title: FHM Ovary Trenbolone High Dose (1 µg/L ) #3

status: Public on Jan 01 2009

city: Alachua

first: Barbara

middle: Joan

last: Carter

address: 12085 Research Drive

department: R&D

institute: Applied Food Technologies

description: RNA Integrity Number (RIN) = 9.5

hyb_protocol: Followed standard Agilent 60-mer oligo microarray processing protocol.  Wash steps included use of stabilization and drying solution.

scan_protocol: Agilent Technologies Scanner G2505B US22502637. Scanned images were processed using Agilent Feature Extraction 9.1.3.1 software for spot identification and for quantification of the fluorescent signal intensities. The fluorescent signal intensity for each oligo spot was calculated using local background subtraction. Quality control algorithms in the software detected poor quality spots, which were excluded from subsequent analyses.

data_processing: A statistical analysis was performed in order to identify differentially expressed genes between the control and 1 µg/L treatment groups using SAS 9.1 (SAS Institute, Cary, NC). Data were analyzed using two-stage mixed model ANOVA following the procedure described by Wolfinger et al. (2001). This approach centers around two interconnected ANOVA models, the “normalization” model and the “gene” model. The first stage is to normalize the data by outputting residuals from an ANOVA containing the effects of array and treatment. The treatment effect is fixed and the array effect is random. A second ANOVA uses the residuals from the first ANOVA to test differences among treatments with a separate ANOVA for each gene. The treatment difference for each gene was determined using a one degree of freedom F-test (P < 0.05).  Because one aim of this project was to discover novel genes and pathways involved in the response to 17β-trenbolone, we did not use a multiple testing correction.  Thus, some of the genes identified as altered are expected to be false positives.

organism: Pimephales promelas

label_protocol: LOW RNA INPUT FLUORESCENT LINEAR AMPLIFICATION KIT (Agilent Technologies, Inc., Santa Clara, CA).  We followed the manufacturer's protocol for cDNA synthesis, cRNA labeling, and amplification.

growth_protocol: Adult fathead minnows (Pimephales promelas) were cultured at the Columbia Environmental Research Center (CERC), USGS and both sexes were housed separately before the experiment. Fish were held in the test system for one day prior to initiation of the chemical exposure at 20.3 ± 0.5 °C under an 14:10 light:dark photo-period.

extract_protocol:
RNEasy Plus Mini-spin columns (Qiagen, Valenci, CA)
We ran samples on Agilent 2100 Bioanalyzer to determine quality of total RNA.  The four samples in each group (control and high dose) with highest RNA Integrity Number (RIN) were used on microarrays.

treatment_protocol: Fish were exposed to 17β-trenbolone for 4 days using a flow-through exposure system. Nominal water concentrations of 0.1 and 1 µg/L 17β-trenbolone were used. For each exposure, a stock solution was prepared in 100 % ethanol and slowly added to the exposure tanks in a proportional flow-through diluter system (6.5 L tank capacity; filled with 4 L of well water) at a flow rate of 0.5 ml/12.5 min. Control tanks had only ethanol added (solvent control). The final concentration of ethanol was 0.03 %. There were four replicate tanks for each treatment, with six fish per replicate at a ratio of three males to three females, for a total of 12 females per treatment. After 4 days of chemical exposure, fish were removed from the test tanks and anesthetized with MS-222 (tricaine methanesulfonate). The weight of each fish was recorded and liver, brain (without pituitary) and gonad tissues were collected, placed in RNALater (Ambion, Austin, TX), and stored at -20 °C until used for RNA extraction. The female fathead minnows were adults with a mean weight of 1.1 ± 0.25 g. Animals were not fed during exposure. No mortality was observed during the experiment.  For microarray analysis, gonad RNA was sampled from 4 females each from the control and 1 µg/L treatment groups only.

tag: Adult fathead minnow ovary (exposed 2 of 4)


title: Calf 129 gd T cells PBS

status: Public on Feb 10 2009

type: RNA

city: Bozeman

first: Jodi

middle: Fern

last: Hedges

state: MT

address: 960 Technology Blvd.

department: Veterinary Molecular Biology

country: USA

institute: Montana State University

description: gd T cells derived from peripheral blood of calf 129 stimulated 4 hours with PBS

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix GeneChip Operating Software V.1.2

label: biotin

molecule: total RNA

organism: Bos taurus

label_protocol: RNA was amplified using Affymetrix One-cycle protocol with approximately 1.7 micrograms of total RNA as described in the GeneChip® Expression Analysis Technical Manual (June 2004).

extract_protocol: PBLs were stained with GD3.8 directly conjugated to FITC, washed, and sorted on a Vantage SE cell sorter (BD Immunocytometry Systems) as previously described.  Sorted cells were rested overnight, stimulated for 4 hours then lysed in Buffer RLT and genomic DNA sheared using Qiashredder columns then frozen at -80oC.  RNA was extracted following the manufacturer’s protocol for RNeasy (Qiagen) column purification.

tag: purified gd T cells derived from peripheral blood stimulated with PBS for 4 hours


title: FHM Ovary Trenbolone High Dose (1 µg/L ) #4

state: FL

description: RNA Integrity Number (RIN) = 9.6

tag: Adult fathead minnow ovary (exposed 3 of 4)


title: Calf 129 gd T cells MDP

description: gd T cells derived from peripheral blood of calf 129 stimulated 4 hours with MDP

extract_protocol: PBLs were stained with GD3.8 directly conjugated to FITC, washed, and sorted on a Vantage SE cell sorter (BD Immunocytometry Systems) as previously described.  Sorted cells were stimulated for 4 hours then immediately lysed in Buffer RLT and genomic DNA sheared using Qiashredder columns then frozen at -80oC.  RNA was extracted following the manufacturer’s protocol for RNeasy (Qiagen) column purification.

tag: purified gd T cells derived from peripheral blood stimulated with MDP for 4 hours


title: 4 day N2B27 treatment-library2-replicate2

status: Public on Dec 31 2008

city: shanghai

first: huang

last: bing

state: shanghai

address: yueyang road 320

department: chemistry

country: China

institute: Chinese Academy of Sciences

description: analysis of mouse microRNAs expression under neural differentiation

hyb_protocol: Microscope glass slides were activated as described.The antisense sequences of microRNAs were used for probes. The melting temperatures of all probes were adjusted to 55 ± 3 °C as described.In addition, each probe contains a 5′ C6-amino modified 10 deoxyadenosines spacer at the 5′ end of the probe.The probes were dissolved in printing buffer (2× SSC/1 M betaine hydrochloride/5% formamide/0.01% SDS, pH 8.5) at the concentration of 20 μM, and then printed onto the epoxy coated slides with PixSys 5500 spotting robot in quadruplicate under 60% humidity. The printed microarrays were further chemically covalently coupled under 60% humidity overnight. Before hybridization, printed microarrays were quenched by quenching buffer (0.1 M Tris–HCl/50 mM ethanolamine, pH 8.0). Small RNA cDNA libraries of samples were amplified and labeled by PCR using the 5′primer (5′-Cy5-CTGGAATTCTGACGATCTGC) and the 3′primer (5′-ACCGAATTCACAGTCAGACC) as described [11]. The PCR product was precipitated, washed, resuspended in 10 μl ddH2O, and cleaned up by a Sephadex G-50 column. Heat the PCR product at 95 °C for 3 min to denature and chill on ice immediately. Combine the PCR product with equal volume of 2× hybridization buffer (8× SSC/0.2% SDS, pH 7.0) that has been heated to 48 °C and mix thoroughly. Immediately, inject the mixture into the hybridization chamber. Hybridization was carried out at 45 °C for 16 h. After hybridization, slides were washed (2× SSC/0.03% SDS, 2 min; 0.2× SSC, 2 min; 0.1× SSC, 1 min) at 25 °C.

scan_protocol: scaned by ScanArray5000

data_processing: Signal intensities for each spot were calculated by subtracting local background from total intensities. No further process was performed.

organism: Mus musculus

source_name: P19C6, N2B27 treated, 4 day

label_protocol: labeled by PCR using a Cy5 labeled primer

extract_protocol: The total RNAs were extracted with the RNarose reagent (Watson and Sangon).

treatment_protocol: For N2B27 induction,nearly confluent P19 cells were dissociated into single cells by Trypsin-EDTA ,and allowed to aggregate in the bacteriological petri dishes at a seeding density of 1 × 105/ml in N2B27 medium (1:1 mix of DMEM/F12 supplemented with 25 μg/ml insulin, 100 μg/ml apo-transferrin, 6 ng/ml progesterone, 16 μg/ml putrescine, 30 nM sodium selenite, 50 μg/ml bovine serum albumin fraction V, and neurobasal medium supplemented with B27 without Vitamin A). After 4 days of culture in suspension, the cell aggregates were collected, rinsed once with phosphate-buffered saline (PBS), fixed in 4% paraformaldehyde for 30 min, incubated in 20% sucrose overnight, embedded in cryomedium OCT,cryo-sectioned at a thickness of 15 μm, and stored at −20°C for further use. The factors and inhibitors, such as bone morphogenetic protein 4 (BMP4) (10 ng/ml), Noggin (100 ng/ml), SU5402 (5 μM), U0126 (5 μM), Wortmannin (100 nM), or U73122 (100 nM), were added at the beginning of the suspension culture, and were present throughout the experiments. To caudalize the N2B27-induced neural stem cells, the RA (2 μM) was added to the N2B27 medium for another 2–4 days, and the cell aggregates cultured in N2B27 medium for 6–8 days served as the control.

tag: P19C6, a subclone of the mouse EC P19 cell line

tag: 4 day treatment


title: low starch vs high starch roots (017)

status: Public on Jan 04 2009

city: Raleigh

first: Earl

middle: William

last: Taliercio

state: NC

address: 3127 Ligon St

institute: USDA/ARS

description: Gene profiling cotton roots before and after starch filling

hyb_protocol: protocol of MoGene (St Louis, MO)

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software

data_processing: for LSR values and statistics calculated from three reps including dye swap

organism: Gossypium hirsutum

source_name: total RNA from 3 week old roots low in starch

label_protocol: MicroMax kit from Perkin Elmer

extract_protocol: polyribosomeal RNA isolation

tag: cultvar STV4793R

source_name: total RNA from 7 week old roots increasing in starch

growth_protocol:
Greenhouse grown
Greenhouse grown

tag: cultivar STV4793R


title: FHM Ovary Trenbolone Control 4

description: RNA Integrity Number (RIN) = 10.0

source_name: FHM Ovary Trenbolone Control 4

tag: Adult fathead minnow ovary


title: FHM Ovary Trenbolone High Dose (1 µg/L ) #2

description: RNA Integrity Number (RIN) = 9.7

tag: Adult fathead minnow ovary (exposed 1 of 4)


title: Calf 150 gd T cells MDP

description: gd T cells derived from peripheral blood of calf 150 stimulated 4 hours with MDP

extract_protocol: PBLs were stained with GD3.8, and anti-Mouse IgG magnetic beads and sorted with MACS magnetic bead system (Miltenyi Biotec) as previously described to a purity of >98%.  Sorted cells were rested overnight then stimulated for 4 hours, lysed in Buffer RLT and genomic DNA sheared using Qiashredder columns then frozen at -80oC.  RNA was extracted following the manufacturer’s protocol for RNeasy (Qiagen) column purification.


title: 345366

status: Public on Jun 01 2009

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description:
LynDN-2 vs WT-3
Date:2008/06/26

hyb_protocol: Agilent : 750.0 ng at 62 degree_C during 16 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Interslide norm. : quantile, Intraslide norm. : printtiploess, Background norm. : none, Software used : limmagui --> VALUE data obtained from log of processed Red signal/processed Green signal.

label_protocol: Ambion

extract_protocol: Qiagen

tag: Tissue

value: skin


title: FHM Ovary Trenbolone Control 6

description: RNA Integrity Number (RIN) = 9.4

source_name: FHM Ovary Trenbolone Control 6


title: 4 day N2B27 treatment-library2-replicate1


title: FHM Ovary Trenbolone Control 1

description: RNA Integrity Number (RIN) = 9.9

source_name: FHM Ovary Trenbolone control 1

tag: Adult fathead minnow  ovary


title: FHM Ovary Trenbolone Control 3

description: RNA Integrity Number (RIN) = 9.8

source_name: FHM Ovary Trenbolone Control 3


title: FHM Ovary Trenbolone High Dose (1 µg/L ) #5

description: RNA Integrity Number (RIN) = 9.8

tag: Adult fathead minnow ovary (exposed 4 of 4)


title: 0 hour N2B27 treatment-library1-replicate1

source_name: P19C6, N2B27 treated, 0 hour

tag: 0 hour treatment


title: cotton stems from greenhouse(015)

description: Gene profiling cotton greenhouse grown stems before and after starch filling

source_name: total RNA from 7 Week old stems high in starch

source_name: total RNA from 5 week old stems low in starch harvested 6-24-04


title: JF1 mid-log replicate 3

status: Public on Dec 26 2008

city: Oklahoma City

first: Lydgia

last: Jackson

state: OK

address: 975 NE 10th Street

department: Microbiology and Immunology

institute: University of Oklahoma Health Sciences Center

hyb_protocol: Arrays were hybridized using streptavidin phycoerythrin according to Affymetrix protocol ProkGE-WS2v3_450

