title: wd_systemic_vs_spit_systemic2s

description: Potato leaves From Solanum tuberosum var. Kennebec will be wounded and oral secretions from 4th instar CPB will be isolated and added to the plants as described by Kruzmane et al (2002, Physiol. Plantarum 115:577-584).  The leaf from the 6th node of the potato plant will be wounded or wounded and treated with oral secretions from CPB. Unwounded leaves from node 1-5 of the wounded  and wounded plus oral secretions plants will be harvested as systemic material. The leaves will be harvested after 4 hrs and RNA will be isolated. 4 hrs was chosen because this represents a time when early and late induced genes should both be present. In addition, the leaf from the 6th node will be subjected to feeding by CPB that have been raised on potato leaves and starved for 16 hrs immediately prior to infestation. Insects will be allowed to feed for 1 hr and the leaves will be harvested after 3 additional hrs. An additional set of plants will be used to infest the leaf on the 6th node for 4 hrs. Leaves from the 6th node will be collected from uninfested plants after 4 hrs as a control. Three sets of 6-12 plants will be used for each sample.

treatment_protocol: Wound and spit systemic 4 hr

treatment_protocol: Wounded systemic 4 hr


title: aphid_vs_PLRV_3d_3

status: Public on Sep 01 2007

type: RNA

city: Rockville

first: Jia

last: Liu

state: MD

address: 9712 Medical Center Drive

country: USA

institute: Plant Genomics

description: Potato plants (cv. Russet Burbank) were grown as in vitro plantlets, and transplanted into 12-cm pots in Sunshine Mix #2 (peat/perlite mix) supplemented with slow release fertilizer (Osmocoat) in the greenhouse.  The experiment was conducted in the summer of 2004 at Moscow, ID.  Plantings were staggered to facilitate collection of volatiles and leaf samples during a short harvest window for all times of all treatments.  Infectious Green Peach Aphids were raised on PLRV-infected potato plants; test plants were infected by placing 10 infectious aphids on a leaf in a clip cage for 48 h.  The control plants for PLRV were similarly treated with aphids that had been raised on uninfected potato plants.  A local isolate of PVYO was inoculated mechanically using purified virus (5 ìg ml-1) in buffer (50 mM Na2HPO4, 20 mM Na2SO3 pH 7.0) lightly rubbed onto a leaf previously dusted with carborundum.  Control plants for PVY were treated in the same manner using buffer without PVY.  The RNA samples were made from systemically affected leaves, excluding the actual leaves inoculated by aphids or that received the mechanical infection.  Leaf volatiles were concurrently collected from equivalent plants; aliquots of frozen leaf samples were sent for metabolite analysis prior to RNA extraction.  Leaf harvests were made 1, 3, 7, 14, and 28 d post-inoculation.

hyb_protocol: Hybridization with indirectly labeled mRNA (SGED_SOP_6.1.1, SGED_SOP_6.2.1-4)

scan_protocol: Axon 4000B scanner. Both the 635nm (red, Cy5) and 532nm (green, Cy3) channels are scanned simultaneously at 100% laser power, the PMT set between 600 and 950. Slides are scanned at a resolution of 10micron

data_processing: The TIFF images were quantified using Genepix 5.0. Local background was subtracted from the signal value and the data was normalized using the quantile method in the limma package of bioconductor.

molecule: total RNA

organism: Solanum tuberosum

label_protocol: Amino allyl labeling and direct labeling (SGED_SOP_5.1.1 + SGED_SOP_6.1.1)

growth_protocol: Greenhouse, ambient + supplemental light (metal halide)

extract_protocol: Phenol method with carbohydrate-enriched tissue such as tubers and trizol for other tissues such as leaves (SGED_SOP_3.1.1 + SGED_SOP_3.3.1)

treatment_protocol: PLRV aphid-infected, 3d

tag: Solanum tuberosum, Leaf, Biotic stress

treatment_protocol: Sham Inoc - aphid control, 3d


title: aphid_vs_PLRV_1d_2

treatment_protocol: PLRV aphid-infected, 1d

treatment_protocol: Sham Inoc - aphid control, 1d


title: aphid_vs_PLRV_1d_3


title: control_vs_PVY_1d_2

treatment_protocol: PVY innoculated, 1d

treatment_protocol: PVY-Buffer control, 1d


title: wd_systemic_vs_spit_systemic3s

growth_protocol: Grown for 4 weeks in greenhouse


title: PPV1_vs_Mock1_systemic_leaf

description: Objectives: Our work focuses on the responses of Solanaceous plants to viruses that cause economically important diseases in tree fruits.  Using mock inoculated leaf tissue as a reference, we plan to compare the gene expression profiles of Nicotiana Benthamiana plants infected with one of three viruses; Plum Pox Potyvirus (PPV), Tomato Ringspot Nepovirus (ToRSV), and Prunus Nectrotic Ringspot Nepovirus (PNRSV).  Our goals are as follows: (1) Identify genes that are induced/repressed in response to individual viruses. (2) Identify genes that are induced/repressed in response to all 3 viruses. (3) Compare results to existing potato array data to look for similarities in responses to other pathogens.  Experimental Design: Nicotiana benthamiana plants were inoculated with one of three viruses: PPV, ToRSV, or PNRSV.  3 week old plants were inoculated by rubbing virus infected plant sap onto leaves dusted with carborundum.  Control plants were mock inoculated using sap from healthy plants.  All plants were maintained in a growth chamber at 22C for 18 days.  8 plants were inoculated with each virus or mock inoculated.  This experiment was repeated twice.  4 biological replicates derived from 2 virus infected plants from each replica experiment (4 plants) are to be used for hybridizations.  RNA from all mock inoculated plants was similarly pooled to create 4 biological replicates.  Each replicate control will serve as a universal reference sample that is to be hybridized pair wise with each of the three virus infected samples.  RNA extraction: After 18 days, un-inoculated leaves displaying clear symptoms were harvested and immediately frozen in liquid N2.  Total RNA was purified using Trizol according to TIGRs listed protocol.  RNA was subsequently treated with Turbo DNA-free RNase (Ambion cat#1907).  Finally, total RNA was further purified on RNeasy columns (Qiagen) according to manufacturer’s instructions and quantified using a Nanodrop spectrophotometer.

organism: Nicotiana benthamiana

growth_protocol: Grown for 18 days in growth chamber (16h/8h light/darkness, 50% humidity, 22°C) in Jiffy mix 50/50.

treatment_protocol: Systemically infected with plant sap containing plum pox virus

tag: Nicotiana benthamiana, Whole leaf, Biotic stress

treatment_protocol: Mock infected with sap from healthy plant


title: control_vs_PVY_3d_2

treatment_protocol: PVY innoculated, 3d

treatment_protocol: PVY-Buffer control, 3d


title: aphid_vs_PLRV_1d_1


title: WT3_vs_hrp2_4d

description: Tomato seeds (Solanum lycopersicum Mill., cultivar Marion) were germinated in vermiculite and 10-day old seedlings were transplanted into 4-inch plastic pots containing a mixture of composted pine bark and vermiculite (3:1) amended with lime and fertilizer. Plants were incubated in a growth chamber (constant 30oC, 14-h photoperiod; 180 ?mol s-1 m-2 light intensity) for 18-21 days before inoculation. Seedlings received a complete liquid fertilizer approximately 7 and 14 days after transplanting. Unwounded roots were inoculated with R. solanacearum by drenching the soil in each pot with 40 ml of water containing 1´107 CFU ml-1 of the wild type or 1´108 CFU ml-1 of the hrp mutant. Non inoculated plants received 40 ml of water. Four days after inoculation, a piece of each stem from about 1-cm above the soil line to just below the cotyledon node was excised, immediately plunged into liquid nitrogen, and stored at -80oC. A separate 0.5-cm stem section from the cotyledon node was removed aseptically from each plant and the number of bacteria in the section determined by dilution plating. Stem pieces from plants systemically colonized by R. solanacearum were pulverized in a mortar under liquid nitrogen, and total RNA was extracted with the Tri-Reagent (Molecular Research Center) and then treated with RNase-free recombinant DNase (Ambion) according to the recommended protocols from TIGR and stored at -70oC.

organism: Solanum lycopersicum

growth_protocol: 14 h light/10 h dark at 30 C in pine bark + vermiculite

treatment_protocol: Colonized by a  Ralstonia solanacearum hrp mutant, 4 days post inoculation

tag: Solanum lycopersicum, Stem between soil line and cotyledeon, Biotic stress

treatment_protocol: Colonized by wild-type Ralstonia solanacearum, 4 days post inoculation


title: wd_systemic_vs_spit_systemic1s


title: PPV2_vs_Mock2_systemic_leaf


title: control_vs_PVY_1d_1


title: wd_systemic_vs_spit_systemic2


title: WT_vs_uc_4d_2

treatment_protocol: None, 4 days post inoculation


title: ctrl_vs_4h_infested3swap

treatment_protocol: Infest with CPB 4 hr

treatment_protocol: Control 4 hr


title: WT2_vs_hrp1_4d


title: Mock4_vs_PNRSV4_systemic_leaf

treatment_protocol: Systemically infected with sap containing prunus necrotic ringspot virus


title: wd_systemic_vs_spit_systemic3

treatment_protocol: Wound and spit systemic 4 hr

treatment_protocol: Wounded systemic 4 hr


title: Mock2_vs_PPV2_systemic_leaf


title: ctrl_vs_4h_infested2swap


title: wounded_vs_wounded_spit3swap

treatment_protocol: Wound and spit 4 hr

treatment_protocol: Wounded 4 hr


title: wd_systemic_vs_spit_systemic1


title: WT_vs_uc_4d_3


title: ctrl_vs_4h_infested2


title: hrp3_vs_WT2_4d


title: uc3_vs_WT2_4d


title: ctrl_vs_4h_infested3


title: hrp2_vs_uc3_4d


title: uc2_vs_WT1_4d


title: uc_vs_hrp_4d_3


title: ctrl_vs_4h_infested1swap


title: hrp1_vs_uc2_4d


title: wounded_vs_wounded_spit2swap


title: ctrl_vs_4h_infested1


title: hrp2_vs_WT1_4d


title: WT_vs_uc_4d_1


title: uc_vs_hrp_4d_1


title: PNRSV2_vs_Mock2_systemic_leaf


title: uc_vs_hrp_4d_2


title: aphid_vs_PLRV_7d_3

treatment_protocol: PLRV aphid-infected, 7d

treatment_protocol: Sham Inoc - aphid control, 7d


title: wounded_vs_wounded_spit1swap


title: WT_vs_hrp_4d_3_FD


title: wounded_vs_wounded_spit1


title: ctrl_vs_1h_infested2swap

treatment_protocol: Infest with CPB 1hr


title: wounded_vs_wounded_spit2


title: WT_vs_hrp_4d_2


title: ctrl_vs_1h_infested3

treatment_protocol: Infest with CPB 1 hr


title: WT_vs_hrp_4d_1_FD


title: ctrl_vs_1h_infested1swap


title: WT_vs_hrp_4d_3


title: ctrl_vs_1h_infested1


title: ctrl_vs_complex_Stbr_96h_1

description: Whole plants of a clone of S. cajamarquence and a clone of S. tuberosum were spray inoculated with Phytophthora infestans sporangial suspension 3000 sporangias/ml until run off. Two isolates were used: PE84006 (race 0) and POX067 (avr 8, 9). Leaves in the middle part of the plants were collected at 72 h and 96 h after inoculation. Leaves of untreated plants were collected as control treatment.

growth_protocol: Grown for 93 days in screenhouse (16h/8h light/darkness, 22%/96% minimum/maximum average humidity, 6 C/28 C minimum/max average temperature) in peat-clay substrate

treatment_protocol: Challenged with Phytophthora infestans  complex race

treatment_protocol: Unchallenged


title: WT_vs_hrp_4d_2_FD


title: Mock_96h_leaf_vs_Ps_1

description: Nicotiana benthamiana plants were grown to the 8th true leaf development stage with 16 h light at 150  mol s-1 m-2 with 25/17oC day/night temperatures. Colletotrichum orbiculare strain ATCC20767 and Pseudomonas syringae pv. tabaci strain BPIC4 was grown in pure cultures to obtain syringae pv. tabaci strain BPIC4 was grown in pure cultures to obtain conidia and cells, respectively. Leaves of N. benthamiana plants were inoculated by spraying a suspension of 2 X 106 spores/ml in sterile H2O for C. orbiculare as described by Shen et al. (2001) or by infiltrating with a needle-less syringe 2 X 105 CFU/ml in sterile 10 mM MgCl2 for P. syringae pv. tabaci according to Rommens et al. (1995). For a control, healthy leaves were sprayed with sterile H2O or infiltrated with sterile 10 mM MgCl2 and then incubated under the same conditions for the same period of time as the pathogen-inoculated plants. Total RNA was extracted at 12 hours and 1, 2, 3 and 4 days after inoculation. The first and second mature leaf was excised and immediately frozen at -70 C.

