title: M61_Catheter_rep2_150711

tag: C. albicans strains SC5314 (Gillum et al., 1984), GDH2346 and M61 were used in this work.  Strain GDH2346 was from a patient with denture stomatitis and provided by Julia Douglas, University of Glasgow, UK.  Strain M61 was obtained from an intravascular line culture at the University Hospitals of Cleveland (Kuhn et al., 2002).  The strains were cultured according to methods reported in Chandra et al. (2001) and Kuhn et al. (2002).  Model biofilms of strains GDH2346 and SC5314 were grown on denture acrylic (Chandra et al., 2001) and model biofilms of strains M61 and SC5314 were formed on silicone elastomer catheter material (Kuhn et al., 2002) as described previously.  Samples were grown for 6, 12, and 48 hours.  Additionally, planktonics cultures of each strain were grown and collected for each surface and time combination.  Samples were flash-frozen in liquid nitrogen and stored at -80ºC until used.


title: M61_Catheter_rep2_150708

status: Public on Aug 01 2007

type: RNA

city: Urbana

first: Lois

last: Hoyer

state: IL

address: 2001 S Lincoln Ave

department: Pathobiology

country: USA

institute: University of Illinois

description:
To determine an appropriate normalization method for the data, MA-plots, as described in Dudoit et al. (2002), were used to initially analyze the fluorescence (R [cy5], G [cy3]) data.  These are plots of the intensity log-ratio M = log2R/G vs. the mean log intensity A =  log2(R/G).  A global normalization model of log2 transformed fluorescence data was used (Wolfinger et al., 2001).  The residuals from this model, which are regarded as a crude indicator of relative expression level and are referred to as ‘normalized expression levels’, were then subjected to individual gene-specific models.  The normalization and gene models were fit using the MIXED procedure of SAS (SAS Institute Inc, 2000).  SAS code for this analysis was based on code available in the Introductory Manual for Mixed Model Analysis of Microarray Data (MANMADA, 2002).
To assess the magnitude and significance of the effects of the strains, surface, time, and their interactions on the normalized expression level of each gene, least square means using the LSMEANS option of SAS (SAS Institute Inc, 2000) were calculated as described in the MANMADA (2002).  The LSMEANS statement calculates the mean value for each target category, adjusted for the other terms in the model.  For each pairwise comparison, the difference between the two normalized expression levels and their standard errors are calculated along with the results of t-tests for the statistical significance of the difference between the means in each pair (Littell et al., 1996).  The resulting p-values are Bonferroni adjusted using the ‘bon’ option with LSMEANS of SAS (SAS Institute, Inc.)

hyb_protocol: The samples of cDNA coupled with fluorescent dyes were resuspended in a solution containing 50% formamide, 10X SSC, and 0.2% sodium dodecyl sulfate. The appropriate Cy3-cDNA and Cy5-cDNA samples were then mixed and heated for 2 min at 100°C before the samples were applied to the microarray slide. Samples were hybridized for 20 h at 42°C, and the slides washed, dried, and then analyzed as described below.

scan_protocol: Arrays were scanned on a GenePix 4000B scanner (Axon Instruments, Foster City, Calif.), and data were quantified by using GenePix Pro version 4.0.

data_processing: VALUE as presented here is the log of the ratio of medians and was calculated in the GenePix Pro version 4.0. Further description of data processing is detailed in the Description section above.

molecule: total RNA

organism: Candida albicans

source_name: Strain_M61 Surface_Catheter 48 hour Biofilm

label_protocol: The methods for labeling probes and hybridization to microarrays were adapted from protocols developed by The Institute for Genomic Research (TIGR, http://pga.tigr.org/protocols.html).  cDNA was synthesized using Superscript II RT (Invitrogen Life Technologies; 100 units of reverse transcriptase) in reaction mixtures containing 0.5 mM (total) deoxynucleoside triphosphates (aminoallyl-dUTP and deoxynucleoside triphosphates [4:1]).  After cDNA synthesis overnight at 42°C, the RNA was hydrolyzed with 1 N NaOH and 0.5 M EDTA. The reaction was neutralized with 1 N HCl.  The cDNA was purified using the Qiagen QIAquick PCR purification kit and modified protocol (TIGR).  The cDNA was recovered and dried in a Speed-Vac (ThermoLabs). The cDNA was coupled with fluorescent dyes by resuspension in 0.05 M sodium bicarbonate buffer, pH 9.0, and incubation with either Cy3 or Cy5 dye (Amersham Biosciences) for 1 h at room temperature in the dark. Unincorporated dye was removed using a Qiagen QIAquick PCR purification kit, and the samples were dried in a Speed-Vac.

extract_protocol: Total RNA was obtained from cells using a hot phenol extraction method (Collart and Oliviero, 1993).  Total RNA was further purified using RNeasy kit (Qiagen) according to the manufacturer’s suggested protocol (Mackenzie et al., 1997).

tag: C. albicans strains SC5314 (Gillum et al., 1984), GDH2346 and M61 were used in this work.  Strain GDH2346 was from a patient with denture stomatitis and provided by Julia Douglas, University of Glasgow, UK.  Strain M61 was obtained from an intravascular line culture at the University Hospitals of Cleveland (Kuhn et al., 2002).  The strains were cultured according to methods reported in Chandra et al. (2001) and Kuhn et al. (2002).  Model biofilms of strains GDH2346 and SC5314 were grown on denture acrylic (Chandra et al., 2001) and model biofilms of strains M61 and SC5314 were formed on silicone elastomer catheter material (Kuhn et al., 2002) as described previously.  Samples were grown for 6, 12, and 48 hours.  Additionally, planktonic cultures of each strain were grown and collected for each surface and time combination.  Samples were flash-frozen in liquid nitrogen and stored at -80ºC until used.

source_name: Strain_M61 Surface_Catheter 12 hour Planktonic


title: M61_Catheter_rep2_150717

source_name: Strain_M61 Surface_Catheter 12 hour Biofilm


title: Sample # 1109-1

city: Aarhus N

first: Lars

last: Dyrskjot

address: Brendstrupgaardsvej

department: Department of Molecular Medicine

country: Denmark

institute: Aarhus University Hospital, Skejby

description: Standard affymetrix protocol

data_processing: RMA normalized

label: Streptavidin-phycoerythrin

organism: Homo sapiens

source_name: Bladder tumor biopsy

tag: T2-4 bladder tumor

tag: Survival (months)


title: M61_Catheter_rep2_150712

source_name: Strain_M61 Surface_Catheter 6 hour Planktonic

source_name: Strain_M61 Surface_Catheter 6 hour Biofilm


title: Sample # 1055-1

description: Standard affymetrix protocol


title: M61_Catheter_rep2_150713


title: Sample # 1044-1

description: Standard affymetrix protocol


title: M61_Catheter_rep1_150577

source_name: Strain_M61 Surface_Catheter 48 hour Planktonic


title: Sample # 1041-1

description: Standard affymetrix protocol


title: Sample # 1015-1

description: Standard affymetrix protocol


title: Sample # 1037-1

description: Standard affymetrix protocol


title: M61_Catheter_rep1_150571


title: M61_Catheter_rep1_150574


title: 752-1

description: Standard affymetrix protocol


title: 981-1

description: Standard affymetrix protocol


title: M61_Catheter_rep1_150569


title: 882-1

description: Standard affymetrix protocol


title: M61_Catheter_rep1_150572


title: M61_Catheter_rep1_150573


title: 575-1

description: Standard affymetrix protocol


title: M61_Catheter_rep1_150579


title: 805-1

description: Standard affymetrix protocol


title: M61_Catheter_rep1_150568


title: 724-1

description: Standard affymetrix protocol


title: 748-1

description: Standard affymetrix protocol


title: 217-16

description: Standard affymetrix protocol


title: 523-1

description: Standard affymetrix protocol


title: M61_Catheter_rep1_150576


title: 621-5

description: Standard affymetrix protocol


title: GDH2346_Denture_rep2_150684

source_name: Strain_GDH2346 Surface_Denture 48 hour Planktonic

source_name: Strain_GDH2346 Surface_Denture 48 hour Biofilm


title: GDH2346_Denture_rep2_150683

source_name: Strain_GDH2346 Surface_Denture 48 hour biofilm


title: M61_Catheter_rep1_150575


title: GDH2346_Denture_rep2_150685

source_name: Strain_GDH2346 Surface_Denture 6 hour Biofilm


title: M61_Catheter_rep1_150578


title: GDH2346_Denture_rep2_150686

source_name: Strain_GDH2346 Surface_Denture 6 hour biofilm


title: GDH2346_Denture_rep2_150689

source_name: Strain_GDH2346 Surface_Denture 12 hour biofilm

source_name: Strain_GDH2346 Surface_Denture 12 hour Planktonic


title: GDH2346_Denture_rep2_150690

source_name: Strain_GDH2346 Surface_Denture 12 hour planktonic

source_name: Strain_GDH2346 Surface_Denture 12 hour Biofilm


title: GDH2346_Denture_rep2_150693


title: GDH2346_Denture_rep2_150694


title: 472-1

description: Standard affymetrix protocol


title: M61_Catheter_rep1_150570


title: GDH2346_Denture_rep2_150687

source_name: Strain_GDH2346 Surface_Denture 6 hour planktonic


title: GDH2346_Denture_rep2_150691

source_name: Strain_GDH2346 Surface_Denture 6 hour Planktonic


title: GDH2346_Denture_rep2_150688


title: GDH2346_Denture_rep1_150588


title: GDH2346_Denture_rep2_150692


title: GDH2346_Denture_rep1_150586


title: GDH2346_Denture_rep1_150591


title: GDH2346_Denture_rep1_150587


title: GDH2346_Denture_rep1_150592


title: SC5314_Catheter_rep2_150696

source_name: Strain_SC5314 Surface_Catheter 48 hour Planktonic

label_protocol: The methods for labeling probes and hybridization to microarrays were adapted from protocols developed by The Institute for Genomic Research (TIGR, http://pga.tigr.org/protocols.html).  cDNA was synthesized using Superscript II RT (Invitrogen Life Technologies; 100 units of reverse transcriptase) in reaction mixtures containing 0.5 mM (total) deoxynucleoside triphosphates (aminoallyl-dUTP and deoxynucleoside triphosphates [4:1]).  After cDNA synthesis overnight at 42°C, the RNA was hydrolyzed with 1 N NaOH and 0.5 M EDTA. The reaction was neutralized with 1 N HCl.  The cDNA was purified using the Qiagen QIAquick PCR purification kit and modified protocol (TIGR).  The cDNA was recovered and dried in a Speed-Vac (ThermoLabs).  The cDNA was coupled with fluorescent dyes by resuspension in 0.05 M sodium bicarbonate buffer, pH 9.0, and incubation with either Cy3 or Cy5 dye (Amersham Biosciences) for 1 h at room temperature in the dark. Unincorporated dye was removed using a Qiagen QIAquick PCR purification kit, and the samples were dried in a Speed-Vac.