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000

data_processing: Data was processed using Genechip Operating Software (GCOS) version 1.4 (Affymetrix, Inc.)  GCOS data was then imported into GeneSpring GX 7.3.1 (Agilent Technologies) and normalized per chip by dividing each measurement by the 50th percentile of all the measurements in that sample and per gene by dividing each gene by the median of its measurements across all samples.  The cross-gene error model was operating based on replicates.  The normalized data from all samples were filtered on genes flagged as present or marginal with the resulting gene list used for further gene expression analysis and clustering.

organism: Neisseria gonorrhoeae

source_name: FA19mtrR mutant cells harvested at mid-log phase; 0.6 @600 OD

label_protocol: Biotinylated cRNA was prepared according to Affymetrix Genechip® Expression Analysis Technical Manual prokaryotic protocol from 10ug of total RNA

growth_protocol: Isolates were grown to mid-log phase in GC broth @ 37°C with supplements and sodium bicarbonate: Shafer, W.M., L. F. Guymon, I. Lind, and P. F. Sparling. 1984. Identification of an envelope mutation (env-10) resulting in increased antibiotic susceptibilit

extract_protocol: RNA was isolated by a hot phenol method according to: Ducey, T. F., M. B. Carson, J. Orvis, A. P. Stintzi, and D. W. Dyer. 2005.  Identification of the iron-responsive genes of Neisseria gonorrhoeae in microarray analysis in defined medium. J. Bacteriol.

tag: FA19mtrR mutant


title: JF1 mid-log replicate 2


title: JF1 mid-log replicate 1


title: 345471

description:
LynDN-3 vs WT-2
Date:2008/06/26


title: L. monocytogenes wild without iron

status: Public on Dec 25 2008

city: Normal

first: Arunachalam Muthaiyan

email: amuthai@gmail.com, bjwilkin@ilstu.edu

state: IL

address: Julian Hall

department: Biological Sciences

institute: Illinois State University

description:
Several controls were employed to minimise technical and biological variations, and ensure the quality of the data: i) each ORF was present quadruplicate in each array, ii) each RNA preparation was used to make probes for at least two-separate arrays with reversal of incorporated dye.
For all supplementary raw data files - Channel A = Cy3; Channel B= Cy5.

hyb_protocol: Purified labeled L. monocytogenes cDNA from test and control samples were hybridised on L. monocytogenes version 2 oligonucleotide microarray representing Open Reading Frames (ORFs) from L. monocytogenes strains EGD-e, 4b F2365, 1/2a F6854 and 4b H7858, obtained from Pathogen Functional Genomic Research Centre (http://pfgrc.tigr.org). Before hybridization, microarray slides were pre-hybridized with pre-hybridization buffer at 42˚C for 45 min. Pre-hybridized slides were washed with water (4 times) and isopropanol (3 times) for 2 min each and dried by centrifugation. Purified probes were speed-vaced and resuspended in hybridization buffer. The probes in hybridization buffer were applied to the microarray slides covered with lifterslips (Erie Scientific Co.). Hybridized slides were sealed in a water tight hybridization chamber. These chambers were incubated for 14-16 h in a 42˚C water bath. Hybridized arrays were then washed 2 times with low stringency, medium stringency, and high stringency buffers for 10 min at room temperature using a reciprocal shaking table.

scan_protocol: Hybridised slides were scanned using a GenePix 4000B microarray scanner (Axon Instruments) with Acuity 4.0 software and scans were stored as single TIFF images.

data_processing:
TIFF images of the hybridised arrays were analysed using the TIGR spotfinder software (www.tigr.org/software), and the local background was subsequently subtracted. The data set was normalised using the LOWESS algorithm by the TIGR-MIDAS (www.tigr.org/software) software. The normalized log2 ratio of test/control signal for each spot was recorded. The averaged log2 ratio for each gene on the six replicate slides was ultimately calculated. Significant changes of gene expression were identified with SAM (Significance-Analysis-of-Microarrays:
http://www-stat.stanford.edu/~tibs/SAM/) software using one class mode.

organism: Listeria monocytogenes

source_name: L. monocytogenes EGDe wild without iron

label_protocol: cDNA was synthesized from the purified RNA by the Institute of Genomics Research microarray protocol (TIGR). In this process 2 μg of the purified RNA was annealed with random hexamers as primers (Invitrogen) (70°C/5min and snap frozen in ice/1min), and extended overnight at 42°C with SuperScript II reverse transcriptase (Invitrogen) in the presence of 0.1 M dithiothreitol 12.5 mM DNTP/aa-UTP (Ambion) mix. Residual RNA was removed and cDNA was purified with a QIAquick PCR purification kit (Qiagen). Purified aminoallyl-modified cDNA was then recovered, labeld with Cy3 or Cy5 mono-functional NHS ester cyanogen dyes (Amersham Pharmacia Biotech, Piscataway, NJ), and purified, using Qiagen PCR purification kits following the manufacturers instructions.

extract_protocol: RNA was extracted from control samples using the Qiagen RNA extraction kit (Qiagen, Valencia, CA). In each case, 5 ml samples were mixed with bacterial RNA protect solution (Qiagen) to stabilise the transcripts, and the cells were recovered by centrifugation. Pelleted cells were resuspended in 1 ml of Trizol (Invitrogen), mechanically broken using the FastPrep system (Qbiogene, Irvine CA) at a speed setting of 6.0 for 40 seconds, and their lysate RNA was extracted from the cell lysate as per the manufacturer’s instructions. Extracted RNA was purified and residual DNA fragments were removed by DNAase (Qiagen) treatment using the RNeasy mini kit (Qiagen).

tag: Listeria monocytogenes EGDe wild

source_name: L. monocytogenes EGDe wild with iron


title: L. monocytogenes fur mutant without iron 2

source_name: L. monocytogenes Fur mutant without iron

tag: L. monocytogenes EGDe Fur mutant

source_name: L. monocytogenes Fur mutant with iron

extract_protocol: RNA was extracted from control and test samples using the Qiagen RNA extraction kit (Qiagen, Valencia, CA). In each case, 5 ml samples were mixed with bacterial RNA protect solution (Qiagen) to stabilise the transcripts, and the cells were recovered by centrifugation. Pelleted cells were resuspended in 1 ml of Trizol (Invitrogen), mechanically broken using the FastPrep system (Qbiogene, Irvine CA) at a speed setting of 6.0 for 40 seconds, and their lysate RNA was extracted from the cell lysate as per the manufacturer’s instructions. Extracted RNA was purified and residual DNA fragments were removed by DNAase (Qiagen) treatment using the RNeasy mini kit (Qiagen).


title: L. monocytogenes wild/fur mutant without iron 1

source_name: L. monocytogenes EGDe without iron

tag: L. monocytogenes EGDe wild

source_name: L. monocytogenes fur mutant without iron

tag: L. monocytogenes EGDe fur mutant


title: L. monocytogenes wild/fur mutant with iron 1

source_name: L. monocytogenes EGDe wild strain with iron

tag: L. monocytogenes EGDe wild strain

source_name: L. monocytogenes EGDe fur mutant with iron


title: L. monocytogenes in absence of iron

source_name: L. monocytogenes with iron

source_name: L. monocytogenes without iron


title: L. monocytogenes wild/fur mutant without iron 2

source_name: L. monocytogenes EGDe fur mutant without iron

tag: L. monocytogenes Fur mutant

source_name: L. monocytogenes wild type without iron

tag: L. monocytogenes wild


title: L. monocytogenes fur mutant without iron 1


title: Psychrobacter arcticus- 22°C vs -6°C- replicate 5

status: Public on Dec 10 2008

city: East Lansing

first: Peter

middle: W

last: Bergholz

state: MI

address: 540 Plant and Soil Sciences

department: Center for Microbial Ecology

institute: Michigan State University

description: Here we report that P. arcticus 273-4 exhibits two states of growth metabolism over temperature, a fast growth state at Topt and a resource efficiency state at temperature < 4°C. While numerous discoveries are reported, three hypotheses were the focus of this transcriptome analysis: i) transcriptomes at low temperature would be more similar to each other than to the transcriptomes at optimal growth temperatures, ii) genes for cold acclimation proteins such as RNA and protein chaperones, fatty acid desaturase and translation factors such as rbfA would be transcribed at higher levels during growth at low temperatures, and iii) acetate metabolism and energy metabolism would be up-regulated at low temperature to compensate for increased energy demand per generation. It was also expected that exchange of isozyme expression of temperature would be detectable in the microarray experiment. The transcriptome results were compared to a small scale proteome analysis and knockout mutants were also generated to test specific hypotheses resulting from the microarray. To the best of our knowledge, this is the first report of transcriptome analysis during growth below 0°C.

hyb_protocol: Amino-allyl labeled cDNAs were resuspended in 4.5 μl 0.1 M Na2CO3, pH 9.0 for 10 min at room temperature and combined with 4.5 μl Cy3 or Cy5 NHS-ester in DMSO (GE Biosciences, Piscataway, NJ). Dye incorporation reactions were incubated at 25°C for 1.5 h. Equipicomolar nucleotide amounts of dye-labeled cDNA samples were hybridized such that neither Cy3 nor Cy5 exceeded 550 pmoles. cDNAs were dried in a SpeedVac for 1.5 h. Hybridization mix was prepared by resuspending cDNA pellets in 50 μl 5X SSC, 25% formamide, 0.1% SDS and 0.1 mg/ml Salmon Testes DNA (Sigma-Aldrich). Glass slide arrays were prehybridized by incubation in 5X SSC, 0.1% SDS, 0.1 mg ml-1 BSA for 60 min at 49°C. Slides were then washed twice in room temperature 0.1X SSC for 5 min. Slides were washed twice for 30 sec in sterile water. Prehybridized slides were then immediately dried by centrifugation for 3 min at 1600 rpm in a Sorvall RT 6000D centrifuge with an H1000B hanging basket rotor. Lifterslips (22 x 60 mm, Erie Scientific, Portsmouth, NH) were washed in sterile water followed by 100% ethanol and dried under filtered forced air. Hybridization mix was preheated to 95°C for 10 min, then pipeted onto the slide. Hybridization cassettes were sealed and incubated in a 49°C water bath shaking at 30 rpm for 20 h.

scan_protocol: Slides were scanned using a Genepix 4000B scanner (Molecular Devices, Sunnyvale, CA). Images were analyzed using Genepix 6.0 software and results were analyzed for quality using the marray and arrayQuality packages in R 2.3.0 (http://www.r-project.org/). Only slides passing the quality control analysis were included in the biological analysis.

data_processing: Statistical significance of the temperature effect on gene expression was computed using R/MAANOVA 1.0 to determine statistical significance and LIMMA 2.7.10 to calculate pairwise comparisons of gene expression. In both cases data were normalized using regional (print-tip) lowess normalization. Normalized data were fit to a mixed-effects ANOVA model with gene, dye and temperature as fixed terms. Slide and biological replicate were random terms. F tests were carried out using the variance shrinking Fs statistic to determine the statistical significance of differential expression with 500 permutations to evaluate the distribution of Fs. Genes were considered differentially expressed if P < 0.01 after Benjamini-Hochberg P-value adjustment for multiple hypothesis testing. The false discovery rate for the statistically significant genes was estimated according to the method of Storey using the qvalue package in R. All pairwise temperature comparison coefficients were estimated using LIMMA.

