title: 50 mg/kg ANIT, 2 hr, bile duct, biological replicate 5

description:
Gene expression data
80_50mg_2hr_bileduct.CEL

source_name: Rat bile ducts from animal 2 hr after dosing with ANIT in the vehicle


title: Male Bull 2 sample 3

status: Public on Feb 24 2010

type: RNA

city: Madrid

first: Pablo

last: Bermejo-Álvarez

state: Madrid

address: Ctra La Coruña Km 5,9

department: Reproducción Animal

country: Spain

institute: INIA

description: Gene expression data from male Day 7 blastocysts produced with sorted semen from Bull2

hyb_protocol: Labelled cRNA was fragmented in fragmentation buffer (5× buffer: 200 mM Tris-acetate (pH 8.1)/500 mM KOAc/150 mM MgOAc) and hybridised to the microarrays in 200µl of hybridization solution containing 15µg labelled target in 1× Mes buffer (0.1 M Mes/1.0 M NaCl/20 mM EDTA 0.01%/Tween20) and 0.1mg/ml herring sperm DNA, 10% DMSO, 0.5mg/ml BSA, 50 pM control oligonucleotide B2 and 1x eukaryotic hybridization controls (bioB, bioC, bioD, cre). Both control oligonucleotide B2 and eukaryotic hybridisation controls were purchased from Affymetrix. Hybridization mix was applied to Bovine Genome array (Affymetrix), and arrays were placed on a rotisserie and rotated at 60 rpm for 16h at 45°C. Following hybridization, the arrays were washed and stained with a streptavidin-phycoerythrin conjugate (Molecular Probes).

scan_protocol: The arrays were scanned using a confocal scanner (GC3000_Affymetrix). The image data were analysed by GeneChip Operating Software (GCOS 1.4, Affymetrix)

data_processing: For the Bioinformatic analysis dChip (www.dchip.org) and Affy/AffyPLM (Bioconductor) software were used to look for samples acting as outliers and Partek Genomics Suite 6.4 (Partek® software, Copyright © 2008 Partek Inc., St. Louis, MO, USA.Partek) to perform gene expression analysis. RMA processing was used for normalizing the data as well as a global median normalisation. The change in each gene expression was calculated by determining the fold change (ratio) of the mean intensity of each group.

label: biotin

molecule: total RNA

organism: Bos taurus

source_name: Male blastocysts from Bull 2

label_protocol: Labelled cRNA was synthesized with a linear RNA amplification method (Message Amp Premier kit, Ambion) following provider´s instructions and using 50 ng of total RNA as template for reverse transcription.

growth_protocol: Details for embryo production are provided in Biology of Reproduction 2008; 79:594-597.

extract_protocol: Total RNA was isolated and purified using RNaeasy Micro kit (Qiagen).

treatment_protocol: Blastocysts were snap frozen on Day 7 post-insemination and kept at -80 ºC until analysis.

tag: cell type

value: blastocyst

tag: genotype

value: Mixed breed

tag: age

value: Day 7 post insemination

tag: gender

value: Male


title: Control Individual 9

city: Québec

first: Christopher

last: Sauvage

state: QC

address: 1030 Avenue de la médecine - Pavillon Marchand

department: Biology

country: Canada

institute: University Laval

description: Control Individual 9

hyb_protocol: Microarray were hybridized using Cy3/Cy5 dyes (Genisphere) as detailed in St-Cyr et al. (2008)

scan_protocol: Transcription profiles from selected and control lines were measured using the Scanarray laser instrument (Packard Bioscience). Pictures were analysed and gene expression levels quantified using the Quantarray software with the histogram quantification method.

data_processing: Data from the two life stages were exported in text format and were separately analysed using a mixed model ANOVA and the R/MAANOVA package (Kerr and Churchill 2000; Wu et al. 2002). Normalization algorithm: Lowess

organism: Salvelinus fontinalis

source_name: Liver and caecum pyloric tissue mixed

label_protocol: Messenger RNA from each sample was reverse-transcribed and labelled using the Genisphere 3DNA Array 50 kit provided by Invitrogen, using the Superscript II retro-transcriptase enzyme and Cy3/Cy5 dyes (Genisphere), according to the manufacturer’s recommendations (Invitrogen protocol: http://web.uvic.ca/cbr/grasp/). Then, cDNA was purified using Microcon YM30 (Millipore, Beford, MA, USA)

extract_protocol:
Whole individuals were stored at -80°C prior to any sampling
All RNA extractions were performed on ice (4°C) and following the same protocol to reduce technical biases in genes expression measures. Entire “control” and “selected” fry were individually homogenised in a mixture composed of 4ml Trizol® reagent (Sigma) and 20 µL isopropanol (Sigma), using a Qiagen homogenizer, whereas approximately 150 mg of liver and pyloric caeca of individual juveniles were treated in the same way. Total RNA was extracted using the Purelink Micro to midi total RNA purification system kit (Invitrogen), according to the manufacturer’s recommendations. Subsequently, RNA integrity and quantity was controlled using a Nanodrop instrument (ND-1000, Nanodrop).

treatment_protocol: Samples were treated with DNAse enzyme prior to labeling

tag: fish line

value: control

tag: tissue type

value: mixed liver and caecum pyloric tissue

value: 16 weeks old juveniles fish


title: Vehicle control, 6 hr, hepatocyte, biological replicate 1

city: Research Triangle Park

first: Neal

middle: F

last: Cariello

state: NC

address: 5 Moore Drive, Bldg 9, Rom 2011

department: Safety Assessment

country: USA

institute: GlaxoSmithKline

description:
Gene expression data
157_0mg_6hr_Hep.CEL

hyb_protocol: Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.

organism: Rattus norvegicus

source_name: Rat hepatocytes from animal 6 hr after dosing with the vehicle, 10 ml/kg corn oil

label_protocol: Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies

growth_protocol: Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.

extract_protocol: RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.

treatment_protocol: Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.

tag: strain

value: Sprague Dawley

value: 8 weeks old

tag: tissue

value: liver

value: hepatocyes

tag: isolation method

value: Laser Capture Microdissection


title: Selected Individual 8

description: Selected Individual 8

value: selected


title: 50 mg/kg ANIT, 2 hr, bile duct, biological replicate 4

description:
Gene expression data
79_50mg_2hr_bileduct.CEL

value: bile duct


title: Selected Individual 14

description: Selected Individual 14


title: Selected Individual 17

description: Selected Individual 17


title: Control Individual 12

description: Control Individual 12


title: Control Individual 18

description: Control Individual 18


title: Control Individual 20

description: Control Individual 20


title: Control Individual 8

description: Control Individual 8


title: Selected Individual 9

description: Selected Individual 9


title: Selected Individual 7

description: Selected Individual 7


title: 50 mg/kg ANIT, 2 hr, bile duct, biological replicate 3

description:
Gene expression data
78_50mg_2hr_bileduct.CEL


title: 50 mg/kg ANIT, 2 hr, bile duct, biological replicate 2

description:
Gene expression data
77_50mg_2hr_bileduct.CEL


title: Vehicle control, 2 hr, bile duct, biological replicate 1

description:
Gene expression data
51_0mg_2hr_bileduct.CEL

source_name: Rat bile ducts from animal 2 hr after dosing with the vehicle, 10 ml/kg corn oil


title: Vehicle control, 2 hr, bile duct, biological replicate 5

description:
Gene expression data
55_0mg_2hr_bileduct.CEL


title: Vehicle control, 2 hr, bile duct, biological replicate 2

description:
Gene expression data
52_0mg_2hr_bileduct.CEL


title: Control Individual 7

description: Control Individual 7


title: Vehicle control, 2 hr, bile duct, biological replicate 4

description:
Gene expression data
54_0mg_2hr_bileduct.CEL


title: 50 mg/kg ANIT, 2 hr, bile duct, biological replicate 1

description:
Gene expression data
76_50mg_2hr_bileduct.CEL


title: Selected Individual 5

description: Selected Individual 5


title: Control Individual 5

description: Control Individual 5


title: Control Individual 6

description: Control Individual 6


title: Vehicle control, 2 hr, bile duct, biological replicate 3

description:
Gene expression data
53_0mg_2hr_bileduct.CEL


title: 50 mg/kg ANIT, 2 hr, hepatocyte, biological replicate 4

description:
Gene expression data
179_50mg_2hr_hepatocyte.CEL

source_name: Rat hepatocytes from animal 2 hr after dosing with ANIT in the vehicle


title: 50 mg/kg ANIT, 2 hr, hepatocyte, biological replicate 5

description:
Gene expression data
180_50mg_2hr_hepatocyte.CEL


title: Selected Individual 6

description: Selected Individual 6


title: Brassica napus_root_Cu-starvation (2 weeks) vs. full nutrition

first: Anja

last: Buhtz

address: Campus de Montegancedo, M40,km38

institute: Centro de Biotecnologia y Genomica de Plantas

description: Chip contained 714 plant microRNA probes (Sanger miRBase 11.0) plus additional 85 custom probes for the detection of small RNA sequences derived from Brassica napus phloem sap (Bn_PsRNAs).

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 µL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing:
Data were analyzed by first subtracting the background and then normalizing the signals by removing system related variation (sample amount variations, different labeling dyes and signal gain differences of scanners) using a locally-weighted regression filter (cyclic LOWESS).  For two color experiments, the ratio of the two sets of detected signals (log2 transformed, balanced) and p-values of the t-test were calculated; differentially detected signals were those with less than 0.01 p-values.
The VALUE column represents the statistically significant log2 ratios of Cy3 (-Cu) and Cy5 (FN) labeled transcripts [Log2 (Signal Cy3 / Signal Cy5)].

organism: Brassica napus

source_name: Brassica napus, root, 2 weeks without copper

label_protocol: Microarray assay was performed using the service provider LC Sciences (Houston, TX). The assay started from 2 to 5 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (from Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags were used for the two RNA samples in dual-sample experiments. On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry.

growth_protocol: For hydroponic growth, Brassica napus seeds were germinated on wet filter paper for 1 week. Germ buds were transferred to plastic boxes containing nutrient medium for 10 weeks. Nutrient medium: 0.6 mM NH4NO3, 1 mM Ca(NO3)2*4H2O, 0.04 mM Fe-EDTA, 0.5 mM K2HPO4, 0.5 mM K2SO4, 0.4 mM Mg(NO3)2*6H2O. Micro nutrients added: 0.8 µM ZnSO4*7H2O, 9 µM MnCl2*4H2O, 0.1 µM Na2MoO4*2H2O, 23 µM H3BO3, 0.3 µM CuSO4*5H2O. The pH was adjusted to 4.7 with 37 % HCl. Nutrient solutions were changed after 4 weeks, and then renewed once a week. After 5 to 6 weeks, media were constantly aerated by an aquarium air pump.

extract_protocol: Total RNA from 100 mg frozen material of root tissue was isolated by using Trizol reagent (Invitrogen) according to manufacturer’s instructions.

treatment_protocol: Copper starvation was applied for two weeks before flowering started by changing to medium without copper. Here, the 0.3 µM CuSO4*5H2O were omitted from the full nutrient solution.

tag: cultivar

value: Drakkar

value: 10 weeks

value: root

tag: developmental stage

value: flowering

tag: cultivation type

value: hydroponically

tag: treatment

value: copper starvation

source_name: Brassica napus, root, full nutrition

value: full nutrition


title: Brassica napus_leaf_Cu-starvation (2 weeks) vs. full nutrition

source_name: Brassica napus, leaf, 2 weeks without copper

extract_protocol: Total RNA from 100 mg frozen material of leaf tissue was isolated by using Trizol reagent (Invitrogen) according to manufacturer’s instructions.