source_name: Strain_SC5314 Surface_Catheter 48 hour Biofilm


title: SC5314_Catheter_rep2_150697

source_name: Strain_SC5314 Surface_Catheter 6 hour Biofilm


title: GDH2346_Denture_rep1_150590


title: SC5314_Catheter_rep2_150695

source_name: Strain_SC5314 Surface_Catheter 48 hour biofilm


title: GDH2346_Denture_rep1_150589


title: GDH2346_Denture_rep1_150593


title: SC5314_Catheter_rep1_150667

source_name: Strain_SC5314 Surface_Catheter 6 hour biofilm


title: SC5314_Catheter_rep2_150703

source_name: Strain_SC5314 Surface_Catheter 6 hour Planktonic


title: SC5314_Catheter_rep2_150705

source_name: Strain_SC5314 Surface_Catheter 12 hour Planktonic


title: SC5314_Catheter_rep2_150701

source_name: Strain_SC5314 Surface_Catheter 12 hour biofilm


title: GDH2346_Denture_rep1_150595

source_name: Strain_GDH2346 Surface_Denture 48 hour biofilm


title: SC5314_Catheter_rep2_150706


title: SC5314_Catheter_rep1_150666


title: SC5314_Catheter_rep2_150698


title: SC5314_Catheter_rep1_150625


title: GDH2346_Denture_rep1_150594

source_name: Strain_GDH2346 Surface_Denture 48 hour Biofilm


title: SC5314_Catheter_rep1_150664


title: GDH2346_Denture_rep1_150596

source_name: Strain_GDH2346 Surface_Denture 6 hour biofilm


title: GDH2346_Denture_rep1_150597

source_name: Strain_GDH2346 Surface_Denture 6 hour Biofilm


title: SC5314_Catheter_rep2_150702

source_name: Strain_SC5314 Surface_Catheter 12 hour Biofilm


title: SC5314_Catheter_rep2_150704

source_name: Strain_SC5314 Surface_Catheter 6 hour planktonic


title: SC5314_Catheter_rep1_150665


title: SC5314_Catheter_rep2_150700


title: SC5314_Catheter_rep2_150699


title: SC5314_Catheter_rep1_150624


title: SC5314_Catheter_rep1_150622


title: SC5314_Catheter_rep1_150614


title: SC5314_Catheter_rep1_150623


title: SC5314_Catheter_rep1_150612


title: SC5314_Denture_rep2_150745

hyb_protocol: The cDNA was coupled with fluorescent dyes by resuspension in 0.05 M sodium bicarbonate buffer, pH 9.0, and incubation with either Cy3 or Cy5 dye (Amersham Biosciences) for 1 h at room temperature in the dark. Unincorporated dye was removed using a Qiagen QIAquick PCR purification kit, and the samples were dried in a Speed-Vac. The samples of cDNA coupled with fluorescent dyes were resuspended in a solution containing 50% formamide, 10X SSC, and 0.2% sodium dodecyl sulfate. The appropriate Cy3-cDNA and Cy5-cDNA samples were then mixed and heated for 2 min at 100°C before the samples were applied to the microarray slide. Samples were hybridized for 20 h at 42°C, and the slides washed, dried, and then analyzed as described below.

source_name: Strain_SC5314 Surface_Denture 6 hour biofilm

label_protocol: The methods for labeling probes and hybridization to microarrays were adapted from protocols developed by The Institute for Genomic Research (TIGR, http://pga.tigr.org/protocols.html).  cDNA was synthesized using Superscript II RT (Invitrogen Life Technologies; 100 units of reverse transcriptase) in reaction mixtures containing 0.5 mM (total) deoxynucleoside triphosphates (aminoallyl-dUTP and deoxynucleoside triphosphates [4:1]).  After cDNA synthesis overnight at 42°C, the RNA was hydrolyzed with 1 N NaOH and 0.5 M EDTA. The reaction was neutralized with 1 N HCl.  The cDNA was purified using the Qiagen QIAquick PCR purification kit and modified protocol (TIGR).  The cDNA was recovered and dried in a Speed-Vac (ThermoLabs).

source_name: Strain_SC5314 Surface_Denture 48 hour Planktonic


title: SC5314_Denture_rep2_150750

source_name: Strain_SC5314 Surface_Denture 6 hour planktonic

source_name: Strain_SC5314 Surface_Denture 12 hour Biofilm


title: SC5314_Denture_rep2_150744

source_name: Strain_SC5314 Surface_Denture 6 hour Biofilm


title: SC5314_Denture_rep1_150563

source_name: Strain_SC5314 Surface_Denture 48 hour Biofilm


title: SC5314_Denture_rep2_150742

source_name: Strain_SC5314 Surface_Denture 12 hour Planktonic


title: SC5314_Catheter_rep1_150615


title: SC5314_Denture_rep2_150747


title: SC5314_Catheter_rep1_150613

source_name: Strain_SC5314 Surface_Catheter 6 hour Biofilm


title: SC5314_Denture_rep2_150751

source_name: Strain_SC5314 Surface_Denture 12 hour biofilm

source_name: Strain_SC5314 Surface_Denture 6 hour Planktonic


title: SC5314_Denture_rep2_150741


title: SC5314_Denture_rep2_150749


title: SC5314_Denture_rep2_150748

source_name: Strain_SC5314 Surface_Denture 48 hour biofilm


title: SC5314_Denture_rep1_150565


title: SC5314_Denture_rep2_150746


title: SC5314_Denture_rep2_150740


title: SC5314_Denture_rep1_150564


title: SC5314_Denture_rep1_150562


title: SC5314_Denture_rep1_150556


title: SC5314_Denture_rep1_150561


title: SC5314_Denture_rep2_150743


title: SC5314_Denture_rep1_150559


title: SC5314_Denture_rep1_150566(2)


title: SC5314_Denture_rep1_150557


title: SC5314_Denture_rep1_150558


title: SC5314_Denture_rep1_150560


title: SC5314_Denture_rep1_150567

data_processing: VALUE as presented here is the log of the ratio of medians and was calculated in the GenePix Pro version 4.0.  Further description of data processing is detailed in the Description section above.


title: M6

status: Public on Jul 31 2007

type: genomic

city: Heidelberg

first: Stefan

middle: M

last: Pfister

address: INF 580

department: Molecular Genetics

country: Germany

institute: German Cancer Research Center

description: array-PAMS

data_processing: genepix 6.0

molecule: genomic DNA

tag: M6 methylation-sensitive restriction

tag: M6 methylation-specific restriction


title: M20

description: array-PAMS

tag: M20 methylation-sensitive restriction

tag: M20 methylation-specific restriction


title: Genomic copy number changes in tumor cells T1 from a xenograft

city: Baltimore

first: Jonathan

last: Pevsner

state: MD

address: 707 N. Broadway

department: Neurology

institute: Kennedy Krieger Institute

description: All procedures were carried out in the Johns Hopkins Cancer Center microarray core facility (http://www.hopkinskimmelcancercenter.org/kpr/spcore-microarray.cfm).

hyb_protocol: Hybridization mixtures were denatured, centrifuged, and added to hybridization chambers for 40 hourse at 65oC in a rotating oven.

scan_protocol: Arrays were scanned with an Agilent G2565BA scanner with default settings.

data_processing: Log ratio and other values were obtained from the scanner software.

label_protocol: Samples were labeled suing a BioPrime Array CGH Genomic Labeling Module (Invitrogen).

extract_protocol: Genomic DNA was isolated with a commercial kit, and concentration and quality were assessed using a NanoDrop spectrophotometer.

tag: P493 cells with a luciferase construct (control cells)

tag: Tumor cells cultured from a mouse xenograft


title: M11a

description: array-PAMS

tag: M11a methylation-sensitive restriction

tag: M11a methylation-specific restriction


title: M9

description: array-PAMS

tag: M9 methylation-sensitive restriction

tag: M9 methylation-specific restriction


title: Cb

description: array-PAMS

source_name: Cb (pool of 5 donors)

tag: Cb methylation-sensitive restriction

tag: Cb methylation-specific restriction


title: M4

description: array-PAMS

tag: M4 methylation-sensitive restriction

tag: M4 methylation-specific restriction


title: M14

description: array-PAMS

tag: M14 methylation-sensitive restriction

tag: M14 methylation-specific restriction


title: M1

description: array-PAMS

tag: M1 methylation-sensitive restriction

tag: M1 methylation-specific restriction


title: KELH0070_HC10_29Fna

city: Toronto

first: Mark

middle: J

last: Cameron

state: Ontario

address: 3-913 TMDT, MaRS Centre, 101 College St.

country: Canada

institute: UHN

description: Peripheral blood was collected longitudinally from SARS patients during hospitalization into heparinized tubes and processed for further analysis within 2-3 hours of collection.  RNA was stabilized and purified using Paxgene Blood Collection Tubes and Paxgene RNA kits (Qiagen, Mississauga, ON, Canada).

hyb_protocol: similar to direct labelling protocol listed at UHN Microarray facility web site.

