title: NO.31


title: NO.29

status: Public on Jan 08 2007

type: RNA

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

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

label: biotin

molecule: total RNA

organism: Arabidopsis thaliana

treatment_protocol: No treatment

tag: Developmental stage

value: 21-day-old plants, vegetative stage

tag: Tissue

value: complete plant


title: NO.11

institute: Nottingham Arabidopsis Stock Centre (NASC)

tag: Stock Code


title: NO.12


title: NO.20-2

treatment_protocol: 20uM t-zeatin for 3h


title: Buchanan-Wollaston_A-9-bwoll-Co1_SLD

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

value: fully expanded leaves

tag: Genetic background

value: Columbia

tag: Genetic variation

value: Coi1 transgenic


title: NO.33


title: NO.30


title: NO.19-2


title: RIKEN-GODA9A-6

source_name: de-etiolated

treatment_protocol: 1uM 6-deoxotyphasterol for 3h

value: 7-day-old seedlings

value: whole plant

value: Col


title: RIKEN-GODA9B-6


title: RIKEN-GODA1A-M

source_name: Wassilewskija

treatment_protocol: no treatment

value: seedling


title: RIKEN-GODA4A-M

source_name: gibberellin deficient (leaky)

value: Ler


title: NO.28


title: RIKEN-GODA2B-M


title: RIKEN-GODA4B-M


title: RIKEN-GODA8A-6

treatment_protocol: 1uM 3-dehydroteasterone for 3h


title: RIKEN-GODA7B-6

treatment_protocol: 1uM 3-dehydro-6-deoxoteasterone for 3h


title: RIKEN-GODA3A-M


title: RIKEN-GODA8B-6


title: RIKEN-GODA3B-M


title: RIKEN-GODA1B-M


title: RIKEN-GODA2A-M


title: RIKEN-GODA7A-6


title: RIKEN-GODA6A-6

treatment_protocol: 1uM teasterone for 3h


title: RIKEN-GODA3B-6

treatment_protocol: 1uM 6-deoxocathasterone for 3h


title: RIKEN-GODA3A-6


title: RIKEN-GODA2B-6

treatment_protocol: 10uM campestanol for 3h


title: RIKEN-GODA2A-6


title: RIKEN-GODA4B-6

treatment_protocol: 1uM cathasterone for 3h


title: RIKEN-GODA1A-6

treatment_protocol: mock treatment for 3h


title: RIKEN-GODA12B-6

treatment_protocol: 100nM castasterone for 3h


title: RIKEN-GODA12A-6


title: RIKEN-GODA5A-6

treatment_protocol: 1uM 6-deoxoteasterone for 3h


title: RIKEN-GODA1B-6


title: RIKEN-GODA6B-6


title: RIKEN-GODA10A-6

treatment_protocol: 1uM typhasterol  for 3h


title: RIKEN-GODA4A-6


title: RIKEN-GODA5B-6


title: RIKEN-GODA11B-6

treatment_protocol: 1uM 6-deoxocastasterone for 3h


title: S1500_2H_B

treatment_protocol: Transferred to the MGRL agar medium containing 1500uM sulfate for 2 hr

value: 10-day-old plant

value: root


title: RIKEN-GODA11A-6


title: S1500_24H_A

treatment_protocol: Transferred to the MGRL agar medium containing 1500uM sulfate for 24 hr


title: S1500_12H_B

treatment_protocol: Transferred to the MGRL agar medium containing 1500uM sulfate for 12 hr


title: RIKEN-GODA13B-6

treatment_protocol: 10nM brassinolide for 3h


title: S1500_24H_B


title: RIKEN-GODA10B-6


title: S1500_8H_A

treatment_protocol: Transferred to the MGRL agar medium containing 1500uM sulfate for 8 hr


title: S1500_8H_B


title: RIKEN-GODA13A-6


title: S1500_4H_A

treatment_protocol: Transferred to the MGRL agar medium containing 1500uM sulfate for 4 hr


title: S1500_0H_B

treatment_protocol: No treatment


title: S1500_2H_A


title: S1500_0H_A


title: S1500_4H_B


title: S1500_12H_A


title: S0_8H_B

treatment_protocol: Transferred to the MGRL agar medium containing 0uM sulfate for 8 hr


title: S0_2H_A

treatment_protocol: Transferred to the MGRL agar medium containing 0uM sulfate for 2 hr


title: S0_4H_A

treatment_protocol: Transferred to the MGRL agar medium containing 0uM sulfate for 4 hr


title: S0_24H_B

treatment_protocol: Transferred to the MGRL agar medium containing 0uM sulfate for 24 hr


title: S0_24H_A


title: S0_2H_B


title: S0_12H_A

treatment_protocol: Transferred to the MGRL agar medium containing 0uM sulfate for 12 hr


title: S0_8H_A


title: RIKEN-YAMAUCHI1B

treatment_protocol: incubated for 96 hours in the dark at 22C

value: dry seeds

value: seeds


title: JD AT+EO TIME EXP3 UNINF 5D

treatment_protocol: Plants were mock-inoculated by placing in settling towers for 15 minutes, then returned to the growth chamber. At 5 days post-mock-inoculation, leaves number 7 to 10 were harvested. All harvests were done in the middle of the light period.

value: 34-day old rosette-stage plants

value: leaves


title: S0_4H_B


title: RIKEN-YAMAUCHI2B

treatment_protocol: incubated for 96 hours in the dark at 4C


title: JD AT+EO TIME EXP3 UNINF 3D

treatment_protocol: Plants were mock-inoculated by placing in settling towers for 15 minutes, then returned to the growth chamber. At 3 days post-mock-inoculation, leaves number 7 to 10 were harvested. All harvests were done in the middle of the light period.

value: 32-day old rosette-stage plants


title: S0_12H_B


title: RIKEN-YAMAUCHI1A


title: JD AT+EO TIME EXP3 UNINF 18H

treatment_protocol: Plants were mock-inoculated by placing in settling towers for 15 minutes, then returned to the growth chamber. At 18 hours post-mock-inoculation, leaves number 7 to 10 were harvested. All harvests were done in the middle of the light period.

value: 29-day old rosette-stage plants


title: JD AT+EO TIME EXP3 EO INF 6H

treatment_protocol: Plants were inoculated via settling tower with 10-day old cultures of Erysiphe orontii. At 6 hours post-inoculation, leaves number 7 to 10 were harvested. All harvests were done in the middle of the light period.


title: JD AT+EO TIME EXP3 UNINF 12H

treatment_protocol: Plants were mock-inoculated by placing in settling towers for 15 minutes, then returned to the growth chamber. At 12 hours post-mock-inoculation, leaves number 7 to 10 were harvested. All harvests were done in the middle of the light period.


title: JD AT+EO TIME EXP3 EO INF 5D

treatment_protocol: Plants were inoculated via settling tower with 10-day old cultures of Erysiphe orontii.  At 5 days post-inoculation, leaves number 7 to 10 were harvested. All harvests were done in the middle of the light period.


title: JD AT+EO TIME EXP3 UNINF 4D

treatment_protocol: Plants were mock-inoculated by placing in settling towers for 15 minutes, then returned to the growth chamber. At 4 days post-mock-inoculation, leaves number 7 to 10 were harvested. All harvests were done in the middle of the light period.

value: 33-day old rosette-stage plants


title: RIKEN-YAMAUCHI2A


title: JD AT+EO TIME EXP3 EO INF 2D

treatment_protocol: Plants were inoculated via settling tower with 10-day old cultures of Erysiphe orontii.  At 2 days post-inoculation, leaves number 7 to 10 were harvested. All harvests were done in the middle of the light period.

value: 31-day old rosette-stage plants


title: JD AT+EO TIME EXP3 EO INF 24H

treatment_protocol: Plants were inoculated via settling tower with 10-day old cultures of Erysiphe orontii.  At 24 hours post-inoculation, leaves number 7 to 10 were harvested. All harvests were done in the middle of the light period.

value: 30-day old rosette-stage plants


title: JD AT+EO TIME EXP3 UNINF 24H

treatment_protocol: Plants were mock-inoculated by placing in settling towers for 15 minutes, then returned to the growth chamber. At 24 hours post-mock-inoculation, leaves number 7 to 10 were harvested. All harvests were done in the middle of the light period.


title: JD AT+EO TIME EXP3 EO INF 4D

treatment_protocol: Plants were inoculated via settling tower with 10-day old cultures of Erysiphe orontii.  At 4 days post-inoculation, leaves number 7 to 10 were harvested. All harvests were done in the middle of the light period.


title: JD AT+EO TIME EXP3 EO INF 18H

treatment_protocol: Plants were inoculated via settling tower with 10-day old cultures of Erysiphe orontii.  At 18 hours post-inoculation, leaves number 7 to 10 were harvested. All harvests were done in the middle of the light period.


title: JD AT+EO COL WT EXP2 18H INFECTED


title: JD AT+EO COL WT EXP2 12H UNINFECTED


title: JD AT+EO COL WT EXP2 18H UNINFECTED


title: JD AT+EO TIME EXP3 EO INF 3D

treatment_protocol: Plants were inoculated via settling tower with 10-day old cultures of Erysiphe orontii.  At 3 days post-inoculation, leaves number 7 to 10 were harvested. All harvests were done in the middle of the light period.


title: JD AT+EO TIME EXP3 UNINF 2D

treatment_protocol: Plants were mock-inoculated by placing in settling towers for 15 minutes, then returned to the growth chamber. At 2 days post-mock-inoculation, leaves number 7 to 10 were harvested. All harvests were done in the middle of the light period.


title: JD AT+EO COL WT EXP2 06H UNINFECTED

treatment_protocol: Plants were mock-inoculated by placing in settling towers for 15 minutes, then returned to the growth chamber. At 6 hours post-mock-inoculation, leaves number 7 to 10 were harvested. All harvests were done in the middle of the light period.


title: JD AT+EO COL WT EXP2 04D UNINFECTED


title: JD AT+EO COL WT EXP2 06H INFECTED


title: JD AT+EO COL WT EXP2 12H INFECTED

treatment_protocol: Plants were inoculated via settling tower with 10-day old cultures of Erysiphe orontii.  At 12 hours post-inoculation, leaves number 7 to 10 were harvested. All harvests were done in the middle of the light period.


title: JD AT+EO COL WT EXP2 24H INFECTED


title: JD AT+EO COL WT EXP2 03D UNINFECTED


title: JD AT+EO COL WT EXP2 02D UNINFECTED


title: JD AT+EO COL WT EXP2 04D INFECTED


title: JD AT+EO COL WT EXP2 05D UNINFECTED

treatment_protocol: Plants were mock-inoculated by placing in settling towers for 15 minutes, then returned to the growth chamber. At 5 days post-mock-inoculation, leaves number 7 to 10 were harvested. All harvests were done in the middle of the light period.


title: JD AT+EO COL WT EXP2 24H UNINFECTED


title: JD AT+EO TIME EXP3 EO INF 12H


title: JD AT+EO COL WT 12H UNINFECTED


title: JD AT+EO COL WT EXP2 03D INFECTED


title: JD AT+EO COL WT 18H INFECTED


title: JD AT+EO COL WT 12H INFECTED


title: JD AT+EO COL WT EXP2 02D INFECTED


title: JD AT+EO COL WT 18H UNINFECTED


title: JD AT+EO COL WT 24H UNINFECTED


title: JD AT+EO COL WT 06H UNINFECTED


title: JD AT+EO COL WT EXP2 05D INFECTED


title: JD AT+EO COL WT 24H INFECTED


title: JD AT+EO COL WT 06H INFECTED


title: JD AT+EO COL WT 04D UNINFECTED


title: JD AT+EO COL WT 02D UNINFECTED


title: JD AT+EO COL WT 04D INFECTED


title: JD AT+EO COL WT 03D UNINFECTED


title: JD AT+EO COL WT 03D INFECTED


title: JD AT+EO COL WT 02D INFECTED


title: JD AT+EO COL WT 05D INFECTED


title: 2530

treatment_protocol: Virulent pathogen (Pseudomonas syringae ES4326) infection, 4h

value: 4-week old plants at 10-11 rossette lead stage (just before bolting)

value: leaf


title: 2526

treatment_protocol: Virulent pathogen (Pseudomonas syringae ES4326) infection, 24h


title: 2509

treatment_protocol: Avirulent pathogen (Pseudomonas syringae ES4326 avrRpt2) infection, 24h


title: 2504

treatment_protocol: Avirulent pathogen (Pseudomonas syringae ES4326 avrRpt2) infection, 4h


title: 2528

treatment_protocol: Virulent pathogen (Pseudomonas syringae ES4326) infection, 16h


title: 2529

treatment_protocol: Virulent pathogen (Pseudomonas syringae ES4326) infection, 8h


title: 2798

treatment_protocol: no treatment


title: 2507

treatment_protocol: Mock treatment (10mM MgCl2 solution), 8h


title: 2511

treatment_protocol: Avirulent pathogen (Pseudomonas syringae ES4326 avrRpt2) infection, 48h


title: 2794


title: 2796


title: 2512

treatment_protocol: Mock treatment (10mM MgCl2 solution), 48h


title: 2505

treatment_protocol: Mock treatment (10mM MgCl2 solution), 4h


title: 2506

treatment_protocol: Avirulent pathogen (Pseudomonas syringae ES4326 avrRpt2) infection, 8h


title: JD AT+EO TIME EXP3 UNINF 6H


title: 2797


title: 2792


title: 2795


title: 2525

treatment_protocol: Virulent pathogen (Pseudomonas syringae ES4326) infection, 48h


title: 2787


title: 2788


title: 2786

treatment_protocol: Mock treatment (10mM MgCl2 solution), 24h


title: 2789

treatment_protocol: Mock treatment (10mM MgCl2 solution), 16h


title: 2527


title: 2503

treatment_protocol: No Treatment


title: 2790

treatment_protocol: Avirulent pathogen (Pseudomonas syringae ES4326 avrRpt2) infection, 16h


title: 2510


title: 2785


title: 2791


title: 2784


title: 2793


title: 2783


title: BC482-2

treatment_protocol: Conidiospores of Botrytis cinerea were collected with sterile water from 2-week-old plates, pelletted and resuspended in 24 g L-1 sterile potato dextrose broth (Difco, Detroit, USA). Conidiospores were diluted to 5X10^5 spores/ml and pre-germinated at RT for 3 hours. Four 5 ul droplets were placed on each of 4-5 fully expanded rosette leaves per plant. Plants were watered right before the experiment, leaving 500 ml of watered on the bottom of the flat, then inoculated, covered with a clear plastic lid. Leaves were harvested 48 hpi.

