title: G-V_THP-1+DbTx_Rep1.

hyb_protocol: The preparation and processing of labeled, fragmented cRNA and hybridization cocktail for hybridization has been performed according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA). Immediately after the hybridization, the hybridized probe arrays underwent an automated washing and staining protocol on an Affymetrix Fluidics Station (Replicate-1).

scan_protocol: We scanned the GeneChips and processed the signals using Affymetrix genechip scanner and expression analysis algorithm (Affymetrix, Santa Clara, CA).

source_name: THP-1+ treated with DbTx_Rep1.

growth_protocol: Human macrophage (THP-1) cells were cultured in 72 cm2 flask in DMEM culture medium supplemented with 10% fetal bovine serum (FBS). The cells were maintained at 37°C in a humidified atmosphere of 5% CO2 and 95% air. The culture medium containing THP-1 cells were exposed to Daboiatoxin (0.5 mM, EC50~1 mM) isolated from Daboia russelli russelli venom without bacterial infection. (Replicate 1).

treatment_protocol: Group V:- Human monocytic macrophage (THP-1) cells were exposed to Daboiatoxin (0.5 mM, EC50~1 mM) isolated from Daboia russelli russelli venom without bacterial infection. (Replicate 1).

tag: Human monocytic macrophage (THP-1) cells were exposed to Daboiatoxin without bacterial infection. (Replicate 1)


title: T00306154: cardiomyocytes, 24 hour conditioned

status: Public on Jun 01 2010

type: RNA

city: Pittsburgh

first: John

middle: Michael

last: Krill-Burger

state: PA

address: Rm. WG21.3 Shadyside Hospital

country: USA

institute: University of Pittsburgh Medical Center

description:
Cardiac media was diluted 50% with conditioned hesc media while FBS and HS percentages were held constant at 5% and 10% respectively.
RNA extracted after 24 hours.

hyb_protocol: GE Healthcare Amersham CodeLink Gene Expression System: Single-Assay Bioarray Hybridization and Detection protocol Detection dye: streptavidin - Alexa Fluor 647

scan_protocol: Scanned using a GenePix 4000B at 600 PMT and CodeLink software (version 5.0).

data_processing:
The threshold was calculated by removing the top 10% and bottom 10% of negative controls and averaging the remaining intensities. The threshold was subtracted from each of the discovery probes. An average was computed for the following positive controls: LEUB, HISB, FIXB, GND, ENTF, and ARAB. The averages of each of these positive controls was grouped together with its average on all the other arrays in this series. By taking the median of each group, a global median was created which represents the median value for a positive control across all of the arrays. Correction factors for this array were calculated by dividing the average of each positive control by its corresponding global median. It was observed that the arrays behaved differently at high intensity levels compared to low intensity levels. As the positive controls increased in intensity, the correction factors also steadily increased or steadily decreased. Therefore, a correction factor derived from a low intensity positive control was not a good correction for high intensity probes. To accommodate for the effect of intensity, the correction factor for each positive control was graphed versus its intensity and a best-fit regression line was created. The equation of the best-fit line was used to calculate a correction factor for each individual discovery probe based on where it fit into the slope of the correction factors. Negative values were replaced by a placeholder of ".0001".
In summary, the data was normalized by comparing each positive control to its median value across arrays and correcting based on the slope of the positive controls versus intensity. Note that the data was never median normalized or log transformed.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: cardiomyocytes, 24 hour conditioned

label_protocol: GE Healthcare Amersham CodeLink iExpress Assay Reagent Kit protocol

extract_protocol: Extracted using Invitrogen Trizol LS Reagent and Invitrogen's RNA isolation protocol supplied with the reagent.

tag: Rat neonatal cardiomyocytes harvested from day 1 ventricles (n=24). Cells purified via serial Percoll gradients and plated at 2.5x10^5 cells per 100 mm sq dish.


title: G-V_THP-1+DbTx_Rep2.

status: Public on May 31 2010

city: Augusta

first: Pachiappan

last: Arjunan

state: Georgia

address: 1120 15th ST, Laney walker Blvd,

department: Anatomy, Unit on Retinal Vascular Neurobiology, BMB

institute: NUS, NIH, GRU

description: Total RNA was isolated from Daboiatoxin treated (n = 5 flasks for each replicate) THP-1 cells using RNeasy® mini kit. The target chip hybridization followed successful Genechip Test3 arrays hybridization. All relevant procedures, such as amplification of cDNA, fragmentation of cRNA for hybridization, and concurrent assessment of expression levels of genes were carried out. Briefly, we synthesized double-stranded cDNA from the total RNA isolated from the THP-1 cells exposed to DbTx. We generated biotin-labeled cRNAs by in-vitro transcription from the ds-cDNA. The cRNAs were fragmented before hybridization, and a hybridization cocktail was prepared and hybridized to the oligonucleotide probes on the HG-U133A GeneChip arrays for 16h incubation at 45°C. Immediately after the hybridization, the hybridized probe arrays underwent an automated washing and staining protocol on an Affymetrix Fluidics Station. We scanned the GeneChips and processed the signals using Affymetrix genechip scanner and expression analysis algorithm (Affymetrix, Santa Clara, CA).

hyb_protocol: The preparation and processing of labeled, fragmented cRNA and hybridization cocktail for hybridization has been performed according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA). Immediately after the hybridization, the hybridized probe arrays underwent an automated washing and staining protocol on an Affymetrix Fluidics Station (Replicate-2).

data_processing: Three chips were used for each experiment (Group) according to MIAME guidelines. Expression values for each gene were calculated using the Affymetrix Microarray suite (MAS v5.0) software. Using the 50th percentile of each chip’s (per chip normalization) intensity range, expression values were normalized across the sample set by scaling the average of the intensities of all genes to constant target intensity of 800 and a comparison of signal intensities using Microsoft® Excel showed results from duplicate chips highly correlated with R values = 0.96. These data were further categorized and analyzed using stringent filter (statistical inclination) in order to identify the target genes. Hence, the resultant data were further put into marketable GeneSpring v7.0 (Silicon Genetics, Redwood City, CA, USA http://www.silicongenetics.com/cgi/SiG.cgi/Products/ GeneSpring?index.smf) for temporal sequence analyses by parametric test based on cross gene error model (PCGEM). Relative expression data for each probe set were generated by normalization over the median of the entire experiment set (per gene normalization).

label: Biotin

organism: Homo sapiens

source_name: THP-1+ treated with DbTx_Rep2.

label_protocol: cRNA was labeled with Biotin according to the manufacturer’s instructions (Enzo BioArrayTM HighYieldTM RNA Transcript Labeling Kit, Affymetrix, Santa Clara, CA).

growth_protocol: Human macrophage (THP-1) cells were cultured in 72 cm2 flask in DMEM culture medium supplemented with 10% fetal bovine serum (FBS). The cells were maintained at 37°C in a humidified atmosphere of 5% CO2 and 95% air. The culture medium containing THP-1 cells were exposed to Daboiatoxin (0.5 mM, EC50~1 mM) isolated from Daboia russelli russelli venom without bacterial infection. (Replicate 2).

extract_protocol: All glasswares used for RNA isolation were treated with diethyl pyrocarbonate (DEPC) to ensure RNase-free environment. They were filled with DEPC-treated water (1.0ml DEPC in 1L of sterile DD-H2O), allowed to stand overnight at 37°C and then autoclaved to eliminate residual DEPC. Total RNA was isolated from THP-1 cells Total RNA was isolated from Daboiatoxin treated (n = 5 flasks for each replicate) THP-1 cells using RNeasy® mini kit. The RNA sample was subsequently treated with RNase-free Dnase-I at room temperature for 20min and stored at -80°C until use. The isolated RNA was subjected to several levels of testing before using for microarray hybridization. The purity and quantity of the RNA was determined by A260/A280 ratios and then A260, respectively, using Biophotometer (Eppendorf, CA, USA). RNA samples that had good OD values (1.8–2.0) were further tested on gels for the integrity of both the 28S and 18S ribosomal RNA by denaturing agarose gels and visualized with ethidium bromide under UV light.

treatment_protocol: Group V:- Human monocytic macrophage (THP-1) cells were exposed to Daboiatoxin (0.5 mM, EC50~1 mM) isolated from Daboia russelli russelli venom without bacterial infection. (Replicate 2).

tag: Human monocytic macrophage (THP-1) cells were exposed to Daboiatoxin without bacterial infection. (Replicate 2)


title: G-(III)_THP-1+B. pseudomallei 24h+DbTx_Rep2.

description: Total RNA was isolated from THP-1 cells infected with B. pseudomallei (n = 5 flasks for each replicate) and treated with Daboiatoxin using RNeasy® mini kit. The target chip hybridization followed successful Genechip Test3 arrays hybridization. All relevant procedures, such as amplification of cDNA, fragmentation of cRNA for hybridization, and concurrent assessment of expression levels of genes were carried out. Briefly, we synthesized double-stranded cDNA from the total RNA isolated from the THP-1 cells infected with with B. pseudomallei, and treated with DbTx. We generated biotin-labeled cRNAs by in-vitro transcription from the ds-cDNA. The cRNAs were fragmented before hybridization, and a hybridization cocktail was prepared and hybridized to the oligonucleotide probes on the HG-U133A GeneChip arrays for 16h incubation at 45°C. Immediately after the hybridization, the hybridized probe arrays underwent an automated washing and staining protocol on an Affymetrix Fluidics Station. We scanned the GeneChips and processed the signals using Affymetrix genechip scanner and expression analysis algorithm (Affymetrix, Santa Clara, CA).

hyb_protocol: The preparation and processing of labeled, fragmented cRNA and hybridization cocktail for hybridization has been performed according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA). Immediately after the hybridization, the hybridized probe arrays underwent an automated washing and staining protocol on an Affymetrix Fluidics Station (Replicate-3).

data_processing: Three chips were used for each experiment according to MIAME guidelines. Expression values for each gene were calculated using the Affymetrix Microarray suite (MAS v5.0) software. Using the 50th percentile of each chip’s (per chip normalization) intensity range, expression values (200 − 44,913.8) were normalized across the sample set by scaling the average of the intensities of all genes to constant target intensity of 800 and a comparison of signal intensities using Microsoft® Excel showed results from duplicate chips highly correlated with R values = 0.96. These data were further categorized and analyzed using stringent filter (statistical inclination) in order to identify the target genes. Hence, the resultant data were further put into marketable GeneSpring v7.0 (Silicon Genetics, Redwood City, CA, USA http://www.silicongenetics.com/cgi/SiG.cgi/Products/ GeneSpring?index.smf) for temporal sequence analyses by parametric test based on cross gene error model (PCGEM). Relative expression data for each probe set were generated by normalization over the median of the entire experiment set (per gene normalization).

organism:
Homo sapiens
Burkholderia pseudomallei

source_name: THP-1+ Infected with B. pseudomallei 24h and treated with Daboiatoxin_Rep2.

growth_protocol: Human macrophage (THP-1) cells were cultured in 72 cm2 flask in DMEM culture medium supplemented with 10% fetal bovine serum (FBS). The cells were maintained at 37°C in a humidified atmosphere of 5% CO2 and 95% air. The culture medium containing THP-1 cells were infected with with Burkholderia pseudomallei (A600 nm = OD 0.6, ~5 x 107 cfu/ml) for 24h, and treated with Daboiatoxin (0.5 mM, EC50~1 mM) isolated from Daboia russelli russelli venom served as a treatment.(Replicate 2).

extract_protocol: All glasswares used for RNA isolation were treated with diethyl pyrocarbonate (DEPC) to ensure RNase-free environment. They were filled with DEPC-treated water (1.0ml DEPC in 1L of sterile DD-H2O), allowed to stand overnight at 37°C and then autoclaved to eliminate residual DEPC. Total RNA was isolated from THP-1 cells infected with B. pseudomallei (n = 5 flasks for each replicate) and treated with Daboiatoxin using RNeasy® mini kit. The RNA sample was subsequently treated with RNase-free Dnase-I at room temperature for 20min and stored at -80°C until use. The isolated RNA was subjected to several levels of testing before using for microarray hybridization. The purity and quantity of the RNA was determined by A260/A280 ratios and then A260, respectively, using Biophotometer (Eppendorf, CA, USA). RNA samples that had good OD values (1.8–2.0) were further tested on gels for the integrity of both the 28S and 18S ribosomal RNA by denaturing agarose gels and visualized with ethidium bromide under UV light.

