title: CDd7_2 biological rep2

source_name: Endometrial biopsy collected at day 7 of the oestrous ccycle from hiefers resulted in calf delivery after embryo transfer

value: yes


title: NPd7_3  biological rep3

status: Public on Mar 25 2010

type: RNA

city: Bonn

first: Dessie

last: Salilew-Wondim

state: NRW

address: Endenicher Allee 15

department: Animal breeding and husbandry group

country: Germany

institute: University of Bonn

hyb_protocol: The biotin-labeled cRNA was fragmented. Following this, a hybridization cocktail consisting of fragmented and labeled cRNA, control oligonucleotide B2 (3nM), 20X eukaryotic hybridization controls (bioB, bioC, bioD, cre), 2X hybridization mix, DMSO and RNAse free water were mixed to a final volume of 200 µl and heated to 99°C for 5 followed by warming at 45°C for 5 min. The samples were then hybridized to GeneChip® Bovine Genome Array for 16 h at 45°C in hybridization oven. For each sample of CDd7, CDd14, NPd7 or NPd14, three biotin labeled cRNA hybridizations were performed.

scan_protocol: The arrays were washed and stained using Fluidics Station 450/250 and scanned using the GeneChip® scanner 3000 integrated with Affymetrix® Microarray Suite software as recommended in GeneChip® expression wash, stain and scan user manual (P/N 702731).

data_processing: The microarray data normalization and background correction was performed using guanine cytosine robust multi-array analysis (gcrma) . The quality of the arrays after hybridization was evaluated by assessing the absent and present calls of the control probesets. Differentially expressed genes were generated using linear models for microarray data analysis (LIMMA).  For this, we used R software, (www.r-project.org) and bioconductor packages (www.bioconductor.org).

label: biotin

molecule: total RNA

organism: Bos taurus

source_name: Endometrial biopsy collected at day 7 of the oestrous ccycle from hiefers resulted in no pregnancy after embryo transfer

label_protocol: The cRNA  was biotin labeled using the GeneChip® IVT Labeling Kit (Affymetrix, Inc., Santa Clara, CA, USA) according to GeneChip® expression analysis technical manual (P/N 702232)

extract_protocol:
Total RNA was extracted from three pools of each endometrial sample (CDd7, CDd14, NPd7 or NPd14 ) using RNeasy mini kit (Qiagen).
RNA amplification was perfomed using MEGAscript® T7 Kit (Ambion, Inc., Austin, TX, USA) according to GeneChip® expression analysis technical manual (P/N 702232)

tag: day of the oestrous cycle

tag: pregnancy

value: no


title: NPd7_2 biological rep2


title: CDd14_2 biological rep2

source_name: Endometrial biopsy collected at day 14 of the oestrous ccycle from hiefers resulted in calf delivery after embryo transfer


title: 0.5uM Bio treated expanded CD34+ cells

status: Public on Mar 26 2010

city: Randwick

first: Kap-Hyoun

last: Ko

state: NSW

address: High Street

department: Cord and Marrow Transplant Facility

country: Australia

institute: Sydney Children's Hospital

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using average normalisation with Illumina Beadstudio

label: Biotin

organism: Homo sapiens

source_name: Umbilical cord blood

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

growth_protocol: CD34+ cells were seeded at a density of 1-2 x 105 cells/ml in Iscove’s Modified Dulbecco’s medium (IMDM) with 10% heat-inactivated foetal calf serum (FCS), 2mM L-glutamine, 100U/ml penicillin/streptomycin and a cytokine cocktail of Flt3 ligand (FLT3L), stem cell factor (SCF) and thrombopoietin (TPO), all at a concentration of 100ng/ml

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: CD34+ cells were exposed to 0.5µM 6-bromoindirubin 3’-oxime (BIO)

tag: tissue

value: Umbilical cord blood

tag: cell type


title: CDd7_3 biological rep3


title: CDd7_1 biological rep1


title: NPd7_1 biological rep1


title: CDd14_1 biological rep1


title: STT4934-SFT-FFPE-aRNA

city: Stanford

first: Andrew

last: Beck

state: CA

address: Stanford

country: USA

institute: Stanford University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-09/76725.gif

hyb_protocol: not provided

scan_protocol: Scanner Model = GenePix 4000A

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

source_name: aRNA-UHR

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: aRNA-UHR

source_name: STT4934-SFT-formalin fixed paraffin embedded tissue-aRNA

tag: preservation

value: formalin fixed paraffin embedded tissue

tag: disease state

value: solitary fibrous tumor


title: CDd14_2 biological rep3


title: Resistance to tunicamycin

type: genomic

city: Houston

first: Richard

last: Sucgang

state: TX

address: 1 Baylor Plaza

department: Biochemistry and Molecular Biology

institute: Baylor College of Medicine

hyb_protocol: The hybridization protocol is detailed in Pan et al, 2007, Methods 41(2):206-221

scan_protocol: Slides were quantified on a GenePix 4000B using GenePix Pro 6.0.1.27

data_processing: Images were not normalized, and the LocalFeature quantification was used to subtract the background. No normalization was involved, data reported is the default output from GenePix 6.0 software. We found that normalization was unnecessary for our paper.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Yeast essential genes variomics library pool

label_protocol: Tag regions were labeled by PCR amplification using universal primers, one of which was appropriately linked to the corresponding dye (either Cy5 or Cy3).

growth_protocol: Cells were sporulated, and selected in the appropriate selection media as described in Pan et al, 2007, Methods 41(2):206-221.

extract_protocol: Genomic DNA was isolated using the Epicentre MasterPure yeast genomic DNA extraction kit (MPY80200)

tag: agent

value: tunicamycin

value: control (untreated)


title: NPd14_3 biological rep3

source_name: Endometrial biopsy collected at day 14 of the oestrous ccycle from hiefers resulted in no pregnancy after embryo transfer


title: Resistance to cycloheximide

treatment_protocol: Cells were sporulated, and selected in the appropriate selection media as described in Pan et al, 2007, Methods 41(2):206-221.

value: cycloheximide


title: Patient_01 (miRNA)

city: Little Rock

first: Yiming

last: Zhou

state: AR

address: 4301 West Markham St., Slot 776

institute: Myeloma Institute for Research and Therapy

description: miRNA expression of CD138 selected plasma cells

data_processing:
Purified miRNA was hybridized to the Human miRNA Microarray platform (Agilent, Santa Clara, CA) following the Agilent version 2.0 protocol (June 2008) explicitly for target labeling, hybridization, washing, scanning, and image analysis.
Total gene signal from GeneView data files, which were extracted using default miRNA settings in Agilent Feature Extraction (v9.5.x), was used as signal for miRNAs. We took advantage of spiked-in controls spotted in Agilent's platform, which were external references and served as microarray controls in the hybridization protocol. We averaged intensities of positive controls on each array and then normalized miRNA signals by equalizing these averages among all  arrays.

source_name: CD138 selected plasma cells

extract_protocol: TRIzol reagent (Invitrogen, Carlsbad, CA) (500 µl) was added to dry cell pellets, which were vigorously pipetted. After incubation at room temperature (5 minutes), chloroform (100 µl) was added, and the sample was briefly vortexed and again incubated at room temperature (5 minutes). After centrifugation (15 minutes, 12,000g, 4°C), the upper aqueous phase of samples was transferred to a new RNase-free microcentrifuge tube containing 250 µl of isopropanol. Following pulse-vortexing and incubation at room temperature (5 minutes), total RNA was precipitated (20 minutes, 14,000g, 4°C). Following removal of the supernatant, the RNA pellet was washed in 500 µl of 70% ethanol (30 minutes, 14,000g, 4°C), RNA pellets were allowed to air-dry (10 minutes) and were resuspended in 20 µl of RNase-free water. Total RNA samples were evaluated spectrophotometrically using a Nanodrop spectrophotometer. A260 values were used to quantify the samples, and A260/A280 ratios were used to determine relative purity; generally, RNA samples with A260/A280 ≥1.6 were routed to analysis.

tag: patient

value: multiple myeloma

value: CD138+ selected plasma cells


title: Resistance to rapamycin

value: rapamycin


title: Rat 13, Day 21, 8 mm

city: Silver Spring

first: Rasha

last: Hammamieh

state: MD

address: 503 Robert Grant Ave

department: Molecular Pathology

institute: Walter Reed Army Institute of Research

description: Gene expression 21 day post 8 mm defect created in calvarial bone

hyb_protocol: The 0.5µg of cRNA extracted from each of the CSD and non-CSD sampels were hybridized onto a microarray slide at 65⁰C for 17 h in a rotisserie chamber at 10 rpm the microarray slides were washed with wash buffer with 0.005% Triton X-102 for 1 min. at RT, followed by wash buffer 2 at 37⁰C for 1 min and drying in the dark for 5 min.

scan_protocol: The slides were scanned with a GenePix 4000B fluorescence scanner (Axon).

data_processing: Data filter and statistical analysis were carried out using GeneSpring(r) 7.3. Local background was subtracted from individual spot intensity and genes that failed 'background check' in any of the experiments were eliminated from further analysis. Each chip was next subjected to intra-chip normalization (LOWESS). Differentially regulated genes were selected using Welch t-test analysis (P < 0.05).

organism: Rattus norvegicus

source_name: Rat 13, Day 21, 8 mm

label_protocol: The Cy-3 labeled RNA applied to Agilent rat whole genome oligo microarray kit (G4131F) was performed according to the manufacturer's instructions.