value: leaf

source_name: Brassica napus, leaf, full nutrition


title: Selected Individual 4

description: Selected Individual 4

value: mixed liver and caecum pyloric tissue


title: SHPKO_WD_rep3

city: Rootstown

first: Yoonkwang

last: Lee

address: 4209 State Route 44

department: Integrative Medical Sciences

institute: Northeast Ohio Medical University

description: replicate 3 of KOWD

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation using Illumina's BeadStudio software

organism: Mus musculus

source_name: mouse islets

label_protocol: Biotinylated cRNA were prepared with the Illumina Totalprep kit

growth_protocol: Mouse were fed chow and a western diet for 6 months. The diet regimen started when they were at 4 month old

extract_protocol: RNA was extracted with  QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed using a 1% agarose gel.

treatment_protocol: To isolate the islets from pancreas, pancreas were perfused with collagenase solution.

value: male

value: 10 months

value: islets

tag: genotype/variation

value: SHPKO

tag: growth protocol

value: Western diet


title: Control Individual 3

description: Control Individual 3

value: control

value: 16 weeks old juveniles fish


title: Brassica napus_phloem_S-starvation (2 weeks) vs. full nutrition

description: Chip contained 623 plant microRNA probes (Sanger miRBase 10.0) plus additional 85 custom probes for the detection of small RNA sequences derived from Brassica napus phloem sap (Bn_PsRNAs).

data_processing:
Data were analyzed by first subtracting the background and then normalizing the signals by removing system related variation (sample amount variations, different labeling dyes and signal gain differences of scanners) using a locally-weighted regression filter (cyclic LOWESS).  For two color experiments, the ratio of the two sets of detected signals (log2 transformed, balanced) and p-values of the t-test were calculated; differentially detected signals were those with less than 0.01 p-values.
The VALUE column represents the statistically significant log2 ratios of Cy3 (-S) and Cy5 (FN) labeled transcripts [Log2 (Signal Cy3 / Signal Cy5)].

source_name: Brassica napus, phloem sap, 2 weeks without sulfur

extract_protocol: Total RNA from phloem sap was isolated by Trizol LS reagent (Invitrogen) according to manufacturer’s instructions.

treatment_protocol: Sulfur starvation was applied for two weeks before flowering started by changing to medium without sulfur. Here, 0.5 mM K2SO4 were substituted by 0.5 mM K2HPO4 and instead of ZnSO4*7H2O and CuSO4*5H2O as micro nutrients, 1 µM ZnCl2 and 1 µM CuCl2*2H2O were added for low sulfate experiments.

value: phloem sap

value: sulfur starvation

source_name: Brassica napus, phloem sap, full nutrition


title: Brassica napus_phloem_Cu-starvation (2 weeks) vs. full nutrition

source_name: Brassica napus, phloem sap, 2 weeks without copper

value: Drakkar

value: 10 weeks


title: Selected Individual 2

description: Selected Individual 2

value: selected


title: Selected Individual 3

description: Selected Individual 3


title: Brassica napus_leaf_S-starvation (2 weeks) vs. full nutrition

source_name: Brassica napus, leaf, 2 weeks without sulfur

value: flowering

value: hydroponically


title: SHPKO_WD_rep2

description: replicate 2 of KOWD


title: Brassica napus_root_S-starvation (2 weeks) vs. full nutrition

source_name: Brassica napus, root, 2 weeks without sulfur

value: root

value: full nutrition


title: Control Individual 2

description: Control Individual 2

value: mixed liver and caecum pyloric tissue


title: Control Individual 4

description: Control Individual 4


title: 50 mg/kg ANIT, 2 hr, hepatocyte, biological replicate 3

description:
Gene expression data
178_50mg_2hr_hepatocyte.CEL

value: Sprague Dawley

value: 8 weeks old

value: liver

value: hepatocyes

value: Laser Capture Microdissection


title: WT_WD_rep3

description: replicate 3 of WTWD

value: male

value: 10 months

value: islets

value: WT

value: Western diet


title: SHPKO_WD_rep1

description: replicate 1 of KOWD

value: SHPKO


title: 50 mg/kg ANIT, 2 hr, hepatocyte, biological replicate 2

description:
Gene expression data
177_50mg_2hr_hepatocyte.CEL


title: 50 mg/kg ANIT, 2 hr, hepatocyte, biological replicate 1

description:
Gene expression data
176_50mg_2hr_hepatocyte.CEL


title: Control Individual 1

description: Control Individual 1

value: control

value: 16 weeks old juveniles fish


title: SHPKO_Chow_rep2

description: replicate 2 of KOC

value: chow (control)


title: WT_WD_rep1

description: replicate 1 of WTWD


title: SHPKO_Chow_rep3

description: replicate 3 of KOC


title: Brassica napus_phloem_Fe-starvation (3 weeks) vs. full nutrition

description: Chip contained 653 plant microRNA probes (Sanger miRBase 10.1) plus additional 85 custom probes for the detection of small RNA sequences derived from Brassica napus phloem sap (Bn_PsRNAs).

data_processing:
Data were analyzed by first subtracting the background and then normalizing the signals by removing system related variation (sample amount variations, different labeling dyes and signal gain differences of scanners) using a locally-weighted regression filter (cyclic LOWESS).  For two color experiments, the ratio of the two sets of detected signals (log2 transformed, balanced) and p-values of the t-test were calculated; differentially detected signals were those with less than 0.01 p-values.
The VALUE column represents the statistically significant log2 ratios of Cy3 (-Fe) and Cy5 (FN) labeled transcripts [Log2 (Signal Cy3 / Signal Cy5)].

source_name: Brassica napus, phloem sap, 3 weeks without iron

treatment_protocol: Iron starvation was applied for three weeks before flowering started by changing to medium without iron. Here, the 0.04 mM Fe-EDTA was omitted from the medium.

value: Drakkar

value: 10 weeks

value: phloem sap

value: flowering

value: hydroponically

value: iron starvation


title: WT_WD_rep2

description: replicate 2 of WTWD


title: Brassica napus_root_Fe-starvation (3 weeks) vs. full nutrition

source_name: Brassica napus, root, 3 weeks without iron

value: root

value: full nutrition


title: Selected Individual 1

description: Selected Individual 1

value: selected

value: mixed liver and caecum pyloric tissue


title: WT_Chow_rep2

description: replicate 2 of WTC

value: male

value: 10 months

value: islets


title: WT_Chow_rep3

description: replicate 3 of WTC

value: WT


title: Vehicle control, 2 hr, hepatocyte, biological replicate 5

description:
Gene expression data
155_0mg_2hr_hepatocyte.CEL

source_name: Rat hepatocytes from animal 2 hr after dosing with the vehicle, 10 ml/kg corn oil

value: Sprague Dawley

value: 8 weeks old

value: liver

value: hepatocyes

value: Laser Capture Microdissection


title: Vehicle control, 2 hr, hepatocyte, biological replicate 4

description:
Gene expression data
154_0mg_2hr_hepatocyte.CEL


title: Vehicle control, 2 hr, hepatocyte, biological replicate 3

description:
Gene expression data
153_0mg_2hr_hepatocyte.CEL


title: Vehicle control, 2 hr, hepatocyte, biological replicate 2

description:
Gene expression data
152_0mg_2hr_hepatocyte.CEL


title: Brassica napus_inflorescence stem vs. phloem under full nutrition

data_processing:
Data were analyzed by first subtracting the background and then normalizing the signals by removing system related variation (sample amount variations, different labeling dyes and signal gain differences of scanners) using a locally-weighted regression filter (cyclic LOWESS).  For two color experiments, the ratio of the two sets of detected signals (log2 transformed, balanced) and p-values of the t-test were calculated; differentially detected signals were those with less than 0.01 p-values.
The VALUE column represents the statistically significant log2 ratios of Cy5 (phloem) and Cy3 (inflorescence stem) labeled transcripts [Log2 (Signal Cy5 / Signal Cy3)].

value: Drakkar

value: 10 weeks

value: phloem sap

source_name: Brassica napus, inflorescence stem, full nutrition

extract_protocol: Total RNA from 100 mg frozen material of inflorescence stem tissue was isolated by using Trizol reagent (Invitrogen) according to manufacturer’s instructions.

value: inflorescence stem


title: 250 µM nicotine treatment, biological replicate 3

status: Public on Feb 23 2010

city: Ithaca

first: John

middle: Sawyer

last: Ramsey

state: NY

address: Comstock Hall

institute: Cornell University

description: Technical Replicate

hyb_protocol: Agilent 2 color microarray protocol hybridization steps were followed

scan_protocol: Agilent scanner and Agilent Feature Extraction Software

data_processing: No background subtraction, Loess normalization within arrays. Linear model and statistical analysis conducted in R, using the LIMMA package

label: Alexa Fluor 555

organism: Myzus persicae

source_name: control diet: aphid heads collected after 24 hours feeding

label_protocol: Ambion Aminoallyl MessageAmp II indirect labeling kit was used, with Alexa Fluor 555 and 647

growth_protocol:
Aphids were transferred onto diet from cabbage plants. Aphid heads were dissected after 24 hours of feeding.
Aphids were reared on liquid diet containing 20 amino acids and sucrose, with or without nicotine

extract_protocol: Ambion Ribopure was used to collect aphid RNA

value: head

tag: diet

value: 24 hours feeding on control diet

label: Alexa fluor 647

source_name: 250 µM nicotine diet: aphid heads collected after 24 hours feeding

value: 24 hours feeding on 250 µM nicotine diet


title: Brassica napus_leaf_Fe-starvation (3 weeks) vs. full nutrition

source_name: Brassica napus, leaf, 3 weeks without iron

value: leaf

value: flowering

value: hydroponically

value: iron starvation

value: full nutrition


title: SHPKO_Chow_rep1

description: replicate 1 of KOC

value: male

value: 10 months

value: islets

value: SHPKO

value: chow (control)


title: 250 µM nicotine treatment, technical replicate of nichead 250_1

description: Biological Replicate


title: Vehicle control, 2 hr, hepatocyte, biological replicate 1

description:
Gene expression data
151_0mg_2hr_hepatocyte.CEL

value: Sprague Dawley

value: 8 weeks old

value: liver

value: hepatocyes

value: Laser Capture Microdissection


title: WT_Chow_rep1

description: replicate 1 of WTC

value: WT


title: 100 µM nicotine treatment, technical replicate of nichead 100_2

description: Technical Replicate

value: head

value: 24 hours feeding on control diet

source_name: 100 µM nicotine diet: aphid heads collected after 24 hours feeding

value: 24 hours feeding on 100 µM nicotine diet


title: 100 µM nicotine treatment, biological replicate 3

description: Biological Replicate


title: 100 µM nicotine treatment, biological replicate 2

description: Biological Replicate


title: 250 µM nicotine treatment, biological replicate 2

description: Biological Replicate

value: 24 hours feeding on 250 µM nicotine diet


title: 100 µM nicotine treatment, biological replicate 1

description: Biological Replicate


title: Sp-CONT-Biorep1

city: Salamanca

first: Luis

last: Quintales

address: Calle Zacarías González, 2

department: Universidad de Salamanca / CSIC

institute: Instituto de Biología Funcional y Genómica (IBFG)

description: Platform GPL7715-CustomCDF

hyb_protocol: Platform hybridization was performed using 5 micrograms of single stranded sense DNA, labelled with biotin and fragmented to an average size of 100 nucleotides. Hybridization was performed following the instructions of the Affymetrix assay manual for each platform.

scan_protocol: Affymetrix standard protocol using Affymetirix Fluidics 450 and Scanner 3000

data_processing: RMA

organism: Schizosaccharomyces pombe 972h-

source_name: Wildtype S.pombe strain

label_protocol: Target labeling preserving the original polarity of RNAs was performed following the instructions of the GeneChip whole transcript sense target labelling assay manual from Affymetrix.

