title: JH003_ATH1_A9-Hammond-CS2

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 66.53
Background Stdev (float) = 1.40
Background Max (float) = 70.1
Background Min (float) = 63.8
Noise Avg (float) = 3.45
Noise Stdev (float) = 0.26
Noise Max (float) = 4.5
Noise Min (float) = 3.0
RawQ (float) = 2.46
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 752
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: JH003_ATH1_A9-Hammond-CS2.DAT

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 = 4501 (type integer); Parameter Upper right corner y coordinate = 243 (type integer); Parameter Lower right corner x coordinate = 4491 (type integer); Parameter Lower right corner y coordinate = 4515 (type integer); Parameter Lower left corner x coordinate = 221 (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 = 0.417048 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;


title: JH003_ATH1_A5-Hammond-KR1_repeat

status: Public on Jan 08 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) = 61.05
Background Stdev (float) = 1.05
Background Max (float) = 63.7
Background Min (float) = 57.9
Noise Avg (float) = 3.05
Noise Stdev (float) = 0.15
Noise Max (float) = 3.5
Noise Min (float) = 2.7
RawQ (float) = 2.37
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 443
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: JH003_ATH1_A5-Hammond-KR1_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 = 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 = 4501 (type integer); Parameter Upper right corner y coordinate = 239 (type integer); Parameter Lower right corner x coordinate = 4495 (type integer); Parameter Lower right corner y coordinate = 4509 (type integer); Parameter Lower left corner x coordinate = 224 (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 = 0.459434 (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 Atmosphere = Normal; Parameter Humidity = 80 %; Parameter Temperature = imbibed for 3-5 days at 4 ; Performer: John,,Hammond

extract_protocol: Qiagen / Trizol; Protocol: Qiagen RNAeasy kit protocol ; Protocol Type = nucleic_acid_extraction; Performer: John,,Hammond

treatment_protocol: 1/10 MS nutrient solution without any potassium ; Performer: John,,Hammond

tag: OrganismPart

value: all root material

tag: Ecotype

tag: NASC:Growth Stage


title: JH003_ATH1_A17-Hammond-KR3

institute: Nottingham Arabidopsis Stock Centre (NASC)

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 73.96
Background Stdev (float) = 2.11
Background Max (float) = 78.6
Background Min (float) = 68.4
Noise Avg (float) = 3.75
Noise Stdev (float) = 0.16
Noise Max (float) = 4.1
Noise Min (float) = 3.3
RawQ (float) = 2.62
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 276
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: JH003_ATH1_A17-Hammond-KR3.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 = 230 (type integer); Parameter Upper left corner y coordinate = 231 (type integer); Parameter Upper right corner x coordinate = 4501 (type integer); Parameter Upper right corner y coordinate = 235 (type integer); Parameter Lower right corner x coordinate = 4498 (type integer); Parameter Lower right corner y coordinate = 4505 (type integer); Parameter Lower left corner x coordinate = 227 (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 = 0.414786 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;


title: JH003_ATH1_A3-Hammond-CS1

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 79.33
Background Stdev (float) = 1.86
Background Max (float) = 84.7
Background Min (float) = 74.8
Noise Avg (float) = 4.72
Noise Stdev (float) = 0.16
Noise Max (float) = 5.1
Noise Min (float) = 4.2
RawQ (float) = 2.91
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 680
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: JH003_ATH1_A3-Hammond-CS1.DAT

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 = 233 (type integer); Parameter Upper right corner x coordinate = 4502 (type integer); Parameter Upper right corner y coordinate = 264 (type integer); Parameter Lower right corner x coordinate = 4472 (type integer); Parameter Lower right corner y coordinate = 4534 (type integer); Parameter Lower left corner x coordinate = 201 (type integer); Parameter Lower left corner y coordinate = 4503 (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 = 0.279383 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

treatment_protocol: 1/10 MS nutrient solution containing 2 mM Caesium ; Performer: John,,Hammond

value: shoots


title: JH003_ATH1_A4-Hammond-FR1

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 79.15
Background Stdev (float) = 0.93
Background Max (float) = 82.4
Background Min (float) = 76.6
Noise Avg (float) = 5.27
Noise Stdev (float) = 0.16
Noise Max (float) = 5.7
Noise Min (float) = 4.8
RawQ (float) = 3.03
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 473
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: JH003_ATH1_A4-Hammond-FR1.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 = 230 (type integer); Parameter Upper right corner x coordinate = 4503 (type integer); Parameter Upper right corner y coordinate = 231 (type integer); Parameter Lower right corner x coordinate = 4504 (type integer); Parameter Lower right corner y coordinate = 4501 (type integer); Parameter Lower left corner x coordinate = 232 (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 = 0.242569 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;


title: JH003_ATH1_A6-Hammond-CR1

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 66.48
Background Stdev (float) = 0.73
Background Max (float) = 68.8
Background Min (float) = 64.5
Noise Avg (float) = 3.44
Noise Stdev (float) = 0.11
Noise Max (float) = 3.9
Noise Min (float) = 3.2
RawQ (float) = 2.50
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 252
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: JH003_ATH1_A6-Hammond-CR1.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 = 230 (type integer); Parameter Upper left corner y coordinate = 232 (type integer); Parameter Upper right corner x coordinate = 4500 (type integer); Parameter Upper right corner y coordinate = 262 (type integer); Parameter Lower right corner x coordinate = 4471 (type integer); Parameter Lower right corner y coordinate = 4532 (type integer); Parameter Lower left corner x coordinate = 201 (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 = 0.460692 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;


title: JH003_ATH1_A2-Hammond-KS1

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 76.52
Background Stdev (float) = 1.71
Background Max (float) = 81.5
Background Min (float) = 72.9
Noise Avg (float) = 3.94
Noise Stdev (float) = 0.18
Noise Max (float) = 4.6
Noise Min (float) = 3.5
RawQ (float) = 2.83
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 513
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: JH003_ATH1_A2-Hammond-KS1.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 = 229 (type integer); Parameter Upper left corner y coordinate = 231 (type integer); Parameter Upper right corner x coordinate = 4499 (type integer); Parameter Upper right corner y coordinate = 247 (type integer); Parameter Lower right corner x coordinate = 4484 (type integer); Parameter Lower right corner y coordinate = 4518 (type integer); Parameter Lower left corner x coordinate = 214 (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 = 0.547880 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;


title: JH003_ATH1_A1-Hammond-FS1

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 78.42
Background Stdev (float) = 2.40
Background Max (float) = 84.1
Background Min (float) = 73.1
Noise Avg (float) = 4.70
Noise Stdev (float) = 0.27
Noise Max (float) = 5.6
Noise Min (float) = 4.3
RawQ (float) = 2.81
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 517
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: JH003_ATH1_A1-Hammond-FS1.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 = 230 (type integer); Parameter Upper right corner x coordinate = 4504 (type integer); Parameter Upper right corner y coordinate = 221 (type integer); Parameter Lower right corner x coordinate = 4514 (type integer); Parameter Lower right corner y coordinate = 4491 (type integer); Parameter Lower left corner x coordinate = 242 (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 = 0.287155 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;


title: JB001_ATH1_A2-1-Boyce-cdpk6-yfp-4-1

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 90.52
Background Stdev (float) = 2.07
Background Max (float) = 96.6
Background Min (float) = 86.7
Noise Avg (float) = 5.69
Noise Stdev (float) = 0.36
Noise Max (float) = 6.6
Noise Min (float) = 4.9
RawQ (float) = 3.50
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 343
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: JB001_ATH1_A2-1-Boyce-cdpk6-yfp-4-1.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 = 232 (type integer); Parameter Upper right corner x coordinate = 4502 (type integer); Parameter Upper right corner y coordinate = 243 (type integer); Parameter Lower right corner x coordinate = 4491 (type integer); Parameter Lower right corner y coordinate = 4513 (type integer); Parameter Lower left corner x coordinate = 221 (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 = 0.329057 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

growth_protocol: unknown; Parameter location = Growth Room; Parameter Humidity = 100%; Parameter Temperature = 22 C; Parameter Lighting = 16 hrs light; Parameter Medium = S; Performer: Joy,,Boyce

extract_protocol: Qiagen Plant RNAeasy kit; Protocol: Seedlings harvested and snap-frozen in liquid nitrogen and RNA extracted as described in the Qiagen RNAeasy kit. ; Protocol Type = nucleic_acid_extraction; Performer: Joy,,Boyce

value: whole seedling

tag: GeneticModification

value: cdpk6-yfp transgene

tag: StrainOrLine

value: cdpk6-yfp 4


title: JB001_ATH1_A2-2-Boyce-cdpk6-yfp-4-2

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 93.79
Background Stdev (float) = 2.02
Background Max (float) = 100.8
Background Min (float) = 90.5
Noise Avg (float) = 6.05
Noise Stdev (float) = 0.33
Noise Max (float) = 6.8
Noise Min (float) = 5.4
RawQ (float) = 3.62
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 449
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: JB001_ATH1_A2-2-Boyce-cdpk6-yfp-4-2.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 = 231 (type integer); Parameter Upper right corner x coordinate = 4502 (type integer); Parameter Upper right corner y coordinate = 226 (type integer); Parameter Lower right corner x coordinate = 4507 (type integer); Parameter Lower right corner y coordinate = 4496 (type integer); Parameter Lower left corner x coordinate = 237 (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 = 0.300583 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;


title: St.Clair_1-84_379_Mt-0_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet

