title: DB001_ATH1_A2-Brown-cal

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 73.96
Background Stdev (float) = 1.98
Background Max (float) = 79.0
Background Min (float) = 68.8
Noise Avg (float) = 4.31
Noise Stdev (float) = 0.14
Noise Max (float) = 4.8
Noise Min (float) = 3.9
RawQ (float) = 2.80
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 501
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: DB001_ATH1_A2-Brown-cal.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 = 234 (type integer); Parameter Upper right corner x coordinate = 4497 (type integer); Parameter Upper right corner y coordinate = 273 (type integer); Parameter Lower right corner x coordinate = 4458 (type integer); Parameter Lower right corner y coordinate = 4543 (type integer); Parameter Lower left corner x coordinate = 192 (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 = 0.364181 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

treatment_protocol: Leaves from seedlings, grown aseptically (14-17 days) on MS agar, excised and transferred to callus induction medium (Gamborg's B5 Basil Medium with minimal organics, 2.0% glucose, 0.5mgl-1 MES, 0.5mgl-1 2,4-D, 0.05mgl-1 Kinetin. pH 5.7). Incubated in darkness, at 22oC for 2 weeks. Callus transferred to high differentiating liquid media (MS 0.2% sucrose, 4% mannitol, 0.2mgl-1 auxins (2,4-D, NAA, IAA) 1mgl-1 BA, pH5.7). Incubated at 22oC on a rotary shaker (105rpm). Sample taken at day =2 ; Performer: David,,Brown

value: 2 day timepoint


title: Birnbaum_1-9_StageII-2_Rep2_ATH1

status: Public on Jan 22 2007

type: RNA

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

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

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

label: biotin

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Stage II

tag: Tissue

value: Where cells transition from being optically dense to a more transparent appearance as they begin longitudinal expansion (about 0.30 mm from the root tip)

tag: Genetic background

value: Columbia


title: Birnbaum_1-13_StageIII-2_Rep2_ATH1

institute: Nottingham Arabidopsis Stock Centre (NASC)

source_name: Stage III

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


title: Birnbaum_1-17_wol-2_Rep2_ATH1

value: Marks cells in stele and starts to fade from the elongation zone


title: Birnbaum_1-25_J0571-1_Rep1_ATH1

value: Marks ground tissue (endodermis and cortex) and the QC


title: Birnbaum_1-14_StageIII-3_Rep3_ATH1


title: Birnbaum_1-22_gl2-1_Rep1_ATH1

value: Marks atrichoblasts from the QC up.


title: Birnbaum_1-11_StageII-4_Rep4_ATH1


title: Birnbaum_1-10_StageII-3_Rep3_ATH1


title: Birnbaum_1-5_StageI-2_Rep2_ATH1

source_name: Stage I

value: Where the root tip reaches its full diameter (about 0.15 mm from the root tip)


title: Birnbaum_1-8_StageII-1_Rep1_ATH1


title: Birnbaum_1-4_StageI-1_Rep1_ATH1


title: Birnbaum_1-3_src5-3_Rep3_ATH1

value: Marks the QC and the endodermis at least past the mature hair zone

value: Landsberg


title: Birnbaum_1-16_wol-1_Rep1_ATH1


title: Birnbaum_1-18_wol-3_Rep3_ATH1


title: Birnbaum_1-7_StageI-4_Rep4_ATH1


title: Birnbaum_1-24_gl2-3_Rep3_ATH1


title: Birnbaum_1-21_LRC-3_Rep3_ATH1

value: Lateral root cap plus epidermis


title: Birnbaum_1-6_StageI-3_Rep3_ATH1


title: Birnbaum_1-15_StageIII-4_Rep4_ATH1


title: Birnbaum_1-1_src5-1_Rep1_ATH1


title: Birnbaum_1-26_J0571-2_Rep2_ATH1


title: Birnbaum_1-20_LRC-2_Rep2_ATH1


title: AtGen_D-17_2-DL_REP2_ATH1

description:
location: Growth Room
Humidity: not adjusted
Temperature: 22°C
Lighting: darkness
Medium: Murashige and Skoog / agar 1.2 %
Stratification: 8°C, 48 hour darkness

treatment_protocol:
Treatment before light irradiation:
Amount of dry seeds: 18 mg / sterilisation: 3 min 70 % Ethanol, stir with over-head tumbler -> short centrifugation ->resuspend in 100 % Ethanol ->pipette on sterile filter paper ->air dry in a sterile bench / Growth media: MS agar (1.2 %) covered with a sterile filter paper (Schleicher and Schuell, Rundfilter 595, Dassel, Germany) in petridishes / Stratification: 8° C, 48 h / Germination induction: 2 h red light / Growth: 94 h in complete darkness at 22°C before onset of irradiation.
Light treatment:
4h of complete darkness (dark control)

tag: Stock Code

tag: Developmental stage

value: mainly hypocotyl and cotyledons


title: Pickett_1-4_wild-type_Rep2_ATH1

description:
location: Conviron E7 Growth Chamber
Atmosphere: Normal
Humidity: Standard
Temperature: 29 degrees C
Lighting: 24 hour light
Medium: Fertiloam Peat Light Mix
Nutrients: Commercial fertilizer: Pete's 20-20-20 (no added barium)
Water: standing water
Stratification: 4 degrees C on soil mix for 4 days

value: hypocotyls; cotyledons;meristems; true leaves 1 and 2; true leaves primordial initals

value: wild-type


title: Birnbaum_1-19_LRC-1_Rep1_ATH1


title: AtGen_D-26_1-FS_REP2_ATH1

description:
location: Growth Room
Humidity: not adjusted
Temperature: 22°C
Lighting: 4 d darkness --> 45 min continuous far-red light
Medium: Murashige and Skoog / agar 1.2 %
Stratification: 8°C, 48 hour darkness

treatment_protocol:
Treatment before light irradiation:
Amount of dry seeds: 18 mg / sterilisation: 3 min 70 % Ethanol, stir with over-head tumbler -> short centrifugation ->resuspend in 100 % Ethanol ->pipette on sterile filter paper ->air dry in a sterile bench / Growth media: MS agar (1.2 %) covered with a sterile filter paper (Schleicher and Schuell, Rundfilter 595, Dassel, Germany) in petridishes / Stratification: 8° C, 48 h / Germination induction: 2 h red light / Growth: 94 h in complete darkness at 22°C before onset of irradiation.
Light treatment:
continuous far-red light / time course: 45 min continuous far-red light / light intensity: 10 µmol m-2 s-1 / filter: 715 nm DAL interference filter (Schott, Mainz, Germany), lamba(max) = 715 nm, half-bandwidth = 15 nm / light source: Leitz Prado 500-W universal projector (Leitz, Wetzlar, Germany) together with Osram Xenophot longlife lamps (Osram, Berlin, Germany) / Temperature: 22°C


title: Pickett_1-3_wild-type_Rep1_ATH1


title: AtGen_D-44_3-RS_REP3_ATH1

description:
location: Growth Room
Humidity: not adjusted
Temperature: 22°C
Lighting: 4 d darkness --> 45 min continuous red light
Medium: Murashige and Skoog / agar 1.2 %
Stratification: 8°C, 48 hour darkness

treatment_protocol:
Treatment before light irradiation:
Amount of dry seeds: 18 mg / sterilisation: 3 min 70 % Ethanol, stir with over-head tumbler -> short centrifugation ->resuspend in 100 % Ethanol ->pipette on sterile filter paper ->air dry in a sterile bench / Growth media: MS agar (1.2 %) covered with a sterile filter paper (Schleicher and Schuell, Rundfilter 595, Dassel, Germany) in petridishes / Stratification: 8° C, 48 h / Germination induction: 2 h red light / Growth: 94 h in complete darkness at 22°C before onset of irradiation
Light treatment:
light treatment: continuous red light / time course: 45 min continuous red light / light intensity: 10 µmol m-2 s-1 / filter: KG65 double glas filter (Balzers, Liechtenstein), lamba(max) = 650 nm, half-bandwidth = 15 nm / light source: Leitz Prado 500-W universal projector (Leitz, Wetzlar, Germany) together with Osram Xenophot longlife lamps (Osram, Berlin, Germany) / Temperature: 22°C


