title: hESC_H7_FGF2-

status: Public on Nov 16 2013

city: Chicago

first: Sergey

last: Malchenko

state: IL

address: 2300 Children's Plaza

institute: Northwestern University's Feinberg School of Medicine

description: Human embryonic stem cell line H7 grown without FGF2

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

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

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

source_name: Human embryonic stem cell line H7

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

growth_protocol: The cells were grown in StemPro medium (Invitrogen, Carlsbad, CA) on a matrigel substrate (BD Bioscience, San Jose, CA)

extract_protocol: Total RNA isolation from the cell lines was performed with the PureZOL RNA isolation reagent (Bio-Rad), followed by DNAse treatment (Promega), according to the manufacturer's instructions. Purity and integrity of the isolated RNA was assessed on the ND-1000 Spectrophotometer (Thermo Fisher Scientific)

treatment_protocol: FGF2+ samples were grown with 20ng/ml of FGF2. In the FGF2- samples, FGF2 was withdrawn following day after plating.

tag: treatment

value: embryo

tag: cell line


title: RD7 E18.5 5-3-07

status: Public on Mar 15 2012

type: RNA

city: Boston

first: Neena

middle: B

last: Haider

state: Massachusetts

address: 20 Staniford Steret

department: Ophthalmology

country: USA

institute: Schepens Eye Research Institute/MEE/Harvard Medical School

hyb_protocol: Samples were labeled using the Affymetrix Eukaryotic Target Labeling Assays to generate biotin-labeled samples for hybridization to Affymetrix GeneChips.

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

data_processing: MAS5 data in the Sample data tables. Data were further processed using the following steps. Data quality was assessed using the affyPLM package for R. Differential expression analysis was performed using the Linear Models for Microarray Analysis portion of Bioconductor. Genes found to be differentially expressed for each pair wise comparison using a FDR-adjusted p-value of 0.001 and at least a 2 fold change were combined and used to perform clustering analysis. A self-organizing map  (SOM) clustering algorithm was applied to genes showing significant expression differences as judged by mean log2 intensity per strain. The gap statistic was used to estimate the optimal number of clusters. Additional analysis was performed using BRB Array Tools for Excel 2007, as well as the Stanford Statistical Analysis of Microarrays  (SAM) plug-in for Excel 2007. Subsequent pathway analysis based on genes found to be statistically significant by these methods was performed using Ingenuity Pathway Analysis software. Gene ontology and further annotation of genes was performed using the Affymetrix NetAffx database, BRB Array Tools, the Database for Annotation, Visualization, and Integrated Discovery (DAVID) (http://david.abcc.ncifcrf.gov), and the UCSC Genome Browser.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: RD7 E18.5 pool

label_protocol: Labeling was performed by the UNMC Microarray Core facility

extract_protocol: RNA was isolated at E18.5 and P30.5 as previously described  (Haider et al. 2009). Briefly, eyes were enucleated and placed in PBS on ice. Retinas were dissected using a stereo microscope (Zeiss Stemi SV 11) and RNA was isolated by TRIzol extraction. A total of 30 retinas were collected from 15 mice of each strain at similar time points during the day. Equimolar amounts of RNA isolated from ten retinas were pooled into three separate pools from each strain and time point.

tag: tissue

value: retina

tag: strain

tag: development age


title: RD7 E18.5 4-19-07


title: hESC_CM14_FGF2-

description: Human embryonic stem cell line CM14 grown without FGF2

organism: Homo sapiens

source_name: Human embryonic stem cell line CM14

tag: developmental stage


title: RD7 E18.5 4-12-07


title: hESC_CM7_FGF2-

description: Human embryonic stem cell line CM7 grown without FGF2

source_name: Human embryonic stem cell line CM7


title: hESC_H9_FGF2+

description: Human embryonic stem cell line H9 grown with FGF2

source_name: Human embryonic stem cell line H9


title: RD7 P30.5 4-19-07

source_name: RD7 P30.5 pool


title: RD7 P30.5 5-3-07


title: RD7 P30.5 4-12-07


title: NOD.NON-H2-NB1 P30.5 4-19-07

source_name: NOD.NON-H2-nb1 P30.5 pool


title: hESC_H9_FGF2-

description: Human embryonic stem cell line H9 grown without FGF2


title: hESC_H14_FGF2+

description: Human embryonic stem cell line H14 grown with FGF2

source_name: Human embryonic stem cell line H14


title: hESC_H14_FGF2-

description: Human embryonic stem cell line H14 grown without FGF2


title: C57BL6/J E18.5 4-19-07

source_name: C57BL6/J E18.5 pool


title: P. aeruginosa isolated from patient M3M1

status: Public on Oct 31 2011

type: genomic

city: Bozeman

first: Kate

last: McInnerney

state: MT

address: 109 Lewis Hall

department: Microbiology

institute: Montana State University

description:
M3M1
Clinical samples were isolated from sputa of chronically-infected CF patients undergoing treatment at the Necker Hopital Enfants-Malades in Paris. Samples were streaked to purity, then archived as -80°C glycerol stocks.

hyb_protocol: Labeled DNA was hybridized for 16 hr at 50C to the Pae_G1a GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix 7G scanner.

data_processing: CEL files were imported into GeneSpring (version 7.3a) and were normalized per chip to the 50% percentile.  Normalized values were then log2 transformed in Excel.

