title: EGT 2

description: no additional information

source_name: Malignant melanoma cisplatin EGT

value: Exposed to electrogenetherapeutic pulses


title: C5D28R2_vs_C0D28R2

status: Public on Dec 31 2009

type: RNA

city: Antwerpen

first: Dries

last: Knapen

address: Groenenborgerlaan 171

department: Biology

country: Belgium

institute: University of Antwerp

description: Microarray is part of a loop design.

hyb_protocol: Agilent's two-colour microarray-based gene expression analysis protocol version 5.7.

data_processing: Data analysis was performed using the R package limma. Background correction: normexp. Normalization: loess.

molecule: total RNA

organism: Danio rerio

source_name: cadmium 5 uM day 28 replicate 2

extract_protocol: Trizol RNA extraction according to Invitrogen's instructions

tag: tissue

value: liver

source_name: cadmium 0 uM day 28 replicate 2


title: PHBE RSV 24h vs. PHBE mock

status: Public on Nov 16 2009

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

country: USA

institute: NIEHS

description: Primary human bronchial epithelial cells were left uninfected or were infected with RSV at multiplicity of infection (MOI) of 2.5 plaque forming unit (pfu)/cell. After 24 hr total cellular RNA was isolated using the TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturers’ instructions.

hyb_protocol: For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol.

scan_protocol: Slides were washed as indicated in the Agilent 60-mer oligo microarray processing protocol and then scanned with an Agilent Scanner. Data was obtained using the Agilent Feature Extraction software (v9.1), using defaults for all parameters.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.1), using defaults for all parameters and loaded into GeneSpring (v7.3).

organism: Homo sapiens

source_name: PHBE RSV 24h

label_protocol: Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 500ng of total RNA, Cy5 labeled cRNA was produced according to manufacturer’s protocol.

growth_protocol: The primary human bronchial epithelial (PHBE) cells were grown as a monolayer at 37oC in a 5% CO2 humidified chamber in a serum-free epithelial cell growth medium .

extract_protocol: Total cellular RNA was isolated using the TRIzol reagent (Invitrogen, Carlsbad, CA).

tag: Normal Human Bronchial Epithelial Cells infected with 2.5 plaque forming units (pfu)/cell for 24 hours.

source_name: PHBE mock

label_protocol: Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

tag: Uninfected Normal Human Bronchial Epithelial Cells


title: NSCL61-2

status: Public on Dec 01 2009

city: Sapporo

first: Toru

last: Kondo

address: Kita-15, Nishi-7, Kita-ku,

department: Institute for Genetic Medicine

country: Japan

institute: Hokkaido University

hyb_protocol: Labeled probes were hybridized to the GeneChip Mouse Genome 430 2.0 array (Affymetrix) according to the manufacturer’s instructions.

data_processing: The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix) to generate CEL data. The CEL data were then analyzed with dChip software, which can normalize and process multiple datasets simultaneously.

label: biotin

organism: Mus musculus

source_name: mouse NSC

label_protocol: Five micrograms of total RNA were labeled with biotin by in vitro transcription (IVT) using the One-Cycle Target Labeling procedure for biotin labeling by in vitro transcription (Affymetrix) according to the manufacturer’s instruction.

growth_protocol: Neuroepithelial cells were prepared from embryonic day 14.5 mouse telencephalon and expanded in serum-free Dulbecco's Modified Eagle's medium (DMEM)/F12 medium containing bovine insulin (10 μg/ml), human transferrin (100 μg/ml), BSA (100 μg/ml), progesterone (60 ng/ml), putrescine (16 μg/ml), sodium selenite (40 ng/ml), N-acetylcysteine (60 μg/ml), forskolin (5 μM), PDGF (10 ng/ml), penicillin, streptomycin, and bFGF as floating spheres.

extract_protocol: Total RNA was prepared using the RNeasy Mini Kit (QIAGEN).

tag: strain

tag: genome/variation

tag: developmental stage

value: E14.5 embryo

value: brain

tag: cell type

value: Neural Stem Cells, Glioma Initiating Cell-like

tag: cell line


title: BbreveUCC2003_Ribose_vs_Glucose DYE SWAP

city: Utrecht

first: Aldert

last: Zomer

address: Yalelaan 1

department: Department of Infectious Diseases and Immunology,Faculty of Veterinary Medicine

country: Netherlands

institute: Utrecht University

description: Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5).

hyb_protocol: Labelled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050).

scan_protocol: Following hybridization, all microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A).

data_processing:
DNA-microarray data were processed as previously described (Garcia De La Nava, J., D. F. Santaella, J. C. Alba, J. M. Carazo, O. Trelles & A. Pascual-Montano, (2003) Engene: the processing and exploratory analysis of gene expression data. Bioinformatics 19: 657-658., van Hijum, S. A. F. T., J. Garcia De La Nava, O. Trelles, J. Kok & O. P. Kuipers, (2003) MicroPreP: a cDNA microarray data pre-processing framework. Appl. Bioinformatics. 2: 241-244., van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77). Data were Lowess normalized. The VALUE column contains normalized log10 ribose/glucose ratios from a single array experiment.
Differential expression tests were performed with the Cyber-T implementation of a variant of the t-test (Long, A. D., H. J. Mangalam, B. Y. Chan, L. Tolleri, G. W. Hatfield & P. Baldi, (2001) Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in  Escherichia coli  K12. J. Biol. Chem. 276: 19937-19944.). A gene was considered differentially expressed when p < 0.001 and an expression ratio of >3 or <0.33 relative to the control. Final data presented are the average of two independent array experiments.

organism: Bifidobacterium breve UCC2003

source_name: Bifidobacterium breve UCC2003 grown in mMRS with glucose

label_protocol: Labelling was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

growth_protocol: Method for cell disruption was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

extract_protocol: RNA isolation, RNA quality control and complementary DNA synthesis was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

treatment_protocol: Bifidobacterium breve UCC200 was grown in modified de Man, Rogosa and Sharpe (mMRS) medium (De Man, J. C., A. Rogosa & M. E. Sharpe, (1960) A medium for the cultivation of lactobacilli. J. Appl. Bacteriol. 23: 130-135), made from first principles, supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany) and 1% (w/v) of glucose solution as the sole carbon source. Strain was grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) till OD600 was 0.5 .

tag: growth stage

value: exponential

tag: carbon source

value: glucose

source_name: Bifidobacterium breve UCC2003 grown in mMRS with ribose

treatment_protocol: Bifidobacterium breve UCC200 was grown in modified de Man, Rogosa and Sharpe (mMRS) medium (De Man, J. C., A. Rogosa & M. E. Sharpe, (1960) A medium for the cultivation of lactobacilli. J. Appl. Bacteriol. 23: 130-135), made from first principles, supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany) and 1% (w/v) of ribose solution as the sole carbon source. Strain was grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) till OD600 was 0.5 .

value: ribose


title: BbreveUCC2003_Ribose_vs_Glucose

value: Ribose


title: ECT 2

status: Public on Nov 01 2009

city: Ljubljana

first: Vid

last: Mlakar

address: Korytkova 2

department: Department for molecular genetics

country: Slovenia

institute: Faculty of Medicine

description: no additional information

hyb_protocol: All hybridizations were performed on HS400 (Tecan) according to the manufacturer’s instructions (Schott Nexterion). 2 micro g of both (Cy3 and Cy5) labeled aaRNA were disolved in 60 micro l hybridization buffer and used in hybridization. Wash 2, Wash 3, Wash 4 and 10 mg/ml BSA were provided in Nexterion 70mer Oligo Microarraying Kit (Schott Nexterion) Step   Temp   Wash (s)   Soak (s)   Agitation   Drying (s) Liquid 1         25          30          30                                     0,1% SDS 2         25          30           0                                      water 3         42          10          30 min                                10 mg/ml BSA 4         40          20           0                                      10 mg/ml BSA 5         40                                                                injection sample 6         40                       60 min     Medium                  hybridization 7         25          60          30                                      Wash 2 8         25          60          30                                      Wash 3 9         25          60          30                                      Wash 4 10

scan_protocol: LS200 laser scanner (Tecan) at 6 micro m resolution was used for scanning the microarrays at 543 nm (Cy3) and 633 nm (Cy5) excitation vawelenght. Scanner was operated using GenePro software.

data_processing:
We used Array-Pro Analyzer 4.5 (Media Cybernetics, Bethesda, MD, USA) for feature extraction after imaging of microarrays.
Out of each feature we extracted:
Median raw intensity for chanel 1 and 2
Mean raw intensity for chanel 1 and 2
Standard deviation of raw intensity for chanel 1 and 2
Median background intensity for chanel 1 and 2
Mean background intensity for chanel 1 and 2
Standard deviation of background intensity for chanel 1 and 2
Acuity (Molecular devices, USA) was used for filtration of bad signals, Lowess normalization and microarray data analysis. Features showing signal intensity of more than 65000 were flagged as bad. Features with signal less than 2 times the intensity of background or coefficient of variation (CV, ratio between standard deviation of the background and the median feature intensity) greater than 0.3 were considered not significantly expressed and were filtered out. Log2 ratios were normalized using LOWESS fit and median from four replicates was used to calculate average gene expression for single sample.