scan_protocol: Scanned at 16 bits using the Genepix Axon Scanner at 10micro-meter resolution at 635 nm (Cy5) and 532 nm (Cy3) using Genepix Pro 6.0 analysis software (Molecular Devices Corporation)

data_processing: Each quantified output file was run though the following pre-processing steps using R (URL: www.r-project.org)and the Limma package. For Minimum Intensity filtering, R and G values were treated with a surrogate replacement policy for estimating sub-threshold values. The raw merged R and G channels were lowess-normalized (grouped by print-tip), normalized between chips using quantile normalization and transformed to log2 ratios (70).

source_name: Universal RNA

label_protocol: Universal RNA probes was prepared by direct labeling of universal aRNA with Cy-3 fluorescent dye

extract_protocol: Universal human reference RNA was purchased from Stratagene and was amplified using MessageAMP aRNA kits (Ambion) as per manufacturer's instructions prior to labeling

tag: Tissue:Universal RNA

source_name: PBMC

label_protocol: Sample probes were prepared by direct labeling with Cy-5 fluorescent dye

extract_protocol: Total RNA was isolated using Paxgene blood collection tubes then amplified using the MessageAmp aRNA kit (Ambion) as per the manufacturer's instructions.

tag: Tissue:Blood, Patient id:HC10, Age:29, Sex:F, DSO:na, Status:healthy control


title: Genomic copy number changes in tumor cells T3 from a xenograft

tag: Independent set of tumor cells cultured from a mouse xenograft


title: M16

description: array-PAMS

tag: M16 methylation-sensitive restriction

tag: M16 methylation-specific restriction


title: M11b

description: array-PAMS

tag: M11b methylation-sensitive restriction

tag: M11b methylation-specific restriction


title: Genomic copy number changes in two parental P493 cell lines

tag: P493 cells with a luciferase construct (control cells)

tag: P493 cells (parental line, i.e. control cells)


title: M13

description: array-PAMS

tag: M13 methylation-sensitive restriction

tag: M13 methylation-specific restriction


title: M18

description: array-PAMS

tag: M18 methylation-sensitive restriction

tag: M18 methylation-specific restriction


title: M19

description: array-PAMS

tag: M19 methylation-sensitive restriction

tag: M19 methylation-specific restriction


title: KELH0068_HC8_23Mna

tag: Tissue:Blood, Patient id:HC8, Age:23, Sex:M, DSO:na, Status:healthy control


title: M7

description: array-PAMS

tag: M7 methylation-sensitive restriction

tag: M7 methylation-specific restriction


title: M3

description: array-PAMS

tag: M3 methylation-sensitive restriction

tag: M3 methylation-specific restriction


title: M10

description: array-PAMS

tag: M10 methylation-sensitive restriction

tag: M10 methylation-specific restriction


title: KELH0069_HC9_26Fna

tag: Tissue:Universal RNA

tag: Tissue:Blood, Patient id:HC9, Age:26, Sex:F, DSO:na, Status:healthy control


title: KELH0067_HC7_28Mna

tag: Tissue:Blood, Patient id:HC7, Age:28, Sex:M, DSO:na, Status:healthy control


title: M15

description: array-PAMS

tag: M15 methylation-sensitive restriction

tag: M15 methylation-specific restriction


title: M12

description: array-PAMS

tag: M12 methylation-sensitive restriction

tag: M12 methylation-specific restriction


title: KELH0066_HC6_20Mna

tag: Tissue:Blood, Patient id:HC6, Age:20, Sex:M, DSO:na, Status:healthy control


title: M2

description: array-PAMS

tag: M2 methylation-sensitive restriction

tag: M2 methylation-specific restriction


title: M5

description: array-PAMS

tag: M5 methylation-sensitive restriction

tag: M5 methylation-specific restriction


title: M21

description: array-PAMS

tag: M21 methylation-sensitive restriction

tag: M21 methylation-specific restriction


title: M17

description: array-PAMS

tag: M17 methylation-sensitive restriction

tag: M17 methylation-specific restriction


title: KELH0002_P-2_53F7

tag: Tissue:Blood, Patient id:P-2, Age:53, Sex:F, DSO:7, Status:pre-pO2 nadir


title: KELH0065_HC5_29Fna

tag: Tissue:Universal RNA

tag: Tissue:Blood, Patient id:HC5, Age:29, Sex:F, DSO:na, Status:healthy control


title: KELH0027_P-22_17M9

tag: Tissue:Blood, Patient id:P-22, Age:17, Sex:M, DSO:9, Status:post-pO2 nadir


title: KELH0008_P-8_51F1

tag: Tissue:Blood, Patient id:P-8, Age:51, Sex:F, DSO:1, Status:pre-pO2 nadir


title: KELH0061_HC1_32Mna

tag: Tissue:Blood, Patient id:HC1, Age:32, Sex:M, DSO:na, Status:healthy control


title: KELH0054_P-40_53F0

tag: Tissue:Blood, Patient id:P-40, Age:53, Sex:F, DSO:0, Status:pre-pO2 nadir


title: KELH0004_P-4_33F7

tag: Tissue:Blood, Patient id:P-4, Age:33, Sex:F, DSO:7, Status:post-pO2 nadir


title: KELH0009_P-9_31F27

tag: Tissue:Blood, Patient id:P-9, Age:31, Sex:F, DSO:27, Status:convalescent


title: KELH0020_P-19_48F20

tag: Tissue:Blood, Patient id:P-19, Age:48, Sex:F, DSO:20, Status:post-pO2 nadir


title: KELH0039_P-30_83F11

tag: Tissue:Blood, Patient id:P-30, Age:83, Sex:F, DSO:11, Status:pre-pO2 nadir


title: KELH0030_P-24_81F10

tag: Tissue:Blood, Patient id:P-24, Age:81, Sex:F, DSO:10, Status:post-pO2 nadir


title: KELH0017_P-17_45F0

tag: Tissue:Blood, Patient id:P-17, Age:45, Sex:F, DSO:0, Status:pre-pO2 nadir


title: KELH0028_P-23_52M5

tag: Tissue:Blood, Patient id:P-23, Age:52, Sex:M, DSO:5, Status:pre-pO2 nadir


title: KELH0044_P-33_52F30

tag: Tissue:Blood, Patient id:P-33, Age:52, Sex:F, DSO:30, Status:post-pO2 nadir


title: KELH0031_P-24_81F22

tag: Tissue:Blood, Patient id:P-24, Age:81, Sex:F, DSO:22, Status:post-pO2 nadir


title: KELH0011_P-11_26M12

tag: Tissue:Blood, Patient id:P-11, Age:26, Sex:M, DSO:12, Status:post-pO2 nadir


title: A4 Cy3 to C1 Cy5

city: columbia

first: lakshmi

middle: praveena

last: yarru

state: MO

address: 920 east campus dr

department: Division of Animal science

institute: University of Missouri

description: Aflatoxin is a toxic secondary metabolite produced by the fungi Aspergillus flavus and A. parasiticus. Ingredients of livestock and poultry feed are often contaminated with aflatoxin.  Aflatoxin affects many species including humans, dogs, cats, pigs, cattle, and poultry, with liver being the major organ affected. A chicken model was used to evaluate the effect of aflatoxin on hepatic gene expression. Seventy five day-old male broiler chicks were assigned to three dietary treatments (5 replicates of 5 chicks each) from hatch to day 21. The diets contained 0, 1 and 2 mg/kg aflatoxin/kg of feed. Feed intake, body weight gain, liver weights and serum chemistry were evaluated at the end of the study and liver samples were collected in RNase free tubes and stored at -80 ºC. Aflatoxin reduced (P ≤ 0.05) feed intake, body weight, serum total proteins, serum calcium and phosphorus but increased (P < 0.01) liver weights in a dose dependent manner. Microarray experiments were conducted using chicken long oligo arrays, to identify the changes in hepatic gene expression in chicks fed 0 (control) and 2mg/kg aflatoxin/kg of feed. A loop design was followed for microarray experiments with three technical and four biological replicates per treatment group. RNA was extracted from liver tissue and its quality was determined using gel electrophoresis. High quality RNA was purified from DNA contamination, reverse transcribed to cDNA and was used for microarray hybridizations. Microarray data was analyzed using a 2-step ANOVA model using GenePix and MAANOVA softwares, and the differentially expressed genes were identified using SAM, TIGR, and Cluster softwares. The microarray data was validated using real time PCR. The genes associated with antioxidant, detoxification and immune systems were down regulated and the genes involved in cell proliferation were up regulated in birds fed aflatoxin compared to controls

hyb_protocol: CUSTOM PROTOCOL

scan_protocol: GENEPIX 6.0

data_processing: JMAANOVA program; intensity based LOWESS normalization are performed

organism: Gallus gallus

source_name: Aflatoxin treated; C1

label_protocol: AMERSHAM DYE KIT PROTOCOL

extract_protocol: QIAGEN KIT PROTOCOL

tag: CHICKEN LIVER AFLATOXIN TREATMENT @2 PPM IN THE DIET

source_name: control; A4

tag: CHICKEN LIVER CONTROL TREATMENT @ 0 PPM OF AFLATOXIN IN THE DIET


title: KELH0064_HC4_24Fna

tag: Tissue:Universal RNA

tag: Tissue:Blood, Patient id:HC4, Age:24, Sex:F, DSO:na, Status:healthy control


title: C1 Cy3 to A2 Cy5

description: Aflatoxin is a toxic secondary metabolite produced by the fungi Aspergillus flavus and A. parasiticus. Ingredients of livestock and poultry feed are often contaminated with aflatoxin.  Aflatoxin affects many species including humans, dogs, cats, pigs, cattle, and poultry, with liver being the major organ affected. A chicken model was used to evaluate the effect of aflatoxin on hepatic gene expression. Seventy five day-old male broiler chicks were assigned to three dietary treatments (5 replicates of 5 chicks each) from hatch to day 21. The diets contained 0, 1 and 2 mg/kg aflatoxin/kg of feed. Feed intake, body weight gain, liver weights and serum chemistry were evaluated at the end of the study and liver samples were collected in RNase free tubes and stored at -80 ºC. Aflatoxin reduced (P ≤ 0.05) feed intake, body weight, serum total proteins, serum calcium and phosphorus but increased (P < 0.01) liver weights in a dose dependent manner. Microarray experiments were conducted using chicken long oligo arrays, to identify the changes in hepatic gene expression in chicks fed 0 (control) and 2mg/kg aflatoxin/kg of feed. A loop design was followed for microarray experiments with three technical and four biological replicates per treatment group. RNA was extracted from liver tissue and its quality was determined using gel electrophoresis. High quality RNA was purified from DNA contamination, reverse transcribed to cDNA and was used for microarray hybridizations. Microarray data was analyzed using a 2-step ANOVA model using GenePix and MAANOVA softwares, and the differentially expressed genes wereidentified using SAM, TIGR, and Cluster softwares. The microarray data was validated using real time PCR. The genes associated with antioxidant, detoxification and immune systems were doenregulated and genes involved in cell proliferation were up-regulated in birds fed aflatoxin compared to controls