extract_protocol: Tissues from each individual defect were harvested using the trephine for the same size and total RNA was isolated using 1 ml Tri Reagent according to the manufacturer's directions in lysing matrix D tubes and homogenized using the FastPrep24 at 4.0 mls for 30 sec. and stored on ice for 1 min. This sequence was repeated 4x. total RNA was further purified by RNeasy columns according to the manufacturer's specifications, quantified by Nanodrop and its integrity confirmed by Bioanalyzer.

treatment_protocol: Using a drill press and copiou irrigation with saline, a trephine was used to create the 4 or 8 mm defect. The surgical site was then closed in standard fashion using a non-resorpable suture. No additional treatments were applied to either defect and the animals were survived in their home environment for the respective period of time.

value: Calvarial bone with healing tissue plug

tag: age

value: 12 weeks

tag: gender

value: male

tag: defect size

value: 8 mm


title: Rat 15, Day 21, 8 mm

source_name: Rat 15, Day 21, 8 mm


title: Rat 12, Day 21, 8 mm

source_name: Rat 12, Day 21, 8 mm


title: Rat 14, Day 14, 8 mm

description: Gene expression 14 day post 8 mm defect created in calvarial bone

source_name: Rat 14, Day 14, 8 mm


title: Rat 15, Day 14, 8 mm

source_name: Rat 15, Day 14, 8 mm


title: Rat 11, Day 21, 4 mm

description: Gene expression 21 day post 4 mm defect created in calvarial bone

source_name: Rat 11, Day 21, 4 mm

value: 4 mm


title: Rat 14, Day 21, 8 mm

source_name: Rat 14, Day 21, 8 mm


title: Rat 10, Day 21, 4 mm

source_name: Rat 10, Day 21, 4 mm


title: Rat 11, Day 21, 8 mm

source_name: Rat 11, Day 21, 8 mm


title: Rat 13, Day 21, 4 mm

source_name: Rat 13, Day 21, 4 mm


title: Rat 12, Day 21, 4 mm

source_name: Rat 12, Day 21, 4 mm


title: Rat 10, Day 21, 8 mm

source_name: Rat 10, Day 21, 8 mm


title: Rat 10, Day 14, 8 mm

source_name: Rat 10, Day 14, 8 mm


title: Rat 14, Day 21, 4 mm

source_name: Rat 14, Day 21, 4 mm


title: Rat 15, Day 21, 4 mm

source_name: Rat 15, Day 21, 4 mm


title: Rat 11, Day 14, 8 mm

source_name: Rat 11, Day 14, 8 mm


title: Rat 20, Day 14, 4 mm

description: Gene expression 14 day post 4 mm defect created in calvarial bone

source_name: Rat 20, Day 14, 4 mm


title: Rat 17, Day 14, 4 mm

source_name: Rat 17, Day 14, 4 mm


title: Rat 12, Day 14, 8 mm

source_name: Rat 12, Day 14, 8 mm


title: Rat 16, Day 14, 4 mm

source_name: Rat 16, Day 14, 4 mm


title: Rat 15, Day 10, 8 mm

description: Gene expression 10 day post 8 mm defect created in calvarial bone

source_name: Rat 15, Day 10, 8 mm


title: caryopses at T 5:00 PM, biological rep2

city: Tuebingen

first: Joachim

last: Kilian

address: Auf der Morgenstelle 1

department: ZMBP Plant Physiology

institute: University of Tuebingen

description: Gene expression data from developing Barley caryopses 12 days after anthesis, at 5:00 PM; 20 h after start of experiment, 11 h after onset of light

hyb_protocol: After fragmentation of cRNA using the RNA Fragmentation Reagents (Ambion), 13.5µg of cRNA was hybridized to Affymetrix Barley1 GeneChips (GEO accsession GPL1340) according to manufacturers manual. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the protocol 'EukGE-WS2V4'.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® scanner GS3000 7G according to manufacturers manual.

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 200.

organism: Hordeum vulgare

source_name: Barley caryopses

label_protocol: 1µg of total RNA were used to synthesize amplified labeled cRNA (MessageAmp™ II aRNA Amplification Kit; Ambion).

growth_protocol: Barley plants were grown in the green house in 10 cm pots in soil with additional lighting from Xenon light bulbs (15h light [6:00 AM - 9:00 PM], 9h dark [9:00 PM - 6:00 AM]; ~24°C; 40% rel. Humidity, October 2006)

extract_protocol: 100mg of pooled homogenized plant material was mixed with 900µl of sarcosyl buffer (1% sodium lauryl sarcosinate, 0.1M Tris-HCl pH 7.5, 0.1M NaCl, 20mM EDTA, 50mM beta-mercaptoethanol) and purification of nucleic acids was done by three steps of phenol-chloroform-isoamylalcohol (25:24:1) extractions. Precipitation of nucleic acids was performed with sodium acetate (pH 5.2) and 1 volume isopropanol. After centrifugation, sediment was washed with ethanol and purified RNA was dissolved in DEPC treated water. Incubation at 65°C for 5min, followed by centrifugation at 4°C was performed to remove residual high molecular weight polysaccharides. The obtained RNA solution was purified following the RNeasy (Quiagen) clean up protocol. RNA quantity and integrity were assessed using RNA 6000 Nano LabChip Kit and the BioAnalyzer software (Agilent).

value: whole carypses from the mid region of the spike, awns removed

tag: genotype

value: Hordeum vulgare cultivar 'Golden Promise'

value: 11 to 12 days after anthesis


title: Rat 18, Day 14, 4 mm

source_name: Rat 18, Day 14, 4 mm


title: Rat 14, Day 10, 8 mm

source_name: Rat 14, Day 10, 8 mm


title: caryopses at T 8:00 PM, biological rep1

description: Gene expression data from developing Barley caryopses 12 days after anthesis, at 8:00 PM; 23 h after start of experiment, 1 hr before turn off the light


title: caryopses at T 5:00 PM, biological rep1


title: Rat 15, Day 14, 4 mm

source_name: Rat 15, Day 14, 4 mm


title: caryopses at T 8:00 PM, biological rep2


title: caryopses at T 2:00 PM, biological rep2

description: Gene expression data from developing Barley caryopses 12 days after anthesis, at 2:00 PM; 17 h after start of experiment, 8 h after onset of light


title: STT200-SFT-FS

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70701.gif

source_name: UHR

value: UHR

value: frozen


title: caryopses at T 2:00 PM, biological rep1


title: Rat 13, Day 10, 4 mm

description: Gene expression 10 day post 4 mm defect created in calvarial bone

source_name: Rat 13, Day 10, 4 mm


title: caryopses at T 7:00 AM, biological rep1

description: Gene expression data from developing Barley caryopses 12 days after anthesis, at 7:00 AM; 10 h after start of experiment, 1 h after onset of light


title: caryopses at T 6:00 AM, biological rep2

description: Gene expression data from developing Barley caryopses 12 days after anthesis, at 6:00 AM; 9 h after start of experiment, directly before onset of light


title: Rat 12, Day 10, 4 mm

source_name: Rat 12, Day 10, 4 mm


title: STT2913-Fibromatosis-FFPE-aRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-09/76714.gif

source_name: aRNA-UHR

value: aRNA-UHR

source_name: STT2913-Fibromatosis-formalin fixed paraffin embedded tissue-aRNA

value: formalin fixed paraffin embedded tissue

value: desmoid type fibromatosis


title: caryopses at T 6:00 AM, biological rep1


title: Rat 12, Day 10, 8 mm

source_name: Rat 12, Day 10, 8 mm


title: Rat 11, Day 10, 8 mm

source_name: Rat 11, Day 10, 8 mm


title: Rat 10, Day 10, 8 mm

source_name: Rat 10, Day 10, 8 mm


title: Rat 13, Day 10, 8 mm

source_name: Rat 13, Day 10, 8 mm


title: caryopses at T 7:00 AM, biological rep2


title: Rat 11, Day 10, 4 mm

source_name: Rat 11, Day 10, 4 mm


title: caryopses at T 10:00 PM, biological rep2

description: Gene expression data from developing Barley caryopses 11 days after anthesis, at 10:00 PM; 1 h after turn off the light (start of experiment)


title: c- 7 hpi

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

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner.

data_processing: The data were analyzed with GeneSpring version 7.1 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Macaca mulatta

source_name: infected Macaca mulatta kidney epithelial cells

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: Virus replication allowed to progress for 3 or 7 hours after infection in MK2 cell, while control cell were mock infected with PBS solution and followed incubation steps identical to infected cells.