source_name: Malignant melanoma

label_protocol: Preparation of labeled aaRNA was performed with an Amino Allyl MessageAmpTM II aRNA Amplification Kit (Ambion) according to the manufacturer’s recommendations. For each hybridization, we labelled 5 micro g of tumour mRNA. After removing the excess dye, the RNAs were dissolved in Nexterion Hybridization solution (Schott Nexterion).

growth_protocol: Human malignant melanoma cells (SK-MEL28) were grown as monolayer in MEM with Glutamax (Gibco), supplemented with 10% FBS (Gibco) and gentamicin (30 μg/mL) (Gibco). Cells were routinely subcultured twice a week and incubated in an atmosphere with 5% CO2 at 37°C.

extract_protocol: RNA from cells was isolated using TRI REAGENTTM (Sigma Aldrich) and a PureLinkTM Micro-to-Midi Total RNA Purification System (Invitrogen), according to the manufacturer's instructions. Briefly, cells were trypsinized, washed in MEM with FBS for trypsin inactivation and resuspended in PBS. After centrifugation at 1500 x g for 5 min, all excess liquid was removed and 1 mL of TRI REAGENTTM was added to each sample. Samples were mixed by hand for 15 s and allowed to stand for 2 - 15 min at room temperature. The resulting mixture was centrifuged at 12000 x g for 15 min at 4 ºC. The aqueous phase was transferred to a fresh microcentrifuge tube and an equal amount of 70% ethanol was added. Samples were transferred to a PureLinkTM Micro-to-Midi Total RNA Purification System column (Invitrogen) and processed according to the manufacturer's protocol. All samples were washed from the column with 75 µl of RNAse free water.

value: Malignant melanoma cell line SK-MEL28

tag: protocol

value: Not treated

source_name: Malignant melanoma cisplatin ECT

treatment_protocol: Confluent cell cultures were trypsinized, washed in MEM with FBS for trypsin inactivation and once in electroporation buffer (125 mM saccharose; 10 mM K2HPO4; 2,5 mM KH2PO4; 2 mM MgCl2·6H20) at 4°C. Final cell suspension was prepared in electroporation buffer at 4°C at a concentration of 22 x 106 cells/mL. Aliquots of final cell suspension (3 x 106 cells) were placed between two parallel electrodes and subjected to eight electric pulses for electrochemotherapy (electric field intensity 1300 V/cm, pulse duration 100 μs and frequency 1 Hz) or eight electric pulses for electrogenetherapy (electric field intensity 600 V/cm, pulse duration 5 ms and frequency 1 Hz). One aliquot of cell suspension was not subjected to any electric pulses and served as control treatment. After electroporation, cells were incubated at room temperature for 5 minutes, diluted in normal growth media and then plated in culture flasks for 16 hours.

value: Exposed to electrochemotherapeutic pulses


title: BbreveUCC2003_Ribose+Glucose_vs_Glucose DYE SWAP

data_processing:
DNA-microarray data were processed as previously described (Garcia De La Nava, J., D. F. Santaella, J. C. Alba, J. M. Carazo, O. Trelles & A. Pascual-Montano, (2003) Engene: the processing and exploratory analysis of gene expression data. Bioinformatics 19: 657-658., van Hijum, S. A. F. T., J. Garcia De La Nava, O. Trelles, J. Kok & O. P. Kuipers, (2003) MicroPreP: a cDNA microarray data pre-processing framework. Appl. Bioinformatics. 2: 241-244., van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77). Data were Lowess normalized. The VALUE column contains normalized log10 (ribose+glucose)/glucose ratios from a single array experiment.
Differential expression tests were performed with the Cyber-T implementation of a variant of the t-test (Long, A. D., H. J. Mangalam, B. Y. Chan, L. Tolleri, G. W. Hatfield & P. Baldi, (2001) Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in  Escherichia coli  K12. J. Biol. Chem. 276: 19937-19944.). A gene was considered differentially expressed when p < 0.001 and an expression ratio of >3 or <0.33 relative to the control. Final data presented are the average of two independent array experiments.

source_name: Bifidobacterium breve UCC2003 grown in mMRS with combination of ribose and glucose

treatment_protocol: Bifidobacterium breve UCC200 was grown in modified de Man, Rogosa and Sharpe (mMRS) medium (De Man, J. C., A. Rogosa & M. E. Sharpe, (1960) A medium for the cultivation of lactobacilli. J. Appl. Bacteriol. 23: 130-135), made from first principles, supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany) and 0.5% (w/v) of ribose and 0.5% (w/v) of glucose solution as the sole carbon source. Strain was grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) till OD600 was 0.5 .

value: ribose and glucose


title: NSCL61-sox11-2

scan_protocol: The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix) to generate CEL data.

value: p53-/-, sox11-expressing


title: PHBE untreated vs. PHBE dsRNA 2h

description: Primary human bronchial epithelial cells were left untreated or were treated with 1 ug/ml dsRNA (poly I:C). After 2 hr total cellular RNA was isolated using the TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturers’ instructions.

scan_protocol: Slides were washed as indicated in the Agilent 60-mer oligo microarray processing protocol and then scanned with an Agilent Scanner. Data was obtained using the Agilent Feature Extraction software (v7.5), using defaults for all parameters.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using defaults for all parameters and loaded into GeneSpring (v7.3).

source_name: PHBE untreated

tag: Untreated Normal Human Bronchial Epithelial Cells

source_name: PHBE dsRNA 2h

tag: Normal Human Bronchial Epithelial Cells treated with 1 ug/ml dsRNA for 2 hours


title: NSCL61-sox11-1


title: Cisplatin ECT 2

description: no additional information

treatment_protocol: no treatment

treatment_protocol: Confluent cell cultures were trypsinized, washed in MEM with FBS for trypsin inactivation and once in electroporation buffer (125 mM saccharose; 10 mM K2HPO4; 2,5 mM KH2PO4; 2 mM MgCl2·6H20) at 4°C. Final cell suspension was prepared in electroporation buffer at 4°C at a concentration of 22 x 106 cells/mL. For clonogenic assay, 90 μL of final cell suspension was mixed with 10 μL of CDDP solution in concentration range from 2 to 80 μg/mL. 50 μL of the mixture (1 x 106 cells) was placed between two parallel electrodes and subjected to eight electric pulses with electric field intensity 1300 V/cm, pulse duration 100 μs and frequency 1 Hz. Other 50 μL of mixture (1 x 106 cells)  served as a control of CDDP treatment alone. For adhesion, migration and invasion assays, the volume of cell suspension subjected to electric pulses was 100 μL (2 x 106 cells). After electroporation cells were incubated at room temperature for 5 minutes, dilluted in 2 mL of growth media and then plated for clonogenic assay. For adhesion, migration and invasion assays, cells were plated in petri dishes for 48 h in MEM with serum.

value: Treated with cisplatin and electroporation


title: BbreveUCC2003_Ribose+Glucose_vs_Glucose

value: Ribose and glucose


title: NSCL61-1


title: Cisplatin 3

description: no additional information

source_name: Malignant melanoma cisplatin

value: Treated with cisplatin


title: PHBE dsRNA 2h vs. PHBE untreated


title: Glis3WT pancreas vs Glis3KO pancreas

status: Public on Nov 15 2009

description: Total RNAs were extracted using RNeasy mini kit (Qiagen, Valencia, CA) from WT P3 pancreas or from Glis3zf/zf P3 pancreas according to the manufacturer's protocols. RNA samples from 2 pups for each WT or Glis3zf/zf pups were pooled, then analyzed. Gene expression analysis was conducted using Agilent Mouse Whole Oligo Microarrays (Agilent Technologies, Palo Alto, CA).  Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 500ng of total RNA, Cy3 or Cy5 labeled cRNA was produced according to manufacturer’s protocol.  For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol.  Slides were washed as indicated in this protocol and then scanned with an Agilent Scanner.  Two arrays were utilized for each comparison allowing for dye reversals.  Data was obtained using the Agilent Feature Extraction software (v7.5), using defaults for all parameters and loaded into the Rosetta Resolver® system (v6.0) (Rosetta Biosoftware, Kirkland, WA).

scan_protocol: Slides were washed as indicated in the Agilent 60-mer oligo microarray processing protocol and then scanned with an Agilent Scanner. Data was obtained using the Agilent Feature Extraction software, using defaults for all parameters.

label: Cy 3

source_name: Glis3WT pancreas

extract_protocol: Total RNAs were extracted using RNeasy mini kit (Qiagen) from WT P3 pancreas

tag: Total RNAs from Pancreas of Glis3 WT P3 pups

label: Cy 5

source_name: Glis3KO pancreas

extract_protocol: Total RNAs were extracted using RNeasy mini kit (Qiagen) from Glis3zf/zf P3 pancreas

tag: Total RNAs from Pancreas of Glis3zf/zf P3 pups, which have a deletion mutation in exon 4.


