title: WT 3 week cold, biological rep3


title: WT warm, biological rep3 [2]

status: Public on Jun 30 2013

type: RNA

city: Beltsville

first: Sunchung

last: Park

state: MD

address: 10300 Baltimore ave, Bldg001

department: ARS-NEA

country: USA

institute: USDA -ARS

description: Arabidopsis WT Col-0 grown at 22⁰C in soil under a 12 h photoperiod for approx 23 d

hyb_protocol: Hybridization and washing were carried out according to the Gene Chip manufacturer's protocol (Affymetrix)

scan_protocol: Scan protocols were carried out according to the Gene Chip manufacturer's protocol (Affymetrix)

data_processing: The data were analyzed with LIMMA package of Bioconductor using GC-RMA normalization procedure.

label: biotin

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Arabidopsis Col-0 grown at 22⁰C

label_protocol: RNA was amplified and biotinylated using a MessageAmp kit (Ambion) according to the manufacturer's protocol

growth_protocol: Plants were grown in soil at 22⁰C under a 12 h photoperiod in a growth chamber for approx 23 d

extract_protocol: RNA was extracted using the RNeasy plant mini kit (Qiagen)

treatment_protocol: Plants were treated for 3 weeks at 4⁰C under a 12 h photoperiod and harvested at ZT4

tag: tissue

value: entire aerial part

tag: cultivar/ecotype

tag: genotype/variation

value: wild type


title: camta1/2/3 24h cold biological rep3

description: Gene expression data from Arabidopsis thaliana camta1/2/3 mutant at 4°C for 24 hrs

data_processing: The data were analyzed with LIMMA package of Bioconductor using GCRMA normalization procedure.

source_name: Arabidopsis thaliana camta1/2/3 mutant grown at 22°C and treated at 4°C for 24 hrs

growth_protocol: Plants were grown in soil at 22°C under a 12 hr photoperiod for 3 weeks

treatment_protocol: Plants were treated at 4°C under a 12 hr photoperiod for 24 h

value: camta1/2/3 mutant


title: WT 3 week cold, biological rep2

description: Arabidopsis WT Col-0 grown at 22⁰C in soil under a 12 h photoperiod for approx 23 d followed by 3 weeks at 4⁰C under a 12 h photoperiod

source_name: Arabidopsis Col-0 grown at 22⁰C followed by 3 weeks at 4⁰C


title: camta1/2/3 24h cold biological rep1


title: WT warm, biological rep2 [2]


title: camta1/2/3 warm biological rep3

description: Gene expression data from Arabidopsis thaliana camta1/2/3 mutant at 22°C

source_name: Arabidopsis thaliana camta1/2/3 mutant grown at 22°C


title: rsa1 salt 12 h rep2

status: Public on Jul 07 2013

city: College Park

first: Jianhua

last: Zhu

address: 2102 Plant Sciences Building

department: Plant Science and Landscape Architecture

institute: University of Maryland

description: Gene expression data from Arabidopsis rsa1-1 plants with salt stress for 24 h

hyb_protocol: Following fragmentation, 10 µg of cRNA was hybridized for 16 h at 45°C on Affymetrix ATH1 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The datasets were subjected to the Robust Multiarray Averaging (RMA) normalization method. The normalized data were further analyzed and p-values were generated by the affymGUI component of Bioconductor in statistics environment R with the default parameters.Genes were selected by the RankProd (non-paramteric method based on the estimated percentage of false discoveries (p value < 0.05)) method.

source_name: Arabidopsis rsa1-1, salt, 24 h.

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

growth_protocol: Arabidopsis seedlings on Murashige and Skoog (MS) medium agar plates (1x MS salts, 2% sucrose, 1.2% agar, pH 5.7) were  grown under cool, white light (~120 μmol m-2 s-1) at 21℃ with a 16-h-light/8-h-dark photoperiod.

extract_protocol: Total RNA was extracted with Trizol reagent (Invitrogen) following the manufacturer's instructions.

treatment_protocol: Six-day-old wild type and rsa1-1 mutant plants were subjuected to salt stress with 120 mM NaCl for 0 and 24 h.

value: seedlings

tag: treatment

value: Salt with 120 mM NaCl for 24 h

tag: genotype

tag: genetic background

value: Columbia gl1 expressing RD29A::LUC transgene

tag: age

value: Seven-day-old


title: camta1/2/3 24h cold biological rep2


title: camta1/2/3 warm biological rep2


title: camta1/2/3 warm biological rep1


title: WT salt 12 h rep2

description: Gene expression data from Arabidopsis wild type plants with salt stress for 24 h

source_name: Arabidopsis wild type, salt, 24 h.


title: camta2/3 warm biological rep2

description: Gene expression data from Arabidopsis thaliana camta2/3 mutant at 22°C

source_name: Arabidopsis thaliana camta2/3 mutant grown at 22°C

value: camta2/3 mutant


title: camta2/3 warm biological rep1


title: rsa1 salt 12 h rep3


title: WT 24h cold, biological rep2

description: Gene expression data from Arabidopsis thaliana Col-0 WT at 4°C for 24 hrs

source_name: Arabidopsis thaliana Col-0 WT grown at 22°C and treated at 4°C for 24 hrs


title: WT 24h cold, biological rep1


title: camta1/2 warm biological rep3

description: Gene expression data from Arabidopsis thaliana camta1/2 mutant at 22°C

source_name: Arabidopsis thaliana camta1/2 mutant grown at 22°C

value: camta1/2 mutant


title: WT warm, biological rep3

description: Gene expression data from Arabidopsis thaliana Col-0 WT at 22°C

source_name: Arabidopsis thaliana Col-0 WT grown at 22°C


title: camta2/3 warm biological rep3


title: WT warm, biological rep1


title: camta1/2 warm biological rep2


title: camta1/3 warm biological rep3

description: Gene expression data from Arabidopsis thaliana camta1/3 mutant at 22°C

source_name: Arabidopsis thaliana camta1/3 mutant grown at 22°C

value: camta1/3 mutant


title: camta1/2 warm biological rep1


title: WT 24h cold, biological rep3


title: camta1/3 warm biological rep1


title: WT warm, biological rep2


title: camta1/3 warm biological rep2


title: 3d old, no treatment, rep2

city: Toronto

first: Malcolm

middle: M.

last: Campbell

state: ON

address: 25 Willcocks Street

department: Cell & Systems Biology

country: Canada

institute: University of Toronto

hyb_protocol: Affymetrix protocol: Eukaryotic target preparation: Eukaryotic target hybridization.

scan_protocol: Affymetrix protocol: GeneChip Scanner 3000 7G Affymetrix 00-0073.

data_processing: Analysis performed using the BioConductor suite in R. All 12 arrays were pre-processed together using GCRMA. Expression data were filtered to remove probe sets which reported low transcript abundance and low variance across all arrays (minimum intensity of 100 on at least two arrays, minimum inter-quartile range of 0.5 on the log2-scale). The pre-processed data were analysed as a 2 X 2 factorial complete randomized ANOVA using the linear model for microarray (limma) package in R (R Development Core Team, 2009). The linear model was parameterized by group means with a manually defined sum-to-zero contrast matrix to test directly for the contrasts of interest: the main and interaction effects overall, as well as the effect of the co-treatment with sucrose and SMX. A Benjamini-Hochberg false discovery rate of 0.1 was applied to the output of all tests (Benjamini and Hochberg, 1995).

source_name: 3d old, no treatment

label_protocol: Affymetrix protocol: Eukaryotic target preparation: One-cycle target labeling assay.

growth_protocol: Wild-type Arabidopsis thaliana (Col) seeds were sown in sterile liquid MS growth media in 24-well plates and wrapped in light-blocking foil. Plates were cold-stratified at 4C for three days, then exposed to light for six hours to promote germination. Seedlings were grown for three days at 21C prior to RNA extraction.

extract_protocol: Total RNA extracted using RNeasy extraction kit (Qiagen).

tag: ecotype

value: Columbia

value: Whole seedling

value: Wild type


title: 3d old, both 10mM sucrose and 0.2µM SMX, rep1

source_name: 3d old, both 10mM sucrose and 0.2µM SMX


title: 3d old, 10mM sucrose only, rep3

source_name: 3d old, 10mM sucrose only


title: 3d old, 0.2µM SMX only, rep2

source_name: 3d old, 0.2µM SMX only


title: 3d old, no treatment, rep1


title: irradiated leaf (WT 1d), biological rep2

status: Public on Jun 01 2013

city: Jeongeup-si

first: Jin-Hong

last: Kim

state: Jeonbuk-do

address: 29 Geumgu-gil

country: South Korea

institute: Korea Atomic Energy Research Institute

hyb_protocol: Hybridization, washing, and staining of the biotin-labeled cRNA with GeneChip® Arabidopsis ATH1 Genome Array were performed as recommended by the Affymetrix GeneChip® Expression Analysis Technical Manual.

scan_protocol: GeneChip arrays were scanned using Affymetrix GeneChip® Scanner 3000 7G.

data_processing: The scanned data were extracted through Affymetrix Command Console 1.1 software to generate raw CEL files. Expression data were generated from the CEL files using MAS5.0 algorithm in Affymetrix Expression Console 1.2 software.