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


title: St.Clair_1-79_276_Mt-0_0.02%-silwet_Rep1_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-87_370_Mt-0_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-83_323_Mt-0_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-80_308_Mt-0_0.02%-silwet_Rep2_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-88_280_Mt-0_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-90_360_Mt-0_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: JB001_ATH1_A1-2-Boyce-Kan-2

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 142.62
Background Stdev (float) = 3.00
Background Max (float) = 150.6
Background Min (float) = 135.4
Noise Avg (float) = 10.35
Noise Stdev (float) = 0.62
Noise Max (float) = 12.4
Noise Min (float) = 8.7
RawQ (float) = 4.92
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 382
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: JB001_ATH1_A1-2-Boyce-Kan-2.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 = 231 (type integer); Parameter Upper right corner x coordinate = 4502 (type integer); Parameter Upper right corner y coordinate = 230 (type integer); Parameter Lower right corner x coordinate = 4503 (type integer); Parameter Lower right corner y coordinate = 4500 (type integer); Parameter Lower left corner x coordinate = 233 (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 = 0.328673 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

value: Aequorin transgene

value: aeq+


title: St.Clair_1-73_291_Mt-0_0.02%-silwet_Rep1_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-74_320_Mt-0_0.02%-silwet_Rep2_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-75_376_Mt-0_0.02%-silwet_Rep3_ATH1

description: Treatment: 0.02% silwet


title: JB001_ATH1_A3-1-Boyce-Kan-3

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 95.64
Background Stdev (float) = 2.06
Background Max (float) = 100.9
Background Min (float) = 91.3
Noise Avg (float) = 5.95
Noise Stdev (float) = 0.36
Noise Max (float) = 6.8
Noise Min (float) = 5.2
RawQ (float) = 3.67
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 258
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: JB001_ATH1_A3-1-Boyce-Kan-3.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 = 232 (type integer); Parameter Upper right corner x coordinate = 4502 (type integer); Parameter Upper right corner y coordinate = 248 (type integer); Parameter Lower right corner x coordinate = 4487 (type integer); Parameter Lower right corner y coordinate = 4519 (type integer); Parameter Lower left corner x coordinate = 217 (type integer); Parameter Lower left corner y coordinate = 4503 (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 = 0.364884 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;


title: St.Clair_1-72_374_Kin-0_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1

description: Biological replicate 3

source_name: Kin-0, 0.30 mM SA in 0.02% silwet, 52hr

tag: ecotype

tag: treatment

value: 0.30 mM SA in 0.02% silwet

tag: time point

value: 52 hr post-treatment


title: St.Clair_1-76_283_Mt-0_0.02%-silwet_Rep1_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-89_314_Mt-0_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-81_356_Mt-0_0.02%-silwet_Rep3_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-71_315_Kin-0_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1

description: Biological replicate 2


title: St.Clair_1-77_302_Mt-0_0.02%-silwet_Rep2_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-69_369_Kin-0_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1

description: Biological replicate 3

source_name: Kin-0, 0.30 mM SA in 0.02% silwet, 28hr

value: 28 hr post-treatment


title: St.Clair_1-68_306_Kin-0_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1

description: Biological replicate 2


title: St.Clair_1-82_294_Mt-0_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-66_380_Kin-0_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1

description: Biological replicate 3

source_name: Kin-0, 0.30 mM SA in 0.02% silwet, 4hr

value: 4 hr post-treatment


title: St.Clair_1-62_309_Kin-0_0.02%-silwet_Rep2_ATH1

description: Biological replicate 2

source_name: Kin-0, 0.02% silwet, 52hr

value: 0.02% silwet


title: St.Clair_1-63_372_Kin-0_0.02%-silwet_Rep3_ATH1

description: Biological replicate 3


title: St.Clair_1-70_278_Kin-0_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1

description: Biological replicate 1


title: St.Clair_1-64_270b_Kin-0_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1

description: Biological replicate 1


title: St.Clair_1-65_322_Kin-0_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1

description: Biological replicate 2


title: St.Clair_1-61_274_Kin-0_0.02%-silwet_Rep1_ATH1

description: Biological replicate 1


title: St.Clair_1-59_303_Kin-0_0.02%-silwet_Rep2_ATH1

description: Biological replicate 2

source_name: Kin-0, 0.02% silwet, 28hr


title: JB001_ATH1_A1-1-Boyce-Kan-1

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 89.78
Background Stdev (float) = 2.06
Background Max (float) = 97.7
Background Min (float) = 86.1
Noise Avg (float) = 5.24
Noise Stdev (float) = 0.36
Noise Max (float) = 6.4
Noise Min (float) = 4.4
RawQ (float) = 3.50
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 300
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: JB001_ATH1_A1-1-Boyce-Kan-1.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 = 231 (type integer); Parameter Upper right corner x coordinate = 4502 (type integer); Parameter Upper right corner y coordinate = 228 (type integer); Parameter Lower right corner x coordinate = 4506 (type integer); Parameter Lower right corner y coordinate = 4498 (type integer); Parameter Lower left corner x coordinate = 236 (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 = 0.389437 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;


title: St.Clair_1-56_319_Kin-0_0.02%-silwet_Rep2_ATH1

description: Biological replicate 2

source_name: Kin-0, 0.02% silwet, 4hr


title: St.Clair_1-58_281_Kin-0_0.02%-silwet_Rep1_ATH1

description: Biological replicate 1


title: St.Clair_1-57_377_Kin-0_0.02%-silwet_Rep3_ATH1

description: Biological replicate 3


title: St.Clair_1-123_444_Van-0_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-124_318_Van-0_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-126_455_Van-0_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-121_330_Van-0_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-125_390_Van-0_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-55_269b_Kin-0_0.02%-silwet_Rep1_ATH1

description: Biological replicate 1


title: St.Clair_1-122_384_Van-0_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-116_387_Van-0_0.02%-silwet_Rep2_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-118_348_Van-0_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-60_365_Kin-0_0.02%-silwet_Rep3_ATH1

description: Biological replicate 3


title: St.Clair_1-120_434_Van-0_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-119_378_Van-0_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-112_327_Van-0_0.02%-silwet_Rep1_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-114_438_Van-0_0.02%-silwet_Rep3_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-110_375_Van-0_0.02%-silwet_Rep2_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-115_312_Van-0_0.02%-silwet_Rep1_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-109_347_Van-0_0.02%-silwet_Rep1_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-111_430_Van-0_0.02%-silwet_Rep3_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-108_358_Tsu-1_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-113_381_Van-0_0.02%-silwet_Rep2_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-105_352_Tsu-1_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-107_313_Tsu-1_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-102_350_Tsu-1_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-106_298_Tsu-1_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-99_354_Tsu-1_0.02%-silwet_Rep3_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-93_349_Tsu-1_0.02%-silwet_Rep3_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-100_268b_Tsu-1_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-50_329_Est_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet

source_name: Est


title: St.Clair_1-91_267b_Tsu-1_0.02%-silwet_Rep1_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-51_386_Est_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-95_301_Tsu-1_0.02%-silwet_Rep2_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-94_271_Tsu-1_0.02%-silwet_Rep1_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-98_307_Tsu-1_0.02%-silwet_Rep2_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-53_316_Est_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-96_351_Tsu-1_0.02%-silwet_Rep3_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-97_296_Tsu-1_0.02%-silwet_Rep1_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-48_397_Est_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-52_279b_Est_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-101_324_Tsu-1_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-49_288c_Est_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-103_272_Tsu-1_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-47_334_Est_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-92_321_Tsu-1_0.02%-silwet_Rep2_ATH1

description: Treatment: 0.02% silwet


title: JH003_ATH1_A14-Hammond-KS3

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 66.75
Background Stdev (float) = 1.32
Background Max (float) = 70.2
Background Min (float) = 63.1
Noise Avg (float) = 3.27
Noise Stdev (float) = 0.17
Noise Max (float) = 3.9
Noise Min (float) = 3.0
RawQ (float) = 2.48
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 544
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: JH003_ATH1_A14-Hammond-KS3.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 = 231 (type integer); Parameter Upper right corner x coordinate = 4502 (type integer); Parameter Upper right corner y coordinate = 245 (type integer); Parameter Lower right corner x coordinate = 4490 (type integer); Parameter Lower right corner y coordinate = 4515 (type integer); Parameter Lower left corner x coordinate = 218 (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 = 0.454783 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;


