title: M40t90_2

description: growth in LB until exponential phase_90 minutes after addition of 40 ng/ml mitomycin_replicate 2


title: Mt0_1

status: Public on Mar 07 2012

type: RNA

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

country: Germany

institute: University Medicine Greifswald

description: growth in LB until exponential phase_t0 = before addition of mitomycin_replicate 1

hyb_protocol: Hybridization was performed by Roche NimbleGen (Madison, WI, USA) following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by Roche NimbleGen (Madison, WI USA) following their standard operating protocol. See www.nimblegen.com.

data_processing:
An aggregated expression value was computed for each Genbank annotated CDS and newly defined transcribed region as the median log2 expression signal intensity of probes lying entirely within the corresponding region.
The expression intensity was computed from the raw intensity data using a model of signal shift and drift and correcting for probe affinity variations as described in (Nicolas et al., 2009, Bioinformatics 25, 2341-2347)
To control for possible cross-hybridization artefacts the sequence of each probe was BLAST-aligned against the whole chromosome sequence and probes with a SeqS value above the 1.5 cut-off were discarded (Wei et al., 2008 Nucl. Acids Res. 36, 2926-2938).

molecule: total RNA

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: Bacillus subtilis cells

label_protocol: 10 µg of RNA were converted into Cy3-labeled cDNA by Roche NimbleGen (Madison, WI, USA) using the BaSysBio protocol for strand-specific hybridization (Rasmussen et al., 2009).

growth_protocol: The complete description of the growth protocols can be found in the Supplementary Online Material (Nicolas, Mäder, Dervyn et al., to be submitted).

extract_protocol: Total RNA was isolated by the method described by Eymann et al. (PMID: 11948165) with minor modifications. The quality of the RNA preparations was assessed by means of the Agilent 2100 Bioanalyzer.

treatment_protocol:
The study comprised adaptation to stresses such as treatment with oxidative agents, nutrient starvation, temperature and osmotic variations.
Detailed treatment protocols are available in the Supplementary Online Material (Nicolas, Mäder, Dervyn et al., to be submitted)

tag: strain

tag: condition

tag: replicate


title: Salt_1

description: growth in SMM medium until OD500 of 0.4_10 minutes after addition of 0.4 M NaCl_replicate 1

value: growth in SMM medium until OD500 of 0.4 10 minutes after addition of 0.4 M NaCl


title: M40t45_2

description: growth in LB until exponential phase_45 minutes after addition of 40 ng/ml mitomycin_replicate 2


title: SMM_3

description: growth in SMM medium until OD500 of 0.4_before stress_replicate 3


title: M40t45_1

description: growth in LB until exponential phase_45 minutes after addition of 40 ng/ml mitomycin_replicate 1


title: M40t90_3

description: growth in LB until exponential phase_90 minutes after addition of 40 ng/ml mitomycin_replicate 3


title: SMM_1

description: growth in SMM medium until OD500 of 0.4_before stress_replicate 1


title: SMM_2

description: growth in SMM medium until OD500 of 0.4_before stress_replicate 2


title: M0t90_1

description: growth in LB until exponential phase_90 minutes after t0_replicate 1


title: dia0_1

description: growth in LB until  OD600 of 0.6_before addition of diamide_replicate 1


title: Salt_2

description: growth in SMM medium until OD500 of 0.4_10 minutes after addition of 0.4 M NaCl_replicate 2


title: M40t90_1

description: growth in LB until exponential phase_90 minutes after addition of 40 ng/ml mitomycin_replicate 1


title: M40t45_3

description: growth in LB until exponential phase_45 minutes after addition of 40 ng/ml mitomycin_replicate 3


title: Etha_3

description: growth in BMM medium until OD500 of 0.4_10 minutes after addition of 4 % ethanol_replicate 3

value: growth in BMM medium until OD500 of 0.4 10 minutes after addition of 4 % ethanol


title: Heat_1

description: growth in BMM medium until OD500 of 0.4_10 minutes after shifting from 37 °C to 48 °C_replicate 1

value: growth in BMM medium until OD500 of 0.4 10 minutes after shifting from 37 °C to 48 °C


title: Heat_2

description: growth in BMM medium until OD500 of 0.4_10 minutes after shifting from 37 °C to 48 °C_replicate 2


title: HiOs_1

description: growth in SMM medium until OD578 of 1_addition of 1.2 M NaCl_replicate 1


title: BMM_2

description: growth in BMM medium until OD500 of 0.4_before stress_replicate 2


title: BMM_3

description: growth in BMM medium until OD500 of 0.4_before stress_replicate 3


title: LoTm_3

description: growth in SMM medium until OD578 of 1_growth temperature of 16 °C_replicate 3

value: growth in SMM medium until OD578 of 1 growth temperature of 16 °C


title: Etha_1

description: growth in BMM medium until OD500 of 0.4_10 minutes after addition of 4 % ethanol_replicate 1


title: Etha_2

description: growth in BMM medium until OD500 of 0.4_10 minutes after addition of 4 % ethanol_replicate 2


title: HiOs_3

description: growth in SMM medium until OD578 of 1_addition of 1.2 M NaCl_replicate 3


title: BMM_1

description: growth in BMM medium until OD500 of 0.4_before stress_replicate 1


title: LoTm_2

description: growth in SMM medium until OD578 of 1_growth temperature of 16 °C_replicate 2


title: HiOs_2

description: growth in SMM medium until OD578 of 1_addition of 1.2 M NaCl_replicate 2


title: Heat_3

description: growth in BMM medium until OD500 of 0.4_10 minutes after shifting from 37 °C to 48 °C_replicate 3


title: Cold_3

description: growth in BMM medium until OD500 of 0.4_60 minutes after shifting from 37 °C to 18 °C_replicate 3


title: HiTm_2

description: growth in SMM medium until OD578 of 1_growth temperature of 51 °C_replicate 2

value: growth in SMM medium until OD578 of 1 growth temperature of 51 °C


title: HiTm_1

description: growth in SMM medium until OD578 of 1_growth temperature of 51 °C_replicate 1


title: HiTm_3

description: growth in SMM medium until OD578 of 1_growth temperature of 51 °C_replicate 3


title: Cold_2

description: growth in BMM medium until OD500 of 0.4_60 minutes after shifting from 37 °C to 18 °C_replicate 2


title: Cold_1

description: growth in BMM medium until OD500 of 0.4_60 minutes after shifting from 37 °C to 18 °C_replicate 1


title: LPhT_1

description: growth in low phosphate medium_stationary phase_replicate 1

value: growth in low phosphate medium stationary phase


title: LPh_3

description: growth in low phosphate medium_exponential phase_replicate 3

value: growth in low phosphate medium exponential phase


title: SMMPr_3

description: growth in SMM medium until OD578 of 1_growth temperature of 37 °C_replicate 3

value: growth in SMM medium until OD578 of 1 growth temperature of 37 °C


title: HPh_2

description: growth in high phosphate medium_exponential phase_replicate 2

value: growth in high phosphate medium exponential phase


title: LPh_1

description: growth in low phosphate medium_exponential phase_replicate 1


title: LoTm_1

description: growth in SMM medium until OD578 of 1_growth temperature of 16 °C_replicate 1


title: SMMPr_1

description: growth in SMM medium until OD578 of 1_growth temperature of 37 °C_replicate 1


title: LPhT_3

description: growth in low phosphate medium_stationary phase_replicate 3


title: T1.0H_1

description: batch fermentation in modified M9 medium_60 minutes after glucose consumption

value: batch fermentation in modified M9 medium 60 minutes after glucose consumption


title: T5.0H_1

description: batch fermentation in modified M9 medium_300 minutes after glucose consumption

value: batch fermentation in modified M9 medium 300 minutes after glucose consumption


title: LPh_2

description: growth in low phosphate medium_exponential phase_replicate 2


title: LPhT_2

description: growth in low phosphate medium_stationary phase_replicate 2


title: HPh_1

description: growth in high phosphate medium_exponential phase_replicate 1


title: T4.0H_1

description: batch fermentation in modified M9 medium_240 minutes after glucose consumption

value: batch fermentation in modified M9 medium 240 minutes after glucose consumption


title: T0.0H_1

description: batch fermentation in modified M9 medium_time of glucose consumption

value: batch fermentation in modified M9 medium time of glucose consumption


title: SMMPr_2

description: growth in SMM medium until OD578 of 1_growth temperature of 37 °C_replicate 2


title: T1.30H_1

description: batch fermentation in modified M9 medium_90 minutes after glucose consumption

value: batch fermentation in modified M9 medium 90 minutes after glucose consumption


title: T3.30H_1

description: batch fermentation in modified M9 medium_210 minutes after glucose consumption

value: batch fermentation in modified M9 medium 210 minutes after glucose consumption


title: HPh_3

description: growth in high phosphate medium_exponential phase_replicate 3


title: T2.30H_1

description: batch fermentation in modified M9 medium_150 minutes after glucose consumption

value: batch fermentation in modified M9 medium 150 minutes after glucose consumption


title: T2.0H_1

description: batch fermentation in modified M9 medium_120 minutes after glucose consumption

value: batch fermentation in modified M9 medium 120 minutes after glucose consumption


title: T0.30H_1

description: batch fermentation in modified M9 medium_30 minutes after glucose consumption

value: batch fermentation in modified M9 medium 30 minutes after glucose consumption


title: T-0.40H_1

description: batch fermentation in modified M9 medium_40 minutes before glucose consumption

value: batch fermentation in modified M9 medium 40 minutes before glucose consumption


title: ferm_1

description: growth in synthetic medium until OD578 of 0.5_anaerobic coditions in the absence of nitrate_replicate 1


title: ferm_2

description: growth in synthetic medium until OD578 of 0.5_anaerobic coditions in the absence of nitrate_replicate 2


title: ferm_3

description: growth in synthetic medium until OD578 of 0.5_anaerobic coditions in the absence of nitrate_replicate 3


title: T-1.40H_1

description: batch fermentation in modified M9 medium_100 minutes before glucose consumption

value: batch fermentation in modified M9 medium 100 minutes before glucose consumption


title: T-3.40H_1

description: batch fermentation in modified M9 medium_220 minutes before glucose consumption

value: batch fermentation in modified M9 medium 220 minutes before glucose consumption


title: T-2.40H_1

description: batch fermentation in modified M9 medium_160 minutes before glucose consumption

value: batch fermentation in modified M9 medium 160 minutes before glucose consumption


title: nit_2

description: growth in synthetic medium until OD578 of 0.5_anaerobic coditions in the presence of nitrate_replicate 2


title: nit_1

description: growth in synthetic medium until OD578 of 0.5_anaerobic coditions in the presence of nitrate_replicate 1


title: nit_3

description: growth in synthetic medium until OD578 of 0.5_anaerobic coditions in the presence of nitrate_replicate 3


title: T-4.40H_1

description: batch fermentation in modified M9 medium_280 minutes before glucose consumption

value: batch fermentation in modified M9 medium 280 minutes before glucose consumption


title: T-1.10H_1

description: batch fermentation in modified M9 medium_70 minutes before glucose consumption

value: batch fermentation in modified M9 medium 70 minutes before glucose consumption


title: T-5.40H_1

description: batch fermentation in modified M9 medium_340 minutes before glucose consumption

value: batch fermentation in modified M9 medium 340 minutes before glucose consumption


