title: DV001_ATH1_A8-degra-Egh

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 92.64
Background Stdev (float) = 3.10
Background Max (float) = 101.0
Background Min (float) = 84.7
Noise Avg (float) = 6.25
Noise Stdev (float) = 0.31
Noise Max (float) = 7.1
Noise Min (float) = 5.5
RawQ (float) = 3.44
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 432
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: DV001_ATH1_A8-degra-Egh.DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 230 (type integer); Parameter Upper left corner y coordinate = 232 (type integer); Parameter Upper right corner x coordinate = 4497 (type integer); Parameter Upper right corner y coordinate = 249 (type integer); Parameter Lower right corner x coordinate = 4482 (type integer); Parameter Lower right corner y coordinate = 4519 (type integer); Parameter Lower left corner x coordinate = 215 (type integer); Parameter Lower left corner y coordinate = 4502 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.257494 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

source_name: De Grauwe_1-8_GA4-etr1-30min_Rep1_ATH1

treatment_protocol: This plant was sprayed with GA4, which was dissolved in water, and harvested 30min. after treatment. ; Performer: Liesbeth,,De Grauwe

value: Col

tag: StrainOrLine


title: JP001_ATH1_A3-Pritc-CTR_repeat

status: Public on Jan 22 2007

type: RNA

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 68.70
Background Stdev (float) = 1.39
Background Max (float) = 72.8
Background Min (float) = 65.0
Noise Avg (float) = 4.22
Noise Stdev (float) = 0.20
Noise Max (float) = 4.8
Noise Min (float) = 3.7
RawQ (float) = 2.57
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 1453
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: JP001_ATH1_A3-Pritc-CTR_repeat.DAT

hyb_protocol: EukGE-WS2v4; Protocol Type = Hybridization; Parameter Wash A1 Recovery Mixes = 0 (type integer); Parameter Wash A1 Temperature (C) = 25 (type integer); Parameter Number of Wash A1 Cycles = 10 (type integer); Parameter Mixes per Wash A1 Cycle = 2 (type integer); Parameter Wash B Recovery Mixes = 0 (type integer); Parameter Wash B Temperature (C) = 50 (type integer); Parameter Number of Wash B Cycles = 4 (type integer); Parameter Mixes per Wash B Cycle = 15 (type integer); Parameter Stain Temperature (C) = 25 (type integer); Parameter First Stain Time (seconds) = 600 (type integer); Parameter Wash A2 Recovery Mixes = 0 (type integer); Parameter Wash A2 Temperature (C) = 25 (type integer); Parameter Number of Wash A2 Cycles = 10 (type integer); Parameter Mixes per Wash A2 Cycle = 4 (type integer); Parameter Second Stain Time (seconds) = 600 (type integer); Parameter Third Stain Time (seconds) = 600 (type integer); Parameter Wash A3 Recovery Mixes = 0 (type integer); Parameter Wash A3 Temperature (C) = 30 (type integer); Parameter Number of Wash A3 Cycles = 15 (type integer); Parameter Mixes per Wash A3 Cycle = 4 (type integer); Parameter Holding Temperature (C) = 25 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Fluidics Station, Parameter: Parameter Station Number = 1 (type integer), Parameter: Parameter Position = 2 (type integer); Performers: John,Y,Okyere, , Janet,,Higgins

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 233 (type integer); Parameter Upper left corner y coordinate = 229 (type integer); Parameter Upper right corner x coordinate = 4503 (type integer); Parameter Upper right corner y coordinate = 213 (type integer); Parameter Lower right corner x coordinate = 4521 (type integer); Parameter Lower right corner y coordinate = 4483 (type integer); Parameter Lower left corner x coordinate = 251 (type integer); Parameter Lower left corner y coordinate = 4499 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.390291 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

label: biotin

molecule: total RNA

organism: Arabidopsis thaliana

label_protocol: Preparation of biotin-labeled cRNA; RNA samples were quality controlled using the Agilent 2100 Bioanalyzer. 100 pmol T7-(dT)24 primer (5'-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-(dT)24-3')  was hybridized with the Total RNA ( 8 - 12ug) at 70°C for 10 minutes. First strand cDNA was synthesized by reverse transcription using 400 units SuperScript II Reverse Transcriptase in a reaction containing 50 mM Tris-HCl (pH 8.3), 75 mM KCl, 3 mM MgCl2, 10 mM dithiothreitol (DTT) and 0.5 mM dNTPs at 42C for 1 hour.  The reaction was then put on ice for 2 mins, followed by second strand cDNA synthesis.  130ul of the second strand reaction mix was added to the 20ul  first strand synthesis reaction. The second strand reaction mix  contained 40 units E. coli DNA polymerase I, 10 units E. coli DNA ligase, 2 units  E. coli RNase H and 0.2 mM dNTPs in a buffer containing 20 mMTris-HCl (pH 6.9), 90 mM KCl, 4.6 mM MgCl2, 10mM (NH4)SO4 and 0.15 mM ß-NAD+. The reaction was incubated at 16 C for 2 hours.  10 units T4 DNA Polymerase was added and the reaction incubated for a further 5 minutes at 16 C, then the reaction was terminated using EDTA.  The double-stranded cDNA was cleaned up using the cDNA Cleanup Spin Column supplied in the Affymetrix GeneChip Sample Cleanup Module.  The double-stranded cDNA was used as a template for in Vitro transcription of biotin-labeled cRNA using the ENZO BioArray RNA Transcript Labeling Kit supplied by Affymetrix.  The Transcript Labeling kit produces large amounts of hybridizable biotin-labeled RNA targets by in Vitro transcription from bacteriophage T7 RNA polymerase promoters.  The reaction mixture containing Biotin-Labeled ribonucleotides (ATP, GTP, CTP, UTP with Bio-UTP and Bio-CTP), DTT, RNase inhibitor mix and T7 RNA polymerase was incubated at 37 C for 5 hrs, gently mixing every 30 minutes during the incubation. This produced an average of 40ug biotin-labeled cRNA . The biotin-labeled cRNA  was cleaned up using the cRNA Cleanup Spin Column supplied in the Affymetrix GeneChip Sample Cleanup Module.  The quantity and quality of the cRNA was measured using the Agilent 2100 Bioanalyzer. The total amount of cRNA was calculated, the starting quantity of RNA subtracted to give the quantity of adjusted cRNA.  The cRNA was fragmented by metal-induced hydrolysis to break down full-length cRNA to 35-200 base fragments.  15ug of adjusted cRNA was used to prepare 300ul of hybridization cocktail of which 200ul was hybridized with the GeneChip.   ; Protocol Type = labeling; Performers: John,Y,Okyere, Janet,,Higgins

growth_protocol: unknown; Parameter location = Growth Room; Parameter Humidity = 70%; Parameter Temperature = 22oC; Parameter Lighting = 18 hour days; Parameter Medium = compost; Parameter Nutrients = osmocote slow release fertiliser mixed in compost; Parameter Water = 3 x per week; Performer: Jeremy,,Pritchard

extract_protocol: Qiagen / Trizol; Protocol: Qiagen RNAeasy kit protocol ; Protocol Type = nucleic_acid_extraction; Performer: Jeremy,,Pritchard

treatment_protocol: Aphid cages attached to leaves- no aphids ; Performer: Jeremy,,Pritchard

tag: OrganismPart

value: 2 mature rosette leaves

tag: Ecotype

tag: NASC:Growth Stage


title: JP001_ATH1_A2-Pritc-CTR

institute: Nottingham Arabidopsis Stock Centre (NASC)