source_name: control; A2

label_protocol: AMERSHAM KIT PROTOCOL

tag: MALE CHICKEN LIVER CONTROL TREATMENT WITH 0 PPM OF AFLATOXIN IN THE DIET

label_protocol: AMERSHAM DYES KIT PROTOCOL

tag: MALE CHICKEN LIVER AFLATOXIN TREATMENT @ 2PPM OF AFLATOXIN IN THE DIET


title: KELH0060_P-50_31M10

tag: Tissue:Blood, Patient id:P-50, Age:31, Sex:M, DSO:10, Status:post-pO2 nadir


title: KELH0045_P-33_52F40

tag: Tissue:Blood, Patient id:P-33, Age:52, Sex:F, DSO:40, Status:post-pO2 nadir


title: A4 Cy3 to C4 Cy5

source_name: Aflatoxin treated; C4

tag: MALE CHICKEN LIVER AFLATOXIN TREATMENT IN DIET @ 2PPM


title: A3 Cy3 to C4 Cy5

tag: CHICKEN LIVER AFLATOXIN TREATED @ 2PPM IN THE DIET

source_name: control; A3


title: KELH0010_P-11_26M0

tag: Tissue:Blood, Patient id:P-11, Age:26, Sex:M, DSO:0, Status:post-pO2 nadir


title: A2 Cy3 to C3 Cy5

source_name: Aflatoxin treated; C3

tag: CHICKEN LIVER AFLATOXIN TREATMENT WITH DIET 2 PPM OF AFLATOXIN

tag: CHICKEN LIVER CONTROL TREATMENT WITH DIET 0 PPM OF AFLATOXIN


title: KELH0051_P-36_63F1

tag: Tissue:Blood, Patient id:P-36, Age:63, Sex:F, DSO:1, Status:pre-pO2 nadir


title: KELH0048_P-34_63M32

tag: Tissue:Blood, Patient id:P-34, Age:63, Sex:M, DSO:32, Status:post-pO2 nadir


title: KELH0033_P-25_46F18

tag: Tissue:Blood, Patient id:P-25, Age:46, Sex:F, DSO:18, Status:post-pO2 nadir


title: A2 Cy3 to C2 Cy5

source_name: Aflatoxin treated; C2

tag: CHICKEN LIVER AFLATOXIN TREATMENT DIET 2 PPM

tag: CHICKEN LIVER TREATMENT CONTROL DIET WITH 0PPM OF AFLATOXIN


title: KELH0019_P-19_48F12

tag: Tissue:Blood, Patient id:P-19, Age:48, Sex:F, DSO:12, Status:post-pO2 nadir


title: A3 Cy3 to C3 Cy5

tag: CHICKEN LIVER AFLATOXIN TREATMENT IN DIET WITH 2 PPM CONCENTRATION

tag: CHICKEN LIVER CONTROL TREATMENT IN DIET WITH 0 PPM OF AFLATOXIN


title: KELH0042_P-33_52F15

tag: Tissue:Universal RNA

tag: Tissue:Blood, Patient id:P-33, Age:52, Sex:F, DSO:15, Status:post-pO2 nadir


title: A1 Cy3 to C1 Cy5

description: Aflatoxin is a toxic secondary metabolite produced by the fungi Aspergillus flavus and A. parasiticus. Ingredients of livestock and poultry feed are often contaminated with aflatoxin.  Aflatoxin affects many species including humans, dogs, cats, pigs, cattle, and poultry, with liver being the major organ affected. A chicken model was used to evaluate the effect of aflatoxin on hepatic gene expression. Seventy five day-old male broiler chicks were assigned to three dietary treatments (5 replicates of 5 chicks each) from hatch to day 21. The diets contained 0, 1 and 2 mg/kg aflatoxin/kg of feed. Feed intake, body weight gain, liver weights and serum chemistry were evaluated at the end of the study and liver samples were collected in RNase free tubes and stored at -80 ºC. Aflatoxin reduced (P ≤ 0.05) feed intake, body weight, serum total proteins, serum calcium and phosphorus but increased (P < 0.01) liver weights in a dose dependent manner. Microarray experiments were conducted using chicken long oligo arrays, to identify the changes in hepatic gene expression in chicks fed 0 (control) and 2mg/kg aflatoxin/kg of feed. A loop design was followed for microarray experiments with three technical and four biological replicates per treatment group. RNA was extracted from liver tissue and its quality was determined using gel electrophoresis. High quality RNA was purified from DNA contamination, reverse transcribed to cDNA and was used for microarray hybridizations. Microarray data was analyzed using a 2-step ANOVA model using GenePix and MAANOVA softwares, and the differentially expressed genes were identified using SAM, TIGR, and Cluster softwares. The microarray data was validated using real time PCR. The genes associated with antioxidant, detoxification and immune systems were down regulated and genes involed in cell proliferation were up regulated  in birds fed aflatoxin compared to controls

source_name: control; A1

tag: CHICKEN LIVER CONTROL TREATMENT 0PPM OF AFLATOXIN IN DIET


title: KELH0012_P-11_26M15

tag: Tissue:Blood, Patient id:P-11, Age:26, Sex:M, DSO:15, Status:pre-pO2 nadir


title: KELH0015_P-15_78F16

tag: Tissue:Blood, Patient id:P-15, Age:78, Sex:F, DSO:16, Status:post-pO2 nadir


title: A1 Cy3 to C2 Cy5

tag: CHICKEN LIVER CONTROL TREATMENT DIET 0 PPM AFLATOXIN


title: KELH0014_P-14_75M2

tag: Tissue:Blood, Patient id:P-14, Age:75, Sex:M, DSO:2, Status:post-pO2 nadir


title: KELH0035_P-26_79M18

tag: Tissue:Blood, Patient id:P-26, Age:79, Sex:M, DSO:18, Status:post-pO2 nadir


title: KELH0062_HC2_31Fna

tag: Tissue:Blood, Patient id:HC2, Age:31, Sex:F, DSO:na, Status:healthy control


title: KELH0049_P-34_63M56

tag: Tissue:Blood, Patient id:P-34, Age:63, Sex:M, DSO:56, Status:post-pO2 nadir


title: Halobacterium_oxygen3_H_540min, Array 10675

city: Seattle

first: Amy

middle: K

last: Schmid

state: WA

institute: Institute for Systemsbiology

description: High-oxygen 540 minutes post-shift vs. reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-65

scan_protocol: ScanArray 5000, using Packard BioChip ScanArray software. See http://www.systemsbiology.org/Scientists_and_Research/Technology/ISB_Facilities/Microarray for microarray scanning details

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:316

label: Alexa 547

organism: Halobacterium salinarum NRC-1

source_name: Halobacterium NRC1, aerobic 540 minutes after shift.

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0%) oxygen in a turbidostat for 24hr.  Sample was harvested at 540 minutes after rapidly shifting to high (~100%; 5microM) oxygen for 12 hours.

extract_protocol: Total DNA-free RNA prepared using the Absolutely RNA miniprep kit (Stratagene) and analyzed by PCR to rule out DNA contamination, with Agilent Bioanalyzer to verify integrity, and in the spectrophotometer for quantification.

tag: Halobacterium NRC-1 in standard growth medium at 37C; at 100% oxygen.

label: Alexa 647

source_name: Halobacterium NRC-1, reference

growth_protocol: Mid-log phase (OD600-0.5 - 0.6) Halobacterium NRC-1 grown at 225 rpm

tag: Halobacterium NRC-1 standard reference grown in standard growth media to mid-log phase (OD600 0.5-0.6).


title: Halobacterium_oxygen3_H_660min, Array 10682

description: High-oxygen 660 minutes post-shift vs. reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-70

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:321

source_name: Halobacterium NRC1, aerobic 660 minutes after shift.

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0%) oxygen in a turbidostat for 24hr.  Sample was harvested at 660 minutes after rapidly shifting to high (~100%; 5microM) oxygen for 12 hours.


title: Halobacterium_oxygen3_H_600min, Array 10678

description: High-oxygen 600 minutes post-shift vs. reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-68

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:319

source_name: Halobacterium NRC1, aerobic 600 minutes after shift.

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0%) oxygen in a turbidostat for 24hr.  Sample was harvested at 600 minutes after rapidly shifting to high (~100%; 5microM) oxygen for 12 hours.


title: Halobacterium_oxygen3_H_660min, Array 10679

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-69

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:320


title: KELH0025_P-21_38M8

tag: Tissue:Blood, Patient id:P-21, Age:38, Sex:M, DSO:8, Status:pre-pO2 nadir


title: Halobacterium_oxygen3_H_600min, Array 10677

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-67

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:318


title: Halobacterium_oxygen3_H_540min, Array 10676

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-66

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:317


title: KELH0037_P-28_57M10

tag: Tissue:Blood, Patient id:P-28, Age:57, Sex:M, DSO:10, Status:post-pO2 nadir


title: KELH0034_P-26_79M8

tag: Tissue:Blood, Patient id:P-26, Age:79, Sex:M, DSO:8, Status:post-pO2 nadir


title: Halobacterium_oxygen3_H_420min, Array 10688

description: High-oxygen 420 minutes post-shift vs. reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-64

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:315

source_name: Halobacterium NRC1, aerobic 420 minutes after shift.