title: aero_1

description: growth in synthetic medium until OD578 of 0.5_aerobic coditions_replicate 1


title: Glucon_3

description: growth in M9 medium until OD600 of 0.5_with gluconate_replicate 3

value: growth in M9 medium until OD600 of 0.5 with gluconate


title: T3.0H_1

description: batch fermentation in modified M9 medium_180 minutes after glucose consumption

value: batch fermentation in modified M9 medium 180 minutes after glucose consumption


title: Glucon_2

description: growth in M9 medium until OD600 of 0.5_with gluconate_replicate 2


title: Pyr_2

description: growth in M9 medium until OD600 of 0.5_with pyruvate_replicate 2

value: growth in M9 medium until OD600 of 0.5 with pyruvate


title: Gly_2

description: growth in M9 medium until OD600 of 0.5_with glycerol_replicate 2

value: growth in M9 medium until OD600 of 0.5 with glycerol


title: Pyr_3

description: growth in M9 medium until OD600 of 0.5_with pyruvate_replicate 3


title: G+S_2

description: growth in M9 medium until OD600 of 0.5_with glutamic acid and succinic acid_replicate 2

value: growth in M9 medium until OD600 of 0.5 with glutamic acid and succinic acid


title: G+S_3

description: growth in M9 medium until OD600 of 0.5_with glutamic acid and succinic acid_replicate 3


title: Mal_1

description: growth in M9 medium until OD600 of 0.5_with L malic acid_replicate 1

value: growth in M9 medium until OD600 of 0.5 with L malic acid


title: aero_3

description: growth in synthetic medium until OD578 of 0.5_aerobic coditions_replicate 3


title: Mal_2

description: growth in M9 medium until OD600 of 0.5_with L malic acid_replicate 2


title: Glucon_1

description: growth in M9 medium until OD600 of 0.5_with gluconate_replicate 1


title: Fru_3

description: growth in M9 medium until OD600 of 0.5_with D fructose_replicate 3

value: growth in M9 medium until OD600 of 0.5 with D fructose


title: Fru_1

description: growth in M9 medium until OD600 of 0.5_with D fructose_replicate 1


title: G+S_1

description: growth in M9 medium until OD600 of 0.5_with glutamic acid and succinic acid_replicate 1


title: Glu_3

description: growth in M9 medium until OD600 of 0.5_with D glucose_replicate 3

value: growth in M9 medium until OD600 of 0.5 with D glucose


title: Glu_2

description: growth in M9 medium until OD600 of 0.5_with D glucose_replicate 2


title: Mal_3

description: growth in M9 medium until OD600 of 0.5_with L malic acid_replicate 3


title: Fru_2

description: growth in M9 medium until OD600 of 0.5_with D fructose_replicate 2


title: Glu_1

description: growth in M9 medium until OD600 of 0.5_with D glucose_replicate 1


title: Gly_1

description: growth in M9 medium until OD600 of 0.5_with glycerol_replicate 1


title: aero_2

description: growth in synthetic medium until OD578 of 0.5_aerobic coditions_replicate 2


title: M+G_3

description: growth in M9 medium until OD600 of 0.5_with D glucose and L malic acid_replicate 3

value: growth in M9 medium until OD600 of 0.5 with D glucose and L malic acid


title: M+G_1

description: growth in M9 medium until OD600 of 0.5_with D glucose and L malic acid_replicate 1


title: M+G_2

description: growth in M9 medium until OD600 of 0.5_with D glucose and L malic acid_replicate 2


title: IC2209

type: genomic

city: Raleigh

first: Ignazio

last: Carbone

state: NC

address: 851 Main Campus Drive, Suite 233

department: Plant Pathology

country: USA

institute: North Carolina State University - Center for Integrated Fungal Research

description: NRRL:  29473x29506-1-9

hyb_protocol: Each sample was analyzed by the Microarray Laboratories of Expression Analysis (Raleigh-Durham NC).  Briefly, 300-350 ng of fragmented genomic DNA was diluted in hybridization buffer (MES, NaCl, EDTA, Tween 20, Herring Sperm DNA, Acetylated BSA) containing biotin-labeled OligoB2 and Eukaryotic Hybridization Controls (Affymetrix).  The hybridization cocktail was denatured at 99°C for 5 minutes, incubated at 45°C for 5 minutes and then injected into a GeneChip cartridge. The GeneChip array was incubated at 42°C for at least 16 hours in a rotating oven at 60 rpm.  GeneChips were washed with a series of nonstringent (25°C) and stringent (50°C) solutions containing variable amounts of MES, Tween20 and SSPE. The microarrays were then stained with streptavidin-phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution.

scan_protocol: Fluorescent images were detected in a GeneChip® Scanner 3000 and array data was extracted using the GeneChip Operating System v 1.1 (Affymetrix). Arrays images were further inspected for defects or debris. Quality control was based on a comparison of the conformity of hybridization controls, scaling factor, and noise; percent detection metrics were analyzed to determine if any outliers were present.

data_processing: For the parent-offspring trio heat maps, array data for all strains examined using aCGH were imported into JMP genomics (SAS, Cary, NC, USA) for further transformation and normalization.  Data were log2 transformed and normalized using Loess normalization.  Because we are interested in detecting differences in hybridization intensities no background correction was applied.  For the genome-wide parentage plots, the A. flavus probe data were normalized using Loess normalization but not log2 transformed.

label: biotin

molecule: genomic DNA

organism: Aspergillus flavus

source_name: mycelia

label_protocol: Genomic DNA was labeled using the BioPrime DNA labeling System (Invitrogen Catalogue No. 18094-011) as follows: (1) fungal DNA in the amount of 300-350 ng was mixed with 60 μl of 2.5X random primers (BioPrime kit) and 132 μl of dH2O, (2) the reaction mixture was denatured in an Eppendorf thermocycler at 99°C for 10 min, and then cooled at 4°C for 15 min, (3) 15 μl of 10X dNTPs containing biotin dCTP and 3 μl Klenow polymerase were added and incubated at 25°C in a thermocycler for 18 h, (4) the reaction mixture was precipitated by adding 15 μl of 3M NaOAc and 400 μl of cold 95% ethanol, followed by incubation at 20°C for 15 min, (5) samples were centrifuged at high speed in a refrigerated microcentrifuge for 20 min, and (6) the pellets were washed with 500 μl ice-cold 70% ethanol, centrifuged, and then vacuum dried with heating for 10 min.  DNA was resuspended in 100 μl of dH2O and 5 μl was used to check the quality of the labeled DNA on a gel.

growth_protocol: Isolates were grown in Potato Dextrose Broth (DifcoTM) for up to 5 days before the mycelia was harvested and lyophilized.

extract_protocol: Total genomic DNA was extracted from freeze-dried mycelia using either the Qiagen maxiprep kit (Qiagen, Valencia, CA) or the MasterPure Yeast DNA Purification Kit (Epicentre Technologies, Madison, WI) following the manufacturer’s protocol.


title: M9stat_3

description: growth in M9 medium with glucose_stationary phase_replicate 3

value: growth in M9 medium with glucose stationary phase


title: M9stat_2

description: growth in M9 medium with glucose_stationary phase_replicate 2


title: IC1775

description: NRRL:  35737x29506-9-6


title: Pyr_1

description: growth in M9 medium until OD600 of 0.5_with pyruvate_replicate 1


title: IC2171

description: NRRL:  29530x18543-1-7


title: IC2207

description: NRRL:  29473x29506-1-7


title: IC1719

description: NRRL:  35736x21882-1-4


title: IC2205

description: NRRL:  29473x29506-1-5


title: IC1650

description: NRRL:  29507x18543-2-1


title: M9stat_1

description: growth in M9 medium with glucose_stationary phase_replicate 1


title: M9tran_3

description: growth in M9 medium with glucose_transition phase_replicate 3

value: growth in M9 medium with glucose transition phase


title: M9tran_1

description: growth in M9 medium with glucose_transition phase_replicate 1


title: IC1751

description: NRRL:  29537x29536-2-12


title: M9tran_2

description: growth in M9 medium with glucose_transition phase_replicate 2


title: M9exp_3

description: growth in M9 medium with glucose_exponential phase_replicate 3

value: growth in M9 medium with glucose exponential phase


title: IC1766

description: NRRL:  62358


title: IC308

description: NRRL:  29537


title: cotyledon_Tendral_WMVinfected_3dpi_rep1_cDNA

city: Espinardo

first: Daniel

last: Gonzalez-Ibeas

state: Murcia

address: Campus de Espinardo s/n

department: Biologia Estres y Patologia Vegetal

country: Spain

institute: CEBAS-CSIC

description:
GSM745567
cDNA synthesis protocol: Double stranded cDNA was synthesised by the SMART procedure with PrimeScript (Takara Bio Inc., Otsu, Shiga, Japan) reverse transcriptase (method B), with some modifications. Twelve micrograms of total RNA were mixed with 2 µl of oligo(dT)-16mer (50 µM), 2 µl of SMART IV oligonucleotide  AAGCAGTGGTATCAACGCAGAGTGGG (50 µM) and sterile miliQ water up to 22 µl of total volume in a microcentrifuge tube (200 µl). The mixture was incubated at 70 C for 3 minutes and cooled on ice for 2 minutes. To the previous RNA/primer mixture, 8 µl of 5X buffer (250 mM Tris-HCl, pH 8.3, 375 mM KCl, 30 mM MgCl2, not supplied with the enzyme), 4 µl of dNTPs (10 mM each), 4µl of DTT (100 mM), 2 µl of RNAse inhibitor (Invitrogen, Carlsbad, CA, USA) and 2 µl (400 units) of PrimeScript (Takara Bio Inc., Otsu, Shiga, Japan) reverse transcriptase were added. The mixture was incubated at 42 C for 60 minutes and at 70 ºC for 15 minutes. One µl of RNAse A (20mg/ml) (Invitrogen, Carlsbad, CA, USA) was added and incubated at 37 C for 10 minutes.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: Data were normalised using the normalisation algorithm RMA with the package oligo version 1.8.2 (Carvalho et al. 2007, Biostatistics 8 (2): 485-499) written in R (R Development Core Team, http://www.R-project.org).

organism: Cucumis melo

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Germination of melon seeds was carried out in Petri dishes for 48 h at 25 ºC. After germination, seeds were sown in 0.5 L pots and kept in growth chambers (MLR-351H from Sanyo) with 16 h light/25 ºC and 8 h dark/18 ºC for about three weeks.

extract_protocol: Cotyledon samples were independently frozen in liquid N2 and stored at -80 ºC. RNA extracts were prepared from these samples using Tri-Reagent (Sigma Chemical Co., St. Louis, MO, USA) following the manufacturer´s instructions. To eliminate traces of genomic DNA, total RNA was incubated with DNAse I (New England Biolabs, London, UK) 10 min at 37 ºC. Then, reaction volume was adjusted to 100 µl and the aqueous phase extracted with phenol:chloroform:isoamilalcohol (125:24:1). Total RNA was precipitated with 10 % (v/v) NaCl 3M and 2.5 v of absolute ethanol by centrifugation (12.000 g, 20 min, 4º C).