growth_protocol: 100 ml yeast extract (YE) medium at 30 ºC and 170 rpm until OD595=0.2 (4 X 106 cells/ml)

extract_protocol: Total RNA was prepared by resuspending the cell pellets in 20 μl extraction buffer (100 mM EDTA pH 8.0, 100 mM NaCl, 50 mM Tris-Hcl pH 8.0), 20 μl phenol/chloroform, 2 μl 10% SDS, 200 μl glass beads (425-600 μm, SIGMA G-8772). Cells were mechanically disrupted in a Fast-Prep (Savant BIO 101) and the cell lysate was extracted with phenol, phenol/chloroform and chloroform/isoamyl alcohol before precipitation with 0.3 M sodium acetate and ethanol. RNA was resuspended in 50 μl of sterile water with Diethyl pyrocarbonate (SIGMA D-5758) and was furher purified through a RNeasy mini kit (Quiagen) following the suppliers specifications.

treatment_protocol: Two separate cultures developed from independent single colonies were processed in parallel throughout the entire experiment (biological duplicates). Cells from a 30 ml volume were collected by centrifugation at 2000 rpm for 2 minutes and the pellet was frozen immediately in liquid nitrogen (control samples). Hydrogen peroxyde (SIGMA, H-1009) was added to the rest of the culture at a final concentration of 0.5 mM and incubation proceed for 30 minutes after which 30 ml of culture were processed as above

tag: oxidative stress

value: no


title: Sp-H2O2-Biorep2

description: Platform GPL2529-CustomCDF

hyb_protocol: Hybridization was performed using 5 micrograms of cRNA, labelled with biotin and fragmented to an average size of 100 nucleotides. Hybridization was performed following the instructions of the Affymetrix assay manual for each platform.

label_protocol: Target labeling was performed following the instructions of the GeneChip whole transcript double-stranded target-labelling assay Affymetrix manual.

value: yes


title: Sp-H2O2-Biorep1

description: Platform GPL7715-CustomCDF


title: Sp-H2O2-Biorep2

description: Platform GPL7715-CustomCDF


title: Sp-CONT-Biorep2

description: Platform GPL2529-CustomCDF


title: 250 µM nicotine treatment, biological replicate 1

description: Biological Replicate


title: Sp-CONT-Biorep2

description: Platform GPL7715-CustomCDF


title: Cytoplasmic GSH sample3, biological rep1

status: Public on Feb 22 2010

city: Murcia

first: Pedro

last: Diaz-Vivancos

address: Campus Universitario de Espinardo, 25

department: Plant Breeding

institute: CEBAS-CSIC

description: Gene expression data when GSH is localized in the cytoplasm.

hyb_protocol: The target cRNAs were fragmented, combined with hybridization and spike controls, then hybridized to the Genechip Arabidopsis ATH1 Genome Array (Affymetrix, Inc., Santa Clara, CA) for 16 h. Following hybridization, the arrays were washed and stained with streptavidin phycoerythrin conjugate using an automated GeneChip® Fluidics Station 450

scan_protocol: GeneChips were scanned with a GeneChip® Scanner 3000 7G using a 570 nm excitation wavelength laser. Microarray quality controls were assessed using GeneChip® Operating Software (Affymetrix)..

data_processing:
Raw intensity values from the scanned Arabidopsis ATH1 Genome Arrays were analyzed using the Robust Multichip Average method (RMA).
A significance test was undertaken by calculating a null hypothesis through a permuted modified t-statistic across the replicates for each array comparison. The log2 means of the normalized intensity values of the biological replicates were compared as ratios, where a log2 ratio of ±1.0 and a p-value of < 0.01 was selected as worthy of further study.

label: Biotin

organism: Arabidopsis thaliana

source_name: GSHc3, 174 h after inoculation

label_protocol: Double-stranded cDNA was generated from each of the eighteen total-RNA samples and transcribed to obtain biotin-labeled cRNA.

growth_protocol: The growth of A. thaliana cultures was performed as described by Pellny et al., (2009).

extract_protocol: Total RNA was extracted from frozen cell pellet using RNeasy Plant Mini Kit (Qiagen) according to manufacturer’s protocol.

treatment_protocol: The logarithmic growth phase of the cultures was prolonged by either diluting the cultures or replenishing the media (media change). Samples were harvested at the indicated stages and cell pellets were snap frozen in liquid nitrogen and stored at −80°C.

tag: sample source

value: Cell suspensions

tag: treatment protocol

value: Media change

tag: gsh localization

value: Cytoplasmic GSH

tag: time (post-inoculation)


title: Sp-CONT-Biorep1

description: Platform GPL2529-CustomCDF


title: Sp-H2O2-Biorep1

description: Platform GPL2529-CustomCDF


title: Cytoplasmic GSH sample2, biological rep3

source_name: GSHc2, 102 h after inoculation

value: Control


title: Cytoplasmic GSH sample3, biological rep2


title: Cytoplasmic GSH sample2, biological rep1


title: Ovary_TNFvsCONTROL

city: Barcelona

first: Diego

last: Crespo

state: Barcelona

address: Avenida Diagonal 645

department: Physiology

institute: University of Barcelona

description: Combined data from dye swap samples

hyb_protocol: The slides were pretreated with 1% BSA(fraction V), 20 × SSC, 10% SDS (30 min at 50°C) and washed with 2 × SSC (3 min) and 0.2 × SSC (3 min) and hybridized overnight in cocktail containing 50 × Denhardt's, 20 × SSC, 10% SDS, 10μg/μl polyadenylate and 10 μg/μl yeast tRNA. All chemicals were from Sigma-Aldrich.

scan_protocol: Scanning was performed with ScanArray 5000 (GSI Lumonics) and images were processed with GenePix Pro 5.0 (Axon). The measurements in spots were filtered by criteria I/B ≥ 3 and (I-B)/(SI + SB) ≥ 0.6, where I and B are the mean signal and background intensities and SI, SB are the standard deviations. After subtraction of median background from median signal intensities, the expression ratios (ER) were calculated. Locally weighted non-linear regression (Lowess) normalization was performed, first for the whole slide and next for twelve rows and four columns per slide. The differential expression was assessed by the difference of the mean log2 expression ratios between the slides with reverse labelling (6 spot replicates per gene on each slide, Student´s t-test, p < 0.01). The log2 ER ranked up or down-regulated genes were analyzed interrogating the functional classes of Gene Ontology (GO) and compared by the sums of ranked genes (Student's t-test, p < 0.05).

data_processing: The measurements in spots were filtered by criteria I/B ≥ 3 and (I-B)/(SI + SB) ≥ 0.6, where I and B are the mean signal and background intensities and SI, SB are the standard deviations. After subtraction of mean background, LOWESS normalization was performed. To assess differential expression of genes, the normalized log intensity ratios (expression ratio) were analyzed with Student's t-test (P <0.05).

organism: Oncorhynchus mykiss

source_name: TNF

label_protocol: Total RNA from pooled control and TNFα-treated brown trout preovulatory follicles (n = 20) from each of a total of three females was labelled with Cy3-dUTP and Cy5-dUTP (GE Healthcare, Barcelona, Spain) using SuperScript III Transcriptase. The cDNA synthesis reaction was performed at 50ºC for 2 h in a 20 µl reaction volume, followed with RNA degradation with 0.2 M NaOH at 37ºC for 15 min and alkaline neutralization with 0.6 M Hepes. Labeled cDNA was purified with Microcon YM30 (Millipore, Madrid, Spain).

extract_protocol: Total RNA from ovarian tissue was isolated using TRIzol Reagent (Invitrogen, Barcelona, Spain), following the manufacturer’s instructions and guidelines. Quantification was carried out with Qubit fluorometer (Invitrogen). cDNA synthesis was performed on 5 μg DNase-treated (RQ1 DNase, Promega, Barcelona, Spain) total RNA using SuperScript III Transcriptase (Invitrogen), oligo(dT) primer and random hexamer primers (Promega), according to the manufacturer's protocols. The RNA was stored at -80°C until use.

treatment_protocol: Reproductively mature female brown trout (Salmo trutta) from a cultured stock at the Piscifactoria de Bagà (Generalitat de Catalunya, Bagà, Spain) were kept under natural conditions of temperature and photoperiod. After dissection, brown trout preovulatory ovaries were placed in Hank´s balanced salt solution (HBSS) and individual ovarian follicles were manually separated with forceps from each ovary on ice. To collect ovarian tissue for RNA extraction, preovulatory follicles from each of a total of three females were incubated (400 follicles/50 ml) in HBSS-BSA in the absence or presence of rtTNFα (100 ng/ ml, dissolved directly in HBSS-BSA), at 15ºC for 24 h with gentle shaking (100 rpm). At the end of the incubation follicles (previously de-yolked by gentle pressure) were removed, flash frozen in liquid nitrogen and stored at -80ºC until assayed.

value: preovulatory follicles

source_name: Control


title: Cytoplasmic GSH sample1, biological rep1

source_name: GSHc1, 78 h after inoculation


title: Replicate 4

city: Seattle

first: Ludmila

last: Chistoserdova

state: WA

address: 616 NE Northlake Place

department: Chemical Engineering

institute: University of Washington

description: Biological replicate (S2B_Ea2B)

hyb_protocol: Hybridization was carried out by Mogene.

scan_protocol: Scanning was carried out by Mogene.

data_processing: The data in the INV_VALUE column were computed by taking the Log2 of the ratio of the Lowess normalized Alexa_647 signal (rDyeNormSignal) divided by the Lowess normalized Alexa_555 signal (gDyeNormSignal) for each spot.  The VALUE column reports Normalized log2 ratio test (ethylamine) versus reference (succinate).

organism: Methylorubrum extorquens

source_name: Succinate-grown cells

label_protocol: cDNA production and labelling were carried out by Mogene.

growth_protocol: Cells were grown at 28 ºC in batch culture using a mineral salts medium described previously ( Okubo et al., OMICS. 2007, 11:325-340.). Succinate was used at 40 mM and ethylamine was used at 20mM. Antibiotic concentrations were (in μg ml-1): tetracycline, 10; kanamycin, 50; rifamycin 50.

extract_protocol: Total RNA was isolated as described by Okubo et al., OMICS. 2007, 11:325-340.

treatment_protocol: Cells were processed as previously described ( Okubo et al., OMICS. 2007, 11:325-340.).

source_name: Ethylamine-grown cells


title: pCA24N-hnsK57N biofilm

city: State College

first: Thomas

middle: K.

last: Wood

state: PA

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

description: RNA extracted from biofilm cells of E. coli K-12 hha hns / pCA24N-hnsK57N after 7 hours of growth in LB with glasswool at 37ºC

hyb_protocol: Following affymetrix protocol. Prepared hybridization cocktail for Single Probe Array (49 Format) with total 200 ul volume including 1X hybrization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labelled cDNA. After loading of hybridization cocktail in Affymetrix E. coli Antisense Genome Array, the hybridization was performed at 45ºC, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS).

scan_protocol: Following affymetrix protocol. After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Escherichia coli K-12

source_name: pCA24N-hnsK57N biofilm

label_protocol:
Following affymetrix protocol.
cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

extract_protocol: The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB medium with 10 g of submerged glass wool (Corning Glass Works, Corning, NY) for forming biofilm. After incubation for 7 h at 37°C with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104).

