title: pMG1_IrrE 0 min, biological rep2

status: Public on Jul 29 2010

type: RNA

city: Beijing

first: Ming

last: Chen

address: Zhongguancun Nandajie 12th,Haidian Zone

country: China

institute: Biotechnology Research Institute, Chinese academy of Agricultural Sciences

description: RNA extracted from cells of E. coli K-12 JM109 with pMG1-IrrE before salt shock

hyb_protocol: The biotin-labeled target was hybridized to the Affymetrix GeneChip E. coli 2.0 array at 45ºC for 16 hour at 60 rpm using the Hybridization Oven 640 (Affymetrix), then a three-step fluorescent staining was conducted using the Fluidics Station 450 (Affymetrix) during the washing and staining procedure.

scan_protocol: The data were collected by using Affymetrix GeneChip Scanner 3000.

data_processing: Affymetrix GeneChip Operating Software (GCOS) Version 1.4  Details: Intra-chip normalizations were performed using Affymetrix Gene Chip Operating Software (GCOS). Default statistical parameters were used to normalize each chip to the same target intensity (1500) as described in the Affymetrix GeneChip Expression Analysis manual. All nine possible inter-chip comparisons were performed in GCOS. The data were subsequently exported to a Microsoft Excel spreadsheet for manipulation. Consensus “detection p-value”, “change p-value”, and “signal log ratios” were calculated, and the default E. coli array p-value cutoff parameters were applied to these consensus values to estimate the transcript change between two conditions and the transcript presence under each condition. Background-subtracted data sets were used to calculate up-regulated and down-regulated genes based on fold changes of greater than 2.

label: biotin

molecule: total RNA

organism: Escherichia coli

source_name: E. coli K12 strain JM109 harboring pMG1-IrrE

label_protocol: Affymetrix Technical Manual, Prokaryotic Sample and Array Processing

growth_protocol: E.coli cells with pMG1 grown with aeration in LB media at 37º C until early log phase (0.4) and were treated with 1 mol/L NaCl for 10 min, after that the cells were harvested to extract RNA. LB medium recipe is as follow: 10g tryptone, 5g yeast extract, 10g NaCl per 1 liter.

extract_protocol: Total RNA was extracted using the commercial product TRIzol Reagent (Invitrogen, Carlsbad, CA).Disrupt about 107cells with a homogenizer with 1ml TRIzol Reafent on ice. Store the homogenate for 5 minutes at room temperature to permit the complete dissociation of nucleoprotein complexes. Next, supplement the homogenate with 0.2 ml chloroform per 1 ml of TRI Reagent, cover the samples tightly and shake vigorously for 15 seconds. Store the resulting mixture at room temperature for 2-15 minutes and centrifuge at 12,000 g for 15 minutes at 4 C. Following centrifugation, the mixture separates into a lower red phenol-chloroform phase, interphase and the colorless upper aqueous phase. Transfer the aqueous phase to a fresh tube. Precipitate RNA from the aqueous phase by mixing with isopropanol. Use 0.5 ml of isopropanol per 1 ml of TRI Reagent used for the initial homogenization. Store samples at room temperature for 5-10 minutes and centrifuge at 12,000 g for 8 minutes at 4 - 25 C. Remove the supernatant and wash the RNA pellet ( by vortexing) with 75% ethanol and subsequent centrifugation at 7,500 g for 5 minutes at 4 - 25 C. Add at least 1 ml of 75% ethanol per 1 ml TRI Reagent used for the initial homogenization. Remove the ethanol wash and briefly air-dry the RNA pellet for 3 - 5 min. Dissolve RNA in DEPC-treated water by passing solution a few times through a pipette tip. Using an on-column DNase digestion with RNase-free DNase I (Qiagen) to purify the total RNA.

treatment_protocol: Treatment protocol- E.coli cells with pMG1 grown in LB media with  at 37º C until early log phase (0.4), then were treated with 1 mol/L NaCl for 0min,10 min,60min,after that the cells were harvested to extract RNA.

tag: cell line


title: pMG1_IrrE 10 min, biological rep3

description: RNA extracted from cells of E. coli K-12 JM109 with pMG1-IrrE after 1 M NaCl shock for 10 min


title: pMG1_IrrE 0 min, biological rep3


title: pMG1 60 min, biological rep2

description: RNA extracted from cells of E. coli K-12 JM109 with pMG1 after 1 M NaCl shock for 60min

source_name: E. coli K12 strain JM109 harboring pMG1


title: pMG1 10 min, biological rep3

description: RNA extracted from cells of E. coli K-12 JM109 with pMG1 after 1 M NaCl shock for 10 min


title: pMG1 60 min, biological rep3


title: pMG1_IrrE 60 min, biological rep1

description: RNA extracted from cells of E. coli K-12 JM109 with pMG1-IrrE after 1 M NaCl shock for 60min


title: pMG1 60 min, biological rep1


title: pMG1 10 min, biological rep1


title: pMG1_IrrE 10 min, biological rep1


title: pMG1_IrrE 0 min, biological rep1


title: pMG1 10 min, biological rep2


title: pMG1_IrrE 60 min, biological rep3


title: pMG1 0 min, biological rep3

description: RNA extracted from cells of E. coli K-12 JM109 with pMG1 before salt shock


title: pMG1 0 min, biological rep2


title: pMG1_IrrE 60 min, biological rep2


title: pMG1_IrrE 10 min, biological rep2


title: pMG1 0 min, biological rep1


title: Yeast slt2 deficient 2 hours rep3

status: Public on Jul 25 2010

city: Madrid

first: Miguel

middle: Angel

last: Rodriguez-Gabriel

address: Campus Cantoblanco

department: Molecular Biology

country: Spain

institute: Universidad Autonoma de Madrid

description: Treated slt2 deficient cells

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Default protocol with GeneChip(R) Scanner 3000 7G

data_processing: The raw data were normalized and summarized with RMA software in the Affymetrix(R) Expression Console. p-values were obtained froma Student's t-test

label: Biotin plus Streptavicin-Phycoeritrin

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae liquid culture

label_protocol: One-Cycle IVT cDNA synthesis

extract_protocol: Total RNA from Saccharomyces cerevisiae was obtained by hot-phenol protol extraction.

treatment_protocol:
BY4741 background strain, slt2 deficient, grown in YEPD rich media at 30ºC to exponential phase. Sodium arsenate 100 micromolar was added and the cells harvested by filtration after 2 hours.
Slt2 deficient cells. Treated with sodium arsenate 100 micromolar for 2 hours

tag: genetic background

tag: genotype

value: slt2 deficient


title: Yeast slt2 deficient 0 minutes rep1

description: Untreated slt2 deficient cells

treatment_protocol:
BY4741 background strain, slt2 deficient, grown in YEPD rich media at 30ºC to exponential phase
Slt2 deficient cells (untreated)


title: Yeast slt2 deficient 0 minutes rep2

description: Untreated slt2 deficient cells


title: Yeast slt2 deficient 2 hours rep2

description: Treated slt2 deficient cells


title: Yeast 2 hours rep2

description: Treated wild type cells

treatment_protocol:
BY4741 strain grown in YEPD rich media at 30ºC to exponential phase. Sodium arsenate 100 micromolar was added and the cells harvested by filtration after 2 hours
Treated cells (sodium arsenate 100 micromolar 2 hours)

value: wild-type


title: Yeast 2 hours rep1

description: Treated wild type cells


title: Yeast slt2 deficient 2 hours rep1

description: Treated slt2 deficient cells


title: Yeast 0 minutes rep2

description: Control sample of untreated wild type cells

treatment_protocol:
BY4741 strain grown in YEPD rich media at 30ºC to exponential phase
Control cells (untreated)


title: Yeast 0 minutes rep3


title: Yeast 2 hours rep3

description: Treated wild type cells


title: miRNA expression profile of SCLC cell line HTB-184 vs. normal lung

status: Public on Jul 24 2010

city: Debrecen

first: Beata

last: Scholtz

address: Nagyerdei krt 98.

department: Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen Medical and Health Science Center

description: None.

hyb_protocol: Hybridization was peformed at LC Sciences.

scan_protocol: Scanning was peformed at LC Sciences.

data_processing: 1. Each miRNA is detected by 4 spots on the microarray. 2. Raw values were averaged for the 4 spots, resulting in the Cy5 or Cy3 signal mean.  3. Background values for the entire microarray were determined for each channel separately, and used for background correction of Cy5 or Cy3 signal means.  4. Background corrected mean signal values for the Cy5 and Cy3 channels were used for all further calculations.  Steps 1-4 of data analysis were performed by LC Sciences staff.   Background corrected mean signal values were used to determine the geometric means for all 4 microarrays.  The geometric mean of the arrays was used to normalize background corrected mean signal values.  Comparative analysis of the 4 microarrays revealed that certain miRNAs have significantly outlier values in one cell line - these values were deleted from the affected dataset, and replaced with "null" value.  No values were deleted from the normal lung datasets.

organism: Homo sapiens

label_protocol: Cy5 labelling was peformed at LC Sciences.

extract_protocol: Trizol reagent (Invitrogen) according to the manufacturer’s instructions.

tag: HTB-184 cell line obtained from ATCC, cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin at 37 °C with 5% CO2.

source_name: Normal lung 4

label_protocol: Cy3 labelling was peformed at LC Sciences.

tag: Total RNA was isolated from surgical samples of 6 tumor-free patients, and mixed at equal ratios.


title: Yeast slt2 deficient 0 minutes rep3

description: Untreated slt2 deficient cells


title: miRNA expression profile of SCLC cell line H69 vs. normal lung

description: None.

tag: H69 cell line obtained from ATCC, cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin at 37 °C with 5% CO2.

source_name: Normal lung 1


title: Yeast 0 minutes rep1


title: miRNA expression profile of SCLC cell line HTB-172 vs. normal lung

description: None.

tag: HTB-172 cell line obtained from ATCC, cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin at 37 °C with 5% CO2.

source_name: Normal lung 2


title: miRNA expression profile of SCLC cell line HTB-173 vs. normal lung

description: None.

tag: HTB-173 cell line obtained from ATCC, cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin at 37 °C with 5% CO2.

source_name: Normal lung 3


title: Magnetically sorted untouched CD8+CD45R0-T cells from donor B stimulated with anti CD3/CD8 beads+IFNα2 for 48 hours

status: Public on Jul 23 2010

city: Pamplona

first: Iranzu

last: Gonzalez

state: Navarra

address: Avda. Pio XII nº 55

department: Hepathology and Gene Therapy

institute: Center for applied medical research

description: no additional information

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133A 2.0 chip according to the protocols provided by the manufacturer.

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

data_processing: RMA

source_name: Human CD8 T cells

label_protocol: The cDNA was prepared from 5 microg total RNA using the One –Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthezising the cRNA using the IVT labeling kit (Affimetrix). The synthezised cRNA was purified with the GeneChip Sample Cleanup Module (Affimetrix).

growth_protocol: Untouched CD8+CD45RO- cells  were cultured at a concentration of 500.000 cells/mL with culture medium alone (resting) or culture medium containing IFNa2, anti-CD3/CD28 Beads alone or anti-CD3/CD28 Beads together with IFNa2 or IFNa5.

