title: Human_IPAH_LungArteries

city: Giessen

first: Jochen

last: Wilhelm

address: Gaffkystrasse 10

department: ECCPS Microarray Unit

institute: Uniklinikum Giessen

description:
Individual spot weights were used througout the data analysis. The spot weight factors were determined according to the spots intensity, saturation and homogeneity. The following R code was used to calculate the spot weights:
# object: data object of type list with following fields:
#  R: Cy5 spot intensity "F635 Mean"
#  G: Cy3 spot intensity "F532 Mean"
#  Rb: Cy5 background intensity "B635 Median"
#  Gb: Cy3 background intensity "B532 Median"
#  R.cv: Cy5 spot homogeneity (coefficient of variation of R) x 100 "F635 CV"
#  G.cv: Cy3 spot homogeneity (coefficient of variation of G) x 100 "F532 CV"
#  R.sat: Cy5 saturation in % "F635 % Sat."
#  G.sat: Cy3 saturation in % "F532 % Sat."
#  R.int: Cy5 relative spot intensity "% > B635+2SD"
#  G.int: Cy3 relative spot intensity "% > B532+2SD"
getWeights <- function(object, badFlag = -100)
{
nGenes <- dim(object)[1]
nOrigins <- dim(object)[2]
m = -1/(75^2-50^2)
b = 1-min*m
cv  = object$R.cv^2 + object$G.cv^2
w.cv = m*cv+b
int = (100-object$R.int)^2 + (100-object$G.int)^2
w.int = m*int+b
sat = object$R.sat^2 + object$G.sat^2
w.sat = m*sat+b
w = pmin(w.sat,w.int,w.cv)
w[w<0] = 0
w[w>1] = 1
if (!is.na(badFlag)) w[object$Flags==badFlag] <- 0
colnames(w) = colnames(object)
w
}

hyb_protocol: Hybridization and washing were carried out following the Agilent 60-mer oligo microarray processing protocol version 4.1.

scan_protocol: Slides were scanned with the Axon A4100 scanner. PMT gains were adjusted to get 5-50 saturated spots. Image analysis was performed with GenePix Pro 4.1.

data_processing:
Data was analyzed using R (www.r-project.org) and limma (http://bioinf.wehi.edu.au/limma/).
MA data were LOESS - normalized (span=0.1).
Normalized Cy3 and Cy5 intensities were obtained from back-transformation of the normalized MA data.

source_name: IPAH

label_protocol: mRNA was preamplified using the BD Atlas SMART Fluorescent Probe Amplification Kit (Clontech / BD Biosciences, Palo Alto, CA, USA) with 24 PCR cycles.

extract_protocol: Lysis buffer for mRNA extraction consisted of 4 mol/L of guauidine thiocyanate (GTC), 25 mmol/L of Na3citrate, 0.5% sarcosyl, and 0.72% β-mercaptoethanol. After incubation for 10 minutes at room temperature, total RNA was isolated using the RNeasy Mini Kit (QIAgen, Hilden, Germany) including a DNA digestion step (RNAse Free DNase Set, QIAgen).

treatment_protocol:
After explantation, lungs were rinsed with ice-cold preservation buffer and
imediately frozen at -80°C.
Cryosections (6 μm) from lung tissue were mounted on glass slides. After hemalaun staining for 45 seconds, the sections were subsequently immersed in 70% and 96% ethanol and stored in 100% ethanol until use. Not more than 10 sections were prepared at once to restrict the storage time. Intrapulmonary arteries with a diameter <750 μm were selected and microdissected under optical control using the Laser Microbeam System (P.A.L.M., Bernried, Germany). Afterwards, the vessel profiles were isolated by a sterile 30-gauge needle. Needles with adherent vessels were transferred into a reaction tube containing 200 μl of RNA lysis buffer.

tag: Pooled RNA from laser-microdissected arteries from lungs of 3 IPAH patients

tag: gender

value: male & female

tag: age

tag: IPAH

value: Heath & Edwards grade 3-4

tag: arteries

value: <750 µm diameter

source_name: Donor

tag: Pooled RNA from laser-microdissected arteries from lungs of 3 healthy donors:

tag: histology

value: no pathological features of the arteries


title: B. thetaiotaomicron tdk strain in vivo, simple sugar diet 1 of 3

status: Public on Nov 21 2008

type: RNA

city: Ann Arbor

first: Eric

middle: Charles

last: Martens

state: MI

address: 1150 West Medical Center Drive

department: Dept. of Microbiology and Immunology

country: USA

institute: University of Michigan Medical School

description: B. thetaiotaomicron tdk mutant strain ('wild-type' parent for gene deletion strains), grown in vivo in the cecum of NMRI inbred mouse fed a glucose (35%) / sucrose (35%) 'simple sugar' diet. Extracted 10d after colonization. Replicate 1 of 3.

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: Signals normalized to 500 using Affymetrix MAS5 software

label: Biotin

molecule: total RNA

organism: Bacteroides thetaiotaomicron

source_name: bacterial

label_protocol: Enzo Biochemicals Bioarray terminal labeling kit

extract_protocol: Qiagen RNAeasy column and Ambion DNAfree DNAseI treatment

tag: strain VPI-5482


title: B. thetaiotaomicron responses to purified host glycans and components: heparin 1

description: B. thetaiotaomicron grown in minimal medium plus 0.5% heparin, 5ml culture in an anaerobic tube. Replicate 1 of 2.

data_processing: Data values for B. thetaiotamicron genes normalized to 500 in Affymetrix MAS5 software (excluded other species that were on chip using electronic mask)

label: biotin

extract_protocol: Qiagen RNAeasy mini column and Ambion DNAfree DNAseI digestion


title: B. thetaiotaomicron responses to purified host glycans and components: heparin 2

description: B. thetaiotaomicron grown in minimal medium plus 0.5% heparin, 5ml culture in an anaerobic tube. Replicate 2 of 2.


title: 5ml tube culture in minimal medium plus 1M PMG glycans; rep 2 of 2

description: 5ml tube culture with minimal medium 1M PMG glycans (0.5%) of B. thetaiotaomicron VPI-5482; grown to mid-log phase; replicate 2 of 2

data_processing: Data normalized to 500 in Affymetrix MAS5 software

extract_protocol: Qiagen RNeasy mini column extraction; Ambion DNA free treatment


title: B. thetaiotaomicron responses to purified host glycans and components: alpha mannan 1

description: B. thetaiotaomicron grown in minimal medium plus 0.5% alpha-mannan, 5ml culture in an anaerobic tube. Replicate 1 of 2.


title: B. thetaiotaomicron responses to purified host glycans and components: hyaluronan 2

description: B. thetaiotaomicron grown in minimal medium plus 0.5% hyaluronan, 5ml culture in an anaerobic tube. Replicate 2 of 2.


title: 5ml tube culture in minimal medium plus 300mM PMG glycans;  rep 1 of 2

description: 5ml tube culture with minimal medium 300mM PMG glycans (0.5%) of B. thetaiotaomicron VPI-5482; grown to mid-log phase; replicate 1 of 2


title: 5ml tube culture in minimal medium plus 300mM PMG glycans; rep 2 of 2

description: 5ml tube culture with minimal medium 300mM PMG glycans (0.5%) of B. thetaiotaomicron VPI-5482; grown to mid-log phase; replicate 2 of 2


title: SLE-7 #1 @36wks, asymptomatic on treatment with sirolimus (-2101366109)

city: Cambridge

first: Padmalatha

last: Reddy

state: MA

address: 35 Cambridgepark Drive

institute: WYETH

description: Cohort ID = 3:2000023007

hyb_protocol: Affymetrix standard hybridization protocol

scan_protocol: Affymetrix standard scan protocol

data_processing: Affymetrix MAS 5.0 algorithm

molecule: polyA RNA

organism: Mus musculus

label_protocol: Affymetrix in-vitro labeling protocol

extract_protocol: RNA was extracted from mouse kidney

tag: Disease_status:asymptomatic on treatment with sirolimus

tag: Strain:NZB/W F1


title: B. thetaiotaomicron responses to purified host glycans and components: chondroitin sulfate 2

description: B. thetaiotaomicron grown in minimal medium plus 0.5% chondroitin sulfate, 5ml culture in an anaerobic tube. Replicate 2 of 2.


title: Expression profiling on Mef2c deficient multipotent progenitor cells   Replicate3

first: Fernando

last: Camargo

address: 9 Cambridge Center

institute: Whitehead Institute

description: 15000 multipotent progenitor cells (MPPs) (Linneg c-kit+ Sca-1+) from poly(I:C)- induced mutant (Mx1-Cre Mef2cf/f  ) and control (Mef2cf/f ) mice were flow sorted. Mice were induced on 4 consecutive days with 250 g poly(I:C). Two days after last induction bone marrow was isolated, lineage depleted and ultimately stained with appropriate antibodies (Lin markers: B220, Ter119, gr-1, mac1, and CD3. ; c-kit, and sca-1). MPPs were sorted into PBS. Eventually cells were pelleted and resuspended in SuperAmp lysis solution (Miltenyi Biotec).

hyb_protocol: The corresponding Cy3 and Cy5 labled cDNAs were combined and hybridized overnight (17hours, 650C) to an Agilent Whole Mouse Oligo Microarray 4x44K using Agilent’s recommended hybridization chamber and oven.  Finally the microarrays were washed once with 6xSSPE buffer containing 0.005% N-lauroylsarcosine for 1 min at room temperature followed by a second wash with pre-heated  0.06 x SSPE buffer (370C) containing 0.005% N-lauroylsarcosine for 1 min. The last wash was performed with acetonitrile for 30 sec.

scan_protocol: Fluorescence signals of the hybridized Agilent Oligo Arrays were detected using Agilent’s DNA microarray scanner according to their protocol.

data_processing: Data were analyzed using the limma package from Bioconductor. Spots were not background corrected before within array loess normalization.  After between array normalization using the quantile method on A-values (average intensities), log2 ratios (mutant / control) were calculated.

source_name: Mx1-cre+ Mef2cfl/fl  (Mutant)

label_protocol: 250 ng of cDNA was used for Cy3 labeling which was performed by Milteniy Biotec’s according to their protocol. The corresponding Cy3 and Cy5 labled cDNAs were combinded

extract_protocol: flow sorted cells were peletted and resuspended in SuperAmp lysis soltion provided by Miltenyi Biotec. The samples were sent on dry ice to Miltenyi Biotec. Miltenyi Biotec performed the SuperAmp RNA amplicfication according to their procedure, wich is based on a global PCR protocol using mRNA-derived cDNA. mRNA was isolated via magnetic bead technology. Amplified cDNA samples were quantified.

tag: multipotent progenitor cells (MPPs) from Mef2c deficient mice (Mx1-cre+ Mef2cfl/fl ) were used.

source_name: Mef2cfl/fl  (Control)

label_protocol: 250 ng of cDNA was used for Cy5 labeling which was performed by Milteniy Biotec’s according to their protocol.

extract_protocol: flow sorted cells were peletted and resuspended in SuperAmp lysis soltion provided by Miltenyi Biotec. The samples were sent on dry ice to Miltenyi Biotec. All further steps were performed by Miltenyi Biotec. Miltenyi Biotec performed the SuperAmp RNA amplicfication according to their procedure, wich is based on a global PCR protocol using mRNA-derived cDNA. mRNA was isolated via magnetic bead technology. Amplified cDNA samples were quantified.

tag: multipotent progenitor cells (MPPs) from control (Mef2cf/f  ) mice were used.


title: B. thetaiotaomicron responses to purified host glycans and components: hyaluronan 1

description: B. thetaiotaomicron grown in minimal medium plus 0.5% hyaluronan, 5ml culture in an anaerobic tube. Replicate 1 of 2.


title: Ventral striatum VS-SDpcb

city: Syracuse

first: Frank

middle: A

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

hyb_protocol: 16hrs 45C 60rpm

organism: Rattus norvegicus

source_name: brain

label_protocol: Ovation (Nugen)

extract_protocol: Qiagen RNeasy

tag: P55-65 males


title: EF2505 2

city: Houston

first: Scott

middle: E

last: Evans

state: TX

address: 1400 Holcombe Blvd

department: Pulmonary Medicine - Unit 1462

institute: University of Texas-M.D. Anderson Cancer Center

description: EF2505-III treated

hyb_protocol: cRNA was hybridized to BeadChips per Illumina instructions.

scan_protocol: Chips were scanned using level 3 signal using a BeadStation 500 scanner.

data_processing: Data was processed using Illumina BeadStudio v3.  Matrix tables were generated both without normalization and with rank invariant normalization, using sham group as the reference group.

source_name: EF2505-III treated

label_protocol: cRNA was hybridized to BeadChips prior to labeling with Cy3-Streptavidin per Illumina instructions.

growth_protocol: MLE-15s grown in monolayer to approximately 80% confluence in 6 well plates

extract_protocol: total RNA extracted using Qiagen Rneasy per manufacturers instructions.  cRNA amplification using Ambion total prep kit per manufacturers instructions.

treatment_protocol: MLE-15 cells were treated with sham (PBS), NTHi lysate (100 ug/ml) or EF2505-III (40 ug/ml) for 2 hours.