value: 4-week old rosette-stage plants


title: BC181-2

treatment_protocol: Conidiospores of Botrytis cinerea were collected with sterile water from 2-week-old plates, pelletted and resuspended in 24 g L-1 sterile potato dextrose broth (Difco, Detroit, USA). Conidiospores were diluted to 5X10^5 spores/ml and pre-germinated at RT for 3 hours. Four 5 ul droplets were placed on each of 4-5 fully expanded rosette leaves per plant. Plants were watered right before the experiment, leaving 500 ml of watered on the bottom of the flat, then inoculated, covered with a clear plastic lid. Leaves were harvested 18 hpi.


title: CT482-2

treatment_protocol: Four 5 ul droplets of sterile potato dextrose broth were placed on each of 4-5 fully expanded rosette leaves per plant. Plants were watered right before the experiment, leaving 500 ml of watered on the bottom of the flat, then inoculated, covered with a clear plastic lid. Leaves were harvested 48 hpi.


title: BC181-1


title: JD AT+EO COL WT 05D UNINFECTED

treatment_protocol: Plants were mock-inoculated by placing in settling towers for 15 minutes, then returned to the growth chamber. At 5 days post-mock-inoculation, leaves number 7 to 10 were harvested. All harvests were done in the middle of the light period.


title: CT182-1

treatment_protocol: Four 5 ul droplets of sterile potato dextrose broth were placed on each of 4-5 fully expanded rosette leaves per plant. Plants were watered right before the experiment, leaving 500 ml of watered on the bottom of the flat, then inoculated, covered with a clear plastic lid. Leaves were harvested 18 hpi.


title: CT481-1


title: BC481-1


title: BC482-1


title: CT181-1


title: CT482-1


title: 2508


title: CT181-2


title: BC182-1


title: Pracharoenwattana_1-2_mdhB_Rep2_ATH1

description:
location: Growth Room
Temperature: 22 C
Lighting: continuous light
Medium: Half strength Murashige and Skoog agar
Nutrients: 1% sucrose
Stratification: 2 days 4 C on agar

value: whole seeds

value: T-DNA inserts in At2g22780 and At5g09660


title: Pracharoenwattana_1-4_ColA_Rep1_ATH1

value: wild type segregant from a T-DNA heterozygote


title: Pracharoenwattana_1-6_ColC_Rep3_ATH1


title: Pracharoenwattana_1-1_mdhA_Rep1_ATH1


title: Quick_A104_5-0hr_Rep4_ATH1

description:
location: Growth Room
Atmosphere: Normal
Humidity: 50 %
Temperature: 20°C
Lighting: 10 h
Medium: Humax compost
Water: every 2-3 days

treatment_protocol: This sample is rep 4, steady state elevated 0h control.

value: developing leaf insertions 19-21


title: Quick_A52_5-0hr_Rep2_ATH1

treatment_protocol: This sample is rep 2, steady-state grown in elevated CO2, 0h control.


title: Quick_A26_5-0hr_Rep1_ATH1

treatment_protocol: This sample is from the steady state elevated control where plants were grown as above but in an elevated carbon dioxide atmosphere at 750 ppm. The plants were at the same stage when placed into the cuvette system and the same three leaves were harvested at time 0 h after the same 24 h adjustment period. These are therefore acting as elevated carbon dioxide steady state controls.


title: Pracharoenwattana_1-3_mdhC_Rep3_ATH1


title: Quick_A111_3-24hr_Rep2m_ATH1

treatment_protocol: This sample is taken from the mature leaves of plants that have had the above treatments for 24h. This sample is Rep 2 24 h ASm.

value: mature leaves


title: Quick_A1_1-0hr_Rep1_ATH1

treatment_protocol: This sample is rep 1, 0h A.


title: Quick_A53_0-0hr_Rep3_ATH1

treatment_protocol: This sample is rep 3, 0h control.


title: Thornton_1-2_Col+trichoderma_Rep1_ATH1

description:
location: Growth Room
Temperature: 19
Lighting: 16h photoperiod
Medium: compost
Treatment: with soil fungus
Water: when needed

source_name: Col + trichoderma

value: whole plant (leaves and roots)

value: Col


title: Quick_A78_5-0hr_Rep3_ATH1

treatment_protocol: This sample is rep 3, steady-state, elevated CO2 0hr control.


title: Quick_A94_3-24hr_Rep4_ATH1

treatment_protocol: This sample is rep 4, 24h AS.


title: Quick_A102_3-96hr_Rep4_ATH1

treatment_protocol: This sample is rep 4, 96h AS.


title: Quick_A79_0-0hr_Rep4_ATH1

treatment_protocol: This sample is rep 4, 0h control.


title: Pracharoenwattana_1-5_ColB_Rep2_ATH1


title: Quick_A27_0-0hr_Rep2_ATH1

treatment_protocol: This sample is rep 2, 0h control.


title: Thornton_1-1_Control_Rep1_ATH1

description:
location: Growth Room
Temperature: 19
Lighting: 16h photoperiod
Medium: compost
Water: when needed

source_name: Col


title: Quick_A98_3-48hr_Rep4_ATH1

treatment_protocol: This sample is rep 4, 48h AS.


title: Quick_A107_3-24hr_Rep1m_ATH1

treatment_protocol: This sample is taken from the mature leaves of plants that have had the above treatments for 24h. This sample is Rep 1 24 h ASm.


title: Quick_A90_3-12hr_Rep4_ATH1

treatment_protocol: This sample is rep 4, 12h AS.


title: Quick_A86_3-4hr-Rep4_ATH1

treatment_protocol: This sample is rep 4, 4h AS.


title: Quick_A82_3-2hr_Rep4_ATH1

treatment_protocol: This sample is rep 4, 2h AS.


title: Quick_A72_3-48hr_Rep3_ATH1

treatment_protocol: This sample is rep 3, 48h AS.


title: Quick_A64_3-12hr_Rep3_ATH1

treatment_protocol: This sample is rep 3, 12h AS.


title: Quick_A76_3-96hr_Rep3_ATH1

treatment_protocol: This sample is rep 3, 96h AS.


title: Quick_A46_3-48hr_Rep2_ATH1

treatment_protocol: This sample is rep 2, 48h AS.


title: Quick_A68_3-24hr_Rep3_ATH1

treatment_protocol: This sample is rep 3, 24h AS.


title: Quick_A60_3-4hr-Rep3_ATH1

treatment_protocol: This sample is rep 3, 4h AS.


title: Quick_A34_3-4hr-Rep2_ATH1

treatment_protocol: This sample is rep 2, 4h AS.


title: Quick_A17_3-24hr_Rep1_ATH1

treatment_protocol: This sample is from the 24h AS treatment, rep 1.


title: Quick_A56_3-2hr_Rep3_ATH1

treatment_protocol: This sample is rep 3, 2h AS.


title: Quick_A38_3-12hr_Rep2_ATH1

treatment_protocol: This sample is rep 2, 12h AS.


title: Quick_A12_3-12hr_Rep1_ATH1

treatment_protocol: This sample is from the 12h AS treatment, rep 1.


title: Quick_A9_3-4hr-Rep1_ATH1

treatment_protocol: This sample is from the 4h ES treatment, rep 1.


title: Quick_A24_3-96hr_Rep1_ATH1

treatment_protocol: This sample is from the 96h AS treatment, rep 1.


title: Quick_A30_3-2hr_Rep2_ATH1

treatment_protocol: This sample is rep 2, 2h AS.


title: Quick_A93_2-24hr_Rep4_ATH1

treatment_protocol: This sample is rep 4, 24h E.


title: Quick_A20_3-48hr_Rep1_ATH1

treatment_protocol: This sample is from the 48h AS treatment, rep 1.


title: Quick_A42_3-24hr_Rep2_ATH1

treatment_protocol: This sample is rep 2, 24h AS.


title: Quick_A110_2-24hr_Rep2m_ATH1

treatment_protocol: This sample is taken from the mature leaves of plants that have had the above treatments for 24h. This sample is Rep 2 24 h Em.


title: Quick_A81_2-2hr_Rep4_ATH1

treatment_protocol: This sample is rep 4, 2h E.


title: Quick_A8_3-4hr-Rep1_ATH1

treatment_protocol: This sample is from the 4h AS treatment, rep 1.


title: Quick_A85_2-4hr-Rep4_ATH1

treatment_protocol: This sample is rep 4, 4h E.


title: Quick_A16_3-24hr_Rep1_ATH1


title: Quick_A50_3-96hr_Rep2_ATH1

treatment_protocol: This sample is rep 2, 96h AS.


title: Quick_A89_2-12hr_Rep4_ATH1

treatment_protocol: This sample is rep 4, 12h E.


title: Quick_A101_2-96hr_Rep4_ATH1

treatment_protocol: This sample is rep 4, 96h E.


title: Quick_A4_3-2hr_Rep1_ATH1

treatment_protocol: This sample is from the 2h AS treatment, rep 1.


title: Quick_A106_2-24hr_Rep1m_ATH1

treatment_protocol: This sample is taken from the mature leaves of plants that have had the above treatments for 24h. This sample is Rep 1 24 h Em.


title: Quick_A97_2-48hr_Rep4_ATH1

treatment_protocol: This sample is rep 4, 48h E.


title: Quick_A63_2-12hr_Rep3_ATH1

treatment_protocol: This sample is rep 3, 12h E.


title: Quick_A67_2-24hr_Rep3_ATH1

treatment_protocol: This sample is rep 3, 24h E.


title: Quick_A33_2-4hr-Rep2_ATH1

treatment_protocol: This sample is rep 2, 4h E.


title: Quick_A23_2-96hr_Rep1_ATH1

treatment_protocol: This sample is from the 96h E treatment, rep 1.


title: Quick_A11_2-12hr_Rep1_ATH1

treatment_protocol: This sample is from the 12h E treatment, rep 1.


title: Quick_A37_2-12hr_Rep2_ATH1

treatment_protocol: This sample is rep 2, 12h E.


title: Quick_A71_2-48hr_Rep3_ATH1

treatment_protocol: This sample is rep 3, 48h E.


title: Quick_A19_2-48hr_Rep1_ATH1

treatment_protocol: This sample is from the 48h E treatment, rep 1.


title: Quick_A29_2-2hr_Rep2_ATH1

treatment_protocol: This sample is rep 2, 2h E.


title: Quick_A15_2-24hr_Rep1_ATH1

treatment_protocol: This sample is from the 24h E treatment, rep 1.


title: Quick_A41_2-24hr_Rep2_ATH1

treatment_protocol: This sample is rep 2, 24h E.


title: Quick_A55_2-2hr_Rep3_ATH1

treatment_protocol: This sample is rep 3, 2h E.


title: Quick_A45_2-48hr_Rep2_ATH1

treatment_protocol: This sample is rep 2, 48h E.


title: Quick_A100_1-96hr_Rep4_ATH1

treatment_protocol: This sample is rep 4, 96h A.


title: Quick_A80_1-2hr_Rep4_ATH1

treatment_protocol: This sample is rep 4, 2h A.


title: Quick_A75_2-96hr_Rep3_ATH1

treatment_protocol: This sample is rep 3, 96h E.


