title: Prunus mume_Ruantiaohongmei_fruits_rep1

description:
Gene expression in fruits of Prunus mume
Array 1-3 R2

source_name: Prunus mume_Ruantiaohongmei_fruits_rep1

value: mixed stages


title: ES__CSC14_passage29_Female____197.1296.1.2

status: Public on May 14 2012

type: genomic

city: La Jolla

first: Kristopher

middle: L.

last: Nazor

state: CA

address: 10550 North Torrey Pines Road

department: Regenerative Medicine

country: USA

institute: The Scripps Research Institute

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using HiScan using standard recommended Illumina scanner setting

data_processing: Genome Studio software v2010.3

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

tag: loring pipeline sample id

tag: loring pipeline stem cell matrix version

value: stem cell matrix version 342

tag: cell type

value: embryonic stem cell, undifferentiated

tag: cell line

tag: passage number

tag: gender

value: Female


title: 3hr_C1

status: Public on May 13 2012

type: RNA

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description: Control mice 3hrs after naphthalene injury.

hyb_protocol: Based on Affymetrix protocols.

scan_protocol: Based on Affymetrix protocols.

data_processing: RMA signal intensity calculation using GeneSpring GX.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Terminal bronchiolar epithelial cells, control mice, 3hr

label_protocol: Based on Affymetrix protocols.

extract_protocol: Guanidinium thiocyanate (GITC).

tag: strain

value: mixture of FVB/N and C57BL/6

tag: genotype

value: control

tag: tissue

value: lung

value: terminal bronchiolar epithelial cells

tag: treatment

value: naphthalene injury

tag: treatment duration


title: 3hr_C2


title: hMSCs Donor 097 Day 0

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

country: Japan

institute: National Center for Child Health and Development

description: Gene expression in human synovial MSCs

hyb_protocol: Biotinylated cRNA was hybridized with a probe array for 16h at 45C, and the hybridized biotinylated cRNA was stained with streptavidin-PE.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner (Palo Alto).

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

source_name: Human synovial MSCs in a monolayer culture

label_protocol: standard Affymetrix protocol

growth_protocol: Human synovial MSCs were plated at 100cells/cm2 in 150 cm2 culture dish in complete culture medium (CCM: αMEM containing 10% fetal bovine serum , 100 units/ml penicillin , 100 μg/ml streptomycin , and 250 ng/ml amphotericin B), and incubated at 37°C with 5% humidified CO2 for 14days. 2.5×105 human synovial MSCs suspended in 35µl of CCM were aggregated using the hanging drop technique and incubated at 37°C with 5% humidified CO2 for 3days.

extract_protocol: QIAizol (Qiagen) and RNeasy mini kit (Qiagen) was used according to the manufacturer's instructions.

treatment_protocol: Human synovial MSCs cultured in monolayer culture and human synovial MSC-aggregates were homoginized in QIAzol.

value: synovial MSCs

value: MSCs in a monolayer culture

tag: donor

value: Donor 097


title: 72hr_C2

description: Control mice 72hrs after naphthalene injury.

source_name: Terminal bronchiolar epithelial cells, control mice, 72hr


title: 0hr_C3

description: Control mice 0hr after naphthalene injury.

source_name: Terminal bronchiolar epithelial cells, control mice, 0hr


title: Phenobarbital_3days_Rep5

status: Public on May 12 2012

city: Wooster

first: Reed

last: Johnson

address: 1680 Madison Ave.

department: Entomology

institute: The Ohio State University

hyb_protocol: Microarray slides were prepared for prehybridization by passing them array-side down twice over steam from a beaker of boiling water and dried briefly on a warm adjustable-temperature block. The oligonucleotides were cross-linked to the array in a Stratalinker (Stratagene) set at 6000 ujoules (x 1000). Excess oligonucleotides were removed by washing the microarray slide quickly in 0.2% SDS and agitating vigorously for 2 minutes, then washing 2X in molecular biology-grade water (Eppendorf). Slides were transferred to Coplin jars containing prehybridization buffer (20% formamide, 5X Denhardt’s, 6X SSC, 0.1%SDS, 25ug/mL tRNA) in a 42°C waterbath for 1 hour with occasional shaking. Slides were washed in molecular biology-grade water 5X, followed by one wash in isopropanol, and spun dry in a ChipMate (Tomy). Slides were placed in Corning hybridization chambers with a LifterSlip (Eerie Scientific) positioned over the area of the spotted oligonucleotides. For each pair of Cy5/Cy3 probes to be hybridized together, one dried probe was suspended in 15 uL nuclease-free water and then transferred to the second probe for suspension. The probes were heated to 95°C for 2-3 min, chilled on ice for 5 min and kept at room temperature. To each labeled probe pair, 15 uL of pre-warmed (50°C) 2X hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) was added and the entire volume pipetted under the Lifterslip edge. A drop of hybridization solution was placed in each chamber well for humidity. Chambers were incubated in a light-proof hybridization oven at 42°C overnight. Microarray slides were transferred to a Coplin jar containing Wash 1 (1X SSC, 0.2% SDS) at 42°C for 8 minutes with agitation. The slides were agitated in Wash 2 (0.1X SSC, 0.2% SDS) for 8 min at room temperature followed by two successive washes in Wash 3 (0.1X SSC) for 8 min at room temperature. The slides were spun dry and stored in a dark container until scanning.

scan_protocol: Microarray slides were scanned on an Axon 4000B Scanner using GenePix v6.0 software. Arrays were scanned using 33% power and manually-adjusted PMT values to achieve an overall count ratio of 1.0 from both channels.

data_processing: LIMMA/Bioconductor/R was used for normalization of the spot intensity data.  NORMEXP was used for background correction, with an offset of 50, followed by a LOESS normalization within arrays.  Finally, SCALE was used to normalize between arrays.

organism: Apis mellifera

label_protocol: For each reverse transcription reaction, 15 ug of total RNA was suspended in 18.5 uL nuclease-free water containing 2 ug oligo-dT16 primer (Operon) and denatured for 10 min at 70°C. A cocktail containing 6.0 uL 5X first strand buffer (Invitrogen), 3.0 uL 0.1M DTT, 0.6 uL 50X amino-allyl dNTP mix (25mM each dATP, dCTP, dGTP, 15mM dTTP, 10mM amino-allyl-dUTP (Sigma)), 2.0 uL Superscript III (Invitrogen, 200U/uL), and 0.5 uL RNase inhibitor (Fisher, 40U/uL) was added to each reaction and incubated overnight at 46°C in a hybridization oven. RNA was hydrolyzed by adding 10 uL 1M NaOH and 10 uL 0.5M EDTA with a 15 min incubation at 65°C followed by neutralized with 10 uL 1M HCl. The 1st cDNA was purified using the Qiagen Qiaquick PCR purification kit, following manufacturer’s instructions with substitutions for the wash buffer (phosphate wash buffer: 5mM KPO4, pH 8.0, 80% EtOH) and elution buffer (phosphate elution buffer: 4mM KPO4, pH8.5). 1st cDNA was eluted from the column twice using 30 ul phosphate elution buffer and dried completely in a SpeedVac. Single-use CyDye label (Cy5, GE Healthcare) was suspended in 9 uL fresh 0.1M Na2CO3 pH 9.0 and transferred to the cDNA pellet for suspension. Labeling reactions were incubated 1 hour in complete darkness. The pH of the labeling reaction was adjusted with 35 uL 3M NaOAc pH5.2. The labeled-cDNA was purified using the Qiagen Qiaquick PCR purification kit following manufacturer’s instructions and eluted twice using 40ul elution buffer. The entire sample was analyzed on a spectrophotometer at 260 nm, 320 nm, 550 nm, 650 nm, and 750 nm to calculate pmoles of cDNA synthesized and label incorporation. Labeled probes were then dried to completion in a SpeedVac and stored at -20°C until hybridization.

extract_protocol: Total RNA was isolated from 10 whole workers by first grinding in liquid nitrogen with a mortar and pestle, then extracting with Trizol.

treatment_protocol: Newly emerged adult worker bees were isolated in groups of approximately 100 and fed phenobarbital candy (2.5 ug/g) for 3 days and maintained in a 34 degree dark incubator.

tag: caste

value: Worker

tag: age

value: 3 days

treatment_protocol: Newly emerged adult worker bees were isolated in groups of approximately 100 and fed plain candy for 3 days and maintained in a 34 degree dark incubator.


title: hMSC-aggregates Donor 097 Day 3

description: Gene expression in human synovial MSC-aggregates

source_name: Human synovial MSC-aggregates cultured in hanging drop culture for 3 days

value: synovial MSC-aggregates


title: ES__CM6_passage19_Female____244.622.1.1


title: Phenobarbital_3days_Rep4


title: ES__WA09_passage39_Female____87.1429.1.1


title: Phenobarbital_3days_Rep2

treatment_protocol: Newly emerged adult worker bees were isolated in groups of approximately 100 and fed sugar candy for 3 days and maintained in a 34 degree dark incubator.


title: ES__FES22_passage44_Male____23.93.1.1

value: Male


title: 0hr_C2


title: hMSCs Donor 079 Day 0

description: Gene expression in human synovial MSCs

value: Donor 079


title: 0hr_C1


title: hMSCs Donor 083 Day 0

description: Gene expression in human synovial MSCs

value: Donor 083


title: 3hr_C3


title: ES__MEL4_passage35_Female____127.378.3.1

value: stem cell matrix version 342


title: Phenobarbital_3days_Rep1

treatment_protocol: Newly emerged adult worker bees were isolated in groups of approximately 100 and fed phenobarbital-treated candy (2.5 ug/g) for 3 days and maintained in a 34 degree dark incubator.


title: hMSC-aggregates Donor 079 Day 3

value: MSC-aggregates cultured in hanging drop culture for 3 days


title: ES__WA09_passage39_Female____87.1429.2.1

value: embryonic stem cell, undifferentiated

value: Female


title: Phenobarbital_3days_Rep3


title: Muscle_AQM_9-14d_loaded_UU58

city: Uppsala

first: Monica

last: Llano-Diez

address: Akademiska sjukhuset, Ing.85, 3tr

department: Neuroscience

country: Sweden

institute: Uppsala university

description:
Experimental rat ICU model. AQM.
Loaded leg.
UU58_100909

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Rat Gene 1.0 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Analyses of the gene expression data were carried out in the freely available statistical computing language R using packages available from the Bioconductor project. The raw data were normalized using the robust multi-array average (RMA), background-adjusted, and log-transformed summarized values as first suggested by Li and Wong in 2001.

organism: Rattus norvegicus

source_name: gastrocnemius muscle, treated with non-depolarizing NMBA and mechanically ventilated, 9d to 14d group, loaded leg

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 g total RNA (Expression Analysis Technical Manual, 2007, Affymetrix).

extract_protocol: Total RNA was extracted according to the standard Affymetrix protocol including Trizol extraction and RNeasy column cleanup.

treatment_protocol:
Briefly, the following surgery and instrumentation was completed with sterile technique: 1) Precordial silver wire electrocardiogram (ECG) electrodes were implanted subcutaneously. 2) An aortic catheter (28-gauge Teflon) was inserted via the left carotid artery to record arterial blood pressure. 3) A 0.9-mm Renathane catheter was threaded into the left jugular vein to administer parental solutions. 4) Three subcutaneous EEG needle electrodes were placed into the skull above the right and left temporal lobes, and a third reference electrode was placed in the neck region. 5) Temperature was measured by a vaginal thermistor and servo-regulated at 37°C. 6) A silicone cannula was inserted in the urethra to continuously record urine output.
During surgery or any possible irritating manipulation, the anesthetic isoflurane level was at >1.5%, which maintained the following states: 1) the electroencephalogram (EEG) was synchronized and dominated by high-voltage slow-wave activity; 2) mean arterial pressure was 100 mmHg, the heart rate, 420 beats/min, and 3) there were no evident EEG, blood pressure or heart rate responses to surgical manipulation. Isoflurane was delivered into the inspiratory gas stream by a precision mass-flow controller. After the initial surgery, Isoflurane was gradually lowered (over 1-2 days) and maintained at <0.5% during the remaining experimental period. Rats were ventilated through a per os coaxial tracheal cannula at 72 breaths/min with an inspiratory and expiratory ratio of 1:2 and a minute volume of 180–200 ml and gas concentrations of 50% O2, 47% N2, and 3% CO2, delivered by a precision volumetric respirator. Intermittent respiratory hyperinflations (6 per hour at 15 cmH2O), positive end-expiratory pressure (1.5 cmH2O), and expiratory CO2 monitoring were continuous. Neuromuscular blockade (NMBA) was induced on the first day (100 µg iv. alpha-cobrotoxin) and maintained by continuous infusion (250 µg/day, iv). Mechanical ventilation was initiated immediately after the NMBA induction. The left leg of the animal was activated for 6 hours at the shortest duration and 12 hours per day at durations 12 hours and longer throughout the experiment, using a mechanical lever arm that produced a continuous passive maximal ankle joint flexions-extensions at a speed of 13.3 cycles per minute. Gastrocnemius muscles were dissected from the loaded left leg and the unloaded right leg immediately after euthanasia.