value: BW25113 hha hns / pCA24N-hnsK57N

tag: time

value: 7 hours

tag: medium

value: LB

tag: cell type

value: biofilm

value: biofilm grown on glass wool, 37C


title: pCA24N-hns biofilm

description: RNA extracted from biofilm cells of E. coli K-12 hha hns / pCA24N-hns after 7 hours of growth in LB with glasswool at 37ºC

source_name: pCA24N-hns biofilm

tag: strain

value: BW25113 hha hns / pCA24N-hns


title: Cytoplasmic GSH sample1, biological rep3


title: Replicate 3

description: Biological replicate (S1B_Ea1B)

data_processing: The data in the VALUE column were computed by taking the Log2 of the ratio of the Lowess normalized Alexa_647 signal (rDyeNormSignal) divided by the Lowess normalized Alexa_555 signal (gDyeNormSignal) for each spot.  The VALUE column reports Normalized log2 ratio test (ethylamine) versus reference (succinate).


title: Cytoplasmic GSH sample1, biological rep2


title: Cytoplasmic GSH sample2, biological rep2


title: Nuclear GSH sample3, biological rep3

description: Gene expression data when GSH is localized into the nucleus.

source_name: GSHn3, 78 h after inoculation

value: Nuclear GSH


title: Nuclear GSH sample3, biological rep2


title: Nuclear GSH sample2, biological rep3

source_name: GSHn2, 198 h after inoculation


title: Non adherent macrophage of mafb null and WT

city: TSUKUBA

first: Michito

last: Hamada

state: IBARAKI

address: 1-1-1 tennodai

department: anatomy and embryogy

country: Japan

institute: University of Tsukuba

description: Data was analyzed by Excel software

hyb_protocol: Agilent Mouse Oligo Microarray Kit（G4121A）

scan_protocol: Agilent G2565AA microarray scanner

data_processing: Data were analyzed by Feature Extraction Software Version A.7.5.1 using linear and lowess normalization methods. Additional processing/filtering was carried out using Microsoft Excel.

source_name: WT macrophage

label_protocol: Low RNA Input Linear Amplification Kit（Agilent）、Cyanine3-CTP&Cyanine5-CTP（PerkinElmer）

extract_protocol: RNeasy mini Kit (Qiagen)

tag: tissue

value: fetal liver

value: macrophage

tag: culture condition

value: M-CSF induced in non adherent culture dish

tag: genome/variation

value: wild type

source_name: Mafb null macrophage

value: Mafb null


title: Nuclear GSH sample2, biological rep2

value: Cell suspensions


title: B24 In Vivo

city: Lausanne

first: Frederic

last: Raymond

address: Campus EPFL - Quartier de l'Innovation

department: Functional Genomics

country: Switzerland

institute: Nestle Institute of Health Sciences

description:
B24
Biopsies obtained from females of age 12-15 years devoid of neuromuscular disease, during surgery for idiopathic scoliosis.

hyb_protocol: Hybridized to an Illumina HumanRef-8 v2 Expression Beadchip following Illumina recommendations.

scan_protocol: The hybridized biotinylated cRNA was stained with streptavidin-Cy3 and quantitated using an Illumina BeadArray Reader (scanner)

data_processing:
Five biological replicates of each condition (cell culture and biopsy) were hybridized onto an Illumina HumanRef-8 array. Signal intensity analysis and preprocessing were performed using the BeadStudio software. The preprocessing algorithm produces an average expression value for each oligonucleotide probe sequence along with a detection p-value. After a background reduction, data were normalized using the quantile algorithm. Then, normalized data were transferred into GeneSpring GX (Agilent) where they were log transformed (log2) and averaged over replicates for each of the experimental conditions. Differential expression was analyzed comparing the cell cultures versus the biopsies with a paired t-test corrected with the Benjamini-Hochberg algorithm.

Non-normalized data is available in the supplementary file 'GSE17503_non-normalized_data.txt', which is linked to the Series GSE17503 record.

organism: Homo sapiens

source_name: Paravertebral muscle biopsy

label_protocol: Single stranded cRNA was generated and labeled incorporating biotinylated UTP (Illumina TotalPrep RNA Amplification Kit, Applied Biosystems/Ambion, Austin, TX,USA)

extract_protocol: Total RNA was extracted from cultured myotubes with RNeasy kit (Qiagen, Valencia, CA, USA).

value: paravertebral muscle

tag: gender

value: female


title: B25 In Vivo

description:
B25
Biopsies obtained from females of age 12-15 years devoid of neuromuscular disease, during surgery for idiopathic scoliosis.


title: Cytoplasmic GSH sample3, biological rep3

value: Media change

value: Cytoplasmic GSH


title: Replicate 2

description: Biological replicate (S2_Ea2)


title: B22 In Vivo

description:
B22
Biopsies obtained from females of age 12-15 years devoid of neuromuscular disease, during surgery for idiopathic scoliosis.


title: Nuclear GSH sample2, biological rep1

value: Control


title: Nuclear GSH sample3, biological rep1


title: Nuclear GSH sample1, biological rep3

source_name: GSHn1, 6 h after inoculation

value: 6 h


title: B26 In Vivo

description:
B26
Biopsies obtained from females of age 12-15 years devoid of neuromuscular disease, during surgery for idiopathic scoliosis.


title: B26 In Vitro

description:
B26
Cell culture obtained through explant technique from biopsies.
Biopsies obtained from females of age 12-15 years devoid of neuromuscular disease, during surgery for idiopathic scoliosis.

source_name: Paravertebral muscle cells in culture

value: paravertebral muscle cells


title: B19 In Vitro

description:
B19
Cell culture obtained through explant technique from biopsies.
Biopsies obtained from females of age 12-15 years devoid of neuromuscular disease, during surgery for idiopathic scoliosis.


title: Replicate 1

description: Biological replicate (S1_Ea1)


title: B25 in Vitro

description:
B25
Cell culture obtained through explant technique from biopsies.
Biopsies obtained from females of age 12-15 years devoid of neuromuscular disease, during surgery for idiopathic scoliosis.


title: B19 In Vivo

description:
B19
Biopsies obtained from females of age 12-15 years devoid of neuromuscular disease, during surgery for idiopathic scoliosis.


title: B24 In Vitro

description:
B24
Cell culture obtained through explant technique from biopsies.
Biopsies obtained from females of age 12-15 years devoid of neuromuscular disease, during surgery for idiopathic scoliosis.


title: Nuclear GSH sample1, biological rep2


title: 12h LIF-treated EpiSCs

status: Public on Feb 21 2010

city: Münster

first: Boris

last: Greber

address: Röntgenstraße 20

department: Cell and Developmental Biology

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

hyb_protocol: According to manufacturer's instructions. Hybridization time: 18h

scan_protocol: Illumina iScan system using default settings

data_processing: Cubic Spline normalization with background subtraction in BeadStudio. Values below 50% of the detection threshold intensity (detection p value = 0.010) were set to "Null" (= not expressed / detectable).

source_name: cell culture from E3 epiblast stem cells

label_protocol: Ambion TotalPrep RNA Amplification Kit. RNA in put: 400ng, IVT: 12h

growth_protocol: Grown on inactivated mouse embryonic fibroblasts (CF1) in KSR medium supplemented with 5 ng/ml FGF2. At semiconfluence change to KSR medium with  1000 U/ml LIF for 12h.

extract_protocol: Qiagen RNeasy kit with on-column DNA digestion

treatment_protocol: see below

tag: cell line


title: 12h CH-treated EpiSCs

growth_protocol: Grown on inactivated mouse embryonic fibroblasts (CF1) in KSR medium supplemented with 5 ng/ml FGF2. At semiconfluence change to KSR medium with  3uM CHIR99021 for 12h.


title: 12h PL-treated ES cells

source_name: cell culture from OG2 embryonic stem cells

growth_protocol: Grown on gelatin in KSR medium supplemented with 1uM PD0325901, 3uM CHIR99021, and 1000 U/ml LIF. Then switch to PD + LIF for 12h. Cells were harvested directly on the culture dish.


title: B22 In Vitro

description:
B22
Cell culture obtained through explant technique from biopsies.
Biopsies obtained from females of age 12-15 years devoid of neuromuscular disease, during surgery for idiopathic scoliosis.


title: 12h PJ-treated ES cells

growth_protocol: Grown on gelatin in KSR medium supplemented with 1uM PD0325901, 3uM CHIR99021, and 1000 U/ml LIF. Then switch to PD + 1uM JAK inhibitor I for 12h. Cells were harvested directly on the culture dish.


title: 12h FL-treated ES cells

growth_protocol: Grown on gelatin in KSR medium supplemented with 1uM PD0325901, 3uM CHIR99021, and 1000 U/ml LIF. Then switch to 10 ng/ml FGF2 + LIF for 12h. Cells were harvested directly on the culture dish.


title: 12h PD-treated EpiSCs

growth_protocol: Grown on inactivated mouse embryonic fibroblasts (CF1) in KSR medium supplemented with 5 ng/ml FGF2. At semiconfluence change to KSR medium with 1uM PD0325901 for 12h.


title: 12h untreated EpiSCs

growth_protocol: Grown on inactivated mouse embryonic fibroblasts (CF1) in KSR medium supplemented with 5 ng/ml FGF2. At semiconfluence change to KSR medium without supplements for 12h.


title: Nuclear GSH sample1, biological rep1


title: 12h FJ-treated ES cells

growth_protocol: Grown on gelatin in KSR medium supplemented with 1uM PD0325901, 3uM CHIR99021, and 1000 U/ml LIF. Then switch to 10 ng/ml FGF2 + 1uM JAK inhibitor I for 12h. Cells were harvested directly on the culture dish.


title: 3h PCL-treated EpiSCs

growth_protocol: Grown on inactivated mouse embryonic fibroblasts (CF1) in KSR medium supplemented with 5 ng/ml FGF2. At semiconfluence change to KSR medium with 1uM PD0325901 / 3uM CHIR99021 / 1000 U/ml LIF for 3h.


title: 12h PCL-treated EpiSCs

growth_protocol: Grown on inactivated mouse embryonic fibroblasts (CF1) in KSR medium supplemented with 5 ng/ml FGF2. At semiconfluence change to KSR medium with 1uM PD0325901 / 3uM CHIR99021 / 1000 U/ml LIF for 12h.


title: 3h CH-treated EpiSCs

growth_protocol: Grown on inactivated mouse embryonic fibroblasts (CF1) in KSR medium supplemented with 5 ng/ml FGF2. At semiconfluence change to KSR medium with 3uM CHIR99021 for 3h.


title: 3h untreated EpiSCs

growth_protocol: Grown on inactivated mouse embryonic fibroblasts (CF1) in KSR medium supplemented with 5 ng/ml FGF2. At semiconfluence change to KSR medium without supplements for 3h.

value: E3 (hybrid background)


title: 3h LIF-treated EpiSCs

growth_protocol: Grown on inactivated mouse embryonic fibroblasts (CF1) in KSR medium supplemented with 5 ng/ml FGF2. At semiconfluence change to KSR medium with 1000 U/ml LIF for 3h.


title: CGR8 embryonic stem cells

source_name: cell culture from CGR8 embryonic stem cells

growth_protocol: Grown on gelatin in KSR medium supplemented with 1uM PD0325901, 3uM CHIR99021, and 1000U LIF. Cells were harvested directly on the culture dish.

treatment_protocol: untreated


title: E3 epiblast stem cells

growth_protocol: Grown on inactivated mouse embryonic fibroblasts (CF1) in KSR medium supplemented with 5 ng/ml FGF2. Cells were harvested at subconfluence with collagenase IV with minimal feeder contamination.


title: 3h PD-treated EpiSCs

growth_protocol: Grown on inactivated mouse embryonic fibroblasts (CF1) in KSR medium supplemented with 5 ng/ml FGF2. At semiconfluence change to KSR medium with 1uM PD PD0325901 for 3h.