title: Quick_A74_1-96hr_Rep3_ATH1

treatment_protocol: This sample is rep 3, 96h A.


title: Quick_A88_1-12hr_Rep4_ATH1

treatment_protocol: This sample is rep 4, 12h A.


title: Quick_A105_1-24hr_Rep1m_ATH1

treatment_protocol: This sample is taken from the mature leaves of plants that have had the above treatments for 24h. This sample is Rep 1 24 h Am.


title: Quick_A96_1-48hr_Rep4_ATH1

treatment_protocol: This sample is rep 4, 48h A.


title: Quick_A109_1-24hr_Rep2m_ATH1

treatment_protocol: This sample is taken from the mature leaves of plants that have had the above treatments for 24h. This sample is Rep 2 24 h Am.


title: Quick_A3_2-2hr_Rep1_ATH1

treatment_protocol: This sample is from the 2h E treatment, rep 1.


title: Quick_A70_1-48hr_Rep3_ATH1

treatment_protocol: This sample is rep 3, 48h A.


title: Quick_A66_1-24hr_Rep3_ATH1

treatment_protocol: This sample is rep 3, 24h A.


title: Quick_A84_1-4hr-Rep4_ATH1

treatment_protocol: This sample is rep 4, 4h A.


title: Quick_A7_2-4hr-Rep1_ATH1

treatment_protocol: This sample is from the 4h E treatment, rep 1.


title: Quick_A62_1-12hr_Rep3_ATH1

treatment_protocol: This sample is rep 3, 12h A.


title: Quick_A92_1-24hr_Rep4_ATH1

treatment_protocol: This sample is rep 4, 24h A.


title: Quick_A49_2-96hr_Rep2_ATH1

treatment_protocol: This sample is rep 2, 96h E.


title: Quick_A40_1-24hr_Rep2_ATH1

treatment_protocol: This sample is rep 2, 24h A.


title: Quick_A58_1-4hr-Rep3_ATH1

treatment_protocol: This sample is rep 3, 4h A.


title: Quick_A54_1-2hr_Rep3_ATH1

treatment_protocol: This sample is rep 3, 2h A.


title: Quick_A6_1-4hr-Rep1_ATH1

treatment_protocol: This sample is from the 4h A treatment, rep 1.


title: Quick_A48_1-96hr_Rep2_ATH1

treatment_protocol: This sample is rep 2, 96h A.


title: Quick_A28_1-2hr_Rep2_ATH1

treatment_protocol: This sample is rep 2, 2h A.


title: Quick_A2_1-2hr_Rep1_ATH1

treatment_protocol: This sample is from the 2h A treatment, rep 1.


title: Quick_A32_1-4hr-Rep2_ATH1

treatment_protocol: This sample is rep 2, 4h A.


title: Quick_A18_1-48hr_Rep1_ATH1

treatment_protocol: This sample is from the 48h A treatment, rep 1.


title: Quick_A10_1-12hr_Rep1_ATH1

treatment_protocol: This sample is from the 12h A treatment, rep 1.


title: Quick_A44_1-48hr_Rep2_ATH1

treatment_protocol: This sample is rep 2, 48h A.


title: ATGE_84_B

value: seeds, stage 10, w/o siliques


title: Quick_A36_1-12hr_Rep2_ATH1

treatment_protocol: This sample is rep 2, 12h A.


title: Quick_A22_1-96hr_Rep1_ATH1

treatment_protocol: This sample is from the 96h A treatment, rep 1.


title: ATGE_83_C

value: seeds, stage 9, w/o siliques


title: ATGE_81_C

value: seeds, stage 7, w/o siliques


title: Quick_A14_1-24hr_Rep1_ATH1

treatment_protocol: This sample is from the 24h A treatment, rep 1.


title: ATGE_83_A


title: ATGE_79_B

value: seeds, stage 6, w/o siliques


title: ATGE_79_A


title: ATGE_82_C

value: seeds, stage 8, w/o siliques


title: ATGE_83_B


title: ATGE_82_A


title: ATGE_81_A


title: ATGE_82_B


title: ATGE_79_C


title: ATGE_81_B


title: Quick_A59_2-4hr-Rep3_ATH1

treatment_protocol: This sample is rep 3, 4h E.


title: ATGE_84_D


title: ATGE_77_F

value: siliques, w/  seeds stage 4


title: ATGE_78_F

value: siliques, w/  seeds stage 5


title: ATGE_76_C

description:
Photoperiod: long day
Relative humidity: 50-60%
Substrate: soil
Temperature: 23oC

value: siliques, w/  seeds stage 3


title: ATGE_76_A


title: ATGE_77_E


title: ATGE_78_D


title: ATGE_76_B


title: ATGE_52_C

description:
Photoperiod: continuous light
Relative humidity: 65%
Substrate: soil
Temperature: 23oC

value: shoot apex, inflorescence (after bolting)


title: ATGE_49_C


title: ATGE_78_E


title: ATGE_50_A


title: ATGE_77_D


title: ATGE_49_B


title: ATGE_51_A


title: ATGE_52_A


title: ATGE_47_A


title: ATGE_51_C


title: ATGE_50_B


title: ATGE_52_B


title: ATGE_50_C


title: ATGE_47_C


title: ATGE_48_B


title: ATGE_49_A


title: ATGE_51_B


title: ATGE_46_C


title: ATGE_48_C


title: ATGE_48_A


title: ATGE_46_B


title: ATGE_29_B2

description:
Photoperiod: continuous light
Relative humidity: 65%
Substrate: soil
Temperature: 23oC
Tissue comments: apex + flowers up to stage 7/8


title: ATGE_27_C

value: stem, 2nd internode


title: ATGE_46_A


title: ATGE_8_A

value: shoot apex, transition (before bolting)


title: ATGE_29_A2


title: ATGE_28_A2

description:
Photoperiod: continuous light
Relative humidity: 65%
Substrate: soil
Temperature: 23oC
Tissue comments: tissue sampled includes part of the stem (approx. 1 mm below and above the branching point), part of the side shoot (approx. 1 mm in length) as well as the base of the 1st cauline leaf

value: 1st node


title: ATGE_28_C2


title: ATGE_27_A


title: ATGE_28_B2


title: ATGE_27_B


title: ATGE_2_A

value: hypocotyl


title: ATGE_4_A

value: shoot apex, vegetative + young leaves


title: ATGE_8_C


title: ATGE_4_B


title: ATGE_4_C


title: ATGE_6_A

value: shoot apex, vegetative


title: ATGE_2_C


title: ATGE_92_C

description:
Photoperiod: long day
Substrate: soil
Temperature: 20oC

value: flower


title: ATGE_6_B


title: ATGE_8_B


title: ATGE_47_B


title: ATGE_6_C


title: ATGE_2_B


title: ATGE_92_B


title: ATGE_73_C

description:
Photoperiod: continuous light
Substrate: soil
Temperature: 23oC

value: mature pollen


title: ATGE_92_A


title: ATGE_84_A

value: seeds, stage 10, w/o siliques


title: ATGE_73_A


title: ATGE_59_B

description:
Photoperiod: continuous light
Relative humidity: 65%
Substrate: soil
Temperature: 23oC
Tissue comments: size similar to wildtype flowers stage12

value: flower stage 12 equivalent; filamentous organs in whorls two and three


title: ATGE_73_B


title: ATGE_59_C


title: ATGE_55_A

value: flower stage 12 equivalent; flowers without sepals, petals replaced by sec. flowers


title: ATGE_55_C


title: ATGE_56_C

value: flower stage 12 equivalent; flowers without sepals, petals; carpeloid structures on sepals


title: ATGE_54_B

value: flower stage 12 equivalent; flowers converted to leaf-like structures; some shoot characteristics


title: ATGE_57_B

value: flower stage 12 equivalent; flowers without petals, stamens


title: ATGE_58_C

value: flower stage 12 equivalent; flowers without stamens, carpels; replaced by sepals and petals; indeterminate


title: ATGE_58_A


title: ATGE_59_A


title: ATGE_57_A


title: ATGE_58_B


title: ATGE_54_A


title: ATGE_54_C


title: ATGE_57_C


title: ATGE_53_A

value: flower stage 12 equivalent; multi-carpel gyneoceum; enlarged meristem; increased organ number


title: ATGE_42_D

value: flowers stage 15, petals


title: ATGE_56_B


title: ATGE_53_C


title: ATGE_45_C

value: flowers stage 15, carpels


title: ATGE_53_B


title: ATGE_43_C

value: flowers stage 15, stamen


title: ATGE_43_B


title: ATGE_56_A


title: ATGE_43_A


title: ATGE_55_B


title: ATGE_45_B


title: ATGE_45_A


title: ATGE_41_B

value: flowers stage 15, sepals


title: ATGE_42_C


title: ATGE_41_C


title: ATGE_42_B


title: ATGE_40_C

value: flowers stage 15, pedicels


title: ATGE_40_B


title: ATGE_39_C

value: flowers stage 15


title: ATGE_37_A

value: flowers stage 12, carpels


title: ATGE_36_C

value: flowers stage 12, stamens


title: ATGE_39_B


title: ATGE_36_B


title: ATGE_36_A


title: ATGE_29_C2

value: shoot apex, inflorescence (after bolting)


title: ATGE_37_B


title: ATGE_35_B

value: flowers stage 12, petals


title: ATGE_34_C

value: flowers stage 12, sepals


title: ATGE_37_C


title: ATGE_34_B


title: ATGE_41_A


title: ATGE_35_A


title: ATGE_35_C


title: ATGE_39_A


title: ATGE_33_B

value: flowers stage 12


title: ATGE_34_A


title: ATGE_32_B2

value: flowers stage 10/11


title: ATGE_32_C2


title: ATGE_33_A


title: ATGE_33_C


title: ATGE_32_A2


title: ATGE_31_C2

value: flowers stage 9


title: ATGE_31_B2


title: ATGE_40_A


title: ATGE_31_A2


title: ATGE_98_C

description:
Photoperiod: continuous light
Substrate: 0.5x GM
Temperature: 20oC

value: root


title: ATGE_95_B

description:
Photoperiod: continuous light
Substrate: 0.5x GM, 5% sucrose
Temperature: 20oC
Tissue comments: the majority of the plants resembled 7-day-old plants of the reference sample (ATGE no. 7)


title: ATGE_95_A


title: ATGE_99_C

description:
Photoperiod: continuous light
Substrate: 0.5x GM, 5% sucrose
Temperature: 20oC


title: ATGE_99_A


title: ATGE_94_C

description:
Photoperiod: continuous light
Substrate: 0.5x GM
Temperature: 20oC
Tissue comments: the majority of the plants resembled 7-day-old plants of the reference sample (ATGE no. 7)


title: ATGE_94_B


title: ATGE_98_A


title: ATGE_95_C


title: ATGE_99_B


title: ATGE_98_B


title: ATGE_9_B

value: roots


title: ATGE_3_C

description:
Photoperiod: continuous light
Relative humidity: 65%
Substrate: soil
Temperature: 23oC
Tissue comments: sampled tissue contaminated with soil


title: ATGE_91_B

description:
Photoperiod: long day
Substrate: 1xMS, 1% sucrose
Temperature: 22oC

value: leaf


title: ATGE_94_A


title: ATGE_93_B


title: ATGE_90_D

description:
Photoperiod: short day (10/14)
Temperature: 22oC

value: veg rosette (for phase change)


title: ATGE_93_A


title: ATGE_9_A


title: ATGE_90_B


title: ATGE_3_A


title: ATGE_91_C


title: ATGE_9_C


title: ATGE_93_C


title: ATGE_91_A


title: ATGE_3_B


title: ATGE_90_A


title: ATGE_89_B

description:
Photoperiod: short day (10/14)
Substrate: soil
Temperature: 22oC


title: ATGE_89_A


title: ATGE_25_A

value: senescing leaves


title: ATGE_87_A


title: ATGE_26_C

value: cauline leaves


title: ATGE_89_C


title: ATGE_20_B

value: leaf 7, proximal half


title: ATGE_87_B


title: ATGE_87_C


title: ATGE_20_C


title: ATGE_26_B


title: ATGE_26_A


title: ATGE_25_C


title: ATGE_20_A


title: ATGE_21_A

value: leaf 7, distal half


title: ATGE_17_A

description:
Photoperiod: continuous light
Relative humidity: 65%
Substrate: soil
Temperature: 23oC
Tissue comments: approx. 1 cm long flowering time (n=20): rosette: 11.1 +/- 0.8 cauline: 2.8 +/- 0.6 total: 13.9 +/- 1.1

value: rosette leaf # 12


title: ATGE_18_A


title: ATGE_16_C

description:
Photoperiod: continuous light
Relative humidity: 65%
Substrate: soil
Temperature: 23oC
Tissue comments: leaf #12 was approx. 1 cm long flowering time (n=20): rosette: 11.1 +/- 0.8 cauline: 2.8 +/- 0.6 total: 13.9 +/- 1.1