treatment_protocol: infiltrating with a needle-less syringe 2 X 105 CFU/ml in sterile 10 mM MgCl2 for P. syringae pv.tabaci, 48h

tag: Nicotiana benthamiana, Leaves, Biotic stress

treatment_protocol: sprayed with water or infiltrated with sterile 10mM MgCl2, 48h


title: ctrl_vs_1h_infested2


title: ctrl_vs_complex_Stbr_72h_1_FD


title: ctrl_vs_complex_Stbr_96h_3


title: Mock_96h_leaf_vs_Ps_3

growth_protocol: 16 h light at 150  mol s-1 m-2 with 25/17oC day/night temperatures

treatment_protocol: infiltrating with a needle-less syringe 2 X 105 CFU/ml in sterile 10 mM MgCl2 for P. syringae pv.tabaci, 96h

treatment_protocol: sprayed with water or infiltrated with sterile 10mM MgCl2, 96h


title: ctrl_vs_complex_Stbr_96h_2


title: ctrl_vs_1h_infested3swap


title: Mock_12h_leaf_vs_Ps_2_FD

treatment_protocol: infiltrating with a needle-less syringe 2 X 105 CFU/ml in sterile 10 mM MgCl2 for P. syringae pv.tabaci, 24h

treatment_protocol: sprayed with water or infiltrated with sterile 10mM MgCl2, 24h


title: Mock_72h_leaf_vs_Ps_2

treatment_protocol: infiltrating with a needle-less syringe 2 X 105 CFU/ml in sterile 10 mM MgCl2 for P. syringae pv.tabaci, 12h

treatment_protocol: sprayed with water or infiltrated with sterile 10mM MgCl2, 12h


title: WT_vs_hrp_4d_1

treatment_protocol: Colonized by a  Ralstonia solanacearum hrp mutant, 4 days post inoculation

treatment_protocol: Colonized by wild-type Ralstonia solanacearum, 4 days post inoculation


title: ctrl_vs_complex_Stbr_72h_2


title: ctrl_vs_complex_Stbr_72h_1


title: Mock_96h_leaf_vs_Ps_2

treatment_protocol: infiltrating with a needle-less syringe 2 X 105 CFU/ml in sterile 10 mM MgCl2 for P. syringae pv.tabaci, 72h

treatment_protocol: sprayed with water or infiltrated with sterile 10mM MgCl2, 72h


title: ctrl_vs_complex_Stbr_72h_3


title: Mock_72h_leaf_vs_Ps_1


title: Mock_48h_leaf_vs_Ps_3


title: wounded_vs_wounded_spit3

treatment_protocol: Wound and spit 4 hr

treatment_protocol: Wounded 4 hr


title: Mock_72h_leaf_vs_Ps_3


title: Mock_48h_leaf_vs_Ps_2


title: Mock_24h_leaf_vs_Ps_3


title: ctrl_vs_complex_Scjm_96h_2


title: ctrl_vs_complex_Scjm_96h_1


title: Mock_24h_leaf_vs_Ps_2


title: Mock_48h_leaf_vs_Ps_1


title: ctrl_vs_complex_Scjm_96h_3


title: ctrl_vs_complex_Scjm_72h_1


title: Mock_24h_leaf_vs_Ps_1


title: Mock_12h_leaf_vs_Ps_1


title: ctrl_vs_race0_Stbr_96h_1

treatment_protocol: Challenged with Phytophthora infestans race 0


title: Mock_96h_leaf_vs_Cg_3

treatment_protocol: spraying a suspension of 2 X 106 spores/ml in sterile H2O for C. orbiculare , 96h


title: ctrl_vs_race0_Stbr_96h_3

treatment_protocol: Unchallenged


title: Mock_12h_leaf_vs_Ps_2


title: Potato_vs_N_benthamiana_2

description: Six different Solanaceae species, Potato (Solanum tuberosum), Tomato (Lycopersicum esculentum), Pepper (Capsicum annuum), Tobacco (Nicotiana tabacum), Petunia and Nicotiana benthamiana were grown at 25C, 16h light and 8h darkness. Mature leaves were harvested after 4-6 weeks. RNA was isolated using Qiagen RNeasy. Tomato, pepper, petunia tobacco and N. benthamiana samples were hybridized against potato samples.

growth_protocol: 25C; 16 hr light, 8 hr dark

treatment_protocol: No treatment

tag: Nicotiana benthamiana, leaves, Development

tag: Solanum tuberosum, leaves, Development


title: Potato_vs_Pepper_2

organism: Capsicum annuum

tag: Capsicum annuum, leaves, Development


title: ctrl_vs_race0_Stbr_72h_3


title: Mock_72h_leaf_vs_Cg_3

treatment_protocol: spraying a suspension of 2 X 106 spores/ml in sterile H2O for C. orbiculare , 72h


title: ctrl_vs_complex_Scjm_72h_2

treatment_protocol: Challenged with Phytophthora infestans  complex race


title: Potato_vs_Tomato_2

tag: Solanum lycopersicum, leaves, Development


title: Potato_vs_Tobacco_2

organism: Nicotiana tabacum

tag: Nicotiana tabacum, leaves, Development


title: ctrl_vs_complex_Scjm_72h_3


title: Mock_48h_leaf_vs_Cg_3

treatment_protocol: spraying a suspension of 2 X 106 spores/ml in sterile H2O for C. orbiculare , 48h

treatment_protocol: sprayed with water or infiltrated with sterile 10mM MgCl2, 48h


title: Mock_24h_leaf_vs_Cg_3

treatment_protocol: spraying a suspension of 2 X 106 spores/ml in sterile H2O for C. orbiculare , 24h

treatment_protocol: sprayed with water or infiltrated with sterile 10mM MgCl2, 24h


title: Mock_12h_leaf_vs_Ps_3

treatment_protocol: infiltrating with a needle-less syringe 2 X 105 CFU/ml in sterile 10 mM MgCl2 for P. syringae pv.tabaci, 48h


title: Potato_vs_Tobacco_1


title: Potato_vs_Petunia_2

organism: Petunia x hybrida

tag: Petunia hybrida, leaves, Development


title: ctrl_vs_race0_Stbr_72h_1


title: ctrl_vs_race0_Stbr_96h_2


title: Potato_vs_N_benthamiana_1


title: Potato_vs_Pepper_1


title: ctrl_vs_race0_Scjm_96h_2


title: Potato_vs_Petunia_1


title: Mock_96h_leaf_vs_Cg_2

treatment_protocol: sprayed with water or infiltrated with sterile 10mM MgCl2, 96h


title: ctrl_vs_race0_Stbr_72h_2


title: ctrl_vs_race0_Scjm_96h_1


title: Potato_vs_Tomato_1


title: Resis(N)_mock_vs_TMV_3h_4

description: TMV-resistant (N), -susceptible (n), and enhanced susceptible mutant sun1-1 (N) tomato were grown in asceptic conditions in growth chambers (25º, 16hr/8hr light dark).  4-5 week old tomato were treated with TMV leaf sap or mock leaf sap, and leaf tissue was collected after 3, 9, and 27 hours.    RNA was isolated from each sample (leaf tissue from one plant/one treatment/one timepoint), using standard TIGR protocols, and 25ug of total RNA was labeled using TIGR indirect labeling protocols.  The experiment was repeated three times.

growth_protocol: Grown for 28-35 days in growth chamber(16h/8h light/dark, 25º in Sunshine mix #1)

treatment_protocol: Challenged with TMV sap, 3hr

tag: Solanum lycopersicum, Leaf and petiole, Biotic stress

treatment_protocol: Mock treated with leaf sap, 3hr


title: Mock_12h_leaf_vs_Cg_3

treatment_protocol: spraying a suspension of 2 X 106 spores/ml in sterile H2O for C. orbiculare , 12h

treatment_protocol: sprayed with water or infiltrated with sterile 10mM MgCl2, 12h


title: Mock_72h_leaf_vs_Cg_2

treatment_protocol: sprayed with water or infiltrated with sterile 10mM MgCl2, 72h


title: sun1-1(N)_mock_vs_TMV_9h_3

treatment_protocol: Challenged with TMV sap, 9hr

treatment_protocol: Mock treated with leaf sap, 9hr


title: Resis(N)_mock_vs_TMV_9h_4

treatment_protocol: Challenged with TMV sap, 3 hr


title: ctrl_vs_race0_Scjm_72h_1

treatment_protocol: Challenged with Phytophthora infestans race 0

treatment_protocol: Unchallenged


title: Mock_24h_leaf_vs_Cg_2


title: Mock_12h_leaf_vs_Cg_2


title: Resis(N)_mock_vs_TMV_27h_4

treatment_protocol: Mock treated with leaf sap, 27hr


title: ctrl_vs_race0_Scjm_72h_2


title: ctrl_vs_race0_Scjm_72h_3


title: Mock_48h_leaf_vs_Cg_2

treatment_protocol: spraying a suspension of 2 X 106 spores/ml in sterile H2O for C. orbiculare , 48h


title: sun1-(N)_mock_vs_TMV_27h_1

treatment_protocol: Challenged with TMV sap, 27hr


title: wt_FRc_12hr_vs_fri_FRc_12hr_2

description: Treatment of the seeds. The Solanum lycopersicum var. Money Maker wild type (MM) and fri1-1 mutant seeds were incubated on distilled-water saturated cotton wool in clear plastic boxes wrapped in black plastic sheets in darkness during 3 hours at 25°C. After that, the seeds were treated as follows: a) 24 hr of continuous irradiation with far-red light, FRc; b) 24 hr of FRc follow by a 10 min red light pulse (Rp), FRc+Rp; and c) complete darkness. After the light treatments, the seeds were incubated in darkness (25°C) until sampling.   Red light (35umol/m2sec) was provided by 40W fluorescent lamps (Phillips 40/15) in combination with a red translucid acrylic. FRc light (100 umol/m2sec) was provided by a set of 150W incandescent internal reflector lamps (Phillips) in combination with a red acetate filter, six 2mm thick blue acrylic filters Paolini 2031 and 10cm water filter.  Total RNA isolation. The seeds were grinded in liquid nitrogen and extracted with two volumes of extraction buffer (1% SDS, 6% p-aminosalycilic acid, 1% NaCl, 6% water-saturated phenol and 2% 2-mercaptoethanol) and two volumes of acid phenol:chloroform solution. The aqueous phase was sequentially extracted with one volume of acid phenol:chloroform solution and one volume of chloroform. The nucleic acids in the aqueous phase were precipitated with 0.15 volumes of 3M NaCl and 2.5 volumes of 100% ethanol at –80°C for 20 minutes. After centrifugation, the pellet was washed with 70% ethanol, resuspended in RNase-free water and precipitated with one volume of 4M LiCl over night at 4°C. The LiCl was removed after centrifugation and the pellet was rinsed with 2M LiCl and resuspended in RNase-free water. The total RNA was treated with RNase-free DNase (Promega) and cleaned up with mini spin columns (RNeasy Plant Mini Kit, Qiagen). The mRNA was amplificated with Message Amp II aRNA Amplification Kit (Ambion) and concentrated by vacumm centrifugation.

growth_protocol: Incubation in distilled water-saturated cotton wool in clear plastic boxes cover with black plastic sheets at 25ºC

treatment_protocol: 24hr FRc

tag: Solanum lycopersicum, Whole seed, Development


title: sun1-(N)_mock_vs_TMV_27h_3


title: Mock_96h_leaf_vs_Cg_1

treatment_protocol: spraying a suspension of 2 X 106 spores/ml in sterile H2O for C. orbiculare , 96h


title: fri_FRc_Rp30h_vs_wtFRc_Rp30h_2_FD


title: sun1-1(N)_mock_vs_TMV_3h_3

treatment_protocol: Mock treated with leaf sap, 3h


title: Mock_72h_leaf_vs_Cg_1

treatment_protocol: spraying a suspension of 2 X 106 spores/ml in sterile H2O for C. orbiculare , 72h


title: sun1-1(N)_mock_vs_TMV_9h_2


title: sun1-1(N)_mock_vs_TMV_9h_1


title: sun1-1(N)_mock_vs_TMV_3h_2

treatment_protocol: Challenged with TMV sap, 3hr


title: sun1-1(N)_mock_vs_TMV_3h_1


title: sun1-(N)_mock_vs_TMV_27h_2


title: wt_dark24hr_vs_wt_FRc24hr_2

treatment_protocol: Darkness


title: Resis(N)_mock_vs_TMV_9h_3


title: Mock_24h_leaf_vs_Cg_1

treatment_protocol: spraying a suspension of 2 X 106 spores/ml in sterile H2O for C. orbiculare , 24h

treatment_protocol: sprayed with water or infiltrated with sterile 10mM MgCl2, 24h


title: Resis(N)_mock_vs_TMV_27h_3


title: Resis(N)_mock_vs_TMV_27h_2


title: wt_FRc_3hr_vs_fri_FRc_3hr_2


title: Resis(N)_mock_vs_TMV_3h_2


title: Resis(N)_mock_vs_TMV_3h_3


title: Resis(N)_mock_vs_TMV_27h_1


title: Mock_48h_leaf_vs_Cg_1

treatment_protocol: sprayed with water or infiltrated with sterile 10mM MgCl2, 48h


title: Resis(N)_mock_vs_TMV_9h_2

treatment_protocol: Challenged with TMV sap, 9hr


title: Resis(N)_mock_vs_TMV_9h_1

treatment_protocol: Mock treated with leaf sap, 9hr


title: wtFRc_Rp30h_vs_fri_FRc_Rp30h_2

treatment_protocol: 24hr FRc follow by a 10 min Rp


title: Mock_12h_leaf_vs_Cg_1

treatment_protocol: spraying a suspension of 2 X 106 spores/ml in sterile H2O for C. orbiculare , 12h

treatment_protocol: sprayed with water or infiltrated with sterile 10mM MgCl2, 12h


title: wt_dark12hr_vs_wt_FRc12hr_2


title: wtFRc_Rp51h_vs_fri_FRc_Rp51h_2


title: ST_roots_pr_vs_mock_15d_2

description: Plant-parasitic nematodes and especially the root-knot nematodes are ubiquitous pathogens. Eggs of root-knot  nematodes (Meloidogyne javanica) were extracted from greenhouse cultures and second-stage juveniles (J2) were hatched in tap, sterile water on 30 µm sieves. Solanum tubersum cv. Desiree explants, i.e., stem including an axillary bud, were sectioned, under sterile conditions from in vitro growing seedlings and transferred to Magenta boxes containing Gamborg's media. Seedlings, 4 weeks post transferring to Gamborg's media were planted in pots containing autoclaved quartz sand. Three weeks later the plants were infected with 3000 M. javanica infective juveniles, applied to the soil in tap, sterile water. Control uninfected plants were mock-inoculated with tap, sterile water. Roots from 6 infected and 6 mock-inoculated plants were collected at a series of time points, including 5, 10 and 15 days post nematode infection/mock inoculation. Roots were observed under the microscope, and nematode feeding sites were selectively dissected, from young lateral roots. To control for the effect of tissue sectioning on gene expression, young lateral roots of the mock inoculated roots were dissected similarly to the infected roots, and collected. Dissected roots were snapped-freeze in liquid nitrogen and immediately stored in -80 C freezer. Total RNA was extracted using Qiagen RNAEasy kit. The experiment for each time point was duplicated, each duplicate derived from independent biological repeat. All RNA samples were amplified using the Ambion kit Message Amp catalog no. 1750, using as starting material 2.5 to 5 µg of total RNA.