tag: 2h treatment of MLE-15 cells


title: EF2505 1

description: EF2505-III treated


title: 5ml tube culture in minimal medium plus 1M PMG glycans; rep 1 of 2

description: 5ml tube culture with minimal medium 1M PMG glycans (0.5%) of B. thetaiotaomicron VPI-5482; grown to mid-log phase; replicate 1 of 2


title: Expression profiling on Mef2c deficient multipotent progenitor cells Replicate1


title: Expression profiling on Mef2c deficient multipotent progenitor cells   Replicate2

data_processing: Data were analyzed using the limma package from Bioconductor. Spots were background corrected using a normal and exponential convolutional model and an offset of 50 was added.  After loess normalization by print tip, log2 ratios were calculated.


title: Ventral striatum VS-WKY


title: Ventral striatum VS-SD


title: Vermis-SHR


title: EF2505 4

description: EF2505-III treated


title: 5ml tube culture in minimal medium plus 100mM PMG glycans; pooled late phases rep2

description: 5ml tube culture with minimal medium 100mM PMG glycans (0.5%) of B. thetaiotaomicron VPI-5482; pool of 3 sample points in later growth phases; replicate 2 of 2


title: 5ml tube culture in minimal medium plus 100mM PMG glycans; pooled late phases rep1

description: 5ml tube culture with minimal medium 100mM PMG glycans (0.5%) of B. thetaiotaomicron VPI-5482; pool of 3 sample points in later growth phases; replicate 1 of 2


title: Vermis-SDpcb


title: EF2505 3

description: EF2505-III treated


title: Vermis-SD


title: Vermis-WKY


title: B. thetaiotaomicron responses to purified host glycans and components: chondroitin sulfate 1

description: B. thetaiotaomicron grown in minimal medium plus 0.5% chondroitin sulfate, 5ml culture in an anaerobic tube. Replicate 1 of 2.


title: B. thetaiotaomicron responses to purified host glycans and components: LacNAc disaccharide 1

description: B. thetaiotaomicron grown in minimal medium plus 0.5% LacNAc disaccharide (galactose-beta1,4-N-acteylglucosamine), 5ml culture in an anaerobic tube. Replicate 1 of 2.


title: B. thetaiotaomicron responses to purified host glycans and components: LacNAc disaccharide 2

description: B. thetaiotaomicron grown in minimal medium plus 0.5% LacNAc disaccharide (galactose-beta1,4-N-acteylglucosamine), 5ml culture in an anaerobic tube. Replicate 2 of 2.


title: NTHi 2

description: NTHi lysate treated

source_name: NTHi lysate treated


title: B. thetaiotaomicron responses to purified host glycans and components: LacNAc monosaccharides 2

description: B. thetaiotaomicron grown in minimal medium plus 0.25% LacNAc monosaccharide components (galactose and N-acteylglucosamine), 5ml culture in an anaerobic tube. Replicate 2 of 2.


title: B. thetaiotaomicron responses to purified host glycans and components: LacNAc monosaccharides 1

description: B. thetaiotaomicron grown in minimal medium plus 0.25% LacNAc monosaccharide components (galactose and N-acteylglucosamine), 5ml culture in an anaerobic tube. Replicate 1 of 2.


title: B. thetaiotaomicron responses to purified host glycans and components: core 1 disaccharide 1

description: B. thetaiotaomicron grown in minimal medium plus 0.5% core 1 disaccharide (galactose-beta-1,3-N-acteylgalactosamine), 5ml culture in an anaerobic tube. Replicate 1 of 2.


title: Substantia nigra SN_VTA-SDpcb


title: NTHi 1

description: NTHi lysate treated


title: Sham 2

description: Sham treated

source_name: PBS treated


title: B. thetaiotaomicron responses to purified host glycans and components: core 1 monosaccharides 2

description: B. thetaiotaomicron grown in minimal medium plus 0.25% each of the monosaccharides found in mucin core 1 (galactose and N-acteylgalactosamine), 5ml culture in an anaerobic tube. Replicate 2 of 2.


title: 5ml tube culture in minimal medium plus 100mM PMG glycans; early phase rep1

description: 5ml tube culture with minimal medium 100mM PMG glycans (0.5%) of B. thetaiotaomicron VPI-5482; grown to middle of first phase; replicate 1 of 2


title: NTHi 4

description: NTHi lysate treated


title: 5ml tube culture in minimal medium plus 100mM PMG glycans; early phase rep2

description: 5ml tube culture with minimal medium 100mM PMG glycans (0.5%) of B. thetaiotaomicron VPI-5482; grown to middle of first phase; replicate 2 of 2


title: B. thetaiotaomicron responses to purified host glycans and components: core 1 disaccharide 2

description: B. thetaiotaomicron grown in minimal medium plus 0.5% core 1 disaccharide (galactose-beta-1,3-N-acteylgalactosamine), 5ml culture in an anaerobic tube. Replicate 2 of 2.


title: Substantia nigra SN_VTA-SHR


title: Sham 3

description: Sham treated


title: Sham 1

description: Sham treated


title: Pre-frontal cortex PFC-SD


title: 5ml tube culture minimal medium plus neutral PMG glycans 0.5%, rep1 of 2

description: 5ml tube culture with minimal medium neutral PMG glycans (0.5%) of B. thetaiotaomicron VPI-5482; grown to mid-log phase; replicate 1 of 2


title: B. thetaiotaomicron responses to purified host glycans and components, minimal glucose 1

description: B. thetaiotaomicron grown in minimal medium plus 0.5% glucose, 5ml culture in an anaerobic tube. Serves as reference for other cultures on pure carbon sources. Replicate 1 of 2.


title: Substantia nigra SN_VTA-WKY


title: 800ml chemostat minimal medium plus unfractionated PMG glycans, phase 1, rep 3

description: 800ml minimal unfractionated PMG glycans (0.5%) medium chemostat culture of B. thetaiotaomicron VPI-5482; grown to middle of first logarithmic growth phase; replicate 3 of 3


title: Pre-frontal cortex PFC-WKY


title: Pre-frontal cortex PFC-SDpcb


title: 5ml tube culture minimal medium plus glucose 0.5%, rep1 of 2

description: 5ml tube culture with minimal medium glucose (0.5%) of B. thetaiotaomicron VPI-5482; grown to mid-log phase; replicate 1 of 2


title: 800ml chemostat minimal medium plus unfractionated PMG glycans, phase 2, rep 2

description: 800ml minimal unfractionated PMG glycans (0.5%) medium chemostat culture of B. thetaiotaomicron VPI-5482; grown to middle of second logarithmic growth phase; replicate 2 of 3


title: areA-0-2

city: Peoria

first: Robert

last: Butchko

state: IL

address: 1815 N. University St.

institute: U.S. Dept. of Agriculture

hyb_protocol: Hybridization conducted by Nimblegen.

scan_protocol: Scan conducted by Nimblegen.

data_processing: Robust multiarray analysis following Bolstad, B., Irizarry, R., Astrand, M. and Speed, T. (2003) Bioinformatics, 19, 185–193.

organism: Fusarium fujikuroi

source_name: Fusarium fujikuroi

label_protocol: Biotin labeling conducted by Nimblegen.

growth_protocol:
F. fujikuroi was cultivated for 2 days in 300 ml Erlenmeyer flasks with 100 ml Darken medium (Darken et al., 1959) with 2.0 g/l L-glutamine instead of (NH4)2SO4 on a rotary shaker at 28 °C.   One ml of this culture was used to inoculate 100 ml ICI media containing 1.8 g/l L-glutamine (Geissman et al., 1966). After 4 days the mycelia was harvested, washed with deionized water, added to fresh ICI medium without nitrogen for 4 h of growth, harvested a second time and then added to fresh ICI media without nitrogen or with 9.2 g/l L-glutamine.
	Darken, M.A., Jensen, A.A.L., and Shu, P. (1959) Production of gibberellic acid by fermentation. Appl Microbiol 7: 301-306.

Geissman, T. A., Verbiscar, A. J., Phinney, B. O., and Cragg, G. 1966. Studies on the biosynthesis of gibberellins from (-)-kaurenoic acid in cultures of Gibberella fujikuroi. Phytochem 5: 933-947.

extract_protocol: RNAgents Total RNA isolation kit (Promega, Mannheim, Germany).

treatment_protocol: without nitrogen source

tag: Fusarium fujikuroi areA deletion (delta areA-T19) strain


title: B. thetaiotaomicron responses to purified host glycans and components: core 1 monosaccharides 1

description: B. thetaiotaomicron grown in minimal medium plus 0.25% each of the monosaccharides found in mucin core 1 (galactose and N-acteylgalactosamine), 5ml culture in an anaerobic tube. Replicate 1 of 2.


title: 800ml chemostat minimal medium plus unfractionated PMG glycans, phase 2, rep 3

description: 800ml minimal unfractionated PMG glycans (0.5%) medium chemostat culture of B. thetaiotaomicron VPI-5482; grown to middle of second logarithmic growth phase; replicate 3 of 3


title: 800ml chemostat minimal medium plus unfractionated PMG glycans, phase 2, rep 1

description: 800ml minimal unfractionated PMG glycans (0.5%) medium chemostat culture of B. thetaiotaomicron VPI-5482; grown to middle of second logarithmic growth phase; replicate 1 of 3


title: 5ml tube culture minimal medium plus glucose 0.5%, rep2 of 2

description: 5ml tube culture with minimal medium glucose (0.5%) of B. thetaiotaomicron VPI-5482; grown to mid-log phase; replicate 2 of 2


title: Hippocampus Hipp-SHR


title: 5ml tube culture neutral PMG glycans, replicate 2

description: 5ml tube culture with minimal medium neutral PMG glycans (0.5%) of B. thetaiotaomicron VPI-5482; grown to mid-log phase; replicate 2 of 2


title: NTHi 3

description: NTHi lysate treated


title: areA-100-1

treatment_protocol: 100 mM glutamine


title: 800ml chemostat minimal medium plus unfractionated PMG glycans, phase 1, rep 1

description: 800ml minimal unfractionated PMG glycans (0.5%) medium chemostat culture of B. thetaiotaomicron VPI-5482; grown to middle of first logarithmic growth phase; replicate 1 of 3


title: LB 1 mM IAA 7 h biofilm cells run with 2nd DMF

city: College Station

first: Jintae

last: Lee

department: Chemical Engineering

institute: Texas A&M University

description: For the microarray experiments, 10 g glass wool (Corning Glass Works, Corning, N.Y.) were used to form biofilms in 250 mL LB in 1 L Erlenmeyer shake flasks which were inoculated with overnight cultures of P. aeruginosa PAO1 diluted that were 1:100.  For P. aeruginosa with 1 mM indole-acetic acid , 1 mM  indole-acetic acid in 250 L DMF, or 250 L DMF alone were added to cells grown in LB.  The cells were shaken at 250 rpm and 37oC for 7 h to form biofilms on the glass wool, and RNA was isolated from the biofilm cells

hyb_protocol: The biotin-labeled target was hybridized to the Affymetrix GeneChip P. aeruginosa Genome Array (Affymetrix, P/N 900339) at 50C for 16 hour at 60 rpm using the Hybridization Oven 640 (Affymetrix), then a three-step fluorescent staining was conducted using the Fluidics Station 450 (Affymetrix) during the washing and staining procedure.

scan_protocol: The microarray was scanned at 570 nm to get an image file by the GeneChip Scanner 3000 (Affymetrix).  Using GeneChip® Operating Software, total cell intensity was scaled automatically in the software to an average value of 500.

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Pseudomonas aeruginosa PAO1

source_name: Strain: P. aeruginosa PAO1 wild type

label_protocol: The total RNA samples were first converted into cDNA through a reverse transcription reaction with poly-A RNA controls spiked into the same reaction mixture to monitor the entire target labeling process.  The cDNA was then digested with DNase I (Amersham Biosciences) to produce 50-200 bp fragments, which was checked by running the fragmented cDNA on a 2% agarose gel.  The fragmented cDNA was labeled at the 3’ termini by the Enzo BioArray Terminal Labeling Kit with Biotin-ddUTP (Affymetrix, P/N 900181).

extract_protocol: To lyse the cells, 1.0 mL RLT buffer (Qiagen, Inc., Valencia, CA) and 0.2 mL 0.1 mm zirconia/silica beads (Biospec) were added to the frozen bead beater tubes containing the cell pellets. The tubes were closed tightly and beat for 50 seconds at the maximum speed in a mini bead beater (cat. no. 3110BX, Biospec). The total RNA was isolated by following the protocol of the RNeasy Mini Kit (Qiagen) including an on-column DNase digestion with RNase-free DNase I (Qiagen).

tag: RNA extracted from biofilm cells of P. aeruginosa PAO1 wild type after 7 h of growth in LB and indole-acetic acid  (1 mM) with glass wool at 37oC


title: Substantia nigra SN_VTA-SD


title: Hippocampus Hipp-SDpcb


title: areA-100-2

growth_protocol:
F. fujikuroi was cultivated for 2 days in 300 ml Erlenmeyer flasks with 100 ml Darken medium (Darken et al., 1959) with 2.0 g/l L-glutamine instead of (NH4)2SO4 on a rotary shaker at 28 °C.   One ml of this culture was used to inoculate 100 ml ICI media containing 1.8 g/l L-glutamine (Geissman et al., 1966). After 4 days the mycelia was harvested, washed with deionized water, added to fresh ICI medium without nitrogen for 4 h of growth, harvested a second time and then added to fresh ICI media without nitrogen or with 9.2 g/l L-glutamine.
Darken, M.A., Jensen, A.A.L., and Shu, P. (1959) Production of gibberellic acid by fermentation. Appl Microbiol 7: 301-306.

