title: breast surgical IMC 4

description:
IMC 5 (583MS20)
Gene expression data from sugical breast cancer specimens.


title: LD green/ HD red

status: Public on Apr 25 2011

type: RNA

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

country: Italy

institute: European Brain Research Institute

description: Single preparation in dye-swap

hyb_protocol: Microarray hybridizations were carried out in Agilent’s SureHyb Hybridization Chambers containing 825 ng of Cyanine 3-labelled and 825 ng of Cyanine5-labelled cRNA per hybridization. The hybridization reaction were performed at  65°C for 17 hours using Agilent’s Genen Expression Hybridization Kit into the single genome human chip.After hybridization, slides were washed with Agilent Gene Expression Wash Buffer 1, Gene Expression Wash Buffer 2 and Acetonitril for one minute at room temperature

scan_protocol: Chips were scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version 9.1) and the GE2-v4_91 extraction protocol.

data_processing: The signal values used for the subsequent analysis (for both channels)  are median feature signals, non background substracted. Microsoft Excel software was used to filter out unreliable features (essentially features with expression values smaller than background + 3 Standard deviations of the background) and to perform the dye swap normalization. Agilent GeneSpring GX Software (v 7.3) was used for the LOWESS normalization. To select differentially expressed genes, up- and down-regulated features were selected both from the dye-swap normalized data and from the LOWESS normalized data, then these two sets were intersected.

molecule: total RNA

organism: Homo sapiens

source_name: Human intestinal Caco-2 cells

label_protocol: 500ng of Poly A+RNA were labelled, using Cyanine 3-CTP or Cyanine 5-CTP (Perkin Elmer) in separate labelling reactions, with the Agilent Low Imput Linear Amplification Kit and purified with Qiagen’s RNeasy mini spin columns

growth_protocol:
Caco-2 cells were mantained in high glucose DMEM supplemented with 10% HIFBS (Hyclone),  1% Non Essential Amino Acid, 4mM Glutamine and antibiotics in incubator with 10% CO2. Low density cells (LD) were subcultured for at least 10 passages when cell reach 50% of confluence before applying the differetiation protocol. High density cells (HD) were subcultured for at least 10 passages when cell reach 90-100% of confluence before applying the differetiation protocol.
For differentiation procedure Caco-2 cells were seeded with a cells density of 3E05 cell x cm2 on PET inserts (Falcon 3090) and let to differenentiate for 21 days. Medium was changed three times a week.

extract_protocol: Total RNA was extracted using TRIzol following manufacturer's instructions

tag: cell type

tag: passage

tag: protocol

value: low density (LD)

tag: age

value: 21-days differentiated

tag: tissue

value: intestine

value: high density (HD)


title: CALU-1

city: West Point

first: Michael

last: Nebozhyn

state: PA

address: Mail Stop WP53B-120, 770 Sumneytown Pike, Building 53, P.O. Box 4

department: GpGx/Computational System biology

country: USA

institute: Merck, Inc

description: lung cancer cell line

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques. Arrays are hybridized for 18 hours at 45oC with vigorous mixing. Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed. Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Standard RefRMA pipleline as implemented in APT (Affymetrix Power Tools software) using default settings

label: Biotin

source_name: ATCC

label_protocol: Standard 1xAffy amplification protocol

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation. Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.

tag: cell line


title: A549

description: lung cancer cell line


title: CALU3

description: lung cancer cell line


title: myotube_ETOH_6h_rep3

city: Berkeley

first: Jen-Chywan

last: Wang

state: CA

address: 315 Morgan Hall, UC Berkeley

department: Nutritional Sciences & Toxicology

institute: UC Berkeley

description:
ETOH.6h.3
replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were pre-processed using lumi package in R with bgAdjust.affy for background correction, quantile normalization, and slide effect removed using linear model.

label: biotin

organism: Mus musculus

source_name: C2C12 myotubes

label_protocol: Biotin-labeled cRNA samples were prepared with 750 ng of total RNA template.  Following synthesis and purification, the biotin-labeled samples were evaluated by both 260/280 absorbance spectrophotometry and capillary electrophoresis.

extract_protocol: Total cellular RNA was isolated utilizing the NucleoSpin RNA II kit (Macherey-Nagel) per manufacturers’ directions.  RNA isolates were first quantified by standard spectrophotometry, and then qualitatively evaluated by capillary electrophoresis employing the Bio-Rad Experion system following the manufacturers’ instruction.

value: myotube

tag: agent

value: ETOH

tag: time


title: myotube_ETOH_6h_rep1

description:
ETOH.6h.1
replicate 1


title: Stickleback_Exposed to Predator Cues_rep2

status: Public on Apr 24 2011

city: Urbana

first: Yibayiri

middle: Osee

last: Sanogo

state: IL

address: 505 S. Goodwin

department: Integrative Biology

institute: University of Illinois at Urbana-Champaign

description:
EXP_3
This sample is of brain of stickleback exposed to predator cues. It is the second of  five samples exposed to predator cues.

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

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

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction using the package Oligo in R Bioconductor (http://www.r-project.org).

organism: Gasterosteus aculeatus

source_name: Stickleback brain  exposed to predator cues_6 days

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

growth_protocol: The fish were maintained in our laboratory in 104L tanks under 8:16h light/dark photoperiod during the winter period (November to March). An average of 10% of the water in the tanks was recycled each day. The adult fish were fed ad libitum with a mixture of bloodworms, serpula and mysis

extract_protocol: Whole fish brains were individually dissected and placed immediately on ice in 500ml of TRIzol¨ Reagent (Invitrogen, Carlsbad, CA). Total RNA was isolated immediately from individual brains using TRIzol¨ Reagent according to the manufacturerÕs recommendation followed by on column purification with RNeasy kit (QIAGEN GmbH, Hilden, Germany).

treatment_protocol: During the six-day exposure to cues of predators, sticklebacks were exposed to olfactory, visual and tactile cues of rainbow trout, Oncorhynchus mykiss, a natural predator, in order to simulate real predation risk

tag: stress

value: predator cues

value: Adult

tag: sex

value: Female

tag: origin

value: Putah Creek, CA

value: whole brain


title: Stickleback_Not exposed to Predator Cues_rep2

description:
CON_5
This sample is of control brain of stickleback. It is the second of  five control samples not exposed to predator cues.

source_name: Stickleback brain not exposed to predator cues_6 days

value: control


title: Stickleback_Exposed to Predator Cues_rep4

description:
EXP_4
This sample is of brain of sticklebackexposed to predator cues. It is the fourth of  five samples exposed to predator cues.


title: Stickleback_Not exposed to Predator Cues_rep4

description:
CON_2
This sample is of control brain of stickleback. It is the fourth of  five control samples not exposed to predator cues.


title: Stickleback_Exposed to Predator Cues_rep5

description:
EXP_5
This sample is of brain of sticklebackexposed to predator cues. It is the fifth of  five samples exposed to predator cues.


title: LD red/ HD green

description: Single preparation in dye-swap


title: Stickleback_Not exposed to Predator Cues_rep3

description:
CON_3
This sample is of control brain of stickleback. It is the third of  five control samples not exposed to predator cues.


title: Stickleback_Exposed to Predator Cues_rep3

description:
EXP_1
This sample is of brain of sticklebackexposed to predator cues. It is the third of  five samples exposed to predator cues.


title: Stickleback_Not exposed to Predator Cues_rep5

description:
CON_1
This sample is of control brain of stickleback. It is the fifth of  five control samples not exposed to predator cues.


title: U87-SupernatantConcentratedPellet-SerumFree

status: Public on Apr 23 2011

city: Seattle

first: Shile

last: Zhang

state: WA

address: 1441 N 34th Street

institute: Institute for systems biology

description: miRNA expression

hyb_protocol: The purified labeled miRNA probes were hybridized to human miRNA V2 oligo microarrays in a rotating hybridization oven at 10 rpm for 20h at 55 C.

scan_protocol: The chips were scanned at 5-um resolution by using a PerkinElmer ScanArray Express array scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Further, expression data was consolidated to make representative expression profile for each probe and then normalized using quantile method

source_name: Cell Culture Media

label_protocol: 100ng of total RNA was dephosphorylated with calf intestinal alkaline phosphate, and denatured with heat in the presence of dimethyl sulfoxide (DMSO). T4 RNA ligase added the Cyanine 3-cytidine biphosphate (pCp) to the dephosphorylated single stranded RNA. MicroBioSpin 6 columns (Bio-Rad, Hercules, CA) were used to remove any unincorporated cyanine dye from the samples.