value: rosette leaf # 10


title: ATGE_21_B


title: ATGE_18_B


title: ATGE_16_A


title: ATGE_19_C

value: leaf 7, petiol


title: ATGE_19_A


title: ATGE_19_B


title: ATGE_18_C


title: ATGE_21_C


title: ATGE_16_B


title: ATGE_17_B


title: ATGE_17_C


title: ATGE_25_B


title: ATGE_15_B

value: rosette leaf # 8


title: ATGE_13_B

value: rosette leaf # 4


title: ATGE_12_B

value: rosette leaf # 2


title: ATGE_10_C

value: rosette leaf #4, 1cm long


title: ATGE_11_B


title: ATGE_13_A


title: ATGE_12_A

description:
Photoperiod: continuous light
Relative humidity: 65%
Substrate: soil
Temperature: 23oC
Tissue comments: leaf #12 was approx. 1 cm long, flowering time (n=20):, rosette: 11.1 +/- 0.8 cauline: 2.8 +/- 0.6, total: 13.9 +/- 1.1


title: ATGE_5_B

description:
Photoperiod: continuous light
Relative humidity: 65%
Substrate: soil
Temperature: 23oC

value: leaves 1 + 2


title: ATGE_14_B

value: rosette leaf # 6


title: ATGE_5_C


title: ATGE_10_A


title: ATGE_1_A

value: cotyledons


title: ATGE_15_C


title: ATGE_11_A


title: ATGE_12_C


title: ATGE_14_A


title: ATGE_101_B

value: seedling, green parts


title: ATGE_13_C


title: ATGE_5_A


title: ATGE_101_A


title: ATGE_14_C


title: ATGE_1_C


title: ATGE_100_B


title: ATGE_11_C


title: ATGE_1_B


title: ATGE_100_A


title: ATGE_101_C


title: ATGE_10_B


title: ATGE_15_A


title: ATGE_100_C


title: ATGE_97_C


title: ATGE_97_B


title: ATGE_97_A


title: ATGE_23_C

value: developmental drift; whole plant after transition, but before bolting


title: ATGE_22_C


title: ATGE_96_A


title: ATGE_24_A


title: ATGE_23_A


title: ATGE_24_B


title: ATGE_23_B


title: AtGen_6-9422_Heatstress(3h)+3hrecovery-Roots-6.0h_Rep2

description:
location: Growth Room
Atmosphere: Normal
Humidity: 50%
Temperature: 24
Lighting: 16 hour days
Medium: Murashige and Skoog
Water: N/A

treatment_protocol:
At day 16, stress treatment started at 3 hours of light treatment.
Heat stress (38°C, samples taken at 0.25, 0.5, 1.0, 3.0h of hs and +1, +3, +9, +21h recovery at 25°C),Group Nover/von Koskull-Döring

value: Roots


title: ATGE_22_B


title: AtGen_6-9421_Heatstress(3h)+3hrecovery-Roots-6.0h_Rep1


title: ATGE_22_A


title: ATGE_24_C


title: ATGE_7_A2


title: AtGen_6-9512_Heatstress(3h)+9hrecovery-Shoots-12.0h_Rep2

value: Shoots


title: AtGen_6-9622_Heatstress(3h)+21hrecovery-Roots-24.0h_Rep2


title: AtGen_6-9621_Heatstress(3h)+21hrecovery-Roots-24.0h_Rep1


title: AtGen_6-9412_Heatstress(3h)+3hrecovery-Shoots-6.0h_Rep2


title: ATGE_7_B2


title: ATGE_96_C


title: ATGE_96_B


title: AtGen_6-9611_Heatstress(3h)+21hrecovery-Shoots-24.0h_Rep1


title: AtGen_6-9522_Heatstress(3h)+9hrecovery-Roots-12.0h_Rep2


title: AtGen_6-9612_Heatstress(3h)+21hrecovery-Shoots-24.0h_Rep2


title: AtGen_6-9521_Heatstress(3h)+9hrecovery-Roots-12.0h_Rep1


title: ATGE_7_C2


title: AtGen_6-9411_Heatstress(3h)+3hrecovery-Shoots-6.0h_Rep1


title: AtGen_6-9822_Heatstress(3h)+1hrecovery-Roots-4.0h_Rep2


title: AtGen_6-9321_Heatstress-Roots-3.0h_Rep1


title: AtGen_6-9322_Heatstress-Roots-3.0h_Rep2


title: AtGen_6-9212_Heatstress-Shoots-1.0h_Rep2


title: AtGen_6-9722_Heatstress-Roots-0.25h_Rep2


title: AtGen_6-9122_Heatstress-Roots-0.5h_Rep2


title: AtGen_6-9221_Heatstress-Roots-1.0h_Rep1


title: AtGen_6-9712_Heatstress-Shoots-0.25h_Rep2


title: AtGen_6-9821_Heatstress(3h)+1hrecovery-Roots-4.0h_Rep1


title: AtGen_6-9121_Heatstress-Roots-0.5h_Rep1


title: AtGen_6-9222_Heatstress-Roots-1.0h_Rep2


title: AtGen_6-9311_Heatstress-Shoots-3.0h_Rep1


title: AtGen_6-9111_Heatstress-Shoots-0.5h_Rep1


title: AtGen_6-9812_Heatstress(3h)+1hrecovery-Shoots-4.0h_Rep2


title: AtGen_6-9711_Heatstress-Shoots-0.25h_Rep1


title: AtGen_6-9112_Heatstress-Shoots-0.5h_Rep2


title: AtGen_6-8622_Woundingstress-Roots-24.0h_Rep2

treatment_protocol:
At day 16, stress treatment started at 3 hours of light treatment.
Wounding stress (Punctured with pins), Group Harter


title: AtGen_6-9211_Heatstress-Shoots-1.0h_Rep1


title: AtGen_6-9811_Heatstress(3h)+1hrecovery-Shoots-4.0h_Rep1


title: AtGen_6-8612_Woundingstress-Shoots-24.0h_Rep2


title: AtGen_6-8621_Woundingstress-Roots-24.0h_Rep1


title: AtGen_6-9721_Heatstress-Roots-0.25h_Rep1


title: AtGen_6-8525_Woundingstress-Roots-12.0h_Rep2


title: AtGen_6-8511_Woundingstress-Shoots-12.0h_Rep1


title: AtGen_6-8424_Woundingstress-Roots-6.0h_Rep2


title: AtGen_6-8611_Woundingstress-Shoots-24.0h_Rep1


title: AtGen_6-8423_Woundingstress-Roots-6.0h_Rep1


title: AtGen_6-8524_Woundingstress-Roots-12.0h_Rep1


title: AtGen_6-8512_Woundingstress-Shoots-12.0h_Rep2


title: AtGen_6-8412_Woundingstress-Shoots-6.0h_Rep2


title: AtGen_6-8325_Woundingstress-Roots-3.0h_Rep2


title: AtGen_6-8224_Woundingstress-Roots-1.0h_Rep1


title: AtGen_6-8225_Woundingstress-Roots-1.0h_Rep2


title: AtGen_6-8324_Woundingstress-Roots-3.0h_Rep1


title: AtGen_6-9511_Heatstress(3h)+9hrecovery-Shoots-12.0h_Rep1


title: AtGen_6-8214_Woundingstress-Shoots-1.0h_Rep2


title: AtGen_6-8313_Woundingstress-Shoots-3.0h_Rep1


title: AtGen_6-8314_Woundingstress-Shoots-3.0h_Rep2


title: AtGen_6-8124_Woundingstress-Roots-0.5h_Rep1


title: AtGen_6-8724_Woundingstress-Roots-0.25h_Rep2


title: AtGen_6-8111_Woundingstress-Shoots-0.5h_Rep1


title: AtGen_6-8112_Woundingstress-Shoots-0.5h_Rep2


title: AtGen_6-7521_UV-Bstress-Roots-12.0h_Rep1

treatment_protocol:
At day 16, stress treatment started at 3 hours of light treatment.
UV-B stress (15 min. 1.18 W/m2 Philips TL40W/12), Group Harter


title: AtGen_6-8126_Woundingstress-Roots-0.5h_Rep2


title: AtGen_6-8712_Woundingstress-Shoots-0.25h_Rep2


title: AtGen_6-7621_UV-Bstress-Roots-24.0h_Rep1


title: AtGen_6-8411_Woundingstress-Shoots-6.0h_Rep1


title: AtGen_6-7522_UV-Bstress-Roots-12.0h_Rep2


title: AtGen_6-7511_UV-Bstress-Shoots-12.0h_Rep1


title: AtGen_6-7421_UV-Bstress-Roots-6.0h_Rep1


title: AtGen_6-7611_UV-Bstress-Shoots-24.0h_Rep1


title: AtGen_6-7612_UV-Bstress-Shoots-24.0h_Rep2


title: AtGen_6-8715_Woundingstress-Shoots-0.25h_Rep1


title: AtGen_6-7622_UV-Bstress-Roots-24.0h_Rep2


title: AtGen_6-7512_UV-Bstress-Shoots-12.0h_Rep2


title: AtGen_6-7411_UV-Bstress-Shoots-6.0h_Rep1


title: AtGen_6-7412_UV-Bstress-Shoots-6.0h_Rep2


title: AtGen_6-7422_UV-Bstress-Roots-6.0h_Rep2


title: AtGen_6-7312_UV-Bstress-Shoots-3.0h_Rep2


title: AtGen_6-8723_Woundingstress-Roots-0.25h_Rep1


title: AtGen_6-7322_UV-Bstress-Roots-3.0h_Rep2


title: AtGen_6-7121_UV-Bstress-Roots-0.5h_Rep1


title: AtGen_6-7311_UV-Bstress-Shoots-3.0h_Rep1


title: AtGen_6-8211_Woundingstress-Shoots-1.0h_Rep1


title: AtGen_6-7212_UV-Bstress-Shoots-1.0h_Rep2


title: AtGen_6-7211_UV-Bstress-Shoots-1.0h_Rep1


title: AtGen_6-7111_UV-Bstress-Shoots-0.5h_Rep1


title: AtGen_6-7721_UV-Bstress-Roots-0.25h_Rep1


title: AtGen_6-7321_UV-Bstress-Roots-3.0h_Rep1


title: AtGen_6-7712_UV-Bstress-Shoots-0.25h_Rep2


title: AtGen_6-7122_UV-Bstress-Roots-0.5h_Rep2


title: AtGen_6-7722_UV-Bstress-Roots-0.25h_Rep2


title: AtGen_6-5622_Genotoxicstress-Roots-24.0h_Rep2

treatment_protocol:
At day 16, stress treatment started at 3 hours of light treatment.
Genotoxic stress (1.5µg/ml bleomycin + 22 µg/ml mitomycin), Group Puchta. Bleomycin + mitomycin were added to the indicated concentration in the Media. To add the reagents the raft was lifted out A magnetic stir bar and a stirrer were used to mix the media and the added reagents. After the rafts were put back in the boxes, they were transferred back to the climate chamber.


title: AtGen_6-5612_Genotoxicstress-Shoots-24.0h_Rep2

treatment_protocol:
At day 16, stress treatment started at 3 hours of light treatment
Genotoxic stress (1.5µg/ml bleomycin + 22 µg/ml mitomycin), Group Puchta. Bleomycin + mitomycin were added to the indicated concentration in the Media. To add the reagents the raft was lifted out A magnetic stir bar and a stirrer were used to mix the media and the added reagents. After the rafts were put back in the boxes, they were transferred back to the climate chamber.


title: AtGen_6-7221_UV-Bstress-Roots-1.0h_Rep1


title: AtGen_6-7222_UV-Bstress-Roots-1.0h_Rep2


title: AtGen_6-5621_Genotoxicstress-Roots-24.0h_Rep1


title: AtGen_6-7711_UV-Bstress-Shoots-0.25h_Rep1


title: AtGen_6-7112_UV-Bstress-Shoots-0.5h_Rep2


title: AtGen_6-5522_Genotoxicstress-Roots-12.0h_Rep2


title: AtGen_6-5511_Genotoxicstress-Shoots-12.0h_Rep1


title: AtGen_6-9312_Heatstress-Shoots-3.0h_Rep2


title: AtGen_6-5521_Genotoxicstress-Roots-12.0h_Rep1


title: AtGen_6-5512_Genotoxicstress-Shoots-12.0h_Rep2


title: AtGen_6-5611_Genotoxicstress-Shoots-24.0h_Rep1


title: AtGen_6-5421_Genotoxicstress-Roots-6.0h_Rep1


title: AtGen_6-5321_Genotoxicstress-Roots-3.0h_Rep1


title: AtGen_6-5422_Genotoxicstress-Roots-6.0h_Rep2


title: AtGen_6-5312_Genotoxicstress-Shoots-3.0h_Rep2


title: AtGen_6-4621_Droughtstress-Roots-24.0h_Rep1

treatment_protocol:
At day 16, stress treatment started at 3 hours of light treatment.
Drought stress, Group Kudla. The plants were stressed by 15 min. dry air stream (clean bench) until 10% loss of fresh weight; then incubation in closed vessels in the climate chamber.