source_name: Arabidopsis (WT) leaves 1 d after gamma irradiation

label_protocol: Conversion of RNA into ds cDNA and generation of biotin-labeled cRNA from the ds cDNA were performed as recommended by the Affymetrix GeneChip® Expression Analysis Technical Manual.

growth_protocol: Plants were grown in a growth chamber with a 16-h photoperiod at 22/18oC (day/night).

extract_protocol: Total RNA was extracted from the leaf powder using RNeasy Plant Mini Kit (Qiagen) according to the supplier’s recommendation  Kit (Qiagen, Chatsworth, CA, USA) according to the supplier’s recommendation.  For complete DNA removal, RNase-Free DNase Set  (Qiagen, Chatsworth, CA, USA) provided efficient on-column digestion  Total RNA was extracted from leaves using RNeasy Plant Mini Kit

treatment_protocol: Rosette leaves were frozen immediately after detachment and ground in liquid nitrogen to fine powder.

value: rosette leaf only

tag: developmental stage

value: 29d after seeds were sown


title: 3d old, 10mM sucrose only, rep1


title: 3d old, 0.2µM SMX only, rep1


title: irradiated leaf (WT 5d), biological rep1

source_name: Arabidopsis (WT) leaves 5 d after gamma irradiation

value: 33d after seeds were sown


title: 3d old, 0.2µM SMX only, rep3


title: irradiated leaf (WT 5d), biological rep2


title: control leaf (WT 1d), biological rep1

source_name: Arabidopsis (WT) leaves - control (1 d)


title: control leaf (cmt 5d), biological rep1

source_name: Arabidopsis (cmt) leaves - control (5 d)


title: 3d old, both 10mM sucrose and 0.2µM SMX, rep2


title: control leaf (WT 5d), biological rep1

source_name: Arabidopsis (WT) leaves - control (5 d)


title: control leaf (WT 5d), biological rep2


title: control leaf (cmt 1d), biological rep1

source_name: Arabidopsis (cmt) leaves - control (1 d)


title: 3d old, no treatment, rep3


title: 3d old, both 10mM sucrose and 0.2µM SMX, rep3


title: control leaf (cmt 1d), biological rep2


title: control leaf (WT 1d), biological rep2


title: irradiated leaf (cmt 1d), biological rep2

source_name: Arabidopsis (cmt) leaves 1 d after gamma irradiation


title: control leaf (cmt 5d), biological rep2


title: irradiated leaf (WT 1d), biological rep1


title: irradiated leaf (cmt 5d), biological rep2

source_name: Arabidopsis (cmt) leaves 5 d after gamma irradiation


title: irradiated leaf (cmt 1d), biological rep1


title: leaves WT Na2S rep3

status: Public on Apr 25 2013

city: Sevilla

first: Cecilia

last: Gotor

address: Avda. Américo Vespucio, 49

country: Spain

institute: Instituto de Bioquímica Vegetal y Fotosíntesis

description: Gene expression data from leaves (WT) grown in presence of Na2S

hyb_protocol: Following fragmentation, 10 µg of biotinylated cRNA were hybridized to Affymetrix chips (ATH1). Each sample was added to a hybridization solution containing 100mM 2-(N-morpholino)ethanesulfonic acid, 1 M Na+, and 20mM of EDTA in the presence of 0.01% of Tween-20 to a final cRNA concentration of 0.05 µg/ml. Hybridization was performed for 16 h at 45ºC . Each microarray was washed and stained with streptavidin-phycoerythrin in a Fluidics station 450 (Affymetrix).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: GeneChip intensities were background-corrected, normalized and sumarized by RMA method, using the “Affy” package from Bioconductor.

source_name: Leaves of 30 days-old plants (WT) in presence of Na2S

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 500 ng total RNA (GeneChip 3' IVT Express Kit).

growth_protocol: Arabidopsis thaliana (accession Col-0) and the des1-1 mutant (SALK_103855 ) were grown in soil under a photoperiod of 16 h of white light (120 μE m-2 s-1) at 20ºC and 8 h dark at 18ºC.

extract_protocol: RNA was prepared using TRIzol (Invitrogen) and the RNeasy Mini Kit (Qiagen). RNA was quantified and the RNA quality was assessed with a 2100 Bioanalyzer from Agilent Technologies

treatment_protocol: After growing for 20 days, plants were separated into two batches; one irrigated with water and the other with 200 mM Na2S for 10 additional days.

value: WT

value: leaf


title: leaves WT Na2S rep2


title: irradiated leaf (cmt 5d), biological rep1


title: leaves WT water rep2

description: Gene expression data from leaves (WT)

source_name: Leaves of 30 days-old plants (WT)

value: water


title: leaves WT water rep3

description: Gene expression data from leaves (WT)


title: leaves des1 water rep3

description: Gene expression data from leaves (des1)

source_name: Leaves of 30 days-old plants (des1)


title: leaves des1 Na2S rep3

description: Gene expression data from leaves (des1) grown in presence of Na2S

source_name: Leaves of 30 days-old plants (des1) in presence of Na2S


title: leaves WT water rep1

description: Gene expression data from leaves (WT)


title: leaves des1 Na2S rep2


title: leaves des1 water rep1

description: Gene expression data from leaves (des1)


title: leaves des1 water rep2

description: Gene expression data from leaves (des1)


title: leaves des1 Na2S rep1


title: Atwrky40_high light_rep3

status: Public on Apr 17 2013

city: Bundoora

first: Reena

last: Narsai

address: 5 Ring road

country: Australia

institute: La trobe University

description: Gene expression data from leaves of Atwrky40 KO Arabidopsis plants, treated with high light for 1h at 1000 μE m-2s-1

hyb_protocol: Following fragmentation, cRNA was hybridized, washed and stained as per manufacterers' instructions.

scan_protocol: GeneChips were scanned using the approved Affymetrix scanner.

data_processing: The data were analyzed with Affymetrix Gene Expression colsole using the Microarray Suite version 5.0 (MAS 5.0) under Affymetrix default analysis settings.

source_name: Arabidopsis leaves from 21-day old Atwrky40 KO plants, treated with high light for 1h at 1000 μE m-2s-1

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

growth_protocol: Arabidopsis seeds were sown on soil, cold stratified for 2 days before growing for 21-days under a 16-h light/8-h dark photoperiod.

extract_protocol: Total RNA extracted using the Qiagen Rneasy kit as per manufacturer's instructions.

treatment_protocol: For the HL treatment, 21-day old plants were treated with high light for 1h at 1000 μE m–2s–1 and snap frozen.

value: Atwrky40 KO

value: 21-day old plants

value: high light for 1h at 1000 μE m-2s-1


title: Atwrky63_high light_rep1

description: Gene expression data from leaves of Atwrky63 KO Arabidopsis plants, treated with high light for 1h at 1000 μE m-2s-1

source_name: Arabidopsis leaves from 21-day old Atwrky63 KO plants, treated with high light for 1h at 1000 μE m-2s-1

value: Atwrky63 KO


title: OE_WRKY63.3_high light_rep1

description: Gene expression data from leaves of Atwrky63.3 OE Arabidopsis plants, treated with high light for 1h at 1000 μE m-2s-1

source_name: Arabidopsis leaves from 21-day old Atwrky63.3 OE plants, treated with high light for 1h at 1000 μE m-2s-1

value: Atwrky63.3 OE


title: OE_WRKY63.3_high light_rep2


title: OE_WRKY63.3_rep1

description: Gene expression data from leaves of Atwrky63.3 OE Arabidopsis plants

source_name: Arabidopsis leaves from 21-day old Atwrky63.3 OE plants


title: OE_WRKY63.3._high light_rep3


title: Atwrky40_high light_rep2


title: OE_WRKY40.4_high light_rep2

description: Gene expression data from leaves of Atwrky40.4 OE Arabidopsis plants, treated with high light for 1h at 1000 μE m-2s-1

source_name: Arabidopsis leaves from 21-day old Atwrky40.4 OE plants, treated with high light for 1h at 1000 μE m-2s-1

value: Atwrky40.4 OE


title: Col0_high light_rep1

description: Gene expression data from leaves of Col0 Arabidopsis plants, treated with high light for 1h at 1000 μE m-2s-1

source_name: Arabidopsis leaves from 21-day old Col0 plants, treated with high light for 1h at 1000 μE m-2s-1


title: Atwrky63_rep3

description: Gene expression data from leaves of Atwrky63 KO Arabidopsis plants

source_name: Arabidopsis leaves from 21-day old Atwrky63 KO plants


title: OE_WRKY40.4_rep3

description: Gene expression data from leaves of Atwrky40.4 OE Arabidopsis plants

source_name: Arabidopsis leaves from 21-day old Atwrky40.4 OE plants


title: OE_WRKY40.4_high light_rep3


title: Atwrky63_high light_rep2


title: Col0_high light_rep2


title: OE_WRKY63.3_rep3


title: Atwrky40_high light_rep1


title: Col0_high light_rep3


title: Atwrky63_high light_rep3


title: OE_WRKY63.3_rep2


title: OE_WRKY40.4_high light_rep1


title: Atwrky63_rep1


title: Atwrky63_rep2


title: OE_WRKY40.4_rep1


title: Atwrky40_rep3

description: Gene expression data from leaves of Atwrky40 KO Arabidopsis plants

source_name: Arabidopsis leaves from 21-day old Atwrky40 KO plants


title: OE_WRKY40.4_rep2


title: Atwrky40_rep2


title: Col0_rep3

description: Gene expression data from leaves of Col0 Arabidopsis plants

source_name: Arabidopsis leaves from 21-day old Col0 plants


title: tor mutant with glucose treatment, biological rep1

status: Public on Apr 05 2013

city: Boston

first: Jen

last: Sheen

state: MA

address: 185 Cambridge st. CPZN7620

department: Molecular Biology

institute: Massachusetts General Hospital

description: Gene expression data from Arabidopsis tor seedlings with 2 hours glucose treatment, replicate 1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on the Arabidopsis ATH1 GeneChips using the Affymetrix 640 Hybridization Oven. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 7G with AutoLoader.

