus


title: WL_Pia-Exp1-R1dH2O

description:
Resistant rice at 1 day after treatment with H2O (Exp1)
Gene expression in the fourth leaves of rice (Pia) at 1 day after treatment with water


title: WL_Pia-Exp1-R3d15B

description:
Resistant rice at 3 days after inoculation with rice blast fungus P91-15B (Exp1)
Gene expression in the fourth leaves of rice (Pia) at 3 days after inoculation with avirulent line of rice blast fungus


title: WL_Pia-Exp1-R2dH2O

description:
Resistant rice at 2 days after treatment with H2O (Exp1)
Gene expression in the fourth leaves of rice (Pia) at 2 days after treatment with water


title: MZM in BXD2-LTR:Fc

city: Birmingham

first: Hui-Chen

last: Hsu

state: AL

address: SHEL 311, 1825 University Blvd

institute: University of Alabama at Birmingham

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Illumina's GenomeStudio v2011.1.

organism: Mus musculus

source_name: Mouse spleen marginal zone macrophages

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent.

treatment_protocol: BXD2 mice and BXD2-Ifnar-/- mice were administered PBS and a third group of BXD2 mice were administered sLTβR-Fc (i.v. with 25 μg per mouse).  All mice were sacrified 10 hours later.  Spleen MZMs were FACS sorted as CD11b(low) F4/80(neg) I-Ab(neg) and SIGN-R1(+) cells.  Each chip is a result derived from MZMs isolated from the spleen of 2 mice from each group.

tag: strain

value: BXD2 sLTβR-Fc

tag: age

value: spleen


title: WL_Pia-Exp1-R2d15B

description:
Resistant rice at 2 days after inoculation with rice blast fungus P91-15B (Exp1)
Gene expression in the fourth leaves of rice (Pia) at 2 days after inoculation with avirulent line of rice blast fungus


title: MZM in BXD2 mice (2)

description: replicate 2


title: 682.sepsis_with_ARDS

city: San Francisco

first: Alisha

last: Holloway

state: CA

address: 1650 Owens Street

institute: Gladstone Institutes

hyb_protocol: Labeled cDNA was hybridized to the Affymetrix Human GeneChip® Gene 1.0 ST array (Affymetrix, Santa Clara, CA), integrating 28,869 genes with 764,885 probes (~26 probes per gene).

scan_protocol: Affymetrix GCS3000

data_processing: CEL files were generated using AGCC 4.0.0.1567G. The values in the CEL files were then normalized with the RMA normalization method, using the Affymetrix Power Tools suite, version 1.12.0.

source_name: blood

label_protocol: The NuGEN Ovation® Whole Blood Reagent (NuGEN technology, San Carlos, CA) was used for amplification, fragmentation and biotin-labeling, which enables gene expression of whole blood RNA without the need for additional globin reduction.

growth_protocol: Whole blood was stored in coded and de-identified PAXgeneTM tubes (PreAnalytiX, Hombrechtikon, CH) tubes at -80° Celsius.

extract_protocol: RNA was extracted using the PAXgeneTM miRNA kit (Qiagen, Valencia, CA) and processed in two separate batches balanced for cases and sepsis alones using identical materials and methods. Quality, quantity and purity of the RNA was assessed by electrophoresis (Bioanalyzer, Agilent, Inc) and spectrophotometry.

treatment_protocol: RNA stabilized at room temperature as per protocol

tag: gender

value: female

tag: shock

tag: disease state

value: sepsis with ARDS


title: MZM in BXD2 mice (1)

description: replicate 1


title: 669.sepsis_with_ARDS

value: male


title: 684.excluded

value: not meeting the Berlin definition of sepsis with ARDS and that they were excluded from analysis


title: LNCaP, Pin1 siRNA-2

first: Akifumi

last: Kushiyama

address: 2-2-6, Nihonbashi Bakurocho, Chuo-ku

institute: The Institute for Adult Diseases, Asahi Life Foundation

hyb_protocol: Probe was incubated with affymetrix human gene 1.0 ST array, according to manufacturers' instructions

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing:
GeneChip Operating Software, 1.3
HuEx-1_0-st-v2.r2.dt1.hg18.full.ps
HuEx-1_0-st-v2.r2.dt1.hg18.full.mps

source_name: LNCaP cell transfected with Pin1 siRNA-2

label_protocol: Probe was labeled by GeneChip WT Terminal Labeling Kit

growth_protocol: prostate cancer cell lines LNCaP and DU145, purchased from American Type Culture Collection (Manassas, Va., USA) were maintained in RPMI 1640 (Nissui Pharmaceutical, Tokyo) and DMEM, respectively, containing 10% (vol/vol) fetal calf serum at 37°C in 5% CO2 in air.

extract_protocol: Trizol, followed by the RNAeasy kit (Qiagen, Crawley, UK)