title: E3R reverted EpiSCs

source_name: cell culture from E3R epiblast stem cells


title: OG2 embryonic stem cells

value: OG2 (hybrid background)


title: bovine embryo at 16 cell stage, biological rep 2

status: Public on Feb 20 2010

city: Urbana

first: Dan

last: Xie

state: IL

address: 3215 Digital Computer Lab, MC-278, 1304 W. Springfield Ave

department: Bioengineering

institute: University of Illinois at Urbana and Champaign

description: Gene expression data from embryo at 16 cell stage

hyb_protocol: Following a 16-hour hybridization the chip was washed and stained utilizing an Affymetrix GeneChipâ Fluidics Station 450 and Affymetrix GeneChipâ Command Console Software.   Initial staining utilized streptavidin-conjugated phycoerythrin dye (Invitrogen Corporation, Carlsbad, CA).  This stain was enhanced with biotinylated goat anti-streptavidin antibody (Vector Laboratories, Burlingame, CA), then counterstained with the conjugated phycoerythrin.

scan_protocol: The chip was scanned with an Affymetrix GeneChipâ Scanner model 3000 7G Plus.  Files of the fluorescence intensities were utilized to generate corresponding probe expression levels utilizing Affymetrix Expression Console version 1.1, and quality control values were checked.

data_processing: The data were analyzed with dChip. Normalization was under default settings.

source_name: Bovine embryo at sixteen cells stage

label_protocol: RNA was prepared utilizing three rounds of amplification and hybridized to Affymetrix GeneChipâ Bovine Genome Expression Arrays (Affymetrix, Inc., Santa Clara, CA)  utilizing Ambion’s MessageAmp TM II aRNA Amplification and MessageAmpTM II-Biotin Enhanced Kits (Applied Biosystems, Foster City, CA) according to the manufacturers’ instructions.

extract_protocol: Total RNA extraction was carried out using the mirVana RNA extraction kit according to the manufacturers protocols (Applied Biosciences/Ambion, Austin, TX ).

treatment_protocol: Human embryos: Supernumerary human embryos were obtained from patients at the Boston IVF Clinic through informed consent with the approval of the Internal Review Board of Harvard University.  Embryos thus obtained were cultured in a two-step culture system (Sage/Biopharma, CT) in micro-drops at 37? C and 5% CO2 under oil (Sage, CT) as described previously.  Embryos from each stage were segregated into three groups.  Each group was considered to be a biologic replicate: embryos within each replicate were pooled for further analysis.  The blastocyst embryos were graded according to the Gardner scale. Mouse embryos: Briefly, female mice were impregnated, and embryos were flushed from the oviducts.  Individual embryos were morphologically staged by light microscopy.  Bovine embryos: Ovaries were washed and 2-6 mm follicles were aspirated.  Only oocytes surrounded by several cell layers of dense cumulus were selected for culture.  Oocytes were washed three times in TL-HEPES (0.22mM sodium pyruvate, 3mg/ml BSA, pH 7.4), and we placed maturation media that had been equilibrated in 5% carbon dioxide and air (39°C, high humidity).  The maturation medium consisted of TC199 supplemented with 3ml of bovine LH and FSH (Sioux Biochemical), 0.25mM sodium pyruvate, and 10% fetal calf serum.  After 20 hours of incubation in maturation media, oocytes were removed, washed in TL-HEPES and  placed in groups of 10 oocytes each into 44 μl microdrops of IVF-Talp (Biowhittaker, Walkersburg, MD) supplemented with 0.22mM sodium pyruvate, and 6 mg/ml essentially fatty acid-free BSA. Live sperm were separated by centrifugation in a percoll gradient (Sigma, P1985).  Eggs were fertilized by adding one million/ml of sperm,  2.0μg heparin (Sigma H-3125), pencillamine, hypotaurine and epinephrine (Sigma-P-4875, H-1384, E-4250) to each drop of fertilization media. Oocytes were removed from the fertilization media after 18-22 hours, washed in TL-HEPES, placed in a 1.5 ml tube, and vortexed for 2 min to remove cumulus cells. Twenty-five cumulus-free oocytes were placed in each 50μl drop of SOF culture medium, supplemented with 8 mg/ml of fatty acid-free BSA, nonessential and essential amino acids and pyruvate. The IVF conditions were optimized for each species. To minimize the influence of IVF conditions to cross-species comparison, we subsequently based the comparisons on either relative expression changes or co-expression patterns.

tag: development stage

value: embryo at sixteen cells stage


title: bovine embryo at 16 cell stage, biological rep 1


title: bovine embryo at morula stage, biological rep 2

description: Gene expression data from morula

source_name: Bovine morula

value: morula


title: E3 EpiSCs

growth_protocol: Grown on inactivated mouse embryonic fibroblasts (CF1) in KSR medium supplemented with 5 ng/ml FGF2. Cells were harvested with collagenase IV with minimal feeder contamination.


title: bovine embryo at 8 cell stage, biological rep 2

description: Gene expression data from embryo at 8 cell stage

source_name: Bovine embryo at eight cells stage

value: embryo at eight cells stage


title: bovine blastocyst, biological rep 2

description: Gene expression data from blastocyst

source_name: Bovine blastocyst

value: blastocyst


title: bovine embryo at 4 cell stage, biological rep 2

description: Gene expression data from embryo at 4 cell stage

source_name: Bovine embryo at four cells stage

value: embryo at four cells stage


title: Mtf2_RNAi_3_2days

description: gene expression of cells transfected with  plasmid pSuper-Mtf2-RNAi-3 and selected by Puromycin(1mg/ml) for 2 days

hyb_protocol: 825 ng of labeled RNA was fragmented and hybridized on the slide in a rotating hybridzation oven at 60C overnight. Slides were washed according to the manufactureres protocols using Agilent wash buffers.

scan_protocol: Slides were scanned in an Axon 4000B scanner using GenePix 6 software to generate gpr files.

data_processing: Data normalized with dChip.

source_name: Mtf2_RNAi_3, 2days

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the Quick-Amp One-Color  (Agilent) according to the manufactruers instructions. Total amount of cRNA and dye incorporation was measured using a nanodrop instrument.

extract_protocol: Extracted by Trizol  Reagent(Invitrogen 15596-018)

treatment_protocol: Plasmids were transfected into the E14 mESC cell lines by lipofectamine 2000 and selected by Puromycin (1 mg/ml) after 1 day of transfection. The sample of 2 days maintained in puromycin was harvested.

value: E14 mESC


title: bovine oocyte, biological rep 2

description: Gene expression data from oocyte

source_name: Bovine oocyte

value: oocyte


title: bovine embryo at 2 cell stage, biological rep 1

description: Gene expression data from embryo at 2 cell stage

source_name: Bovine embryo at two cells stage

value: embryo at two cells stage


title: bovine embryo at morula stage, biological rep 1

description: Gene expression data from morula


title: bovine oocyte, biological rep 1

description: Gene expression data from oocyte


title: bovine embryo at 2 cell stage, biological rep 2


title: bovine embryo at 8 cell stage, biological rep 1


title: bovine embryo at 1 cell stage, biological rep 1

description: Gene expression data from zygote before divide

source_name: Bovine embryo at one cell stage

value: embryo at one cell stage


title: mouse blastocyst, biological rep 2

description: Gene expression data from blastocyst

source_name: Mouse blastocyst


title: bovine embryo at 4 cell stage, biological rep 1


title: Luci_RNAi_2days

description: gene expression of cells transfected with plasmid pSuper-Luciferase-RNAi and selected by Puromycin(1mg/ml) for 2 days

source_name: Luci_RNAi, 2days


title: bovine embryo at 1 cell stage, biological rep 2


title: T9 epiblast stem cells

source_name: cell culture from T9 epiblast stem cells

value: T9 (129 background)


title: mouse blastocyst, biological rep 3

description: Gene expression data from blastocyst


title: pSuper_2days

description: gene expression of cells transfected with vector pSuper and selected by Puromycin(1mg/ml) for 2 days

source_name: pSuper, 2days


title: mouse embryo at morula stage, biological rep 1

description: Gene expression data from morula

source_name: Mouse morula


title: mouse blastocyst, biological rep 1

description: Gene expression data from blastocyst


title: mouse embryo at morula stage, biological rep 2

description: Gene expression data from morula


title: mouse embryo at 8 cell stage, biological rep 3

source_name: Mouse embryo at eight cell stage

value: embryo at eight cell stage


title: mouse embryo at 4 cell stage, biological rep 3

source_name: Mouse embryo at four cell stage

value: embryo at four cell stage


title: bovine blastocyst, biological rep 1

description: Gene expression data from blastocyst


title: mouse embryo at 4 cell stage, biological rep 1


title: mouse embryo at 4 cell stage, biological rep 2


title: mouse embryo at 8 cell stage, biological rep 1


title: mouse embryo at 2 cell stage, biological rep 3

source_name: Mouse embryo at two cell stage

value: embryo at two cell stage


title: mouse embryo at 1 cell stage, biological rep 1

source_name: Mouse embryo at one cell stage


title: mouse embryo at 1 cell stage, biological rep 3


title: mouse embryo at 2 cell stage, biological rep 1


title: mouse embryo at 1 cell stage, biological rep 2


title: EP2KO_Cumulus_H14

city: Tokyo

first: Eri

last: Segi-Nishida

state: Tokyo

address: Niijuku 6-3-1

institute: Tokyo University of Science

hyb_protocol: For each sample, 20 µg of the cRNA product was fragmented and hybridized for 18 h into Affymetrix GeneChip Murine Genome U74Av2 microarrays. Each microarray was washed and stained with streptavidin-phycoerythrin.

scan_protocol: The GeneChips were scanned with the GeneArray Scanner2500 (Agilent Technologies) according to the GeneChip Expression Analysis Technical Manual procedure (Affymetrix).

data_processing: The robust multi-array analysis (RMA) expression measure that represents the log transformation of (background corrected and normalized) intensities of the GeneChips was used. The RMA measures were calculated using the R package program, which is freely available on the web site (http://www.bioconductor.org). Using the k-means clustering algorithm, these genes were classified into nine clusters on the basis of the similarity of their expression profiles.

source_name: EP2KO, Cumulus, hCG 14h

label_protocol: One hundred ng of total RNA from WT cumulus cells at 0, 3, 9 and 14 h after hCG injection was used to generate double-strand cDNA with the T7-oligo (dT)24 primer (GE Healthcare Bioscience) according to the GeneChip Eukaryotic Small Sample Target Labeling Assay Version I protocol. After second-strand synthesis, in vitro transcription was performed using a MEGAscript High Yield Transcription kit (Ambion). The cRNA synthesized after the first cycle of in vitro transcription was then used as a template in a second cycle of first-strand cDNA synthesis with random primers (Invitrogen Life Technologies). Then, the second-strand synthesis was performed in the presence of the oligo(dT)24 primer. For the second-strand cDNA synthesis, in vitro transcription was performed using an ENZO BioArray HighYield RNA Transcription Labeling kit (ENZO Diagnostics) to generate biotin-labeled cRNA.

growth_protocol: Follicular growth and ovulation were stimulated in mice at 3-4 weeks of age by the following hormonal regimen: intraperitoneal (ip) injection of 5 IU PMSG followed 48 h later by ip injection of 5 IU hCG.

extract_protocol: Total RNA of cumulus cells was then obtained with an RNeasy Mini Kit (QIAGEN) according to manufacturer’s instructions.