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

treatment_protocol: Culture medium was removed and cells were incubated with 3 ml of virus seed at MOI=5 in 150 ml culture flasks.  The virus was adsorbed for 30-45 min, then virus seed was removed, cells washed with PBS, culture medium was added and cells were incubated for indicated time at 37C.

tag: infection

value: Monkey pox virus

tag: virus replication time

value: 7 hours


title: Rat 12, Day 7, 8 mm

description: Gene expression 7 day post 8 mm defect created in calvarial bone

source_name: Rat 12, Day 7, 8 mm


title: Rat 14, Day 7, 8 mm

source_name: Rat 14, Day 7, 8 mm


title: b- Control

source_name: Macaca mulatta kidney epithelial cells

value: Mock infected


title: Rat 10, Day 7, 8 mm

source_name: Rat 10, Day 7, 8 mm


title: Rat 15, Day 7, 4 mm

description: Gene expression 7 day post 4 mm defect created in calvarial bone

source_name: Rat 15, Day 7, 4 mm


title: Rat 14, Day 7, 4 mm

source_name: Rat 14, Day 7, 4 mm


title: Insulin sensitive patient 13 - omental adipose tissue

city: Worcester

first: Olga

middle: Theresa

last: Hardy

state: MA

address: 373 Plantation Street, Biotech Two, Suite 100

department: Molecular Medicine

institute: University of Massachusetts

description: Gene expression data from human adipose tissue obtained during gastric bypass surgery.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133plus2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000, with 7G upgrade

data_processing: The data were analyzed with the Bioconductor statistical environment using RMA and Expression Console software using RMA.

source_name: Obese male

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.

extract_protocol:
Paired samples of omental and subcutaneous adipose were obtained from fasting patients during gastric bypass surgery. Whole adipose tissue was dissected to remove fibrotic tissue and obvious vasculature, and frozen in 0.5 cm3 sections in liquid nitrogen.
Total RNA was isolated from frozen human tissues by homogenizing the tissue in TRIzol.  RNA quality was assessed using a denaturing agarose gel.   Total RNA was purified using RNeasy Mini-Kit.

value: omental adipose

tag: metabolic status

value: insulin sensitive


title: Rat 13, Day 7, 8 mm

source_name: Rat 13, Day 7, 8 mm

value: Calvarial bone with healing tissue plug

value: 12 weeks


title: c- 3 hpi

value: 3 hours


title: caryopses at T 10:00 PM, biological rep1

source_name: Barley caryopses


title: Insulin sensitive patient 14 - omental adipose tissue

source_name: Obese female

value: female


title: Rat 23, Day 5, 8 mm

description: Gene expression 5 day post 8 mm defect created in calvarial bone

source_name: Rat 23, Day 5, 8 mm

value: male

value: 8 mm


title: Rat 15, Day 7, 8 mm

source_name: Rat 15, Day 7, 8 mm


title: c- Control


title: Rat 10, Day 7, 4 mm

source_name: Rat 10, Day 7, 4 mm

value: 4 mm


title: Rat 12, Day 7, 4 mm

source_name: Rat 12, Day 7, 4 mm


title: Rat 13, Day 7, 4 mm

source_name: Rat 13, Day 7, 4 mm


title: b- 7 hpi


title: a- Control


title: b- 3 hpi


title: a- 3 hpi


title: a- 7 hpi


title: Patient_01

description: Gene expression data from CD138+ selected plasma cells

hyb_protocol: mRNA purification, cDNA synthesis, cRNA preparation, and hybridization to the Human Genome U133Plus 2.0 GeneChip microarrays (Affymetrix, Santa Clara, CA) were performed as previously described PMID: 17105814

scan_protocol: mRNA purification, cDNA synthesis, cRNA preparation, and hybridization to the Human Genome U133Plus 2.0 GeneChip microarrays (Affymetrix, Santa Clara, CA) were performed as previously described PMID: 17105815

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 500.

source_name: CD138 selected plasma cells

label_protocol: mRNA purification, cDNA synthesis, cRNA preparation, and hybridization to the Human Genome U133Plus 2.0 GeneChip microarrays (Affymetrix, Santa Clara, CA) were performed as previously described PMID: 17105813

extract_protocol: mRNA purification, cDNA synthesis, cRNA preparation, and hybridization to the Human Genome U133Plus 2.0 GeneChip microarrays (Affymetrix, Santa Clara, CA) were performed as previously described in PMID: 17105813

value: multiple myeloma

value: CD138+ selected plasma cells

tag: risk score

tag: proliferation index


title: Insulin sensitive patient 15 - omental adipose tissue


title: Rat 20, Day 5, 8 mm

source_name: Rat 20, Day 5, 8 mm


title: Insulin sensitive patient 7 - omental adipose tissue


title: Rat 21, Day 5, 8 mm

source_name: Rat 21, Day 5, 8 mm


title: Rat 19, Day 5, 8 mm

source_name: Rat 19, Day 5, 8 mm


title: 131h 31.5C rep2

city: Wilmington

first: Kevin

last: Portune

state: NC

address: 601 S. College Road

institute: University of North Carolina, Wilmington

description:
Pooled reference of coral larvae raised at three temperatures (28C, 30C, 31.5C) of 12, 24.5, 42.5, 89, and 131 hours after fertilization.
Coral larvae raised at 31.5C for 131 hours after fertilization hybridized against pooled reference.

hyb_protocol: Cy3 and Cy5 labeled cDNAs were mixed together in a hybridization buffer containing 0.25% SDS, 25mM HEPES, and 3x SSC. The hybridization mixtures were boiled for 2min at 99°C then allowed to cool at room temperature for 5 minutes. The cooled hybridization mixtures were pipetted under an mSeries Lifterslip (Erie Scientific), and hybridization took place in Corning hybridization chambers overnight at 63°C. Microarrays were washed twice in 0.6x SSC and 0.01% SDS followed by a rinse in 0.06x SSC and dried via centrifugation.

scan_protocol: Slides were immediately scanned using an Axon 4000B scanner.

data_processing: Spot intensities were extracted, background subtracted, and block-wise lowess normalized using TIGR Spotfinder 2.2.4 (Saeed et al., 2003). Duplicated spots were averaged over the median of intensities.

organism: Acropora palmata

source_name: Common reference

label_protocol: 1 µg of total RNA was amplified using the MessageAmp II aRNA kit (Ambion). For cDNA synthesis, 3 µg of aRNA per sample were primed with 3.5 nmol random pentadecamer for 10min at 70°C. Reverse transcription (RT) lasted for 2 hours at 42°C using a master mix containing a 3:2 ratio of aminoallyl-dUTP to TTP. Following RT, single-stranded RNA was hydrolyzed by incubating the RT reactions in 10 uL 0.5M EDTA and 10 uL 1M NaOH for 15min at 65°C. After hydrolysis, RT reactions were cleaned using the MinElute Cleanup kit (Qiagen). Cy3 and Cy5 dyes (GE Healthcare) were dissolved in 17uL DMSO, and the coupling reactions lasted for 2hr at room temperature in the dark. Dye-coupled cDNAs were cleaned using the MinElute Cleanup kit (Qiagen).

extract_protocol: Total RNA of coral larvae was isolated using Qiazol (Qiagen) according to manufacturer’s instructions. Larvae were homogenized for 2 minutes using a Mini-Beadbeater (Biospec) with 0.1 mm and 0.55 mm silica beads to disrupt cellular structures. RNA pellets were cleaned further with RNeasy Mini columns (Qiagen).

tag: sample

value: pooled reference

tag: developmental stage

value: coral larvae

tag: growth protocol

value: raised at 31.5C

value: 131 hours after fertilization


title: Rat 16, Day 5, 8 mm

source_name: Rat 16, Day 5, 8 mm

tag: tissue


title: Rat 18, Day 5, 8 mm

source_name: Rat 18, Day 5, 8 mm


title: CD4_anti-CD3_IL2_TGFb_IL6_rep1,2,3,4

city: Scottsdale

first: Cheryl

middle: E

last: Myers

state: AZ

address: 13400 E Shea Blvd

department: Immunology

institute: Mayo Clinic College of Medicine

description:
504_1_3.txt: Treg_cy3; T-effector_cy5
US45102967_251486813481_H_1_3.txt: Treg_cy3; T-effector_cy5
503_1_4.txt: Treg_cy5; T-effector_cy3
US45102967_251486813481_H_1_2.txt: Treg_cy5; T-effector_cy3

hyb_protocol: Agilent In Situ Hybridization Kit Plus was used according to manufacturers instructions

scan_protocol: GE2-v5_95_Feb07 (Read Only), using Agilent Technologies Scanner G2505B US45102967

data_processing:
Images were quantified using Agilent Feature Extraction Software (version A.9.5.1.1).
Agilent Feature Extraction Software (v 9.5.1.1) was used for background subtraction and LOWESS normalization. The normalized data was derived by averaging the ratio of (Treg/T-effector) in each treatment condition.

label: cy3, cy5

organism: Mus musculus

source_name: CD4+ cells from lymph node

label_protocol: Agilent Low RNA Input Linear Amplification Kit PLUS, two color,  was used according to manufacturers instructions

growth_protocol: CD4+ cells were grown in plates coated with 1ug/ml anti-CD3, for 4days

extract_protocol: Trizol, followed by Rneasy MiniKit (Qiagen)

treatment_protocol: Cells were incubated for three days with IL2 (100 units/ml), TGFb at 4ng/ml, and IL6 at 25ng/ml.