treatment_protocol: Group (III):- Human monocytic macrophage (THP-1) cells were infected with Burkholderia pseudomallei (A600 nm = OD 0.6, ~5 x 107 cfu/ml) and treated with Daboiatoxin (0.5 mM, EC50~1 mM) isolated from Daboia russelli russelli venom served as a treatment. (Replicate 2).

tag: Human monocytic macrophage (THP-1) cells were infected with Burkholderia pseudomallei (A600 nm = OD 0.6, ~5 x 107 cfu/ml) and treated with Daboiatoxin (0.5 mM, EC50~1 mM) isolated from Daboia russelli russelli venom served as a treatment (Replicate 2).


title: G-IV_THP-1+B. pseudomallei 24h+CAZ_Rep1.

description: Total RNA was isolated from THP-1 cells infected with B. pseudomallei (n = 5 flasks for each replicate) and treated with commercial antimicrobial drug ceftazidime using RNeasy® mini kit. The target chip hybridization followed successful Genechip Test3 arrays hybridization. All relevant procedures, such as amplification of cDNA, fragmentation of cRNA for hybridization, and concurrent assessment of expression levels of genes were carried out. Briefly, we synthesized double-stranded cDNA from the total RNA isolated from the THP-1 cells infected with with B. pseudomallei, and treated with CAZ. We generated biotin-labeled cRNAs by in-vitro transcription from the ds-cDNA. The cRNAs were fragmented before hybridization, and a hybridization cocktail was prepared and hybridized to the oligonucleotide probes on the HG-U133A GeneChip arrays for 16h incubation at 45°C. Immediately after the hybridization, the hybridized probe arrays underwent an automated washing and staining protocol on an Affymetrix Fluidics Station. We scanned the GeneChips and processed the signals using Affymetrix genechip scanner and expression analysis algorithm (Affymetrix, Santa Clara, CA).

source_name: THP-1+ Infected with B. pseudomallei 24h and treated with ceftazidime_Rep1.

growth_protocol: Human macrophage (THP-1) cells were cultured in 72 cm2 flask in DMEM culture medium supplemented with 10% fetal bovine serum (FBS). The cells were maintained at 37°C in a humidified atmosphere of 5% CO2 and 95% air. The culture medium containing THP-1 cells were infected with with Burkholderia pseudomallei (A600 nm = OD 0.6, ~5 x 107 cfu/ml) for 24h, and treated with commercial antimicrobial drug ceftazidime (10mg/ml) served as a drug control. (Replicate 1).

extract_protocol: All glasswares used for RNA isolation were treated with diethyl pyrocarbonate (DEPC) to ensure RNase-free environment. They were filled with DEPC-treated water (1.0ml DEPC in 1L of sterile DD-H2O), allowed to stand overnight at 37°C and then autoclaved to eliminate residual DEPC. Total RNA was isolated from THP-1 cells infected with B. pseudomallei (n = 5 flasks for each replicate) and treated with commercial antimicrobial drug ceftazidime using RNeasy® mini kit. The RNA sample was subsequently treated with RNase-free Dnase-I at room temperature for 20min and stored at -80°C until use. The isolated RNA was subjected to several levels of testing before using for microarray hybridization. The purity and quantity of the RNA was determined by A260/A280 ratios and then A260, respectively, using Biophotometer (Eppendorf, CA, USA). RNA samples that had good OD values (1.8–2.0) were further tested on gels for the integrity of both the 28S and 18S ribosomal RNA by denaturing agarose gels and visualized with ethidium bromide under UV light.

treatment_protocol: Group IV :- Human monocytic macrophage (THP-1) cells were infected with Burkholderia pseudomallei (A600 nm = OD 0.6, ~5 x 107 cfu/ml) and treated with commercial antimicrobial drug ceftazidime (10mg/ml) served as a drug control. (Replicate 1).

tag: Human monocytic macrophage (THP-1) cells were infected with Burkholderia pseudomallei and treated with commercial antimicrobial drug ceftazidime (10mg/ml) served as a drug control. (Replicate 1).


title: G-IV_THP-1+B. pseudomallei 24h+CAZ_Rep2.

description: Total RNA was isolated from THP-1 cells infected with B. pseudomallei (n = 5 flasks for each replicate) and treated with standared antimicrobial drug ceftazidime using RNeasy® mini kit. The target chip hybridization followed successful Genechip Test3 arrays hybridization. All relevant procedures, such as amplification of cDNA, fragmentation of cRNA for hybridization, and concurrent assessment of expression levels of genes were carried out. Briefly, we synthesized double-stranded cDNA from the total RNA isolated from the THP-1 cells infected with with B. pseudomallei, and treated with CAZ. We generated biotin-labeled cRNAs by in-vitro transcription from the ds-cDNA. The cRNAs were fragmented before hybridization, and a hybridization cocktail was prepared and hybridized to the oligonucleotide probes on the HG-U133A GeneChip arrays for 16h incubation at 45°C. Immediately after the hybridization, the hybridized probe arrays underwent an automated washing and staining protocol on an Affymetrix Fluidics Station. We scanned the GeneChips and processed the signals using Affymetrix genechip scanner and expression analysis algorithm (Affymetrix, Santa Clara, CA).

source_name: THP-1+ Infected with B. pseudomallei 24h and treated with ceftazidime_Rep2.

growth_protocol: Human macrophage (THP-1) cells were cultured in 72 cm2 flask in DMEM culture medium supplemented with 10% fetal bovine serum (FBS). The cells were maintained at 37°C in a humidified atmosphere of 5% CO2 and 95% air. The culture medium containing THP-1 cells were infected with with Burkholderia pseudomallei (A600 nm = OD 0.6, ~5 x 107 cfu/ml) for 24h, and treated with commercial antimicrobial drug ceftazidime (10mg/ml) served as a drug control. (Replicate 2).

treatment_protocol: Group IV :- Human monocytic macrophage (THP-1) cells were infected with Burkholderia pseudomallei (A600 nm = OD 0.6, ~5 x 107 cfu/ml) and treated with commercial antimicrobial drug ceftazidime (10mg/ml) served as a drug control. (Replicate 2).

tag: Human monocytic macrophage (THP-1) cells were infected with Burkholderia pseudomallei and treated with commercial antimicrobial drug ceftazidime (10mg/ml) served as a drug control. (Replicate 2).


title: G-(II)_THP-1+B. pseudomallei 24h_Rep3.

description: Total RNA was isolated from B. pseudomallei (n = 5 flasks for each replicate) infected THP-1 cells using RNeasy® mini kit. The target chip hybridization followed successful Genechip Test3 arrays hybridization. All relevant procedures, such as amplification of cDNA, fragmentation of cRNA for hybridization, and concurrent assessment of expression levels of genes were carried out. Briefly, we synthesized double-stranded cDNA from the total RNA isolated from the THP-1 cells infected with with B. pseudomallei. We generated biotin-labeled cRNAs by in-vitro transcription from the ds-cDNA. The cRNAs were fragmented before hybridization, and a hybridization cocktail was prepared and hybridized to the oligonucleotide probes on the HG-U133A GeneChip arrays for 16h incubation at 45°C. Immediately after the hybridization, the hybridized probe arrays underwent an automated washing and staining protocol on an Affymetrix Fluidics Station. We scanned the GeneChips and processed the signals using Affymetrix genechip scanner and expression analysis algorithm (Affymetrix, Santa Clara, CA).

source_name: THP-1+ Infected with B. pseudomallei_Rep3.

growth_protocol: Human macrophage (THP-1) cells were cultured in 72 cm2 flask in DMEM culture medium supplemented with 10% fetal bovine serum (FBS). The cells were maintained at 37°C in a humidified atmosphere of 5% CO2 and 95% air. The culture medium containing THP-1 cells were infected with with Burkholderia pseudomallei (A600 nm = OD 0.6, ~5 x 107 cfu/ml) for 24h served as a disease control. (Replicate 3)

extract_protocol: All glasswares used for RNA isolation were treated with diethyl pyrocarbonate (DEPC) to ensure RNase-free environment. They were filled with DEPC-treated water (1.0ml DEPC in 1L of sterile DD-H2O), allowed to stand overnight at 37°C and then autoclaved to eliminate residual DEPC. Total RNA was isolated from B. pseudomallei (n = 5 flasks for each replicate) infected THP-1 cells using RNeasy® mini kit. The RNA sample was subsequently treated with RNase-free Dnase-I at room temperature for 20min and stored at -80°C until use. The isolated RNA was subjected to several levels of testing before using for microarray hybridization. The purity and quantity of the RNA was determined by A260/A280 ratios and then A260, respectively, using Biophotometer (Eppendorf, CA, USA). RNA samples that had good OD values (1.8–2.0) were further tested on gels for the integrity of both the 28S and 18S ribosomal RNA by denaturing agarose gels and visualized with ethidium bromide under UV light.

treatment_protocol: Human monocytic macrophage (THP-1) cells were infected with Burkholderia pseudomallei (A600 nm = OD 0.6, ~5 x 107 cfu/ml) for 24h served as a disease control (Replicate 3).

tag: Group II :- Human monocytic macrophage (THP-1) cells were infected with Burkholderia pseudomallei (A600 nm = OD 0.6, ~5 x 107 cfu/ml) as a disease control (Replicate 3).


title: G-(III)_THP-1+B. pseudomallei 24h+DbTx_Rep1.

source_name: THP-1+ Infected with B. pseudomallei 24h and treated with Daboiatoxin_Rep1.

growth_protocol: Human macrophage (THP-1) cells were cultured in 72 cm2 flask in DMEM culture medium supplemented with 10% fetal bovine serum (FBS). The cells were maintained at 37°C in a humidified atmosphere of 5% CO2 and 95% air. The culture medium containing THP-1 cells were infected with with Burkholderia pseudomallei (A600 nm = OD 0.6, ~5 x 107 cfu/ml) for 24h, and treated with Daboiatoxin (0.5 mM, EC50~1 mM) isolated from Daboia russelli russelli venom served as a treatment.(Replicate 1).

treatment_protocol: Group (III):- Human monocytic macrophage (THP-1) cells were infected with Burkholderia pseudomallei (A600 nm = OD 0.6, ~5 x 107 cfu/ml) and treated with Daboiatoxin (0.5 mM, EC50~1 mM) isolated from Daboia russelli russelli venom served as a treatment. (Replicate 1).

tag: Human monocytic macrophage (THP-1) cells were infected with Burkholderia pseudomallei (A600 nm = OD 0.6, ~5 x 107 cfu/ml) and treated with Daboiatoxin (0.5 mM, EC50~1 mM) isolated from Daboia russelli russelli venom served as a treatment (Replicate 1).


title: G-(III)_THP-1+B. pseudomallei 24h+DbTx_Rep3.

source_name: THP-1+ Infected with B. pseudomallei 24h and treated with Daboiatoxin_Rep3.

growth_protocol: Human macrophage (THP-1) cells were cultured in 72 cm2 flask in DMEM culture medium supplemented with 10% fetal bovine serum (FBS). The cells were maintained at 37°C in a humidified atmosphere of 5% CO2 and 95% air. The culture medium containing THP-1 cells were infected with with Burkholderia pseudomallei (A600 nm = OD 0.6, ~5 x 107 cfu/ml) for 24h, and treated with Daboiatoxin (0.5 mM, EC50~1 mM) isolated from Daboia russelli russelli venom served as a treatment.(Replicate 3).

treatment_protocol: Group (III):- Human monocytic macrophage (THP-1) cells were infected with Burkholderia pseudomallei (A600 nm = OD 0.6, ~5 x 107 cfu/ml) and treated with Daboiatoxin (0.5 mM, EC50~1 mM) isolated from Daboia russelli russelli venom served as a treatment. (Replicate 3).

tag: Human monocytic macrophage (THP-1) cells were infected with Burkholderia pseudomallei (A600 nm = OD 0.6, ~5 x 107 cfu/ml) and treated with Daboiatoxin (0.5 mM, EC50~1 mM) isolated from Daboia russelli russelli venom served as a treatment (Replicate 3).