data_processing: The data were analyzed in FlexArray using RMA (background correction and normalization) and also dChip (subtract MM from PM). dChip(PM-MM) log(2) with p-value, RMA log(2) signal intensity with p-value data can be found on Series (GSE40245_torC-torG.txt.gz and GSE40245_wtC-wtG.txt.gz).

source_name: Arabidopsis seedlings

label_protocol: Total RNA (5µg) were amplified and biotinylated using the BioArrayTM HighYieldTM RNA transcript labelling kit (Enzo) according to the manufacturer’s instructions.  The RNA was then fragmented in fragmentation buffer (40 mM Tris-Acetate, pH 8.1, 100 mM KOAc, 30 mM MgOAc), 94 degree for 35 minutes.

growth_protocol: Arabidopsis wild type (Col-0) and estradiol inducible RNAi-tor plants were grown in 6-well plates containing 1 ml of liquid medium (0.5 x MS, pH 5.7) in a controlled room for 3 days at 22oC, 60% relative humidity, 75 uE light and 12 hr photoperiod.

extract_protocol: Total RNA was extracted using RNeasy plant mini kit (Qiagen) according to the manufacturer’s protocol

treatment_protocol: Seedlings were treated with or without 15 mM glucose for 2 hours

value: seedlings

value: glucose

value: tor mutant

value: 3 days


title: tor mutant without treatment, biological rep2

description: Gene expression data from Arabidopsis tor seedlings without treatment, replicate 2


title: tor mutant with glucose treatment, biological rep3

description: Gene expression data from Arabidopsis tor seedlings with 2 hours glucose treatment, replicate 3


title: tor mutant with glucose treatment, biological rep2

description: Gene expression data from Arabidopsis tor seedlings with 2 hours glucose treatment, replicate 2


title: wild type (Col) without treatment, biological rep1

description: Gene expression data from Arabidopsis WT seedlings without treatment, replicate 1

value: wild type


title: wild type (Col) without treatment, biological rep2

description: Gene expression data from Arabidopsis WT seedlings without treatment, replicate 2


title: Atwrky40_rep1


title: tor mutant without treatment, biological rep1

description: Gene expression data from Arabidopsis tor seedlings without treatment, replicate 1


title: Col0_rep1


title: A2QK HS-2

status: Public on Apr 09 2013

city: Shulin City, Taipei County

first: Hsiang-chin

last: Liu

address: 9F., No.332, Xuefu Rd.

country: Taiwan

institute: Academia sinica

description:
10h2
Gene expression at heat shock condition (37°C for 1 hr).

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Arabidopsis Genome Arrays. GeneChips were washed and stained in the Affymetrix® GeneChip® Fluidics Station 450.

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

data_processing: The data were RMA normalized using GeneSpring 11.5.1.

source_name: whole seedling of 7-day-old plants at 37°C for 1 hr, overexpression of HSFA2 in QK

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

growth_protocol: The seeds were sowed in 0.5X MS medium, then treated in 4°C for 3 days to synchronize the germination and grown in 22°C for 7 days with 16 h of light (120 mmol m-2 s-1).

extract_protocol: Total RNA of plant tissues was isolated according to the method of Oñate-Sánchez and Vicente-Carbajosa (2008, BMC Research Notes, 1, 93 (PMID 18937828)).

treatment_protocol: The samples were incubated for 1 h at 37°C in a water bath.

tag: strain/background

value: mixed (Col-0 and Ws)

value: overexpression of HSFA2 in QK (hsfa1 quadruple mutant)

value: whole seedling

value: 7 days

tag: condition

value: heat shock (37°C)


title: A2QK HS-1

description:
10h1
Gene expression at heat shock condition (37°C for 1 hr).


title: wild type (Col) glucose treatment, biological rep3

description: Gene expression data from Arabidopsis WT seedlings with 2 hours glucose treatment, replicate 3


title: QK control-1

description:
qc1
Gene expression at control condition (22°C).

source_name: whole seedling of 7-day-old plants at control condition, hsfa1 quadruple mutant (QK)

value: hsfa1 quadruple mutant (QK)

value: control (22°C)


title: QK control-2

description:
qc2
Gene expression at control condition (22°C).


title: Wild type (Col-0) control-1

description:
cc1
Gene expression at control condition (22°C).

source_name: whole seedling of 7-day-old plants at control condition, wild type


title: Wild type (Col-0) HS-1

description:
ch1
Gene expression at heat shock condition (37°C for 1 hr).

source_name: whole seedling of 7-day-old plants at 37°C for 1 hr, wild type


title: wild type (Col) glucose treatment, biological rep1

description: Gene expression data from Arabidopsis WT seedlings with 2 hours glucose treatment, replicate 1


title: QK HS-2

description:
qh2
Gene expression at heat shock condition (37°C for 1 hr).

source_name: whole seedling of 7-day-old plants at 37°C for 1 hr, hsfa1 quadruple mutant (QK)


title: A2QK control-2

description:
10c2
Gene expression at control condition (22°C).

source_name: whole seedling of 7-day-old plants at control condition, overexpression of HSFA2 in QK


title: tor mutant without treatment, biological rep3

description: Gene expression data from Arabidopsis tor seedlings without treatment, replicate 3


title: Wild type (Col-0) HS-2

description:
ch2
Gene expression at heat shock condition (37°C for 1 hr).


title: A2QK control-1

description:
10c1
Gene expression at control condition (22°C).


title: wild type (Col) glucose treatment, biological rep2

description: Gene expression data from Arabidopsis WT seedlings with 2 hours glucose treatment, replicate 2


title: QK HS-1

description:
qh1
Gene expression at heat shock condition (37°C for 1 hr).


title: Wild type (Col-0) control-2

description:
cc2
Gene expression at control condition (22°C).


title: low R/FR_mock spray, biological rep 3

status: Public on Apr 03 2013

city: Utrecht

first: Ronald

last: Pierik

address: Padualaan 8

department: Plant Ecophysiology

country: Netherlands

institute: Utrecht University

hyb_protocol: The (#900720) GeneChip Hybridization, Wash and Stain Kit was used for hybridization, washing, staining and scanning of the chips.

scan_protocol: The software program Affymetrix 'GeneChip Command Console (v3.1)' was used to operate the staning, washing and scanning of the GeneChips and visual inspection of the array images. Chips were scanned using the Affymetrix 3000G scanner

data_processing: Data were processed using the Bioconductor packages in R and using the RMA normalization algorithm.

source_name: Arabidopsis petioles, 2h low R/FR treatment

label_protocol: The Affymetrix 3'IVT-Express Labeling Kit was used to synthesize Biotin-labeled cRNA. From each RNA sample 100 ng was used as input for the labelling reactions.

growth_protocol: Arabidopsis thaliana plants were sown, stratified (4˚C) for 3 days and then transferred to a growth chamber (9 h. light (180 µmol / m2 / s, 20°C, 70% RH, R/FR = 2.2), 15 h dark) where they were transferred to individual pots after 10 d and gwon until 4 weeks old.

extract_protocol: Total RNA was isolated from homogenized material using the RNeasy plant mini kit (Qiagen) with on-column DNA digestion following the company’s instructions

treatment_protocol: Plants were put in each of the four conditions (control light with mock spray, control light with 0.5 mM SA spray, low R:FR (0.2) with mock spray, low R:FR (0.2) with 0.5 mM SA spray) for 2h. One petiole (approx. 5 mm length) per plant was harvested in liquid N2. 3 petioles/biological replicate were pooled.

tag: organ

value: petiole

value: 4 weeks old

value: low R/FR, mock spray


title: wild type (Col) without treatment, biological rep3

description: Gene expression data from Arabidopsis WT seedlings without treatment, replicate 3


title: leaves WT Na2S rep1

description: Gene expression data from leaves (WT) grown in presence of Na2S

source_name: Leaves of 30 days-old plants (WT) in presence of Na2S

value: WT

value: leaf


title: Col0_rep2

description: Gene expression data from leaves of Col0 Arabidopsis plants

value: 21-day old plants


title: CHLD dex biol rep1

status: Public on Apr 01 2013

city: Berlin

first: Hagen

last: Schlicke

address: Philippstr. 13, building 12

department: Institute of Biology

country: Germany

institute: Humboldt University Berlin

description:
Gene expression data from Arabidosis seedlings
A504_04_CHLD

hyb_protocol: Following fragmentation, 12.5 µg of cRNA were hybridized for 16 hr at 45C on GeneChip ATH1 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400. Hybridisation was performed at KFB Regensburg, Germany.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000. Scaning was performed at KFB Regensburg, Germany.