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen)  and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

treatment_protocol: IFNa doses used was 500 IU/mL. Anti-CD3/CD28 beads were used at a ratio of 1 bead per 10 cells

tag: cell type

value: CD8+CD45R0-T cells

tag: donor

value: B

tag: stimulated

value: yes

tag: agent

value: anti CD3/CD8 beads+IFNα2

tag: time

value: 48 hours

tag: donor ethnicity

value: Caucasian

tag: health status

value: healthy


title: Magnetically sorted untouched CD8+CD45R0-T cells from donor B unstimulated

description: no additional information

value: no


title: Magnetically sorted untouched CD8+CD45R0-T cells mRNA from a three donors pooled sample stimulated 7 hours with IFN α5

description: three donors pooled sample

growth_protocol: Untouched CD8+CD45RO-cells  were cultured at a concentration of 500.000 cells/mL with culture medium alone (resting) or culture medium containing IFNa2 or IFNa5.

treatment_protocol: IFN alfa 2 or IFN alfa 5 at 500 IU/mL

value: 7 hours

tag: donor pool ethnicity


title: Magnetically sorted untouched CD8+CD45R0-T cells from donor C unstimulated

description: no additional information

value: C


title: Magnetically sorted untouched CD8+CD45R0-T cells from donor A stimulated with IFNα2 for 48 hours

description: no additional information

value: A


title: Magnetically sorted untouched CD8+CD45R0-T cells from donor C stimulated with IFNα2 for 48 hours

description: no additional information


title: Magnetically sorted untouched CD8+CD45R0-T cells from donor B stimulated with anti CD3/CD8 beads for 48 hours

description: no additional information

value: anti CD3/CD8 beads


title: Magnetically sorted untouched CD8+CD45R0-T cells from donor C stimulated with anti CD3/CD8 beads for 48 hours

description: no additional information


title: Magnetically sorted untouched CD8+CD45R0-T cells from donor B stimulated with IFNα2 for 48 hours

description: no additional information


title: Magnetically sorted untouched CD8+CD45R0-T cells from donor C stimulated with anti CD3/CD8 beads+IFNα2 for 48 hours

description: no additional information


title: Magnetically sorted untouched CD8+CD45R0-T cells from donor A stimulated with anti CD3/CD8 beads+IFNα5 for 48 hours

description: no additional information

value: anti CD3/CD8 beads+IFNα5


title: naph_ben_set2_2B (array set 2)

status: Public on Jul 22 2010

city: Amherst

first: Derek

last: Lovley

state: MA

address: University of Massachusetts at Amherst, Dept. of Microbiology, Morrill IV north room 202

department: Microbiology

country: USA

institute: University of Massachusetts Amherst

description: no additional information

hyb_protocol: Combimatrix 100 ul cap.

scan_protocol: Slide was scanned using GenePix software and a GenePix 4000b scanner.

data_processing:
The raw total intensities were treated as follows to generate the M Log2 ratios for this work. Background signal was calculated from a set of negative control spots incorporated into the array. As the negative control sequences are not design specific (ie. are found in all of the ESOAs independent of the organism being sampled) some will inevitably demonstrate strong cross hybridization with the sample of interest. To avoid this issue the negative control spots were ranked according to their total intensity. The average of the lowest 30% was calculated. Background signal was calculated as this mean + 2 standard deviations.
The background signal was then subtracted from the total intensity for each spot. Probes whose signal was not greater than zero after background subtraction were omitted from further analysis. For the remaining data, the logged ratios [M=log2 (Ex/Ct)] are then calculated and Lowess global normalization is performed. During the data preprocessing, M vs. A plots before and after normalization, and side-by-side box plots for all arrays are used to assess array quality.(3) LIMMA mixed model analysis (R-package LIMMA(2))is applied to the normalized logged ratios to identify differentially expressed genes. Specifically, biological replicates are treated as a randomized block to allow for modeling correlations within them. LIMMA calculates a moderated t statistic for each probe, which is the ratio of the estimated   mean logged intensity ratio and the Empirical   Bayes estimate of its standard error. The   P-value of each oligo is then corrected for   multiple comparisons according to Benjamini and   Hockberg's procedure(1) to control the false   discovery rate. Oligos are ranked according to   the adjusted P-values and were called   differentially expressed if the adjusted   P-values are < 0.001. Note that multiple   oligonucleotide probes from the same gene are   analyzed separately and a gene is called   differentially expressed if at least half of its   probes are called differentially expressed.   1. Benjamini, Y., and Y. Hochberg. 1995.   Controlling the False Discovery Rate - a   Practical and Powerful Approach to Multiple   Testing. Journal of the Royal Statistical   Society Series B-Methodological 57:289-300.   2. Smyth, G. K. 2004. Linear models and   empirical bayes methods for assessing   differential expression in microarray   experiments. Stat Appl Genet Mol Biol   3:Article3.   3. Smyth, G. K., and T. Speed. 2003.   Normalization of cDNA microarray data. Methods   31:265-73.

organism: delta proteobacterium NaphS2

source_name: NaphS2 grown with naphthalene as the electron donor

label_protocol: 300 ng total RNA was amplified using the Ambion MessageAmpII-Bacteria kit, ethanol precipitated and resuspended to 1 mg/ml in RNase-free H2O, 10 ug was subsequently labeled with the MicroMax ASAP direct RNA labeling kit.

extract_protocol: Total RNA was isolated using a phenol extraction protocol.

tag: NaphS2 was grown with naphthalene as the electron donor and sulfate as the electron acceptor

source_name: NaphS2 grown with pyruvate as the electron donor

tag: NaphS2 was grown with pyruvate as the electron donor and sulfate as the electron acceptor


title: Magnetically sorted untouched CD8+CD45R0-T cells from donor A stimulated with anti CD3/CD8 beads for 48 hours

description: no additional information


title: Magnetically sorted untouched CD8+CD45R0-T cells from donor A unstimulated

description: no additional information


title: Magnetically sorted untouched CD8+CD45R0-T cells from donor C stimulated with anti CD3/CD8 beads+IFNα5 for 48 hours

description: no additional information


title: naph_pyr_set1_3B (array set 2)

description: no additional information

source_name: NaphS2 was grown in batch culture using Naphthalene as the electron donor

tag: NaphS2 was grown in batch culture with naphthalene as the electron donor and sulfate as the electron acceptor.

tag: NaphS2 was grown in batch culture with pyruvate as the electron donor and sulfate as the electron acceptor.


title: Magnetically sorted untouched CD8+CD45R0-T cells mRNA from a three donors pooled sample stimulated 7 hours with IFN α2

description: three donors pooled sample


title: Magnetically sorted untouched CD8+CD45R0-T cells from donor A stimulated with anti CD3/CD8 beads+IFNα2 for 48 hours

description: no additional information


title: naph_ben_set2_3B (array set 2)

description: no additional information

tag: NaphS2 was grown with naphthalene as the electron donor and sulfate as the electron acceptor.

source_name: NaphS2 grown with benzoate as the electron donor

tag: NaphS2 was grown with benzoate as the electron donor and sulfate as the electron acceptor


title: Magnetically sorted untouched CD8+CD45R0-T cells mRNA from a three donors pooled sample unstimulated

description: three donors pooled sample


title: naph_ben_set2_1A (array set 2)

description: no additional information

tag: NaphS2 was grown with naphthalene as the electron  donor and sulfate as the electron acceptor.

tag: NaphS2 as grown with benzoate as the electron donor and sulfate as the electron acceptor.


title: naph_ben_set2_3A (array set 2)

description: no additional information


title: naph_ben_set2_1B (array set 2)

description: no additional information

tag: NaphS2 wasd grown with naphthalene as the electron donor and sulfate as the electron acceptor


title: naph_ben_set2_2A (array set 2)

description: no additional information

tag: NaphS2 was grown with benzoate as the electron donor and sulfate as the electron acceptor.


title: naph_pyr_set2_2B (array set 2)

description: no additional information

source_name: NaphS2 was grown in batch culture using naphthalene as the electron donor

source_name: NaphS2 was grown in batch culture using pyruvate as the electron donor


title: naph_pyr_set2_3A (array set 2)

description: no additional information

source_name: NaphS2 was grown in batch culture with pyruvate as the electron donor


title: naph_pyr_set2_1B (array set 2)

description: no additional information


title: ben_pyr_set2_2B (array set 2)

description: no additional information

data_processing:
The raw total intensities were treated as follows to generate the M Log2 ratios for this work. Background signal was calculated from a set of negative control spots incorporated into the array. As the negative control sequences are not design specific (ie. are found in all of the ESOAs independent of the organism being sampled) some will inevitably demonstrate strong cross hybridization with the sample of interest. To avoid this issue the negative control spots were ranked according to their total intensity. The average of the lowest 30% was calculated. Background signal was calculated as this mean + 2 standard deviations. The background signal was then subtracted from the total intensity for each spot. Probes whose signal was not greater than zero after background subtraction were omitted from further analysis. For the remaining data, the logged ratios [M=log2 (Ex/Ct)] are then calculated and Lowess global normalization is performed. During the data preprocessing, M vs. A plots before and after normalization, and side-by-side box plots for all arrays are used to assess array quality.(3) LIMMA mixed model analysis (R-package LIMMA(2))is applied to the normalized logged ratios to identify differentially expressed genes. Specifically, biological replicates are treated as a randomized block to allow for modeling correlations within them. LIMMA calculates a moderated t statistic for each probe, which is the ratio of the estimated mean logged intensity ratio and the Empirical Bayes estimate of its standard error. The P-value of each oligo is then corrected for multiple comparisons according to Benjamini and Hockberg's procedure(1) to control the false discovery rate. Oligos are ranked according to the adjusted P-values and were called differentially expressed if the adjusted P-values are < 0.001. Note that multiple oligonucleotide probes from the same gene are analyzed separately and a gene is called differentially expressed if at least half of its probes are called differentially expressed.
1. Benjamini, Y., and Y. Hochberg. 1995. Controlling the False Discovery Rate - a Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society Series B-Methodological 57:289-300.
2. Smyth, G. K. 2004. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3:Article3.
3. Smyth, G. K., and T. Speed. 2003. Normalization of cDNA microarray data. Methods 31:265-73.

source_name: NaphS2 was grown in batch culture using benzoate as the electron donor

tag: NaphS2 was grown in batch culture with benzoate as the electron donor and sulfate as the electron acceptor.

source_name: NaphS2 was grown in batch culture using Pyruvate as the electron donor


title: naph_pyr_set2_2A (array set 2)

description: no additional information


title: ben_pyr_set2_1A (array set 2)

description: no additional information

tag: Strain NaphS2 was grown in batch culture using benzoate as the electron donor and sulfate as the electron acceptor.

tag: Strain NaphS2 was grown in batch culture using pyruvate as the electron donor and sulfate as the electron acceptor.


title: naph_pyr_set2_1A (array set 2)

description: no additional information


title: naph_pyr_set1_1B (array set 1)

description: no additional information

source_name: NaphS2 grown with naphthalene as electron donor

tag: NaphS2 was grown with naphthalene as electron donor and sulfate as electron acceptor

source_name: NaphS2 grown with pyruvate as electron donor

tag: NaphS2 was grown with pyruvate as electron donor and sulfate as electron acceptor


title: naph_pyr_set1_3A (array set 1)

description: no additional information


title: ben_pyr_set2_3B (array set 2)

description: no additional information


title: PCA_wt_ppcA_BR3A

description: total RNA was directly labeled with the Micromax ASAP labeling kit, using 10 ug total RNA for each sample.

hyb_protocol: Combimatrix 100 ul volume cap.