value: Sprague-Dawley

value: female

value: gactrocnemius muscle

value: non-depolarizing neuromuscular blocking agent (NMBA)

value: passive loading

tag: time

value: 9-14 days


title: Muscle_AQM_9-14d_loaded_UU60

description:
Experimental rat ICU model. AQM.
Loaded leg.
UU60_100909


title: Muscle_AQM_5-8d_loaded_UU56

description:
Experimental rat ICU model. AQM.
Loaded leg.
UU56_100909

source_name: gastrocnemius muscle, treated with non-depolarizing NMBA and mechanically ventilated, 5d to 8d group, loaded leg

value: 5-8 days


title: Muscle_AQM_5-8d_loaded_UU54

description:
Experimental rat ICU model. AQM.
Loaded leg.
UU54_100909


title: Muscle_AQM_5-8d_loaded_UU44

description:
Experimental rat ICU model. AQM.
Loaded leg.
UU44_100216


title: hMSC-aggregates Donor 083 Day 3


title: Muscle_AQM_9-14d_loaded_UU46

description:
Experimental rat ICU model. AQM.
Loaded leg.
UU46_100216


title: Muscle_AQM_9-14d_loaded_UU52

description:
Experimental rat ICU model. AQM.
Loaded leg.
UU52_100216


title: Muscle_AQM_9-14d_loaded_UU48

description:
Experimental rat ICU model. AQM.
Loaded leg.
UU48_100216


title: Muscle_AQM_9-14d_loaded_UU50

description:
Experimental rat ICU model. AQM.
Loaded leg.
UU50_100216


title: Muscle_AQM_5-8d_loaded_UU42

description:
Experimental rat ICU model. AQM.
Loaded leg.
UU42_100216


title: Muscle_AQM_6h-4d_loaded_UU38

description:
Experimental rat ICU model. AQM.
Loaded leg.
UU38_100216

source_name: gastrocnemius muscle, treated with non-depolarizing NMBA and mechanically ventilated, 6h to 4d group, loaded leg

value: 6hr-4 days


title: Muscle_AQM_6h-4d_loaded_UU36

description:
Experimental rat ICU model. AQM.
Loaded leg.
UU36_100216


title: SKOV3.ip1-S116A_rep3

city: Houston

first: Xuemei

last: Xie

state: Texas

address: 1515 Holcombe Blvd

department: Breast Medical Oncology

institute: The University of Texas MD Anderson Cancer Center

hyb_protocol: The fragmented cRNA was used for hybridization to the Affymetrix HGU133 chip overnight at 45°C with rotation.

scan_protocol: Using a GeneArray Scanner (Hewlett-Pacrkard, Palo Alto, CA, USA).

data_processing: The data pre-processing and statistical analysis were performed in R [version 2.12.2 (2011-02-25)]. As part of the standard quality control(QC) analysis, the data were first quantified using the MAS5 algorithm. The Robust Multiarray Analysis (RMA) algorithm that borrows strength across arrays was used to normalize and quantify the data.

label: Biotin

label_protocol: The double-stranded cDNA was transcribed into cRNA in the presence of biotin-labeled ribonucleotides using the ENZO BioArray HighYield RNA Transcript Labeling Kit (Affymetrix) as described by the manufacturer.

growth_protocol: SKOV3.ip1 human ovarian cancer cells were cultured in DMEM/F12 medium supplemented with 10% FBS and 100 units/mL penicillin-streptomycin.

extract_protocol: Total RNA was extracted and purified using RNeasy mini kit (Qiagen, Inc.) according to the manufacturer’s instructions.

treatment_protocol: SKOV3.ip1 cells were stably transfected with a vector containing nonphosphorylatable PEA-15 (SKOV3.ip1-S116A; Ser116 of PEA-15 substituted with alanine) or a vector containing phosphomimetic PEA-15 (SKOV3.ip1-S116D; Ser16 of PEA-15 substituted with aspartic acid).

tag: genotype/variation

value: ovarian cancer cells

tag: stably transfected with

value: vector containing nonphosphorylatable PEA-15 (Ser116 substituted with alanine)


title: SKOV3.ip1-S116D_rep3

source_name: SKOV3.ip1-S116D_phosphomimetic PEA-15

value: vector containing phosphomimetic PEA-15 (Ser104 and Ser116 substituted with aspartic acid)


title: SKOV3.ip1-S116A_rep2


title: SKOV3.ip1-S116D_rep1


title: Muscle_AQM_6h-4d_loaded_UU28

description:
Experimental rat ICU model. AQM.
Loaded leg.
UU28_100217


title: Muscle_AQM_6h-4d_loaded_UU34

description:
Experimental rat ICU model. AQM.
Loaded leg.
UU34_100216


title: Muscle_AQM_6h-4d_loaded_UU32

description:
Experimental rat ICU model. AQM.
Loaded leg.
UU32_100216


title: SKOV3.ip1-S116D_rep2


title: Muscle_AQM_6h-4d_loaded_UU24

description:
Experimental rat ICU model. AQM.
Loaded leg.
UU24_100217


title: Muscle_AQM_6h-4d_loaded_UU30

description:
Experimental rat ICU model. AQM.
Loaded leg.
UU30_100217


title: SKOV3.ip1-S116A_rep1


title: Muscle_AQM_6h-4d_loaded_UU20

description:
Experimental rat ICU model. AQM.
Loaded leg.
UU20_100217


title: Sn leaf_7_1_C_July18_Cy5

city: New Haven

first: shenghua

last: yuan

state: CT

address: 165 Prospect St.

department: Ecology and Evolutionary Biology

institute: Yale University

description:
MSMI_13470398.gpr
Sample 98

hyb_protocol: The labeled cDNA was hybridized overnight at 50C to cDNA microarrays, followed by a second hybridization of the dye molecules with the specific primers on the cDNAs. Advalytix SlideBooster hybridization station.

scan_protocol: Axon GenPix 4100 scanner at two wavelength, 652 and 532 nm, using GenePix software (V. 5) producing two-channel images.

data_processing: We loaded the GAL file for the SAM 1.2 maize microarray, aligned the spots using a template grid. Obvious anomalies in the grids were flagged as bad spots and then fluorescence intensity was assessed with GenePix. These results were queried for quality control. Features with signal to noise ratios less than ten were flagged bad and excluded from further analysis. The intersity values on each array were then normalized with the ratip of medians protocol according to the use manual. Prior to the high-throughput regression analysis, the fluorescence intensity were normalized by conducting mixed model ANOVAs with array and dye included as fixed effects: yij=X+Ai+Dj+(AXD)ij+Eij, where yij is the fluorescence intensity on the ith array and labeled with the jth dye, X is the mean, Ai is the effect of the ith array (i = 1-49 for Andropogon gerardii; i=1-50 for Sorghastrum nutans), Dj is the effect of the jth dye, (AXD)ij is the array-dye interaction and Eij is the stochastic error.

organism: Sorghastrum nutans

label_protocol: Genisphere kit (Array 900) Expression Array Detection kit

growth_protocol: Individuals of Andropogon gerardii and Sorghastrum nutans were sampled from the natural population in field from RaMP of Konza prairie in 2006

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions and purified with RNAeasy kit (Qiagen)

treatment_protocol: The RaMP facility can manipuate precipitation (ambient precipitation and altered precipitation) and temperature (ambient temperature and warming).

value: leaf

tag: precipitation

value: ambient

tag: temperature

value: control


title: Muscle_AQM_6h-4d_loaded_UU22

description:
Experimental rat ICU model. AQM.
Loaded leg.
UU22_100217


title: Sn leaf_11_2_D_July18_Cy5

description:
MSMI_13470399.gpr
Sample 99

value: varied


title: Sn leaf_11_1_C_July18_Cy3

description:
MSMI_13470399.gpr
Sample 99

value: warm


title: Sn leaf_2_4_B_June1_Cy5

description:
MSMI_13470397.gpr
Sample 97


title: Sn leaf_7_4_B_July18_Cy3

description:
MSMI_13470398.gpr
Sample 98


title: Sn leaf_2_1_C_July24_Cy5

description:
MSMI_13470396.gpr
Sample 96


title: Muscle_AQM_9-14d_unloaded_UU59

description:
Experimental rat ICU model. AQM.
Unloaded leg.
UU59_100909

source_name: gastrocnemius muscle, treated with non-depolarizing NMBA and mechanically ventilated, 9d to 14d group, unloaded leg

value: no loading


title: Sn leaf_2_1_C_June1_Cy3

description:
MSMI_13470397.gpr
Sample 97


title: Muscle_AQM_6h-4d_loaded_UU14

description:
Experimental rat ICU model. AQM.
Loaded leg.
UU14_100202

value: Sprague-Dawley


title: Muscle_AQM_6h-4d_loaded_U12

description:
Experimental rat ICU model. AQM.
Loaded leg.
U12_100127

value: female


title: Sn leaf_12_2_D_July24_Cy5

description:
MSMI_13465952.gpr
Sample 95


title: Sn leaf_12_2_D_July24_Cy3

description:
MSMI_13465952.gpr
Sample 95


title: Muscle_AQM_6h-4d_loaded_UU18

description:
Experimental rat ICU model. AQM.
Loaded leg.
UU18_100217

value: gactrocnemius muscle


title: Muscle_AQM_9-14d_unloaded_UU57

description:
Experimental rat ICU model. AQM.
Unloaded leg.
UU57_100909

value: non-depolarizing neuromuscular blocking agent (NMBA)


title: LCM SS14-3 chief

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42335.gif

hyb_protocol: not provided

scan_protocol: 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: pooled aged matched control samples 2x amplified

label_protocol: not provided

extract_protocol: not provided

tag: reference

source_name: SS14-3 chief

tag: infection

value: infected

tag: cell type

value: chief


title: Muscle_AQM_9-14d_unloaded_UU49

description:
Experimental rat ICU model. AQM.
Unloaded leg.
UU49_100216

tag: gender

value: 9-14 days


title: Muscle_AQM_9-14d_unloaded_UU45

description:
Experimental rat ICU model. AQM.
Unloaded leg.
UU45_100216

tag: strain


title: Sn leaf_7_4_D_Aug22_Cy3

description:
MSMI_13497102.gpr
Sample 90


title: Sn leaf_3_1_A_Aug22_Cy5_2

description:
MSMI_13465950.gpr
Sample 93


title: Muscle_AQM_5-8d_unloaded_UU41

description:
Experimental rat ICU model. AQM.
Unloaded leg.
UU41_100216

source_name: gastrocnemius muscle, treated with non-depolarizing NMBA and mechanically ventilated, 5d to 8d group, unloaded leg

value: 5-8 days


title: Sn leaf_3_2_D_Aug22_Cy3_2

description:
MSMI_13465950.gpr
Sample 93


title: Muscle_AQM_5-8d_unloaded_UU53

description:
Experimental rat ICU model. AQM.
Unloaded leg.
UU53_100909


title: Muscle_AQM_5-8d_unloaded_UU55

description:
Experimental rat ICU model. AQM.
Unloaded leg.
UU55_100909


title: Muscle_AQM_9-14d_unloaded_UU47

description:
Experimental rat ICU model. AQM.
Unloaded leg.
UU47_100216


title: Sn leaf_10_1_C_June1_Cy5

description:
MSMI_13497104.gpr
Sample 92


title: Sn leaf_5_1_C_Aug22_Cy3_2

description:
MSMI_13497103.gpr
Sample 91


title: Sn leaf_7_1_C_June1_Cy5

description:
MSMI_13497101.gpr
Sample 89


title: Muscle_AQM_6h-4d_unloaded_UU37

description:
Experimental rat ICU model. AQM.
Unloaded leg.
UU37_100216

source_name: gastrocnemius muscle, treated with non-depolarizing NMBA and mechanically ventilated, 6h to 4d group, unloaded leg