data_processing: The data were analyzed with Affymetrix GeneChip Command Console and Expression Console Software. Primary data presented here were analysed at KFB Regensburg, Germany.

source_name: green tissue of 3 weeks old Arabidopsis seedlings

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip 3'IVT Kit, Affymetrix 2008). Labeling was performed at KFB Regensburg, Germany.

growth_protocol: Seedlings were grown on soil in a 10h light 14h dark rhytmn at 23°C after 3 days of stratification.

extract_protocol: Extraction of total RNA was performed using InviTrap® Spin Plant RNA Mini Kit (Invitek, Germany) according to the manufacturer's instructions.

treatment_protocol: One set of seedlings was treated with 20µg/ml dexamethasone (dex).The other set of seedlings was treated with 20µM ß-estradiol.

value: seedling

value: 3 weeks old

value: green tissue

tag: agent

value: dexamethasone (dex)

value: CHLD reduction


title: CHLD dex biol rep2

description:
Gene expression data from Arabidosis seedlings
A504_05_CHLD


title: CHLM estr biol rep1

description:
Gene expression data from Arabidosis seedlings
A504_10_CHLM

value: ß-estradiol

value: CHLM overexpression


title: CHLM estr biol rep3

description:
Gene expression data from Arabidosis seedlings
A504_12_CHLM


title: Col-0 dex biol rep3

description:
Gene expression data from Arabidosis seedlings
A504_03_Col

value: control


title: CHLM estr biol rep2

description:
Gene expression data from Arabidosis seedlings
A504_11_CHLM


title: Col-0 dex biol rep1

description:
Gene expression data from Arabidosis seedlings
A504_01_Col


title: Col-0 estr biol rep3

description:
Gene expression data from Arabidosis seedlings
A504_09_Col


title: CHLD dex biol rep3

description:
Gene expression data from Arabidosis seedlings
A504_06_CHLD


title: Col-0 dex biol rep2

description:
Gene expression data from Arabidosis seedlings
A504_02_Col


title: Col-0 estr biol rep2

description:
Gene expression data from Arabidosis seedlings
A504_08_Col


title: Total RNA from atcsp1-1, cold rep 2

status: Public on Mar 31 2013

city: Riverside

first: Piyada

last: Juntawong

state: CA

address: 900 University ave

department: Botany and Plant Sciences

institute: University of California Riverside

description: SAMPLE 36

hyb_protocol: Hybridizations were performed at 45 °C for 16 h, in a rotating platform with 10 µg of biotin-labeled aRNA for total and polysome RNAs and 7-10 µg of biotin-labeled aRNA for IP RNA.

scan_protocol: GeneChips were scanned by use of the Affymetrix GeneChip Workstation Scanner 3000.

data_processing: R/Bioconductor (v. 2.12.0), RMA normalization

source_name: Total RNA_atcsp1-1_cold

label_protocol: Amplified RNA (aRNA) synthesis and biotin-labeling was conducted with 150 total or polysomal RNA, or 3-6 ng immunoprecipitated (IP) RNA using GeneChip® 3’ IVT expression  (Affymetrix)

growth_protocol: Plants were grown in soil (Sunshine Mix LC1, JM McConkey, Sumner, WA) containing 150 g Osmocote 14-14-14 fertilizer (Scotts catalog #90036) and 75 g Marathon pesticide (Crop production services, Riverside, CA) per 3.8 ft3 of soil in a controlled environmental growth room (16 h at ~100 uE sec-1m-2 light: 8 h dark at 23C).

extract_protocol:
Extraction of polysome by differential centrifugation through sucrose gradients was based on the procedures of Zanetti et al. (2005) and Mustroph et al. (2009); Total RNA and polysomal RNA (≥ 2 ribosomes per mRNA; typically gradient fractions 7 to 13) were extracted by use of TRIzol solution (Invitrogen) according to the manufacturer’s protocol. Total RNAs were subjected to DNAse treatment by use of RNase-Free DNAse Set (Qiagen, Chatsworth, CA) according to the manufacturer’s protocol. Total and polysomal RNA were cleaned by use of the RNAeasy Plant mini kit (Qiagen).

For CSP immunopurification for RNA analyses, rosette leaves of 25-d-old plants were collected and cross-linked with formaldehyde solution (Niranjanakumari et al., 2002). Briefly, leaves were washed with ice-cold ddH2O and cross-linked by bathing in 1% (v/v) formaldehyde (Molecular biology grade, Fisher, Fremont, CA) for 15 min by vacuum infiltration. Cross-linking was stopped by addition of 2 M glycine [pH 7.0] to a final concentration of 125 mM and vacuum-infiltrated for 5 min. Leaves were washed twice with ice-cold ddH2O, ground in liquid nitrogen and stored at -80 °C. One mL pulverized frozen plant tissue was thawed in 2 mL extraction buffer, mixed and centrifuged at 16,000 g at 4°C for 15 min to obtain a supernatant and passed through Miracloth. The clarified extracts were added to the antibody-coated Protein A beads (described above) and incubated at 4°C for 2 h with gentle shaking. The supernatant (Unbound fraction) was removed and the beads were washed 4 times by resuspension in 6 mL wash buffer (200 mM Tris-HCl [pH 9.0], 200 mM KCl, 36 mM MgCl2, 25 mM EGTA, 5 mM DTT, 1 mM PMSF, 50 μg/mL cycloheximide, 50 μg/mL chloramphenicol, 1.125 % (v/v) Triton X-100, 0.125 % (v/v) Brij-35, 0.125 % (v/v) Tween-40, 0.125 % (v/v) NP-40) and centrifuged to discard the wash solution. To elute the bound CSP1 and any associated molecules, 150 μL elution buffer (100 mM Tris-HCL [pH 8.0], 25 mM EDTA, 1 % (w/v) SDS) was added to the beads, which were incubated 10 min at room temperature with shaking, and centrifuged to obtain the eluate fraction. Elution were repeated by addition of 150 μL elution buffer following by incubation at 65°C for 10 min. The eluate was combined and 2 μL proteinase K (20 μg/mL) was added, and incubated at 65°C for 1 h to reverse the cross-linking. Immunopurified RNAs were extracted with TRIzol (Invitrogen) according to the manufacturer’s protocol and further purified by use of the RNAeasy plant mini kit column (Qiagen).

anti-CSP1 antibody: the rabbit polyclonal antiserum was generated against  a peptide (C15 AGNGDQRGATKGGN163) specific to *Arabidopsis thaliana *CSP1(At4g36020). The antiserum was subsequently affinity purified using the CSP1 peptide (anti-CSP1, Gencript, Piscataway, NJ)

treatment_protocol: 25-d-old plants grown in 5.08cm square pots were placed in a 4C chamber (16 h, ~ 50 uE sec-1 m-2 light: 8 h dark) for 12 h or in a 23C growth chamber (16 h, ~ 100 uE sec-1 m-2 light: 8 h dark). Cold treatment began 2 h following the initiation of light period (ZT2). Cold-treated or control rosette leaves were collected at specific time points, flash frozen in liquid nitrogen unless otherwise indicated and stored at -80C.

value: 25 days

value: 12h cold (4C)

value: rosettes

tag: molecule subtype

value: Total RNA


title: Total RNA from atcsp1-1, non-stress rep 2

description: SAMPLE 35

source_name: Total RNA_atcsp1-1_non-stress

value: 12h non-stress


title: Total RNA from atcsp1-1, cold rep 1

description: SAMPLE 32


title: tga1_tga4_root_2h_KNO3_rep2

city: Santiago

first: Jose

middle: Miguel

last: Alvarez

state: Santiago

address: Alameda 340

department: Genética Molecular y Microbiología

country: Chile

institute: Pontificia Universidad Católica

description:
TGA1 and TGA4 double mutant seedlings (tga1/tga4), treated with 5 mM KNO3 for 2 hours. Roots were cut and total RNA was extracted using TriZol.
tga1_tga4 KNO3 2H R2

hyb_protocol: ATH1 chips were hybridized using the GeneChip Hybridization, Wash and Stain kit from Affymetrix

scan_protocol: Chips were scanned using the Affymetrix GeneChip Scanner 3000 7G and the Affymetrix GeneChip Command Console Scan Control 1.1.0.845 software

data_processing: The summarized probe set data was generated using R/bioconductor (affy library). Normalization of the data was performed using rma. Normalized data was subjected to a two-way ANOVA analysis with a false discovery rate of 5 %.

source_name: tga1_tga4 roots, treated with 5 mM KNO3 for 2 hours

label_protocol: Bioitinylated cRNA was prepared using the GeneChip 3'IVT kit from Affymetrix

growth_protocol: Arabidopsis seedlings of the Col 0 and tga1/tga4 genotypes were grown on hydroponic medium containing 1X MS salts without Nitrogen, supplemented with 0.5 mM ammonium succinate as Nitrogen source and 3 mM sucrose on a Percival chamber under a photoperiod of 16 hours of light (100 μE/m2/sec) and 8 hours of dark at 22°C for 14 days.