treatment_protocol: The viral isolate used in this study was WMV-M116, kindly provided by Dr. Moriones (Estación Experimental “La Mayora”-CSIC, Málaga, Spain). Mechanical inoculations were carried out using standard procedures. Dehydrated viral inoculum was first revived by mechanical inoculation of squash fully-expanded cotyledons. Systemically infected squash leaves were harvested after 15 days post-inoculation (dpi) and used as inoculum source for melons. Squash leaves were ground in a sterile mortar in the presence of inoculation buffer (0.2 M phosphate buffer pH 8.0, 0.1 % v/v β-mercaptoethanol, 0.03 g/mL active charcoal) and, then, carborundum (0.037 mm diameter) dusted 7 days old melon cotyledons were rubbed with this infectious mixture. Control non-infected melon cotyledons were rubbed using only inoculation buffer (mock-inoculated controls).

tag: tissue

value: cotyledon

tag: reference sample from accession gse30111 (rna source)

tag: genotype

value: Tendral

tag: physiological condition

value: WMV infected

tag: days post-inoculation


title: IC311

description: NRRL:  35737


title: IC307

description: NRRL:  29536


title: IC1179

description: NRRL:  18543 (=IC1179, AF36)


title: IC310

description: NRRL:  35736


title: IC301

description: NRRL:  29530


title: IC278

description: NRRL:  29507


title: B60_1

description: biofilm formation_strong biofilm = 60h of growth in MSgg medium without shaking_replicate 1


title: B36_1

description: biofilm formation_early biofilm = 36h of growth in MSgg medium without shaking_replicate 1


title: B36_2

description: biofilm formation_early biofilm = 36h of growth in MSgg medium without shaking_replicate 2


title: M9exp_1

description: growth in M9 medium with glucose_exponential phase_replicate 1


title: B60_2

description: biofilm formation_strong biofilm = 60h of growth in MSgg medium without shaking_replicate 2


title: cotyledon_Tendral_mock_7dpi_rep3 (cDNA study)

value: mock inoculated


title: IC244

description: NRRL:  29473


title: IC277

description: NRRL:  29506


title: BT_1

description: biofilm formation_control for no biofilm = 24h of growth in MSgg medium under shaking_replicate 1

value: biofilm formation control for no biofilm = 24h of growth in MSgg medium under shaking


title: cotyledon_Tendral_mock_7dpi_rep1 (cDNA study)


title: Sw_2

description: 18h of growth on soft plates_replicate 2

value: 18h of growth on soft plates


title: cotyledon_Tendral_WMVinfected_1dpi_rep3_cDNA

description:
GSM745566
cDNA synthesis protocol: Double stranded cDNA was synthesised by the SMART procedure with PrimeScript (Takara Bio Inc., Otsu, Shiga, Japan) reverse transcriptase (method B), with some modifications. Twelve micrograms of total RNA were mixed with 2 µl of oligo(dT)-16mer (50 µM), 2 µl of SMART IV oligonucleotide  AAGCAGTGGTATCAACGCAGAGTGGG (50 µM) and sterile miliQ water up to 22 µl of total volume in a microcentrifuge tube (200 µl). The mixture was incubated at 70 C for 3 minutes and cooled on ice for 2 minutes. To the previous RNA/primer mixture, 8 µl of 5X buffer (250 mM Tris-HCl, pH 8.3, 375 mM KCl, 30 mM MgCl2, not supplied with the enzyme), 4 µl of dNTPs (10 mM each), 4µl of DTT (100 mM), 2 µl of RNAse inhibitor (Invitrogen, Carlsbad, CA, USA) and 2 µl (400 units) of PrimeScript (Takara Bio Inc., Otsu, Shiga, Japan) reverse transcriptase were added. The mixture was incubated at 42 C for 60 minutes and at 70 ºC for 15 minutes. One µl of RNAse A (20mg/ml) (Invitrogen, Carlsbad, CA, USA) was added and incubated at 37 C for 10 minutes.


title: cotyledon_Tendral_mock_7dpi_rep2 (cDNA study)


title: Sw_1

description: 18h of growth on soft plates_replicate 1


title: BC_1

description: 18h of growth on plates_around 1000 colonies per plate_replicate 1

value: 18h of growth on plates around 1000 colonies per plate


title: BC/t_2

description: 18h of growth on plates_around 1000 colonies per plate_technical replicate of replicate 2

value: technical replicate of replicate 2


title: BC/t_1

description: 18h of growth on plates_around 1000 colonies per plate_technical replicate of replicate 1

value: technical replicate of replicate 1


title: M9exp_2

description: growth in M9 medium with glucose_exponential phase_replicate 2


title: BC_2

description: 18h of growth on plates_around 1000 colonies per plate_replicate 2


title: cotyledon_Tendral_mock_3dpi_rep3 (cDNA study)


title: BT_2

description: biofilm formation_control for no biofilm = 24h of growth in MSgg medium under shaking_replicate 2


title: cotyledon_Tendral_mock_1dpi_rep2 (cDNA study)


title: cotyledon_Tendral_mock_3dpi_rep2 (cDNA study)


title: cotyledon_Tendral_mock_1dpi_rep3 (cDNA study)


title: cotyledon_Tendral_mock_3dpi_rep1 (cDNA study)


title: cotyledon_Tendral_mock_1dpi_rep1 (cDNA study)


title: cotyledon_Tendral_WMVinfected_7dpi_rep2 (cDNA study)


title: cotyledon_Tendral_WMVinfected_7dpi_rep1 (cDNA study)


title: BI_1

description: 18h of growth on plates_around 100 colonies per plate_replicate 1

value: 18h of growth on plates around 100 colonies per plate


title: BI_2

description: 18h of growth on plates_around 100 colonies per plate_replicate 2


title: cotyledon_Tendral_WMVinfected_7dpi_rep3 (cDNA study)


title: C90_1

description: competence_time=90 minutes after induction_replicate 1


title: cotyledon_Tendral_WMVinfected_3dpi_rep3 (cDNA study)


title: Rat cardiac myocytes Non target 48 hrs-2

city: Miami

first: Salil

last: Sharma

state: Florida

address: 1600 NW 10th Ave

department: Molecular and Cellular Pharmacology

institute: University of Miami

description:
2010-03-16_354093_650pmt_0635.gpr
THE CONSTRUCTS WERE TAGGED WITH RFP

hyb_protocol: Biotinylated cRNA samples were fragmented, diluted in a formamide-containing hybridization buffer, and loaded on to the surface of MEEBO microarray slides enclosed in custom hybridization chambers.  The slides were hybridized for 16-18 hours under constant rotation in a Model 400 hybridization oven (Scigene, Sunnyvale, CA).

scan_protocol: After hybridization, the microarray slides were washed under stringent conditions, stained with Streptavidin-Alexa-647 (Invitrogen), and scanned using an Axon GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA).

data_processing: Spot intensities for each probe were calculated by subtracting median local background from median local foreground for each spot. Spot intensities were transformed by taking the base 2 logarithm of each value. The spot intensities were then normalized by subtracting the 70th percentile of the spot intensities of probes against rat genes and adding back a scaling factor (grand mean of 70th percentile). Data for low quality spots, control sequences, and non-rat probes were removed.

organism: Rattus norvegicus

source_name: NON TARGET NEONATAL CARDIAC MYOCYTES_TOTAL RNA 48 hours

label_protocol: Biotin-labeled complementary RNA (cRNA) was prepared from DNase treated total RNA by the method of Van Gelder et al., (1). Briefly, an oligonucleotide containing a 5'-T7-promoter sequence and a 3' T24VN sequence was used to prime reverse transcription of RNA catalyzed by Superscript II (Invitrogen, Carlsbad, CA). Double-stranded cDNA was prepared from the 1st strand product by the method of Gubler & Hoffman (2), and purified on a PCR purification column (Qiagen, Valencia, CA). The double-stranded cDNA was then used as a template for in vitro transcription with T7 RNA polymerase using a high yield transcription kit (Ambion, Austin, TX) and including biotin-16-UTP (Ambion) in the reaction mixture.

extract_protocol: Total RNA was extracted using miRVana RNA isolation kit from AMBION using manufacturer's protocol.

treatment_protocol: primary cultures of neonatal rat cardiac myocytes were either transfected with miR142 lentiviral construct or a non target lentiviral construct from Open Biosystems Inc. 48 hours post transfection, total RNA was extracted.

value: Sprague Dawley

tag: cell type

value: neonatal rat cardiac myocytes

tag: treatment group

value: non target control overexpressed using lentivirus


title: cotyledon_Tendral_WMVinfected_3dpi_rep2 (cDNA study)


title: Rat cardiac myocytes Non target 48 hrs-3

description:
2010-03-16_354096_650pmt_0635.gpr
THE CONSTRUCTS WERE TAGGED WITH RFP


title: Rat cardiac myocytes Non target 48 hrst-1

description:
2010-03-16_354086_650pmt_0635.gpr
THE CONSTRUCTS WERE TAGGED WITH RFP


title: Rat cardiac myocytes miR142OE 48 hrs-1

description:
2010-03-16_355294_650pmt_0635.gpr
THE CONSTRUCTS WERE TAGGED WITH RFP

source_name: MIR142OE NEONATAL CARDIAC MYOCYTES_TOTAL RNA_48 hours

value: miR142 overexpressed using lentivirus


title: Rat cardiac myocytes miR142OE 48 hrs-2

description:
2010-03-16_355296_650pmt_0635.gpr
THE CONSTRUCTS WERE TAGGED WITH RFP


title: Rat cardiac myocytes miR142OE 48 hrs-3

description:
2010-03-16_355297_650pmt_0635.gpr
THE CONSTRUCTS WERE TAGGED WITH RFP


title: C30_1

description: competence_time=30 minutes after induction_replicate 1


title: C90_2

description: competence_time=90 minutes after induction_replicate 2


title: Gly_3

description: growth in M9 medium until OD600 of 0.5_with glycerol_replicate 3

value: growth in M9 medium until OD600 of 0.5 with glycerol


title: G180_3

description: germination_time=180 minutes after induction_replicate 3


title: C30_2

description: competence_time=30 minutes after induction_replicate 2


title: miRNA expression analysis in RWPE-1, biological replicate 2

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

department: Diagnostics

institute: Fraunhofer Institute for Cell Therapy and Immunology

description: miRNA expression analysis in prostate epithelial cell line RWPE-1

hyb_protocol: according to CombiMatrix miRNA microarray hybridization protocol

scan_protocol: Arrays were scanned using a GenePix 4200 Scanner and the GenePix Pro 6.1 Software (Molecular Devices) with following settings: laser power: 40%, PMT: 500, resolution: 5µm, Focus: 85µm.

data_processing: The data were analyzed with R (version 2.9.0) and BioConductor (version 2.4). Expression levels were normalized (quantile normalization) and a linear model was fitted using the R package limma in order to identify differentially expressed miRNAs. Reliable variance estimations were obtained by empirical Bayes moderated t-statistics. False discovery rate was controlled by Benjamini-Hochberg adjustment.

organism: Homo sapiens

source_name: Prostate epithelial cell line RWPE-1

label_protocol: 1µg microRNA was Cy-5-labeled using the Mirus Bio Label IT miRNA Labeling Kit according to the manufacturer`s protocol

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

tag: cell line

value: prostate epithelial


title: miRNA expression analysis in RWPE-1, biological replicate 3


title: miRNA expression analysis in LNCaP, biological replicate 3

description: miRNA expression analysis in early prostate cancer cell line LNCaP.