growth_protocol: 16 hour light/8 hour dark at 25 C in sand

treatment_protocol: 15 days post mock-inoculation

tag: Solanum tuberosum, Dissected elongation zone of young lateral roots, Biotic stress

treatment_protocol: A mixture of 5,10 and 15 days of infection and mock inoculation

tag: Solanum tuberosum, Mixture of dissect. elong. zone and RKN feeding sites of YLR, Biotic stress


title: ST_roots_pr_vs_rkn_15d_1

treatment_protocol: 15 days post infection

tag: Solanum tuberosum, Dissected nematode feeding sites of young lateral roots, Biotic stress


title: wt_FRc_27hr_vs_wt_FRc_Rp51hr_2

treatment_protocol: 24hr FRc


title: ST_roots_pr_vs_rkn_5d_1_FD

treatment_protocol: 5 days post infection


title: wt_FRc_6hr_vs_wt_FRc_27hr_2


title: Susc(n)_mock_vs_TMV_3h_3

treatment_protocol: Mock treated with leaf sap, 3h


title: Susc(n)_mock_vs_TMV_3h_2


title: ST_roots_pr_vs_rkn_15d_2


title: Resis(N)_mock_vs_TMV_3h_1


title: wt_FRc_27hr_vs_wt_FRc_Rp30hr_2


title: Susc(n)_mock_vs_TMV_27h_3

treatment_protocol: Challenged with TMV sap, 27hr

treatment_protocol: Mock treated with leaf sap, 27hr


title: Susc(n)_mock_vs_TMV_27h_2


title: ST_roots_pr_vs_mock_15d_1


title: wt_dark9hr_vs_wt_FRc9hr_2

treatment_protocol: Darkness


title: Susc(n)_mock_vs_TMV_9h_2


title: Susc(n)_mock_vs_TMV_27h_1


title: ST_roots_pr_vs_mock_10d_2

treatment_protocol: 10 days post mock-inoculation


title: wt_dark9hr_vs_wt_FRc9hr


title: Susc(n)_mock_vs_TMV_9h_1


title: ST_roots_pr_vs_rkn_10d_2

treatment_protocol: 10 days post infection


title: ST_roots_pr_vs_rkn_10d_1


title: wt_dark24hr_vs_wt_FRc24hr


title: Susc(n)_mock_vs_TMV_9h_3


title: ST_roots_pr_vs_mock_10d_1


title: wt_FRc_3hr_vs_fri_FRc_3hr


title: ST_roots_pr_vs_rkn_5d_2


title: wt_dark12hr_vs_wt_FRc12hr


title: ST_roots_pr_vs_mock_5d_2

treatment_protocol: 5 days post mock-inoculation


title: B_Leaf_control_2_vs_first_drought_1_FD

description: Seed of 4 lines of S. tuberosum var andigena were sown and, after transplanting, grown in 3 gal nursery containers in a greenhouse with natural daylight.  The seeds were sown in July and the drought stress experiment began in September.  Drought stress was administered by withholding water and monitored by measuring the rate of photosynthesis (PS; LiCor 6400).  We found that loss of photosynthetic capability (ie a PS rate of 0-2 mM CO2/m2/sec) correlated with a severe drought stress.  Control plants were watered normally and maintained a PS rate of 18-20 mM CO2/m2/sec.  After drought stress, the treated plants were re-watered and PS measurements taken again.  After the first cycles of stress, control and treated plants were harvested and roots, tubers and shoots were stored at –80°C for RNA extractions.  The drought experiment was then repeated for the remaining plants such that they were exposed to a second cycle of stress.  For each line of S. andigena, there were 2 control and 2 treated plants per cycle of stress.  RNA was extracted following the acid phenol protocol of TIGR.

growth_protocol: Greenhouse, in natural daylight

treatment_protocol: Drought stressed once

tag: Solanum tuberosum, Leaves, Abiotic stress

treatment_protocol: Control


title: C_Tuber_control_1_vs_second_drought_1

treatment_protocol: Drought stressed twice

tag: Solanum tuberosum, Tuber, Abiotic stress


title: wt_FRc_Rp51h_vs_fri_FRc_Rp51h

treatment_protocol: 24hr FRc follow by a 10 min Rp


title: wt_FRc_12hr_vs_fri_FRc_12hr


title: C_Tuber_control_1_vs_first_drought_2


title: Susc(n)_mock_vs_TMV_3h_1

treatment_protocol: Challenged with TMV sap, 3hr


title: B_Tuber_control_2_vs_second_drought_1


title: C_Tuber_control_2_vs_second_drought_1


title: C_Tuber_control_1_vs_first_drought_1


title: ST_roots_pr_vs_rkn_5d_1


title: C_Tuber_control_2_vs_second_drought_2


title: wt_FRc_27hr_vs_wt_FRc_Rp_30hr


title: B_Tuber_control_1_vs_second_drought_2


title: wt_FRc_27hr_vs_wt_FRc_Rp_51hr


title: B_Leaf_control_2_vs_second_drought_1


title: 72h_control_vs_SA_MJ_2

description: Potato cultivar Russet Norkotah was grown in a growth chamber at 16 hour light/8 hour dark at 22°C fertilized with Osmocote.  Plants were from tissue culture, transplanted to soil and used approximately 4 weeks after transplanting.  RNA was extracted from leaves using Trizol.  Plants were sprayed with one of four treatments, either 1mM salicylic acid, 100 µM methyl jasmonate, 1 mg/ml arachidonic acid or 100 µM methyl jasmonate plus 1 mM salicylic acid together.   Samples were harvested at 3, 24 and 72 hours after spraying.  Each salicylic acid or arachidonic acid treatment has 3 biological replicates done in parallel, using leaves pooled from 2 plants.  The control for SA or AA treated plants were water sprayed plants, from which leaves of 3 different plants were pooled at each timepoint, done side-by-side with the treated samples. Methyl jasmonate or MJ+SA treatments had 2 biological replicates each, using leaves pooled from 2 plants. A separate set of water sprayed plants (from the SA and AA control treatments) were used as controls, and pooled leaves from 3 plants were used at each time-point, and done in parallel with the treated samples.

growth_protocol: Growth chamber, 16h light/8h dark at 22C, fertilized with osmocoat

treatment_protocol: 72h, 1mM salicylic acid and 100uM methyl jasmonate

tag: Solanum tuberosum, Leaves, petioles, Biotic stress

treatment_protocol: 72h, water sprayed control


title: B_Leaf_control_1_vs_second_drought_2


title: B_Leaf_control_2_vs_second_drought_2


title: B_Tuber_control_1_vs_second_drought_1


title: B_Tuber_control_2_vs_second_drought_2


title: wt_FRc_Rp30h_vs_fri_FRc_Rp30h


title: C_Tuber_control_1_vs_second_drought_2


title: 72h_control_vs_SA_MJ_1


title: B_Tuber_control_2_vs_first_drought_2


title: ST_roots_pr_vs_mock_5d_1

treatment_protocol: A mixture of 5,10 and 15 days of infection and mock inoculation


title: 24h_control_vs_SA_MJ_1

treatment_protocol: 24h, 1mM salicylic acid and 100uM methyl jasmonate

treatment_protocol: 24h, water sprayed control


title: Stigma_vs_Stage12_3

description: Floral Nectaries – Many plants secrete a rich floral nectar to entice visitation by insect and avian pollinators.  In turn, these pollinators transfer pollen between flowers increasing plant fecundity.  The nectary is the floral organ that secretes nectar into the base of the flower.  The size and abundance of the ornamental tobacco nectaries (Nicotiana sp.) will permit us to isolate up to several grams of nectaries at each stage to obtain the necessary amounts of RNA for probe preparation.  Our primary goals to understand the biochemistry the nectary, so that we can manipulate nectary function to increase pollinator visitation. We have previously conducted an EST study and have identified 13596 cDNAs from three different stages of nectary development (Stage 6, immature, presecretory nectaries; Stage 12, mature nectaries at floral anthesis; and nectaries, 44 hours after fertilization.  In our efforts to evaluate the transcriptional program for the Nicotiana nectary we are proposing to evaluate nectary mRNAs by hybridization with the potato microarrays.    We have preliminary evidence that wholesale transcriptional reprogramming (60% of the transcriptome) occurs during nectary maturation and again following fertilization. Our goal is to understand these processes at a biochemical level so that we can begin manipulating nectary function to improve nectar quality and quantity thereby increasing the attractiveness of flowers to insect pollinators.  Such improvements have the potential to result in increases in insect visitation, seedset, and ultimately yield for insect pollinated crops.  We are also making significant efforts to understand the restructuring of the nectary during its lifecycle. Many changes occur during nectary development and the observed transcriptional reprogramming makes sense the when these many changes are accounted for.

organism: Nicotiana langsdorffii x Nicotiana sanderae

growth_protocol: Green house grown, 16h light, 8h darkness

tag: Nicotiana langsdorffii x sanderae, Stigma, Development

tag: Nicotiana langsdorffii x sanderae, Nectary, Development


title: B_Tuber_control_1_vs_first_drought_1


title: 3h_control_vs_SA_MJ_2

treatment_protocol: 3h, 1mM salicylic acid and 100uM methyl jasmonate

treatment_protocol: 3h, water sprayed control


title: B_Tuber_control_2_vs_first_drought_1


title: B_Leaf_control_1_vs_second_drought_1


title: B_Tuber_control_1_vs_first_drought_2


title: 24h_control_vs_SA_MJ_2


title: Stage12_vs_Stigma_2


title: wt_FRc_6hr_vs_wt_FRc_27hr

treatment_protocol: 24hr FRc


title: B_Leaf_control_1_vs_first_drought_1


title: A_Tuber_control_1_vs_second_drought_2


title: A_Tuber_control_2_vs_first_drought_2


title: A_Tuber_control_2_vs_first_drought_1


title: A_Tuber_control_1_vs_first_drought_2


title: B_Leaf_control_2_vs_first_drought_1


title: A_Leaf_control_2_vs_first_drought_1


title: A_Tuber_control_1_vs_first_drought_1


title: 3h_control_vs_SA_MJ_1


title: Stigma_vs_Stage12_2


title: A_Leaf_control_1_vs_first_drought_1


title: 72h_control_vs_AA_3

treatment_protocol: 72h, 1mg/ml arachidonic acid


title: A_Leaf_control_2_vs_first_drought_2


title: A_Leaf_control_1_vs_first_drought_2


title: Stage12_vs_Stigma_3


title: Stigma_vs_Stage12_1


title: Stage12_vs_Stigma_1


title: Stage3_vs_PF4_2


title: 72h_control_vs_AA_2


title: 72h_control_vs_AA_1


title: Son1_mock_vs_TMV_1h_2

description: TMV-resistant, TMV-susceptible and enhanced susceptibility mutant tomato were grown in asceptic conditions.  At approximately 5 weeks, leaves were mock inoculated, TMV inoculated, or left untreated.  Leaf tissue was collected 1hour after treatment.  RNA was isolated and purified; hybridizations were performed using 130ug of total RNA from plants mock inoculated versus TMV inoculated and untreated.  Each RNA sample is from two pooled plants.  Two replicates were completed.

growth_protocol: 16 h light/ 8 h dark 25C

treatment_protocol: TMV

tag: Solanum lycopersicum, Leaves, petioles, Biotic stress

treatment_protocol: Mock


title: Son1_untreated_vs_mock_1h_2

treatment_protocol: Untreated


title: 24h_control_vs_AA_3

treatment_protocol: 24h, 1mg/ml arachidonic acid


title: D51_mock_vs_TMV_1h_2


title: Son1_mock_vs_TMV_1h_1


title: PF2_vs_Stage12_2


title: PF4_vs_PF2_2


title: VF36_mock_vs_TMV_1h_2


title: 24h_control_vs_AA_2


title: Son1_untreated_vs_mock_1h_1


title: D51_mock_vs_TMV_1h_1


title: PF4_vs_Stage3_2


title: PF2_vs_PF4_2


title: 24h_control_vs_AA_1


title: VF36_untreated_vs_mock_1h_1


title: D51_untreated_vs_mock_1h_2


title: Stage12_vs_PF2_2


title: VF36_untreated_vs_mock_1h_2


title: 3h_control_vs_AA_2

treatment_protocol: 3h, 1mg/ml arachidonic acid


title: VF36_mock_vs_TMV_1h_1


title: Root_control_vs_salt_stress_9h_3

description: Potato seedlings were subjected to cold, heat and salt stress. Expression profiles were captured at three different time-points, 3h, 9h and 27h from two different tissues, roots and leaves. The experiment was preformed independently three times. Commercially available true potato seeds (Variety Gilroy) were germinated on rafts floating on hydroponic medium in Magenta boxes. Plants were grown for 5 weeks prior to stress application under long day conditions (16h light and 8h dark) at 25C with gentle agitation. To initiate stress the medium was replaced with fresh medium pre-chilled to 4C (cold stress), pre-heated to 35C (heat stress) or supplemented with 100mM NaCl (salt stress). Cold and heat stress were maintained for the duration of the experiment by placing the Magenta boxes on ice or in a water-bath at 35C. For every individual sample two boxes of plants were used pooling a total of 6 plants per sample. For each time-point a single control sample was used by changing the media in a similar way as for the stress induction. A total of six boxes were combined for the pooled reference samples. Plants were harvested at the appropriate time and snap-frozen in liquid nitrogen. Roots and aerial tissue was separated prior to freezing. The tissue was stored at -80C freezer until isolation. Total RNA was isolated using RNeasy isolation kit. The intactness of the RNA was verified on gel and the concentration was adjusted to 3ug/ul by ethanol precipitation and re-suspension.