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0%) oxygen in a turbidostat for 24hr.  Sample was harvested at 420 minutes after rapidly shifting to high (~100%; 5microM) oxygen for 12 hours.


title: KELH0006_P-6_55F4

tag: Tissue:Blood, Patient id:P-6, Age:55, Sex:F, DSO:4, Status:pre-pO2 nadir


title: Halobacterium_oxygen3_H_420min, Array 10673

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-63

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:314


title: Human_P493_cells_parental control line_tet resistant

description: SNP genotyping was performed at the Johns Hopkins SNP Center. The BeadStudio output is also posted at http://pevsnerlab.kennedykrieger.org/microarraydata/Gao_Dang/

hyb_protocol: Hybridization was performed at the Johns Hopkins SNP Center.

scan_protocol: Scans were performed at the Johns Hopkins SNP Center.

data_processing: Data processing was performed using BeadStudio software (Illumina)(v.2.3.41).

label: SNPs were identified by single-base extension.

source_name: Human P493 cells

label_protocol: SNPs were analyzed at the Johns Hopkins SNP Center (http://snpcenter.grcf.jhmi.edu/).

extract_protocol: Genomic DNA was isolated using an extraction kit.

tag: This is one of two parental P493 cells used in this study. These cells are tetracycline resistant, and serve as a control cell line.


title: Human_P493_tumor_cells_retrieved_from_a_xenograft_2of2

tag: This is one of two tumor cell lines retrieved from xenografts and compared to parental P493 cell line controls P493Luc and P493TR.


title: Halobacterium_oxygen3_H_360min, Array 10672

description: High-oxygen 360 minutes post-shift vs. reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-62

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:313

source_name: Halobacterium NRC1, aerobic 360 minutes after shift.

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0%) oxygen in a turbidostat for 24hr.  Sample was harvested at 360 minutes after rapidly shifting to high (~100%; 5microM) oxygen for 12 hours.


title: KELH0059_P-46_32F0

source_name: Universal RNA

tag: Tissue:Universal RNA

tag: Tissue:Blood, Patient id:P-46, Age:32, Sex:F, DSO:0, Status:pre-pO2 nadir


title: KELH0026_P-21_38M16

source_name: PBMC

tag: Tissue:Blood, Patient id:P-21, Age:38, Sex:M, DSO:16, Status:pre-pO2 nadir


title: KELH0024_P-21_38M5

tag: Tissue:Blood, Patient id:P-21, Age:38, Sex:M, DSO:5, Status:pre-pO2 nadir


title: Halobacterium_oxygen3_H_300min, Array 10670

description: High-oxygen 300 minutes post-shift vs. reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-60

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:311

source_name: Halobacterium NRC1, aerobic 300 minutes after shift.

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0%) oxygen in a turbidostat for 24hr.  Sample was harvested at 300 minutes after rapidly shifting to high (~100%; 5microM) oxygen for 12 hours.


title: Halobacterium_oxygen3_H_300min, Array 10687

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-59

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:310


title: Halobacterium_oxygen3_H_240min, Array 10686

description: High-oxygen 240 minutes post-shift vs. reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-58

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:309

source_name: Halobacterium NRC1, aerobic 240 minutes after shift.

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0%) oxygen in a turbidostat for 24hr.  Sample was harvested at 240 minutes after rapidly shifting to high (~100%; 5microM) oxygen for 12 hours.


title: Halobacterium_oxygen3_H_360min, Array 10671

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-61

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:312


title: Human_P493_cells_parental control line

tag: This is one of two parental P493 cells used in this study. These cells conditionally express MYC upon removal of tetracycline in a xenograft model in SCID mice.


title: KELH0052_P-37_52F4

tag: Tissue:Blood, Patient id:P-37, Age:52, Sex:F, DSO:4, Status:pre-pO2 nadir


title: KELH0055_P-41_24F27

tag: Tissue:Blood, Patient id:P-41, Age:24, Sex:F, DSO:27, Status:convalescent


title: Halobacterium_oxygen3_H_240min, Array 10685

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-57

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:308


title: Halobacterium_oxygen3_H_180min, Array 10666

description: High-oxygen 180 minutes post-shift vs. reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-56

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:307

source_name: Halobacterium NRC1, aerobic 180 minutes after shift.

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0%) oxygen in a turbidostat for 24hr.  Sample was harvested at 180 minutes after rapidly shifting to high (~100%; 5microM) oxygen for 12 hours.


title: KELH0050_P-34_63M79

hyb_protocol: similar to direct labelling protocol listed at UHN Microarray facility web site.

data_processing: Each quantified output file was run though the following pre-processing steps using R (URL: www.r-project.org)and the Limma package. For Minimum Intensity filtering, R and G values were treated with a surrogate replacement policy for estimating sub-threshold values. The raw merged R and G channels were lowess-normalized (grouped by print-tip), normalized between chips using quantile normalization and transformed to log2 ratios (70).

tag: Tissue:Blood, Patient id:P-34, Age:63, Sex:M, DSO:79, Status:pre-pO2 nadir


title: Halobacterium_oxygen3_H_180min, Array 10665

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-55

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:306


title: KELH0013_P-12_72M14

tag: Tissue:Blood, Patient id:P-12, Age:72, Sex:M, DSO:14, Status:post-pO2 nadir


title: KELH0001_P-1_47F37

tag: Tissue:Blood, Patient id:P-1, Age:47, Sex:F, DSO:37, Status:convalescent


title: Halobacterium_oxygen3_H_060min, Array 10658

description: High-oxygen 060 minutes post-shift vs. reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-50

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:301

source_name: Halobacterium NRC1, aerobic 060 minutes after shift.

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0%) oxygen in a turbidostat for 24hr.  Sample was harvested at 060 minutes after rapidly shifting to high (~100%; 5microM) oxygen for 12 hours.

tag: Halobacterium NRC-1 in standard growth medium at 37C; at 100% oxygen.

tag: Halobacterium NRC-1 standard reference grown in standard growth media to mid-log phase (OD600 0.5-0.6).


title: Halobacterium_oxygen3_H_060min, Array 10657

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-49

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:300


title: Halobacterium_oxygen3_H_090min, Array 10660

description: High-oxygen 090 minutes post-shift vs. reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-52

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:303

source_name: Halobacterium NRC1, aerobic 090 minutes after shift.

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0%) oxygen in a turbidostat for 24hr.  Sample was harvested at 090 minutes after rapidly shifting to high (~100%; 5microM) oxygen for 12 hours.


title: Halobacterium_oxygen3_H_120min, Array 10663

description: High-oxygen 120 minutes post-shift vs. reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-53

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:304

source_name: Halobacterium NRC1, aerobic 120 minutes after shift.

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0%) oxygen in a turbidostat for 24hr.  Sample was harvested at 120 minutes after rapidly shifting to high (~100%; 5microM) oxygen for 12 hours.


title: Halobacterium_oxygen3_H_090min, Array 10659

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-51

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:302


title: KELH0046_P-34_63M2

tag: Tissue:Blood, Patient id:P-34, Age:63, Sex:M, DSO:2, Status:post-pO2 nadir


title: KELH0063_HC3_32Mna

tag: Tissue:Blood, Patient id:HC3, Age:32, Sex:M, DSO:na, Status:healthy control


title: Human_P493_tumor_cells_retrieved_from_a_xenograft_1of2

tag: This is one of two tumor samples that were retrieved from xenografts. They were compared to two control P493 cell lines (P493Luc and P493TR) to assess changes in genome stability.


title: Halobacterium_oxygen3_L2H_000min, Array 10639

description: High-oxygen 000 minutes post-shift vs. reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-37

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:288

source_name: Halobacterium NRC1, aerobic 000 minutes after shift.

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0%) oxygen in a turbidostat for 24hr.  Sample was harvested at 000 minutes after rapidly shifting to high (~100%; 5microM) oxygen for 12 hours.

tag: Halobacterium NRC-1 in standard growth medium at 37C; at 0% oxygen.


title: Halobacterium_oxygen3_H_010min, Array 10643

description: High-oxygen 010 minutes post-shift vs. reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-41

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:292

source_name: Halobacterium NRC1, aerobic 010 minutes after shift.

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0%) oxygen in a turbidostat for 24hr.  Sample was harvested at 010 minutes after rapidly shifting to high (~100%; 5microM) oxygen for 12 hours.

tag: Halobacterium NRC-1 in standard growth medium at 37C; at 95.8% oxygen.


title: Halobacterium_oxygen3_H_030min, Array 10647

description: High-oxygen 030 minutes post-shift vs. reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-45

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:296

source_name: Halobacterium NRC1, aerobic 030 minutes after shift.

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0%) oxygen in a turbidostat for 24hr.  Sample was harvested at 030 minutes after rapidly shifting to high (~100%; 5microM) oxygen for 12 hours.


title: Halobacterium_oxygen3_H_045min, Array 10649

description: High-oxygen 045 minutes post-shift vs. reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-47

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:298

source_name: Halobacterium NRC1, aerobic 045 minutes after shift.

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0%) oxygen in a turbidostat for 24hr.  Sample was harvested at 045 minutes after rapidly shifting to high (~100%; 5microM) oxygen for 12 hours.

source_name: Halobacterium NRC-1, reference


title: Halobacterium_oxygen3_H_120min, Array 10664

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-54

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:305


title: Halobacterium_oxygen3_H_020min, Array 10645

description: High-oxygen 020 minutes post-shift vs. reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-43

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:294

source_name: Halobacterium NRC1, aerobic 020 minutes after shift.