molecule: genomic DNA

organism: Pseudomonas aeruginosa

source_name: P. aeruginosa clinical isolate from CF lung

label_protocol: 10ug genomic DNA was fragmented with DNAse I (5-10m at 37C) and labeled with biotin per the Affymetrix prokaryotic protocol.

growth_protocol: Isolates were streaked to purity on PIA and grown overnight at 37⁰C in MH broth.

extract_protocol: Genomic DNA extractions were performed using a CTAB method of phenol/chloroform extraction (Ausubel et al. 2002 Short Protocols in Molecular Biology 1:2.11-2.12) after overnight culture in Pseudomonas F broth.

tag: isolate type

value: clinical

tag: date of isolation

tag: mutation frequency

tag: resistance profile

value: (S) ami, tic, tob, cip


title: PA01 control

description:
PA01
Archived PA01 lab strain stocks received from contributing author Michael Franklin, Montana State University. Exhibits some sequence/expression differences relative to reports for Genbank AE004091.

source_name: P. aeruginosa laboratory isolate

value: laboratory


title: hESC_CM7_FGF2+

description: Human embryonic stem cell line CM7 grown with FGF2


title: hESC_H7_FGF2+

description: Human embryonic stem cell line H7 grown with FGF2


title: P. aeruginosa isolated from patient I3M1

description:
I3M1
Clinical samples were isolated from sputa of chronically-infected CF patients undergoing treatment at the Necker Hopital Enfants-Malades in Paris. Samples were streaked to purity, then archived as -80°C glycerol stocks.

value: (R) ami


title: P. aeruginosa isolated from patient I1NM

description:
I1NM
Clinical samples were isolated from sputa of chronically-infected CF patients undergoing treatment at the Necker Hopital Enfants-Malades in Paris. Samples were streaked to purity, then archived as -80°C glycerol stocks.

value: (R) ami, tic; (I) cip


title: P. aeruginosa isolated from patient I2M1

description:
I2M1
Clinical samples were isolated from sputa of chronically-infected CF patients undergoing treatment at the Necker Hopital Enfants-Malades in Paris. Samples were streaked to purity, then archived as -80°C glycerol stocks.

value: (R) ami, cip, tic


title: C57BL6/J E18.5 5-3-07


title: C57BL6/J E18.5 4-20-07


title: P. aeruginosa isolated from patient M3M2

description:
M3M2
Clinical samples were isolated from sputa of chronically-infected CF patients undergoing treatment at the Necker Hopital Enfants-Malades in Paris. Samples were streaked to purity, then archived as -80°C glycerol stocks.


title: P. aeruginosa isolated from patient M1M

description:
M1M
Clinical samples were isolated from sputa of chronically-infected CF patients undergoing treatment at the Necker Hopital Enfants-Malades in Paris. Samples were streaked to purity, then archived as -80°C glycerol stocks.


title: C57BL6/J P30.5 4-19-07

source_name: C57BL6/J P30.5 pool


title: P. aeruginosa isolated from patient I3M2

description:
I3M2
Clinical samples were isolated from sputa of chronically-infected CF patients undergoing treatment at the Necker Hopital Enfants-Malades in Paris. Samples were streaked to purity, then archived as -80°C glycerol stocks.

value: (R) ami, cip, tic (I) tob


title: P. aeruginosa isolated from patient I4NM

description:
I4NM
Clinical samples were isolated from sputa of chronically-infected CF patients undergoing treatment at the Necker Hopital Enfants-Malades in Paris. Samples were streaked to purity, then archived as -80°C glycerol stocks.


title: C57BL6/J P30.5 4-12-07


title: CD630_sigH4-cy5_WT4-cy3

status: Public on Aug 22 2011

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

description: Biological replicate 4 of 4.

hyb_protocol: samples were applied to microarrays enclosed in Agilent hybridization chambers for 17h at 65°C. After hybridization, slides were washed with Agilent washing buffers

scan_protocol: Scanned on an GenePix Pro 6 dual-channel laser scanner

data_processing: R limma package - Function used - Background correction : backgroundCorrect normexp ; Normalization : normalizeWithinArrays loess - Correlation of spot duplicat : duplicateCorrelation - Adjust to linear method : lmFit - Statistical analysis : eBayes, decideTests global BH.

organism: Clostridioides difficile

source_name: strain C630E grown 10h in TY (reference)

label_protocol: 10 µg of total RNA and pdN6 primer were heated at 70°C for 5 min, then reversed transcribed at 42°C for 3 h in the presence of 800 U SuperScript III Reverse Transcriptase (Invitrogen), each dATP, dTTP, dGTP,  dCTP. cDNA were then incubated with cy5 or cy3 dyes 1h at room temperature in the dark.

growth_protocol: C.difficile  630E strain 10h vs sigH mutant 10h grown for 10 hours in TY medium.

extract_protocol: Total RNA was extracted using phenol, Trizol reagent and chloroform/isoamylalcohol.

value: C630E Mullany

tag: genotype/variation

value: wild type

tag: time

source_name: sigH mutant grown 10h in TY (test)

value: sigH mutant


title: hESC_CM14_FGF2+

description: Human embryonic stem cell line CM14 grown with FGF2


title: CD630_WT1-10h-cy3_WT1-4h-cy5

description: Biological replicate 1 of 4.