organism: Psychrobacter arcticus 273-4

source_name: mid-exponential growth at -6°C

label_protocol: Three 5 μg aliquots of total RNA were denatured with 6 μg random hexamers (Invitrogen, Carlsbad, CA) in a 17.5 μl volume for 10 min at 70°C and snap-cooled for 5 min on ice. Denatured total RNA mixtures were reverse transcribed to amino-allyl labeled cDNAs by combining the total RNA mixture with 6 μl 5X First Strand Synthesis Buffer, 3 μl 0.1 M dithiothreitol, 1 μl RNaseOUT (Invitrogen), 1.2 μl 25X dNTPs (3 aa-dUTP:2 dTTP), and 2 μl Superscript II reverse transcriptase (Invitrogen). Amino-allyl dUTP was obtained from Ambion (Austin, TX). Reactions were incubated at 42°C overnight and stopped by addition of 10 μl 0.5 M EDTA. RNA was hydrolyzed by incubation with 10 μl 1 M NaOH at 65°C for 15 min. RNA hydrolysis was neutralized with 10 μl 1 M HCl. Amino-allyl labeled cDNAs were purified according to the amino-allyl labeling protocol published by The Institute for Genomic Research (TIGR) (Hegde et al 2000).

growth_protocol:
Growth Media and Procedure: For all experiments, single colonies of Psychrobacter arcticus 273-4 were used to inoculate primary cultures in marine broth (MB) which grew to OD600 ~ 0.8 at 4°C. One liter of MB consisted of 3% (w/v) sea salts (Sigma-Aldrich, St. Louis, MO), 5 g/l tryptone (BD, Sparks, MD) and 1 g/l yeast extract (Difco). A 1% (v/v) inoculum of this starter culture was transferred to 7 ml of acetate medium. One liter acetate medium contained 75 g l-1 sea salts (Sigma-Aldrich), 50 mM MOPS buffer (Sigma-Aldrich), 20 mM sodium acetate (Baker), 5 mM NH4Cl (Baker), pH 7.0 with NaOH, 1 mM K2HPO4 (Baker), 1X Wolfe’s Vitamins, and 1X trace minerals mix. Wolfe’s Vitamins (1000X) and trace minerals solutions were made according to M1 defined medium from Kostka and Nealson (31).
P. arcticus 273-4 was acclimatized to the acetate medium through two passages to OD600 ~ 0.8 at 4°C with shaking at 150 rpm before inoculation into experimental samples. A 5 ml inoculum from the final starter culture of P. arcticus in acetate medium was introduced to 500 ml acetate medium in 300 cm2 untreated and vent-capped Falcon tissue culture flask. Cultures were allowed to grow without shaking at -6°C, 0°C, 17°C or 22°C until they reached an OD600 between 0.09 and 0.25 (mid-exponential phase at all temperatures).

extract_protocol:
When cultures reached mid- exponential phase, 25 ml of culture was preserved with 2 volumes of RNAprotect Bacteria Reagent (Qiagen, Valencia, CA) which had been chilled to the growth temperature of the culture. Cells in RNAprotect were incubated at room temperature for 5 min then pelleted by centrifugation in a Sorvall RC-5B centrifuge at 4°C. Cells were resuspended in 1 ml room temperature RNAprotect and pelleted again in an Eppendorf 5417R centrifuge at 4°C. Supernatant was decanted and the cell pellet was frozen at -80°C.
RNA extractions were performed according to the RNEasy mini kit (Qiagen) with some modifications. Specificially, lysozyme digestion was carried out for 30 min. Following cell lysis using buffer RLT (Qiagen), 1 μl each of a two-fold dilution series of SpotReport mRNAs (Stratagene) ranging from 1 ng to 1 pg of RNA were added to the lysate as controls for RNA degradation during sample preparation. Purified RNAs were analysed by gel electrophoresis in a 1X FA gel containing 0.67% formaldehyde and 1.2% agarose.

tag: Growth Temperature

tag: Optical Density (OD600) at Harvest

tag: Growth Rate

source_name: mid-exponential growth at 22°C


title: Psychrobacter arcticus- 0°C vs -6°C- replicate 5

source_name: mid-exponential growth at 0°C


title: L. monocytogenes wild/fur mutant with iron 2


title: Psychrobacter arcticus- 22°C vs 0°C- replicate 4


title: Psychrobacter arcticus- 17°C vs -6°C- replicate 5

source_name: mid-exponential growth at 17°C


title: Psychrobacter arcticus- 22°C vs 0°C- replicate 5


title: Psychrobacter arcticus- 17°C vs 0°C- replicate 5


title: Psychrobacter arcticus- 22°C vs 0°C- replicate 3


title: Psychrobacter arcticus- 17°C vs -6°C- replicate 4


title: Psychrobacter arcticus- 0°C vs -6°C- replicate 4


title: Psychrobacter arcticus- 22°C vs 17°C- replicate 5


title: Psychrobacter arcticus- 22°C vs 0°C- replicate 2


title: Psychrobacter arcticus- 0°C vs -6°C- replicate 3


title: Psychrobacter arcticus- 22°C vs -6°C- replicate 3


title: Psychrobacter arcticus- 22°C vs -6°C- replicate 4


title: Psychrobacter arcticus- 22°C vs -6°C- replicate 2


title: Psychrobacter arcticus- 22°C vs 0°C- replicate 1


title: Psychrobacter arcticus- 17°C vs -6°C- replicate 3

growth_protocol:
Growth Media and Procedure: For all experiments, single colonies of Psychrobacter arcticus 273-4 were used to inoculate primary cultures in marine broth (MB) which grew to OD600 ~ 0.8 at 4°C. One liter of MB consisted of 3% (w/v) sea salts (Sigma-Aldrich, St. Louis, MO), 5 g/l tryptone (BD, Sparks, MD) and 1 g/l yeast extract (Difco). A 1% (v/v) inoculum of this starter culture was transferred to 7 ml of acetate medium. One liter acetate medium contained 75 g l-1 sea salts (Sigma-Aldrich), 50 mM MOPS buffer (Sigma-Aldrich), 20 mM sodium acetate (Baker), 5 mM NH4Cl (Baker), pH 7.0 with NaOH, 1 mM K2HPO4 (Baker), 1X Wolfe’s Vitamins, and 1X trace minerals mix. Wolfe’s Vitamins (1000X) and trace minerals solutions were made according to M1 defined medium (Kostka and Nealson 1998).
P. arcticus 273-4 was acclimatized to the acetate medium through two passages to OD600 ~ 0.8 at 4°C with shaking at 150 rpm before inoculation into experimental samples. A 5 ml inoculum from the final starter culture of P. arcticus in acetate medium was introduced to 500 ml acetate medium in 300 cm2 untreated and vent-capped Falcon tissue culture flask. Cultures were allowed to grow without shaking at -6°C, 0°C, 17°C or 22°C until they reached an OD600 between 0.09 and 0.25 (mid-exponential phase at all temperatures).


title: Psychrobacter arcticus- 17°C vs 0°C- replicate 2


title: Psychrobacter arcticus- 22°C vs 17°C- replicate 4


title: Myeloblasts_2

city: Modena

first: Francesco

last: Ferrari

address: Via G. Campi 287

department: Department of Biomedical Sciences

country: Italy

institute: University of Modena and Reggio Emilia

description: In vitro differentiated normal human myeloblasts

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner GCS3000.

data_processing: The data were analyzed using Bioconductor packages and RMA pre-processing procedure

organism: Homo sapiens

label_protocol: RNA samples from cells of different donors were pooled to obtain 5 μg of total cellular RNA that were used for target synthesis according to the standard one-cycle Affymetrix protocol, supplied by the manufacturer (Affymetrix, Santa Clara, CA).

growth_protocol: Monoblasts (CD14+ precursors) and myeloblasts (CD14- precursors) were obtained by in vitro differentiation of cord blood (CB) derived CD34+ cells performed as already described by Montanari et al. Briefly, CB CD34+ cells were cultured in IMDM added with 20% FCS (Bio-Whittaker, Walkersville, MD, USA), in the presence of human hematopoietic cytokines: SCF (50 ng/ml), Flt3-ligand (Flt3-l) (50 ng/ml), IL-11 (50 ng/ml), IL-6 (10 ng/ml), IL-3 (10 ng/ml) and G-CSF (10 ng/ml) (all from R&D Systems, Minneapolis, MN, USA). After 7 days of culture, hematopoietic cells were analyzed, by flow cytometry, for CD14 antigen expression, estimated at about 25-30% of the entire cell population. Then monoblasts (CD14+) and myeloblasts (CD14-) cell fractions were obtained by immunomagnetic separation using the MACS technology (Miltenyi). Differentiation of CD34+ cells was monitored by morphological analysis of MGG-stained cytospins and by flow-cytometric analysis of CD34, CD38 and CD14 surface antigen expression.

extract_protocol: Total cellular RNA was isolated by means of RNeasy Mini Kit (Qiagen, Valencia, CA) following manufacturer's recommendations.

tag: type

value: in vitro differentiated cells derived from CD34+ stem/progenitor cells from healthy donors


title: Myeloblasts_1

source_name: In vitro differentiated normal human myeloblasts


title: Myeloblasts_3


title: Psychrobacter arcticus- 22°C vs 17°C- replicate 2

tag: Growth temperature


title: Psychrobacter arcticus- 22°C vs 17°C- replicate 3


title: Monoblasts_3

description: In vitro differentiated normal human monoblasts


title: Monoblasts_2

source_name: In vitro differentiated normal human monoblasts


title: Monoblasts_1


title: Psychrobacter arcticus- 17°C vs 0°C- replicate 1


title: Megakaryoblasts_1

description: In vitro differentiated normal human megakaryoblasts

growth_protocol: Megakaryoblasts were obtained by in vitro differentiation of CD34+ cells performed as already described by Tenedini et al. Briefly, megakaryocytes were obtained from CD34+ cells cultivated in serum-free medium supplemented with 50 ng/mL SCF and 100ng/mL thrombopoietin (TPO; Genzyme, Boston, MA) for 14-16 days and subsequently selected by means of a magnetic beads sorting procedure using monoclonal antibody directed against CD41a antigen (Dako, Milan, Italy).


title: Psychrobacter arcticus- 17°C vs 0°C- replicate 4


title: Erythroblasts_2

description: In vitro differentiated normal human erythroblasts

growth_protocol: Normal human erythroblasts were obtained from cord blood CD34+ hematopoietic progenitors cultured in IMDM (Euroclone) supplemented with 20% BIT (Stem Cell Technologies), 50 ng/ml SCF and 4 U/ml Erythropoietin (R&D Systems, Minneapolis, MN) for 8-10 days[63]. Differentiation of CD34+ cells was monitored daily by morphological analysis of May and Grunwald - Giemsa (MGG) stained cytospins and by flow-cytometric analysis of glycophorin A (GPA) surface antigen expression, using the phycoerythrin (PE)-conjugated mouse anti-human GPA monoclonal antibody (MoAb) (Becton Dickinson Systems, Mountain View, CA, USA).


title: field grown cotton stems (019)

description: Gene profiling field grown stems before and after starch filling

source_name: total RNA from stems low in starch harvested 6-24-04

tag: cultvar STV4793R

source_name: total RNA from stems increasing in starch harvested 7-7-04

growth_protocol:
field grown
field grown

tag: cultivar STV4793R


title: Psychrobacter arcticus- 17°C vs 0°C- replicate 3


title: Erythroblasts_1

source_name: In vitro differentiated normal human erythroblasts


title: Erythroblasts_3


title: Megakaryoblasts_2

source_name: In vitro differentiated normal human megakaryoblasts


title: Psychrobacter arcticus- 0°C vs -6°C- replicate 1

description: Here we report that P. arcticus 273-4 exhibits two states of growth metabolism over temperature, a fast growth state at Topt and a resource efficiency state at temperature < 4°C.  While numerous discoveries are reported, three hypotheses were the focus of this transcriptome analysis:  i) transcriptomes at low temperature would be more similar to each other than to the transcriptomes at optimal growth temperatures, ii) genes for cold acclimation proteins such as RNA and protein chaperones, fatty acid desaturase and translation factors such as rbfA would be transcribed at higher levels during growth at low temperatures, and iii) acetate metabolism and energy metabolism would be up-regulated at low temperature to compensate for increased energy demand per generation.  It was also expected that exchange of isozyme expression of temperature would be detectable in the microarray experiment.  The transcriptome results were compared to a small scale proteome analysis and knockout mutants were also generated to test specific hypotheses resulting from the microarray.  To the best of our knowledge, this is the first report of transcriptome analysis during growth below 0°C.