Geissman, T. A., Verbiscar, A. J., Phinney, B. O., and Cragg, G. 1966. Studies on the biosynthesis of gibberellins from (-)-kaurenoic acid in cultures of Gibberella fujikuroi. Phytochem 5: 933-947.


title: Sham 4

description: Sham treated


title: Pre-frontal cortex PFC-SHR


title: Hippocampus Hipp-WKY


title: areA-0-1


title: 800ml chemostat minimal medium plus unfractionated PMG glycans, phase 1, rep 2

description: 800ml minimal unfractionated PMG glycans (0.5%) medium chemostat culture of B. thetaiotaomicron VPI-5482; grown to middle of first logarithmic growth phase; replicate 2 of 3


title: Dorsal striatum DS-WKY


title: S1-100-2

tag: Fusarium fujikuroi IMI58289 (Commonwealth Mycological Institute, Kew, UK)


title: B. thetaiotaomicron responses to purified host glycans and components, minimal glucose 2

description: B. thetaiotaomicron grown in minimal medium plus 0.5% glucose, 5ml culture in an anaerobic tube. Serves as reference for other cultures on pure carbon sources. Replicate 2 of 2.


title: Hippocampus Hipp-SD


title: 800ml minimal medium glucose chemostat 3

description: 800ml minimal glucose (0.5%) medium chemostat culture of B. thetaiotaomicron VPI-5482; grown to mid-log phase; replicate 3 of 3


title: S1-100-1


title: LB 7HI 7h biofilm cells

description: For the microarray experiments, 10 g glass wool (Corning Glass Works, Corning, N.Y.) were used to form biofilms in 250 mL in 1 L Erlenmeyer shake flasks which were inoculated with overnight cultures of P. aeruginosa PAO1 diluted that were 1:100.  For P. aeruginosa with 7-hydroxyindole and indole, 500 uM 7-hydroxyindole in 250 uL DMF, 1000 uM indole in 250 uL DMF, or 250 uL DMF alone were added to cells grown in LB.  The cells were shaken at 250 rpm and at 37oC for 7 h to form biofilms on the glass wool, and RNA was isolated from the biofilm cells.

hyb_protocol: The biotin-labeled target was hybridized to the Affymetrix GeneChip P. aeruginosa Genome Array (Affymetrix, P/N 900339) at 50°C for 16 hour at 60 rpm using the Hybridization Oven 640 (Affymetrix), then a three-step fluorescent staining was conducted using the Fluidics Station 450 (Affymetrix) during the washing and staining procedure.

source_name: Channel 1

tag: RNA extracted from biofilm cells of P. aeruginosa PAO1 wild type after 7 h of growth in LB and 7-hydroxyindole with glass wool at 37oC


title: LB DMF 7h biofilm cells

tag: RNA extracted from biofilm cells of P. aeruginosa PAO1 wild type after 7 h of growth in LB and 0.1 % DMF with glass wool at 37oC


title: S1-0-2


title: Dorsal striatum DS-SD


title: V. parahaemolyticus cDNA 3%LB at 20°C vs gDNA non-replicating

status: Public on Nov 20 2008

type: mixed

city: Suita

first: Kaori

last: Izutsu

state: Osaka

address: 1-1 Yamadaoka

department: Research Institute for Microbial Diseases

country: Japan

institute: Osaka University

hyb_protocol: Cy3- or Cy5- labeled probes (21.6 µl each) were mixed and 18 μl 20X SSC (3 M NaCl, 0.3 M HOC(COONa)(CH2COONa)2), 7.2 μl human CotI DNA (Invitrogen) and 3.6 μl 10% SDS was added. Hybridisation mixtures were incubated at 96ºC for 5 min, chilled on ice and kept at 55ºC until application onto microarray slides. Slides were covered with a MAUI AO Lid and insertion into MAUI hybridization chambers (BioMicro Systems) before application of the pre-warmed hybridisation mixture and 16 h incubation at 55ºC followed. After hybridisation, slides were washed twice in 2X SSC, 0.1 % SDS at 55ºC for 10 min, twice in 0.2X SSC, 0.1 % SDS at room temperature for 10 min, twice in 0.2X SSC at room temperature for 10 min and finally in ethanol for 1 min.

scan_protocol: Slides were scanned with a ScanArrayExpress scanner (PerkinElmer). Obtained data was analysed by ScanArrayExpress software version 3.0 (PerkinElmer).

data_processing: LOWESS normalised, background subtracted data obtained from log2 of processed Cy3 signal/processed Cy5 signal.

molecule: genomic DNA

organism: Vibrio parahaemolyticus

source_name: Genomic DNA from non-replicating cells

label_protocol: For generation of aminoallyl-labelled product from gDNA, the general procedures accompanying BioPrime Array CGH Genomic Labelling System (Invitrogen) were followed with a few modifications. Genomic DNA (2 μg) was incubated for 5 min at 95ºC with 20 μl 2.5X random primer solution in 44 μl reactions. Mixtures were cooled on ice for 3 min before addition of 5 μl 10X dNTP-aminoallyl dUTP (5 mM dATP, dCTP and dGTP, 2 mM dTTP and 3 mM aadUTP, Sigma) and 1 μl Exo-Klenow polymerase (40U, Invitrogen) and a further incubation at 37ºC for 1 h. Reactions were cleaned, precipitated and washed. For generation of aminoallyl-labelled product from total RNA, reagents included in SuperScript™ III Reverse Transcriptase Kit (Invitrogen) were used. In brief, 20 μg RNA was mixed with 10 μg random hexamers in a 22 μl reaction that was incubated at 70ºC for 5 min before cooling on ice. Addition of 5X First-Strand Buffer (8 μl), 0.1 M DTT (2 μl), SuperScript™ III RT (4 μl) and 10X dNTP-aminoallyl dUTP (4 μl) was followed by a 3 h incubation at 46ºC. Samples were cleaned, precipitated and washed. Finally, aminoallyl-labelled nucleic acids were resuspended in 10 μl 50 mM NaCO3 (pH 9.0), and 10 μl of either Cy3 or Cy5 monofunctional reactive dye (GE Healthcare) was added. Mixtures were incubated in the dark for 1 h at room temperature and unincorporated dye was removed on CENTRI-SEP Columns (Princeton Separations) following the manufacturer’s instructions before precipitation and wash.

growth_protocol: To obtain non-replicating bacteria, cells were spread onto Luria-Bertani (LB) Agar followed by a 24 h incubation t 20ºC and a 24 h incubation at 4ºC. Other samples were grown at 37ºC in liquid LB with 3% NaCl or liquid M9 with 3% NaCl and 0.4% glucose until an OD600 of 0.2, 0.5 or 3.0 was reached.

extract_protocol: Genomic DNA was purified using the DNeasy Tissue Kit (Qiagen) according to the manufacturer's instruction. RNA was extracted using TRIzol Reagent (Invitrogen) and purified with RNeasy Mini Kit (Qiagen) following the manufacturers protocols.

tag: Strain

source_name: cDNA derived from cells grown at 20°C in LB 3% NaCl harvested at OD600=0.5


title: V. parahaemolyticus cDNA 3%M90.4%glucose vs gDNA non-replicating

source_name: cDNA derived from cells grown at 37°C in M9 3% NaCl and 0.4% glucose harvested at OD600=0.5


title: LB 2nd DMF 7h biofilm cells run with IAA sample


title: Dorsal striatum DS-SDpcb


title: ATRA-treated Day4  0.05uM_Replicate_3

city: St. Louis

first: Michael

last: Diamond

state: MO

address: McDonnell Pediatric Research Building, Room 7264

department: Division of Infectious Diseases

institute: Washington University in St. Louis

description: With HL60 multipotent promyelocytic leukemia cell line, we performed experiments that lead to two different cell fate attractors by treatments of varying dosage and duration of the differentiation agent all-trans-retinoic acid (ATRA).

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

organism: Homo sapiens

source_name: untreated HL60 Promyelocytic Cells

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-labe

growth_protocol: RPMI1640 with 10%FBS

extract_protocol: Total RNA extracted using Trizol following instructions from Agilent

treatment_protocol: ATRA Untreated

tag: HL60 multipotent promyelocytic leukemia cell Line

source_name: ATRA-treated HL60 Promyelocytic Cells

treatment_protocol: Day4   0.05uM   ATRA


title: EhHMGB1 overexpression p3m sample 2

city: Charlottesville

first: Carol

last: Gilchrist

state: VA

address: Dept. of Medicine/Division of Infectious Diseases, Building MR4, Rm 2126,PO Box 801365

department: Medicine

institute: University of Virginia

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

data_processing: gcrma

organism: Entamoeba histolytica

source_name: EhHMGB1 overexpression p3m sample 2

label_protocol: SPIA

tag: EhHMGB1 overexpression p3m sample 2


title: S1-0-1


title: Control pGir sample 2

source_name: Control pGir sample 2

tag: Control pGir sample 2


title: V. parahaemolyticus cDNA 3%LB early logarithmic growth at 37°C vs cDNA 3%LB late logarithmic/early stationary growth

organism: Vibrio parahaemolyticus RIMD 2210633

source_name: cDNA derived from cells grown at 37°C in LB 3% NaCl harvested at OD600=3.0

source_name: cDNA derived from cells grown at 37°C in LB 3% NaCl harvested at OD600=0.2


title: EhHMGB1 overexpression p3m sample 3

source_name: EhHMGB1 overexpression p3m sample 3

tag: EhHMGB1 overexpression p3m sample 3


title: Control (incubated as GSM296164 but without IAM blocking) (Sample B)

type: protein

city: Kgs Lyngby

first: Per

last: Hagglund

address: Soltofts plads

department: Department of Systems Biology

country: Denmark

institute: Technical University of Denmark

description: Sample preparation: Barley embryo protein extract, treated with iodoacetamide (IAM) during extraction, was incubated ± thioredoxin for 1 h at RT. Remaining cysteine residues were completely reduced by tris(2-carboxyethyl)phosphine (TCEP) under denaturing conditions and ICAT-labeled (+Trx, ICATL; -Trx, ICATH), essentially as recommended by the manufacturer (Applied Biosystems). The ICATL and ICATH labeled samples were mixed 1:1 and subjected to trypsin digestion followed by isolated of ICAT labeled peptides by avidin affinity chromatography and LC-MS/MS analysis on an Agilent 1100 nanoflow HPLC (Agilent, Palo Alto CA) coupled to a QSTAR quadrupole time-of-flight mass spectrometer (Applied Biosystems). Data were acquired in information dependent mode with a cycle of a survey mass spectrum followed by tandem mass spectra of the three most intense multiply charged ions (1 s each) after which the selected ions were placed on an exclusion list for 45 s. References: Bønsager BC, Finnie C, Roepstorff P, Svensson B (2007) Spatio-temporal changes in germination and radical elongation of barley seeds tracked by proteome analysis of dissected embryo, aleurone layer, and endosperm tissues. Proteomics 7:4528-4540.

data_processing: Data processing and peptide quantification. The raw data .wiff files were processed with the Mascot script for Analyst (QS 2.0) version 1.6b20 (Matrix Science, London, UK).   The charge state was determined from the survey spectrum with a default charge setting of multiply charged precursors. The MS/MS data was centroided and de-isotoped without MS/MS averaging to generate the Mascot Generic Format (MGF) peak list. Spectra with less than 10 peaks were rejected. Database searches of the centroided data were performed using the Mascot search engine (Matrix Science) against the Viridiplantae (Green Plants) subset of Swiss-Prot 54.6, nrNCBI (downloaded on 20071206) and the Barley EST database (barley gene index [HvGI] release 9.0). The following search criteria were used: MS mass tolerance 0.2 Da; MS/MS tolerance 0.2 Da; no trypsin miss-cleavage allowed. Variable modifications: ICATH (cysteine), ICATL (cysteine), carbamidomethyl (cysteine) and oxidation (methionine). Tentative consensus sequences (TC sequences) identified in HvGI release 9.0 were blasted (http://www.ncbi.nlm.nih.gov/blast) against the nrNCBI database. Quantification of ICAT labeled peptide pairs was performed using the software MS quant version 1.4.3a12 (http://www.msquant.sourceforge.net). Spectra were manually validated and peptides with a sequence tag of at least three amino acids and a Mascot score of 20 were accepted.

molecule: protein

organism: Hordeum vulgare

source_name: Barley embryo protein extract, thioredoxin untreated

growth_protocol: Dissected embryos from seeds from the malting barley (Hordeum vulgare) cultivar Barke (2002 harvest) germinated for 48 h as previously described (Bønsager et al., 2007).