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0%) oxygen in a turbidostat for 24hr.  Sample was harvested at 020 minutes after rapidly shifting to high (~100%; 5microM) oxygen for 12 hours.

tag: Halobacterium NRC-1 in standard growth medium at 37C; at 98.7% oxygen.


title: Halobacterium_oxygen3_H_005min, Array 10641

description: High-oxygen 005 minutes post-shift vs. reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-39

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:290

source_name: Halobacterium NRC1, aerobic 005 minutes after shift.

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0%) oxygen in a turbidostat for 24hr.  Sample was harvested at 005 minutes after rapidly shifting to high (~100%; 5microM) oxygen for 12 hours.

tag: Halobacterium NRC-1 in standard growth medium at 37C; at 91.1% oxygen.


title: Halobacterium_oxygen3_H_020min, Array 10646

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-44

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:295

growth_protocol: Mid-log phase (OD600-0.5 - 0.6) Halobacterium NRC-1 grown at 225 rpm


title: Halobacterium_oxygen3_H_045min, Array 10656

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-48

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:299


title: Halobacterium_oxygen3_H_005min, Array 10642

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-40

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:291


title: Halobacterium Oxygen2 L 70 min 1

description: low oxygen, 70 minutes series 2 vs. reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:286

label: Alexa 532

source_name: Halobacterium NRC-1,  70 minutes after shift from high to low oxygen, series 2

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to high (~90-100%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from high to low (~0-10%) oxygen, and sample was harvested 70 minutes after the shift.

treatment_protocol: 10mL of cells were harvested from turbidostat, pelleted at 13,000rpm for 0.5 min, and snap-frozen in a dry-ice ethanol bath.  Samples were stored at -80C until RNA extraction

tag: Halobacterium NRC-1 in standard growth medium at 37C

tag: cells at 0.4% oxygen in turbidostat


title: Halobacterium Oxygen2 L 380 min dye swap 1

description: reference vs.low oxygen, 380 minutes series 2

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35

source_name: Halobacterium NRC-1, 380 minutes after shift from high to low oxygen, series 2

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to high (~90-100%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from high to low (~0-10%) oxygen, and sample was harvested 380 minutes after the shift.

tag: cells at 0% oxygen in turbidostat


title: Halobacterium Oxygen2 L 160 min dye swap 1

description: reference vs.low oxygen, 160 minutes series 2

source_name: Halobacterium NRC-1, 160 minutes after shift from high to low oxygen, series 2

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to high (~90-100%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from high to low (~0-10%) oxygen, and sample was harvested 160 minutes after the shift.


title: Halobacterium Oxygen2 L 290 min dye swap 1

description: reference vs.low oxygen, 290 minutes series 2

source_name: Halobacterium NRC-1, 290 minutes after shift from high to low oxygen, series 2

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to high (~90-100%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from high to low (~0-10%) oxygen, and sample was harvested 290 minutes after the shift.


title: Halobacterium Oxygen2 L 110min 1

description: low oxygen, 110_minutes series 2 vs. reference

source_name: Halobacterium NRC-1,  110 minutes after shift from high to low oxygen, series 2

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to high (~90-100%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from high to low (~0-10%) oxygen, and sample was harvested 110 minutes after the shift.

tag: cells at 0.1% oxygen in turbidostat


title: Halobacterium_oxygen3_H_030min, Array 10648

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-46

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:297


title: Halobacterium Oxygen2 L 380 min 1

description: low oxygen, 380 minutes series 2 vs. reference


title: Halobacterium_oxygen3_LO2_-05min, Array 10684

description: low oxygen 5min pre-shift vs. reference

source_name: Halobacterium NRC1, anaerobic 5 minute pre-shift

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0%) oxygen in a turbidostat for 24hr.  Sample was harvested at 5 minutes prior to rapidly shifting to high (~100%; 5microM) oxygen for 12 hours.

tag: Halobacterium NRC-1 in standard growth medium at 37C; cells at 0% oxygen


title: Halobacterium Oxygen2 L 200 min 1

description: low oxygen, 200 minutes series 2 vs. reference

source_name: Halobacterium NRC-1,  5 minutes after shift from high to low oxygen, series 2

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to high (~90-100%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from high to low (~0-10%) oxygen, and sample was harvested 200 minutes after the shift.


title: Halobacterium Oxygen2 L 70 min dye swap 1

description: reference vs.low oxygen, 70 minutes series 2

source_name: Halobacterium NRC-1, 70 minutes after shift from high to low oxygen, series 2


title: Halobacterium Oxygen2 L 110 min dye swap 1

description: reference vs.low oxygen, 110 minutes series 2

source_name: Halobacterium NRC-1, 110 minutes after shift from high to low oxygen, series 2


title: Halobacterium Oxygen2 L 160 min 1

description: low oxygen, 160 minutes series 2 vs. reference

source_name: Halobacterium NRC-1,  160 minutes after shift from high to low oxygen, series 2


title: Halobacterium_oxygen3_L2H_000min, Array 10640

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-38

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:289

source_name: Halobacterium NRC1, aerobic 000 minutes after shift.


title: Halobacterium Oxygen2 L 55 min dye swap 1

description: reference vs.low oxygen, 55 minutes series 2

source_name: Halobacterium NRC-1, 55 minutes after shift from high to low oxygen, series 2

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to high (~90-100%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from high to low (~0-10%) oxygen, and sample was harvested 55 minutes after the shift.

tag: cells at 0.7% oxygen in turbidostat


title: Halobacterium_oxygen3_H_010min, Array 10644

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-42

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:293

source_name: Halobacterium NRC1, aerobic 010 minutes after shift.


title: Halobacterium Oxygen2 L 290 min 1

description: low oxygen, 290 minutes series 2 vs. reference


title: Halobacterium_oxygen3_LO2_-05min, Array 10638

description: low oxygen 5min pre-shift vs. reference

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-36

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:287


title: Halobacterium Oxygen2 L 200 min dye swap 1

description: reference vs.low oxygen, 200 minutes series 2

source_name: Halobacterium NRC-1, 200 minutes after shift from high to low oxygen, series 2


title: Halobacterium Oxygen2 L 45 min dye swap 1

description: reference vs.low oxygen, 45 minutes series 2

source_name: Halobacterium NRC-1, reference

source_name: Halobacterium NRC-1, 45 minutes after shift from high to low oxygen, series 2

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to high (~90-100%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from high to low (~0-10%) oxygen, and sample was harvested 45 minutes after the shift.

tag: cells at 1.1% oxygen in turbidostat


title: Halobacterium Oxygen2 L 55 min 1

description: low oxygen,55 minutes series 2 vs. reference

source_name: Halobacterium NRC-1,  55 minutes after shift from high to low oxygen, series 2


title: Halobacterium Oxygen2 L 25 min dye swap 1

description: reference vs.low oxygen, 25 minutes series 2

source_name: Halobacterium NRC-1, 25 minutes after shift from high to low oxygen, series 2

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to high (~90-100%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from high to low (~0-10%) oxygen, and sample was harvested 25 minutes after the shift.

tag: cells at 1.6% oxygen in turbidostat


title: Halobacterium Oxygen2 L 30 min 1

description: low oxygen, 30 minutes series 2 vs. reference

source_name: Halobacterium NRC-1, 30 minutes after shift from high to low oxygen, series 2

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to high (~90-100%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from high to low (~0-10%) oxygen, and sample was harvested 30 minutes after the shift.

tag: cells at 1.4% oxygen in turbidostat


title: Halobacterium Oxygen2 L 35 min dye swap 1

description: reference vs.low oxygen, 35 minutes series 2

source_name: Halobacterium NRC-1, 35 minutes after shift from high to low oxygen, series 2

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to high (~90-100%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from high to low (~0-10%) oxygen, and sample was harvested 35 minutes after the shift.


title: Halobacterium Oxygen2 H2L 10 min dye swap 1

description: reference vs.low oxygen, 10 minutes series 2

source_name: Halobacterium NRC-1, 10 minutes after shift from high to low oxygen, series 2

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to high (~90-100%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from high to low (~0-10%) oxygen, and sample was harvested 10 minutes after the shift.

tag: cells at 4.3% oxygen in turbidostat


title: Halobacterium Oxygen2 H2L 20 min dye swap 1

description: reference vs.low oxygen, 20 minutes series 2

source_name: Halobacterium NRC-1, 20 minutes after shift from high to low oxygen, series 2

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to high (~90-100%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from high to low (~0-10%) oxygen, and sample was harvested 20 minutes after the shift.

tag: cells at 2.9% oxygen in turbidostat


title: Halobacterium Oxygen2 L 25 min 1

description: low oxygen, 25 minutes series 2 vs. reference

source_name: Halobacterium NRC-1,  25 minutes after shift from high to low oxygen, series 2


title: Halobacterium Oxygen2 H2L 10 min 1

description: low oxygen, 10 minutes series 2 vs. reference


title: Halobacterium Oxygen2 L 30 min dye swap 1

description: reference vs.low oxygen, 30 minutes series 2


title: Halobacterium Oxygen2 H2L 0 min 1

description: high to low oxygen series 2, 0 minutes vs. reference

source_name: Halobacterium NRC-1, 0 minutes, during shift from high to low oxygen, series2

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to high (~90-100%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from high to low (~0-10%) oxygen, and sample was harvested during the shift.

tag: cells at 98.5% oxygen in turbidostat


title: Halobacterium Oxygen2 L 35 min 1

description: low oxygen, 35 minutes series 2 vs. reference

source_name: Halobacterium NRC-1,  35 minutes after shift from high to low oxygen, series 2


title: Halobacterium Oxygen2 H2L 20 min 1

description: low oxygen, 20 minutes series 2 vs. reference

source_name: Halobacterium NRC-1,  20 minutes after shift from high to low oxygen, series 2


title: Halobacterium Oxygen1 L2H 770 min 1

description: low to high oxygen, 770 minutes vs. reference

source_name: Halobacterium NRC-1, 770 minutes, during second shift from low to high oxygen