tag: cell type

value: Treg

label: cy5, cy3

value: T-effector


title: Insulin sensitive patient 11 - omental adipose tissue

value: omental adipose


title: MDA-MB-231 S1b, biological rep2

city: New York

first: Mi-Young

last: Kim

state: NY

address: 1275 York Ave

institute: MSKCC

description: Gene expression data MDA-MB-231-S1b cells

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: MAS 5

source_name: Isolated seeder cell popuation2

label_protocol: Biotin

growth_protocol: Subconfluent, in DMEM containing 10% FBS

extract_protocol: RNA was isolated by using USB RNA extraction kit

tag: cell line lineage


title: Rat 15, Day 5, 8 mm

source_name: Rat 15, Day 5, 8 mm


title: Insulin sensitive patient 9 - omental adipose tissue

source_name: Obese male

value: insulin sensitive


title: CD4_anti-CD3_IL2_IL6_rep1,2,3

description:
504_1_4.txt: Treg_cy3; T-effector_cy5
479_1_4.txt: Treg_cy3; T-effector_cy5
504_1_1.txt: Treg_cy5; T-effector_cy3


title: Insulin resistant patient 15 - omental adipose tissue

source_name: Obese female

value: insulin resistant


title: Insulin sensitive patient 10 - omental adipose tissue


title: Rat 17, Day 5, 8 mm

source_name: Rat 17, Day 5, 8 mm

value: Calvarial bone with healing tissue plug

value: 12 weeks


title: Insulin sensitive patient 8 - omental adipose tissue

value: female


title: Insulin sensitive patient 6 - omental adipose tissue


title: CD4_anti-CD3_IL2_rep1,2,3

description:
479_1_3.txt: Treg_cy3; T-effector_cy5
503_1_2.txt: Treg_cy5; T-effector_cy3
US45102967_483_H_1_4.txt: Treg_cy5; T-effector_cy3


title: Rat 22, Day 5, 8 mm

source_name: Rat 22, Day 5, 8 mm

value: male


title: CD4_anti-CD3_IL2_TGFb_rep1,2,3

description:
504_1_2.txt: Treg_cy3; T-effector_cy5
US45102967_251486813481_H_1_4.txt: Treg_cy3; T-effector_cy5
503_1_3.txt: Treg_cy5; T-effector_cy3


title: Insulin sensitive patient 12 - omental adipose tissue


title: Rat 14, Day 5, 8 mm

source_name: Rat 14, Day 5, 8 mm

value: 8 mm


title: 131h 31.5C rep1


title: 131h 30C rep2

description:
Pooled reference of coral larvae raised at three temperatures (28C, 30C, 31.5C) of 12, 24.5, 42.5, 89, and 131 hours after fertilization.
Coral larvae raised at 30C for 131 hours after fertilization hybridized against pooled reference.

value: raised at 30C


title: 131h 30C rep1


title: 131h 28C rep2

description:
Pooled reference of coral larvae raised at three temperatures (28C, 30C, 31.5C) of 12, 24.5, 42.5, 89, and 131 hours after fertilization.
Coral larvae raised at 28C for 131 hours after fertilization hybridized against pooled reference.

value: raised at 28C


title: 131h 28C rep1


title: 89h 31.5C rep2

description:
Pooled reference of coral larvae raised at three temperatures (28C, 30C, 31.5C) of 12, 24.5, 42.5, 89, and 131 hours after fertilization.
Coral larvae raised at 31.5C for 89 hours after fertilization hybridized against pooled reference.

value: 89 hours after fertilization


title: Rat 12, Day 5, 8 mm

source_name: Rat 12, Day 5, 8 mm


title: Rat 11, Day 5, 8 mm

source_name: Rat 11, Day 5, 8 mm


title: 89h 31.5C rep1

value: pooled reference


title: Insulin resistant patient 13 - omental adipose tissue


title: Rat 21, Day 5, 4 mm

description: Gene expression 5 day post 4 mm defect created in calvarial bone

source_name: Rat 21, Day 5, 4 mm

value: 4 mm


title: MDA-MB-231 S1b, biological rep1


title: MDA-MB-231 S1a, biological rep1

description: Gene expression data MDA-MB-231-S1a cells

source_name: Isolated seeder cell popuation1


title: Rat 19, Day 5, 4 mm

source_name: Rat 19, Day 5, 4 mm


title: NPd14_1 biological rep1

source_name: Endometrial biopsy collected at day 14 of the oestrous ccycle from hiefers resulted in no pregnancy after embryo transfer

tag: day of the oestrous cycle

tag: pregnancy

value: no


title: 89h 30C rep2

description:
Pooled reference of coral larvae raised at three temperatures (28C, 30C, 31.5C) of 12, 24.5, 42.5, 89, and 131 hours after fertilization.
Coral larvae raised at 30C for 89 hours after fertilization hybridized against pooled reference.

source_name: Common reference

source_name: 89h 30C rep2

value: coral larvae

tag: age


title: Insulin resistant patient 11 - omental adipose tissue

tag: gender


title: Parental MDA-MB-231, biological rep1

description: Gene expression data parental MDA-MB-231 cells

source_name: parental MDA-MB-231 cells

value: parental MDA-MB-231-1


title: Insulin resistant patient 12 - omental adipose tissue


title: Rat 20, Day 5, 4 mm

source_name: Rat 20, Day 5, 4 mm

tag: defect size


title: Insulin resistant patient 14 - omental adipose tissue


title: Insulin resistant patient 10 - omental adipose tissue


title: Insulin resistant patient 9 - omental adipose tissue


title: Rat 18, Day 5, 4 mm

source_name: Rat 18, Day 5, 4 mm


title: MDA-MB-231 S1a, biological rep2

description: Gene expression data MDA-MB-231-S1a  cells


title: Parental MDA-MB-231, biological rep2

value: parental MDA-MB-231-2


title: 13690762 - SL2 vs H2O2

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

country: France

institute: INRA

description: Identification of genes involved in early Arabidopsis response to pathogenic and non-pathogenic bacteria.

hyb_protocol: H2O2 Cy5 / SL2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: whole plant - Media : in vitro half MS medium, pH 5,4 with MES-KOH, and 1% sucrose hygrometry : 100% Temperature : 22°C Light : long day – 16h of light, 8h of dark

treatment_protocol: Name:MgCl2 - control buffer - control buffer,mock inoculation:time 2hour . mock treatment with 10mM MgCl2

tag: ecotype

value: 14 day

treatment_protocol: Name:Salmonella typhimurium - biotic stress - pathogen infection,salmonella typhimurium:time 2hour . Salmonella typhimurium strain 14028s


title: Insulin resistant patient 8 - omental adipose tissue

description: Gene expression data from human adipose tissue obtained during gastric bypass surgery.

value: omental adipose


title: 89h 30C rep1

source_name: 89h 30C rep1


title: 13690761 - H2O2 vs SL2

hyb_protocol: SL2 Cy5 / H2O2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Rat 17, Day 5, 4 mm

source_name: Rat 17, Day 5, 4 mm


title: 13690758 - EC2 vs H2O2

hyb_protocol: H2O2 Cy5 / EC2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:Escherichia coli - biotic stress - pathogen infection,escherichia coli:time 2hour . Escherichia coli DH5A


title: 89h 28C rep2

description:
Pooled reference of coral larvae raised at three temperatures (28C, 30C, 31.5C) of 12, 24.5, 42.5, 89, and 131 hours after fertilization.
Coral larvae raised at 28C for 89 hours after fertilization hybridized against pooled reference.

source_name: 89h 28C rep2


title: 13690757 - H2O2 vs EC2

hyb_protocol: EC2 Cy5 / H2O2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 89h 28C rep1

source_name: 89h 28C rep1


title: 13690756 - EC1 vs H2O1

hyb_protocol: H2O1 Cy5 / EC1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 42.5h 31.5C rep1

description:
Pooled reference of coral larvae raised at three temperatures (28C, 30C, 31.5C) of 12, 24.5, 42.5, 89, and 131 hours after fertilization.
Coral larvae raised at 31.5C for 42.5 hours after fertilization hybridized against pooled reference.

value: raised at 31.5C

value: 42.5 hours after fertilization


title: Insulin sensitive patient 15 - subcutaneous adipose tissue

source_name: Obese female

value: subcutaneous adipose

value: insulin sensitive


title: 13688439 - PS2 vs H2O2

hyb_protocol: H2O2 Cy5 / PS2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:Pseudomonas syringea - biotic stress - pathogen infection,pseudomonas syringea:time 2hour .


title: 42.5h 31.5C rep2


title: 42.5h 30C rep2

description:
Pooled reference of coral larvae raised at three temperatures (28C, 30C, 31.5C) of 12, 24.5, 42.5, 89, and 131 hours after fertilization.
Coral larvae raised at 30C for 42.5 hours after fertilization hybridized against pooled reference.


title: Insulin resistant patient 6 - omental adipose tissue

value: female

value: insulin resistant


title: Insulin resistant patient 7 - omental adipose tissue


title: 13690755 - H2O1 vs EC1

hyb_protocol: EC1 Cy5 / H2O1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Insulin sensitive patient 13 - subcutaneous adipose tissue

source_name: Obese male

value: male


title: Insulin sensitive patient 12 - subcutaneous adipose tissue


title: Rat 14, Day 5, 4 mm

source_name: Rat 14, Day 5, 4 mm

value: Calvarial bone with healing tissue plug

value: 12 weeks


title: Rat 11, Day 5, 4 mm

source_name: Rat 11, Day 5, 4 mm


title: Insulin sensitive patient 14 - subcutaneous adipose tissue


title: Rat 10, Day 10, 4 mm

description: Gene expression 10 day post 4 mm defect created in calvarial bone

source_name: Rat 10, Day 10, 4 mm


title: 42.5h 30C rep1

value: pooled reference

value: raised at 30C


title: Rat 13, Day 5, 4 mm

source_name: Rat 13, Day 5, 4 mm

value: 4 mm


title: Rat 10, Day 5, 4 mm

source_name: Rat 10, Day 5, 4 mm


title: Rat 12, Day 5, 4 mm

source_name: Rat 12, Day 5, 4 mm


title: Rat 16, Day 5, 4 mm

source_name: Rat 16, Day 5, 4 mm


title: 13688437 - H2O2 vs PS2

hyb_protocol: PS2 Cy5 / H2O2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 42.5h 28C rep2

description:
Pooled reference of coral larvae raised at three temperatures (28C, 30C, 31.5C) of 12, 24.5, 42.5, 89, and 131 hours after fertilization.
Coral larvae raised at 28C for 42.5 hours after fertilization hybridized against pooled reference.