hyb_protocol: Amino-allyl labeled cDNAs were resuspended in 4.5 μl 0.1 M Na2CO3, pH 9.0 for 10 min at room temperature and combined with 4.5 μl Cy3 or Cy5 NHS-ester in DMSO (GE Biosciences, Piscataway, NJ).  Dye incorporation reactions were incubated at 25°C for 1.5 h.  Equipicomolar nucleotide amounts of dye-labeled cDNA samples were hybridized such that neither Cy3 nor Cy5 exceeded 550 pmoles.  cDNAs were dried in a SpeedVac for 1.5 h.  Hybridization mix was prepared by resuspending cDNA pellets in 50 μl 5X SSC, 25% formamide, 0.1% SDS and 0.1 mg/ml Salmon Testes DNA (Sigma-Aldrich). 	Glass slide arrays were prehybridized by incubation in 5X SSC, 0.1% SDS, 0.1 mg ml-1 BSA for 60 min at 49°C.  Slides were then washed twice in room temperature 0.1X SSC for 5 min.  Slides were washed twice for 30 sec in sterile water.  Prehybridized slides were then immediately dried by centrifugation for 3 min at 1600 rpm in a Sorvall RT 6000D centrifuge with an H1000B hanging basket rotor.  Lifterslips (22 x 60 mm, Erie Scientific, Portsmouth, NH) were washed in sterile water followed by 100% ethanol and dried under filtered forced air.  Hybridization mix was preheated to 95°C for 10 min, then pipeted onto the slide.  Hybridization cassettes were sealed and incubated in a 49°C water bath shaking at 30 rpm for 20 h.

scan_protocol: Slides were scanned using a Genepix 4000B scanner (Molecular Devices, Sunnyvale, CA).  Images were analyzed using Genepix 6.0 software and results were analyzed for quality using the marray and arrayQuality packages in R 2.3.0 (http://www.r-project.org/).  Only slides passing the quality control analysis were included in the biological analysis.

data_processing: Statistical significance of the temperature effect on gene expression was computed using R/MAANOVA 1.0 to determine statistical significance and LIMMA 2.7.10 to calculate pairwise comparisons of gene expression.  In both cases data were normalized using regional (print-tip) lowess normalization.  Normalized data were fit to a mixed-effects ANOVA model with gene, dye and temperature as fixed terms.  Slide and biological replicate were random terms.  F tests were carried out using the variance shrinking Fs statistic to determine the statistical significance of differential expression with 500 permutations to evaluate the distribution of Fs.  Genes were considered differentially expressed if P < 0.01 after Benjamini-Hochberg P-value adjustment for multiple hypothesis testing.  The false discovery rate for the statistically significant genes was estimated according to the method of Storey using the qvalue package in R. All pairwise temperature comparison coefficients were estimated using LIMMA.

label_protocol: Three 5 μg aliquots of total RNA were denatured with 6 μg random hexamers (Invitrogen, Carlsbad, CA) in a 17.5 μl volume for 10 min at 70°C and snap-cooled for 5 min on ice.  Denatured total RNA mixtures were reverse transcribed to amino-allyl labeled cDNAs by combining the total RNA mixture with 6 μl 5X First Strand Synthesis Buffer, 3 μl 0.1 M dithiothreitol, 1 μl RNaseOUT (Invitrogen), 1.2 μl 25X dNTPs (3 aa-dUTP:2 dTTP), and 2 μl Superscript II reverse transcriptase (Invitrogen).  Amino-allyl dUTP was obtained from Ambion (Austin, TX).  Reactions were incubated at 42°C overnight and stopped by addition of 10 μl 0.5 M EDTA.  RNA was hydrolyzed by incubation with 10 μl 1 M NaOH at 65°C for 15 min.  RNA hydrolysis was neutralized with 10 μl 1 M HCl.  Amino-allyl labeled cDNAs were purified according to the amino-allyl labeling protocol published by The Institute for Genomic Research (TIGR) (Hegde et al 2000).

growth_protocol:
Growth Media and Procedure: For all experiments, single colonies of Psychrobacter arcticus 273-4 were used to inoculate primary cultures in marine broth (MB) which grew to OD600 ~ 0.8 at 4°C.  One liter of MB consisted of 3% (w/v) sea salts (Sigma-Aldrich, St. Louis, MO), 5 g/l tryptone (BD, Sparks, MD) and 1 g/l yeast extract (Difco).  A 1% (v/v) inoculum of this starter culture was transferred to 7 ml of acetate medium.  One liter acetate medium contained 75 g l-1 sea salts (Sigma-Aldrich), 50 mM MOPS buffer (Sigma-Aldrich), 20 mM sodium acetate (Baker), 5 mM NH4Cl (Baker), pH 7.0 with NaOH, 1 mM K2HPO4 (Baker), 1X Wolfe’s Vitamins, and 1X trace minerals mix.  Wolfe’s Vitamins (1000X) and trace minerals solutions were made according to M1 defined medium from Kostka and Nealson (31).
P. arcticus 273-4 was acclimatized to the acetate medium through two passages to OD600 ~ 0.8 at 4°C with shaking at 150 rpm before inoculation into experimental samples.  A 5 ml inoculum from the final starter culture of P. arcticus in acetate medium was introduced to 500 ml acetate medium in 300 cm2 untreated and vent-capped Falcon tissue culture flask.  Cultures were allowed to grow without shaking at -6°C, 0°C, 17°C or 22°C until they reached an OD600 between 0.09 and 0.25 (mid-exponential phase at all temperatures).

extract_protocol:
When cultures reached mid- exponential phase, 25 ml of culture was preserved with 2 volumes of RNAprotect Bacteria Reagent (Qiagen, Valencia, CA) which had been chilled to the growth temperature of the culture.  Cells in RNAprotect were incubated at room temperature for 5 min then pelleted by centrifugation in a Sorvall RC-5B centrifuge at 4°C.  Cells were resuspended in 1 ml room temperature RNAprotect and pelleted again in an Eppendorf 5417R centrifuge at 4°C.  Supernatant was decanted and the cell pellet was frozen at -80°C.
	RNA extractions were performed according to the RNEasy mini kit (Qiagen) with some modifications.  Specificially, lysozyme digestion was carried out for 30 min.  Following cell lysis using buffer RLT (Qiagen), 1 μl each of a two-fold dilution series of SpotReport mRNAs (Stratagene) ranging from 1 ng to 1 pg of RNA were added to the lysate as controls for RNA degradation during sample preparation.  Purified RNAs were analysed by gel electrophoresis in a 1X FA gel containing 0.67% formaldehyde and 1.2% agarose.

growth_protocol:
Growth Media and Procedure: For all experiments, single colonies of Psychrobacter arcticus 273-4 were used to inoculate primary cultures in marine broth (MB) which grew to OD600 ~ 0.8 at 4°C.  One liter of MB consisted of 3% (w/v) sea salts (Sigma-Aldrich, St. Louis, MO), 5 g/l tryptone (BD, Sparks, MD) and 1 g/l yeast extract (Difco).  A 1% (v/v) inoculum of this starter culture was transferred to 7 ml of acetate medium.  One liter acetate medium contained 75 g l-1 sea salts (Sigma-Aldrich), 50 mM MOPS buffer (Sigma-Aldrich), 20 mM sodium acetate (Baker), 5 mM NH4Cl (Baker), pH 7.0 with NaOH, 1 mM K2HPO4 (Baker), 1X Wolfe’s Vitamins, and 1X trace minerals mix.  Wolfe’s Vitamins (1000X) and trace minerals solutions were made according to M1 defined medium (Kostka and Nealson 1998).
P. arcticus 273-4 was acclimatized to the acetate medium through two passages to OD600 ~ 0.8 at 4°C with shaking at 150 rpm before inoculation into experimental samples.  A 5 ml inoculum from the final starter culture of P. arcticus in acetate medium was introduced to 500 ml acetate medium in 300 cm2 untreated and vent-capped Falcon tissue culture flask.  Cultures were allowed to grow without shaking at -6°C, 0°C, 17°C or 22°C until they reached an OD600 between 0.09 and 0.25 (mid-exponential phase at all temperatures).


title: CD34+_PB_2

description: Stem/progenitor hematopoietic cells CD34+ from periferal blood (PB)

growth_protocol: Peripheral blood hemopoietic stem and progenitor cells, were obtained from healthy donors who received recombinant human G-CSF (Lenograstim, Rhone-Poulenc Rorer, Milan, Italy), administered subcutaneously at 10 ug/kg per day for 5-6 days. Hematopoietic stem/progenitor CD34+ cell purification was then performed as described for cord blood samples: mononuclear cells were isolated by Ficoll-Hypaque gradient separation, washed twice with PBS, and then CD34+ cells separated using a magnetic cell sorting procedure (EasySep Human CD34 Positive Selection Kit, StemCell Technologies).

value: primary cells from healthy donors


title: Psychrobacter arcticus- 0°C vs -6°C- replicate 2


title: High AP3 producing Actinosynnema pretiosum (ATCC:31565) rifampicin mutant_Biolreplicate3_day8

status: Public on Dec 01 2008

type: mixed

city: Singapore

last: Nissom

address: 20 Biopolis Way

country: Singapore

institute: Bioprocessing Technology Institute

description: Biological replicate : r50D1 rifampicin resistant clone derived from Actinosynnema pretiocum (ATCC:31565) day 8 sample vs gDNA reference 2 technical repeats

hyb_protocol: Slides were pre-hybridized with 5x saline sodium citrate buffer(SSC), 50% deionised formamide, 0.1% sodium dodecyl sulphate(SDS) and 1 % Bovine serum albumin for 2 hour at 42oC. Labelled cDNA and gDNA was cleaned up using mineluate columns per manufacture’s protocol (Qiagen, USA). Hybridisation mixture comprising of labelled cDNA from 10ug of total RNA, 0.1ug of labelled gDNA, 5 x SSC, 25% deionised formamide and 0.1% SDS were heated at 95oC for 5 minutes, cooled on ice before sample was applied to the microarray slides and enclosed in hybridisation chambers for 16 hours at 42oC. Cover slips of the microarray were firsted removed in SSC and 0.2% SDS before being washed in twice in 2 x SSC for 5 mintues each wash, two five minutes wash in 0.1 x SSC with 0.1%SDS and final two washes of 5 mintues each in 0.1x SSC. Slides were subsequently dried by centrifuging at 129g for 3 minutes.

scan_protocol: Slides were scanned on a Axon GenePixÔ 4000B scanner and images were analysed using GenePix Pro 4.1. Expression data was exported into microsoft Excel for normalisation and further analysis

data_processing: Zero or negative value background corrected readings were assigned a value of one.  Quantile normalization was carried out based on the method described in Mehra et al. {Mehra, 2006 157 /id}.  Briefly, log2(cDNA/gDNA) was first calculated for each data point, before the log ratio of each array was sorted in ascending order and ranked accordingly.  The “reference” array was generated by taking the median value of each rank.  To normalize the data, percentile values from each of the array to be normalized was replaced by the corresponding value from the reference array before unsorting back to the original order. Technical replicates were averaged and standard deviation was calculated for log intensity ratios for each probe. Probe with log intensity ratios more then 1 standard deviation from the average were treated as outliers and discarded. Technical replicates were then averaged again. Each chip was then scale normalized {Quackenbush, 2002 301 /id} by subtracting the 16s log ratio from each data point.

organism: Actinosynnema pretiosum

source_name: Rifampicin resistant mutant, derived from Actinosynnema pretiosum, cultured in YMG day 8

label_protocol:
10ug of total RNA was incubated with 2ug of randomer hexamer. Incubated at 70Co for 5 mintues and placed on ice. 1pmole of Cy3 labelled dUTP, low dT-dNTP mix Rnase inhibitor and 2uL of RevertAidTM H- Minus M- MuLV Reverse Transcriptase (Fermentas Life Sciences, MD) was added. Mixture is incubated at room temperature for 10 minutes folloed by 42Co for 2 hours
10 µg of total RNA were primed with 2 µl of 100 µM random DNA primer (N9) at 70°C for 5min, then reversed transcribed at 42°C for 1 h in the presence of 400 U RevertAidTM H- Minus M- MuLV Reverse Transcriptase (Fermentas Life Sciences, MD), and 25 µM each dATP, dCTP, dGTP, with 12.5 µM dTTP, and 25 µM Cy3-labelled dUTP.

growth_protocol: Spores from single colonies were cultured in Vegetative medium (5 g/l meat extract, 5/l g peptone, 5 g/l yeast extract, 2.5 g/l enzyme hydrolysate of casein, 20 g/l glucose, 1.5 g/l NaCl) for 2 days at 26oC. 2mL of seed culture was used to innoculate 320mL of YMG media (4 g/l yeast extract, 10 g/l malt extract, 4 g/l glucose, pH 7.2) Cultures were incubated at 26oC shekn at 190rpm. Samples were taken at day 2, 4, 6 and 8 of the culture. The samples were centrifuged at 3000g at 4oC for 15 mintues. The supernatent was used for Ansamitocin-P3 analysis and the volume of the cell pellet estimated(PCV) before freezing and storing at -80oC.