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0.5%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from low to high (~90-100%, 5uM) oxygen, equilibrated at high oxygen for 6 hours, back to low oxygen for 6 hours, then harvested 20 minutes after a second rapid shift back to high oxygen (770 total minutes elapsed in time course).

tag: cells at 85.2% oxygen in turbidostat


title: Halobacterium Oxygen2 H2L 5 min dye swap 1

description: reference vs.low oxygen, 5 minutes series 2

growth_protocol: Mid-log phase (OD600-0.5 - 0.6) Halobacterium NRC-1 grown at 225 rpm

source_name: Halobacterium NRC-1, 5 minutes after shift from high to low oxygen, series 2

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to high (~90-100%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from high to low (~0-10%) oxygen, and sample was harvested 5 minutes after the shift.

tag: cells at 40.7% oxygen in turbidostat


title: Halobacterium Oxygen1 L2H 760 min 1

description: low to high oxygen, 760 minutes vs. reference

source_name: Halobacterium NRC-1, 760 minutes, during second shift from low to high oxygen

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0.5%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from low to high (~90-100%, 5uM) oxygen, equilibrated at high oxygen for 6 hours, back to low oxygen for 6 hours, then harvested 10 minutes after a second rapid shift back to high oxygen (760 total minutes elapsed in time course).

tag: cells at 84.7% oxygen in turbidostat


title: Halobacterium Oxygen2 H2L 5 min 1

description: low oxygen, 5 minutes series 2 vs. reference

source_name: Halobacterium NRC-1,  5 minutes after shift from high to low oxygen, series 2


title: Halobacterium Oxygen1 L2H 780 min 1

description: low to high oxygen, 780 minutes vs. reference

source_name: Halobacterium NRC-1, 780 minutes, during second shift from low to high oxygen

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0.5%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from low to high (~90-100%, 5uM) oxygen, equilibrated at high oxygen for 6 hours, back to low oxygen for 6 hours, then harvested 30 minutes after a second rapid shift back to high oxygen (780 total minutes elapsed in time course).


title: Halobacterium Oxygen1 L 747 min 1

description: low oxygen, 747 minutes vs. reference

source_name: Halobacterium NRC-1, 747 minutes, 385 minutes after shift from high back to low oxygen

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0.5%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from low to high (~90-100%, 5uM) oxygen, equilibrated at high oxygen for 6 hours, then harvested 385 minutes after shifting back to low oxygen (747 total minutes elapsed in time course).

tag: cells at 0.8% oxygen in turbidostat

source_name: Halobacterium NRC-1, reference


title: Halobacterium Oxygen1 L2H 780 min dye swap 1

description: reference vs.low to high oxygen, 780 minutes

source_name: Halobacterium NRC-1, 780 minutes, during second shift from low back to high oxygen


title: Halobacterium Oxygen1 L2H 750 min 1

description: low to high oxygen, 750 minutes vs. reference

source_name: Halobacterium NRC-1, 750 minutes, during second shift from low to high oxygen

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0.5%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from low to high (~90-100%, 5uM) oxygen, equilibrated at high oxygen for 6 hours, back to low oxygen for 6 hours, then harvested during a second rapid shift back to high oxygen (750 total minutes elapsed in time course).

tag: cells at 54.0% oxygen in turbidostat


title: Halobacterium Oxygen1 L2H 770 min dye swap 1

description: reference vs.low to high oxygen, 770 minutes

tag: Halobacterium NRC-1 in standard growth medium at 37C

source_name: Halobacterium NRC-1, 770 minutes, during second shift from low back to high oxygen


title: Halobacterium Oxygen1 L2H 755 min dye swap 1

description: reference vs.low to high oxygen, 755 minutes

source_name: Halobacterium NRC-1, 755 minutes, during second shift from low back to high oxygen

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0.5%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from low to high (~90-100%, 5uM) oxygen, equilibrated at high oxygen for 6 hours, back to low oxygen for 6 hours, then harvested 5 minutes after a second rapid shift back to high oxygen (755 total minutes elapsed in time course).

tag: cells at 82.5% oxygen in turbidostat


title: Halobacterium Oxygen1 L 567 min 1

description: low oxygen, 567 minutes vs. reference

source_name: Halobacterium NRC-1, 567 minutes, 205 minutes after shift from high back to low oxygen

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0.5%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from low to high (~90-100%, 5uM) oxygen, equilibrated at high oxygen for 6 hours, then harvested 205 minutes after shifting back to low oxygen (567 total minutes elapsed in time course).


title: Halobacterium Oxygen2 H2L 0 min dye swap 1

description: reference vs. high to low oxygen series 2, 0 minutes

source_name: Halobacterium NRC-1, 0 minutes, during shift from high to low oxygen, series 2


title: Halobacterium Oxygen1 L 567 min dye swap 1

description: reference vs.low oxygen, 567 minutes


title: Halobacterium Oxygen1 L2H 750 min dye swap 1

description: reference vs.low to high oxygen, 750 minutes

source_name: Halobacterium NRC-1, 750 minutes, during second shift from low back to high oxygen


title: Halobacterium Oxygen1 L2H 755 min 1

description: low to high oxygen, 755 minutes vs. reference

source_name: Halobacterium NRC-1, 755 minutes, during second shift from low to high oxygen


title: Halobacterium Oxygen1 L 747 min dye swap 1

description: reference vs.low oxygen, 747 minutes


title: Halobacterium Oxygen1 L2H 760 min dye swap 1

description: reference vs.low to high oxygen, 760 minutes

source_name: Halobacterium NRC-1, 760 minutes, during second shift from low back to high oxygen


title: Halobacterium Oxygen1 L 477 min dye swap 1

description: reference vs.low oxygen, 477 minutes

source_name: Halobacterium NRC-1, 477 minutes, 115 minutes after shift from high back to low oxygen

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0.5%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from low to high (~90-100%, 5uM) oxygen, equilibrated at high oxygen for 6 hours, then harvested 115 minutes after shifting back to low oxygen (477 total minutes elapsed in time course).

tag: cells at 1.7% oxygen in turbidostat


title: SiHa sample 1

city: Leiden

first: Jan

last: Oosting

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: Leiden University Medical Center

description: Gene expression data

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data files of all arrays were normalized using sequence information in Robust Multi_Chip Average (GCRMA) method.

label: biotin

source_name: SiHa

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: cells were grown semiconfluent in RPMI 1640, supplemented with 10% FCS, streptomycin, and penicillin at 37ºC and 5% CO2

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

tag: Cervical cancer cell line (HPV 16)


title: SiHa sample 2

description: Gene expression data


title: Halobacterium Oxygen1 L 407 min 1

description: low oxygen, 407 minutes vs. reference

source_name: Halobacterium NRC-1, 407 minutes, 45 minutes after shift from high back to low oxygen

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0.5%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from low to high (~90-100%, 5uM) oxygen, equilibrated at high oxygen for 6 hours, then harvested 45 minutes after shifting back to low oxygen (407 total minutes elapsed in time course).

tag: cells at 3.0% oxygen in turbidostat


title: Halobacterium Oxygen1 L 417 min dye swap 1

description: reference vs.low oxygen, 417 minutes

source_name: Halobacterium NRC-1, 417 minutes, 55 minutes after shift from high back to low oxygen

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0.5%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from low to high (~90-100%, 5uM) oxygen, equilibrated at high oxygen for 6 hours, then harvested 55 minutes after shifting back to low oxygen (417 total minutes elapsed in time course).

tag: cells at 2.7% oxygen in turbidostat


title: Halobacterium Oxygen1 L 417 min 1

description: low oxygen, 417 minutes vs. reference


title: Halobacterium Oxygen1 L 432 min 1

description: low oxygen, 432 minutes vs. reference

source_name: Halobacterium NRC-1, 432 minutes, 70 minutes after shift from high back to low oxygen

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0.5%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from low to high (~90-100%, 5uM) oxygen, equilibrated at high oxygen for 6 hours, then harvested 55 minutes after shifting back to low oxygen (432 total minutes elapsed in time course).

tag: cells at 2.4% oxygen in turbidostat


title: Halobacterium Oxygen1 L 407 min dye swap 1

description: reference vs.low oxygen, 407 minutes


title: CC8 sample 1

description: Gene expression data

tag: Cervical cancer cell line (HPV 45)


title: CC8 sample 2

description: Gene expression data


title: CC11+ sample 1

description: Gene expression data

tag: Cervical cancer cell line (HPV 67)


title: HeLa sample 2

description: Gene expression data

source_name: HeLa

tag: Cervical cancer cell line (HPV 18)


title: HeLa sample 1

description: Gene expression data


title: Halobacterium Oxygen1 L 477 min 1

description: low oxygen, 477 minutes vs. reference


title: Halobacterium Oxygen1 L 392 min dye swap 1

description: reference vs. low oxygen, 392 minutes

source_name: Halobacterium NRC-1, 392 minutes, 30 minutes after shift from high back to low oxygen

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0.5%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from low to high (~90-100%, 5uM) oxygen, equilibrated at high oxygen for 6 hours, then harvested 30 minutes after shifting back to low oxygen (392 total minutes elapsed in time course).

tag: cells at 3.7% oxygen in turbidostat


title: Halobacterium Oxygen1 L 432 min dye swap 1

description: reference vs.low oxygen, 432 minutes

source_name: Halobacterium NRC-1, reference

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0.5%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from low to high (~90-100%, 5uM) oxygen, equilibrated at high oxygen for 6 hours, then harvested 70 minutes after shifting back to low oxygen (432 total minutes elapsed in time course).


title: CC11+ sample 2

description: Gene expression data


title: CSCC7 sample 2

description: Gene expression data


title: Halobacterium Oxygen1 L 387 min 1

description: low oxygen, 387 minutes vs. reference

source_name: Halobacterium NRC-1, 387 minutes, 25 min after shift from high back to low oxygen

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0.5%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from low to high (~90-100%, 5uM) oxygen, equilibrated at high oxygen for 6 hours, then harvested 25 minutes after shifting back to low oxygen (387 total minutes elapsed in time course).