source_name: Common reference

value: coral larvae

value: raised at 28C


title: 13688434 - PS1 vs H2O1

hyb_protocol: H2O1 Cy5 / PS1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 24.5h 31.5C rep2

description:
Pooled reference of coral larvae raised at three temperatures (28C, 30C, 31.5C) of 12, 24.5, 42.5, 89, and 131 hours after fertilization.
Coral larvae raised at 31.5C for 24.5 hours after fertilization hybridized against pooled reference.

value: 24.5 hours after fertilization


title: 42.5h 28C rep1


title: 13688431 - H2O1 vs PS1

hyb_protocol: PS1 Cy5 / H2O1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: 14 day


title: Insulin sensitive patient 10 - subcutaneous adipose tissue


title: 24.5h 31.5C rep1


title: Insulin sensitive patient 11 - subcutaneous adipose tissue


title: 13688382 - SL1 vs H2O1

hyb_protocol: H2O1 Cy5 / SL1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688381 - H2O1 vs SL1

hyb_protocol: SL1 Cy5 / H2O1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Rat 22, Day 3, 8 mm

description: Gene expression 3 day post 8 mm defect created in calvarial bone

hyb_protocol: The 0.5µg of cRNA extracted from each of the CSD and non-CSD sampels were hybridized onto a microarray slide at 65⁰C for 17 h in a rotisserie chamber at 10 rpm the microarray slides were washed with wash buffer with 0.005% Triton X-102 for 1 min. at RT, followed by wash buffer 2 at 37⁰C for 1 min and drying in the dark for 5 min.

source_name: Rat 22, Day 3, 8 mm

value: 8 mm


title: Rat 21, Day 3, 8 mm

source_name: Rat 21, Day 3, 8 mm


title: 24.5h 30C rep1

description:
Pooled reference of coral larvae raised at three temperatures (28C, 30C, 31.5C) of 12, 24.5, 42.5, 89, and 131 hours after fertilization.
Coral larvae raised at 30C for 24.5 hours after fertilization hybridized against pooled reference.


title: Rat 20, Day 3, 8 mm

source_name: Rat 20, Day 3, 8 mm


title: 24.5h 30C rep2


title: Rat 19, Day 3, 8 mm

source_name: Rat 19, Day 3, 8 mm


title: Insulin sensitive patient 9 - subcutaneous adipose tissue

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133plus2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.


title: Insulin sensitive patient 8 - subcutaneous adipose tissue


title: Insulin sensitive patient 7 - subcutaneous adipose tissue


title: Insulin sensitive patient 6 - subcutaneous adipose tissue


title: 24.5h 28C rep2

description:
Pooled reference of coral larvae raised at three temperatures (28C, 30C, 31.5C) of 12, 24.5, 42.5, 89, and 131 hours after fertilization.
Coral larvae raised at 28C for 24.5 hours after fertilization hybridized against pooled reference.

hyb_protocol: Cy3 and Cy5 labeled cDNAs were mixed together in a hybridization buffer containing 0.25% SDS, 25mM HEPES, and 3x SSC. The hybridization mixtures were boiled for 2min at 99°C then allowed to cool at room temperature for 5 minutes. The cooled hybridization mixtures were pipetted under an mSeries Lifterslip (Erie Scientific), and hybridization took place in Corning hybridization chambers overnight at 63°C. Microarrays were washed twice in 0.6x SSC and 0.01% SDS followed by a rinse in 0.06x SSC and dried via centrifugation.


title: Rat 17, Day 3, 8 mm

source_name: Rat 17, Day 3, 8 mm


title: Interleukin_6_1

city: Vienna

first: Martin

last: Bilban

country: Austria

institute: Medical University of Vienna

description: Affymetrix

hyb_protocol: standard Affymetrix protocols

scan_protocol: standard Affymetrix protocols

data_processing: Bioconductor / RMA Signal Extraction

source_name: whole liver, treated with IL-6

label_protocol: Affymetrix WT labeling kit

growth_protocol: 10-week old male C57BL6 mice were fasted for 16 h overnight and then given either saline or IL-6 (100 ng/mouse) injections intraperitoneally for 1 h. Mice were euthanized using CO2, and the livers were collected and snap-frozen in liquid nitrogen and stored at -80 C until further use.

extract_protocol: Tissues were homogenized in STAT60 reagent (TelTest Inc) using a Tissue Lyser (Qiagen) at 30 Hz for 2 min. RNA was extracted according to the manufacturer’s protocol.

value: 10-week old

tag: sex

tag: strain

value: liver


title: Rat 16, Day 3, 8 mm

source_name: Rat 16, Day 3, 8 mm


title: Insulin resistant patient 15 - subcutaneous adipose tissue

source_name: Obese female

value: subcutaneous adipose

tag: metabolic status


title: Insulin resistant patient 14 - subcutaneous adipose tissue

source_name: Obese male


title: Rat 14, Day 3, 8 mm

source_name: Rat 14, Day 3, 8 mm


title: Insulin resistant patient 13 - subcutaneous adipose tissue


title: 24.5h 28C rep1


title: Saline_3

description: Affymetrix

source_name: whole liver, treated with saline (control)


title: Interleukin_6_3

description: Affymetrix


title: Rat 15, Day 3, 8 mm

source_name: Rat 15, Day 3, 8 mm


title: 12h 31.5C rep2

description:
Pooled reference of coral larvae raised at three temperatures (28C, 30C, 31.5C) of 12, 24.5, 42.5, 89, and 131 hours after fertilization.
Coral larvae raised at 31.5C for 12 hours after fertilization hybridized against pooled reference.

value: raised at 31.5C

value: 12 hours after fertilization


title: Interleukin_6_2

description: Affymetrix


title: 12h 31.5C rep1


title: Saline_1

description: Affymetrix


title: Insulin resistant patient 12 - subcutaneous adipose tissue

value: insulin resistant


title: Saline_2

description: Affymetrix

value: male


title: Rat 13, Day 3, 8 mm

source_name: Rat 13, Day 3, 8 mm

value: Calvarial bone with healing tissue plug


title: Rat 12, Day 3, 8 mm

source_name: Rat 12, Day 3, 8 mm

value: 12 weeks


title: Insulin resistant patient 11 - subcutaneous adipose tissue

value: female


title: Insulin resistant patient 10 - subcutaneous adipose tissue


title: 12h 30C rep2

description:
Pooled reference of coral larvae raised at three temperatures (28C, 30C, 31.5C) of 12, 24.5, 42.5, 89, and 131 hours after fertilization.
Coral larvae raised at 30C for 12 hours after fertilization hybridized against pooled reference.

value: pooled reference

source_name: 12h 30C rep2


title: 12h 28C rep1

description:
Pooled reference of coral larvae raised at three temperatures (28C, 30C, 31.5C) of 12, 24.5, 42.5, 89, and 131 hours after fertilization.
Coral larvae raised at 28C for 12 hours after fertilization hybridized against pooled reference.

source_name: 12h 28C rep1


title: 12h 30C rep1

source_name: Common reference

source_name: 12h 30C rep1


title: 12h 28C rep2

source_name: 12h 28C rep2


title: Rat 22, Day 3, 4 mm

description: Gene expression 3 day post 4 mm defect created in calvarial bone

source_name: Rat 22, Day 3, 4 mm

value: 4 mm


title: Resistant Time 0 vs Susceptible Time 1 FR29

city: St Lucia

first: Sean

last: McWilliam

state: Queensland

address: 306 Carmody Road

department: Agriculture and Food

institute: CSIRO

hyb_protocol: Fluorescently labelled cDNAs were mixed in 50 µL hybridisation mixture containing 50% deionised formamide, 4 × SSC, 0.5% SDS, 20 µg polydA and 10 µg bovine hyblock DNA (Applied Genetics Laboratories, Melbourne, Vic., Australia). The mixture was heated at 95°C for 5 min and incubated at 45°C for 45 min before application onto the microarray slides. Hybridisation was conducted in a humidified slide chamber (ArrayIt, Telechem International Inc.) at 45°C for 16 h. Slides were washed in 0.2 × SSC, 0.1% SDS for 15 min, 0.2 × SSC for 15 min, 0.06 × SSC for 5 min and spun at 500 rpm for 5 min at room temperature (Sigma 4K15)

scan_protocol: Scanned on an GenePix 4000A optical scanner Images were quantified using GenePixPro 5.1 image analysis software

data_processing: An ANOVA mixed-effect model was employed to normalize the data as previously described (Reverter et al. 2005).

organism: Ovis aries

source_name: Skin biopsy

label_protocol: 5µg of total RNA were primed with 5ug of Random Primerat 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 1mmol/L each dATP, dCTP, dGTP, with 0.6mmol/L µM aa-dUTP, 0.4mmol/L dCTP, purified and incubat for 1hr RT with Cy3 or Cy5 (post-Labelling Reactive Dye Pack, Amersham Biosciences)

extract_protocol: Total RNA was prepared from the skin samples using TRI reagent in accordance with the manufacturer’s recommendations (Sigma, St Louis, MO, USA).