title: Glis3KO pancreas vs Glis3WT pancreas

data_processing: Data was obtained using the Agilent Feature Extraction software (v7.5), using defaults for all parameters and loaded into the Rosetta Resolver® system (v6.0) (Rosetta Biosoftware, Kirkland, WA).


title: R1881, biological rep3

status: Public on Dec 30 2009

city: Ann Arbor

first: Adaikkalam

last: Vellaichamy

state: MI

address: 1400 E. Med. Center Dr.

institute: University of Michigan

description: Gene expression data from R1881 treated cells

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Probe intensity values were converted to expression values using the Robust Multi-Array Average (RMA) method following Irizarry et al (Irizarry, RA, Hobbs, B, Collin, F, Beazer-Barclay, YD, Antonellis, KJ, Scherf, U, Speed, TP (2003) Exploration, Normalization, and Summaries of High Density Oligonucleotide Array Probe Level Data. Biostatistics. Vol. 4, Number 2: 249-264). Log2 transformed expression values were obtained. This was implemented in the R statistical language using the affy package of Bioconductor.

source_name: LNCaP cells treated with R1881

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

growth_protocol: LNCaP cells were grown in RPMI 1640 medium at 37C, under 5% CO2 and 90% humidity

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

treatment_protocol: Cells were deprived of androgen in RPMI medium containing charcoal stripped serum, and treated with 1nM of R1881 for 48h

value: metastistic prostate cancer cell, androgen receptor positive

value: LNCaP


title: Cisplatin 1

description: no additional information


title: Colorectal_cancer_16

hyb_protocol: All hybridizations were performed on HS400 (Tecan) according to the manufacturer’s instructions (Schott Nexterion). 2 micro g of both (Cy3 and Cy5) labeled aaRNA were disolved in 60 micro l hybridization buffer and used in hybridization. Wash 2, Wash 3, Wash 4 and 10 mg/ml BSA were provided in Nexterion 70mer Oligo Microarraying Kit (Schott Nexterion) Step   Temp   Wash (s)   Soak (s)   Agitation   Drying (s) Liquid 1         25          30          30                                     0,1% SDS 2         25          30           0                                      water 3         42          10          30 min                                10 mg/ml BSA 4         40          20           0                                      10 mg/ml BSA 5         40                                                                injection sample 6         40                       60 min     Medium                  hybridization 7         25          60          30                                      Wash 2 8         25          60          30                                      Wash 3 9         25          60          30                                      Wash 4 10	                                                           120

scan_protocol: LS200 laser scanner (Tecan) at 6 micro m resolution was used for scanning the microarrays at 543 nm (Cy3) and 633 nm (Cy5) excitation wavelength. Scanner was operated using GenePro software.

data_processing:
Using GenePix software we extracted for each feature:
Median raw intensity for channel 1 and 2
Mean raw intensity for channel 1 and 2
Standard deviation of raw intensity for channel 1 and 2
Median background intensity for channel 1 and 2
Mean background intensity for channel 1 and 2
Standard deviation of background intensity for channel 1 and 2
Features not exceeding background by factor 2, showing coefficient of variation above 0,5 and saturated features were filtered out using Orange canvase program package (AI lab, Ljubljana). Data was normalized using LOWESS method and Log2 ratios were calculated.

source_name: Colorectal cancer

extract_protocol: Total RNA was isolated using TRI REAGENTTM (Sigma Aldrich) and a PureLinkTM Micro-to-Midi Total RNA Purification System (Invitrogen), according to the manufacturer’s instructions. 50 – 100 mg of tissue was homogenized in TRI REAGENTTM using PT 3100 homogenizer (Polytron). The homogenate was centrifuged at 12000 x g for 10 min at 4 ºC to remove insoluble material and the supernatant was transferred to a fresh microcentrifuge tube.  Samples were allowed to sit at room temperature for 5 min, and 0.2 ml of chloroform was added per 1 ml of TRI REAGENTTM. Samples were mixed by hand for 15 s and allowed to stand for 2 – 15 min at room temperature. The resulting mixture was centrifuged at 12000 x g for 15 min at 4 ºC. The aqueous phase was transferred to a fresh microcentrifuge tube and an equal amount of 70% ethanol was added. Samples were transferred to a PureLinkTM Micro-to-Midi Total RNA Purification System column and processed according to the manufacturer’s protocol. All samples were washed from the column with 75 micro l of RNAse free water.

treatment_protocol: Sample was stabilised in RNAlater (Ambion) immediately after extraction and stored according to manufacturers recommendations (over night +4 ºC and -20 ºC)

tag: Gender

value: female

tag: Tissue

value: Colorectal cancer

tag: TN status

value: T3 N0

tag: KRAS status

value: normal

source_name: Normal colon

value: Corresponding normal tissue


title: EGT 1

description: no additional information

source_name: Malignant melanoma cisplatin EGT

value: Exposed to electrogenetherapeutic pulses


title: Lung_Adenocarcinoma_13

data_processing: Features not exceeding background by factor 2, showing coeficient of variation above 0,5 and saturated features were filtered out using Orange canvase program package (AI lab, Ljubljana). Data was normalized using LOWESS method and Log2 ratios were calculated. Median value was calculated for replicate spots.

value: male

value: Lung adenocarcinoma

tag: TNM status

value: T2 N0 M0

value: Lung corresponding normal


title: Lung_Adenocarcinoma_16

value: T4 N2 M0


title: Cisplatin 2

description: no additional information

value: Malignant melanoma cell line SK-MEL28

value: Not treated


title: Lung_Adenocarcinoma_17

value: T2 N2 M0


title: Lung_Adenocarcinoma_15

value: T1 N0 M0


title: Lung_Adenocarcinoma_12


title: Lung_Adenocarcinoma_2

value: T3 N2 M0


title: Colorectal_cancer_5

value: T3 N2


title: Colorectal_cancer_15


title: Colorectal_cancer_6

value: T3 N1


title: Lung_Adenocarcinoma_18

value: female


title: Colorectal_cancer_11

value: Colorectal cancer


title: Lung_Adenocarcinoma_20


title: Lung_Adenocarcinoma_11


title: Colorectal_cancer_1

value: colorectal cancer

value: T3 N0

value: normal

value: corresponding normal tissue


title: Colorectal_cancer_2

value: male

value: T1 N0

value: Corresponding normal tissue


title: Colorectal_cancer_12


title: Colorectal_cancer_13


title: Colorectal_cancer_14


title: cow_7384_PMN_NEB_cy3

status: Public on Dec 25 2009

city: Tjele

first: Kasey

middle: M

last: Moyes

address: Blichers Allé 20, P.O. BOX 50

department: Animal Health, Welfare, and Disease

country: Denmark

institute: University of Aarhus

description: 7384 24-3

hyb_protocol: A 13,257 oligonucleotide microarray was used for gene expression profiling (Loor et al., 2007). Prior to hybridization, slides were denatured in boiling water, rinsed in ethanol, and blocked in prehybridization buffer. Probes, consisting of the experimental sample and reference (control), were denatured by boiling and hybridized to the array under cover slips for 2 d at 42 oC. Slides were then washed for 4 min each in 1 x SSC 0.03% SDS, 0.2 x SSC, 0.1 x SSC, and 0.05 x SSC prior to scanning. All samples were hybridized to duplicate slides and repeated with reverse labeling for a total of 2 slides, or 4 spots per gene per experiment.

scan_protocol: Slides were scanned for both dye channels (Cy3 and Cy5) with a Scanarray 4000 (GSI-Lumonics, Billerica,MA) dual-laser confocal scanner and images were edited and processed using GenePix 6.0 (Axon Instruments, Inc., CA).

data_processing: Oligonucleotides that were flagged with -100 by GenePix were removed from the analysis, and the remaining data were normalized to control for dye effects using the median of control elements on the microarray.  In a subsequent normalization step, the log2 normalized ratio of PMN versus reference (i.e., RNA mixture of  different bovine tissues) signal intensities were adjusted for global dye and PMN effects and normalized by Lowess.  A mixed-effects model was then fitted to the adjusted ratios (PMN/reference) using Proc MIXED of SAS (2003).  The model consisted of treatment (TRT; NEB and PEB).  The fixed effect was dye with cow and microarray as random effects.  Statistical significance probability values for TRT effects were adjusted for the number of comparisons using Benjamini and Hochberg’s FDR.  Differentially expressed genes were based on FDR P-value ≤ 0.05, which corresponded to an unadjusted P ≤ 0.01.

organism: Bos taurus

source_name: Pooled RNA from bovine tissues

label_protocol: Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using Superscript III Kit (Invitrogen) according to manufacturer's instructions. Samples were purified using the QIAGEN PCR purification kit before hybridization.