scan_protocol: Slide was scanned using GenePix software and a GenePix 4000b scanner

data_processing:
The raw total intensities were treated as follows to generate the M Log2 ratios for this work.  Background signal was calculated from a set of negative control spots incorporated into the array.  As the negative control sequences are not design specific (ie. are found in all of the ESOAs independent of the organism being sampled) some will inevitably demonstrate strong cross hybridization with the sample of interest.  To avoid this issue the negative control spots were ranked according to their total intensity.  The average of the lowest 30% was calculated.  Background signal was calculated as this mean + 2 standard deviations.  The background signal was then subtracted from the total intensity for each spot.  Probes whose signal was not greater than zero after background subtraction were omitted from further analysis.  For the remaining data, the logged ratios [M=log2 (Ex/Ct)] are then calculated and Lowess global normalization is performed. During the data preprocessing, M vs. A plots before and after normalization, and side-by-side box plots for all arrays are used to assess array quality.(3)  LIMMA mixed model analysis (R-package LIMMA(2))is applied to the normalized logged ratios to identify differentially expressed genes.  Specifically, biological replicates are treated as a randomized block to allow for modeling correlations within them. LIMMA calculates a moderated t statistic for each probe, which is the ratio of the estimated mean logged intensity ratio and the Empirical Bayes estimate of its standard error. The P-value of each oligo is then corrected for multiple comparisons according to Benjamini and Hockberg's procedure(1) to control the false discovery rate. Oligos are ranked according to the adjusted P-values and were called differentially expressed if the adjusted P-values are < 0.001.  Note that multiple oligonucleotide probes from the same gene are analyzed separately and a gene is called differentially expressed if at least half of its probes are called differentially expressed.
1.	Benjamini, Y., and Y. Hochberg. 1995. Controlling the False Discovery Rate - a Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society Series B-Methodological 57:289-300.
2.	Smyth, G. K. 2004. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3:Article3.
3.	Smyth, G. K., and T. Speed. 2003. Normalization of cDNA microarray data. Methods 31:265-73.

organism: Geobacter sulfurreducens

source_name: ppcA mutant adapted on ferric citrate

label_protocol: Micromax ASAP direct RNA labeling protocol

extract_protocol: Qiagen RNEasy Midi Kit protocol, DNAse Treatment with Ambion DNA-free kit.

tag: Geobacter sulfurreducens was grown anaerobically to mid-log in batch freshwater media with ferric citrate as the terminal electron acceptor and acetate as the electron donor.

source_name: wildtype grown on ferric citrate


title: PCA_wt_ppcA_BR3B


title: PCA_wt_ppcA_BR2B


title: PCA_wt_ppcA_BR1A


title: naph_pyr_set1_1A (array set 1)

description: no additional information


title: PCA_wt_ppcA_BR1B


title: ben_pyr_set2_3A (array set 2)

description: no additional information


title: ben_pyr_set2_2A (array set 2)

description: no additional information


title: ben_pyr_set2_1B (array set 2)

description: no additional information


title: PCA_wt_ppcA_BR2A


title: ben_pyr_set1_3B (array set 1)

description: no additional information

source_name: NaphS2 grown with benzoate as electron donor

tag: NaphS2 was grown with benzoate as electron donor and sulfate as electron acceptor


title: naph_ben_set1_2A (array set 1)

description: no additional information


title: naph_ben_set1_2B (array set 1)

description: no additional information


title: naph_ben_set1_3A (array set 1)

description: no additional information

tag: NaphS2 grown with naphthalene as electron donor and sulfate as electron acceptor

tag: NaphS2 grown with benzoate as electron donor and sulfate as electron acceptor


title: ben_pyr_set1_3A (array set 1)

description: no additional information


title: naph_ben_set1_3B (array set 1)

description: no additional information


title: naph_pyr_set1_3B (array set 1)

description: no additional information


title: naph_pyr_set1_2B (array set 1)

description: no additional information


title: naph_ben_set1_1B (array set 1)

description: no additional information


title: naph_pyr_set1_2A (array set 1)

description: no additional information


title: ben_pyr_set1_1A (array set 1)

description: no additional information

tag: NaphS2 was grown with benzoate as electron donor and sulfate as electron acceptor.

tag: NaphS2 was grown with pyruvate as the electron donor and sulfate as the electron acceptor


title: naph_ben_set1_1A (array set 1)

description: no additional information


title: ben_pyr_set1_1B (array set 1)

description: no additional information


title: gura_mnox_fum_2A

description: total RNA was amplified using the Ambion MessageAmp II- Bacteria kit for polyadenylation and subsequent amplification of total RNA. aRNA was ethanol precipitated and resuspended in nuclease-free water to a total concentration of ~1 ug/ul.

hyb_protocol: Combimatrix 100ul cap.

organism: Geotalea uraniireducens

source_name: Manganese oxide as electron acceptor

label_protocol: Micromax ASAP direct labeling of 10 ug aRNA

extract_protocol: For reference see:In situ expression of nifD in Geobacteraceae in subsurface sediments. Appl Environ Microbiol. 2004 Dec;70(12):7251-9. PMID: 15574924

tag: G. uraniumreducens was grown with manganese oxide as the electron acceptor

source_name: Fumarate as electron acceptor

tag: G. uraniumreducens was grown with fumarate as the electron acceptor


title: ben_pyr_set1_2B (array set 1)

description: no additional information


title: gura_feox_fum_2B

source_name: Iron oxide as electron acceptor

tag: G. uraniumreducens was grown with iron oxide as the electron acceptor

tag: G. uraniumreducens was grown with fumarate as the electron acceptor.


title: ben_pyr_set1_2A (array set 1)

description: no additional information


title: gura_mnox_fum_1A


title: gura_mnox_fum_2B


title: gura_feox_fum_1A

source_name: Iron oxide as Electron Acceptor

tag: G. uraniumreducens was grown using iron oxide as the electron acceptor

tag: G. uraniumreducens was grown using fumarate as the electron acceptor.


title: gura_mnox_fum_3B

tag: G. uraniumreducens was grown using manganese oxide as the electron acceptor

tag: G. uraniumreducens was grown using fumarate as the electron acceptor


title: gura_mnox_fum_1B


title: gura_mnox_fum_3A


title: gura_feox_fum_3A


title: gura_feox_fum_3B


title: gura_feox_fum_1B


title: Resistant versus Sensitive replicate 3 bis

status: Public on Jul 16 2010

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

institute: IGTP

description: NP-18AR versus NP-18 biological replicate 3 of 3. Technical replicate 3 of 3.

hyb_protocol: Three biological replicate experiments were performed confronting TK/GCV resistant cell lines versus de parental TK/GCV sensitive NP-18 pancreatic cancer derived cell line. For all three three biological replicates each experimental pair of labelled samples was co-hybridized on at least two separate microarrays with dye swapping to correct for dye bias effects. Thus, up to nine microarray hybridizations were processed , totalling 9 array datasets.

scan_protocol: Fluorescent images were obtained using an Agilent G2565BA scanner at 100% PMT 100% laser power settings and quantified through the GenePix 6.0 software (Axon, Molecular Devices, Sunnywale, CA) using the irregular feature finding option.

data_processing: Extracted raw data were filtered and normalized using the Limma package developed within the Bioconductor project in the R statistical programming environment. The two channels were balanced by lowess normalization using 0.3 as the span parameter with reduced weights in control and poor quality spots, followed by scaling across chips. Target genes were considered as differentially expressed when above the 95% rank in the B empirical Bayes statistic and a set fold change. All quantitative and statistical analyses were performed using using Limma package in the R. environment (Smyth 2004).

label_protocol: 500 ng of total RNA were reverse transcribed, amplified, labelled by in vitro transcription using the Low Input Linear Amplification Kit (Agilent 5184-3523), and hybridized following the manufacturer’s instructions (SSC wash Agilent 60-mer oligo microarray processing protocol, Version 4.1, April 2004).

growth_protocol: NP-18 and NP-18AR cells were cultured in RPMI medium supplemented with 10% FBS and penicillin (10.000U/ml) and streptomycin (10 mg/ml), at 37ºC and 5% CO2 and 100% humidity.

extract_protocol: Total RNA was extracted using a commercial kit (Rneasy, Qiagen)

tag: cell line

value: NP-18AR3 pancreatic cancer derived cell line

tag: sensitivity

value: TK/GCV resistant cell line 3

tag: source

value: biological replicate 3, cultured cells from independently generated clone, different from NP-18AR1 and NP-18AR2

value: TK/GCV sensitive cell line

value: biological replicate 3, third of three independently treated cell cultures from same parental clone NP-18


title: gura_feox_fum_2A


title: Resistant versus Sensitive replicate 3 dye swap

description: NP-18AR versus NP-18 biological replicate 3 of 3. Technical replicate 2 of 3.

value: NP-18 pancreatic cancer derived cell line


title: Resistant versus Sensitive replicate 2 bis dye swap

description: NP-18AR versus NP-18 biological replicate 2 of 3. Technical replicate 4 of 4.

value: NP-18AR2 pancreatic cancer derived cell line

value: TK/GCV resistant cell line 2

value: biological replicate 2, cultured cells from independently generated clone, different from NP-18AR1 and NP-18AR3

value: biological replicate 2, second of three independently treated cell cultures from same parental clone NP-18


title: Resistant versus Sensitive replicate 2 dye swap

description: NP-18AR versus NP-18 biological replicate 2 of 3. Technical replicate 2 of 4.


title: Resistant versus Sensitive replicate 2 bis

description: NP-18AR versus NP-18 biological replicate 2 of 3. Technical replicate 3 of 4.


title: Resistant versus Sensitive replicate 1 dye swap

description: NP-18AR versus NP-18 biological replicate 1 of 3. Technical replicate 2 of 2.

value: NP-18AR1 pancreatic cancer derived cell line

value: TK/GCV resistant cell line 1

value: biological replicate 1, cultured cells from independently generated clone, different from NP-18AR2 and NP-18AR3

value: biological replicate 1, first of three independently treated cell cultures from same parental clone NP-18


title: Resistant versus Sensitive replicate 2

description: NP-18AR versus NP-18 biological replicate 2 of 3. Technical replicate 1 of 4.


title: Resistant versus Sensitive replicate 1

description: NP-18AR versus NP-18 biological replicate 1 of 3. Technical replicate 1 of 2.


title: Resistant versus Sensitive replicate 3

description: NP-18AR versus NP-18 biological replicate 3 of 3. Technical replicate 1 of 3.


title: vtrB replicate 2

city: Suita

first: Toshio

last: Kodama

state: Osaka

address: 3-1 Yamadaoka

country: Japan

institute: OSAKA university

hyb_protocol: Cy3- or Cy5-labeled probes (apploximately 20 µl for each) were mixed, and 3 µl of 10% SDS, 6 µl of 1 mg/ml human Cot-1 DNA (Invitrogen) and 15 µl of 20X SSC (3 M NaCl, 0.3 M trisodium citrate 2H2O, pH 7.0) were added to the mixture. After incubation at 96˚C for 2 min, the denatured sample was applied to a microarray slide and incubated on an MAUI hybridization chamber at 60˚C for 16h. The slide was then washed twice in 2X SSC/0.1% SDS solution at 60˚C for 10 min, twice in 0.2X SSC/0.1% SDS solution at room temperature for 10 min, and twice in 0.2X SSC solution at room temperature for another 10 min. Finally, the slide was briefly rinsed with ethanol and dried by centrifugation.

scan_protocol: Scanned with a ScanArrayExpress scanner (PerkinElmer). Obtained data were analyzed by the ScanArrayExpress software ver. 3.0.