treatment_protocol: 48 h after the transfection of Pin1 or control siRNAs

tag: cell line

value: LNCaP

value: prostate cancer

tag: phenotype

value: androgen dependent


title: 686.sepsis_alone

value: sepsis alone


title: DU145, Pin1 siRNA-1

source_name: DU145 cell transfected with Pin1 siRNA-1

value: androgen independent


title: DU145, control siRNA

source_name: DU145 cell transfected with control siRNA


title: 654.sepsis_with_ARDS


title: 649.sepsis_with_ARDS


title: 632.sepsis_alone


title: 690.sepsis_alone


title: LNCaP, Pin1 siRNA-1

source_name: LNCaP cell transfected with Pin1 siRNA-1


title: 623.excluded


title: 618.sepsis_alone


title: 641.sepsis_alone


title: MZM in BXD2-IFNarKO

description: replicate 1


title: 661.sepsis_alone


title: 677.sepsis_with_ARDS


title: LNCaP, control siRNA

source_name: LNCaP cell transfected with control siRNA


title: 617.sepsis_alone


title: 605.sepsis_with_ARDS


title: 631.sepsis_alone


title: 582.sepsis_with_ARDS


title: 597.sepsis_alone


title: 571.sepsis_alone


title: 547.sepsis_with_ARDS


title: 550.sepsis_alone


title: 524.sepsis_alone


title: 523.sepsis_alone


title: 569.sepsis_with_ARDS


title: 509.sepsis_with_ARDS


title: 563.sepsis_with_ARDS


title: 495.sepsis_with_ARDS


title: 558.sepsis_with_ARDS


title: 476.excluded


title: 460.sepsis_with_ARDS


title: 474.sepsis_with_ARDS


title: 428.sepsis_alone


title: 486.sepsis_with_ARDS


title: 410.sepsis_with_ARDS


title: 491.sepsis_alone


title: 408.sepsis_alone


title: 470.sepsis_with_ARDS


title: 431.sepsis_alone


title: 455.sepsis_alone


title: 561.sepsis_with_ARDS


title: 407.sepsis_with_ARDS

value: other


title: 409.sepsis_alone


title: 412.sepsis_alone


title: 446.sepsis_with_ARDS


title: 400.sepsis_with_ARDS


title: 388.sepsis_with_ARDS


title: 403.sepsis_with_ARDS


title: 391.excluded


title: 387.sepsis_alone


title: 337.sepsis_with_ARDS


title: 357.sepsis_alone


title: 348.sepsis_alone


title: 356.sepsis_with_ARDS


title: 405.sepsis_alone


title: 350.sepsis_alone


title: 369.sepsis_with_ARDS


title: 320.sepsis_with_ARDS


title: 324.sepsis_with_ARDS


title: 308.excluded


title: 333.sepsis_alone


title: 325.sepsis_alone


title: 786-0 + L46R NF2

city: London

first: Stephen

last: Henderson

address: Paul O'Gorman Building

department: Cancer Institute

country: United Kingdom

institute: UCL

hyb_protocol: Following fragmentation, 1 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HuGene1.0ST array.  Genechips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affymetrix HuGene1.0ST chips were scanned using the Affymetrix Scanner 3000 7G and the MAS 5.1 software according to the manufacturers' protocol (http://www.affymetrix.com/support/technical/datasheets/mas_datasheet.pdf).

data_processing: Data was preprocessed, normalized and summarised using the RMA algorithm from the Bioconductor `affy` package and annotations from Bioconductor Hugene1.0stv cdf file

label_protocol: cDNA was generated using the WT Expression kit (ambion) and subsequently labeled using the GeneChip WT terminal labeling kit (affymetrix) acording to the manufacturers instructions

growth_protocol: All cell lines were grown in DMEM under standard conditions

extract_protocol: Total RNA was isolated using the RNeasy kit (Qiagen) according to the manufacturers instructions.

treatment_protocol: Cell lines were infected with lentiviruses expressing either wt Merlin or Merlin L46R mutant. 24 hours after infection, fresh media containing 2.5ug/ml puromycin was added (drug selection) and cells grown for a further 24 hours, i.e. cells were harvested 48hour after infection.

value: renal carcinoma cell line 786-0

tag: nf2 mutational status of cell line

value: wild type

tag: lentiviral infection with nf2 (either wt or l46r inactive mutant)


title: SN12C + L46R NF2 rep1

description: SN12C-mutant a

value: renal carcinoma cell line SN12C

value: mutant


title: SN12C + wt NF2 rep1

description: SN12C-wt a


title: 786-0 + wt NF2


title: BCPAP + L46R NF2

description: BCPAP-mutant

source_name: BCPAP

value: thyroid carcinoma cell line BCPAP


title: SN12C + L46R NF2 rep2

description: SN12C-mutant b


title: 301.sepsis_alone


title: 8505C + L46R NF2, rep1

description: 8505C-mutant a

value: thyroid carcinoma cell line 8505C


title: 8505C + L46R NF2, rep2

description: 8505C-mutant b


title: HMLE + L46R NF2

description: HMLE-mutant

source_name: HMLE

value: breast immortalized cell line HMLE


title: BCPAP + wt NF2

description: BCPAP-wt


title: IOMM-Lee + wt NF2, rep1

description: IOMM-Lee-wt

source_name: IOMM-Lee

value: meningioma cell line IOMM-Lee


title: HMLE + wt NF2

description: HMLE-wt


title: MDA-MB-23 + L46R NF2 rep2

description: MDA-MB-231-mutant b

value: breast carcinoma cell line MDA-MB-231


title: 8505Cwt NF2, rep2

description: 8505C-wt b


title: SF1335 + L46R NF2, rep1

description: SF1335-mutant a

value: meningioma cell line SF1336


title: 8505C + wt NF2, rep1

description: 8505C-wt a


title: MDA-MB-231+ wt NF2, rep2

description: MDA-MB-231-wt b


title: MDA-MB-231 + wt NF2, rep1

description: MDA-MB-231-wt a


title: MDA-MB-231 + L46R NF2 rep1

description: MDA-MB-231-mutant a


title: SF1335 + wt NF2, rep2

description: SF1335-wt b

value: meningioma cell line SF1335


title: IOMM-Lee + L46R NF2, rep1

description: IOMM-Lee-mutant


title: SF1335 + L46R NF2, rep2

description: SF1335-mutant b

value: meningioma cell line SF1337


title: WL_Pia-Exp1-R1d15B

description:
Resistant rice at 1 day after inoculation with rice blast fungus P91-15B (Exp1)
Gene expression in the fourth leaves of rice (Pia) at 1 day after inoculation with avirulent line of rice blast fungus

tag: cultivar

value: Nipponbare

tag: tissue

value: Fourth leaves

value: Pia

value: Resistant

value: avirulent line of rice blast fungus


title: siNF2-Sparse, rep1

description:
siNF2-sparse a
Gene expression data from sparse HMLE cells transfected with NF2 siRNA

data_processing: Data was preprocessed, normalized and summarized using the RMA algorithm from the Bioconductor `affy` package and annotations from Bioconductor Hugene1.0stv cdf file

growth_protocol: HMLE cells were grown in DMEM/F12  supplemented with 5% Horse serum, 20 ng/ml EGF, 0.5 µg/ml hydrocortisone, 100 ng/ml cholera toxin and 10 µg/ml insulin.