extract_protocol: Total RNA was extracted using TRIZol (Invitrogen) and cleaned using the RNeasy mini kit Column (QIAGEN).

tag: tissue

value: mixed

tag: sample type

value: reference standard

source_name: neutrophils, negative energy balance

tag: breed

value: Holstein

value: blood

value: neutrophil

tag: diet

value: restricted

tag: s. uberis infection

value: infected


title: Colorectal_cancer_10

value: T4 N0


title: Colorectal_cancer_7

value: female

value: T3 N2


title: Colorectal_cancer_4

value: Colorectal cancer

value: T4 N2


title: Colorectal_cancer_3

value: T2 N0

value: normal


title: Lung_Adenocarcinoma_14

value: male

value: Lung adenocarcinoma

value: T2 N0 M0

value: Lung corresponding normal


title: Colorectal_cancer_8

value: T1 N0

value: Corresponding normal tissue


title: Lung_Adenocarcinoma_10

value: T3 N1 M0


title: Colorectal_cancer_9

value: T3 N1


title: Limbal epithelial cells versus Bone marrow mesenchymal stem cells, replicate2

city: Hyderabad

first: geeta

middle: Kashyap

last: vemuganti

state: Andhrapradesh

address: Road No.2

department: C-TRACER

country: India

institute: L.V.Prasad Eye Institute

description: Contains both Biological replicate 1 and 2. Limbal epithelial cells, Bone marrow meschymal stem cells.

hyb_protocol: 825ng of labeled cRNA of the respective sample was used for hybridization in following combinations - LEC (Cy3) and MLC-L (Cy5), LEC (Cy3) and MSC-BM (Cy5), and MLC-L (Cy3) and MSC-BM (Cy5). Hybridization was performed for 17 hrs, 10 rpm at 65⁰C.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.9.5.3.1).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization was done using Genespring (GX v 10.0).

source_name: Limbal epithelial cell

label_protocol: 500ng of RNA from LEC, MLC-L and MSC-BM was used. Labeling was done using Quick Amp labeling kit (Agilent) as per the manufacturer’s protocol. Briefly, using T7 promoter element coupled oligodT primer cDNA was generated and using T7 polymerase and from cDNA, labeled cRNA was generated via an in vitro transcription reaction using T7 RNA polymerase and Cy3 (for LEC and MC-L) or Cy5 (MC-L and MSC-BM) CTP.

growth_protocol: LEC were grown on denuded human amniotic membrane by explant culture techinique. The source of MLC-L were the adherent spindle cells originated in the late limbal explant cultures which were subsequently passaged using Dulbecco's modified essential medium and 10% Fetal calf serum. MSC-BM were isolated by ficoll density gradient centrifugation and adherent the plastic surface and cultured them in DMEM/10%  FCS.

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

value: epithelial

source_name: Bone marrow mesenchymal stem cells

value: bone marrow


title: day 14, PRAME replicate 1

city: Seattle

first: Vivian

middle: G.

last: Oehler

state: WA

address: 1100 Fairview Ave. North, D4-100

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

description: day 14, PRAME replicate 1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array (HU-133A). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
Image (DAT), cell intensity (CEL), and chip (CHP) files were generated using MAS 5.0 software (Affymetrix, Santa Clara, CA).  Individual arrays were screened for quality.
Expression values for individual probe sets were extracted from CEL files using the Bioconductor  and gcRMA programs to background adjust, normalize and log-transform the data.

source_name: PRAME replicate 1, day 14 in culture

label_protocol:
One microgram of high quality RNA was amplified using a single-stranded linear amplification protocol (SLAP).  This protocol is published (PMID 14706461).  Biotin-labeling was performed using the Enzo BioArrayTM High Yield RNA Transcript Labeling Kit (Axxora, LLC, San Diego, CA).
Standard Affymetrix protocols and guidelines were followed as published in the GeneChipTM Expression Analysis Technical Manual.

growth_protocol: Hematopoietic cells from peripheral blood stem cell products from healthy donors without malignancy were thawed and cultured overnight in media containing Iscove's Modified Dulbecco's Medium (IMDM), 20% FBS, 1% penicillin/streptomycin/ fungisome, 10-4 M beta mercaptoethanol, 100 ng/ml of stem cell factor (SCF), 30 ng/ml IL3, and 50 ng/ml IL6.  The following day the cells were transduced with either lentiviral vectors containing PRAME or the control vector.  A double transduction protocol was used.  After the second transduction cells were resuspended in media containing X-vivo 15, 1% lot-tested BSA, 2mM glutamine, 10-4 M beta mercaptoethanol, 100 ng/ml of SCF, 30 ng/ml IL3, and 50 ng/ml IL6.  Cells were sorted using GFP fluorescence after transduction on Day 0.  To examine the effects of PRAME protein expression on in vitro myeloid differentiation, after GFP selection, cells were cultured in 100 ng/ml of SCF, 30 ng/ml IL3, 20 ng/ml IL6, 20 ng/ml G-CSF, and 20 ng/ml GM-CSF and total RNA was extracted on days 4, 7, and 14.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Invitrogen, Carlsbad, CA).

treatment_protocol: Cells for each day were spun down and resuspended in Trizol.

tag: condition

value: PRAME

tag: replicate

tag: time point

value: day 14 in culture

value: mononuclear hematopoietic cells


title: Mesenchymal-like cells of limbus versus Bone marrow mesenchymal stem cells, replicate1

description: Contains both Biological replicate 1 and 2. Mesenchymal-like cells of limbus, Bone marrow meschymal stem cells.

source_name: Mesenchymal-like cell

value: limbal stroma


title: Lung_Adenocarcinoma_6


title: Control monkeys received orally dosed with Thalidomide 3

city: Louisville

first: Thomas

middle: B

last: Knudsen

state: KY

address: 501 S Preston St

department: Birth Defects Center

institute: University of Louisville

hyb_protocol: followed a protocol described in the Gene Logic GeneChip® Analysis Manual (Gaithersburg, USA).

data_processing: Probe-level data normalization from the 6 *.cel files used the robust multichip average (RMA) method with perfect-match (PM) but not mismatch (MM) data from the microarrays. RMA returns a single file containing the 51,886 probes in 6 columns of normalized data, representing the log2-intensity of each probe. To query differential transcript abundance between sample groups, the log2 ratio of treated (Q) to reference (R) was computed for all 6 samples, with R being the average of the 3 controls. The 6 columns were centered to MEDIAN = 0.00 and scaled to STDEV = 0.50 [Singh et al. 2005; Green et al. 2007]. These data were loaded to GeneSpring GX7.3 software (Agilent Technologies, Redwood City CA, USA) for one-way analysis of variance (ANOVA) by treatment group. Due to the small sample size (n=3) and limited annotation of the Cynomalgus genome for this preliminary analysis we relaxed the selection criterion by not applying a false-discovery rate filter. Genes or probes passing the statistical (ANOVA) filter at a P-value of 0.05 were subjected to K-means clustering, with cluster Set 1 and Set 2 that were up-regulated and down-regulated, respectively, in the thalidomide-exposed versus control embryos. Entrez gene identifiers (id) and human Locus Link ids were used for bioinformatics evaluation.

organism: Macaca fascicularis

source_name: Whole embryos

growth_protocol: Treated on gestation day 26 and Whole embryos were rapidly removed from the uterus using a stereomicroscope and immersed in sterilized physiological saline.

extract_protocol: Total RNA was isolated from each day 26 embryo, amplified to cRNA, and biotin-labeled for analysis on the Affymetrix NHP GeneChip® Array at Gene Logic Inc. (Gaithersburg, MD, USA) using the TRIzol method and RNeasy columns according to protocols from Affymetrix (Santa Clara, CA, USA). The 28S/18S rRNA ratio of isolated RNA was assessed using a Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA)

treatment_protocol: Treated with Thalidomide

value: Whole Embryo

tag: agent

value: Thalidomide


title: Control monkeys received orally dosed with Thalidomide 2

scan_protocol: followed a protocol described in the Gene Logic GeneChip® Analysis Manual (Gaithersburg, USA).


title: Limbal epithelial cells versus Bone marrow mesenchymal stem cells, replicate1


title: siSelT-5 vs pU6-m3 vector control; replicate 1

city: Bethesda

first: Dolph

middle: L

last: Hatfield

state: MD

address: 37 Convent Drive, Rm. 6032A

department: LCP

institute: NIH/NCI

description: Biological replicate 1 of 2 for siSelT-5.

hyb_protocol: Mouse oligoarrays obtained from the NCI Microarray Facility, Frederick, MD, USA, were used for the experiments. For hybridization, 10 µl each of the Cy3 and Cy5 labeled cDNAs were combined and mixed with 1 µL COT-1 DNA, preheated at 100°C for 1 min to denature the cDNA and snap cooled on ice. This mixture was added to 20 µl of 2x F-hybridization buffer (50% formamide, 10x SSC, 0.2% SDS) and pre-warmed at 42°C. The total cDNA/hybridization solution mixture was loaded onto each prehybridized slide and slides placed in hybridization chambers and incubated overnight at 42°C. Post-hybridization washing included 5 min in 2x SSC + 0.1% SDS, 5 min in 1x SSC and 5 min in 0.2x SSC, after which the slides were dried by centrifugation.