extract_protocol: Total RNA was extracted using the TriZol reagent as indicated by the manufacturer.

treatment_protocol: Plants were treated at the onset of the light period on day 15 with 5 mM KNO3 or 5 mM KCl as control for 2 hours. Roots were cut and frozen on liquid nitrogen.

value: TGA1 and TGA4 double mutant

value: root

value: 15 days old

value: 5 mM KNO3

tag: time

value: 2 hours


title: Polysomal RNA from 35S:AtCSP1-FH#11, cold rep 1

description: SAMPLE 22

source_name: Polysomal RNA_35S:AtCSP1-FH#11_cold

value: Polysomal RNA


title: Polysomal RNA from atcsp1-1, cold rep 1

description: SAMPLE 34

source_name: Polysomal RNA_atcsp1-1_cold


title: Total RNA from atcsp1-1, non-stress rep 1

description: SAMPLE 31


title: Polysomal RNA from atcsp1-1, cold rep 2

description: SAMPLE 38


title: Polysomal RNA from 35S:AtCSP1-FH#11, non-stress rep 2

description: SAMPLE 27


title: Total RNA from 35S:AtCSP1-FH#11, non-stress rep 2

description: SAMPLE 25

source_name: Total RNA_35S:AtCSP1-FH#11_non-stress


title: Polysomal RNA from atcsp1-1, non-stress rep 2

description: SAMPLE 37

source_name: Polysomal RNA_atcsp1-1_non-stress


title: tga1_tga4_root_2h_KCl_rep2

description:
TGA1 and TGA4 double mutant seedlings (tga1/tga4), treated with 5 mM KCl for 2 hours. Roots were cut and total RNA was extracted using TriZol.
tga1_tga4 KCl 2H R2

source_name: tga1_tga4 roots, treated with 5 mM KCl for 2 hours

value: seedling

value: 5 mM KCl


title: Polysomal RNA from 35S:AtCSP1-FH#11, non-stress rep 1

description: SAMPLE 21


title: Polysomal RNA from 35S:AtCSP1-FH#11, cold rep 2

description: SAMPLE 28


title: Col 0_root_2h_KNO3_rep2

description:
Col 0 wild-type seedlings, treated with 5 mM KNO3 for 2 hours. Roots were cut and total RNA was extracted using TriZol.
Col 0 KNO3 2H R2

source_name: Col 0 roots, treated with 5 mM KNO3 for 2 hours

value: wild-type


title: Col-0 estr biol rep1

description:
Gene expression data from Arabidosis seedlings
A504_07_Col

value: 3 weeks old

value: green tissue

value: ß-estradiol


title: Total RNA from 35S:AtCSP1-FH#11, cold rep 1

description: SAMPLE 20

source_name: Total RNA_35S:AtCSP1-FH#11_cold

value: 25 days


title: Polysomal RNA from 35S:HF-RPL18, non-stress rep 3

description: SAMPLE 15

source_name: Polysomal RNA_35S:HF-RPL18_non-stress


title: Total RNA from 35S:HF-RPL18, cold rep 2

description: SAMPLE 8

source_name: Total RNA_35S:HF-RPL18_cold

value: 12h cold (4C)


title: Total RNA from 35S:HF-RPL18, non-stress rep 2

description: SAMPLE 7

source_name: Total RNA_35S:HF-RPL18_non-stress

value: rosettes


title: Polysomal RNA from 35S:HF-RPL18, cold rep 3

description: SAMPLE 16

source_name: Polysomal RNA_35S:HF-RPL18_cold


title: Polysomal RNA from 35S:HF-RPL18, cold rep 2

description: SAMPLE 10


title: Polysomal RNA from 35S:HF-RPL18, non-stress rep 2

description: SAMPLE 9


title: Total RNA from 35S:AtCSP1-FH#11, non-stress rep 1

description: SAMPLE 19

value: Total RNA


title: Total RNA from 35S:HF-RPL18, cold rep 1

description: SAMPLE 2


title: Polysomal RNA from 35S:HF-RPL18, non-stress rep 1

description: SAMPLE 3

value: 12h non-stress


title: Total RNA from 35S:HF-RPL18, cold rep 3

description: SAMPLE 14


title: Total RNA from 35S:HF-RPL18, non-stress rep 1

description: SAMPLE 1


title: Total RNA from 35S:AtCSP1-FH#11, cold rep 2

description: SAMPLE 26


title: Total RNA from 35S:HF-RPL18, non-stress rep 3

description: SAMPLE 13


title: Polysomal RNA from 35S:HF-RPL18, cold rep 1

description: SAMPLE 4


title: Cycloheximide, Dexamethasone 3

status: Public on Mar 26 2013

city: SAS Nagar

first: Ram

middle: Kishor

last: Yadav

state: Punjab

address: Sector 81

department: Biology

country: India

institute: Indian Institute of Science Education and Research Mohali

description: Gene expression data from ~28 days old plant

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on ATH1 chip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. Affymetrix Hybridization oven 640

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000 with 7G upgrade

data_processing: The probe set-to-locus mappings for the ATH1 chip were obtained from TAIR (2009). The normalization of the raw data Cel files was performed with the  MAS5 algorithm using the default settings of the corresponding R  function of the affy package (Gautier et al., 2004). The quality of  the Affymetrix GeneChips was assessed with analysis routines provided  by the affyPLM and arrayQualityMetrics packages (Bolstad et al., 2005;  Kauffmann et al., 2009).

label: Biotin

source_name: ap1-1;cal1-1 shoot apical meristem

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

growth_protocol: Arabidopsis thaliana 35S::WUS-GR ap1-1;cal1-1 plants were grown in growth room for 28 days. The shoot apices from these plants were used for RNA isolation after respective treatments.

extract_protocol: RNA was isolated using RNeasy kit (Qiagen).

treatment_protocol: 35S::WUS-GR; ap1-1;cal1-1 SAMs were either treated with 10μM Dex or mock solution for four hour. SAMs were simultaneously treated with 10μM Dex and 10μM Cycloheximide (Cyc), protein synthesis inhibitor and Cyc alone for four hours.

value: Cycloheximide, Dexamethasone


title: Cycloheximide, Dexamethasone 2


title: Mock 1

value: Mock


title: Dexamethasone 1

value: Dexamethasone


title: Mock 3


title: Cycloheximide 2

value: Cycloheximide


title: Mock 2


title: Dexamethasone 2


title: Cycloheximide, Dexamethasone 1


title: Dexamethasone 3


title: Polysomal RNA from atcsp1-1, non-stress rep 1

description: SAMPLE 33


title: Cycloheximide 1


title: Cycloheximide 3


title: ActD+Tm(+) ire1a/ire1b rep1

status: Public on Mar 19 2013

city: Yokohama

first: Yukihisa

last: Shimada

state: Kanagawa

address: Maiokacho, Totsuka

department: Kihara Institute for Biological Science

country: Japan

institute: Yokohama City University

hyb_protocol: Affymetrix standard protocol

scan_protocol: GeneChip Scanner 3000

source_name: 10 day old seedlings

label_protocol: 3' INV Express Kit

growth_protocol: Seedlings were grown for 10 days at 22 degrees.

extract_protocol: Rneasy Plant Miini Kit (Quagen)

treatment_protocol: Seedlings were treated with or without tunicamycin (5 mg/l) for 5 h in the presence of actinomycin D (75 micro molar). ActD was added 2 hours before tunicamycin or mock treatment. For mock, DMSO (solvent for tunicamycin) was added instead of tunicamycin.

value: ire1a ire1b mutant

value: tunicamycin

value: Columbia (Col-0)


title: ActD+Mock(-) WT rep3

value: Wild type

value: mock


title: ActD+Tm(+) ire1a/ire1b rep3


title: ActD+Tm(+) WT rep3


title: ActD+Mock(-) WT rep2


title: ActD+Mock(-) ire1a/ire1b rep2


title: ActD+Mock(-) ire1a/ire1b rep3


title: ActD+Tm(+) ire1a/ire1b rep2


title: wt rep1

status: Public on Mar 08 2013

city: Warsaw

first: Maciej

last: Kotliński

state: Mazowieckie

address: Pawinskiego 5a

department: Laboratory of Microarray Analysis

country: Poland

institute: University of Warsaw / Institute of Biochemistry and Biophysics, PAS

hyb_protocol: 15 µg of labeled and fragmented aRNA were hybridized with Arabidopsis ATH1 genome arrays, according to the manufacturer’s recommendations (Affymetrix). Affymetrix Fluidics Stations 450 were used.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. The signals were recorded and processed using Affymetrix® GeneChip® Command Console® Software (AGCC).

data_processing: CEL files were gennerated with AGCC. CEL files were further analyzed with the Partek Genomics Suite (Partek). Upon importing the data, a GC-RMA background correction, quantile normalization, log2 transformation were conducted. Median Polish was used for probset summarization.