source_name: strain C630E grown 4h in TY (test)

growth_protocol: C.difficile strain C630E was grown for 4h or 10 hours in TY medium.

source_name: strain 630E in TY 10H of growth (reference)


title: CD630_sigH1-cy3_WT1-cy5

description: Biological replicate 1 of 4.


title: WT vs. DglnR N_starvation_rep1

status: Public on Jul 01 2011

city: Erlangen

first: Weber

last: Simone

state: Bavaria

address: Ulmenweg 18

department: Medicine

country: Germany

description: Replicate 1

hyb_protocol: following fragmentation, each 300ng of Cy3-labeled and Cy-5 labeled cRNA were mixed and hybridisied for 17h at 65°C on 8x15K Agilent Msmeg_v1 arrays. Arrays were washed according to the protocol (two-color Microarray-based gene expression protocol)

scan_protocol: Microarrays were scanned using Agilent G2565B Microarray Scanner. Data were extracted using Feature Extraction Version: FE Version 9.5.3.1 (Agilent Technologies Germany). Each target (6760 features) was spotted twice

data_processing: Data analysis was performed using GeneSpringXI (Agilent Technologies)

organism: Mycolicibacterium smegmatis

source_name: wt grown in N-depleted media for 30min

label_protocol: Cy3- and Cy5-labeled cRNA were prepared according to the agilent protocol from 300ng total RNA (two-color microarray based gene expression analysis protocoll v5.7, 2008)

growth_protocol: As described before (Amon et al., 2008), cells were grown in 7H9 medium until exponential growth phase (oD600 0.8-1).

extract_protocol: Total RNA was prepared as described before (Amon et al., 2008) using the NucleoSpin® RNA II kit (Macherey-Nagel, Düren).

treatment_protocol: Cells were harvested by centrifugation (4,000 x g, 10 min, 4°C), washed once and resuspended in 7H9-N medium (Amon et al., 2008). After 30 minutes of incubation in 7H9-N medium at 37°C, 7 ml samples were taken for RNA preparation. The samples were centrifuged (8,000 xg, 3 min, 4°C) and the cell pellet was frozen in liquid nitrogen.

value: MC2 155; strain SMR5

source_name: glnr mutant grown in N-depleted media for 30min

value: MC2 155; strain MH1 (DglnR)


title: CD630_WT4-10h-cy5_WT4-4h-cy3

description: Biological replicate 4 of 4.


title: WT vs. DamtR N surplus_ dyeswap_rep1

description: Replicate 1, dye swap

source_name: amtR mutant grown in N-containing media for 30min

value: MC2 155, DamtR (YL1)

source_name: Wt-strain grown in N-containing media for 30 min


title: C57BL6/J P30.5 5-3-07


title: CD630_sigH2-cy5_WT2-cy3

description: Biological replicate 2 of 4.


title: WT vs. DamtR N surplus_dyeswap_rep2

description: Replicate 2, dye swap


title: WT vs. DglnR N_starvation_dye swap_rep2

description: Replicate 2, dye swap


title: WT vs. DglnR N_starvation_rep2

description: Replicate 2


title: WT with vs. without N_dye swap_rep2

description: Replicate 2, dye swap

source_name: wt grown in N-containing media for 30min


title: WT with vs. without N_rep1

description: Replicate 1


title: WT vs. DamtR N surplus_rep1

description: Replicate 1


title: CD630_WT3-10h-cy3_WT3-4h-cy5

description: Biological replicate 3 of 4.


title: WT with vs. without N_rep2

description: Replicate 2


title: WT vs. DglnR N_starvation_dye swap_rep1

description: Replicate 1, dye swap


title: WT vs. DamtR N surplus_rep2

description: Replicate 2


title: WT with vs. without N_dye swap_rep1

description: Replicate 1, dye swap


title: DamtR with vs. DamtR without N_dyeswap_ rep1

description: Replicate 1, dye swap

source_name: amtR mutant grown in N-depleted media for 30min


title: WT vs. DamtR without N_ dyeswap_rep1

description: Replicate 1, dye swap

source_name: Wt-strain grown in N-depleted media for 30 min


title: WT vs. DamtR without N_rep1

description: Replicate 1


title: WT vs. DamtR without N_ dyeswap_rep2

description: Replicate 2, dye swap


title: WT vs. DamtR without N_rep2

description: Replicate 2

value: MC2 155; strain SMR6


title: CD630_WT2-10h-cy5_WT2-4h-cy3

description: Biological replicate 2 of 4.


title: DamtR with vs. DamtR without N_ rep2

description: Replicate 2,


title: DglnR_without vs. with N_dyeswap_rep2

description:
replicate 2, dye swap
DglnR2+N (Cy5) vs. DglnR2-N (Cy3) (dye swap)
AG-Sonnewald_252606210003_S02_GE2-v5_95_Feb07_2_4.txt: cy3ByCy5Signal

hyb_protocol: following fragmentation, 300ng of Cy3-labeled and Cy-5 labeled cRNA each were mixed and hybridisied for 17h at 65°C on 8x15K Agilent Msmeg_v1 arrays. Arrays were washed according to the protocol (two-color Microarray-based gene expression protocol)

source_name: glnR mutant grown in N-containing media for 30min

label_protocol: Cy3- and Cy5-labeled cRNA were prepared according to the Agilent protocol from 300ng total RNA (two-color microarray based gene expression analysis protocoll v5.7, 2008)