value: 6hr-4 days


title: Muscle_AQM_5-8d_unloaded_UU43

description:
Experimental rat ICU model. AQM.
Unloaded leg.
UU43_100216


title: Muscle_AQM_6h-4d_unloaded_UU31

description:
Experimental rat ICU model. AQM.
Unloaded leg.
UU31_100216


title: Sn leaf_5_4_D_Aug22_Cy5

description:
MSMI_13497103.gpr
Sample 91


title: Sn leaf_12_4_D_Aug22_Cy3

description:
MSMI_13491145.gpr
Sample 88


title: Muscle_AQM_6h-4d_unloaded_UU29

description:
Experimental rat ICU model. AQM.
Unloaded leg.
UU29_100217


title: Muscle_AQM_6h-4d_unloaded_UU33

description:
Experimental rat ICU model. AQM.
Unloaded leg.
UU33_100216


title: Sn leaf_7_1_C_Aug22_Cy5

description:
MSMI_13497102.gpr
Sample 90


title: Sn leaf_7_4_D_June1_Cy3

description:
MSMI_13497101.gpr
Sample 89


title: Muscle_AQM_6h-4d_unloaded_UU35

description:
Experimental rat ICU model. AQM.
Unloaded leg.
UU35_100216


title: Muscle_AQM_6h-4d_unloaded_UU27

description:
Experimental rat ICU model. AQM.
Unloaded leg.
UU27_100217


title: Muscle_AQM_6h-4d_unloaded_UU23

description:
Experimental rat ICU model. AQM.
Unloaded leg.
UU23_100217


title: Sn leaf_9_4_A_Aug22_Cy5

description:
MSMI_13491143.gpr
Sample 86


title: Sn leaf_12_1_C_July18_Cy3

description:
MSMI_13491144.gpr
Sample 87


title: Sn leaf_6_4_B_Aug22_Cy5

description:
MSMI_13491141.gpr
Sample 85


title: Sn leaf_12_1_D_July18_Cy5

description:
MSMI_13491144.gpr
Sample 87


title: Sn leaf_2_1_C_Aug22_Cy5_2

description:
MSMI_13491145.gpr
Sample 88


title: Sn leaf_9_1_C_Aug22_Cy3

description:
MSMI_13491143.gpr
Sample 86


title: Muscle_AQM_6h-4d_unloaded_UU21

description:
Experimental rat ICU model. AQM.
Unloaded leg.
UU21_100217


title: Sn leaf_15_2_D_Aug22_Cy5

description:
MSMI_13490796.gpr
Sample 83


title: Sn leaf_4_1_C_Aug22_Cy3

description:
MSMI_13491139.gpr
Sample 84


title: Sn leaf_4_2_D_Aug22_Cy5

description:
MSMI_13491139.gpr
Sample 84


title: Sn leaf_15_1_A_Aug22_Cy3

description:
MSMI_13490796.gpr
Sample 83


title: Sn leaf_10_1_C_Aug22_Cy5

description:
MSMI_13490776.gpr
Sample 82


title: Muscle_AQM_6h-4d_unloaded_UU13

description:
Experimental rat ICU model. AQM.
Unloaded leg.
UU13_100202


title: mimetic pattern 4th at 1h 1

city: Tsukuba

first: Ryo

last: Futahashi

address: Central6, Higashi 1-1-1

institute: National Institute of Advanced Industrial Science and Technology

description: Cryptic green vs. cryptic black 9

hyb_protocol: Hybridization was performed using an In situ Hybridization Kit Plus (Agilent Technologies). One microgram of each Cy3-labelled cRNA and Cy5-labelled cRNA were mixed, fragmented and hybridized to each oligo-microarray at 65 °C for 17 h at 4 rpm. The arrays were washed in 6x saline sodium citrate (SSC), 0.005% TritonX-102 for 10 min at room temperature and in 0.1x SSC, 0.005% TritonX-102 for 5 min at 4 °C.

scan_protocol: Intensities of the hybridized probes were detected with an Agilent G2565BA Microarray Scanner with 10 mm scan resolution, and the signals were extracted with G2565AA Feature Extraction Software v. 7.1 (Agilent Technologies).

data_processing: Normalization was performed ‘per spot’ and ‘per chip’ using the GENESPRING program. The low expression level spots in all cells were removed (fluorescence intensity is appxiometry lower than 100).

organism: Papilio xuthus

source_name: Papilio xuthus cryptic green

label_protocol: Total RNA (400 ng each for Cy3 and Cy5) was converted to cDNAs with T7 promoter oligo-dT primer and Moloney Murine Leukemia Virus reverse transcriptase. Second-strand cDNA was transcribed to cRNA with T7 RNA polymerase and 10 mM Cy3 or Cy5.

growth_protocol: For microarray experiment of mimetic pattern, total epidermal RNAs of 6 developmental stages (0, 4, 8, 11, 16 hours after HCS of the 3rd molting period and intermolt (day 2) of the 3rd instar) were isolated from white (abdominal 2-4 segments) and black (abdominal 4-5 segments) regions independently. For microarray experiment of cryptic pattern, total epidermal RNAs of 5 developmental stages (1, 4, 10, 13 hours after HCS of the 4th molting period and intermolt (day 2) of the 4th instar) were isolated from thorax (thoracic 2 segment with no markings), eyespot (thoracic 3 segment), abdomen (abdominal 3-4 segments with no markings), and V-shaped markings (abdominal 4-5 segments) regions independently.

extract_protocol: Total RNA extracted using TRI reagent following manufacturer's instructions

value: 4th instar molt at 1h

value: epidermis, green thoracic region

source_name: Papilio xuthus cryptic black

value: epidermis, eyespot region


title: Muscle_AQM_6h-4d_unloaded_U11

description:
Experimental rat ICU model. AQM.
Unloaded leg.
U11_100127


title: Muscle_AQM_9-14d_unloaded_UU51

description:
Experimental rat ICU model. AQM.
Unloaded leg.
UU51_100216


title: mimetic pattern 4th intermolt 2

description: Cryptic green vs. cryptic black 8

value: 4th instar intermolt

value: epidermis, green abdominal region

value: epidermis, V-shaped region


title: Sn leaf_7_1_C_July24_Cy5

description:
MSMI_13490775.gpr
Sample 81

value: leaf

value: varied

value: warm


title: Sn leaf_10_4_B_Aug22_Cy3

description:
MSMI_13490776.gpr
Sample 82

value: ambient


title: Sn leaf_7_4_B_July24_Cy3

description:
MSMI_13490775.gpr
Sample 81

value: control


title: mimetic pattern 4th intermolt 1

description: Cryptic green vs. cryptic black 7


title: Sn leaf_3_2_D_Aug22_Cy3_1

description:
MSMI_13512898.gpr
Sample 79


title: mimetic pattern 3rd at 16h

description: Mimetic white vs. mimetic black 6

source_name: Papilio xuthus mimetic white

value: 3rd instar molt at 16h

value: epidermis, white region

source_name: Papilio xuthus mimetic black

value: epidermis, black region


title: Sn leaf_5_1_C_Aug22_Cy3_1

description:
MSMI_13490773.gpr
Sample 80


title: Sn leaf_5_4_C_Aug22_Cy5

description:
MSMI_13490773.gpr
Sample 80


title: mimetic pattern 3rd at 4h

description: Mimetic white vs. mimetic black 5

value: 3rd instar molt at 4h


title: Sn leaf_2_1_C_Aug22_Cy5_1

description:
MSMI_13512897.gpr
Sample 78


title: Sn leaf_3_1_A_Aug22_Cy5_1

description:
MSMI_13512898.gpr
Sample 79


title: Sn leaf_2_4_D_Aug22_Cy3

description:
MSMI_13512897.gpr
Sample 78


title: LCM SS7-5 parietal

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40629.gif

value: pooled aged matched control samples 2x amplified

source_name: SS7-5 parietal

value: 7 d

value: infected

value: parietal


title: LCM SS2-4 parietal

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41299.gif

source_name: SS2-4 parietal

value: 2 d


title: Sn leaf_12_1_C_Aug22_Cy5

description:
MSMI_13513589.gpr
Sample 77


title: Sn leaf_12_2_D_Aug22_Cy3

description:
MSMI_13513589.gpr
Sample 77


title: LCM mock7-3 mucus producing

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40619.gif

source_name: mock7-3 mucus producing

value: pit


title: LCM mock2-4 chief

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42029.gif

source_name: mock2-4 chief

value: chief


title: Sn leaf_3_2_D_July24_Cy3

description:
MSMI_13512895.gpr
Sample 75


title: Sn leaf_11_2_D_Aug22_Cy3

description:
MSMI_13512896.gpr
Sample 76


title: Sn leaf_3_1_C_July24_Cy5

description:
MSMI_13512895.gpr
Sample 75


title: LCM mock2-1 parietal

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41281.gif

source_name: mock2-1 parietal


title: Sn leaf_11_1_A_Aug22_Cy5

description:
MSMI_13512896.gpr
Sample 76


title: Sn leaf_9_1_C_July18_Cy5

description:
MSMI_13512894.gpr
Sample 74


title: mimetic pattern 3rd intermolt

description: Mimetic white vs. mimetic black 3

value: 3rd instar intermolt


title: LCM SS14-4 parietal

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42328.gif

source_name: SS14-4 parietal


title: Sn leaf_9_4_B_July18_Cy3

description:
MSMI_13512894.gpr
Sample 74

value: leaf


title: mimetic pattern 4th at 10h 2

description: Cryptic green vs. cryptic black 4

value: 4th instar molt at 10h

value: epidermis, green abdominal region

value: epidermis, V-shaped region


title: LCM mock7-2 chief

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40617.gif

source_name: mock7-2 chief

value: control


title: mimetic pattern 4th at 13h 1

description: Cryptic green vs. cryptic black 5

value: 4th instar molt at 13h

value: epidermis, green thoracic region

value: epidermis, eyespot region


title: LCM mock14-4 chief

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42323.gif

source_name: mock14-4 chief


title: Sn leaf_10_4_D/B_June1_Cy3

description:
MSMI_13497104.gpr
Sample 92

value: varied


title: Sn leaf_15_2_D_July18_Cy5

description:
MSMI_13465951.gpr
Sample 94


title: mimetic pattern 4th at 13h 2

description: Cryptic green vs. cryptic black 6


title: Sn leaf_5_1_C_July18_Cy5

description:
MSMI_13513588.gpr
Sample 73

value: ambient


title: mimetic pattern 4th at 1h 2

description: Cryptic green vs. cryptic black 10

value: 4th instar molt at 1h


title: Muscle_AQM_6h-4d_unloaded_UU19

description:
Experimental rat ICU model. AQM.
Unloaded leg.
UU19_100217

value: Sprague-Dawley

value: female

value: gactrocnemius muscle

value: non-depolarizing neuromuscular blocking agent (NMBA)

value: no loading

value: 6hr-4 days


title: Muscle_AQM_6h-4d_unloaded_UU17

description:
Experimental rat ICU model. AQM.
Unloaded leg.
UU17_100217


title: Sn leaf_2_4_B_July24_Cy3

description:
MSMI_13470396.gpr
Sample 96

value: leaf


title: Sn leaf_4_1_C_July24_Cy5

description:
MSMI_13512904.gpr
Sample 71


title: Sn leaf_5_4_B_July18_Cy3

description:
MSMI_13513588.gpr
Sample 73

value: warm


title: Sn leaf_3_2_D_July18_Cy3

description:
MSMI_13513585.gpr
Sample 72


title: Muscle_AQM_6h-4d_loaded_UU16

description:
Experimental rat ICU model. AQM.
Loaded leg.
UU16_100202

source_name: gastrocnemius muscle, treated with non-depolarizing NMBA and mechanically ventilated, 6h to 4d group, loaded leg

value: passive loading


title: LCM mock7-4 chief

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40623.gif

source_name: pooled aged matched control samples 2x amplified

source_name: mock7-4 chief

value: 7 d

value: chief


title: Sn leaf_3_1_A_July18_Cy5

description:
MSMI_13513585.gpr
Sample 72


title: LCM mock14-1 mucus producing

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42319.gif

value: pooled aged matched control samples 2x amplified

source_name: mock14-1 mucus producing

value: control

value: pit


title: Sn leaf_15_1_C_July24_Cy3

description:
MSMI_13512903.gpr
Sample 70

value: varied


title: Sn leaf_10_4_B_July24_Cy3

description:
MSMI_13512902.gpr
Sample 69


title: Sn leaf_10_1_C_July24_Cy5

description:
MSMI_13512902.gpr
Sample 69


title: Sn leaf_4_2_D_July24_Cy3

description:
MSMI_13512904.gpr
Sample 71

value: ambient


title: Sn leaf_11_2_D_July24_Cy5

description:
MSMI_13512901.gpr
Sample 68


title: LCM mock7-4 parietal

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40624.gif

source_name: mock7-4 parietal

value: parietal


title: Sn leaf_6_1_A_Aug22_Cy3

description:
MSMI_13491141.gpr
Sample 85


title: Sn leaf_15_2_B_July24_Cy5

description:
MSMI_13512903.gpr
Sample 70


title: Sn leaf_11_1_C_July24_Cy3

description:
MSMI_13512901.gpr
Sample 68


title: Muscle_AQM_6h-4d_unloaded_UU15

description:
Experimental rat ICU model. AQM.
Unloaded leg.
UU15_100202

source_name: gastrocnemius muscle, treated with non-depolarizing NMBA and mechanically ventilated, 6h to 4d group, unloaded leg