source_name: Early prostate cancer cell line LNCaP

value: LNCaP

tag: tumor

value: prostate cancer

tag: tumor stage

value: early


title: cotyledon_Tendral_WMVinfected_1dpi_rep3 (cDNA study)

value: cotyledon

value: Tendral

value: WMV infected


title: cotyledon_Tendral_WMVinfected_1dpi_rep1 (cDNA study)


title: cotyledon_Tendral_WMVinfected_1dpi_rep2 (cDNA study)


title: miRNA expression analysis in LNCaP, biological replicate 1


title: miRNA expression analysis in RWPE-1, biological replicate 1


title: miRNA expression analysis in PC3, biological replicate 3

description: miRNA expression analysis in late prostate cancer cell line PC3.

source_name: Late prostate cancer cell line PC3

value: late


title: miRNA expression analysis in Du-145, biological replicate 3

description: miRNA expression analysis in late prostate cancer cell line Du-145.

source_name: Late prostate cancer cell line Du-145


title: miRNA expression analysis in Du-145, biological replicate 1


title: miRNA expression analysis in LNCaP, biological replicate 2


title: miRNA expression analysis in Du-145, biological replicate 2


title: miRNA expression analysis in PC3, biological replicate 2


title: G150_3

description: germination_time=150 minutes after induction_replicate 3


title: G180_1

description: germination_time=180 minutes after induction_replicate 1


title: cotyledon_Tendral_WMVinfected_3dpi_rep1 (cDNA study)


title: cotyledon_TGR-1551_mock_7dpi_rep2 (cDNA study)

value: mock inoculated


title: cotyledon_TGR-1551_mock_7dpi_rep3 (cDNA study)


title: cotyledon_TGR-1551_mock_3dpi_rep3 (cDNA study)


title: cotyledon_TGR-1551_mock_7dpi_rep1 (cDNA study)


title: G180_2

description: germination_time=180 minutes after induction_replicate 2


title: G150_2

description: germination_time=150 minutes after induction_replicate 2


title: miRNA expression analysis in PC3, biological replicate 1


title: G150_1

description: germination_time=150 minutes after induction_replicate 1


title: G135_1

description: germination_time=135 minutes after induction_replicate 1


title: G135_3

description: germination_time=135 minutes after induction_replicate 3


title: IC201

description: NRRL:  21882 (=IC201, IC316, afla-guard)


title: cotyledon_TGR-1551_mock_3dpi_rep2 (cDNA study)


title: cotyledon_TGR-1551_mock_3dpi_rep1 (cDNA study)


title: MTB1254 Day 0 rep 1

city: Stanford

first: SMD

last: Staff

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Strain Comparison, Stress by growth condition
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75090.gif

hyb_protocol: 10 ul of hybridization solution (labeled cDNA, 5 ug tRNA, 3.8x SSC, 0.27% SDS) was sealed under a coverslip with rubber cement and hybridized overnight at 65 C for the DNA microarray. Oligonucleotide microarrays were first prehybridized for 1 h in 5x SSC, 1% BSA, and 0.1% SDS and washed with H2O and isopropanol. After the prehybridization, 10 ul of hybridization solution (labeled cDNA, 5 ug tRNA, 2x SSC, 25% formamide, and 0.1% SDS) was hybridized overnight at 54 C.

scan_protocol: Microarrays were scanned using a GenePix 4000A (Axon Instruments, Inc.). The intensities of the two dyes at each spot were quantified using ScanAlyze (M. Eisen, Lawrence Berkeley National Lab, Berkeley, CA).

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

organism: Mycobacterium tuberculosis

source_name: MTB1254 Day 0

label_protocol: Both a PCR gene product microarray and a 70-mer oligonucleotide-based microarray (tuberculosis oligonucleotide set; QIAGEN) were used. Labeled cDNA was prepared as follows: 2 ug total RNA and 4.4ug of random oligonucleotide hexamers were incubated for 2 min at 98 C, cooled on ice, combined with Stratascript RTase buffer, 0.5 mM dA,G,CTP, 0.02 mM dTTP, 1.5 nmol Cy3 or Cy5-dUTP (Amersham Biosciences), and 1.8 ul Stratascript RTase (Stratagene) in a total volume of 25 ul, and incubated for 10 min at 25 C and 90 min at 42 C. cDNA was purified by microcon-10 (Amicon) filtration.

growth_protocol: Clinical isolate 1254, 7H9 medium (supplemented with BSA, NaCl, glucose, and glycerol), 250-ml vented tissue culture flasks, 90 rpm shaking, and a starting culture density of OD 0.15 were used, unless otherwise indicated. RNA samples isolated from OD 0.15 cultures of the M. tuberculosis strain being assayed on the same day were used for the reference sample in each experiment. Cells were collected with a 4-min centrifugation step and frozen on dry ice.

extract_protocol: Cell debris was separated by a 45-s centrifugation. The supernatant was transferred to 2-ml Heavy Phase Lock Gel I tubes (Eppendorf) containing 300 ul chloroform, inverted rapidly for 15 s, and incubated 2 min. Samples were centrifuged for 5 min, and the aqueous phase was added to 270 ul isopropanol, followed by addition of 270 ul of the following mixture: 0.8 M sodium citrate and 1.2 M NaCl. Samples were incubated for 10 min at 4 C and centrifuged for 15 min at 4 C. The RNA pellets were washed with 1 ml 75% ethanol, centrifuged 5 min, and air-dried. After suspension of the RNA pellets in 90 ul water, 10 ul DNase I 10x buffer, and 6 U DNase I (Ambion) were added, and the samples were incubated for 30 min. Final purification of RNA was by RNeasy column (QIAGEN).

treatment_protocol: Cell pellets were suspended in 1 ml TRIzol reagent (GIBCO BRL) and transferred to 2-ml screw cap tubes containing 0.5 ml 0.1-mm diameter zirconia/silica beads (BioSpec Products).

tag: treatment

value: control

tag: strain name

value: H37Rv (wild_type)

value: Control (Growth curve) 0 days


title: cotyledon_TGR-1551_mock_1dpi_rep3 (cDNA study)


title: MTB1254 Day 0 vs low Oxygen Day 4 rep 4

description:
Simple annotation: Strain Comparison, Stress by growth condition
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75057.gif

source_name: MTB1254 Day 4

value: NRP (Wayne Growth)/4 days


title: S8_5

description: induction of sporulation_time=8h_replicate 5

value: induction of sporulation_time=8h


title: S8_4

description: induction of sporulation_time=8h_replicate 4


title: S7_6

description: induction of sporulation_time=7h_replicate 6

value: induction of sporulation_time=7h


title: H37 Rv3132-34 KO 0 days vs Rv3132-34 KO (complemented) hypoxia 4 day rep 1

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75654.gif

source_name: H37Rv No treatment

value: H37Rv-Delta-dosR::kan plus DosR

source_name: CO NRP Day 4


title: cotyledon_TGR-1551_mock_1dpi_rep2 (cDNA study)


title: H37 Rv3132-34 KO 0 days vs Rv3132-34 KO (complemented) hypoxia 4 day rep 4

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75657.gif


title: cotyledon_TGR-1551_WMVinfected_7dpi_rep2 (cDNA study)


title: MTB1254 Day 0 rep 2

description:
Simple annotation: Strain Comparison, Stress by growth condition
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75091.gif


title: H37 Rv3132-34 KO 0 days vs Rv3132-34 KO (complemented) hypoxia 4 day rep 3

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75656.gif


title: cotyledon_TGR-1551_WMVinfected_7dpi_rep3 (cDNA study)


title: S7_5

description: induction of sporulation_time=7h_replicate 5


title: cotyledon_TGR-1551_mock_1dpi_rep1 (cDNA study)


title: cotyledon_TGR-1551_WMVinfected_7dpi_rep1 (cDNA study)


title: S6_5

description: induction of sporulation_time=6h_replicate 5

value: induction of sporulation_time=6h


title: S6_4

description: induction of sporulation_time=6h_replicate 4


title: MTB1254 Day 0 vs low Oxygen Day 4 rep 2

description:
Simple annotation: Strain Comparison, Stress by growth condition
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75055.gif


title: H37Rv 0 day ctrl vs Rv3132-34 KO hypoxia 4 day rep 2

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75659.gif

source_name: Rv3132 4KO No treatment

source_name: KO NRP Day 4


title: MTB1254 Day 0 vs low Oxygen Day 4 rep 6

description:
Simple annotation: Strain Comparison, Stress by growth condition
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75059.gif


title: MTB1254 Day 0 vs low Oxygen Day 4 rep 5

description:
Simple annotation: Strain Comparison, Stress by growth condition
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75058.gif


title: cotyledon_TGR-1551_WMVinfected_3dpi_rep2 (cDNA study)


title: S7_4

description: induction of sporulation_time=7h_replicate 4


title: H37Rv 0 day ctrl vs Rv3132-34 KO hypoxia 4 day rep 3

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75660.gif


title: MTB1254 Day 0 rep 3

description:
Simple annotation: Strain Comparison, Stress by growth condition
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75092.gif


title: H37 Rv3132-34 KO 0 days vs Rv3132-34 KO (complemented) hypoxia 4 day rep 2

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75655.gif


title: cotyledon_TGR-1551_WMVinfected_3dpi_rep1 (cDNA study)


title: cotyledon_TGR-1551_WMVinfected_3dpi_rep3 (cDNA study)


title: H37Rv 0 day ctrl vs Rv3132-34 KO hypoxia 4 day rep 1

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75658.gif


title: H37Rv 0 day ctrl vs Rv3132-34 KO hypoxia 4 day rep 4

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75661.gif


title: MTB1254 Day 0 vs low Oxygen Day 4 rep 3

description:
Simple annotation: Strain Comparison, Stress by growth condition
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75056.gif


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 24hrs + 0.5 mM DNO 40min rep 1

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75607.gif

source_name: 1254 No treatment

value: 1254 (wild_type)

value: 0.5mM of diethylenetriamine/nitric oxide for 24 hours + 0.05mM DNO 40 min


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 8hrs rep 4

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75594.gif

source_name: 0.5mM DNO 8h

value: 0.5mM of diethylenetriamine/nitric oxide for 8 hours


title: H37Rv Ctrl vs 0.05 mM DETA/NO 40min rep 2

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19136.gif

source_name: Control

source_name: Rv 0.05mM DNO 40m

value: 0.05mM of diethylenetriamine/nitric oxide for 40 minutes


title: MTB strain 1254 Ctrl vs 0.05 mM DETA/NO 40min rep 1

description:
Simple annotation: Stress, Stress by growth condition
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18438.gif

source_name: Strain: MTB strain 1254 Treatment: Control

source_name: Strain: MTB strain 1254 Treatment: 0.05 mM DETA/NO for 40min


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 24hrs + 0.5 mM DNO 40min rep 4

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75610.gif

source_name: 0.5mM DNO 24h + 0.05mM DNO 40min


title: CDC1551 Ctrl vs 0.05 mM DETA/NO 40 min rep 1

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75646.gif

source_name: CDC1551 No treatment

value: CDC1551 (wild_type)


title: MTB strain 1254 Ctrl vs 2hr Hypoxia rep 3

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75620.gif

source_name: GasPak 2h 1256

value: Exposing for 2 hour to 0.2% O2 (hypoxia)


title: MTB1254 Day 0 vs low Oxygen Day 4 rep 1

description:
Simple annotation: Strain Comparison, Stress by growth condition
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75054.gif