value: MC2 155, DglnR

tag: growth protocol

value: N-containing media

source_name: glnR mutant grown in N-depleted media for 30 min

value: N-depleted media


title: DglnR_without vs. with N_dyeswap_rep1

description:
replicate 1, dye swap
DglnR1+N (Cy5) vs. DglnR1-N (Cy3) (dye swap)
AG-Sonnewald_252606210003_S02_GE2-v5_95_Feb07_2_1.txt: cy3ByCy5Signal


title: DglnR_without vs. with N_rep2

description:
replicate 2
DglnR2-N (Cy5) vs. DglnR1+N (Cy3)
AG-Sonnewald_252606210003_S02_GE2-v5_95_Feb07_2_3.txt: cy5ByCy3Signal

source_name: glnR mutant grown in N-depletd media for 30min

source_name: glnR mutant grown in N-containing media for 30 min


title: Growth of APEC in chicken serum compared to LB, replicate 2

status: Public on Apr 01 2011

city: Birmingham

first: Chrystala

last: Constantinidou

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

description:
Avian pathogenic Escherichia coli.
Biological replicates 2 of 4.

hyb_protocol: For each of four biological replicates, equal quantities of Cy5- and Cy3-labeled cDNA from APEC cultured in chicken serum or LB were added to hybridization solution. Hybridization was performed using the Gene Expression Hybridization Kit (Agilent Technologies).

scan_protocol: Slides were scanned with a GenePix 4000B scanner (Axon Instruments), and the fluorescence intensities were collected with the ImaGene software (BioDiscovery, El Segundo, CA).

data_processing: Analyses were performed using R. The median signal intensities for each spot were background-corrected and log-transformed. The LOWESS procedure was used to correct the intensity-dependent dye bias for each 2-color array.  Then linear models were fitted to the normalized data for each gene.  The moderated-t test was applied using the R package limma to detect the differentially expressed genes between APEC grown in chicken serum and APEC grown in LB.  The correlation among replicate spots within each array was analyzed using the ‘duplicateCorrelation’ function from the limma package and the correlation structure was utilized in the linear model analysis.  The set of p-values was converted to q values for false discovery rate control using the R package q-value developed by Storey et al.  Along with q-values, estimates of fold-change were computed.

organism: Escherichia coli APEC O1

source_name: Total RNA from APEC O1:K1:H7 cultured in LB

label_protocol: Five micrograms of total RNA was used for labelling, and cDNA was synthesized and labelled with Fairplay® III Microarray labelling kit (Agilent Technologies - Stratagene Products) according to the recommendations of the manufacturer and labelled with the CyTM 3 or 5 Mono-Reactive Dye Pack (GE Healthcare). Labelled cDNA was purified and quantified according to the manufacturer’s instructions.

growth_protocol: Overnight cultures of E. coli strains were diluted 1: 100 into LB medium and incubated at 37°C with shaking at 160 RPM until an OD600 of 1.0 (Eppendorf Biophotometer) was attained. These cultures were again diluted 1:5 into fresh LB or chicken serum, and then incubated 3 hours at 37°C.

extract_protocol: RNA from APEC cultured both in LB and chicken serum was extracted using an RNeasy Mini Kit (QIAGEN) with a 1-h on-column DNase digestion (QIAGEN) according to the manufacturer’s instructions.

tag: condition

value: LB media

source_name: Total RNA from APEC O1:K1:H7 cultured in chicken serum

value: chicken serum


title: DglnR_without vs. with N_rep1

description:
replicate 1
DglnR1-N (Cy5) vs. DglnR1+N (Cy3)
AG-Sonnewald_252606210003_S02_GE2-v5_95_Feb07_2_2.txt: cy5ByCy3Signal


title: Growth of APEC in chicken serum compared to LB, replicate 1

description:
Avian pathogenic Escherichia coli.
Biological replicates 1 of 4.


title: Growth of APEC in chicken serum compared to LB, replicate 3

description:
Avian pathogenic Escherichia coli.
Biological replicates 3 of 4.


title: P. aeruginosa isolated from patient M2NM

description:
M2NM
Clinical samples were isolated from sputa of chronically-infected CF patients undergoing treatment at the Necker Hopital Enfants-Malades in Paris. Samples were streaked to purity, then archived as -80°C glycerol stocks.

source_name: P. aeruginosa clinical isolate from CF lung

value: clinical

value: (R) tob, ami


title: Growth of APEC in chicken serum compared to LB, replicate 4

description:
Avian pathogenic Escherichia coli.
Biological replicates 4 of 4.


title: cKO_P55

status: Public on Jan 06 2011

city: Kiel

first: Robert

last: Haesler

address: Schittenhelmstr. 12

department: IKMB / 1st Dept. of Medicine

institute: University Clinic of Schleswig Holstein

description: mouse skin Adam 10 knockout

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol for Mouse Gene 1.0 arrays, using the AGCC (Affymetrix) software.

scan_protocol: Image aquisition was performed according to the standard Affymetrix protocol for Mouse Gene 1.0 arrays using the AGCC (Affymetrix) software.

data_processing:
Data was processed using the AGCC (Affymetrix) software and normalized using the RMA method. Signals, that were not stronger than the 95th percentile of all intron probes on the array were excluded from further analysis.
probe group file: MoGene-1_0-st-v1.r4.pgf
meta-probeset file: MoGene-1_0-st-v1.r4.mps

source_name: Adam10 knockout mouse

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol for Mouse Gene 1.0 arrays.