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 104.81
Background Stdev (float) = 1.40
Background Max (float) = 110.6
Background Min (float) = 101.4
Noise Avg (float) = 6.24
Noise Stdev (float) = 0.23
Noise Max (float) = 6.8
Noise Min (float) = 5.4
RawQ (float) = 3.58
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 412
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: JP001_ATH1_A2-Pritc-CTR.DAT

hyb_protocol: EukGE-WS2v4; Protocol Type = Hybridization; Parameter Wash A1 Recovery Mixes = 0 (type integer); Parameter Wash A1 Temperature (C) = 25 (type integer); Parameter Number of Wash A1 Cycles = 10 (type integer); Parameter Mixes per Wash A1 Cycle = 2 (type integer); Parameter Wash B Recovery Mixes = 0 (type integer); Parameter Wash B Temperature (C) = 50 (type integer); Parameter Number of Wash B Cycles = 4 (type integer); Parameter Mixes per Wash B Cycle = 15 (type integer); Parameter Stain Temperature (C) = 25 (type integer); Parameter First Stain Time (seconds) = 600 (type integer); Parameter Wash A2 Recovery Mixes = 0 (type integer); Parameter Wash A2 Temperature (C) = 25 (type integer); Parameter Number of Wash A2 Cycles = 10 (type integer); Parameter Mixes per Wash A2 Cycle = 4 (type integer); Parameter Second Stain Time (seconds) = 600 (type integer); Parameter Third Stain Time (seconds) = 600 (type integer); Parameter Wash A3 Recovery Mixes = 0 (type integer); Parameter Wash A3 Temperature (C) = 30 (type integer); Parameter Number of Wash A3 Cycles = 15 (type integer); Parameter Mixes per Wash A3 Cycle = 4 (type integer); Parameter Holding Temperature (C) = 25 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Fluidics Station, Parameter: Parameter Station Number = 1 (type integer), Parameter: Parameter Position = 1 (type integer); Performers: John,Y,Okyere, , Janet,,Higgins

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 231 (type integer); Parameter Upper left corner y coordinate = 231 (type integer); Parameter Upper right corner x coordinate = 4500 (type integer); Parameter Upper right corner y coordinate = 239 (type integer); Parameter Lower right corner x coordinate = 4493 (type integer); Parameter Lower right corner y coordinate = 4509 (type integer); Parameter Lower left corner x coordinate = 223 (type integer); Parameter Lower left corner y coordinate = 4501 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.366088 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;


title: ik_L2_T5.5_r1

city: Boston

first: Timothy

middle: S

last: Gardner

state: MA

address: 44 Cummington St.

department: Biomedical Engineering

country: USA

institute: Boston University

description: GeneChips were washed and stained with an FS450 fluidics machine and scanned using a GeneChip Scanner 3000

hyb_protocol: Following fragmentation, cDNA was hybridized for 16 hr at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

organism: Escherichia coli

source_name: Escherichia coli

label_protocol: Biotinylated cDNA was prepared according to the standard Affymetrix E. coli protocol

extract_protocol: RNAEasy with RNAProtect(Qiagen)

tag: K12 EMG2 on LB with 0.2 percent glucose, 5.5 hours post-incubation


title: ik_L2_T6_r1

scan_protocol: GeneChips were washed and stained with an FS450 fluidics machine and scanned using a GeneChip Scanner 3000

tag: K12 EMG2 on LB with 0.2 percent glucose, 6 hours post-incubation


title: Birnbaum_1-23_gl2-2_Rep2_ATH1

description:
Media: MS + 4.5% sucrose
Light: 16h light 8h dark

data_processing: The data were analysed using Affymetrix Microarray Suite 5.0 (MAS5)

tag: Tissue

value: Marks atrichoblasts from the QC up.

tag: Genetic background

value: Columbia


title: ik_L2_T8_r1

data_processing: GeneChips were washed and stained with an FS450 fluidics machine and scanned using a GeneChip Scanner 3000

tag: K12 EMG2 on LB with 0.2 percent glucose, 8 hours post-incubation


title: ik_L2_T5_r1

tag: K12 EMG2 on LB with 0.2 percent glucose, 5 hours post-incubation


title: ik_L2_T3_r1

tag: K12 EMG2 on LB with 0.2 percent glucose, 3 hours post-incubation


title: ik_L2_T3.5_r1

tag: K12 EMG2 on LB with 0.2 percent glucose, 3.5 hours post-incubation


title: ik_L2_T4_r1

tag: K12 EMG2 on LB with 0.2 percent glucose, 4 hours post-incubation


title: ik_L2_T2.5_r1

tag: K12 EMG2 on LB with 0.2 percent glucose, 2.5 hours post-incubation


title: ik_L2_T4.5_r1

tag: K12 EMG2 on LB with 0.2 percent glucose, 4.5 hours post-incubation


title: ccdB_W1863_90_r1

tag: E.coli W1863 wt lambda- with ccdB upregulation 90 minutes after induction


title: ccdB_W1863_30_r1

tag: E.coli W1863 wt lambda- with ccdB upregulation 30 minutes after induction


title: lacZ_MG1063_120_r1

tag: E.coli MG1063 (recA56 = recA-) with lacZ upregulation 120 minutes after induction


title: ccdB_MG1063_120_r1

tag: E.coli MG1063 (recA56 = recA-) with ccdB upregulation 120 minutes after induction


title: Birnbaum_1-12_StageIII-1_Rep1_ATH1

source_name: Stage III

value: Where root hairs are fully elongated (about 0.45 to 2 mm from the root tip)


title: ccdB_W1863_60_r1

tag: E.coli W1863 wt lambda- with ccdB upregulation 60 minutes after induction


title: lacZ_W1863_60_r1

tag: E.coli W1863 wt lambda- with lacZ upregulation 60 minutes after induction


title: ccdB_W1863_0_r1

tag: E.coli W1863 wt lambda- with ccdB upregulation 0 minutes after induction


title: lacZ_W1863_90_r1

tag: E.coli W1863 wt lambda- with lacZ upregulation 90 minutes after induction


title: lacZ_W1863_30_r1

tag: E.coli W1863 wt lambda- with lacZ upregulation 30 minutes after induction


title: ccdB_MG1063_90_r1

tag: E.coli MG1063 (recA56 = recA-) with ccdB upregulation 90 minutes after induction


title: ccdB_MG1063_60_r2

tag: E.coli MG1063 (recA56 = recA-) with ccdB upregulation 60 minutes after induction


title: ccdB_MG1063_0_r1

tag: E.coli MG1063 (recA56 = recA-) with ccdB upregulation 0 minutes after induction


title: ccdB_MG1063_0_r2


title: ccdB_MG1063_60_r1


title: ccdB_MG1063_90_r2


title: ccdB_MG1063_30_r2

tag: E.coli MG1063 (recA56 = recA-) with ccdB upregulation 30 minutes after induction


title: lacZ_MG1063_90_r2

tag: E.coli MG1063 (recA56 = recA-) with lacZ upregulation 90 minutes after induction


title: lacZ_MG1063_90_r1


title: lacZ_MG1063_30_r2

tag: E.coli MG1063 (recA56 = recA-) with lacZ upregulation 30 minutes after induction


title: ccdB_MG1063_30_r1


title: lacZ_W1863_0_r1

tag: E.coli W1863 wt lambda- with lacZ upregulation 0 minutes after induction


title: lacZ_MG1063_60_r1

tag: E.coli MG1063 (recA56 = recA-) with lacZ upregulation 60 minutes after induction


title: lacZ_MG1063_60_r2


title: lacZ_K12_60_r1

tag: E.coli K12 with lacZ upregulation 60 minutes after induction


title: lacZ_K12_120_r1

tag: E.coli K12 with lacZ upregulation 120 minutes after induction


title: lacZ_MG1063_30_r1


title: lacZ_K12_90_r1

tag: E.coli K12 with lacZ upregulation 90 minutes after induction


title: lacZ_K12_0_r1

tag: E.coli K12 with lacZ upregulation 0 minutes after induction


title: lacZ_MG1063_0_r2

tag: E.coli MG1063 (recA56 = recA-) with lacZ upregulation 0 minutes after induction