value: Sprague-Dawley


title: mimetic pattern 3rd at 11h

description: Mimetic white vs. mimetic black 2

value: 3rd instar molt at 11h

value: epidermis, white region

value: epidermis, black region


title: mimetic pattern 4th at 4h 1

description: Cryptic green vs. cryptic black 1

source_name: Papilio xuthus cryptic green

value: 4th instar molt at 4h

value: epidermis, green thoracic region

source_name: Papilio xuthus cryptic black

value: epidermis, eyespot region


title: LCM mock14-3 parietal

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42322.gif

source_name: mock14-3 parietal


title: mimetic pattern 4th at 10h 1

description: Cryptic green vs. cryptic black 3

value: 4th instar molt at 10h


title: Sn leaf_10_1_C_July18_Cy5

description:
MSMI_13512900.gpr
Sample 67

value: leaf

value: warm


title: Sn leaf_2_4_B_July18_Cy3

description:
MSMI_13512457.gpr
Sample 66


title: Sn leaf_9_1_C_June7_Cy5

description:
MSMI_13512456.gpr
Sample 65


title: mimetic pattern 3rd at 8h

description: Mimetic white vs. mimetic black 1

source_name: Papilio xuthus mimetic white

value: 3rd instar molt at 8h

source_name: Papilio xuthus mimetic black


title: Sn leaf_10_4_B_July18_Cy3

description:
MSMI_13512900.gpr
Sample 67


title: mimetic pattern 4th at 4h 2

description: Cryptic green vs. cryptic black 2

value: epidermis, green abdominal region

value: epidermis, V-shaped region


title: Sn leaf_9_4_A_June7_Cy3

description:
MSMI_13512456.gpr
Sample 65


title: JN vs DB10_3

city: Pathumthani

first: nitsara

last: karoonuthaisiri

state: Pathumthani

address: Paholyothin

department: Central

country: Thailand

institute: BIOTEC

hyb_protocol: The probe was resuspended in hybridization solution (50% Formamide; 5x SSC; 0.1% SDS; 1 mg/ml Human Placental DNA; 10mM Tris, pH 7.5) and placed onto the post-processed slides. The slides were hybridized at 420C for 16 hrs before they were washed according to Corning’s protocol.

scan_protocol: The slides were scanned with GenePix 4000B (Molecular Devices, Sunnyvale, CA). Microarray spots on scanned images are located using GenePix Pro version 6.1.

data_processing: All “empty” and “bad” spots were removed from the analysis. “Empty” spots were failed PCR products whereas “bad” spots were flagged by visual inspection of the spot images. From the remaining spots, only the spots with intensities more than one standard deviation above the background intensity were further analyzed. The processed data were normalized within each array by the median-nomalization method, and across arrays, using the Aroma package (Bengtsson, available from: http://www.maths.lth.se/help/R/aroma/) run in R project environment (http://cran.r-project.org). Data from replicated spots were averaged before clustering. Logarithmic base 2 values of intensities from both Cy3- and Cy5- samples (M values) were used as inputs for clustering. Cluster program was used to perform hierarchical clustering and Treeview program was used to visualized the clustered results (Eisen et al., 1998)

organism: Penaeus monodon

source_name: pooled testis from juvenile shrimp

label_protocol: The RNA from testis of pooled male juveniles was labeled with Cy3 dye as a reference and those from testes of broodstocks were labeled with Cy5 dye. The Cy3- and Cy5-samples were mixed together and hybridized onto the arrays overnight. The hybridized slides were washed according to Corning’s instruction.

extract_protocol: RNA samples were extracted from testes of male shrimp. Contaminated genomic DNA was removed by treatment with DNase I at 0.15 U/μg total RNA at 37°C for 30 min.

value: testis

tag: developmental stage

value: juvenile

value: pooled from 114 shrimp

source_name: testis from Domesticated-broodstock shrimp 10 months

value: 10 months

tag: variety

value: Domesticated-broodstock shrimp


title: JN vs DB10_4

tag: tissue


title: Sn leaf_2_1_C_July18_Cy5

description:
MSMI_13512457.gpr
Sample 66

value: varied


title: Sn leaf_6_1_B_June7_Cy5

description:
MSMI_13512453.gpr
Sample 64

value: ambient


title: Sn leaf_6_4_A_June7_Cy3

description:
MSMI_13512453.gpr
Sample 64

value: control


title: LCM SS14-4 mucus producing

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42327.gif

value: pooled aged matched control samples 2x amplified

source_name: SS14-4 mucus producing

value: infected

value: pit


title: Sn leaf_4_1_A_June7_Cy3

description:
MSMI_13512452.gpr
Sample 63


title: LCM SS7-6 chief

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40633.gif

source_name: SS7-6 chief

value: 7 d

value: chief


title: JN vs DB10_1


title: JN vs DB14_4

source_name: testis from Domesticated-broodstock shrimp 14 months

value: 14 months


title: JN vs DB14_3


title: Sn leaf_4_2_B_June7_Cy5

description:
MSMI_13512452.gpr
Sample 63

value: leaf


title: Sn leaf_2_1_C_June7_Cy5

description:
MSMI_13512451.gpr
Sample 62

value: warm


title: JN vs DB10_2


title: LCM mock7-2 mucus producing

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40616.gif

source_name: mock7-2 mucus producing


title: Sn leaf_2_4_D_June7_Cy3

description:
MSMI_13512451.gpr
Sample 62


title: Sn leaf_3_1_C_June7_Cy5

description:
MSMI_13512541.gpr
Sample 61


title: JN vs DB14_2


title: Sn leaf_13_2_B_June7_Cy5

description:
MSMI_13512539.gpr
Sample 60


title: Sn leaf_3_2_D_June7_Cy3

description:
MSMI_13512541.gpr
Sample 61


title: LCM SS7-6 mucus producing repeat

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40632.gif

source_name: SS7-6 mucus producing repeat


title: LCM mock7-2 parietal

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40618.gif

source_name: pooled aged matched control samples 2x amplified

source_name: mock7-2 parietal

value: parietal


title: Sn leaf_15_1_C_July18_Cy3

description:
MSMI_13465951.gpr
Sample 94


title: LCM mock14-4 parietal

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42324.gif

source_name: mock14-4 parietal


title: Sn leaf_15_1_C_June7_Cy3

description:
MSMI_13512538.gpr
Sample 59


title: Sn leaf_12_1_A_June7_Cy5

description:
MSMI_13465993.gpr
Sample 58


title: JN vs DB18_4

value: testis

source_name: testis from Domesticated-broodstock shrimp 18 months

value: 18 months


title: LCM SS14-3 mucus producing

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42325.gif

source_name: SS14-3 mucus producing


title: LCM SS14-3 parietal

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42326.gif

source_name: SS14-3 parietal


title: Sn leaf_12_2_A_June7_Cy3

description:
MSMI_13465993.gpr
Sample 58


title: Sn leaf_15_2_B_June7_Cy5

description:
MSMI_13512538.gpr
Sample 59


title: JN vs DB14_1

value: juvenile

value: pooled from 114 shrimp


title: Sn leaf_13_1_A_June7_Cy3

description:
MSMI_13512539.gpr
Sample 60


title: Sn leaf_11_2_D_June7_Cy3

description:
MSMI_13465994.gpr
Sample 57


title: Sn leaf_11_1_C_June7_Cy5

description:
MSMI_13465994.gpr
Sample 57


title: JN vs DB18_1

value: Domesticated-broodstock shrimp


title: JN vs DB18_3


title: Sn leaf_10_4_D_June7_Cy5

description:
MSMI_13465995.gpr
Sample 56

value: varied


title: LCM mock2-2 parietal

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41287.gif

source_name: mock2-2 parietal

value: 2 d


title: Sn leaf_10_1_C_June7_Cy3

description:
MSMI_13465995.gpr
Sample 56

value: control


title: JN vs DB18_2


title: Sn leaf_7_4_D_June7_Cy5

description:
MSMI_13465996.gpr
Sample 55

value: ambient


title: LCM mock14-1 parietal

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42320.gif

value: pooled aged matched control samples 2x amplified

source_name: mock14-1 parietal


title: Sn leaf_9_4_A_June1_Cy3

description:
MSMI_13491128.gpr
Sample 54


title: Sn leaf_9_1_C_June1_Cy5

description:
MSMI_13491128.gpr
Sample 54


title: mimetic pattern 3rd at 0h

description: Mimetic white vs. mimetic black 4

source_name: Papilio xuthus mimetic white

value: 3rd instar molt at 0h

value: epidermis, white region

value: epidermis, black region


title: JN vs WBE_2

source_name: testis from wild-broodstock shrimp from east coast of Thailand


title: JN vs WBE_3

source_name: pooled testis from juvenile shrimp

value: wild-broodstock shrimp from east coast of Thailand


title: Sn leaf_7_1_C_June7_Cy3

description:
MSMI_13465996.gpr
Sample 55

value: leaf


title: JN vs WBE_1


title: Sn leaf_15_2_B_June1_Cy3

description:
MSMI_13491132.gpr
Sample 53

value: warm


title: Sn leaf_3_2_B_June1_Cy5

description:
MSMI_13491136.gpr
Sample 52


title: Sn leaf_15_1_A_June1_Cy5

description:
MSMI_13491132.gpr
Sample 53


title: LCM SS7-5 mucus producing

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40626.gif

source_name: SS7-5 mucus producing

value: 7 d

value: infected

value: pit


title: LCM mock7-3 parietal

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40621.gif

source_name: mock7-3 parietal

value: parietal


title: LCM mock2-1 chief

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41279.gif

source_name: mock2-1 chief

value: chief


title: Sn leaf_3_1_C_June1_Cy3

description:
MSMI_13491136.gpr
Sample 52


title: LCM SS2-4 chief

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41298.gif

source_name: SS2-4 chief


title: LCM SS2-5 mucus producing

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42030.gif

source_name: SS2-5 mucus producing


title: JN vs WBW_2

value: testis

value: juvenile

value: pooled from 114 shrimp

source_name: testis from wild-broodstock shrimp from west coast of Thailand


title: JN vs WBW_3

value: wild-broodstock shrimp from west coast of Thailand


title: Ag leaf_13_2_B_July18_Cy5

description:
MSMI_13513584.gpr
Sample 50

organism: Andropogon gerardi

value: varied


title: LCM mock14-3 mucus producing

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42321.gif

source_name: pooled aged matched control samples 2x amplified

source_name: mock14-3 mucus producing

value: control


title: LCM mock2-4 mucus producing

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41289.gif

value: pooled aged matched control samples 2x amplified

source_name: mock2-4 mucus producing

value: 2 d


title: Ag leaf_11_2_D_July18_Cy5

description:
MSMI_13513583.gpr
Sample 49

value: ambient


title: JN vs WBW_1


title: Sn leaf_12_1_A_June1_Cy3

description:
MSMI_13491137.gpr
Sample 51


title: Ag leaf_13_1_C_July18_Cy3

description:
MSMI_13513584.gpr
Sample 50


title: Sn leaf_12_2_A_June1_Cy5

description:
MSMI_13491137.gpr
Sample 51


title: Ag leaf_11_1_C_July18_Cy3

description:
MSMI_13513583.gpr
Sample 49


title: Ag leaf_7_4_B_July18_Cy3

description:
MSMI_13513162.gpr
Sample 48


title: Ag leaf_2_4_B_June1_Cy5

description:
MSMI_13513161.gpr
Sample 47


title: Ag leaf_7_1_C_July18_Cy5

description:
MSMI_13513162.gpr
Sample 48


title: Ag leaf_2_1_C_June1_Cy3

description:
MSMI_13513161.gpr
Sample 47


title: Breast Cancer Tissue 47

first: Francisco

middle: J.

last: Esteva

state: TX

address: 1515 Holcombe Blvd, Unit 1354

department: Department of Breast Medical Oncology

institute: MD Anderson Cancer Center

description: Gene expression data from breast cancer tissue

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized to affymetrix U133A arrays overnight at 42C. Microarrays were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000DX. This system is manufactured by Affymetrix Inc in Santa Clara, CA.

data_processing: Microarray data were normalized using RMA method via Partek software and absolute expression values were obtained.

source_name: Human breast cancer

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from at least 1 ug total RNA using the BioArray High Yield RNA transcript labeling kit (Enzo Laboratories).

extract_protocol: total RNA was extracted from the specimens using Qiagen RNeasy kit following the manufacturer’s instructions (http://www.qiagen.com).

tag: er

value: NEG

tag: pr

value: POS

value: IIIC

value: RD


title: Ag leaf_2_1_C_July24_Cy5

description:
MSMI_13513160.gpr
Sample 46

value: leaf


title: Breast Cancer Tissue 49


title: Ag leaf_2_4_B_July24_Cy3

description:
MSMI_13513160.gpr
Sample 46

value: warm


title: Breast Cancer Tissue 48


title: 110330_MM9_HuMA_M-dcn3

city: Philadelphia

first: Renato

middle: V.

last: Iozzo

state: PA

address: 1020 Locust St. Rm 336

department: Pathology, Anatomy, and Cell Biology

institute: Thomas Jefferson University

description:
Decorin 3
cDNA derived from total RNA.