treatment_protocol: HMLE cells were transfected with Lipofectamine RNAiMax and 10nM stealth NF2 or scramble negative control siRNAs (Invitrogen). 2 days later, when 10cm dishes were ~90% confluent, either medium was changed (Dense) or split to 5x15cm dishes (Sparse) and cells harvested the next day (3 days after siRNA transfection)

value: NF2 knockdown

tag: cell density

value: sparse


title: SN12C + wt NF2 rep2

description: SN12C-wt b

value: renal carcinoma cell line SN12C

value: wild type


title: SF1335 + wt NF2, rep1

description: SF1335-wt a

value: mutant


title: DU145, Pin1 siRNA-2

source_name: DU145 cell transfected with Pin1 siRNA-2

tag: cell type

value: prostate cancer

value: androgen independent


title: siNF2-Sparse, rep2

description:
siNF2-sparse b
Gene expression data from sparse HMLE cells transfected with NF2 siRNA

value: breast immortalized cell line HMLE

tag: genotype/variation


title: Scramble-Sparse, rep3

description:
shScramble-sparse c
Gene expression data from sparse HMLE cells transfected with scramble control siRNA

value: control


title: siNF2-Dense, rep1

description:
siNF2-dense a
Gene expression data from dense HMLE cells transfected with NF2 siRNA

value: dense


title: Scramble-Sparse, rep1

description:
siScramble-sparse a
Gene expression data from sparse HMLE cells transfected with scramble control siRNA


title: Scramble-Dense, rep2

description:
siScramble-dense b
Gene expression data from dense HMLE cells transfected with scramble control siRNA


title: Scramble-Sparse, rep2

description:
siScramble-sparse b
Gene expression data from sparse HMLE cells transfected with scramble control siRNA


title: siNF2-Dense, rep2

description:
siNF2-dense b
Gene expression data from dense HMLE cells transfected with NF2 siRNA


title: ER-RNA, hypoxia, RNA pool out of 5 independent biological experiments

city: Berlin

first: Michael

last: Fähling

address: Charitéplatz 1

department: Institut für Vegetative Physiologie

country: Germany

institute: Charité - Universitätsmedizin Berlin

hyb_protocol: The biotinylated cDNA was added to a hybridization cocktail for hybridization to the Mouse Gene 1.0ST Array (Hybridization Wash and Stain Kit, Affymetrix). The hybridization in the Affymetrix hybridization oven 640 at 45°C and 60 rpm for 16 h, the staining and washing processed in the Fluidics Station 450.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Partek Genomics Suite 6.4 software. Normalization according to RMA method.
probe group file: HuGene-1_0-st-v1

label_protocol: Random-primed cDNA synthesis was performed using the Ambion® WT Expression Kit (Ambion, Austin, Texas, USA). Subsequently, cDNA was fragmented with a combination of uracil DNA glucosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE1) and then labeled using the WT terminal labeling kit (Affymetrix Inc., Santa Clara, CA, USA).

growth_protocol: Human fibrosarcoma HT1080 cells obtained from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH; ACC 315) and cultured in Dulbecco’s modified Eagle’s medium (high glucose; PAA Laboratories GmbH), supplemented with 10% heat-inactivated fetal calf serum, 50 U/ml penicillin, 50 g/ml streptomycin, 15 mM Hepes, and 2 mmol/l glutamine, at 37 °C, 5% CO2.

extract_protocol: Total RNA was isolated from cultured cells using RNA-BeeTM (CS-105B; AMS Biotechnology, Europe) according to the manufacturer’s protocol. Isolation of an endoplasmatic reticulum fraction was performed using the ER0100 Sigma Endoplasmic Reticulum Isolation Kit (Sigma-Aldrich Chemie GmbH, Germany) according to the manufacturer’s protocol. RNA was extracted from the ER fraction using RNA-BeeTM. RNA integrity was checked by analyzing on the 2100 Bioanalyzer (Agilent technologies, PA, USA).

treatment_protocol: Cells were maintained in a medium containing 0.4% fetal calf serum for at least 24 h prior to the start and during the experiments. For hypoxic conditions the cells were incubated in a hypoxic chamber where the O2 content was reduced to 1% by gas exchange with 95% nitrogen and 5% CO2. Control cells were incubated under atmospheric conditions (21% O2, 5% CO2, 37 °C).

value: fibrosarcoma cells

tag: culture condition

value: hypoxic (1% O2, 5% CO2, 37°C) for 36hr

tag: molecule subtype

value: ER-RNA


title: ER-RNA, control, RNA pool out of 5 independent biological experiments

value: control/atmospheric (21% O2, 5% CO2, 37 °C) for 36h


title: Post-PHx-Mdr2/KO Liver Tumor (HCC) (PHx3M)

city: Jerusalem

first: Daniel

last: Goldenberg

address: Ein Kerem

department: Gene therapy

country: Israel

institute: Hadassah medical center

hyb_protocol: According to manufacturer protocol (Affymetrix)

data_processing: Partek, GC-RMA

source_name: Liver, Tumor, PHx

growth_protocol: Regular growth on normal diet

extract_protocol: Tri-reagent

treatment_protocol: 70% PHx of both male and female Mdr2-KO mice at the age of either 3 or 6 months

tag: gender,

value: Male

tag: treatment

value: Partial hepatectomy

value: Liver tumor (HCC)

value: FVB/N

tag: genotype


title: Scramble-Dense, rep3

description:
shScramble-dense c
Gene expression data from dense HMLE cells transfected with scramble control siRNA


title: Post-PHx-Mdr2/KO Liver (PHx1M)

scan_protocol: According to manufacturer protocol (Affymetrix)

source_name: Liver, PHx

value: Liver

tag: strain


title: Post-PHx-Mdr2/KO Liver Tumor (HCC) (PHx2F)

label_protocol: According to manufacturer protocol (Affymetrix)

value: Female


title: Post-PHx-Mdr2/KO Liver (PHx2F)


title: total-RNA, control, RNA pool out of 5 independent biological experiments

value: total RNA


title: NestinCre;Sirt1lox/lox NSCs/neural progenitors biological replicate 2

city: Stanford

first: Victoria

last: Rafalski

address: 300 Pasteur Drive Alway M314

department: Genetics

institute: Stanford University

description: Gene expression data from proliferating adult NSCs/neural progenitors lacking active SIRT1

hyb_protocol: Following fragmentation and labeling, single-stranded DNA was hybridized at 45C on Affymetrix GeneChip Mouse Gene 1.0STArray according to manufacturer's protocol. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: The data were adjusted for background and then normalized using Robust Multiarray Analysis (RMA).

source_name: Proliferating adult NSCs/neural progenitors experimental 2

label_protocol: Biotinylated single-stranded DNA were prepared according to Affymetrix Whole Transcript Sense Targeting Labeling Assay protocol.