title: T60_N0000_r3

tag: untreated cells after 60 min


title: lacZ_K12_30_r1

tag: E.coli K12 with lacZ upregulation 30 minutes after induction


title: lacZ_MG1063_0_r1


title: ccdB_K12_60_r1

tag: E.coli K12 with ccdB upregulation 60 minutes after induction


title: ccdB_K12_0_r1

tag: E.coli K12 with ccdB upregulation 0 minutes after induction


title: ccdB_K12_120_r1

tag: E.coli K12 with ccdB upregulation 120 minutes after induction


title: T60_N0025_r3

tag: cells 60 min after treatment by norfloxacin


title: T60_N0000_r1


title: ccdB_K12_90_r1

tag: E.coli K12 with ccdB upregulation 90 minutes after induction


title: ccdB_K12_30_r1

tag: E.coli K12 with ccdB upregulation 30 minutes after induction


title: T60_N0000_r2


title: T36_N0025_r2

tag: cells 36 min after treatment by norfloxacin


title: T24_N0000_r2

tag: untreated cells after 24 min


title: T60_N0025_r1


title: T24_N0000_r1


title: T36_N0025_r1


title: T24_N0025_r2

tag: cells 24 min after treatment by norfloxacin


title: T24_N0000_r3


title: T60_N0025_r2


title: T48_N0025_r2

tag: cells 48 min after treatment by norfloxacin


title: T24_N0025_r3


title: T48_N0025_r3


title: T36_N0025_r3


title: T12_N0025_r3

tag: cells 12 min after treatment by norfloxacin


title: T24_N0025_r1


title: T12_N0025_r2


title: T12_N0025_r1


title: T48_N0025_r1


title: luc2_U_N0025_r2

tag: luciferase 0.025ug/ml norfloxacin


title: T0_N0025_r2

tag: cells prior to treatment by norfloxacin


title: luc2_U_N0000_r2

tag: luciferase no drug


title: luc2_U_N0000_r1


title: T0_N0025_r1


title: luc2_U_N0025_r1


title: recA_D_N1000_r2

tag: recA deletion 1.0 ug/ml norfloxacin


title: WT_D_N1000_r1

tag: wild-type 1.0 ug/ml norfloxacin


title: WT_D_N1000_r2


title: recA_D_N0050_r2

tag: recA deletion 0.05 ug/ml norfloxacin


title: recA_D_N1000_r1


title: T0_N0025_r3


title: recA_D_N0050_r1


title: WT_N0075_r2

tag: wild-type cells with 0.075 ug/ml norfloxacin


title: WT_N0000_r1

tag: wild-type cells without norfloxacin


title: WT_N0000_r2


title: uspA__U_N0075_r2

tag: uspA upregulation, 0.075 mg/mL norfloxacin


title: WT_N0050_r1

tag: wild-type cells with 0.050 ug/ml norfloxacin


title: sbcB__U_N0075_r3

tag: sbcB upregulation, 0.075 mg/mL norfloxacin


title: WT_N0075_r1


title: WT_N0050_r2


title: WT_N0025_r1

tag: wild-type cells with 0.025 ug/ml norfloxacin


title: recA_D_N0000_r1

tag: recA deletion 0 ug/ml norfloxacin


title: uspA__U_N0075_r3


title: recA_D_N0000_r2


title: WT_N0025_r2


title: sbcB__U_N0075_r1


title: rstB__U_N0075_r3

tag: rstB upregulation, 0.075 mg/mL norfloxacin


title: ruvC__U_N0075_r1

tag: ruvC upregulation, 0.075 mg/mL norfloxacin


title: uspA__U_N0075_r1


title: ruvC__U_N0075_r3


title: ruvC__U_N0075_r2


title: rimI__U_N0075_r3

tag: rimI upregulation, 0.075 mg/mL norfloxacin


title: pyrC__U_N0075_r2

tag: pyrC upregulation, 0.075 mg/mL norfloxacin


title: rstB__U_N0075_r1


title: sbcB__U_N0075_r2


title: rimI__U_N0075_r1


title: pyrC__U_N0075_r1


title: rstB__U_N0075_r2


title: rimI__U_N0075_r2


title: nrdA__U_N0075_r1

tag: nrdA upregulation, 0.075 mg/mL norfloxacin


title: nupC__U_N0075_r3

tag: nupC upregulation, 0.075 mg/mL norfloxacin


title: nrdA__U_N0075_r3


title: yoeB__U_N0075_r1

tag: yoeB upregulation, 0.075 mg/mL norfloxacin


title: yoeB__U_N0075_r2


title: nrdA__U_N0075_r2


title: murI__U_N0075_r1

tag: murI upregulation, 0.075 mg/mL norfloxacin


title: minD__U_N0075_r2

tag: minD upregulation, 0.075 mg/mL norfloxacin


title: minE__U_N0075_r3

tag: minE upregulation, 0.075 mg/mL norfloxacin


title: minE__U_N0075_r2


title: nrdB__U_N0075_r1

tag: nrdB upregulation, 0.075 mg/mL norfloxacin


title: minE__U_N0075_r1


title: pyrC__U_N0075_r3


title: minD__U_N0075_r3


title: murI__U_N0075_r2


title: nrdB__U_N0075_r3


title: murI__U_N0075_r3


title: nupC__U_N0075_r1


title: menC__U_N0075_r3

tag: menC upregulation, 0.075 mg/mL norfloxacin


title: nupC__U_N0075_r2


title: yoeB__U_N0075_r3


title: menC__U_N0075_r1


title: menB__U_N0075_r3

tag: menB upregulation, 0.075 mg/mL norfloxacin


title: menC__U_N0075_r2


title: menB__U_N0075_r1


title: menB__U_N0075_r2


title: mcrB__U_N0075_r3

tag: mcrB upregulation, 0.075 mg/mL norfloxacin


title: minD__U_N0075_r1


title: mcrB__U_N0075_r2


title: mcrB__U_N0075_r1


title: mcrC__U_N0075_r1

tag: mcrC upregulation, 0.075 mg/mL norfloxacin


title: ldrA__U_N0075_r3

tag: ldrA upregulation, 0.075 mg/mL norfloxacin


title: mcrC__U_N0075_r2


title: ldrA__U_N0075_r1


title: mcrC__U_N0075_r3


title: holD__U_N0075_r3

tag: holD upregulation, 0.075 mg/mL norfloxacin


title: holD__U_N0075_r1


title: hlpA__U_N0075_r1

tag: hlpA upregulation, 0.075 mg/mL norfloxacin


title: hlpA__U_N0075_r2


title: hscA__U_N0075_r2

tag: hscA upregulation, 0.075 mg/mL norfloxacin


title: IHF___U_N0075_r1

tag: IHF upregulation, 0.075 mg/mL norfloxacin


title: hlpA__U_N0075_r3


title: gyrI__U_N0075_r3

tag: gyrI upregulation, 0.075 mg/mL norfloxacin


title: hscA__U_N0075_r3


title: gyrI__U_N0075_r1


title: hscA__U_N0075_r1


title: IHF___U_N0075_r3


title: gyrA__U_N0075_r3

tag: gyrA upregulation, 0.075 mg/mL norfloxacin


title: gyrI__U_N0075_r2


title: galF__U_N0075_r2

tag: galF upregulation, 0.075 ug/ml norfloxacin


title: gcvR__U_N0075_r2

tag: gcvR upregulation, 0.075 mg/mL norfloxacin


title: holD__U_N0075_r2


title: gyrA__U_N0075_r1


title: folA__U_N0075_r2

tag: folA upregulation, 0.075 ug/ml norfloxacin


title: gyrA__U_N0075_r2


title: galF__U_N0075_r3


title: folA__U_N0075_r1


title: fklB__U_N0075_r3

tag: fklB upregulation, 0.075 ug/ml norfloxacin


title: fklB__U_N0075_r2


title: gcvR__U_N0075_r1


title: galF__U_N0075_r1


title: folA__U_N0075_r3


title: ldrA__U_N0075_r2


title: era___U_N0075_r3

tag: era upregulation, 0.075 ug/ml norfloxacin


title: fis___U_N0075_r1

tag: fis upregulation, 0.075 ug/ml norfloxacin


title: dnaT__U_N0075_r2

tag: dnaT upregulation, 0.075 ug/ml norfloxacin


title: era___U_N0075_r1


title: dnaT__U_N0075_r3


title: fis___U_N0075_r3


title: era___U_N0075_r2


title: emrR__U_N0075_r3

tag: emrR upregulation, 0.075 ug/ml norfloxacin


title: emrR__U_N0075_r1


title: dnaT__U_N0075_r1


title: fklB__U_N0075_r1


title: fis___U_N0075_r2


title: dnaA__U_N0075_r2