growth_protocol: All experiments were carried out in accordance with the animal care guidelines of the University of Kiel (acceptance no.: V 742-72 241.121-3 (20-2/04) and (76-7/00)). Mice were maintained in a 12-h light-dark cycle under standard conditions and were provided with food and water ad libitum. Procedures involving animals and their care were conducted in conformance with national and international laws and policies. Blood was drawn from the mice by cardiac puncture under general anesthesia.

extract_protocol: Qiagen RNA extraction (Rneasy) according to the manufacturers guidelines

value: primary skin cells

value: Adam10 knockout


title: WT_P60

description: mouse skin Adam 10 wildtype

source_name: Adam10 wildtype mouse

value: Adam10 wildtype


title: Kidney Cortex F2 pool vs. 552561_F2_344

status: Public on Jan 13 2011

city: Seattle

first: Jonathan

middle: M

last: Derry

state: WA

address: 1100 Fairview Ave N

institute: Sage Bionetworks

description: Derry J, Zhong H, Molony C et al ABSTRACT:  To identify the genes and pathways that underlie cardiovascular and metabolic phenotypes we performed an integrated analysis of a mouse C57BL/6J x A/J F2 (B6AF2) cross by relating genome-wide gene expression data from adipose, kidney, and liver tissues to physiological endpoints measured in the population. We have identified a large number of trait QTLs including loci driving variation in cardiac function on chromosomes 2 and 6 and a hotspot for adiposity, energy metabolism, and glucose traits on chromosome 8. Integration of adipose gene expression data identified a core set of genes that drive the chromosome 8 adiposity QTL. This chromosome 8 trans eQTL signature contains genes associated with mitochondrial function and oxidative phosphorylation and maps to a subnetwork with conserved function in humans that was previously implicated in human obesity. In addition, human eSNPs corresponding to orthologous genes from the signature show enrichment for association to type II diabetes in the DIAGRAM cohort, supporting the idea that the chromosome 8 locus perturbs a molecular network that in humans senses variations in DNA and in turn affects metabolic disease risk. We functionally validate predictions from this approach by demonstrating metabolic phenotypes in knockout mice for three genes from the trans eQTL signature, Akr1b8, Emr1, and Rgs2. In addition we show that the transcriptional signatures for knockout of two of these genes, Akr1b8 and Rgs2, map to the F2 network modules associated with the chromosome 8 trans eQTL signature and that these modules are in turn very significantly correlated with adiposity in the F2 population. Overall this study demonstrates how integrating gene expression data with QTL analysis in a network-based framework can aid in the elucidation of the molecular drivers of disease that can be translated from mice to humans.

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

source_name: Kidney Cortex

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: sample type

value: Kidney Cortex F2 pool

tag: animal id

tag: gender

value: M

tag: generation

value: kidney cortex


title: cKO_P69

description: mouse skin Adam 10 knockout


title: WT_P58

description: mouse skin Adam 10 wildtype


title: WT_P59

description: mouse skin Adam 10 wildtype


title: cKO_P68

description: mouse skin Adam 10 knockout


title: Kidney Cortex F2 pool vs. 552560_F2_343


title: Liver confinement timecourse LS6L vs LS24L

status: Public on Nov 24 2010

city: Galway

first: Michael

middle: Taylor

last: Cairns

address: University Road

department: MRI

country: Ireland

institute: NUI Galway

description: The fish used in the study were sexually immature, mixed sex, adult rainbow trout from two lines of fish selectively bred for either a high (HR) or low (LR) corticosteroid response to a standardized confinement stressor. The selection programme used to generate the HR and LR lines of trout has been described previously (Pottinger and Carrick, 1999 and 2001). In brief, single parent matings of individuals identified as either HR or LR by their corticosteroid response to a series of standardized confinement stressors were used to generate F1 lines of HR and LR progeny. An individual-within-family selection process was adopted to establish the F2 and subsequently the F3 generation, used in this study. The F3 generation hatched during spring 2003 and these fish were therefore in their second year (18 months old) at the time of this study. The mean weight and fork length of the two lines at the time of the study was LR: 181 g, 24.7 cm; HR: 185 g, 24.9 cm.

hyb_protocol: Cy3-labelled and Cy5-labelled cDNA were dried and resuspended in 22 microL of hybridisation mix (5X Denhardt, 3.5X SSC, 0.3% SDS (Bio-Rad), 0.5 microg/microL yeast tRNA (Invitrogen), 0.5 microg/microL polyA RNA (Invitrogen) and 50 % formamide). Slides were prehybridized with a solution containing 50mM ethanolamine, 100mM Tris base, 0.1% SDS, pH 9.0 at 50 ºC for 15 min followed by two washes in 18 MW water. Next slides were incubated in a solution containing 4X SSC and 0.1% SDS at 50 ºC for 15 min followed by one wash with 18 MW water and centrifugation (260g) for 3 minutes at room temperature. Slides were incubated in prehybridisation solution (3.5X SSC, 0.3% SDS, 1% BSA) at 42 ºC for 1h. Slides were washed 5 times with 18 MW water and dried by centrifugation (260g) for 3 min. Before hybridisation, Cy3- and Cy5-labelled targets were pooled and denatured at 100 ºC for 2 min. Targets were applied to the microarray slide and covered with a coverslip (Erie Scientific). Hybridisation of the slides was performed in a hybridisation chamber (Genetix) humidified with 3X SSC at an annealing temperature of 42 ºC overnight followed by immersion of slides in 2% SSC, 0.1% SDS for the removal of the coverslip. Slides were washed with 1X SSC for 2 min and followed by 2 washes with 0.2X SSC for 2 min each. Slides were dried by centrifugation (260g) for 3 min at room temperature and immediately scanned.