tag: flock

value: Armidale

tag: genotype

value: RES

tag: time

value: T0 (Prior to commencement of treatment to induce fleece rot)

value: skin

value: SUS

value: T1 (2-3 days post commencment)


title: Susceptible Time 0 vs Susceptible Time 2 FR30

value: T2 (11 days post commencment)


title: Resistant Time 0 vs Susceptible Time 2 FR31


title: Resistant Time 0 vs Susceptible Time 0 FR28


title: Resistant Time 1 vs Susceptible Time 0 FR27


title: Resistant Time 1 vs Resistant Time 2 FR26


title: Rat 21, Day 3, 4 mm

source_name: Rat 21, Day 3, 4 mm


title: Insulin resistant patient 9 - subcutaneous adipose tissue

value: subcutaneous adipose


title: Rat 19, Day 3, 4 mm

source_name: Rat 19, Day 3, 4 mm


title: Resistant Time 1 vs Resistant Time 2 FR25


title: Insulin resistant patient 7 - subcutaneous adipose tissue


title: Insulin resistant patient 8 - subcutaneous adipose tissue


title: Rat 17, Day 3, 4 mm

source_name: Rat 17, Day 3, 4 mm


title: INTN7R

city: Galway

first: Michael

middle: Taylor

last: Cairns

address: University Road

department: MRI

country: Ireland

institute: NUI Galway

hyb_protocol: The two cDNA samples per slide (e.g. reference cDNA Cy3 labelled and experimental cDNA Cy5 labelled) were mixed and appropriate blockers were added (sheared salmon sperm genomic DNA, poly dA). The cDNA mixture was concentrated by precipitation with 3M sodium acetate and absolute ethanol at -20oC for 30 min. followed by centrifugation at 12500 x g for 30 min. Following removal of supernatant, the cDNA pellet was resuspended in 70 µl slide hyb buffer #1 (Ambion) and was then denatured at 95oC for 2 min. Slides were placed in Pre-Hyb solution (3xSSC, 0.1 % BSA, 0.1 % SDS) in 50 ml Sarsted tubes pre-warmed @ 42 °C and pre-hybed @ 42 °C for 30 min. Slides were rinsed 3 times in water and spun dry for 3 min @ 1600rpm. The hybridisation mixture was then added to the pre-hybed microarray slide using a coverslip (Erie Scientific). Hybridisation was performed in a Genetix hybidisation chamber (Genetix, UK) at 42 °C for 16 h. Following hybridisation the slides were washed (2 x 5 min. washes using 0.2XSSC/0.1% SDS and 2 x 5 min. washes using 0.2XSSC) using an Advawash automatic washing station (Advalytix).

scan_protocol: Microarray slides were scanned in two channels (543 & 633nm) at 5 µM resolution using a confocal laser scanner (ScanArray Express, Perkin Elmer)

data_processing:
TIFF image files were imported into Genepix Pro (version 5.0.1.24) (Axon instruments) for feature finding and alignment using a batch alignment process. Features were flagged as present, absent or bad by this software program and pixel intensities for feature and background were quantified. Output Genepix results (GPR) files were imported into the Genespring GX 7.3 software program (Agilent technologies). To account for dye swap, the signal channel and control channel measurements for appropriate samples were reversed. Values below 0.01 were set to 0.01. A Lowess curve was fit to the log-intensity versus log-ratio plot using 20.0% of the data to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.
VALUE column represents Log2 Ratio (CONTROL/REFERENCE) or Log2 Ratio (EXPERIMENTAL/REFERENCE).

organism:
Sparus aurata
Enteromyxum leei

source_name: INTESTINE, EXPOSED NOT INFECTED FISH 7  201g, 20cm  Tank 25-8

label_protocol: Ten micrograms of total RNA per individual fish (control/experimental) and ten micrograms of reference RNA per slide were indirectly labelled following an "in house" protocol with the red fluorescent dye ester cyanine 5 (Cy5) and green fluorescent dye ester Cyanine 3 (Cy3) both from GE Healthcare (UK). In brief, cDNA was synthesised using Superscript III MMLV reverse transcriptase (Invitrogen) incorporating aminoallyl dUTP (Sigma Aldrich). Synthesis took place at 42 oC for 2 hours. RNA was hydrolysed with 10M NaOH/0.5M EDTA for 15 minutes and the reaction was then neutralised with 1M HEPES. Reverse transcription reactions were purified using Microcon 30 columns (Millipore, UK) according to manufacturer~s instructions. Purified cDNAs were dried using a vacuum concentrator (Eppendorf) and were then resuspended in 0.1M sodium bicarbonate buffer. Cy dyes were resuspended in the same buffer and coupling to the Cy dye ester took place in the dark for 2 hours at room temperature. The removal of unincorporated dye was performed using the Illustra CyScribe GFX purification kit (GE Healthcare). Labelled cDNA samples were tested for successful dye incorporation using a Nanodrop spectrophotometer (Nanodrop technologies).

growth_protocol: Gilthead sea bream were checked for the absence of the parasite and acclimated to the experimental conditions two weeks before the beginning of the experiment. Day length followed natural changes and water was heated in order to keep temperature always above 18oC, the range was 18-23 oC. Water was 5 micrometer-filtered and UV irradiated, and salinity was 37.5~. Water flow was 10L/min and oxygen content of outlet water remained higher than 85%saturation. All fish were fed daily a commercial dry pellet diet at about 1% of body weight.

extract_protocol: Qiagen RNeasy Maxi combination protocol with Qiazol reagent

treatment_protocol: One fish group was exposed to E. leei-contaminated effluent (recipient group = R). R fish (n= 66, average weight = 134 g) were placed in two replicated 200L fibre-glass tanks which were set to receive exclusively the effluent water from another tank containing 24 infected (donors = D; average weight = 127.3 g; prevalence of infection = 54%) gilthead sea bream. The D to R fish ratio was 0.8. Other 66 naïve fish were allocated in two replicated tanks (control group = CTRL) under the same conditions, but without receiving contaminated effluent. Over the course of the study, day length followed natural changes and water was heated in order to keep temperature always above 18 oC, the range was 18-23 oC. Water was 5 micrometer-filtered and UV irradiated, and salinity was 37.5~. Water flow was 10L/min and oxygen content of outlet water remained higher than 85%saturation. All fish were fed daily a commercial dry pellet diet at about 1% of body weight. Disease signs and daily mortalities were recorded throughout the experiments. The parasitic status of dead fish was checked by microscopic examination of fresh intestinal scrapings. Fish were sampled after 113 days post exposure. Feeding was stopped one day prior to the sampling to ensure that the digestive tract was empty. Head kidney and posterior intestine were rapidly excised, frozen in liquid nitrogen, and stored at -80 oC until RNA extraction and analysis.

tag: pathogen

value: Enteromyxum leei

tag: pathogen exposure

value: EXPOSED, NON-INFECTED

tag: fish description

organism: Sparus aurata

source_name: PATHOGEN EXPOSURE REFERENCE  POOL OF ALL RNA  (EXCEPT HKI1,HKI2,HKI3,HKC7,HKN2, HKN3, HKN4,HKN5,HKN7,INTN1, INTN5, INTN8, HKC7,  HKC8, HKI1, HKI2, HKI3, HKI6, INTC3, INTC5, INTC6)

value: REFERENCE


title: Rat 18, Day 3, 4 mm

source_name: Rat 18, Day 3, 4 mm

tag: tissue

value: male


title: INTN7F

description: Head kidney and posterior intestine were rapidly excised, frozen in liquid nitrogen, and stored at -80 oC until RNA extraction and analysis.


title: Rat 14, Day 3, 4 mm

source_name: Rat 14, Day 3, 4 mm

value: Calvarial bone with healing tissue plug


title: Resistant Time 1 vs Susceptible Time 1 FR24


title: Rat 16, Day 3, 4 mm

source_name: Rat 16, Day 3, 4 mm

value: 12 weeks


title: Susceptible Time 0 vs Susceptible Time 1 FR23


title: INTN6R

source_name: INTESTINE, EXPOSED NOT INFECTED FISH 6  197g, 19cm  Tank 25-6


title: Rat 13, Day 3, 4 mm

source_name: Rat 13, Day 3, 4 mm


title: INTN6F


title: Resistant Time 0 vs Susceptible Time 2 FR21

value: Trangie


title: INTN5R

source_name: INTESTINE, EXPOSED NOT INFECTED FISH 5  188g, 19cm  Tank 23-10


title: Resistant Time 0 vs Susceptible Time 2 FR20


title: INTN5F


title: Rat 16, Day 1, 8 mm

description: Gene expression 1 day post 8 mm defect created in calvarial bone

source_name: Rat 16, Day 1, 8 mm

value: 8 mm


title: Rat 13, Day 1, 8 mm

source_name: Rat 13, Day 1, 8 mm


title: Rat 14, Day 1, 8 mm

source_name: Rat 14, Day 1, 8 mm


title: Resistant Time 0 vs Susceptible Time 0 FR22


title: Rat 12, Day 1, 8 mm

source_name: Rat 12, Day 1, 8 mm


title: Susceptible Time 1 vs Susceptible Time 2 FR18


title: INTN4R

source_name: INTESTINE, EXPOSED NOT INFECTED FISH 4  172g, 19.5cm  Tank 23-9


title: Resistant Time 0 vs Susceptible Time 2 FR19

source_name: Skin biopsy


title: Resistant Time 0 vs Susceptible Time 1 FR16


title: Susceptible Time 1 vs Susceptible Time 2 FR17


title: INTN4F


title: Rat 18, Day 1, 4 mm

description: Gene expression 1 day post 4 mm defect created in calvarial bone

data_processing: Data filter and statistical analysis were carried out using GeneSpring(r) 7.3. Local background was subtracted from individual spot intensity and genes that failed 'background check' in any of the experiments were eliminated from further analysis. Each chip was next subjected to intra-chip normalization (LOWESS). Differentially regulated genes were selected using Welch t-test analysis (P < 0.05).!Sample_data_row_count = 41090