tag: dnaA upregulation, 0.075 ug/ml norfloxacin


title: dnaN__U_N0075_r2

tag: dnaN upregulation, 0.075 ug/ml norfloxacin


title: dam___U_N0075_r2

tag: dam upregulation, 0.075 ug/ml norfloxacin


title: dnaA__U_N0075_r1


title: dnaN__U_N0075_r3


title: dnaN__U_N0075_r1


title: cspF__U_N0075_r3

tag: cspF upregulation, 0.075 ug/ml norfloxacin


title: dam___U_N0075_r1


title: cspF__U_N0075_r1


title: dam___U_N0075_r3


title: dnaA__U_N0075_r3


title: crp___U_N0075_r2

tag: crp upregulation, 0.075 ug/ml norfloxacin


title: crp___U_N0075_r3


title: crp___U_N0075_r1


title: gcvR__U_N0075_r3


title: cspF__U_N0075_r2


title: crcB__U_N0075_r3

tag: crcB upregulation, 0.075 ug/ml norfloxacin


title: crcB__U_N0075_r2


title: bcp___U_N0075_r2

tag: bcp upregulation, 0.075 ug/ml norfloxacin


title: bcp___U_N0075_r1


title: b2618_U_N0075_r3

tag: b2618 upregulation, 0.075 ug/ml norfloxacin


title: b2618_U_N0075_r1


title: cpxR__U_N0075_r2

tag: cpxR upregulation, 0.075 ug/ml norfloxacin


title: luc___U_N0000_r2

tag: luc upregulation, 0.000 ug/ml norfloxacin


title: crcB__U_N0075_r1


title: luc___U_N0000_r3


title: zipA__U_N0075_r3

tag: zipA upregulation, 0.075ug/ml norfloxacin


title: zipA__U_N0075_r1


title: luc___U_N0075_r3

tag: luc upregulation, 0.075ug/ml norfloxacin


title: uvrA___U_N0025_r1

tag: uvrA upregulation, amp 50ug/ml, 0.0125% arabinose, 0.025ug/ml norfloxacin OD ~0.3


title: uvrA___U_N0025_r2


title: luc___U_N0075_r1


title: cpxR__U_N0075_r3


title: luc___U_N0000_r1


title: luc___U_N0075_r2


title: zipA__U_N0075_r2


title: umuD___U_N0025_r3

tag: umuD upregulation, amp 50ug/ml, 0.0125% arabinose, 0.025ug/ml norfloxacin OD ~0.3


title: yebF__U_N0075_r1

tag: yebF upregulation, 0.075ug/ml norfloxacin


title: yebF__U_N0075_r2


title: umuD___U_N0025_r2


title: b2618_U_N0075_r2


title: yebF__U_N0075_r3


title: umuD___U_N0025_r1


title: uvrA___U_N0025_r3


title: ruvA___U_N0025_r2

tag: ruvA upregulation, amp 50ug/ml, 0.0125% arabinose, 0.025ug/ml norfloxacin OD ~0.3


title: sulA___U_N0025_r3

tag: sulA upregulation, amp 50ug/ml, 0.0125% arabinose, 0.025ug/ml norfloxacin OD ~0.3


title: ruvA___U_N0025_r3


title: relE___U_N0025_r3

tag: relE upregulation, amp 50ug/ml, 0.0125% arabinose, 0.025ug/ml norfloxacin OD ~0.3


title: relE___U_N0025_r2


title: relE___U_N0025_r1


title: sulA___U_N0025_r2


title: sulA___U_N0025_r1


title: recA___U_N0025_r3

tag: recA upregulation, amp 50ug/ml, 0.0125% arabinose, 0.025ug/ml norfloxacin OD ~0.3


title: SG001_AG_2ASWGcR

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 86.48
Background Stdev (float) = 4.66
Background Max (float) = 95.2
Background Min (float) = 74.5
Noise Avg (float) = 3.06
Noise Stdev (float) = 0.28
Noise Max (float) = 3.7
Noise Min (float) = 2.2
RawQ (float) = 2.37
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 36
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: SG001_AG_2ASWGcR.DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 233 (type integer); Parameter Upper left corner y coordinate = 234 (type integer); Parameter Upper right corner x coordinate = 4499 (type integer); Parameter Upper right corner y coordinate = 258 (type integer); Parameter Lower right corner x coordinate = 4476 (type integer); Parameter Lower right corner y coordinate = 4523 (type integer); Parameter Lower left corner x coordinate = 211 (type integer); Parameter Lower left corner y coordinate = 4499 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.362711 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

growth_protocol: unknown; Parameter location = Growth Room; Parameter Atmosphere = Normal; Parameter Humidity = 70 %; Parameter Temperature = 22/18 day/night; Parameter Lighting = 10/14 h  day/night; Parameter Medium = hydroponic culture; Parameter Nutrients = nutrient after Siedlecka Krupa 2002 submitted to Acta Physiologiae Plantarum; Parameter Stratification = stratification for 3 days at 4 C ; Performer: Stanislaw,,Gawronski

extract_protocol: Gawronki Trizol Extraction Protocol; Protocol: ored at -20 C degree)  12. centrifuge for 5 minutes at 2-8 Celsius degree and 7500 rpm  13. discard the ethanol   14. air - dry the pellet (shortly)  15. dissolve the pellet in 100 uL RNAse free water    and then was the ethanol precipitation   ; Protocol Type = nucleic_acid_extraction; Performer: Stanislaw,,Gawronski

tag: OrganismPart

value: roots

tag: Ecotype

tag: NASC:Growth Stage


title: recA___U_N0025_r2


title: ruvA___U_N0025_r1


title: SG001_AG_4ASWG25PbR

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 97.80
Background Stdev (float) = 5.55
Background Max (float) = 113.7
Background Min (float) = 87.3
Noise Avg (float) = 3.52
Noise Stdev (float) = 0.48
Noise Max (float) = 4.9
Noise Min (float) = 2.6
RawQ (float) = 2.85
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 33
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: SG001_AG_4ASWG25PbR.DAT

hyb_protocol: EukGE-WS2v4; Protocol Type = Hybridization; Parameter Wash A1 Recovery Mixes = 0 (type integer); Parameter Wash A1 Temperature (C) = 25 (type integer); Parameter Number of Wash A1 Cycles = 10 (type integer); Parameter Mixes per Wash A1 Cycle = 2 (type integer); Parameter Wash B Recovery Mixes = 0 (type integer); Parameter Wash B Temperature (C) = 50 (type integer); Parameter Number of Wash B Cycles = 4 (type integer); Parameter Mixes per Wash B Cycle = 15 (type integer); Parameter Stain Temperature (C) = 25 (type integer); Parameter First Stain Time (seconds) = 600 (type integer); Parameter Wash A2 Recovery Mixes = 0 (type integer); Parameter Wash A2 Temperature (C) = 25 (type integer); Parameter Number of Wash A2 Cycles = 10 (type integer); Parameter Mixes per Wash A2 Cycle = 4 (type integer); Parameter Second Stain Time (seconds) = 600 (type integer); Parameter Third Stain Time (seconds) = 600 (type integer); Parameter Wash A3 Recovery Mixes = 0 (type integer); Parameter Wash A3 Temperature (C) = 30 (type integer); Parameter Number of Wash A3 Cycles = 15 (type integer); Parameter Mixes per Wash A3 Cycle = 4 (type integer); Parameter Holding Temperature (C) = 25 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Fluidics Station, Parameter: Parameter Station Number = 1 (type integer), Parameter: Parameter Position = 4 (type integer); Performers: John,Y,Okyere, , Janet,,Higgins