title: Pickett_1-2_ADD3_Rep2_ATH1

value: Col-3 gl1

tag: Genetic variation

value: EMS Mutant


title: AtGen_D-47_3-US_REP3_ATH1

description:
location: Growth Room
Humidity: not adjusted
Temperature: 22°C
Lighting: 4 d darkness --> 5 min UV-A/B light --> 40 min darkness
Medium: Murashige and Skoog / agar 1.2 %
Stratification: 8°C, 48 hour darkness

treatment_protocol:
Treatment before light irradiation:
Amount of dry seeds: 18 mg / sterilisation: 3 min 70 % Ethanol, stir with over-head tumbler -> short centrifugation ->resuspend in 100 % Ethanol ->pipette on sterile filter paper ->air dry in a sterile bench / Growth media: MS agar (1.2 %) covered with a sterile filter paper (Schleicher and Schuell, Rundfilter 595, Dassel, Germany) in petridishes / Stratification: 8° C, 48 h / Germination induction: 2 h red light / Growth: 94 h in complete darkness at 22°C before onset of irradiation


title: AtGen_D-46_3-AS_REP3_ATH1

description:
location: Growth Room
Humidity: not adjusted
Temperature: 22°C
Lighting: 4 d darkness --> 5 min UV-A light --> 40 min darkness
Medium: Murashige and Skoog / agar 1.2 %
Stratification: 8°C, 48 hour darkness

treatment_protocol:
Treatment before light irradiation:
Amount of dry seeds: 18 mg / sterilisation: 3 min 70 % Ethanol, stir with over-head tumbler -> short centrifugation ->resuspend in 100 % Ethanol ->pipette on sterile filter paper ->air dry in a sterile bench / Growth media: MS agar (1.2 %) covered with a sterile filter paper (Schleicher and Schuell, Rundfilter 595, Dassel, Germany) in petridishes / Stratification: 8° C, 48 h / Germination induction: 2 h red light / Growth: 94 h in complete darkness at 22°C before onset of irradiation
Light treatment:
UV-A light pulse / time course: 5 min UV-A light pulse followed by 40 min of darkness / light intensity: 7 W m-2 / filter: WG327 quarz filter, 3 mm, (Schott, Mainz, Germany), cut-off filter with half-maximal transmission at 327 nm / light source: 6 x Philips TL 40W/12 UV fluorescent tubes, lamba(max) = 310 nm, half-bandwidth = 40 nm / Temperature: 22°C / literature: PMID 14739338


title: AtGen_D-43_3-PS_REP3_ATH1

description:
location: Growth Room
Humidity: not adjusted
Temperature: 22°C
Lighting: 4 d darkness --> 1 min red light --> 44 min darkness
Medium: Murashige and Skoog / agar 1.2 %
Stratification: 8°C, 48 hour darkness

treatment_protocol:
Treatment before light irradiation:
Amount of dry seeds: 18 mg / sterilisation: 3 min 70 % Ethanol, stir with over-head tumbler -> short centrifugation ->resuspend in 100 % Ethanol ->pipette on sterile filter paper ->air dry in a sterile bench / Growth media: MS agar (1.2 %) covered with a sterile filter paper (Schleicher and Schuell, Rundfilter 595, Dassel, Germany) in petridishes / Stratification: 8° C, 48 h / Germination induction: 2 h red light / Growth: 94 h in complete darkness at 22°C before onset of irradiation
Light treatment:
red light pulse / time course: 1 min red light pulse followed by 44 min of darkness / light intensity: 50 µmol m-2 s-1 / filter: KG65 double glas filter (Balzers, Liechtenstein), lamba(max) = 650 nm, half-bandwidth = 15 nm / light source: Leitz Prado 500-W universal projector (Leitz, Wetzlar, Germany) together with Osram Xenophot longlife lamps (Osram, Berlin, Germany) / Temperature: 22°C


title: AtGen_D-39_3-UL_REP3_ATH1

description:
location: Growth Room
Humidity: not adjusted
Temperature: 22°C
Lighting: 4 d darkness --> 5 min UV-A/B light --> 4 h darkness
Medium: Murashige and Skoog / agar 1.2 %
Stratification: 8°C, 48 hour darkness


title: AtGen_D-45_3-BS_REP3_ATH1

description:
location: Growth Room
Humidity: not adjusted
Temperature: 22°C
Lighting: 4 d darkness --> 45 min continuous blue light
Medium: Murashige and Skoog / agar 1.2 %
Stratification: 8°C, 48 hour darkness

treatment_protocol:
Treatment before light irradiation:
Amount of dry seeds: 18 mg / sterilisation: 3 min 70 % Ethanol, stir with over-head tumbler -> short centrifugation ->resuspend in 100 % Ethanol ->pipette on sterile filter paper ->air dry in a sterile bench / Growth media: MS agar (1.2 %) covered with a sterile filter paper (Schleicher and Schuell, Rundfilter 595, Dassel, Germany) in petridishes / Stratification: 8° C, 48 h / Germination induction: 2 h red light / Growth: 94 h in complete darkness at 22°C before onset of irradiation
Light treatment:
continuous blue light / time course: 45 min continuous blue light / light intensity: 10 µmol m-2 s-1 / filter: 453 nm DAL interference filter (Schott, Mainz, Germany), lamba(max) = 453 nm, half-bandwidth = 18 nm / light source: Leitz Prado 500-W universal projector (Leitz, Wetzlar, Germany) together with Osram Xenophot longlife lamps (Osram, Berlin, Germany) / Temperature: 22°C


title: AtGen_D-40_3-WL_REP3_ATH1

description:
location: Growth Room
Humidity: not adjusted
Temperature: 22°C
Lighting: 4 d darkness --> 4 h continuous white light
Medium: Murashige and Skoog / agar 1.2 %
Stratification: 8°C

treatment_protocol:
Treatment before light irradiation:
Amount of dry seeds: 18 mg / sterilisation: 3 min 70 % Ethanol, stir with over-head tumbler -> short centrifugation ->resuspend in 100 % Ethanol ->pipette on sterile filter paper ->air dry in a sterile bench / Growth media: MS agar (1.2 %) covered with a sterile filter paper (Schleicher and Schuell, Rundfilter 595, Dassel, Germany) in petridishes / Stratification: 8° C, 48 h / Germination induction: 2 h red light / Growth: 94 h in complete darkness at 22°C before onset of irradiation
Light treatment:
continuous white light / time course: 4 h continuous white light / light intensity: 10 µmol m-2 s-1 / filter: 10 % neutral glas filter (Balzers, Liechtenstein) / light source: Leitz Prado 500-W universal projector (Leitz, Wetzlar, Germany) together with Osram Xenophot longlife lamps (Osram, Berlin, Germany) / Temperature: 22°C


title: AtGen_D-35_3-PL_REP3_ATH1

description:
location: Growth Room
Humidity: not adjusted
Temperature: 22°C
Lighting: 4 d darkness --> 1 min red light --> 4 h darkness
Medium: Murashige and Skoog / agar 1.2 %
Stratification: 8°C, 48 hour darkness

treatment_protocol:
Treatment before light irradiation:
Amount of dry seeds: 18 mg / sterilisation: 3 min 70 % Ethanol, stir with over-head tumbler -> short centrifugation ->resuspend in 100 % Ethanol ->pipette on sterile filter paper ->air dry in a sterile bench / Growth media: MS agar (1.2 %) covered with a sterile filter paper (Schleicher and Schuell, Rundfilter 595, Dassel, Germany) in petridishes / Stratification: 8° C, 48 h / Germination induction: 2 h red light / Growth: 94 h in complete darkness at 22°C before onset of irradiation
Light treatment:
red light pulse / time course: 1 min red light pulse followed by 4 h of darkness / light intensity: 50 µmol m-2 s-1 / filter: KG65 double glas filter (Balzers, Liechtenstein), lamba(max) = 650 nm, half-bandwidth = 15 nm / light source: Leitz Prado 500-W universal projector (Leitz, Wetzlar, Germany) together with Osram Xenophot longlife lamps (Osram, Berlin, Germany) / Temperature: 22°C