title: St.Clair_1-44_310_Est_0.02%-silwet_Rep2_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-45_388_Est_0.02%-silwet_Rep3_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-42_383_Est_0.02%-silwet_Rep3_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-43_275b_Est_0.02%-silwet_Rep1_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-40_285_Est_0.02%-silwet_Rep1_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-46_293_Est_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-39_394_Est_0.02%-silwet_Rep3_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-41_326b_Est_0.02%-silwet_Rep2_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-34_346_Cvi-1_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-27_449_Cvi-1_0.02%-silwet_Rep3_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-35_373_Cvi-1_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-36_454b_Cvi-1_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-25_345_Cvi-1_0.02%-silwet_Rep1_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-37_290_Est_0.02%-silwet_Rep1_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-32_367_Cvi-1_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-28_339_Cvi-1_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-26_371_Cvi-1_0.02%-silwet_Rep2_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-38_332_Est_0.02%-silwet_Rep2_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-31_343_Cvi-1_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-20_361_Cvi-1_0.02%-silwet_Rep2_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-16_277b_Col-0_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-30_433_Cvi-1_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-23_363_Cvi-1_0.02%-silwet_Rep2_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-21_429_Cvi-1_0.02%-silwet_Rep3_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-22_341_Cvi-1_0.02%-silwet_Rep1_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-14_328_Col-0_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-18_357-2_Col-0_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-15_400_Col-0_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-11_333_Col-0_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-19_336_Cvi-1_0.02%-silwet_Rep1_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-6_398_Col-0_0.02%-silwet_Rep3_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-13_287b_Col-0_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-12_407_Col-0_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-10_292b_Col-0_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-24_437_Cvi-1_0.02%-silwet_Rep3_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-9_353_Col-0_0.02%-silwet_Rep3_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-7_273b_Col-0_0.02%-silwet_Rep1_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-8_311_Col-0_0.02%-silwet_Rep2_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-2_331_Col-0_0.02%-silwet_Rep2_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-3_404_Col-0_0.02%-silwet_Rep3_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-5_325_Col-0_0.02%-silwet_Rep2_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-4_284b_Col-0_0.02%-silwet_Rep1_ATH1

description: Treatment: 0.02% silwet


title: Penfield_1-12_embryo-control_Rep3_ATH1

description:
stratification: 3 days at 4 degrees celsius
sterilisation: 100% ethanol rinse
Growth substrate type: Agar (100-200 seeds per plate)
Growth medium: Seeds were sown on MS medium, stratified for 3 days at 4 degrees celsius, then tranferred to a growth room at 22 degrees celsius under continuous white light at 80-100 umol m-2 for 24 hours

tag: Stock Code

tag: Developmental stage

tag: Tissue

value: embryo


title: Penfield_1-7_endosperm-PAC_Rep1_ATH1

description:
stratification: 3 days at 4 degrees celsius
sterilisation: 100% ethanol rinse
Growth substrate type: Agar (100-200 seeds per plate)
Growth medium: Seeds were sown on MS medium supplented with 20uM PAC(Greyhound Chromatography, Birkenhead, UK), stratified for 3 days at 4 degrees celsius, then tranferred to a growth room at 22 degrees celsius under continuous white light at 80-100 umol m-2 for 24 hours

value: endosperm


title: Penfield_1-5_endosperm-ABA_Rep2_ATH1

description:
stratification: 3 days at 4 degrees celsius
sterilisation: 100% ethanol rinse
Growth substrate type: Agar (100-200 seeds per plate)
Growth medium: Murashige and Skoog basal salt mixture
Growth protocol: Seeds were sown on MS medium supplented with 20uM ABA (mixed iosmers, sigma), stratified for 3 days at 4 degrees celsius, then tranferred to a growth room at 22 degrees celsius under continuous white light at 80-100 umol m-2 for 24 hours


title: Penfield_1-3_endosperm-control_Rep3_ATH1

description:
stratification: 3 days at 4 degrees celsius
sterilisation: 100% ethanol rinse
Location: Greenhouse
Growth substrate type: Agar (100-200 seeds per plate)
Growth medium: Murashige and Skoog basal salt mixture
Growth protocol: Seeds were sown on MS medium, stratified for 3 days at 4 degrees celsius, then tranferred to a growth room at 22 degrees celsius under continuous white light at 80-100 umol m-2 for 24 hours.


title: Penfield_1-18_embryo-PAC_Rep3_ATH1

description:
stratification: 3 days at 4 degrees celsius
sterilisation: 100% ethanol rinse
Growth substrate type: Agar (100-200 seeds per plate)
Growth medium: Seeds were sown on MS medium supplemented with 20uM paclobutrazol (Greyhound chromatography, Birkenhead, UK), stratified for 3 days at 4 degrees celsius, then tranferred to a growth room at 22 degrees celsius under continuous white light at 80-100 umol m-2 for 24 hours


title: Penfield_1-4_endosperm-ABA_Rep1_ATH1


title: JB001_ATH1_A3-2-Boyce-cdpk-yfp-1

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 91.47
Background Stdev (float) = 2.46
Background Max (float) = 99.9
Background Min (float) = 87.1
Noise Avg (float) = 5.98
Noise Stdev (float) = 0.32
Noise Max (float) = 6.8
Noise Min (float) = 5.3
RawQ (float) = 3.46
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 672
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: JB001_ATH1_A3-2-Boyce-cdpk-yfp-1.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 = 230 (type integer); Parameter Upper right corner x coordinate = 4502 (type integer); Parameter Upper right corner y coordinate = 227 (type integer); Parameter Lower right corner x coordinate = 4507 (type integer); Parameter Lower right corner y coordinate = 4497 (type integer); Parameter Lower left corner x coordinate = 237 (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 = 0.314107 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;


title: Penfield_1-13_embryo-ABA_Rep1_ATH1

description:
stratification: 3 days at 4 degrees celsius
sterilisation: 100% ethanol rinse
Growth substrate type: Agar (100-200 seeds per plate)
Growth medium: Seeds were sown on MS medium supplemented with 20uM ABA (mixed isomers, Sigma), stratified for 3 days at 4 degrees celsius, then tranferred to a growth room at 22 degrees celsius under continuous white light at 80-100 umol m-2 for 24 hours


title: St.Clair_1-1_289b_Col-0_0.02%-silwet_Rep1_ATH1

description: Treatment: 0.02% silwet


title: Penfield_1-11_embryo-control_Rep2_ATH1


title: Penfield_1-16_embryo-PAC_Rep1_ATH1


title: Penfield_1-17_embryo-PAC_Rep2_ATH1


title: Penfield_1-2_endosperm-control_Rep2_ATH1


title: Penfield_1-9_endosperm-PAC_Rep3_ATH1


title: Penfield_1-14_embryo-ABA_Rep2_ATH1


title: Penfield_1-15_embryo-ABA_Rep3_ATH1


title: Penfield_1-8_endosperm-PAC_Rep2_ATH1


title: Penfield_1-10_embryo-control_Rep1_ATH1


title: Fukuda_1-12_10B_Rep2_ATH1

description:
harvesting: collection after treatment -  10 days
growth media type: liquid culture media
nutrients: MS1  MS salts, 1 ug /ml 2,4-dichlorphenoxyacetic acid and 3% sucrose
nutrients: MS2  MS salts, 3% sucrose, 1 uM brassinolide and 10 mM H3BO3
average daily temperature: 27C

treatment_protocol: For in vitro tracheary element (xylem vessel element) transdifferentiation, a 7.5 ml aliquot of 7-day-old subcultured cells was transferred into 42.5 ml of fresh medium that included 1 uM brassinolide and 10 mM H3BO3. Cells were collected by centrigugation after 10 days of culture.

value: Col-0 suspension cells


title: Murray_3-4_D7-GROWTH_Rep1_ATH1

description:
growth media type: liquid culture media
light regime: continuous darkness
MSS medium: 100 ml MS salts, 3% sucrose, 0.5 mg/l NAA, 0.05 mg/l kinetin
average daily temperature: 27C

treatment_protocol: An aliquot of 5 ml of an early stationary phase MM2d cell suspension (7 days after previous subculture) was inoculated into 100 ml fresh MSS-medium (MS-salt, 3% sucrose, 0.5mg/l NAA, 0.05mg/l kinetin). Cells were incubated under continuous darkness by rotating at 130 rpm at a temperature of 27C and samples were taken every two days for analysis. The D7 sample was taken at day 7 after subculture into fresh medium (exp. variable; time course).