growth_protocol: 25C, 16 h light, 8 h dark

treatment_protocol: Salt stress, 150mM NaCl, 9 h

tag: Solanum tuberosum, Roots, Abiotic stress

treatment_protocol: Control, 9 h


title: 72h_control_vs_MJ_1

treatment_protocol: 72h, 100uM methyl jasmonate


title: D51_untreated_vs_mock_1h_1


title: Root_control_vs_salt_stress_9h_2


title: 72h_control_vs_MJ_2


title: 3h_control_vs_AA_3


title: Stage12_vs_Stage9_2


title: Root_control_vs_salt_stress_9h_1


title: Root_control_vs_salt_stress_3h_3

treatment_protocol: Salt stress, 150mM NaCl, 3 h

treatment_protocol: Control, 3 h


title: Stage9_vs_Stage12_2


title: Root_control_vs_salt_stress_3h_1


title: 24h_control_vs_MJ_1

treatment_protocol: 24h, 100uM methyl jasmonate


title: 24h_control_vs_MJ_2


title: Root_control_vs_salt_stress_27h_3

treatment_protocol: Salt stress, 150mM NaCl, 27 h

treatment_protocol: Control, 27 h


title: Stage6_vs_Stage3_2


title: Root_control_vs_heat_stress_9h_3

treatment_protocol: Heat stress, 35C, 9 h


title: Root_control_vs_salt_stress_3h_2


title: Stage6_vs_Stage9_2


title: 72h_control_vs_SA_2

treatment_protocol: 72h, 1mM salicylic acid

treatment_protocol: 72h, water sprayed control


title: Root_control_vs_salt_stress_27h_1


title: Root_control_vs_heat_stress_3h_2

treatment_protocol: Heat stress, 35C, 3 h


title: Root_control_vs_heat_stress_3h_3


title: Root_control_vs_heat_stress_9h_1


title: 72h_control_vs_SA_3


title: Root_control_vs_heat_stress_9h_2


title: Root_control_vs_salt_stress_27h_2


title: Root_control_vs_heat_stress_27h_3

treatment_protocol: Heat stress, 35C, 27 h


title: PF4_vs_Stage3_1


title: 3h_control_vs_MJ_1

treatment_protocol: 3h, 100uM methyl jasmonate

treatment_protocol: 3h, water sprayed control


title: 72h_control_vs_SA_1


title: Stage3_vs_PF4_1


title: Root_control_vs_heat_stress_27h_1


title: Root_control_vs_heat_stress_3h_1


title: PF4_vs_PF2_1


title: 3h_control_vs_SA_3

treatment_protocol: 3h, 1mM salicylic acid


title: 24h_control_vs_SA_3

treatment_protocol: 24h, 1mM salicylic acid

treatment_protocol: 24h, water sprayed control


title: Root_control_vs_heat_stress_27h_2


title: PF2_vs_PF4_1


title: Root_control_vs_control_stress_9h_3

treatment_protocol: No stress, 9 h

treatment_protocol: Control, 9 h


title: Stage3_vs_Stage6_2


title: 3h_control_vs_MJ_2


title: 24h_control_vs_SA_2


title: PF2_vs_Stage12_1


title: Stage12_vs_Stage9_1


title: 3h_control_vs_SA_2


title: 24h_control_vs_SA_1


title: Root_control_vs_control_stress_9h_2


title: Root_control_vs_control_stress_9h_1


title: Root_control_vs_control_stress_27h_3

treatment_protocol: No stress, 27 h


title: 3h_control_vs_SA_1


title: Root_control_vs_control_stress_3h_2

treatment_protocol: No stress, 3 h

treatment_protocol: Control, 3 h


title: Root_control_vs_control_stress_3h_1


title: Stage9_vs_Stage6_1


title: Stage9_vs_Stage12_1


title: Stage12_vs_PF2_1


title: Root_control_vs_cold_stress_9h_3

treatment_protocol: Cold stress, 4C, 9 h


title: Root_control_vs_control_stress_3h_3


title: Root_control_vs_control_stress_27h_1

treatment_protocol: Control, 27 h


title: Stage3_vs_Stage6_1


title: Stage6_vs_Stage9_1


title: Root_control_vs_cold_stress_9h_2


title: Root_control_vs_cold_stress_3h_2

treatment_protocol: Cold stress, 4C, 3 h


title: Petunia_control_vs_cold_48h_2

description: Seven different Solanaceae species, Potato (Solanum tubersosum), Tomato (Lycopersicum esculentum), Eggplant (Solanum melongena), Pepper (Capsicum annuum), Tobacco (Nicotiana tabacum), Petunia and Nicotiana benthamiana were subjected to cold stress. Plants were grown at 25 C for 4-6 weeks after wich cold stress was initiated by exposing the plants to 4 C for 4, 8, 12, 24 and 48 hours. Control samples were isolated from  plants just before the cold stress was initated.  RNA was isolated using Qiagen RNeasy.

growth_protocol: 4 C; 16 h light, 8 h dark

treatment_protocol: Cold, 48 h

tag: Petunia hybrida, leaves, Abiotic stress

growth_protocol: 25 C; 16 h light, 8 h dark

treatment_protocol: Abiotic control, 0 h


title: Stage6_vs_Stage3_1


title: Root_control_vs_control_stress_27h_2


title: Root_control_vs_cold_stress_3h_3


title: Root_control_vs_cold_stress_27h_2

treatment_protocol: Cold stress, 4C, 27 h


title: Root_control_vs_cold_stress_9h_1


title: Petunia_control_vs_cold_12h_2

treatment_protocol: Cold, 12 h


title: Root_control_vs_cold_stress_27h_1


title: Petunia_control_vs_cold_8h_2

treatment_protocol: Cold, 8 h


title: ctrl_vs_modroughtstolonSU_1_FD

description: The response to moderate and heavy drought of two Solanum tuberosum ssp. Andigena varieties, Sullu (NP 03.03) and SA 2563 (NP 03.01), planted in rain- and soil water protected fields in the Peruvian highlands are compared. Previous experiments indicate that Sullu has a greater capacity for yield maintenance under drought than SA 2563. Both clones have similar morphological properties, vegetative periods and rooting depths, so it can be assumed that the cause for increased drought tolerance of clone NP 03.03 is rather due to physiological or biochemical mechanisms, than to drought escape by deep rooting or earliness. Sullu and SA 2563 were planted in a random block design with 5 plants per bloc and 7 repetitions per treatment.  Treatments: (1) drought stress, (2) irrigated control The plants were drip-irrigated in both treatments until tuberization (until day 84 after planting). Subsequently, the irrigation was stopped in the drought field, but continued in the control field. The soil moisture content in the control field was kept near field capacity.   Planting date: October 05 2004 Start of drought treatment (during tuberization, 84 days after planting): December 28 2004  First sampling (soil water potential: -0.3 mPa 114 days after planting): January 27 2005 Second sampling (soil water potential –0.6 MPa, 134 days after planting): February 15 2005 Harvest: March 19 2005 (165 days after planting)  The experimental design includes gene expression analysis in leaves, roots and stolons at two time points, when soil water potential reaches -0.3 and –0.6 MPa. Gene expression changes will be set in relation with physiological and agronomical data obtained in the same experiment.

growth_protocol: Field, drought from day 85 after planting on

treatment_protocol: Moderate drought

tag: Solanum tuberosum, Pool of all stolones of 3 plants, Abiotic stress

growth_protocol: Field, irrigated during whole vegetative period

treatment_protocol: Control


title: Leaf_control_vs_salt_stress_9h_3

treatment_protocol: Salt stress, 150mM NaCl, 9 h


title: Petunia_control_vs_cold_4h_2

treatment_protocol: Cold, 4 h


title: Root_control_vs_cold_stress_27h_3


title: Leaf_control_vs_salt_stress_9h_1


title: ctrl_vs_hv_drought_root_SU_2

treatment_protocol: Heavy drought

tag: Solanum tuberosum, Pool of 3 roots of 3 plants, Abiotic stress


title: Leaf_control_vs_salt_stress_3h_1

treatment_protocol: Salt stress, 150mM NaCl, 3 h


title: Root_control_vs_cold_stress_3h_1


title: Leaf_control_vs_salt_stress_9h_2

treatment_protocol: Control, 9 h


title: N_tabacum_control_vs_cold_4h_2

tag: Nicotiana benthamiana, leaves, Abiotic stress


title: Leaf_control_vs_salt_stress_3h_3


title: Leaf_control_vs_salt_stress_3h_2


title: Leaf_control_vs_salt_stress_27h_2

treatment_protocol: Salt stress, 150mM NaCl, 27 h


title: Stage9_vs_Stage6_2


title: C_annuum_control_vs_cold_12h_2

tag: Capsicum annuum, leaves, Abiotic stress


title: Leaf_control_vs_salt_stress_27h_3


title: ctrl_vs_hv_drought_stolon_SU_1


title: Leaf_control_vs_heat_stress_9h_3

treatment_protocol: Heat stress, 35C, 9 h


title: ctrl_vs_mo_drought_root_SU_1


title: C_annuum_control_vs_cold_48h_2


title: Leaf_control_vs_salt_stress_27h_1


title: ctrl_vs_hv_drought_stolon_SU_2


title: C_annuum_control_vs_cold_8h_2


title: ctrl_vs_mo_drought_stolon_SU_2


title: Leaf_control_vs_heat_stress_9h_1


title: C_annuum_control_vs_cold_4h_2


title: Leaf_control_vs_heat_stress_3h_3

treatment_protocol: Heat stress, 35C, 3 h

treatment_protocol: Control, 3 h


title: ctrl_vs_mo_drought_stolon_SU_1


title: Leaf_control_vs_heat_stress_3h_2


title: Leaf_control_vs_heat_stress_9h_2


title: Leaf_control_vs_heat_stress_27h_1

treatment_protocol: Heat stress, 35C, 27 h

treatment_protocol: Control, 27 h


title: S_melongena_control_vs_cold_48h_2

organism: Solanum virginianum

treatment_protocol: Cold, 48 h

tag: Solanum melongena, leaves, Abiotic stress

treatment_protocol: Abiotic control, 0 h


title: Leaf_control_vs_heat_stress_27h_3


title: Leaf_control_vs_control_stress_9h_3

treatment_protocol: No stress, 9 h


title: Leaf_control_vs_heat_stress_3h_1


title: Leaf_control_vs_heat_stress_27h_2


title: ctrl_vs_hv_drought_leaf_SU_1

tag: Solanum tuberosum, Pool of leaf 3, 4, 5 of 3 plants, Abiotic stress


title: S_melongena_control_vs_cold_12h_2

treatment_protocol: Cold, 12 h


title: Leaf_control_vs_control_stress_9h_1


title: S_melongena_control_vs_cold_8h_2

treatment_protocol: Cold, 8 h


title: N_tabacum_control_vs_cold_8h_2


title: ctrl_vs_hv_drought_leaf_SU_2

treatment_protocol: Control


title: Leaf_control_vs_control_stress_3h_3

treatment_protocol: No stress, 3 h


title: S_melongena_control_vs_cold_24h_2

treatment_protocol: Cold, 24 h


title: Leaf_control_vs_control_stress_9h_2


title: ctrl_vs_mo_drought_leaf_SU_2

treatment_protocol: Moderate drought


title: Leaf_control_vs_control_stress_3h_1


title: S_melongena_control_vs_cold_4h_2

treatment_protocol: Cold, 4 h


title: Leaf_control_vs_control_stress_3h_2


title: L_esculentum_control_vs_cold_48h_2

tag: Lycopersicon esculentum, leaves, Abiotic stress


title: Leaf_control_vs_control_stress_27h_1

treatment_protocol: No stress, 27 h


title: Leaf_control_vs_control_stress_27h_2


title: Leaf_control_vs_control_stress_27h_3


title: Leaf_control_vs_cold_stress_9h_2

treatment_protocol: Cold stress, 4C, 9 h

treatment_protocol: Control, 9 h


title: Leaf_control_vs_cold_stress_3h_3

treatment_protocol: Cold stress, 4C, 3 h


title: Leaf_control_vs_cold_stress_27h_1

treatment_protocol: Cold stress, 4C, 27 h


title: Leaf_control_vs_cold_stress_27h_3


title: Leaf_control_vs_cold_stress_9h_1


title: ctrl_vs_hv_drought_stolon_SA_2

treatment_protocol: Heavy drought


title: Leaf_control_vs_cold_stress_3h_1

treatment_protocol: Control, 3 h


title: Leaf_control_vs_cold_stress_27h_2

treatment_protocol: Control, 27 h


title: Leaf_control_vs_cold_stress_9h_3


title: ctrl_vs_mo_drought_leaf_SA_1


title: ctrl_vs_mo_drought_leaf_SU_1


title: L_esculentum_control_vs_cold_4h_2

treatment_protocol: Abiotic control, 0 h


title: Petunia_control_vs_cold_24h_1

tag: Petunia hybrida, Leaves, Abiotic stress


title: Petunia_control_vs_cold_48h_1

treatment_protocol: Cold, 48 h


title: L_esculentum_control_vs_cold_12h_2

treatment_protocol: Cold, 12 h


title: ctrl_vs_hv_drought_leaf_SA_1


title: Petunia_control_vs_heat_48h_2

description: Seven different Solanaceae species, Potato (Solanum tubersosum), Tomato (Lycopersicum esculentum), Eggplant (Solanum melongena), Pepper (Capsicum annuum), Tobacco (Nicotiana tabacum), Petunia and Nicotiana benthamiana were subjected to heat stress. Plants were grown for 4-6 weeks at 25 C after which heat stress was initiated by exposing the plants to 35 C for 6, 12, 24, 48 and 96 hours. Control samples were isolated from plants just before initiating the heat stress. RNA was isolated using Qiagen RNeasy.