growth_protocol: NSCs/neural progenitors were isolated from 8-week-old Sirt1lox/lox and NestinCre;Sirt1lox/lox mice, grown as neurospheres in neurobasal media with B27 supplement and EGF and bFGF for one passage before being dissociated and plated at equal density on poly-D-lysine- coated plates. Proliferating cells were collected for total RNA at early passage 2.

extract_protocol: Qiagen Rneasy kit

tag: age

tag: passage

value: passage 2

tag: sirt1 expression

value: lacks active SIRT1


title: Scramble-Dense, rep1

description:
siScramble-dense a
Gene expression data from dense HMLE cells transfected with scramble control siRNA

tag: cell line


title: Post-PHx-Mdr2/KO Liver Tumor (HCC) (PHx1M)


title: NestinCre;Sirt1lox/lox NSCs/neural progenitors biological replicate 1

source_name: Proliferating adult NSCs/neural progenitors experimental 1


title: Post-PHx-Mdr2/KO Liver (PHx6F)


title: Post-PHx-Mdr2/KO Liver Tumor (HCC) (PHx4M)


title: total-RNA, hypoxia, RNA pool out of 5 independent biological experiments


title: Post-PHx-Mdr2/KO Liver (PHx3M)


title: Sirt1lox/lox NSCs/neural progenitors biological replicate 3

description: Gene expression data from proliferating adult NSCs/neural progenitors expressing active SIRT1

source_name: Proliferating adult NSCs/neural progenitors control 3

value: expresses active SIRT1


title: Post-PHx-Mdr2/KO Liver Tumor (HCC) (PHx5M)


title: Post-PHx-Mdr2/KO Liver (PHx5M)


title: Post-PHx-Mdr2/KO Liver (PHx4M)


title: NestinCre;Sirt1lox/lox NSCs/neural progenitors biological replicate 3

source_name: Proliferating adult NSCs/neural progenitors experimental 3


title: Sirt1lox/lox NSCs/neural progenitors biological replicate 1

source_name: Proliferating adult NSCs/neural progenitors control 1


title: Sirt1lox/lox NSCs/neural progenitors biological replicate 2

source_name: Proliferating adult NSCs/neural progenitors control 2


title: polysomal RNA, control untreated, bio.rep2

city: Povo

first: Toma

last: Tebaldi

state: Trento

address: via Sommarive n. 9

department: Centre for Integrative Biology

country: Italy

institute: University of Trento

hyb_protocol: Hybridization, blocking and washing were performed according to Agilent protocol: “One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling)”: (https://www.chem.agilent.com/Library/usermanuals/Public/G4140-90040_GeneExpression_One-Color_v6.0.pdf)

scan_protocol: Hybridized microarray slides were scanned with an Agilent DNA Microarray Scanner (G2505C, Agilent Technologies, Santa Clara, CA) at 5 micron resolution with the manufacturer’s software (Agilent ScanControl 8.1.3). The scanned TIFF images were analyzed numerically using the Agilent Feature Extraction Software version 10.7.7.1 according to the Agilent standard protocol GE1_107_Sep09.

data_processing: The scanned TIFF images were analyzed numerically and the background corrected using the Agilent Feature Extraction Software version 10.7.7.1 according to the Agilent standard protocol GE1_107_Sep09. The output of Feature Extraction was analyzed with the R software environment for statistical computing (http://www.r-project.org/) and the Bioconductor library of biostatistical packages (http://www.bioconductor.org/). Signal intensities across arrays were normalized with the quantile normalization algorithm.

source_name: SH-SY5Y cells_polysomal RNA_control untreated

growth_protocol: SH-SY5Y cells were maintained in DMEM supplemented with 10% Fetal Bovine Serum (FBS), 2 mM L-glutamine, penicillin 100.000 U.I./l and streptomycin 100 mg/l. Cells were cultured at 37 °C in humid atmosphere of 5% CO2. All experiments were performed in DMEM using medium without phenol red, FBS, and antibiotics to avoid any interference with protein. If not specified differently, cells were grown to 80% of confluence before each assay.

extract_protocol: Cells were washed once with phosphate buffer saline (PBS) and treated directly on the plate with 300 µl lysis buffer [10 mM NaCl, 10 mM MgCl2, 10 mM Tris–HCl, pH 7.5, 1% Triton X-100, 1% sodium deoxycholate, 0.2 U/µl RNase inhibitor (Fermentas) and 1 mM dithiothreitol] and transferred to an Eppendorf tube. After a few minute incubation on ice with occasional vortexing, the extracts were centrifuged for 10 min at 12000 g at 4°C. The supernatant was stored at –80°C or loaded directly onto a 15–50% linear sucrose gradient containing 30 mM Tris–HCl, pH 7.5, 100 mM NaCl, 10 mM MgCl2, and centrifuged in an Sorvall rotor for 120 min at 40000 rpm. Polysomal fractions were collected monitoring the absorbance at 254 nm and treated directly with proteinase K. After phenol–chloroform extraction and isopropanol precipitation, polysomal RNA was resuspended in 30 µl of water. RNA quality was assessed by agarose gel electrophoresis and the Agilent 2100 Bioanalyzer platform.

treatment_protocol: SH-SY5Y cells were seeded at a density of 2.5 × 104 cells/cm2 and maintained for 3 days in the growth medium, until the 80% confluence was reached. The control experiments were performed in DMEM using medium without phenol red, FBS, and antibiotics to avoid any interference with protein.

tag: treated with

value: none (untreated control)

tag: rna fraction

value: cytoplasmic RNA; polysomal RNA


title: polysomal RNA, control untreated, bio.rep1


title: total RNA, control untreated, bio.rep1

source_name: SH-SY5Y cells_total RNA_control untreated

extract_protocol: Total RNA was extracted using TRIZOL reagent according to the manufacturer's protocol. Briefly, the aqueous phase was used for RNA precipitation with an equal volume of isopropanol. The RNA pellet was washed once with 75% ethanol, then air-dried and re-dissolved in 20 μl of RNase-free water. RNA was quantified using a spectrophotometer and its quality was checked by agarose gel electrophoresis and by Agilent 2100 Bioanalyzer platform, following the manifacturer’s guidelines for sample preparation and analysis of data (Agilent 2100 Bioanalyzer 2100 Expert User's Guide, http://www.agilent.com).