value: 7 days after subculture to fresh media

value: cell suspension


title: Fukuda_1-11_10A_Rep1_ATH1


title: Fukuda_1-10_8B_Rep2_ATH1

description:
harvesting: collection after treatment -  8 days
growth media type: liquid culture media
nutrients: MS1  MS salts, 1 ug /ml 2,4-dichlorphenoxyacetic acid and 3% sucrose
nutrients: MS2  MS salts, 3% sucrose, 1 uM brassinolide and 10 mM H3BO3
average daily temperature: 22C

treatment_protocol: For in vitro tracheary element (xylem vessel element) transdifferentiation, a 7.5 ml aliquot of 7-day-old subcultured cells was transferred into 42.5 ml of fresh medium that included 1 uM brassinolide and 10 mM H3BO3. Cells were collected by centrigugation after 8 days of culture.


title: Fukuda_1-8_6B_Rep2_ATH1

description:
harvesting: collection after treatment -  6 days
growth media type: liquid culture media
nutrients: MS1  MS salts, 1 ug /ml 2,4-dichlorphenoxyacetic acid and 3% sucrose
nutrients: MS2  MS salts, 3% sucrose, 1 uM brassinolide and 10 mM H3BO3
average daily temperature: 27C

treatment_protocol: For in vitro tracheary element (xylem vessel element) transdifferentiation, a 7.5 ml aliquot of 7-day-old subcultured cells was transferred into 42.5 ml of fresh medium that included 1 uM brassinolide and 10 mM H3BO3. Cells were collected by centrigugation after 6 days of culture.


title: Murray_3-1_D1-GROWTH_Rep1_ATH1

treatment_protocol: An aliquot of 5 ml of an early stationary phase MM2d cell suspension (7 days after previous subculture) was inoculated into 100 ml fresh MSS-medium (MS-salt, 3% sucrose, 0.5mg/l NAA, 0.05mg/l kinetin). Cells were incubated under continuous darkness by rotating at 130 rpm at a temperature of 27C and samples were taken every two days for analysis. The D1 sample was taken at day 1 after subculture into fresh medium (exp. Variable; time course).

value: 1 day after subculture to fresh media


title: Murray_3-2_D3-GROWTH_Rep1_ATH1

treatment_protocol: An aliquot of 5 ml of an early stationary phase MM2d cell suspension (7 days after previous subculture) was inoculated into 100 ml fresh MSS-medium (MS-salt, 3% sucrose, 0.5mg/l NAA, 0.05mg/l kinetin). Cells were incubated under continuous darkness by rotating at 130 rpm at a temperature of 27C and samples were taken every two days for analysis. The D3 sample was taken at day 3 after subculture into fresh medium (exp. variable; time course).

value: 3 days after subculture to fresh media


title: Penfield_1-1_endosperm-control_Rep1_ATH1


title: Murray_3-3_D5-GROWTH_Rep1_ATH1

treatment_protocol: An aliquot of 5 ml of an early stationary phase MM2d cell suspension (7 days after previous subculture) was inoculated into 100 ml fresh MSS-medium (MS-salt, 3% sucrose, 0.5mg/l NAA, 0.05mg/l kinetin). Cells were incubated under continuous darkness by rotating at 130 rpm at a temperature of 27C and samples were taken every two days for analysis. The D5 sample was taken at day 5 after subculture into fresh medium (exp. variable; time course).

value: 5 days after subculture to fresh media


title: Penfield_1-6_endosperm-ABA_Rep3_ATH1


title: Fukuda_1-9_8A_Rep1_ATH1


title: Fukuda_1-7_6A_Rep1_ATH1


title: Weigel_2-34_CHIP-214-A_Rep1_ATH1

description:
germplasm: flc-3
light regime1: short day
light regime2: long day
growth media type: soil
average daily humidity:
average daily temperature: 23C

treatment_protocol: LD 7 days

value: transition to flowering, 10-18 leaves

value: apical region

tag: Genetic variation

value: fast neutron flc allele in Col-0 background, early flowering


title: Fukuda_1-3_2A_Rep1_ATH1

description:
harvesting: collection after treatment -  2 days
growth media type: liquid culture media
nutrients: MS1  MS salts, 1 ug /ml 2,4-dichlorphenoxyacetic acid and 3% sucrose
nutrients: MS2  MS salts, 3% sucrose, 1 uM brassinolide and 10 mM H3BO3
average daily temperature: 27C

treatment_protocol: For in vitro tracheary element (xylem vessel element) transdifferentiation, a 7.5 ml aliquot of 7-day-old subcultured cells was transferred into 42.5 ml of fresh medium that included 1 uM brassinolide and 10 mM H3BO3. Cells were collected by centrigugation after 2 days of culture.


title: Fukuda_1-6_4B_Rep2_ATH1

description:
harvesting: collection after treatment -  4 days
growth media type: liquid culture media
nutrients: MS1  MS salts, 1 ug /ml 2,4-dichlorphenoxyacetic acid and 3% sucrose
nutrients: MS2  MS salts, 3% sucrose, 1 uM brassinolide and 10 mM H3BO3
average daily temperature: 22C

treatment_protocol: For in vitro tracheary element (xylem vessel element) transdifferentiation, a 7.5 ml aliquot of 7-day-old subcultured cells was transferred into 42.5 ml of fresh medium that included 1 uM brassinolide and 10 mM H3BO3. Cells were collected by centrigugation after 4 days of culture.


title: Weigel_2-35_CHIP-214-B_Rep2_ATH1

value: vegetative plant, 10-18 leaves


title: Fukuda_1-4_2B_Rep2_ATH1


title: Weigel_2-32_CHIP-213-B_Rep2_ATH1

treatment_protocol: LD 5 days


title: Weigel_2-26_CHIP-211-B_Rep2_ATH1

treatment_protocol: LD 0 days


title: Weigel_2-22_CHIP-210-A_Rep1_ATH1

description:
germplasm: flc-3 in FRI-Sf-2 in Col
light regime1: short day
light regime2: long day
growth media type: soil
average daily humidity:
average daily temperature: 23C

source_name: FLC-3 IN FRI-SF-2 IN COL

value: fast neutron flc allele in FRI-Sf-2 in Col-0 background, early flowering


title: Weigel_2-27_CHIP-211-C_Rep3_ATH1


title: Weigel_2-25_CHIP-211-A_Rep1_ATH1


title: Weigel_2-20_CHIP-209-B_Rep2_ATH1


title: Weigel_2-30_CHIP-212-C_Rep3_ATH1

treatment_protocol: LD 3 days


title: Weigel_2-17_CHIP-208-B_Rep2_ATH1


title: Weigel_2-29_CHIP-212-B_Rep2_ATH1


title: Weigel_2-28_CHIP-212-A_Rep1_ATH1


title: Weigel_2-18_CHIP-208-C_Rep3_ATH1


title: Fukuda_1-2_0B_Rep2_ATH1

description:
harvesting: collection after treatment -  0 days
growth media type: liquid culture media
nutrients: MS1  MS salts, 1 ug /ml 2,4-dichlorphenoxyacetic acid and 3% sucrose
nutrients: MS2  MS salts, 3% sucrose, 1 uM brassinolide and 10 mM H3BO3
average daily temperature: 22C

treatment_protocol: no treatment


title: Weigel_2-31_CHIP-213-A_Rep1_ATH1


title: Weigel_2-16_CHIP-208-A_Rep1_ATH1


title: Weigel_2-23_CHIP-210-B_Rep2_ATH1


title: Weigel_2-36_CHIP-214_D_Rep3_ATH1


title: Weigel_2-13_CHIP-207-A_Rep1_ATH1


title: Weigel_2-24_CHIP-210-C_Rep3_ATH1


title: Weigel_2-14_CHIP-207-B_Rep2_ATH1


title: Weigel_2-19_CHIP-209-A_Rep1_ATH1


title: Weigel_2-21_CHIP-209-C_Rep3_ATH1


title: Weigel_2-12_CHIP-206-C_Rep3_ATH1

description:
germplasm: FRI-Sf-2 in Col
light regime1: short day
light regime2: long day
growth media type: soil
average daily humidity:
average daily temperature: 23C

source_name: FRI-Sf-2 in Col


title: Weigel_2-15_CHIP-207-C_Rep3_ATH1


title: Weigel_2-11_CHIP-206-B_Rep2_ATH1


title: Fukuda_1-5_4A_Rep1_ATH1


title: Weigel_2-7_CHIP-205-A_Rep1_ATH1


title: Weigel_2-4_CHIP-204-A_Rep1_ATH1


title: Weigel_2-3_CHIP-203-C_Rep3_ATH1


title: Weigel_2-2_CHIP-203-B_Rep2_ATH1


title: Weigel_2-6_CHIP-204-C_Rep3_ATH1


title: Yang_1-8_CPR5NPR1-2_Rep2_ATH1

description:
average daily humidity: 70%
light source: fluorescent
photoperiod: 16 hr
average daily temperature: 23 C

value: 2 weeks old

value: aerial parts of plant

value: double mutant completely resistant to P. parasitica


title: Yang_1-9_CPR5SCV1-1_Rep1_ATH1

value: Suppressor of cprV double mutant has wild-type susceptibility to P. parasitica, slightly enhanced susceptibility to P. syringae and resistance to B. cinerea.