scan_protocol: Slides were scanned for each fluoroprobe at 10 µm using a Genepix 4000B (Axon Instruments). Images were analyzed with GenePix Pro 3.0 software (Axon Instruments).

data_processing: For data processing, data files (in gpr format) and image (in jpeg format) were imported into the microarray database (mAdb) and analyzed by software tools provided by the National Cancer Institute, Center for Cancer Research in collaboration with the National Institutes of Health, Center for Information Technology, Bioinformatics and Molecular Analysis Section. The 50th Percentile (Median) method was used for normalization.

source_name: murine fibroblast cell line

label_protocol: 10-15 µg of total RNA in combination with oligo dT was used to generate cDNA, using the Fairplay II Microarray Labeling Kit (Stratagene) and labeled with monofunctional dye (Cy3 or Cy5) using the Fairplay coupling buffer. These reactions were carried out according to manufacturer's protocol.

growth_protocol: pU6-m3 transfected NIH 3T3 were stabilized with 150µg/ml hygromycin B and grown in DMEM supplemented with 10% FBS and antibiotic-antimycotic solution supplemented with 100 nM sodium selenite.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) following manufacturer's instructions

tag: cell line

value: NIH 3T3

tag: transfection

value: pU6-m3 vector

growth_protocol: siSelT-5 transfected NIH 3T3 were stabilized with 150µg/ml hygromycin B and grown in DMEM supplemented with 10% FBS and antibiotic-antimycotic solution supplemented with 100 nM sodium selenite.

value: pU6-m3 containing the siRNA target sequence designated siSelT-5, spanning nucleotides 971-989 of Selt (GenBank accession number NM_001040396).


title: Mesenchymal-like cells of limbus versus Bone marrow mesenchymal stem cells, replicate2


title: Limbal epithelial cells versus Mesenchymal-like cells, replicate 1

description: Contains both Biological replicate 1 and 2. Limbal epithelial cells, Mesenchymal-like cells.

source_name: Mesenchymal-like cells


title: siSelT-1 vs pU6-m3 vector control; replicate 1

description: Biological replicate 1 of 2 for siSelT-1.

growth_protocol: siSelT-1 transfected NIH 3T3 were stabilized with 150µg/ml hygromycin B and grown in DMEM supplemented with 10% FBS and antibiotic-antimycotic solution supplemented with 100 nM sodium selenite.

value: pU6-m3 containing the siRNA target sequence designated siSelT-1, spanning nucleotides 205-224 of Selt (GenBank accession number NM_001040396).


title: Limbal epithelial cells versus Mesenchymal-like cells, replicate 2


title: day 14, PRAME replicate 2

description: day 14, PRAME replicate 2

source_name: PRAME replicate 2, day 14 in culture


title: day 7, PRAME replicate 2

description: day 7, PRAME replicate 2

source_name: PRAME replicate 2, day 7 in culture

value: day 7 in culture


title: day 7, control replicate 2

description: day 7, control replicate 2

source_name: control replicate 2, day 7 in culture

value: control


title: siSelT-1 vs pU6-m3 vector control; replicate 2

description: Biological replicate 2 of 2 for siSelT-1.


title: day 14, control replicate 2

description: day 14, control replicate 2

source_name: control replicate 2, day 14 in culture


title: day 14, control replicate 1

description: day 14, control replicate 1

source_name: control replicate 1, day 14 in culture


title: siSelT-5 vs pU6-m3 vector control; replicate 2

description: Biological replicate 2 of 2 for siSelT-5.


title: Control monkeys capsule only3

description: Control monkeys capsule only

label_protocol: followed a protocol described in the Gene Logic GeneChip® Analysis Manual (Gaithersburg, USA).

treatment_protocol: Untreated

value: untreated


title: Control monkeys received orally dosed with Thalidomide 1


title: day 4, PRAME replicate 2

description: day 4, PRAME replicate 2

source_name: PRAME replicate 2, day 4 in culture

value: day 4 in culture


title: day 7, PRAME replicate 1

description: day 7, PRAME replicate 1

source_name: PRAME replicate 1, day 7 in culture


title: day 4, PRAME replicate 1

description: day 4, PRAME replicate 1

source_name: PRAME replicate 1, day 4 in culture


title: Control monkeys capsule only1

description: Control monkeys capsule only


title: Control monkeys capsule only2

description: Control monkeys capsule only


title: day 4, control replicate 2

description: day 4, control replicate 2

source_name: control replicate 2, day 4 in culture


title: day 4, control replicate 1

description: day 4, control replicate 1

source_name: control replicate 1, day 4 in culture


title: Chitosan 3h Treatment 2

status: Public on Oct 31 2009

city: San Giuliano Terme

first: Pierdomenico

last: Perata

state: Pisa

address: Via Guidiccioni 8-10

department: Institute of Life Sciences

country: Italy

institute: Sant'Anna School of Advanced Studies

description: no additional description required

hyb_protocol: Affymetrix standard hybridization protocol

scan_protocol: Affymetrix standard scan protocol

data_processing: GC-RMA algorithm

label: Biotin

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

label_protocol: Affymetrix standard labeling protocol

growth_protocol: Seeds were sterilized with diluted bleach (10-min incubation in 1.7% sodium hypochlorite, rinsed and washed seven times in sterile water) and incubated in 2.5 mL of liquid growing media (Murashige and Skoog half-strength solution in six-well plates) containing 30 mM sucrose. The plates were incubated in the dark at 4°C for two days (vernalization, to promote homogeneous germination) and then transferred to 23°C for four days under continuous light before the treatments.

extract_protocol: Total RNA was extracted from the seedling samples using the Ambion RNAqueous kit (Ambion). RNA quality was assessed by agarose gel electrophoresis and spectrophotometry. RNA was processed for use on Affymetrix Arabidopsis ATH1 GeneChip arrays.

treatment_protocol: Arabidopsis seedlings. Ecotype: Columbia 0; Age: 4 days; Germination: aerobic; Medium: Murashige-Skoog medium, half-strenght, sucrose 30 mM, 23°C, continuous light; Treated for 3 hours with chitosan under continuous light.

tag: growth stage

value: seedling

tag: ecotype

value: Columbia 0

tag: age

value: 4 days

tag: germination

value: aerobic

tag: growth conditions

value: Murashige-Skoog growth conditions, half-strength, sucrose 30 mM, 23°C, continuous light

tag: treatment


title: (129S1xB6) F1 XY gonad M6

status: Public on Oct 30 2009

city: Bar Harbor

first: Steven

middle: C

last: Munger

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description: Reference sample includes 4 pairs of e11.5 XY gonads, 3 pairs of e11.5 XX gonads, 4 e11.5 XY whole embryos, and 2 e11.5 XX whole embryos.

hyb_protocol: To each array, 900ng each of Cy5-labeled experimental and Cy3-labeled reference cRNA were co-hybridized at 65C for 17h according to Syed and Threadgill 2006.

scan_protocol: Microarrays were scanned using an Agilent scanner, and raw data were collected using feature extraction software (Agilent).

data_processing: Probe level data were imported into BRB-ArrayTools software (version 3.7.0), and normalized using the Lowess smoother function.

source_name: e11.5 XY mouse gonads (1 pair)

label_protocol: 200-450ng total RNA from each sample was amplified into cRNA using the Low RNA Input Linear Amplification kit (Agilent) and labeled with 1.5uL Cy5-CTP according to protocols established by Agilent and modified by us (see Syed and Threadgill 2006).

growth_protocol: C57BL/6J (stock# 000664) and 129S1/SvImJ (stock# 002448) mice were obtained from The Jackson Laboratory. Timed matings were established, embryos were collected from pregnant mothers at embryonic day 11.5 (e11.5), where e0.5 is defined as noon on the day a mating plug was detected. Embryos were staged more precisely by counting tail somites distal to the hindlimbs according to Hacker et al (1995). Embryos that fell within a 17-21 tail somite window were included in this study.

extract_protocol: Total RNA isolated from e11.5 XY gonads (separated from mesonephroi) using Trizol reagent according to standard protocols optimized in lab. Glycogen was added (10ug) as a carrier molecule to improve RNA yield.

treatment_protocol: Gonads were dissected away from mesonephroi in sterile PBS and stored in RNAlater RNA stabilization solution (Ambion) at -80C.