growth_protocol: The HepG2 and U87 cells were obtained from the American Type Culture Collection (ATCC, Manassas, VA) and grown in recommended medium containing 10% fetal bovine serum (FBS), 100U/ml penicillin and 100 μg/ml streptomycin (Invitrogen, Carlsbad, CA) at 37 °C under 5% CO2.

extract_protocol: Total RNA was isolated from 300ul of medium samples or 500,000 cells using miRNeasy mini kit per the manufacturer’s protocol (Qiagen, Valencia, CA)

treatment_protocol: For serum depletion experiments, the cells were inoculated and grown for 24 hours with 10% FBS containing media prior to switching to serum-free media. Serum free medium contained the basic medium as provided by Invitrogen (Carlsbad, CA) with 100U/ml penicillin and 100μg/ml streptomycin.

tag: cell culture condition

value: SupernatantConcentratedPellet-SerumFree


title: U87-Pellet-SerumFree

description: miRNA expression

value: Pellet-SerumFree


title: U87-OriginalPellet-SerumFree

description: miRNA expression

value: OriginalPellet-SerumFree


title: U87-ConcentratedPellet-SerumFree

description: miRNA expression

value: ConcentratedPellet-SerumFree


title: U87-SupernatantConcentratedPellet-Serum

description: miRNA expression

value: SupernatantConcentratedPellet-Serum


title: U87-Media-2hrs-Serum

description: miRNA expression


title: U87-ConcentratedPellet-Serum

description: miRNA expression

value: ConcentratedPellet-Serum


title: U87-Cells-2hrs-SerumFree

description: miRNA expression

source_name: Cell Culture


title: U87-OriginalPellet-Serum

description: miRNA expression

value: OriginalPellet-Serum


title: U87-Media-2hrs-SerumFree

description: miRNA expression


title: U87-Cells-2hrs-Serum

description: miRNA expression


title: U87-Pellet-Serum

description: miRNA expression

value: Pellet-Serum


title: T98-Cell-Cytoplastic+Nuclear

description: miRNA expression

value: Cell-Cytoplastic+Nuclear


title: Stickleback_Exposed to Predator Cues_rep1

description:
EXP_2
This sample is of brain of stickleback exposed to predator cues. It is the first of  five samples exposed to predator cues.


title: T98-Original Control-Serum

description: miRNA expression

value: Original Control-Serum


title: HepG2-Media-6hrs-SerumFree

description: miRNA expression


title: T98Cell-Nuclear

description: miRNA expression


title: HepG2-Media-24hrs-SerumFree, 2

description: miRNA expression


title: T98-Media-Original

description: miRNA expression

value: Media-Original


title: HepG2-Media-0hrs-SerumFree

description: miRNA expression


title: HepG2-Cells-24hrs-SerumFree

description: miRNA expression


title: T98-Supernatant-Serum

description: miRNA expression

value: Supernatant-Serum


title: T98-Pellet

description: miRNA expression

value: Pellet


title: T98-Media-Concentrated-Supernatant-Serum

description: miRNA expression

value: Media-Concentrated-Supernatant-Serum


title: HepG2-Cells-2hrs-SerumFree

description: miRNA expression


title: HepG2-Cells-6hrs-SerumFree

description: miRNA expression


title: T98-Cell-Cytoplastic

description: miRNA expression

value: Cell-Cytoplastic


title: HepG2-Media-2hrs-SerumFree

description: miRNA expression


title: HepG2-Media-30hrs-SerumFree+RNase

description: miRNA expression


title: HepG2-Media-30hrs-SerumFree

description: miRNA expression


title: HepG2-Media-2hrs-Serum-2hr

description: miRNA expression


title: HepG2-Media-Pellet-SerumFree

description: miRNA expression

value: Media-Pellet-SerumFree


title: HepG2-Cells-30hrs-SerumFree

description: miRNA expression


title: HepG2-Media-24hrs-SerumFree

description: miRNA expression


title: HepG2-Media-Control-Serum

description: miRNA expression

value: Media-Control-Serum


title: HepG2-Media-Concentrated-2hrs-SerumFree

description: miRNA expression


title: HepG2-Media-Prespin-SerumFree

description: miRNA expression

value: Media-Prespin-SerumFree


title: HepG2-Media-6hrs-Serum

description: miRNA expression


title: HepG2-Media-30hrs-Serum

description: miRNA expression


title: HepG2-Cells-6hrs-Serum

description: miRNA expression


title: HepG2-Cells-30hrs-Serum

description: miRNA expression


title: BEAS-Cell-2hrs-Serum

description: miRNA expression

value: BEAS


title: A549-Media-Control-Serum

description: miRNA expression


title: A549-Media-6hrs-Serum

description: miRNA expression


title: A549-Media-2hrs-Serum

description: miRNA expression


title: A549-Media-2hrs-SerumFree, 2

description: miRNA expression


title: HepG2-Media-24hrs-Serum

description: miRNA expression


title: HepG2-Cells-Control-Serum

description: miRNA expression

value: Cells-Control-Serum


title: HepG2-Cells-2hrs-Serum

description: miRNA expression


title: HepG2-Cells-24hrs-Serum

description: miRNA expression


title: HepG2-Media-Concentrated-Supernatant-2hrs-SerumFree

description: miRNA expression


title: A549-Media-6hrs-SerumFree, 2

description: miRNA expression


title: BEAS-Media-2hrs-Serum

description: miRNA expression


title: A549-Media-24hrs-SerumFree, 2

description: miRNA expression


title: A549-Media-0.5hrs-SerumFree

description: miRNA expression


title: A549-Media-24hrs-Serum

description: miRNA expression


title: A549-Media-0.5hrs-Serum

description: miRNA expression


title: BEAS-Media-2hrs-SerumFree

description: miRNA expression


title: Stickleback_Not exposed to Predator Cues_rep1

description:
CON_4
This sample is of control brain of stickleback. It is the first of  five control samples not exposed to predator cues.

value: control

value: Adult

value: Female

value: Putah Creek, CA

value: whole brain


title: A549-Cells-Control-Serum

description: miRNA expression


title: A549-Cells-6hrs-SerumFree, 2

description: miRNA expression


title: A549-Cells-2hrs-Serum, 2

description: miRNA expression


title: A549-Cells-2hrs-SerumFree, 2

description: miRNA expression


title: A549-Cells-24hrs-SerumFree, 2

description: miRNA expression


title: A549-Cells-24hrs-Serum

description: miRNA expression


title: A549-Supernatant-Concentrated-SerumFree-2hrs

description: miRNA expression


title: A549-Cells-6hrs-Serum

description: miRNA expression


title: A549-Prespin-SerumFree-2hrs

description: miRNA expression


title: A549-Pelet-SerumFree-2hrs

description: miRNA expression


title: A549-Cells-6hrs-SerumFree

description: miRNA expression


title: A549-Cells-2hrs-SerumFree

description: miRNA expression


title: A549-Cells-24hrs-SerumFree

description: miRNA expression


title: A549-Media-Concentrated-SerumFree-2hrs

description: miRNA expression


title: myotube_ETOH_6h_rep2

description:
ETOH.6h.2
replicate 2

value: myotube

value: ETOH


title: T5

city: Pamplona

first: Paul

middle: C.

last: Schröder

email: pschrode@unav.es, fjcorrales@unav.es

state: Navarra

address: Avda. Pío XII, 55

department: Gene Therapy & Hepatology

country: Spain

institute: CIMA (Center for Applied Medical Research) University of Navarra

hyb_protocol: The chemically fragmented cRNA (15 µg) was hybridized to the Affymetrix Mouse Genome MOE430A 2.0 array (Affymetrix, CA, USA).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 from Affymetrix.

data_processing: RMA

source_name: tumor liver tissue

label_protocol: From total RNA, cDNA and then the biotin-labeled antisense cRNA were obtained following the recommendations indicated in the corresponding kits (Affymetrix, CA, USA).

extract_protocol: Tissue specimens were obtained by laparotomy and flash frozen in liquid nitrogen and stored at -80º. RNA extraction was performed using RNeasy Mini kit (Qiagen, West Sussex, UK) according to the manufacturer’s standard protocol. Integrity of RNA was assessed by on-chip electrophoresis using Experion (Bio-Rad, Mississauga, ON, Canada). RNA quality was assessed by ratios A260/A280 close to 2.

value: liver

tag: genotype/variation

value: MAT1A deficient

tag: strain

value: 129 SvJ


title: T4


title: T3


title: T1


title: Low density (10), rep 3

city: Chile

first: Sebastian

last: Boltana

state: Bio BIO

address: Edmundo Larenas s/n, Barrio Universitario. Biotechnology Center

department: Oceanografia

country: Chile

institute: Universidad de Concepcion

description: Seabass 1_10c

hyb_protocol: Each sample (1.65 μg of RNA) was hybridized to a D. labrax array at 65 °C for 17 hours using Agilent’s GE Hybridization Kit. Washes were conducted as recommended by the manufacturer using Agilent’s Gene Expression Wash Pack with stabilization and drying solution.