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 233 (type integer); Parameter Upper left corner y coordinate = 235 (type integer); Parameter Upper right corner x coordinate = 4497 (type integer); Parameter Upper right corner y coordinate = 259 (type integer); Parameter Lower right corner x coordinate = 4474 (type integer); Parameter Lower right corner y coordinate = 4524 (type integer); Parameter Lower left corner x coordinate = 209 (type integer); Parameter Lower left corner y coordinate = 4500 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.438757 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

treatment_protocol: between developmental stages 3.90 and 5.10 (complete rosette growth and first flower bud visible) along with nutrients changes - 25 ppm of Pb as Pb(NO3)2 was added to the nutrient solution twice (in week interval) ; Performer: Stanislaw,,Gawronski


title: SG001_AG_1ASWGcL

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 85.32
Background Stdev (float) = 4.48
Background Max (float) = 99.6
Background Min (float) = 76.8
Noise Avg (float) = 3.00
Noise Stdev (float) = 0.41
Noise Max (float) = 4.2
Noise Min (float) = 2.2
RawQ (float) = 2.45
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 23
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: SG001_AG_1ASWGcL.DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 236 (type integer); Parameter Upper left corner y coordinate = 233 (type integer); Parameter Upper right corner x coordinate = 4501 (type integer); Parameter Upper right corner y coordinate = 225 (type integer); Parameter Lower right corner x coordinate = 4510 (type integer); Parameter Lower right corner y coordinate = 4490 (type integer); Parameter Lower left corner x coordinate = 244 (type integer); Parameter Lower left corner y coordinate = 4498 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.398717 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

value: rosette leaves


title: SG001_AG_6ASWG50PbR

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 192.65
Background Stdev (float) = 6.66
Background Max (float) = 215.3
Background Min (float) = 180.4
Noise Avg (float) = 5.90
Noise Stdev (float) = 0.64
Noise Max (float) = 8.3
Noise Min (float) = 4.8
RawQ (float) = 4.16
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 10
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: SG001_AG_6ASWG50PbR.DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 233 (type integer); Parameter Upper left corner y coordinate = 235 (type integer); Parameter Upper right corner x coordinate = 4499 (type integer); Parameter Upper right corner y coordinate = 259 (type integer); Parameter Lower right corner x coordinate = 4475 (type integer); Parameter Lower right corner y coordinate = 4524 (type integer); Parameter Lower left corner x coordinate = 210 (type integer); Parameter Lower left corner y coordinate = 4500 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.324287 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

treatment_protocol: between developmental stages 3.90 and 5.10 (complete rosette growth and first flower bud visible) along with nutrients changes - 50 ppm of Pb as Pb(NO3)2 was added to the nutrient solution twice (in week interval) ; Performer: Stanislaw,,Gawronski

value: root


title: PW001_AG_A4-White-NPO2

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 52.95
Background Stdev (float) = 1.28
Background Max (float) = 57.0
Background Min (float) = 50.8
Noise Avg (float) = 1.59
Noise Stdev (float) = 0.18
Noise Max (float) = 2.0
Noise Min (float) = 1.3
RawQ (float) = 1.52
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 50
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: PW001_AG_A4-White-NPO2.DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 234 (type integer); Parameter Upper left corner y coordinate = 235 (type integer); Parameter Upper right corner x coordinate = 4500 (type integer); Parameter Upper right corner y coordinate = 266 (type integer); Parameter Lower right corner x coordinate = 4471 (type integer); Parameter Lower right corner y coordinate = 4531 (type integer); Parameter Lower left corner x coordinate = 205 (type integer); Parameter Lower left corner y coordinate = 4500 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.947989 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

growth_protocol: unknown; Parameter Humidity = 80% in growth cabinet; Parameter Light = 16h day length until hydroponics, then constant light in growth cabinet; Parameter Medium = MS in polycarbonate discs until 21 days, then hydroponics in growth cabinet; Parameter Temperature = 24 C; Parameter Water = Hydropoincs; Parameter Nutrients = 1% sucrose in agar, then see in-vivo treatment; Parameter Treatment = None; Parameter Location = Growth room until 21 days, then hydroponics in Saxcil growth cabinet; Performer: Philip,,White

extract_protocol: TriZOL; Protocol:   ; Protocol Type = nucleic_acid_extraction; Performer: Philip,,White

treatment_protocol: This source has no KH2PO4 or KOH (No Potassium!). It has 0.27mM additional Ca(H2PO4)2. ; Performer: Philip,,White

value: Rosette leaves

tag: Age time point

value: 28 hours after nutrient removal


title: luc___U_N0025_r2

tag: luc upregulation, amp 50ug/ml, 0.0125% arabinose, 0.025ug/ml norfloxacin OD ~0.3


title: SG001_AG_5ASWG50PbL

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 75.36
Background Stdev (float) = 3.22
Background Max (float) = 85.3
Background Min (float) = 69.7
Noise Avg (float) = 2.71
Noise Stdev (float) = 0.35
Noise Max (float) = 3.6
Noise Min (float) = 2.1
RawQ (float) = 2.21
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 38
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: SG001_AG_5ASWG50PbL.DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 234 (type integer); Parameter Upper left corner y coordinate = 232 (type integer); Parameter Upper right corner x coordinate = 4499 (type integer); Parameter Upper right corner y coordinate = 239 (type integer); Parameter Lower right corner x coordinate = 4494 (type integer); Parameter Lower right corner y coordinate = 4504 (type integer); Parameter Lower left corner x coordinate = 229 (type integer); Parameter Lower left corner y coordinate = 4497 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.495869 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;


title: mazF___U_N0025_r2

tag: mazF_chpA upregulation, amp 50ug/ml, 0.0125% arabinose, 0.025ug/ml norfloxacin OD ~0.3


title: mazF___U_N0025_r1


title: CH001_AG_A1-Howar-410(2)

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 56.06
Background Stdev (float) = 0.95
Background Max (float) = 59.7
Background Min (float) = 54.8
Noise Avg (float) = 1.58
Noise Stdev (float) = 0.12
Noise Max (float) = 1.9
Noise Min (float) = 1.4
RawQ (float) = 1.62
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 13
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: CH001_AG_A1-Howar-410(2).DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 236 (type integer); Parameter Upper left corner y coordinate = 234 (type integer); Parameter Upper right corner x coordinate = 4501 (type integer); Parameter Upper right corner y coordinate = 237 (type integer); Parameter Lower right corner x coordinate = 4499 (type integer); Parameter Lower right corner y coordinate = 4502 (type integer); Parameter Lower left corner x coordinate = 233 (type integer); Parameter Lower left corner y coordinate = 4499 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 1.924722 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

growth_protocol: unknown; Parameter Atmosphere = Normal; Parameter Humidity = 60%; Parameter Light =  16hs dark; Parameter Medium = M2 compost; Parameter Temperature =  16hrs 15oC (dark); Parameter Water = twice weekly; Performer: Caroline,,Howard

extract_protocol: Unknown; Protocol Type = nucleic_acid_extraction; Performer: Caroline,,Howard