title: Yang_1-7_CPR5NPR1-1_Rep1_ATH1


title: Weigel_2-5_CHIP-204-B_Rep2_ATH1


title: Yang_1-1_WT(COL)-1_Rep1_ATH1


title: Weigel_2-10_CHIP-206-A_Rep1_ATH1


title: Yang_1-10_CPR5SCV1-2_Rep2_ATH1


title: Yang_1-2_WT(COL)-2_Rep2_ATH1


title: Schroeder_1-3_JS45-control-48h_Rep1_ATH1

description:
nutrients: media with potassium (48 hours)
growth media type: hydroponics  (4-5 weeks)
humidity: average daily humidity  (70%) 4-5 weeks
light source: fluorescent  (4-5 weeks)
photoperiod: 16 hr  (4-5 weeks)
average daily temperature: 22C  (4-5 weeks)

treatment_protocol: Plants were transferred from control to control nutrient solution (1.0 mM Ca(NO3)2, 0.5 mM KH2PO4, 1.25 mM KNO3, 0.5 mM MgSO4, 20 uM FeNaEDTA, 0.5 uM CuSO4, 0.5 uM MnSO4, 10 uM H3BO3, 0.05 uM Na2MoO4, 0.25 uM NaCl, 0.5 uM ZnSO4) (exp. Variable) for 48 hours (exp. Variable)

value: Mix of roots from 4 to 5 week-old plants

value: root


title: Yang_1-4_CPR5-2_Rep2_ATH1


title: Yang_1-3_CPR5-1_Rep1_ATH1


title: Weigel_2-8_CHIP-205-B_Rep2_ATH1


title: Schroeder_1-6_JS43-control-96h_Rep1_ATH1

description:
nutrients: media with potassium (96 hours)
growth media type: hydroponics  (4-5 weeks)
humidity: average daily humidity  (70%) 4-5 weeks
light source: fluorescent  (4-5 weeks)
photoperiod: 16 hr  (4-5 weeks)
average daily temperature: 22C  (4-5 weeks)

treatment_protocol: Plants were transferred from control to control nutrient solution (1.0 mM Ca(NO3)2, 0.5 mM KH2PO4, 1.25 mM KNO3, 0.5 mM MgSO4, 20 uM FeNaEDTA, 0.5 uM CuSO4, 0.5 uM MnSO4, 10 uM H3BO3, 0.05 uM Na2MoO4, 0.25 uM NaCl, 0.5 uM ZnSO4) (exp. variable) for 96 hours (exp. variable)


title: Schroeder_1-12_JS44-starve-96h_Rep1_ATH1

description:
nutrients: media without potassium (96 hours)
growth media type: hydroponics  (4-5 weeks)
humidity: average daily humidity  (70%) 4-5 weeks
light source: fluorescent  (4-5 weeks)
photoperiod: 16 hr  (4-5 weeks)
average daily temperature: 22C  (4-5 weeks)

treatment_protocol: Plants were transferred from control to potassium free nutrient solution (1.0 mM Ca(NO3)2, 0.5 mM H3PO4, 1.25 mM HNO3, 0.5 mM MgSO4, 20 uM FeNaEDTA, 0.5 uM CuSO4, 0.5 uM MnSO4, 10 uM H3BO3, 0.05 uM Na2MoO4, 0.25 uM NaCl, 0.5 uM ZnSO4) (exp. Variable) for 96 hours (exp. variable)


title: Weigel_2-1_CHIP-203-A_Rep1_ATH1


title: Yang_1-5_NPR1-1_Rep1_ATH1


title: Schroeder_1-9_JS46-starve-48h_Rep1_ATH1

description:
nutrients: media without potassium (48 hours)
growth media type: hydroponics  (4-5 weeks)
humidity: average daily humidity  (70%) 4-5 weeks
light source: fluorescent  (4-5 weeks)
photoperiod: 16 hr  (4-5 weeks)
average daily temperature: 22C  (4-5 weeks)

treatment_protocol: Plants were transferred from control to potassium free nutrient solution (1.0 mM Ca(NO3)2, 0.5 mM H3PO4, 1.25 mM HNO3, 0.5 mM MgSO4, 20 uM FeNaEDTA, 0.5 uM CuSO4, 0.5 uM MnSO4, 10 uM H3BO3, 0.05 uM Na2MoO4, 0.25 uM NaCl, 0.5 uM ZnSO4) (exp. variable) for 48 hours (exp. variable)


title: Raghavan_1-2_1MM-1HR-A_Rep1_ATH1

description:
Sample: hormone - 2,4-D, 1 mM ,  duration: 1 hour
growth media substrate: phytagel  -  1 %  for 14 days
light regime:  darkness  - 48 hours
photoperiod:  16 hr  - 14 day
nutrients:  MS medium  for 14 days
sugar :  sucrose, 1.5 %, 14 days
average daily temperature:  14 days
temperature: 4 C  for 48 hours

treatment_protocol: The chemical 2,4-D was dissolved in water and the pH was adjusted to 7.0. Plates were flooded with 1 mL of stock solutions of 2,4-D.

value: At this stage the plants had developed four rosette leaves 1.04

value: whole plant


title: Yang_1-11_CPR5NPR1SVI1-1_Rep1_ATH1

value: triple mutant


title: Zarka_4-3_MT-P15-15A_Rep1_ATH1

description:
:
growth media substrate: phytagar (0.80%)
light intensity: 100 umol m-2 s-1
light regime: continuous light
light source: fluorescence
nutrients: Gamborg's B5 salts 1X
stratification: cold (4oC)  for 4 days
average daily temperature: 24C  (10 days)
vitamins: Gamborg's B5 salts  1X

treatment_protocol: Four plates, each containing approximately 100 35S::ZAT12 (p15-8) plants, were individually harvested after 10 d of growth.

value: 10 day old

value: zat12 overexpressor under 35S promoter


title: Yang_1-6_NPR1-2_Rep2_ATH1


title: Zarka_4-2_MT-WTB(ZAT12)_Rep2_ATH1

treatment_protocol: Four plates, each containing approximately 100 wild type plants, were indidually harvested after 10 d of growth.


title: Newbury_1-21_Petraea-control-leaves(PLO)_Rep3_ATH1

description:
location: Growth Room
Atmosphere: Normal
Humidity: 80
Temperature: 25
Lighting: 10hrs
Medium: Full mineral medium
Water: weekly

organism: Arabidopsis lyrata subsp. petraea

source_name: petraea

value: 10-16 rosette leaves

value: Rosette leaves


title: Cain_1-4_CDB1-Knockout_Rep2_ATH1

description:
location: Growth Room
Humidity: 80%
Lighting: 16h days, standard brightness
Temperature: 20 degC
Medium: 1/2 MS10 media

value: Whole seedlings

tag: Genetic background

value: Complete knockout


title: Beynon_1-8-cat-ReferenceMix_Rep1_ATH1

description:
location: Agar plates
Atmosphere: Normal
Lighting: 16hr photoperiod
Harvest: harvests at mid-day, 6hr into day period