scan_protocol: Microarray slides were scanned with Agilent Technologies Scanner model G2505C. Spot intensities and other quality control features were extracted with Agilent’s Feature Extraction software version 10.4.0.0.

data_processing: Percentile shift normalization was made to adjust all spot intensities in an array. This normalization takes each column in an experiment independently, and computes the median expression values for this array, across all spots. It then subtracts this value from the expression value of each entity (Bolstad et al, 2003). After Percentile normalization, all data were filtered by comparison of the standard deviation expression among groups (filter by expression). The entities that had values lesser or greater than the standard deviation value were retained. This filter procedure allowed selected genes that have outlier samples, and filter out genes that have a low variation in expression values across all samples. For each transcript two or more probes at non-overlapping positions as near as possible to the 3'-end of each transcript are present in the sea bream microarray platform. The variability between two probes for the same transcript was evaluated using a Pearson correlation coefficient between Probe_1 and Probe_2 for each gene within each experiment. Pearson correlation coefficients also were conduced to estimate the technical variability among arrays, thus ensuring the repeatability and accuracy of the results. A non-parametric Spearman rank-correlation test was used to assess correlation between expression values measured respectively with quantitative real-time PCR and microarray. Statistical test implemented in GeneSpring software GX 11.0 (one-way ANOVA) was used to select transcripts that were differentially expressed (P < 0.05) between control/treatment. One-way ANOVAs were used by search differences in the transcriptomic profile among the different treatments. Pearson and Spearman correlation coefficients were conduced to estimate the technical variability among arrays and qRT-PCR. The statistical test were made using SPSS 17.0 and R Bioconductor software.

organism: Dicentrarchus labrax

source_name: Liver, low density

label_protocol: A loop microarray design approach was taken for the study. All experimental RNA samples were labelled with one dye (Cy3) and each stimulated sample was compared to the low density sample (8-10 kg/m3) labelled with the same dye (Cy3). Denatured samples of RNA were reversed transcribed and indirectly labelled with Cy3. RNA labelling was performed according to the manufacturer’s instructions. Briefly, total RNA (500 ng) was amplified and Cy3-labeled with Agilent’s One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labelling kit) along with Agilent’s One-Color RNA SpikeIn Kit.

extract_protocol: Total RNA was extracted from cell cultures using 1mL of TriReagent (Molecular Research Center) per well cell culture, following the manufacturer’s instructions. RNA concentration was quantified using Nanodrop ND-1000, and RNA integrity and quality was assessed using a Bioanalyzer 2100 with the RNA 6000 Nano LabChip kit (Agilent Technologies). The RNA integrity number (RIN) was calculated for each sample using the Agilent 2100 Expert software. Only RNAs with a RIN number > 7 were processed (to reduce experimental biases). Total RNA (2μg) was used to synthesize cDNA with SuperScript III Transcriptase (Invitrogen) and oligo-dT primer (Promega).

treatment_protocol: Adult European seabass (Dicentrarchus labrax) of body weight 30e40 g were obtained from the Centro de Investigación y Formación Pesquera y Acuícola El Toruño (Puerto de Santa María, Cádiz, Spain). The ﬁsh were acclimatized to laboratory conditions for 15 days before experiments. Fish were held in tanks with recirculating water under a photoperiod of 12 h light/12 h dark and natural conditions of temperature (19-21Cº) and fed twice a day with a commercial diet (Skretting). For density experiments, ﬁsh were exposed to a crowding stress by increasing the density of the tanks from 8-10 kg/m3 (hereon, low density conditions) to 50 kg/m3 (hereon, high density conditions).

tag: developmental stage

value: adult

tag: treatment

value: acclimation to low density

tag: density

tag: treatment duration

value: 15 day


title: T2


title: High density (50), rep 1

description: Seabass 1_50a

source_name: Liver, high density

value: acclimation to high density


title: High density (50), rep 2

description: Seabass 1_50b


title: Low density (10), rep 2

description: Seabass 1_10b


title: NT4

source_name: peritumor liver tissue


title: NT5


title: NT3


title: A549-Media-30hrs-SerumFree

description: miRNA expression


title: A549-Media-6hrs-SerumFree

description: miRNA expression


title: High density (50), rep 3

description: Seabass 1_50c


title: NT2


title: Low density (10), rep 1

description: Seabass 1_10a


title: PGN 6h (2)

description: Pool of 3 cultures.

hyb_protocol: Each sample (1.65 μg of RNA) was hybridized to an S. aurata array (ID 024502, Agilent) at 65 °C for 17 hours using Agilent’s GE Hybridization Kit. Washes were conducted as recommended by the manufacturer using Agilent’s Gene Expression Wash Pack with stabilization and drying solution.

scan_protocol: Microarrays slides were scanned with Agilent Technologies Scanner model G2505B. Spot intensities and other quality control features were extracted with Agilent’s Feature Extraction software version 10.4.0.0. One-channel TIFF images were imported into the GeneSpring software GX 11.0. The assessment of spot quality was done by ratio (R) between the difference of signal and background intensities (SI − SB) and sum of their standard deviations (SDI + SDB).

organism: Sparus aurata

source_name: Head-Kidney macrophages, PGN, 6h

label_protocol: A loop microarray design approach was taken for the study. All experimental RNA samples were labelled with one dye (Cy3) and each stimulated sample was compared to the control sample (pool without stimulation) labelled with the same dye (Cy3). Denatured samples of RNA were reversed transcribed and indirectly labelled with Cy3. RNA labelling was performed according to the manufacturer’s instructions. Briefly, total RNA (500 ng) was amplified and Cy3-labeled with Agilent’s One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labelling kit) along with Agilent’s One-Color RNA SpikeIn Kit.

extract_protocol: Total RNA was extracted from cell cultures using 1mL of TriReagent (Molecular Research Center) per well cell culture, following the manufacturer’s instructions. RNA concentration was quantified using Nanodrop ND-1000, and RNA integrity and quality were assessed using a Bioanalyzer 2100 with the RNA 6000 Nano LabChip kit (Agilent Technologies). The RNA integrity number (RIN) was calculated for each sample using the Agilent 2100 Expert software. Only RNAs with a RIN number > 7 were processed (to reduce experimental biases). Total RNA (2μg) was used to synthesize cDNA with SuperScript III Transcriptase (Invitrogen) and oligo-dT primer (Promega).

treatment_protocol: For microarray screening, 36 head-kidney macrophage cell cultures were or were not stimulated with PGN and LPS from E. coli O111:B4 strain (10 μg/mL): cell cultures without stimulation (control, n = 9), stimulated with PGN for 1 hour (n = 9), for 6 hours (n = 9), and with LPS during 6 hours (n = 9). Individuals RNAs were grouped into pools from 3 cell cultures for each time point and treatment.

tag: cell type

value: head-kidney macrophages

value: peptidoglycan (PGN) from E. coli (0111:B4)

tag: treatment exposure

value: 6 hours


title: PGN 6h (3)

description: Pool of 3 cultures.


title: PGN 1h (2)

description: Pool of 3 cultures.

source_name: Head-Kidney macrophages, PGN, 1h

value: 1 hours


title: PGN 1h (3)

description: Pool of 3 cultures.


title: PGN 6h (1)

description: Pool of 3 cultures.


title: PGN 1h (1)

description: Pool of 3 cultures.


title: LPS 6h (3)

description: Pool of 3 cultures.

source_name: Head-Kidney macrophages, LPS, 6h

value: lipopolysaccharide (LPS) from E. coli (0111:B4)


title: NT1


title: A549-Media-control

description: miRNA expression

value: Media-control


title: A549-Media-2hrs-SerumFree

description: miRNA expression


title: A549-Cells-2hrs-Serum

description: miRNA expression


title: LPS 6h (2)

description: Pool of 3 cultures.


title: spheroid-derived cells_rep3

city: Atlanta

first: Roman

middle: F. N.