tag: tissue

value: gonad

tag: sex

value: XY

tag: developmental stage

tag: strain

source_name: pooled gonads and whole mouse embryos e11.5

value: gonads and whole embryos

value: pooled XY and XX samples

value: Sox9-ECFP(C57BL/6J) x CD-1


title: (B6x129S1) F1 XY gonad C2


title: C57BL/6J XY gonad H4


title: No Chitosan Control 1

description: no additional description required

treatment_protocol: Arabidopsis seedlings. Ecotype: Columbia 0; Age: 4 days; Germination: aerobic; Medium: Murashige-Skoog medium, half-strenght, sucrose 30 mM, 23°C, continuous light; Treated for 3h with chitosan under continuous light.

value: mock treatment


title: 129S1/SvImJ XY gonad A6


title: day 7, control replicate 1

description: day 7, control replicate 1

source_name: control replicate 1, day 7 in culture

value: mononuclear hematopoietic cells


title: C57BL/6J XY gonad H3


title: (B6x129S1) F1 XY gonad E1


title: (B6x129S1) F1 XY gonad C3


title: (B6x129S1) F1 XY gonad F2


title: Chitosan 3h Treatment 1

description: no additional description required

value: chitosan treatment for 3 hours under continuous light.


title: 129S1/SvImJ XY gonad A3


title: 129S1/SvImJ XY gonad A4


title: 129S1/SvImJ XY gonad G3


title: No Chitosan Control 2

description: no additional description required


title: C57BL/6J XY gonad H2


title: (129S1xB6) F1 XY gonad L2


title: 129S1/SvImJ XY gonad D4


title: C57BL/6J XY gonad K2


title: (B6x129S1) F1 XY gonad C4


title: (129S1xB6) F1 XY gonad M3


title: (129S1xB6) F1 XY gonad L4


title: 1:14 HDM inflammatory (Cy3)

status: Public on Oct 01 2009

first: John

last: Tomfohr

address: 111 T.W. Alexander Dr. P.O. Box 12233

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, May 06, 2005 20:11:17

source_name: Stratagene Universal Human Reference RNA

tag: Reference RNA

source_name: 1:14 HDM inflammatory

tag: subject id = 1:14 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 1:14 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, May 06, 2005 19:47:48

source_name: 1:14 LPS inflammatory

tag: subject id = 1:14 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 1:14 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, May 06, 2005 20:35:31

source_name: 1:14 saline inflammatory

tag: subject id = 1:14 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: C57BL/6J XY gonad H1


title: 1:15 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Tuesday, April 26, 2005 13:10:41

source_name: 1:15 saline inflammatory

tag: subject id = 1:15 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 1:16 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, May 06, 2005 11:16:04

source_name: 1:16 HDM inflammatory

tag: subject id = 1:16 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 1:15 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Tuesday, April 26, 2005 10:54:35

source_name: 1:15 HDM inflammatory

tag: subject id = 1:15 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 1:16 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, May 06, 2005 13:22:35

source_name: 1:16 saline inflammatory

tag: subject id = 1:16 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:01 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, March 16, 2005 10:30:50

source_name: 2:01 saline inflammatory

tag: subject id = 2:01 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 1:16 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, May 06, 2005 11:23:22

source_name: 1:16 LPS inflammatory

tag: subject id = 1:16 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:02 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, April 14, 2005 12:33:34

source_name: 2:02 LPS inflammatory

tag: subject id = 2:02 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:03 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, April 15, 2005 09:53:34

source_name: 2:03 HDM inflammatory

tag: subject id = 2:03 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:02 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, April 14, 2005 12:47:08

source_name: 2:02 HDM inflammatory

tag: subject id = 2:02 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:03 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, April 15, 2005 09:36:29

source_name: 2:03 LPS inflammatory

tag: subject id = 2:03 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:05 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, April 13, 2005 16:03:50

source_name: 2:05 HDM inflammatory

tag: subject id = 2:05 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:07 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, April 14, 2005 09:17:33

source_name: 2:07 HDM inflammatory

tag: subject id = 2:07 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:06 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Tuesday, April 19, 2005 09:26:33

source_name: 2:06 LPS inflammatory

tag: subject id = 2:06 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:07 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, April 14, 2005 09:32:13

source_name: Stratagene Universal Human Reference RNA

tag: Reference RNA

source_name: 2:07 saline inflammatory

tag: subject id = 2:07 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:07 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, April 14, 2005 09:03:16

source_name: 2:07 LPS inflammatory

tag: subject id = 2:07 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:05 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, April 13, 2005 15:47:04

source_name: 2:05 LPS inflammatory

tag: subject id = 2:05 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:06 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, May 06, 2005 08:12:46

source_name: 2:06 saline inflammatory

tag: subject id = 2:06 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:08 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, April 15, 2005 11:41:51

source_name: 2:08 LPS inflammatory

tag: subject id = 2:08 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:01 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, April 14, 2005 11:00:14

source_name: 2:01 LPS inflammatory

tag: subject id = 2:01 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:08 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, April 15, 2005 12:02:00

source_name: 2:08 saline inflammatory

tag: subject id = 2:08 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:03 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, April 15, 2005 10:39:13

source_name: 2:03 saline inflammatory

tag: subject id = 2:03 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:05 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, April 13, 2005 16:18:05

source_name: 2:05 saline inflammatory

tag: subject id = 2:05 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = no


title: mouse mast cells (16 hours) -3

city: Budapest

first: Zoltan

last: Wiener

address: Nagyvarad ter 4.

department: Dept of Genetics, Cell- and Immunobiology

country: Hungary

institute: Semmelweis University

description: Washing according to Agilent Dual-Color Gene Expression Protocol version 5.5

scan_protocol: Agilent Scanner, extended dynamic range (high value: 100%, low value: 10%)

data_processing: Agilent Feature Extraction Software version 9, with default 4x44K settings

source_name: Mouse in vitro-differentiated mast cells, treated by unspecific goat IgG (control, 16 hours), replicate 3

growth_protocol: Bone marrow cells were differentiated in RPMI + 10% FCS + 5 ng/ml mouse IL-3 + 40 ng/ml mouse SCF for >4 weeks.

extract_protocol: RNA was extracted by Qiagen RNeasy Micro Kit. The quality and quantity of the RNA was checked by Agilent Bioanalyzer and Nanodrop, respectively.

treatment_protocol: control goat IgG, 15 ug/ml, 16 hours, in vitro

tag: Mouse in vitro-differentiated mast cells, treated by unspecific goat IgG (control)

source_name: Mouse in vitro-differentiated mast cells, treated by an agonist anti-mouse TIM-3 antibody (16 hours), replicate 3

treatment_protocol: agonist polyclonal goat anti-mouse TIM3 antibody (RnD Systems), 15 ug/ml, 16 hours, in vitro

tag: Mouse in vitro-differentiated mast cells, treated by an agonist anti-mouse TIM-3 antibody (RnD Systems)


title: mouse mast cells (16 hours) -4

hyb_protocol: Agilent Dual-Color Gene Expression Protocol version 5.5

source_name: Mouse in vitro-differentiated mast cells, treated by unspecific goat IgG (control, 16 hours), replicate 4

source_name: Mouse in vitro-differentiated mast cells, treated by an agonist anti-mouse TIM-3 antibody (16 hours), replicate 4


title: 2:09 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, April 15, 2005 15:25:33

source_name: 2:09 saline inflammatory

tag: subject id = 2:09 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:01 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, March 16, 2005 13:19:59

source_name: 2:01 HDM inflammatory

tag: subject id = 2:01 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 1:15 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Tuesday, April 26, 2005 10:40:29

source_name: 1:15 LPS inflammatory

tag: subject id = 1:15 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:10 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, April 06, 2005 16:00:25

source_name: Stratagene Universal Human Reference RNA

source_name: 2:10 saline inflammatory

tag: subject id = 2:10 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:06 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, May 06, 2005 07:55:38

source_name: 2:06 HDM inflammatory

tag: subject id = 2:06 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:10 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, April 06, 2005 15:42:29

tag: Reference RNA

source_name: 2:10 HDM inflammatory

tag: subject id = 2:10 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: IgE/antigen-activated mouse mast cells (16 hours) -3

source_name: Mouse in vitro-differentiated IgE/antigen-activated mast cells, treated by unspecific goat IgG (control, 16 hours), replicate 3

label_protocol: Agilent Dual-Color Gene Expression Protocol version 5.5

treatment_protocol: Cells were sensitized by 5 ug/ml anti-DNP IgE (Sigma) for 1 hour and then treated by 100 ng/ml DNP-HSA (Sigma) and 15 ug/ml unspecific goat IgG for 16 hours, in vitro.

tag: Mouse in vitro-differentiated mast cells, sensitized by 5 ug/ml anti-DNP IgE (Sigma) for 1 hour. Cells were then treated by 100 ng/ml DNP-HSA (Sigma) and unspecific goat IgG (control).

source_name: Mouse in vitro-differentiated, IgE/antigen-activated mast cells, treated by an agonist anti-mouse TIM-3 antibody (16 hours), replicate 3

treatment_protocol: Cells were sensitized by 5 ug/ml anti-DNP IgE (Sigma) for 1 hour and then treated by 100 ng/ml DNP-HSA (Sigma) and 15 ug/ml agonist polyclonal goat anti-mouse TIM3 antibody (RnD Systems) for 16 hours, in vitro.