treatment_protocol: Reference Spike Mix

value: 1.04-4_rosette_leaves> 1mm

value: whole shoot


title: Zarka_4-4_MT-P15-8B_Rep2_ATH1


title: Beynon_1-7-cat-SpikeMix7_Rep1_ATH1

treatment_protocol: Spike Mix 7


title: Newbury_1-12_Halleri-highZn-leaves(HLH)_Rep3_ATH1

organism: Arabidopsis halleri

source_name: halleri

treatment_protocol: 25um Zinc


title: Newbury_1-9_Halleri-control-leaves(HLO)_Rep3_ATH1


title: Cain_1-2_WT1_Rep2_ATH1


title: Newbury_1-17_Petraea-highZn-roots(PRH)_Rep2_ATH1

value: whole root system


title: Beynon_1-4-cat-SpikeMix4_Rep1_ATH1

treatment_protocol: Spike Mix 4


title: Newbury_1-6_Halleri-highZn-roots(HRH)_Rep3_ATH1


title: Cain_1-3_CDB1-Knockout_Rep1_ATH1


title: Beynon_1-1-cat-SpikeMix1_Rep1_ATH1

treatment_protocol: Spike Mix 1


title: Beynon_1-2-cat-SpikeMix2_Rep1_ATH1

treatment_protocol: Spike Mix 2


title: Newbury_1-24_Petraea-highZn-leaves(PLH)_Rep3_ATH1


title: Newbury_1-23_Petraea-highZn-leaves(PLH)_Rep2_ATH1


title: Beynon_1-5-cat-SpikeMix5_Rep1_ATH1

treatment_protocol: Spike Mix 5


title: Newbury_1-14_Petraea-control-roots(PRO)_Rep2_ATH1


title: Newbury_1-8_Halleri-control-leaves(HLO)_Rep2_ATH1


title: Newbury_1-20_Petraea-control-leaves(PLO)_Rep2_ATH1


title: Newbury_1-15_Petraea-control-roots(PRO)_Rep3_ATH1


title: Zarka_4-1_MT-WTA(ZAT12)_Rep1_ATH1


title: Newbury_1-11_Halleri-highZn-leavesHLH)_Rep2_ATH1


title: Beynon_1-6-cat-SpikeMix6_Rep1_ATH1

treatment_protocol: Spike Mix 6


title: Beynon_1-3-cat-SpikeMix3_Rep1_ATH1

treatment_protocol: Spike Mix 3


title: Newbury_1-5_Halleri-highZn-roots(HRH)_Rep2_ATH1


title: Cain_1-1_WT1_Rep1_ATH1


title: Newbury_1-22_Petraea-highZn-leaves(PLH)_Rep1_ATH1


title: Newbury_1-2_halleri-control-roots(HRO)_Rep2_ATH1


title: Newbury_1-16_Petraea-highZn-roots(PRH)_Rep1_ATH1


title: Yang_1-12_CPR5NPR1SVI1-2_Rep2_ATH1

value: 2 weeks old

value: aerial parts of plant


title: Newbury_1-1_halleri-control-roots(HRO)_Rep1_ATH1

description:
location: Growth Room
Humidity: 80
Temperature: 25
Lighting: 10hrs
Medium: Full mineral medium
Water: weekly


title: Walters_A-06-Kruger-WH3_REP3

value: unshaded mature rosette leaves


title: Walters_A-10-Kruger-MH1_REP1

value: T-DNA insert


title: Newbury_1-18_Petraea-highZn-roots(PRH)_Rep3_ATH1


title: Walters_A-12-Kruger-MH3_REP3


title: Newbury_1-19_Petraea-control-leaves(PLO)_Rep1_ATH1


title: Walters_A-07-Kruger-ML1_REP1


title: Newbury_1-4_Halleri-highZn-roots(HRH)_Rep1_ATH1


title: Walters_A-04-Kruger-WH1_REP1


title: Newbury_1-10_Halleri-highZn-leaves(HLH)_Rep1_ATH1


title: Newbury_1-3_Halleri-control-roots(HRO)_Rep1_ATH1


title: Walters_A-05-Kruger-WH2_REP2


title: Walters_A-03-Kruger-WL3_REP3


title: Walters_A-08-Kruger-ML2_REP2


title: Walters_A-09-Kruger-ML3_REP3


title: Walters_A-02-Kruger-WL2_REP2


title: Yang_1-6_old-pod_Rep3_ATH1

description:
Light: 24 hour light
Medium: compost: Levington M3
Temperature: 19oC
Location: Glasshouse

value: mature and senescing siliques


title: Walters_A-11-Kruger-MH2_REP2


title: Yang_1-2_old-pod_Rep1_ATH1


title: Yang_1-4_old-pod_Rep2_ATH1


title: Yang_1-1_young-pod_Rep1_ATH1


title: Yang_1-3_young-pod_Rep2_ATH1


title: Yang_1-5_young-pod_Rep3_ATH1


title: Walters_A-01-Kruger-WL1_REP1


title: Diamond_A-4-Diamo-met_SLD

description:
Location: Cell Culture Incubator
Atmosphere: Normal
Humidity:
Temperature: 24C
Medium: Murashige and Skoog
Treatment: NAA, Kinetin
Nutrients: Sucrose

source_name: Ler

value: Cell culture


title: Diamond_A-3-Diamo-met_SLD


title: Diamond_A-3-Diamo-fum_SLD


title: Werner_1-5_wildtype-2hr-zearalenone(c2t)_Rep1_ATH1

description:
location: Growth Room
Humidity: 50%
Temperature: 22°C
Lighting: 16h light/8h dark
Medium: Murashige and Skoog
Treatment: zearalenone
Nutrients: 2.5% sucrose
Water: liquid medium
Stratification: 48h

value: 15 DAG seedlings


title: Diamond_A-1-Diamo-met_SLD


title: Diamond_A-4-Diamo-fum_SLD


title: Werner_1-8_mutant-24hr-zearalenone(j4t)_Rep1_ATH1

source_name: zorro

value: Columbia JE100

value: EMS mutant


title: Diamond_A-1-Diamo-fum_SLD


title: Diamond_A-2-Diamo-met_SLD


title: Werner_1-6_wildtype-24hr-zearalenone(c4t)_Rep1_ATH1


title: Werner_1-4_mutant-24hr-control(j4s)_Rep1_ATH1

description:
location: Growth Room
Humidity: 50%
Temperature: 22°C
Lighting: 16h light/8h dark
Medium: Murashige and Skoog
Treatment:
Nutrients: 2.5% sucrose
Water: liquid medium
Stratification: 48h


title: Werner_1-1_wildtype-2hr-control(c2s)_Rep1_ATH1

description:
location: Growth Room
Humidity: 50%
Temperature: 22°C
Lighting: 16h light/8h dark
Medium: Murashige and Skoog
Nutrients: 2.5% sucrose
Water: liquid medium
Stratification: 48h


title: Werner_1-3_mutant-2hr-control(j2s)_Rep1_ATH1


title: Werner_1-7_mutant-2hr-zearalenone(j2t)_Rep1_ATH1


title: Bird_1-6_low-light-highCO2_Rep1_ATH1

description:
location: Growth Room
Atmosphere: Elevated carbon dioxide
Humidity: 50-60%
Temperature: 21 degrees C
Lighting: 10 hrs light 14 hrs dark
Medium: Compost
Treatment: Intercept insecticide
Nutrients: None
Water: 2-3 days as needed
Stratification: 4 degrees C for 3 days

value: Centre of rosette up to leaf 11


title: Bird_1-3_low-light-ambientCO2_Rep1_ATH1

description:
location: Growth Room
Atmosphere: Normal
Humidity: 50-60%
Temperature: 21 degrees C
Lighting: 10 hrs light 14 hrs dark
Medium: Compost
Treatment: Intercept insecticide
Nutrients: None
Water: 2-3 days as needed
Stratification: 4 degrees C for 3 days


title: Bird_1-2_medium-light-ambientCO2_Rep1_ATH1


title: Bird_1-4_high-light-highCO2_Rep1_ATH1


title: Diamond_A-2-Diamo-fum_SLD


title: Bird_1-1_high-light-ambientCO2_Rep1_ATH1


title: Bird_1-5_medium-light-highCO2_Rep1_ATH1


title: Werner_1-2_wildtype-24hr-control(c4s)_Rep1_ATH1


title: Brueggemann_A-6-Brueg-Pps_SLD

description:
location: Growth Room
Atmosphere: Normal
Humidity: 70%
Temperature: 21degreeC (day) 16degreeC (night)
Lighting: 12 hr light: 12 hr dark
Medium: Compost
Nutrients: none
Water: top watering as needed	 1-2 times a week
Stratification: no

treatment_protocol:
"Peronospora parasitica on susceptible host" TREATMENT:
rpp7 Plants (susceptible host) were sprayed with Peronospora parasitica Hiks-1 spores (2*10e4 spores per ml or above) until run-off.
After spraying, plants were coverd with propagator lids and transferred to an 18 degree C (day and night) growth room for 3 days before sampling (sampling done 6 hours into the light period)

value: 3.90:Rosette Growth Complete

value: whole above ground rosettes


title: Brueggemann_A-3-Brueg-vis_SLD

description:
location: Growth Room
Atmosphere: Normal
Humidity: 70%
Temperature: 21?C (day) 16?C (night)
Lighting: 12 hr light: 12 hr dark
Medium: Compost
Nutrients: none
Water: top watering as needed	 1-2 times a week
Stratification: no

treatment_protocol:
Visible Light Only TREATMENT: Background photosynthetically active radiation (400nm-700nm): 20 micromol m-2 s-1
Duration: 1.5 photoperiods (samples taken 6 hours into the second day of treatment with supplementary UV-B)


title: Brueggemann_A-5-Brueg-Mck_SLD

treatment_protocol: "Mock" TREATMENT:Plants were sprayed with H2O as a mock treatment.After spraying, plants were coverd with propagator lids and transferred to an 18 degree C (day and night) growth room for 3 days before sampling (sampling done 6 hours into the light period)