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

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

data_processing: The raw data (.pair) was processed (RMA normalized) using Bioconductor in R, heatmaps were rendered using MeV (version 4.8.1) in the TM4 package from Dana-Farber Institute.

organism:
Homo sapiens
Mus musculus

source_name: Mus musculus xenograft tumor decorin treated

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

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen) on liquid nitrogen snap frozen tumor xenografts according to the manufacturer's protocol. RNA integrity was verified using an Agilent Bioanalyzer 2100 on an RNA 6000 Nano kit.

treatment_protocol: Mice were injected intraperitoneally daily with 10mg/kg decorin proteoglycan.

tag: treatment

value: decorin for 23 days at 10mg/kg

value: mouse stroma + human MDA-MB-231 tumor xenograft

tag: mouse strain

value: SCID

value: female

tag: age of mouse

value: 35 days


title: Breast Cancer Tissue 46

tag: age

value: IIB


title: 110330_MM9_HuMA_M-dcn4

description:
Decorin 4
cDNA derived from total RNA.


title: LCM mock2-1 mucus producing

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41277.gif

source_name: mock2-1 mucus producing

tag: time

value: pit


title: LCM SS2-5 chief

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42031.gif

source_name: SS2-5 chief

value: infected

value: chief


title: Ag leaf_12_2_D_July24_Cy3

description:
MSMI_13513159.gpr
Sample 45

tag: precipitation

value: varied


title: LCM mock2-2 mucus producing

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41283.gif

value: pooled aged matched control samples 2x amplified

source_name: mock2-2 mucus producing

value: 2 d

value: control


title: LCM mock7-4 mucus producing

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40622.gif

source_name: mock7-4 mucus producing

value: 7 d


title: 110330_MM9_HuMA_M-dcn2

description:
Decorin 2
cDNA derived from total RNA.


title: Breast Cancer Tissue 45

value: NEG

value: POS

value: IIIC

value: RD


title: Breast Cancer Tissue 44

value: IIIB


title: Ag leaf_10_1_C_June1_Cy5

description:
MSMI_13470394.gpr
Sample 42

value: leaf

tag: temperature


title: Ag leaf_3_2_D_Aug22_Cy3_2

description:
MSMI_13470395.gpr
Sample 43

value: ambient

value: warm


title: Ag leaf_15_2_D_July18_Cy5

description:
MSMI_13513158.gpr
Sample 44


title: Ag leaf_15_1_C_July18_Cy3

description:
MSMI_13513158.gpr
Sample 44


title: Ag leaf_3_1_A_Aug22_Cy5_2

description:
MSMI_13470395.gpr
Sample 43


title: Ag leaf_10_4_D/B_June1_Cy3

description:
MSMI_13470394.gpr
Sample 42


title: Breast Cancer Tissue 43

value: IIIA


title: Ag leaf_12_2_D_July24_Cy5

description:
MSMI_13513159.gpr
Sample 45


title: 110330_MM9_HuMA_M-dcn10a

description:
Decorin 10A
cDNA derived from total RNA.

value: decorin for 23 days at 10mg/kg

value: mouse stroma + human MDA-MB-231 tumor xenograft

value: SCID

value: female

value: 35 days


title: Breast Cancer Tissue 42


title: 110330_MM9_HuMA_M-dcn12a

description:
Decorin 12A
cDNA derived from total RNA.


title: Ag leaf_7_4_D_Aug22_Cy3

description:
MSMI_13470392.gpr
Sample 40


title: LCM SS2-3 parietal

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41296.gif

tag: reference

value: pooled aged matched control samples 2x amplified

source_name: SS2-3 parietal

value: 2 d

value: infected

value: parietal


title: 110330_MM9_HuMA_M-dcn8a

description:
Decorin 8A
cDNA derived from total RNA.


title: 110330_MM9_HuMA_M-cnt1

description:
Control 1
cDNA derived from total RNA.

source_name: Mus musculus xenograft tumor control


title: Ag leaf_7_1_C_Aug22_Cy5

description:
MSMI_13470392.gpr
Sample 40

value: control


title: LCM SS2-4 mucus producing

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41297.gif

source_name: SS2-4 mucus producing

tag: infection

value: pit


title: Breast Cancer Tissue 41

value: POS

value: NEG

value: IIB

value: RD


title: Ag leaf_2_1_C_Aug22_Cy5_2

description:
MSMI_13470401.gpr
Sample 38

value: leaf

value: varied


title: 110330_MM9_HuMA_M-cnt2

description:
Control 2
cDNA derived from total RNA.


title: Ag leaf_12_4_D_Aug22_Cy3

description:
MSMI_13470401.gpr
Sample 38

value: warm


title: Ag leaf_7_4_D_June1_Cy3

description:
MSMI_13470391.gpr
Sample 39

value: ambient


title: Breast Cancer Tissue 40

value: IIA


title: 110330_MM9_HuMA_M-cnt5a

description:
Control 5A
cDNA derived from total RNA.

value: mouse stroma + human MDA-MB-231 tumor xenograft

value: SCID

value: female


title: LCM SS2-5 parietal

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41300.gif

value: pooled aged matched control samples 2x amplified

source_name: SS2-5 parietal

value: 2 d

tag: cell type


title: 110330_MM9_HuMA_M-cnt6a

description:
Control 6A
cDNA derived from total RNA.

tag: gender

value: 35 days


title: LCM mock7-3 chief

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40620.gif

source_name: mock7-3 chief

value: 7 d

value: control

value: chief


title: 110330_MM9_HuMA_M-cnt2-1

description:
Control 2-1
cDNA derived from total RNA.


title: Ag leaf_12_1_D_July18_Cy5

description:
MSMI_13491134.gpr
Sample 37


title: Ag leaf_12_1_C_July18_Cy3

description:
MSMI_13491134.gpr
Sample 37


title: Breast Cancer Tissue 38

value: POS

value: NEG


title: Ag leaf_9_4_A_Aug22_Cy5

description:
MSMI_13512534.gpr
Sample 36


title: Ag leaf_9_1_C_Aug22_Cy3

description:
MSMI_13512534.gpr
Sample 36


title: Breast Cancer Tissue 39

value: IIB

value: RD


title: Breast Cancer Tissue 50

value: IV


title: Ag leaf_5_4_D_Aug22_Cy5

description:
MSMI_13470393.gpr
Sample 41

value: leaf

value: varied

value: warm


title: 110330_MM9_HuMA_M-cnt4a

description:
Control 4A
cDNA derived from total RNA.