source_name: Rat 18, Day 1, 4 mm

value: 4 mm


title: Rat 11, Day 1, 8 mm

source_name: Rat 11, Day 1, 8 mm


title: INTN3R

source_name: INTESTINE, EXPOSED NOT INFECTED FISH 3  195g, 19.5cm  Tank 23-6


title: Resistant Time 0 vs Susceptible Time 1 FR15


title: INTI6R

source_name: INTESTINE, INFECTED FISH 6  199g, 19cm  Tank 25-4

value: INFECTED


title: INTN3F

source_name: PATHOGEN EXPOSURE REFERENCE  POOL OF ALL RNA  (EXCEPT HKI1,HKI2,HKI3,HKC7,HKN2, HKN3, HKN4,HKN5,HKN7,INTN1, INTN5, INTN8, HKC7,  HKC8, HKI1, HKI2, HKI3, HKI6, INTC3, INTC5, INTC6)


title: INTI5R

source_name: INTESTINE, INFECTED FISH 5  203g, 19.25cm  Tank 25-2


title: Rat 17, Day 1, 4 mm

source_name: Rat 17, Day 1, 4 mm


title: INTI6F


title: Rat 13, Day 1, 4 mm

source_name: Rat 13, Day 1, 4 mm


title: Resistant Time 0 vs Susceptible Time 0 FR14

value: RES


title: No pregnancy vs calf delivery rep 3

description: Analysis  was performed by comparing the gene expression of embryo biopsies that resulted in calf delivery and embryos biopsies resulted in no pregnancy

hyb_protocol: Labelled cDNA hybridised using the ready made bovine cDNA array (BlueChip version 3, kindly provided by prof. Andre Sirard, (Laval university, Quebec, Canada).The array consisting of more than 2200 targets genes derived from suppression subtractive hybridization of bovine embryo and tissues

scan_protocol: Array scanning and image analysis was performed using Axon GenePix 4000B scanner and GenePix Pro analysis software (version 4.0) (Axon Instruments, Foster City, CA), respectively

data_processing: Data analysis was perfomed using R programme and  bioconductor packages. The values from each channel were log2 transformed and normalized using the LOESS algorithm to remove intensity dependent effects within the calculated values.  a mean log2-transformed value of (Cy5/Cy3) was calculated for the replicates to obtain one value per clone. Differentially expressed genes were obtained using linear models for microarray data (LIMMA)

source_name: Biopsied embryos consisting of 60-70% of inner cell mass and trophectoderm

label_protocol: 3 µg of amplified RNA from each embryo biopsies ( calf delivery and No pregnancy) was used as template in reverse transcription reactions incorporating amino-modified dUTPs into the cDNA using the cyscribe post-labelling kit (Amersham Biosciences, Freiburg, Germany). The Purified aminoallyl labelled cDNA samples from each group were differentially labelled indirectly using N-hydroxysuccinate-derived Cy3 and Cy5 dyes a. To avoid variation due to dye coupling, amplified RNA samples from the same group were labelled reversibly either with Cy3 or Cy5 for target and dye-swap hybridizations. The reaction was then purified with CyScribeTM GFXTM Purification kit (Amersham Biosciences, Freiburg, Germany)

growth_protocol: Embryos were developed in vio and flushed afer 7 days of development

extract_protocol: Total RNA was extracted from three independent pools consisting of 10 of embryo biopsies that resulted in calf delivery or no pregnancy using the PicoPureTM RNA isolation kit according to the manufacturer's instruction. Genomic DNA contamination was removed by performing on column DNA digestion using RNase-free DNase set (Qiagen, Hilden, Germany).

tag: embryo biopsy result

value: no pregnancy

tag: stage of embryo

value: blastocyst stage embryo

value: calf delivery


title: Resistant Time 0 vs Susceptible Time 0 FR13

value: SUS

value: T0 (Prior to commencement of treatment to induce fleece rot)

value: skin


title: Resistant Time 1 vs Susceptible Time 0 FR12

value: T1 (2-3 days post commencment)


title: INTI2R

source_name: INTESTINE, EXPOSED NOT INFECTED FISH 2  185g, 20cm  Tank 23-5

value: Enteromyxum leei

value: EXPOSED, NON-INFECTED


title: INTI5F

value: REFERENCE


title: INTI2F


title: No pregnancy vs calf delivery rep 1


title: No pregnancy vs calf delivery rep 2


title: Resistant Time 0 vs Resistant Time 0 FR10


title: INTI1R

source_name: INTESTINE, INFECTED FISH 1  174g, 19.25cm  Tank 23-2


title: Resistant Time 1 vs Susceptible Time 0 FR11


title: Calf delivery vs no pregnancy rep 3


title: Calf delivery vs no pregnancy rep 2


title: Resistant Time 1 vs Resistant Time 2 FR8

value: T2 (11 days post commencment)


title: Resistant Time 1 vs Resistant Time 2 FR7


title: Resistant Time 1 vs Susceptible Time 1 FR5


title: INTI1F


title: Resistant Time 1 vs Resistant Time 2 FR9


title: Resistant Time 1 vs Susceptible Time 1 FR6


title: Calf delivery vs no pregnancy rep 1


title: Resistant Time 0 vs Susceptible Time 0 FR1


title: Susceptible Time 0 vs Susceptible Time 1 FR3


title: Resistant Time 0 vs Susceptible Time 0 FR2


title: Susceptible Time 0 vs Susceptible Time 1 FR4


title: delta-arcS 3

city: Marburg an der Lahn

first: Jürgen

last: Lassak

state: Hessen

address: Karl-von-Frisch Strasse

department: Ecophysiology

institute: Max-Planck-Institute for Terrestrial Microbiology

hyb_protocol: Samples were loaded onto the arrays and hybridization was done over night (16 hours) at 45°C, using argon pressure to move the samples within the arrays.

scan_protocol: After the hybridization the chip is washed with the “febit GT-standard (external incubation)” hybridization profile and a standard detection using the appropriate filter set in  the Geniom® One Instrument.

data_processing: To assess the reproducibility of the biological replicates, the Pearson Correlation Coefficients were calculated. For the normalization procedure the “Quantile normalization” method was applied

organism: Shewanella oneidensis MR-1

source_name: total bacterial cells

label_protocol: febit uses the MICROBExpressTM kit from Ambion to remove 16S and 23S rRNA from RNA samples. For each array 3 μg of total RNA were purified according to the manufacturer’s instructions. Following, the MessageAmpTMII-Bacteria kit from Ambion was applied for labelling the mRNA. The kit provides a transcription of RNA in cDNA, following a transcription in cRNA while enrichment of all nucleic acid molecules is included. After labelling samples were dried in a speed-vac and fragmented with a fragmentation buffer. Finally, febit’s proprietary standard Longmer Hybridization Buffer (15 μl per array) was added.

growth_protocol: cells were grown aerobically in LB to logarithmic phase (OD600nm=0.6)

extract_protocol: Total RNA was extracted from S. oneidensis MR-1 cells using the hot phenol method. Residual chromosomal DNA was removed using Turbo DNA-freeTM (Applied Biosystems) following the manufacturer’s instructions.

treatment_protocol: no treatment

tag: cell type

value: logarithmic aerobic growing cells

value: delta-arcS


title: INTC8F

source_name: INTESTINE, CONTROL FISH 8  182g, 19.25cm  Tank 22-8

value: CONTROL


title: wild type 2

value: wild-type


title: delta-arcS 1


title: INTC7F

source_name: INTESTINE, CONTROL FISH 7  170g, 19.5cm  Tank 22-7


title: INTC2R

source_name: INTESTINE, CONTROL FISH 2  175g, 19cm  Tank 21-4


title: wild type 3


title: 13748253_c6b4

status: Public on Jul 30 2010

city: Vicksburg

first: Kurt

middle: A

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

description: Control, 6 month vs Reference

hyb_protocol: Products of the cDNA synthesis reactions were hybridized onto microarrays.  Two µL of blocking agent, locked nucleic acid (LNA) dT Blocker (Genisphere) was included in each hybridization.  RNA sample probes were hybridized at 55 ºC overnight (~16h) then washed for 20 min in 60 ºC 2x standard saline citrate (SSC) including 0.2% sodium dodecyl sulfate (SDS), 20 min in 2x SSC at room temperature, and 20 min in 0.2x SSC also at room temperature.  Slides were then spin dried for 2 min at 800 rcf.  Slides were subsequently hybridized to A647 and Cy3 labeled secondary hybridization probes in 100 µL hybridization buffer with 1 µL of Anti-Fade Reagent for 4h at 60ºC.  reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 30 seconds with Acetonitrile, and dried with Agilent Stabilization and Drying Solution.

scan_protocol: An Axon GenePix® 4000B Microarray Scanner (Molecular Devices Inc.) was used to scan microarray images at 5 μm resolution.  Grids were manually fit to microarray spots using GenePix Software (Molecular Devices).  Data for which the spot intensity was less than the background intensity plus 2x the background standard deviation for ≥1 signal channel were excluded from analysis.

data_processing: Data were LOWESS-normalized using Acuity Software (Molecular Devices) providing Cy3:A647 ratio values calculated using background-normalized median-signal intensities.  Statistical analyses were conducted using Bayesian Analysis of Gene Expression Levels (BAGEL) software version 3.62 (Townsend and Hartl, 2002).  Non-overlapping 97.5% confidence intervals (C.I.) among treatments were established a priori as statistically significant differences in expression.

organism: Pimephales promelas

source_name: Control, 6 month

label_protocol: Experimental samples were labeled with Cyanine-3 (Cy3) and the Reference fathead minnow brain samples were labeled with A647 dye.  Probes for microarray hybridizations were prepared from 500 ng total RNA / sample following the Genisphere®, Array 900™ Alexa Fluor 647 and Cy3 secondary hybridization labeling protocol (Genisphere, Hatfield, PA) according to the manufacturer’s instructions.