title: Brueggemann_A-4-Brueg-PpH_SLD

treatment_protocol: "Peronospora parasitica on resistant plant" TREATMENT: Col-5 plants (resistant host) sprayed with P. parasitica Hiks-1 spores (2*10e4 spores per ml or above) until run-off. After spraying, plants were coverd with propagator lids and transferred to an 18 degree C (day and night) growth room for 3 days before sampling (sampling done 6 hours into the light period)


title: Brueggemann_A-2-Brueg-uva_SLD

treatment_protocol:
UV-A TREATMENT: UV-A source: Philips TL12 40W tubes covered with 1 layer (0.1mm) of "Mylar D"
UV-A fluence rate (320nm-400): 3.7 micromol m-2 s-1
Background photosynthetically active radiation (400nm-700nm): 20 micromol m-2 s-1
Duration: 1.5 photoperiods (samples taken 6 hours into the second day of treatment with supplementary UV-B)


title: Lindsey_1-25_torpedo-meristem_Rep1_ATH1

description:
location: Growth Room
Atmosphere: Normal
Humidity: ca. 30%
Lighting: 16 hour day
Nutrients: Compost
Water: watering every other day

value: torpedo embryo, meristem tissue


title: Lindsey_1-26_torpedo-meristem_Rep2_ATH1


title: Lindsey_1-1_globular-apical_Rep1_ATH1

description:
location: Growth Room
Atmosphere: Normal
Humidity: 50%
Temperature: 23oC
Lighting: 16h day 8h night
Medium: compost
Water: every 2 days
Stratification: 4oC 72hrs dark

value: globular embryo, apical tissue


title: Lindsey_1-4_globular-basal_Rep1_ATH1

value: globular embryo, basal tissue


title: Lindsey_1-24_torpedo-apical_Rep6_ATH1

value: torpedo embryo, apical tissue


title: Lindsey_1-6_globular-basal_Rep3_ATH1


title: Brueggemann_A-1-Brueg-uvb_SLD

treatment_protocol:
UV-B TREATMENT: UV-B source: Philips TL12 40W tubes covered with 1 layer (0.12mm) of "Diacel" cellulose diacetate UV-B fluence rate (280nm-320nm): 4.5 micromol m-2 s-1
Background photosynthetically active radiation (400nm-700nm): 20 micromol m-2 s-1
Duration: 1.5 photoperiods (samples taken 6 hours into the second day of treatment with supplementary UV-B)


title: Lindsey_1-3_globular-apical_Rep3_ATH1


title: Lindsey_1-2_globular-apical_Rep2_ATH1


title: Lindsey_1-5_globular-basal_Rep2_ATH1


title: Lindsey_1-27_torpedo-meristem_Rep3_ATH1


title: Lindsey_1-22_torpedo-apical_Rep4_ATH1


title: Lindsey_1-23_torpedo-apical_Rep5_ATH1


title: Lindsey_1-21_torpedo-basal_Rep6_ATH1

value: torpedo embryo, basal tissue


title: Lindsey_1-17_torpedo-cotyledon_Rep3_ATH1

value: embryo cotyledon


title: Lindsey_1-18_torpedo-root_Rep3_ATH1

value: embryo root


title: Lindsey_1-15_torpedo-cotyledon_Rep2_ATH1


title: Lindsey_1-19_torpedo-basal_Rep4_ATH1


title: Lindsey_1-14_torpedo-root_Rep1_ATH1


title: Lindsey_1-16_torpedo-root_Rep2_ATH1


title: Lindsey_1-20_torpedo-basal_Rep5_ATH1


title: Newbury_1-7_Halleri-control-leaves(HLO)_Rep1_ATH1

value: 10-16 rosette leaves

value: Rosette leaves


title: Lindsey_1-9_heart-stage-cotyledon_Rep3_ATH1

value: heart stage embryo, cotyledon pole


title: Shirras_1-5_Calcicole_Rep3_ATH1

description:
location: Growth Room
Atmosphere: Normal
Humidity: 34
Temperature: 23
Lighting: 160 mM/m2/s
Medium: sand
Treatment: 1 mM CaCl2
Nutrients: 0.5 X Long Ashton
Water: Daily
Stratification: 48 hrs 4oC

value: Whole plant


title: Lindsey_1-11_heart-stage-root_Rep2_ATH1

value: heart stage embryo, root pole


title: Lindsey_1-8_heart-stage-cotyledon_Rep2_ATH1


title: Shirras_1-4_Non-Calcicole_Rep2_ATH1


title: Lindsey_1-10_heart-stage-root_Rep1_ATH1


title: Turner_A-1-Turne-Mut-Top1_SLD

description:
location: Growth Room
Atmosphere: Normal
Humidity: 65%
Temperature: 22 degrees
Lighting: 24 hour
Medium: compost
Treatment: Intercept insecticide
Nutrients: none supplied
Water: every 3-4 days
Stratification:

source_name: cov

value: inflorescence stem tip


title: Turner_A-4-Turne-Mut-Base2_SLD

value: inflorescence stem base


title: Shirras_1-1_Calcicole_Rep1_ATH1


title: Lindsey_1-12_heart-stage-root_Rep3_ATH1


title: Turner_A-5-Turne-WT-Top1_SLD


title: Turner_A-2-Turne-Mut-Top2_SLD


title: Newbury_1-13_Petraea-control-roots(PRO)_Rep1_ATH1

description:
location: Growth Room
Atmosphere: Normal
Humidity: 80
Temperature: 25
Lighting: 10hrs
Medium: Full mineral medium
Water: weekly

value: whole root system


title: Turner_A-8-Turne-WT-Base2_SLD


title: Shirras_1-7_Non-Calcicole_Rep3_ATH1


title: Buchanan-Wollaston_A-10-bwoll-Co2_SLD

description:
location: Growth Room
Atmosphere: Normal
Humidity: not controlled
Temperature: 18
Lighting: 12h day
Medium: compost
Treatment: none
Nutrients: none
Water: as needed
Stratification:

value: fully expanded leaves

value: Columbia

value: Coi1 transgenic


title: Turner_A-3-Turne-Mut-Base1_SLD


title: Shirras_1-3_Non-Calcicole_Rep1_ATH1


title: Lindsey_1-7_heart-stage-cotyledon_Rep1_ATH1


title: Turner_A-7-Turne-WT-Base1_SLD


title: Buchanan-Wollaston_A-7-bwoll-Ei1_SLD

value: Ein2 transgenic


title: Buchanan-Wollaston_A-8-bwoll-Ei2_SLD


title: Shirras_1-8_Non-Calcicole_Rep4_ATH1


title: Buchanan-Wollaston_A-6-bwoll-NG2_SLD

source_name: NahG

value: NahG transgenic


title: Lindsey_1-13_torpedo-cotyledon_Rep1_ATH1


title: Turner_A-6-Turne-WT-Top2_SLD


title: Shirras_1-2_Calcicole_Rep2_ATH1


title: Buchanan-Wollaston_A-1-bwoll-C0G_SLD


title: Buchanan-Wollaston_A-3-bwoll-C0S_SLD


title: Buchanan-Wollaston_A-4-bwoll-C5S_SLD


title: Buchanan-Wollaston_A-2-bwoll-C5G_SLD


title: Shirras_1-6_Calcicole_Rep4_ATH1


title: Buchanan-Wollaston_A-5-bwoll-NG1_SLD


title: McCormac_1-2_wildtype-Contrl_Rep1_ATH1

description:
location: Growth Room
Humidity: in sealed petri dish therefore 80%
Temperature: 23oC
Lighting: 3d growth in darkness followed by 3d continuous white light
Medium: Murashige and Skoog basal salts solidified with agar
Treatment: control
Nutrients: 1.5 w/v sucrose
Stratification: no (seeds were vernalised prior to germination)

treatment_protocol: WT seedlings which had not been treated with Norflurazon and therefore are the control sample.

value: whole young seedlings in entirety with cotyledons, hypocotyl and primary roots - (no emerged true leaves).


title: Urwin_A-2-Urwin-Inf_SLD

description:
location: Sanyo MLR3500 growth cabinet
Atmosphere: Normal
Humidity: Ambient
Temperature: 20.5
Lighting: 16:8 light:dark
Medium: ½MS10 media	 0.2 % phytagel
Treatment: n/a
Nutrients: ½MS10 media
Water: n/a
Stratification: on moist filter paper @ 4 oC for 3 days

treatment_protocol: At 21 days germination (Growth Stage 3.4/3.5) Arabidopsis plants were challenged with rigorously sterilised,infective nematodes of H. schachtii as before (Urwin et al., (1997) Plant Journal 12: 455-461). 35 sterile J2s were pipetted onto small ~0.5 mm2 squares of sterile GF/A filter paper. The GF/A paper was left in direct contact with the zone of elongation on 3 lateral roots per plant for 48 hours. Sections of root containing syncytia have been excised from the thin and transparent roots of Arabidopsis and collected into RNAlater solution (Ambion) at 21 days post infection (Growth Stage 6.1). The female nematode has been removed.