title: AtGen_D-41_3-DS_REP3_ATH1

treatment_protocol:
Treatment before light irradiation:
Amount of dry seeds: 18 mg / sterilisation: 3 min 70 % Ethanol, stir with over-head tumbler -> short centrifugation ->resuspend in 100 % Ethanol ->pipette on sterile filter paper ->air dry in a sterile bench / Growth media: MS agar (1.2 %) covered with a sterile filter paper (Schleicher and Schuell, Rundfilter 595, Dassel, Germany) in petridishes / Stratification: 8° C, 48 h / Germination induction: 2 h red light / Growth: 94 h in complete darkness at 22°C before onset of irradiation
Light treatment:
45 min of complete darkness (dark control)


title: AtGen_D-42_3-FS_REP3_ATH1

treatment_protocol:
Treatment before light irradiation:
Amount of dry seeds: 18 mg / sterilisation: 3 min 70 % Ethanol, stir with over-head tumbler -> short centrifugation ->resuspend in 100 % Ethanol ->pipette on sterile filter paper ->air dry in a sterile bench / Growth media: MS agar (1.2 %) covered with a sterile filter paper (Schleicher and Schuell, Rundfilter 595, Dassel, Germany) in petridishes / Stratification: 8° C, 48 h / Germination induction: 2 h red light / Growth: 94 h in complete darkness at 22°C before onset of irradiation
Light treatment:
continuous far-red light / time course: 45 min continuous far-red light / light intensity: 10 µmol m-2 s-1 / filter: 715 nm DAL interference filter (Schott, Mainz, Germany), lamba(max) = 715 nm, half-bandwidth = 15 nm / light source: Leitz Prado 500-W universal projector (Leitz, Wetzlar, Germany) together with Osram Xenophot longlife lamps (Osram, Berlin, Germany) / Temperature: 22°C


title: AtGen_D-34_3-FL_REP3_ATH1

description:
location: Growth Room
Humidity: not adjusted
Temperature: 22°C
Lighting: 4 d darkness --> 4 h continuous far-red light
Medium: Murashige and Skoog / agar 1.2 %
Stratification: 8°C, 48 hour darkness

treatment_protocol:
Treatment before light irradiation:
Amount of dry seeds: 18 mg / sterilisation: 3 min 70 % Ethanol, stir with over-head tumbler -> short centrifugation ->resuspend in 100 % Ethanol ->pipette on sterile filter paper ->air dry in a sterile bench / Growth media: MS agar (1.2 %) covered with a sterile filter paper (Schleicher and Schuell, Rundfilter 595, Dassel, Germany) in petridishes / Stratification: 8° C, 48 h / Germination induction: 2 h red light / Growth: 94 h in complete darkness at 22°C before onset of irradiation
Light treatment:
continuous far-red light / time course: 4 h continuous far-red light / light intensity: 10 µmol m-2 s-1 / filter: 715 nm DAL interference filter (Schott, Mainz, Germany), lamba(max) = 715 nm, half-bandwidth = 15 nm / light source: Leitz Prado 500-W universal projector (Leitz, Wetzlar, Germany) together with Osram Xenophot longlife lamps (Osram, Berlin, Germany) / Temperature: 22°C


title: Pickett_1-1_ADD3_Rep1_ATH1


title: AtGen_D-30_2-AS_REP2_ATH1


title: AtGen_D-48_3-WS_REP3_ATH1

description:
location: Growth Room
Humidity: not adjusted
Temperature: 22°C
Lighting: 4 d darkness --> 45 min continuous white light
Medium: Murashige and Skoog / agar 1.2 %
Stratification: 8°C, 48 hour darkness

treatment_protocol:
Treatment before light irradiation:
Amount of dry seeds: 18 mg / sterilisation: 3 min 70 % Ethanol, stir with over-head tumbler -> short centrifugation ->resuspend in 100 % Ethanol ->pipette on sterile filter paper ->air dry in a sterile bench / Growth media: MS agar (1.2 %) covered with a sterile filter paper (Schleicher and Schuell, Rundfilter 595, Dassel, Germany) in petridishes / Stratification: 8° C, 48 h / Germination induction: 2 h red light / Growth: 94 h in complete darkness at 22°C before onset of irradiation
Light treatment:
continuous white light / time course: 45 min continuous white light / light intensity: 10 µmol m-2 s-1 / filter: 10 % neutral glas filter (Balzers, Liechtenstein) / light source: Leitz Prado 500-W universal projector (Leitz, Wetzlar, Germany) together with Osram Xenophot longlife lamps (Osram, Berlin, Germany) / Temperature: 22°C


title: AtGen_D-32_2-WS_REP2_ATH1


title: AtGen_D-29_2-BS_REP2_ATH1


title: AtGen_D-38_3-AL_REP3_ATH1

description:
location: Growth Room
Humidity: not adjusted
Temperature: 22°C
Lighting: 4 d darkness --> 5 min UV-A light --> 4 h darkness
Medium: Murashige and Skoog / agar 1.2 %
Stratification: 8°C, 48 hour darkness

treatment_protocol:
Treatment before light irradiation:
Amount of dry seeds: 18 mg / sterilisation: 3 min 70 % Ethanol, stir with over-head tumbler -> short centrifugation ->resuspend in 100 % Ethanol ->pipette on sterile filter paper ->air dry in a sterile bench / Growth media: MS agar (1.2 %) covered with a sterile filter paper (Schleicher and Schuell, Rundfilter 595, Dassel, Germany) in petridishes / Stratification: 8° C, 48 h / Germination induction: 2 h red light / Growth: 94 h in complete darkness at 22°C before onset of irradiation
Light treatment:
UV-A light pulse / time course: 5 min UV-A light pulse followed by 4 h of darkness / light intensity: 7 W m-2 / filter: WG327 quarz filter, 3 mm, (Schott, Mainz, Germany), cut-off filter with half-maximal transmission at 327 nm / light source: 6 x Philips TL 40W/12 UV fluorescent tubes, lamba(max) = 310 nm, half-bandwidth = 40 nm / Temperature: 22°C / literature: PMID 14739338


title: AtGen_D-31_2-US_REP2_ATH1

treatment_protocol:
"Treatment before light irradiation:
Amount of dry seeds: 18 mg
Sterilization: 3 min 70 % Ethanol, stir with over-head tumbler -> short zentrifugation ->resuspend in 100 % Ethanol ->pipette on steril filter paper ->air dry in a sterile bench
Growth media: MS agar (1.2 %) covered with a sterile filter paper (Schleicher and Schuell, Rundfilter 595, Dassel, Germany) in petridishes
Stratification: 8° C, 48 h / Germination induction: 2 h red light
Growth: 94 h in complete darkness at 22°C before onset of irradiation
Light treatment:
UV-A/B light pulse / time course: 5 min UV-A/B light pulse followed by 40 min of darkness
Light intensity: 7 W m-2 / filter: WG307 quarz filter, 3 mm, (Schott, Mainz, Germany), cut-off filter with half-maximal transmission at 307 nm
Light source: 6 x Philips TL 40W/12 UV fluorescent tubes, lamba(max) = 310 nm, half-bandwidth = 40 nm
Temperature: 22°C
Literature: PMID 14739338


title: AtGen_D-36_3-RL_REP3_ATH1

description:
location: Growth Room
Humidity: not adjusted
Temperature: 22°C
Lighting: 4 d darkness --> 4 h continuous red light
Medium: Murashige and Skoog / agar 1.2 %
Stratification: 8°C, 48 hour darkness