tag: cells at 4.1% oxygen in turbidostat


title: CC10A sample 2

description: Gene expression data


title: Halobacterium Oxygen1 L 392 min 1

description: low oxygen, 392 minutes vs. reference


title: Halobacterium Oxygen1 L 387 min dye swap 1

description: reference vs.low oxygen, 387 minutes

source_name: Halobacterium NRC-1, 387 minutes, 25 minutes shift from high back to low oxygen


title: Halobacterium Oxygen1 H2L 382 min dye swap 1

description: reference vs. high to low oxygen, 362 minutes

source_name: Halobacterium NRC-1, 382 minutes, during shift from high back to low oxygen

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0.5%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from low to high (~90-100%, 5uM) oxygen, equilibrated at high oxygen for 6 hours, then harvested 20 minutes after shifting back to low oxygen (382 total minutes elapsed in time course).

tag: cells at 4.8% oxygen in turbidostat


title: Halobacterium Oxygen1 L 397 min 1

description: low oxygen, 397 minutes vs. reference

source_name: Halobacterium NRC-1, 397 minutes, 35 minutes after shift from high back to low oxygen

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0.5%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from low to high (~90-100%, 5uM) oxygen, equilibrated at high oxygen for 6 hours, then harvested 35 minutes after shifting back to low oxygen (397 total minutes elapsed in time course).

tag: cells at 3.5% oxygen in turbidostat

growth_protocol: Mid-log phase (OD600-0.5 - 0.6) Halobacterium NRC-1 grown at 225 rpm


title: CSCC7 sample 1

description: Gene expression data


title: CC10A sample 1

description: Gene expression data


title: CC11- sample 1

description: Gene expression data


title: Halobacterium Oxygen1 L 397 min dye swap 1

description: reference vs. low oxygen, 397 minutes


title: Halobacterium Oxygen2 L 45 min 1

description: low oxygen, 45 minutes series 2 vs. reference

source_name: Halobacterium NRC-1,  45 minutes after shift from high to low oxygen, series 2

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to high (~90-100%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from high to low (~0-10%) oxygen, and sample was harvested 45 minutes after the shift.


title: Halobacterium Oxygen1 H2L 382 min 1

description: high to low oxygen, 382 minutes vs. reference


title: CC10B sample 2

description: Gene expression data


title: CaSki sample 1

description: Gene expression data

source_name: CaSki


title: CaSki sample 2

description: Gene expression data


title: CSCC1 sample 1

description: Gene expression data


title: CC11- sample 2

description: Gene expression data


title: CSCC1 sample 2

description: Gene expression data


title: Halobacterium Oxygen1 H 367 min dye swap 1

description: reference vs. high to low oxygen, 367 minutes

source_name: Halobacterium NRC-1, 5 minutes after shift from high back to low oxygen

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0.5%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from low to high (~90-100%, 5uM) oxygen, equilibrated at high oxygen for 6 hours, then harvested 5 minutes after shifting back to low oxygen (367 total minutes elapsed in time course).

tag: cells at 21.5% oxygen in turbidostat


title: Halobacterium Oxygen1 H2L 362 min 1

description: high to low oxygen, 362 minutes vs. reference

source_name: Halobacterium NRC-1, 362 minutes, during shift from high back to low oxygen

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0.5%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from low to high (~90-100%, 5uM) oxygen, equilibrated at high oxygen for 6 hours, then harvested while shifting back to low oxygen (362 total minutes elapsed in time course).

tag: cells at 86.0% oxygen in turbidostat


title: Halobacterium Oxygen1 H 360 min 1

description: high oxygen 360 minutes after shift vs. reference

source_name: Halobacterium NRC-1, aerobic 360 minutes after shift from low to high oxygen

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0.5%) oxygen in a turbidostat for 12hr.  Sample was harvested 360 minutes after rapidly shifting to high (~90-100%, 5uM) oxygen.

tag: cells at 90.3% oxygen in turbidostat


title: Halobacterium Oxygen1 H2L 372 min 1

description: high to low oxygen, 372 minutes vs. reference

source_name: Halobacterium NRC-1, 372 minutes, during shift from high back to low oxygen

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0.5%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from low to high (~90-100%, 5uM) oxygen, equilibrated at high oxygen for 6 hours, then harvested 10 minutes after shifting back to low oxygen (372 total minutes elapsed in time course).

tag: Halobacterium NRC-1 in standard growth medium at 37C

tag: cells at 7.9% oxygen in turbidostat


title: Halobacterium Oxygen1 H 360 min dye swap 1

description: reference vs. high oxygen 360 minutes after shift


title: Halobacterium Oxygen1 H2L 372 min dye swap 1

description: reference vs. high to low oxygen, 372 minutes


title: Halobacterium Oxygen1 H 90 min 1

description: high oxygen 90 minutes after shift vs. reference

source_name: Halobacterium NRC-1, aerobic 90 minutes after shift from low to high oxygen

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0.5%) oxygen in a turbidostat for 12hr.  Sample was harvested 90 minutes after rapidly shifting to high (~90-100%, 5uM) oxygen.

tag: cells at 94.1% oxygen in turbidostat


title: Halobacterium Oxygen1 H 30 min dye swap 1

description: reference vs. high oxygen 30 minutes after shift

source_name: Halobacterium NRC-1, aerobic 30 minutes after shift from low to high oxygen

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0.5%) oxygen in a turbidostat for 12hr.  Sample was harvested 30 minutes after rapidly shifting to high (~90-100%, 5uM) oxygen.

tag: cells at 93.1% oxygen in turbidostat


title: Halobacterium Oxygen1 H 180 min dye swap 1

description: reference vs. high oxygen 180 minutes after shift

source_name: Halobacterium NRC-1, aerobic 180 minutes after shift from low to high oxygen

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0.5%) oxygen in a turbidostat for 12hr.  Sample was harvested 180 minutes after rapidly shifting to high (~90-100%, 5uM) oxygen.

tag: cells at 93.0% oxygen in turbidostat


title: CC10B sample 1

description: Gene expression data

growth_protocol: cells were grown semiconfluent in RPMI 1640, supplemented with 10% FCS, streptomycin, and penicillin at 37ºC and 5% CO2


title: Halobacterium Oxygen1 H2L 362 min dye swap 1

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0.5%) oxygen in a turbidostat for 12hr.  Culture was rapidly shifted to from low to high (~90-100%, 5uM) oxygen, equilibrated at high oxygen for 6 hours, then harvested 2 minutes after shifting back to low oxygen (362 total minutes elapsed in time course).


title: Halobacterium Oxygen1 H2L 367 min 1

description: high to low oxygen, 367 minutes vs. reference


title: Halobacterium Oxygen1 H 45 min dye swap 1

description: reference vs. high oxygen 45 minutes after shift

source_name: Halobacterium NRC-1, aerobic 45 minutes after shift from low to high oxygen

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0.5%) oxygen in a turbidostat for 12hr.  Sample was harvested 45 minutes after rapidly shifting to high (~90-100%, 5uM) oxygen.

tag: cells at 93.9% oxygen in turbidostat


title: Halobacterium Oxygen1 H 90 min dye swap 1

description: reference vs. high oxygen 90 minutes after shift


title: tdt-1_3days_rep3

city: Salt Lake City

first: David

last: Goeres

state: UT

department: Biology

institute: University of Utah

description: Please note this experiment is dye-swapped with respect to previous two replicates.

hyb_protocol: Agilent Gene Expression Hybridization Kit

scan_protocol: Agilent G2565BA Microarray Scanner, Agilent Feature Extraction software

data_processing: Cy3 and Cy5 intensities were normalized using Linear LOWESS normalization in Agilent Feature Extraction software. Control features were removed, and log base 10 ratios were converted to log base 2.

organism: Arabidopsis thaliana

source_name: tdt-1, whole seedlings, 3 days

label_protocol: Agilent Low RNA Input Linear Amplification kit

growth_protocol:
Grown on MS Agar Plates,
Constant Light Conditions,
Growth Temperature:  22 C

extract_protocol: Agilent Plant RNA Isolation Mini Kit

tag: Tissue

value: Whole Seedlings,

tag: Age

value: 3 days

source_name: wild type, whole seedlings, 3 days


title: Halobacterium Oxygen1 H 180 min 1

description: high oxygen 180 minutes after shift vs. reference

source_name: Halobacterium NRC-1, reference


title: Halobacterium Oxygen1 H 20 min dye swap 1

description: reference vs. high oxygen 20 minutes after shift

source_name: Halobacterium NRC-1, aerobic 20 minutes after shift from low to high oxygen

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0.5%) oxygen in a turbidostat for 12hr.  Sample was harvested 20 minutes after rapidly shifting to high (~90-100%, 5uM) oxygen.

tag: cells at 93.7% oxygen in turbidostat


title: Halobacterium Oxygen1 H 45 min 1

description: high oxygen 45 minutes after shift vs. reference


title: Halobacterium Oxygen1 H 30 min 1

description: high oxygen 30 minutes after shift vs. reference


title: tdt-1_3days_rep1


title: Halobacterium Oxygen1 H 10 min dye swap 1

description: reference vs. high oxygen 10 minutes after shift

source_name: Halobacterium NRC-1, aerobic 10 minutes after shift from low to high oxygen

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0.5%) oxygen in a turbidostat for 12hr.  Sample was harvested ten minutes after rapidly shifting to high (~90-100%, 5uM) oxygen.

tag: cells at 94.7% oxygen in turbidostat


title: Halobacterium Oxygen1 H 10 min 1

description: high oxygen 10 minutes after shift vs. reference


title: Halobacterium Oxygen1 H 05 min dye swap 1

description: reference vs. high oxygen 5 minutes after shift

source_name: Halobacterium NRC-1, aerobic 5 minutes after shift from low to high oxygen

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0.5%) oxygen in a turbidostat for 12hr.  Sample was harvested five minutes after rapidly shifting to high (~90-100%, 5uM) oxygen.

tag: cells at 92.2% oxygen in turbidostat


title: tdt-1_3days_rep2