title: Human monocytic macrophage (THP-1) cell lines served as untreated control (Replicate 3)

description: The untreated control (THP-1) cells were harvested and the total RNA was extracted. The target chip hybridization followed successful Genechip Test3 arrays hybridization. All relevant procedures, such as amplification of cDNA, fragmentation of cRNA for hybridization, and concurrent assessment of expression levels of genes were carried out. Briefly, we synthesized double-stranded cDNA from the total RNA isolated from the THP-1 cells. We generated biotin-labeled cRNAs by in-vitro transcription from the ds-cDNA. The cRNAs were fragmented before hybridization, and a hybridization cocktail was prepared and hybridized to the oligonucleotide probes on the HG-U133A GeneChip arrays for 16h incubation at 45°C. Immediately after the hybridization, the hybridized probe arrays underwent an automated washing and staining protocol on an Affymetrix Fluidics Station. We scanned the GeneChips and processed the signals using Affymetrix genechip scanner and expression analysis algorithm (Affymetrix, Santa Clara, CA).

growth_protocol: Human macrophage (THP-1) cells were cultured in 72 cm2 flask in DMEM culture medium supplemented with 10% fetal bovine serum (FBS). The cells were maintained at 37°C in a humidified atmosphere of 5% CO2 and 95% air. The culture medium was changed four times a week.

extract_protocol: All glasswares used for RNA isolation were treated with diethyl pyrocarbonate (DEPC) to ensure RNase-free environment. They were filled with DEPC-treated water (1.0ml DEPC in 1L of sterile DD-H2O), allowed to stand overnight at 37°C and then autoclaved to eliminate residual DEPC. Total RNA was isolated from untreated (n = 5 flasks for each replicate) THP-1 cells using RNeasy® mini kit. The RNA sample was subsequently treated with RNase-free Dnase-I at room temperature for 20min and stored at -80°C until use. The isolated RNA was subjected to several levels of testing before using for microarray hybridization. The purity and quantity of the RNA was determined by A260/A280 ratios and then A260, respectively, using Biophotometer (Eppendorf, CA, USA). RNA samples that had good OD values (1.8–2.0) were further tested on gels for the integrity of both the 28S and 18S ribosomal RNA by denaturing agarose gels and visualized with ethidium bromide under UV light.

treatment_protocol: Human monocytic macrophage (THP-1) cell lines grown in the culture medium without any bacterial infection served as untreated control (Replicate 3 for Ctrl).

tag: Human monocytic macrophage (THP-1) cell lines served as untreated control (R-3).


title: Human monocytic macrophage (THP-1) cell lines served as untreated control (Replicate 1)

hyb_protocol: The preparation and processing of labeled, fragmented cRNA and hybridization cocktail for hybridization has been performed according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA). Immediately after the hybridization, the hybridized probe arrays underwent an automated washing and staining protocol on an Affymetrix Fluidics Station (Replicate1).

source_name: Monocytic macrophage (THP-1) cell lines served as untreated control (R-1)

treatment_protocol: Human monocytic macrophage (THP-1) cell lines grown in the culture medium without any bacterial infection served as untreated control.

tag: Human monocytic macrophage (THP-1) cell lines served as untreated control.


title: G-(II)_THP-1+B. pseudomallei 24h_Rep2.

source_name: THP-1+ Infected with B. pseudomallei_Rep2.

growth_protocol: Human macrophage (THP-1) cells were cultured in 72 cm2 flask in DMEM culture medium supplemented with 10% fetal bovine serum (FBS). The cells were maintained at 37°C in a humidified atmosphere of 5% CO2 and 95% air. The culture medium containing THP-1 cells were infected with with Burkholderia pseudomallei (A600 nm = OD 0.6, ~5 x 107 cfu/ml) for 24h served as a disease control. (Replicate 2)

treatment_protocol: Human monocytic macrophage (THP-1) cells were infected with Burkholderia pseudomallei (A600 nm = OD 0.6, ~5 x 107 cfu/ml) for 24h served as a disease control (Replicate 2).

tag: Group II :- Human monocytic macrophage (THP-1) cells were infected with Burkholderia pseudomallei (A600 nm = OD 0.6, ~5 x 107 cfu/ml) as a disease control (Replicate 2).


title: G-(II)_THP-1+B. pseudomallei 24h_Rep1.

source_name: THP-1+ Infected with B. pseudomallei_Rep1.

growth_protocol: Human macrophage (THP-1) cells were cultured in 72 cm2 flask in DMEM culture medium supplemented with 10% fetal bovine serum (FBS). The cells were maintained at 37°C in a humidified atmosphere of 5% CO2 and 95% air. The culture medium containing THP-1 cells were infected with with Burkholderia pseudomallei (A600 nm = OD 0.6, ~5 x 107 cfu/ml) for 24h served as a disease control. (Replicate 1)

treatment_protocol: Human monocytic macrophage (THP-1) cells were infected with Burkholderia pseudomallei (A600 nm = OD 0.6, ~5 x 107 cfu/ml) for 24h served as a disease control (Replicate 1).

tag: Group II :- Human monocytic macrophage (THP-1) cells were infected with Burkholderia pseudomallei (A600 nm = OD 0.6, ~5 x 107 cfu/ml) as a disease control (Replicate 1).


title: Newborn wild-type inner ear pool, replicate A1, GCRMA-normalized

city: Houston

first: Fred

middle: A.

last: Pereira

state: TX

address: One Baylor Plaza

department: Hufftington Center on Aging

institute: Baylor College of Medicine

description: The objective of our study is to identify direct COUP-TFI targets in the mouse inner ear. We performed a total of 8 microarray experiments using Affymetrix MG-U74Av2 chips. Two sets of hybridizations (experimental replicates) were performed at a different point in time, each set consisting of one RNA pool per genotype hybridized in duplicate.

hyb_protocol: A hybridization cocktail containing Affymetrix spike-in controls and fragmented labeled cRNA was loaded onto a GeneChip® array.  The array was hybridized overnight at 45°C with rotation at 60 rpm then washed and stained with a strepavidin, R-phycoerythrin conjugate stain.  Signal amplification was done using biotinylated antistreptavidin.

scan_protocol: The stained array was scanned on the Affymetrix GeneChip® Scanner 3000.  The images were analyzed and quality control metrics recorded using Affymetrix GCOS software version 1.1.2.

data_processing: Microarray raw data was normalized using GCRMA software.

organism: Mus musculus

source_name: Newborn mouse whole inner ears

label_protocol: The Baylor College of Medicine Microarray Core Facility first conducted Sample Quality checks using the Agilent Bioanalyzer, and then used the Affymetrix Genechip™ microarray system as follows:  samples were labeled using the standard Affymetrix T7 oligo(dT) primer protocol.  Five ug of total RNA was reverse transcribed to produce double-stranded cDNA.  The cDNA product was used as a template for the in vitro transcription reaction, producing biotin-labeled cRNA.  The labeled cRNA was qualified using the Agilent Bioanalyzer. 15.0 µg of the labeled cRNA was fragmented and re-checked for concentration.

extract_protocol: Whole P0 inner ears were placed in RNA Later (Ambion) after dissection, stored at 4C overnight and then at -20C until genotype was determined. Total RNA was isolated using the RNeasy Mini Kit (Qiagen), following the manufacturer’s instructions, and quantified by NanoDrop spectrophotometry (Wilmington, DE).

tag: genotype

value: wild-type

tag: tissue

value: newborn whole inner ears

tag: strain


title: Newborn wild-type inner ear pool, replicate B2, dChip-normalized

data_processing: Microarray raw data was normalized using dChip software.


title: Newborn wild-type inner ear pool, replicate A2, GCRMA-normalized


title: Newborn wild-type inner ear pool, replicate B1, dChip-normalized


title: Newborn wild-type inner ear pool, replicate B1, GCRMA-normalized


title: Newborn wild-type inner ear pool, replicate A2, dChip-normalized


title: Newborn wild-type inner ear pool, replicate B2, GCRMA-normalized


title: Newborn COUP-TFI-/- inner ear pool, replicate B2, GCRMA-normalized

value: COUP-TFI-/-


title: Newborn COUP-TFI-/- inner ear pool, replicate A2, GCRMA-normalized


title: Newborn wild-type inner ear pool, replicate A1, dChip-normalized


title: Newborn COUP-TFI-/- inner ear pool, replicate B1, GCRMA-normalized


title: Human monocytic macrophage (THP-1) cell lines served as untreated control (Replicate 2)

tag: Human monocytic macrophage (THP-1) cell lines served as untreated control (R-2).


title: Newborn COUP-TFI-/- inner ear pool, replicate A1, dChip-normalized


title: Newborn COUP-TFI-/- inner ear pool, replicate A1, GCRMA-normalized


title: Newborn COUP-TFI-/- inner ear pool, replicate A2, dChip-normalized


title: Newborn COUP-TFI-/- inner ear pool, replicate B1, dChip-normalized


title: Newborn COUP-TFI-/- inner ear pool, replicate B2, dChip-normalized


title: Pantoea stewartii pv stewartii strain DC283-c

status: Public on Mar 16 2010

type: genomic

city: Waedenswil

first: Frederique

last: Pasquer

address: Schloss

department: Plant Protection

country: Switzerland

institute: Agroscope Changins-Waedenswil Research Station ACW

description:
Replicate 3 of 3.
227206-stew

hyb_protocol: Prior to hybridisation, 3 mg of labelled DNA in 100 ml of 2 x Hybridisation buffer (NimbleGen® System, Inc., Madison, Wi, United States of America) and 40 ml Hybridisation Component A (NimbleGen® System, Inc.), 0.3 microl of 3’ labelled Cy3-CPK6 50 nM (Integrated DNA Technologies, Coralville, Ia, United States of America) and ddH2O up to 200 ml were denatured for 5 min at 95°C and cooled. Hybridisation was performed during 16 hrs at 4°C with a pump rate of 1ml/min in an aHybTM hybridisation station (Miltenyi Biotec, Bergisch-Gladbach, Germany). Washings were performed at 20°C in the station with NimbleGen® buffers I to III for 1 min each, respectively. The last washing buffer was incubated 1 min on the slide before blow-drying with high-pressure air.

scan_protocol: Slides were scanned at a gain of 500 to 600 at 532 nm wavelength and 5 microm resolution with a Genepix 4100A scanner (Axon Instrument, Sunnyvale, California, United States of America).

data_processing: Signals of each slide were smoothed using the NMPP program (Wang et al., 2006). Normalisation per chip to 50th percentile and further analyses were performed in GeneSpring GX v7.3.1 (Agilent Technologies, Basel, Switzerland).

molecule: genomic DNA

organism: Pantoea stewartii

source_name: Pantoea stewartii pv stewartii strain DC283 DNA

label_protocol: Labelling was performed by overnight incubation at 37°C of 10 mg DNA with 50ml with 40 U of Klenow fragment (Fermentas), 5ml of 10 x buffer, 1 ml of Cyanine-3 labelled dUTP (Perkin Elmer, Schwerzenbach, Switzerland), 0.5 mM of dNTP (without dTTP) (Fermentas). Samples were purified using a PCR purification kit (Qiagen, Basel, Switzerland), and quality and concentration checked using a ND-1000 spectrophotometer (NanoDrop®, Witec AG, Littau, Switzerland).

extract_protocol: Genomic bacterial DNA was extracted following the protocol described in Maniatis Sambrook (Sambrook et al., 1989). DNA was sonicated in a Bioruptor (Diagenode, Liege, Belgium) to obtain fragments of approximately 500 bp.

tag: pathovar

value: stewartiia


title: Rat 17 Replicate 2, Shunt collaterals versus Control arteries

status: Public on May 26 2010

city: Bad Nauheim

first: Kerstin

last: Troidl

address: Ludwigstr. 43

country: Germany

institute: Max-Planck-Institute for Heart and Lung Research

description: Biological replicate 3, technical replicate 2: shunted collaterals versus control arteries

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. Samples were hybridized and washed according to the default Agilent Hybridization and wash protocols.

scan_protocol: Scanned on an Agilent G2565AA scanner

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.7.5.1). Agilent Feature Extraction Software (v 7.5.1) was used for background subtraction and LOWESS normalization. After Quantile interarray normalization, Log10 Intensity Ratios of Shunt/Control were calculated.