last: Mezencev

state: GA

address: 310 Ferst Dr

department: School of Biology

institute: Georgia Institute of Technology

description: culture of OVCAR-3-derived spheroids

hyb_protocol: as per manufacturer's protocol

scan_protocol: as per manufacturer's protocol

data_processing: Affymetrix Expression Console Software Version 5.0 using the default MAS5.0 3'-expression workflow

source_name: epithelial ovarian cancer

label_protocol: mRNA was labeled using the IVT Labeling Kit (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions

growth_protocol: Spheroid-derived cells cultured in ultra-low attachment Petri dishes (Corning Incorporated, Corning, NY) in DMEM/F12 (1:1) medium supplemented with 0.4% bovine serum albumin (BSA, Sigma-Aldrich, St. Louis, MO), 20 ng/mL epidermal growth factor (EGF, Invitrogen), 10 ng/mL basic fibroblast growth factor (bFGF, Sigma-Aldrich), 5 µg/ml insulin (Sigma-Aldrich) and 1% antibiotic-antimycotic solution.

extract_protocol: RNA extracted using Arcturus PicoPure RNA Isolation Kit (Applied Biosciences, Carlsbad, CA) according to the manufacturer’s instructions

value: OVCAR-3_derived stem cell-like cells

tag: culture type

value: suspension culture


title: spheroid-derived cells_rep1

description: culture of OVCAR-3-derived spheroids


title: A549-Media-2hrs

description: miRNA expression


title: spheroid-derived cells_rep2

description: culture of OVCAR-3-derived spheroids


title: A549-Media-24hrs-SerumFree

description: miRNA expression


title: WT3

source_name: wild type liver tissue

value: wild type

tag: tissue


title: WT5


title: ovarian carcinoma OVCAR-3 cell line_rep2

description: subconfluent culture of OVCAR-3 cell line

growth_protocol: cells maintained in RPMI 1640 medium supplemented with 10% FBS (Atlanta Biologicals, Lawrenceville, GA) and 1% antibiotic-antimycotic solution (Mediatech-Cellgro, Manassas, VA)

tag: cell line

value: OVCAR-3 parental (progenitor)

value: adherent culture


title: LPS 6h (1)

description: Pool of 3 cultures.


title: WT4

value: liver


title: Control (2)

description: Pool of 3 cultures.

source_name: Head-Kidney macrophages, control


title: ovarian carcinoma OVCAR-3 cell line_rep1


title: WT2


title: breast biopsy, sample 11 rep 1

status: Public on Apr 22 2011

city: Nashville

first: Jennifer

last: Pietenpol

state: TN

address: 652 Preston Research Building, 23rd Avenue South at Pierce

institute: Vanderbilt University Medical Center

description:
6826-A- 589JP54
Gene expression data from pretreatment breast needle biopsies.

hyb_protocol: See Vanderbilt Microarray Shared Resource (http://array.mc.vanderbilt.edu/).

data_processing: The data were analyzed for differentially expressed probes between responder and non-responder patient tumor samples. Data was RMA summarized, quantile normalized and log2 transformed using GeneSpring GX Software (Agilent).

source_name: breast needle biopsy, pretreatment, non-pCR

growth_protocol: All samples are from frozen primary breast needle biopsies.

extract_protocol: Frozen biopsies were sectioned and laser capture microdissected for invasive tumor cells, and total RNA was isolated according to the manufacturer's instructions.

treatment_protocol: All samples are from pretreatment patients.

value: breast tumor biopsy

value: pre-dose-dense docetaxel

tag: pathological complete response

value: no

tag: sample

tag: replicate


title: ovarian carcinoma OVCAR-3 cell line_rep3


title: Control (3)

description: Pool of 3 cultures.

value: adult


title: breast biopsy, sample 12 rep 2

description:
6827-B- 589JP57
Gene expression data from pretreatment breast needle biopsies.

scan_protocol: See Vanderbilt Microarray Shared Resource (http://array.mc.vanderbilt.edu/).


title: breast biopsy, sample 8 rep 2

description:
6819-B- 589JP39
Gene expression data from pretreatment breast needle biopsies.

label_protocol: See Vanderbilt Microarray Shared Resource (http://array.mc.vanderbilt.edu/).


title: breast biopsy, sample 11 rep 2

description:
6826-B- 589JP55
Gene expression data from pretreatment breast needle biopsies.


title: breast biopsy, sample 9 rep 1

description:
6820-A- 589JP46
Gene expression data from pretreatment breast needle biopsies.


title: Control (1)

description: Pool of 3 cultures.


title: breast biopsy, sample 7 rep 2

description:
6817-B- 589JP51
Gene expression data from pretreatment breast needle biopsies.


title: breast biopsy, sample 12 rep 1

description:
6827-A- 589JP56
Gene expression data from pretreatment breast needle biopsies.


title: breast biopsy, sample 10 rep 2

description:
6821-B- 589JP37
Gene expression data from pretreatment breast needle biopsies.


title: breast biopsy, sample 8 rep 1

description:
6819-A- 589JP38
Gene expression data from pretreatment breast needle biopsies.


title: breast biopsy, sample 9 rep 2

description:
6820-B- 589JP47
Gene expression data from pretreatment breast needle biopsies.


title: breast biopsy, sample 10 rep 1

description:
6821-A- 589JP36
Gene expression data from pretreatment breast needle biopsies.


title: breast biopsy, sample 7 rep 1

description:
6817-A- 589JP50
Gene expression data from pretreatment breast needle biopsies.


title: breast biopsy, sample 6 rep 1

description:
6815-A- 589JP48
Gene expression data from pretreatment breast needle biopsies.


title: breast biopsy, sample 6 rep 2

description:
6815-B- 589JP49
Gene expression data from pretreatment breast needle biopsies.


title: WT1


title: breast biopsy, sample 5 rep 1

description:
6814-A- 589JP44
Gene expression data from pretreatment breast needle biopsies.


title: breast biopsy, sample 3 rep 2

description:
6812-B- 589JP43
Gene expression data from pretreatment breast needle biopsies.


title: breast biopsy, sample 4 rep 2

description:
6813-B- 589JP52
Gene expression data from pretreatment breast needle biopsies.

source_name: breast needle biopsy, pretreatment, pCR

value: yes


title: breast biopsy, sample 5 rep 2

description:
6814-B- 589JP45
Gene expression data from pretreatment breast needle biopsies.


title: breast biopsy, sample 4 rep 1

description:
6813-A- 589JP32
Gene expression data from pretreatment breast needle biopsies.


title: breast biopsy, sample 2 rep 2

description:
6811-B- 589JP41
Gene expression data from pretreatment breast needle biopsies.


title: breast biopsy, sample 3 rep 1

description:
6812-A- 589JP42
Gene expression data from pretreatment breast needle biopsies.


title: breast biopsy, sample 2 rep 1

description:
6811-A- 589JP40
Gene expression data from pretreatment breast needle biopsies.


title: breast biopsy, sample 1 rep 1

description:
6807-A- 589JP35
Gene expression data from pretreatment breast needle biopsies.


title: breast biopsy, sample 1 rep 2

description:
6807-B- 589JP53
Gene expression data from pretreatment breast needle biopsies.


title: 2% polydextrose vessel 4

city: Turku

first: Esa

last: Alhoniemi

address: Itäinen Pitkäkatu 4 C

country: Finland

institute: Pharmatest Services Ltd

hyb_protocol: Affymetrix standard protocol; after fragmentation, 15 ug of cRNA was hybridized for 16 hours at 45 C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in Affymetrix Fluidics Station.

scan_protocol: Affymetrix standard protocol using type M10 scanner

data_processing: The analysis was performed using R/Bioconductor, and the data was normalized using GC-RMA algorithm.

source_name: 2% PDX fermentation metabolite-treated, 24h

label_protocol: Affymetrix standard protocol

growth_protocol: Caco-2 cells were maintained in Dulbecco's modified Eagle's medium supplemented with non-essential amino acids (Invitrogen, Carlsbad, CA, US), 1 mM sodium Puryvate (Invitrogen), and 20 Uml-1 penicillin (Invitrogen), 20 µgml-1 streptomycin (Invitrogen), 0.5 µgml-1 amphotericin (Invitrogen), and 5 % fetal bovine serum (Invitrogen) at +37 °C in 5 % air atmosphere.

extract_protocol: Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.

treatment_protocol: Polydextrose was fermented with semi-continuous colon silmulator in which a single unit consists of four sequentially connected glass vessels, V1 to V4, in which the conditions are adjusted to represent the different compartments of the colon, V1 representing ascending colon, V2 transverse colon, V3 descending colon, and V4 sigmoid/rectum area. The simulation was performed for 48 hours as in Makivuokko H, Nurmi J, Nurminen P, Stowell J, Rautonen N (2005) In vitro effects on polydextrose by colonic bacteria and caco-2 cell cyclooxygenase gene expression. Nutr Cancer 52 (1):94-104. Non-differentiated Caco-2 cells were treated with 5mM butyrate, 100 mM NaCl and 10 % (vol/vol) containing 0%, 1% and 2% polydextrose fermentation metabolites from which bacterial cells and other debris was removed by centifugation (10 000 × g, 5 minutes)diluted in serum-free DMEM for 24 hours.