value: mouse stroma + human MDA-MB-231 tumor xenograft


title: Ag leaf_6_4_B_Aug22_Cy5

description:
MSMI_13513511.gpr
Sample 35

value: ambient


title: Breast Cancer Tissue 36

value: IIIA

value: IIA


title: Ag leaf_6_1_A_Aug22_Cy3

description:
MSMI_13513511.gpr
Sample 35


title: Ag leaf_4_2_D_Aug22_Cy5

description:
MSMI_13513510.gpr
Sample 34


title: Ag leaf_7_1_C_June1_Cy5

description:
MSMI_13470391.gpr
Sample 39


title: Ag leaf_15_2_D_Aug22_Cy5

description:
MSMI_13513508.gpr
Sample 33


title: Ag leaf_15_1_A_Aug22_Cy3

description:
MSMI_13513508.gpr
Sample 33


title: Ag leaf_7_1_C_July24_Cy5

description:
MSMI_13513505.gpr
Sample 31


title: Ag leaf_10_1_C_Aug22_Cy5

description:
MSMI_13513506.gpr
Sample 32


title: Ag leaf_7_4_B_July24_Cy3

description:
MSMI_13513505.gpr
Sample 31


title: Ag leaf_10_4_B_Aug22_Cy3

description:
MSMI_13513506.gpr
Sample 32


title: Ag leaf_5_1_C_Aug22_Cy3_1

description:
MSMI_13512562.gpr
Sample 30


title: Ag leaf_5_4_C_Aug22_Cy5

description:
MSMI_13512562.gpr
Sample 30


title: Ag leaf_3_1_A_Aug22_Cy5_1

description:
MSMI_13512450.gpr
Sample 29


title: Ag leaf_4_1_C_Aug22_Cy3

description:
MSMI_13513510.gpr
Sample 34


title: Ag leaf_2_1_C_Aug22_Cy5_1

description:
MSMI_13512449.gpr
Sample 28


title: Breast Cancer Tissue 35


title: Breast Cancer Tissue 34

value: IIIC


title: Breast Cancer Tissue 32

value: I


title: Breast Cancer Tissue 30


title: Ag leaf_3_2_D_Aug22_Cy3_1

description:
MSMI_13512450.gpr
Sample 29


title: Breast Cancer Tissue 31


title: Ag leaf_2_4_D_Aug22_Cy3

description:
MSMI_13512449.gpr
Sample 28


title: Breast Cancer Tissue 29

value: IIIB


title: Breast Cancer Tissue 33


title: LCM SS14-4 chief relabeled

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43105.gif

value: pooled aged matched control samples 2x amplified

source_name: SS14-4 chief

value: infected


title: LCM SS28-4 parietal relabeled

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43121.gif

source_name: SS28-4 parietal

value: parietal


title: LCM SS14-6 parietal relabeled

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43340.gif

source_name: SS14-6 parietal


title: Ag leaf_12_1_C_Aug22_Cy5

description:
MSMI_13512448.gpr
Sample 27

value: control


title: Ag leaf_11_1_A_Aug22_Cy5

description:
MSMI_13512447.gpr
Sample 26


title: Ag leaf_11_2_D_Aug22_Cy3

description:
MSMI_13512447.gpr
Sample 26


title: LCM mock14-3 chief relabeled

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43101.gif

source_name: pooled aged matched control samples 2x amplified

source_name: mock14-3 chief

value: chief


title: Breast Cancer Tissue 27

value: NEG

value: POS

value: pCR


title: Ag leaf_12_2_D_Aug22_Cy3

description:
MSMI_13512448.gpr
Sample 27

value: leaf

value: varied


title: Ag leaf_9_4_B_July18_Cy3

description:
MSMI_13513617.gpr
Sample 24

value: warm


title: Ag leaf_3_2_D_July24_Cy3

description:
MSMI_13513618.gpr
Sample 25

value: ambient


title: Ag leaf_5_1_C_July18_Cy5

description:
MSMI_13513616.gpr
Sample 23


title: Breast Cancer Tissue 28

value: RD


title: Ag leaf_5_4_B_July18_Cy3

description:
MSMI_13513616.gpr
Sample 23


title: Ag leaf_9_1_C_July18_Cy5

description:
MSMI_13513617.gpr
Sample 24


title: Breast Cancer Tissue 24


title: Ag leaf_3_1_C_July24_Cy5

description:
MSMI_13513618.gpr
Sample 25


title: LCM mock28-3 chief relabeled

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43115.gif

source_name: mock28-3 chief


title: Breast Cancer Tissue 26

description: Gene expression data from breast cancer tissue

source_name: Human breast cancer


title: Ag leaf_3_1_A_July18_Cy5

description:
MSMI_13513615.gpr
Sample 22


title: Breast Cancer Tissue 23

value: IIB


title: LCM SS28-3 mucus producing relabeled

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43117.gif

source_name: SS28-3 mucus producing

value: pit


title: LCM SS2-3 chief relabeled

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43322.gif

source_name: SS2-3 chief

value: 2 d


title: Breast Cancer Tissue 22

value: IIIC


title: LCM SS7-3 chief relabeled

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43324.gif

value: pooled aged matched control samples 2x amplified

source_name: SS7-3 chief

value: 7 d


title: LCM mock14-1 chief relabeled

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43100.gif

source_name: mock14-1 chief


title: LCM mock28-3 mucus producing relabeled

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43114.gif

source_name: mock28-3 mucus producing


title: Ag leaf_4_1_C_July24_Cy5

description:
MSMI_13513614.gpr
Sample 21


title: Ag leaf_3_2_D_July18_Cy3

description:
MSMI_13513615.gpr
Sample 22


title: Breast Cancer Tissue 21

value: IIIA


title: Ag leaf_10_1_C_July24_Cy5

description:
MSMI_13513537.gpr
Sample 19

value: control


title: Ag leaf_4_2_D_July24_Cy3

description:
MSMI_13513614.gpr
Sample 21


title: Ag leaf_15_2_B_July24_Cy5

description:
MSMI_13513538.gpr
Sample 20


title: Ag leaf_10_4_B_July24_Cy3

description:
MSMI_13513537.gpr
Sample 19


title: Breast Cancer Tissue 37

value: IIIB

value: IIA


title: Breast Cancer Tissue 20

value: NEG

value: POS


title: LCM SS14-5 parietal relabeled

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43334.gif

source_name: SS14-5 parietal

value: infected

value: parietal


title: Ag leaf_15_1_C_July24_Cy3

description:
MSMI_13513538.gpr
Sample 20

value: leaf


title: Ag leaf_11_2_D_July24_Cy5

description:
MSMI_13513536.gpr
Sample 18

value: ambient

value: warm


title: Ag leaf_11_1_C_July24_Cy3

description:
MSMI_13513536.gpr
Sample 18


title: LCM SS2-3 mucus producing relabeled

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43320.gif

source_name: SS2-3 mucus producing


title: LCM mock28-1 chief relabeled

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43108.gif

source_name: mock28-1 chief

value: chief


title: Breast Cancer Tissue 19

value: pCR


title: Ag leaf_10_1_C_July18_Cy5

description:
MSMI_13513535.gpr
Sample 17

value: varied


title: Breast Cancer Tissue 18


title: Ag leaf_5_1_C_Aug22_Cy3_2

description:
MSMI_13470393.gpr
Sample 41


title: Ag leaf_2_1_C_July18_Cy5

description:
MSMI_13513533.gpr
Sample 16


title: Ag leaf_10_4_B_July18_Cy3

description:
MSMI_13513535.gpr
Sample 17


title: LCM mock2-2 chief relabeled

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43315.gif

source_name: mock2-2 chief

value: 2 d


title: Ag leaf_9_1_C_June7_Cy5

description:
MSMI_13512737.gpr
Sample 15


title: Ag leaf_6_4_A_June7_Cy3

description:
MSMI_13512736.gpr
Sample 14


title: Ag leaf_9_4_A_June7_Cy3

description:
MSMI_13512737.gpr
Sample 15


title: Ag leaf_6_1_B_June7_Cy5

description:
MSMI_13512736.gpr
Sample 14


title: Ag leaf_2_4_B_July18_Cy3

description:
MSMI_13513533.gpr
Sample 16


title: Breast Cancer Tissue 16


title: LCM mock28-2 parietal relabeled

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43113.gif

value: pooled aged matched control samples 2x amplified

source_name: mock28-2 parietal


title: Ag leaf_4_1_A_June7_Cy3

description:
MSMI_13512735.gpr
Sample 13


title: Ag leaf_4_2_B_June7_Cy5

description:
MSMI_13512735.gpr
Sample 13


title: Breast Cancer Tissue 17


title: LCM SS14-6 mucus producing relabeled

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43337.gif

source_name: SS14-6 mucus producing

value: pit


title: Breast Cancer Tissue 13


title: Breast Cancer Tissue 15

value: IIIC


title: Breast Cancer Tissue 25

value: IIB


title: Ag leaf_2_1_C_June7_Cy5

description:
MSMI_13512734.gpr
Sample 12

value: control


title: Ag leaf_3_1_C_June7_Cy5

description:
MSMI_13512733.gpr
Sample 11


title: Breast Cancer Tissue 14

value: IIIA


title: Breast Cancer Tissue 12

value: NEG

value: I


title: LCM mock2-4 parietal relabeled

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43317.gif

source_name: mock2-4 parietal


title: Ag leaf_2_4_D_June7_Cy3

description:
MSMI_13512734.gpr
Sample 12


title: LCM mock28-2 mucus producing relabeled

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43111.gif

source_name: mock28-2 mucus producing


title: Ag leaf_3_2_D_June7_Cy3

description:
MSMI_13512733.gpr
Sample 11


title: LCM SS14-6 chief relabeled

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43106.gif

source_name: pooled aged matched control samples 2x amplified

source_name: SS14-6 chief

value: infected


title: Ag leaf_13_2_B_June7_Cy5

description:
MSMI_13513185.gpr
Sample 10


title: Ag leaf_13_1_A_June7_Cy3

description:
MSMI_13513185.gpr
Sample 10


title: Breast Cancer Tissue 11

value: POS


title: Breast Cancer Tissue 9


title: LCM SS28-5 mucus producing relabeled

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43122.gif

source_name: SS28-5 mucus producing


title: Ag leaf_15_2_B_June7_Cy5

description:
MSMI_13513184.gpr
Sample 9

value: leaf


title: LCM mock28-3 parietal relabeled

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43116.gif

source_name: mock28-3 parietal

value: parietal


title: Ag leaf_12_2_A_June7_Cy3

description:
MSMI_13513182.gpr
Sample 8

value: warm


title: Breast Cancer Tissue 10

description: Gene expression data from breast cancer tissue

source_name: Human breast cancer


title: Ag leaf_10_4_D_June7_Cy5

description:
MSMI_13513180.gpr
Sample 6


title: Ag leaf_11_2_D_June7_Cy3

description:
MSMI_13513181.gpr
Sample 7

value: ambient


title: LCM SS7-6 parietal relabeled

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43329.gif

source_name: SS7-6 parietal

value: 7 d


title: Breast Cancer Tissue 8

value: pCR


title: Ag leaf_11_1_C_June7_Cy5

description:
MSMI_13513181.gpr
Sample 7


title: Breast Cancer Tissue 7

value: IIA


title: LCM SS28-3 chief relabeled

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43118.gif

value: pooled aged matched control samples 2x amplified

source_name: SS28-3 chief

value: chief


title: LCM mock14-4 mucus producing relabeled

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43103.gif

source_name: mock14-4 mucus producing

value: pit


title: Ag leaf_10_1_C_June7_Cy3

description:
MSMI_13513180.gpr
Sample 6

value: varied


title: Ag leaf_9_1_C_June1_Cy5

description:
MSMI_13512637.gpr
Sample 4

value: control


title: Breast Cancer Tissue 5


title: Ag leaf_7_4_D_June7_Cy5

description:
MSMI_13512638.gpr
Sample 5


title: LCM mock28-2 chief relabeled

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43112.gif

source_name: mock28-2 chief


title: Breast Cancer Tissue 6


title: Ag leaf_9_4_A_June1_Cy3

description:
MSMI_13512637.gpr
Sample 4


title: Ag leaf_15_1_A_June1_Cy5

description:
MSMI_13512635.gpr
Sample 3


title: LCM mock28-1 mucus producing relabeled

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43107.gif

source_name: mock28-1 mucus producing


title: Ag leaf_15_2_B_June1_Cy3

description:
MSMI_13512635.gpr
Sample 3


title: Ag leaf_3_1_C_June1_Cy3

description:
MSMI_13512634.gpr
Sample 2


title: Breast Cancer Tissue 3

value: IIIB


title: Ag leaf_12_1_A_June1_Cy3

description:
MSMI_13512633.gpr
Sample 1


title: LCM SS28-4 mucus producing relabeled

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43119.gif

source_name: SS28-4 mucus producing


title: Ag leaf_12_2_A_June1_Cy5

description:
MSMI_13512633.gpr
Sample 1


title: Ag leaf_3_2_B_June1_Cy5

description:
MSMI_13512634.gpr
Sample 2


title: LCM SS14-5 mucus producing relabeled

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43331.gif

source_name: SS14-5 mucus producing


title: LCM mock28-1 parietal relabeled

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43109.gif

source_name: mock28-1 parietal


title: LCM SS28-5 chief relabeled

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43123.gif

source_name: SS28-5 chief


title: Ag leaf_15_1_C_June7_Cy3

description:
MSMI_13513184.gpr
Sample 9


title: Breast Cancer Tissue 2

value: NEG


title: 13_4_MPG_18

status: Public on May 11 2012

city: Perth

first: Sulev

last: Koks

state: Western Australia

address: 90 South Street

department: Centre for Molecular Medicine and Innovative Therapeutics

country: Australia

institute: Murdoch University

description: Gene expression data from mid-gestational placenta

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

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000

data_processing: The raw intensity data (cel files) were analyzed with rma.

source_name: placenta

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: Frozen in liquid nitrogen

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

value: placenta

tag: gestational age


title: LCM SS28-5 parietal relabeled

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43124.gif

source_name: SS28-5 parietal

value: infected


title: 97 Control (subset)

city: Umea

first: Matilda

last: Rentoft

address: NUS

department: Medical Biosciences

institute: Umea University

description: SAMPLE 78

hyb_protocol: Hybridization were performed according to manufacturers protocol (WG-DASL) (illumina)

scan_protocol: Arrays were scanned with a BeadArray Reader (Illumina) and data was extracted using GenomeStudio software (Illumina).

data_processing: Data were normalized using Cubiq spline. No background correction were done.

label: Cy3 + Cy5

source_name: Tongue, FFPE

label_protocol: Labeling were performed according to manufacturers protocol (WG-DASL) (illumina)

extract_protocol: RNA were extracted using the High Pure RNA Paraffin Kit according to the manufacturer’s protocol

value: Man

tag: quality (ctdiff)

tag: detected genes (p<0.05)


title: LCM SS7-3 parietal relabeled

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43326.gif

source_name: pooled aged matched control samples 2x amplified

source_name: SS7-3 parietal


title: 14_5_MPG_17.1

tag: tissue


title: Ag leaf_12_1_A_June7_Cy5

description:
MSMI_13513182.gpr
Sample 8

value: leaf


title: 21 Control (subset)

description: SAMPLE 77


title: 95 Control (subset)

description: SAMPLE 75


title: 94 Control (subset)

description: SAMPLE 69

value: Woman


title: 18 Control (subset)

description: SAMPLE 74


title: 15_6_MPG_17.3


title: 20 Control (subset)

description: SAMPLE 66


title: 100 Control (subset)

description: SAMPLE 71


title: 38 Control (subset)

description: SAMPLE 76


title: 16_8_MPG_18.8


title: 17 Control (subset)

description: SAMPLE 68


title: 15 Control (subset)

description: SAMPLE 72


title: 96 Control (subset)

description: SAMPLE 67


title: 16 Control (subset)

description: SAMPLE 64


title: 93 Control (subset)

description: SAMPLE 65


title: 46 Tumour (subset)

description: SAMPLE 60

tag: tnm


title: 83 Tumour (subset)

description: SAMPLE 42


title: 32 Tumour (subset)

description: SAMPLE 34


title: 56 Tumour (subset)

description: SAMPLE 55


title: 84 Tumour (subset)

description: SAMPLE 23


title: 91 Tumour (subset)

description: SAMPLE 40


title: 101 Control (subset)

description: SAMPLE 63


title: Breast Cancer Tissue 4

tag: er

tag: pr

value: POS

value: IIIA


title: 26 Tumour (subset)

description: SAMPLE 22


title: 14 Tumour (subset)

description: SAMPLE 39


title: 50 Tumour (subset)

description: SAMPLE 47


title: 68 Tumour (subset)

description: SAMPLE 35


title: 42 Tumour (subset)

description: SAMPLE 45


title: 98 Control (subset)

description: SAMPLE 73


title: 92 Tumour (subset)

description: SAMPLE 21


title: 34 Tumour (subset)

description: SAMPLE 43


title: 1 Tumour (subset)

description: SAMPLE 29


title: 51 Tumour (subset)

description: SAMPLE 28


title: 40 Tumour (subset)

description: SAMPLE 51


title: Ag leaf_7_1_C_June7_Cy3

description:
MSMI_13512638.gpr
Sample 5

value: ambient


title: 69 Tumour (subset)

description: SAMPLE 44


title: 63 Tumour (subset)

description: SAMPLE 61


title: 53 Tumour (subset)

description: SAMPLE 20


title: 45 Tumour (subset)

description: SAMPLE 18


title: 43 Tumour (subset)

description: SAMPLE 26


title: Breast Cancer Tissue 1

value: pCR


title: 102 Tumour (subset)

description: SAMPLE 14


title: Patient5_mother

city: Utrecht

first: Wigard

last: Kloosterman

address: Universiteitsweg 100

country: Netherlands

institute: University Medical Center Utrecht

description: Genomic DNA extracted from sample was genotyped using the Illumina HumanHap300v1 Genotyping BeadChip.

hyb_protocol: RA1-resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining, BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on an iScan (Illumina).

data_processing: Data processing was done using GenomeStudio (Illumina).

label: Biotin (C, G), DNP (A,T)

source_name: DNA from blood, patient 5 mother

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (MSM) and primer/neutralization mix (MA1-MA2-0.1N NaOH). After incubation, the amplified DNA was fragmented with fragmentation mix (FMS), precipitated with isopropanol and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed using proteinase K and repeated phenol-chloroform extractions.

tag: individual

value: patient 5 mother

value: female

value: blood

tag: treatment

tag: disease state

value: not applicable


title: 47 Tumour (subset)

description: SAMPLE 10

tag: age


title: 64 Tumour (subset)

description: SAMPLE 11


title: 9 Tumour (subset)

description: SAMPLE 5


title: Patient5

source_name: DNA from blood, patient 5

value: patient 5

value: multiple congenital abnormalities and mental retardation


title: 95 Control


title: 36 Tumour (subset)

description: SAMPLE 3


title: 15 Control


title: 38 Control


title: 21 Control


title: 98 Control


title: 37 Control


title: 17 Control


title: 94 Control


title: 97 Control


title: 18 Control


title: 100 Control


title: 39 Tumour (subset)

description: SAMPLE 8


title: Q334-S

city: Brisbane

first: Amy

last: McCart Reed

state: QLD

address: Building 71/918 Herston

department: UQCCR

institute: The University of Queensland

hyb_protocol: Illumina WG-DASL protocol followed as directed.