label_protocol: Low Input RNA Fluorescent Linear Amplification Kit, Agilent (#5184-3523)

extract_protocol: Total RNA molecules were extracted by using the default protocol of the Absolutely RNA Nanoprep Kit, Stratagene (#400753).

treatment_protocol: Arteries were extracted from the rat hindlimb. Immediately thereafter the arteries were snapfrozen in liquid Nitrogen for storage until RNA extraction.

value: Shunt arteries

value: Control arteries


title: Rat 15 Replicate 2, Shunt collaterals versus Control arteries

description: Biological replicate 2, technical replicate 2: shunted collaterals versus control arteries


title: P35S::EBB1_Apex_rep2

status: Public on May 28 2010

city: Houghton

first: Victor

last: Busov

state: MI

address: 1400 Townsend Drive

department: Forest Resources and Environmental Science

institute: Michigan Technological University

description: Gene expression data from apex of P35S::EBB1.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Poplar Genome Array. GeneChips were washed and stained in the Affymetrix GeneChip® Fluidics Station 450. The Affymetrix eukaryotic hybridization control kit and Poly-A RNA control kit were used to ensure efficiency of hybridization and cRNA amplification. Hybridizations were conducted with one replicate of all times and treatments concurrently.

scan_protocol: Arrays were scanned with an Affymetrix GeneChip® Scanner 3000 at 570nm. Each array image was visually screened to discount for signal artifacts, scratches or debris.

data_processing: The data were processed with RMAExpress (http://rmaexpress.bmbolstad.com/) using default analysis settings, quantile normalization and median polish.

organism: Populus tremula x Populus alba

source_name: Apices from EBB1-overexpressing plant

label_protocol: Biotinylated cRNA were prepared according to the standard one_cycle Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). All cRNA was synthesized at the same time.

growth_protocol: Greenhouse conditions.

extract_protocol: We isolated RNA from about 0.3g tissue. RNA was extracted as previously described (Busov VB,at al, 2003, Plant Physiol 132: 1283-1291) using QIAGEN kits.

treatment_protocol: Apices from EBB1-overexpressing plant and control, about 0.5 cm, was fixed in liquid Nitrogen and stored  at -80oC until RNA extraction.

tag: clone

value: INRA 717-IB5

value: apex


title: Salmonella Typhimurium strain DT204-b

description:
Replicate 2 of 3.
149784S1-DT204

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: Salmonella Typhimurium strain DT204 DNA


title: Rat 17 Replicate 1, Shunt collaterals versus Control arteries

description: Biological replicate 3, technical replicate 1: shunted collaterals versus control arteries


title: Control_Apex_rep1

description: Gene expression data from apex of wild type.

source_name: Apices from control

value: INRA 717-IB6

value: wild type


title: Micrococcus luteus-a

description:
Replicate 1 of 2.
148747-Mluteus

organism: Micrococcus luteus

source_name: Micrococcus luteus DNA


title: Salmonella Typhimurium strain LT2-b

description:
Replicate 2 of 2.
227130-LT2

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

source_name: Salmonella Typhimurium strain LT2 DNA


title: Salmonella Typhimurium strain DT204-a

description:
Replicate 1 of 3.
148741-DT204


title: Rat 15 Replicate 1, Shunt collaterals versus Control arteries

description: Biological replicate 2, technical replicate 1: shunted collaterals versus control arteries


title: Pantoea agglomerans strain C9-1w-b

description:
Replicate 2 of 2.
227208-C9-1w

organism: Pantoea agglomerans

source_name: Pantoea agglomerans strain C9 DNA

value: C9-1 white


title: Control_Apex_rep2

value: INRA 717-IB7


title: Micrococcus luteus-b

description:
Replicate 2 of 2.
149766-Mluteus


title: Pantoea agglomerans strain C9-1w-a

description:
Replicate 1 of 2.
227045-C9-1w


title: Salmonella Typhimurium strain LT2-a

description:
Replicate 1 of 2.
227122-LT2


title: Rat 8 Replicate 2, Shunt collaterals versus Control arteries

description: Biological replicate 1, technical replicate 2: shunted collaterals versus control arteries


title: P35S::EBB1_Apex_rep1

value: INRA 717-IB4


title: Pantoea stewartii pv stewartii strain DC283-a

description:
Replicate 1 of 3.
148451-stew


title: Pantoea agglomerans strain C9-1-a

description:
Replicate 1 of 3.
149779-C9-1


title: Rat 8 Replicate 1, Shunt collaterals versus Control arteries

description: Biological replicate 1, technical replicate 1: shunted collaterals versus control arteries


title: Pantoea agglomerans strain C9-1-b

description:
Replicate 2 of 3.
149782-C9-1


title: Salmonella Typhimurium strain DT204-c

description:
Replicate 3 of 3.
227016S1-DT204


title: Pantoea stewartii pv stewartii strain DC283-b

description:
Replicate 2 of 3.
227026-stew


title: Pantoea agglomerans strain C9-1-c

description:
Replicate 3 of 3.
227222-C9-1


title: Pantoea agglomerans strain ATCC 27155T-b

description:
Replicate 2 of 2.
227207-27155T

source_name: Pantoea agglomerans strain ATCC 27155T DNA

value: ATCC 27155T


title: Pantoea agglomerans strain ATCC 27155T-a

description:
Replicate 1 of 2.
227072-27155T


title: E. coli strain B-b

description:
Replicate 2 of 2.
194279-B

organism: Escherichia coli B

source_name: E. coli strain B DNA

value: B


title: E. coli strain K12-c

description:
Replicate 3 of 4.
194266-K12

organism: Escherichia coli K-12

source_name: E. coli strain K12 DNA


title: E. coli strain K12-a

description:
Replicate 1 of 4.
149777-K12


title: E. coli strain K12-b

description:
Replicate 2 of 4.
194223-K12


title: E. coli strain K12-d

description:
Replicate 4 of 4.
194277-K12


title: E. coli strain B-a

description:
Replicate 1 of 2.
148473-A


title: MCF-7 macroH2A Replicate 1

status: Public on Jan 31 2010

city: Dallas

first: W. Lee

last: Kraus

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

hyb_protocol: Standard hybridization to Affymetrix U133A 2.0 microarray.

scan_protocol: Standard scanning protocol using GeneChip Scanner.

data_processing: The raw data were processed by Affymetrix GCOS software to obtain detection calls and signal values, and then normalized by scaling. Signals were then used in further analysis, namely batch effect adjusted and log2 median-normalized using COMBAT R.

source_name: MCF-7 macroH2A Replicate 1

label_protocol: Seven μg of total RNA were subjected to One-Cycle Target Labeling Assay (Affymetrix) to generate biotinylated cRNA targets for hybridization to Affymetrix U133A 2.0 microarray.

extract_protocol: Total RNA was prepared using Trizol Reagent according to the manufacturer’s instructions (Invitrogen) and was further purified using RNeasy columns (Qiagen).

tag: MCF-7 macroH2A Replicate 1


title: GBM Spheroid culture 3

status: Public on Feb 13 2010

city: Heidelberg

first: Aurelie

last: Ernst

address: Im Neuenheimer Feld 280

institute: DKFZ

hyb_protocol: Labeled, amplified material (700 to 1250 ng per array) was hybridized to the Illumina Human whole genome Sentrix-6 V2 BeadChip® array according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Microarray scanning was done using a Beadstation array scanner, setting adjusted to a scaling factor of 1 and PMT settings at 430.

data_processing: Raw data extraction was done using the beadarray R package (svn release 1.7.0) from bioconductor.org. Bead outliers were removed when their expression value dropped below a threshold: the imaging system background, non-specific binding and cross hybridization signal. Individual bead types were flagged as filtered when their bead replicate count dropped below 17. All data was used for the mean expression value calculation within beadarray. Finally, we excluded a bead type when the bead type’s filter flag was set across all samples. Data analysis was done by variance stabilizing and spline normalizing the signals using the algorithms from the lumi R package (release 1.1.0) from bioconductor.org.

source_name: primary glioblastoma

label_protocol: Labeling was achieved by use of the incorporation of biotin-16-UTP.

growth_protocol: Glioblastoma samples were enzymatically dissociated and resuspended in stem-cell medium made of DMEM/F-12 medium containing 20% BIT serum-free supplement, basic fibroblast growth factor (bFGF) and epidermal growth factor (EGF) at 20ng/ml each (all Provitro, Berlin, Germany)

extract_protocol: RNA  was isolated from the spheroid cultures using the RNeasy kit (Qiagen, Hilden, Germany). RNA quality and concentration were assessed with the Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA).

value: brain

tag: cell type

value: glioblastoma

tag: class

value: WHO IV


title: MCF-7 macroH2A Replicate 3

source_name: MCF-7 macroH2A Replicate 3

tag: MCF-7 macroH2A Replicate 3


title: Non-neoplastic brain culture 1

source_name: non-neoplastic human brain tissue sample of 1 individual (bulbus olfactorius)

value: non-neoplastic

value: normal


title: GBM Spheroid culture 7


title: GBM Spheroid culture 9


title: GBM Spheroid culture 10


title: GBM Spheroid culture 5


title: Reference normal brain 2

description: Normal brain

source_name: non-neoplastic human brain tissue sample of 1 individual


title: GBM Spheroid culture 4


title: GBM Spheroid culture 1


title: GBM Spheroid culture 6


title: MCF-7 macroH2A Replicate 2

source_name: MCF-7 macroH2A Replicate 2

tag: MCF-7 macroH2A Replicate 2


title: GBM Spheroid culture 8


title: GBM Spheroid culture 2

source_name: secondary glioblastoma


title: Reference normal brain 1

description: Normal brain pool

source_name: non-neoplastic human brain tissue samples of 5 individuals (age range: 26–82)


title: BW25113 ompA/pCA24N

status: Public on Jan 20 2010

city: State College

first: Thomas

middle: K.

last: Wood

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

description: RNA extracted from suspension cells of E. coli BW25113 ompA/pCA24N after 7 h of growth in LB+0.1 mM IPTG at 37ºC.

hyb_protocol: Following affymetrix protocol. Prepared hybridization cocktail for Single Probe Array (49 Format) with total 80 ul volume including 1X hybrization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labelled cDNA. After loading of hybridization cocktail in Affymetrix E. coli Antisense Genome Array, the hybridization was performed at 45ºC, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS)

scan_protocol: Following affymetrix protocol. After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS)

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Escherichia coli

source_name: E. coli BW25113 ompA/pCA24N suspension cells

label_protocol:
Following affymetrix protocol.
cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181)

extract_protocol: The overnight culture was used to 1:100 inoculate 25 ml of fresh LB medium with 0.1 mM IPTG and 30 ug/mL chloramphenicol. After incubation for 7 h at 37°C with shaking (250 rpm), cells were collected. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit.

tag: strain/genotype

value: E. coli K-12 BW25113 ompA/pCA24N

tag: growth

value: suspension cells of E. coli K-12 ompA/pCA24N after 7 hours of growth in LB with 0.1 mM IPTG and 30 ug/mL chloramphenicol at 37ºC


description: RNA extracted from glasswool biofilm cells of E. coli K-12 BW25113 wild type after 15 hours of growth in LB at 37ºC

hyb_protocol: Following affymetrix protocol. Prepared hybridization cocktail for Single Probe Array (49 Format) with total 200 ul volume including 1X hybrization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labelled cDNA. After loading of hybridization cocktail in Affymetrix E. coli Antisense Genome Array, the hybridization was performed at 45ºC, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS)

source_name: E. coli K-12 BW25113 wild type glasswool biofilm cells

extract_protocol: Overnight culture were 1:100 reinoculated into 250 mL LB culture with ~10 g glasswool. Biofilm cells from glasswool surfaces were collected after 37˚C incubation for 15 h. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit.

value: E. coli K-12 BW25113 wild type


title: BW25113 ompA polystyrene biofilm cells

description: RNA extracted from polystyrene biofilm cells of E. coli K-12 BW25113 ompA after 15 hours of growth in LB at 37ºC

source_name: E. coli K-12 BW25113 ompA polystyrene biofilm cells

extract_protocol: Overnight culture were 1:100 reinoculated into 300 mL LB culture with ~30 g polystyrene particles. Biofilm cells from polystyrene surfaces were collected after 37˚C incubation for 15 h. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit.