value: non-differentiated Caco-2 intestinal epithelial cell line


title: 1% polydextrose vessel 4

source_name: 1% PDX fermentation metabolite-treated, 24h


title: 1% polydextrose vessel 1


title: 2% polydextrose vessel 1


title: 2% polydextrose vessel 2


title: 0% polydextrose vessel 4

source_name: 0% PDX fermentation metabolite-treated, 24h


title: 5 mM butyrate

source_name: 5 mM butyrate treated, 24h


title: 1% polydextrose vessel 2


title: 2% polydextrose vessel 3


title: 0% polydextrose vessel 3


title: Medium-only

source_name: medium treated, 24h


title: 0% polydextrose vessel 1


title: 1% polydextrose vessel 3


title: 100 mM NaCl

source_name: 100 mM NaCl treated, 24h


title: 0% polydextrose vessel 2


title: Bevacizumab (Avastin) 17.1 (MouseWG-6)

city: Houston

first: Tina

last: Cascone

state: TX

address: 1515 Holcombe Blvd.

department: Cancer Medicine

institute: UT MD Anderson Cancer Center

hyb_protocol: Each of 1.5 ug of biotinylated cRNAs was hybridized to both Illumina Human WG-6 V3 and Mouse WG-6 V2 microarrays at the same time.

scan_protocol: Signals were developed by Amersham fluorolink streptavidin-Cy3 (GE Health care Bio-Sciences, Little Chalfont, UK). Gene expression data were collected by using Illumina bead Array Reader confocal scanner (BeadStation 500GXDW; Illumina Inc.)

data_processing: Read out files from the Illumina scanner were normalized using RMA and log2base transformed using the BRB-ArrayTools developed by Richard Simon and the BRB-Tools development team. Class comparison between vehicle and drug-treated mice was performed by the BRB-ArrayTools using a p-value statistical cut-off and estimation of the false discovery rate.

label: Biotin labeled

source_name: Subcutaneous xenograft (murine) from a mouse treated with bevacizumab (10 mg/kg) 17.1

label_protocol: Biotin labeled cRNA samples for hybridization were prepared by using Illumina Total Prep RNA Amplification Kit (Ambion Inc., Austin, TX). One microgram of total RNA was used for the synthesis of cDNA and followed by an amplification and biotin labeling.

extract_protocol: Total RNA was isolated from the cancer tissues by using mirVanaTM miRNA isolation Kit (Ambion Inc., Austin, TX) according to manufacturer’s protocol.

value: Athymic nude mouse

tag: gender

value: male

tag: age

value: 5-8 weeks

tag: xenografts

value: 2 million human H1975 NSCLC cells

value: lung adenocarcinoma

value: bevacizumab


title: Bevacizumab (Avastin) 18.1 (MouseWG-6)

source_name: Subcutaneous xenograft (murine) from a mouse treated with bevacizumab (10 mg/kg) 18.1


title: 4-Va24-3-N

city: Chicago

first: Albert

last: Bendelac

address: 929 East 57th Street, GCIS W506

department: Pathology

institute: The University of Chicago

hyb_protocol: 12µg of fragmented cRNA was hybridized to the array for 16 hours at 45°C and 60 rpm.  The array was washed and stained with streptavidin phycoerythrin according to the Affymetrix GeneChip protocol.

scan_protocol: The array was scanned using the Affymetrix Gene Chip Scanner 3000 7G and the CEL intensity files was generated using Gene Chip Operating Software (MicroArray Suite 5.0).

data_processing: Data was generated using MicroArray Suite 5.0 and scaled to a median intensity of 500.

source_name: Individual #4, CD1d-aGC+ Va24- T cell clone #3, resting

label_protocol: Biotin-labeled cRNA was generated using the Genechip Expression 3´ amplification IVT labeling kit (Affymetrix).

extract_protocol: Trizol protocol (Invitrogen) followed by the RNeasy Mini kit (Qiagen)

treatment_protocol: Stimulated 18 days prior to analysis with feeder cells consisting of irradiated allogenic PBMC (50,000/well) and irradiated EBV-transformed cells (5,000/well), in medium containing 1μg/ml PHA and 100U/ml human IL-2.

value: CD1d-aGC+ Va24- T cell clone


title: Vehicle 5.2 (PBS) control (MouseWG-6)

source_name: Subcutaneous xenograft (murine) from a mouse treated with control (PBS) vehicle 5.2

value: athymic nude mouse

value: PBS


title: 4-Va24-4-S

source_name: Individual #4, CD1d-aGC+ Va24- T cell clone #4, stimulated

treatment_protocol: Stimulated 3 days prior to analysis with feeder cells consisting of irradiated allogenic PBMC (50,000/well) and irradiated EBV-transformed cells (5,000/well), in medium containing 1μg/ml PHA and 100U/ml human IL-2.


title: 4-Va24-3-S

source_name: Individual #4, CD1d-aGC+ Va24- T cell clone #3, stimulated


title: Bevacizumab (Avastin) 19.1 (MouseWG-6)

source_name: Subcutaneous xenograft (murine) from a mouse treated with bevacizumab (10 mg/kg) 19.1


title: Vehicle 7.1 (PBS) control (MouseWG-6)

source_name: Subcutaneous xenograft (murine) from a mouse treated with control (PBS) vehicle 7.1


title: 4-NKT-9-N

source_name: Individual #4, NKT cell clone #9, resting

value: NKT cell clone


title: A880STM1 in glycerol, biological rep2

city: Taipei

first: yu-chen

last: Huang

address: Academia Sinica. 128 Sec. 2

country: Taiwan

institute: Institute of Molecular Biology

description: Gene expression from A880/STM1 in glycerol

hyb_protocol: Following fragmentation, 1.1 ug of cRNA were hybridized for 16.5 hr at 45 C with GeneChip (Yeast 2.0). Washing and staining were done in the Affymetrix GeneChip Fluidics Station-450.

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

data_processing: Data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Saccharomyces cerevisiae

source_name: A880STM1 in glycerol

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (GeneChip Expression Analysis Technical Manual rev5, Affymetrix).

growth_protocol: Yeast cells were culture in SC (0.67% yeast nitrogen base without amino acids and 0.2% dropout mix) with 2% glucose to 1 OD600. Cells were then washed with and diluted into SC with 2% glycerol and cultured for an additional 12 hours to a cell density of 0.4-0.8 OD600.

extract_protocol: Total yeast RNAs were extracted from whole cells with phenol-chloroform according to Del Aguila et al. [BMC Mol Biol, 6, 9 (2005)].

tag: genotype/variation

tag: cell

value: whole cell

tag: growth phase

value: early log phase


title: 4-NKT-1-N

source_name: Individual #4, NKT cell clone #1, resting


title: A880STM1K in glycerol, biological rep1

description: Gene expression from A880/STM1K in glycerol

source_name: A880STM1K in glycerol


title: Mouse suprachiasmatic nucleus expression at CT2 and CT14

city: Kyoto

first: Hitoshi

last: Okamura

department: Department of Systems Biology

country: Japan

institute: Kyoto University, Graduate School of Pharmaceutical Sciences

hyb_protocol: Hybridization was performed with the GeneChip Mouse Genome 430 2.0 array (Affymetrix) according to the manufacturer's protocol.

scan_protocol: The GeneChip was scanned with the GeneChip Scanner 3000 (Affymetrix) following the manufacturer's instructions.

data_processing: Values were normalized with the MAS5 (GCOS 1.4) algorithm, using the default analysis settings and global scaling as normalization method. The resulting value of mean target intensity (TGT) was 111.55.

source_name: Pool of suprachiasmatic nucleus punches taken at CT2 and CT14

label_protocol: Biotin-labeled cRNA were prepared according to the standard one-cycle target labelling protocol (Affymetrix) with 2.5 μg of total RNA.

extract_protocol: RNeasy Micro Kit (QIAGEN).

tag: strain

value: 2 months

value: suprachiasmatic nucleus (SCN)

tag: treatment

value: constant darkness

tag: time

value: CT2, CT14

tag: sample type

value: pool


title: Vehicle 2.1 (PBS) control (MouseWG-6)

source_name: Subcutaneous xenograft (murine) from a mouse treated with control (PBS) vehicle 2.1

value: Athymic nude mouse


title: 4-Va24-4-N

source_name: Individual #4, CD1d-aGC+ Va24- T cell clone #4, resting

tag: cell type


title: 4-NKT-9-S

source_name: Individual #4, NKT cell clone #9, stimulated


title: 4-NKT-1-S

source_name: Individual #4, NKT cell clone #1, stimulated


title: A880STM1K in glycerol, biological rep2


title: 13690907 - Col0 13dap_rep3 vs. Col0 16dap_rep3

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: WP3 : Biodiversity of seed traits : state of the art

hyb_protocol: Col0 16dap_rep3 Cy5 / Col0 13dap_rep3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 6.0, Cy3:pmt voltage 532nm,500V,laser power 30%, Cy5:635nm,pmt voltage 500V,laser power 30%