scan_protocol: ScanArray Express HT Microarray Scanner (Perkin Elmer) - GenePix software (GenePix Pro 6.0.1.25) was used for feature acquisition from the TIF images (Molecular Devices Corp).

data_processing: Intensity values used were signal median values and local background was automatically subtracted. Data from the time course experiment was analysed using separate channel analysis of two color data using Limma. The raw data from this loop experiment was normalised within slide using the 'printtiploess' method and the 'normexp' background correction method (Smyth and Speed, 2003). Log2 fold changes and standard errors were estimated by using linear models and empirical Bayes moderated F statistics for each gene. P values were adjusted for multiple testing by using the method of Benjamini and Hochberg (Smyth, 2004).

organism: Oncorhynchus mykiss

label_protocol: Five microg of total RNA was used to synthesize labelled cDNA using the ChipShotTM Direct Labeling and Clean-Up System (Promega) following the manufacturer¢s protocol. Labelled cDNA was quantified using a NanoDropTM ND 1000 spectrophotometer (Thermo Scientific).

growth_protocol: Prior to the study the fish were held in 1000-litre circular glassfibre tanks. Each tank received a single pass flow-through (20 litres min-1) of untreated Windermere lake water at ambient temperature (annual range approx 4oC - 17oC). Stocking densities were in the order of 20 g/litre. The fish were fed three times weekly with commercial pellets (Skretting Standard Expanded 40) at a ration size of approx 5% body weight.

extract_protocol: Total RNA was isolated using the RNeasy Midi Kit (Qiagen) following the manufacturer's recommended protocol after homogenising 0.2 - 0.3 mg of tissue in Qiazol reagent (Qiagen). Contaminating genomic DNA was degraded using an on-column DNase I treatment using RNase-free DNase Kit (Qiagen). The quality of RNA was checked using the Agilent Bioanalyser 2100. RNA integrity numbers (RIN) were 10 for most of the samples. Total RNA was quantified by UV spectrophotometry at 260 nm (Eppendorf Biophotometer).

treatment_protocol: A time-course study using HR and LR fish from the F3 generation was carried out during August and September 2004. During July, LR and HR fish (LR weight: 181.3 g; length: 24.7 cm; HR weight: 184.7 g; length: 24.9 cm) were distributed between twenty-two 1000 litre holding tanks (approx 110 fish/tank, 11 for each line). Each tank was supplied with a constant flow of untreated Windermere lake water (20 litres min-1) at ambient temperature (mean 16.7 oC). After a 2 week period of acclimation, LR fish from a single holding tank were transferred to twenty-two 50 litre confinement tanks, 5 fish per tank, each supplied with a constant flow of lake water. At intervals (0, 2, 4, 6, 8, 24, 48, 96, 168, 336, 504h) a total of 6 fish (3 fish from each of two tanks) were sampled, with undisturbed LR fish in pairs of holding tanks acting as controls. At each time-point livers were collected and immediately frozen in liquid nitrogen for subsequent analysis. The confinement and sampling procedure was repeated 1 week later for the HR fish. Fish were fasted for 2 days prior to the study and offered food on day 3 of the study and three times weekly thereafter. Plasma cortisol was measured by a validated radioimmunoassay procedure (Pottinger and Carrick, 2001).

tag: genetic line

value: Low response

value: stress


title: Liver confinement timecourse LS6L vs HS6L

value: High response


title: Liver confinement timecourse LS24L vs LS168L


title: cKO_P67

description: mouse skin Adam 10 knockout

tag: tissue


title: WT_P57

description: mouse skin Adam 10 wildtype


title: In vivo-3

status: Public on Nov 10 2010

city: Reno

first: Gnanaratnam

last: Giritharan

state: Nevada

address: 645 Sierra Rose Drive, Suite 205

institute: Nevada Center for Reproductive Medicine

hyb_protocol: The samples were hybridized to mouse Affymetrix 430 2.0 GeneChips, then washed and stained on fluidics stations

scan_protocol: The samples were scanned at 3 µm resolution according to the manufacturer’s instructions (GeneChip Analysis Technical Manual, www.affymetrix.com).

data_processing:
Programmatic identifier: GeneChip.CallGEBaseCall
Algorithm: ExpressionStat 5.0

source_name: Embryos produced in vivo

label_protocol: In each pool, five embryo equivalents of total RNA was used for reverse transcription followed by linear amplification of antisense cDNA strand, fragmentation and biotin labeling by using NuGEN Ovation Biotin System (NuGEN Technologies Inc., San Carlos, CA).  Briefly, RNA is converted to cDNA with a unique DNA/RNA heteroduplex at one end.  A linear isothermal DNA amplification process was conducted using DNA/RNA chimeric primer, DNA polymerase and RNase H in a homogeneous isothermal assay that provides highly efficient amplification of DNA sequences.  The amplified cDNA strands were subjected to an enzymatic fragmentation and the fragmented product was then labeled with biotin.