growth_protocol: 35 C; 16 h light, 8 h dark

treatment_protocol: Heat, 48 h


title: N_benthamiana_control_vs_cold_48h_1

tag: Nicotiana benthamiana, Leaves, Abiotic stress


title: S_tuberosum_control_vs_cold_8h_2

treatment_protocol: Cold, 8 h

tag: Solanum tuberosum, leaves, Abiotic stress


title: SmutansUA159_BHI_rep4

city: Gainesville

first: Robert

middle: A

last: Burne

state: FL

address: 1600 SW Archer Rd. BOX 100424

department: Oral Biology

institute: University of Florida

description: S. mutans manL wildtype

hyb_protocol: Hybridizations were carried out in the dark for 17 h at 42°C.  The slides were then washed according to TIGR protocols.

scan_protocol: The slides were scanned using a GenePix Scanner (Axon Instruments Inc., Union City, CA).

data_processing:
After the slides were scanned, singlechannel
images were loaded into TIGR Spotfinder software
and overlaid. A spot grid was created according to TIGR specifications
and then manually adjusted to fit all spots within the grid. The intensity
values of each spot were measured and saved into “.mev” and “.tav” files. Data
were normalized using LOWESS and iterative log mean centering with default
settings, followed by in-slide replicate analysis using TIGR microarray data
analysis software. Spots that were
flagged as bad because of either low intensity values or signal saturation were
automatically discarded.

organism: Streptococcus mutans

source_name: S. mutans UA159 grown in BHI

label_protocol:
All RNAs were purified as described above and used to generate cDNA according to the protocol provided
by TIGR with the following minor modifications.
The amount of RNA in each reaction was increased to 10 ug, and the
molar ratio of dTTP:aa-dUTP was increased to 1:1.5. In addition, SuperscriptIII
reverse transcriptase (Invitrogen, Gaithersburg, MD) was used to increase
cDNA yields.

growth_protocol:
Growth Media: Brain-Heart Infusion
OD600: 0.5

extract_protocol:
Briefly, 50-ml cultures that were intended for use in
microarray experiments were grown under the desired
conditions and harvested by centrifugation at 4°C. Pelleted cells were resuspended
in 400 ul of diethyl pyrocarbonate-treated water, 800 ul of RNA protect
reagent (QIAGEN, Inc., Chatsworth, CA) was added, and the samples were
incubated at room temperature for 5 min with vortexing for 10 s at 1-min
intervals. Cells were then pelleted, resuspended in 500 ul Tris-EDTA (50:10)
buffer, and transferred to 1.5-ml screw-cap tubes containing sterile glass beads
(avgerage diameter, 0.1 mm; Biospec, Bartlesville, OK), 100 ul of 1% sodium
dodecyl sulfate, and 650 ul of acid phenol:chloroform (5:1). The mixture was
homogenized twice in a bead beater for 40 s and chilled on ice for 2 min between
cycles. Samples were centrifuged for 30 min at maximum speed at 4°C. Two
additional hot acid-phenol:chloroform extractions were performed by incubating
the samples at 65°C for 10 min and transferring them to an ice bath for another
10 min, followed by centrifugation at maximum speed for 10 min at 4°C. The
aqueous phase was collected and extracted once with chloroform:isoamyl-alcohol
(24:1). RNA was precipitated with 1/10 volume of 3 M sodium acetate, pH 5, and
an equal volume of isopropanol at -20°C for 1 h, followed by multiple washes
with 70% ethanol, one wash with 99% ethanol, and drying in vacuo. RNA was
resuspended in 52 ul of diethyl pyrocarbonate-treated water; 1 ul was used to estimate RNA concentration, and 1 ul was used to verify RNA quality in a
formaldehyde gel. The remaining 50-ul sample was digested with DNase I (Ambion, Austin, TX), and then the RNA was repurified and treated on column with DNase I using an RNeasy mini kit (QIAGEN, Inc., Chatsworth, CA) as recommendedby the supplier.

tag: Strain UA159


title: Petunia_control_vs_cold_8h_1


title: SmutansUA159_BHI_rep5

description: S. mutans manL wildtype


title: ctrl_vs_mo_drought_stolon_SA_2

treatment_protocol: Control


title: N_benthamiana_control_vs_cold_24h_1

treatment_protocol: Cold, 24 h


title: SmutansUA159_BHI_rep3

description: S. mutans manL wildtype


title: ctrl_vs_hv_drought_leaf_SA_2


title: SmutansUA159_BHI_rep6

description: S. mutans manL wildtype


title: Petunia_control_vs_heat_96h_2

treatment_protocol: Heat, 96 h


title: Leaf_control_vs_cold_stress_3h_2

tag: Solanum tuberosum, Leaves, Abiotic stress


title: ctrl_vs_mo_drought_leaf_SA_2

treatment_protocol: Moderate drought


title: SmutansUA159_BHI_rep2

description: S. mutans manL wildtype


title: N_benthamiana_control_vs_cold_8h_1


title: SmutansJAM1_BHI_rep6

description: S. mutans manL knockout mutant

source_name: S. mutans JAM1 grown in BHI

tag: Strain JAM1

value: Knockout of S. mutans manL gene via insertion of a kanamycin cassette.


title: ctrl_vs_mo_drought_stolon_SA_1


title: N_tabacum_control_vs_cold_48h_1

tag: Nicotiana tabacum, Leaves, Abiotic stress


title: Petunia_control_vs_heat_12h_2

treatment_protocol: Heat, 12 h


title: N_tabacum_control_vs_cold_8h_1


title: ctrl_vs_hv_drought_stolon_SA_1


title: Petunia_control_vs_heat_24h_2

treatment_protocol: Heat, 24 h


title: S_tuberosum_control_vs_cold_12h_2


title: N_benthamiana_control_vs_cold_12h_1


title: Petunia_control_vs_cold_12h_1


title: L_esculentum_control_vs_cold_8h_2


title: SmutansJAM1_BHI_rep5

description: S. mutans manL knockout mutant


title: N_tabacum_control_vs_cold_24h_1


title: SmutansUA159_BHI_rep1

description: S. mutans manL knockout mutant

tag: Growth Media

value: Brain-Heart Infusion


title: S_tuberosum_control_vs_cold_4h_2

treatment_protocol: Cold, 4 h


title: N_tabacum_control_vs_cold_12h_1


title: Petunia_control_vs_cold_4h_1


title: N_benthamiana_control_vs_heat_96h_2


title: N_benthamiana_control_vs_heat_48h_2


title: S_tuberosum_control_vs_cold_48h_2


title: Petunia_control_vs_heat_6h_2

treatment_protocol: Heat, 6 h


title: SmutansJAM1_BHI_rep4

description: S. mutans manL knockout mutant


title: N_benthamiana_control_vs_cold_4h_1


title: C_annuum_control_vs_cold_12h_1

tag: Capsicum annuum, Leaves, Abiotic stress


title: C_annuum_control_vs_cold_4h_1


title: SmutansJAM1_BHI_rep3

description: S. mutans manL knockout mutant


title: C_annuum_control_vs_cold_8h_1


title: N_benthamiana_control_vs_heat_12h_2


title: C_annuum_control_vs_cold_48h_1


title: S_melongena_control_vs_cold_8h_1

tag: Solanum melongena, Leaves, Abiotic stress


title: S_melongena_control_vs_cold_24h_1


title: SmutansJAM1_BHI_rep2

description: S. mutans manL knockout mutant


title: N_benthamiana_control_vs_heat_6h_2


title: S_melongena_control_vs_cold_4h_1


title: S_melongena_control_vs_cold_48h_1


title: S_melongena_control_vs_cold_12h_1


title: C_annuum_control_vs_cold_24h_1


title: N_benthamiana_control_vs_heat_24h_2


title: N_tabacum_control_vs_heat_48h_2

tag: Nicotiana tabacum, leaves, Abiotic stress


title: N_tabacum_control_vs_heat_96h_2


title: SmutansJAM1_BHI_rep1

description: S. mutans manL knockout mutant


title: L_esculentum_control_vs_cold_4h_1

tag: Solanum lycopersicum, Leaves, Abiotic stress


title: L_esculentum_control_vs_cold_8h_1


title: N_tabacum_control_vs_heat_24h_2


title: L_esculentum_control_vs_cold_12h_1


title: L_esculentum_control_vs_cold_48h_1


title: N_tabacum_control_vs_heat_12h_2


title: S_tuberosum_control_vs_cold_24h_1


title: S_tuberosum_control_vs_cold_4h_1


title: N_tabacum_control_vs_heat_6h_2


title: Skeletal muscle sample from fine needle-stimulated hindlimb

city: Suita

first: Osamu

last: Ishida

state: Osaka

address: 5-7-1 Fujishorodai

department: Regenerative Medicine

country: Japan

institute: National Cardiovascular Center

description: None.

hyb_protocol: Hybridized with GeneChip Rat Genome 230 2.0 Array (Affymetrix) according to the manufacturer's instruction.

scan_protocol: Using GeneChip scanner 3000 (Affymetrix)

label: biotin

organism: Rattus norvegicus

source_name: hindlimb skeletal muscle

label_protocol: Using GeneChip One-Cycle Target Labeling and Control Reagent (Affymetrix) according to the manufacturer's instruction.

extract_protocol: Using an RNeasy kit (Qiagen) according to the manufacturer's instruction

treatment_protocol: With 0.14 mm diameter stainless steel needle, one hundred pricks were applied to a 10 mm by 10 mm square region of the left hindlimb to adductor muscle. Muscle sample were harvested 24 hours after the fine needle stimulation.

tag: Strain

value: Lewis, Gender:Male, Body Weight:275g, Tissue:Skeletal muscle sample from fine nnedle-stimulated hindlimb


title: L_esculentum_control_vs_cold_24h_1


title: S_tuberosum_control_vs_cold_8h_1


title: Skeletal muscle sample from control hindlimb

description: None.

scan_protocol: Using GeneChip scanner 3000 (Affymetrix).

extract_protocol: Using an RNeasy kit (Qiagen) according to the manufacturer's instruction.

treatment_protocol: No treatment

value: Lewis, Gender:Male, Body weight:275g, Tissue:skeletal muscle sample from non fine needle-stimulated hindlimb


title: C_annuum_control_vs_heat_96h_2

tag: Capsicum annuum, leaves, Abiotic stress


title: FRI1169 non-hemolytic variant batch culture replicate #1

city: St Paul

first: Jeremy

middle: M

last: Yarwood

state: MN

department: Corporate Research

description: Microarray experiment protocols were based in large part on those described in Schuster, M., C. P. Lostroh, T. Ogi, and E. P. Greenberg. 2003. Identification, timing, and signal specificity of Pseudomonas aeruginosa quorum-controlled genes: a transcriptome analysis. J. Bacteriol. 185:2066-79.

hyb_protocol: Labeled, fragmented cDNA was prepared for hybridization to S. aureus microarrays using the Prokaryotic Sample and Array Processing Protocol (Affymetrix) at 45oC. Following hybridization, wash and staining procedures were carried out on GeneChip Fluidics Station-450s (Affymetrix) using the ProkGE-WS2v3_450 procedure.

scan_protocol: Following washing and staining, the microarrays were scanned on a GeneChip GeneChip Scanner 300.

data_processing:
Microarray images were inspected by eye to
confirm grid alignment and the absence of any chip irregularities. Initial analysis was conducted to confirm that overall chip intensity (OCI) and standard deviation were within acceptable range. OCI values represent the “brightness” or pre-normalization average intensity of the array and although this value typically varies between arrays it should not vary dramatically within an experiment. The standard deviation value represents background noise present of the microarray and again, should not vary dramatically within an experiment. Standard deviation is calculated by determining the standard deviation of intensity of all the genes called absent. Expression of BioB, C, D, and Cre, which are spiked in cDNA hybridization controls at 1.5pM, 5.0pM, 25.0pM,
and 100pM respectively, were observed for appropriate increasing expression values.Analysis of expression profiling experiments.
We used the Affymetrix Microarray Software suite (MAS) (version 5.0) to determine transcript levels and whether there were differences in transcript levels when different samples were compared. Affymetrix scaling was used to normalize data from different arrays. A scale factor is derived from the mean signal of all of the probe sets on an array and a user-defined target signal. The signal from each individual probe set is multiplied by this scale factor. For comparison analyses, the log2 ratio for absolute transcript signals obtained from a given pair of arrays was calculated by using MAS. A statistical algorithm of the software also assigned a change call for each transcript pair, which indicated whether the level of a transcript was significantly increased, decreased, or not changed compared to the level for the baseline sample. The baseline samples were those derived from cultures of wild-type FRI1169. Graphical analysis of the signal log ratios from each experiment (any pair of arrays) revealed a normal distribution with a mean very close to zero (no change). Only the fold-changes for transcripts of Agr-regulated virulence factors with significant increases or decreases compared to the baseline in both replicate experiments are shown in Table 1 (Yarwood et al, J. Bacteriol. in press).