tag: Same as for Sample (Trx-treated) except IAM addition after thioredoxin incubation was omitted.


title: V. parahaemolyticus cDNA 3%LB at 37°C vs cDNA 3%M90.4%glucose

source_name: cDNA derived from cells grown at 37°C in LB 3% NaCl harvested at OD600=0.6


title: LB indole 7 h biofilm cells

hyb_protocol: The biotin-labeled target was hybridized to the Affymetrix GeneChip P. aeruginosa Genome Array (Affymetrix, P/N 900339) at 50oC for 16 hour at 60 rpm using the Hybridization Oven 640 (Affymetrix), then a three-step fluorescent staining was conducted using the Fluidics Station 450 (Affymetrix) during the washing and staining procedure.

tag: RNA extracted from biofilm cells of P. aeruginosa PAO1 wild type after 7 h of growth in LB and indole (1000 uM) with glass wool at 37oC


title: V. parahaemolyticus cDNA 3%LB at 37°C vs gDNA non-replicating

source_name: cDNA derived from cells grown at 37°C in LB 3% NaCl harvested at OD600=0.5


title: V. parahaemolyticus gDNA 3%M90.4%glucose at 37°C vs gDNA non-replicating

type: genomic

source_name: Genomic DNA from cells grown at 37°C in M9 3% NaCl and 0.4% glucose harvested at OD600=0.5


title: Barley embryo extract incubated +/- Trx (Sample A)

description: Sample preparation:  Barley embryo protein extract, treated with iodoacetamide (IAM) during extraction, was incubated ± thioredoxin and after 1 h incubation at RT, IAM was again added (final concentration 10 mM) to irreversibly block cysteines reduced by thioredoxin. Excess IAM was removed and remaining cysteine residues were completely reduced by tris(2-carboxyethyl)phosphine (TCEP) under denaturing conditions and ICAT-labeled (+Trx, ICATL; -Trx, ICATH), essentially as recommended by the manufacturer (Applied Biosystems). The ICATL and ICATH labeled samples were mixed 1:1 and subjected to trypsin digestion followed by isolated of ICAT labeled peptides by avidin affinity chromatography and LC-MS/MS analysis on an Agilent 1100 nanoflow HPLC (Agilent, Palo Alto CA) coupled to a QSTAR quadrupole time-of-flight mass spectrometer (Applied Biosystems). Data were acquired in information dependent mode with a cycle of a survey mass spectrum followed by tandem mass spectra of the three most intense multiply charged ions (1 s each) after which the selected ions were placed on an exclusion list for 45 s.  References:  Bønsager BC, Finnie C, Roepstorff P, Svensson B (2007) Spatio-temporal changes in germination and radical elongation of barley seeds tracked by proteome analysis of dissected embryo, aleurone layer, and endosperm tissues. Proteomics 7:4528-4540.

source_name: Barley embryo protein extract, thioredoxin treated


title: ATRA-treated Day4  0.05uM_Replicate_2


title: ATRA-treated Day4  0.05uM_Replicate_1


title: Non-additive expression between synthetic allopolyploid Allo738 and their progenitors

city: Bethesda

first: Misook

last: Ha

state: MD

address: NIH

institute: National Heart Lung Blood Institute

description: Total 8 replications ( 4 biological replications and dye-swap experiments were performed for each biological replication).

hyb_protocol: Each lyophilized probe was re-suspended in 40 μL of hybridization solution (0.25 M Na2HPO4, 0.25 M NaH2PO4, pH 7.4, and 3.5% SDS, w/v). The solution was heated for 2 min at 95 °C, chilled immediately in ice, and applied directly to the array. After covering the array with a 24 × 40 mm coverslip (Sigma, St Louis, MO), the slide was placed in a microarray hybridization chamber (Corning Incorporated, Corning, NY). Hybridization was performed overnight (16 h) at 60 °C in a hybridization oven. After hybridization, the slides were washed for 2 min in 2× SSC, 0.03% (w/v) SDS, 2 min in 0.2× SSC, and 2 min in 0.05× SSC. Immediately after the last wash, the slides were dried by centrifugation (3 min at 500 r.p.m.).

scan_protocol: Slides were scanned using Genepix 4000B

data_processing:
The data were processed using a lowess function to remove nonlinear components and analyzed using a linear model. This linear model was employed to partition variation in the observed data relative to technical and biological variation. Given that each feature is represented once on an array, the linear model is
Yijklm ¼ m1Ai 1Dj 1Tk 1Gl 1AGil 1DGjl 1TGkl 1TDGjkl 1eijklm
where µ represents the overall mean effect; A, D, T, and G represent main fixed effects from the array, dye, treatment (e.g., RNA from two species), and gene, respectively; and i = 1, ..., 8, k = 1, 2, j = 1, 2, and l = 1, ..., 27,648 (including 26,090 70-mer Arabidopsis oligos plus controls). The interaction terms AG, DG, TG, and TDG represent array-by-gene, dye-by-gene, treatment-by-gene, and treatment-by-dye-by-gene interactions, and {varepsilon}ijklm denotes the random error and is used to test for significance of main and interaction effects in the model. Due to confounding and/or aliasing issues involving the array, dye, and treatment terms, not all two-way interactions are included in the model. The model residuals are assumed to be normally distributed with a common variance [i.e., {varepsilon}ijklm iid N(0, {sigma}2)], unless evidence of variance nonconstancy is observed. In such a case, a per gene variance is assumed [i.e., {varepsilon}ijklm independent N(0, {sigma}l2)].
We tested differential expression using significant differences in T + TG terms for a particular gene because we are interested in changes in expression beyond the average treatment effect. The hypotheses reflect whether a gene, g, has undergone differential expression between treatments, t and t' (e.g., A. thaliana and A. arenosa).
A standard t-test statistic is used for this comparison, based on the normality assumption for the residuals. To control for multiple testing errors the false discovery rate (FDR) of BENJAMINI and HOCHBERG (1995) was employed as it provides weak control of the familywise error rate (FWER) and controls the FDR below level {alpha}. The FDR is defined as the expected proportion of incorrect rejections of H0, relative to the total number of rejections. The significance level {alpha} = 0.05 was chosen for these investigations. All analyses of variance models were fit using standard statistical packages

label: Either Cy3 or Cy5, dye-swap experiments

organism:
Arabidopsis thaliana
Arabidopsis arenosa

source_name: Leaves before bolting

label_protocol: We used 500 ng of mRNA in each labeling reaction using Cy3- or Cy5-dCTP (Amersham Biosciences). The Cy3-dCTP reaction was mixed with the Cy5-dCTP reaction for one hybridization

extract_protocol: Total RNA was isolated using Trizol reagent (Invitrogen, San Diego) according to the manufacturer's recommendations. Each RNA sample was quantified by measuring 260/280 ratios using a UV-spectrometer (GeneQuant pro; Amersham Biosciences, Arlington Heights, IL) and by agarose–formaldehyde gel electrophoresis. Total RNA was subjected to mRNA isolation, using a Micro-FastTrack 2.0 mRNA isolation kit (Invitrogen). Equal amounts of mRNA from A. thaliana and A. arenosa were mixed as a midparent value to detect nonadditive gene expression in the allotetraploids

tag: A synthetic allopolyploid line generated by hybridization of Arabidopsis thaliana and Arabidopsis arenosa.

source_name: Artificial mix of mRNAs from Leaf tissues of A. thaliana and A. arenosa

tag: Arabidopsis thaliana and Arabidopsis arenosa are progenitor species of the synthetic allopolyploid line, Allo738


title: Control pGir sample 3

source_name: Control pGir sample 3

tag: Control pGir sample 3


title: ATRA-treated Day3  0.05uM_Replicate_3

treatment_protocol: Day3   0.05uM   ATRA


title: V. parahaemolyticus gDNA 3%LB at 20°C vs gDNA non-replicating

source_name: Genomic DNA from non-replicating cells

source_name: Genomic DNA from cells grown at 20°C in LB 3% NaCl harvested at OD600=0.5


title: ATRA-treated Day3  0.05uM_Replicate_2

source_name: untreated HL60 Promyelocytic Cells


title: ATRA-treated Day3  0.05uM_Replicate_1

source_name: ATRA-treated HL60 Promyelocytic Cells


title: V. parahaemolyticus gDNA 3%LB at 37°C vs gDNA non-replicating

source_name: Genomic DNA from cells grown at 37°C in LB 3% NaCl harvested at OD600=0.5


title: EhHMGB1 overexpression 3m sample 1

source_name: EhHMGB1 overexpression 3m sample 1

tag: EhHMGB1 overexpression 3m sample 1


title: ATRA-treated Day2  0.05uM_Replicate_3

treatment_protocol: Day2   0.05uM   ATRA


title: ATRA-treated Day2  0.05uM_Replicate_2


title: ATRA-treated Day2  0.05uM_Replicate_1


title: Pten+/-;Mlh1-/- mouse with Invasion 4

city: New York

first: Ayesha

last: Joshi

address: 1300 York Avenue, Pathology

department: Pathology and Laboratory Medicine

institute: Weill Medical College of Cornell University

description: Pten+/-;Mlh1-/- mouse with invasive carcinoma

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

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

growth_protocol: Pten+/- and Mlh1+/- were maintained as separate lines. Pten+/-; Mlh1-/- mice were generated by crossing the two lines. Female mice were allowed to age and sacrificed between 16-32 weeks of age and uteri harvested

extract_protocol: All RNAs were extracted using the Trizol reagent as per manufacturer's instructions.

treatment_protocol: Uteri were dissected out and a quarter segment was snap frozen for RNA extraction.


title: ATRA-treated Day1  0.05uM_Replicate_2

treatment_protocol: Day1   0.05uM   ATRA


title: ATRA-treated Day1  0.05uM_Replicate_3


title: Pten+/-  mouse with Invasion 2

description: Pten+/-;Mlh1+/+ mouse with invasive carcinoma


title: Pten+/-;Mlh1-/- mouse with CAH8

description: Pten+/-;Mlh1-/- mouse with CAH

source_name: Pten+/-;Mlh1-/- mouse with CAH

tag: Pten+/-;Mlh1-/- mouse with CAH


title: Pten+/-  mouse with Invasion 1

source_name: Pten+/-;Mlh1+/+ mouse with invasive carcinoma


title: ATRA-treated Day0  0.05uM_Replicate_2

treatment_protocol: Day0   0.05uM   ATRA


title: ATRA-treated Day4 1uM_Replicate_2

treatment_protocol: Day4    1uM    ATRA


title: Pten+/-;Mlh1-/- mouse with CAH7

description: Pten+/-;Mlh1-/- mouse with CAH


title: ATRA-treated Day0  0.05uM_Replicate_1


title: ATRA-treated Day1  0.05uM_Replicate_1


title: Pten+/-;Mlh1-/- mouse with Invasion 3

source_name: Pten+/-;Mlh1-/- mouse with invasive carcinoma


title: Pten+/-  mouse with CAH4

description: Pten+/-;Mlh1+/+ mouse with CAH

source_name: Pten+/-;Mlh1+/+ mouse with CAH

tag: Pten+/-;Mlh1+/+ mouse with CAH


title: Pten+/-;Mlh1-/- mouse with CAH6

description: Pten+/-;Mlh1-/- mouse with CAH


title: ATRA-treated Day4 1uM_Replicate_1


title: Pten+/-  mouse with CAH3

description: Pten+/-;Mlh1+/+ mouse with CAH


title: Wild type mouse 42

description: Wild type mouse with no lesions

source_name: Wild type mouse with no lesions

tag: Wild type mouse with no lesions


title: ATRA-treated Day3 1uM_Replicate_2

treatment_protocol: Day3    1uM     ATRA


title: ATRA-treated Day3 1uM_Replicate_1


title: Pten+/-  mouse with CAH1

description: Pten+/-;Mlh1+/+ mouse with CAH


title: ATRA-treated Day3 1uM_Replicate_3


title: Wild type mouse 30

description: Wild type mouse with no lesions


title: Pten+/-  mouse with CAH2

description: Pten+/-;Mlh1+/+ mouse with CAH


title: ATRA-treated Day1 1uM_Replicate_2

treatment_protocol: Day1     1uM   ATRA


title: ATRA-treated Day2 1uM_Replicate_3

treatment_protocol: Day2     1uM   ATRA


title: ATRA-treated Day2 1uM_Replicate_2


title: Pten+/-;Mlh1-/- mouse with CAH5

description: Pten+/-;Mlh1-/- mouse with CAH


title: ATRA-treated Day2 1uM_Replicate_1


title: ATRA-treated Day0  0.05uM_Replicate_3


title: ATRA-treated Day1 1uM_Replicate_1


title: ATRA-treated Day0 1uM_Replicate_1

treatment_protocol: Day0     1uM   ATRA


title: Wild type mouse 15

description: Wild type mouse with no lesions


title: SA01 P32 vs. VUB01 P85

status: Public on Nov 19 2008

city: Evry cedex

first: Anselme

middle: Louis

last: Perrier

address: 5 rue desbrueres

department: I-Stem, AFM

country: France

institute: INSERM/UEVE UMR 861,

description: DATA exportation with Genocensus software

hyb_protocol: After addition of tRNA (48 mg) plus a quantity of human Cot DNA (Invitrogen, Carlsbad, CA) equal to 50 times the mass of the labeled DNAs, the resulting products were concentrated by vacuum centrifugation, resuspended in 43 mL of hybridization solution (Ambion, Austin, TX) and deposited on the array under a coverslip. Hybridization in a sealed chamber (Corning Life Sciences, Acton, MA) was for 66 hours at 55_C, a post hybridization treatement was done.