treatment_protocol: WT and Ptger2-/- mice were sacrificed at different time points (0, 3, 9, 14 h) after hCG injection. At time points before ovulation (at post-hCG, 0, 3 or 9 h), ovaries were collected and large antral follicles visible on the surface of the ovary were ruptured using a 30-gauge needle allowing the COCs to flow out into phosphate-buffered saline containing 0.3% BSA (0.3% BSA/PBS). Using glass capillaries, cumulus cells and the oocyte were surgically stripped, and cumulus cells were removed from the oocytes. At 14 h after hCG, the COCs were collected from the ampullary of the oviducts and treated with 0.1% hyaluronidase (Sigma-Aldrich) to strip the COCs of cumulus cells.

tag: genotype

value: female

tag: age

value: 3-4 weeks

value: ovary

value: cumulus cell

tag: human chorionic gonadotropin (hcg) treatment

value: yes

tag: hcg treatment time

value: 14 hr


title: mouse embryo at 8 cell stage, biological rep 2


title: EP2KO_Cumulus_H0

source_name: EP2KO, Cumulus, PMSG 48h, hCG 0h

value: no

value: 0 hr


title: EP2KO_Cumulus_H3

source_name: EP2KO, Cumulus, hCG 3h

value: 3 hr


title: mouse embryo at 2 cell stage, biological rep 2


title: D-487 Normal liver

status: Public on Feb 19 2010

type: genomic

city: Columbus

first: Kellie

middle: J.

last: Archer

state: OH

address: 1841 Neil Ave

department: Division of Biostatistics

institute: Ohio State University

description:
Methylated channel=Cy3; Unmethylated=Cy5
Proportion methylated

hyb_protocol: After extension and ligation, the ligated products were amplified using universal primers and hybridized to an Illumina GoldenGate Methylation BeadArray Cancer Panel I for interrogating CpG sites. The array hybridization was conducted under a temperature gradient.

scan_protocol: The sentrix array was scanned using Illumina's BeadArray reader and software.

data_processing: Background was estimated separately for the methylated and unmethylated states as the average intensity of the negative control beads for the red (Rbi)  and green channels (Gbi), respectively, and was then subtracted from the beadtype intensities on array i. The maximum of the background subtracted intensities and 0 was then used to calculate the proportion methylated.

label: Cy3, Cy5

molecule: genomic DNA

source_name: liver tissue

label_protocol: After bisulfite treatment, the remaining procedures were identical to the GoldenGate genotyping assay, using Illumina-supplied reagents and conditions.

growth_protocol: Liver tissue from 20 HCV-HCC patients and their corresponding non-tumorous cirrhotic tissues were procured.

extract_protocol: DNA was isolated using QIA amp DNA Mini Kit (Qiagen) according to the manufacturer’s instructions. The EZ DNA methylation kit (Zymo Research) was used for bisulfite conversion of all DNA (1 mg) samples.

treatment_protocol: Cirrhotic liver tissue from 16 HCV-cirrhotic patients without concomintant HCC were also procured as well as 20 normal liver samples.

tag: disease state

value: Normal

value: liver


title: D-242 Normal liver


title: WT_Cumulus_H3

source_name: WT, Cumulus, hCG 3h

value: WT


title: WT_Cumulus_H14

source_name: WT, Cumulus, hCG 14h


title: D-85 Normal liver


title: Resistant hybrid pool_rep2

city: Cordeirópolis

first: Leonardo

middle: Pires

last: Boava

state: São Paulo

address: Via Anhanguera, km158

country: Brazil

institute: Centro de citricultura 'Sylvio Moreira' /IAC

description: This sample is of resistant hybrid pool inoculated with P. parasitica . It is the second of two biological replicates used in this experiment

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Citrus sunki x Citrus trifoliata

source_name: leaves

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol:
The selected hybrids were the most resistant and susceptible to P. parasitica infection according to Boava and Siviero et al.  Three buds from each hybrid and parental lines were collected and grafted onto 6-month-old Rangpur lime rootstocks.
After six month, plants were inoculated by the disc method, which was performed by placing a mycelial block onto the center of a cut made in the stem and covered with parafilm. After 48 hours, leaves were harvested individually, separately flash frozen in liquid nitrogen, and then stored at 80°C prior to RNA isolation.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).

tag: authority

value: Citrus sunki Hort. ex. Tan. x Poncirus trifoliata (L.) Raf cv. Rubidoux

value: F1 (Citrus Sunki x Poncirus trifoliata)

tag: phenotype

value: Resistant to P. parasitica

tag: phytophtora inoculation

value: inoculated


title: WT_Cumulus_H9

source_name: WT, Cumulus, hCG 9h

value: 9 hr


title: D-80 Normal liver


title: D-91 Normal liver


title: WT_Cumulus_H0

source_name: WT, Cumulus, PMSG 48h, hCG 0h

value: female


title: Whole retina DA repicate 1

city: Basel

first: Jacek

last: Krol

address: Maulbeerstrasse 66

department: Epigenetics

institute: Friedrich Miescher Institute for Biomedical Research

description: dark adapted for 3h

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Standard Affymetrix procedures

data_processing: Quality control and background normalization was performed using Refiner 4.1 from Genedata AG (Basel, Switzerland). Expression value estimates were obtained using the GC-RMA implementation in Refiner 4.1. Quantile-normalization and median scaling of the genes called present (detection p value <0.05) was performed in Genedata’s Analyst 4.1 package. Data analysis was performed using Expressionist Analyst 4.1 from Genedata AG. Genes were required to pass a t-test (1-way ANOVA) with a p < 0.05.

source_name: whole retina; dark adapted

label_protocol: Biotinylated cRNA were prepared according to the two-cycle target labeling Affymetrix protocol.

growth_protocol: Adult 7-8 weeks old C57BL/6 mice bred in a pathogen-free environment with ad libitum access to food and drinking water. LA (light adapted) animals were kept in a room with the light phase (450 lux) from 6:00 am (ZT0) to 6:00 pm (ZT12). For dark adaptation, animals were kept in a dark chamber with maximum of 0.4 lux

extract_protocol: Laser capture microscopy was used to isolate retina cell layers. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Animals were light adapted for 6h or dark adapted for 3h

value: retina whole retina

tag: treatment

value: dark adapted


title: Susceptible hybrid pool _rep1

description: This sample is of susceptible hybrid pool inoculated with P. parasitica . It is the first of two biological replicates used in this experiment

value: Susceptible to P. parasitica


title: Whole retina DA repicate 2

description: dark adapted for 3h


title: D-162 Normal liver


title: Resistant hybrid pool_rep1

description: This sample is of resistant hybrid pool inoculated with P. parasitica . It is the first of two biological replicates used in this experimen


title: Poncirus trifoliata_rep2

description: This sample is of Poncirus trifoliata inoculated with P. parasitica . It is the second of two biological replicates used in this experiment

organism: Citrus trifoliata

value: Poncirus trifoliata (L.) Raf cv. Rubidoux

value: Poncirus trifoliata


title: Citrus Sunki_rep1

description: This sample is of Citrus Sunki inoculated with P. parasitica . It is the first of two biological replicates used in this experiment

organism: Citrus sunki

value: Citrus sunki Hort. ex. Tan.

value: Citrus Sunki


title: Poncirus trifoliata_rep1

description: This sample is of Poncirus trifoliata inoculated with P. parasitica . It is the first of two biological replicates used in this experiment


title: GCL DA repicate 2

description: dark adapted for 3h

source_name: ganglion cell layer; dark adapted

value: retina ganglion cell layer


title: D-84 Normal liver

value: Normal


title: IPL DA repicate 2

description: dark adapted for 3h

source_name: inner plexiform layer; dark adapted

value: retina inner plexiform layer


title: EP2KO_Cumulus_H9

source_name: EP2KO, Cumulus, hCG 9h

value: 3-4 weeks

value: ovary

tag: cell type

value: cumulus cell

value: yes


title: D-407 Normal liver

value: liver


title: D-71 Normal liver


title: GCL DA repicate 1

description: dark adapted for 3h


title: D-260 Normal liver


title: D-386 Normal liver


title: IPL DA repicate 1

description: dark adapted for 3h


title: D-486 Normal liver


title: mouse embryo at morula stage, biological rep 3

description: Gene expression data from morula

source_name: Mouse morula

value: morula


title: INL DA repicate 2

description: dark adapted for 3h

source_name: inner nuclear layer; dark adapted

value: retina inner nuclear layer


title: D-245 Normal liver


title: D-254 Normal liver


title: D-232 Normal liver


title: ONL+OS/IS DA replicate 2

description: dark adapted for 3h

source_name: photoreceptor layer; dark adapted

value: retina photoreceptor layer


title: D-190 Normal liver


title: Whole retina LA repicate 2

description: light adapted for 6h

source_name: whole retina; light adapted

value: retina whole retina

value: light adapted


title: ONL+OS/IS DA replicate 1

description: dark adapted for 3h

value: dark adapted


title: D-79 Normal liver


title: D-194 Normal liver


title: IPL LA repicate 2

description: light adapted for 6h

source_name: inner plexiform layer; light adapted


title: INL DA repicate 1

description: dark adapted for 3h


title: GCL LA repicate 1

description: light adapted for 6h

source_name: ganglion cell layer; light adapted


title: GCL LA repicate 2

description: light adapted for 6h


title: D-308 Cirrhosis non-HCC

value: Cirrhosis non-HCC


title: D-74 Normal liver


title: D-75 Normal liver


title: IPL LA repicate 1

description: light adapted for 6h


title: D-273 Cirrhosis non-HCC


title: INL LA repicate 2

description: light adapted for 6h

source_name: inner nuclear layer; light adapted


title: INL LA repicate 1

description: light adapted for 6h


title: Whole retina LA repicate 1

description: light adapted for 6h


title: D-309 Cirrhosis

source_name: liver tissue

value: Cirrhosis


title: ONL+OS/IS LA replicate 1

description: light adapted for 6h

source_name: photoreceptor layer; light adapted


title: D-234 Cirrhosis non-HCC


title: D-309 Tumor

value: Tumor


title: ONL+OS/IS LA replicate 2

description: light adapted for 6h


title: D-129 Cirrhosis non-HCC


title: D-388 Cirrhosis


title: D-388 Tumor


title: D-187 Cirrhosis non-HCC


title: D-134 Cirrhosis non-HCC


title: D-111 Cirrhosis non-HCC


title: D-108 Cirrhosis non-HCC


title: D-130 Cirrhosis non-HCC


title: GL24PV_bio1_tech2

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

country: Italy

institute: University of Verona

description: All the procedures provided were performed as indicated by Combimatrix protocols available at Combimatrix website (www.combimatric.com)

hyb_protocol: Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 1% SDS, 0.2% BSA) for 60 minutes at 37 °C. Hybridization was performed at 37°C for 16 hours in hybridization solution (6X SSPE, 0.8% BSA, 12% DI Formamide, 2.5% SDS). Hybridization washings were performed as following: - wash with 6X SSPET wash solution (6X SSPE, 0.05% Tween-20). - wash with 3X SSPET wash solution (3X SSPE, 0.05% Tween-20). - 2 washes with 0.5X SSPET wash solution (0.5X SSPE, 0.05% Tween-20).

scan_protocol: Scanning was performed using Perkin Elmer ScanArray 4000XL microarray scanner and ScanArray Express 4.0 acquisition software. Laser was set at 60% of power. PMT gain was set at 60%.

data_processing: Raw data was extracted using Microarray Imager 5.8.0 software (Combimatrix). Data were quantile-normalized using Blist 0.6 software (Combimatrix).