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 20min rep 1

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75599.gif

source_name: 0.5mM DNO 20 min

value: 0.5mM of diethylenetriamine/nitric oxide for 20 minutes


title: S6_6

description: induction of sporulation_time=6h_replicate 6

source_name: Bacillus subtilis cells


title: S6/t_3

description: induction of sporulation_time=6h_technical replicate of replicate 3

value: technical replicate of replicate 3


title: MTB strain 1254 Ctrl vs 5.0 mM DETA/NO 40min rep 1

description:
Simple annotation: Stress, Stress by growth condition
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74762.gif

source_name: Strain: MTB strain 1254 Treatment: 5.0 mM DETA/NO for 40min

value: 5.0mM of diethylenetriamine/nitric oxide for 40 minutes


title: S6/t_2

description: induction of sporulation_time=6h_technical replicate of replicate 2

value: technical replicate of replicate 2


title: CDC1551 Ctrl vs 0.05 mM DETA/NO 40 min rep 2

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75647.gif

value: control


title: cotyledon_TGR-1551_WMVinfected_1dpi_rep3 (cDNA study)

value: cotyledon

value: WMV infected


title: S6_1

description: induction of sporulation_time=6h_replicate 1


title: S6/t_1

description: induction of sporulation_time=6h_technical replicate of replicate 1

value: technical replicate of replicate 1


title: S6_2

description: induction of sporulation_time=6h_replicate 2


title: S6_3

description: induction of sporulation_time=6h_replicate 3


title: MTB strain 1254 Ctrl vs high aeration rep2

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75630.gif

source_name: No treatment


title: S5_3

description: induction of sporulation_time=5h_replicate 3

value: induction of sporulation_time=5h


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 24hrs rep 4

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75606.gif

source_name: 0.5mM DNO 24h

value: 0.5mM of diethylenetriamine/nitric oxide for 24 hours


title: MTB strain 1254 Ctrl vs 0.5 mM KCN 1hr rep 2

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75612.gif

source_name: KCN 0.5mM 1h

value: 0.5mM Potassium cyanide 1 hour


title: MTB strain 1254 Ctrl vs 1.0 mM DETA/NO 40min rep 1

description:
Simple annotation: Stress, Stress by growth condition
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19036.gif

value: 1254 (wild_type)

source_name: Strain: MTB strain 1254 Treatment: 1.0 mM DETA/NO for 40min

value: 1.0mM of diethylenetriamine/nitric oxide for 40 minutes


title: S5_2

description: induction of sporulation_time=5h_replicate 2


title: cotyledon_TGR-1551_WMVinfected_1dpi_rep1 (cDNA study)


title: MTB strain 1254 Ctrl vs high aeration + 0.001 mM DETA/NO rep 3

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75622.gif

source_name: High aeration and 0.001mMDNO

value: 0.001 mM of diethylenetriamine/nitric oxide


title: cotyledon_TGR-1551_WMVinfected_1dpi_rep2 (cDNA study)


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 5min rep 4

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75590.gif

source_name: 1254 No treatment

source_name: 0.5mM DNO 5min

value: 0.5mM of diethylenetriamine/nitric oxide for 5 minutes


title: S5_1

description: induction of sporulation_time=5h_replicate 1


title: MTB strain 1254 Ctrl vs 0.5 mM KCN 20min + 0.05 mM DETA/NO 40min rep 1

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75614.gif

value: 0.5mM Potassium cyanide plus 40 min. 0.05mM DNO


title: S4_3

description: induction of sporulation_time=4h_replicate 3

value: induction of sporulation_time=4h


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 5min rep 2

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75588.gif


title: MTB strain 1254 Ctrl vs high aeration + 0.05 mM DETA/NO rep 2

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75627.gif

value: 0.05 mM of diethylenetriamine/nitric oxide


title: MTB strain 1254 Ctrl vs low aeration + 0.001 mM DETA/NO rep 2

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75632.gif


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 20min rep 4

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75602.gif

value: 0.5mM of diethylenetriamine/nitric oxide for 20 minutes


title: MTB strain 1254 Ctrl vs low aeration + 0.01 mM DETA/NO rep 1

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75634.gif

value: 0.01 mM of diethylenetriamine/nitric oxide


title: MTB strain 1254 Ctrl vs low aeration + 0.01 mM DETA/NO rep 3

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75636.gif


title: MTB strain 1254 Ctrl vs 0.05 mM DETA/NO 40min rep 7

description:
Simple annotation: Stress, Stress by growth condition
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74758.gif

value: 0.05mM of diethylenetriamine/nitric oxide for 40 minutes


title: MTB strain 1254 Ctrl vs low aeration (0.2% oxygen) 2hr rep 2

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75644.gif

value: control


title: S4_2

description: induction of sporulation_time=4h_replicate 2


title: S4_1

description: induction of sporulation_time=4h_replicate 1


title: S3_3

description: induction of sporulation_time=3h_replicate 3

value: induction of sporulation_time=3h


title: MTB strain 1254 Ctrl vs 0.5 mM KCN + 2hr hypoxia rep 3

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75619.gif

source_name: KCN 0.5mM GasPak 2h

value: 0.5mM Potassium cyanide plus 2 hours-hipoxia


title: MTB strain 1254 Ctrl vs 1.0 mM DETA/NO 40min rep 3

description:
Simple annotation: Stress, Stress by growth condition
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19038.gif


title: S3_2

description: induction of sporulation_time=3h_replicate 2


title: MTB strain 1254 Ctrl vs 0.05 mM DETA/NO 40min rep 6

description:
Simple annotation: Stress, Stress by growth condition
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18443.gif


title: MTB strain 1254 Ctrl vs high aeration + 0.01 mM DETA/NO rep 1

description:
Simple annotation: Stress, Miscellaneous
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19187.gif

source_name: Control

source_name: High aeration + 0.01mM DNO


title: S3_1

description: induction of sporulation_time=3h_replicate 1


title: MTB strain 1254 Ctrl vs 0.005 mM DETA/NO 40min rep 3

description:
Simple annotation: Stress, Stress by growth condition
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19034.gif

source_name: Strain: MTB strain 1254 Treatment: Control

source_name: Strain: MTB strain 1254 Treatment: 0.005 mM DETA/NO for 40min

value: 0.005mM of diethylenetriamine/nitric oxide for 40 minutes


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 1hr rep 4

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75581.gif

source_name: 0.5mM DNO 1h

value: 0.5mM of diethylenetriamine/nitric oxide for 1 hour


title: MTB strain 1254 Ctrl vs high aeration rep1

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75629.gif


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 8hrs rep 3

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75593.gif

source_name: 0.5mM DNO 8h

value: 0.5mM of diethylenetriamine/nitric oxide for 8 hours


title: MTB strain 1254 Ctrl vs high aeration rep3

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75631.gif


title: H37Rv ctrl vs Rv3132-34 KO (complemented)  0.05 mM DETA/NO 40min rep 3

description:
Simple annotation: Stress, Miscellaneous
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19151.gif

value: H37Rv-Delta-dosR::kan plus DosR

source_name: Rv3133Comp 0.05mM DNO 40m


title: S2_3

description: induction of sporulation_time=2h_replicate 3

source_name: Bacillus subtilis cells

value: induction of sporulation_time=2h


title: S2_1

description: induction of sporulation_time=2h_replicate 1


title: S2_2

description: induction of sporulation_time=2h_replicate 2


title: S1_2

description: induction of sporulation_time=1h_replicate 2

value: induction of sporulation_time=1h


title: S1_3

description: induction of sporulation_time=1h_replicate 3


title: S1_1

description: induction of sporulation_time=1h_replicate 1


title: S0_3

description: induction of sporulation_time=0_replicate 3

value: induction of sporulation_time=0


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 24hrs + 0.5 mM DNO 40min rep 3

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75609.gif

value: 1254 (wild_type)

value: 0.5mM of diethylenetriamine/nitric oxide for 24 hours + 0.05mM DNO 40 min


title: S0_2

description: induction of sporulation_time=0_replicate 2


title: S0_1

description: induction of sporulation_time=0_replicate 1


title: MTB strain 1254 Ctrl vs high aeration + 0.001 mM DETA/NO rep 2

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75621.gif

value: 0.001 mM of diethylenetriamine/nitric oxide


title: MTB strain 1254 Ctrl vs 2hr Hypoxia rep 1

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19132.gif

source_name: 1254 HypoxiaGP 2h

value: Exposing for 2 hour to 0.2% O2 (hypoxia)


title: H37Rv ctrl vs Rv3132-34 KO (complemented)  0.05 mM DETA/NO 40min rep 1

description:
Simple annotation: Stress, Miscellaneous
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19149.gif


title: MTB strain 1254 Ctrl vs 0.05 mM DETA/NO 40min rep 4

description:
Simple annotation: Stress, Stress by growth condition
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18441.gif

source_name: Strain: MTB strain 1254 Treatment: 0.05 mM DETA/NO for 40min


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 24hrs rep 2

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75604.gif

source_name: 0.5mM DNO 24h

value: 0.5mM of diethylenetriamine/nitric oxide for 24 hours


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 40min rep 1

description:
Simple annotation: Stress, Stress by growth condition
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19041.gif

source_name: Strain: MTB strain 1254 Treatment: 0.5 mM DETA/NO for 40min

value: 0.5mM of diethylenetriamine/nitric oxide for 40 minutes


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 2hrs rep 1

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75583.gif

source_name: 0.5mM DNO 2h

value: 0.5mM of diethylenetriamine/nitric oxide for 2 hours


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 16hrs rep 2

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75596.gif

value: control

source_name: 0.5mM DNO 16h

value: 0.5mM of diethylenetriamine/nitric oxide for 16 hours


title: MTB strain 1254 Ctrl vs 1.0 mM DETA/NO 40min rep 4

description:
Simple annotation: Stress, Stress by growth condition
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74761.gif

source_name: Strain: MTB strain 1254 Treatment: 1.0 mM DETA/NO for 40min

value: 1.0mM of diethylenetriamine/nitric oxide for 40 minutes


title: H37Rv ctrl vs Rv3132-3134 KO  0.05 mM DETA/NO 40min rep 4

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75652.gif

source_name: Rv3132 4KO No treatment

value: 0.05mM of diethylenetriamine/nitric oxide for 40 minutes


title: MTB strain 1254 Ctrl vs 0.05 mM DETA/NO 40min rep 2

description:
Simple annotation: Stress, Stress by growth condition
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18439.gif


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 16hrs rep 1

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75595.gif

source_name: 1254 No treatment


title: CDC1551 Ctrl vs 0.05 mM DETA/NO 40 min rep 5

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75650.gif

source_name: CDC1551 No treatment

value: CDC1551 (wild_type)


title: LBGstat_3

description: growth in LB medium with added glucose_stationary phase_replicate 3

value: growth in LB medium with added glucose stationary phase


title: MTB strain 1254 Ctrl vs 0.5 mM KCN + 2hr hypoxia rep 1

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75617.gif

source_name: KCN 0.5mM GasPak 2h

value: 0.5mM Potassium cyanide plus 2 hours-hipoxia


title: LBGstat_2

description: growth in LB medium with added glucose_stationary phase_replicate 2


title: MTB strain 1254 Ctrl vs low aeration + 0.05 mM DETA/NO rep 1

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75640.gif

value: 0.05 mM of diethylenetriamine/nitric oxide


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 2hrs rep 3

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75585.gif


title: MTB strain 1254 Ctrl vs high aeration + 0.005 mM DETA/NO rep 2

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75625.gif

value: 0.005 mM of diethylenetriamine/nitric oxide


title: MTB strain 1254 Ctrl vs high aeration + 0.01 mM DETA/NO rep 2

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75623.gif

value: 0.01 mM of diethylenetriamine/nitric oxide


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 24hrs + 0.5 mM DNO 40min rep 2