scan_protocol: Slides were scanned (Agilent Technologies, Santa Clara, CA), data were extracted with GenePix 6 (Axon InstrumentseMolecular Devices, Sunnyvale, CA),

data_processing: All data is lowess normalized, ratio value is CY5/CY3. Copy number analysis was performed with GenoCensus (IntegraGen), which includes block Loess normalization

label_protocol: A genomic DNA labeling kit (Enzo, Farmingdale, NY) was used to label the sample DNA with Cy5. The labeled products were purified with QiaQuick polymerase chain reaction (PCR) purification kits (Qiagen, Valencia, CA).

growth_protocol: Human embryonic stem cells derived by Cellartis AB grown on STO feeders. Manual dissection was systematically used to passage the cells rather than enzymatic methods.

extract_protocol: Genomic DNA was isolated from hESC using the Wizard® Genomic DNA Purification Kit (Promega, Charbonnieres, France).

tag: human embryonic stem cells

source_name: VUB01 P85

label_protocol: A genomic DNA labeling kit (Enzo, Farmingdale, NY) was used to label the sample DNA with Cy3. The labeled products were purified with QiaQuick polymerase chain reaction (PCR) purification kits (Qiagen, Valencia, CA).

growth_protocol: Human embryonic stem cells derived as described by Mateizel, I. et al. Hum. Reprod. 21, 503-511 (2006) and grown on STO feeders. Manual dissection was systematically used to passage the cells rather than enzymatic methods.


title: H1 P41 vs. Control

growth_protocol: Human embryonic stem cells derived grown on STO feeders. Manual dissection was systematically used to passage the cells rather than enzymatic methods.

source_name: Control

tag: control male human genomic DNA


title: SA01 P30 vs. VUB01 P93

growth_protocol: Human embryonic stem cells derived grown on STO feeders. Manual dissection was systematically used to passage the cells

source_name: VUB01 P93

growth_protocol: Human embryonic stem cells grown on STO feeders. Manual dissection was systematically used to passage the cells


title: H1 P53 vs. Control

extract_protocol: Genomic DNA was using the Wizard® Genomic DNA Purification Kit (Promega, Charbonnieres, France).


title: H9 P74 vs. Control

label_protocol: Genomic DNA was isolated from hESC using the Wizard® Genomic DNA Purification Kit (Promega, Charbonnieres, France).

growth_protocol: Human embryonic stem cells grown on STO feeders. Manual dissection was systematically used to passage the cells rather than enzymatic methods.

tag: female human embryonic stem cells

tag: female control human DNA


title: Gene expression difference between A. suecica and their progenitor species

description: 8 replicate measurements. Four biological replications were performed and each biological replication was measured by dye-swap experiments. One biological replication was performed using 12 plants per species. Four biological replications were performed with different pools of the plants and extraction. To exclude dye effect, A.suecica and midparent value were reversely labeled and hybridized for individual biological replication.

data_processing:
We applied a linear model to exclude technical variation by arrays and dyes and biological variation by different plant populations. The linear model is
Log (Yigkl) = µ + Gi + Tj + Ak + Dl + (G*T)ij + (G*A)ik + (G*D)il + (G*T*D)ijl + ɛijkl
Where Y represents raw intensity after background level is subtracted; G, T, A, and D are main sources of variation from gene (G), treatment (plant species, T), array (A) and dye (D); i = 1,…, 31818; j = 1, 2; k = 1, 2, 3, 4;l = 1,2; µ represents the overall mean. The interaction terms, G*T, G*A, G*D, and G*T*D mean gene-by-species, gene-by-array, gene-by-dye and gene-by-species-by-dye. ɛijkl represents random error.
To test difference of mRNA expression between A.suecica and mid-parent value (MPV), t-tests were employed for individual genes (pergene-variance).
The null hypothesis, H0: (T)A.suecica + (G*T)i,A.suecica = (T)MPV + (G*T)i,MPV  was examined by p-value. Overall type I error rate of multiple testing was controlled to be below 0.05 employing the false discovery rate of Benjamini and Hotchberg.

label: Cy3 and Cy5, dye swap

organism: Arabidopsis suecica

source_name: Leaf tissue mRNAs from Arabidopsis suecica

label_protocol: We used 500 ng of mRNA in each labeling reaction using Cy3- or Cy5-dCTP (Amersham Biosciences). The Cy3-dCTP reaction was mixed with the Cy5-dCTP reaction for one hybridization, and then an equal amount of RNA samples was reversely labeled for another hybridization.

growth_protocol: All plants were grown in a growth chamber at 22 degree and under 16 hour of light per day.

tag: Natural allopolyploid species formed by interspecific hybridization between extant A.thaliana and A.arenosa species.

growth_protocol: All plants were grown in a graoth chamber at 22 degree and under 16 hour of light per day.

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies), following the manufacture instruction. mRNAs were isolated from total RNA using a Micro-FastTrack 2.0 mRNA isolation kit (Invitrogen). Equal amount of mRNA from A.thaliana and A.arenosa were combined as a midparent value to detect nonadditive expression in a natural allopolyploid species, A.suecica.

tag: A.thaliana and A.arenosa are extant progenitor species of A.suecica


title: SA01 P32 vs. VUB05 P40

source_name: VUB05 P40


title: H9 P34 vs. Control

tag: female control human genomic DNA


title: Sa strain 1183 biological rep 2

type: other

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from_Sa strain 1183 bilogical rep 2

hyb_protocol: Following fragmentation, 3-7 ug of cDNA were hybridized for 16 hr at 40C on our custom Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis with a scale filter for Se genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

molecule: other

organism: Staphylococcus aureus

source_name: Sa strain 1183 bilogical rep 2

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 3-7 ug cDNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: For microarray experiments, cultures were prepared by inoculating 50 ml of TSB with the appropriate strain (in triplicates for each strain) and incubated at 37C with shaking at 180rpm overnight.

extract_protocol: Cells were collected by centrifugation and resuspended in 4 mL of QIAGEN Buffer P1 supplemented with 10 mg/mL RNase A. Lysostaphin was added to a final concentration of 50 mg/mL and the cell suspensions were incubated at 37C for 1 hour. Protoplasts were lysed by adding 200 mL of a saturated SDS (in 45% EtOH) solution and incubating at room temperature for 5 min. 1.3 mL of 5M sodium perchlorate was added followed by gentle inversion. Lysates were extracted 3x with choroform, in each extraction 1 volume of cholorom was added, followed by vigorous vortexing and centrifugation at 14,000 rpm for 10 min. The acqueous upper phase was collected. Chromosomal DNA was precipitated by adding 2.5 volumes of ice-cold 100% EtOH followed by vigorous vortexing. The DNA was fished out with a glass rod and washed twice with 70% EtOH. The Chromosomal DNA was allowed to air dry follwed by resuspension in TE buffer.


title: VUB05-HD P103 vs. Control

source_name: VUB05-HD P103

tag: male human embryonic stem cells

tag: Female human genomic DNA


title: Non-additive expression between synthetic allopolyploid Allo733 and their progenitors

source_name: leaves before bolting

tag: A synthetic allopolyploid line generated by hybridization of Arabidopsis thaliana and Arabidopsis arenosa

source_name: Artificial mix of mRNAs from Leaf tissues of A. thaliana and A. arenosa

tag: Arabidopsis thaliana and Arabidopsis arenosa are progenitor species of the synthetic allopolyploid line, Allo733


title: Sa strain 1183 biological rep 3

description: Gene expression data from_Sa strain 1183 bilogical rep 3

source_name: Sa strain 1183 bilogical rep 3


title: ATRA-treated Day0 1uM_Replicate_2

source_name: untreated HL60 Promyelocytic Cells

tag: HL60 multipotent promyelocytic leukemia cell Line

source_name: ATRA-treated HL60 Promyelocytic Cells


title: Sa strain 1179 (RF122) biological rep 3

description: Gene expression data from_Sa strain 1179 (RF122) bilogical rep 3

source_name: Sa strain 1179 (RF122) bilogical rep 3


title: VUB05 P40 vs. VUB01 P85


title: Sa strain 1183 biological rep 1

description: Gene expression data from_Sa strain 1183 bilogical rep 1

source_name: Sa strain 1183 bilogical rep 1


title: Sa strain 1179 (RF122) biological rep 2

description: Gene expression data from_Sa strain 1179 (RF122) bilogical rep 2

source_name: Sa strain 1179 (RF122) bilogical rep 2


title: SA01 P83 vs. VUB01 P150

growth_protocol: Human embryonic stem cells derived as described by Mateizel, I. et al. Hum. Reprod. 21, 503-511 (2006) and grown on STO feeders. Manual dissection was systematically used to passage the cells


title: SA01 P41 vs. Control

tag: controle male human genomic DNA


title: Sa strain 1179 (RF122) biological rep 1

description: Gene expression data from_Sa strain 1179 (RF122) bilogical rep 1

source_name: Sa strain 1179 (RF122) bilogical rep 1


title: Sa strain 1173 biological rep 1

description: Gene expression data from_Sa strain 1173 bilogical rep 1

source_name: Sa strain 1173 bilogical rep 1


title: Sa strain 1178 biological rep 2

description: Gene expression data from_Sa strain 1178 bilogical rep 2

source_name: Sa strain 1178 bilogical rep 2


title: Sa strain 1174 biological rep 3

description: Gene expression data from_Sa strain 1174 bilogical rep 3

source_name: Sa strain 1174 bilogical rep 3


title: Sa strain 1178 biological rep 1

description: Gene expression data from_Sa strain 1178 bilogical rep 1

source_name: Sa strain 1178 bilogical rep 1


title: Sa strain 1178 biological rep 3

description: Gene expression data from_Sa strain 1178 bilogical rep 3

source_name: Sa strain 1178 bilogical rep 3


title: Sa strain 1173 biological rep 2

description: Gene expression data from_Sa strain 1173 bilogical rep 2

source_name: Sa strain 1173 bilogical rep 2


title: Sa strain 1174 biological rep 1

description: Gene expression data from_Sa strain 1174 bilogical rep 1

source_name: Sa strain 1174 bilogical rep 1


title: Sa strain 1170 biological rep 1

description: Gene expression data from_Sa strain 1170 bilogical rep 1

source_name: Sa strain 1170 bilogical rep 1


title: Sa strain 1171 biological rep 1

description: Gene expression data from_Sa strain 1171 bilogical rep 1

source_name: Sa strain 1171 bilogical rep 1


title: Sa strain 1173 biological rep 3

description: Gene expression data from_Sa strain 1173 bilogical rep 3

source_name: Sa strain 1173 bilogical rep 3


title: Sa strain 1171 biological rep 3

description: Gene expression data from_Sa strain 1171 bilogical rep 3

source_name: Sa strain 1171 bilogical rep 3


title: Sa strain 1174 biological rep 2

description: Gene expression data from_Sa strain 1174 bilogical rep 2

source_name: Sa strain 1174 bilogical rep 2


title: Sa strain 1167 biological rep 1

description: Gene expression data from_Sa strain 1167 bilogical rep 1

source_name: Sa strain 1167 bilogical rep 1


title: Sa strain 1168 (Newbould) biological rep 1

description: Gene expression data from_Sa strain 1168 (Newbould) bilogical rep 1

tag: 1168 (Newbould)


title: Control pGir sample 1

source_name: Control pGir sample 1

tag: Control pGir sample 1


title: Sa strain 1166 biological rep 3

description: Gene expression data from_Sa strain 1166 bilogical rep 3

source_name: Sa strain 1166 bilogical rep 3


title: HemeLimitation_PgC06

city: Parkville

first: Helen

last: Mitchell

address: 720 Swanston St

department: School of Dental Science

country: Australia

institute: The University of Melbourne

description: No additional information

hyb_protocol: Slides hybridised using either heme-excess or heme-limited samples labelled with Cy3, combined with a universal genomic reference labelled with Cy5. Prior to hybridisation, microarray slides were immersed for 1 h in blocking solution (35% formamide, 1% BSA, 0.1% SDS, 5X SSPE [1X SSPE is 150 mM NaCl, 10 mM NaH2PO4, 1 mM EDTA]) at 42ºC.  After blocking slides were briefly washed in H2O followed by 99% ethanol and then dried by centrifugation.  Labelled cDNAs were resuspended in 55 µL of hybridization buffer (35% formamide, 5X SSPE, 0.1% SDS, 0.1 mg/mL Salmon Sperm DNA) denatured at 95ºC for 5 min then applied to slides and covered with LifterSlips (Erie Scientific).  Hybridisation was performed at 42ºC for 16 h.  Following hybridisation slides were successively washed in 0.1% SDS plus 2X SSC [1X SSC is 150 mM NaCl 15 mM sodium citrate] (5 min at 42 ºC, all further washes performed at room temperature), 0.1% SDS plus 0.1X SSC (10 min), 0.1X SSC (4 washes, 1 min each), and then quickly immersing in 0.01X SSC, then 99% ethanol and using centrifugation to dry the slides.