value: E. coli K-12 BW25113 ompA mutant


description: RNA extracted from polystyrene biofilm cells of E. coli K-12 BW25113 wild type after 15 hours of growth in LB at 37ºC

source_name: E. coli K-12 BW25113 wild type polystyrene biofilm cells


title: BW25113 ompA/pCA24N_ompA

description: RNA extracted from suspension cells of E. coli BW25113 ompA/pCA24N_ompA after 7 h of growth in LB+0.1 mM IPTG at 37ºC.

source_name: E. coli K-12 ompA/pCA24N_ompA suspension cells

value: E. coli K-12 BW25113 ompA/pCA24N_ompA

value: suspension cells of E. coli K-12 ompA/pCA24N_ompA after 7 hours of growth in LB with 0.1 mM IPTG and 30 ug/mL chloramphenicol at 37ºC


title: BW25113 ompA mutant LB 15 h 37C polystyrene biofilm cell (repeat)

description: RNA extracted from polystyrene biofilm cells of E. coli K-12 ompA after 15 hours of growth in LB at 37ºC

hyb_protocol: Following affymetrix protocol. Prepared hybridization cocktail for Single Probe Array (49 Format) with total 80 ul volume including 1X hybrization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labelled cDNA. After loading of hybridization cocktail in Affymetrix E. coli Genome 2.0 Array, the hybridization was performed at 45ºC, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS)

source_name: E. coli K-12 BW25113 ompA mutant polystyrene biofilm cells

extract_protocol: The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB medium with 30 g of submerged polystyrene particles for forming biofilm. After incubation for 15 h at 37°C with shaking (250 rpm), the polystyrene particles was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the polystyrene particles in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104).

value: polystyrene biofilm cells of E. coli K-12 ompA mutant after 15 hours of growth in LB at 37ºC


title: BW25113 w/t LB 15 h 37C polystyrene biofilm cell (repeat)

description: RNA extracted from polystyrene biofilm cells of E. coli K-12 wild type after 15 hours of growth in LB at 37ºC


title: BW25113 ompA glasswool biofilm cells

description: RNA extracted from glasswool biofilm cells of E. coli K-12 BW25113 ompA after 15 hours of growth in LB at 37ºC

source_name: E. coli K-12 BW25113 ompA glasswool biofilm cells


title: Ovary at P3, wild-type, replicate 1

status: Public on Jan 01 2010

first: Henriette

last: Uhlenhaut

address: Meyerhofstrasse 1

department: Developmental Biology Unit

institute: EMBL

description: Expression profiles of neonatal (P3) ovaries

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17hr at 45C on Affymetrix Mouse Genome 430 2.0 Arrays (P3) and  Affymetrix Mouse Gene 1.0 ST Arrays (Adult). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: MAS 5

source_name: Mouse ovary, P3, wildtype

label_protocol: Biotinylated cRNAs were prepared according to the standard GeneChip WT Sense Target Labeling Assay Manual protocol (Affymetrix) from 300ng total RNA. For the P3 samples, 1µg RNA was labeled according to the CodeLink Bioarray Processing Protocol (Amersham).

growth_protocol: Mice were housed in specific pathogen-free controlled conditions. Food and water were available ad libitum. All experiments were carried out in accordance with the principles and guidelines of the LAR/European Molecular Biology Laboratory (EMBL).

extract_protocol: RNeasy (Qiagen) RNA isolation from animal tissues according to standard protocol, including on-column DNase digestion.

treatment_protocol: Ovaries/testes were removed from euthanized animals after perfusion with PBS and snap-frozen in liquid nitrogen (no perfusion for P3). Adult expression profiles represent single organ samples (single animals), whereas P3 profiles represent pools of >10 females per chip.

value: ovary

value: wild type

tag: developmental stage

value: newborn


title: Ovary at P3, wild-type, replicate 2


title: Ovary at P3, Foxl2 KO, replicate 1

source_name: Mouse ovary, P3, Foxl2 KO

value: Foxl2 KO


title: Rpb1-S2A-3

city: New York

first: Harm

middle: van

last: Bakel

state: New York

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

description: Rpb1-S2A RNA vs. wild type RNA, Replicate 3

hyb_protocol: 750 ng of labeled cRNA was hybridized per sample, according to standard Agilent protocols.

scan_protocol: Microarrays were scanned using an Agilent Microarray Scanner G2565CA (Agilent Technologies)

data_processing: Spot quantification was carried out using Feature Extraction software v9.5 (Agilent Technologies). Following quantification, the microarray data was lowess-normalized and an expression ratio was calculated for each microarray feature by dividing the signal intensity of the Rpb3-S2A sample by that of the wild type control.

organism: Schizosaccharomyces pombe

source_name: Rpb1-S2A total RNA

label_protocol: For each sample, 500 µg of total RNA was converted into labeled cRNA with nucleotides coupled to a fluorescent dye using the Low RNA Input Linear Amplification Kit (Agilent Technologies).

growth_protocol: A culture of 100ml was grown at 32°C in YES medium until mid-log phase, pelleted and snap-frozen in liquid nitrogen.

extract_protocol: RNA was prepared by acidic phenol extraction at 65°C for 1 hour with brief vortexing every 10 minutes. The water phase was re-extracted with acidic phenol-chloroform-IAA (24:24:1) and the RNA precipitated. About 250 µg of RNA were purified on Qiagen RNeasy column and eluted with 30 µl H20.

value: "552 h- rpb1-CTD-S2A-kanR"

source_name: Wild type total RNA


title: Lsk1-del-3

description: Lsk1-del RNA vs. wild type RNA, Replicate 3

data_processing: Spot quantification was carried out using Feature Extraction software v9.5 (Agilent Technologies). Following quantification, the microarray data was lowess-normalized and an expression ratio was calculated for each microarray feature by dividing the signal intensity of the Lsk1-del sample by that of the wild type control.

source_name: Lsk1-del total RNA


title: Rpb1-S2A-2

description: Rpb1-S2A RNA vs. wild type RNA, Replicate 2


title: TCDD exposed embryos, replicate 2

city: Hamilton

first: Andrew

middle: G.

last: McArthur

state: Ontario

address: 1280 Main Street West

department: Biochemistry & Biomedical Sciences

country: Canada

institute: McMaster University

description: TCDD exposed embryos, replicate 2

hyb_protocol: cRNA samples were hybridized to Agilent 22k zebrafish microarrays using the Agilent Gene Expression Hybridization Kit.  Labeled cRNAs were combined with the Agilent 25x fragmentation buffer and incubated at 60°C for 30 minutes.  This was followed by mixing with 2x hybridization buffer, after which 100 ul of the product was spread evenly across the surface of an Agilent 22K zebrafish microarray.  The loaded microarray was incubated at 60°C for 17 hours with rotation in an Agilent DNA Microarray Hybridization Oven.  Post-hybridization, microarray slides were washed, air-dried, and stored in darkness with desiccation.

scan_protocol: Raw hybridization results were obtained by laser-excited fluorescence scanning in an Agilent DNA Micorarray Scanner.

data_processing: Analysis of raw microarray data was performed using Agilent’s feature extraction protocol, which includes spot finding, spot analysis, background subtraction (using local background plus global background based on spots along the central tendency line for red versus green intensity), dye normalization (linear and lowess algorithms, using spots along the central tendency line as for background subtraction), and final calculation of Cy5/Cy3 ratios and log2 transformed fold change for each spot. Data were additionally median centered among all microarray results prior to statistical analyses.

organism: Danio rerio

source_name: Universal RNA Reference Sample

label_protocol: RNA samples were checked for quality using a NanoDrop ND-1000 spectrophotometer and an Agilent 2100 BioAnalyzer.  cDNA synthesis from 600 ng of total RNA was performed using the Agilent Low RNA Input Linear Fluorescent Amplification Plus kit, following the manufacturer’s instructions. cRNA was synthesized from the cDNA template, with incorporation of cyanine-3-CTP (Perkin Elmer). Labeled cRNA was purified using the Qiagen RNeasy Mini kit with quantity and quality was assessed by NanoDrop spectrophotometer and Agilent BioAnalyzer.

growth_protocol: Adult fish were maintained according to the guidelines set forth by the zebrafish handbook. Embryos were kept in egg water (60 μg/ml Instant Ocean Salts) in a 28°C incubator with no light.

extract_protocol: Total RNA was isolated from pooled tissues using RNA STAT-60.

treatment_protocol: Separate groups of 30 embryos generated from TL adults were placed in 15 ml egg water in a 10-cm glass petri and at 1, 2, 3, 4, 5, and 6-dpf were exposed for 6 hr to 0.1% dimethyl sulfoxide (DMSO), 2 nM 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), or 10 uM tert-butylhydroquinone (tBHQ) (4 groups per compound per time point). Embyros were frozen immediately after the 6 hr exposure and RNA isolated for microarray analysis. The Universal RNA Reference Sample was created by mixing equal amounts of total RNA from 2 replicates each from all toxicants (TCDD, tBHQ, DMSO) and timepoints (1, 2, 3, 4, 5, 6-dpf).

tag: Strain

value: TL

tag: Age

value: 1-6 days post-fertilization

source_name: 4 days post-fertilization TCDD exposed Danio rerio embryos, replicate 2

label_protocol: RNA samples were checked for quality using a NanoDrop ND-1000 spectrophotometer and an Agilent 2100 BioAnalyzer.  cDNA synthesis from 600 ng of total RNA was performed using the Agilent Low RNA Input Linear Fluorescent Amplification Plus kit, following the manufacturer’s instructions. cRNA was synthesized from the cDNA template, with incorporation of cyanine-5-CTP (Perkin Elmer). Labeled cRNA was purified using the Qiagen RNeasy Mini kit with quantity and quality was assessed by NanoDrop spectrophotometer and Agilent BioAnalyzer.

treatment_protocol: Separate groups of 30 embryos generated from TL adults were placed in 15 ml egg water in a 10-cm glass petri and at 4 dpf were exposed for 6 hr to 2 nM 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Embyros were frozen immediately after the 6 hr exposure and RNA isolated for microarray analysis.

value: 4 days post-fertilization


title: Lsk1-del-2

description: Lsk1-del RNA vs. wild type RNA, Replicate 2


title: Lsk1-del-4

description: Lsk1-del RNA vs. wild type RNA, Replicate 4


title: Rpb1-S2A-4

description: Rpb1-S2A RNA vs. wild type RNA, Replicate 4


title: TCDD exposed embryos, replicate 1

description: TCDD exposed embryos, replicate 1

source_name: 4 days post-fertilization TCDD exposed Danio rerio embryos, replicate 1


title: Ovary at P3, Foxl2 KO, replicate 2


title: TCDD exposed embryos, replicate 3

description: TCDD exposed embryos, replicate 3

source_name: 4 days post-fertilization TCDD exposed Danio rerio embryos, replicate 3


title: tBHQ exposed embryos, replicate 4

description: tBHQ exposed embryos, replicate 4

source_name: 4 days post-fertilization tBHQ exposed Danio rerio embryos, replicate 4

treatment_protocol: Separate groups of 30 embryos generated from TL adults were placed in 15 ml egg water in a 10-cm glass petri and at 4 dpf were exposed for 6 hr to 10 uM tert-butylhydroquinone (tBHQ). Embyros were frozen immediately after the 6 hr exposure and RNA isolated for microarray analysis.


title: Rpb1-S2A-1

description: Rpb1-S2A RNA vs. wild type RNA, Replicate 1


title: Lsk1-del-1

description: Lsk1-del RNA vs. wild type RNA, Replicate 1


title: tBHQ exposed embryos, replicate 3

description: tBHQ exposed embryos, replicate 3

source_name: 4 days post-fertilization tBHQ exposed Danio rerio embryos, replicate 3


title: DMSO exposed embryos, replicate 4

description: DMSO exposed embryos, replicate 4

source_name: 4 days post-fertilization DMSO exposed Danio rerio embryos, replicate 4

treatment_protocol: Separate groups of 30 embryos generated from TL adults were placed in 15 ml egg water in a 10-cm glass petri and at 4 dpf were exposed for 6 hr to 0.1% dimethyl sulfoxide (DMSO). Embyros were frozen immediately after the 6 hr exposure and RNA isolated for microarray analysis.