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75608.gif

value: 1254 (wild_type)


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 5min rep 3

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75589.gif

source_name: 0.5mM DNO 5min

value: 0.5mM of diethylenetriamine/nitric oxide for 5 minutes


title: LBGstat_1

description: growth in LB medium with added glucose_stationary phase_replicate 1


title: MTB strain 1254 Ctrl vs low aeration + 0.01 mM DETA/NO rep 2

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75635.gif


title: H37Rv Ctrl vs 0.05 mM DETA/NO 40min rep 3

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19137.gif

source_name: Control

value: H37Rv (wild_type)

source_name: Rv 0.05mM DNO 40m


title: MTB strain 1254 Ctrl vs low aeration + 0.05 mM DETA/NO rep 3

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75642.gif


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 5min rep 1

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75587.gif


title: MTB strain 1254 Ctrl vs 0.5 mM KCN 20min + 0.05 mM DETA/NO 40min rep 2

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75615.gif

source_name: KCN 0.5mM 20m and 0.05mM DNO 40mn

value: 0.5mM Potassium cyanide plus 40 min. 0.05mM DNO


title: LBGtran_2

description: growth in LB medium with added glucose_transition phase_replicate 2

value: growth in LB medium with added glucose transition phase


title: LBGtran_3

description: growth in LB medium with added glucose_transition phase_replicate 3


title: MTB strain 1254 Ctrl vs low aeration + 0.005 mM DETA/NO rep 3

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75639.gif


title: LBGexp_3

description: growth in LB medium with added glucose_exponential phase_replicate 3

value: growth in LB medium with added glucose exponential phase


title: LBGexp_1

description: growth in LB medium with added glucose_exponential phase_replicate 1


title: LBstat_3

description: growth in LB medium_stationary phase_replicate 3

value: growth in LB medium stationary phase


title: LBGexp_2

description: growth in LB medium with added glucose_exponential phase_replicate 2


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 24hrs rep 3

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75605.gif

value: control

value: 0.5mM of diethylenetriamine/nitric oxide for 24 hours


title: MTB strain 1254 Ctrl vs 0.5 mM KCN 1hr rep 3

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75613.gif

source_name: KCN 0.5mM 1h

value: 0.5mM Potassium cyanide 1 hour


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 20min rep 2

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75600.gif

source_name: 0.5mM DNO 20 min

value: 0.5mM of diethylenetriamine/nitric oxide for 20 minutes


title: MTB strain 1254 Ctrl vs 1.0 mM DETA/NO 40min rep 2

description:
Simple annotation: Stress, Stress by growth condition
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19037.gif

source_name: Strain: MTB strain 1254 Treatment: Control

value: 1.0mM of diethylenetriamine/nitric oxide for 40 minutes


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 20min rep 3

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75601.gif


title: H37Rv ctrl vs Rv3132-3134 KO  0.05 mM DETA/NO 40min rep 3

description:
Simple annotation: Stress, Miscellaneous
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19147.gif

value: 0.05mM of diethylenetriamine/nitric oxide for 40 minutes


title: MTB strain 1254 Ctrl vs low aeration + 0.001 mM DETA/NO rep 3

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75633.gif

value: 0.001 mM of diethylenetriamine/nitric oxide


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 8hrs rep 1

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75591.gif

source_name: 0.5mM DNO 8h

value: 0.5mM of diethylenetriamine/nitric oxide for 8 hours


title: LBstat_2

description: growth in LB medium_stationary phase_replicate 2

source_name: Bacillus subtilis cells


title: MTB strain 1254 Ctrl vs high aeration + 0.005 mM DETA/NO rep 1

description:
Simple annotation: Stress, Miscellaneous
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19184.gif

source_name: High aeration + 0.005mM DNO

value: 0.005 mM of diethylenetriamine/nitric oxide


title: CDC1551 Ctrl vs 0.05 mM DETA/NO 40 min rep 3

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75648.gif

value: CDC1551 (wild_type)


title: LBstat_1

description: growth in LB medium_stationary phase_replicate 1


title: MTB strain 1254 Ctrl vs low aeration (0.2% oxygen) 2hr rep 1

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75643.gif

value: 1254 (wild_type)

source_name: No treatment


title: LBtran_3

description: growth in LB medium_transition phase_replicate 3

value: growth in LB medium transition phase


title: MTB strain 1254 Ctrl vs 0.05 mM DETA/NO 40min rep 5

description:
Simple annotation: Stress, Stress by growth condition
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18442.gif

source_name: Strain: MTB strain 1254 Treatment: 0.05 mM DETA/NO for 40min


title: MTB strain 1254 Ctrl vs low aeration (0.2% oxygen) 2hr rep 3

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75645.gif


title: H37Rv ctrl vs Rv3132-3134 KO  0.05 mM DETA/NO 40min rep 1

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19145.gif


title: MTB strain 1254 Ctrl vs 5.0 mM DETA/NO 40min rep 3

description:
Simple annotation: Stress, Stress by growth condition
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19045.gif

source_name: Strain: MTB strain 1254 Treatment: 5.0 mM DETA/NO for 40min

value: 5.0mM of diethylenetriamine/nitric oxide for 40 minutes


title: MTB strain 1254 Ctrl vs high aeration + 0.001 mM DETA/NO rep 1

description:
Simple annotation: Stress, Miscellaneous
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19181.gif

source_name: High aeration + 0.001mM DNO


title: LBtran_1

description: growth in LB medium_transition phase_replicate 1


title: LBtran_2

description: growth in LB medium_transition phase_replicate 2


title: LBexp_3

description: growth in LB medium_exponential phase_replicate 3

value: growth in LB medium exponential phase


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 16hrs rep 4

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75598.gif

source_name: 1254 No treatment

source_name: 0.5mM DNO 16h

value: 0.5mM of diethylenetriamine/nitric oxide for 16 hours


title: H37Rv ctrl vs Rv3132-34 KO (complemented)  0.05 mM DETA/NO 40min rep 2

description:
Simple annotation: Stress, Miscellaneous
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19150.gif

value: H37Rv-Delta-dosR::kan plus DosR

source_name: Rv3133Comp 0.05mM DNO 40m


title: LBexp_2

description: growth in LB medium_exponential phase_replicate 2


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 2hrs rep 2

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75584.gif

source_name: 0.5mM DNO 2h

value: 0.5mM of diethylenetriamine/nitric oxide for 2 hours


title: LBexp_1

description: growth in LB medium_exponential phase_replicate 1


title: H37Rv Ctrl vs 0.05 mM DETA/NO 40min rep 1

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19135.gif

source_name: Control

value: control

value: H37Rv (wild_type)


title: MTB strain 1254 Ctrl vs 0.005 mM DETA/NO 40min rep 1

description:
Simple annotation: Stress, Stress by growth condition
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19032.gif

source_name: Strain: MTB strain 1254 Treatment: 0.005 mM DETA/NO for 40min

value: 0.005mM of diethylenetriamine/nitric oxide for 40 minutes


title: Total RNA upon scramble miR reconstitution in LNCaP, biological replicate 2

description: For identifying direct targets of scramble miR a AGO2-RNA co-immunoprecipitation as described by (Beitzinger et al. 2007) was performed. Total mRNAs were identified by using Affymetrix Genechips.

hyb_protocol: GeneChips were proceed using the Affymetrix GCS3000 7G system according to manufacturer`s protocol.

data_processing: The data were analyzed with R (version 2.9.0) and BioConductor (version 2.4). Quality assessment of arrays included exploration of distributions of probe intensities across all arrays, of average background values, and RNA quality was examined by RNA degradation plots. Diagnostic plots based on a probe level model (PLM) have been used to rule out chips with spatial artifacts (Chip pseudo-images, normalized unscaled standard error (NUSE) plot and relative log expression (RLE) plot). Background adjusted normalized data was retrieved by the GCRMA (robust multi-array average) procedure.

source_name: Total RNA in prostate cancer cell line LNCaP upon scramble miR reconstitution

label_protocol: 2µg RNA were analyzed on Affymetrix GeneChip Human Genome U133A 2.0 Arrays according to the manufacturer`s protocol.

growth_protocol: Cells were grown in medium to confluency (LNCaP cells: RPMI 1640 medium with L-glutamine (PAA) (10%FCS (Biochrom), 100Units/ml penicillin, 100 µg/ml streptomycin (PAA) and 10mM HEPES buffer (Biochrom), PC-3 and Du-145 cells: DMEM/F-12 medium with L-glutamine (PAA) (10\%FCS (Biochrom), 100Units/ml penicillin, 100 µg/ml streptomycin (PAA)), and RWPE-1 cells: Keratinocyte-Serum free medium (Gibco-BRL) (5ng/ml human recombinant EGF and 0.05mg/ml bovine pituary extract (Gibco-BRL))).

treatment_protocol: Cells were transfected using the Nucleofector 2 Technology (Amaxa) according to the instructions. For miRNA reconstitution 2.5ug plasmid DNA for each miRNA was used. AGO2 RNA co-immunoprecipitation (AGO2 co-IP) was performed using AG02-1 11A antibody (Ascenion).

value: LNCaP

value: prostate cancer

value: early


title: MTB strain 1254 Ctrl vs low aeration + 0.005 mM DETA/NO rep 2

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75638.gif


title: MTB strain 1254 Ctrl vs high aeration + 0.05 mM DETA/NO rep 1

description:
Simple annotation: Stress, Miscellaneous
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19190.gif

source_name: High aeration + 0.05mM DNO

value: 0.05 mM of diethylenetriamine/nitric oxide


title: MTB strain 1254 Ctrl vs high aeration + 0.05 mM DETA/NO rep 3

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs//75628.gif


title: THP1-LPS-4

city: Copenhagen

first: Lasse

last: Folkersen

address: Artellerivej

department: Bioinformatics

country: Denmark

institute: National Genome Center

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

data_processing:
CEL files were RMA normalized and log2 transformed using the apt-probeset-summarize algorithm as implemented in Affymetrix Power Tools 1.12.0. Meta probe sets were selected from the Affymetrix defined core set of well-established genes.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

label_protocol: The RNA was then hybridized and scanned on the Affymetrix® Genechip® Human Exon 1.0 ST array (Affymetrix, Santa Clara, CA, USA) following manufacturer’s protocols at the Karolinska Institute microarray core facility.

growth_protocol: THP-1 cells (monocyte cell line) (ATCC , Manassas, VA, USA) were maintained in culture in RPMI 1640 medium containing 10% fetal bovine serum, 1mM sodium pyruvate , 100 units/ml penicillin and 100 μg/ml streptomycin at 37°C with 5% CO2. For differentiation of THP-1 cells into macrophages a protocol using conditioned media as previously described by Whatling et al was used. To confirm differentiation of THP-1 monocytes into macrophages CD11b expression was measured using FACS and quantitative polymerase chain reaction (qPCR) (Text S2).