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

organism: Arabidopsis thaliana

source_name: Col0 16dap

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

growth_protocol: seed - Media: soil Temp: 22°C Light: 16h (days) H: 60%

extract_protocol: Col0 16dap_rep3:2.3ug. (Qiagen RNeasy)

treatment_protocol: no treatment

tag: ecotype

tag: developmental stage

value: 16 days after j0 (Boyes et al. Plant Cell 2001)

source_name: Col0 13dap

extract_protocol: Col0 13dap_rep3:4.41ug. (Qiagen RNeasy)

value: 13 days after j0 (Boyes et al. Plant Cell 2001)


title: 13690909 - Col0 10dap_rep3 vs. Col0 13dap_rep3

hyb_protocol: Col0 13dap_rep3 Cy5 / Col0 10dap_rep3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 10dap

extract_protocol: Col0 10dap_rep3:2.5ug. (Qiagen RNeasy)

value: 10 days after j0 (Boyes et al. Plant Cell 2001)


title: 13561273 - Col0 10dap_rep3 vs. Col0 7dap_rep3

hyb_protocol: Col0 7dap_rep3 Cy5 / Col0 10dap_rep3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 7dap

extract_protocol: Col0 7dap_rep3:4.41ug. (Qiagen RNeasy)

value: 7 days after j0 (Boyes et al. Plant Cell 2001)


title: A880 in glycerol, biological rep2

description: Gene expression from A880 in glycerol

source_name: A880 in glycerol


title: 13690910 - Col0 13dap_rep3 vs. Col0 10dap_rep3

hyb_protocol: Col0 10dap_rep3 Cy5 / Col0 13dap_rep3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: A880 in glycerol, biological rep1

description: Gene expression from A880 in glycerol


title: A880STM1 in glycerol, biological rep1


title: 13690911 - Col0 7dap_rep3 vs. Col0 10dap_rep3

hyb_protocol: Col0 10dap_rep3 Cy5 / Col0 7dap_rep3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13690908 - Col0 16dap_rep3 vs. Col0 13dap_rep3

hyb_protocol: Col0 13dap_rep3 Cy5 / Col0 16dap_rep3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13561270 - Col0 4dap_rep3 vs. Col0 7dap_rep3

hyb_protocol: Col0 7dap_rep3 Cy5 / Col0 4dap_rep3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 4dap

extract_protocol: Col0 4dap_rep3:4.36ug. (Qiagen RNeasy)

value: 4 days after j0 (Boyes et al. Plant Cell 2001)


title: 13552311 - Col0 7dap_rep3 vs. Col0 4dap_rep3

hyb_protocol: Col0 4dap_rep3 Cy5 / Col0 7dap_rep3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 4-CD4-3-N

source_name: Individual #4, CD4 T cell clone #3, resting

value: CD4 T cell clone


title: 4-CD4-3-S

source_name: Individual #4, CD4 T cell clone #3, stimulated


title: 13561504 - Col0 10dap_rep2 vs. Col0 7dap_rep2

hyb_protocol: Col0 7dap_rep2 Cy5 / Col0 10dap_rep2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: seed - Media: soil Temp: 22°C Light: 16 h (day) H: 60%

extract_protocol: Col0 7dap_rep2:7.6ug. (Qiagen RNeasy)

extract_protocol: Col0 10dap_rep2:5.67ug. (Qiagen RNeasy)


title: 4-CD4-2-S

source_name: Individual #4, CD4 T cell clone #2, stimulated


title: June 6th Gills S

city: Plouzane

first: Arnaud

last: Huvet

address: Ifremer centre de Brest BP 70

department: Physiologie Fonctionnelle des Organismes Marins

institute: IFREMER

hyb_protocol: Equimolar amounts of cDNA samples and cDNA reference, labeled with Cy5 and Cy3 respectively, were SpeedVac evaporated and mixed into a single pool with the hybridization buffer (ChipHyb™ hybridization buffer, Ventana Discovery, Tucson, AZ, USA). They were then co-hybridized on the same microarray slide in a Ventana hybridization station (Ventana Discovery, Tucson, AZ, USA). Hybridizations were performed at the INRA IFR 140 transcriptomic facility (Rennes, France). Following pre-hybridization (with ChipSpread buffer, containing 4×SSC and 0.2% SDS), hybridization was conducted overnight at 42°C in a humidified chamber, according to manufacturer’s instructions. The arrays were washed twice with Ribowash solution (0.1 M Tris, 0.05 M EDTA, and 0.4 M NaCl), twice with 0.1×SSC and finally centrifuged to dry.

scan_protocol: After the hybridization step, microarray slides were scanned using a Scanner Genepix 4000B (Axon Instruments Inc.) according to the following parameters: Cy 5 Photo Multiplier Tube (PMT): 550 and Cy 3 PMT: 590.

data_processing: This process was repeated for each of the hybridized slides. The images (16-bits TIF images) were then analyzed with Genepix pro 5.1 software (Axon Instruments Inc.) according to manufacturer’s instructions. Spots were filtered for quality according to the following criteria: spot shape, median intensity of the spot, homogeneity of the local background pixels and spot pixel intensities. Spots showing inadequate signals were eliminated, as were those with noisy backgrounds and those with more than 20% saturated pixels in both channels. Transformation and normalization of hybridization data were performed to minimize variation arising from technical differences in RNA quality, probe labeling, and hybridization conditions between experiments. First, a logarithmic transformation was performed for each signal intensity (giving “log values”). The “log values” were median centered. Correction was next performed for differences in the variance across the range of gene expression levels using the formula: (corrected Cy5 log value)i = (Cy5 log value)i – (Cy3 log value)i + (mean Cy3 log value), where Cy5 log value represents sample signal intensity, Cy3 log value represents the reference signal intensity, and mean Cy3 log value represents the mean of all green values obtained for the gene “i” across the different conditions.

organism: Magallana gigas

source_name: pool of 8 sensitive oyster gills, sampled the 6th June 2005

extract_protocol: Total RNA was isolated using Extract-All (Eurobio), RNA quality was assessed by Agilent 6000 nano reagents (Agilent), and RNA concentration was measured using an ND-1000 spectrophotometer (Nanodrop).

treatment_protocol: in situ rearing before summer mortality (South Britanny, France)

value: pool of 8 gills oysters

tag: line

value: sensitive

tag: field

value: in situ rearing (South Britanny, France)

value: males and females

tag: tissue

value: gills

source_name: pool of 10 wild oyster

label_protocol: 5µg of total RNA directly labeled by reverse transcription using the Direct ShipShot labeling kit (Promega). All these Cy3 reference samples were pooled and then divided once more into several samples to obtain homogeneous reference.

extract_protocol: Total RNA was isolated using Extract-All (Eurobio). RNA quality was assessed by Agilent 6000 nano reagents (Agilent). RNA concentration was measured using an ND-1000 spectrophotometer (Nanodrop).

value: pool of 10 oysters

value: no selection (wild oysters)

tag: sampling

value: the 10th May 2007

value: Brest, France

value: all tissues (whole oyster)


title: 13561500 - Col0 7dap_rep2 vs. Col0 10dap_rep2

hyb_protocol: Col0 10dap_rep2 Cy5 / Col0 7dap_rep2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: June 20th Gills S

source_name: pool of 8 sensitive oyster gills, sampled the 20th June 2005

label_protocol: 5µg of total RNA directly labeled by reverse transcription using the Direct ShipShot labeling kit (Promega).