growth_protocol: Fathead minnow were maintained in 10 gallon aquaria including glass wool filtration systems, air stones, breeding substrates (3 PVC pipe cut in longitudinal section) where water changes were conducted every 28d.  Fish were fed frozen brine shrimp daily.

extract_protocol: RNA was prepared using the RNeasy mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: 2 male and 4 female adult fish were allocated to each experimental unit (10 gallon aquarium).  Eight experimental units were maintained as controls and another 8 were dosed with RDX that averaged 0.83mg/L over the course of the year long Assay.  5 male fish were collected from each the control and RDX-exposure condition at 1d, 1mo, 3mo, 6mo, 9mo, and 12 mo time periods.  Both liver and brain tissues were collected and immediately transferred to RNA Later (Ambion, Austin TX) and RNA fixed following manufacturer's recommendations.

value: brain

source_name: Reference Sample

value: Pooled brain tissue reference used for main experiment


title: INTC4R

source_name: INTESTINE, CONTROL FISH 4  158g, 19cm  Tank 21-7


title: INTC7R


title: delta-arcS 2


title: wild type 1


title: INTC8R


title: INTC2F


title: INTC1R

source_name: INTESTINE, CONTROL FISH 1  185g: 18.75cm  tank 21-2


title: INTC4F


title: root_highN_rep1

status: Public on Mar 24 2010

city: St. Louis

first: Dan

last: Ruzicka

state: MO

address: 975 N. Warson Rd.

institute: Donald Danforth Plant Science Center

hyb_protocol: Follow Affymetrix suggested standard method;  wash and stain protocol: mini_euk2v3-450, with fluidics station 450

scan_protocol: Genechipscanner 3000 with 7G upgrade, Software: GCOS v1.4

data_processing: Signal intenisty data were summarized with MAS5.0 algorithm, natural log transformed and processed with JMP genomics 3.0 software.  The probelist was filtered for expressed genes based on Affmetrix expression console sofware PMA designation.  ANOVA analysis was performed on all expressed genes to identify significantly differential probesets.

organism: Solanum lycopersicum

source_name: wild-type 76R

label_protocol: RNA samples were prepared for microarray analysis using the MessageAmp Premier RNA Amplification Kit (Ambion, Foster City CA) with 200 ng total RNA as input

growth_protocol: tomato plants transplanted into field soil collected at Durst Farm, Yolo County CA

extract_protocol: 53 hours post-treatment, patch roots were excised, washed, and frozen.  RNA was extracted using a modified Qiagen Rneasy extraction kit

treatment_protocol: The high N treatment was 65ug NH4+-N per gram of soil. Ammonium treatments were injected into discrete soil patches

value: root


title: root_highN_rep2


title: INTC1F


title: root_highN_rep3


title: root_lowN_rep2

treatment_protocol: The low N treatment was 6.5ug NH4+-N per gram of soil. Ammonium treatments were injected into discrete soil patches


title: root_lowN_rep1


title: root_lowN_rep3


title: root_water_control_rep3

treatment_protocol: water


title: root_water_control_rep1


title: HFF replicate 2

city: San Francisco

first: Sanjay

last: Chandriani

address: 513 Parnassus Avenue

institute: UCSF

description: All infections were performed with either BCBL-1-derived KSHV or rKSHV.219.

hyb_protocol: Samples were hybridized to the custom tiling microarrays according the manufacturer’s protocol (Agilent). Hybridized microarrays were washed according to the manufacturer’s protocol (Agilent),

scan_protocol: Microarrays were scanned on the GenePix 4000B scanner (Axon instruments) and all feature intensities collected using the GenePix Pro 6.0 software.

data_processing:
TIFF images of scanned slides were analyzed using Feature Extraction Software version 9.5.3 (Agilent) using a custom grid file (017577_D_F_20070822). LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.
Data of identical probes were averaged.
Data were subject to a further linear normalization step by the average of the features detecting the spike-in transcripts.  Only features that did not have any feature non-uniformity or population outlier flags contributed to the averages used for determining the normalization factor.
Remove any data that failed any of the following spot quality filters: 1. gIsFound = 1 AND rIsFound = 1; 2. no PopnOL or NonUnifOL detected; 3. g OR r IsWellAboveBackground.
Data of every probe was centered to the average of the corresponding control samples.
Data for host genes were removed and probes against viral sequences were ordered by position in genome.

source_name: HFF cells

label_protocol: The Quick Amp labeling kit (Agilent) was used according to the manufacturer’s protocol to generate Cy5/Cy3 labeled cRNA from 450ng of total RNA, which contains mix of spike-in transcripts A + B (Agilent).  An equal amount of the spike-in transcript mix are added to both Cy5 and Cy3 labeled samples.  The spike-in transcripts are detected by E1A probes on the array and are used for a linear normalization subsequent to the LOWESS normalization performed by the Agilent feature extraction software.

extract_protocol: HFF and SLK cell samples were harvested in RLT buffer and RNA was isolated using the RNeasy Mini kit according to the manufacturer’s protocol (Qiagen)

tag: infection

value: Mock

tag: virus

organism:
Homo sapiens
Human gammaherpesvirus 8
Human herpesvirus 8 strain rKSHV.219

source_name: Common reference:  mix of several different cell types (BJAB, BCBL, SLK, HFF, HUVEC, TIME), both infected and uninfected.

tag: common reference

value: mix of several different cell types (BJAB, BCBL, SLK, HFF, HUVEC, TIME), infected and uninfected


title: STE6

city: Birmingham

first: Molly

middle: Bray

last: Bray

state: AL

address: 720 20th Street S

department: Genetics

institute: Univ of Alabama at Birmingham

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
STE6

hyb_protocol: A total of 0.75 micrograms of biotin-labeled cRNA was applied to a BeadChip and allowed to hybridize overnight at 55°C for approximately 18 hours, followed by washing and staining with streptavidin-Cy3 prior to visualization.

scan_protocol: BeadChips were visualized using the BeadStation scanner, which uses a dual-laser confocal scanner with 0.8 µm resolution to determine fluorescence values for each bead on the chip.

data_processing: After scanning the probe arrays, the resulting images were analyzed using the BeadStudio software (V3, Illumina, Inc., San Diego, CA), which calculates the mean fluorescence signal across all replicates of each gene/transcript, along with a probability that the mean signal for each gene/transcript on the chip is greater than background (i.e., detection p-value).  Both non-normalized and normalized (qspline) data were generated for each tissue type.

source_name: Cardiomyocytes, stearic acid

label_protocol: Total RNA was converted to cDNA by reverse transcription using Superscript II reverse transcriptase and T7-(dT)24 primers, followed by second-strand synthesis to generate double-stranded cDNA.

extract_protocol: RNA was extracted from all tissues using a standard protocol and Tri-reagent.

treatment_protocol: Isolated, cultured adult rat cardiomyocytes were challenged with 1% BSA (control) or 0.4 mM octanoate, palmitate, stearate, oleate, or linoleate conjugated to 1% BSA for 24 h, after which RNA was isolated and utilized for gene expression analysis.

value: Wistar

tag: gender

value: male

tag: developmental stage

value: adult

value: wildtype

value: cardiomyocytes

tag: treatment

value: exposed to 1%BSA + stearic acid


title: HFF stably infected with rKSHV.219 replicate 2

organism:
Homo sapiens
Human herpesvirus 8 strain rKSHV.219

source_name: HFF cells stably infected with rKSHV.219

value: Stable, latent

value: rKSHV.219 (P-type strain)


title: STE7

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
STE7

tag: strain


title: HFF replicate 1


title: HFF stably infected with rKSHV.219 replicate 1


title: STE4

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
STE4


title: root_water_control_rep2


title: STE5

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
STE5


title: PAL8

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
PAL8

source_name: Cardiomyocytes, palmitic acid

value: exposed to 1%BSA + palmitic acid


title: SLK replicate 2

source_name: SLK cells


title: SLK stably infected with rKSHV.219 replicate 1

source_name: SLK cells stably infected with rKSHV.219


title: SLK stably infected with rKSHV.219 replicate 2


title: STE8

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
STE8


title: SLK replicate 1


title: STE1

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
STE1


title: BCBL-1 replicate 2

organism:
Homo sapiens
Human gammaherpesvirus 8

source_name: BCBL-1 cells stably infected with KSHV

extract_protocol: BJAB and BCBL-1 samples were harvested in RNA-Bee solution and RNA was isolated according to the manufacturer’s protocol (Tel-Test, Inc.). BJAB and BCBL-1 RNA’s that were subject to microarray analysis were then re-purified using the RNeasy Mini kit according to the manufacturer’s protocol (Qiagen)

value: KSHV (P-type strain)


title: STE2

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
STE2


title: BJAB replicate 2

organism: Homo sapiens

source_name: BJAB cells


title: BCBL-1 replicate 1


title: BJAB replicate 1


title: STE3

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
STE3


title: PAL6

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
PAL6


title: PAL7

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
PAL7


title: PAL1

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
PAL1


title: OLE6

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
OLE6

source_name: Cardiomyocytes, oleic acid

value: exposed to 1%BSA + oleic acid


title: PAL2

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
PAL2


title: OLE7

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
OLE7


title: PAL5

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
PAL5


title: PAL4

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
PAL4


title: OLE5

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
OLE5


title: OLE8

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
OLE8


title: OLE1

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
OLE1


title: OLE2

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
OLE2


title: OLE4

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
OLE4


title: PAL3

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
PAL3