extract_protocol: DEPC treated water equvilent to 0.5 x volume of cell pellet was added to the cell pellet. After cell pellet has thawed, it is subjected to 5 more cycles of freezing thawing in liquid nitrogen and a 55oC waterbath respectively. The cell pellet is then treated with lysozyme (3.5 mg/ml) at 37oC  for 20 min. The supernatent removed through centrifugation and the pellet mixed with Rnawiz (Ambion, USA) and RiboPureTM-Bacteria Kit (Ambion, USA) was used as per manufecturer's protocol. Optional Dnase cleanup step was also performed.

tag: Derived from Actinosynnema pretiosum (ATCC:31565) Resistant to 50ug/mL rifampicin

molecule: genomic DNA

source_name: Actinosynnema pretiosum sheared genomic DNA

label_protocol: Actinosynnema pretiosum genomic DNA was sheared by sonicating on ice with the Vibra-CellTM  fitted with a 3mm probe (Sonics and Materials, CT)  for 1 min. 0.1ug of sheared gDNA was incubated with 300µg/mL random DNA octomers at 96Co for 5 mintues then placed on ice. It was then incubated with 50U of klenow fragments (New England Biolabs, USA), 120µM each of dATP, dCTP,dGTP, 60µM of dTTP and 40µM of Cy5-labelled dUTP at 37oC for 2 hours.

tag: Strain

value: ATCC number:31565


title: CD34+_PB_1

source_name: Stem/progenitor hematopoietic cells CD34+ from periferal blood (PB)


title: High AP3 producing Actinosynnema pretiosum (ATCC:31565) rifampicin mutant_Biolreplicate2_day8


title: High AP3 producing Actinosynnema pretiosum (ATCC:31565) rifampicin mutant_Biolreplicate1_day8

description: Biological replicate : r50D1 rifampicin resistant clone derived from Actinosynnema pretiocum (ATCC:31565) day 8 sample vs gDNA reference 3 technical repeats


title: Actinosynnema pretiosum (ATCC:31565)_Biolreplicate2_day8

description: Biological replicate : Wildtype Actinosynnema pretiocum (ATCC:31565) day 8 sample vs gDNA reference 2 technical repeats

source_name: Actinosynnema pretiosum cultured in YMG day 8


title: High AP3 producing Actinosynnema pretiosum (ATCC:31565) rifampicin mutant_Biolreplicate2_day6

description: Biological replicate : r50D1 rifampicin resistant clone derived from Actinosynnema pretiocum (ATCC:31565) day 6 sample vs gDNA reference 2 technical repeats

source_name: Rifampicin resistant mutant, derived from Actinosynnema pretiosum, cultured in YMG day 6


title: Psychrobacter arcticus- 22°C vs 17°C- replicate 1

label_protocol: Amino-allyl dUTP was obtained from Ambion (Austin, TX).  Reactions were incubated at 42°C overnight and stopped by addition of 10 μl 0.5 M EDTA.  RNA was hydrolyzed by incubation with 10 μl 1 M NaOH at 65°C for 15 min.  RNA hydrolysis was neutralized with 10 μl 1 M HCl.  Amino-allyl labeled cDNAs were purified according to the amino-allyl labeling protocol published by The Institute for Genomic Research (TIGR) (Hegde et al 2000).


title: Actinosynnema pretiosum (ATCC:31565)_Biolreplicate3_day8


title: High AP3 producing Actinosynnema pretiosum (ATCC:31565) rifampicin mutant_Biolreplicate3_day6


title: CD34+_CB_2

description: Stem/progenitor hematopoietic cells CD34+ from cord blood (CB)

growth_protocol: Human CD34+ cells were purified from umbilical cord blood samples: mononuclear cells were isolated by Ficoll-Hypaque gradient separation, washed twice with PBS, and then CD34+ cells separated using a magnetic cell sorting procedure (EasySep Human CD34 Positive Selection Kit, StemCell Technologies).


title: Actinosynnema pretiosum (ATCC:31565)_Biolreplicate1_day8

description: Biological replicate : Wildtype Actinosynnema pretiocum (ATCC:31565) day 8 sample vs gDNA reference 3 technical repeats


title: Psychrobacter arcticus- 17°C vs -6°C- replicate 2


title: Psychrobacter arcticus- 22°C vs -6°C- replicate 1


title: CD34+_BM_1

description: Stem/progenitor hematopoietic cells CD34+ from bone marrow (BM)

growth_protocol: Human CD34+ cells were purified from bone marrow blood samples: mononuclear cells were isolated by Ficoll-Hypaque gradient separation, washed twice with PBS, and then CD34+ cells separated using a magnetic cell sorting procedure (EasySep Human CD34 Positive Selection Kit, StemCell Technologies).


title: CD34+_BM_2

source_name: Stem/progenitor hematopoietic cells CD34+ from bone marrow (BM)


title: Psychrobacter arcticus- 17°C vs -6°C- replicate 1


title: CD34+_CB_1

source_name: Stem/progenitor hematopoietic cells CD34+ from cord blood (CB)


title: High AP3 producing Actinosynnema pretiosum (ATCC:31565) rifampicin mutant_Biolreplicate1_day6


title: Actinosynnema pretiosum (ATCC:31565)_Biolreplicate3_day6

description: Biological replicate : Wildtype Actinosynnema pretiocum (ATCC:31565) day 6 sample vs gDNA reference 2 technical repeats

source_name: Actinosynnema pretiosum cultured in YMG day 6


title: Actinosynnema pretiosum (ATCC:31565)_Biolreplicate2_day6


title: High AP3 producing Actinosynnema pretiosum (ATCC:31565) rifampicin mutant_Biolreplicate3_day4

description: Biological replicate : r50D1 rifampicin resistant clone derived from Actinosynnema pretiocum (ATCC:31565) day 4 sample vs gDNA reference 2 technical repeats

source_name: Rifampicin resistant mutant, derived from Actinosynnema pretiosum, cultured in YMG day 4


title: Actinosynnema pretiosum (ATCC:31565)_Biolreplicate1_day6

description: Biological replicate : Wildtype Actinosynnema pretiocum (ATCC:31565) day 6 sample vs gDNA reference 3 technical repeats


title: High AP3 producing Actinosynnema pretiosum (ATCC:31565) rifampicin mutant_Biolreplicate2_day4


title: Actinosynnema pretiosum (ATCC:31565)_Biolreplicate3_day4

description: Biological replicate : Wildtype Actinosynnema pretiocum (ATCC:31565) day 4 sample vs gDNA reference 2 technical repeats

source_name: Actinosynnema pretiosum cultured in YMG day 4


title: Actinosynnema pretiosum (ATCC:31565)_Biolreplicate3_day2

description: Biological replicate : Wildtype Actinosynnema pretiocum (ATCC:31565) day 2 sample vs gDNA reference 2 technical repeats

source_name: Actinosynnema pretiosum cultured in YMG day 2


title: High AP3 producing Actinosynnema pretiosum (ATCC:31565) rifampicin mutant_Biolreplicate3_day2

description: Biological replicate : r50D1 rifampicin resistant clone derived from Actinosynnema pretiocum (ATCC:31565) day 2 sample vs gDNA reference 2 technical repeats

source_name: Rifampicin resistant mutant, derived from Actinosynnema pretiosum, cultured in YMG day 2


title: Actinosynnema pretiosum (ATCC:31565)_Biolreplicate1_day2

description: Biological replicate : Wildtype Actinosynnema pretiocum (ATCC:31565) day 2 sample vs gDNA reference 3 technical repeats


title: Actinosynnema pretiosum (ATCC:31565)_Biolreplicate2_day4


title: Actinosynnema pretiosum (ATCC:31565)_Biolreplicate2_day2


title: High AP3 producing Actinosynnema pretiosum (ATCC:31565) rifampicin mutant_Biolreplicate1_day4


title: High AP3 producing Actinosynnema pretiosum (ATCC:31565) rifampicin mutant_Biolreplicate2_day2


title: High AP3 producing Actinosynnema pretiosum (ATCC:31565) rifampicin mutant_Biolreplicate1_day2


title: Actinosynnema pretiosum (ATCC:31565)_Biolreplicate1_day4

description: Biological replicate : Wildtype Actinosynnema pretiocum (ATCC:31565) day 4 sample vs gDNA reference 3 technical repeats


title: Adipose tissue-derived MSC 2

city: Roma

first: Nathalie

last: Saulnier

address: Largo Francesco Vito,1

institute: Università Cattolica del Sacro Cuore di Roma

description: Adipose tissue-derived stromal cells (ATSC) hold great promises for the regenerative medicine, due to their in vitro high proliferative capacity and multilineage differentiation potential. In particular, the hepatic differentiation of ATSC has been so far reported in vitro and in vivo. Molecular mechanisms allowing the differentiation of these cells toward another tissue lineage are however poorly understood. The aim of this study is to compare the transcriptome of ATSC cultured under standard procedure and ATSC cultured for 4 weeks under an hepatogenic regimen.

hyb_protocol: Biotin-labeled cRNA was purified and chemically fragmented according to Affymetrix's protocol. Ten micrograms of fragmented and biotin-labeled cRNA were hybridized onto Human Focus array at 45°C for 16 hours in a rotisserie oven set at 60RPM. The following day, the chip was washed and labeled with streptavidin-phycoerythrin in a fluidic station using the EukGE-WS2v5 protocol according to Affymetrix' s recommendation.

scan_protocol: Arrays were read with the geneChip Affymetrix 3000 7G scanner.

data_processing: Data were generated by using Affymetrix MAS 5.0 software. Briefly, the signal value was calculated from the combined background-adjusted, PerfectMatch and MisMatch values of the probe set using predefined algorithms of MAS 5.0 software. Data set was further exported to GeneSpring software for normalization, statistical analysis and functional categorization.

label: Biotin

source_name: Human subcutaneous adipose tissue

label_protocol: Labeling protocol was accomplished according to Affymetrix recommended protocol. Briefly, following cDNA synthesis, the material was amplified and labeled with biotinylated dNTPs during an in vitro transcription (IVT) using the GeneChip Expression 3' Amplification One-Cycle target Labeling and Control Reagents (Affymetrix Inc.)

growth_protocol: AT was extensively washed in PBS, dissected into small pieces and digested with 0.1% collagenase for 30 minutes at 37°C. Then, the solution was filtered through a 100um mesh filter, and the cell suspension was cultured in DMEM supplemented with 10% FBS and 2ng/ml FGF-beta. Cells were expanded in vitro and harvested at culture passage 4 for this experiement.

extract_protocol: Total RNA was isolated using the RNeasy mini kit (Qiagen) according to the manufacturer's instructions. An additional on-column DNase incubation was added, allowing the selective removal of genomic DNA during the isolation procedure. RNA was quantified by UV spectrophotometer and quality was assessed on agarose gel.

tag: Adipose tissue was retrieved from a female (42 year old) patient


title: Adipose tissue-derived hepatocyte-like cells 1

growth_protocol: AT was extensively washed in PBS, dissected into small pieces and digested with 0.1% collagenase for 30 minutes at 37°C. Then, the solution was filtered through a 100um mesh filter, and the cell suspension was cultured in DMEM supplemented with 10% FBS and 2ng/ml FGF-beta. Cells were expanded in vitro up to culture passage 4, before initiating the hepatogenic conversion.

treatment_protocol: At passage culture 4, cells were submitted to the in vitro hepatogenic regimen. Briefly, serum was depleted for 48 hours. Cells were cultured for 2 weeks in the induction medium consisting in DMEM supplemented with 2% FBS, 4.9mM nicotinamide, 20ng/ml hepatocyte growth factor, and 10ng/ml fibroblast growth factor beta. Then, cells were cultured for 2 other weeks in maturation medium containing DMEM supplemented with 2% FBS, 4.9mM nicotinamdie and 20ng/ml oncostatin M.

tag: Adipose tissue was obtained from a patient (male, 52 year old) undergoing partial abdominolasty


title: Adipose tissue-derived hepatocyte-like cells 2

tag: Adipose tissue was obtained from a female (42 year old ) patient undergoing partial abdominoplasty.


title: Ad-F7 transduction + anti-IFNAR2 treatment in primary human macrophages (Experiment 2)

status: Public on Nov 30 2008

city: Montreal

first: Eduardo

last: Hernandez

state: Quebec

address: 3755 Cote-Sainte-Catherine Road

department: Molecular Oncology Group

country: Canada

institute: Lady Davis Institute for Medical Research (JGH)

description: See illumina's sample preparation

hyb_protocol: From illumina

scan_protocol: From illumina

data_processing: BeadStudio from illumina, J-Express from Molmine and  R

source_name: Macrophages Ad-F7 + anti-IFNAR2

label_protocol: Ambion, TotalPrep, for biotin labeling and illumina's protocol for Cy3 labeling.