tag: sample

tag: gender


title: BY4741 in glycerol, biological rep2

description: Gene expression from BY4741 in glycerol

source_name: BY4741 in glycerol

value: whole cell

value: early log phase


title: June 6th Gills R

source_name: pool of 8 resistant oyster gills, sampled the 6th June 2005

value: resistant


title: June 20th Gills R

source_name: pool of 8 resistant oyster gills, sampled the 20th June 2005


title: 13550763 - Col0 13dap_rep2 vs. Col0 10dap_rep2

hyb_protocol: Col0 10dap_rep2 Cy5 / Col0 13dap_rep2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: 10 days after j0 (Boyes et al. Plant Cell 2001)

extract_protocol: Col0 13dap_rep2:3.6ug. (Qiagen RNeasy)

value: 13 days after j0 (Boyes et al. Plant Cell 2001)


title: 4-CD4-2-N

source_name: Individual #4, CD4 T cell clone #2, resting


title: BY4741 in glycerol, biological rep1

description: Gene expression from BY4741 in glycerol


title: May 25th Gills S

source_name: pool of 8 sensitive oyster gills, sampled the 25th May 2005


title: 1-Va24-7-S

source_name: Individual #1, CD1d-aGC+ Va24- T cell clone #7, stimulated

value: CD1d-aGC+ Va24- T cell clone


title: May 25th Gills R

source_name: pool of 8 resistant oyster gills, sampled the 25th May 2005


title: 1-Va24-7-N

source_name: Individual #1, CD1d-aGC+ Va24- T cell clone #7, resting


title: 13561256 - Col0 10dap_rep2 vs. Col0 13dap_rep2

hyb_protocol: Col0 13dap_rep2 Cy5 / Col0 10dap_rep2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 13dap

source_name: Col0 10dap


title: 1-Va24-4-S

source_name: Individual #1, CD1d-aGC+ Va24- T cell clone #4, stimulated


title: 13550750 - Col0 7dap_rep2 vs. Col0 4dap_rep2

hyb_protocol: Col0 4dap_rep2 Cy5 / Col0 7dap_rep2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 4dap

extract_protocol: Col0 4dap_rep2:5.639ug. (Qiagen RNeasy)

value: 4 days after j0 (Boyes et al. Plant Cell 2001)

source_name: Col0 7dap

value: 7 days after j0 (Boyes et al. Plant Cell 2001)


title: June 20th Muscle R

source_name: pool of 8 resistant oyster muscle, sampled the 20th June 2005

value: pool of 8 muscle oysters

value: muscle


title: 1-Va24-4-N

hyb_protocol: 12µg of fragmented cRNA was hybridized to the array for 16 hours at 45°C and 60 rpm.  The array was washed and stained with streptavidin phycoerythrin according to the Affymetrix GeneChip protocol.

source_name: Individual #1, CD1d-aGC+ Va24- T cell clone #4, resting


title: June 20th Muscle S

source_name: pool of 8 sensitive oyster muscle, sampled the 20th June 2005

value: sensitive

value: in situ rearing (South Britanny, France)

value: males and females

source_name: pool of 10 wild oyster


title: ZES, Pig 4751, LAD

first: Andrew

middle: D

hyb_protocol: The resulting cDNA was hybridized to the GeneChip Porcine Genome array for 16 hours at 45 degrees C.

scan_protocol: Arrays were scanned with the Affymetrix GeneChip Scanner 3000

data_processing: Affymetrix .CEL files were processed using the Affymetrix Expression Console Software version 5.0. Files were procssed using the default MAS5 3' expression workflow.

organism: Sus scrofa

source_name: Pig 4751 implanted with zotarolimus-eluting stent in the left anterior descending artery

label_protocol: 3 micrograms of amplified cDNA was fragmented and labeled with Encore Biotin Module according to the manufacturer's instructions.

growth_protocol: Stented arteries were collected at 28 days following angioplasty and implantation.

extract_protocol: RNA was extracted using the Rneasy kit according to the manufacturer's instructions.

treatment_protocol: Tissues was manually dissected from each stent and 10-20 mg was ground with a Polytron homogenizer in Rneasy lysis buffer.

tag: breed

value: Yorkshire farm pigs

tag: stent

value: zotarolimus-eluting stent


title: ZES, Pig 4751, RCA

source_name: Pig 4751 implanted with zotarolimus-eluting stent in the right coronary artery


title: 1-NKT-22-S

source_name: Individual #1, NKT cell clone #22, stimulated

value: NKT cell clone


title: ZES, Pig 4757, LAD

source_name: Pig 4757 implanted with zotarolimus-eluting stent in the left anterior descending artery


title: 13561259 - Col0 4dap_rep2 vs. Col0 7dap_rep2

hyb_protocol: Col0 7dap_rep2 Cy5 / Col0 4dap_rep2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13550748 - Col0 13dap_rep2 vs. Col0 16dap_rep2

hyb_protocol: Col0 16dap_rep2 Cy5 / Col0 13dap_rep2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 16dap

extract_protocol: Col0 16dap_rep2:5.42ug. (Qiagen RNeasy)

value: 16 days after j0 (Boyes et al. Plant Cell 2001)


title: 13552415 - Col0 16dap_rep2 vs. Col0 13dap_rep2

hyb_protocol: Col0 13dap_rep2 Cy5 / Col0 16dap_rep2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: SES, Pig 4750, LAD

source_name: Pig 4750 implanted with a sirolimus-eluting stent in the left anterior descending artery

value: sirolimus-eluting stent


title: ZES, Pig 4757, RCA

source_name: Pig 4757 implanted with zotarolimus-eluting stent in the right coronary artery


title: May 25th Muscle S

source_name: pool of 8 sensitive oyster muscle, sampled the 25th May 2005

value: pool of 10 oysters

value: no selection (wild oysters)

value: the 10th May 2007

value: Brest, France

value: all tissues (whole oyster)


title: 13561493 - Col0 10dap vs. Col0 7dap

hyb_protocol: Col0 7dap Cy5 / Col0 10dap Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,530V,laser power 100%, Cy5:635nm,pmt voltage 700V,laser power 100%

growth_protocol: seed - Media : soil Hygrometry : 60% Temperature : 22°C Light : 16 h (day)

extract_protocol: Col0 7dap:2.5ug. (Qiagen RNeasy)

extract_protocol: Col0 10dap:650ng. (Qiagen RNeasy)

value: 10 days after j0 (Boyes et al. Plant Cell 2001)


title: May 25th Muscle R

source_name: pool of 8 resistant oyster muscle, sampled the 25th May 2005

value: resistant


title: 1-NKT-14-N

source_name: Individual #1, NKT cell clone #14, resting

extract_protocol: Trizol protocol (Invitrogen) followed by the RNeasy Mini kit (Qiagen)


title: June 6th Muscle S

source_name: pool of 8 sensitive oyster muscle, sampled the 6th June 2005

value: pool of 8 muscle oysters


title: BMS, Pig 4747, LAD

source_name: Pig 4747 implanted with a bare metal stent in the left anterior descending artery

value: bare metal stent


title: SES, Pig 4745, LCX

source_name: Pig 4745 implanted with sirolimus-eluting stent in the left circumflex artery


title: 1-NKT-14-S

source_name: Individual #1, NKT cell clone #14, stimulated


title: SES, Pig 4745, RCA

source_name: Pig 4745 implanted with sirolimus-eluting stent in the right coronary artery


title: 1-NKT-4-N

source_name: Individual #1, NKT cell clone #4, resting


title: June 6th Muscle R

source_name: pool of 8 resistant oyster muscle, sampled the 6th June 2005

value: muscle

source_name: pool of 10 wild oyster


title: 1-NKT-22-N

source_name: Individual #1, NKT cell clone #22, resting


title: 1-NKT-4-S

source_name: Individual #1, NKT cell clone #4, stimulated


title: SES, Pig 4750, RCA

source_name: Pig 4750 implanted with a sirolimus-eluting stent in the right coronary artery


title: 13561489 - Col0 10dap vs. Col0 13dap

hyb_protocol: Col0 13dap Cy5 / Col0 10dap Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 13dap

extract_protocol: Col0 13dap:5.4ug. (Qiagen RNeasy)

value: 13 days after j0 (Boyes et al. Plant Cell 2001)

source_name: Col0 10dap


title: 13561490 - Col0 7dap vs. Col0 10dap

hyb_protocol: Col0 10dap Cy5 / Col0 7dap Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 7dap

value: 7 days after j0 (Boyes et al. Plant Cell 2001)


title: 13552334 - Col0 16dap vs. Col0 13dap

hyb_protocol: Col0 13dap Cy5 / Col0 16dap Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 16dap

extract_protocol: Col0 16dap:650ng. (Qiagen RNeasy)


title: June 20th Gonad R

source_name: pool of 8 resistant oyster gonad, sampled the 20th June 2005

value: pool of 8 gonad oysters

value: in situ rearing (South Britanny, France)

value: males and females

value: gonad


title: 13561491 - Col0 13dap vs. Col0 10dap

hyb_protocol: Col0 10dap Cy5 / Col0 13dap Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13561497 - Col0 13dap vs. Col0 16dap

hyb_protocol: Col0 16dap Cy5 / Col0 13dap Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: 16 days after j0 (Boyes et al. Plant Cell 2001)


title: BMS, Pig 4747, RCA

source_name: Pig 4747 implanted with a bare metal stent in the right coronary artery

value: Yorkshire farm pigs


title: June 6th Gonad S

source_name: pool of 8 sensitive oyster gonad, sampled the 6th June 2005

value: sensitive

value: pool of 10 oysters

value: no selection (wild oysters)


title: May 25th Gonad S

source_name: pool of 8 sensitive oyster gonad, sampled the 25th May 2005

value: the 10th May 2007

value: Brest, France

value: all tissues (whole oyster)


title: May 25th Gonad R

source_name: pool of 8 resistant oyster gonad, sampled the 25th May 2005

value: resistant


title: June 20th Gonad S

source_name: pool of 8 sensitive oyster gonad, sampled the 20th June 2005


title: BMS, Pig 4746, LAD

source_name: Pig 4746 implanted with a bare metal stent in the left anterior descending artery.