extract_protocol: total mRNA was extracted using TRIZOL® reagent (Invitrogen, Carlsbad, CA, USA) and purified using the RNeasy Mini Kit following the manufacturer’s instructions and included a DNase treatment (Qiagen, Valencia, CA, USA). RNA concentration and quality were analyzed using Nanodrop 1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA) respectively.

treatment_protocol: THP-1 macrophages were then either left unstimulated (control) or stimulated with 1ug/ml LPS (LPS-stimulated) from Escherichia coli O55:B5 for 2 hours (Sigma Chemical Co., St. Louis, MO, USA) to induce an acute inflammatory response. To confirm an induction of the inflammatory response in the THP-1 macrophages, TNF mRNA levels were measured in control and LPS-stimulated samples

tag: agent

value: LPS

tag: sample pair


title: Total RNA upon scramble miR reconstitution in LNCaP, biological replicate 1

scan_protocol: GeneChips were proceed using the Affymetrix GCS3000 7G system according to manufacturer`s protocol.


title: AGO2-RNA upon scramble miR reconstitution in LNCaP, biological replicate 2

description:
AGO2 bound RNA
For identifying direct targets of scramble miR a AGO2-RNA co-immunoprecipitation as described by (Beitzinger et al. 2007) was performed. AGO2-bound mRNAs were identified by using Affymetrix Genechips.

source_name: AGO2 bound RNA in prostate cancer cell line LNCaP upon scramble miR reconstitution

extract_protocol: Trizol extraction of AGO2 bound RNA was performed according to the manufacturer's instructions.


title: MTB strain 1254 Ctrl vs low aeration + 0.001 mM DETA/NO rep 1

description:
Simple annotation: Stress, Miscellaneous
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19196.gif

source_name: Low aeration + 0.001mM DNO

value: 0.001 mM of diethylenetriamine/nitric oxide


title: Total RNA upon scramble miR reconstitution in LNCaP, biological replicate 3


title: MTB strain 1254 Ctrl vs high aeration + 0.005 mM DETA/NO rep 3

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75626.gif

source_name: High aeration and 0.005mM DNO

value: 0.005 mM of diethylenetriamine/nitric oxide


title: THP1-LPS-3


title: THP1-control-3


title: AGO2-RNA upon scramble miR reconstitution in LNCaP, biological replicate 3


title: MTB strain 1254 Ctrl vs 0.005 mM DETA/NO 40min rep 2

description:
Simple annotation: Stress, Stress by growth condition
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19033.gif

source_name: Strain: MTB strain 1254 Treatment: Control

value: 1254 (wild_type)


title: THP1-control-4


title: AGO2-RNA upon scramble miR reconstitution in LNCaP, biological replicate 1


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 1hr rep 2

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75577.gif

source_name: 0.5mM DNO 1h

value: 0.5mM of diethylenetriamine/nitric oxide for 1 hour


title: MTB strain 1254 Ctrl vs 0.5 mM KCN 20min + 0.05 mM DETA/NO 40min rep 3

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75616.gif

value: 0.5mM Potassium cyanide plus 40 min. 0.05mM DNO


title: MTB strain 1254 Ctrl vs 2hr Hypoxia rep 2

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19133.gif

source_name: 1254 HypoxiaGP 2h

value: Exposing for 2 hour to 0.2% O2 (hypoxia)


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 8hrs rep 2

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75592.gif

source_name: 0.5mM DNO 8h

value: 0.5mM of diethylenetriamine/nitric oxide for 8 hours


title: MTB strain 1254 Ctrl vs 5.0 mM DETA/NO 40min rep 4

description:
Simple annotation: Stress, Stress by growth condition
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19046.gif

source_name: Strain: MTB strain 1254 Treatment: 5.0 mM DETA/NO for 40min

value: 5.0mM of diethylenetriamine/nitric oxide for 40 minutes


title: THP1-control-2


title: THP1-LPS-2


title: Total RNA upon miR-205 reconstitution in LNCaP, biological replicate 3

description: For identifying direct targets of miR-205 a AGO2-RNA co-immunoprecipitation as described by (Beitzinger et al. 2007) was performed. Total mRNAs were identified by using Affymetrix Genechips.

source_name: Total RNA in prostate cancer cell line LNCaP upon miR-205 reconstitution


title: THP1-LPS-1


title: Total RNA upon miR-205 reconstitution in LNCaP, biological replicate 1


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 2hrs rep 4

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75586.gif

source_name: 1254 No treatment

value: 0.5mM of diethylenetriamine/nitric oxide for 2 hours


title: THP1-control-1


title: AGO2-RNA upon miR-205 reconstitution in LNCaP, biological replicate 1

description:
AGO2 bound RNA
For identifying direct targets of miR-205 a AGO2-RNA co-immunoprecipitation as described by (Beitzinger et al. 2007) was performed. AGO2-bound mRNAs were identified by using Affymetrix Genechips.

source_name: AGO2 bound RNA in prostate cancer cell line LNCaP upon miR-205 reconstitution


title: MTB strain 1254 Ctrl vs 5.0 mM DETA/NO 40min rep 2

description:
Simple annotation: Stress, Stress by growth condition
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19044.gif

value: control


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 1hr rep 3

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75579.gif


title: H37Rv Ctrl vs 0.05 mM DETA/NO 40min rep 4

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75651.gif

source_name: H37Rv No treatment

value: H37Rv (wild_type)

source_name: H37Rv DS 0.05DNO 40min

value: 0.05mM of diethylenetriamine/nitric oxide for 40 minutes


title: AGO2-RNA upon miR-205 reconstitution in LNCaP, biological replicate 2

value: LNCaP


title: AGO2-RNA upon miR-205 reconstitution in LNCaP, biological replicate 3

value: prostate cancer


title: H37Rv ctrl vs Rv3132-34 KO (complemented)  0.05 mM DETA/NO 40min rep 4

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75653.gif

source_name: Rv3133COMP0 No treatment

value: H37Rv-Delta-dosR::kan plus DosR


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 1hr rep 1

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75575.gif


title: Keratinocytes_IL4_subject3

city: Boston

first: William

middle: R

last: Swindell

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard University

description: primary human keratinocytes treated with IL4

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray TM Scanner 3000.

data_processing: Robust Multichip Average (RMA)

source_name: primary keratinocytes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Monolayer NHK cultures were established and used in the second or third passage (Elder 1991, J. Invest. Dermatol. 96: 425-433). Cultures were grown to 40 or 80% confluence, or maintained to 4 days postconfluency.

extract_protocol: RNA was extracted using QIAGEN RNEasy mini kits

treatment_protocol: Cultures were starved of growth factors in unsupplemented M154 medium (Invitrogen/Cascade Biologics, Portland, OR) for 24 hours before use. Cultures were stimulated 24 hours with recombinant human cytokines and growth factors from R&D Systems (Minneapolis, MN).

value: primary keratinocytes


title: Total RNA upon miR-203 reconstitution in LNCaP, biological replicate 2

description: For identifying direct targets of miR-203 a AGO2-RNA co-immunoprecipitation as described by (Beitzinger et al. 2007) was performed. Total mRNAs were identified by using Affymetrix Genechips.

source_name: Total RNA in prostate cancer cell line LNCaP upon miR-203 reconstitution

value: early


title: Total RNA upon miR-203 reconstitution in LNCaP, biological replicate 3


title: MTB strain 1254 Ctrl vs 0.005 mM DETA/NO 40min rep 4

description:
Simple annotation: Stress, Stress by growth condition
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74757.gif

source_name: Strain: MTB strain 1254 Treatment: 0.005 mM DETA/NO for 40min

value: 0.005mM of diethylenetriamine/nitric oxide for 40 minutes


title: Keratinocytes_TNF_subject2

description: primary human keratinocytes treated with TNF

value: TNF-treated


title: Total RNA upon miR-203 reconstitution in LNCaP, biological replicate 1


title: Total RNA upon miR-205 reconstitution in LNCaP, biological replicate 2


title: Keratinocytes_IL4_subject2


title: Keratinocytes_TNF_subject3


title: AGO2-RNA upon miR-203 reconstitution in LNCaP, biological replicate 3

description:
AGO2 bound RNA
For identifying direct targets of miR-203 a AGO2-RNA co-immunoprecipitation as described by (Beitzinger et al. 2007) was performed. AGO2-bound mRNAs were identified by using Affymetrix Genechips.

source_name: AGO2 bound RNA in prostate cancer cell line LNCaP upon miR-203 reconstitution


title: MTB strain 1254 Ctrl vs 0.5 mM KCN 1hr rep 1

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75611.gif

value: 1254 (wild_type)

source_name: KCN 0.5mM 1h

value: 0.5mM Potassium cyanide 1 hour


title: AGO2-RNA upon miR-203 reconstitution in LNCaP, biological replicate 2


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 24hrs rep 1

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75603.gif

source_name: 0.5mM DNO 24h

value: 0.5mM of diethylenetriamine/nitric oxide for 24 hours


title: CDC1551 Ctrl vs 0.05 mM DETA/NO 40 min rep 4

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75649.gif

source_name: CDC1551 No treatment

value: CDC1551 (wild_type)


title: Keratinocytes_TNF_subject1


title: AGO2-RNA upon miR-203 reconstitution in LNCaP, biological replicate 1


title: MTB strain 1254 Ctrl vs high aeration + 0.01 mM DETA/NO rep 3

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75624.gif

value: 0.01 mM of diethylenetriamine/nitric oxide


title: MTB strain 1254 Ctrl vs 0.5 mM KCN + 2hr hypoxia rep 2

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75618.gif

source_name: KCN 0.5mM GasPak 2h

value: 0.5mM Potassium cyanide plus 2 hours-hipoxia


title: MTB strain 1254 Ctrl vs low aeration + 0.05 mM DETA/NO rep 2

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75641.gif

value: 0.05 mM of diethylenetriamine/nitric oxide


title: Total RNA upon miR-130a reconstitution in LNCaP, biological replicate 3

description: For identifying direct targets of miR-130a a AGO2-RNA co-immunoprecipitation as described by (Beitzinger et al. 2007) was performed. Total mRNAs were identified by using Affymetrix Genechips.

source_name: Total RNA in prostate cancer cell line LNCaP upon miR-130a reconstitution


title: Total RNA upon miR-130a reconstitution in LNCaP, biological replicate 2


title: Keratinocytes_IL17A_replicate3

description: primary human keratinocytes treated with IL17A


title: Keratinocytes_IL17A_replicate2


title: MTB strain 1254 Ctrl vs 0.05 mM DETA/NO 40min rep 3

description:
Simple annotation: Stress, Stress by growth condition
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18440.gif

source_name: Strain: MTB strain 1254 Treatment: Control

value: control

source_name: Strain: MTB strain 1254 Treatment: 0.05 mM DETA/NO for 40min


title: Keratinocytes_IL13_subject3

description: primary human keratinocytes treated with IL13


title: Keratinocytes_IL4_subject1


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 40min rep 3

description:
Simple annotation: Stress, Stress by growth condition
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74759.gif

source_name: Strain: MTB strain 1254 Treatment: 0.5 mM DETA/NO for 40min

value: 0.5mM of diethylenetriamine/nitric oxide for 40 minutes


title: miRNA scramble expression in LNCaP, biological replicate 2

description: Gene expression data from LNCaP cells transfected with miRNA scramble.

hyb_protocol: Affymetrix GeneChip Human Genome U133A 2.0 Arrays were processed according to the manufacturer`s protocol.

scan_protocol: GeneChips were processed using the Affymetrix GCS3000 7G system according to manufacturer`s protocol.