title: polysomal RNA, control untreated, bio.rep3


title: total RNA, control untreated, bio.rep2


title: total RNA, rAHL treated 2h, bio.rep1

source_name: SH-SY5Y cells_total RNA_rAHL treated 2h

treatment_protocol: SH-SY5Y cells were seeded at a density of 2.5 × 104 cells/cm2 and maintained for 3 days in the growth medium, until the 80% confluence was reached. All experiments were performed in  the presence of 3nM rAHL oligomers for 2h in DMEM using medium without phenol red, FBS, and antibiotics   to avoid any interference with protein.

value: 3nM rAHLfor 2hrs


title: s1p_T12_NHDF

city: Lebanon

first: Tammara

last: Wood

state: NH

address: WTRB 674

department: Biomedical Data Science

institute: Dartmouth Medical School

description:
S1P Treatment Time Course 2 12h
EXPT_ID: 62414
PRINT_ID: 1064

hyb_protocol: Hybridized using Agilent Hyb Kit.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner, and image intensity data were extracted and analyzed with GenePix Pro analysis software.

data_processing: Data for both channels were Lowess-normalized and then the log(2) ratio was taken. Data were filtered for genes with >80% good data.

label_protocol: Labeled using Agilent Quick Amp Labeling Kit.

extract_protocol: Total RNA isolated using Qiagen RNeasy Mini Kit.

treatment_protocol: Storage of human tissue in RNAlater.

value: cultured normal human dermal fibroblasts

source_name: Stratagene Universal Human Reference

extract_protocol: Total RNA isolated by Stratagene.