extract_protocol: Qiagen RNeasy Plus extraction kit

treatment_protocol: Transduction of primary human macrophages with Ad-F7 and treatment of cells with anti-IFNAR2

tag: Human macrophages transduced with adenoviral vector expression the active form of IRF-7 (IRF-7 D247-467; Ad-F7) and treatment of cells with neutralizing antibody for the type I IFN receptor (IFNAR2). RNA collected at 24 hours.


title: D562 cell line relative to normal diploid cell

type: genomic

city: Tsurumi-ku, Yokohama

first: Katsuyuki

last: Hayashi

state: Kanagawa

address: 1-1-43, Suehiro-cho

department: Business Development

country: Japan

institute: DNA Chip Research Inc

description: D562 cell line relative to normal duploid cell

hyb_protocol: The samples were hybridized for 40 hours using the Agilent Oligo aCGH Hybridization Kit according to the manufacturer's instructions.

scan_protocol: Arrays were scanned on an Agilent carousel scanner following maufacturer's instructions. Agilent Feature Extractor software was used to extract the data.

data_processing: Data were extracted using Agilent's Feature Extraction software, version 9.1 (P/N G2565BA), Cy3 corresponding to the Processed Signal column of FE file, Cy5 corresponding to the rProcessedSignal column of FE file. Normalized log2 ratio (Cy3/Cy5) was calculated using CGH-v4_95_Feb07 protocol of FE software.

source_name: Normal human diploid genomic DNA

label_protocol: The samples were labeled using the Agilent Geomic DNA Labeling Kit PLUS (Agilent p/n 5188-5309) according to manufacturer's instructions. Genomic DNA was fragmented using restriction exzymes. Random hexamers were used to prime an Exo-Klenow fragment DNA polymerase reaction incorporating CyDye labeled dUTP.

growth_protocol: Five of the esophageal squamous cell carcinoma (ESCC) cell lines (TE1, TE2, TE3, YES1, and YES2) were maintained in RPMI1640 (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (Hyclone, Logan, UT). Five of the (HNSCC) cell lines (Ca9-22, H1, HSC2, HSC3, and D562) were maintained in DMEM (Dulbecco’s modified Eagle medium) /F12 (Invitrogen) with 10% fetal bovine serum (Hyclone). These cells were cultured in 5% CO2 at 37°C.

extract_protocol: Chromosomal DNA was isolated from ESCC and HNSCC cell lines using FlexiGene(QIAGEN) according manufacturer's protocol.

tag: Purchased from Promega

tag: Pharyngeal squamous cell carcinoma cell line


title: Ad-GFP transduction + IgG treatment in primary human macrophages (control Experiment 2)

description: See illumina's sample preparation

source_name: Ad-GFP + IgG

treatment_protocol: Transduction of primary human macrophages with Ad-GFP and treatment of cells with IgG

tag: Human Macrophages transduced with adenoviral vector expression GFP and treatment of cells with control isotype (IgG). RNA collected at 24 hours.


title: HSC3 cell line relative to normal diploid cell

description: HSC3 cell line relative to normal duploid cell

tag: Oral squamous cell carcinoma cell line


title: Ca9-22 cell line relative to normal diploid cell

description: Ca9-22 cell line relative to normal duploid cell


title: Ad-GFP transduced primary human macrophages (control Experiment 1)

description: See illumina's sample preparation

source_name: Macrophages Ad-GFP control

extract_protocol: Qiagen RNA extraction

treatment_protocol: Transduction of primary human macrophages with Ad-GFP.

tag: Human Macrophages transduced with control GFP expressing adenoviral vector. RNA collected at 24 hours.


title: Propionate-rep2

status: Public on Nov 01 2008

city: Suita

first: Toru

last: Tobe

state: Osaka

address: 2-2 Yamadaoka

department: Graduate School of Medicine

institute: Osaka University

description: no additional information

hyb_protocol: The labeled cDNA probes were then dissolved in water, mixed with hybridization buffer (5x SSC, 0.5% SDS, 1 mg/ml yeast RNA), and heat-denatured. Hybridization was carried out at 50 °C for 16 h. Slides were washed with 2x SSC containing 0.2% SDS at 50 °C twice, then with 0.2x SSC containing 0.2% SDS at 20 °C twice.

scan_protocol: The slides were scanned for fluorescence intensity using a GMS 418 array scanner (Genetic Microsystems), and the information was converted to 16-bit image files.

data_processing: The signal density of each spot was quantified using IMAGENE software (BioDiscovery). We first corrected the intensity of each spot by subtracting the local background. The mean values of the negative control spots containing yeast oligo DNA and the spots containing spotting buffer alone were determined, with the standard deviation (SD). Normalization was performed using Intensity dependent (Lowess) normalization procedure in GeneSpring GX software.

organism: Escherichia coli

source_name: Total RNA from wild type EHEC harboring pGEM vector labeled with Cy5.

label_protocol: Fluorescent-labeled cDNA probes were synthesized in a reverse-transcriptase reaction with AMVXL (XL Life Science) and Cy3-dUTP or Cy5-dUTP (Amersham Pharmacia) and the mixture of specific primers made from the total EHEC RNA. The specific primer was a 16-mer oligo DNA that was anti-sense to the downstream sequence of the spotted oligo DNA for each gene. Labeled cDNA probes were purified by Centri-sep (Princeton Separations), phenol-chloroform extraction, and ethanol precipitation.

growth_protocol: Bacteria were grown in DMEM at 37C to logarithmic phase.

extract_protocol: Total RNA was extracted from bacteria harvested from 10 ml culture by using TRI reagent (Sigma) according to the manufacturer’s instruction.

treatment_protocol: 20 mM of NaCl, sodium acetate, sodium propionate, or sodium butyrate was added to DMEM

tag: Enterohaemorrhagic E. coli O157:H7 Sakai grown with propionate

source_name: Total RNA from wild type EHEC harboring pGEM-PchA labeled with Cy3.

tag: Enterohaemorrhagic E. coli O157:H7 Sakai grown with NaCl


title: Propionate-rep1

description: no additional information

source_name: Total RNA from wild type EHEC harboring pGEM vector labeled with Cy3.

source_name: Total RNA from wild type EHEC harboring pGEM-PchA labeled with Cy5.


title: YES2 cell line relative to normal diploid cell

description: YES2 cell line relative to normal duploid cell

tag: Esophageal squamous cell carcinoma cell line


title: H1 cell line relative to normal diploid cell

description: H1 cell line relative to normal duploid cell


title: Acetate-rep1

description: no additional information

tag: Enterohaemorrhagic E. coli O157:H7 Sakai grown with acetate

source_name: Total RNA from wild type EHEC harboring pGEM-ler labeled with Cy5.


title: Ad-F7 transduction + IgG treatment in primary human macrophages (Experiment 2)

description: See illumina's sample preparation

source_name: Macrophages Ad-F7 + IgG

treatment_protocol: Transduction of primary human macrophages with Ad-F7 and treatment of cells with IgG

tag: Human Macrophages transduced with adenoviral vector expression the active form of IRF-7 (IRF-7 D247-467; Ad-F7) and treatment of cells with control isotype (IgG). RNA collected at 24 hours.


title: Adipose tissue-derived MSC

growth_protocol: AT was extensively washed in PBS, dissected into small pieces and digested with 0.1% collagenase for 30 minutes at 37°C. Then, the solution was filtered through a 100um mesh filter, and the cell suspension was cultured in DMEM supplemented with 10% FBS and 2ng/ml FGF-beta. Cells were expanded in vitro and harvested at culture passage 4 for this experiment.

tag: Adipose tissue (AT) was obtained from a patient (male, 52 year old) undergoing partial abdominoplasty.


title: Butyrate-rep2

description: no additional information

data_processing: The signal density of each spot was quantified using IMAGENE software (BioDiscovery). We first corrected the intensity of each spot by subtracting the local background. The mean values of the negative control spots containing yeast oligo DNA and the spots containing spotting buffer alone were determined, with the standard deviation (SD). For each gene/CDS one of two probes was selected for further analysis.

tag: Enterohaemorrhagic E. coli O157:H7 Sakai grown with butyrate

source_name: Total RNA from ler mutant of EHEC harboring pGEM vector labeled with Cy3.


title: Ad-F7 transduced primary human macrophages (Experiment 1)

description: See illumina's sample preparation protocol

data_processing: Bead Studio from illumina, J-Express from Molmine and R

source_name: Macrophages Ad-F7

label_protocol: Ambion, TotalPrep, for biotin labelling and illumina's protocol for Cy3 labeling

treatment_protocol: Transduction of primary human microphages with Ad-F7.

tag: Human macrophages transduced with adenoviral vector expressing the active form of IRF-7 (IRF-7 D247-467; Ad-F7). RNA collected at 24 hours.


title: Ad-GFP transduction + anti-IFNAR2 treatment in primary human macrophages (Experiment 2)

description: See illumina's sample preparation

source_name: Macrophages Ad-GFP + anti-IFNAR2

treatment_protocol: Transduction of primary human macrophages with Ad-GFP and treatment of cells with anti-IFNAR2

tag: Human Macrophages transduced with adenoviral vector expression GFP (Ad-GFP) and treatment of cells with neutralizing antibody for the type I IFN receptor (anti-IFNAR2). RNA collected at 24 hours.


title: Acetate-rep2

description: no additional information

source_name: Total RNA from wild type EHEC harboring pGEM-ler labeled with Cy3.


title: HSC2 cell line relative to normal diploid cell

description: HSC2 cell line relative to normal duploid cell


title: TE3 cell line relative to normal diploid cell

description: TE3 cell line relative to normal duploid cell


title: TE1 cell line relative to normal diploid cell

description: TE1 cell line relative to normal duploid cell


title: YES1 cell line relative to normal diploid cell

description: YES1 cell line relative to normal duploid cell


title: Ad-F3 transduced primary human macrophages (Experiment 1)

description: See illumina's sample preparation

source_name: Macrophages Ad-F3

treatment_protocol: Transduction of primary human macrophages with Ad-F3

tag: Human Macrophages were transduced with adenoviral factor expressing the active form of IRF-3 (IRF-3 5D; Ad-F3). RNA collected at 24 hours.


title: TE2 cell line relative to normal diploid cell

description: TE2 cell line relative to normal duploid cell


title: Butyrate-rep1

description: no additional information

source_name: Total RNA from ler mutant of EHEC harboring pGEM vector labeled with Cy5.


title: PA14 WT w/10 mM uracil LB 37C 7h biofilms

status: Public on Nov 12 2008

city: College Station

first: Akihiro

last: Ueda

state: TX

address: 3122 TAMU

department: Chemical Engineering

institute: Texas A&M University

description:
RNA extracted from biofilm cells of P. aeruginosa PA14-WT with 10 mM uracil supplement at 37C at 250 rpm after 7 hours of growth in LB with glass wool
Channel 1

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

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

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Pseudomonas aeruginosa

source_name: P. aeruginosa PA14, wild type, 10mM uracil

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

extract_protocol: The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB medium with 10 g of submerged glass wool (Corning Glass Works, Corning, NY) for forming biofilm. After incubation for 7 h at 37°C with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104).

tag: RNA extracted from biofilm cells of P. aeruginosa PA14-WT strain with 10 mM uracil supplement at 37C at 250 rpm after 7 hours of growth in LB with glass wool


title: LAPC4_prostate_cancer_cell_line-untreated

city: Baltimore

first: Srinivasan

last: Yegnasubramanian

state: MD

address: 1650 Orleans Street, CRB1 Rm 1M53

institute: Johns Hopkins University

hyb_protocol: Affymetrix hgU133a manufacturer's recommended protocol

source_name: LAPC4 prostate cancer cells

growth_protocol: Grown/propagated in RPMI 1640 with 10% FBS and 1 nM R1881

extract_protocol: Qiagen RNeasy kit

treatment_protocol: Untreated

tag: Androgen sensitive


title: PREC_prostate_normal_epithelial_cells-untreated

scan_protocol: Affymetrix hgU133a manufacturer's recommended protocol

source_name: PrEC normal prostate epithelial cells

growth_protocol: Grown/propagated in RPMI 1640 with 10% FBS

tag: Normal prostate epithelial cells grown in primary culture


title: LNCaP_prostate_cancer_cell_line-untreated

source_name: LNCaP prostate cancer cells

label_protocol: Affymetrix hgU133a manufacturer's recommended protocol

tag: Androgen sensitive prostate cancer cell line


title: Biofilms after 3 days, biological replicate 3

city: Cambridge

first: Helga

last: Mikkelsen

address: Building O, Downing Site

department: Department of Biochemistry

country: United Kingdom

institute: University of Cambridge

description: Gene expression data from 3-day-old biofilms in a continuous flow system

hyb_protocol: Following fragmentation, cDNA was hybridized for 16 hr at 50degC on GeneChip P. aeruginosa Genome Arrays. The GeneChips were then washed and stained in an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using a GeneChip Scanner 3000 (Affymetrix).