treatment_protocol:
Treatment before light irradiation:
Amount of dry seeds: 18 mg / sterilisation: 3 min 70 % Ethanol, stir with over-head tumbler -> short centrifugation ->resuspend in 100 % Ethanol ->pipette on sterile filter paper ->air dry in a sterile bench / Growth media: MS agar (1.2 %) covered with a sterile filter paper (Schleicher and Schuell, Rundfilter 595, Dassel, Germany) in petridishes / Stratification: 8° C, 48 h / Germination induction: 2 h red light / Growth: 94 h in complete darkness at 22°C before onset of irradiation
Light treatment:
light treatment: continuous red light / time course: 4 h continuous red light / light intensity: 10 µmol m-2 s-1 / filter: KG65 double glas filter (Balzers, Liechtenstein), lamba(max) = 650 nm, half-bandwidth = 15 nm / light source: Leitz Prado 500-W universal projector (Leitz, Wetzlar, Germany) together with Osram Xenophot longlife lamps (Osram, Berlin, Germany) / Temperature: 22°C


title: AtGen_D-28_2-RS_REP2_ATH1


title: AtGen_D-37_3-BL_REP3_ATH1

description:
location: Growth Room
Humidity: not adjusted
Temperature: 22°C
Lighting: 4 d darkness --> 4 h continuous blue light
Medium: Murashige and Skoog / agar 1.2 %
Stratification: 8°C, 48 hour darkness

treatment_protocol:
Treatment before light irradiation:
Amount of dry seeds: 18 mg / sterilisation: 3 min 70 % Ethanol, stir with over-head tumbler -> short centrifugation ->resuspend in 100 % Ethanol ->pipette on sterile filter paper ->air dry in a sterile bench / Growth media: MS agar (1.2 %) covered with a sterile filter paper (Schleicher and Schuell, Rundfilter 595, Dassel, Germany) in petridishes / Stratification: 8° C, 48 h / Germination induction: 2 h red light / Growth: 94 h in complete darkness at 22°C before onset of irradiation
Light treatment:
continuous blue light / time course: 4 h continuous blue light / light intensity: 10 µmol m-2 s-1 / filter: 453 nm DAL interference filter (Schott, Mainz, Germany), lamba(max) = 453 nm, half-bandwidth = 18 nm / light source: Leitz Prado 500-W universal projector (Leitz, Wetzlar, Germany) together with Osram Xenophot longlife lamps (Osram, Berlin, Germany) / Temperature: 22°C


title: AtGen_D-27_2-PS_REP2_ATH1


title: AtGen_D-25_2-DS_REP2_ATH1


title: AtGen_D-33_3-DL_REP3_ATH1

treatment_protocol:
Treatment before light irradiation:
Amount of dry seeds: 18 mg / sterilisation: 3 min 70 % Ethanol, stir with over-head tumbler -> short centrifugation ->resuspend in 100 % Ethanol ->pipette on sterile filter paper ->air dry in a sterile bench / Growth media: MS agar (1.2 %) covered with a sterile filter paper (Schleicher and Schuell, Rundfilter 595, Dassel, Germany) in petridishes / Stratification: 8° C, 48 h / Germination induction: 2 h red light / Growth: 94 h in complete darkness at 22°C before onset of irradiation
Light treatment:
4h of complete darkness (dark control)


title: AtGen_D-23_2-UL_REP2_ATH1


title: AtGen_D-24_2-WL_REP2_ATH1

description:
location: Growth Room
Humidity: not adjusted
Temperature: 22°C
Lighting: 4 d darkness --> 4 h continuous white light
Medium: Murashige and Skoog / agar 1.2 %
Stratification: 8°C, 48 hour darkness


title: AtGen_D-21_2-BL_REP2_ATH1


title: AtGen_D-22_2-AL_REP2_ATH1


title: AtGen_D-18_2-FL_REP2_ATH1


title: AtGen_D-15_1-US_REP1_ATH1


title: AtGen_D-19_2-PL_REP2_ATH1


title: AtGen_D-16_1-WS_REP1_ATH1


title: AtGen_D-13_1-BS_REP1_ATH1


title: AtGen_D-14_1-AS_REP1_ATH1


title: AtGen_D-10_1-FS_REP1_ATH1


title: AtGen_D-20_2-RL_REP2_ATH1


title: AtGen_D-6_1-AL_REP1_ATH1


title: AtGen_D-8_1-WL_REP1_ATH1

treatment_protocol:
Treatment before light irradiation:
Amount of dry seeds: 18 mg / sterilisation: 3 min 70 % Ethanol, stir with over-head tumbler -> short centrifugation ->resuspend in 100 % Ethanol ->pipette on sterile filter paper ->air dry in a sterile bench / Growth media: MS agar (1.2 %) covered with a sterile filter paper (Schleicher and Schuell, Rundfilter 595, Dassel, Germany) in petridishes / Stratification: 8° C, 48 h / Germination induction: 2 h red light / Growth: 94 h in complete darkness at 22°C before onset of irradiation.
Light treatment:
continuous white light / time course: 4 h continuous white light / light intensity: 10 µmol m-2 s-1 / filter: 10 % neutral glas filter (Balzers, Liechtenstein) / light source: Leitz Prado 500-W universal projector (Leitz, Wetzlar, Germany) together with Osram Xenophot longlife lamps (Osram, Berlin, Germany) / Temperature: 22°C


title: AtGen_D-9_1-DS_REP1_ATH1

description:
location: Growth Room
Humidity: not adjusted
Temperature: 22°C
Lighting: darkness
Medium: Murashige and Skoog / agar 1.2 %
Stratification: 8°C, 48 hour darkness

treatment_protocol:
Treatment before light irradiation:
Amount of dry seeds: 18 mg / sterilisation: 3 min 70 % Ethanol, stir with over-head tumbler -> short centrifugation ->resuspend in 100 % Ethanol ->pipette on sterile filter paper ->air dry in a sterile bench / Growth media: MS agar (1.2 %) covered with a sterile filter paper (Schleicher and Schuell, Rundfilter 595, Dassel, Germany) in petridishes / Stratification: 8° C, 48 h / Germination induction: 2 h red light / Growth: 94 h in complete darkness at 22°C before onset of irradiation.
Light treatment:
45 min of complete darkness (dark control)


title: AtGen_D-11_1-PS_REP1_ATH1


title: AtGen_D-5_1-BL_REP1_ATH1


title: AtGen_D-4_1-RL_REP1_ATH1


title: AtGen_D-3_1-PL_REP1_ATH1


title: AtGen_D-12_1-RS_REP1_ATH1

treatment_protocol:
Treatment before light irradiation:
Amount of dry seeds: 18 mg / sterilisation: 3 min 70 % Ethanol, stir with over-head tumbler -> short centrifugation ->resuspend in 100 % Ethanol ->pipette on sterile filter paper ->air dry in a sterile bench / Growth media: MS agar (1.2 %) covered with a sterile filter paper (Schleicher and Schuell, Rundfilter 595, Dassel, Germany) in petridishes / Stratification: 8° C, 48 h / Germination induction: 2 h red light / Growth: 94 h in complete darkness at 22°C before onset of irradiation
Light treatment:
light treatment: continuous red light / time course: 45 min continuous red light / light intensity: 10 µmol m-2 s-1 / filter: KG65 double glas filter (Balzers, Liechtenstein), lamba(max) = 650 nm, half-bandwidth = 15 nm / light source: Leitz Prado 500-W universal projector (Leitz, Wetzlar, Germany) together with Osram Xenophot longlife lamps (Osram, Berlin, Germany) / Temperature: 22°C