label: Alexa Fluor 647

organism: Vitis riparia

source_name: Gloire de Montpellier, leaf, Plasmopara viticola, 24h

label_protocol: Total RNA (1 ug) was amplified by using the SuperScript Indirect RNA Amplification System (Invitrogen), to incorporate amino-allyl UTP molecules (aRNA) and fluorescently labelled by using the Alexa Fluor 647 reactive Dye

growth_protocol: In vitro plants of Vitis vinifera riparia cv. Gloire de Montpellier grown at 27°C and a 16 h photoperiod (50 μE/m2/s) as described in Blaich (1977)

extract_protocol: Total RNA was isolated form leaves of V. riparia cv Gloire de Montpellier according to Reid et al., 2006.

treatment_protocol: Fully expanded leaves of 8 to 10-week-old in vitro grapevine plants were infected by application of 50μL drops containing 50,000 sporangia per mL of Plasmopara viticola on the adaxial leaf surface. Leaf disks corresponding to infected tissue were cut and collected at 12 and 24 hours post-inoculation (hpi), immediately frozen in liquid nitrogen and stored at -80°C

value: leaf

tag: infection

value: Plasmopara viticola

tag: time point

tag: cultivar

value: Gloire de Montpellier


title: D-114 Cirrhosis non-HCC

tag: tissue


title: GL24PV_bio3_tech2


title: Susceptible hybrid pool _rep2

description: This sample is of susceptible hybrid pool inoculated with P. parasitica . It is the second of two biological replicates used in this experiment

source_name: leaves

value: Citrus sunki Hort. ex. Tan. x Poncirus trifoliata (L.) Raf cv. Rubidoux

value: F1 (Citrus Sunki x Poncirus trifoliata)

value: Susceptible to P. parasitica

value: inoculated


title: GL12PV_bio3_tech1

source_name: Gloire de Montpellier, leaf, Plasmopara viticola, 12h


title: GL24PV_bio2_tech1


title: GL12PV_bio2_tech2


title: GL24PV_bio2_tech2


title: D-527 Cirrhosis-Replicate

value: liver


title: D-527 Tumor


title: D-527 Tumor-Replicate


title: D-527 Cirrhosis


title: GL12PV_bio3_tech2


title: GL12PV_bio2_tech1


title: GL24W_bio3_tech1

source_name: Gloire de Montpellier, leaf, water, 24h

treatment_protocol: Fully expanded leaves of 8 to 10-week-old in vitro grapevine plants were mock-inoculated by application of 50μL drops of distilled water on the adaxial leaf surface as a control, with the same procedure. Leaf disks corresponding to infected tissue were cut and collected at 12 and 24 hours post-inoculation (hpi), immediately frozen in liquid nitrogen and stored at -80°C

value: water


title: GL24PV_bio1_tech1


title: D-606 Tumor


title: GL12PV_bio1_tech2


title: GL12PV_bio1_tech1


title: GL24PV_bio3_tech1


title: GL24W_bio2_tech2


title: GL24W_bio3_tech2


title: D-127 Cirrhosis non-HCC


title: D-606 Cirrhosis


title: D-138 Cirrhosis non-HCC


title: D-109 Cirrhosis non-HCC


title: GL24W_bio1_tech1

growth_protocol: In vitro plants of Vitis riparia cv. Gloire de Montpellier grown at 27°C and a 16 h photoperiod (50 μE/m2/s) as described in Blaich (1977)

extract_protocol: Total RNA was isolated form leaves of V. riparia cv Gloir de Montpellier according to Reid et al., 2006.


title: D-513 Tumor


title: GL24W_bio2_tech1


title: D-614 Cirrhosis-Replicate


title: D-122 Cirrhosis non-HCC


title: D-614 Tumor-Replicate


title: D-123 Cirrhosis non-HCC


title: GL12W_bio3_tech2

source_name: Gloire de Montpellier, leaf, water, 12h


title: GL12W_bio2_tech1


title: GL12W_bio3_tech1


title: GL12W_bio2_tech2


title: GL12W_bio1_tech1


title: D-614 Tumor


title: D-513 Cirrhosis


title: PN24PV_bio3_tech1

organism: Vitis vinifera

source_name: Pinot Noir leaf, Plasmopara viticola, 24h

growth_protocol: In vitro plants of Vitis vinifera cv. Pinot Noir grown at 27°C and a 16 h photoperiod (50 μE/m2/s) as described in Blaich (1977)

extract_protocol: Total RNA was isolated form leaves of V. vinifera cv Pinot Noir according to Reid et al., 2006.

value: Pinot Noir


title: D-614 Cirrhosis


title: PN24PV_bio2_tech2


title: D-128 Cirrhosis non-HCC


title: D-524 Tumor-Replicate


title: D-524 Cirrhosis


title: D-524 Tumor


title: PN24PV_bio1_tech2


title: PN24PV_bio3_tech2


title: PN24PV_bio1_tech1


title: D-541 Tumor


title: D-524 Cirrhosis-Replicate


title: D-541 Tumor-Replicate


title: PN12PV_bio3_tech1

source_name: Pinot Noir leaf, Plasmopara viticola, 12h


title: D-541 Cirrhosis-Replicate


title: PN12PV_bio2_tech2


title: GL12W_bio1_tech2


title: PN12PV_bio3_tech2


title: D-607 Tumor-Replicate


title: D-607 Cirrhosis-Replicate


title: GL24W_bio1_tech2


title: PN12PV_bio2_tech1


title: PN12PV_bio1_tech1


title: PN24W_bio3_tech2

source_name: Pinot Noir leaf, water, 24h


title: D-607 Cirrhosis


title: PN12PV_bio1_tech2


title: D-607 Tumor


title: PN24W_bio3_tech1


title: PN24W_bio2_tech1


title: D-541 Cirrhosis


title: PN24W_bio1_tech2


title: D-605 Cirrhosis


title: D-605 Tumor


title: SOP/pI vs. Epithelial cells hyb2

city: Paris

first: Michel

last: Gho

address: 9 quai Saint Bernard

country: France

institute: CNRS

description: Cy3 and Cy5 labelled aRNA samples were mixed in equal proportions (600 pmol) and fragmented with the RNA Fragmentation Reagents (Ambion) to enhance aRNA hybridization, dried up to 60ul of final volume, and hybridized on INDAC oligonucleotide microarrays.

hyb_protocol: Labeled probes (60 µl) were mixed with 60 µl of 4X hybridization buffer and 120 µl of deionised formamide, denatured at 95°C for 5min and hybridized at 37°C for 12 hours with the Automated Slide Processor (ASP) of Amersham. Slides were successively washed at 37°C in 1X SCC/0.2% SDS for 20 min, in 0.1X SCC/0.2% SDS for 2x10 min, in 0.1X SCC for 10 min, rinsed in isopropanol and air dried.

scan_protocol: Images were obtained with a GenePix 4200AL (Axon Instruments) at 10 um resolution and 5% of laser power. Fluorescence measurements are made using Array Vision quantification software (Imaging Research Inc).

data_processing: Normalization of raw data was performed by LIMMA. The flagged spots and controls were removed from the analysis. No background correction was performed before normalization. Lowess normalization was used to normalize the M-values for each array separately (within-array normalization).

organism: Drosophila melanogaster

source_name: SOP/pI

extract_protocol: Total RNA extracted using Picopure RNA isolation kit (Molecular Devices-Arcturus) following manufacturer’s instructions. Around 0.1 – 0.5 ug of total RNA from sample. Amplification RNA was amplified using MesageAMP II aRNA amplification kit (Ambion).  Two rounds of in vitro amplification following manufacturer’s instructions. UTP-amino allyls were integrated during the second round (Amino allyl MessageAmp II kit, Ambion). 20-50 ug of aRNA were obtained for sample.

tag: sample type

value: SOP/pI were laser microdissected from fixed notum of pupae at 16 h APF. SOP/pI were identified by specific expression of GFP. Around 1000 microdissected cells for sample.

value: SOP/pI

source_name: Epithelial cells

label_protocol:
Amino allyl aRNA was labelled according the "Dye Coupling and Labeled aRNA Cleanup" protocol of the Amino Allyl MessageAmpTM II aRNA Amplification Kit (Ambion) 600 pmol of incorporated dye was used for hybridization.
All Channels

value: Epithelial cells were laser microdissected from fixed notum of pupae at 16 h APF.

value: Epithelial cells


title: D-588 Tumor


title: PN24W_bio2_tech2


title: D-569 Tumor


title: PN12W_bio3_tech2

source_name: Pinot Noir leaf, water, 12h


title: PN24W_bio1_tech1


title: D-569 Cirrhosis


title: D-514 Cirrhosis


title: D-514 Tumor


title: D-507 Cirrhosis-Replicate


title: D-507 Tumor


title: D-507 Cirrhosis


title: 24h_Ifnb_s22_(MoEx-1_0-st-v1)_2

city: Roslin

first: Sobia

last: Raza

state: Midlothian

address: Roslin Biocentre

department: Roslin Institute

country: United Kingdom

institute: University of Edinburgh

description: RMA expression value derived from Expression Console software; Core-Gene-Level analysis

hyb_protocol: Samples were hybridized with GeneChip Mouse Exon 1.0 ST Arrays (Affymetrix) and scanned at the Wellcome Trust Sanger Institute.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data was normalized using the RMA package within the Affymetrix Expression Console software and annotated. Transcripts which might be considered to be differentially expressed at each time point compared to 0 h were identified using the Empirical Bayes function within the Bioconductor package of the R statistical program using a 1.5 fold cut-off and a p-value of 0.05. According to this analysis 2,300 transcripts were considered to be differentially expressed. Data corresponding to these transcripts was then loaded into the network visualization tool BioLayout Express3D using a Pearson correlation cut-off of 0.9 to filter edges. The the graph-based clustering algorithm MCL and an explorative network based approach was applied to analyse transcriptional changes over time.

source_name: 24-hours Interferon-beta treated macrophages

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Bone marrow derived macrophages (BMDM) were prepared from femurs of 8-9 week old male Balb-C mice. RPMI 1640 medium (Sigma-Aldrich, Gillingham, UK) supplemented with 10% heat inactivated foetal bovine serum (FBS) (Sigma-Aldrich Gillingham, UK), 25 U/ml penicillin (Invitrogen, Paisley, UK), 25 µg/ml streptomycin (Invitrogen, Paisley, UK), and 2 mM L-glutamine (Invitrogen) (complete medium) was used for culture of the BMDM. Briefly, bone marrow cells were cultured for 6 days in complete medium in the presence of 10,000 U/ml CSF1 (colony stimulating factor-1) on 10 cm square bacteriological plastic plates, with a re-supplement of CSF1 on day 5. On day 6 cells were harvested, counted, re-suspended in complete medium with 10,000 U/ml CSF1 and plated out onto 6-well tissue culture plates at a density of 1 million cells per well and cultured for a further 24 h.

extract_protocol: Total RNA was harvested from the cells using an RNeasy Mini kit (Qiagen, Crawley, UK) according to manufacturer's instructions. RNA was quantified and quality controlled using a NanoDrop spectrophotometer (NanoDrop Technologies, Delaware, USA) and BioAnalyser 2100 (Agilent, California, USA). Replicate 300 ng samples of total RNA derived from two separate wells per time point were labeled using the Affymetrix whole transcript labeling protocol.

treatment_protocol: On day 7 of growth BMDM cells were treated with 10 U/ml recombinant mouse interferon-beta (Ifn-β) (PBL Interferon Source, New Jersey, USA) and harvested 1, 2, 4, 8 and 24 h following treatment or collected pre-treatment (0 h). Duplicate biological replicates for each time-point were processed for hybridization to the Mouse Exon 1.0 ST Arrays.