data_processing:
Preliminary data processing was performed using Affymetrix GCOS 1.4 and total signal target was scaled to 500 for all arrays. Normalisation was performed using
The resulting output data was analysed using R 2.5.0 (r-project.org) and the BioConductor packages affyPLM, GCRMA and LIMMA (bioconductor.org).
Normalisation was carried out using quantile normalisation, no background correction, perfect match probes only and median polish summary.

source_name: P. aeruginosa biofilms in a continuous flow system after 3 days of growth

label_protocol: Biotinylated RNA was prepared from 12 mg total RNA as previously described (Hentzer et al. 2005, Biofilms 2, 27-61).

growth_protocol: All samples were grown in AGSY medium (56 mM alanine, 17 mM K2HPO4, 86 mM NaCl, 100 μM CaCl2, 10 mM MgSO4, 5 µM FeCl2, 7.5 µM ZnCl2, 0.5% v/v glycerol, 3 g/L yeast extract, pH 7) at 37degC. Planktonic cells were grown with vigorous shaking for three hours (late exponential phase) or nine hours (early stationary phase), colonies were grown on 1.5% agar for 15 or 40 hours, and biofilms were grown for three days in silicone tubes, 6 mm i.d. under a continuous flow of 50 ml/h for 3 days.

extract_protocol: RNA was extracted using the RNeasy Mini Purification Kit (Qiagen) following the supplier's instructions.

treatment_protocol: All cells were harvested directly into RNAlater (Ambion), kept at 5degC overnight and stored at -80degC until use.

tag: Biofilms grown for 3 days in silicone tubes


title: Biofilms after 3 days, biological replicate 2


title: PC3_prostate_cancer_cell_line-untreated

source_name: PC-3 prostate cancer cell line

tag: PC3 androgen receptor negative prostate cancer cell line


title: Colonies after 40 hrs, biological replicate 3

description: Gene expression data from large colonies

source_name: P. aeruginosa colonies on agar plates after 40h of growth

tag: Colonies pigmented and differentiated, 5-7 mm diametre


title: Biofilms after 3 days, biological replicate 1


title: 13-S_T1628 (parental)

city: Washington, DC

first: Norman

middle: H

last: Lee

state: DC

address: 2300  I Street, N.W.

department: Pharmacology & Physiology

institute: The George Washington University Medical Center

description: no additional information

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45C on the GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained on the Affymetrix Fluidics Station 450 using Fluidics Script EukGE-WS2v5.

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

data_processing: The data were analyzed with the Affymetrix GeneChip Operating Software 1.4 (GCOS 1.4) using Affymetrix default analysis settings and global scaling to a target intensity value of 500.

organism: Rattus norvegicus

source_name: T1628 (Inbred Dahl salt-sensitive (SS/Jr) rat kidney )

label_protocol: Biotinylated cRNA was generated according to the standard Affymetrix protocol from 5 ug of total RNA (GeneChip Expression Analysis Technical Manual; Affymetrix).

extract_protocol: Tissue was processed and extracted using TRIzol reagent (Invitrogen) and total RNA was purified using RNeasy columns (Qiagen) according to manufacturer's protocols.

tag: Inbred Dahl salt-sensitive (SS/Jr) adult male rat; tissue

value: kidney


title: Colonies after 40 hrs, biological replicate 2


title: Colonies after 15 hrs, biological replicate 3

description: Gene expression data from small fast growing colonies

source_name: P. aeruginosa colonies on agar plates after 15h of growth

tag: Colonies unpigmented and flat, 0.5-1mm diametre


title: Colonies after 15 hrs, biological replicate 2


title: Colonies after 40 hrs, biological replicate 1


title: C42B_prostate_cancer_cell_line-untreated

source_name: C42B prostate cancer cell line

growth_protocol: Grown/propagated in RPMI 1640 with 10% FBS.

tag: This is a prostate cancer cell line that is an androgen independent variant of the LNCaP prostate cancer cell line. It is directly derived from the LNCaP cell line.


title: CWR22Rv1_prostate_cancer_cell_line-untreated

source_name: CWR22Rv1 prostate cancer cell line

tag: CWR22Rv1 prostate cancer cell line


title: 15-D1MCO4x1x3Bx1_8051 (congenic)

description: no additional information

source_name: 8051(Congenic S.LEW.D1MCO4x1x3Bx1 rat kidney)

tag: Congenic S.LEW.D1MCO4x1x3Bx1 adult male rat; tissue


title: DU145_prostate_cancer_cell_line-untreated

source_name: DU-145 prostate cancer cell line

tag: Androgen receptor negative prostate cancer cell line


title: 1S_prostate_normal_stromacells-untreated

hyb_protocol: Affymetrix U133A manufacturer's recommended protocol

source_name: 1s normal prostate stromal cells, basal conditions

growth_protocol: Cells were propagated in Iscove’s media (Life Technologies, Inc.) containing 10% fetal bovine serum and 1 nM R1881

treatment_protocol: No treatment

tag: These are a batch of normal prostate stromal cells propagated in primary culture. These cells are not immortalized.


title: 9-D1MCO4x1x3Bx1_8090 (congenic)

description: no additional information

source_name: 8090 (Congenic S.LEW.D1MCO4x1x3Bx1 rat kidney)


title: 14-S_T1626 (parental)

description: no additional information

source_name: T1626 (Inbred Dahl salt-sensitive (SS/Jr) rat kidney )


title: Adamts16-2600 (Replicate 1)

description: no additional information

source_name: NRK-52E (rat kidney epithelial) cell line transfected with siRNA: Adamts16-2600

growth_protocol: Cells were cultured in 100 mm dishes containing DMEM medium supplemented with 10% fetal bovine serum and grown at 37C and 5% CO2.

extract_protocol: Cells were processed and extracted using TRIzol reagent (Invitrogen) and total RNA was purified using RNeasy columns (Qiagen) according to manufacturer's protocols.

treatment_protocol: Cells were seeded at 20% confluence in 60 mm plates and cultured for 6 hours before transfection with the small interfering RNA (siRNA) duplex using Lipofectamine 2000 (Invitrogen), following the manufacturer's protocol. Briefly, the siRNA duplex mixed with 200 ul of OptiMEM and Lipofectamine 2000 mixed with 200 ul of OptiMEM were simultaneously incubated at room temperature for 5 minutes. Subsequently, the two mixtures were combined and incubated at room temperature for 20 minutes. The siRNA:Lipofectamine complex was added to the cells (at a final siRNA duplex concentration of 100 pmol per milliliter of culture medium) and left in the plate for 48 hours after which the cells were harvested for RNA extraction.

tag: NRK-52E cells were transfected with siRNA (according to treatment protocol). siRNA

value: Adamts16-2600 (NM_001107332). Sense sequence:CCTATATTTCTGTGCGCAAdTdT. Antisense sequence:TTGCGCACAGAAATATAGGdTdT


title: Scrambled control (Replicate 3)

description: no additional information

source_name: NRK-52E (rat kidney epithelial) cell line transfected with siRNA: Scrambled control

value: Scrambled control. Sense sequence:CCTCCAATGTGCTCGGTAATdTdT. Antisense sequence:ATTACCGAGCACATTGGAGGdTdT


title: 7-D1MCO4x1x3Bx1_8054 (congenic)

description: no additional information

source_name: 8054 (Congenic S.LEW.D1MCO4x1x3Bx1 rat kidney)


title: 4-S_T1655 (parental)

description: no additional information

source_name: T1655 (Inbred Dahl salt-sensitive (SS/Jr) rat kidney )


title: Colonies after 15 hrs, biological replicate 1


title: 4ST_prostate_normal_stromalcells-untreated

source_name: 4ST prostate normal stromal cells

growth_protocol: Grown/propagated in Iscove's media with 10% FBS and 1nM R1881

tag: Normal stromal cells from a the prostate gland grown in primary culture. Not transformed or immortalized.


title: Planktonic cells stat phase, biological replicate 2

description: Genee expresion data from planktonic cells in early stationary phase

source_name: P. aeruginosa planktonic cells after 9h of growth

tag: Cultures pigmented, OD~9


title: Adamts16-3488 (Replicate 1)

description: no additional information

source_name: NRK-52E (rat kidney epithelial) cell line transfected with siRNA: Adamts16-3488

value: Adamts16-3488 (NM_001107332). Sense sequence:AGAAGTACGTCTCCGGAAAdTdT. Antisense sequence:TTTCCGGAGACGTACTTCTdTdT


title: Adamts16-3488 (Replicate 2)

description: no additional information


title: Planktonic cells exp phase, biological replicate 1

description: Gene expression data from planktonic cells in late exponential phase

source_name: P. aeruginosa planktonic cells after 3h of growth

tag: Cultures colourless, OD~1


title: Scrambled control (Replicate 2)

description: no additional information


title: Planktonic cells stat phase, biological replicate 3


title: Adamts16-2600 (Replicate 2)

description: no additional information


title: Scrambled control (Replicate 1)

description: no additional information


title: Planktonic cells exp phase, biological replicate 3


title: array-CGH - GBM20sw

status: Public on Oct 30 2008

city: Rennes

first: Marie

last: de Tayrac

address: 2 avenue du Professeur Léon Bernard

description: Low quality spots were flagged according to default FE criteria and corresponding values were removed.

hyb_protocol: Tumor and control DNAs were pooled and hybridized with 50microg of Human Cot I DNA at 65°C with rotation for 48 hours. Washing was performed according to the Agilent protocol.

scan_protocol: Arrays were analyzed using the Agilent G2565BA microarray scanner and the Feature Extraction software (FE v9.4.1, CGH_44k_1005 protocol).

data_processing: Data preprocessing was carried out using limma (R package) from Bioconductor with adaptation to array CGH data files. Quality control was performed by visualization of the spatial distribution of probes; background array images and examination of boxplots, histograms, global MvA plots and per chromosome MvA plots. Median pixel feature intensity values were median normalized. Missing values were imputed by the use of the k-nearest neighbors method implemented in impute (R package).

source_name: GBM20 - blood DNA

label_protocol: 5microg DNA were double-digested with AluI and RsaI (Promega, Madison, WI, USA) for 2h at 37C. The digested DNA was labeled by random priming using the Bioprime DNA Labeling Kit (Invitrogen, Carlsbad, USA).  DNA was labeled with Cy3-dUTP (PerkinElmer, Waltham, USA) . Labeled product was purified with Microcon YM (Millipore, Billerica, MA, USA).

extract_protocol: Classical saline extraction from peripheral blood leucocytes. The quantification of DNA was done by spectrophotometry (Nanodrop, Labtech); integrity and purity were analyzed on 1% agarose gel.

tag: Age

value: 76; Gender:Male; WHO grade IV

source_name: GBM20 - tumor DNA

extract_protocol: DNA was extracted with Macherey Nagel NucleoSpin Tissue Kit. The quantification of DNA was done by spectrophotometry (Nanodrop, Labtech); integrity and purity were analyzed on 1% agarose gel.