scan_protocol: Illumina BeadScan

data_processing: The data were normalised using quantile normalisation with lumi bioconductor package in R

source_name: Breast tissue

extract_protocol: RNA was extracted with the Roche High Pure RNA Paraffin kit, according to manufacturer's instructions

value: Breast tissue

tag: tissue type

value: RM-NS

tag: sample id


title: 9C

label_protocol: Illumina WG-DASL protocol followed as directed.

value: DCIS


title: 96 Control


title: 20 Control


title: 4B

value: IDC-S


title: 93 Control

value: Man


title: 16A-DUPL

description: Replicate

value: IDC

tag: replicate

value: Replicate


title: 7B


title: 101 Control


title: 4D

value: DCIS-S


title: LCM SS28-4 chief relabeled

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43120.gif

tag: reference

value: pooled aged matched control samples 2x amplified

source_name: SS28-4 chief

tag: infection

value: infected

tag: time

value: chief


title: 54 Tumour

tag: gender

value: Woman


title: Q326-S


title: 10B


title: 46 Tumour

tag: quality (ctdiff)


title: 63 Tumour

tag: detected genes (p<0.05)


title: 1E

tag: tissue

value: BC-NS


title: 16 Control


title: 11E


title: Patient2_father

description: Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.

source_name: DNA from blood, patient 2 father

value: patient 2 father

value: male

value: blood


title: Patient3_mother

source_name: DNA from blood, patient 3 mother

value: patient 3 mother

value: female

value: not applicable


title: 2E

value: Breast tissue


title: 8D


title: 54 Tumour (subset)

description: SAMPLE 62

tag: tnm


title: 77 Tumour


title: Patient3

source_name: DNA from blood, patient 3

value: patient 3

value: multiple congenital abnormalities and mental retardation


title: 87 Tumour


title: 29 Tumour

value: Man


title: 12D


title: 16B

value: IDC-S


title: 56 Tumour


title: Patient3_father

source_name: DNA from blood, patient 3 father

value: patient 3 father


title: 66 Tumour


title: 3B


title: Patient1_father

source_name: DNA from blood, patient 1 father

value: patient 1 father


title: 8 Tumour


title: Patient2_mother

source_name: DNA from blood, patient 2 mother

value: patient 2 mother


title: 80 Tumour


title: 48 Tumour


title: 6C

value: DCIS


title: 31 Tumour

value: Woman


title: Patient1_mother

source_name: DNA from blood, patient 1 mother

value: patient 1 mother


title: Patient1

source_name: DNA from blood, patient 1

value: patient 1


title: 40 Tumour


title: 13C


title: Patient2

source_name: DNA from blood, patient 2

value: patient 2


title: 10C


title: 14A

value: IDC


title: 17D

value: DCIS-S


title: 42 Tumour


title: 58 Tumour


title: 8C


title: 8A


title: 10 Tumour


title: 50 Tumour


title: Control

city: Darlinghurst

first: Warren

last: Kaplan

state: NSW

address: 384 Victoria Street

department: Peter Wills Bioinformatics Centre

institute: Garvan Institute of Medical Research

description: RNA from pooled eyes, Control

hyb_protocol: Labeled, fragmented RNA hybridized to Affymetrix Human Gene 1.0 ST Gene Arrays at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturers instructions.

scan_protocol: Arrays were scanned at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturers instructions.

data_processing: Data was RMA normalised using NormalizeAffymetrixST (version 1) GenePattern module from the Peter Wills Bioinformatics Centre's GenePattern Server: http://pwbc.garvan.unsw.edu.au/gp

source_name: Control

label_protocol: RNA was fragmented, biotin labeled at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturers instructions.

growth_protocol: Eyes were enucleated and placed in TRIzol on dry ice according to the manufacturer’s instructions (Purelink RNA Minikit, Invitrogen

extract_protocol: Total RNA was extracted with the RNeasy Minikit (Qiagen) and DNase-treated with the DNase kit (Qiagen) according to manufacturer’s instructions. RNA quality was assessed by RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Dz13 (20 µg in 1.68 µl H2O containing DOTAP/DOPE) was administered once, intravitreally to I-0 C57BL/6 mice. These mice had previously been exposed to 75% oxygen for 4 d and returned to room air to render the inner retina relatively hypoxic. Alternatively the mice were injected with Dz13scr (20 µg) or the vehicle alone. Ten days following DNAzyme administration, at I-10, the mice were sacrificed, the eyes enucleated, cross-sectioned and stained.

value: Control

value: eye


title: Vehicle

description: RNA from pooled eyes, Vehicle

source_name: Pooled eyes, incubated with Vehicle

value: Vehicle


title: 15C

value: Breast tissue


title: 69 Tumour

source_name: Tongue, FFPE


title: 83 Tumour


title: 34 Tumour


title: 12E

value: BC-NS


title: 25 Tumour

value: Man


title: Dz13

description: RNA from pooled eyes, Dz13

source_name: Pooled eyes, incubated with Dz13


title: 91 Tumour


title: 68 Tumour


title: 14 Tumour


title: 81 Tumour


title: 32 Tumour


title: 49 Tumour


title: HeLa CTR RNAi replicate 2 B

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

country: Germany

institute: LMU Munich

description: HeLa cells; Luciferase knockdown; biological replicate 2

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: R/bioconductor, 'oligo' package, default parameters

source_name: Luciferase knockdown

growth_protocol: HeLa cells were cultured at 37°C in Dulbecco´s Modified Eagle´s Medium (Invitrogen) supplemented with 10% fetal calf serum (Invitrogen) and penicillin/streptomycin

extract_protocol: Total RNA was isolated from HeLa cells employing the RNeasy Kit (Qiagen) with additional RNase-free DNase (Qiagen) on column digestion. The quality and quantity of the RNA was determined using the Agilent RNA 6000 NanoLabChip kit and Agilent 2100 bioanalyzer.

treatment_protocol: siRNAs were transfected using Oligofectamine and OPTIMEM (Invitrogen) according to suppliers protocol. 2x10^5 cells at 40-50% confluency were transfected with 200 pmol siRNA and collected 72h later.

tag: cell line

value: HeLa cells

tag: batch

value: B

tag: RNAi

value: Luciferase


title: 16C


title: 9D


title: 14C


title: HeLa CTR RNAi replicate 1 B

description: HeLa cells; Luciferase knockdown; biological replicate 1


title: 3E


title: 57 Tumour


title: Nrest_4A

first: Joanna

last: DiSpirito

address: 3610 Hamilton Walk, University of Pennsylvania

department: Microbiology

institute: University of Pennsylvania

description: Murine FACS-sorted naïve (CD44lo) CD8 T cells cultured 4hrs ex vivo media only

hyb_protocol: After purification, 1.65 μg of cRNA was fragmented and hybridized to the array for 17 hr. at 65°C.

scan_protocol: Microarray slides were hybridized overnight, then washed and scanned with Agilent G2565BA Microarray Scanner. Images were analyzed with Feature Extraction 9.5 (Agilent Technologies, CA).

data_processing: Mean foreground intensities were obtained for each spot and imported into the mathematical software package “R”, which was used for all data input, diagnostic plots, normalization and quality checking steps of the analysis process using scripts developed in-house by Peter White specifically for this analysis. In outline, the Cy3 (green) intensities were not background corrected (this has been shown to only introduce noise), and corrected for the scanner offset (40 was subtracted for each intensity). The dataset was filtered to remove positive control elements and any elements that had been flagged as bad. Using the negative controls on the arrays, the background threshold was determined and all values less than this value were set to the threshold value. Finally, the data was normalized using the Quantile Normalization package in “R” (Bolstad et al., 2003).

label_protocol: Approximately 200 ng of total RNA was amplified and labeled with Cy3 using the Low RNA Input Linear Amp Kit PLUS, One-Color (Agilent Technologies, CA). This labeling reaction produces 0.25 – 2.0 µg of Cy3-labeled cRNA (anti-sense), by first Converting mRNA primed with an oligo (d)T-T7 primer into dsDNA with MMLV-RT and then amplifying the sample using T7 RNA Polymerase in the presence of Cy3-CTP.

extract_protocol: Following 4hr culture, cells were lysed in TRIzol reagent followed by phenol+chloroform extraction and purification using RNEasy mini columns (QIAGEN).

treatment_protocol: FACS-purified naïve (CD44lo) and memory phenotype (CD44hi) CD8+ T cells were cultured for four hours in media alone (Iscove’s DMEM + 8% FBS (HI) + 100U/mL Pennicillin + 100ug/mL Streptomycin + 2mM L-glutamine + 50uM β-mercaptoethanol) or in media with PMA (10ng/mL) and ionomycin (500ng/mL).

tag: strain

value: Female

tag: cell type


title: 41 Tumour

tag: age


title: Nstim_4C

description: Murine FACS-sorted naïve (CD44lo) CD8 T cells cultured 4hrs ex vivo, stimulated with PMA+ionomycin


title: HeLa SNF2L RNAi replicate 2

description: HeLa cells; SNF2L knockdown; biological replicate 2

source_name: SNF2L knockdown


title: Patient7_mother

description: Genomic DNA extracted from sample was genotyped using the Illumina HumanCNV370-QuadV3 DNA Analysis BeadChip.

source_name: DNA from blood, patient 7 mother

tag: individual

value: patient 7 mother

value: female

value: blood

tag: treatment

tag: disease state

value: not applicable


title: Dz13scrambled

description: RNA from pooled eyes, Dz13scrambled

source_name: Pooled eyes, incubated with Dz13scrambled


title: Patient7

source_name: DNA from blood, patient 7

value: patient 7

value: male

value: multiple congenital abnormalities and mental retardation


title: Mstim_4D

description: Murine FACS-sorted memory (CD44hi) CD8 T cells cultured 4hrs ex vivo, stimulated with PMA+ionomycin


title: Mrest_4B

description: Murine FACS-sorted memory (CD44hi) CD8 T cells cultured 4hrs ex vivo media only


title: HeLa SNF2L RNAi replicate 3

description: HeLa cells; SNF2L knockdown; biological replicate 3


title: 13E

source_name: Breast tissue

tag: tissue type

tag: sample id


title: 15E


title: 10A-DUPL

description: Replicate

value: IDC

tag: replicate

value: Replicate


title: HeLa CTR RNAi replicate 3 B

description: HeLa cells; Luciferase knockdown; biological replicate 3


title: 24 Tumour

tag: gender


title: 89 Tumour

value: Woman

tag: quality (ctdiff)


title: Mstim_3D

source_name: Murine FACS-sorted memory (CD44hi) CD8 T cells cultured 4hrs ex vivo, stimulated with PMA+ionomycin


title: HeLa SNF2L RNAi replicate 1

description: HeLa cells; SNF2L knockdown; biological replicate 1


title: 90 Tumour

tag: detected genes (p<0.05)


title: Mrest_3B

source_name: Murine FACS-sorted memory (CD44hi) CD8 T cells cultured 4hrs ex vivo media only


title: 9A

tag: tissue

value: Breast tissue


title: 3A


title: 1 Tumour

tag: tnm


title: HeLa CTR RNAi replicate 2 A

tag: cell line

value: A


title: 1A


title: 13 Tumour


title: 59 Tumour

value: Man


title: HeLa CTR RNAi replicate 1 A

value: HeLa cells

tag: batch


title: 11C

value: DCIS


title: HeLa SNF2H RNAi replicate 2

description: HeLa cells; SNF2H knockdown; biological replicate 2

source_name: SNF2H knockdown

tag: RNAi


title: Nstim_2C

source_name: Murine FACS-sorted naïve (CD44lo) CD8 T cells cultured 4hrs ex vivo, stimulated with PMA+ionomycin

tag: strain


title: Nstim_3C

tag: cell type


title: Nrest_3A

source_name: Murine FACS-sorted naïve (CD44lo) CD8 T cells cultured 4hrs ex vivo media only


title: HeLa SNF2H RNAi replicate 3

description: HeLa cells; SNF2H knockdown; biological replicate 3


title: 7D

value: DCIS-S


title: 13A


title: 2B

value: IDC-S


title: Mstim_2D

value: Female


title: 51 Tumour

tag: age


title: HeLa SNF2H RNAi replicate 1

description: HeLa cells; SNF2H knockdown; biological replicate 1


title: 6E

value: BC-NS


title: 1B


title: 71 Tumour


title: 43 Tumour


title: Nrest_2A


title: Mrest_2B


title: Mstim_1D


title: 17B


title: 11A


title: Mrest_1B


title: 26 Tumour


title: 84 Tumour


title: 11B


title: Nstim_1C


title: BCR-ABL+, NUP98-HOXA9+ replicate 4

city: Rochester

first: John

last: Ashton

state: NY

address: 575 Elmwood Ave

institute: University of Rochester

description: Gene expression from lineage negative BCR-ABL+/NUP98-HOXA9+ bone marrow cells

hyb_protocol: Biotin-labeled cDNA was hybridized overnight with Affymetrix Mouse 430 2.0 arrays according to manufacturer's protocols.  Post hybridization, arrays were washed and stained with strepavidin conjugated R-phycoerythrin.