value: bare metal stent


title: 13561496 - Col0 4dap vs. Col0 7dap

hyb_protocol: Col0 7dap Cy5 / Col0 4dap Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 4dap

extract_protocol: Col0 4dap:1ug. (Qiagen RNeasy)

value: 4 days after j0 (Boyes et al. Plant Cell 2001)


title: June 6th Gonad R

hyb_protocol: Equimolar amounts of cDNA samples and cDNA reference, labeled with Cy5 and Cy3 respectively, were SpeedVac evaporated and mixed into a single pool with the hybridization buffer (ChipHyb™ hybridization buffer, Ventana Discovery, Tucson, AZ, USA). They were then co-hybridized on the same microarray slide in a Ventana hybridization station (Ventana Discovery, Tucson, AZ, USA). Hybridizations were performed at the INRA IFR 140 transcriptomic facility (Rennes, France). Following pre-hybridization (with ChipSpread buffer, containing 4×SSC and 0.2% SDS), hybridization was conducted overnight at 42°C in a humidified chamber, according to manufacturer’s instructions. The arrays were washed twice with Ribowash solution (0.1 M Tris, 0.05 M EDTA, and 0.4 M NaCl), twice with 0.1×SSC and finally centrifuged to dry.

source_name: pool of 8 resistant oyster gonad, sampled the 6th June 2005


title: MCF10A_Keap1 siNA_rep4

city: Baltimore

first: Abena

last: Agyeman

state: MD

address: 615 N Wolfe St

department: Biochemistry and Molecular Biology

institute: Johns Hopkins School of Public Health

description: Gene expression after 24hr Keap1 siRNA exposure

hyb_protocol: Cy3-labeled samples (0.825 ug) were used for hybridization at 65ºC for 17 hours in a hybridization oven with rotation. After hybridization, microarrays were washed and dried in a walk-in ozone-controlled enclosure according to the Agilent microarray processing protocol.

scan_protocol: Microarrays were scanned using an Agilent G2565A Scanner controlled by Agilent Scan Control 7.0 software.

data_processing: Data were extracted with Agilent Feature Extraction 9.5.3.1 software.

source_name: non tumorigenic human breast epithelial MCF10A cell line: Keap1 siNA_rep4

label_protocol: Sample amplification and labeling procedures were carried out using a Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies) with minor modifications. Briefly, 0.4 µg total RNA was reverse-transcribed into cDNA by MMLV-RT using an oligo dT primer (System Biosciences, Mountain View, CA) that incorporates a T7 promoter sequence. The cDNA was then used as a template for in vitro transcription in the presence of T7 RNA polymerase and Cyanine-3 labeled CTP (Perkin Elmer, Waltham, MA). The labeled cRNA was purified using RNeasy mini kit (Qiagen). RNA spike-in controls (Agilent Technologies) were added to RNA samples before amplification and labeling according to the manufacturer’s protocol.

growth_protocol: MCF10A (American Type Culture Collection, Manassas, VA) cells were cultured in (DMEM)/F12 minus L-lysine and L-arginine for SILAC. Medium was supplemented with 5% horse serum, 20ng/ml epidermal Growth Factor, 0.5 µg/ml hydrocortisone, 100 ng/ml cholera toxin and 10 µg/ml insulin at 37°C in a humidified environment with 5% CO2. For light medium 12C6 L-lysine:2HCL and 12C6 L-arginine-HCl were supplemented and for heavy medium 13C6 L-lysine:2HCl and 13C6 L-arginine:HCl were added (Cambridge Isotope Laboratories, Andover, MA).

extract_protocol: Total MCF10A RNA was isolated from cell pellets using TriZol reagent (Invitrogen), followed by RNeasy mini kit with DNase on-column digestion (Quiagen, Valencia, CA). MCF10A RNA was quantified with a NanoDrop ND-1000 (Thermo Scientific) followed by quality assessment with a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) according to the manufacturer’s protocol.

treatment_protocol: Cells were transfected with 30nM KEAP1 or non targeting control (NTC) siRNA in heavy and light SILAC media respectively by reverse transfection.  Cells were treated with 15 µM sulforaphane (SFN) or acetonitrile vehicle in heavy and light medium respectively 24 hours after plating. RNA was collected 24 hours after plating. The SFN treatment and KEAP1 knockdown experiments each had four biological replicates

tag: cell line

tag: treatment protocol

value: Keap1 siRNA


title: 13552324 - Col0 7dap vs. Col0 4dap

hyb_protocol: Col0 4dap Cy5 / Col0 7dap Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: 7 days after j0 (Boyes et al. Plant Cell 2001)


title: 1-NKT-1-N

source_name: Individual #1, NKT cell clone #1, resting

value: NKT cell clone


title: 1-CD4-4-N

source_name: Individual #1, CD4 T cell clone #4, resting

value: CD4 T cell clone


title: MCF10A_Keap1 siNA_rep2

source_name: non tumorigenic human breast epithelial MCF10A cell line: Keap1 siNA_rep2


title: MCF10A_Keap1 siNA_rep3

source_name: non tumorigenic human breast epithelial MCF10A cell line: Keap1 siNA_rep3


title: BMS, Pig 4746, RCA

source_name: Pig 4746 implanted with a bare metal stent in the right coronary artery


title: Bevacizumab (Avastin) 18.1 (HumanWG-6)

hyb_protocol: Each of 1.5 ug of biotinylated cRNAs was hybridized to both Illumina Human WG-6 V3 and Mouse WG-6 V2 microarrays at the same time.

source_name: Subcutaneous xenograft (murine) from a mouse treated with bevacizumab (10 mg/kg) 18.1

extract_protocol: Total RNA was isolated from the cancer tissues by using mirVanaTM miRNA isolation Kit (Ambion Inc., Austin, TX) according to manufacturer’s protocol.

tag: strain

value: Athymic nude mouse

value: male

tag: age

value: 5-8 weeks

tag: xenografts

value: 2 million human H1975 NSCLC cells

value: lung adenocarcinoma

value: bevacizumab


title: MDA-MB-231_Paclitaxel_Rep2

city: Washington DC

first: Nesrin

last: Rechache

state: Washington DC

address: W401 Research Building  Georgetown University Medical Center  3970 Reservoir Rd NW

institute: Georgetown University

description: Gene expression data from MDA-MB-231 cells grown in normal growth media with 1uM Verapamil and 7nM of Paclitaxel

hyb_protocol: 10 ug of fragmented cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scan protocol Standard Protocol for Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with Affymetrix Expression Console version 1.1.2 using Affymetrix default analysis settings and PLIER workflow as normalization method.

source_name: Verapamil and Paclitaxel

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNA isolated from three independent passages of sensitive, Docetaxel and Paclitaxel resistant cell lines using Trizol (Invitrogen; Carlsbad, CA), 2 ml per T-75 flask, followed by Qiagen RNeasy cleanup protocol.

treatment_protocol: Cells were grown in T75 flasks and cultured in normal growth media with 1µM Verapamil for the sensitive cells, 7nM Paclitaxel for Paclitaxel resistant cells and 2nM Docetaxel for Docetaxel resistant cells.

tag: source tissue

value: mammary gland

value: adherant epithelial cells


title: 1-CD4-1-N

hyb_protocol: 12µg of fragmented cRNA was hybridized to the array for 16 hours at 45°C and 60 rpm.  The array was washed and stained with streptavidin phycoerythrin according to the Affymetrix GeneChip protocol.

source_name: Individual #1, CD4 T cell clone #1, resting

tag: cell type


title: 1-NKT-1-S

source_name: Individual #1, NKT cell clone #1, stimulated


title: MDA-MB-231_Paclitaxel_Rep3


title: 1-CD4-1-S

source_name: Individual #1, CD4 T cell clone #1, stimulated