data_processing: LOWESS normalaized, background subtracted data obtained from log2 of processed Cy3 signal/processed Cy5 signal.

organism: Vibrio parahaemolyticus

source_name: wild type

label_protocol: First, 20 µg of total RNA were primed with 2 µl of 5 µg/µl random hexamer at 70˚C for 5 min then reversed transcribed at 46˚C for 2 h in the presence of 800 U SuperScript III RTase (Invitrogen), and 5 mM each dATP, dTTP, dCTP, with 2 mM dTTP, 3 mM aminoallyl-modified dUTP (Sigma). The aminoallyl-labeled cDNA was purified by phenol-chloroform extraction and ethanol precipitation. Precipitated cDNA was dried and resuspended in 10 µl of 50 mM NaHCO3. After adding 10 µl of dimethyl sulfoxide solution containing Cy3 or Cy5 mnonofunctional reactive dye (GE healthcare), the sample was incubated at room temperature in the dark for 1h to allow the dye to couple with DNA. the fluorescently labeled DNA was finally purified by the CentriCep spin column (Princeton Sepatations Inc.).

growth_protocol: Cells were grown to the OD600=1.0 at 37˚C in Luria-Bertani containing medium 0.5% NaCl.

extract_protocol: Total RNA was purified using Trizol (Invitrogen) and digested DNA with TURBO DNA-free (Ambion), then carryed out RNeasy mini Kit (Qiagen) according to the mnufacture's instruction.

tag: strain

source_name: vtrB

value: RIMD 2210633 vtrB mutant


title: vtrB replicate 3


title: vtrB replicate 1


title: vtrA replicate 3

source_name: vtrA

value: RIMD 2210633 vtrA mutant


title: Magnetically sorted untouched CD8+CD45R0-T cells from donor B stimulated with anti CD3/CD8 beads+IFNα5 for 48 hours

description: no additional information

source_name: Human CD8 T cells

tag: cell type

value: CD8+CD45R0-T cells

tag: donor

value: B

tag: stimulated

value: yes

tag: agent

value: anti CD3/CD8 beads+IFNα5

tag: time

value: 48 hours

tag: donor ethnicity

value: Caucasian

tag: health status

value: healthy


title: vtrA replicate 1


title: vtrA replicate 2


title: Dox treatment, mouse rep4

status: Public on Jul 15 2010

city: Durham

first: ASHUTOSH

last: CHILKOTI

state: NC

address: BME, PO Box 90281, Duke University

department: BME

institute: Duke University

hyb_protocol: The bybridization was performed according to the Affymetrix protocol of enkaryotic samples (Expression Analysis Technical Manual, P/N 702232 Rev.3, Affymetrix) by Duke Microarray Facility

scan_protocol: Microarraye were scanned by Duke Microarray Facility with Affemetrix Genechip Scanner 7G with AGCC software.

data_processing: The data were processed and analyzed by Partek genomic suite 6.4. The algorithm of robust multi-array analysis (RMA) was used to process raw data. There was no scaling process. Pairwise comparisons between gene expression profiles of differentially treated mice were performed via the one-way ANOVA test and differentially expressed genes were selected from volcano plots.

organism: Mus musculus

source_name: 48 hours after free Dox treatment

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, P/N 702232 Rev.3, Affymetrix) by Duke Microarray Facility.

growth_protocol: 2.5-5x105 C26 cells were injected subcutanousely to dorsal flank of Balb/c mouse which gave 95% tumor-take.

extract_protocol: At 48 hours after the treatment, subcutaneous tumors were collected and immediately merged into RNAlater reagent. Total RNA was later isolated from the tumor tissues by using RNeasy kit

treatment_protocol: Mice with subcutaneous tumor (size=~50 mm3) were treated with PBS-control, free Dox, or CP-Dox respectively at day 8 after tumor inoculation.

tag: tissue

value: C26 murine colon carcinoma xenograft on Balb/c mice

value: Balb/c

tag: age

value: 6 weeks


title: PBS_Control, mouse rep4

source_name: 48 hours after PBS control treatment


title: PBS_Control, mouse rep2


title: CP-Dox treatment, mouse rep4

source_name: 48 hours after CP-Dox treatment


title: PBS_Control, mouse rep3


title: Dox treatment, mouse rep3


title: Dox treatment, mouse rep2


title: CP-Dox treatment, mouse rep1


title: CP-Dox treatment, mouse rep3


title: Dox treatment, mouse rep1


title: Clorgyline_6hr_con

status: Public on Jul 17 2010

city: Stanford

first: Donna

middle: M

last: Peehl

state: CA

department: Department of Urology

institute: Stanford University School of Medicine

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-11/77515.gif

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1240, 6000; Software: type: feature extraction; Performer: Hongjuan,,Zhao

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

source_name: Strategene Reference

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: Strategene Reference

source_name: E-CA-88 cells no drug treatment control for  6 hrs

label_protocol:
Extract preparation: Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 2 (red).; Protocol Type = Extract preparation; Parameter Extraction method = TRIZOL RNA Isolation Protocol; Parameter Extraction method reference = "Invitrogen/Carlsbad, USA"; Parameter Extracted molecule = RNA
Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 40 ug; Parameter Type of label = Cy5

growth_protocol: Parameters that describe the conditions under which the biological sample was grown or propagated; Protocol Type = Growth Conditions; Parameter Media = "PFMR-4A w/o EGF and 10 nM 1,25-dihydroxyvitamin D3, 1 uM all-trans retinoic acid, 1 ng/ml TGF-beta, and 1 nM R1882"

treatment_protocol: Experimentally pertinent treatments performed on the original biological sample that was used to generate the extract that was labelled and scanned in Channel 2 (red).; Protocol Type = Treatment; Parameter Time = 6 hr; Parameter Compound Based Treatment = control

tag: tissue type

value: cancerous prostate

value: epithelial


title: PBS_Control, mouse rep1


title: Clorgyline_6hr_exp

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-11/77514.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1240, 6760; Software: type: feature extraction; Performer: Hongjuan,,Zhao

source_name: E-CA-88 cells treated with 1 uM clorgyline for 6 hrs

treatment_protocol: Experimentally pertinent treatments performed on the original biological sample that was used to generate the extract that was labelled and scanned in Channel 2 (red).; Protocol Type = Treatment; Parameter Time = 6 hr; Parameter Compound Based Treatment = 1 uM clorgyline


title: CP-Dox treatment, mouse rep2


title: Clorgyline_24hr_con

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-11/77516.gif

source_name: Strategen Reference

source_name: E-CA-88 cells no drug treatment control for 24 hrs

treatment_protocol: Experimentally pertinent treatments performed on the original biological sample that was used to generate the extract that was labelled and scanned in Channel 2 (red).; Protocol Type = Treatment; Parameter Time = 24 hr; Parameter Compound Based Treatment = control


title: Stage II colorectal cancer tissue samples (FFPE) 48

status: Public on Jul 13 2010

type: genomic

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description: Pooled DNA from the blood of 18 healthy individuals

hyb_protocol: Hybridization protocol available via www.agilent.com

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

data_processing: Median Signal intensity minus median Background intensity; excluding negative values

molecule: genomic DNA

source_name: colorectal cancer

label_protocol: DNA labeling protocol according to Enzo Life Sciences

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

value: colorectal cancer

tag: tumor stage

value: stage II

source_name: male reference DNA


title: Clorgyline_24hr_exp

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-11/77518.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1000, 6000; Software: type: feature extraction; Performer: Hongjuan,,Zhao

source_name: E-CA-88 cells treated with 1 uM clorgyline for 24 hrs

treatment_protocol: Experimentally pertinent treatments performed on the original biological sample that was used to generate the extract that was labelled and scanned in Channel 2 (red).; Protocol Type = Treatment; Parameter Time = 24 hr; Parameter Compound Based Treatment = 1 uM clorgyline


title: Clorgyline_96hr_exp

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-11/77520.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1520, 5440; Software: type: feature extraction; Performer: Hongjuan,,Zhao

source_name: E-CA-88 cells treated with 1 uM clorgyline for 96 hrs

treatment_protocol: Experimentally pertinent treatments performed on the original biological sample that was used to generate the extract that was labelled and scanned in Channel 2 (red).; Protocol Type = Treatment; Parameter Time = 96 hr; Parameter Compound Based Treatment = 1 uM clorgyline


title: Stage II colorectal cancer tissue samples (FFPE) 45

description: Pooled DNA from the blood of 18 normal individuals was used as reference

value: Pooled DNA from the blood of 18 healthy individuals


title: Stage II colorectal cancer tissue samples (FFPE) 49


title: Stage II colorectal cancer tissue samples (FFPE) 37

description: Normal colon mucosa from each patient was used as reference in the oaCGH experiments

source_name: normal colorectum mucosa

value: normal colon mucosa obtained from the same patient as ch1


title: Stage II colorectal cancer tissue samples (FFPE) 22


title: Stage II colorectal cancer tissue samples (FFPE) 41


title: Stage II colorectal cancer tissue samples (FFPE) 3


title: Stage II colorectal cancer tissue samples (FFPE) 47


title: Stage II colorectal cancer tissue samples (FFPE) 38


title: Clorgyline_96hr_con

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-11/77519.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1080, 5440; Software: type: feature extraction; Performer: Hongjuan,,Zhao

source_name: E-CA-88 cells no drug treatment control for 96 hrs

treatment_protocol: Experimentally pertinent treatments performed on the original biological sample that was used to generate the extract that was labelled and scanned in Channel 2 (red).; Protocol Type = Treatment; Parameter Time = 96 hr; Parameter Compound Based Treatment = control


title: donorF2_IRA860J/cm2_24hpostincubation_biolrep2

status: Public on Jul 10 2010

city: Düsseldorf

first: Christian

last: Calles

address: Auf'm Hennekamp 50

department: Molecular Ageing Research/Cellbiology

country: Germany

institute: Institut fuer umweltmedizinische Forschung (IUF)

description: no additional description

hyb_protocol: After purification, fragmentation and a further quality and purity control with the Agilent Bioanalyzer 2100 system 9 µg of the labeled cRNA were hybridized on the Affymetrix HG-U133A Microarray according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.

scan_protocol: The hybridized arrays were scanned using Microarray Suite (MAS) Software (Affymetrix) according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.

data_processing: The raw data containing .cel-files were normalised in the free statistical software R Version 2.0.1 with the BioCconductor affy-package using the robust multichip average (RMA) method. A separate normalisation procedure for array samples of each of the three different fibroblast cells lead to better results regarding how often commonly regulated genes were found in total and therefore was used for this study.

source_name: human dermal fibroblasts IRA irradiated with 860J/cm2

label_protocol: The in vitro transcription into biotinylated cRNA was performed with the IVT Labeling Kit (Affymetrix) according to the manufacturers protocols.

growth_protocol: Human dermal fibroblasts were isolated from foreskin of different donors. Cells cultivated in Eagle’s minimum essential medium with Earle’s salts (MEM, PAA Laboratories Pasching, Austria) supplemented with 10% fetal bovine serum (Gibco, Karlsruhe Germany), 1% antibiotics/antimycotics (penicillin, streptomycin, amphotericin B), 1% glutamine (Gibco) and were cultivated on 100 mm plastic culture dishes (Greiner, Solingen, Germany) at 37°C in humidified air with 5% CO2. Cells were used between passages five and ten, grown to 100% confluency before treatment. At least 24 hours before IRA irradiation media was changed to serum-free MEM.