source_name: 18-d old shoots

label_protocol: 100 ng of isolated RNA were used for aRNA synthesis and labeling using a GeneChip 3` IVT - Express Kit (Affymetrix)

growth_protocol: Seedlings were cultivated in medium containing 1/2 Murashige and Skoog (MS) salts (Sigma-Aldrich), 0.5% (w/v) sucrose and 0.8% agar, pH 5.8.

extract_protocol: Total RNA from shoots of 18-d-old seedlings was extracted using the RNeasy plant mini kit (Qiagen) according to the manufacturer’s protocol, followed by Turbo DNase treatment (Ambion). The quantity and quality of the isolated RNA was determined using a NanoDrop ND1000 spectrophotometer (Nanodrop technologies) and RNA integrity was assessed with a Bioanalyzer 2100 (Agilent Technologies).

value: shoots

value: 18 days

value: wild type


title: ActD+Mock(-) ire1a/ire1b rep1


title: brm-1 rep3


title: ActD+Tm(+) WT rep2


title: ga1-3/brm-1 rep2


title: ga1-3 rep3


title: wt rep2


title: ga1-3/brm-1 rep3


title: ActD+Mock(-) WT rep1


title: ga1-3 rep1


title: ga1-3/brm-1 rep1


title: brm-1 rep2


title: ga1-3 rep2


title: brm-1 rep1


title: ActD+Tm(+) WT rep1


title: wt rep3


title: rcf1-1_cold_12 h_rep2

status: Public on Feb 25 2013

description: Gene expression data from Arabidopsis rcf1-1 plants with cold stress for 12 h

data_processing: The datasets were subjected to the Robust Multiarray Averaging (RMA) normalization method. The normalized data were further analyzed and p-values were generated by the affymGUI component of Bioconductor in statistics environment R with the default parameters.Genes were selected by the RankProd (non-paramteric method based on the estimated percentage of false discoveries (p value < 0.05)) method. Normalized expression values presented in Matrix table are log2 values.

source_name: Arabidopsis rcf1-1, cold at 4°C,12 h.

growth_protocol: Arabidopsis seedlings on Murashige and Skoog (MS) medium agar plates (1x MS salts, 2% sucrose, 0.6% agar, pH 5.7) were  grown under cool, white light (~120 μmol m-2 s-1) at 21 ± 1℃ with a 16-h-light/8-h-dark photoperiod.

treatment_protocol: Fourteen-day-old wild type and rcf1-1 mutant plants were subjuected to cold stress at 4°C for 0, 12, and 24 h.

value: seedlings

value: cold at 4°C

value: Fourteen-day-old


title: rcf1-1_cold_24 h_rep1

description: Gene expression data from Arabidopsis rcf1-1 plants with cold stress for 24 h

source_name: Arabidopsis rcf1-1, cold at 4°C, 24 h.


title: rcf1-1_cold_12h_rep1


title: rcf1-1_cold_24 h_rep2


title: WT_cold_12 h_rep2

description: Gene expression data from Arabidopsis wild type plants with cold stress for 12 h

source_name: Arabidopsis wild type, cold at 4°C,12 h.


title: rcf1-1_cold_0 h_rep1

description: Gene expression data from Arabidopsis rcf1-1 plants without cold stress

source_name: Arabidopsis rcf1-1, cold, control.

value: Control


title: WT_cold_24 h_rep2

description: Gene expression data from Arabidopsis wild type plants with cold stress for 24 h

source_name: Arabidopsis wild type, cold at 4°C, 24 h.


title: WT_cold_24 h_rep1


title: WT_cold_0 h_rep1

description: Gene expression data from Arabidopsis wild type plants without cold stress

source_name: Arabidopsis wild type, cold, control.


title: WT_cold_12 h_rep1


title: EV_3d_C

status: Public on Jan 31 2013

city: Campinas

first: Camila

last: Caldana

state: Sao Paulo

address: Rua Giuseppe Máximo Scolfaro, 10.000

country: Brazil

institute: Brazilian Bioethanol Science and Technology Laboratory

description:
2 week-old transgenic plants (Arabidopsis Col-0 background, inducible empty vector) non-induced plants for 3 days
Gene expression data from empty inducible vector

hyb_protocol: performed by Atlas Biolabs

scan_protocol: performed by Atlas Biolabs

data_processing: The data were analyzed with GCRMA (Wu et al., 2004).

source_name: 2 week-old transgenic plants; 3 days non-induced plants, EV

label_protocol: Labling procedure performed using MessageAmpTM II-Biotin Enhanced Kit

growth_protocol: Transgenic amiR-tor seeds were surfaced sterilized and germinated in MS plates with hygromycin at continuous light.

extract_protocol: RNA extraction performed using Rneasy Plant MiniKit (Qiagene)

treatment_protocol: Two weeks-old transgenic seedlings were transferred to MS plate with 20µM estradiol to induce the overexpression of amiR-tor (consequently, repression of AtTOR levels) under the control of an estradiol-(EST) inducible promoter. Identically treated wild-type Col-0 and pER8 empty-vector (EV) transformed seedlings were served as controls. All the genotypes were also transferred to MS plate without EST as an additional control. Seedlings were harvested after 0, 3 and 6 (amiR-tor lines) days.

value: 3 days non-treated

tag: cultivar

value: Arabidopsis Col-0 background, inducible artificial micro RNA

value: WT (Empty Vector)


title: EV_6d_C

description:
2 week-old transgenic plants (Arabidopsis Col-0 background, inducible empty vector) non-induced plants for 6 days
Gene expression data from empty inducible vector

source_name: 2 week-old transgenic plants; 6 days non-induced plants, EV

value: 6 days non-treated


title: WT_cold_0 h_rep2


title: amiR-tor20_3d_E

description:
2 week-old transgenic plants (Arabidopsis Col-0 background, inducible artificial micro RNA) estradiol-induced plants for 3 days
Gene expression data from empty inducible vector

source_name: 2 week-old transgenic plants; 3 days estradiol-induced plants, amiR-tor 20

value: 3 days estradiol-treated

value: amiR-tor 20


title: EV_6d_E

description:
2 week-old transgenic plants (Arabidopsis Col-0 background, inducible empty vector) estradiol-induced plants for 6 days
Gene expression data from empty inducible vector

source_name: 2 week-old transgenic plants; 6 days estradiol-induced plants,EV

value: 6 days estradiol-treated


title: amiR-tor20_6d_E

description:
2 week-old transgenic plants (Arabidopsis Col-0 background, inducible artificial micro RNA) estradiol-induced plants for 6 days
Gene expression data from empty inducible vector

source_name: 2 week-old transgenic plants; 6 days estradiol-induced plants, amiR-tor 20


title: amiR-tor17_6d_C

description:
2 week-old transgenic plants (Arabidopsis Col-0 background, inducible artificial micro RNA) non-induced plants for 6 days
Gene expression data from empty inducible vector

source_name: 2 week-old transgenic plants; 6 days non-induced plants, amiR-tor 17

value: amiR-tor 17


title: amiR-tor9_6d_C

source_name: 2 week-old transgenic plants; 6 days non-induced plants, amiR-tor 9

value: amiR-tor 9


title: amiR-tor20_3d_C

description:
2 week-old transgenic plants (Arabidopsis Col-0 background, inducible artificial micro RNA) non-induced plants for 3 days
Gene expression data from empty inducible vector

source_name: 2 week-old transgenic plants; 3 days non-induced plants, amiR-tor 20


title: amiR-tor17_6d_E

source_name: 2 week-old transgenic plants; 6 days estradiol-induced plants, amiR-tor 17


title: amiR-tor9_6d_E

source_name: 2 week-old transgenic plants; 6 days estradiol-induced plants, amiR-tor 9


title: rcf1-1_cold_0 h_rep2


title: amiR-tor17_3d_E

source_name: 2 week-old transgenic plants; 3 days estradiol-induced plants, amiR-tor 17


title: EV_3d_E

description:
2 week-old transgenic plants (Arabidopsis Col-0 background, inducible empty vector) estradiol-induced plants for 3 days
Gene expression data from empty inducible vector

source_name: 2 week-old transgenic plants; 3 days estradiol-induced plants,EV


title: amiR-tor17_3d_C

source_name: 2 week-old transgenic plants; 3 days non-induced plants, amiR-tor 17


title: amiR-tor9_3d_E

source_name: 2 week-old transgenic plants; 3 days estradiol-induced plants, amiR-tor 9


title: amiR-tor9_3d_C

source_name: 2 week-old transgenic plants; 3 days non-induced plants, amiR-tor 9


title: amiR-tor20_6d_C

source_name: 2 week-old transgenic plants; 6 days non-induced plants, amiR-tor 20


title: anac017-2_mutant_14-day-seedling-leaf_water_treated_3h_rep1

status: Public on Jan 30 2013

city: Perth

first: Estelle

last: Giraud

state: WA

address: UWA 35 Stirling Highway Crawley

department: ARC CoE Plant Energy Biology

institute: University of Western Australia

description: gene expression data from anac017-2 arabidopsis 14-day-old seedlings treated with water control for 3h

hyb_protocol: Following fragmentation, 10 ug of labelled aRNA were hybridized for 16 hr at 45C on GeneChip ATH1 Arabidopsis Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using a Affymetrix GeneChip Scanner 3000 (7G)

data_processing: The data were analyzed with GC - Robust Multi-array Average (GC-RMA) 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: leaf tissue water treated 3h