scan_protocol: GenePix 4000B microarray scanner (Molecular Devices) at 532 nm (Cy3) and 635 nm (Cy5) with a 10 µm resolution and laser power at 100 %. PMT setting adjusted to obtain a 1:1 ratio of Cy3:Cy5. Pictures of both channels saved as 16-bit tiff files

data_processing: Image analysis was performed using the GenePix Pro 6.0 software (Molecular Devices), and “morph” background values were used as the background estimates in further analysis.  Spots were filtered and flagged as "bad" if circularity <60, diameter <= 50 or F pixels (area) <30.  The LIMMA software package (Smyth, 2005) was used to normalize the within-array data by subtracting the "morph" background and using the "control" method to fit a global loess curve through the whole library titration series spots (MSP controls) and then applying that curve to all the other spots. Between-array normalization was also carried out for all arrays in the series using the "scale" method.  Spots classified as "bad" were down-weighted to 1 % for these analyses.  The "VALUE" data are the mean (as spots were printed in triplicate) of the normalized log2 (gDNA reference/ test sample) ratios.

organism: Porphyromonas gingivalis

source_name: Total RNA, heme-limitation

label_protocol: cDNA synthesized from 10 µg total RNA using the SuperScript plus Indirect cDNA labelling system (Invitrogen) primed with 5 µg random hexamers.  cDNA labelled using the Cy3 post-labelling reactive dye pack (GE) and purified using the purification module of the Invitrogen labelling system.

extract_protocol:
Samples stabilized with 0.2 Volumes of 5 % Phenol in Absolute ethanol, then pelleted by centrifugation and frozen in liquid nitrogen.
Total RNA extracted using Trizol (Invitorgen) according to manufacturers instructions but enhanced with mechanical lysis (Precellys 24 homogenizer - Bertin Technologies, Lysing Matrix B Glass Beads - MP Biomedicals).  RNA was further purified using Illustra RNAspin Mini RNA Isolation kit (GE) according to manufacturers instructions including on-column DNase treatment.

tag: Porphyromonas gingivalis W50, grown in continuous culture under conditions of heme-limitation (BHI with 0.1 µg/mL hemin). Biological replicate 1 (Each heme-limitation sample is from a separate chemostat).

source_name: Genomic DNA Reference

label_protocol: 400 ng of genomic DNA used to synthesize dUTP incorporated DNA  with the BioPrime Plus Array CGH Indirect Genomic Labelling System (Invitrogen) and then labelled using the Cy5 post-labelling reactive dye pack (GE) and purified using the purification module of the Invitrogen labelling system.

extract_protocol: Genomic DNA extracted using the DNeasy Blood and Tissue Kit (Qiagen) in accordance with Manufacturers instructions.

tag: Genomic DNA from Porphyromonas gingivalis W50 used as reference sample


title: Sa strain 1168 (Newbould) biological rep 2

description: Gene expression data from_Sa strain 1168 (Newbould) bilogical rep 2


title: Dorsal striatum DS-SHR

source_name: brain

tag: P55-65 males


title: Sa strain 1167 biological rep 3

description: Gene expression data from_Sa strain 1167 bilogical rep 3

source_name: Sa strain 1167 bilogical rep 3


title: Sa strain 1170 biological rep 3

description: Gene expression data from_Sa strain 1170 bilogical rep 3

source_name: Sa strain 1170 bilogical rep 3


title: Sa strain 1168 (Newbould) biological rep 3

description: Gene expression data from_Sa strain 1168 (Newbould) bilogical rep 3


title: Sa strain 1170 biological rep 2

description: Gene expression data from_Sa strain 1170 bilogical rep 2

source_name: Sa strain 1170 bilogical rep 2


title: Sa strain 1171 biological rep 2

description: Gene expression data from_Sa strain 1171 bilogical rep 2

source_name: Sa strain 1171 bilogical rep 2


title: Sa strain 1167 biological rep 2

description: Gene expression data from_Sa strain 1167 bilogical rep 2

source_name: Sa strain 1167 bilogical rep 2


title: NsrR_Flagtag_rep3

city: Richardson

first: Stephen

last: Spiro

address: 800 W Campbell Road

department: Molecular and Cell Biology

institute: University of Texas at Dallas

description: High fluorescence ratios indicate sites bound by NsrR in vivo in cultures grown in the absence of nitrate.

hyb_protocol: Following Oxford Gene Technology protocols (www.ogt.co.uk).

scan_protocol: Arrays were scanned on an Agilent array scanner, following the manufacturer's protocols.

data_processing: The value is the simple linear ratio of the processed Cy5 and Cy3 signals.

organism: Escherichia coli

source_name: Anaerobic, plus nitrate, IP

extract_protocol: Chromatin was extracted and processed according to Oxford Gene Technology protocols (www.ogt.co.uk).

tag: Escherichia coli, expressing NsrR with a C-terminal Flag-tag, was grown anaerobically in L broth supplemented with glucose and nitrate.

source_name: Anaerobic, minus nitrate, IP

tag: Escherichia coli, expressing NsrR with a C-terminal Flag-tag, was grown anaerobically in L broth supplemented with glucose.


title: HemeExcess_PgC07

description: No additional information

source_name: Total RNA, heme-excess

tag: Porphyromonas gingivalis W50, grown in continuous culture under conditions of heme-excess (BHI with 5.0 µg/mL hemin). Biological replicate 1 (Each heme-excess sample is from a separate chemostat).


title: HemeLimitation_PgC08

description: No additional information

tag: Porphyromonas gingivalis W50, grown in continuous culture under conditions of heme-limitation (BHI with 0.1 µg/mL hemin). Biological replicate 2 (Each heme-limitation sample is from a separate chemostat).


title: HemeExcess_PgC09

description: No additional information

tag: Porphyromonas gingivalis W50, grown in continuous culture under conditions of heme-excess (BHI with 5.0 µg/mL hemin). Biological replicate 2 (Each heme-excess sample is from a separate chemostat).


title: HemeExcess_PgC11

description: No additional information

tag: Porphyromonas gingivalis W50, grown in continuous culture under conditions of heme-excess (BHI with 5.0 µg/mL hemin). Biological replicate 3 (Each heme-excess sample is from a separate chemostat).


title: Sa strain 1166 biological rep 2

description: Gene expression data from_Sa strain 1166 bilogical rep 2

source_name: Sa strain 1166 bilogical rep 2


title: NsrR_Flagtag_rep2

data_processing: The value is the simple linear ratio of the processed Cy3 and Cy5 signals.

label_protocol: Following Oxford Gene Technology protocols (www.ogt.co.uk).


title: NsrR_Flagtag_rep1


title: HemeLimitation_PgC10

description: No additional information

tag: Porphyromonas gingivalis W50, grown continuous culture under conditions of heme-limitation (BHI with 0.1 µg/mL hemin). Biological replicate 3 (Each heme-limitation sample is from a separate chemostat).


title: Expression divergence between Arabidopsis thaliana and Arabidopsis arenosa in leaves

description: Total 8 replications ( 4 biological replications and dye-swap experiments were performed for each biological replication).

organism: Arabidopsis thaliana

source_name: mRNAs from leaves before bolting

tag: A. thaliana isogenic autotetraploids (At4, accession no. CS3900)

organism: Arabidopsis arenosa

source_name: mRNA from leaves before bolting

tag: A. arenosa (Aa, accession no. CS3901)


title: Sa strain 1166 biological rep 1

description: Gene expression data from_Sa strain 1166 bilogical rep 1

source_name: Sa strain 1166 bilogical rep 1


title: Sa strain 315 biological rep 1

description: Gene expression data from_Sa strain 315 bilogical rep 1

source_name: Sa strain 315 bilogical rep 1


title: Eilenburg-0 vs Loch Ness-0 Replicate 2 (R/G)

status: Public on Nov 18 2008

city: Lausanne

first: Johann

last: Weber

state: VD

address: Genopode Building

department: Center for integrative Genomics

country: Switzerland

institute: University of Lausanne

hyb_protocol: Hybridisation buffer was 3xSSC and 0,4%SDS. Incubation at 64°C O/N without agitation. Washing conditions: twice for 5 minutes in 2xSSC 0.1% SDS, twice for 1 minute in 0.2xSSC,  1 minute in 0.1xSSC, 5 minutes in 0.1xSSC 0.1% TritonX100. All washes at room temperature.

scan_protocol: Agilent microarray scanner, 10 μm resolution

data_processing: GenePix Pro 6.0 was used to analyse the images and  generate gpr files; raw data without background substraction were print-tip loess normalized to calculate M values. Bioconductor open source software was used for data processing.

label_protocol: Total RNA from the seedling pools was amplified using the MessageAmpTM aRNA II kit (Ambion, NY, U.S.A.). 5 microgram of amplified RNA were reverse transcribed into cyanin3 or cyanin 5 labeled cDNA, purified with QiaquickTM columns (Qiagen, Netherlands) and hybridized on custom microarrays (GEO accession number GPL6147)

growth_protocol: stratified for 48 hrs at 4°C, grown in tissue culture on basic solid medium with macro- and micronutrients (0.5 x MS) and 0.9% agar (Duchefa, Netherlands), supplemented with 2% sucrose at 21°C under continuous light of 130 μE intensity. Plant material for RNA analysis was harvested  at 9 days after germination.

extract_protocol: Total RNA from plants was isolated using the Plant RNeasyTM kit (QIAGEN, Netherlands) according to the manufacturer’s instructions.

tag: Arabidopsis thaliana accession Eil-0

source_name: Loch Ness-0

tag: Arabidopsis thaliana accession Lc-0


title: Sa strain 315 biological rep 3

description: Gene expression data from_Sa strain 315 bilogical rep 3

source_name: Sa strain 315 bilogical rep 3


title: Eilenburg-0 vs Loch Ness-0 Replicate 3 (R/G)


title: RDE2_X3339_FlightvsGround_G412_M9_7DS523_only2subs

city: Irvine

last: McClelland

state: CA

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

description:
Salmonella enterica subsp. enterica serovar Typhimurium 14028s
biological replicate, Date of Scan Thu Dec 14 18:20:40 2006

hyb_protocol: overnight hyb on Corning UltraGAPS slides at 42°C in 25% formamide / 5xSSC / 0.1% BSA

scan_protocol: Perkin Elmer ScanArray 5000 scanner, image acquisition with ScanArray Express 3.0.1 software, spot quantification using Quantarray 3.0 software, adaptive quantification, protocol STv7S_01_051201; only the first two subarrays were scanned

data_processing: normalized based on total signal for each channel, background subtracted VALUE data obtained from log of normalized background subtracted ch1/ch2 signal. Data were extracted for only two subarrays - duplicated second subarray data for processing and uploading to GEO - second and third subarray therefore have identical numbers.

organism: Salmonella enterica

source_name: X3339 total RNA after microgravity on ground on M9 minimal media

label_protocol: incorporation of Cy3-dCTP with Superscript RT and random hexamers

extract_protocol: RNeasy kit (QIAGEN)

tag: Salmonella typhimurium X3339 total RNA harvested after exposure to space flight, grown in M9 minimal media

source_name: Typhimurium X3339 gDNA from overnight cultures in LB

label_protocol: incorporation of Cy5-dCTP using Klenow enzyme and random hexamers

extract_protocol: SIGMA GenElute bacterial genomic DNA extraction

tag: Salmonella typhimurium X3339 grown O/N in LB at 37C with aeration


title: Eilenburg-0 vs RIL2076 (G/R)

tag: Recombinant inbred line from a cross between Eil-0 and Lc-0


title: Eilenburg-0 vs Loch Ness-0 Replicate 3 (G/R)


title: RDE2_X3339_FlightvsGround_G43_M9_7DS524

description:
Salmonella enterica subsp. enterica serovar Typhimurium 14028s
biological replicate, Date of Scan Thu Dec 14 18:40:49 2006

scan_protocol: Perkin Elmer ScanArray 5000 scanner, image acquisition with ScanArray Express 3.0.1 software, spot quantification using Quantarray 3.0 software, adaptive quantification, protocol STv7S_01_051201

data_processing: normalized based on total signal for each channel, background subtracted VALUE data obtained from log of normalized background subtracted ch1/ch2 signal.