extract_protocol: RNA was extracted using the NucleoSpin RNA II kit (Macherey-Nagel, Düren, Germany) according to the manufacturers instruction. RNA quality and purity were assessed using an Agilent Bioanalyzer 2100 system (Agilent Technologies, Palo Alto, CA). The RNA was then utilized to synthesize first- and second-strand cDNA by using the Affymetrix One-Cycle cDNA Synthesis Kit (Affymetrix UK Ltd, High Wycombe,UK) with an subsequent clean up with the GeneChip Sample Cleanup Kit (Affymetrix).

treatment_protocol: We used a waterfiltered Hydrosun 500 H 500 IRA lamp (Hydrosun Medizintechnik GmbH, Müllheim, Germany) with an emission in the range of 760-1400 nm leading to an irradiance of 360 mW/cm2 at a distance of 20 cm measured through Hydrosun HBM1 irradiance measuring device (Hydrosun). IRA irradiation lasted 40 min leading to a total dose of 860 J/cm2. The culture dishes were placed on a cooled plate connected to thermostated bath (Thermo Haake GmbH, Karlsruhe, Germany) to maintain temperatures below 37°C during IRA irradiation. For irradiation, medium was replaced by phosphate-buffered saline (37°C, Gibco). Control cells were held on a 37°C thermostated plate under similar conditions without irradiation. Following the treatment cells were cultivated for 24 hours with serum free MEM culture medium at 37°C.

value: primary human dermal fibroblasts

tag: passage

value: between 5-10


title: donorF2_IRA860J/cm2_24hpostincubation_biolrep3

description: no additional description


title: donorF2_shamtreated_24hpostincubation_biolrep2

description: no additional description

source_name: human dermal fibroblasts sham treated control


title: donorF2_IRA860J/cm2_24hpostincubation_biolrep1

description: no additional description


title: donorF3_shamtreated_24hpostincubation_biolrep3

description: no additional description


title: donorF3_IRA860J/cm2_24hpostincubation_biolrep2

description: no additional description


title: donorF1_shamtreated_24hpostincubation_biolrep2

description: no additional description


title: donorF3_shamtreated_24hpostincubation_biolrep1

description: no additional description


title: donorF2_shamtreated_24hpostincubation_biolrep3

description: no additional description


title: donorF3_IRA860J/cm2_24hpostincubation_biolrep1

description: no additional description


title: donorF3_IRA860J/cm2_24hpostincubation_biolrep3

description: no additional description


title: donorF3_shamtreated_24hpostincubation_biolrep2

description: no additional description


title: donorF1_shamtreated_24hpostincubation_biolrep3

description: no additional description


title: donorF2_shamtreated_24hpostincubation_biolrep1

description: no additional description


title: Patient 102n

status: Public on Jul 09 2010

city: Bethesda

first: Ewy

last: Mathe

state: MD

address: 37 Convent Dr.

institute: National Cancer Institute/National Institutes of Health

hyb_protocol: Labeled cDNA was hybridized onto the chips, and processed by direct detection of the biotin-containing transcripts by streptavidin-Alexa 647 conjugate.

scan_protocol: Slides were scanned with the Axon 4000B Scanner (Molecular Device, Inc) and spot intensities were quantified with Genepix (version Pro 6.0.1.00).

data_processing: Mean intensity spot values for each sample were extracted for spots that were not flagged by the image quantification software GenePix (version Pro 6.0.1.00).  In addition, spots were removed if their background intensities were higher than their respective foreground intensities, and if quadruplicate intensity spot values differed by more than 1 (on a log2 scale).  The remaining spots were then normalized using a loess normalization modified for single channel array data, where the true spot intensity is estimated by the average of that spot across all arrays.

source_name: ADC patient, non-cancerous

label_protocol: Five μg of total RNA was converted to biotin-labeled first strand cDNA.

extract_protocol: Total RNA used for quantification of miRNA levels was extracted from esophageal tissue in our laboratory using TRIZOL (Invitrogen, cat. no. 15596-026), according to the manufacturer’s procedures.

tag: cohort

value: US

tag: hybridization date

tag: histology

value: adenocarcinoma

tag: barrett's esophagus

value: Yes

tag: chemoradiation therapy

tag: alcohol consumption

tag: smoking:

tag: ptnm stage

value: IIA

tag: nodal involvement

value: No

tag: survival days

tag: death due to cancer


title: Patient 108n

tag: smoking

value: III


title: Patient 104n


title: Patient 108t

source_name: ADC patient, cancerous

value: Cancerous


title: Patient 107t


title: donorF1_IRA860J/cm2_24hpostincubation_biolrep2

description: no additional description

tag: cell type

tag: donor


title: Patient 107n

tag: tissue type


title: Patient 100t


title: donorF1_shamtreated_24hpostincubation_biolrep1

description: no additional description


title: Patient 105t

value: IV


title: Patient 104t


title: Patient 105n


title: Patient 99n


title: Patient 97n


title: Patient 100n


title: Patient 102t


title: donorF1_IRA860J/cm2_24hpostincubation_biolrep1

description: no additional description


title: Patient 94n


title: donorF1_IRA860J/cm2_24hpostincubation_biolrep3

description: no additional description


title: Patient 93n


title: Patient 91t


title: Patient 95t

source_name: SCC patient, cancerous

value: squamous cell carcinoma

tag: alcohol consumption:

value: II


title: Patient 95n

source_name: SCC patient, non-cancerous


title: Patient 96n


title: Patient 94t


title: Stage II colorectal cancer tissue samples (FFPE) 19

tag: tissue

tag: tumor stage


title: Patient 96t

tag: cohort

tag: hybridization date


title: Patient 87t

tag: histology

tag: barrett's esophagus


title: Patient 93t

tag: chemoradiation therapy

tag: alcohol consumption


title: Patient 82n

tag: ptnm stage

value: I


title: Patient 84n

tag: nodal involvement


title: Patient 83n

tag: survival days


title: Patient 86t

tag: death due to cancer


title: Patient 82t

tag: smoking


title: Patient 87n


title: Patient 90n

value: IIB


title: Patient 91n


title: Patient 89t


title: Patient 89n


title: Patient 86n


title: Patient 99t


title: Patient 88n

tag: smoking:


title: Patient 75t


title: Patient 78n


title: Patient 81n


title: Patient 90t


title: Patient 85t


title: Patient 74n


title: Patient 70t


title: Patient 71n


title: Patient 85n


title: Patient 83t


title: Patient 88t


title: Patient 84t


title: Patient 70n


title: Patient 81t


title: Patient 79n


title: Patient 74t


title: Patient 72n


title: Patient 71t


title: Patient 78t


title: Patient 59t


title: Patient 64t


title: Patient 65n


title: Patient 59n


title: Patient 67n


title: Patient 72t


title: Patient 57t


title: Patient 79t


title: Patient 67t


title: Patient 68t


title: Patient 55n


title: Patient 97t


title: Patient 57n


title: Patient 75n


title: Patient 40n

value: Japanese


title: Patient 62t


title: Patient 61n


title: Patient 65t


title: Patient 41t


title: Patient 41n


title: Patient 40t


title: Patient 62n


title: Patient 55t


title: Patient 64n


title: Patient 68n


title: Patient 36t


title: Patient 38n


title: Patient 61t


title: Patient 37n


title: Patient 63n


title: Patient 58n


title: Patient 37t


title: Patient 58t


title: Patient 35n


title: Patient 35t


title: Patient 56t


title: Patient 56n


title: Patient 52n


title: Patient 39t


title: Patient 28T


title: Patient 34t


title: Patient 52t


title: Patient 28N


title: Patient 24t


title: Patient 23t


title: Patient 22n


title: Patient 36n


title: Patient 23n


title: Patient 21n


title: Patient 20t


title: Patient 24n


title: Patient 19t


title: Patient 25n


title: Patient 22t


title: Patient 16n


title: Patient 12t


title: Patient 12n


title: Patient 10n


title: Patient 11t


title: Patient 13n


title: Patient 39n


title: Patient 38t


title: Patient 10t


title: Patient 11n


title: Patient 20n


title: Patient 19n


title: Patient 34n


title: Patient 16t


title: Patient 26t


title: Patient 25t


title: Patient 26n


title: Patient 6n


title: Patient 6t


title: Patient 5t


title: Patient 7n


title: Patient 9t


title: Patient 5n


title: Patient 21t


title: Patient 4t


title: Patient 14t


title: Patient 13t


title: Patient 14n


title: Patient 8t


title: Patient 9n


title: Patient 8n


title: Patient 15t


title: Patient 7t


title: Patient 3t


title: Patient 4n


title: Patient 3n


title: Patient 1t


title: Patient 2n


title: Patient 1n


title: Patient 2t


title: Patient 15n


title: sh48

status: Public on Jul 08 2010

city: Heidelberg

first: maria

last: shahmoradgoli

state: BW

address: Im Neuenheimer Feld 280

department: Molecular Genetics

institute: German Cancer Research Center

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.

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

growth_protocol: Human HEK293T (human embryonic kidney) cells (ATCC CRL-1573) were cultured in DMEM medium supplemented with 10% (v/v) fetal bovine serum, 100 U/ml penicillin, and 100 μg/ml streptomycin at 37°C and 5% (v/v) CO2

extract_protocol: RNA  was isolated from the HEK293T cells using the RNeasy kit (Qiagen, Hilden, Germany). RNA quality and concentration were assessed with the Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: cell line

tag: cell type

value: human embryonic kidney

tag: atcc


title: ps72

description: control

source_name: control


title: DMSO 1

first: Zsuzsanna

middle: S.

last: Nagy

address: Nagyerdei krt. 98

institute: University of Debrecen

description: 12h treatment

hyb_protocol: Affymetrix Hybridization, Washing/Staining on the Fluidics Station

scan_protocol: Affymetrix GeneChip® Scanner 3000

data_processing: Array quality parameters were as follows: Scaling Factor (6.681, 2.881, 2.967, 2.656 for NC1153_1, DMSO_1, NC1153_2, DMSO_2, respectively), Average Background (65.71, 87.2, 72.77, 79.23), number of present probes for housekeeping probe sets were 3 for GAPDH and b-actin and 2 for spike in probe sets bioB, bioC and bioD on each array. The 3’-end to 5’-end probe intensity ratios were 0.93, 0.91, 0.92 and 0.94 for GAPDH and 4.47, 3.54, 3.89 and 3.82 for b-actin. Differences in percent of probe sets present between compared chips (determined by Affymetrix’s algorhythm) were below 10 percent.

source_name: Kit225 cells treated with DMSO 12h

label_protocol: Affymetrix Labeling (Total RNA). These steps as well as the QC steps were perfomed by MCF according to their standardized procedures.

growth_protocol: Kit225 cells were maintained in RPMI-1640 medium containing 10% fetal calf serum, 2 mM L-glutamine and penicillin-streptomycin supplemented with 20 U/ml human recombinant IL-2.

extract_protocol: QIAGEN RNeasy Kit. RNA samples were analyzed for purity (A260/280 min. 1.9, A260/230 min 1.7) and integrity (capillary electrophoresis for degradation and DNA contamination) on an Agilent 2100 Bioanalyser and the NanoDrop ND-1000 Spectrophotometer. Only RNA samples that passed this Quality Check were used for subsequent hybridization.

treatment_protocol: Kit225 cells at a density of 8x10E5/ml were treated with 25 mM NC1153 or 0.1 % DMSO for 12 hours.