tag: mouse-strain

value: Balb-C

tag: sex

value: Male

value: 8-9 weeks

value: Bone Marrow Derived Macrophage


title: D-588 Cirrhosis

value: Cirrhosis


title: D-464 Cirrhosis


title: 24h_Ifnb_s17_(MoEx-1_0-st-v1)


title: PN24PV_bio2_tech1

value: leaf

value: Plasmopara viticola


title: D-464 Tumor

value: Tumor


title: PN12W_bio3_tech1


title: 8h_Ifnb_s18_(MoEx-1_0-st-v1)_2_2

source_name: 8-hours Interferon-beta treated macrophages


title: D-473 Cirrhosis


title: PN12W_bio2_tech2


title: SOP/pI vs. Epithelial cells hyb1

label_protocol: Amino allyl aRNA was labelled according the "Dye Coupling and Labeled aRNA Cleanup" protocol of the Amino Allyl MessageAmpTM II aRNA Amplification Kit (Ambion) 600 pmol of incorporated dye was used for hybridization.


title: 4h_Ifnb_s16_(MoEx-1_0-st-v1)

source_name: 4-hours Interferon-beta treated macrophages


title: PrrA2 mutant biological rep3

city: Houston

first: Jung Hyeob

last: Roh

state: TX

address: 6431 Fannin St.

department: Microbiology & Molecular Genetics

institute: The University of Texas

description: Gene expression data from anaerobic dark/DMSO condition

hyb_protocol: Target hybridization, staining, and scanning were performed according to the instructions designed for the Pseudomonas aeruginosa genome array by Affymetrix

scan_protocol: Agilent GeneArray scanner under the control of the Affymetrix GCOS

data_processing: .CEL file converted to MAS5 format and analyzed using Affymetrix MAS5 default analysis settings and global scaling as normalization method.

organism: Cereibacter sphaeroides 2.4.1

source_name: R. sphaeroides PrrA2 mutant

label_protocol: cDNA synthesized from total RNA was fragmented and labeled using the Enzo BioArray terminal labeling kit

growth_protocol: Strains were sparged anaerobicallyin the dark with 95%N2-5%CO2 in SIS medium supplemented with 0.1% yeast extract in the presence of DMSO (0.5% vol/vol), as electron acceptor.  When the optical density at 600 nm (OD600) reached approximately 0.4 RNA was isolated from a 50-ml aliquot of the culture.

extract_protocol: Total RNA was extracted by a modified hot-phenol method described in J. Biol. Chem. 279:9146-9155, 2004

treatment_protocol: Total RNA was extracted directly from the culture.

tag: genotype

value: PrrA2 mutant


title: 8h_Ifnb_s23_(MoEx-1_0-st-v1)_2

tag: age


title: 4h_Ifnb_s15_(MoEx-1_0-st-v1)_2_2


title: PN12W_bio1_tech1

description: All the procedures provided were performed as indicated by Combimatrix protocols available at Combimatrix website (www.combimatrix.com)

treatment_protocol: Fully expanded leaves of 8 to 10 week-old in vitro grapevine plants were mock-inoculated by application of 50μL drops of distilled water on the adaxial leaf surface as a control. Leaf disks corresponding to treated tissue were cut and collected at 12 and 24 hours post-inoculation (hpi), immediately frozen in liquid nitrogen and stored at -80°C


title: PN12W_bio2_tech1


title: D-473 Tumor

source_name: liver tissue


title: 2h_Ifnb_s12_(MoEx-1_0-st-v1)

source_name: 2-hours Interferon-beta treated macrophages


title: PN12W_bio1_tech2


title: D-451 Cirrhosis


title: 2h_Ifnb_s10_(MoEx-1_0-st-v1)


title: D-520 Tumor


title: D-520 Cirrhosis


title: D-334 Cirrhosis


title: D-334 Tumor


title: PrrA2 mutant biological rep1


title: PrrA2 mutant biological rep2


title: 1h_Ifnb_s8_(MoEx-1_0-st-v1)_2

source_name: 1-hour Interferon-beta treated macrophages


title: D-345 Cirrhosis


title: 1h_Ifnb_s5_(MoEx-1_0-st-v1)


title: D-451 Tumor


title: D-345 Tumor


title: wild type biological rep1

source_name: R. sphaeroides 2.4.1

value: wild type


title: wild type biological rep2


title: wild type biological rep3


title: 0h_Ifnb_s2_(MoEx-1_0-st-v1)

source_name: 0-hours Interferon-beta treated macrophages


title: RhCMV Δ178Δ182-189

city: Beaverton

first: Rebecca

last: Richards

state: OR

address: 505 NW 185th Ave

department: Microbiology and Immunology

institute: Vaccine and Gene Therapy Institute

description: Test sample (RhCMVΔ178-gag) and reference sample (RhCMV-BAC) were co-hybridized to a NimbleGen RhCMV 68-1 tiling array, and the ratio of Cy3/Cy5 probe intensities was obtained

hyb_protocol: Labeled reference and test viral DNA probes were co-hybridized to the tiling arrays.

scan_protocol: After hybridization to the tiling arrays, the Cy3 and Cy5 signals were scanned

data_processing: SignalMap software (NimbleGen Systems, Inc.) was used to analyze all comparative genome sequencing data.

organism: macacine betaherpesvirus 3

source_name: RhCMVΔ178Δ182-189-gag genomic DNA

label_protocol: Viral DNA was fragmented and labeled with Cy3 (RhCMV-BAC as reference) or Cy5 (deletion viruses)

growth_protocol: Telomerized rhesus fibroblasts were cultured under standard conditions and infected at an MOI of 0.1

extract_protocol: Genomic DNA was prepared as follows: virus was produced in telomerized rhesus fibroblasts (TRFs), supernatants were collected and, after proteinase K treatment, DNA was isolated by cesium chloride gradient centrifugation. The resulting viral DNA was ethanol precipitated and brought to a final concentration of 1ɥg/ɥl.

treatment_protocol: After TRFs reached 100% cytopathic effect, virus was produced in telomerized rhesus fibroblasts (TRFs), supernatants were collected and, after proteinase K treatment, DNA was isolated by cesium chloride gradient centrifugation. The resulting viral DNA was ethanol precipitated and brought to a final concentration of 1ɥg/ɥl.

tag: strain

value: RhCMV strain 68-1

source_name: RhCMV-BAC genomic DNA


title: 0h_Ifnb_s4_(MoEx-1_0-st-v1)


title: RhCMV Δ182-189

source_name: RhCMVΔ182-189-gag genomic DNA


title: RhCMV Δ178

source_name: RhCMVΔ178-gag genomic DNA


title: c HUVEC/ MCF-7  co-culture 2

status: Public on Feb 18 2010

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67572.gif

hyb_protocol: not provided

scan_protocol: GenePix 4000A

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: stratagene human reference

label_protocol: amplified RNA dircect inocorporaton; The protocol was modified for amplified RNA: 1. 6ug of amplified RNA and 10ug of random hexamer primer were mixed in a total volume of 15.4 ul. Then the described protocol was followed.; Protocol Type = Labeling; Performer: Martin,,Buess

extract_protocol: MessageAmpII; Total RNA was amplified using the Message AmpTM II aRNA Kit (Ambion, Austin, TX), according to the manufacturer's instructions.; Protocol Type = Amplification; Performer: Martin,,Buess

tag: reference

value: Stratagene Universal reference; pooled from 11 cell lines

label_protocol: amplified RNA direct incorporation method; The protocol was modified for amplified RNA:  6ug of amplified RNA was mixed with 10ug of random hexamer primer pd(N)6( Procuct number 27-2166-01, Amersham Biosciences) in a total volume of 15.4 ul. Then the protocol was followed as described; Protocol Type = Labeling; Performer: Martin,,Buess

growth_protocol: Endothelial co-culture conditions; Human mammary epithelial cells (HMEC) (Cambrex Bio Science Walkersville, Inc) were expanded in mammary epithelial basal medium supplemented with bovine pituitary extract, human EGF, insulin and antibiotics (Clonetics, Cambrex Bio Science Walkersville, Inc). MCF-7, T47D, MDA-MB231, SKBR-3, Hs578T, BT549 (ATTC) were propagated in DMEM supplemented with 10% FBS (HyClone, Logan UT), glutamine, 100U/ml penicillin and 100 μg/ml streptomycin (GIBCO, Grand Island, N.Y.). HUVEC (ATTC) AND HDMEC (Cambrex Bio Science Walkersville, Inc) were expanded in endothelial basal media (CAMBREX Bio Science Rockland, Inc Rockland, Maine) supplemented with hEGF, Hydrocortisone, GA-1000 (Gentamicin, Amphotericin-B), 5% FBS, VEGF, hFGF-B (w/ heparin), R3 -IGF-and ascorbic acid. For co-culture experiments the cells were cultivated for 48 hours at 50,000 cells/cm2 in endothelial basal media (CAMBREX Bio Science Rockland, Inc Rockland, Maine) with 0.2% FBS, which was a good universal media for all cells involved.; Protocol Type = Biological Sample; Performer: Martin,,Buess

extract_protocol:
RNeasy; Total RNA was isolated using the RNeasy mini kit (QIAGEN), according to the manufacturer's instructions.; Protocol Type = Extract preparation; Performer: Martin,,Buess
MessageAmp II; RNA was amplified using the Message AmpTM II aRNA Kit (Ambion, Austin, TX) according to the manufacturer's instructions.; Protocol Type = Amplification; Performer: Martin,,Buess

value: HUVEC/ MCF-7

tag: cell line

value: co-culture


title: c HDMEC/MDA-MB-231 co-culture 1

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67589.gif


title: c MCF-7 monoculture 1

description:
Simple annotation: Cell-line, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67557.gif

source_name: stratagene universal reference

value: monoculture


title: c HUVEC monoculture 1

description:
Simple annotation: Cell-line, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67551.gif

source_name: HUVEC

value: HUVEC


title: c HDMEC/T47D co-culture 2

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67588.gif


title: c HDMEC /BT549 co-culture 2

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67592.gif


title: c HUVEC/HMEC co-culture 2

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67570.gif

source_name: HUVEC/HMEC

value: HUVEC/HMEC


title: c HUVEC/MDA-MB-231 co-culture 2

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67576.gif

source_name: stratagene human  reference


title: c HDMEC/HMEC co-culture 2

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67584.gif

source_name: HDMEC/HMEC

extract_protocol: MessageAmp II; RNA was amplified using the Message AmpTM II aRNA Kit (Ambion, Austin, TX) according to the manufacturer's instructions.; Protocol Type = Amplification; Performer: Martin,,Buess

value: HDMEC/HMEC


title: c SKBR-3 monoculture 2

description:
Simple annotation: Cell-line, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67568.gif


title: c HDMEC monoculture 1

description:
Simple annotation: Cell-line, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67555.gif

source_name: HDMEC

value: HDMEC


title: c HUVEC/T47D co-culture 2

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67574.gif


title: c HDMEC/HMEC co-culture 1

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67583.gif


title: c HDMEC/Hs578T co-culture 2

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67594.gif


title: c SKBR-3 monoculture 1

description:
Simple annotation: Cell-line, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67567.gif


title: c HUVEC monoculture 2

description:
Simple annotation: Cell-line, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67552.gif

label_protocol: not provided

extract_protocol: not provided

source_name: sample


title: c HDMEC/MCF-7 co-culture 1

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67585.gif


title: c HUVEC/Hs578T co-culture 2

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67580.gif


title: c Hs578T monoculture 1

description:
Simple annotation: Cell-line, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67561.gif


title: c HUVEC/BT549 co-culture 2

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67578.gif


title: c HDMEC/T47D co-culture 1

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67587.gif


title: c Hs578T monoculture 2

description:
Simple annotation: Cell-line, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67562.gif


title: c HUVEC/BT549 co-culture 1

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67577.gif


title: c HUVEC/SKBR3 co-culture 2

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67582.gif


title: c HDMEC/Hs578T co-culture 1

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67593.gif