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 400 ng total RNA input (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Seedlings were grown on GamborgB5 medium supplemented with 3 % sucrose under 16 h light/ 8h dark regime at 22 °C (after 48 hr stratification at dark, at 4°C)

extract_protocol: Qiagen RNeasy plant mini kit (Qiagen) according to manufacturer's instruction. On column Qiagen DNase digestion according to manufacturer's instruction.

treatment_protocol: Seedlings were sprayed either with deionised water (mock), 20mM hydrogen peroxide or 50 µM antimycin A (Sigma) at 4 hours into the light cycle and put back to normal growth conditions for 3 hr before all green leaf tissue was collected.

value: Columbia


title: anac017-2_mutant_14-day-seedling-leaf_AntimycinA_treated_3h_rep3

description: gene expression data from anac017-2 arabidopsis 14-day-old seedlings treated with 50 uM Antimycin A for 3h

source_name: leaf tissue AntimycinA treated 3h


title: anac017-2_mutant_14-day-seedling-leaf_AntimycinA_treated_3h_rep2


title: anac017-2_mutant_14-day-seedling-leaf_water_treated_3h_rep2


title: anac017-2_mutant_14-day-seedling-leaf_H2O2_treated_3h_rep3

description: gene expression data from anac017-2 arabidopsis 14-day-old seedlings treated with 20 mM H2O2 for 3h

source_name: leaf tissue H2O2 treated 3h


title: anac017-1_mutant_14-day-seedling-leaf_water_treated_3h_rep3

description: gene expression data from anac017-1 arabidopsis 14-day-old seedlings treated with water control for 3h


title: anac017-1_mutant_14-day-seedling-leaf_water_treated_3h_rep2


title: anac017-2_mutant_14-day-seedling-leaf_H2O2_treated_3h_rep2


title: anac017-2_mutant_14-day-seedling-leaf_water_treated_3h_rep3


title: anac017-1_mutant_14-day-seedling-leaf_H2O2_treated_3h_rep2

description: gene expression data from anac017-1 arabidopsis 14-day-old seedlings treated with 20 mM H2O2 for 3h


title: anac017-1_mutant_14-day-seedling-leaf_H2O2_treated_3h_rep3


title: anac017-1_mutant_14-day-seedling-leaf_H2O2_treated_3h_rep1


title: anac017-1_mutant_14-day-seedling-leaf_water_treated_3h_rep1


title: anac017-2_mutant_14-day-seedling-leaf_AntimycinA_treated_3h_rep1


title: rao2_EMS_mutant_14-day-seedling-leaf_water_treated_3h_rep2

description: gene expression data from rao2 arabidopsis 14-day-old seedlings treated with water control for 3h


title: anac017-2_mutant_14-day-seedling-leaf_H2O2_treated_3h_rep1


title: anac017-1_mutant_14-day-seedling-leaf_AntimycinA_treated_3h_rep3

description: gene expression data from anac017-1 arabidopsis 14-day-old seedlings treated with 50 uM Antimycin A for 3h


title: rao2_EMS_mutant_14-day-seedling-leaf_H2O2_treated_3h_rep3

description: gene expression data from rao2 arabidopsis 14-day-old seedlings treated with 20 mM H2O2 for 3h


title: rao2_EMS_mutant_14-day-seedling-leaf_water_treated_3h_rep1


title: rao2_EMS_mutant_14-day-seedling-leaf_water_treated_3h_rep3


title: rao2_EMS_mutant_14-day-seedling-leaf_H2O2_treated_3h_rep2


title: anac017-1_mutant_14-day-seedling-leaf_AntimycinA_treated_3h_rep2


title: rao2_EMS_mutant_14-day-seedling-leaf_H2O2_treated_3h_rep1


title: Wild-type_14-day-seedling-leaf_water_treated_3h_rep3

description: gene expression data from wild-type Col:LUC arabidopsis 14-day-old seedlings treated with water control for 3h

value: wildtype


title: anac017-1_mutant_14-day-seedling-leaf_AntimycinA_treated_3h_rep1


title: rao2_EMS_mutant_14-day-seedling-leaf_AntimycinA_treated_3h_rep1

description: gene expression data from rao2 arabidopsis 14-day-old seedlings treated with 50 uM Antimycin A for 3h


title: Wild-type_14-day-seedling-leaf_water_treated_3h_rep1


title: rao2_EMS_mutant_14-day-seedling-leaf_AntimycinA_treated_3h_rep2


title: Wild-type_14-day-seedling-leaf_water_treated_3h_rep2


title: rao2_EMS_mutant_14-day-seedling-leaf_AntimycinA_treated_3h_rep3


title: Wild-type_14-day-seedling-leaf_H2O2_treated_3h_rep3

description: gene expression data from wild-type Col:LUC arabidopsis 14-day-old seedlings treated with 20 mM H2O2 for 3h


title: Wild-type_14-day-seedling-leaf_AntimycinA_treated_3h_rep2

description: gene expression data from wild-type Col:LUC arabidopsis 14-day-old seedlings treated with 50 uM Antimycin A for 3h


title: Wild-type_14-day-seedling-leaf_AntimycinA_treated_3h_rep1


title: Wild-type_14-day-seedling-leaf_AntimycinA_treated_3h_rep3


title: Wild-type_14-day-seedling-leaf_H2O2_treated_3h_rep1


title: rao1-2 mutant seedlings treated with 3 hours antimycin A, rep 1

status: Public on Jan 28 2013

city: Crawley

first: Sophia

middle: Jinq Tyan

last: Ng

address: 35, Stirling Hwy

institute: ARC CoE PEB, UWA

description: Gene expression data from Arabidopsis rao1-2 mutant seedlings treated with 3 hours antimycin A

source_name: 14 day old rao1-2 seedlings

treatment_protocol: Seedlings were sprayed either with deionised water (mock) or 50 µM antimycin A (Sigma) and put back to normal growth conditions for 3 hr before tissues were collected.

value: 14 day old

value: rao1-2 (regulators of alternative oxidase 1a mutants)

value: whole green tissue

value: 50 µM antimycin A for 3 hours


title: rao1-2 mutant seedlings treated with mock water control, rep 1

description: Gene expression data from Arabidopsis rao1-2 mutant seedlings treated with water control

value: water control treatment 3 hours


title: rao1-1 mutant seedlings treated with mock water control, rep 3

description: Gene expression data from Arabidopsis rao1-1 mutant seedlings treated with water control

source_name: 14 day old rao1-1 seedlings

value: rao1-1 (regulators of alternative oxidase 1a mutants)


title: rao1-1 mutant seedlings treated with mock water control, rep 2


title: rao1-1 mutant seedlings treated with 3 hours antimycin A, rep 1

description: Gene expression data from Arabidopsis rao1-1 mutant seedlings treated with 3 hours antimycin A


title: Col-Luc wild-type seedlings treated with mock water control, rep 3

description: Gene expression data from Arabidopsis Col:LUC (wildtype) seedlings treated with water control

source_name: 14 day old Col-Luc (WT) seedlings

value: Col:LUC (wild-type)


title: Col-Luc wild-type seedlings treated with 3 hours antimycin A, rep 2

description: Gene expression data from Arabidopsis Col:LUC (wildtype) seedlings treated with 3 hours antimycin A


title: rao1-2 mutant seedlings treated with mock water control, rep 3


title: Col-Luc wild-type seedlings treated with mock water control, rep 1


title: rao1-2 mutant seedlings treated with mock water control, rep 2


title: Col-Luc wild-type seedlings treated with 3 hours antimycin A, rep 1


title: rao1-2 mutant seedlings treated with 3 hours antimycin A, rep 3


title: rao1-1 mutant seedlings treated with 3 hours antimycin A, rep 3


title: +DEX +CHX, rep3

status: Public on Jan 01 2013

city: Montpellier

first: Gabriel

last: Krouk

address: 2 Place Pierre Viala

country: France

institute: CNRS

hyb_protocol: Affymetrix recommendations.

scan_protocol: Affymetrix recommendations.

data_processing: Mas5 [R].

source_name: Root/protoplasts, +DEX +CHX

label_protocol: NuGEN Kit.

growth_protocol: Plants are grown on MS/2 media.

extract_protocol: QIAGEN Kit.

treatment_protocol: Transformed protoplasts were treated with combinations of CHX (35 µM) or DEX (10 µM). CHX blocks translation into proteins and DEX induced the transcription factor nuclear localization.

value: root/protoplasts

value: +DEX +CHX


title: Col-Luc wild-type seedlings treated with 3 hours antimycin A, rep 3


title: rao1-1 mutant seedlings treated with 3 hours antimycin A, rep 2


title: -DEX +CHX, rep3

source_name: Root/protoplasts, -DEX +CHX

value: -DEX +CHX


title: rao1-1 mutant seedlings treated with mock water control, rep 1


title: Col-Luc wild-type seedlings treated with mock water control, rep 2


title: +DEX +CHX, rep2


title: +DEX +CHX, rep1


title: -DEX +CHX, rep1


title: Spleen_RAG_CD8_alphaplus denritic cells_rep1

status: Public on Jan 22 2013

city: Munich

first: Jacek

last: Puchałka

address: Lindwurmstrasse 2a

department: University Children's Hospital

institute: Munich University Hospital

description:
Strain: C57BL/6 RAG ko
Gender: Female
Age: 10 weeks
Tissue: spleen

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Data were normalized with quantile normalization. The expression values were computed using GC-RMA algorithm. All computations were performed with appropriate functions from the Affy and GCRMA packages of the Bioconductor suite.