title: AtGen_D-1_1-DL_REP1_ATH1

treatment_protocol:
Treatment before light irradiation:
Amount of dry seeds: 18 mg / sterilisation: 3 min 70 % Ethanol, stir with over-head tumbler -> short centrifugation ->resuspend in 100 % Ethanol -> pipette on sterile filter paper ->air dry in a sterile bench / Growth media: MS agar (1.2 %) covered with a sterile filter paper (Schleicher and Schuell, Rundfilter 595, Dassel, Germany) in petridishes / Stratification: 8° C, 48 h / Germination induction: 2 h green light / Growth: 94 h in complete darkness at 22°C before onset of irradiation
Light treatment:
4h of complete darkness (dark control)


title: AtGen_D-2_1-FL_REP1_ATH1


title: IL-12 stimulated T effector cells

city: Palo Alto

first: Junliang

last: Pan

state: CA

address: 3801 Miranda Avenue

department: Pathology

country: USA

institute: Stanford University

description: done by stanford facility

hyb_protocol: done by stanford pan facility

scan_protocol: done by stanford pan facility

data_processing: done by stanford facility

label: biotin-labeled cRNA

organism: Homo sapiens

source_name: human peripheral naive T cells

label_protocol: done by Stanford Pan facility

extract_protocol: RNeasy mini kit

tag: 24-well plates were coated with anti-CD3 and anti-CD28 monoclonal antibodies (1 μg/ml) in phosphate buffered saline overnight at 4 °C. Naïve or memory T cells (0.7 x 106/well) were cultured in RPMI-1640 (GIBCO) supplemented with 10% heat-inactivated FCS, penicillin/streptomycin and glutamine (all from GIBCO), in the presence of 10 ng/ml of IL-12 (R&D Systems). After 2 days, T cells were transferred to a new plate, and fresh medium containing IL-2 (12.5 ng/ml) and IL-12 (2.5 ng/ml) added and cultured for 4 additional days.  T effector cells were FACS-sorted based on expression of cutaneous lymphocyte antigen expression and CD3 positive.


title: AtGen_D-7_1-UL_REP1_ATH1

treatment_protocol:
Treatment before light irradiation:
Amount of dry seeds: 18 mg / sterilisation: 3 min 70 % Ethanol, stir with over-head tumbler -> short centrifugation ->resuspend in 100 % Ethanol ->pipette on sterile filter paper ->air dry in a sterile bench / Growth media: MS agar (1.2 %) covered with a sterile filter paper (Schleicher and Schuell, Rundfilter 595, Dassel, Germany) in petridishes / Stratification: 8° C, 48 h / Germination induction: 2 h red light / Growth: 94 h in complete darkness at 22°C before onset of irradiation


title: Retinoid Acid stimulated T effector cells

description: Hybridization, washing, staining and scanning were all done by Stanford Pan Facility.

hyb_protocol: Hybridization was carried out in Stanford Protein and Nucleic Acid (PAN) facility

scan_protocol: Stanford Pan facility using Agilent scanner

data_processing: value was generated using affymetrix genechip operating software

label: BioArrayHighYield transcript labeling kit to synthesize biotin-labeled cRNA

label_protocol:
Using "Superscript double stranded cDNA synthesis kit" (invitrogen11917-010) for cDNA synthesis.  We used 200 ng to 500 ng of total RNA, whose quality was validated by Agilent BioAnalyzer.
PCR was conducted to amplify cDNA.
Using "BioArrayHighYield transcript labeling kit" to synthesize biotin-labeled cRNA.
cRNA was cleanup, fragmented and analyzed by Agilent BioAnalyzer before hybridization with Affymetrix Chips.

extract_protocol: Total RNA was isolated using a Qiagen RNeasy mini kit.

tag: Human naive T cells were cultured in 96-well plate coated with anti-CD3 and anti-CD28 antibodies in RPMI medium supplemented with 10% FBS and retinoid acid.  After culture for 6 days, T cells were sorted based on expression of alpha4beta7 integrin.


title: 1,25(OH)2 vitamin D3 plus IL-12 stimulated CCR10-negative CLA-positive T cells

description: done by stanford facility

tag: 24-well plates were coated with anti-CD3 and anti-CD28 monoclonal antibodies (1 μg/ml) in phosphate buffered saline overnight at 4 °C. Naïve or memory T cells (0.7 x 106/well) were cultured in RPMI-1640 (GIBCO) supplemented with 10% heat-inactivated FCS, penicillin/streptomycin and glutamine (all from GIBCO), in the presence of 1alpha-25-hydroxyvitamin D3 (1,25(OH)2D3 with 10 ng/ml of IL-12 (R&D Systems). After 2 days, T cells were transferred to a new plate, and fresh medium containing IL-2 (12.5 ng/ml) and IL-12 (2.5 ng/ml) added and cultured for 4 additional days.  The cells were FACS-sorted based on expression of CLA-positive but CCR10-negative.


title: 1,25(OH)2 vitamin D3 plus IL-12 stimulated CCR10-positive CLA-positive T cells

description: done by stanford facility

tag: 24-well plates were coated with anti-CD3 and anti-CD28 monoclonal antibodies (1 μg/ml) in phosphate buffered saline overnight at 4 °C. Naïve or memory T cells (0.7 x 106/well) were cultured in RPMI-1640 (GIBCO) supplemented with 10% heat-inactivated FCS, penicillin/streptomycin and glutamine (all from GIBCO), in the presence of 1alpha-25-hydroxyvitamin D3 (1,25(OH)2D3) from Sigma-Aldrich, and with 10 ng/ml of IL-12 (R&D Systems). After 2 days, T cells were transferred to a new plate, and fresh medium containing IL-2 (12.5 ng/ml) and IL-12 (2.5 ng/ml) added and cultured for 4 additional days.  The cells were FACS-sorted based on expression of CCR10-positive and CLA-positive.


title: Unstimulated T effector cells

description: done by the stanford pan facility

hyb_protocol: done by the stanford PAN facility

scan_protocol: done by the stanford PAN facility

data_processing: done by the stanford pan facility

label: Biotin-labeled cRNA

label_protocol: done by the Stanford PAN facility

extract_protocol: RNeasy mini kit from Qiagen according to manufacturer's instruction

tag: 24-well plates were coated with anti-CD3 and anti-CD28 monoclonal antibodies (1 μg/ml) in phosphate buffered saline overnight at 4 °C. Naïve T cells (0.7 x 10E6/well) were cultured in RPMI-1640 (GIBCO) supplemented with 10% heat-inactivated FCS, penicillin/streptomycin and glutamine (all from GIBCO), in the absence of cholecalciferol (vitamin D3), 25-hydroxyvitamin D3 (25(OH)D3), 1alpha-25-hydroxyvitamin D3 (1,25(OH)2D3), or all-trans retinoic acid (all from Sigma-Aldrich), and without 2.5–10 ng/ml of IL-12 (R&D Systems). After 2 days, T cells were transferred to a new plate, and fresh medium containing IL-2 (12.5 ng/ml) was added and cultured for 4 additional days.  This is called unstimulated T effector cells, which was sorted based on expression of alpha4beta7 integrin (intermediate level) and CD3 marker.


title: NRMRL control replicate01, uninfected batch052005 430_2 chip

status: Public on Jan 20 2007

city: Cincinnati

first: Samuel

last: Hayes

state: OH

address: 26 W. Martin Luther King Dr.

institute: United States Environmental Protection Agency

hyb_protocol: GCOS software, EukGE-WS2

scan_protocol: GCOS software with 3000 Scanner

data_processing: GCOS software, target signal scaling 500; normalization 1; Alpha1 0.05; Alpha2 0.065, Tau 0.015; Gamma1L and 1H 0.0045; Gamma2L and 2H 0.06; and Pertubation 1.1.