value: Unshaded rosette leaves

tag: GeneticModification


title: PW001_AG_A3-White-NOP2

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 51.51
Background Stdev (float) = 1.69
Background Max (float) = 57.8
Background Min (float) = 49.3
Noise Avg (float) = 1.50
Noise Stdev (float) = 0.18
Noise Max (float) = 2.0
Noise Min (float) = 1.2
RawQ (float) = 1.55
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 9
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: PW001_AG_A3-White-NOP2.DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 234 (type integer); Parameter Upper left corner y coordinate = 234 (type integer); Parameter Upper right corner x coordinate = 4500 (type integer); Parameter Upper right corner y coordinate = 250 (type integer); Parameter Lower right corner x coordinate = 4484 (type integer); Parameter Lower right corner y coordinate = 4515 (type integer); Parameter Lower left corner x coordinate = 219 (type integer); Parameter Lower left corner y coordinate = 4499 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 1.118371 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

treatment_protocol: This source has no KH2PO4 (No Phosphate!). It has 0.125mM additional K2SO4. ; Performer: Philip,,White


title: mazF___U_N0025_r3


title: recA___U_N0025_r1


title: MB001_AG_COL

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 57.92
Background Stdev (float) = 1.76
Background Max (float) = 63.4
Background Min (float) = 54.3
Noise Avg (float) = 1.52
Noise Stdev (float) = 0.18
Noise Max (float) = 2.1
Noise Min (float) = 1.3
RawQ (float) = 1.61
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 114
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: MB001_AG_COL.DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 233 (type integer); Parameter Upper left corner y coordinate = 234 (type integer); Parameter Upper right corner x coordinate = 4497 (type integer); Parameter Upper right corner y coordinate = 244 (type integer); Parameter Lower right corner x coordinate = 4487 (type integer); Parameter Lower right corner y coordinate = 4509 (type integer); Parameter Lower left corner x coordinate = 223 (type integer); Parameter Lower left corner y coordinate = 4499 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 1.062617 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

growth_protocol: unknown; Parameter Atmosphere = Normal; Parameter Humidity = Normal; Parameter Light = 24 hour days; Parameter Medium = Murashige Skoog, 1% agar; Parameter Temperature = 22 C; Parameter Nutrients = 1% sucrose; Performer: Cathlene,,Eland

extract_protocol: Qiagen / Trizol; Protocol: Qiagen RNAeasy kit protocol ; Protocol Type = nucleic_acid_extraction; Performer: Cathlene,,Eland

value: Whole seedlings

tag: Sex

value: Male


title: PW001_AG_A2-White-OPK2

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 52.89
Background Stdev (float) = 1.71
Background Max (float) = 58.3
Background Min (float) = 49.5
Noise Avg (float) = 1.43
Noise Stdev (float) = 0.12
Noise Max (float) = 1.8
Noise Min (float) = 1.2
RawQ (float) = 1.52
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 32
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: PW001_AG_A2-White-OPK2.DAT

hyb_protocol: EukGE-WS2v4; Protocol Type = Hybridization; Parameter Wash A1 Recovery Mixes = 0 (type integer); Parameter Wash A1 Temperature (C) = 25 (type integer); Parameter Number of Wash A1 Cycles = 10 (type integer); Parameter Mixes per Wash A1 Cycle = 2 (type integer); Parameter Wash B Recovery Mixes = 0 (type integer); Parameter Wash B Temperature (C) = 50 (type integer); Parameter Number of Wash B Cycles = 4 (type integer); Parameter Mixes per Wash B Cycle = 15 (type integer); Parameter Stain Temperature (C) = 25 (type integer); Parameter First Stain Time (seconds) = 600 (type integer); Parameter Wash A2 Recovery Mixes = 0 (type integer); Parameter Wash A2 Temperature (C) = 25 (type integer); Parameter Number of Wash A2 Cycles = 10 (type integer); Parameter Mixes per Wash A2 Cycle = 4 (type integer); Parameter Second Stain Time (seconds) = 600 (type integer); Parameter Third Stain Time (seconds) = 600 (type integer); Parameter Wash A3 Recovery Mixes = 0 (type integer); Parameter Wash A3 Temperature (C) = 30 (type integer); Parameter Number of Wash A3 Cycles = 15 (type integer); Parameter Mixes per Wash A3 Cycle = 4 (type integer); Parameter Holding Temperature (C) = 25 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Fluidics Station, Parameter: Parameter Station Number = 1 (type integer), Parameter: Parameter Position = 3 (type integer); Performers: John,Y,Okyere, , Janet,,Higgins

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 237 (type integer); Parameter Upper left corner y coordinate = 233 (type integer); Parameter Upper right corner x coordinate = 4502 (type integer); Parameter Upper right corner y coordinate = 219 (type integer); Parameter Lower right corner x coordinate = 4517 (type integer); Parameter Lower right corner y coordinate = 4484 (type integer); Parameter Lower left corner x coordinate = 251 (type integer); Parameter Lower left corner y coordinate = 4498 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 1.162603 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

treatment_protocol: This source has no Ca(NO3)2.4H2O (No Nitrate!). It has 4mM CaSO4.H2O in addition ; Performer: Philip,,White


title: SG001_AG_3ASWG25PbL

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 69.03
Background Stdev (float) = 2.33
Background Max (float) = 77.3
Background Min (float) = 65.7
Noise Avg (float) = 2.50
Noise Stdev (float) = 0.23
Noise Max (float) = 3.2
Noise Min (float) = 2.1
RawQ (float) = 2.13
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 56
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: SG001_AG_3ASWG25PbL.DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 234 (type integer); Parameter Upper left corner y coordinate = 235 (type integer); Parameter Upper right corner x coordinate = 4499 (type integer); Parameter Upper right corner y coordinate = 261 (type integer); Parameter Lower right corner x coordinate = 4473 (type integer); Parameter Lower right corner y coordinate = 4526 (type integer); Parameter Lower left corner x coordinate = 208 (type integer); Parameter Lower left corner y coordinate = 4500 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.735718 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;


title: SP001_AG_SPABA

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 86.26
Background Stdev (float) = 5.43
Background Max (float) = 105.8
Background Min (float) = 76.1
Noise Avg (float) = 3.02
Noise Stdev (float) = 0.54
Noise Max (float) = 5.4
Noise Min (float) = 2.2
RawQ (float) = 2.50
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 97
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: SP001_AG_SPABA.DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 236 (type integer); Parameter Upper left corner y coordinate = 232 (type integer); Parameter Upper right corner x coordinate = 4502 (type integer); Parameter Upper right corner y coordinate = 219 (type integer); Parameter Lower right corner x coordinate = 4516 (type integer); Parameter Lower right corner y coordinate = 4484 (type integer); Parameter Lower left corner x coordinate = 250 (type integer); Parameter Lower left corner y coordinate = 4497 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.560894 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

growth_protocol: unknown; Parameter Media = Half strength MS and 10uM ABA. Imbided 4 days at 4C, dark, then 16hr light/8hr dark; Performer: Sarah,,Pritchard

extract_protocol: Qiagen / Trizol; Protocol: Qiagen RNAeasy kit protocol ; Protocol Type = nucleic_acid_extraction; Performer: Sarah,,Pritchard

value: Whole Seeds


title: luc___U_N0025_r3


title: luc___U_N0025_r1


title: MB001_AG_SKS

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 61.92
Background Stdev (float) = 2.09
Background Max (float) = 68.0
Background Min (float) = 58.2
Noise Avg (float) = 1.56
Noise Stdev (float) = 0.16
Noise Max (float) = 1.9
Noise Min (float) = 1.3
RawQ (float) = 1.70
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 21
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: MB001_AG_SKS.DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 233 (type integer); Parameter Upper left corner y coordinate = 235 (type integer); Parameter Upper right corner x coordinate = 4497 (type integer); Parameter Upper right corner y coordinate = 252 (type integer); Parameter Lower right corner x coordinate = 4481 (type integer); Parameter Lower right corner y coordinate = 4517 (type integer); Parameter Lower left corner x coordinate = 217 (type integer); Parameter Lower left corner y coordinate = 4500 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 1.160874 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