scan_protocol: Arrays were scanned using the Fluidics Station 450 Scanner 3000 from Affymetrix.

data_processing: Array normalization and background subtraction was performed using dCHIP.

source_name: lineage negative BCR-ABL+ and NUP98-HOXA9+ bone marrow cells

label_protocol: Total RNA was converted into biotin-labeled, fragmented cDNA with NuGEN technologies kit according to manufacturer's protocols.

growth_protocol: Primary murine LSK cells were purified from bone marrow and cultured in IMDM supplemented with 10% FBS, 10ng/ML IL3, 10ng/ml IL6, 50ng/ml SCF, and 50ng/ml FLT3 ligand.

extract_protocol: Hematopoietic cells were isolated from the bone marrow of recipient mice after 9 days of in vivo growth and purified by Flourescence activated cell sorting (FACS) based on expression of GFP and YFP.  Total RNA was extracted using the RNAeasy PLUS kit form Qiagen according to manufacturers protocol.

treatment_protocol: LSK cells transduced with BCR-ABL-GFP and NUP98-HOXA(-YFP retroviruses followed by transplant into recipient mice.

tag: oncogenes


title: 62 Tumour


title: 92 Tumour


title: 2A


title: BCR-ABL+, NUP98-HOXA9+ replicate 5


title: 74 Tumour


title: 7C


title: 9B


title: Nrest_1A


title: BCR-ABL+, NUP98-HOXA9+ replicate 6


title: 53 Tumour


title: 2D


title: 45 Tumour


title: 13B


title: BCR-ABL+, NUP98-HOXA9+ replicate 3


title: BCR-ABL+, NUP98-HOXA9+ replicate 1


title: 10E


title: 35 Tumour


title: 17A


title: BCR-ABL+, NUP98-HOXA9+ replicate 2


title: 28 Tumour


title: 102 Tumour


title: 10A


title: 8B


title: NUP98-HOXA9+ replicate 6

description: Gene expression from lineage negative NUP98-HOXA9+ bone marrow cells


title: NUP98-HOXA9+ replicate 5

source_name: lineage negative NUP98-HOXA9+ bone marrow cells


title: NUP98-HOXA9+ replicate 3


title: 16A


title: 7 Tumour


title: 64 Tumour


title: 3D


title: 78 Tumour


title: 3C


title: Q329-S

value: RM-NS


title: NUP98-HOXA9+ replicate 1


title: 47 Tumour


title: 55 Tumour


title: 1D


title: BCR-ABL+ replicate 5

description: Gene expression from lineage negative BCR-ABL+ bone marrow cells

value: BCR-ABL+


title: 88 Tumour


title: NUP98-HOXA9+ replicate 4


title: NUP98-HOXA9+ replicate 2


title: Transgenic mouse 3, age 16 days

city: Sydney

first: Richard

last: Bagnall

address: Missenden Road

department: Molecular Cardiology

institute: Centenary Institute

description: Test

data_processing: comparative threshold (Ct) values were calculated using SDS software v2.4), with automatic baseline settings and a threshold of 0.2. Ct values were imported into DataAssist software version 2.0. snoRNA135 and snoRNA202 were used as reference genes to normalize the data

source_name: Ventricles

label_protocol: 450 ng RNA was reverse transcribed using TaqMan MicroRNA Reverse Transcription Kit, without pre-amplification, and Megaplex RT Primers rodent pool A. Complementary DNA was amplified using a TaqMan rodent microRNA A Array v2.0  with TaqMan Universal PCR Master Mix on an ABI 7900HT Sequence Detection System

extract_protocol: Total RNA was extracted using Trizol reagent. RNAs with a RIN value >9 were used for global microRNA analysis

value: Ventricles

value: C57 black 6

tag: genotype/variation

value: transgenic

value: 16 days


title: Transgenic mouse 2, age 16 days

description: Test


title: Transgenic mouse 1, age 16 days

description: Test


title: Non-transgenic mouse 3, age 16 days

description: Control

value: non-transgenic


title: Non-transgenic mouse 2, age 16 days

description: Control


title: 14A-DUPL

description: Replicate

value: IDC

value: Replicate


title: BCR-ABL+ replicate 4

source_name: lineage negative BCR-ABL+ bone marrow cells


title: 39 Tumour

source_name: Tongue, FFPE


title: BCR-ABL+ replicate 6


title: 1C

value: Breast tissue


title: 30 Tumour

value: Woman


title: Non-transgenic mouse 1, age 16 days

description: Control


title: BCR-ABL+ replicate 3


title: Transgenic mouse 3, age 10 days

description: Test

value: 10 days


title: Transgenic mouse 2, age 10 days

description: Test


title: BCR-ABL+ replicate 1


title: 14B


title: HeLa CTR RNAi replicate 3 A

label_protocol: standard Affymetrix protocol

value: HeLa cells

value: A

value: Luciferase


title: Transgenic mouse 1, age 10 days

description: Test


title: Non-transgenic mouse 3, age 10 days

description: Control


title: 72 Tumour

value: Man


title: 6B

value: IDC-S


title: 9 Tumour


title: 14E

value: BC-NS


title: BCR-ABL+ replicate 2

value: BCR-ABL+


title: 8E


title: BCR-ABL neg, NUP98-HOXA9 neg replicate 4

description: Gene expression from lineage negative bone marrow cells

source_name: lineage negative bone marrow cells


title: BCR-ABL neg, NUP98-HOXA9 neg replicate 5


title: Non-transgenic mouse 2, age 10 days

description: Control

value: Ventricles


title: 36 Tumour


title: 12A


title: BCR-ABL neg, NUP98-HOXA9 neg replicate 6


title: 6D

value: DCIS-S


title: 85 Tumour


title: Non-transgenic mouse 1, age 10 days

description: Control

value: C57 black 6


title: BCR-ABL neg, NUP98-HOXA9 neg replicate 1


title: Gastric cancer  tissue samples (FFPE)_183

status: Public on May 10 2012

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

description:
A pool of DNA from blood of normal individuals
T183_10_55_output_fused
T183

hyb_protocol: As described in Buffart et al, J Pathol. 2007 Jan;211(1):45-51

scan_protocol: Slides were scanned using the Agilent microarray scanner, protocol according to Agilent.

data_processing: Bluefuse software version 3.4 (BlueGnome, Cambridge, UK) was used for automatic feature extraction. Spots were excluded when the quality flag was below 1 or the confidence value was below 0.1. Log2 tumor to normal ratio was calculated for each clone and median block normalization was used to normalize the data.

source_name: Gastric cancer

label_protocol: Labeling was done by random priming (Bioprime DNA Labeling System, Invitrogen, Breda, The Netherlands)

extract_protocol: DNA isolation protocol available via www.vumc.nl/microarrays. Also described in Buffart et al, J Pathol. 2007 Jan;211(1):45-51

value: Gastric cancer

tag: lymph node status

value: negative

tag: survival (years)

tag: comort

value: death due to other reason

source_name: female reference DNA

value: reference:Pooled DNA from the blood of 18 normal male individuals


title: BCR-ABL neg, NUP98-HOXA9 neg replicate 2


title: Gastric cancer  tissue samples (FFPE)_182

description:
A pool of DNA from blood of normal individuals
T182_32_55_output_fused
T182

value: alive

value: reference:Pooled DNA from the blood of 18 normal female individuals


title: BCR-ABL neg, NUP98-HOXA9 neg replicate 3


title: 13D

value: Breast tissue

tag: tissue type

tag: sample id


title: Gastric cancer  tissue samples (FFPE)_181

description:
A pool of DNA from blood of normal individuals
T181_24_55_output_fused
T181

value: positive


title: 15A

value: IDC


title: Gastric cancer  tissue samples (FFPE)_175

description:
A pool of DNA from blood of normal individuals
T175_55_55_output_fused
T175

value: operation mortality


title: Gastric cancer  tissue samples (FFPE)_180

description:
A pool of DNA from blood of normal individuals
T180_12_55_output_fused
T180

value: death due to cancer/recurrence


title: Gastric cancer  tissue samples (FFPE)_173

description:
A pool of DNA from blood of normal individuals
T173_52_55_output_fused
T173


title: 27 Tumour

tag: gender

value: Man

tag: quality (ctdiff)


title: Gastric cancer  tissue samples (FFPE)_177

description:
A pool of DNA from blood of normal individuals
T177_11_58_output_fused
T177

tag: tissue


title: Gastric cancer  tissue samples (FFPE)_172

description:
A pool of DNA from blood of normal individuals
T172_81_55_output_fused
T172


title: Gastric cancer  tissue samples (FFPE)_170

description:
A pool of DNA from blood of normal individuals
T170_63_55_output_fused
T170


title: Gastric cancer  tissue samples (FFPE)_167

description:
A pool of DNA from blood of normal individuals
T167_60_55_output_fused
T167


title: Gastric cancer  tissue samples (FFPE)_171

description:
A pool of DNA from blood of normal individuals
T171_59_55_output_fused
T171


title: microRNA profile of case NCN1

city: Guangzhou

first: Rongrong

last: wei

address: 651 Dongfeng East Road

department: cancer center

country: China

institute: Sun-Yat Sen university

description: Sample was used for hybridization on each miRNA microarray chip containing 917 probes

hyb_protocol: The labeled RNAs were mixed and hybridized to the array with a 1×hybridization solution (5× Denhart’s solution, 0.5% SDS, 5× SSC) in a Hybridization Chamber (Corning Inc, Corning, NY, USA) at 46°C for 12 to 16 hours.

scan_protocol: scanned in a LuxScanTM -10K Scanner (capitalBio Inc.,Beijing, China).

data_processing: quantile normalization across multiple arrays, log 2 transformation of expression levels

source_name: Nasopharyngitis

label_protocol: 2.5 μg of total RNA was employed with 100 nmol/L of pCp-DY647(Dharmacon, Lafayette, CO, USA) and 15 Units of T4 RNA ligase (USB, Cleveland, Oh, USA) in a total reaction volume of 20 µL at 16°C overnight

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: disease state

value: Nasopharyngitis

value: Nasopharyngitis tissue


title: microRNA profile of case NCN2


title: microRNA profile of case NPC111

source_name: Naspharyngeal Carcinoma

tag: survival time (month), status (1-death, 0-survival)

tag: metastasis (1-yes, 0-no)

tag: gender (1-male, 0-female)

tag: age (1 - greater than or equal to 50y, 0 - less than 50y)

tag: max diameter of lymph nodes (1 - greater than or equal to 10mm, 0 - less than 10mm)

value: Naspharyngeal Carcinoma

value: Naspharyngeal Carcinoma tissue


title: microRNA profile of case NCN4


title: microRNA profile of case NPC112


title: microRNA profile of case NCN5


title: microRNA profile of case NCN7


title: microRNA profile of case NCN6


title: Gastric cancer  tissue samples (FFPE)_176

description:
A pool of DNA from blood of normal individuals
T176_13_55_output_fused
T176


title: microRNA profile of case NPC109


title: microRNA profile of case NPC108


title: Gastric cancer  tissue samples (FFPE)_164

description:
A pool of DNA from blood of normal individuals
T164_58_55_output_fused
T164


title: microRNA profile of case NPC101


title: microRNA profile of case NPC107


title: microRNA profile of case NPC106


title: Gastric cancer  tissue samples (FFPE)_166

description:
A pool of DNA from blood of normal individuals
T166_44_55_output_fused
T166


title: microRNA profile of case NPC99


title: microRNA profile of case NPC97


title: microRNA profile of case NPC98


title: Gastric cancer  tissue samples (FFPE)_161

description:
A pool of DNA from blood of normal individuals
T161_22_55_output_fused
T161


title: Gastric cancer  tissue samples (FFPE)_162

description:
A pool of DNA from blood of normal individuals
T162_83_55_output_fused
T162


title: Gastric cancer  tissue samples (FFPE)_160

description:
A pool of DNA from blood of normal individuals
T160_13_58_output_fused
T160


title: Gastric cancer  tissue samples (FFPE)_163

description:
A pool of DNA from blood of normal individuals
T163_21_55_output_fused
T163


title: microRNA profile of case NPC95


title: microRNA profile of case NPC96


title: Gastric cancer  tissue samples (FFPE)_158

description:
A pool of DNA from blood of normal individuals
T158_57_55_output_fused
T158


title: Gastric cancer  tissue samples (FFPE)_156

description:
A pool of DNA from blood of normal individuals
T156_11_55_output_fused
T156