label: Strepavidin Phycoerythrin (SAPE)

organism: Mus musculus

source_name: Neonatal mouse small intestinal tissue, 24 hours

label_protocol: Affymetrix SOP, EukGE-WS2

extract_protocol: TriZol procedure

tag: Swiss Webster neonatal mouse, 4-6 days old


title: NRMRL control replicate03, uninfected batch052005 430_2 chip

source_name: Neonatal small intestinal tissue, 24 hours


title: NRMRL test replicate04, EPA72 batch052005 430_2 chip

source_name: Neonatal mouse small intestinal tissue, 24 hour infection


title: HDAC2 WT E17.5 Ventricle 2A

status: Public on Jan 18 2007

city: Philadelphia

first: Jonathan

middle: A

last: Epstein

state: PA

address: 421, Curie Blvd

department: Cell and Developmental Biology

institute: University of Pennsylvania, School of Medicine

description: Gene expression data during developmental stage of heart at E17.5

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector. Global scaling was applied to allow comparison of gene Signals across multiple microarrays: after exclusion of the highest and lowest 2%, the average total chip Signal was calculated and used to determine what scaling factor was required to adjust the chip average to an arbitrary target of 150. All Signal values from one microarray were then multiplied by the appropriate scaling factor.

label: Biotin

source_name: Mouse wt heart ventricular tissue at E17.5, pool of 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

extract_protocol: Triazol extraction of total RNA was performed according to the manufecturer's protocol.

tag: Strain

value: C57BL/6 X SV129, Age:Embryonic Day 17.5, Tissue:Heart Venticle


title: B6Osb129F1 mouse - spleen - eGFP/CD3 double positive

status: Public on Jan 19 2007

city: Kennett Square

first: K.

middle: John

last: McLaughlin

address: 382 West Street Rd

department: Animal Biology; School of Veterinary Medicine

institute: University of Pennsylvania

description: Methods were as described by the Penn MicroArray Facility

hyb_protocol: The cRNA products were fragmented to 200 nucleotides or less, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Affymetrix Mouse 430 version 2 microarrays. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.

data_processing: Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector. Probe pairs were scored positive or negative for detection of the targeted sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau = 0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call. A weighted mean of probe fluorescence (corrected for nonspecific signal by subtracting the mismatch probe value) was calculated using the One-step Tukey's Biweight Estimate. This Signal value, a relative measure of the expression level, was computed for each assayed gene. Global scaling was applied to allow comparison of gene Signals across multiple microarrays: after exclusion of the highest and lowest 2%, the average total chip Signal was calculated and used to determine what scaling factor was required to adjust the chip average to an arbitrary target of 150. All Signal values from one microarray were then multiplied by the appropriate scaling factor.

source_name: mouse spleen, FACS sorted cells, eGFP/CD3 double positive

label_protocol: 150 ng of total RNA were converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.

extract_protocol: RNA was extracted from sorted cells using RNeasy columns (Quiagen).

treatment_protocol: The spleen was dissociated into a single cell suspension, stained with a PE-conjugated monoclonal antibody specific for CD3 (BD Pharmingen). eGFP and CD3 double positive cells were collected using a FACSVantage Sort (BD Pharmingen).

tag: Strain:C57BL/6-TgN (ACTbEGFP)1Osb X 129S1 F1 ES cell chimera (injection of ES cells in to Bl6 blastocyst)

tag: Sex

value: male

tag: Age

value: 16 months

tag: tissue

value: spleen cells; FACS sorted:eGFP/CD3 positive cells collected


title: HDAC2 KO E17.5 Ventricle 2B

source_name: Mouse wt heart ventricular tissue at E17.5, pool of 3


title: HDAC2 KO E17.5 Ventricle 1B

value: C57BL/6 X SV129, Age:Embryonic Day 17.5, Tissue:Heart Venticlee


title: NRMRL test replicate02, EPA72 batch052005 430_2 chip

source_name: neonatal mouse small intestinal tissue, 24 hour infection


title: NRMRL control replicate04, uninfected batch052005 430_2 chip


title: NRMRL control replicate02, unifected batch052005 430_2 chip


title: NRMRL test replicate03, EPA72, batch052005 430_2 chip

source_name: neonatal small intestinal tissue, 24 hour infection


title: NRMRL test replicate05, EPA72 batch052005 430_2 chip

source_name: Neonatal small intestinal tissue, 24 hour infection


title: NRMRL test replicate01, EPA72 batch052005 430_2 chip


title: IOSE treated with TGFb for 12hr replicate 1

status: Public on Jan 09 2007

city: Columbus

first: Sandya

last: Liyanarachchi

address: Rm 830, 460, W 12th Avenue

department: Human Genetics

institute: OSU

description: gene expression data from IOSE cells treated with TGFb1, time course study

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Robust Multichip Averages

source_name: IOSE cells treated with TGFb for 12hr

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

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

tag: cell line, normal ovarian epithelium, immortalized


title: IOSE treated with TGFb for 3hr replicate 2

source_name: IOSE cells treated with TGFb for 3hr


title: IOSE treated with TGFb for 0hr replicate 1

source_name: IOSE cells treated with TGFb for 0hr


title: brain, cochlea: [17] Sample #17_le1

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

description: Wild-type 8 months old, female

source_name: brain, cochlea


title: IOSE treated with TGFb for 12hr replicate 2


title: IOSE treated with TGFb for 3hr replicate 1


title: IOSE treated with TGFb for 0hr replicate 2


title: IOSE treated with TGFb for 6hr replicate 2

source_name: IOSE cells treated with TGFb for 6hr


title: 1,25(OH)2 vitamin D3 stimulated T effector cells

description: done by stanford facility

tag: 24-well plates were coated with anti-CD3 and anti-CD28 monoclonal antibodies (1 μg/ml) in phosphate buffered saline overnight at 4 °C. Naïve or memory T cells (0.7 x 106/well) were cultured in RPMI-1640 (GIBCO) supplemented with 10% heat-inactivated FCS, penicillin/streptomycin and glutamine (all from GIBCO), in the presence of 1alpha-25-hydroxyvitamin D3 (1,25(OH)2D3) (from Sigma-Aldrich), but without 10 ng/ml of IL-12 (R&D Systems). After 2 days, T cells were transferred to a new plate, and fresh medium containing IL-2 (12.5 ng/ml) was added and the cells were cultured for 4 additional days.  T effector cellls were FACS-sorted based on expression of cutaneous lymphocyte antigen (CLA) and CD3 marker.


title: DEER2

city: Madrid

first: Manuel

last: Nieto-Díaz

state: Madrid

address: Avda. Doctor Arce, 37

department: Neural Plasticity

country: Spain

institute: Instituto de Neurobiología ramón y Cajal (CSIC)

description: Labeling, Hybridization and Scanning were performed by Progenika Medplant company at Spain, following Affymetrix protocols.

data_processing: Value and detection measures were calculated following the standard protocols of Affymetrix, using MAS5 algorithms implemented in GCOS 1.2

label: Affymetrix Fluorochrome

organism: Cervus elaphus

source_name: Antler base sample maximum growth period

growth_protocol: Individual kept in captivity at the Experimental Farm of the University of Castilla-La Mancha at Albacete (Spain)

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) and purified using Rneasy kit (Qiagen, Valen, CA, USA).

treatment_protocol: No treatment besides sample taking. Sample was harvested with the individuales under anaesthesia. After sampling, biopsies were frozen in liquid nitrogen and kept at -80ºC until processing.

tag: Sample of the soft tissues (epidermis, dermis and periostium) overlying the bone at the base of the antler. Harvested during the period of maximum growth of the antler (60 days after casting the previous antler).


title: HDAC2 WT E17.5 Ventricle 1A


title: DEER4

source_name: Antler Tip; End of Gowth

tag: Sample of antler's tip tissues (velvet plus mesenchyme or derivates) harvested at the end of the antler's growth (90 days after casting the previous antlers).


title: DEER3

source_name: Soft tissues frontal bone during antler's maximum growth

tag: Sample of soft tissues (epidermis, dermis and periostium) overlying the frontal bone between the antlers. Harvested using 4mm biopsy punches during the period of maximum antler growth (60 days after casting the previous antlers).