label: biotin-ddUTP

organism: Staphylococcus aureus

source_name: Staphylococcus aureus FRI1169 non-hemolytic variant

label_protocol: Further sample preparation and processing of the S. aureus GeneChip genome arrays were done as described by the manufacturer (Affymetrix) with minor modifications.  For cDNA synthesis we used 12 µg of purified RNA, semirandom hexamer primers with an average G+C content of 75%, and Superscript II reverse transcriptase (Life Technologies). Control RNAs from yeast, Arabidopsis, and Bacillus subtilis genes (provided by S. Lory) were added to the reaction mixtures to monitor assay performance. RNA was removed from the PCR mixtures by alkaline hydrolysis. The cDNA synthesis products were purified and fragmented by brief incubation with DNase I, and the 3' termini of the fragmentation products were labeled with biotin-ddUTP.

growth_protocol: Cultures of the S. aureus FRI1169 wild-type (H) and non-hemolytic variant (N) were inoculated to an optical density (600 nm) of 0.01 from overnight cultures and incubated with shaking at 37oC. Cells were harvested at an optical density (600 nm) of 2 (stationary phase).

extract_protocol: Between 1 x 10^9 and 2 x 10^9 cells were mixed with RNA Protect Bacteria reagent (Qiagen) and treated as recommended by the manufacturer's mechanical disruption and lysis protocol. RNA was purified by using RNeasy mini columns (Qiagen), including the on-column DNase I digestion described by the manufacturer. In addition, we treated the eluted RNA for 1 h at 37°C with DNase I (0.1 U per µg of RNA). DNase I was removed by using DNA-Free (Ambion) or by RNeasy column purification. RNA integrity was monitored by agarose gel electrophoresis of glyoxylated samples.

tag: Non-hemolytic variant derived from biofilm cultures of S. aureus FRI1169 as described in Yarwood et al., J. Bacteriol 2007.


title: FRI1169 non-hemolytic variant batch culture replicate #2

source_name: S. aureus FRI1169 non-hemolytic variant

tag: Non-hemolytic variant isolated from biofilms inoculated with FRI1169 as described in Yarwood et al., J. Bacteriol. 2007.


title: Petunia_control_vs_heat_48h_1


title: C_annuum_control_vs_heat_24h_2


title: C_annuum_control_vs_heat_12h_2


title: Wild-type FRI1169 batch culture replicate #1

source_name: Staphylococcus aureus FRI1169

tag: Clinical isolate


title: Petunia_control_vs_heat_12h_1

tag: Petunia hybrida, Leaves, Abiotic stress


title: N_benthamiana_control_vs_heat_48h_1

tag: Nicotiana benthamiana, Leaves, Abiotic stress


title: Wild-type FRI1169 batch culture replicate #2


title: C_annuum_control_vs_heat_6h_2


title: S_melongena_control_vs_heat_96h_2

tag: Solanum melongena, leaves, Abiotic stress


title: Petunia_control_vs_heat_96h_1


title: Petunia_control_vs_heat_6h_1


title: Petunia_control_vs_heat_24h_1


title: N_benthamiana_control_vs_heat_6h_1


title: N_benthamiana_control_vs_heat_24h_1


title: C_annuum_control_vs_heat_48h_2


title: S_melongena_control_vs_heat_12h_2


title: N_tabacum_control_vs_cold_4h_1


title: S_tuberosum_control_vs_cold_48h_1


title: N_tabacum_control_vs_heat_12h_1


title: S_melongena_control_vs_heat_24h_2


title: S_melongena_control_vs_heat_48h_2


title: N_tabacum_control_vs_heat_24h_1


title: N_tabacum_control_vs_heat_96h_1


title: N_benthamiana_control_vs_heat_96h_1


title: L_esculentum_control_vs_heat_96h_2

tag: Solanum lycopersicum, leaves, Abiotic stress


title: S_melongena_control_vs_heat_6h_2


title: C_annuum_control_vs_heat_48h_1


title: N_benthamiana_control_vs_heat_12h_1


title: S_tuberosum_control_vs_cold_12h_1

tag: Solanum tuberosum, Leaves, Abiotic stress


title: N_tabacum_control_vs_heat_48h_1


title: C_annuum_control_vs_heat_96h_1


title: N_tabacum_control_vs_heat_6h_1


title: L_esculentum_control_vs_heat_48h_2


title: L_esculentum_control_vs_heat_24h_2


title: S_melongena_control_vs_heat_96h_1


title: S_melongena_control_vs_heat_12h_1


title: C_annuum_control_vs_heat_12h_1


title: C_annuum_control_vs_heat_24h_1


title: S_melongena_control_vs_heat_48h_1


title: S_melongena_control_vs_heat_24h_1


title: C_annuum_control_vs_heat_6h_1


title: L_esculentum_control_vs_heat_12h_2


title: S_melongena_control_vs_heat_6h_1


title: L_esculentum_control_vs_heat_6h_2


title: L_esculentum_control_vs_heat_24h_1


title: S_tuberosum_control_vs_heat_24h_2

tag: Solanum tuberosum, leaves, Abiotic stress


title: L_esculentum_control_vs_heat_12h_1


title: S_tuberosum_control_vs_heat_48h_1


title: L_esculentum_control_vs_heat_6h_1


title: L_esculentum_control_vs_heat_48h_1


title: S_tuberosum_control_vs_heat_24h_1


title: S_tuberosum_control_vs_heat_96h_2


title: L_esculentum_control_vs_heat_96h_1


title: S_tuberosum_control_vs_heat_48h_2


title: S_tuberosum_control_vs_heat_6h_2


title: S_tuberosum_control_vs_heat_12h_2


title: S_tuberosum_control_vs_heat_6h_1


title: Res_control_vs_Res_7dpi_1_FD

description: Female whiteflies are used to inoculate the susceptible and resistant tomato genotypes as follows. Whiteflies are caged with TYLCV-infected tomato plants for a 48 h acquisition access period. Then, the viruliferous insects are collected and used to inoculate 20 plants of each genotype. The plants at their 4 leaf-stage are inoculated by caging ten viruliferous whiteflies with the youngest true leaf (more than 1 cm) of each plant, using leaf cages. Mock inoculations are conducted using the same number of non-viruliferous insects. After a 12 h inoculation access period (which ensures 100% infection), the insect cages are removed and the plants are treated with insecticide (imidacloprid). The plants are kept for 3 or 7 days in an insect-proof greenhouse, in natural daylight (12 h light/12 h dark).

growth_protocol: Greenhouse, in natural daylight (12 h light/12 h dark), at 22-26 C

treatment_protocol: Infected with TYLCV by viruliferous whiteflies, 7 dpi

tag: Solanum lycopersicum, Leaves, Biotic stress

treatment_protocol: Non infected


title: S_tuberosum_control_vs_heat_12h_1

treatment_protocol: Abiotic control, 0 h


title: S_tuberosum_control_vs_heat_96h_1


title: Res_mock_7dpi_vs_Res_inf_7dpi_2

treatment_protocol: Mock inoculation by whiteflies, 7 dpi


title: Res_mock_7dpi_vs_Res_inf_7dpi_1


title: Petunia_control_vs_drought_10d_2

description: Seven different Solanaceae species, Potato (Solanum tubersosum), Tomato (Solanum lycopersicum), Eggplant (Solanum melongena), Pepper (Capsicum annuum), Tobacco (Nicotiana tabaccum), Petunia and Nicotiana benthiamana were subjected to drought stress. Drought stress was applied by stopping watering of the plants, control plants were normally watered with nutrient solution. Samples were collected at 0, 1, 3, 5, 7 and 10 days after the first application of the drought stress. RNA was isolated using Qiagen RNeasy.

growth_protocol: 25C; 16 h light, 8 h dark

treatment_protocol: No Watering, 5 days

tag: Petunia hybrida, leaves, Abiotic stress

treatment_protocol: Nutrient solution, 5 days


title: Petunia_control_vs_drought_7d_2

treatment_protocol: No Watering, 10 days

treatment_protocol: Nutrient solution, 10 days


title: Res_mock_3dpi_vs_Res_inf_3dpi_1

treatment_protocol: Infected with TYLCV by viruliferous whiteflies, 3 dpi

treatment_protocol: Mock inoculation by whiteflies, 3 dpi


title: Sus_inf_3dpi_vs_Sus_inf_7dpi_2


title: Petunia_control_vs_drought_1d_2

treatment_protocol: No Watering, 1 days

treatment_protocol: Nutrient solution, 1 days


title: Sus_mock_7dpi_vs_Sus_inf_7dpi_1


title: Sus_control_vs_Sus_mock_3dpi_2


title: Petunia_control_vs_drought_5d_2

treatment_protocol: No Watering, 7 days

treatment_protocol: Nutrient solution, 7 days


title: Res_mock_3dpi_vs_Res_inf_3dpi_2


title: Res_control_vs_Res_mock_3dpi_1


title: Petunia_control_vs_drought_3d_2

treatment_protocol: No Watering, 3 days

treatment_protocol: Nutrient solution, 3 days


title: Res_control_vs_Res_7dpi_2


title: Sus_control_vs_Sus_7dpi_2


title: Res_inf_3dpi_vs_Res_inf_7dpi_1


title: Sus_mock_3dpi_vs_Sus_inf_3dpi_1


title: Sus_inf_3dpi_vs_Sus_inf_7dpi_1


title: N_benthamiana_control_vs_drought_7d_2

tag: Nicotiana benthamiana, leaves, Abiotic stress


title: Sus_control_vs_Sus_mock_3dpi_1


title: Res_control_vs_Res_mock_3dpi_2


title: Res_inf_3dpi_vs_Res_inf_7dpi_2


title: Sus_7dpi_2_vs_Res_7dpi_1C


title: Petunia_control_vs_drought_0d_2

treatment_protocol: No Watering, 0 days

treatment_protocol: Nutrient solution, 0 days


title: N_benthamiana_control_vs_drought_1d_2


title: Sus_mock_7dpi_vs_Sus_inf_7dpi_2

treatment_protocol: Infected with TYLCV by viruliferous whiteflies, 7 dpi


title: N_benthamiana_control_vs_drought_3d_2


title: Sus_mock_3dpi_vs_Sus_inf_3dpi_2


title: Res_control_vs_Res_7dpi_1

treatment_protocol: Non infected


title: N_benthamiana_control_vs_drought_0d_2


title: N_benthamiana_control_vs_drought_5d_2


title: Sus_3dpi_vs_Res_3dpi_2


title: Sus_7dpi_vs_Res_7dpi_2


title: Sus_3dpi_vs_Res_3dpi_1


title: Sus_3dpi_1_vs_Res_3dpi_2C


title: Sus_control_1_vs_Res_control_2C


title: Sus_control_vs_Res_control_2


title: Sus_7dpi_vs_Res_7dpi_1


title: Sus_control_vs_Res_control_1


title: N_tabacum_control_vs_drought_10d_2


title: Sus_control_vs_Sus_7dpi_1


title: Petunia_control_vs_drought_7d_1


title: N_tabacum_control_vs_drought_1d_2


title: Petunia_control_vs_drought_3d_1


title: Petunia_control_vs_drought_5d_1


title: C_annuum_control_vs_drought_7d_2


title: Petunia_control_vs_drought_1d_1


title: C_annuum_control_vs_drought_10d_2


title: Petunia_control_vs_drought_10d_1


title: N_benthamiana_control_vs_drought_3d_1


title: N_benthamiana_control_vs_drought_5d_1


title: Petunia_control_vs_drought_0d_1


title: N_tabacum_control_vs_drought_7d_2


title: N_benthamiana_control_vs_drought_7d_1


title: N_tabacum_control_vs_drought_3d_2


title: C_annuum_control_vs_drought_3d_2


title: N_benthamiana_control_vs_drought_10d_1


title: N_tabacum_control_vs_drought_7d_1

tag: Nicotiana tabacum, Leaves, Abiotic stress


title: N_tabacum_control_vs_drought_10d_1


title: S_melongena_control_vs_drought_10d_2


title: N_benthamiana_control_vs_drought_0d_1


title: S_melongena_control_vs_drought_7d_2


title: N_benthamiana_control_vs_drought_1d_1


title: N_tabacum_control_vs_drought_5d_1


title: N_tabacum_control_vs_drought_3d_1


title: S_melongena_control_vs_drought_5d_2


title: C_annuum_control_vs_drought_1d_2


title: S_melongena_control_vs_drought_1d_2


title: N_tabacum_control_vs_drought_1d_1


title: D01 24h TLR2/1L

city: Los Angeles

first: Philip

middle: T.

state: CA

address: 611 Charles E Young Dr. East, 522 MBI

department: Department of Medicine, Divison of Dermatology

institute: University of California at Los Angeles

description: Timecourse of TLR2/1 stimulated human monocytes with the Mycobacterium tuberculosis derived 19kDa lipopeptide.

hyb_protocol: UCLA Microarray Core Facility

scan_protocol: UCLA Microarray Core Facility

data_processing: UCLA Microarray Core Facility

label: Biotin

organism: Homo sapiens

source_name: Total RNA

label_protocol: UCLA Microarray Core Facility

extract_protocol:
Trizol total RNA extraction based on manufacturer's protocol.
RNA cleanup with RNeasy kit based on manufacturer's protocol.

tag: Primary human peripherial monocytes


title: C_annuum_control_vs_drought_3d_1

tag: Capsicum annuum, Leaves, Abiotic stress


title: C_annuum_control_vs_drought_5d_1


title: S_melongena_control_vs_drought_10d_1

tag: Solanum melongena, Leaves, Abiotic stress


title: C_annuum_control_vs_drought_10d_1


title: N_tabacum_control_vs_drought_0d_1


title: S_melongena_control_vs_drought_7d_1


title: S_melongena_control_vs_drought_0d_2


title: S_melongena_control_vs_drought_5d_1


title: L_esculentum_control_vs_drought_10d_2

tag: Lycopersicon esculentum, leaves, Abiotic stress


title: L_esculentum_control_vs_drought_7d_2


title: C_annuum_control_vs_drought_0d_1


title: C_annuum_control_vs_drought_7d_1


title: C_annuum_control_vs_drought_1d_1


title: S_melongena_control_vs_drought_3d_2


title: S_melongena_control_vs_drought_3d_1


title: CT mix1 3rd

city: Tsukuba

first: Emiko

last: Kitagawa

state: Ibaraki

address: Onogawa 16-1

institute: National Institute of Advanced Industrial Science and Technology

description: Data with flag value 0 were used for LOWESS normalization processing.

hyb_protocol: Hybridized for 16-18 h at 65 C

scan_protocol: Scan Array 4000 (PerkinElmer Japan Co., Ltd) was used for scanning. Array images were analyzed with Gene Pix Pro 4.0 (Axon Instrument).

data_processing: GeneSpring ver 7.3.1 (Agilent Technologies Inc.)