tag: sample type

value: reference


title: polysomal RNA, rAHL treated 2h, bio.rep2

source_name: SH-SY5Y cells_polysomal RNA_rAHL treated 2h


title: s1p_T8_NHDF

description:
S1P Treatment Time Course 2 8h
EXPT_ID: 62410
PRINT_ID: 1064


title: polysomal RNA, rAHL treated 2h, bio.rep3


title: S1P_C18_TC1_T16

description:
S1P Treatment Time Course 1 16h
EXPT_ID: 51999
PRINT_ID: 1064


title: total RNA, control untreated, bio.rep3


title: total RNA, rAHL treated 2h, bio.rep2


title: total RNA, rAHL treated 2h, bio.rep3


title: s1p_T0-3_NHDF

description:
S1P Treatment Time Course 2 0h #3
EXPT_ID: 62409
PRINT_ID: 1064


title: s1p_T4_NHDF

description:
S1P Treatment Time Course 2 4h
EXPT_ID: 62412
PRINT_ID: 1064


title: s1p_T24_NHDF

description:
S1P Treatment Time Course 2 24h
EXPT_ID: 62407
PRINT_ID: 1064


title: s1p_T2_NHDF

description:
S1P Treatment Time Course 2 2h
EXPT_ID: 62413
PRINT_ID: 1064


title: S1P_C18_TC1_T4

description:
S1P Treatment Time Course 1 4h
EXPT_ID: 51997
PRINT_ID: 1064


title: S1P_C18_TC1_T8

description:
S1P Treatment Time Course 1 8h
EXPT_ID: 51998
PRINT_ID: 1064


title: polysomal RNA, rAHL treated 2h, bio.rep1


title: S1P_C18_TC1_T0C

description:
S1P Treatment Time Course 1 0h #3
EXPT_ID: 51995
PRINT_ID: 1064


title: S1P_C18_TC1_T0A

description:
S1P Treatment Time Course 1 0h #1
EXPT_ID: 51993
PRINT_ID: 1064


title: s1p_T0-1_NHDF

description:
S1P Treatment Time Course 2 0h #1
EXPT_ID: 62408
PRINT_ID: 1064


title: s1p_T0-2_NHDF

description:
S1P Treatment Time Course 2 0h #2
EXPT_ID: 62411
PRINT_ID: 1064


title: S1P_C18_TC1_T0B

description:
S1P Treatment Time Course 1 0h #2
EXPT_ID: 51994
PRINT_ID: 1064


title: IL4_TC2_Leni_T12_stripped

description:
IL4 Treatment Time Course 2 12h
EXPT_ID: 60236
PRINT_ID: 1064


title: IL4_TC2_Leni_T24_stripped

description:
IL4 Treatment Time Course 2 24h
EXPT_ID: 60237
PRINT_ID: 1064


title: IL4_TC2_Leni_T4_stripped

description:
IL4 Treatment Time Course 2 4h
EXPT_ID: 60239
PRINT_ID: 1064


title: IL4_TC2_Leni_T0-3_stripped

description:
IL4 Treatment Time Course 2 0h #3
EXPT_ID: 60235
PRINT_ID: 1064


title: IL4_TC1_Leni_T0-1_stripped

description:
IL4 Treatment Time Course 1 0h #1
EXPT_ID: 60172
PRINT_ID: 1064


title: IL4_TC1_Leni_T24_stripped

description:
IL4 Treatment Time Course 1 24h
EXPT_ID: 60176
PRINT_ID: 1064


title: IL4_TC2_Leni_T2_stripped

description:
IL4 Treatment Time Course 2 2h
EXPT_ID: 60238
PRINT_ID: 1064


title: IL4_TC1_Leni_T4_stripped

description:
IL4 Treatment Time Course 1 4h
EXPT_ID: 60178
PRINT_ID: 1064


title: IL4_TC1_Leni_T12_stripped

description:
IL4 Treatment Time Course 1 12h
EXPT_ID: 60175
PRINT_ID: 1064


title: IL4_TC2_Leni_T0-2_stripped

description:
IL4 Treatment Time Course 2 0h #2
EXPT_ID: 60234
PRINT_ID: 1064


title: IL4_TC2_Leni_T8_stripped

description:
IL4 Treatment Time Course 2 8h
EXPT_ID: 60240
PRINT_ID: 1064


title: IL4_TC1_Leni_T8_stripped

description:
IL4 Treatment Time Course 1 8h
EXPT_ID: 60179
PRINT_ID: 1064


title: IL13_TC2_Leni_T24

description:
IL13 Treatment Time Course 2 24h
EXPT_ID: 60127
PRINT_ID: 1064


title: IL13_TC2_Leni_T12

description:
IL13 Treatment Time Course 2 12h
EXPT_ID: 60125
PRINT_ID: 1064


title: IL13_TC2_Leni_T8

description:
IL13 Treatment Time Course 2 8h
EXPT_ID: 60130
PRINT_ID: 1064


title: IL13_TC2_Leni_T2

description:
IL13 Treatment Time Course 2 2h
EXPT_ID: 60128
PRINT_ID: 1064


title: IL4_TC1_Leni_T0-3_stripped

description:
IL4 Treatment Time Course 1 0h #3
EXPT_ID: 60174
PRINT_ID: 1064


title: IL13_TC2_Leni_T4

description:
IL13 Treatment Time Course 2 4h
EXPT_ID: 60129
PRINT_ID: 1064


title: IL13_TC2_Leni_T0-4

description:
IL13 Treatment Time Course 2 0h #1
EXPT_ID: 60123
PRINT_ID: 1064


title: IL13_TC1_Leni_T12

description:
IL13 Treatment Time Course 1 12h
EXPT_ID: 60089
PRINT_ID: 1064


title: IL13_TC1_Leni_T24

description:
IL13 Treatment Time Course 1 24h
EXPT_ID: 60090
PRINT_ID: 1064


title: IL13_TC1_Leni_T8

description:
IL13 Treatment Time Course 1 8h
EXPT_ID: 60093
PRINT_ID: 1064


title: IL4_TC1_Leni_T2_stripped

description:
IL4 Treatment Time Course 1 2h
EXPT_ID: 60177
PRINT_ID: 1064


title: IL4_TC1_Leni_T0-2_stripped

description:
IL4 Treatment Time Course 1 0h #2
EXPT_ID: 60173
PRINT_ID: 1064


title: IL13_TC1_Leni_T4

description:
IL13 Treatment Time Course 1 4h
EXPT_ID: 60092
PRINT_ID: 1064


title: IL4_TC2_Leni_T0-1_stripped

description:
IL4 Treatment Time Course 2 0h #1
EXPT_ID: 60233
PRINT_ID: 1064


title: IL13_TC1_Leni_T0-3

description:
IL13 Treatment Time Course 1 0h #3
EXPT_ID: 60088
PRINT_ID: 1064


title: IL13_TC1_Leni_T2

description:
IL13 Treatment Time Course 1 2h
EXPT_ID: 60091
PRINT_ID: 1064


title: Post-PHx-Mdr2/KO Liver Tumor (HCC) (PHx6F)

tag: tissue


title: IL13_TC1_Leni_T0-1

description:
IL13 Treatment Time Course 1 0h #1
EXPT_ID: 60086
PRINT_ID: 1064


title: IL13_TC1_Leni_T0-2

description:
IL13 Treatment Time Course 1 0h #2
EXPT_ID: 60087
PRINT_ID: 1064


description: Polysomal RNA sample extracted from untreated SH-SY5Y cells.

source_name: SH-SY5Y cells, polysomal RNA, control untreated, bio.rep#3

value: control, untreated

value: polysomal RNA


description: Polysomal RNA sample extracted from SH-SY5Y cells treated with staphylococcal alpha-hemolysin (3nM final concentration) for 2 hours.

source_name: SH-SY5Y cells, polysomal RNA, AHL treated 2h, bio.rep#2

treatment_protocol: SH-SY5Y cells were seeded at a density of 2.5 × 104 cells/cm2 and maintained for 3 days in the growth medium, until the 80% confluence was reached. All experiments were performed in  the presence of 3nM AHL for 2h in DMEM using medium without phenol red, FBS, and antibiotics   to avoid any interference with protein.

value: 3nM AHL, 2 hours


title: MCF7 -Arg 24h

city: Durham

first: Xiaohu

last: Tang

state: NC

address: CIEMAS Rm 2133, 101 Science Dr.

department: Department of Molecular Genetics and Microbiology

institute: Duke University

description: Sample name: MCF7 -Arg

hyb_protocol: Hybridization was performed in Affymetrix  GeneChip® hybridization oven 645, washed in Affymetrix GeneChip® Fluidics Station 450 according to standard Affymetrix GeneChip® Hybridization and wash protocols. (Affymetrix, Santa Clara,CA).

scan_protocol: Fluorescent images were scanned with Affymetrix GeneChip® Scanner 7G according to standard Affymetrix GeneChip® Stain protocols. (Affymetrix, Santa Clara,CA).

data_processing:
Expression data was extracted using the Affymetrix Expression Console version 1.1 (Affymetrix) and further generated by RMAExpress using Quantile/Median Polish normorlization/summarization methods. The results were shown in log2 scale.
All GeneChips were scaled to a median intensity setting of 500.

source_name: MCF7 cells deprived Arginine for 24 hours

label_protocol: Total RNA were assessed for quality with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies,Santa Clara, CA)) and Nanodrop 8000 spectrophotometer (Thermo Scientific/Nanodrop, Wilmington, DE). Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) from total RNA.

growth_protocol: MCF7 or PC3 cells grew in the control full DMEM media supplement with 10% FBS and Penicillin/Streptomycin

extract_protocol: RNA was extracted by RNAeasy kits (Qiagen) according to the manufacturer's instructions.

treatment_protocol: MCF7 or PC3 cells were treated for 24 hours with the control or one (or all amino acids) deprived DMEM media supplemnent with 10% dialysed FBS and Penicillin/Streptomycin

value: deprived of Arginine

tag: time

value: 24 hours


title: total RNA, AHL treated 2h, bio.rep#2

description: Total RNA sample extracted from SH-SY5Y cells treated with staphylococcal alpha-hemolysin (3nM final concentration) for 2 hours.

source_name: SH-SY5Y cells, total RNA, AHL treated 2h, bio.rep#2


title: total RNA, control untreated, bio.rep#3

description: Total RNA sample extracted from untreated SH-SY5Y cells.