value: An insertion mutant

tag: StrainOrLine

value: sks


title: SP001_AG_SP5

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 83.47
Background Stdev (float) = 3.80
Background Max (float) = 95.4
Background Min (float) = 76.7
Noise Avg (float) = 3.02
Noise Stdev (float) = 0.39
Noise Max (float) = 4.3
Noise Min (float) = 2.3
RawQ (float) = 2.53
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 116
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: SP001_AG_SP5.DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 236 (type integer); Parameter Upper left corner y coordinate = 232 (type integer); Parameter Upper right corner x coordinate = 4502 (type integer); Parameter Upper right corner y coordinate = 214 (type integer); Parameter Lower right corner x coordinate = 4522 (type integer); Parameter Lower right corner y coordinate = 4478 (type integer); Parameter Lower left corner x coordinate = 256 (type integer); Parameter Lower left corner y coordinate = 4497 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.457621 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

growth_protocol: unknown; Parameter Media = Half strength MS imbibed 4 days at 4C in dark then 16hr light/8hr; Performer: Sarah,,Pritchard

value: Whole Seedlings


title: lon___U_N0025_r3

tag: lon upregulation, amp 50ug/ml, 0.0125% arabinose, 0.025ug/ml norfloxacin OD ~0.3


title: lon___U_N0025_r2


title: SP001_AG_SP0

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 89.41
Background Stdev (float) = 3.56
Background Max (float) = 101.8
Background Min (float) = 82.7
Noise Avg (float) = 3.30
Noise Stdev (float) = 0.33
Noise Max (float) = 4.6
Noise Min (float) = 2.7
RawQ (float) = 2.62
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 79
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: SP001_AG_SP0.DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 237 (type integer); Parameter Upper left corner y coordinate = 233 (type integer); Parameter Upper right corner x coordinate = 4503 (type integer); Parameter Upper right corner y coordinate = 212 (type integer); Parameter Lower right corner x coordinate = 4525 (type integer); Parameter Lower right corner y coordinate = 4477 (type integer); Parameter Lower left corner x coordinate = 258 (type integer); Parameter Lower left corner y coordinate = 4498 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.451523 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

growth_protocol: unknown; Parameter Media = Half strength MS imbibed in darkness, 4 days at 4C; Performer: Sarah,,Pritchard

value: Whole seeds


title: SP001_AG_SP1_repeat

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 90.61
Background Stdev (float) = 4.70
Background Max (float) = 104.7
Background Min (float) = 81.5
Noise Avg (float) = 2.91
Noise Stdev (float) = 0.33
Noise Max (float) = 3.9
Noise Min (float) = 2.4
RawQ (float) = 2.61
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 24
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: SP001_AG_SP1_repeat.DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 232 (type integer); Parameter Upper left corner y coordinate = 235 (type integer); Parameter Upper right corner x coordinate = 4499 (type integer); Parameter Upper right corner y coordinate = 265 (type integer); Parameter Lower right corner x coordinate = 4470 (type integer); Parameter Lower right corner y coordinate = 4530 (type integer); Parameter Lower left corner x coordinate = 203 (type integer); Parameter Lower left corner y coordinate = 4500 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.655410 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

growth_protocol: unknown; Parameter Media = Half strength MS media imbibed in darkness 4 days at 4C, then 16hr light/8hr dark; Performer: Sarah,,Pritchard

value: Whole germinating seeds


title: lon___U_N0025_r1

description: GeneChips were washed and stained with an FS450 fluidics machine and scanned using a GeneChip Scanner 3000


title: lexA___U_N0025_r1

scan_protocol: GeneChips were washed and stained with an FS450 fluidics machine and scanned using a GeneChip Scanner 3000

tag: lexA upregulation, amp 50ug/ml, 0.0125% arabinose, 0.025ug/ml norfloxacin OD ~0.3


title: lexA___U_N0025_r3

data_processing: GeneChips were washed and stained with an FS450 fluidics machine and scanned using a GeneChip Scanner 3000


title: lexA___U_N0025_r2


title: CH001_AG_A6-Howar-143(2)

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 68.77
Background Stdev (float) = 2.20
Background Max (float) = 76.0
Background Min (float) = 64.8
Noise Avg (float) = 2.09
Noise Stdev (float) = 0.20
Noise Max (float) = 2.7
Noise Min (float) = 1.7
RawQ (float) = 1.94
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 35
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: CH001_AG_A6-Howar-143(2).DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 234 (type integer); Parameter Upper left corner y coordinate = 235 (type integer); Parameter Upper right corner x coordinate = 4499 (type integer); Parameter Upper right corner y coordinate = 255 (type integer); Parameter Lower right corner x coordinate = 4480 (type integer); Parameter Lower right corner y coordinate = 4520 (type integer); Parameter Lower left corner x coordinate = 215 (type integer); Parameter Lower left corner y coordinate = 4500 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 2.081572 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

growth_protocol: unknown; Parameter Atmosphere = Normal; Parameter Humidity = 60%; Performer: Caroline,,Howard


title: CH001_AG_A4-Howar-140(2)

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 73.52
Background Stdev (float) = 2.64
Background Max (float) = 83.3
Background Min (float) = 69.0
Noise Avg (float) = 2.17
Noise Stdev (float) = 0.23
Noise Max (float) = 2.9
Noise Min (float) = 1.9
RawQ (float) = 2.00
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 12
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: CH001_AG_A4-Howar-140(2).DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 234 (type integer); Parameter Upper left corner y coordinate = 234 (type integer); Parameter Upper right corner x coordinate = 4499 (type integer); Parameter Upper right corner y coordinate = 253 (type integer); Parameter Lower right corner x coordinate = 4482 (type integer); Parameter Lower right corner y coordinate = 4518 (type integer); Parameter Lower left corner x coordinate = 216 (type integer); Parameter Lower left corner y coordinate = 4499 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 1.177388 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;


title: PW001_AG_A1-White-NPK2

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 49.06
Background Stdev (float) = 1.29
Background Max (float) = 53.3
Background Min (float) = 46.9
Noise Avg (float) = 1.38
Noise Stdev (float) = 0.15
Noise Max (float) = 1.9
Noise Min (float) = 1.1
RawQ (float) = 1.51
Number Cells Masked (integer) = 312
Number Outlier Cells (integer) = 183
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: PW001_AG_A1-White-NPK2.DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 237 (type integer); Parameter Upper left corner y coordinate = 233 (type integer); Parameter Upper right corner x coordinate = 4502 (type integer); Parameter Upper right corner y coordinate = 212 (type integer); Parameter Lower right corner x coordinate = 4524 (type integer); Parameter Lower right corner y coordinate = 4477 (type integer); Parameter Lower left corner x coordinate = 258 (type integer); Parameter Lower left corner y coordinate = 4497 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 1.444951 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

treatment_protocol: Full nutrient solution: KH2PO4 0.25mM, KOH 0.5mM, MgSO4.7H2O 0.75mM, CaCl2.2H2O 0.025 FeNaEDTA 0.1mM, H3BO3 0.03 mM, MnSO4.4H2O 0.01mM, ZnSO4.7H2O 0.001mM, CuSO4.5H2O 0.003 mM, Na2MoO4.2H2O 0.0005mM ; Performer: Philip,,White


title: dinP___U_N0025_r2

tag: dinP upregulation, amp 50ug/ml, 0.0125% arabinose, 0.025ug/ml norfloxacin OD ~0.3


title: CH001_AG_A3-Howar-413(2)

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 64.52
Background Stdev (float) = 2.17
Background Max (float) = 72.0
Background Min (float) = 60.5
Noise Avg (float) = 1.62
Noise Stdev (float) = 0.16
Noise Max (float) = 2.2
Noise Min (float) = 1.3
RawQ (float) = 1.76
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 12
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: CH001_AG_A3-Howar-413(2).DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 235 (type integer); Parameter Upper left corner y coordinate = 234 (type integer); Parameter Upper right corner x coordinate = 4501 (type integer); Parameter Upper right corner y coordinate = 238 (type integer); Parameter Lower right corner x coordinate = 4498 (type integer); Parameter Lower right corner y coordinate = 4502 (type integer); Parameter Lower left corner x coordinate = 233 (type integer); Parameter Lower left corner y coordinate = 4499 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 2.146128 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;


title: CH001_AG_A5-Howar-141(2)