title: sh72


title: Brain V1 Sample a

status: Public on Jul 06 2010

city: Nantes

first: Mahatsangy

last: Raharijaona

address: Faculte de Medecine - Inserm U915 1 rue gaston Veil

country: France

institute: INSERM

description: AMC V1 third instar larva sample a

hyb_protocol: A first hybridization was performed using a 33P-labelled oligonucleotide (which is found at the extremity of each PCR product) to monitor the amount of cDNA present in each spot. After stripping (3 hours 68°C, 0.1 SSC, 0.2% SDS), arrays were prehybridized for 4 h at 65°C in hybridization solution (5X Denhardt's, 5X SSC, 0.5% SDS) and hybridized with denatured labeled cDNAs for 24 h at 68°C in hybridization solution. Filters were then washed in 0.1X SSC/0.2% SDS solution for 3 hours. Finally, membranes were rinsed in 2x SSC and air-dried before exposure.

scan_protocol: After hybridizations and washes, arrays were exposed ON to phosphoimaging plates (FUJIFILM), which were scanned (with a Fuji BAS 5000, Raytest, Paris France) to quantify signal intensities (ArrayGauge software v1.3; Fuji, Paris, France)

data_processing: The signal intensities depend on the accessible amount of PCR product spotted on the microarray. Hence, for each spot, the corresponding vector signal was used to check the reliability of the measurement. Then the variability due to experimental conditions was eliminated by using a local weighted scattered plot smoother analysis (LOWESS, Dudoit et al. 2002). The data were then filtered and sole the values found two times above the mean of background value and coherent with the vector signal were kept. Data were then log transformed and analysed.

organism: Drosophila melanogaster

source_name: Canton-S (Cs) strain

label_protocol:
For each sample, cDNA were synthesised from 3.0 µg total RNA in the presence of 33[P] dATP (Amersham Pharmacia Biotech, Bucks, United Kingdom), dNTP, Superscript II reverse transcriptase for 2h at 42°C.
3µg Total RNA was mixed with 8 µg oligodT(25) and 0.3 ng cytochrome CG03 mRNA. Samples were heated at 70°C to remove secondary structure and progressively cooled to 42°C to ensure annealing of oligo(dT) with the poly(A) tail. Then, 17 µl of labeling mix (1 µl RNasin, 6 µl 5x first strand buffer, 2 µl 0.1 M DTT, 0.6 µl of 20 mM (each) dATP dGTP dTTP, 0.6 µl of 120 µM dCTP, 3 µl of alpha-33P-dCTP, 1 µl SuperScript II reverse transcriptase, 2.8 µl water) were added and reverse transcription was performed at 42°C for one hour. To improve reverse transcription, 1 µl SuperScript II reverse transcriptase was subsequently added and reaction was carried on for one hour. RNA was removed by treatment at 68°C for 30 min with 1 µl 1% SDS, 1 µl 0.5 M EDTA and 3µl 3 M NaOH. After equilibration (15 min at room temperature) samples were neutralized using 10 µl 1 M Tris-HCl and 3 µl 2N HCl. Next, 2 µg of polyA(80) were added and samples were heated at 100°C for 5 min. Volume was then adjusted to 500 ULwith hybridization buffer (5x SSC, 5x Denhardt's, 0.5% SDS) and samples were heated for 2 hr 30 at 68°C

extract_protocol: Total RNA from third instar larvae (3 µg) were extracted from isolated AMC and CNS, according to Guenin et al. (2007). RNA extractions from third instar larvae were carried out according to the TRIzolTM Reagent protocol (Invitrogen). Four independent extractions were performed for each sample condition. Third instar larvae were collected 30 min after metamorphosis and neural regions were dissected in RNA laterTM (Ambion). To remove traces of genomic DNA, the extracted RNA was digested with RQ1 RNase free DNase (Promega). RNA integrity was checked by denaturing formaldehyde agarose gel electrophoresis and the quantity was assessed by optical density (OD) 260/280 ratios.

treatment_protocol: The prosV strains used in this study have been previously described (Guenin et al., Dev Biol 2007). Strains used are the wild-type Canton-S (Cs) strain; Briefly, they were generated by insertion (prosV1) and remobilization (prosV13, prosV24, ProsV14) of a PGal4 transposon, located 216 pb upstream of the pros transcription initiation site. Strains were kept at 25 °C under a 12h dark/light cycle on standard cornmeal and yeast medium.

tag: strains

tag: tissue

value: Central Nervous System

tag: developmental stage

value: Early third instar larva

tag: pros expression level

value: weak transcript level in CNS and AMC, no protein in larval AMC

tag: lethality stage

value: third instar larva


title: AMC V24 sample a

description: AMC V24 third instar larva sample a

value: Antenno-maximilary complex (AMC)

value: weak transcript level in Central Nervous System

value: pupal


title: NC1153 1

description: 12h treatment

source_name: Kit225 cells treated with NC1153 12h


title: Brain V13 sample a

description: Brain V13 third instar larva sample a

value: overexpression in brain

value: young adult


title: emp48

description: control


title: AMC V1 sample a

description: AMC V1 third instar larva sample a


title: Brain V24 sample a

description: Brain V24 third instar larva sample a

value: pupal or viable


title: Brain V14 sample c

description: Brain V14 third instar larva sample c

value: wild type

value: viable


title: NC1153 2

description: 12h treatment


title: AMC V13 sample a

description: AMC V13 third instar larva sample a


title: over72


title: over24


title: time.zero

description: no incubation time

source_name: no incubation time


title: em24

description: control


title: over48


title: DMSO 2

description: 12h treatment


title: ps48

description: control


title: sh24


title: ps24

description: control


title: AMC V14 sample a

description: AMC V14 third instar larva sample a


title: AMC V14 sample b

description: AMC V14 third instar larva sample b


title: AMC V1 sample c

description: AMC V1 third instar larva sample c

hyb_protocol: A first hybridization was performed using a 33P-labelled oligonucleotide (which is found at the extremity of each PCR product) to monitor the amount of cDNA present in each spot. After stripping (3 hours 68°C, 0.1 SSC, 0.2% SDS), arrays were prehybridized for 4 h at 65°C in hybridization solution (5X Denhardt's, 5X SSC, 0.5% SDS) and hybridized with denatured labeled cDNAs for 24 h at 68°C in hybridization solution. Filters were then washed in 0.1X SSC/0.2% SDS solution for 3 hours. Finally, membranes were rinsed in 2x SSC and air-dried before exposure.membranes were rinsed in 2x SSC and air-dried before exposure.


title: AMC V13 sample c

description: AMC V13 third instar larva sample c


title: AMC V13 sample b

description: AMC V13 third instar larva sample b


title: AMC V24 sample b

description: AMC V24 third instar larva sample b


title: AMC V24 sample c

description: AMC V24 third instar larva sample c


title: AMC V1 sample b

description: AMC V1 third instar larva sample b


title: Brain V14 sample b

description: Brain V14 third instar larva. Sample b

extract_protocol: Total RNA from third instar larvae (3 µg) were extracted from isolated AMC and CNS, according to Guenin et al. (Dev Biol 2007). RNA extractions from third instar larvae were carried out according to the TRIzolTM Reagent protocol (Invitrogen). Four independent extractions were performed for each sample condition. Third instar larvae were collected 30 min after metamorphosis and neural regions were dissected in RNA laterTM (Ambion). To remove traces of genomic DNA, the extracted RNA was digested with RQ1 RNase free DNase (Promega). RNA integrity was checked by denaturing formaldehyde agarose gel electrophoresis and the quantity was assessed by optical density (OD) 260/280 ratios.


title: Brain V13 sample b

description: Brain V13 third instar larva sample b


title: Brain V14 sample a

description: Brain V14 third instar larva. Sample a

value: Wild Type


title: A459 2-3D

status: Public on Jul 01 2010

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

institute: University Medical Center Hamburg-Eppendorf

description: Second RNA isolated from 3D cell culture

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Expression Console version 1.1 using RMA as normalization method.

label: Biotinylated Nucleotides

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 90 ng total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: RNA isolation of cells growing exponentially for 4 days in 2 dimensional cell culture or 3 dimensional cell culture (matrigel embedded cells)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Following cleanup according to Qiagen Rneasy Mini Kit Protocol.

value: lung carcinoma

tag: genotype

value: hypotriploid


title: UT-15 2-3D

value: squamous cell carcinoma

value: p53 deficient


title: RWV horizontal - biological replicate 1

status: Public on Jul 05 2010

city: Mol

first: Rob

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

country: Belgium

institute: SCK-CEN

description: gene expression data from bacteria cultured in horizontal RWV machine

hyb_protocol: Biotinylated cDNA was hybridized to GeneChip® P. aeruginosa Genome arrays (Affymetrix) by incubation in a GeneChip® hybridization oven 640 at 50 °C with orbital shaking at 60 r.p.m. for 16 h in the following MES-buffer [2-(N-morpholino) ethanesulfonic acid]: 0.1 µg/µl herring sperm DNA (Promega), 0.5 µg/µl bovine serum albumine (Invitrogen), 7.8% dimethyl sulfoxide (Sigma-Aldrich), 50 mM B2 control oligo (Affymetrix) in 1x hybridization buffer (made according to instructions of Affymetrix GeneChip®). Microarray slides were washed according to the manufacturer's protocol and stained using a fluidics station 450 (Affymetrix) and applying the Midi_euk2v3_450 protocol. Briefly, the staining procedure was comprised of the following steps: (i) binding of streptavidin (Invitrogen) to the biotin-labeled hybridized cDNA, (ii) binding of a biotin-conjugated streptavidin antibody (Labconsult) and (iii) binding of R-phycoerythrin-conjugated streptavidin (Invitrogen).

scan_protocol: Microarrays were scanned at the emission wavelength of 570 nm where after the data analysis took place.

data_processing: Raw Affymetrix data were pre-processed using the Affy package in BioConductor as follows: (i) background correction based on the robust multichip average (RMA) convolution model (Irizarry et al., 2003), (ii) quantile normalization to make expression values from different arrays more comparable (Bolstad et al., 2003), (iii) summarization of multiple probe intensities for each probe set to one expression value per gene using RMA (Irizarry et al., 2003). To test for differential expression between the different simulated microgravity (LSMMG and RG) conditions and the reference condition (NG) the Bayesian adjusted t-statistics was used as implemented in the LIMMA package (version 2.5.15) (Smyth, 2004). P-values were corrected for multiple testing using the Benjamini and Hochberg’s method to control the false discovery rate (Benjamini and Hochberg, 1995). Microarray analysis was performed on all three biological replicates.

organism: Pseudomonas aeruginosa PAO1

source_name: normal gravity

label_protocol: Fragmented cDNA was end-labelled with biotin-dUTP using the GeneChip® DNA labelling reagent (Affymetrix) and terminal deoxynucleotidyl transferase (Promega) in 1x reaction buffer  (Promega) at 37 °C for 60 min. The reaction was stopped using 0.5 M EDTA.

growth_protocol: The wild type P. aeruginosa PAO1 strain (ATCC 15692) was used in this study and all cultures were grown in Lennox L Broth Base (LB) (Life Technologies) at 28 °C. An overnight shaking culture (125 r.p.m.) of P. aeruginosa in LB was washed and diluted in 0.85% NaCl solution to an OD600 of 1. This bacterial suspension was used to inoculate fresh LB medium at a final concentration of 10-4 CFU/ml.