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: Cadmium chloride and Thiuram treated for 2 h, Cy5

label_protocol: At least 4 µg of mRNA and a 0.4 µM oligo dT12-17 primer (GIBCO BRL; Life Technologies) were denatured at 70 ºC for 5 min, and the labeled cDNA was synthesized.  The reaction mixture contained 0.5 mM each of dATP, dGTP, and dCTP; 0.2 mM dTTP (GIBCO BRL; Life Technologies); 15 mM Cy5-labeled dUTP (PE Applied Biosystems); 200 units of PowerScript Reverse Transcriptase (CLONTEC, Palo Alto, CA); and an appropriate buffer and RNase inhibiter (GIBCO BRL; Life Technologies).  The reactions were performed at 42 ºC for 1h and 30 min.  Another 200 units of transcriptase was added in the tubes 40 min after the beginning of reverse transcription.  The template mRNA was dissolved by the addition of 0.5 N NaOH for 1 h at 65 ºC.  After neutralization with 1 M Tris-HCl, Cy3- and Cy5-labeled cDNA solution was mixed and filtered on Microcon 30 (AMICON).

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking until OD=1. The exponential growing cells were exposed with Cd;10uM and Thiuram;2.5uM (final concentration) for 2 h.

extract_protocol: Hot-phenol& Oligotex-dT30 mRNA purification kit (TaKaRa, Otsu, Japan)

treatment_protocol: Stock solution of cadmium chloride (Wako; 039-12342) or thiuram (Wako; 204-11371) was dissolved with sterilized water or 100% DMSO, respectively.

tag: strain S288C

source_name: control (without treatment for 2h), Cy3

label_protocol: At least 4 µg of mRNA and a 0.4 µM oligo dT12-17 primer (GIBCO BRL; Life Technologies) were denatured at 70 ºC for 5 min, and the labeled cDNA was synthesized.  The reaction mixture contained 0.5 mM each of dATP, dGTP, and dCTP; 0.2 mM dTTP (GIBCO BRL; Life Technologies); 15 mM Cy3-labeled dUTP (PE Applied Biosystems); 200 units of PowerScript Reverse Transcriptase (CLONTEC, Palo Alto, CA); and an appropriate buffer and RNase inhibiter (GIBCO BRL; Life Technologies).  The reactions were performed at 42 ºC for 1h and 30 min.  Another 200 units of transcriptase was added in the tubes 40 min after the beginning of reverse transcription.  The template mRNA was dissolved by the addition of 0.5 N NaOH for 1 h at 65 ºC.  After neutralization with 1 M Tris-HCl, Cy3- and Cy5-labeled cDNA solution was mixed and filtered on Microcon 30 (AMICON).

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking until OD=1, then grown for 2 h without any treatment.

treatment_protocol: without treatment


title: S_melongena_control_vs_drought_1d_1


title: S_melongena_control_vs_drought_0d_1


title: CT mix1 1st


title: L_esculentum_control_vs_drought_3d_2


title: L_esculentum_control_vs_drought_0d_2


title: S_tuberosum_control_vs_drought_7d_2


title: CT mix1 2nd


title: L_esculentum_control_vs_drought_5d_2


title: S_tuberosum_control_vs_drought_10d_2

treatment_protocol: No Watering, 5 days

treatment_protocol: Nutrient solution, 5 days


title: C_annuum_control_vs_drought_5d_2

tag: Capsicum annuum, leaves, Abiotic stress


title: S_tuberosum_control_vs_drought_3d_2


title: L_esculentum_control_vs_drought_5d_1

tag: Solanum lycopersicum, Leaves, Abiotic stress


title: L_esculentum_control_vs_drought_7d_1


title: S_tuberosum_control_vs_drought_0d_2


title: L_esculentum_control_vs_drought_1d_1


title: D11 24h TLR2/1L


title: S_tuberosum_control_vs_drought_1d_2


title: S_tuberosum_control_vs_drought_10d_1

treatment_protocol: No Watering, 10 days

treatment_protocol: Nutrient solution, 10 days


title: SN_uc_vs_SN_c_AF7d_2

description: Nicotiana attenuata and Solanum nigrum were challenged with different insects: Manduca sexta and Tupiocoris notatus in different combinations Goals of the study are first to haracterize the transcriptional response of two native Solanaceous plants (Nicotiana attenuata and Solanum nigrum) to attack from two herbivorous pests common on Solanaceous crops (Manduca sexta and Tupiocoris notatus). And second to identify genes involved in herbivore vaccination phenomenon. After germination, inbred and genetically characterized lines of N. attenuata DI92 and S. nigrum Sn30 originally collected from southwestern Utah in 1988, and Jena Germany in 2000, respectively, were grown in a greenhouse. Eggs of Manduca sexta (abbreviated M. s.) came from the North Carolina State University - Entomology Insectary and were hatched under 37°C. Nymphs and adults of Tupiocoris notatus (abbreviated T. n.) came from laboratory colonies started in 2000 with individuals collected from our Utah field sites. Plant were challenged with these different insect and combinations of them. All plants for a given treatment were enclosed in glass-and-mesh insect cages to avoid cross-infection. After 24 h or 5 days the herbivores and their frass were removed, and the above ground biomass of each plant was flash-frozen in liquid nitrogen and stored at -80 °C until RNA extraction. Three independent replicate cages (biological replicates) were used for each of the 7 treatments resulting in a total of 21 cages per species. RNA extraction was performed according to the protocol using Trizol. The RNA samples represent a pooled sample from 4 plants grown in a cage.

organism: Solanum nigrum

growth_protocol: green house (16h/8h light/darkness, 20-22°C/18-20°C, 65% humidity) in peat-clay-substrate. Planted to field plot after 3 weeks.

treatment_protocol: water spraying on aphid (Aphis fabae) infested plants for 7 days = aphid treatment

tag: Solanum nigrum, Leaves, Biotic stress

treatment_protocol: insecticide spraying (Spruzit, 0.1%) on aphid (Aphis fabae) infested plants for 7 days = control


title: L_esculentum_control_vs_drought_3d_1


title: S_tuberosum_control_vs_drought_7d_1


title: SN_uc_vs_SN_c_AF7d_1


title: S_tuberosum_control_vs_drought_3d_1


title: S_tuberosum_control_vs_drought_5d_2


title: S_tuberosum_control_vs_drought_5d_1


title: L_esculentum_control_vs_drought_10d_1


title: S_tuberosum_control_vs_drought_0d_1


title: L_esculentum_control_vs_drought_0d_1


title: SN_tl_vs_SN_tMeJA24h_3

growth_protocol: green house (16h/8h light/darkness, 20-22°C/18-20°C, 65% humidity) in peat-clay-substrate

treatment_protocol: application of  0.075 mg methyl-jasmonate in 0.01 ml lanolin paste smeared across the leaf surface

treatment_protocol: application of  0.01 ml pure lanolin paste smeared across the leaf surface


title: S_tuberosum_control_vs_drought_1d_1

treatment_protocol: No Watering, 1 days

treatment_protocol: Nutrient solution, 1 days


title: SN_tl_vs_SN_tMeJA24h_1


title: SN_un_vs_SN_c_EP48h_3

treatment_protocol: Epitrix pubescens infestation: 48h, 5 individuals per cage


title: SN_tl_vs_SN_tMeJA24h_2


title: SN_uc_vs_SN_c_AF7d_3


title: NS_uc_5d_vs_NS_simc_MS5d_TN5d_3

growth_protocol: Grown for 21 days in green house (16h/8h light/darkness, 65% humidity, 26 °C) in peat-clay substrate

treatment_protocol: S. nigrum plants challenged with 10 Tupiocoris notatus adults for 1d and no herbivore for 4d, 5d

treatment_protocol: None, 5 days


title: NS_uc_5d_vs_NS_seqc_MS1d_TN4d_3

treatment_protocol: S. nigrum plants challenged with 10 Tupiocoris notatus adults for 1d and 2 Manduca sexta larvae for 4d, 5d


title: NA_uc_24h_vs_NA_c_MS24h_1_FD

organism: Nicotiana attenuata

growth_protocol: Sterile germination, grown for 38 days in green house (16h/8h light/darkness, 65% humidity, 26 °C) in peat-clay substrate

treatment_protocol: Challenged with 15 Manduca sexta neonate larvae for 1d, 24h

tag: Nicotiana attenuata, Leaves, Biotic stress

treatment_protocol: None, 24 h


title: Smad3-independent genes in BxPC-3 cells

city: Beijing

first: yu

last: jian

state: Beijing

address: Qinghuayuan

department: Medical Systems Biology Research Center

country: China

institute: Tsinghua University

description: Confirmation of the Smad3-independent genes via TGFb stimulation in BxPC-3 cells.

hyb_protocol: Labeled control and test samples were quantitatively adjusted based on the efficiency of Cy-dye incorporation and mixed into 80 µL hybridization solution (3×SSC, 0.2% SDS, 25% formamide and 5×Denhart’s). DNA in hybridization solution was denatured at 95℃ for 3 min prior loading on a microarray. Hybridization was performed under LifterSlipTM (Erie Company), which allows for even dispersal of hybridization solutions between the microarray and coverslip. The hybridization chamber was placed on a 3D-Tilting Agitator (CapitalBio Corp.) to facilitate the microfluidic circulation under the coverslip. The array was hybridized at 42℃ overnight and washed with two consecutive washing solutions (0.2% SDS, 2×SSC at 42℃ for 5 min, and 0.2% SSC for 5 min at room temperature).

scan_protocol: Microarrays were scanned with a confocal LuxScanTM scanner (CapitalBio Corp.), and the data of obtained images were extracted with SpotData Software (CapitalBio Corp.).

data_processing: The raw data was normalized using a space and intensity-dependant LOWESS program (Yang et al., 2002). The data from faint spots was removed, in which the intensity was lower than the average intensity plus 2 standard deviations of the negative controls on the array.

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM210nnn/GSM210123/suppl/GSM210123 (S3KD+cy3 + S3KD-cy5.LSR.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM210nnn/GSM210123/suppl/GSM210123 (S3KD+cy5 + S3KD-cy3.LSR.gz

source_name: S3KD (Smad3 knockdown) cells with TGFb stimulation

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method.and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with RNeasy Mini Kit (Qiagen). Because sense oligonucleotide arrays were used here, we took a cDNA labeling approach with Klenow enzyme after reverse transcription.

extract_protocol: Total RNA was extracted with Trizol (Invitrogen, Carlsbad, CA).

treatment_protocol: The cells were stimulated by incubation in the presence (+) of 10 ng/ml of TGF-β for 4 h.

tag: stable Smad3 knockdown BxPC-3 cells

source_name: S3KD (Smad3 knockdown) cells without TGFb stimulation

label_protocol: Fluorescent dye (Cy3 and Cy5-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method.and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with RNeasy Mini Kit (Qiagen). Because sense oligonucleotide arrays were used here, we took a cDNA labeling approach with Klenow enzyme after reverse transcription.

treatment_protocol: The cells were stimulated by incubation in the absence (-) of 10 ng/ml of TGF-β for 4 h.


title: SN_un_vs_SN_c_EP48h_1


title: NS_uc_24h_vs_NS_c_TN5d_3

treatment_protocol: S. nigrum plants challenged with 5 Manduca sexta neonate larvae for 1d and no herbivore for 4d, 5d


title: SN_un_vs_SN_c_EP48h_2


title: NS_uc_24h_vs_NS_c_TN24h_3

treatment_protocol: S. nigrum plants challenged with 10 Tupiocoris notatus adults for 24h, 24h


title: PBMCs__SYS99 070406 A

city: Dallas

first: Florence

last: Allantaz

state: TX

address: 3434 Live Oak Street

institute: Baylor Institute for Immunology Research

description: PBMCs from SoJIA patient.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: PBMCs from SoJIA patient.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: RNeasy Mini

tag: Age

value: 5 yrs, when sample taken.

tag: Gender

value: M

tag: Race

value: White

tag: Illness

value: JIA Systemic Onset

tag: Symptoms

value: Fever arthritis

tag: Treatment


title: Smad2-dependent genes in BxPC-3 cells

description: Confirmation of the Smad2-dependent genes via TGFb stimulation in BxPC-3 cells.

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM210nnn/GSM210122/suppl/GSM210122 (WT+cy3 + S2KD+cy5).LSR.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM210nnn/GSM210122/suppl/GSM210122 (WT+cy5 + S2KD+cy3).LSR.gz

source_name: S2KD (Smad2 knockdown) cells with TGFb stimulation

tag: stable Smad2 knockdown BxPC-3 cells

source_name: WT (control) cells with TGFb stimulation

tag: stable transfetcted with RNAi vector in BxPC-3 cells


title: Smad2-independent genes in BxPC-3 cells

description: Confirmation of the Smad2-independent genes via TGFb stimulation in BxPC-3 cells.