tag: Mouse in vitro-differentiated mast cells, sensitized by 5 ug/ml anti-DNP IgE (Sigma) for 1 hour. Cells were then treated by 100 ng/ml DNP-HSA (Sigma) and an agonist anti-mouse TIM-3 antibody (RnD Systems).


title: 2:10 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, April 06, 2005 15:27:36

source_name: 2:10 LPS inflammatory

tag: subject id = 2:10 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: IgE/antigen-activated mouse mast cells (16 hours) -4

source_name: Mouse in vitro-differentiated IgE/antigen-activated mast cells, treated by unspecific goat IgG (control, 16 hours), replicate 4

source_name: Mouse in vitro-differentiated, IgE/antigen-activated mast cells, treated by an agonist anti-mouse TIM-3 antibody (16 hours), replicate 4


title: mouse mast cells (16 hours)-1

source_name: Mouse in vitro-differentiated mast cells, treated by unspecific goat IgG (control, 16 hours), replicate 1

source_name: Mouse in vitro-differentiated mast cells, treated by an agonist anti-mouse TIM-3 antibody (16 hours), replicate 1


title: IgE/antigen-activated mouse mast cells (16 hours) -2

source_name: Mouse in vitro-differentiated IgE/antigen-activated mast cells, treated by unspecific goat IgG (control, 16 hours), replicate 2

source_name: Mouse in vitro-differentiated, IgE/antigen-activated mast cells, treated by an agonist anti-mouse TIM-3 antibody (16 hours), replicate 2


title: 2:11 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, May 05, 2005 21:21:17

source_name: 2:11 saline inflammatory

tag: subject id = 2:11 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:11 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, May 05, 2005 20:43:30

source_name: 2:11 HDM inflammatory

tag: subject id = 2:11 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:14 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Monday, April 18, 2005 10:49:02

source_name: 2:14 LPS inflammatory

tag: subject id = 2:14 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:14 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Monday, April 18, 2005 11:30:42

source_name: 2:14 saline inflammatory

tag: subject id = 2:14 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:09 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, April 15, 2005 14:52:02

source_name: Stratagene Universal Human Reference RNA

source_name: 2:09 LPS inflammatory

tag: subject id = 2:09 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: IgE/antigen-activated mouse mast cells, replicate 2

source_name: Mouse in vitro-differentiated IgE/antigen-activated mast cells, treated by unspecific goat IgG (control), replicate 2

treatment_protocol: Cells were sensitized by 5 ug/ml anti-DNP IgE (Sigma) for 1 hour and then treated by 100 ng/ml DNP-HSA (Sigma) and 15 ug/ml unspecific goat IgG for 2 hours, in vitro.

source_name: Mouse in vitro-differentiated, IgE/antigen-activated mast cells, treated by an agonist anti-mouse TIM-3 antibody, replicate 2

treatment_protocol: Cells were sensitized by 5 ug/ml anti-DNP IgE (Sigma) for 1 hour and then treated by 100 ng/ml DNP-HSA (Sigma) and 15 ug/ml agonist polyclonal goat anti-mouse TIM3 antibody (RnD Systems) for 2 hours, in vitro.


title: 2:11 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, May 05, 2005 20:08:10

source_name: 2:11 LPS inflammatory

tag: subject id = 2:11 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: mouse mast cells (16 hours) -2

source_name: Mouse in vitro-differentiated mast cells, treated by unspecific goat IgG (control, 16 hours), replicate 2

tag: Mouse in vitro-differentiated mast cells, treated by unspecific goat IgG (control)

source_name: Mouse in vitro-differentiated mast cells, treated by an agonist anti-mouse TIM-3 antibody (16 hours), replicate 2

tag: Mouse in vitro-differentiated mast cells, treated by an agonist anti-mouse TIM-3 antibody (RnD Systems)


title: IgE/antigen-activated mouse mast cells, replicate 3

source_name: Mouse in vitro-differentiated IgE/antigen-activated mast cells, treated by unspecific goat IgG (control), replicate 3

source_name: Mouse in vitro-differentiated, IgE/antigen-activated mast cells, treated by an agonist anti-mouse TIM-3 antibody, replicate 3


title: 2:09 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, April 15, 2005 15:07:57

source_name: 2:09 HDM inflammatory

tag: subject id = 2:09 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:14 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Monday, April 18, 2005 11:14:38

source_name: 2:14 HDM inflammatory

tag: subject id = 2:14 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: IgE/antigen-activated mouse mast cells (16 hours) -1

source_name: Mouse in vitro-differentiated IgE/antigen-activated mast cells, treated by unspecific goat IgG (control, 16 hours), replicate 1

source_name: Mouse in vitro-differentiated, IgE/antigen-activated mast cells, treated by an agonist anti-mouse TIM-3 antibody (16 hours), replicate 1


title: IgE/antigen-activated mouse mast cells, replicate 4

source_name: Mouse in vitro-differentiated IgE/antigen-activated mast cells, treated by unspecific goat IgG (control), replicate 4

source_name: Mouse in vitro-differentiated, IgE/antigen-activated mast cells, treated by an agonist anti-mouse TIM-3 antibody, replicate 4


title: IgE/antigen-activated mouse mast cells, replicate 1

source_name: Mouse in vitro-differentiated, IgE/antigen-activated mast cells, treated by unspecific goat IgG (control), replicate 1

treatment_protocol: Cells were senzsitized by 5 ug/ml anti-DNP IgE (Sigma) for 1 hour and then treated with 100 ng/ml DNP-HSA (Sigma) and 15 ug/ml control goat IgG for 2 hours, in vitro

source_name: Mouse in vitro-differentiated, IgE/antigen-activated mast cells, treated by an agonist anti-mouse TIM-3 antibody, replicate 1

treatment_protocol: Cells were senzsitized by 5 ug/ml anti-DNP IgE (Sigma) for 1 hour and then treated with 100 ng/ml DNP-HSA (Sigma) and 15 ug/ml agonist polyclonal goat anti-mouse TIM3 antibody (RnD Systems) for 2 hours, in vitro


title: 2:15 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Saturday, May 07, 2005 12:55:22

source_name: Stratagene Universal Human Reference RNA

source_name: 2:15 saline inflammatory

tag: subject id = 2:15 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = no


title: mouse mast cells, replicate 4

data_processing: Agilent Feature Extraction Software version 9, with default 4x44K settings

source_name: Mouse in vitro-differentiated mast cells, treated by unspecific goat IgG (control), replicate 4

treatment_protocol: control goat IgG, 15 ug/ml, 2 hours, in vitro

source_name: Mouse in vitro-differentiated mast cells, treated by an agonist anti-mouse TIM-3 antibody, replicate 4

treatment_protocol: agonist polyclonal goat anti-mouse TIM3 antibody (RnD Systems), 15 ug/ml, 2 hours, in vitro


title: 2:15 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Saturday, May 07, 2005 21:29:03

source_name: 2:15 HDM inflammatory

tag: subject id = 2:15 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 3:01 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, April 14, 2005 14:23:29

tag: Reference RNA

source_name: 3:01 saline inflammatory

tag: subject id = 3:01 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = no


title: 3:01 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, May 25, 2005 09:12:35

source_name: 3:01 HDM inflammatory

tag: subject id = 3:01 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = no


title: 2:15 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Saturday, May 07, 2005 20:16:35

source_name: 2:15 LPS inflammatory

tag: subject id = 2:15 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = no


title: 3:02 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Monday, April 18, 2005 09:16:50

source_name: 3:02 HDM inflammatory

tag: subject id = 3:02 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = no


title: mouse mast cells, replicate 1

source_name: Mouse in vitro-differentiated mast cells, treated by unspecific goat IgG (control), replicate 1

source_name: Mouse in vitro-differentiated mast cells, treated by an agonist anti-mouse TIM-3 antibody, replicate 1


title: B16-F10 melanoma cells, biological replicate 3

description: Washing according to Agilent Dual-Color Gene Expression Protocol version 5.7

source_name: B16F10 mouse melanoma cells, in vitro, treated by unspecific goat IgG (control), p18

growth_protocol: DMEM high glucose + 10% FBS + Pen/Str + glutamine

tag: B16F10 mouse melanoma cells, treated by unspecific goat IgG (control) for 2 hours, p18. This is the third biological replicate out of the four.

source_name: B16F10 mouse melanoma cells, in vitro, treated by goat polyclonal anti-mouse TIM3 antibody (RnD Systems), p18

tag: B16F10 mouse melanoma cells, treated by polyclonal agonist goat anti-mouse TIM3 antibody for 2 hours, p18. This is the third biological replicate out of the four.