data_processing: The data were analyzed with R (version 2.9.0) and BioConductor (version 2.4). Quality assessment of arrays included exploration of distributions of probe intensities across all arrays, of average background values, and RNA quality was examined by RNA degradation plots. Diagnostic plots based on a probe level model (PLM) have been used to rule out chips with spatial artifacts (Chip pseudo-images, normalized unscaled standard error (NUSE) plot and relative log expression (RLE) plot). Background adjusted normalized data was retrieved by the RMA (robust multi-array average) procedure. Loss of mRNA expression was conducted by fitting a linear model using the R package limma. Reliable variance estimations were obtained by empirical Bayes moderated t-statistics. False discovery rate was controlled by Benjamini-Hochberg adjustment.

source_name: Prostate cancer cell line LNCaP transfected with miRNA scramble

label_protocol: 2µg RNA were analyzed according to the manufacturer's protocol.

tag: mirna

value: scramble


title: Keratinocytes_IL13_subject2


title: AGO2-RNA upon miR-130a reconstitution in LNCaP, biological replicate 2

description:
AGO2 bound RNA
For identifying direct targets of miR-130a a AGO2-RNA co-immunoprecipitation as described by (Beitzinger et al. 2007) was performed. AGO2-bound mRNAs were identified by using Affymetrix Genechips.

source_name: AGO2 bound RNA in prostate cancer cell line LNCaP upon miR-130a reconstitution

value: LNCaP


title: AGO2-RNA upon miR-130a reconstitution in LNCaP, biological replicate 3

value: prostate cancer


title: AGO2-RNA upon miR-130a reconstitution in LNCaP, biological replicate 1


title: Total RNA upon miR-130a reconstitution in LNCaP, biological replicate 1


title: Keratinocytes_IL17A_replicate1


title: MTB strain 1254 Ctrl vs low aeration + 0.005 mM DETA/NO rep 1

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75637.gif

source_name: 1254 No treatment

value: 0.005 mM of diethylenetriamine/nitric oxide


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 16hrs rep 3

description:
Simple annotation: Stress, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/75597.gif

source_name: 0.5mM DNO 16h

value: 0.5mM of diethylenetriamine/nitric oxide for 16 hours


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 40min rep 4

description:
Simple annotation: Stress, Stress by growth condition
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74760.gif


title: miRNA scramble expression in LNCaP, biological replicate 1

value: early


title: H37Rv ctrl vs Rv3132-3134 KO  0.05 mM DETA/NO 40min rep 2

description:
Simple annotation: Stress, Miscellaneous
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19146.gif

source_name: Control

value: 0.05mM of diethylenetriamine/nitric oxide for 40 minutes


title: MTB strain 1254 Ctrl vs 0.5 mM DETA/NO 40min rep 2

description:
Simple annotation: Stress, Stress by growth condition
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19042.gif


title: Keratinocytes_IL13_subject1

source_name: primary keratinocytes

value: primary keratinocytes


title: miR-205 overexpression in LNCaP, biological replicate 3

description: Gene expression data from LNCaP cells transfected with miR-205.

source_name: Prostate cancer cell line LNCaP transfected with microRNA miR-205


title: miRNA scramble expression in LNCaP, biological replicate 3


title: Keratinocytes_IFNg_subject1

description: primary human keratinocytes treated with IFNg

value: IFNg-treated


title: miR-205 overexpression in LNCaP, biological replicate 2


title: Keratinocytes_IFNg_subject3


title: Keratinocytes_IFNg_subject2


title: VhlΔIE/Apcmin/+

city: Ann Arbor

first: XIANG

last: XUE

state: Michigan

address: 1301 E. Catherine Street

institute: Umich

description: Gene expression data from colons.

hyb_protocol: Following fragmentation, 16 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data was analyzed using the affy Bioconductor packages implemented in the R-statistical environment. RMA was used to normalize the data and fit log2 transformed expression values.

organism: Mus musculus

source_name: Colon

label_protocol: Biotinylated aRNA were prepared according to the Ambion Premier kit protocol from 250 ng total RNA (MessageAmp Premier RNA Amplification Kit Instruction Manual, 2008, Ambion).

growth_protocol: All mice were 129S6/SvEv background and maintained in standard cages in a light and temperature-controlled room and were allowed standard chow and water ad libitum.

treatment_protocol: Colon mucosal scrapings were got from 5 weeks old mice

tag: strain

tag: age

value: 5 weeks old

tag: genotype/variation

value: VhlΔIE/Apcmin/+ (intestine-specific Vhl-knockout, intestinal tumor model)

value: Colon


title: Keratinocytes_IFNa_subject3

description: primary human keratinocytes treated with IFNa

tag: tissue

value: IFNa-treated


title: Keratinocytes_IFNa_subject2


title: miR-205 overexpression in LNCaP, biological replicate 1


title: VhlF/F/Apcmin/+

description: Gene expression data from colons.

value: VhlF/F/Apcmin/+ (Vhl-floxed, intestinal tumor model)


title: miR-203 overexpression in LNCaP, biological replicate 3

description: Gene expression data from LNCaP cells transfected with miR-203.

source_name: Prostate cancer cell line LNCaP transfected with microRNA miR-203


title: miR-130a overexpression in LNCaP, biological replicate 2

description: Gene expression data from LNCaP cells transfected with miR-130a.

source_name: Prostate cancer cell line LNCaP transfected with microRNA miR-130a


title: miR-130a overexpression in LNCaP, biological replicate 1


title: Keratinocytes_untreated_subject1

description: primary human keratinocytes

value: untreated control


title: Keratinocytes_IFNa_subject1


title: miR-130a overexpression in LNCaP, biological replicate 3


title: VhlF/F

description: Gene expression data from colons.

value: VhlF/F (Vhl-floxed)


title: 3-4 hrs(II)

status: Public on Mar 06 2012

city: Princeton

first: Bing

last: He

state: NJ

address: Washington Rd

department: Molecular Biology

institute: Princeton University

description: test-Cy5: RNA are extracted from 3-4 hour ORE R embryos; reference-Cy3: RNA from 0-16hr ORER embryos

hyb_protocol: Temperature : 65 C Hybridization buffer : Agilent Hi-RPM hybridization buffer w/ Agilent Blocking Agent Hybridization volume : 220 uL Duration : 17 hr Rotational speed : 20 rpm Amount of extract labeled : 1000 ng

scan_protocol: Pixel Size : 5 Scan Date : 2010-09-27 Scan Time : 13:16:20 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

data_processing: Data were normalized using the limma package in R. Arrays were first loess normalized using NormalizeWithinArrays, and then all arrays were quantile normalized according to the reference channel using NormalizeBetweenArrays.

organism: Drosophila melanogaster

source_name: RNA from 3-4 hr ORER embryos

label_protocol:
reference URL : http://www.chem.agilent.com/Library/usermanuals/Public/G4140-90051_Two-Color_Tecan.pdf
Kit protocol : Agilent QuickAmp Labeling

extract_protocol:
Extracted molecule : polyA RNA
Extraction description : "TriZol procedure, followed by Qiagen Rneasy Kit clean up"

value: Oregon R

tag: species

value: D. melanogaster

tag: developmental stage

value: embryo 3-4 hr


title: 4-5 hrs(I)

description: test-Cy5: RNA are extracted from 4-5 hour ORE R embryos; reference-Cy3: RNA from 0-16hr ORER embryos

scan_protocol: Pixel Size : 5 Scan Date : 2010-09-27 Scan Time : 12:59:17 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: RNA from 4-5 hr ORER embryos

value: embryo 4-5 hr


title: 3-4 hrs(I)


title: miR-203 overexpression in LNCaP, biological replicate 2

value: LNCaP

value: prostate cancer


title: miR-203 overexpression in LNCaP, biological replicate 1

value: early


title: VhlΔIE

description: Gene expression data from colons.


title: Thalassemia kidney vs control kidney Hyb 2

city: Nashville

first: Hanako

last: Kobayashi

institute: Vanderbilt University

hyb_protocol: 1.65 ug of purified cRNA was fragmented and hybridized to the array for 17 hr at 65 oC.

scan_protocol: Array were scanned on an Agilent G2565BA scanner, and analyzed with Agilent Feature Extraction 9.5.

data_processing: "SAM" statistical analysis package version 3.1 was used for data analysis.

label_protocol: 500 ng of total RNA was amplified using Low RNA Input Linear Amp Kit PLUS, One-color. This labeling reaction produces 0.25-2.0 ug of labeled cRNA, by first converting mRNA primed with an oligo (d)T-T7 primer into dsDNA with MMLV-RT and then amplifying the sample using T7 RNA polymerase.

growth_protocol: a mouse model of beta-thalassemia was generated by deletion of both b-globin genes, beta-major and beta-minor.

extract_protocol: Total RNA extracted using Qiagen RNeasy following manufacturer's instructions

value: kidney

source_name: control

value: control


title: Thalassemia kidney vs control kidney Hyb 4


title: T6PNE untreated

city: La Jolla

first: Roy

middle: M

last: Williams

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

hyb_protocol: As recommended by illumina

scan_protocol: As suggested by illumina using the illumina scanner

data_processing: Raw data filtered on P value for <0.05 with the remaining data normalised using the affy tools R bioconductor normalize.quantiles routine

label: streptavidin Cy3

source_name: T6PNE cells were isolated from human fetal islets; E47 was induced by tamoxifen treatment; untreated

label_protocol: As suggested by illumina

growth_protocol: T6PNE cells were maintained in RPMI (5.5 mM glucose) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin (pen-strep) and grown in 5% CO2, 37°C.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: untreated

value: cell line derived from fetal islets (T6PNE)


title: 4-5 hrs(II)


title: Thalassemia kidney vs control kidney Hyb 1


title: Keratinocytes_untreated_subject2

description: primary human keratinocytes

value: primary keratinocytes


title: Keratinocytes_untreated_subject3

description: primary human keratinocytes


title: T6PNE, BIM5078 treated

source_name: T6PNE cells were isolated from human fetal islets; E47 was induced by tamoxifen treatment; cells were treated with small molecule BIM5078

treatment_protocol: T6PNE cells were treated with 5uM BIM5078 for 48 hours


title: Thalassemia kidney vs control kidney Hyb 3


title: 19-22 hrs(II)

description: test-Cy5: RNA are extracted from 20-22 hrs ORE R embryos; reference-Cy3: RNA from 0-16hr ORER embryos

scan_protocol: Pixel Size : 5 Scan Date : 2010-09-27 Scan Time : 12:24:44 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: RNA from 20-22 hrs ORER embryos

value: embryo 19-22 hr


title: Mid-Late Cycle 14(II)

description: test-Cy5: RNA are extracted from cyc14-15 ORE R embryos; reference-Cy3: RNA from 0-16hr ORER embryos

source_name: RNA from cyc14-15 ORER embryos

value: embryo Mid-Late Cycle 14 (~2.5-3 hr)


title: Cycle 13-early Cycle 14(II)

description: test-Cy5: RNA are extracted from cyc12-13 ORE R embryos; reference-Cy3: RNA from 0-16hr ORER embryos

scan_protocol: Pixel Size : 5 Scan Date : 2010-09-27 Scan Time : 12:42:27 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: RNA from cyc12-13 ORER embryos

value: embryo Cycle 13-Early Cycle 14 (~2-2.5 hr)