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM210nnn/GSM210121/suppl/GSM210121 (S2KD+cy3 + S2KD-cy5).LSR.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM210nnn/GSM210121/suppl/GSM210121 (S2KD+cy5 + S2KD-cy3).LSR.gz

source_name: S2KD (Smad2 knockdown) cells without TGFb stimulation


title: Smad3-dependent genes in BxPC-3 cells

description: Confirmation of the Smad3-dependent genes via TGFb stimulation in BxPC-3 cells.

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM210nnn/GSM210124/suppl/GSM210124 (S3KD+cy3 + WT+cy5).LSR.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM210nnn/GSM210124/suppl/GSM210124 (S3KD+cy5 + WT+cy3).LSR.gz


title: PBMCs__sys85A 041505

description: PBMCs from SoJIA patient.

value: 8 yrs, when sample taken.

value: F

value: AA

value: Fever


title: NS_uc_5d_vs_NS_seqc_MS1d_TN4d_2


title: NS_uc_24h_vs_NS_c_TN24h_2


title: NS_uc_24h_vs_NS_c_TN5d_2


title: Smad4-independent genes in BxPC-3 cells

description: Confirmation of the Smad4-independent genes via TGFb stimulation in BxPC-3 cells.

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM210nnn/GSM210120/suppl/GSM210120 (WT+cy3 + WT-cy5).LSR.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM210nnn/GSM210120/suppl/GSM210120 (WT+cy5 + WT-cy3).LSR.gz

source_name: WT cells with TGFb stimulation

source_name: WT cells without TGFb stimulation

treatment_protocol: The cells were stimulated by incubation in the absence (+) of 10 ng/ml of TGF-β for 4 h.


title: NS_uc_24h_vs_NS_c_MS24h_3

treatment_protocol: S. nigrum plants challenged with 5 Manduca sexta neonate larvae for 24h, 24h


title: PBMCs__sys70A 052102

description: PBMCs from SoJIA patient.

value: 4 yrs, when sample taken.

value: Asian

value: Arthritis


title: PBMCs__sys78A 120804

description: PBMCs from SoJIA patient.


title: PBMCs__sys91A 011106

description: PBMCs from SoJIA patient.


title: PBMCs__sys81A

description: PBMCs from SoJIA patient.

value: 6 yrs, when sample taken.


title: NS_uc_24h_vs_NS_c_MS24h_2


title: Mo17xB73 19 DAP endosperm tissue biological replicate 3

city: Saint Paul

first: Nathan

last: Springer

address: 1445 Gortner Ave

department: Plant Biology

institute: University of Minnesota

description: No other relevant details

hyb_protocol: Hybridization was performed according to the recommended Affymetrix protocols at the University of Minnesota Microarray facility.

scan_protocol: The Genechip 3000 scanner was used to scan each array

data_processing: MAS5.0 values are reported; the .cel file is also available

organism: Zea mays

source_name: Zea mays 19 day after pollination endosperm tissue

label_protocol: Eight ug of total RNA was labeled for each hybridization using the One-Cycle cDNA Synthesis Kit, according to the manufacturer’s instructions (Affymetrix, Santa Clara CA).

growth_protocol: Endosperm tissues were isolated from kernels of inbreds Mo17 and B73, and hybrids Mo17xB73 and B73xMo17 for gene expression analysis. Samples were collected during August 2005 from field-grown maize plants grown on the St. Paul campus Agricultural Experiment Station. Inbred and hybrid crosses were performed at three different dates to produce biological replicates. The crosses for all genotypes within a biological replicate were performed within 30 minutes of each other. Six ears of each genotypes were harvested at 19 DAP. Six endosperms were collected from each of the six ears and pooled for a total of 36 endosperms from each genotype by biological replicate combination. All tissues were flash frozen in a dry-ice cooled ethanol bath, and subsequently stored at −80˚C.

extract_protocol: Initial isolation of 19 DAP endosperm RNAs involved a combination of phenol/chloroform extraction and the TRIzol procedure, and essentially followed published methods (Leiva-Neto et al. 2004).  Briefly, powders for 19 DAP endosperm were homogenized in extraction buffer (50mM TRIS pH 8.0, 150mM LiCl, 5mM EDTA pH 8.0, 1% SDS), extracted twice with an equal volume of 1:1 phenol chloroform, extracted with an equal volume of chloroform, and then extracted with TRIzol according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA).  The 19 DAP endosperm RNAs were further purified using the RNeasy protocol (Qiagen Corp., Valencia, CA).  All purified RNA samples were quantified and qualified using the Nanodrop spectrophotometer (Nanodrop Technologies, Montchanin, DE) and agarose gel electrophoresis.

tag: Stage

value: 19 day after pollination endosperm; Genotype:Mo17xB73


title: PBMCs__sys78A 101304

description: PBMCs from SoJIA patient.


title: NS_uc_5d_vs_NS_simc_MS5d_TN5d_1


title: NS_uc_5d_vs_NS_simc_MS5d_TN5d_2


title: B73 19 DAP endosperm tissue biological replicate 3

description: No other relevant details

value: 19 day after pollination endosperm; Genotype:B73


title: PBMCs__sys74A 110304

description: PBMCs from SoJIA patient.

value: 10 yrs, when sample taken.

value: Hispanic

value: Methotrexate


title: PBMCs__sys68A 111004

description: PBMCs from SoJIA patient.


title: PBMCs__sys69A 022404

description: PBMCs from SoJIA patient.

value: 16 yrs, when sample taken.

value: M

value: Steroids PO


title: B73xMo17 19 DAP endosperm tissue biological replicate 3

description: No other relevant details

value: 19 day after pollination endosperm; Genotype:B73xMo17


title: PBMCs__sys68A 011304

description: PBMCs from SoJIA patient.

value: JIA Systemic Onset

value: Fever arthritis


title: NS_uc_24h_vs_NS_c_TN24h_1


title: B73xMo17 19 DAP endosperm tissue biological replicate 2

description: No other relevant details


title: NS_uc_5d_vs_NS_seqc_MS1d_TN4d_1


title: Mo17 19 DAP endosperm tissue biological replicate 3

description: No other relevant details

value: 19 day after pollination endosperm; Genotype:Mo17


title: PBMCs__sys85B 041505

description: PBMCs from SoJIA patient.

value: 8 yrs, when sample taken.

value: F

value: AA

value: Fever


title: NS_uc_24h_vs_NS_c_MS24h_1


title: PBMCs__sys81B

description: PBMCs from SoJIA patient.

value: 6 yrs, when sample taken.


title: PBMCs__sys78B 101304

description: PBMCs from SoJIA patient.

value: 5 yrs, when sample taken.

value: White

value: Anakinra


title: NS_uc_24h_vs_NS_c_TN5d_1


title: PBMCs__sys78B 120804

description: PBMCs from SoJIA patient.


title: B73 19 DAP endosperm tissue biological replicate 2

description: No other relevant details

value: 19 day after pollination endosperm; Genotype:B73


title: PBMCs__sys53A 050603

description: PBMCs from SoJIA patient.

value: 9 yrs, when sample taken.


title: PBMCs__sys91B 011106

description: PBMCs from SoJIA patient.

value: 4 yrs, when sample taken.


title: B73 19 DAP endosperm tissue biological replicate 1

description: No other relevant details


title: PBMCs__sys62A 033104

description: PBMCs from SoJIA patient.

value: Hispanic

value: Steroids PO, Steroids IV


title: NA_uc_5d_vs_NA_seqc_MS1d_TN4d_2

treatment_protocol: Sequentially challenged with 15 Manduca sexta neonate larvae for 1d followd by 15 Tupiocoris notatus adults for 4 d, 5d


title: Mo17 19 DAP endosperm tissue biological replicate 2

description: No other relevant details


title: NA_uc_24h_vs_NA_c_MS24h_3


title: PBMCs__SYS99 070406 B

description: PBMCs from SoJIA patient.

value: M


title: NA_uc_5d_vs_NA_seqc_MS1d_TN4d_3


title: NA_uc_24h_vs_NA_c_TN5d_3

treatment_protocol: Challenged with 15 Tupiocoris notatus adults for 5d, 5d


title: NA_uc_24h_vs_NA_c_TN24h_3

treatment_protocol: Challenged with 15 Tupiocoris notatus adults for 1d, 24h


title: PBMCs__sys56A 021804

description: PBMCs from SoJIA patient.

value: JIA Systemic Onset

value: Steroids PO, Steroids IV, Methotrexate


title: NA_uc_5d_vs_NA_simc_MS5d_TN5d_3

treatment_protocol: Simultaneously challenged with 15 Manduca sexta neonate larvae (reduced to 2 by day 5) and 15 Tupiocoris notatus adults for 5d, 5d


title: Mo17xB73 19 DAP endosperm tissue biological replicate 1

description: No other relevant details

value: 19 day after pollination endosperm; Genotype:Mo17xB73


title: PBMCs__sys74B 110304

description: PBMCs from SoJIA patient.

value: 10 yrs, when sample taken.

value: Arthritis

value: Methotrexate


title: PBMCs__sys52A 050403

description: PBMCs from SoJIA patient.

value: 14 yrs, when sample taken.

value: F

value: Fever arthritis


title: PBMCs__sys49A 062002

description: PBMCs from SoJIA patient.

value: 11 yrs, when sample taken.

value: White

value: Steroids PO, Methotrexate


title: PBMCs__sys51A 022003

description: PBMCs from SoJIA patient.

value: 2 yrs, when sample taken.


title: Mo17xB73 19 DAP endosperm tissue biological replicate 2

description: No other relevant details


title: B73xMo17 19 DAP endosperm tissue biological replicate 1

description: No other relevant details

value: 19 day after pollination endosperm; Genotype:B73xMo17


title: PBMCs__sys70B 052102

description: PBMCs from SoJIA patient.

value: 4 yrs, when sample taken.

value: Asian


title: PBMCs__sys69B 022404

description: PBMCs from SoJIA patient.

value: 16 yrs, when sample taken.

value: M

value: AA

value: Steroids PO


title: NA_uc_24h_vs_NA_c_TN5d_2


title: NA_uc_5d_vs_NA_simc_MS5d_TN5d_2


title: B73xMo17 13 DAP endosperm tissue biological replicate 3

description: No other relevant details

source_name: Zea mays 13 day after pollination endosperm tissue

growth_protocol: Endosperm tissues were isolated from kernels of inbreds Mo17 and B73, and hybrids Mo17xB73 and B73xMo17 for gene expression analysis.  Samples were collected during August 2005 from field-grown maize plants grown on the St. Paul campus Agricultural Experiment Station.  Inbred and hybrid crosses were performed at three different dates to produce biological replicates.  The crosses for all genotypes within a biological replicate were performed within 30 minutes of each other.  Six ears of each genotypes were harvested at 13 DAP.  Six endosperms were collected from each of the six ears and pooled for a total of 36 endosperms from each genotype by biological replicate combination.  All tissues were flash frozen in a dry-ice cooled ethanol bath, and subsequently stored at −80˚C.

extract_protocol: RNAs for 13 DAP endosperm tissues were isolated using the plant RNeasy kit, according to the manufacturer’s instructions (Qiagen Corp., Valencia, CA).  All purified RNA samples were quantified and qualified using the Nanodrop spectrophotometer (Nanodrop Technologies, Montchanin, DE) and agarose gel electrophoresis.

value: 13 day after pollination endosperm; Genotype:B73xMo17


title: PBMCs__sys44A 112102

description: PBMCs from SoJIA patient.

value: 13 yrs, when sample taken.

value: JIA Systemic Onset


title: B73 13 DAP endosperm tissue biological replicate 3

description: No other relevant details

value: 13 day after pollination endosperm; Genotype:B73


title: PBMCs__sys47A 033104

description: PBMCs from SoJIA patient.

value: 10 yrs, when sample taken.

value: Hispanic


title: Mo17 19 DAP endosperm tissue biological replicate 1

description: No other relevant details

value: 19 day after pollination endosperm; Genotype:Mo17


title: PBMCs__sys51A 012704

description: PBMCs from SoJIA patient.

value: 3 yrs, when sample taken.

value: F

value: White

value: Fever arthritis

value: Steroids PO, Steroids IV


title: NA_uc_24h_vs_NA_c_MS24h_2


title: PBMCs__sys68B 111004

description: PBMCs from SoJIA patient.

value: 6 yrs, when sample taken.


title: PBMCs__sys40A 060202

description: PBMCs from SoJIA patient.

value: Arthritis

value: Infliximab


title: Mo17 13 DAP endosperm tissue biological replicate 3

description: No other relevant details

value: 13 day after pollination endosperm; Genotype:Mo17


title: PBMCs__sys39A 111202

description: PBMCs from SoJIA patient.

value: 5 yrs, when sample taken.


title: PBMCs__sys42A 111402

description: PBMCs from SoJIA patient.

value: 11 yrs, when sample taken.

value: M


title: NA_uc_24h_vs_NA_c_TN24h_2


title: NA_uc_5d_vs_NA_simc_MS5d_TN5d_1


title: PBMCs__sys37A 110502

description: PBMCs from SoJIA patient.

value: 8 yrs, when sample taken.

value: JIA Systemic Onset

value: Steroids PO


title: PBMCs__sys68B 011304

description: PBMCs from SoJIA patient.

value: Hispanic


title: PBMCs__sys56B 021804

description: PBMCs from SoJIA patient.

value: 4 yrs, when sample taken.

value: Steroids PO, Steroids IV, Methotrexate


title: PBMCs__sys53B 050603

description: PBMCs from SoJIA patient.

value: 9 yrs, when sample taken.

value: F


title: Mo17xB73 13 DAP endosperm tissue biological replicate 3

description: No other relevant details

value: 13 day after pollination endosperm; Genotype:Mo17xB73


title: PBMCs__sys51B 022003

description: PBMCs from SoJIA patient.

value: 2 yrs, when sample taken.

value: White

value: Fever arthritis

value: Steroids PO, Methotrexate