title: 3:02 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, April 15, 2005 16:43:45

source_name: 3:02 LPS inflammatory

tag: subject id = 3:02 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = no


title: 3:05 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Tuesday, April 19, 2005 14:34:23

source_name: 3:05 saline inflammatory

tag: subject id = 3:05 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = no


title: 4:12 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Saturday, May 07, 2005 15:58:43

source_name: 4:12 HDM inflammatory

tag: subject id = 4:12 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 3:05 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, May 06, 2005 07:39:52

source_name: 3:05 HDM inflammatory

tag: subject id = 3:05 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = no


title: 3:02 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Monday, April 18, 2005 09:33:46

source_name: Stratagene Universal Human Reference RNA

source_name: 3:02 saline inflammatory

tag: subject id = 3:02 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = no


title: mouse mast cells, replicate 2

source_name: Mouse in vitro-differentiated mast cells, treated by unspecific goat IgG (control), replicate 2

source_name: Mouse in vitro-differentiated mast cells, treated by an agonist anti-mouse TIM-3 antibody, replicate 2

tag: Mouse in vitro-differentiated mast cells, treated by an agonist anti-mouse TIM-3 antibody (RnD Systems)


title: B16-F10 melanoma cells, biological replicate 4

source_name: B16F10 mouse melanoma cells, in vitro, treated by unspecific goat IgG (control), p19

tag: B16F10 mouse melanoma cells, treated by unspecific goat IgG (control) for 2 hours, p19. This is the fourth biological replicate out of the four.

source_name: B16F10 mouse melanoma cells, in vitro, treated by goat polyclonal anti-mouse TIM3 antibody (RnD Systems), p19

tag: B16F10 mouse melanoma cells, treated by polyclonal agonist goat anti-mouse TIM3 antibody for 2 hours, p19. This is the fourth biological replicate out of the four.


title: 3:07 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Monday, May 23, 2005 09:25:58

source_name: 3:07 LPS inflammatory

tag: subject id = 3:07 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: mouse mast cells, replicate 3

source_name: Mouse in vitro-differentiated mast cells, treated by unspecific goat IgG (control), replicate 3

source_name: Mouse in vitro-differentiated mast cells, treated by an agonist anti-mouse TIM-3 antibody, replicate 3


title: B16-F10 melanoma cells, biological replicate 1

source_name: B16F10 mouse melanoma cells, in vitro, treated by unspecific goat IgG (control), p14

tag: B16F10 mouse melanoma cells, treated by unspecific goat IgG (control) for 2 hours, p14. This is the first biological replicate out of the four.

source_name: B16F10 mouse melanoma cells, in vitro, treated by goat polyclonal agonist anti-mouse TIM3 antibody (RnD Systems), p14

tag: B16F10 mouse melanoma cells, treated by polyclonal agonist goat anti-mouse TIM3 antibody for 2 hours, p14. This is the first biological replicate out of the four.


title: 3:07 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Tuesday, April 26, 2005 12:45:45

tag: Reference RNA

source_name: 3:07 HDM inflammatory

tag: subject id = 3:07 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = no


title: 4:12 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Saturday, May 07, 2005 14:56:53

source_name: 4:12 LPS inflammatory

tag: subject id = 4:12 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 4:14 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, April 27, 2005 14:22:15

source_name: 4:14 saline inflammatory

tag: subject id = 4:14 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 1:15 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Tuesday, April 26, 2005 13:01:02

source_name: 1:15 HDM inflammatory

tag: subject id = 1:15 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 1:14 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, May 06, 2005 21:24:22

source_name: 1:14 saline inflammatory

tag: subject id = 1:14 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 4:14 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, April 27, 2005 13:51:14

source_name: 4:14 HDM inflammatory

tag: subject id = 4:14 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: B16-F10 melanoma cells, biological replicate 2

data_processing: Agilent Feature Extraction Software version 9, with default 4x44K settings

source_name: B16F10 mouse melanoma cells, in vitro, treated by unspecific goat IgG (control), p16

tag: B16F10 mouse melanoma cells, treated by unspecific goat IgG (control) for 2 hours, p16. This is the second biological replicate out of the four.

source_name: B16F10 mouse melanoma cells, in vitro, treated by goat polyclonal anti-mouse TIM3 antibody (RnD Systems), p16

tag: B16F10 mouse melanoma cells, treated by polyclonal agonist goat anti-mouse TIM3 antibody for 2 hours, p16. This is the second biological replicate out of the four.


title: 4:15 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, May 06, 2005 21:12:49

source_name: Stratagene Universal Human Reference RNA

source_name: 4:15 saline inflammatory

tag: subject id = 4:15 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:01 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, April 14, 2005 11:06:14

source_name: 2:01 LPS inflammatory

tag: subject id = 2:01 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 4:15 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Saturday, May 07, 2005 06:23:03

source_name: 4:15 HDM inflammatory

tag: subject id = 4:15 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 4:16 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, April 27, 2005 13:07:15

source_name: 4:16 saline inflammatory

tag: subject id = 4:16 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 4:14 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, April 27, 2005 13:35:55

source_name: 4:14 LPS inflammatory

tag: subject id = 4:14 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 1:16 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, May 06, 2005 12:54:50

source_name: 1:16 HDM inflammatory

tag: subject id = 1:16 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 1:16 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, June 03, 2005 09:09:42

source_name: 1:16 LPS inflammatory

tag: subject id = 1:16 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 4:16 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, April 01, 2005 15:26:42

source_name: 4:16 LPS inflammatory

tag: subject id = 4:16 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:01 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, March 16, 2005 14:28:04

source_name: 2:01 HDM inflammatory

tag: subject id = 2:01 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes

tag: Reference RNA


title: 4:12 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Saturday, May 07, 2005 15:39:51

source_name: 4:12 saline inflammatory

tag: subject id = 4:12 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 3:07 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Tuesday, April 26, 2005 10:20:10

source_name: 3:07 saline inflammatory

tag: subject id = 3:07 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = no


title: 1:14 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, May 06, 2005 19:57:35

source_name: 1:14 LPS inflammatory

tag: subject id = 1:14 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 1:14 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, May 06, 2005 20:24:20

source_name: 1:14 HDM inflammatory

tag: subject id = 1:14 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 4:16 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, April 01, 2005 15:52:00

source_name: 4:16 HDM inflammatory

tag: subject id = 4:16 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:02 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, April 14, 2005 12:40:03

source_name: 2:02 LPS inflammatory

tag: subject id = 2:02 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 4:17 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Saturday, May 07, 2005 07:09:40

source_name: 4:17 LPS inflammatory

tag: subject id = 4:17 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 4:17 HDM inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Saturday, May 07, 2005 07:32:34

source_name: Stratagene Universal Human Reference RNA

source_name: 4:17 HDM inflammatory

tag: subject id = 4:17 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 4:17 saline inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Saturday, May 07, 2005 08:12:58

source_name: 4:17 saline inflammatory

tag: subject id = 4:17 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:02 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, April 14, 2005 12:54:58

source_name: 2:02 HDM inflammatory

tag: subject id = 2:02 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:01 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, March 16, 2005 10:39:06

source_name: 2:01 saline inflammatory

tag: subject id = 2:01 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 4:15 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Saturday, May 07, 2005 05:45:19

source_name: 4:15 LPS inflammatory

tag: subject id = 4:15 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 3:01 LPS inflammatory (Cy3)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, May 25, 2005 08:57:37

source_name: 3:01 LPS inflammatory

tag: subject id = 3:01 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = no


title: 1:15 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Tuesday, April 26, 2005 10:47:46

source_name: 1:15 LPS inflammatory

tag: subject id = 1:15 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 1:15 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Tuesday, April 26, 2005 13:18:16

source_name: 1:15 saline inflammatory

tag: subject id = 1:15 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:03 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, April 15, 2005 10:46:43

source_name: 2:03 saline inflammatory

tag: subject id = 2:03 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 1:16 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, May 06, 2005 13:03:15

source_name: 1:16 saline inflammatory

tag: subject id = 1:16 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes

tag: Reference RNA


title: 2:07 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, April 14, 2005 09:40:17

source_name: 2:07 saline inflammatory

tag: subject id = 2:07 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:03 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Friday, April 15, 2005 09:44:28

source_name: 2:03 LPS inflammatory

tag: subject id = 2:03 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:07 HDM inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, April 14, 2005 09:24:35

source_name: 2:07 HDM inflammatory

tag: subject id = 2:07 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = HDM | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes


title: 2:05 saline inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Wednesday, April 13, 2005 16:25:05

source_name: 2:05 saline inflammatory

tag: subject id = 2:05 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = saline | cell type = inflammatory | batch = 2 (2005) | included in published analysis = no


title: 2:07 LPS inflammatory (Cy5)

description: human airway inflammatory cells

data_processing: Processed with FeatureExtraction Version A.7.5.1 on Thursday, April 14, 2005 09:10:36

source_name: 2:07 LPS inflammatory

tag: subject id = 2:07 (1:control, 2:atopy only, 3:asthma only, 4:atopy+asthma) | exposure = LPS | cell type = inflammatory | batch = 2 (2005) | included in published analysis = yes