title: Eilenburg-0 vs Loch Ness-0 Replicate 1 (R/G)


title: Eilenburg-0 vs RIL2076 (R/G)


title: Loch Ness-0 vs RIL2040(G/R)


title: Loch Ness-0 vs RIL2076 (R/G)


title: RDE2_X3339_FlightvsGround_G514_M9_7DS526

description:
Salmonella enterica subsp. enterica serovar Typhimurium 14028s
biological replicate, Date of Scan Fri Dec 15 12:23:04 2006


title: SA01 P49

description: HumanHap300 (317,000 tag SNPs) Genotyping BeadChips from Illumina apply to the 550K array (HumanHap550)

hyb_protocol: The whole-genome amplification process requires 250–750 ng of input gDNA and creates a sufficient quantity of DNA (1000× amplification) to be used on a single BeadChip in the Infinium assay (Illumina MP1 and AMM). After amplification, the product is fragmented using a proprietary reagent (FRG), precipitated with 2-propanol (plus precipitating reagent; PA1), and resus-pended in formamide-containing hybridization buffer (RA1). The DNA samples are denatured at 95°C for 20 min, loaded into the Tecan Flow Through Chambers (Tecan Part No. 760,810), and placed in a humidified container for a minimum of 16 h at 48°C allowing SNP loci to hybridize to the 50mer capture probes (Steemers and Gunderson 2005).

scan_protocol: The Illumina BeadArray Reader is a two-color (543 nm/643 nm) confocal fluorescent scanner with 0.84-μm pixel resolution. The scanner excites the fluorophors generated during signal amplification/staining of the allele-specific (one color) or single-base (two colors) extension products on the BeadChips. The image intensities are extracted using Illumina's BeadScan software.

data_processing: The data for each BeadChip is self-normalized using information contained within the array. This normalization algorithm removes outliers, adjusts for channel-dependent background and global intensity differences, and also scales the data.

label: CY3, CY5

label_protocol: For the single-base extension (SBE) (Infinium II) assay, primers were extended with a polymerase and labeled nucleotide mix (TEM), and stained with repeated application of LTM (staining reagent) and ASM (anti-staining reagent). After staining was complete, the slides were washed with low salt wash buffer (PB1), immediately coated with XC4, and then imaged on the Illumina BeadArray Reader.

growth_protocol: Human embryonic stem cells derived by Cellartis AB and cultured on STO feeder cells in DMEM-F12 medium supplemented with 4ng/ml FGF2

tag: human embryonic stem cells


title: RDE2_X3339_FlightvsGround_F423_M9_7DS525

description:
Salmonella enterica subsp. enterica serovar Typhimurium 14028s
biological replicate, Date of Scan Fri Dec 15 11:40:18 2006

source_name: X3339 total RNA after microgravity in flight on M9 minimal media


title: RDE2_X3339_FlightvsGround_F41_M9_7DS521

description:
Salmonella enterica subsp. enterica serovar Typhimurium 14028s
biological replicate, Date of Scan Thu Dec 14 17:19:53 2006


title: Eilenburg-0 vs Loch Ness-0 Replicate 1 (G/R)


title: Loch Ness-0 vs RIL2040 (R/G)


title: Eilenburg-0 vs Loch Ness-0 Replicate 2 (G/R)


title: Eilenburg-0 vs RIL2040 (R/G)


title: Loch Ness-0 vs RIL2019 (G/R)


title: Eilenburg-0 vs RIL2019 (G/R)


title: Loch Ness-0 vs RIL2011 (G/R)


title: Eilenburg-0 vs RIL2019 (R/G)


title: Loch Ness-0 vs RIL2011 (R/G)


title: Loch Ness-0 vs RIL2019 (R/G)


title: Eilenburg-0 vs RIL2040 (G/R)


title: Eilenburg-0 vs RIL2011 (G/R)


title: Eilenburg-0 vs RIL2011 (R/G)


title: Loch Ness-0 vs RIL1088 (R/G)


title: VUB05-HD P94

source_name: VUB05-HD P94

growth_protocol: Human embryonic stem cells derived as described by Mateizel, I. et al. Hum. Reprod. 21, 503-511 (2006) and cultured on STO feeder cells in DMEM-F12 medium supplemented with 4ng/ml FGF2


title: Loch Ness-0 vs RIL1024 (R/G)


title: Loch Ness-0 vs RIL1088 (G/R)


title: Eilenburg-0 vs RIL1088 (R/G)


title: Eilenburg-0 vs RIL1088 (G/R)


title: Eilenburg-0 vs RIL1050 (R/G)


title: Loch Ness-0 vs RIL1050 (G/R)


title: Loch Ness-0 vs RIL1050 (R/G)


title: Loch Ness-0 vs RIL1024 (G/R)


title: LGMD2A patient_EXP-5_U133B

city: San Sebastian

first: Amets

last: Saenz

state: Gipuzkoa

address: Pº dr Begiristain s/n

country: Spain

institute: Donostia Hospital

description: LGMD2A patient_EXP-5_U133B

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on HG-U133A/B Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Agilent GeneArray Scanner G2500A.

data_processing: Arrays were scanned and raw data were normalized using RMA (Robust Multichip Average)

source_name: Proximal muscle (Deltoids)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Affymetrix Protocol, May 5, 2005).

extract_protocol: RNAPlus (Qbiogene) extraction of total RNA was performed according to the standard protocols for muscle tissue.

tag: Gender

value: Male, Age:13 years

tag: Mutations


title: Eilenburg-0 vs RIL1024 (G/R)


title: Eilenburg-0 vs RIL1050 (G/R)


title: LGMD2A patient_EXP-40_U133B

description: LGMD2A patient_EXP-40_U133B

source_name: Proximal muscle

value: Male, Age:29 years


title: Eilenburg-0 vs RIL1024 (R/G)


title: LGMD2A patient_EXP-41_U133B

description: LGMD2A patient_EXP-41_U133B

value: Female, Age:17 years


title: LGMD2A patient_EXP-36_U133B

description: LGMD2A patient_EXP-36_U133B

value: Male, Age:26 years


title: LGMD2A patient_EXP-9_U133B

description: LGMD2A patient_EXP-9_U133B

source_name: Proximal muscle (Biceps)

value: Female, Age:14 years


title: Control_EXP-38_U133B

source_name: Proximal muscle (Quadriceps)

value: Male, Age:31 years

value: No


title: Loch Ness-0 vs RIL2076 (G/R)


title: Sa strain 315 biological rep 2

description: Gene expression data from_Sa strain 315 bilogical rep 2

source_name: Sa strain 315 bilogical rep 2


title: LGMD2A patient_EXP-35_U133B

description: LGMD2A patient_EXP-35_U133B

value: Male, Age:48 years


title: Control_EXP-39_U133B

value: Male, Age:40 years


title: RDE2_X3339_FlightvsGround_F54_M9_7DS522

description:
Salmonella enterica subsp. enterica serovar Typhimurium 14028s
biological replicate, Date of Scan Thu Dec 14 17:42:05 2006


title: Control_EXP-31_U133B

value: Male, Age:46 years


title: Control_EXP-30_U133B

value: Male, Age:84 years


title: Control_EXP-33_U133B

value: Male, Age:51 years


title: Control_EXP-29_U133B

value: Female, Age:73 years


title: Control_EXP-27_U133B

tag: Gender:Male, Age

value: 50 years


title: Control_EXP-32_U133B


title: LGMD2A patient_EXP-3_U133B

description: LGMD2A patient_EXP-3_U133B

value: Male, Age:37 years


title: LGMD2A patient_EXP-1_U133B

description: LGMD2A patient_EXP-1_U133B

value: Male, Age:34 years


title: Control_EXP-25_U133B

value: Female, Age:57 years


title: Reference pool vs. lung_NCI-H2170

city: Seattle

first: Tao

last: Xie

state: WA

address: 401 Terry Ave. N.

department: Genetics

institute: Rosetta Inpharmatics

description: Samples from a collection of cancer cell lines.

hyb_protocol: Labeled cRNAs were fragmented to an average size of approximately 50 to 100 nucleotides in the presence of 10 mM zinc chloride and adding a hybridization buffer containing 1 M sodium chloride, 0.5 percent sodium sarcosine, 50 mM morpholino-ethane sulfonic acid (pH 6.5), and formamide (final concentration, 30 percent at 40°C); After hybridization, the slides were washed.

scan_protocol: Slides were scanned using a confocal laser scanner (Agilent Technologies, Palo Alto, CA). Fluorescence intensities of the scanned images were quantified, normalized, and balanced.

data_processing: Rosetta Resolver Ratio Experiment using default Rosetta Resolver Agilent Error Model.

source_name: Lung, NCI-H2170 cell line

label_protocol: One round of RT-IVT to cRNA

extract_protocol: Trizol Lysis + RNeasy Column

tag: Cell line derived from lung.

source_name: Reference RNA pool

tag: Common reference RNA pool (Human Universal Reference RNA, Stratagene).

tag: Control.


title: Reference pool vs. lymphoma_BC-1

source_name: Lymphoma, BC-1 cell line

tag: Cell line derived from lymphoma.


title: Reference pool vs. lung_NCI-H226

source_name: Lung, NCI-H226 cell line


title: Reference pool vs. myeloma_OPM-2

source_name: Myeloma, OPM-2 cell line

tag: Cell line derived from myeloma.


title: Reference pool vs. lymphoma_H9

source_name: Lymphoma, H9 cell line


title: Reference pool vs. uterus_MES-SA

source_name: Uterus, MES-SA cell line

tag: Cell line derived from uterus.


title: Reference pool vs. lymphoma_U-937

source_name: Lymphoma, U-937 cell line


title: Reference pool vs. lymphoma_BC-3

source_name: Lymphoma, BC-3 cell line


title: Reference pool vs. melanoma_SK-MEL-3

source_name: Melanoma, SK-MEL-3 cell line

tag: Cell line derived from melanoma.


title: Reference pool vs. melanoma_MALME-3M

source_name: Melanoma, MALME-3M cell line


title: Reference pool vs. lymphoma_JEKO-1

source_name: Lymphoma, JEKO-1 cell line


title: Reference pool vs. lymphoma_SU-DHL-4

source_name: Lymphoma, SU-DHL-4 cell line


title: Reference pool vs. lymphoma_MC116

source_name: Lymphoma, MC116 cell line


title: Reference pool vs. myeloma_NCI-H929

source_name: Myeloma, NCI-H929 cell line


title: Reference pool vs. lymphoma_JM1

source_name: Lymphoma, JM1 cell line


title: Reference pool vs. stomach_Hs 746T

source_name: Stomach, Hs 746T cell line

tag: Cell line derived from stomach.


title: Reference pool vs. lymphoma_RC-K8

source_name: Lymphoma, RC-K8 cell line


title: Reference pool vs. myeloma_LP-1

source_name: Myeloma, LP-1 cell line

source_name: Reference RNA pool


title: Reference pool vs. melanoma_M14

source_name: Melanoma, M14 cell line


title: Reference pool vs. prostate_22Rv1

source_name: Prostate, 22Rv1 cell line

tag: Cell line derived from prostate.


title: Reference pool vs. melanoma_HT-144

source_name: Melanoma, HT-144 cell line


title: Reference pool vs. lung_NCI-H1838

source_name: Lung, NCI-H1838 cell line


title: Reference pool vs. lymphoma_OCI-LY-19

source_name: Lymphoma, OCI-LY-19 cell line


title: Reference pool vs. lymphoma_SC-1

source_name: Lymphoma, SC-1 cell line


title: Reference pool vs. lymphoma_HuT 78

source_name: Lymphoma, HuT 78 cell line


title: Reference pool vs. lymphoma_KARPAS-299

source_name: Lymphoma, KARPAS-299 cell line


title: Reference pool vs. lung_Hs 573.T

source_name: Lung, Hs 573.T cell line


title: Reference pool vs. melanoma_C32

source_name: Melanoma, C32 cell line


title: Reference pool vs. melanoma_G-361

source_name: Melanoma, G-361 cell line


title: Reference pool vs. lymphoma_DB

source_name: Lymphoma, DB cell line


title: Reference pool vs. breast_BT-20

source_name: Breast, BT-20 cell line

tag: Cell line derived from breast.


title: Reference pool vs. breast_HCC38

source_name: Breast, HCC38 cell line


title: Reference pool vs. colon_DLD-1

source_name: Colon, DLD-1 cell line

tag: Cell line derived from colon.


title: Reference pool vs. lymphoma_Hs 445

source_name: Lymphoma, Hs 445 cell line


title: Reference pool vs. myeloma_MOLP-8

source_name: Myeloma, MOLP-8 cell line

source_name: Reference RNA pool


title: Reference pool vs. melanoma_UACC-62

source_name: Melanoma, UACC-62 cell line


title: Reference pool vs. stomach_MKN-45

source_name: Stomach, MKN-45 cell line


title: Reference pool vs. glioblastoma_SNB-19

source_name: Glioblastoma, SNB-19 cell line

tag: Cell line derived from glioblastoma.


title: Reference pool vs. lymphoma_Toledo

source_name: Lymphoma, Toledo cell line


title: Reference pool vs. colon_COLO 320 DM

source_name: Colon, COLO 320 DM cell line


title: Reference pool vs. melanoma_HMCB

source_name: Melanoma, HMCB cell line


title: Reference pool vs. lung_LX-1

source_name: Lung, LX-1 cell line


title: Reference pool vs. lung_SK-LU-1

source_name: Lung, SK-LU-1 cell line


title: Reference pool vs. melanoma_M19-MEL

source_name: Melanoma, M19-MEL cell line


title: Reference pool vs. colon_HCT 116

source_name: Colon, HCT 116 cell line


title: Reference pool vs. lymphoma_RL

source_name: Lymphoma, RL cell line


title: Reference pool vs. glioma_SF-539

source_name: Glioma, SF-539 cell line

tag: Cell line derived from glioma.