extract_protocol: After 24 hours of cultivation, the contents of every bioreactor was gently mixed by pipetting and divided into several aliquots. Ten millilitres of culture from each growth condition was immediately fixed with RNA Protect Reagent (Qiagen), following the manufacturer's instructions, and fixed cell pellets were frozen at -20 °C until RNA extraction. Samples were immediately exposed to different stresses. The extraction of total RNA was performed with the Total RNA Isolation System (Promega). RNA quality and quantity were assessed using the Agilent Bioanalyzer 2100 electrophoresis system and the Nanodrop ND-1000 spectrophotometer (NanoDrop technologies) respectively. cDNA synthesis and further processing for the transcriptomic analysis were performed according to the protocol of the GeneChip® manufacturer (Affymetrix). Ten micrograms of total RNA per sample was used for cDNA synthesis and a Poly-A RNA control was added to the RNA sample using the GeneChip eukaryotic poly-A control kit (Affymetrix). The synthesis of cDNA was performed using denatured total RNA (70 °C for 10 min), 13 ng/µl random hexamer primers (Roche), 0.5 U/µl SUPERase In (Ambion), 25 U/µl SuperScript II reverse transcriptase (Invitrogen), 0.5 nmol/µl deoxynucleoside triphosphates in 1x first strand buffer with 10 nmol/µl dithiothreitol. The latter mix was placed in a Thermocycler operated at 25 °C for 10 min, 37 °C for 60 min, 42 °C for 60 min and 70 °C for 10 min. The remaining RNA was degraded by treatment with 1 N NaOH, incubation for 30 min at 65 °C and subsequent neutralization with 1 N HCl. cDNA was purified using a MiniElute PCR purification kit (Qiagen), where after the concentration of cDNA was assessed using the Nanodrop ND-1000 spectrophotometer (NanoDrop technologies). Eight micrograms of cDNA was fragmented to a size range of 50-200 nucleotides with DNase I (Promega) for 10 min at 37 °C where after the enzyme was inactivated at 99 °C for 10 min. The fragmented cDNA was verified by loading a sample on a 2% agarose gel containing 0.1 %0  (v/v) GelRed (Biotium).

treatment_protocol: Synthecon Rotating Wall Vessel bioreactors (RWV) (50 ml or 10 ml) were filled with inoculated medium so that no headspace (i.e. no bubbles) was present. Other than for stress resistance assays, for which 10 ml capacity bioreactors were used, RWV bioreactors with a capacity of 50 ml were adopted for all experiments. Identical bioreactors were mounted in triplicate on (i) a RWV device in vertical position (LSMMG) (Cellon), (ii) a RWV device in horizontal position (NG) and (iii) the center of the inner Random Positioning Machine (RPM) frame (RG) (Fokker Space), and placed in a large humidified (70%-80% relative humidity) culture chamber, to avoid evaporation of culture medium through the gas-permeable membrane at the back of each vessel (Figure 1). A 25 r.p.m. rotation speed was adopted for the RWV cultures, while RPM-cultures were randomly rotated at 10 r.p.m. (60°/s). Bacteria were grown in the three described test conditions for 24 hours.

tag: strain

tag: culture

value: bacteria cultured in a RWV device in horizontal position (NG)


title: UT-15 2-2D

description: Second RNA isolated from conventional 2D cell culture


title: RPM - biological replicate 2

description: gene expression data from bacteria cultured in RPM machine

source_name: RPM

value: bacteria cultured in a RPM machine (RG)


title: RPM - biological replicate 3


title: A459 3-3D

description: Third RNA isolated from 3D cell culture


title: UT-15 3-2D

description: Third RNA isolated from conventional 2D cell culture


title: RWV horizontal - biological replicate 2


title: A459 3-2D


title: RPM - biological replicate 1


title: UT-15 3-3D

description: Third RNA isolated from 3D cell culture


title: RWV horizontal - biological replicate 3


title: UT-15 1-2D

description: First RNA isolated from conventional 2D cell culture


title: RWV vertical - biological replicate 1

description: gene expression data from bacteria cultured in vertical RWV machine

source_name: RWV

value: bacteria cultured in a RWV device in vertical position (LSMMG)


title: RWV vertical - biological replicate 2


title: A459 2-2D


title: A459 1-3D

description: First RNA isolated from 3D cell culture


title: UT-15 1-3D

description: First RNA isolated from 3D cell culture


title: ERK1/2 null EC, biological rep3

city: Columbus

first: Ruchika

last: Srinivasan

state: OH

address: Rm 840 W12th avenue

institute: The Ohio State University

description: Gene expression data from EC with ERK1/2 deletion

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hours at 44ºC on Mouse Exon 1.0 ST GeneChips.  GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: RMA method was applied to the primary data to correct the technical bias and summarize gene expression values over probe-sets

label: Biotin

source_name: Aortic EC isolated from mouse infected with lentivirus-egfp-Cre

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2007, Affymetrix).

growth_protocol: EC were isolated from mouse aorta

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

treatment_protocol: EC were grown in complete EC media (DMEM-F12+20% FBS+heparin+ECGS+PS) in a 37º incubator with 5% CO2.

value: C57/BL6 (5 generations)

tag: age

value: 4 Weeks

value: aortic endothelial cell

value: Erk1-/-; Erk2fl/fl + lentiviral-Cre


title: ERK1/2 wild type EC, biological rep3

description: Gene expression data from EC with wild type ERK1/2

source_name: Aortic EC isolated from mouse infected with lentivirus-egfp

value: Erk1-/-; Erk2fl/fl + lentiviral-GFP


title: ERK1/2 wild type EC, biological rep1


title: ERK1/2 wild type EC, biological rep2


title: ERK1/2 null EC, biological rep2


title: A459 1-2D


title: ERK1/2 null EC, biological rep1

value: Erk1-/-; Erk2fl/fl + lentiviral-egfp-Cre


title: iPS cell line of  Human Third Molars 101-cl.8

status: Public on Jun 26 2010

city: Amagasaki

first: Hajime

last: Ohgushi

state: Hyogo

address: 3-11-46 Nakouji

department: Research Institute for Cell Engineering

institute: National Institute of Advanced Industrial Science and Technology

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

scan_protocol: GeneChips were scanned using the GCS3000 GeneArray Scanner and AGCC was used for image processing

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

source_name: iPS cell line of  Human Third Molars

label_protocol: cDNA was subjected to in vitro transcription , according to the manufacturer’s protocol (One-Cycle Target Labeling and Control Reagent package).

extract_protocol: Total cellular RNA was isolated with the RNeasy Mini Kit (Qiagen), according to manufacture’s instructions.). Genomic DNA was eliminated by DNase I (TAKARA BIO INC.) treatments.

value: iPS

value: Human third molar


title: iPS cell line of  Human Third Molars 101-cl.5


title: Human Third Molars cell line 101

source_name: Human Third Molars cell line


title: tongue squamous cell carcinoma cell line from ATCC, SCC15

city: Vancouver

first: Ivy

last: Tsui

state: BC

address: 675 West 10th Avenue

department: Cancer Genetics and Developmental Biology

country: Canada

institute: BC Cancer Research Centre

hyb_protocol: Hybridization was performed according to Agilent protocol.

scan_protocol: Arrays were scanned using Axon GenePix 4000B and 4200A scanners. Arrays were scanned at 5um resolution. Array images are analyzed with GenePix Pro 6.1.

data_processing: Agilent feature extraction software was used and each array was median normalized.

source_name: ATCC cell line SCC-15

label_protocol: Agilent labeling kit

extract_protocol: Total RNA was extracted using the TRIzol (Invitrogen, Carlsbad, CA) protocol followed by DNase I treatment.

tag: atcc cell line


title: tongue squamous cell carcinoma cell line from ATCC, SCC15 (CGH)

hyb_protocol: Mix the two reactions (reference and sample) and add 100ul Cot-1 DNA (1ug/ul), and purified using a microcon YM-30 column. Resuspend the probe in 45 uL hybridization solution (36 uL DIGeasy+ 4.5 uL (20mg/mL) sheared Herring Sperm DNA + 4.5 uL (10mg/mL) yeast tRNA). Denature the samples at 85°C  for 5min, and incubate at 45°C for 1 hour to allow Cot-1 to anneal to DNA probe. Add 45uL of the probe solution onto the array slide. Gently lower coverslip (22x60mm, Fisher Scientific) onto slide over probe solution. Place the slide into a pre-warmed (45°C) hybridization cassette (Telechem) and add 10uL of H20 in the lower groove (to control humidity). Incubate for 36 - 40hrs at 45°C.  Wash the slide with  0.1X SSC + 0.1% SDS (pH 7.0, pre-warmed to 45°C) for 5 minutes in the dark with agitation, and with 0.1X SCC 5 times. Dry the slides by centrifuging at 500rcf for 1 minute.

scan_protocol: We are currently using the Axon GenePix 4000B scanner. Array images are analyzed with GenePix Pro 6.1.

data_processing: A three-step normalization procedure, including LOWESS fitting, spatial, and median normalization was used.

label_protocol: Random-primer labelling reaction  1. For each slide combine: (1 reaction tube for reference & 1 reaction tube for sample)  a) DNA (200ng)  b) 5uL of 5X (PB) random primers buffer (Final concentration: 5X Promega Klenow buffer and 7ug/ul random octomers)  c) Dilute to 16.5uL total volume with ddH2O    2. Boil for 10 min at 100°C in PCR machine. Transfer immediately to ice for 2 min  3. Add 4ul of 10X dNTP mix (2mM each dATP, dGTP, dTTP, 1.2mM dCTP) - Vortex very well  4. Add CyeDyes: Vortex and spin prior to adding  • Add 2uL (2nmoles) of Cy3 labelled dCTP to Reference DNA (Novagen Male Genomic)  • Add 2uL (2nmoles) of Cy5 labelled dCTP to sample DNA   5. Add 2.5uL of Klenow (9U/uL) and mix by pipetting   6. Incubate 37oC overnight (~18hours).

extract_protocol: Cells were harvested for DNA extraction when they reached ~ 80% confluency. Genomic DNA was extracted by the standard phenol-chloroform extraction protocol.

source_name: Normal male

tag: reference

value: Novagen pooled normal male genomic DNA


title: iPS cell line of  Human Third Molars 15-cl.39


title: iPS cell line of  Human Third Molars 15-cl.58


title: tongue squamous cell carcinoma cell line from ATCC, SCC25

source_name: ATCC cell line SCCS-25


title: Human Third Molars cell line 15


title: tongue squamous cell carcinoma cell line from ATCC, SCC25 (CGH)


title: tongue squamous cell carcinoma cell line from ATCC, Cal27

source_name: ATCC cell line Cal27


title: YYK014

status: Public on Jun 01 2010

type: other

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

hyb_protocol: Samples were hybridized onto Affymetrix Murine 430A 2.0 arrays using the FS450 Fluidics Work Station

scan_protocol: Arrays were scanned using the Gene Chip Scanner 3000 by the University of Minnesota Biomedical Genomics Center.

data_processing: Data was normalized using GCRMA in R

molecule: other

source_name: polysomal RNA obtained from WT mouse lung

label_protocol: 100 ng of sample RNA was labeled utilizing the Affymetrix Two-Cycle Target Labeling and Control Reagent Kit.

growth_protocol: Balb/c mice doubly knocked out for Eif4ebp1 and Eif4ebp2 were generously provided by Dr. Nahum Sonenberg.  Wild type Balb/c mice were purchased from Charles River Laboratories (Wilmington, MA).  At 5 weeks age, mice were started on AIN-93M purified diet (Research Diets, New Brunswick, NJ) until the end of the experiment.