source_name: SH-SY5Y cells, total RNA, control untreated, bio.rep#3


title: total RNA, AHL treated 2h, bio.rep#3

source_name: SH-SY5Y cells, total RNA, AHL treated 2h, bio.rep#3


source_name: SH-SY5Y cells, polysomal RNA, AHL treated 2h, bio.rep#3


source_name: SH-SY5Y cells, polysomal RNA, control untreated, bio.rep#1


source_name: SH-SY5Y cells, polysomal RNA, control untreated, bio.rep#2


title: MCF7 -Met-Arg 24h

description: Sample name: MCF7 -Met-Arg

source_name: MCF7 cells deprived both Methionine and Arginine for 24 hours

value: deprived of both Methionine and Arginine


source_name: SH-SY5Y cells, polysomal RNA, AHL treated 2h, bio.rep#1


title: MCF7 Con 24h

description: Sample name: MCF7 Con

source_name: MCF7 cells in the control media for 24 hours

value: control media


title: PC3 0 μM Met 48h-rep3

description: Sample name: PC3 0 μM Met-6

source_name: PC3 cells in the 0 μM Methionine media for 48 hours, biological rep3

value: 0 μM Methionine media

value: 48 hours


title: total RNA, control untreated, bio.rep#1

source_name: SH-SY5Y cells, total RNA, control untreated, bio.rep#1

value: total RNA


title: total RNA, control untreated, bio.rep#2

source_name: SH-SY5Y cells, total RNA, control untreated, bio.rep#2


title: total RNA, AHL treated 2h, bio.rep#1

source_name: SH-SY5Y cells, total RNA, AHL treated 2h, bio.rep#1


title: MCF7 DZNep 24h

description: Sample name: MCF7 DZNep

source_name: MCF7 cells treated with 5 μM DZNep for 24 hours

value: 5 μM DZNep


title: MCF7 -Met 24h

description: Sample name: MCF7 -Met

source_name: MCF7 cells deprived Methionine for 24 hours

value: deprived of Methionine


title: IL13_TC2_Leni_T0-5

description:
IL13 Treatment Time Course 2 0h #2
EXPT_ID: 60124
PRINT_ID: 1064

tag: cell type

source_name: Stratagene Universal Human Reference


title: PC3 Con 48h-rep3

description: Sample name: PC3 Con-6

source_name: PC3 cells in the control media for 48 hours, biological rep3


title: PC3 Con 48h-rep2

description: Sample name: PC3 Con-5

source_name: PC3 cells in the control media for 48 hours, biological rep2


title: PC3 20 μM Met 24h-rep3

description: Sample name: PC3 20 μM Met-3

source_name: PC3 cells in the 20 μM Methionine media for 24 hours, biological rep3

value: 20 μM Methionine media


title: PC3 Con 48h-rep1

description: Sample name: PC3 Con-4

source_name: PC3 cells in the control media for 48 hours, biological rep1


title: PC3 0 μM Met 48h-rep1

description: Sample name: PC3 0 μM Met-4

source_name: PC3 cells in the 0 μM Methionine media for 48 hours, biological rep1


title: PC3 5 μM Met 24h-rep2

description: Sample name: PC3 5 μM Met-2

source_name: PC3 cells in the 5 μM Methionine media for 24 hours, biological rep2

value: 5 μM Methionine media


title: PC3 20 μM Met 24h-rep1

description: Sample name: PC3 20 μM Met-1

source_name: PC3 cells in the 20 μM Methionine media for 24 hours, biological rep1


title: PC3 5 μM Met 24h-rep3

description: Sample name: PC3 5 μM Met-3

source_name: PC3 cells in the 5 μM Methionine media for 24 hours, biological rep3


title: PC3 0 μM Met 48h-rep2

description: Sample name: PC3 0 μM Met-5

source_name: PC3 cells in the 0 μM Methionine media for 48 hours, biological rep2


title: PC3 20 μM Met 24h-rep2

description: Sample name: PC3 20 μM Met-2

source_name: PC3 cells in the 20 μM Methionine media for 24 hours, biological rep2


title: PC3 5 μM Met 24h-rep1

description: Sample name: PC3 5 μM Met-1

source_name: PC3 cells in the 5 μM Methionine media for 24 hours, biological rep1


title: PC3 0 μM Met 24h-rep2

description: Sample name: PC3 0 μM Met-2

source_name: PC3 cells in the 0 μM Methionine media for 24 hours, biological rep2


title: PC3 0 μM Met 24h-rep3

description: Sample name: PC3 0 μM Met-3

source_name: PC3 cells in the 0 μM Methionine media for 24 hours, biological rep3


title: PC3 1 μM Met 24h-rep1

description: Sample name: PC3 1 μM Met-1

source_name: PC3 cells in the 1 μM Methionine media for 24 hours, biological rep1

value: 1 μM Methionine media


title: PC3 1 μM Met 24h-rep2

description: Sample name: PC3 1 μM Met-2

source_name: PC3 cells in the 1 μM Methionine media for 24 hours, biological rep2


title: PC3 Con 24h-rep1

description: Sample name: PC3 Con-1

source_name: PC3 cells in the control media for 24 hours, biological rep1


title: PC3 Con 24h-rep2

description: Sample name: PC3 Con-2

source_name: PC3 cells in the control media for 24 hours, biological rep2


title: PC3 0 μM Met 24h-rep1

description: Sample name: PC3 0 μM Met-1

source_name: PC3 cells in the 0 μM Methionine media for 24 hours, biological rep1


title: MCF7 -Trp 24h-rep4

description: Sample name: MCF7 -Trp-4

source_name: MCF7 cells deprived Tryptophan for 24 hours, biological rep4

value: deprived of Tryptophan


title: PC3 Con 24h-rep3

description: Sample name: PC3 Con-3

source_name: PC3 cells in the control media for 24 hours, biological rep3


title: MCF7 -Trp 24h-rep1

description: Sample name: MCF7 -Trp-1

source_name: MCF7 cells deprived Tryptophan for 24 hours, biological rep1


title: MCF7 -Trp 24h-rep3

description: Sample name: MCF7 -Trp-3

source_name: MCF7 cells deprived Tryptophan for 24 hours, biological rep3


title: MCF7 -Tyr 24h-rep4

description: Sample name: MCF7 -Tyr-4

source_name: MCF7 cells deprived Tyrosine for 24 hours, biological rep4

value: deprived of Tyrosine


title: MCF7 -Tyr 24h-rep1

description: Sample name: MCF7 -Tyr-1

source_name: MCF7 cells deprived Tyrosine for 24 hours, biological rep1


title: MCF7 -Thr 24h-rep4

description: Sample name: MCF7 -Thr-4

source_name: MCF7 cells deprived Theronine for 24 hours, biological rep4

value: deprived of Theronine


title: MCF7 -Thr 24h-rep3

description: Sample name: MCF7 -Thr-3

source_name: MCF7 cells deprived Theronine for 24 hours, biological rep3


title: MCF7 -Ser 24h-rep2

description: Sample name: MCF7 -Ser-2

source_name: MCF7 cells deprived Serine for 24 hours, biological rep2

value: deprived of Serine


title: MCF7 -Tyr 24h-rep2

description: Sample name: MCF7 -Tyr-2

source_name: MCF7 cells deprived Tyrosine for 24 hours, biological rep2


title: MCF7 -Thr 24h-rep2

description: Sample name: MCF7 -Thr-2

source_name: MCF7 cells deprived Theronine for 24 hours, biological rep2


title: MCF7 -Ser 24h-rep1

description: Sample name: MCF7 -Ser-1

source_name: MCF7 cells deprived Serine for 24 hours, biological rep1


title: PC3 1 μM Met 24h-rep3

description: Sample name: PC3 1 μM Met-3

source_name: PC3 cells in the 1 μM Methionine media for 24 hours, biological rep3