title: Reference pool vs. prostate_PC-3

source_name: Prostate, PC-3 cell line


title: Reference pool vs. lung_NCI-H2052

source_name: Lung, NCI-H2052 cell line


title: Reference pool vs. melanoma_Hs 294T

source_name: Melanoma, Hs 294T cell line


title: Reference pool vs. lung_NCI-H1734

source_name: Lung, NCI-H1734 cell line


title: Reference pool vs. colon_WiDr

source_name: Colon, WiDr cell line

source_name: Reference RNA pool


title: Reference pool vs. ovary_SK-OV-3

source_name: Ovary, SK-OV-3 cell line

tag: Cell line derived from ovary.


title: Reference pool vs. colon_COLO 320 HSR

source_name: Colon, COLO 320 HSR cell line


title: Reference pool vs. bladder_UM-UC-3

source_name: Bladder, UM-UC-3 cell line

tag: Cell line derived from bladder.


title: Reference pool vs. melanoma_A-375.S2

source_name: Melanoma, A-375.S2 cell line


title: Reference pool vs. liver_huH-7

source_name: Liver, huH-7 cell line

tag: Cell line derived from liver.


title: Reference pool vs. lung_Lu-135

source_name: Lung, Lu-135 cell line


title: Reference pool vs. breast_HCC1937

source_name: Breast, HCC1937 cell line


title: Reference pool vs. colon_SW48

source_name: Colon, SW48 cell line


title: Reference pool vs. myeloma_IM-9

source_name: Myeloma, IM-9 cell line


title: Reference pool vs. colon_LS 180

source_name: Colon, LS 180 cell line


title: Reference pool vs. colon_SW480

source_name: Colon, SW480 cell line


title: Reference pool vs. breast_HCC1428

source_name: Breast, HCC1428 cell line


title: Reference pool vs. ovary_MDAH-2774

source_name: Ovary, MDAH-2774 cell line


title: Reference pool vs. tongue_SCC-25

source_name: Tongue, SCC-25 cell line

tag: Cell line derived from tongue.


title: Reference pool vs. colon_LS513

source_name: Colon, LS513 cell line


title: Reference pool vs. cervix_C-33 A

source_name: Cervix, C-33 A cell line

tag: Cell line derived from cervix.


title: Reference pool vs. breast_Hs 578T

source_name: Breast, Hs 578T cell line

source_name: Reference RNA pool

tag: Common reference RNA pool (Human Universal Reference RNA, Stratagene).


title: Reference pool vs. glioblastoma_U-118 MG

source_name: Glioblastoma, U-118 MG cell line

tag: Control.


title: Reference pool vs. lung_NCI-H2228

source_name: Lung, NCI-H2228 cell line

tag: Cell line derived from lung.


title: Reference pool vs. lymphoma_DOHH-2

source_name: Lymphoma, DOHH-2 cell line

tag: Cell line derived from lymphoma.


title: Reference pool vs. colon_SW1463

source_name: Colon, SW1463 cell line


title: Reference pool vs. colon_Caco-2

source_name: Colon, Caco-2 cell line


title: Reference pool vs. pancreas_MIA PaCa-2

source_name: Pancreas, MIA PaCa-2 cell line

tag: Cell line derived from pancreas.


title: Reference pool vs. lung_NCI-H1395

source_name: Lung, NCI-H1395 cell line


title: Reference pool vs. pancreas_BxPC-3

source_name: Pancreas, BxPC-3 cell line


title: Reference pool vs. lymphoma_ST486

source_name: Lymphoma, ST486 cell line


title: Reference pool vs. colon_HCT-8

source_name: Colon, HCT-8 cell line


title: Reference pool vs. colon_HT-29

source_name: Colon, HT-29 cell line


title: Reference pool vs. lymphoma_SR-786

source_name: Lymphoma, SR-786 cell line


title: Reference pool vs. lung_NCI-H460

source_name: Lung, NCI-H460 cell line


title: Reference pool vs. melanoma_WM-266-4

source_name: Melanoma, WM-266-4 cell line

tag: Cell line derived from melanoma.


title: Reference pool vs. lymphoma_MJ

source_name: Lymphoma, MJ cell line


title: Reference pool vs. lymphoma_SUP-T1

source_name: Lymphoma, SUP-T1 cell line


title: Reference pool vs. colon_COLO 201

source_name: Colon, COLO 201 cell line

source_name: Reference RNA pool


title: LGMD2A patient_EXP-9_U133A

description: LGMD2A patient_EXP-9_U133A

source_name: Proximal muscle (Biceps)

tag: Gender

tag: Mutations


title: Reference pool vs. colon_SW837

source_name: Colon, SW837 cell line


title: Reference pool vs. lymphoma_HH

source_name: Lymphoma, HH cell line


title: Reference pool vs. colon_LoVo

source_name: Colon, LoVo cell line


title: LGMD2A patient_EXP-5_U133A

description: LGMD2A patient_EXP-5_U133A

source_name: Proximal muscle (Deltoids)

value: Male, Age:13 years


title: Reference pool vs. lung_NCI-H2347

source_name: Lung, NCI-H2347 cell line


title: Reference pool vs. colon_COLO205

source_name: Colon, COLO205 cell line


title: Reference pool vs. pancreas_Panc 03.27

source_name: Pancreas, Panc 03.27 cell line


title: LGMD2A patient_EXP-4_U133A

description: LGMD2A patient_EXP-4_U133A

source_name: Proximal muscle (Quadriceps)

value: Male, Age:44 years


title: Reference pool vs. colon_COLO-206F

source_name: Colon, COLO-206F cell line


title: Reference pool vs. pancreas_SU.86.86

source_name: Pancreas, SU.86.86 cell line


title: Reference pool vs. melanoma_WM-115

source_name: Melanoma, WM-115 cell line


title: Reference pool vs. lung_NCI-H69

source_name: Lung, NCI-H69 cell line


title: Reference pool vs. lymphoma_GRANTA-519

source_name: Lymphoma, GRANTA-519 cell line


title: LGMD2A patient_EXP-40_U133A

description: LGMD2A patient_EXP-40_U133A

source_name: Proximal muscle

value: Male, Age:29 years


title: Reference pool vs. colon_SW403

source_name: Colon, SW403 cell line


title: Reference pool vs. bladder_J82

source_name: Bladder, J82 cell line

source_name: Reference RNA pool


title: LGMD2A patient_EXP-41_U133A

description: LGMD2A patient_EXP-41_U133A

value: Female, Age:17 years


title: Reference pool vs. skin_A-431

source_name: Skin, A-431 cell line

tag: Cell line derived from skin.


title: Reference pool vs. bladder_HT-1197

source_name: Bladder, HT-1197 cell line


title: Reference pool vs. lung_A549

source_name: Lung, A549 cell line


title: Reference pool vs. colon_SW1116

source_name: Colon, SW1116 cell line

tag: Cell line derived from colon.


title: Reference pool vs. colon_SW620

source_name: Colon, SW620 cell line


title: Reference pool vs. breast_MCF7

source_name: Breast, MCF7 cell line

tag: Cell line derived from breast.


title: Reference pool vs. lung_NCI-H520

source_name: Lung, NCI-H520 cell line


title: Reference pool vs. myeloma_EJM

source_name: Myeloma, EJM cell line

tag: Cell line derived from myeloma.


title: Reference pool vs. melanoma_A7

source_name: Melanoma, A7 cell line


title: Reference pool vs. lung_NCI-H596

source_name: Lung, NCI-H596 cell line


title: Reference pool vs. bladder_T24

source_name: Bladder, T24 cell line


title: Control_EXP-39_U133A

source_name: Proximal muscle (Quadriceps)


title: Reference pool vs. lung_NCI-H1975

source_name: Lung, NCI-H1975 cell line


title: Control_EXP-32_U133A


title: Reference pool vs. colon_HCT-15

source_name: Colon, HCT-15 cell line


title: Reference pool vs. colon_CX-1

source_name: Colon, CX-1 cell line


title: Control_EXP-30_U133A


title: Reference pool vs. lung_NCI-H1563

source_name: Lung, NCI-H1563 cell line


title: Reference pool vs. colon_LS1034

source_name: Colon, LS1034 cell line

source_name: Reference RNA pool


title: Reference pool vs. ovary_Caov-3

source_name: Ovary, Caov-3 cell line

tag: Cell line derived from ovary.


title: Control_EXP-33_U133A

source_name: Proximal muscle (Deltoids)


title: LGMD2A patient_EXP-35_U133A

description: LGMD2A patient_EXP-35_U133A


title: Control_EXP-38_U133A


title: LGMD2A patient_EXP-3_U133A

description: LGMD2A patient_EXP-3_U133A


title: Control_EXP-28_U133A

value: Male, Age:22 years


title: Control_EXP-31_U133A


title: Reference pool vs. bone_U-2 OS

source_name: Bone, U-2 OS cell line

tag: Cell line derived from bone.


title: Reference pool vs. colon_SK-CO-1

source_name: Colon, SK-CO-1 cell line


title: Reference pool vs. pancreas_PANC-1

source_name: Pancreas, PANC-1 cell line


title: Control_EXP-29_U133A


title: Reference pool vs. colon_NCI-H508

source_name: Colon, NCI-H508 cell line


title: Reference pool vs. melanoma_RPMI-7951

source_name: Melanoma, RPMI-7951 cell line


title: LGMD2A patient_EXP-36_U133A

description: LGMD2A patient_EXP-36_U133A

source_name: Proximal muscle

value: Male, Age:26 years


title: Reference pool vs. tongue_CAL-27

source_name: Tongue, CAL-27 cell line


title: Control_EXP-25_U133A

value: Female, Age:57years

value: No


title: Control_EXP-27_U133A

value: Male, Age:50 years


title: Reference pool vs. stomach_MKN-1

source_name: Stomach, MKN-1 cell line

tag: Cell line derived from stomach.


title: 040853

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

description:
NB4 ATRA #2 vs NB4#2
Date:2007/04/20

hyb_protocol: Agilent : 700.0 ng at 48 degree_C during 17 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Interslide norm. : quantile, Intraslide norm. : printtiploess, Background norm. : none, Software used : limmagui

source_name: NB4 ATRA #2

label_protocol: Invitrogen - Ulysis

extract_protocol: MirVana

tag: Labeling_reference:NB4 ATRA #2

value: NB4 ATRA #2


title: 040854

description:
LR1 ATRA #1 vs LR1#1
Date:2007/04/20

hyb_protocol: Agilent : 750.0 ng at 48 degree_C during 17 hours

source_name: LR1 ATRA #1

tag: Labeling_reference:LR1 ATRA #1

value: LR1 ATRA #1


title: LGMD2A patient_EXP-1_U133A

description: LGMD2A patient_EXP-1_U133A

source_name: Proximal muscle (Quadriceps)


title: LGMD2A patient_EXP-2_U133A

description: LGMD2A patient_EXP-2_U133A

value: Female, Age:33 years


title: Reference pool vs. bladder_TCCSUP

source_name: Bladder, TCCSUP cell line

tag: Cell line derived from bladder.

tag: Common reference RNA pool (Human Universal Reference RNA, Stratagene).


title: Reference pool vs. lung_NCI-H1703

source_name: Lung, NCI-H1703 cell line

tag: Cell line derived from lung.

tag: Control.


title: 040856

description:
LR2 ATRA #2 vs LR2#2
Date:2007/04/20

source_name: LR2 ATRA #2

tag: Labeling_reference:LR2 ATRA #2

value: LR2 ATRA #2


title: 309322

description:
LR1#3 vs LR1 ATRA #2
Date:2007/04/20

source_name: LR1 ATRA #2

tag: Labeling_reference:LR1 ATRA #2

value: LR1 ATRA #2


title: Reference pool vs. colon_SW1417

source_name: Colon, SW1417 cell line

source_name: Reference RNA pool


title: Reference pool vs. colon_LS411N

source_name: Colon, LS411N cell line


title: Reference pool vs. colon_COLO-678

source_name: Colon, COLO-678 cell line


title: Reference pool vs. colon_HRT-18G

source_name: Colon, HRT-18G cell line


title: Reference pool vs. colon_NCI-H747

source_name: Colon, NCI-H747 cell line


title: 040857

description:
NB4#3 vs NB4 ATRA #1
Date:2007/04/20

source_name: NB4 ATRA #1

tag: Labeling_reference:NB4 ATRA #1

value: NB4 ATRA #1


title: 040858

description:
LR2#3 vs LR2 ATRA #3
Date:2007/04/20

source_name: LR2 ATRA #3

tag: Labeling_reference:LR2 ATRA #3

value: LR2 ATRA #3


title: Reference pool vs. bladder_RT-4

source_name: Bladder, RT-4 cell line