title: Adult ovary, Foxl2 mutant, replicate 3

description: Expression profiles of adult ovaries

data_processing: Data were analyzed with RMA using Affymetrix default analysis settings (Expression Console). Up- and downregulated genes were identified using the GeneSpring GX statistical software package (Agilent).

source_name: Mouse ovary, adult,Foxl2 flox/flox x CreEBD

value: Foxl2 mutant

value: adult


title: DMSO exposed embryos, replicate 1

description: DMSO exposed embryos, replicate 1

source_name: 4 days post-fertilization DMSO exposed Danio rerio embryos, replicate 1


title: DMSO exposed embryos, replicate 2

description: DMSO exposed embryos, replicate 2

source_name: 4 days post-fertilization DMSO exposed Danio rerio embryos, replicate 2


title: DMSO exposed embryos, replicate 3

description: DMSO exposed embryos, replicate 3

source_name: 4 days post-fertilization DMSO exposed Danio rerio embryos, replicate 3


title: Adult ovary, wild-type, replicate 1

description: Expression profiles of adult ovaries

source_name: Mouse ovary, adult, wildtype


title: Lpictus_CO2_Hyb6_O4B4

city: San Francisco

first: Anne

last: Todgham

state: CA

address: 1600 Holloway Ave

department: Biology

institute: San Francisco State University

hyb_protocol: Samples were hybridized following Agilent’s Protocol for Two-Color Microarray-Based Gene Expression Analysis (version 5.5, pages 24-35).  The cDNA samples were quantified using a NanoDrop 1000 UV/visible spectrophotometer (Thermo Scientific, Wilmington, DE, USA) to ensure high quality cDNA synthesis and dye incorporation before continuing on to the slide hybridization.  If the cDNA yield of a particular sample was <600 ηg and the specific activity was <8.0 ρmol dye per μg cDNA, cDNA synthesis and labeling was repeated.  Prior to slide hybridization, cDNA samples were fragmented following Agilent’s Gene Expression Hybrization Kit for 4x44K slides.  Briefly, 600ηg of Alexafluor 555-labeled cDNA, 600ηg of Alexafluor 647-labeled cDNA, 11 μL of 10X Blocking Agent and 2.2 μL of 25X Fragmentation Buffer were mixed to a total volume of 55 μL with nuclease-free water and incubated at 60°C for 30 min.  To each array mixture 55 μL of 2X GE Hybridization Buffer HI-RPM was added and then the sample was applied to the microarray slides.  Hybridizations were conducted overnight (~17 h) at 65°C in Agilent Microarray Hybridization Chambers with the hybridization oven rotisserie set at 10rpm.  Following hybridization, the slides were washed in Agilent’s Gene Expression Wash Buffers following manufacturer’s instructions.

scan_protocol: The slides were scanned at 5μm on a GenePix 4000B microarray scanner (Axon Instruments, Molecular Devices, Sunnyvale, CA, USA).  Data from the microarrays were extracted using GenePix Pro 4.0 software (Axon Instruments).

data_processing: Normalization and data analysis were completed using R (R Development Core Team 2008) with the limma software package (Smyth 2005). To avoid violating assumptions of the number or degree of symmetry of differentially expressed genes, a global normalization for dye-bias was applied on a probe-by-probe basis, after averaging over log-ratios from replicate probes within arrays, by including a dye-effect in the linear model.

label: Alexafluor 647

organism: Lytechinus pictus

source_name: Lpictus, echinopluteus, 380ppm CO2, rep4

label_protocol: Indirect coupling of dye following cDNA synthesis with amino-allyl dUTP. cDNA was incubated with 1 μL of either Alexafluor 555 or 647 dye for 1h at room temperature in the dark.

extract_protocol: Total RNA was extracted from a pooled sample of approximate 40,000 early 4-arm urchin larvae.  Total RNA was isolated using TRIzol® Reagent following manufacturer’s instructions (Invitrogen, Carlsbad, CA, USA). RNA was then processed through an additional column clean-up step to remove tRNA and small-sized RNA degradation products.

tag: Species

value: Lytechinus pictus,

tag: Developmental stage

value: echinopluteus,

value: 48 hours post-fertilization,

tag: CO2 treatment

value: 380 ppm CO2,

tag: Replicate culture

label: Alexafluor 555

source_name: Lpictus, echinopluteus, 970ppm CO2, rep4

value: 970 ppm CO2,


title: Conventionalized_6dpf_zebrafish_larvae_replicate3_8301

city: Chapel Hill

middle: F

last: Rawls

state: NC

address: 111 Mason Farm Rd.

department: Department of Cell and Molecular Physiology

institute: University of North Carolina at Chapel Hill

description: Whole 6dpf zebrafish larvae raised germ-free through 3dpf, then colonized with a conventional zebrafish microbiota from 3-6dpf

hyb_protocol: Hybridization performed using standard Affymetrix protocol available at http://www.affymetrix.com/support/technical/manuals.affx

scan_protocol: Scanning performed using standard Affymetrix protocol available at http://www.affymetrix.com/support/technical/manuals.affx

data_processing: Raw expression values were normalized (Invariant set method) and modelled (PM-MM model), and present/absent calls were generated using dChip software (build date Dec.11, 2005).

label_protocol: Total RNA from each replicate pool (12ug RNA/replicate) was used as template for independent cDNA synthesis and in vitro transcription reactions (BioArray HighYield RNA Transcript Labeling Kit; Enzo Life Sciences) to generate biotinylated cRNA targets. cRNA targets (20ug/replicate) were fragmented using standard methods.

extract_protocol: Total RNA was purified from pooled intact zebrafish larvae (28-80 larvae/pool, 3 biological replicate pools/condition) using Trizol reagent (Invitrogen) followed by DNase I digestion (DNA-Free, Ambion) according to manufacturers' protocols.

tag: strain

tag: age

value: 6 days post-fertilization (6dpf)

tag: tissue

value: whole larvae

tag: rearing conditions

value: gnotobiotic

tag: microbial status

value: ex-germ-free conventionalized

tag: replicate

value: 3 of 3


title: Lpictus_CO2_Hyb5_G4O3

source_name: Lpictus, echinopluteus, 970ppm CO2, rep3

source_name: Lpictus, echinopluteus, 540ppm CO2, rep4

value: 540 ppm CO2,


title: Adult ovary, Foxl2 mutant, replicate 2

description: Expression profiles of adult ovaries

value: ovary

tag: genotype


title: Adult testis, wild-type, replicate 3

description: Expression profiles of adult testes

source_name: Mouse testis, adult, wildtype

value: testis

value: wild type


title: Lpictus_CO2_Hyb4_B3G3

source_name: Lpictus, echinopluteus, 540ppm CO2, rep3

source_name: Lpictus, echinopluteus, 380ppm CO2, rep3


title: TCDD exposed embryos, replicate 4

description: TCDD exposed embryos, replicate 4

source_name: Universal RNA Reference Sample

value: TL

value: 1-6 days post-fertilization

source_name: 4 days post-fertilization TCDD exposed Danio rerio embryos, replicate 4

value: 4 days post-fertilization


title: Lpictus_CO2_Hyb2_G2O1

source_name: Lpictus, echinopluteus, 970ppm CO2, rep1

value: Lytechinus pictus

value: echinopluteus

value: 48 hours post-fertilization

value: 970 ppm CO2

source_name: Lpictus, echinopluteus, 540ppm CO2, rep2

value: 540 ppm CO2


title: Lpictus_CO2_Hyb3_O2B2

source_name: Lpictus, echinopluteus, 380ppm CO2, rep2

value: 380 ppm CO2

source_name: Lpictus, echinopluteus, 970ppm CO2, rep2


title: Adult ovary, wild-type, replicate 2

description: Expression profiles of adult ovaries

value: adult


title: Conventionalized_6dpf_zebrafish_larvae_replicate2_8300

source_name: Whole 6dpf zebrafish larvae raised germ-free through 3dpf, then colonized with a conventional zebrafish microbiota from 3-6dpf

value: 6 days post-fertilization (6dpf)

value: whole larvae

value: gnotobiotic

value: 2 of 3


title: tBHQ exposed embryos, replicate 1

description: tBHQ exposed embryos, replicate 1

source_name: 4 days post-fertilization tBHQ exposed Danio rerio embryos, replicate 1


title: Lpictus_CO2_Hyb1_B1G1

source_name: Lpictus, echinopluteus, 540ppm CO2, rep1

source_name: Lpictus, echinopluteus, 380ppm CO2, rep1


title: tBHQ exposed embryos, replicate 2

description: tBHQ exposed embryos, replicate 2

source_name: 4 days post-fertilization tBHQ exposed Danio rerio embryos, replicate 2


title: Adult ovary, Foxl2 mutant, replicate 1

description: Expression profiles of adult ovaries

source_name: Mouse ovary, adult,Foxl2 flox/flox x CreEBD

value: ovary

value: Foxl2 mutant


title: Adult testis, wild-type, replicate 2

description: Expression profiles of adult testes

value: testis

value: wild type


title: Adult testis, wild-type, replicate 1

description: Expression profiles of adult testes


title: Conventionalized_6dpf_zebrafish_larvae_replicate1_8299

value: ex-germ-free conventionalized

value: 1 of 3


title: Germ-free_6dpf_zebrafish_larvae_replicate3_8422

description: Whole 6dpf germ-free zebrafish larvae

source_name: Whole 6dpf germ-free zebrafish larvae

value: germ-free

value: 3 of 3


title: Germ-free_6dpf_zebrafish_larvae_replicate2_8298

description: Whole 6dpf germ-free zebrafish larvae


title: testis_GONSL21

status: Public on Dec 31 2009

city: Galway

first: Michael

last: Cairns

address: University Road

department: NCBES

country: Ireland

institute: NUI Galway

description:
Atlantic salmon (Aquaculture and Catchment Management Services of the Marine Institute (Ireland) in Burrishoole, Newport, Co. Mayo)
Nine microarray hybridisations were carried out in total as part of this design. To compare brain samples total RNA from 10 individual brains (dissected of hypothalamus and pituitary) of precocious fish and 10 brains of non-precocious fish were pooled to give two pools each of five precocious (PA and PB) and non-precocious (NPA and NPB) brains. Each pool of precocious brains was compared in a dye swap experiment with each pool of non-precocious brains

hyb_protocol: Slides were pre-hybridised in 50% formamide, 5x SSC, 0.1% SDS, 0.1 mg/ml BSA at 42 oC for 1 h, then washed twice for 5 min with 0.1x SSC and for 30 s with 18MOhm water. The slides were dried immediately by centrifugation (Eppendorf Multipuropose Centrifuge 5804) at 1500 rpm for 5 min at room temperature in a slide box lined with 3MM Whatman paper (10.8 x 7.4cm). Dust was removed from the surface of the pre-hybridised arrays using an ozone-free air duster (Kenair, UK). The purified, combined Cy5- and Cy3-labelled cDNAs (80 microlitre) were denatured at 95 C in a thermal cycler for 3 min, immediately applied to the array surface and covered with a lifter slip (Erie Scientific, USA). Each array was placed in a pre-warmed Genetix hybridisation chamber. The chamber was sealed and incubated in an oven for 16-18 h at 50 oC. Microarray wash solutions were warmed to 55 oC. All wash steps were carried out in the dark. Each array was dipped in a 50 ml Sarstedt tube filled with wash solution 1 (2X SSC, 0.1% SDS) to dislodge the coverslip. The arrays were washed twice for 5 min on a rotary table in fresh wash solution 1. The arrays were transferred to wash solution 2 (0.1X SSC) and washed twice for 1 min on a rotary table. Finally, the arrays were rinsed by immersion in RNase/DNase-free water to remove any residual salts, followed by brief immersion in 100 % isopropanol (Sigma-Aldrich) at room temperature and brief centrifugation at 1500 rpm for 2 min to dry the slides.