growth_protocol: Embryos grown to expanded blastocyst stage were collected

extract_protocol: Total RNA was extracted from four pools of 10 embryos using PicoPure RNA Isoloation Kit (Arcturus, Sunnyvale, CA) according to the manufacturer’s instructions.  In column DNase treatment was performed using RNase-free DNase set (Qiagen Inc, Valencia, CA, USA) as described in the user guide of the PicoPure RNA isolation kit to remove the residual DNA.

treatment_protocol: snap frozen and stored at -80 C before RNA extraction

tag: cell type

value: Blastocyst stage embryo

tag: group

value: Embryos produced in vivo


title: In vivo-1


title: ICSI-WM-4

source_name: ICSI embryos cultured in WM

value: ICSI embryos cultured in WM


title: ICSI-WM-1


title: ICSI-KSOMaa-2

source_name: ICSI embryos cultured in KSOM

value: ICSI embryos cultured in KSOMaa


title: IVF-WM-2

source_name: IVF embryos cultured in WM

value: IVF embryos cultured in WM


title: ICSI-KSOMaa-4


title: ICSI-WM-3


title: ICSI-WM-2


title: In vivo-4


title: IVF-WM-3


title: ICSI-KSOMaa-3


title: Golden Promise_Amykor treated_repl1

status: Public on Mar 03 2010

description: Golden Promise_Amykor treated_repl1

hyb_protocol: Following fragmentation, 1.65 µg cRNA were used to hybridise the 4x44K Agilent custom made -barley array (017060) for 17h at 65°C using Agilent hybridisation chamber and oven. Washing was performed according to Agilents specifications.

scan_protocol: Microarrays were scanned on an Agilent Scanner (G2505B) using one color scan setting for 4x44k array slides and the protocol GE1_v5_95_Feb07

data_processing: Raw data were extracted by the feature extraction software package (v9.5.3.1/ Agilent Technologies) using a standard protocol and were imported into GeneSpring GX 7.3.1 (Silicon Genetics, Palo Alto, CA, USA) for further analysis. Flags were taken from Feature extraction software. Using GeneSpring three normalisation steps were performed: (i) data transformation: measurements less than 5.0 were set to 5.0; (ii) per chip: normalisation to 50th percentile; (iii) per gene: normalisation to the median. Features passing the quality check (flags present or marginal) and showing changes in expression levels more than 2fold were selected for pairwise comparisons using Volcano Plots.

organism: Hordeum vulgare

source_name: leaves, pool1

label_protocol: Cy3 labeled cRNA was prepared according to the standard Agilent protocol from 500ng total RNA (One_Colour Microarray-based Gene Expression Analysis 5.0.1)

growth_protocol: Plants were planted on March 28th, 2007 in the field at Giessen experimental station at a density of 300 grains•m2 with a dedicated Wintersteiger Precision Space Planter and were further cultivated on soil consisting of 27 cm weakly humous A-horizon on coarse-sandy clay underground in replicated blocks. Each block consisted of eight 0.8 m × 0.5 m plots among which genotypes were randomly distributed. No additional fertilizer was applied. Samples were taken in the middle of the light period on a sunny summer day with full light intensity on August 1st, 2007.

extract_protocol: RNA was isolated from 100mg of pooled leaf material following the method described by Logemann et al (1987; Anal Biochem 163: 16-20) and purified using Qiagen Rneasy Mini Kit according to manufacture's instruction.

treatment_protocol: Arbuscular mycorrhiza inoculum Amykor® Wurzel-Vital (Amykor, Bitterfeld-Wolfen Germany) was incorporated at a concentration of 50mL/qm into the soil of half of the plots as indicated. Amykor® consists of expanded clay based inoculum mainly containing Glomus intraradices and Glomus mosseae. The other part of the plots was treated with expanded clay lacking fungal inoculum. On the following day barley grains (300 grains•m2) were planted with a dedicated Wintersteiger Precision Space Planter. Additional fertilizer was not applied.

tag: genotype

value: wild type

tag: transgene

tag: background

value: Golden Promise

tag: amykor treatment

value: yes


title: Golden Promise_repl2

description: Golden Promise_repl2

source_name: leaves, pool2

value: no


title: ICSI-KSOMaa-1


title: ChGP_repl2

value: transgenic

value: engineered Trichoderma harzianum endochitinase


title: ChGP_repl1


title: Golden Promise_Amykor treated_repl2

description: Golden Promise_Amykor treated_repl2


title: ChGP_Amykor treated_repl2

description: ChGP_Amykor treated_repl2

source_name: leaves, pool4


title: Golden Promise_repl1

description: Golden Promise_repl1


title: GluB_repl2

description:
transgenics were outcrossed from the cultivar Golden Promise into Baronesse
GluB_repl2

value: chimeric (1,3-1,4)-beta glucanase from Bacilius spec.

value: Baronesse


title: ChGP_Amykor treated_repl1

description: ChGP_Amykor treated_repl1


title: GluB_Amykor treated_repl2

description:
transgenics were outcrossed from the cultivar Golden Promise into Baronesse
GluB_Amykor treated_repl2


title: CD630_sigH3-cy3_WT3-cy5

description: Biological replicate 3 of 4.