title: DEER1

source_name: Velvet and mesenchyme tissues from tip of the growing antler

tag: Antler tip tissues (velvet plus mesenchyme) harvestad during the period of antler maximum growth  (60 days after casting the previous antlers).

tag: Adult male individual


title: brain, cochlea: [13] Sample #13_le1

description: Wild-type 5 months old, male


title: IOSE treated with TGFb for 6hr replicate 1


title: brain, cochlea: [15] Sample #15_le1

description: Wild-type 5 months old, female


title: brain, cochlea: [16] Sample #16_le1

description: Wild-type 8 months old, male


title: brain, cochlea: [14] Sample #14_le1

description: Wild-type 5 months old, female


title: brain, cochlea: [6] Sample #6_le1

description: Knockout 5 months old, female


title: brain, cochlea: [18] Sample #18_le1

description: Wild-type 8 months old, female


title: brain, cochlea: [7] Sample #7_le1

description: Knockout 8 months old, male


title: brain, cochlea: [10] Sample #10_le1

description: Wild-type 3 months old, male


title: brain, cochlea: [11] Sample #11_le1

description: Wild-type 3 months old, female


title: brain, cochlea: [3] Sample #3_le1

description: Knockout 3 months old, female


title: brain, cochlea: [5] SAmple #5_le1

description: Knockout 5 months old, female


title: brain, cochlea: [2] Sample #2_le1

description: Knockout 3 months old, female


title: brain, cochlea: [1] Sample #1_le1

description: Knockout 3 months old, male


title: brain, cochlea: [12] Sample #12_le1

description: Wild-type 3 months old, female


title: eye, cornea: TRizol Extraction_le1 8

description: wildtype litter mate to the mice that have the overexpression of tgf beta

source_name: eye, cornea


title: eye, cornea: TRizol Extraction_le1 7


title: brain, cochlea: [4] Sample #4_le1

description: Knockout 5 months old, male


title: brain, cochlea: [8] Sample #8_le1

description: Knockout 8 months old, female


title: eye, cornea: TRizol Extraction_le1 4

description: mice that have the overexpression of tgf beta


title: brain, cochlea: [9] Sample #9_le1

description: Knockout 8 months old, male


title: eye, cornea: TRizol Extraction_le1 3


title: eye, cornea: TRizol Extraction_le1 2


title: eye, cornea: TRizol Extraction_le1 5


title: brain, cerebral cortex: Extract 8_le1

description:
FGF2 +SB202190  #2
Treatment, type=acclimatization, description=growth factor + p38 inhibitor

source_name: brain, cerebral cortex


title: brain, cerebral cortex: Extract 7_le1

description:
FGF2 +SB202190  #1
Treatment, type=wait, description=growth factor + p38  inhibitor


title: WW002_ATH1_A2-willa-ISOX-REP3

status: Public on Jan 08 2007

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 87.00
Background Stdev (float) = 2.69
Background Max (float) = 94.3
Background Min (float) = 82.0
Noise Avg (float) = 4.57
Noise Stdev (float) = 0.19
Noise Max (float) = 5.1
Noise Min (float) = 4.1
RawQ (float) = 3.50
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 613
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: WW002_ATH1_A2-willa-ISOX-REP3.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 = 229 (type integer); Parameter Upper left corner y coordinate = 232 (type integer); Parameter Upper right corner x coordinate = 4501 (type integer); Parameter Upper right corner y coordinate = 264 (type integer); Parameter Lower right corner x coordinate = 4471 (type integer); Parameter Lower right corner y coordinate = 4534 (type integer); Parameter Lower left corner x coordinate = 198 (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 = 0.452309 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

source_name: Willats-ISOXEBEN Treated Rep 3

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 Medium = Murashige and Skooge; Parameter Nutrients = 30g/L sucrose, 0.5mg/L Napthalene acetic acid, 0.05mg/L Kinetin; Parameter Temperature = Unknown; Performer: William,,Willats

extract_protocol: Qiagen / Trizol; Protocol: Qiagen RNAeasy kit protocol ; Protocol Type = nucleic_acid_extraction; Performer: William,,Willats

treatment_protocol: 0.1 mM ISOXABEN ; Performer: William,,Willats

tag: OrganismPart

value: Cell suspension

tag: Ecotype:


title: eye, cornea: TRizol Extraction_le1 1


title: eye, cornea: TRizol Extraction_le1 6


title: JH003_ATH1_A18-Hammond-CR3

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 72.51
Background Stdev (float) = 1.15
Background Max (float) = 75.7
Background Min (float) = 69.9
Noise Avg (float) = 3.85
Noise Stdev (float) = 0.22
Noise Max (float) = 5.0
Noise Min (float) = 3.2
RawQ (float) = 2.68
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 246
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: JH003_ATH1_A18-Hammond-CR3.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 = 4502 (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 = 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 = 0.387619 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

growth_protocol: unknown; Parameter location = Growth Room; Parameter Atmosphere = Normal; Parameter Humidity = 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 containing 2 mM Caesium ; Performer: John,,Hammond

value: all root material

tag: Ecotype

tag: NASC:Growth Stage


title: WW001_ATH1_A1-WILLA-CON

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 67.11
Background Stdev (float) = 1.98
Background Max (float) = 71.9
Background Min (float) = 63.3
Noise Avg (float) = 4.30
Noise Stdev (float) = 0.28
Noise Max (float) = 5.1
Noise Min (float) = 3.5
RawQ (float) = 2.83
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 7023
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: WW001_ATH1_A1-WILLA-CON.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 = 4499 (type integer); Parameter Upper right corner y coordinate = 246 (type integer); Parameter Lower right corner x coordinate = 4486 (type integer); Parameter Lower right corner y coordinate = 4516 (type integer); Parameter Lower left corner x coordinate = 217 (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 = 0.397030 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;


title: brain, cerebral cortex: Extract 6_le1

description:
FGF2 +U0126 #2
Treatment, type=wait, description=growth factor + MEK inhibitor


title: WW002_ATH1_A2-willa-ISOX-REP2

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 113.18
Background Stdev (float) = 1.95
Background Max (float) = 119.6
Background Min (float) = 109.5
Noise Avg (float) = 6.47
Noise Stdev (float) = 0.27
Noise Max (float) = 7.0
Noise Min (float) = 5.5
RawQ (float) = 4.25
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 160
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: WW002_ATH1_A2-willa-ISOX-REP2.DAT

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 = 232 (type integer); Parameter Upper right corner x coordinate = 4501 (type integer); Parameter Upper right corner y coordinate = 259 (type integer); Parameter Lower right corner x coordinate = 4476 (type integer); Parameter Lower right corner y coordinate = 4529 (type integer); Parameter Lower left corner x coordinate = 204 (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 = 0.333102 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

source_name: Willats-ISOXEBEN Treated Rep 2


title: WW002_ATH1_A1-willa-CON-REP3

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 90.36
Background Stdev (float) = 1.45
Background Max (float) = 95.8
Background Min (float) = 87.5
Noise Avg (float) = 5.22
Noise Stdev (float) = 0.35
Noise Max (float) = 6.6
Noise Min (float) = 4.5
RawQ (float) = 3.63
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 580
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: WW002_ATH1_A1-willa-CON-REP3.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 = 234 (type integer); Parameter Upper right corner x coordinate = 4501 (type integer); Parameter Upper right corner y coordinate = 286 (type integer); Parameter Lower right corner x coordinate = 4450 (type integer); Parameter Lower right corner y coordinate = 4556 (type integer); Parameter Lower left corner x coordinate = 178 (type integer); Parameter Lower left corner y coordinate = 4504 (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 = 0.348188 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