value: lateral roots


title: McCormac_1-1_wildtype-NFtreated_Rep1_ATH1

description:
location: Growth Room
Humidity: in sealed petri dish therefore 80%
Temperature: 23oC
Lighting: 3d growth in darkness followed by 3d continuous white light
Medium: Murashige and Skoog basal salts solidified with agar
Treatment: the herbicide Norflurazon was included in the medium at 5 microMolar
Nutrients: 1.5 w/v sucrose
Stratification: no (seeds were vernalised prior to germination)

treatment_protocol: WT seedlings treated with the herbicide Norflurazon.


title: McCormac_1-3_mutant-NFtreated_Rep1_ATH1

description:
location: Growth Room
Humidity: in sealed petri dish therefore 80%
Temperature: 23oC
Lighting: 3d growth in darkness followed by 3d continuous white light
Medium: Murashige and Skoog basal salts solidified with agar
Treatment: growth medium supplemented with 5 micromolar Norflurazon
Nutrients: 1.5 w/v sucrose
Stratification: no (seeds were vernalised prior to germination)

source_name: gun1,gun5 double mutant

treatment_protocol: Seedlings of a double mutant line gun1,gun5 which had been treated with Norflurazon.


title: Villadsen_A-6-villa-man_SLD

description:
location: Growth Room
Atmosphere: Normal
Humidity: -
Temperature: 23 C
Lighting: continuous light
Medium: 1/2 x MS	 0.8% agar
Treatment: none
Nutrients: none
Water: none
Stratification: 72 h at 4C

value: the entire seedlings


title: McCormac_1-5_wildtype-Contrl_Rep2_ATH1

description:
location: Growth Room
Atmosphere: Normal
Humidity: in sealed petri dish therefore 80%
Temperature: 23oC
Lighting: 3d growth in darkness followed by 3d continuous white light
Medium: Murashige and Skoog basal salts solidified with agar
Treatment: control
Nutrients: 1.5 w/v sucrose
Stratification: no (seeds were vernalised prior to germination)

treatment_protocol: Seedlings of WT which had not been treated with Norflurazon.


title: McCormac_1-6_mutant-NFtreated_Rep2_ATH1

treatment_protocol: Seedlings of a double mutant line gun1,gun5 treated with Norflurazon.


title: Deeken_A-1-Deeke-Tum_SLD_REP1

description:
Atmosphere: Normal
Humidity: Normal
Light: 8 hour days
Medium: Compost
Temperature: 22 C during day, 18 C at night

treatment_protocol: Tumour tissue induced at the base of an inflorescence stalk with Agrobacterium tumefaciens

value: Tumour


title: Deeken_A-2-Deeke-Inf_SLD_REP2

treatment_protocol: Inflorescence stalk injured at the base with a injection needle

value: Inflorescence stalk


title: Deeken_A-1-Deeke-Tum_SLD_REP2


title: Villadsen_A-5-villa-DOG_SLD


title: Villadsen_A-2-villa-wat_SLD


title: Deeken_A-2-Deeke-Inf_SLD_REP1


title: Urwin_A-1-Urwin-Con_SLD


title: Short_1-5_ozone_Rep3_ATH1

description:
location: Growth cabinet
Humidity: ~90%
Temperature: 20 degrees
Lighting: 16h day 8h night
Medium: 0.8% agar  1 x MS with full strength vitamins

treatment_protocol: Fumigation with 500ppb Ozone for 6 hours from 10.30am in sealed chambers inside the growth cabinet. Flow rate was 910ml/min. The ozone was bubbled through water before entering fumigation chambers to humidify the gas. Seelings were fumigated in their growth plates and extracted immediately after fumigation.

value: Whole Plant


title: Short_1-4_control_Rep2_ATH1

treatment_protocol: Fumigation with scrubbed air (filtered through charcoal and purafill)  for 6 hours from 10.30am in sealed chambers inside the growth cabinet. Flow rate was 910ml/min. The air was bubbled through water before entering fumigation chambers to humidify the gas. Seelings were fumigated in their growth plates and RNA extracted immediately after fumigation.


title: McCormac_1-4_wildtype-NFtreated_Rep2_ATH1

description:
location: Growth Room
Atmosphere: Normal
Humidity: in sealed petri dish therefore 80%
Temperature: 23oC
Lighting: 3d growth in darkness followed by 3d continuous white light
Medium: Murashige and Skoog basal salts solidified with agar
Treatment: 5 micromolar Norflurazon
Nutrients: 1.5 w/v sucrose
Stratification: no (seeds were vernalised prior to germination)

treatment_protocol: Seedlings of WT which had been treated with Norflurazon.


title: Short_1-6_control_Rep3_ATH1


title: Villadsen_A-3-villa-glc_SLD


title: Villadsen_A-4-villa-OMG_SLD


title: Villadsen_A-1-villa-zer_SLD


title: Short_1-3_ozone_Rep2_ATH1


title: Short_1-2_control_Rep1_ATH1


title: Bramke_A5-warre-S2C

description:
Atmosphere: Normal
Humidity: Normal
Light: 8 hour days
Medium: compost (Levingtons' Plant Protection Mix)
Temperature: 21-22 C
Treatment: None
Water: None

value: Not in stock centre

value: Aerial parts of whole plants


title: Bramke_A2-warre-WTW


title: Short_1-1_ozone_Rep1_ATH1


title: Bramke_A6-warre-S2W


title: Bramke_A1-warre-WTC


title: Bramke_A4-warre-S6W


title: Knight_2-1_wildtype-lt_Rep1_ATH1

treatment_protocol: After 7 days growing in the conditions described, the agar plate was transferred to a high-light growth cabinet (240 microEinsteins; 16h light-8h dark) for 24h prior to start of treatments. After this time, these wild type plants remained in this high light treatment for 3h before being harvested.

value: Cell culture


title: Knight_2-4_sfr6-dk_Rep1_ATH1

treatment_protocol: After 7 days growing in the conditions described, the agar plate was transferred to a high-light growth cabinet (240 microEinsteins; 16h light-8h dark) for 24h prior to start of treatment. After this time, these sfr6 mutant plants were subjected to darkness by wrapping tightly in aluminium foil for 3h before being harvested.

value: EMS Mutant


title: Knight_2-2_wildtype-dk_Rep1_ATH1

treatment_protocol: After 7 days growing in the conditions described, agar plates were transferred to a high-light growth cabinet (240 microEinsteins; 16h light-8h dark) for 24h prior to start of treatments. After this time, mutant and wild type plants were subjected to dark treatment by being wrapped in aluminium foil for 3h whilst control untreated plates remained uncovered in the high-light cabinet. !Samples were harvested immediately after treatment.


title: Bramke_A3-warre-S6C


title: Knight_2-3_sfr6-lt_Rep1_ATH1

treatment_protocol: After 7 days growing in the conditions described, the agar plate was transferred to a high-light growth cabinet (240 microEinsteins; 16h light-8h dark) for 24h prior to start of treatments. After this time, these sfr6 mutant plants remained in this high light treatment for 3h before being harvested.


title: RIKEN-LI5B

treatment_protocol: 5 uM gibberellin treatment for 6 hours

value: seeds

value: Ler


title: RIKEN-LI6B

treatment_protocol: 5 uM gibberellin treatment for 9 hours


title: RIKEN-LI4B

treatment_protocol: 5 uM gibberellin treatment for 3 hours


title: RIKEN-LI6A


title: RIKEN-LI5A


title: RIKEN-LI3B

treatment_protocol: water treatment for 9 hours


title: RIKEN-LI3A


title: RIKEN-LI4A


title: RIKEN-LI1B

treatment_protocol: water treatment for 3 hours


title: RIKEN-LI2A

treatment_protocol: water treatment for 6 hours


title: RIKEN-NAKABAYASHI4A

treatment_protocol: 24 h imbibed in 30 uM ABA

value: 24 h imbibed seed

value: seed


title: RIKEN-NAKABAYASHI2A

treatment_protocol: 24 h imbibed in water


title: RIKEN-LI2B


title: RIKEN-NAKABAYASHI2B


title: RIKEN-NAKABAYASHI4B


title: NO.27

treatment_protocol: No treatment

value: 21-day-old plants, vegetative stage

value: whole plant


title: RIKEN-NAKABAYASHI1B

treatment_protocol: no treatment

value: dry seed


title: NO.15


title: RIKEN-NAKABAYASHI5B

treatment_protocol: 24 h imbibed in 3 uM ABA


title: RIKEN-LI1A


title: RIKEN-NAKABAYASHI1A


title: RIKEN-NAKABAYASHI3A


title: NO.25


title: NO.26


title: NO.14


title: NO.13


title: NO.21-2

treatment_protocol: 20uM t-zeatin for 3h

value: complete plant


title: NO.32


title: NO.10