source_name: strain C630E grown 10h in TY (reference)

tag: strain

value: C630E Mullany

source_name: sigH mutant grown 10h in TY (test)

value: sigH mutant


title: GluB_Amykor treated_repl1

description:
transgenics were outcrossed from the cultivar Golden Promise into Baronesse
GluB_Amykor treated_repl1


title: Baronesse_Amykor treated_repl1

description: Baronesse_Amykor treated_repl1


title: Baronesse_repl2


title: Baronesse_repl1


title: Baronesse_Amykor treated_repl2

description: Baronesse_Amykor treated_repl2


title: GluB_repl1

description:
transgenics were outcrossed from the cultivar Golden Promise into Baronesse
GluB_repl1


title: DamtR with vs. DamtR without N_ rep1

description: Replicate 1,

source_name: amtR mutant grown in N-containing media for 30min

value: MC2 155, DamtR (YL1)

source_name: amtR mutant grown in N-depleted media for 30min


title: Rat neonatal cardiomyocytes, AngII-Cy5 vs control-Cy3, slide_09, dye-swap

status: Public on Aug 31 2006

city: Rotterdam

first: Jasper

last: Saris

state: Zuid holland

address: Dr. Molewaterplein 50

country: Netherlands

institute: Erasmus Medical Center

description: high density plated, purified, serum-deprived purified Wistar Rat neonatal cardiomyocytes

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a Agilent G2505A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 3.0 analysis software.

data_processing: After background correction and removal of flagged values, log base 2 expression ratios were derived

organism: Rattus norvegicus

source_name: Rat neonatal cardiomyocytes, Control-Cy5

label_protocol: The cRNA from prorenin stimulated and control cells was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 50 mM sodium bicarbonate, pH 9.0, followed by quenching with 2.7 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were combined and purified with a QIAquick PCR purification kit.

growth_protocol: Neonatal rat cardiomyocytes, step-wise serum deprived in 4 days, day 5 in DMEM/199 (4:1) plus 1% BSA, plated in high density (1,500,000 cells/dish). After stimulation for 4 hours, cells were chilled, 3x rinsed with cold PBS, and pelleted.

extract_protocol: RNA isolation was accomplished with Sigma-Aldrich Tri-reagent and verified using lab-on-chip and UV-spectrum analysis.

tag: Rat neonatal cardiomyocytes, vehicle incubated for 4 hours. Total RNA of 5 independent preparations was equimolar pooled and lineair amplified.

source_name: Rat neonatal cardiomyocytes, AngII-Cy3

tag: Rat neonatal cardiomyocytes, AngII (100 nM) incubated for 4 hours. Total RNA of 5 independent preparations was equimolar pooled and lineair amplified.


title: Rat neonatal cardiomyocytes, Prorenin-Cy5 vs Ang-Cy3, slide_05

status: Public on Sep 01 2006

source_name: Rat neonatal cardiomyocytes, prorenin-Cy5

tag: Rat neonatal cardiomyocytes, prorenin (2 nM) stimulated for 4 hours. Total RNA of 5 independent preparations was equimolar pooled and lineair amplified.

tag: Rat neonatal cardiomyocytes, AngII (100nM) incubated for 4 hours. Total RNA of 5 independent preparations was equimolar pooled and lineair amplified.


title: Rat neonatal cardiomyocytes, AngII-Cy5 vs Prorenin-Cy3, dye-swap, slide_08,

source_name: Rat neonatal cardiomyocytes, Ang-Cy5

tag: Rat neonatal cardiomyocytes, AngII (100nM) stimulated for 4 hours. Total RNA of 5 independent preparations was equimolar pooled and lineair amplified.

source_name: Rat neonatal cardiomyocytes, Prorenin-Cy3

tag: Rat neonatal cardiomyocytes, prorenin (2 nM) incubated for 4 hours. Total RNA of 5 independent preparations was equimolar pooled and lineair amplified.


title: Rat neonatal cardiomyocytes, control-Cy5 vs prorenin-Cy3, slide-6

growth_protocol: Prepared neonatal rat purified cardiomyocytes were step-wise serum deprived, 4 days, day 5 in DMEM/199 (4:1) plus 1% BSA. Cells were plated in 9.6 cm2 dishes in high density (1,500,000 cells/dish). After stimulation for 4 hours, cells were harvested by chilling on ice, 3x rinsing with cold PBS, followed by pelleting of the cells.

source_name: Rat neonatal cardiomyocytes, prorenin-Cy3


title: Rat neonatal cardiomyocytes, prorenin-Cy5 vs control-Cy3, slide_07

source_name: Rat neonatal cardiomyocytes, control-Cy3


title: Rat neonatal cardiomyocytes, Ang-Cy5 vs control-Cy3, slide_04

source_name: Rat neonatal cardiomyocytes, AngII-Cy5

extract_protocol: RNA isolation was accomplished with Sigma-Aldrich Tri-reagent and verified using lab-on-chip and UV-spectrum analysis. RNA of 5 independent preparations was equimolar pooled and lineair amplified.

tag: Rat neonatal cardiomyocytes, Angiotensin-II stimulated for 4 hours

tag: Rat neonatal cardiomyocytes, vehicle incubated for 4 hours


title: IVF-WM-1


title: IVF-WM-4


title: In vivo-2

source_name: Embryos produced in vivo