title: AtGen_6-5121_Genotoxicstress-Roots-0.5h_Rep1


title: AtGen_6-5122_Genotoxicstress-Roots-0.5h_Rep2


title: AtGen_6-5411_Genotoxicstress-Shoots-6.0h_Rep1


title: AtGen_6-5322_Genotoxicstress-Roots-3.0h_Rep2


title: AtGen_6-4612_Droughtstress-Shoots-24.0h_Rep2


title: AtGen_6-4611_Droughtstress-Shoots-24.0h_Rep1


title: AtGen_6-4522_Droughtstress-Roots-12.0h_Rep2


title: AtGen_6-5111_Genotoxicstress-Shoots-0.5h_Rep1


title: AtGen_6-4622_Droughtstress-Roots-24.0h_Rep2


title: AtGen_6-5112_Genotoxicstress-Shoots-0.5h_Rep2


title: AtGen_6-5311_Genotoxicstress-Shoots-3.0h_Rep1


title: AtGen_6-5222_Genotoxicstress-Roots-1.0h_Rep2


title: AtGen_6-4411_Droughtstress-Shoots-6.0h_Rep1


title: AtGen_6-4412_Droughtstress-Shoots-6.0h_Rep2


title: AtGen_6-4421_Droughtstress-Roots-6.0h_Rep1


title: AtGen_6-5221_Genotoxicstress-Roots-1.0h_Rep1


title: AtGen_6-5212_Genotoxicstress-Shoots-1.0h_Rep2


title: AtGen_6-4512_Droughtstress-Shoots-12.0h_Rep2


title: AtGen_6-4322_Droughtstress-Roots-3.0h_Rep2


title: AtGen_6-4511_Droughtstress-Shoots-12.0h_Rep1


title: AtGen_6-4422_Droughtstress-Roots-6.0h_Rep2


title: AtGen_6-4521_Droughtstress-Roots-12.0h_Rep1


title: AtGen_6-5211_Genotoxicstress-Shoots-1.0h_Rep1


title: AtGen_6-4321_Droughtstress-Roots-3.0h_Rep1


title: AtGen_6-4311_Droughtstress-Shoots-3.0h_Rep1


title: AtGen_6-4112_Droughtstress-Shoots-0.5h_Rep2


title: AtGen_6-4111_Droughtstress-Shoots-0.5h_Rep1


title: AtGen_6-4221_Droughtstress-Roots-1.0h_Rep1


title: AtGen_6-4711_Droughtstress-Shoots-0.25h_Rep1


title: AtGen_6-3421_Saltstress-Roots-6.0h_Rep1

treatment_protocol:
At day 16, stress treatment started at 3 hours of light treatment.
Salt stress (150 mM NaCl), Group Kudla. NaCl was added to a concentration of 150 mM in the Media. To add NaCl the raft was lifted out. A magnetic stir bar and a stirrer were used to mix the media and the added NaCl. After the rafts were put back in the boxes, they were transferred back to the climate chamber.


title: AtGen_6-3512_Saltstress-Shoots-12.0h_Rep2


title: AtGen_6-4122_Droughtstress-Roots-0.5h_Rep2


title: AtGen_6-4222_Droughtstress-Roots-1.0h_Rep2


title: AtGen_6-3611_Saltstress-Shoots-24.0h_Rep1


title: AtGen_6-3422_Saltstress-Roots-6.0h_Rep2


title: AtGen_6-4712_Droughtstress-Shoots-0.25h_Rep2


title: AtGen_6-4212_Droughtstress-Shoots-1.0h_Rep2


title: AtGen_6-4722_Droughtstress-Roots-0.25h_Rep2


title: AtGen_6-4721_Droughtstress-Roots-0.25h_Rep1


title: AtGen_6-3522_Saltstress-Roots-12.0h_Rep2


title: AtGen_6-3511_Saltstress-Shoots-12.0h_Rep1


title: AtGen_6-3412_Saltstress-Shoots-6.0h_Rep2


title: AtGen_6-3621_Saltstress-Roots-24.0h_Rep1


title: AtGen_6-3521_Saltstress-Roots-12.0h_Rep1


title: AtGen_6-3612_Saltstress-Shoots-24.0h_Rep2


title: AtGen_6-4312_Droughtstress-Shoots-3.0h_Rep2


title: AtGen_6-3411_Saltstress-Shoots-6.0h_Rep1


title: AtGen_6-3312_Saltstress-Shoots-3.0h_Rep2


title: AtGen_6-4121_Droughtstress-Roots-0.5h_Rep1


title: AtGen_6-3321_Saltstress-Roots-3.0h_Rep1


title: AtGen_6-3622_Saltstress-Roots-24.0h_Rep2


title: AtGen_6-3322_Saltstress-Roots-3.0h_Rep2


title: AtGen_6-4211_Droughtstress-Shoots-1.0h_Rep1


title: AtGen_6-3211_Saltstress-Shoots-1.0h_Rep1


title: AtGen_6-2612_Osmoticstress-Shoots-24.0h_Rep2

treatment_protocol:
At day 16, stress treatment started at 3 hours of light treatment.
Osmotic stress (300 mM Mannitol), Group Kudla. Mannitol was added to a concentration of 300 mM in the Media. To add Mannitol the raft was lifted out A magnetic stir bar and a stirrer were used to mix the media and the added Mannitol. After the rafts were put back in the boxes, they were transferred back to the climate chamber.


title: AtGen_6-2522_Osmoticstress-Roots-12.0h_Rep2


title: AtGen_6-2512_Osmoticstress-Shoots-12.0h_Rep2


title: AtGen_6-3122_Saltstress-Roots-0.5h_Rep2


title: AtGen_6-3221_Saltstress-Roots-1.0h_Rep1


title: AtGen_6-2521_Osmoticstress-Roots-12.0h_Rep1


title: AtGen_6-2621_Osmoticstress-Roots-24.0h_Rep1


title: AtGen_6-2421_Osmoticstress-Roots-6.0h_Rep1


title: AtGen_6-2622_Osmoticstress-Roots-24.0h_Rep2


title: AtGen_6-3111_Saltstress-Shoots-0.5h_Rep1


title: AtGen_6-3311_Saltstress-Shoots-3.0h_Rep1


title: AtGen_6-3112_Saltstress-Shoots-0.5h_Rep2


title: AtGen_6-2422_Osmoticstress-Roots-6.0h_Rep2


title: AtGen_6-2611_Osmoticstress-Shoots-24.0h_Rep1


title: AtGen_6-2322_Osmoticstress-Roots-3.0h_Rep2


title: AtGen_6-2411_Osmoticstress-Shoots-6.0h_Rep1


title: AtGen_6-2412_Osmoticstress-Shoots-6.0h_Rep2


title: AtGen_6-2311_Osmoticstress-Shoots-3.0h_Rep1


title: AtGen_6-3222_Saltstress-Roots-1.0h_Rep2


title: AtGen_6-2312_Osmoticstress-Shoots-3.0h_Rep2


title: AtGen_6-2221_Osmoticstress-Roots-1.0h_Rep1


title: AtGen_6-2222_Osmoticstress-Roots-1.0h_Rep2


title: AtGen_6-2212_Osmoticstress-Shoots-1.0h_Rep2


title: AtGen_6-5412_Genotoxicstress-Shoots-6.0h_Rep2


title: AtGen_6-2321_Osmoticstress-Roots-3.0h_Rep1


title: AtGen_6-2511_Osmoticstress-Shoots-12.0h_Rep1


title: AtGen_6-2112_Osmoticstress-Shoots-0.5h_Rep2


title: AtGen_6-1611_Cold(4°C)-Shoots-24.0h_Rep1

treatment_protocol:
At day 16, stress treatment started at 3 hours of light treatment.
Cold stress (4°C), Group Kudla.	The Magenta boxes were placed on ice in the cold room (4°C). The environmental light intensity was 20 µEinstein/cm2 sec. An extra light which was installed over the plants had 40 µEinstein/cm2 sec. The plants stayed there.


title: AtGen_6-2211_Osmoticstress-Shoots-1.0h_Rep1


title: AtGen_6-1411_Cold(4°C)-Shoots-6.0h_Rep1


title: AtGen_6-1511_Cold(4°C)-Shoots-12.0h_Rep1


title: AtGen_6-2122_Osmoticstress-Roots-0.5h_Rep2


title: AtGen_6-1622_Cold(4°C)-Roots-24.0h_Rep2


title: AtGen_6-1422_Cold(4°C)-Roots-6.0h_Rep2


title: AtGen_6-1412_Cold(4°C)-Shoots-6.0h_Rep2


title: AtGen_6-1621_Cold(4°C)-Roots-24.0h_Rep1


title: AtGen_6-2111_Osmoticstress-Shoots-0.5h_Rep1


title: AtGen_6-1612_Cold(4°C)-Shoots-24.0h_Rep2


title: AtGen_6-1512_Cold(4°C)-Shoots-12.0h_Rep2


title: AtGen_6-3121_Saltstress-Roots-0.5h_Rep1


title: AtGen_6-1421_Cold(4°C)-Roots-6.0h_Rep1


title: AtGen_6-1521_Cold(4°C)-Roots-12.0h_Rep1


title: AtGen_6-1311_Cold(4°C)-Shoots-3.0h_Rep1


title: AtGen_6-1312_Cold(4°C)-Shoots-3.0h_Rep2


title: AtGen_6-1221_Cold(4°C)-Roots-1.0h_Rep1


title: AtGen_6-1322_Cold(4°C)-Roots-3.0h_Rep2


title: AtGen_6-1122_Cold(4°C)-Roots-0.5h_Rep2


title: AtGen_6-1522_Cold(4°C)-Roots-12.0h_Rep2


title: AtGen_6-1112_Cold(4°C)-Shoots-0.5h_Rep2


title: AtGen_6-2121_Osmoticstress-Roots-0.5h_Rep1


title: AtGen_6-1211_Cold(4°C)-Shoots-1.0h_Rep1


title: AtGen_6-1321_Cold(4°C)-Roots-3.0h_Rep1


title: AtGen_6-1121_Cold(4°C)-Roots-0.5h_Rep1


title: AtGen_6-1212_Cold(4°C)-Shoots-1.0h_Rep2


title: AtGen_6-1222_Cold(4°C)-Roots-1.0h_Rep2


title: AtGen_6-1111_Cold(4°C)-Shoots-0.5h_Rep1


title: AtGen_6-0611_Control-Shoots-24.0h_Rep1

treatment_protocol:
At day 16, stress treatment started at 3 hours of light treatment.
Control plants, Group Kudla. The plants were treated like the treated plants; e.g.: Transfer of Magenta boxes out of the climate chamber. Opening of the boxes and lifting the raft as long as the treatments last. Then boxes were transferred back to the climate chamber.