source_name: Willats-Control Rep 3


title: WW002_ATH1_A1-willa-CON-REP2

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 84.53
Background Stdev (float) = 1.48
Background Max (float) = 90.0
Background Min (float) = 81.8
Noise Avg (float) = 4.69
Noise Stdev (float) = 0.16
Noise Max (float) = 5.2
Noise Min (float) = 4.2
RawQ (float) = 3.42
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 356
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: WW002_ATH1_A1-willa-CON-REP2.DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 230 (type integer); Parameter Upper left corner y coordinate = 232 (type integer); Parameter Upper right corner x coordinate = 4502 (type integer); Parameter Upper right corner y coordinate = 253 (type integer); Parameter Lower right corner x coordinate = 4482 (type integer); Parameter Lower right corner y coordinate = 4523 (type integer); Parameter Lower left corner x coordinate = 211 (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 = 0.317938 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

source_name: Willats-Control Rep 2


title: AM001_ATH1_Control

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 80.02
Background Stdev (float) = 1.42
Background Max (float) = 84.4
Background Min (float) = 77.5
Noise Avg (float) = 5.69
Noise Stdev (float) = 0.29
Noise Max (float) = 6.8
Noise Min (float) = 5.1
RawQ (float) = 3.30
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 850
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: AM001_ATH1_Control.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 = 4505 (type integer); Parameter Upper right corner y coordinate = 209 (type integer); Parameter Lower right corner x coordinate = 4527 (type integer); Parameter Lower right corner y coordinate = 4479 (type integer); Parameter Lower left corner x coordinate = 256 (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 = 0.335717 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

growth_protocol: unknown; Parameter Light = 24hr; Parameter Temperature = 22C; Performer: Alan,,Marchant

extract_protocol: Qiagen / Trizol; Protocol: Qiagen RNAeasy kit protocol ; Protocol Type = nucleic_acid_extraction; Performer: Alan,,Marchant

value: Whole plant


title: WW001_ATH1_A2-WILLA-ISOX

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 85.82
Background Stdev (float) = 3.37
Background Max (float) = 93.0
Background Min (float) = 78.8
Noise Avg (float) = 4.90
Noise Stdev (float) = 0.24
Noise Max (float) = 5.6
Noise Min (float) = 4.3
RawQ (float) = 3.41
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 293
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: WW001_ATH1_A2-WILLA-ISOX.DAT

hyb_protocol: FlexGE-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 = 232 (type integer); Parameter Upper left corner y coordinate = 230 (type integer); Parameter Upper right corner x coordinate = 4501 (type integer); Parameter Upper right corner y coordinate = 227 (type integer); Parameter Lower right corner x coordinate = 4505 (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 = 0.290194 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;


title: AM001_ATH1_axr4-2

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 70.79
Background Stdev (float) = 2.30
Background Max (float) = 77.5
Background Min (float) = 66.2
Noise Avg (float) = 3.96
Noise Stdev (float) = 0.18
Noise Max (float) = 4.5
Noise Min (float) = 3.5
RawQ (float) = 2.80
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 366
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: AM001_ATH1_axr4-2.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 = 4503 (type integer); Parameter Upper right corner y coordinate = 251 (type integer); Parameter Lower right corner x coordinate = 4485 (type integer); Parameter Lower right corner y coordinate = 4521 (type integer); Parameter Lower left corner x coordinate = 214 (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 = 0.395512 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

tag: GeneticModification

value: Mutant see Hobbie and Estelle (1995) Plant J. 7 211-220

tag: StrainOrLine


title: brain, cerebral cortex: Extract 5_le1

description:
FGF2 +U0126 #1
Treatment, type=wait, description=growth factor + MEK inhibitor


title: JH003_ATH1_A15-Hammond-CS3

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 72.43
Background Stdev (float) = 1.70
Background Max (float) = 75.1
Background Min (float) = 66.9
Noise Avg (float) = 4.14
Noise Stdev (float) = 0.24
Noise Max (float) = 4.6
Noise Min (float) = 3.5
RawQ (float) = 2.78
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 333
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: JH003_ATH1_A15-Hammond-CS3.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 = 230 (type integer); Parameter Upper right corner x coordinate = 4503 (type integer); Parameter Upper right corner y coordinate = 235 (type integer); Parameter Lower right corner x coordinate = 4500 (type integer); Parameter Lower right corner y coordinate = 4505 (type integer); Parameter Lower left corner x coordinate = 228 (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 = 0.386568 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

value: shoots


title: JH003_ATH1_A16-Hammond-FR3

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 76.05
Background Stdev (float) = 1.62
Background Max (float) = 79.8
Background Min (float) = 71.4
Noise Avg (float) = 4.01
Noise Stdev (float) = 0.10
Noise Max (float) = 4.2
Noise Min (float) = 3.7
RawQ (float) = 2.74
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 246
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: JH003_ATH1_A16-Hammond-FR3.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 = 4501 (type integer); Parameter Upper right corner y coordinate = 254 (type integer); Parameter Lower right corner x coordinate = 4480 (type integer); Parameter Lower right corner y coordinate = 4524 (type integer); Parameter Lower left corner x coordinate = 209 (type integer); Parameter Lower left corner y coordinate = 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 = 0.339807 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;


title: JH003_ATH1_A13-Hammond-FS3

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 69.44
Background Stdev (float) = 0.90
Background Max (float) = 72.1
Background Min (float) = 67.7
Noise Avg (float) = 3.72
Noise Stdev (float) = 0.15
Noise Max (float) = 4.2
Noise Min (float) = 3.4
RawQ (float) = 2.59
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 381
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: JH003_ATH1_A13-Hammond-FS3.DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 228 (type integer); Parameter Upper left corner y coordinate = 233 (type integer); Parameter Upper right corner x coordinate = 4500 (type integer); Parameter Upper right corner y coordinate = 275 (type integer); Parameter Lower right corner x coordinate = 4459 (type integer); Parameter Lower right corner y coordinate = 4545 (type integer); Parameter Lower left corner x coordinate = 188 (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 = 0.434077 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;


title: JH003_ATH1_A12-Hommond-CR2_repeat

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 63.59
Background Stdev (float) = 1.82
Background Max (float) = 67.3
Background Min (float) = 58.9
Noise Avg (float) = 3.14
Noise Stdev (float) = 0.21
Noise Max (float) = 3.5
Noise Min (float) = 2.5
RawQ (float) = 2.43
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 257
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: JH003_ATH1_A12-Hommond-CR2_repeat.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 = 4500 (type integer); Parameter Upper right corner y coordinate = 238 (type integer); Parameter Lower right corner x coordinate = 4494 (type integer); Parameter Lower right corner y coordinate = 4508 (type integer); Parameter Lower left corner x coordinate = 225 (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 = 0.457466 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;


title: brain, cerebral cortex: Extract 2_le1

description:
CTL(vehicle)#2
Treatment, type=wait, description=control


title: brain, cerebral cortex: Extract 4_le1

description:
FGF2 #2
Treatment, type=wait, description=growth factor


title: brain, cerebral cortex: Extract 3_le1

description:
FGF2 #1
Treatment, type=wait, description=growth factor


title: brain, cerebral cortex: Extract 1_le1

description:
CTL(vehicle)#1
Treatment, type=wait, description=control


title: JH003_ATH1_A8-Hammond-KS2

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 70.86
Background Stdev (float) = 2.10
Background Max (float) = 76.2
Background Min (float) = 65.0
Noise Avg (float) = 3.55
Noise Stdev (float) = 0.12
Noise Max (float) = 4.0
Noise Min (float) = 3.2
RawQ (float) = 2.55
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 682
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: JH003_ATH1_A8-Hammond-KS2.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 = 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 = 225 (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 = 0.415392 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

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


title: JH003_ATH1_A7-Hammond-FS2

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 66.65
Background Stdev (float) = 1.71
Background Max (float) = 71.0
Background Min (float) = 62.9
Noise Avg (float) = 3.47
Noise Stdev (float) = 0.16
Noise Max (float) = 3.9
Noise Min (float) = 3.0
RawQ (float) = 2.48
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: JH003_ATH1_A7-Hammond-FS2.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 = 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 = 228 (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 = 0.435108 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;