scan_protocol: The arrays were scanned as soon as possible after washing. After hybridisation, fluorescence was measured using a confocal laser scanner (ScanArray Express HT, Perkin Elmer, USA). The high-resolution images were inspected using Genepix Pro v5.1.0.16 (Molecular Devices, USA)

data_processing: LIMMA (part of the Bioconductor R package) was applied to the loop design used in this experiment. For this spots were weighted based on feature flagging in Genepix: weak signal and feature irregularity appeared to be the main source of discrepancy therefore features were flagged to avoid these spots (Flag=0). Median local background values were subtracted from median feature values, dye channels were swapped as appropriate and a printtiploess normalisation was applied (log2 fold ratios are given)

organism: Salmo salar

source_name: testis, pool of 10, non-precocious parr, NP2

label_protocol: An indirect labelling method was used to attach Cy5 and Cy3 dyes to the cDNA. All target cDNAs were synthesised in one round. 10 Micrograms of both tester and reference total RNA was used per hybridisation. cDNA was generated by reverse transcription for 2 h at 42 oC using an anchored oligo VdT26, a random primer (V9), both at 1 micrograms/ml, and Stratascript RT enzyme (75U). Amino-allyl (aa) dUTP/dNTPs produced from a 20X stock (10 mM dCTP, dGTP, dATP and 5mM ea. of dTTP and dUTP) were incorporated into the cDNA. This 1:1 ratio of dUTP/dTTP proved to be an effective ratio for the testes tissue. Contaminating enzymes and buffers were removed by purification with the Nucleospin Extract II Kit (Macherey-Nagel, Ger). Eluted cDNA was concentrated using a Vacufuge Concentrator 5301 at 42 oC (Eppendorf, Ger). The resulting cDNA pellets were resuspended in 5 microlitres of sodium bicarbonate (0.1M) (Sigma Aldrich). Cy dyes (Amersham Pharmacia Biotech, UK) were resuspended in 0.1M sodium bicarbonate and coupling to the cDNA took place in the dark for 2 h at room temperature. The labelled cDNA was again purified to remove any uncoupled Cy dye using the Nucleospin Extract II Kit.

growth_protocol: Fish were netted and transferred to an anaesthetic/sedative solution (1:1000 dilution of a stock 100 mg/ml ethyl 4-benzoate; Sigma-Aldrich). Blood samples were collected from the caudal vessels into EDTA (1.5 mg/ml blood; Sigma-Aldrich) and aprotinin (3000 KU/ml blood; Sigma-Aldrich) and fish were killed by spinal section. Fifty precocious male parr and fifty non-precocious male parr (sex determined on dissection) were sampled in January/February 2004. Length and weight measurements were taken. All tissues were removed to RNAlater or snap frozen in liquid nitrogen. Samples were stored at -80oC until RNA extraction.

extract_protocol: All samples were lysed and homogenized in TRIzol reagent (Invitrogen Life Technologies). Qiagen RNeasy midi columns and wash buffers were used to purify the RNA. All samples were DNase treated on-column using the Qiagen DNA-free DNase kit. The concentrations of the RNA samples were determined by UV spectrophotometry (Shimadzu UV-1601 / Eppendorf BioPhotometer) and checked for quality using the Agilent Bioanalyser-derived RNA integrity number (RIN) and by denaturing formaldehyde gel electrophoresis followed by northern blotting and subsequent analysis with a radiolabelled beta-actin probe.

tag: maturation

value: non-precocious

tag: gender

value: Male

value: Parr

value: Testis

source_name: testis, pool of 4, precocious parr, PG1

extract_protocol: All samples were lysed and homogenized in TRIzol reagent (Invitrogen Life Technologies). Qiagen RNeasy midi columns and wash buffers were used to purify the RNA. All samples were DNase treated on-column using the Qiagen DNA-free DNase kit. The concentrations of the RNA samples were determined by UV spectrophotometry (Shimadzu UV-1601 / Eppendorf BioPhotometer) and checked for quality using the Agilent Bioanalyser-derived RNA integrity number (RIN) and by denaturing formaldehyde gel electrophoresis followed by northern blotting and subsequent analysis with a radiolabelled -actin probe.

value: precocious


title: testes_GONSL28

scan_protocol: The arrays were scanned as soon as possible after washing. After hybridisation, fluorescence was measured using a confocal laser scanner (ScanArray Express HT, Perkin Elmer, USA). The high-resolution images were inspected using Genepix Pro v5.1.0.16 (Molecular Devices, USA).

data_processing: LIMMA (part of the Bioconductor R package) was applied to the loop design used in this experiment. For this spots were weighted based on feature flagging in Genepix: weak signal and feature irregularity appeared to be the main source of discrepancy therefore features were flagged to avoid these spots (Flag=0). Median local background values were subtracted from median feature values, dye channels were swapped as appropriate and a printtiploess normalisation was applied (log2 fold ratios are given).

source_name: testis_precocious_pool of 4_PG2

source_name: testis_non-precocious_pool of 10_NP2


title: testis_GONSL33

source_name: testis_precocious_pool of 4_PG3


title: testis_GONSL27

source_name: testis_nonprecocious_pool of 10_NP3

label_protocol: An indirect labelling method was used to attach Cy5 and Cy3 dyes to the cDNA. All target cDNAs were synthesised in one round. 10 Micrograms of both tester and reference total RNA was used per hybridisation. cDNA was generated by reverse transcription for 2 h at 42 oC using an anchored oligo VdT26, a random primer (V9), both at 1 micrograms/ml, and Stratascript RT enzyme (75U). Amino-allyl (aa) dUTP/dNTPs produced from a 20X stock (10 mM dCTP, dGTP, dATP and 5mM ea. of dTTP and dUTP) were incorporated into the cDNA. This 1:1 ratio of dUTP/dTTP proved to be an effective ratio for the testes tissue. Contaminating enzymes and buffers were removed by purification with the Nucleospin Extract II Kit (Macherey-Nagel, Ger). Eluted cDNA was concentrated using a Vacufuge Concentrator 5301 at 42 oC (Eppendorf, Ger). The resulting cDNA pellets were resuspended in 5 microlitres of sodium bicarbonate (0.1M) (Sigma Aldrich). Cy dyes (Amersham Pharmacia Biotech, UK) were resuspended in 0.1M sodium bicarbonate and coupling to the cDNA took place in the dark for 2 h at room temperature. The labelled cDNA was again purified to remove any uncoupled Cy dye using the Nucleospin Extract II Kit


title: testis_GONSL36

source_name: testis_non-precocious_pool of 10_NP1


title: testis_GONSL42


title: testis_GONSL26

source_name: testis_precocious_pool of 4_PG1

source_name: testes_non-precocious_pool of 10_NP3


title: Germ-free_6dpf_zebrafish_larvae_replicate1_8297

description: Whole 6dpf germ-free zebrafish larvae

value: 6 days post-fertilization (6dpf)


title: testes_GONSL29

source_name: testis_non-precocious_pool of 10_NP3


title: testis_GONSL34


title: YJB10283 aCGH

city: Boston

first: Anna

last: Selmecki

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

description: no additional information

hyb_protocol: Slides were hybridized overnight in a 37C waterbath

scan_protocol: Slides were scanned using a ScanArray (Perkin Elmer) and accompanying ScanArray Express software.

data_processing: Data were extracted using GenePix Pro and GeneTraffic software. Global Lowess normalization.

organism: Candida albicans

label_protocol: DNA was digested with HaeIII, purified, and labeled using an Invitrogen Bioprime aCGH labeling kit.

growth_protocol: DNA was isolated after minimal growth in YPAD at 30C

extract_protocol: Phenol Chloroform DNA extraction

source_name: SC5314 (reference)

value: SC5314 (sequenced strain)


title: YJB10971_aCGH

description: FluR, single colony isolate YJB10971 vs. reference strain SC5314

hyb_protocol: Arrays were hybridized in a 37C waterbath overnight

scan_protocol: Arrays were scanned using a ScanArray scanner.

label_protocol: Labeling was done with a BioPrime aCGH kit from Invitrogen.

extract_protocol: gDNA extractions were done using the Hoffman-Winston preparation (phenol/chloroform/isoamyl alcohol and lysis buffer followed by EtOH/salt precipitation).  All gDNA is RNaseA treated.  The same gDNA prep was used to label with Cy3 for this array.


title: YJB10673 aCGH

description: no additional information


title: YJB10656 aCGH

description: no additional information


title: YJB10657 aCGH

description: no additional information


title: YJB10971_CHEFband_aCGH

description: YJB10971 was run on a CHEF gel and the novel chromosome band around 1.5 Mb was  cut from the gel.  DNA was purified from the gel slice and labeled with Cy3.

growth_protocol: Cells were grown minimally in YPAD and normal CHEF gel plug preparation was followed.

extract_protocol: DNA in the CHEF gel band was digested with HaeIII and then isolated from the gel.  DNA was purified and concentrated using phenol chloroform DNA extraction.


title: YJB10653 aCGH

description: no additional information


title: YJB10675 aCGH

description: no additional information


title: YJB10658 aCGH

description: no additional information


title: YJB10654 aCGH

description: no additional information


title: YJB10655 aCGH

description: no additional information


title: YJB10975 aCGH

description: no additional information


title: YJB10821 aCGH

description: no additional information


title: LGD-N5-3659

first: Hushan

last: Yang

address: 1515 Holcombe

institute: UT MD Anderson Cancer Center

description: microRNA expression

hyb_protocol: For each tissue sample, 100 ng total RNA was hybridized with the miRNA array and further processed in accordance with the manufacturer’s instructions.

scan_protocol: The arrays were scanned using an Agilent Technology G2565BA scanner.

data_processing: The scanned images were processed using the Feature Extraction software package version 9.5 (Agilent Technology).

organism: Homo sapiens

source_name: Paired normal tissue of barrett's esophagous tissue with low grade dysplasia 5

label_protocol: Agilent labelling kit following the manufacturer's instruction (Agilent Technologies)

extract_protocol: Total RNAs including small RNAs were extracted from each tissue using the mirVana miRNA extraction kit (Ambion, Austin, TX) according to the manufacturer’s protocol. Total RNA concentrations were measured using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE).

treatment_protocol: These are tissue samples and there are no treatments before RNA extraction.

value: male


title: YJB10984 aCGH

description: no additional information


title: YJB10970 aCGH

description: no additional information


title: YJB10981 aCGH

description: no additional information


title: YJB10955 aCGH

description: no additional information


title: YJB10952 aCGH

description: no additional information


title: LGD-N4-3436

description: microRNA expression

source_name: Paired normal tissue of barrett's esophagous tissue with low grade dysplasia 4


title: LGD-T4-3437

description: microRNA expression

source_name: Barrett's esophagous tissue with low grade dysplasia 4


title: LGD-T5-3660

description: microRNA expression

source_name: Barrett's esophagous tissue with low grade dysplasia 5


title: Exp2Rep1: 0.125 TU Pyr

city: Antwerp

first: Tine

last: Vandenbrouck

address: Groenenborgerlaan 171

department: Department of Biology

country: Belgium

institute: University of Antwerp

description: Hybridization: Reference sample vs pyrene 0.125TU

hyb_protocol: Prior to hybridization, arrays were incubated for 30-45 min at 42°C in a prehybridization solution (50% formamide, 5x saline sodium citrate (SSC), 0.1% sodium dodecyl sulphate (SDS), 0.1mg/mL BSA). The vacuum dried targets (both reference and treatment target) were resuspended in a hybridization solution (50% formamide, 5x SSC, 0.1% SDS, 0.1mg/mL BSA and 0.1mg/mL sheared salmon sperm) and denaturated at 95°C. The cooled targets were subsequently applied onto the prehybridized slides and incubated overnight at 42°C. After hybridization, arrays were washed in solutions with increasing stringency (decreasing concentrations of SSC and SDS) and dried with N2.

scan_protocol: Scanning and analysing of the slides was performed using the Genepix personal 4100 Scanner and Genepix pro Software (both Axon instruments, USA). Cy3 and Cy5 fluorescent signals were scanned at respectively 532 and 635nm and the PMT (photomultiplier tube) values were adjusted to reach a ratio (Cy5/Cy3) around 1. Spots were identified and ratio’s quantified by means of the Genepix software 5.0 (Axon Instruments).