title: AtGen_6-0512_Control-Shoots-12.0h_Rep2


title: AtGen_6-0412_Control-Shoots-6.0h_Rep2


title: AtGen_6-0521_Control-Roots-12.0h_Rep1


title: AtGen_6-0811_Control-Shoots-4.0h_Rep1


title: AtGen_6-0621_Control-Roots-24.0h_Rep1


title: AtGen_6-0612_Control-Shoots-24.0h_Rep2


title: AtGen_6-0821_Control-Roots-4.0h_Rep1


title: AtGen_6-0511_Control-Shoots-12.0h_Rep1


title: AtGen_6-0622_Control-Roots-24.0h_Rep2


title: AtGen_6-0312_Control-Shoots-3.0h_Rep2


title: AtGen_6-0222_Control-Roots-1.0h_Rep2


title: AtGen_6-0822_Control-Roots-4.0h_Rep2


title: AtGen_6-0422_Control-Roots-6.0h_Rep2


title: AtGen_6-0211_Control-Shoots-1.0h_Rep1


title: AtGen_6-0321_Control-Roots-3.0h_Rep1


title: AtGen_6-0122_Control-Roots-0.5h_Rep2


title: AtGen_6-0111_Control-Shoots-0.5h_Rep1


title: AtGen_6-0411_Control-Shoots-6.0h_Rep1


title: AtGen_6-0812_Control-Shoots-4.0h_Rep2


title: AtGen_6-0212_Control-Shoots-1.0h_Rep2


title: AtGen_6-0121_Control-Roots-0.5h_Rep1


title: AtGen_6-0311_Control-Shoots-3.0h_Rep1


title: AtGen_6-0522_Control-Roots-12.0h_Rep2


title: AtGen_6-0221_Control-Roots-1.0h_Rep1


title: AtGen_6-0112_Control-Shoots-0.5h_Rep2


title: AtGen_6-0421_Control-Roots-6.0h_Rep1


title: AtGen_6-0322_Control-Roots-3.0h_Rep2


title: AtGen_6-3212_Saltstress-Shoots-1.0h_Rep2


title: AtGen_6-0722_Control-Roots-0.25h_Rep2


title: AtGen_6-0711_Control-Shoots-0.25h_Rep1


title: Kadalayil_1-2_Pasta2M1.1_Rep1_ATH1

description:
location: Growth Room
Humidity: 43% percent rh
Temperature: 22/20 degrees
Lighting: 0700-1900 (12 hrs)
Medium: MS first  transplanted to soil
Treatment: 50 uM PPT in the MS plate
Water: Once a day from the bottom
Stratification: yes  seeds on MS plates were incubated at 4 degrees in the dark for ~ 84 hrs (3.5 days) before transferring to the growth room

treatment_protocol: Seeds were spread on plates containing 50 uM PPT

value: Harvested on the 41st day after the seeds were sown on MS plates (~3.90)

value: mature leaves


title: AtGen_6-0721_Control-Roots-0.25h_Rep1


title: AtGen_6-0021_Control-Roots-0h_Rep1


title: AtGen_6-0012_Control-Shoots-0h_Rep2


title: Scrase-Field_1-4_camta1-2-Col-0_Rep2_ATH1

description:
location: Greenhouse
Humidity: 100%
Temperature: 20 DegC
Lighting: 16 h light 5 hr dark
Medium: 1 X MS 0.8% agar
Stratification: 4 days in the dark at 4 DegC

value: Whole seedling

value: TDNA insertion into At5g09410


title: AtGen_C-17_2-Pi-24_REP2_ATH1

description:
location: Growth Room
Humidity: 70%
Temperature: 23°C day / 20°C night
Lighting: 8 hrs light / 16 hrs dark
Medium: GS90 : vermiculite (1:1)
Water: when necessary

treatment_protocol: Plants were moved to growth chamber with 20°C day / 18°C night for treatment. As many Phytophthora infestans drops (10 000 spores/drop) on leaves as possible. Trays covered with lid after treatment. Leaves harvested 24 hours post-treatment.

value: leaves


title: AtGen_C-5_2-C-12_REP2_ATH1

treatment_protocol: Plants were moved to growth chamber with 20°C day / 18°C night for treatment. As many Water drops on leaves as possible. Trays covered with lid after treatment. Leaves harvested 12 hours post-treatment.


title: AtGen_6-0011_Control-Shoots-0h_Rep1


title: AtGen_C-18_3-Pi-24_REP3_ATH1


title: AtGen_6-0022_Control-Roots-0h_Rep2


title: AtGen_C-8_2-C-24_REP2_ATH1

treatment_protocol: Plants were moved to growth chamber with 20°C day / 18°C night for treatment. As many Water drops on leaves as possible. Trays covered with lid after treatment. Leaves harvested 24 hours post-treatment.


title: AtGen_C-10_1-Pi-6_REP1_ATH1

treatment_protocol: Plants were moved to growth chamber with 20°C day / 18°C night for treatment. As many Phytophthora infestans drops (10 000 spores/drop) on leaves as possible. Trays covered with lid after treatment. Leaves harvested 6 hours post-treatment.


title: AtGen_C-12_3-Pi-6_REP3_ATH1


title: AtGen_C-15_3-Pi-12_REP3_ATH1

treatment_protocol: Plants were moved to growth chamber with 20°C day / 18°C night for treatment. As many Phytophthora infestans drops (10 000 spores/drop) on leaves as possible. Trays covered with lid after treatment. Leaves harvested 12 hours post-treatment.


title: AtGen_6-0712_Control-Shoots-0.25h_Rep2


title: AtGen_C-14_2-Pi-12_REP2_ATH1


title: AtGen_C-11_2-Pi-6_REP2_ATH1


title: AtGen_C-13_1-Pi-12_REP1_ATH1


title: AtGen_C-6_3-C-12_REP3_ATH1


title: AtGen_C-7_1-C-24_REP1_ATH1


title: AtGen_C-9_3-C-24_REP3_ATH1


title: Scrase-Field_1-3_Col-0-wildtype_Rep2_ATH1

description:
location: 0.8% agar plates, sealed with micropore tape in a growth chamber
Medium: 1 x MS
Lighting: 16 hours light/ 8 hours dark

value: Cell culture experiment


title: Kadalayil_1-1_wildtype_Rep1_ATH1

description:
location: Growth Room
Humidity: 43% percent rh
Temperature: 22/20 degrees
Lighting: 0700-1900 (12 hrs)
Medium: MS first  transplanted to soil
Water: Once a day from the bottom
Stratification: yes  seeds on MS plates were incubated at 4 degrees in the dark for ~ 84 hrs (3.5 days) before transferring to the growth room


title: Scrase-Field_1-1_Col-0-wildtype_Rep1_ATH1


title: Scrase-Field_1-2_camta1-2-Col-0_Rep1_ATH1


title: AtGen_C-4_1-C-12_REP1_ATH1


title: AtGen_C-3_4-C-6_REP3_ATH1

treatment_protocol: Plants were moved to growth chamber with 20°C day / 18°C night for treatment. As many Water drops on leaves as possible. Trays covered with lid after treatment. Leaves harvested 6 hours post-treatment.


title: AtGen_B-35_3-7-1_REP3_ATH1

treatment_protocol: leaves infiltrated with 100µg/ml LPS from P.syringae pv.tomato DC3000, harvested 1 hour later.


title: AtGen_C-2_2-C-6_REP2_ATH1


title: AtGen_C-1_1-C-6_REP1_ATH1


title: AtGen_B-34_3-6-1_REP3_ATH1

treatment_protocol: leaves infiltrated with 1 µM Flg-22, harvested 1 hour later.


title: AtGen_B-36_3-1-4_REP3_ATH1

treatment_protocol: leaves infiltrated with water, harvested 4 hours later.


title: AtGen_B-33_3-5-1_REP3_ATH1

treatment_protocol: leaves infiltrated with 1 µM GST-NPP1, harvested 1 hour later.


title: AtGen_B-26_2-5-4_REP2_ATH1

treatment_protocol: leaves infiltrated with 1 µM GST-NPP1, harvested 4 hours later.


title: AtGen_B-24_2-3-4_REP2_ATH1

treatment_protocol: leaves infiltrated with 1 µM GST, harvested 4 hours later.


title: AtGen_B-28_2-7-4_REP2_ATH1

treatment_protocol: leaves infiltrated with 100µg/ml LPS from P.syringae pv.tomato DC3000, harvested 4 hours later


title: AtGen_B-23_2-2-4_REP2_ATH1

treatment_protocol: leaves infiltrated with 1 mM CaCl2 + 2.5 mM MgCl2, harvested 4 hours later.


title: AtGen_B-19_2-5-1_REP2_ATH1


title: AtGen_B-22_2-1-4_REP2_ATH1


title: AtGen_B-30_3-2-1_REP3_ATH1

treatment_protocol: leaves infiltrated with 1 mM CaCl2 + 2.5 mM MgCl2, harvested 1 hour later.


title: AtGen_B-21_2-7-1_REP2_ATH1


title: AtGen_B-32_3-4-1_REP3_ATH1

treatment_protocol: leaves infiltrated with 10 µM HrpZ, harvested 1 hour later


title: AtGen_B-25_2-4-4_REP2_ATH1

treatment_protocol: leaves infiltrated with 10 µM HrpZ, harvested 4 hours later.


title: AtGen_B-12_1-5-4_REP1_ATH1


title: AtGen_B-20_2-6-1_REP2_ATH1


title: AtGen_B-15_2-1-1_REP2_ATH1

treatment_protocol: leaves infiltrated with water, harvested 1 hour later.


title: AtGen_B-11_1-4-4_REP1_ATH1


title: AtGen_B-16_2-2-1_REP2_ATH1


title: AtGen_B-14_1-7-4_REP1_ATH1


title: AtGen_B-13_1-6-4_REP1_ATH1

treatment_protocol: leaves infiltrated with 1 µM Flg-22, harvested 4 hours later.


title: AtGen_B-18_2-4-1_REP2_ATH1


title: AtGen_B-17_2-3-1_REP2_ATH1

treatment_protocol: leaves infiltrated with 1 µM GST, harvested 1 hour later


title: AtGen_B-9_1-2-4_REP_1_ATH1


title: AtGen_B-7_1-7-1_REP_1_ATH1


title: AtGen_B-10_1-3-4_REP1_ATH1


title: AtGen_B-5_1-5-1_REP_1_ATH1

treatment_protocol: leaves infiltrated with 1 µM GST-NPP1, harvested 1 hour later


title: AtGen_B-8_1-1-4_REP_1_ATH1


title: AtGen_B-6_1-6-1_REP_1_ATH1

treatment_protocol: leaves infiltrated with 1 µM Flg-22, harvested 1 hour later


title: AtGen_B-3_1-3-1_REP_1_ATH1


title: AtGen_B-1_1-1-1_REP_1_ATH1


title: AtGen_B-38_3-3-4_REP3_ATH1


title: Broadley_1-3_A3-Bo-P2-phosphate-starved_Rep2_ATH1

description:
Light: 16 h daylength
Medium: compost
Temperature: 22°C
Humidity: 70-80%
Watering regime: watered daily with deionised water
Stratification: 3 to 5 days in sterile distilled water at 4°C

source_name: oleracea

value: shoot tissue

value: Brassica oleracea var. alboglabra (A12dH)


title: Broadley_1-5_A5-Bo+P2-nutrient-replete_Rep2_ATH1


title: AtGen_B-2_1-2-1_REP_1_ATH1

treatment_protocol: leaves infiltrated with 1 mM CaCl2 + 2.5 mM MgCL2, harvested 1 hour later.


title: AtGen_B-4_1-4-1_REP_1_ATH1


title: AtGen_B-42_3-7-4_REP3_ATH1


title: Newbury_2-21_acc-bulk-control-leaf(ALO)_Rep3_ATH1

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

organism: Arabidopsis halleri

source_name: accumulating bulk

value: Rosette leaves


title: Broadley_1-4_A4-Bo-P3-phosphate-starved_Rep3_ATH1


title: Broadley_1-6_A6-Bo+P3-nutrient-replete_Rep3_ATH1


title: AtGen_C-16_1-Pi-24_REP1_ATH1

treatment_protocol: Plants were moved to growth chamber with 20°C day / 18°C night for treatment. As many Phytophthora infestans drops (10 000 spores/drop) on leaves as possible. Trays covered with lid after treatment. Leaves harvested 24 hours post-treatment.


title: AtGen_B-39_3-4-4_REP3_ATH1


title: Broadley_1-1_A1-Bo+P-nutrient-replete_Rep1_ATH1


title: Newbury_2-20_acc-bulk-control-leaf(ALO)_Rep2_ATH1


title: AtGen_B-41_3-6-4_REP3_ATH1


title: AtGen_B-37_3-2-4_REP3_ATH1


title: Newbury_2-24_acc-bulk-highZn-leaf(ALH)_Rep3_ATH1

treatment_protocol: 25um Zinc


title: Newbury_2-23_acc-bulk-highZn-leaf(ALH)_Rep2_ATH1


title: Newbury_2-18_acc-bulk-highZn-root(ARH)_Rep3_ATH1

value: whole root system


title: Newbury_2-15_acc-bulk-control-root(ARO)_Rep3_ATH1


title: Newbury_2-17_acc-bulk-highZn-root(ARH)_Rep2_ATH1


title: Newbury_2-14_acc-bulk-control-root(ARO)_Rep2_ATH1


title: Newbury_2-8_non-acc-bulk-control-leaf(NLO)_Rep2_ATH1

source_name: non-accumulating bulk


title: Newbury_2-13_acc-bulk-control-root(ARO)_Rep1_ATH1


title: Newbury_2-16_acc-bulk-highZn-root(ARH)_Rep1_ATH1


title: Newbury_2-4_non-acc-bulk-highZn-root(NRH)_Rep1_ATH1


title: Newbury_2-12_non-acc-bulk-highZn-leaf(NLH)_Rep3_ATH1


title: Newbury_2-10_non-acc-bulk-highZn-leaf(NLH)_Rep1_ATH1


title: Newbury_2-19_acc-bulk-control-leaf(ALO)_Rep1_ATH1


title: Newbury_2-6_non-acc-bulk-highZn-root(NRH)_Rep3_ATH1


title: Newbury_2-11_non-acc-bulk-highZn-leaf(NLH)_Rep2_ATH1


title: Newbury_2-5_non-acc-bulk-highZn-root(NRH)_Rep2_ATH1


title: Newbury_2-3_non-acc-bulk-control-root(NRO)_Rep3_ATH1


title: Edwards_1-13_74hr_Rep1_ATH1

description:
location: Growth Room
Temperature: 22 C
Lighting: 12 hour photoperiod
Medium:  MS agar plates with 3% sucrose