title: MCF7 -Met 24h-rep4

description: Sample name: MCF7 -Met-4

source_name: MCF7 cells deprived Methionine for 24 hours, biological rep4


title: MCF7 -Ser 24h-rep3

description: Sample name: MCF7 -Ser-3

source_name: MCF7 cells deprived Serine for 24 hours, biological rep3


title: MCF7 -Met 24h-rep3

description: Sample name: MCF7 -Met-3

source_name: MCF7 cells deprived Methionine for 24 hours, biological rep3


title: MCF7 -Thr 24h-rep1

description: Sample name: MCF7 -Thr-1

source_name: MCF7 cells deprived Theronine for 24 hours, biological rep1


title: MCF7 -Lys 24h-rep3

description: Sample name: MCF7 -Lys-3

source_name: MCF7 cells deprived Lysine for 24 hours, biological rep3

value: deprived of Lysine


title: MCF7 -Ser 24h-rep4

description: Sample name: MCF7 -Ser-4

source_name: MCF7 cells deprived Serine for 24 hours, biological rep4


title: MCF7 -Met 24h-rep2

description: Sample name: MCF7 -Met-2

source_name: MCF7 cells deprived Methionine for 24 hours, biological rep2


title: MCF7 -Tyr 24h-rep3

description: Sample name: MCF7 -Tyr-3

source_name: MCF7 cells deprived Tyrosine for 24 hours, biological rep3


title: MCF7 -Met 24h-rep1

description: Sample name: MCF7 -Met-1

source_name: MCF7 cells deprived Methionine for 24 hours, biological rep1


title: MCF7 -Lys 24h-rep4

description: Sample name: MCF7 -Lys-4

source_name: MCF7 cells deprived Lysine for 24 hours, biological rep4


title: MCF7 -Cys 24h-rep1

description: Sample name: MCF7 -Cys-1

source_name: MCF7 cells deprived Cystine for 24 hours, biological rep1

value: deprived of Cystine


title: S1P_C18_TC1_T32

description:
S1P Treatment Time Course 1 32h
EXPT_ID: 52000
PRINT_ID: 1064

value: cultured normal human dermal fibroblasts

source_name: Stratagene Universal Human Reference

value: reference


title: MCF7 -Cys 24h-rep3

description: Sample name: MCF7 -Cys-3

source_name: MCF7 cells deprived Cystine for 24 hours, biological rep3

value: 24 hours


title: MCF7 -Lys 24h-rep1

description: Sample name: MCF7 -Lys-1

source_name: MCF7 cells deprived Lysine for 24 hours, biological rep1


title: MCF7 -Lys 24h-rep2

description: Sample name: MCF7 -Lys-2

source_name: MCF7 cells deprived Lysine for 24 hours, biological rep2


title: MCF7 -Gly 24h-rep3

description: Sample name: MCF7 -Gly-3

source_name: MCF7 cells deprived Glycine for 24 hours, biological rep3

value: deprived of Glycine


title: MCF7 -Arg 24h-rep3

description: Sample name: MCF7 -Arg-3

source_name: MCF7 cells deprived Arginine for 24 hours, biological rep3

value: deprived of Arginine


title: MCF7 -Gly 24h-rep2

description: Sample name: MCF7 -Gly-2

source_name: MCF7 cells deprived Glycine for 24 hours, biological rep2


title: MCF7 -Cys 24h-rep4

description: Sample name: MCF7 -Cys-4

source_name: MCF7 cells deprived Cystine for 24 hours, biological rep4


title: MCF7 -Gly 24h-rep4

description: Sample name: MCF7 -Gly-4

source_name: MCF7 cells deprived Glycine for 24 hours, biological rep4


title: MCF7 -Cys 24h-rep2

description: Sample name: MCF7 -Cys-2

source_name: MCF7 cells deprived Cystine for 24 hours, biological rep2


title: MCF7 -Gly 24h-rep1

description: Sample name: MCF7 -Gly-1

source_name: MCF7 cells deprived Glycine for 24 hours, biological rep1


title: MCF7 -Arg 24h-rep2

description: Sample name: MCF7 -Arg-2

source_name: MCF7 cells deprived Arginine for 24 hours, biological rep2


title: MCF7 -Arg 24h-rep1

description: Sample name: MCF7 -Arg-1

source_name: MCF7 cells deprived Arginine for 24 hours, biological rep1


title: MCF7 -Phe 24h-rep3

description: Sample name: MCF7 -Phe-3

source_name: MCF7 cells deprived Phenylalanine for 24 hours, biological rep3

value: deprived of Phenylalanine


title: MCF7 -Phe 24h-rep2

description: Sample name: MCF7 -Phe-2

source_name: MCF7 cells deprived Phenylalanine for 24 hours, biological rep2


title: MCF7 -Phe 24h-rep1

description: Sample name: MCF7 -Phe-1

source_name: MCF7 cells deprived Phenylalanine for 24 hours, biological rep1


title: MCF7 -Arg 24h-rep4

description: Sample name: MCF7 -Arg-4

source_name: MCF7 cells deprived Arginine for 24 hours, biological rep4


title: MCF7 -Val 24h-rep3

description: Sample name: MCF7 -Val-3

source_name: MCF7 cells deprived Valine for 24 hours, biological rep3

value: deprived of Valine


title: MCF7 -Val 24h-rep2

description: Sample name: MCF7 -Val-2

source_name: MCF7 cells deprived Valine for 24 hours, biological rep2


title: MCF7 -Leu 24h-rep3

description: Sample name: MCF7 -Leu-3

source_name: MCF7 cells deprived leucine for 24 hours, biological rep3

value: deprived of leucine