data_processing: Prior to the actual statistical analysis, the quality of the microarray spots was assessed. Over-saturated spots and bad quality spots identified during the feature identification process (visual inspection of the slides) were excluded from further analysis. Hereafter, a local background correction was performed on these datasets (BASE). Those spots with foreground levels lower than the background levels for both channels were excluded from the analysis. Spots for which the foreground was smaller than the mean (local) background ±2 standard deviations for both channels were given a ‘weight’ of 0.1. All other included spots are given a weight of 1. Subsequently, microarray datasets were normalized using the variance stabilizing normalization (VSN) (Huber 2002). The significantly differentially expressed genes (between control and treatment) were statistically determined using LIMMA (LInear Model for Microarray Analysis) (Smyth 2004). Results were corrected for multiple testing using the false discovery rate (FDR) and differential gene expression was detected in probes with p<0.05. An additional threshold which was taken into account is the fold induction cut-off (Log2) of (-)0.85. In conclusion, genes with fold inductions outside these thresholds and p-values below 0.05 were selected as differentially expressed.

organism: Daphnia magna

source_name: reference sample

label_protocol: The production of cDNA and subsequent amino-allyl labelling were performed according to the protocol described in detail by Van der Ven et al. (2005) and Soetaert et al. (2006). In brief, 5µg of total RNA was mixed with Lucidea control mRNA spike mix (Amersham, UK) to be reverse-transcribed using the Superscript II, Random hexamer primers (both Invitrogen) in the presence of dNTPs with 2/3 aa-dTTP/dTTP (Sigma-Aldrich, Belgium). After an overnight incubation period (42°C) the amino-allyl-incorporated cDNA was purified using a modified Qiagen PCR spin colomn protocol (Van der Ven et al., 2005). In a next step, Cy3/Cy5 esters (Amersham) were used for covalent coupling to the amino-allyl labelled cDNA. The vacuum dried cDNA samples (dissolved in a 0,1M carbonate buffer (pH 9.0)) were mixed with the Cy3/Cy5 esters (dissolved in 100% DMSO) and incubated for an hour in the dark at room temperature. Hereafter, a second cleanup reaction was performed to establish the removal of the remaining uncoupled dyes (QIAquick PCR purification kit, Qiagen, USA). The quality of eluted and labelled cDNA was analysed using the Nanodrop® spectrophotometer. Samples with an FOI (frequence of incorporated dye) between 20 and 50 were selected for hybridization and an amount of 50 pmol labelled target was vacuum dried.

extract_protocol:
Approximately 40 Daphnia/replicate were collected. Samples were shock-frozen in liquid nitrogen and stored in RNAlater (Ambion, USA) at -80°C.
All RNA extractions were performed using the TRIzol® method (Invitrogen, Belgium) followed by a DNAse treatment using 1U RNAse-free DNAse and 1U RNAse inhibitor (Fermentas, Germany) per 30µl sample and subsequent phenol/chloroform extractions. The purity of the RNA samples was checked using the ND-1000 spectrophotometer (Nanodrop®, USA) through measurement of the 260nm/280nm and 260nm/230nm absorbance. For all used samples these ratios were respectively above 1.90 and 2.10. To verify the intactness of the RNA samples, a denaturating formaldehyde agarose gel electrophoresis was performed to visualize the 18S and 28S ribosomal bands.

treatment_protocol: The organisms were exposed to two PAHs, fluoranthene and pyrene (Sigma-Aldrich, Belgium) both as single compounds and as binary mixtures. EC50 (immobility at 48h) values of the single compounds (when fed) were established to set the concentrations of the individual component exposures equal to 0; 0.062; 0.125 and 0.250 Toxic Units (TU) when one TU is defined as the EC50 (immobility at 48h) of the single compound. For the binary mixtures, concentrations for a total of 6 (to 8) combinations were determined based on a fixed ratio design. During the 96h exposure experiments, 40 Daphnia/replica were kept at a density of 1 organism/10mL OECD standard water (CaCl2.2H2O, 2mM; MgSO4.7H2O, 500μM; NaHCO3, 771μM; KCl, 77.1μM; water hardness, 250 mg CaCO3; pH 7.8; OECD guideline 203, annex 2). Since fluoranthene and pyrene are both poorly soluble in water, a solvent was used. The PAHs were dissolved in acetone; final solvent concentrations of 0.01% were used. Therefore besides the pure OECD water control, an additional solvent control sample was included in each test. Organisms were fed every other day – when test solutions were renewed - with a mixture of P. subcapitata and C. reinhardtii in a 3:1 ratio.

value: whole body extracts (40 organisms)

value: 96h old

source_name: pyrene 0.125 TU


title: Exp1Rep2: 0.0625 TU Pyr

description: Hybridization: Reference sample vs pyrene 0.0625TU

source_name: pyrene 0.0625 TU


title: LGD-N2-1781

description: microRNA expression

source_name: Paired normal tissue of barrett's esophagous tissue with low grade dysplasia 2


title: Exp2Rep1: 0.0625 TU Pyr


title: HGD-N5-8885

description: microRNA expression

source_name: Paired normal tissue of barrett's esophagous tissue with high grade dysplasia 5


title: LGD-T2-1782

description: microRNA expression

source_name: Barrett's esophagous tissue with low grade dysplasia 2


title: LGD-T1-2312

description: microRNA expression

source_name: Barrett's esophagous tissue with low grade dysplasia 1


title: HGD-T5-8887

description: microRNA expression

source_name: Barrett's esophagous tissue with high grade dysplasia 5


title: YJB10885 aCGH

description: no additional information


title: YJB10883 aCGH

description: no additional information


title: LGD-N1-2311

description: microRNA expression

source_name: Paired normal tissue of barrett's esophagous tissue with low grade dysplasia 1


title: HGD-N4-6469

description: microRNA expression

source_name: Paired normal tissue of barrett's esophagous tissue with high grade dysplasia 4

value: female


title: Exp1Rep2: 0.125 TU Pyr


title: HGD-T4-6470

description: microRNA expression

source_name: Barrett's esophagous tissue with high grade dysplasia 4


title: HGD-N3-5305

description: microRNA expression

source_name: Paired normal tissue of barrett's esophagous tissue with high grade dysplasia 3


title: YJB10881 aCGH

description: no additional information

source_name: SC5314 (reference)


title: Exp2Rep1: 0.25 TU Pyr

description: Hybridization: Reference sample vs Pyrene 0.25TU

source_name: pyrene 0.25 TU


title: HGD-T3-5307

description: microRNA expression

source_name: Barrett's esophagous tissue with high grade dysplasia 3


title: YJB9613 aCGH

description: ancestral strain T118 from Leah Cowen et al 2000


title: HGD-N2-3494

description: microRNA expression

source_name: Paired normal tissue of barrett's esophagous tissue with high grade dysplasia 2


title: Exp1Rep2: 0.25 TU Pyr


title: Exp1Rep2: 0.0625 TU Flu + 0.1875 TU Pyr

description: Hybridization: Reference sample vs Mixture of 0.0625 TU Flu and 0.1875 TU Pyr

source_name: mixture of 0.0625 TU fluoranthene and 0.1875 TU pyrene


title: Exp2Rep1: 0.0625 TU Flu + 0.0625 TU Pyr

description: Hybridization: Reference sample vs Mixture of 0.0625 TU Flu and 0.0625 TU Pyr

source_name: reference sample

source_name: mixture of 0.0625 TU fluoranthene and 0.0625 TU pyrene


title: HGD-T2-3495

description: microRNA expression

source_name: Barrett's esophagous tissue with high grade dysplasia 2


title: EAC-N2-40771-13

description: microRNA expression

source_name: Paired normal tissue of Esophageal adenocarcinoma tissue 2


title: LGD-T3-1503

description: microRNA expression

source_name: Barrett's esophagous tissue with low grade dysplasia 3


title: LGD-N3-1502

description: microRNA expression

source_name: Paired normal tissue of barrett's esophagous tissue with low grade dysplasia 3


title: HGD-N1-2731

description: microRNA expression

source_name: Paired normal tissue of barrett's esophagous tissue with high grade dysplasia 1


title: HGD-T1-2732

description: microRNA expression

source_name: Barrett's esophagous tissue with high grade dysplasia 1


title: EAC-T2-40771-3

description: microRNA expression

source_name: Esophageal adenocarcinoma tissue 2

value: Esophageal adenocarcinoma tissue


title: Exp2Rep1: 0.0625 TU Flu + 0.187 TU Pyr

description: Hybridization: Reference sample vs Mixture of 0.0625 TU Flu and 0.187 TU Pyr

source_name: mixture of 0.0625 TU fluoranthene and 0.187 TU pyrene


title: EAC-T6-40839-4

description: microRNA expression

source_name: Esophageal adenocarcinoma tissue 6


title: Exp1Rep2: 0.187 TU Flu + 0.0625 TU Pyr

description: Hybridization: Reference sample vs Mixture of 0.187TU Flu and 0.0625TU Pyr

source_name: mixture of 0.187 TU fluoranthene and 0.0625 TU pyrene


title: EAC-N1-34686-8

description: microRNA expression

source_name: Paired normal tissue of Esophageal adenocarcinoma tissue 1


title: EAC-N6-40839-13

description: microRNA expression

source_name: Paired normal tissue of Esophageal adenocarcinoma tissue 6


title: EAC-T1-34686-3

description: microRNA expression

source_name: Esophageal adenocarcinoma tissue 1


title: YJB10888 aCGH

description: no additional information

source_name: SC5314 (reference)


title: EAC-N4-38521-13

description: microRNA expression

source_name: Paired normal tissue of Esophageal adenocarcinoma tissue 4


title: EAC-T5-36141-1

description: microRNA expression

source_name: Esophageal adenocarcinoma tissue 5


title: EAC-T4-38521-7

description: microRNA expression

source_name: Esophageal adenocarcinoma tissue 4


title: EAC-N5-36141-7

description: microRNA expression

source_name: Paired normal tissue of Esophageal adenocarcinoma tissue 5


title: Exp2Rep1: 0.187 TU Flu + 0.187 TU Pyr

description: Hybridization: Reference sample vs Mixture of 0.187 TU Flu and 0.187 TU Pyr

source_name: reference sample

source_name: mixture of 0.187 TU fluoranthene and 0.187 TU pyrene


title: Exp2Rep1: 0.187 TU Flu + 0.0625 TU Pyr

description: Hybridization: Reference sample vs Mixture of 0.187 TU Flu and 0.0625 TU Pyr


title: Exp2Rep1: 0.125 TU Flu + 0.125 TU Pyr

description: Hybridization: Reference sample vs Mixture of 0.125TU Flu and 0.125TU Pyr

source_name: mixture of 0.125 TU fluoranthene and 0.125 TU pyrene


title: Exp1Rep2: 0.125 TU Flu + 0.125 TU Pyr

description: Hybridization: Reference sample vs Mixture of 0.125TU Flu and 0.125 TU Pyr


title: EAC-N3-42743-12

description: microRNA expression

source_name: Paired normal tissue of Esophageal adenocarcinoma tissue 3


title: Exp2Rep2: 0.0625 TU Flu

description: Hybridization: 0.0625TU Fluoranthene sample versus Reference sample

source_name: fluoranthene 0.0625 TU


title: Exp2Rep1: 0.25 TU Flu + 0.25 TU Pyr

description: Hybridization: Reference sample vs Mixture of 0.25TU Flu and 0.25TUPyr

source_name: mixture of 0.25 TU fluoranthene and 0.25 TU pyrene


title: Exp2Rep1: 0.125 TU Flu

description: Hybridization: Reference sample vs 0.125TU Fluoranthene

source_name: fluoranthene 0.125 TU


title: EAC-T3-42743-7

description: microRNA expression

source_name: Esophageal adenocarcinoma tissue 3


title: Exp1Rep2: 0.125 TU Flu


title: Exp2Rep1: 0.0625 TU Flu

description: Hybridization: Reference sample vs 0.0625TU Fluoranthene


title: Exp1Rep1: 0.185 TU Flu + 0.0625 TU Pyr

description: Hybridization: Mixture of 0.185TUFlu and 0.062TUPyr vs Reference sample

source_name: mixture of 0.185 TU fluoranthene and 0.0625 TU pyrene