value: whole seedlings


title: Newbury_2-7_non-acc-bulk-control-leaf(NLO)_Rep1_ATH1


title: AtGen_B-27_2-6-4_REP2_ATH1


title: AtGen_B-31_3-3-1_REP3_ATH1


title: Edwards_1-10_62hr_Rep1_ATH1


title: Edwards_1-12_70hr_Rep1_ATH1


title: Edwards_1-7_50hr_Rep1_ATH1


title: AtGen_B-29_3-1-1_REP3_ATH1


title: Edwards_1-9_58hr_Rep1_ATH1


title: Edwards_1-11_66hr_Rep1_ATH1


title: Newbury_2-2_non-acc-bulk-control-root(NRO)_Rep2_ATH1


title: Edwards_1-4_38hr_Rep1_ATH1


title: Edwards_1-5_42hr_Rep1_ATH1


title: Edwards_1-6_46hr_Rep1_ATH1


title: Edwards_1-2_30hr_Rep1_ATH1


title: Edwards_1-8_54hr_Rep1_ATH1


title: Hammond_2-3_Col2wildtype_Rep2_ATH1

description:
location: Growth Room
Atmosphere: Normal
Humidity: 80 %
Temperature: 24 degrees C
Lighting: 16 h photoperiod
Medium: 0.8 % agar containing MS salts and 1 % sucrose
Treatment:
Nutrients: MS salts and 1 % sucrose
Water:
Stratification:


title: Hammond_2-5_Col2wildtype_Rep3_ATH1


title: Hammond_2-4_pho1mutant_Rep2_ATH1

value: EMS mutant


title: Edwards_1-1_26hr_Rep1_ATH1


title: Edwards_1-3_34hr_Rep1_ATH1


title: Hammond_2-6_pho1mutant_Rep3_ATH1


title: Hammond_2-1_Col2wildtype_Rep1_ATH1


title: Hammond_2-2_pho1mutant_Rep1_ATH1


title: HUVEC_Bb+IFNg_B

status: Public on Jan 05 2007

city: Stony Brook

first: Lance

middle: E

last: Palmer

state: NY

address: 235 CMM

department: Center for Infectious Diseases

country: USA

institute: University at Stony Brook

description: Human umbilical vein endothelial cells (HUVEC) were isolated from umbilical cords by collagenase perfusion as previously reported (Huang, A. J., M. B. Furie, S. C. Nicholson, J. Fischbarg, L. S. Liebovitch, and S. C. Silverstein. 1988. Effects of human neutrophil chemotaxis across human endothelial cell monolayers on the permeability of these monolayers to ions and macromolecules. J. Cell Physiol 135: 355-366.)

hyb_protocol: Affymetrix HG U133 2.0 Plus arrays were hybridized with 200ul of the hybridization cocktail.  The hybridization was performed in an Affymetrix Hybridization Oven 640 over night at 45C at 60 RPMs.

scan_protocol: Arrays were washed and stained in a Affymetrix Fluidics Station FS 450 as per standard Affymetrix fluidics protocol EukGE-WS2v4.  Arrays were scanned in an Affymetrix 3000 scanner.  Images were analyzed using Affymetrix GCOS software.  The Target Intensity was set to 250.

data_processing: The Robust Multichip Average (RMA) method within the Bioconductor package for the R statistical environment was used for data processing and normalization.

label: Biotin

organism: Homo sapiens

label_protocol: 5ug total RNA was input into 1st strand cDNA reaction.  Followed standard Affymetrix protocol using 2ul  (400 units) SuperScript II  RT.  Second strand as per Affymetrix protocol. Purified cDNA using a Phenol/Chloroform extraction followed by EtOH precipitation.  Pellets resuspended in 22 ul DEPC treated H2O.  The entire sample was used for the IVT reaction. The IVT reaction was done using the Enzo Life Sciences BioArray High Yield RNA Transcription Labeling Kit (T7)  Followed protocol provided with the BioArray High Yield RNA Transcription Labeling Kit. Samples were incubated at 37C overnight in a MJ research PTC100 thermocyler.  The samples were purified using Qiagen RNeasy kit including DNase treatment.  The samples were eluted 2 x with 50ul DEPC treated H2O.  Samples were then EtOH precipitated and resuspended in 33 ul DEPC treated H2O.  The cRNA was quantitated on a spectrophotometer.  20ug of cRNA were fragmented using the standard Affymetrix fragmentation protocol

growth_protocol: HUVEC and B. burgdorferi were grown and cultured as previously described (Gergel, E. I., and M. B. Furie. 2001. Activation of endothelium by Borrelia burgdorferi in vitro enhances transmigration of specific subsets of T lymphocytes. Infect. Immun. 69: 2190-2197.)

extract_protocol: RNA was isolated with TRI Reagent (Sigma Aldrich, Inc.) according to the manufacturer’s instructions.


title: Underwood_1-1_Cor-10e6-24h_Rep1_ATH1

description:
stratification: Stratified 3 days at 4degC
growth protocol: Arabidopsis thaliana accession Col-0 plants were grown in soil in growth chambers with a day/night cycle of 12 h/12 h, a light intensity of 100 µE, and a constant temperature of 20°C. Four- to 5-week-old plants were used for experiments.
Location: Growth chamber
Growth  substrate: Commercial soil
Watering: flats were watered every 2-3 days

treatment_protocol: Plants were inoculated by vacuum infiltration with Pseudomonas syringae DC3118 Coronatine- bacteria at a concentration of 10e6 cfu per ml. Inoculated leaf tissue from at least 15 plants was collected for RNA isolation.

value: Leaves


title: Underwood_1-4_Cor-hrpS-10e6-24h_Rep1_ATH1

treatment_protocol: Plants were inoculated by vacuum infiltration with Pseudomonas syringae DC3118 COR-hrpS double mutant bacteria at a concentration of 10e6 cfu/ml. Inoculated leaf tissue from at least 15 plants was collected for RNA isolation.


title: larvae_wt_control_3

status: Public on Jan 06 2007

city: Detroit

first: Xinxian

last: Deng

state: MI

address: 5047 Gullen Mall

department: Biological Sciences

institute: Wayne State University

description: Total RNA was prepared from roX1+ roX2- male third instar larvae. roX1+ roX2- male was used for the wildtype control.

hyb_protocol: Affymetrix GeneChip® Expression Analysis Technical Manual

data_processing: The Chip Image was analysed using GCOS 1.2 from Affymetrix.

organism: Drosophila melanogaster

source_name: Larvae

extract_protocol: TRIzol standard protocol

tag: Gender

value: male

tag: Stage

value: third instar larvae

tag: Genotype

value: y+ w roX1+ roX2-/ Y


title: larvae_wt_control_1

scan_protocol: Affymetrix GeneChip® Expression Analysis Technical Manual


title: larvae_roX1roX2 mutant_3

description: Total RNA was prepared from roX1- roX2- male third instar larvae. SMC17A was used for the roX1 mutant, which is described in Deng et al., 2005.

label_protocol: Affymetrix GeneChip® Expression Analysis Technical Manual

value: y+ w roX1- roX2-/ Y


title: Underwood_1-2_Cor-10e6-24h_Rep2_ATH1


title: HUVEC_Bb+IFNg_A

tag: Human umbilical vein endothelial cells (HUVEC)


title: Broadley_1-2_A2-Bo-P-phosphate-starved_Rep1_ATH1


title: larvae_wt_control_2


title: HUVEC_IFNg_B


title: larvae_roX1roX2 mutant_2


title: larvae_roX1roX2 mutant_1


title: AtGen_B-40_3-5-4_REP3_ATH1

treatment_protocol: leaves infiltrated with 1 µM GST-NPP1, harvested 4 hours later.


title: HUVEC_Bb_A


title: HUVEC_Bb_B


title: HUVEC_IFNg_A


title: HUVEC_UnStim_A


title: Omentum - 276657

status: Public on Jan 03 2007

city: Phoenix

first: Erin

last: Curley

state: AZ

address: 445 N. 5th Street

institute: IGC

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 40-50
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 6-10
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 120
Prior Therapy: Chemotherapy
Prior Therapy: Radiation
Pathological T: X
Pathological N: X
Pathological M: 1
Pathological Metastatic Sites: Lymph Nodes
Pathological Stage: 4B
Pathological Grade: X
Pathological Staged During or Following Multimodality Therapy: Yes
Primary Site: Cervix Uteri
Histology: Squamous cell carcinoma

source_name: Omentum


title: Breast - 84139

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 40-50
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 14
Mammogram: Yes
Number of years in which a mammogram was obtained?: 11-15
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 26-30
Oophorectomy?: No
Fibrocystic disease?: No
Mammogram calcifications?: No
Pathological T: 1b
Pathological N: 0(i-)
Pathological M: 0
Pathological Stage: 1
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Breast
Histology: Ductal Carcinoma

source_name: Breast


title: Kidney - 38212

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Clinical T: 1a
Clinical N: 0
Clinical M: X
Clinical Stage: Unknown
Clinical Grade: 2
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Papillary renal cell carcinoma

source_name: Kidney


title: Colon - 262819

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 70-80
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 6-10
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 23
Presenting Symptoms: Bright red stools
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: B
Primary Site: Colon
Histology: Adenocarcinoma

source_name: Colon


title: Kidney - 262813

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 70-80
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 36-40
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 14
Pathological T: 3b
Pathological N: 0
Pathological M: 0
Pathological Stage: 3
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: HUVEC_UnStim_B


title: Omentum - 262802

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 80-90
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Presenting Symptoms: Abdominal pain
Pathological T: 3c
Pathological N: X
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Ovary
Histology: Metastatic Papillary Serous Adenocarcinoma


title: Small intestine - 262793

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 7
Presenting Symptoms: Weight loss
Have you ever had mononucleousis?: No
Have you ever had chemotherapy for any previous cancer prior to your current diagnosis?: No
Clinical Stage: 4
Clinical Symptoms: B
Primary Site: Lymph Nodes
Histology: B-cell lymphoma, NOS

source_name: Small intestine


title: Urinary Bladder - 262809

description:
Quality metric = 28S to 18S: 2.0
Patient Age: 70-80
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 21-25
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 30
Prior Therapy: Surgical
Pathological T: 2b
Pathological N: 0
Pathological M: 0
Pathological Stage: 2
Pathological Grade: 3
Pathological Multiple Tumours: No
Pathological Staged During or Following Multimodality Therapy: No
Primary Site: Urinary Bladder
Histology: Papillary transitional cell carcinoma

source_name: Urinary Bladder


title: Vulva - 262795

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 80-90
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 0-5
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 6
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 2
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Vulva
Histology: Keratinizing squamous cell carcinoma

source_name: Vulva


title: Thyroid - 84135

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 30-40
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 54
Clinical T: 1
Clinical N: 0
Clinical M: X
Clinical Stage: Unknown
Clinical Multiple Tumours: No
Clinical Staged During or Following Multimodality Therapy: No
Primary Site: Thyroid
Histology: Papillary carcinoma, follicular variant

source_name: Thyroid


title: Gastroesophageal Junction - 261174

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 25
Have you ever had esophagitis/reflux?: No
Pathological Question: T
Pathological Value: 3
Pathological Question: N
Pathological Value: 1
Pathological Question: M
Pathological Value: 0
Pathological Question: Stage
Pathological Value: 3A
Pathological Question: Grade
Pathological Value: 3
Pathological Question: Multiple Tumors
Pathological Value: No
Pathological Question: Stage During or Following Multimodality Therapy
Pathological Value: No
Primary Site: Gastroesophageal Junction
Pathological Question: Histology
Pathological Value: Adenocarcinoma

source_name: Gastroesophageal junction


title: Colon - 262792

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 70-80
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 30
Presenting Symptoms: Bright red stools
Screening studies performed?: No
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 1
Pathological M: X
Pathological Stage: Unknown
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Colon
Histology: Adenocarcinoma


title: Humerus bone - 256954

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Retreatment T: X
Retreatment N: X
Retreatment M: 1
Retreatment Metastatic Sites: Osseous
Retreatment Stage: 4
Retreatment Grade: X
Primary Site: Stomach
Histology: Metastatic Mucinous Adenocarcinoma

source_name: Humerus bone


title: Ovary - 262794

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 30-40
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Presenting Symptoms: Abdominal pain
Clinical T: 1a
Clinical N: 0
Clinical M: 0
Clinical Stage: 1A
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Ovary
Histology: Mucinous cystic tumor of low malignant potential

source_name: Ovary


title: Uterus - 262807

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Pathological T: 2b
Pathological N: 0
Pathological M: 0
Pathological Stage: 2B
Pathological Grade: 2
Pathological Multiple Tumors: No
Primary Site: Endometrium
Histology: Endometrioid carcinoma