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 56.56
Background Stdev (float) = 1.37
Background Max (float) = 62.1
Background Min (float) = 54.7
Noise Avg (float) = 1.50
Noise Stdev (float) = 0.13
Noise Max (float) = 2.0
Noise Min (float) = 1.3
RawQ (float) = 1.61
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 13
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: CH001_AG_A5-Howar-141(2).DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 233 (type integer); Parameter Upper left corner y coordinate = 234 (type integer); Parameter Upper right corner x coordinate = 4498 (type integer); Parameter Upper right corner y coordinate = 260 (type integer); Parameter Lower right corner x coordinate = 4474 (type integer); Parameter Lower right corner y coordinate = 4525 (type integer); Parameter Lower left corner x coordinate = 209 (type integer); Parameter Lower left corner y coordinate = 4499 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 1.607357 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;


title: CH001_AG_A2-Howar-411(2)

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 64.02
Background Stdev (float) = 2.00
Background Max (float) = 70.8
Background Min (float) = 60.5
Noise Avg (float) = 1.58
Noise Stdev (float) = 0.17
Noise Max (float) = 2.1
Noise Min (float) = 1.3
RawQ (float) = 1.71
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 17
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: CH001_AG_A2-Howar-411(2).DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 235 (type integer); Parameter Upper left corner y coordinate = 234 (type integer); Parameter Upper right corner x coordinate = 4500 (type integer); Parameter Upper right corner y coordinate = 246 (type integer); Parameter Lower right corner x coordinate = 4489 (type integer); Parameter Lower right corner y coordinate = 4510 (type integer); Parameter Lower left corner x coordinate = 224 (type integer); Parameter Lower left corner y coordinate = 4499 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 2.010713 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;


title: dinP___U_N0025_r3


title: yeastcells_treatment6hrsafterO.D.1.0_25ug/ml T2

city: College Station

first: Coran

middle: MH

last: Watanabe

state: TX

address: Texas A&M Dept. Chemistry MS 3255

department: Chemistry

institute: Texas A*M University

description: We have examined the transcriptional response of S. cerevisiae to exposure to pyocyanin at 25 and 250 ?g/ml concentrations.  Our analysis indicates that the changes are consistent with an oxidative stress response, as observed in other studies of the mode of action of pyocyanin toxicity.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip YeastS98 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae cells

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

growth_protocol: Cells were grown in YPD media at 30 degrees Celsius at 250 rpm shaker.

extract_protocol: SDS/double phenol RNA extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were grown to O.D. of 1.0, given 25?g/ml pyocyanin in minimal ethanol, and grown for 6 hours, then collected by centrifugation, frozen in liquid nitrogen, thawed before proecessing.

tag: Saccharomyces cerevisiae, wt, maintianed on YPD plates, started from 48 hrs growth on a new YPD agar plate


title: dinI___U_N0025_r2

tag: dinI upregulation, amp 50ug/ml, 0.0125% arabinose, 0.025ug/ml norfloxacin OD ~0.3


title: dinP___U_N0025_r1


title: dinI___U_N0025_r3


title: dinI___U_N0025_r1


title: Patient 46 GF201 046

status: Public on Jan 20 2007

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

country: Japan

institute: Aichi Cancer Center

description: Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.

hyb_protocol: The GeneFilters were prehybridized for 2 h at 51°C with 0.5 mg/ml of poly-dA (Invitrogen) and 0.5 mg/ml Cot-1 DNA (Invitrogen) in 10 ml of AlkPhos DIRECT hybridization buffer (Amersham Bioscience) and then hybridized for 17 h at 51°C with the denatured radio-labeled probe. Hybridization of the arrays was followed by two washings with a solution containing 2 M of urea, 0.1 % of SDS, 50 mM of Na phosphate buffer (pH 7.0), 150 mM of NaCl, 1 mM of MgCl2 and 0.2 % of AlkPhos DIRECT blocking reagent (Amersham Bioscience). The arrays were then washed twice with a solution containing 2 mM of MgCl2, 50 mM of Tris and 100 mM of NaCl, and with a solution containing 2 mM of MgCl2, 50 mM of Tris and 15 mM of NaCl. All procedures were carried out with the aid of custom-made AutoHybridizers (Fuji Photo Film, Tokyo, Japan).

scan_protocol: The arrays were then exposed for 2 hours to an Imaging Plate and scanned at 25-mm resolution with a BAS5000 phosphoimager (Fuji Photo Film), images of the hybridized arrays were processed with L Process (Fuji Photo Film) and signal intensities quantified with ArrayGauge software (Fuji Photo Film).

data_processing: The raw data were re-scaled to account for the differences in individual hybridization intensities.  We employed a rank-invariant scaling method to select genes (Tseng et al., 2001), which were then used for fitting of a non-linear normalization curve.  Averaged values of the first and the second hybridizations were used for further analyses.

organism: Homo sapiens

source_name: primary lung cancer

label_protocol: Five mg of total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of 100 mCi of [33P]dCTP (Amersham Bioscience, Piscataway, NJ) according to the instructions for the GeneFilters (Invitrogen) with slight modification.

extract_protocol: On average, 50 7 um-thick cryostat sections were prepared for the extraction of total RNA from tumor cell-rich areas, which were identified by a surgical pathologist (YY) using every 10th section stained by May-Giemsa. Careful attention was paid to the microdissection of only such tumor cell-rich areas, yielding an average of 75.4% tumor cell content (Figure 1i). RNAs were then isolated using RNAeasy (Quiagen, Valencia, CA, USA) according to the manufacturer's instruction, and their quality was checked with the RNA 6000 Nano Assay kit and the 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA).

tag: Sample #

tag: Survival Period

tag: status after 5 years

value: Alive

tag: HIST

value: SQ

tag: AGE

tag: SEX

tag: pStage

value: IIB

tag: pT

tag: pN


title: yeastcells_control6hrsafterO.D.1.0_control1.

treatment_protocol: Cells were grown to O.D. of 1.0 and grown for 6 hours, then collected by centrifugation, frozen in liquid nitrogen, thawed before proecessing.


title: Patient 47 GF201 047

value: IB


title: yeastcells_control6hrsafterO.D.1.0_control2.


title: Patient 50 GF201 050

value: Dead

value: IIIB


title: Patient 49 GF201 049

value: IIIA


title: Patient 48 GF201 048


title: Patient 41 GF201 041

value: AD

value: Female

value: IA


title: Patient 43 GF201 043

value: LA

value: Male


title: Patient 44 GF201 044


title: yeastcells_treatment6hrsafterO.D.1.0_25ug/ml T1


title: Patient 40 GF201 040


title: Patient 39 GF201 039


title: Patient 37 GF201 037


title: Patient 38 GF201 038


title: Patient 45 GF201 045


title: Patient 36 GF201 036


title: Patient 42 GF201 042


title: Patient 35 GF201 035


title: Patient 29 GF201 029


title: Patient 34 GF201 034


title: Patient 32 GF201 032


title: Patient 33 GF201 033


title: Patient 25 GF201 025


title: Patient 26 GF201 026


title: Patient 24 GF201 024


title: Patient 30 GF201 030


title: Patient 28 GF201 028


title: Patient 31 GF201 031


title: Patient 23 GF201 023


title: Patient 27 GF201 027


title: Patient 22 GF201 022


title: Patient 17 GF201 017


title: Patient 20 GF201 020


title: Patient 21 GF201 021


title: Patient 18 GF201 018


title: Patient 19 GF201 019


title: Patient 16 GF201 016


title: Patient 15 GF201 015