extract_protocol: Mouse lungs were removed and processed for total and polyribosome bound RNA as described by Mullany 2007 modified for the lung (J Biol Chem, 282: 21244-21252, 2007).  Polyribosome microarray analysis was performed as previously described (Larsson, Cancer Res, 67: 6814-6824, 2007.). The polyribosome stratified RNA was fractionated and ten, 0.5 ml fractions were collected into tubes containing 50 l 10% SDS. RNA in the fractions was purified using Tri-reagent (Sigma) and fractions 7 to10 were combined into the “heavy” fraction (3 or more ribosomes per transcript).

tag: mouse genotype

value: WT

tag: replicate set

value: B


title: HDF

source_name: HDF

value: HDF


title: submaxillary salivary gland epidermoid carcinoma cell line from ATCC, A253 (CGH)

source_name: ATCC cell line A253


title: tongue squamous cell carcinoma cell line from ATCC, SCC9 (CGH)

source_name: ATCC cell line SCC-9


title: tongue squamous cell carcinoma cell line from ATCC, SCC9


title: YYK016

source_name: polysomal RNA obtained from 4ebp1-/-/4ebp2-/- mouse lung

value: A


title: YYK_07

source_name: Total RNA obtained from WT mouse lung


title: iPS cell line of HDF cl.1

source_name: iPS cell line of HDF


title: YYK018

value: C


title: YYK017


title: YYK015


title: submaxillary salivary gland epidermoid carcinoma cell line from ATCC, A253


title: YYK_05

source_name: Total RNA obtained from 4ebp1-/-/4ebp2-/- mouse lung


title: YYK_04


title: tongue squamous cell carcinoma cell line from ATCC, SCC4

source_name: ATCC cell line SCC-4


title: tongue squamous cell carcinoma cell line from ATCC, SCC4 (CGH)


title: YYK_9


title: Fibroblast_infected_rep7

status: Public on Mar 31 2010

city: Seoul

first: Nam-Hyuk

last: Cho

address: 28 Yongon-Dong, Chongno-Gu

department: Microbiology and Immunology

country: South Korea

institute: Seoul National Univ. College of Medicine

description: 27 to 40-mer oligonucleotide probes (1613 probes) were designed for 1472 CDSs of the O. tsutsugamushi genome (GeneBank accession no. AM494475). 1 to 6 probes per CDS were designed and some of the probes were duplicated on the microarray (total 2187 spots on an array). As negative controls, 5 and 15 oligonucleotide probes derived from plant and bacteriophage respectively were spotted on the array at 53 sites per array.

hyb_protocol: The customarray 4x2k microarray was prehybrizied with pre-hybridization solution (combimatrix) at 50'C for 16 hr and then hybridized with the prepared cDNAs or gDNAs at 50'C for 5hr.

scan_protocol: The hybrizided microarray were scanned with GenePix 4000B (Molecular Devices) with 5 um resolution.

data_processing: A local background subtraction method was used and the background-subtracted signal values were imported to Avadis Prophetic software (ver. 3.3, Strand Genomics) for data analysis. Global normalization of gene expression data was done using quantile normalization method embedded in Expander software (ver. 4.1, http://acgt.cs.tau.ac.il/expander/). Data from genomic DNA hybridizatioin were used directly without normalization to evaluate the specificity of microarray system.

organism:
Orientia tsutsugamushi
Mus musculus

source_name: L929 cell line infected with O. tsutsugamushi

label_protocol: cDNAs synthesized using Superscript II reverse transcriptase (Stratagene) and 2 ug of RNA were applied for one-color hybridization by labeling the hybridized cDNAs or chromosomal DNAs with Cy5 fluorescent dye.

growth_protocol: L929 cells or J774A.1 cells were infected with O. tsutsugamushi. At 2 days after infection, the cells were harvested and used for total RNA preparation.

extract_protocol: O. tsutsugamushi-infected L929 or J774A.1 cells were lysed with TRIzol (Invitrogen). Total RNA was prepared according to the manufacturer's instruction and treated with RNase-free DNase (Qiagen) for 30 min and stored at -20 ℃ until use.

treatment_protocol: 1 x 107 ICU of O. tsutsugamushi were used to infect L929 or J774A.1 cells cultured in 6-well plates.

tag: obligate intracellular bacterium

value: Orientia tsutsugamushi


title: Fibroblast_infected_rep6

tag: cell line


title: tongue squamous cell carcinoma cell line from ATCC, Cal27 (CGH)


title: YYK_8


title: Macrophage_infected_rep2

source_name: J774A.1 cell line infected with O. tsutsugamushi


title: Macrophage_infected_rep1


title: Fibroblast_infected_rep3


title: Fibroblast_infected_rep4


title: Fibroblast_infected_rep5


title: J774A.1 genomic DNA Hyb

description: 27 to 40-mer oligonucleotide probes (1613 probes) were designed for 1472 CDSs of the O. tsutsugamushi genome (GeneBank accession no. AM494475). 1 to 6 probes per CDS were designed and some of the probes were duplicated on the microarray (total 2187 spots on an array). As negative controls, 5 and 15 oligonucleotide probes derived from plant and bacteriophage respectively were spotted on the array at 53 sites per array. Genomic DNAs were fragmented by sonication before hybridiation.

source_name: Genomic DNA from J774A.1 cells


title: Fibroblast_infected_rep2


title: Fibroblast_uninfected_rep3

source_name: L929 cell line


title: Fibroblast_uninfected_rep2


title: Fibroblast_infected_rep1


title: YYK_6


title: L929 genomic DNA Hyb

source_name: Genomic DNA from L929 cells


title: O. tsutsugamushi genomic DNA Hyb

organism: Orientia tsutsugamushi

source_name: Genomic DNA from O. tsutsugamushi


title: Fibroblast_uninfected_rep1


title: Seminal vesicle, biological replicate 3

city: Rennes

first: Charles

last: PINEAU

address: Campus de Beaulieu (batiment 24)

description: Gene expression from adult Human seminal vesicle

hyb_protocol: Purified labeled cRNAs (20µg) were fragmented and hybridized (16 hours at 45°C) to HG-U133 Plus 2.0 GeneChip® arrays (Affymetrix).

scan_protocol: Microarrays were scanned with a GeneChip® scanner 3000 7G (Affymetrix). Raw image files (DAT) as well as feature-level data files (CEL) were finally generated using the Affymetrix GeneChip® Command Console (AGCC).

data_processing: Raw data were normalised using the RMA (Robust Multi-array Analysis; Irizari et al., 2003) in the AMEN (Annotation, Mapping, Expression, Network; Chalmel and Primig, 2008) suite of tools.

source_name: Normal seminal vesicle from adult man

label_protocol: 500ng of total RNA were used for the synthsis of biotynilated cRNA (GeneChip® 3’ IVT Express Kit User Manual).

extract_protocol: Total RNA was extracted using Trizol reagent according to the manufacturer instructions and was further cleaned up using a QIAGEN RNeasy Mini column.

value: Seminal vesicle

value: adult


title: blood_breast cancer, CBP4

status: Public on Jan 15 2010

city: Oslo

first: Jørgen

middle: Mømb

last: Aarøe

address: Montebello

department: Genetics

country: Norway

institute: The Norwegian Radium Hospital

description: Collected in pax tubes.

hyb_protocol: 10ug labeled and fragmented cRNA was hybridized onto single channel Applied Biosystems Human Genome Survey microarrays v2.0 for 16 hours at 55ºC according to the manufacturer’s protocol.

scan_protocol: After hybridization, slides were manually washed and prepared according to manufacturers’ recommendations before image capturing using the AB1700 reader. Identification and quantification of gene expression signals, signal-to-noise ratios and flagging of failed spots were conducted using the Applied Biosystems Expression System software. Raw data files were exported for further analysis.

data_processing:
Data analysis was performed using R  and tools from the Bioconductor project, adapted to our needs. Data were log2 transformed while individual measurements with signal-to-noise < 3 or flag values >8191 were set as missing. Probes with more than 5% missing values over all 156 arrays were excluded. Preprocessing left 156 samples and 11217 probes for further analyses. Data were standardized (i.e. centered and scaled) and missing values were imputed with k-nearest neighbors imputation using k = 10. Data were Batch-adjusted using the ANOVA-based batch adjustment function available in the pamr package for R. The 26 technical control samples (ControlReplicates) were then excluded. The signal intensities in biological replicates (blood_control_mens.cycle_reps) were averaged for each probe. Thus, 127 arrays, one from each individual remained for analysis. Finally, within-array normalization was conducted by global mean subtraction.

Raw data is available in the 'GSE16443_raw_data.txt' file, which is linked to the GSE16443 record. The Sample 'characteristics: assay name' value is used as the Sample identifier in the raw data file.  The 26 technical control samples in the raw data file were removed after preprocessing and hence are not represented as Sample records (which report only the processed data).

label: Digoxigenin

source_name: peripheral blood

label_protocol: For each sample, Digoxigenin-UTP labeled cRNA was generated from 500 ng total RNA according to the NanoAmp RT-IVT Labeling Kit Protocol.

extract_protocol: From each woman, 2.5 ml blood was collected in PAXgene tubes and left overnight at room temperature before storing at -80ºC until use. PAXgene tubes were thawed over night in batches of 12 tubes and total RNA was extracted according to the PAXgeneTM Blood RNA Kit Handbook Protocol and Appendix A (April 2001). Total RNA was stored at -80ºC until use. RNA quality and quantity measures were conducted using the 2100 Bioanalyzer (Agilent Technologies, California, USA) and the NanoDrop ND-1000 spectrophotometer (Thermo Scientific, Delaware, USA), respectively.

treatment_protocol: 121 blood samples were collected in PAXgeneTM tubes (PreAnalytiX, Hombrechtikon, Switzerland) from women called in for a second look after a first suspect mammogram. The PAXgene Blood RNA System is a technology that consolidates and integrates the key steps of whole blood collection, nucleic acid stabilization, and RNA purification. The samples were collected prior to a clinical examination that includes diagnostic mammography and biopsy in the case of a positive mammographic finding. In addition, nine control samples were collected from: three pregnant women, one breast-feeding woman and five samples from two healthy controls at different timepoints in their menstrual cycle.

tag: assay name

tag: status

value: Breast cancer

tag: subject age

tag: passed menopause

tag: gender

value: female

tag: estrogen receptor status

value: POS

tag: progesterone receptor status

tag: additional clinical information

value: IDC

tag: tumor grade


title: blood_breast cancer, 901

description: Collected in pax tubes.

value: YES


title: Seminal vesicle, biological replicate 4

tag: tissue


title: blood_breast cancer, 912

description: Collected in pax tubes.

value: NO

value: IDC/DCIS


title: blood_breast cancer, 914

description: Collected in pax tubes.

value: DCIS


title: blood_breast cancer, 878

description: Collected in pax tubes.


title: blood_breast cancer, 839

description: Collected in pax tubes.


title: blood_breast cancer, 898

description: Collected in pax tubes.


title: blood_breast cancer, 818

description: Collected in pax tubes.


title: blood_breast cancer, 896

description: Collected in pax tubes.


title: blood_breast cancer, 900

description: Collected in pax tubes.

value: ILC


title: blood_breast cancer, 829

description: Collected in pax tubes.


title: blood_breast cancer, 844

description: Collected in pax tubes.

value: NEG


title: Seminal vesicle, biological replicate 2

tag: age


title: Seminal vesicle, biological replicate 1


title: blood_breast cancer, 817

description: Collected in pax tubes.


title: blood_breast cancer, 832

description: Collected in pax tubes.