source_name: Uterus


title: Uterus - 256961

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 7
Have you ever been diagnosed as having HPV on your PAP smear?: No
Pathological T: 3b
Pathological N: 0
Pathological M: 0
Pathological Stage: 3B
Pathological Grade: 3
Primary Site: Cervix Uteri
Histology: Squamous cell carcinoma


title: Ovary - 262803

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 14
Presenting Symptoms: Abdominal pain
Pathological T: 3c
Pathological N: 1
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 3
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Ovary
Histology: Transitional cell carcinoma


title: Uterus - 256956

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 30
Pathological T: 1a
Pathological N: 0
Pathological M: 0
Pathological Stage: 1A
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Malignant mixed Mullerian tumor


title: Omentum - 256950

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 40-50
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 31-35
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 13
Presenting Symptoms: Abdominal mass
Presenting Symptoms: Abdominal pain
Pathological T: 3c
Pathological N: 0
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Ovary
Histology: Metastatic Papillary Serous Carcinoma


title: Prostate - 256947

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 70-80
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 10
Presenting Symptoms: Urgency
PSA: Normal
# of years PSA Tested?: 6-10
Cancer discovered by digital exam?: Yes
Current status of disease: Under Therapy
Pathological T: 2c
Pathological N: 0
Pathological M: 0
Pathological Stage: 2
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Gleason Score: 7
Primary Site: Prostate
Histology: Adenocarcinoma, NOS

source_name: Prostate


title: Breast - 256881

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Mammogram: Yes
Number of years in which a mammogram was obtained?: 16-20
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 11-15
Oophorectomy?: No
Fibrocystic disease?: No
Mammogram calcifications?: No
Pathological T: 1c
Pathological N: 1a
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 1
Pathological Multiple Tumors: Yes
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Ductal Carcinoma


title: Pelvic Lymph Node - 256960

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 30-40
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 6-10
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 41
Have you ever been diagnosed as having HPV on your PAP smear?: No
Pathological T: 1b2
Pathological N: 1
Pathological M: 1
Pathological Metastatic Sites: Lymph Nodes
Pathological Stage: 4B
Pathological Grade: X
Primary Site: Cervix Uteri
Histology: Squamous cell carcinoma, non-keratinizing

source_name: Pelvic lymph node


title: Chest wall mass - 254444

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 40-50
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 16-20
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Have you ever had mononucleousis?: No
Have you ever had chemotherapy for any previous cancer prior to your current diagnosis?: No
Clinical Question: Stage
Clinical Value: 4
Clinical Question: Stage During or Following Multimodality Therapy
Clinical Value: No
Clinical Question: Symptoms
Clinical Value: A
Primary Site: Skin
Clinical Question: Histology
Clinical Value: Anaplastic large cell lymphoma, primary cutaneous type

source_name: Chest wall mass


title: Breast - 256882

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 30-40
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Mammogram: No
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 16-20
Oophorectomy?: No
Fibrocystic disease?: No
Mammogram calcifications?: No
Pathological T: 1c
Pathological N: 3a
Pathological M: X
Pathological Stage: 3C
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Positive
Pathological PR: Negative
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Ductal Carcinoma


title: Urinary bladder - 256878

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 40-50
Gender: Female
Ethnic Background: African-American
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 30
Pathological T: 4a
Pathological N: 1
Pathological M: 0
Pathological Stage: 4
Pathological Grade: 3
Pathological Multiple Tumours: No
Pathological Staged During or Following Multimodality Therapy: No
Primary Site: Urinary Bladder
Histology: Keratinizing squamous cell carcinoma

source_name: Urinary bladder


title: Colon - 256880

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 40-50
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 16
Presenting Symptoms: Bright red stools
Screening studies performed?: No
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: B
Primary Site: Colon
Histology: Adenocarcinoma


title: Prostate - 256874

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: No
Presenting Symptoms: Hematuria
Presenting Symptoms: Nocturia
PSA: Normal
Cancer discovered by digital exam?: No
Current status of disease: Under Therapy
Clinical T: 2c
Clinical N: X
Clinical M: 0
Clinical Stage: Unknown
Clinical Grade: 3
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Clinical Gleason Score: 7
Primary Site: Prostate
Histology: Adenocarcinoma, NOS


title: Breast - 254441

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Prior Therapy: Hormonal Treatment
Relapse Since Primary Treatment: No
Oral contraceptives?: No
Oophorectomy?: No
Fibrocystic disease?: No
Clinical T: 4b
Clinical N: 2a
Clinical M: 1
Clinical Metastatic Sites: Pulmonary
Clinical Stage: 4
Clinical Grade: 3
Clinical ER: Positive
Clinical PR: Positive
Clinical HER/2 Neu: Negative
Primary Site: Breast
Histology: Ductal Carcinoma


title: Breast - 254436

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 8
Relapse Since Primary Treatment: No
Mammogram: Yes
Number of years in which a mammogram was obtained?: 0-5
Oral contraceptives?: No
Oophorectomy?: Yes
Fibrocystic disease?: No
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 1
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Positive
Pathological PR: Negative
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Papillary carcinoma


title: Prostate - 254395

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 36-40
Type of Tobacco Use: Chewing Tobacco
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 14
PSA: Elevated
# of years PSA Tested?: 0-5
Cancer discovered by digital exam?: No
Current status of disease: Under Therapy
Pathological T: 2c
Pathological N: 0
Pathological M: 0
Pathological Stage: 2
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Gleason Score: 5-6
Primary Site: Prostate
Histology: Adenocarcinoma, NOS


title: Kidney - 254403

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 28
Clinical T: 1a
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 2
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Papillary renal cell carcinoma


title: Jejunum - 254371

description:
Quality metric = 28S to 18S: 2.0
Patient Age: 70-80
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2
Pathological Grade: 2
Pathological Multiple Tumours: No
Pathological Staged During or Following Multimodality Therapy: No
Primary Site: Jejunum
Histology: Adenocarcinoma

source_name: Jejunum


title: Breast - 254376

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 18
Mammogram: Yes
Number of years in which a mammogram was obtained?: 16-20
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 16-20
Oophorectomy?: No
Fibrocystic disease?: No
Mammogram calcifications?: No
Pathological T: 1c
Pathological N: 0
Pathological M: 0
Pathological Stage: 1
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Negative
Pathological PR: Negative
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Ductal Carcinoma


title: Pelvic sidewall nodule - 254392

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 30-40
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 6-10
Retreatment T: 2b
Retreatment N: 0
Retreatment M: 0
Retreatment Stage: 2B
Retreatment Grade: X
Primary Site: Ovary
Histology: Metastatic Dysgerminoma

source_name: Pelvic sidewall nodule


title: Kidney - 254391

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 80-90
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Clinical T: 3a
Clinical N: 0
Clinical M: 0
Clinical Stage: 3
Clinical Grade: 2
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Chromophobe renal carcinoma


title: Lung - 254375

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 40-50
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 9
Workplace or household smokers?: Yes
Pathological T: 2b
Pathological N: 0
Pathological M: 0
Pathological Stage: 3
Pathological Multiple Tumours: No
Pathological Staged During or Following Multimodality Therapy: No
Primary Site: Lung
Histology: Synovial sarcoma, monophasic fibrous

source_name: Lung


title: Ovary - 254388

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 40-50
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 23
Presenting Symptoms: Abdominal pain
Presenting Symptoms: Bloating
Pathological T: 3c
Pathological N: 1
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 2
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Ovary
Histology: Papillary Serous Carcinoma


title: Liver - 254373

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 80-90
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Diagnosis made by: Colonoscopy
Retreatment T: 3
Retreatment N: 1
Retreatment M: 1
Retreatment Metastatic Sites: Hepatic
Retreatment Stage: 4
Retreatment Grade: 2
Retreatment Multiple Tumors: No
Primary Site: Colon
Histology: Metastatic Adenocarcinoma

source_name: Liver


title: Kidney - 254361

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 40-50
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 1
Clinical T: 1a
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 1
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma

source_name: Kidney


title: Corpus Uteri - 254398

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 13
Pathological T: 1b
Pathological N: 0
Pathological M: 0
Pathological Stage: 1B
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Endometrioid carcinoma

source_name: Corpus Uteri


title: Breast - 254374

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Mammogram: Yes
Number of years in which a mammogram was obtained?: 21-25
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 0-5
Oophorectomy?: No
Fibrocystic disease?: No
Mammogram calcifications?: Yes
Pathological T: 3
Pathological N: 1a
Pathological M: 0
Pathological Stage: 3A
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Negative
Pathological PR: Negative
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Ductal Carcinoma

source_name: Breast


title: Lung - 251055

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 46-50
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 33
Pathological T: 2
Pathological N: 2
Pathological M: 0
Pathological Stage: 3A
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Lung
Histology: Squamous cell carcinoma


title: Colon - 254360

description:
Quality metric = 28S to 18S: 1.9
Patient Age: 80-90
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: B
Primary Site: Colon
Histology: Adenocarcinoma arising in a villous adenoma

source_name: Colon


title: Soft tissue of arm - 254350

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Prior Therapy: Chemotherapy
Prior Therapy: Radiation
Presenting Symptoms: Persistent Cough
Pathological T: 4
Pathological N: 2
Pathological M: 1
Pathological Metastatic Sites: Other
Pathological Stage: 4
Pathological Grade: X
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Lung
Histology: Metastatic Large cell carcinoma

source_name: Soft tissue of arm


title: Uterus - 251054

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 36-40
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Pathological T: 2b
Pathological N: 0
Pathological M: 0
Pathological Stage: 2B
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Malignant mixed Mullerian tumor


title: Breast - 254354

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 80-90
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Mammogram: Yes
Oral contraceptives?: No
Oophorectomy?: No
Fibrocystic disease?: No
Pathological T: 2
Pathological N: 2a
Pathological M: 0
Pathological Stage: 3A
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: Yes
Pathological ER: Positive
Pathological PR: Positive
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Lobular Carcinoma


title: Breast - 254359

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 10
Prior Therapy: Radiation
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 6-10
Mammogram: Yes
Number of years in which a mammogram was obtained?: 0-5
Oral contraceptives?: No
Oophorectomy?: No
Fibrocystic disease?: No
Mammogram calcifications?: Yes
Pathological T: 2
Pathological N: 1mi
Pathological M: 0
Pathological Stage: 2B
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Negative
Pathological PR: Negative
Pathological HER/2 Neu: Positive
Primary Site: Breast
Histology: Ductal Carcinoma


title: Liver - 254357

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 11-15
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Prior Therapy: Chemotherapy
Prior Therapy: Radiation
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Presenting Symptoms: Bright red stools
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Retreatment T: X
Retreatment N: X
Retreatment M: 1
Retreatment Metastatic Sites: Hepatic
Retreatment Stage: 4
Retreatment Grade: X
Primary Site: Colon
Histology: Metastatic Adenocarcinoma


title: Ovary - 251044

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 40-50
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Presenting Symptoms: Abdominal pain
Pathological T: 1a
Pathological N: 0
Pathological M: 0
Pathological Stage: 1A
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Ovary
Histology: Papillary serous tumor of low malignant potential


title: Ovary - 251042

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 40-50
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Prior Therapy: Chemotherapy
Presenting Symptoms: Abdominal pain
Presenting Symptoms: Bloating
Pathological T: 3b
Pathological N: 0
Pathological M: 0
Pathological Stage: 3B
Pathological Grade: 3
Pathological Multiple Tumors: Yes
Pathological Stage During or Following Multimodality Therapy: Yes
Primary Site: Ovary
Histology: Adenocarcinoma with mixed subtypes


title: Uterus - 251038

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Pathological T: 1c
Pathological N: 0
Pathological M: 0
Pathological Stage: 1C
Pathological Grade: 1
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Endometrioid carcinoma


title: Cervix Uteri - 251047

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 40-50
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Have you ever been diagnosed as having HPV on your PAP smear?: No
Pathological T: 1b2
Pathological N: 1
Pathological M: 0
Pathological Stage: 3B
Pathological Grade: 2
Pathological Multiple Tumours: No
Pathological Staged During or Following Multimodality Therapy: No
Primary Site: Cervix Uteri
Histology: Squamous cell carcinoma, keratinizing

source_name: Cervix Uteri


title: Lung - 251053

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 19
Workplace or household smokers?: Yes
Pathological T: 1
Pathological N: 0
Pathological M: 0
Pathological Stage: 1A
Pathological Grade: X
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Lung
Histology: Adenosquamous Carcinoma


title: Breast - 251050

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 30
Mammogram: Yes
Number of years in which a mammogram was obtained?: 21-25
Oophorectomy?: Yes
Fibrocystic disease?: No
Mammogram calcifications?: No
Hormonal therapy (# of Years)?: 0-5
Pathological T: 2
Pathological N: 1a
Pathological M: 0
Pathological Stage: 2B
Pathological Grade: 3
Pathological Multiple Tumors: Yes
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Negative
Pathological PR: Negative
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Ductal Carcinoma