title: array-CGH - GBM10sw

source_name: GBM10 - blood DNA

value: 59; Gender:Male; WHO grade IV

source_name: GBM10 - tumor DNA

tag: GBM10 - tumor DNA


title: array-CGH - GBM13sw

source_name: GBM13 - blood DNA

value: 55; Gender:Male; WHO grade IV

source_name: GBM13 - tumor DNA


title: array-CGH - GBM4sw

source_name: GBM4 - blood DNA

value: 60; Gender:Female; WHO grade IV

source_name: GBM4 - tumor DNA


title: array-CGH - GBM19sw

source_name: GBM19 - blood DNA

value: 63; Gender:Male; WHO grade IV

source_name: GBM19 - tumor DNA


title: array-CGH - GBM11sw

source_name: GBM11 - blood DNA

value: 56; Gender:Female; WHO grade IV

source_name: GBM11 - tumor DNA


title: array-CGH - GBM18sw

source_name: GBM18 - blood DNA

source_name: GBM18 - tumor DNA


title: array-CGH - GBM6sw

source_name: GBM6 - blood DNA

value: 51; Gender:Female; WHO grade IV

source_name: GBM6 - tumor DNA


title: array-CGH - GBM15sw

source_name: GBM15 - blood DNA

value: 72; Gender:Female; WHO grade IV

source_name: GBM15 - tumor DNA


title: array-CGH - GBM16sw

source_name: GBM16 - blood DNA

value: 50; Gender:Female; WHO grade IV

source_name: GBM16 - tumor DNA


title: array-CGH - GBM8sw

source_name: GBM8 - blood DNA

value: 65; Gender:Female; WHO grade IV

source_name: GBM8 - tumor DNA


title: array-CGH - GBM3sw

source_name: GBM3 - blood DNA

source_name: GBM3 - tumor DNA


title: array-CGH - GBM17sw

source_name: GBM17 - blood DNA

source_name: GBM17 - tumor DNA


title: array-CGH - GBM20

source_name: GBM20 - tumor DNA

source_name: GBM20 - blood DNA


title: array-CGH - GBM5sw

source_name: GBM5 - blood DNA

value: 75; Gender:Male; WHO grade IV

source_name: GBM5 - tumor DNA


title: array-CGH - GBM19

source_name: GBM19 - tumor DNA

source_name: GBM19 - blood DNA


title: array-CGH - GBM12sw

source_name: GBM12 - blood DNA

value: 73; Gender:Female; WHO grade IV

source_name: GBM12 - tumor DNA


title: array-CGH - GBM14sw

source_name: GBM14 - blood DNA

value: 48; Gender:Female; WHO grade IV

source_name: GBM14 - tumor DNA


title: array-CGH - GBM18

source_name: GBM18 - tumor DNA

source_name: GBM18 - blood DNA


title: Planktonic cells stat phase, biological replicate 1

source_name: P. aeruginosa planktonic cells after 9h of growth


title: Planktonic cells exp phase, biological replicate 2

source_name: P. aeruginosa planktonic cells after 3h of growth


title: array-CGH - GBM16

source_name: GBM16 - tumor DNA

source_name: GBM16 - blood DNA


title: array-CGH - GBM7sw

source_name: GBM7 - blood DNA

value: 60; Gender:Male; WHO grade IV

source_name: GBM7 - tumor DNA


title: array-CGH - GBM14


title: array-CGH - GBM8

source_name: GBM8 - tumor DNA

source_name: GBM8 - blood DNA


title: array-CGH - GBM1

source_name: GBM1 - tumor DNA

value: 39; Gender:Male; WHO grade IV

source_name: GBM1 -  blood DNA

label_protocol: 5microg DNA were double-digested with AluI and RsaI (Promega, Madison, WI, USA) for 2h at 37C. The digested DNA was labeled by random priming using the Bioprime DNA Labeling Kit (Invitrogen, Carlsbad, USA).  DNA was labeled with Cy5-dUTP (PerkinElmer, Waltham, USA) . Labeled product was purified with Microcon YM (Millipore, Billerica, MA, USA).


title: expression microarray - N4

description: Poor quality spots were flagged according to default FE criteria and corresponding values were removed.

hyb_protocol: 1.65microg of Cy3-labeled RNA were hybridized to each array in a 110microl total volume of hybridization buffer (Agilent Technologies) for 17 hours at 65°C. Washing was performed according to the Agilent protocol.

scan_protocol: Arrays were analyzed using the dynamic autofocus Agilent G2565BA microarray scanner and the Agilent Feature Extraction software (FE v9.4.1, GE1-v5_91_0806 protocol).

data_processing: Median normalization from the processed Multiplicative Detrend FE data was carried out using limma (R package) from Bioconductor. Missing values were imputed by the use of the k-nearest neighbors method implemented in impute (R package).

source_name: N4- control RNA

label_protocol: Agilent’s recommended procedures for microarray-based one-color gene expression analysis were followed. Briefly, 350ng of total RNA with control RNA Spike In were amplified and labeled with Cy3-CTP using the T7-based Low RNA Input Linear Amplification Kit, PLUS, One-Color (Agilent Technologies, Santa Clara, CA). After purification (RNeasy Mini Kit, QIAGEN), labeled cRNAs were quantified for yield and dye incorporation using a Nanodrop spectrophotometer.

extract_protocol: Total RNA was isolated using the NucleoSpin RNAII Kit (Macherey-Nagel, Düren, DE) and quantified via spectrophotometry (Nanodrop, Labtech). RNA integrity was confirmed using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

tag: Non-neoplastic brain tissue from patient undergoing cortectomy for chronic epilepsy.


title: expression microarray - N2

source_name: N2- control RNA


title: array-CGH - GBM6

source_name: GBM6 - tumor DNA

source_name: GBM6 - blood DNA


title: expression microarray - GBM20

source_name: GBM20 - tumor RNA


title: array-CGH - GBM13

source_name: GBM13 - tumor DNA

source_name: GBM13 - blood DNA


title: array-CGH - GBM10

source_name: GBM10 - tumor DNA

source_name: GBM10 - blood DNA


title: array-CGH - GBM7


title: array-CGH - GBM4

source_name: GBM1 -  tumor DNA

source_name: GBM4 - blood DNA


title: expression microarray - GBM18

source_name: GBM18 - tumor RNA


title: expression microarray - GBM17

source_name: GBM17 - tumor RNA


title: array-CGH - GBM12

source_name: GBM12 - tumor DNA

source_name: GBM12 - blood DNA


title: expression microarray - GBM15

source_name: GBM15 - tumor RNA


title: array-CGH - GBM3

source_name: GBM3 -  tumor DNA

value: 60 Gender:Female; WHO grade IV

source_name: GBM3 -  blood DNA


title: expression microarray - GBM13

source_name: GBM13 - tumor RNA


title: expression microarray - N3

source_name: N3- control RNA


title: array-CGH - GBM1sw

source_name: GBM1 -  blood DNA

source_name: GBM1 - tumor DNA


title: expression microarray - N1

source_name: N1- control RNA


title: expression microarray - GBM12

source_name: GBM12 - tumor RNA


title: array-CGH - GBM17

source_name: GBM17 - tumor DNA

source_name: GBM17 - blood DNA


title: array-CGH - GBM15

source_name: GBM15 - tumor DNA

source_name: GBM15 - blood DNA


title: array-CGH - GBM11

source_name: GBM11 - tumor DNA

source_name: GBM11 - blood DNA


title: expression microarray - GBM16

source_name: GBM16 - tumor RNA


title: array-CGH - GBM5

source_name: GBM5 - tumor DNA

source_name: GBM5 - blood DNA


title: array-CGH - GBM2

source_name: GBM2 - tumor DNA

value: 70; Gender:Female; WHO grade IV

source_name: GBM2 - blood DNA


title: KT2440(pCAR1)_succinate_rep1_and_rep2

status: Public on Oct 18 2008

city: Sendai

first: Masatoshi

last: Miyakoshi

state: Miyagi

address: Aoba-ku, Katahira, 2-1-1

department: Department of Environmental Life Sciences

institute: Tohoku University

hyb_protocol: Labeled cDNA was mixed with 50 pM control oligonucleotide B2 (Affymetrix), 1× Hybridization Mix (Affymetrix), and 7% DMSO in a total volume of 200 µl and denatured at 95˚C for 5 min.  Per array, 130 µl of the hybridization cocktail was hybridized at 45˚C for 16 h with a rotation rate of 60 rpm using a GeneChip Hybridization Oven 640 (Affymetrix).  Chips were washed and stained using a Hybridization, Wash, and Stain Kit (Affymetrix) according to the FlexFS450-0002 protocol of GeneChip Fluidics station 450 (Affymetrix).

scan_protocol: Signals were detected using GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The CEL files were generated using Affymetrix GCOS.  The signal intensities at each probe were computed using Affymetrix TAS.  The replications of CEL files were together converted into the BAR files using pCAR1_8b520435FF-3.bpmap for the forward strand and pCAR1_8b520435FR-3.bpmap for the reverse strand; the BAR files with header F indicate the forward strand and with header R indicate the reverse strand of pCAR1.  The intensities were linearly scaled so that the median was 100.  Bandwidth: 30, Threshold: 0, MaxGap: 30, MinRun, 30.

organism: Pseudomonas putida

source_name: Pseudomonas putida KT2440(pCAR1) grown on succinate at exponential phase

label_protocol: Single-strand cDNA was synthesized in 60 µl of 1× First Strand Buffer (Invitrogen, Carlsbad, CA) containing 12 µg of total RNA, 750 ng of random primers (Invitrogen), 1500 units of SuperScript II (Invitrogen), 60 units of RNaseOUT (Invitrogen), 10 mM DTT (Invitrogen), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.4 mM dTTP, and 0.1 mM dUTP (Roche Applied Science, Mannheim, Germany).  After the RNA and random primers were denatured at 70˚C for 10 min and annealed at 25˚C for 10 min, the remaining reagents were added, and the reaction mixture was then incubated at 25˚C for 10 min, 37˚C for 60 min, 42˚C for 60 min, and 70˚C for 10 min.  After cDNA synthesis, template RNA was degraded with one-third volume of 1N NaOH at 65˚C for 30 min; one-third volume of 1N HCl was added to neutralize the reaction mixture before cleanup.  The cDNA was purified using a QIAquick PCR Purification Kit (Qiagen).    The cDNA was fragmented and labeled using GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix).  The purified single-stranded cDNA (~5 µg) was fragmented in 48 µl of 1× cDNA Fragmentation Buffer containing 15 units of Uracil DNA Glycosylase (UDG) and 225 units of Apurinic/apyrimidinic Endonuclease 1 (APE1) at 37˚C for 60 min, and incubated at 93˚C for 2 min.  The fragmented cDNA was labeled in 60 µl of 1× TdT Buffer containing 60 units of Terminal Deoxynucleotidyl Transferase (TdT) and 0.083 mM GeneChip DNA Labeling Reagent at 37˚C for 60 min, and incubated at 70˚C for 2 min.

growth_protocol: 100 ml of NMM-4 (Miyakoshi et al. Transcriptome analysis of Pseudomonas putida KT2440 harboring the completely sequenced IncP-7 plasmid pCAR1. J Bacteriol 2007 Oct;189(19):6849-60. PMID: 17675379) supplemented with 1.0 mg ml-1 sodium succinate or carbazole was inoculated by overnight culture in Luria broth to obtain initial optical densities at 600 nm (OD600) of 0.05. Cultures were incubated at 30˚C in a rotating shaker at 120 rpm to exponential phase.

extract_protocol: Total RNA was extracted using NucleoSpin RNA II (Macherey-Nagel GmbH & Co. KG, Düren, Germany).  The eluted RNA was treated with RQ1 RNase-free DNase (Promega, Madison, WI) at 37˚C for 30 min.  After inactivation of DNase by the addition of the provided stop reagent and subsequent incubation at 65˚C for 10 min, total RNA was repurified using NucleoSpin RNA Clean-up (Macherey-Nagel).

treatment_protocol: A total of 1 × 10^9 cells were mixed with RNA Protect Bacteria reagent (Qiagen, Valencia, CA) as recommended by the manufacturer.

tag: Strain KT2440(pCAR1), Carbon source

value: succinate, Growth phase:exponential


title: CA10_carbazole_rep1_and_rep2

organism: Metapseudomonas resinovorans

source_name: Pseudomonas resinovorans CA10 grown on carbazole at exponential phase

tag: Strain CA10, Carbon source

value: carbazole, Growth phase:exponential


title: KT2440(pCAR1)_carbazole_rep1_and_rep2

source_name: Pseudomonas putida KT2440(pCAR1) grown on carbazole at exponential phase


title: expression microarray - GBM19

source_name: GBM19 - tumor RNA


title: expression microarray - GBM14

source_name: GBM14 - tumor RNA


title: expression microarray - GBM11

source_name: GBM11 - tumor RNA


title: CA10_succinate_rep1_and_rep2

source_name: Pseudomonas resinovorans CA10 grown on succinate at exponential phase


title: expression microarray - GBM10

source_name: GBM10 - tumor RNA

value: 59; Gender:Male; WHO grade IV


title: expression microarray - GBM4

source_name: GBM4 - tumor RNA

value: 60; Gender:Female; WHO grade IV


title: expression microarray - GBM1

source_name: GBM1 - tumor RNA


title: expression microarray - GBM7

source_name: GBM7 - tumor RNA


title: expression microarray - GBM2

source_name: GBM2 - tumor RNA


title: expression microarray - GBM8

source_name: GBM8 - tumor RNA


title: expression microarray - GBM5

source_name: GBM5 - tumor RNA


title: expression microarray - GBM3

source_name: GBM3 - tumor RNA


title: expression microarray - GBM6

source_name: GBM6 - tumor RNA