organism: Mus musculus

source_name: C57BL/6 RAG ko spleen CD8 alpha plus dendritic cells

label_protocol: standard Affymetrix procedures

extract_protocol: ethanol extraction followed by Qiagen RNeasy total RNA cleanup protocol

tag: strain

tag: gender

value: Female

value: 10 weeks

value: spleen


title: Spleen_RAG_CD8_alphaminus denritic cells_rep1

source_name: C57BL/6 RAG ko spleen CD8 alpha minus dendritic cells

tag: tissue


title: +DEX -CHX, rep3

source_name: Root/protoplasts, +DEX -CHX

value: +DEX -CHX


title: Spleen_RAG_CD8_alphaminus denritic cells_rep2


title: rao1-2 mutant seedlings treated with 3 hours antimycin A, rep 2


title: Spleen_RAG_CD8_alphaplus denritic cells_rep2


title: +DEX -CHX, rep2


title: -DEX +CHX, rep2


title: -DEX -CHX, rep3

source_name: Root/protoplasts, -DEX -CHX

value: -DEX -CHX


title: -DEX -CHX, rep2

value: Columbia


title: +DEX -CHX, rep1


title: -DEX -CHX, rep1


title: sim smr1_rep1

status: Public on Dec 31 2012

city: Durham

first: shui

last: wang

state: NC

address: 124 Science Dr

institute: Duke University

description: 10-day-old soil grown plants

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on Affymetrix ATH1 GeneChip (Santa Clara, CA, U.S.A).

scan_protocol: GeneChips were scanned using the Axon Genepix Scanner (Genepix 4000B).

data_processing: The data were normalized with RMA algorithm using Gene-Spring GX (version 12) default analysis settings

source_name: sim smr1_seedling

label_protocol: RNA probes were labelled using the Ambion MessageAmp Premier.

growth_protocol: Arabidopsis seedlings were grown at 21-24°C, 16-hour day length, 60% relative humidity

extract_protocol: Total RNA was isolated from the frozen material using Invitrogen TRIzol.

treatment_protocol: 10-day-old wild type (Col-0), cpr5, sim smr1 and cpr5 sim smr1. Replicates are derived from three independent biological experiments.

tag: ecotype background

tag: genotype/variation

value: sim smr1

value: seedling


title: cpr5 sim smr1_rep3

description: 10-day-old soil grown plants

source_name: cpr5 sim smr1_seedling

value: cpr5 sim smr1


title: cpr5_rep3

description: 10-day-old soil grown plants


title: cpr5_rep1

description: 10-day-old soil grown plants


title: sim smr1_rep2

description: 10-day-old soil grown plants


title: sim smr1_rep3

description: 10-day-old soil grown plants


title: WT_rep2

description: 10-day-old soil grown plants

value: WT


title: WT_rep1

description: 10-day-old soil grown plants


title: cpr5 sim smr1_rep1

description: 10-day-old soil grown plants


title: WT_rep3

description: 10-day-old soil grown plants


title: cpr5 sim smr1_rep2

description: 10-day-old soil grown plants


title: cpr5_rep2

description: 10-day-old soil grown plants


title: Roots at T0 (NPA), rep3

status: Public on Dec 18 2012

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description:
Gene expression data from roots upon NPA treatment for 3 days.
Biological replicate 3 of 3.

hyb_protocol: A mixture of purified and fragmented biotinylated cRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix ATH1 arrays followed by staining and washing in a GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer's procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

data_processing: Data were normalized using RMA as implemented in the Affy package (version 1.36.0) of Bioconductor. Expression values are represented on a log2-scale.

source_name: Roots of seedling grown 3 days on NPA

label_protocol: RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 2 µg of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was converted to double-stranded cDNA in a reverse transcription reaction. Subsequently, the sample was converted and amplified to antisense cRNA and labeled with biotin in an in vitro transcription reaction. All steps were carried out according to the manufacturer's protocol (Affymetrix). All amplification and labeling reactions were performed on a Biomek 3000 ArrayPlex Workstation (Beckman Coulter).

growth_protocol: Arabidopsis thaliana (L). Heynh., Col-0 seeds were germinated vertically on solid.

extract_protocol: RNA was extracted with the RNeasy kit (Qiagen).

value: root

tag: morphology

value: no lateral root initiation

value: 3 days after germination

tag: treatment

value: mock


title: Roots at T2' NAA, rep3

description:
Gene expression data from roots upon lateral root-inducible system (LRIS) treatment with NAA for 6 hours.
Biological replicate 3 of 3.

source_name: Roots of seedling transferred from NPA to NAA for 6 hours

value: lateral root initiation

tag: age

value: NAA

tag: exposure time

value: 6 hours


title: Roots at T2' NAA, rep2

description:
Gene expression data from roots upon lateral root-inducible system (LRIS) treatment with NAA for 6 hours.
Biological replicate 2 of 3.

tag: ecotype


title: Roots at T2 naxillin, rep2

description:
Gene expression data from roots upon lateral root-inducible system (LRIS) treatment with naxillin for 6 hours.
Biological replicate 2 of 3.

source_name: Roots of seedling transferred from NPA to naxillin for 6 hours

value: naxillin


title: Roots at T2' NAA, rep1

description:
Gene expression data from roots upon lateral root-inducible system (LRIS) treatment with NAA for 6 hours.
Biological replicate 1 of 3.


title: Roots at T1' NAA, rep3

description:
Gene expression data from roots upon lateral root-inducible system (LRIS) treatment with NAA for 2 hours.
Biological replicate 3 of 3.

source_name: Roots of seedling transferred from NPA to NAA for 2 hours

value: 2 hours


title: Roots at T1' NAA, rep1

description:
Gene expression data from roots upon lateral root-inducible system (LRIS) treatment with NAA for 2 hours.
Biological replicate 1 of 3.


title: Roots at T1 naxillin, rep3

description:
Gene expression data from roots upon lateral root-inducible system (LRIS) treatment with naxillin for 2 hours.
Biological replicate 3 of 3.

source_name: Roots of seedling transferred from NPA to naxillin for 2 hours


title: Roots at T2 naxillin, rep3

description:
Gene expression data from roots upon lateral root-inducible system (LRIS) treatment with naxillin for 6 hours.
Biological replicate 3 of 3.


title: Roots at T0 (NPA), rep2

description:
Gene expression data from roots upon NPA treatment for 3 days.
Biological replicate 2 of 3.


title: Roots at T1 naxillin, rep1

description:
Gene expression data from roots upon lateral root-inducible system (LRIS) treatment with naxillin for 2 hours.
Biological replicate 1 of 3.


title: Roots at T1 naxillin, rep2

description:
Gene expression data from roots upon lateral root-inducible system (LRIS) treatment with naxillin for 2 hours.
Biological replicate 2 of 3.


title: Roots at T1' NAA, rep2

description:
Gene expression data from roots upon lateral root-inducible system (LRIS) treatment with NAA for 2 hours.
Biological replicate 2 of 3.


title: Roots at T0 (NPA), rep1

description:
Gene expression data from roots upon NPA treatment for 3 days.
Biological replicate 1 of 3.


title: Roots at T2 naxillin, rep1

description:
Gene expression data from roots upon lateral root-inducible system (LRIS) treatment with naxillin for 6 hours.
Biological replicate 1 of 3.


title: axr2-BR-rep1

status: Public on Dec 16 2012

city: Shanghai

first: zhou

middle: xiao

last: yi

address: 300 fenglin Road

country: China

institute: Shanghai Institutes for Biological Science

description: Gene expression data

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization,Wash and Stain Kit (Affymetrix, US) followed the manufacturer’s instructions

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Affymetrix, US) and Command Console Software 3.1 (Affymetrix, US) with default settings

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, US);The trimmed mean target intensity of each array was arbitrarily set to 100

source_name: BR-treated seedlings of axr2

label_protocol: RNA were labled using biotin as described in the affymetrix technical manual (Affymetri, USA)

growth_protocol: Sterilized  seeds were germinated on medium containing 2% sucrose (w/v) and 0.8% agar (w/v). After cold (4℃) treatment for 3 days, seeds were germinated at 22℃ in light (16h light/8h dark cycles) for 8h then transferred to grown in the darkness for 4 days

extract_protocol: Total RNA was extracted with RNeasy plant mini kit (Qiagen, Germany). RNA quality and quantity were tested by Agilent Bioanalyzer 2100 (Agilent technologies, US) and further purified by RNeasy micro kit (QIAGEN, Germany) and RNase-Free DNase Set (QIAGEN, Germany)

treatment_protocol: Seedlings were grown on MS medium with or without 100nM 24-eBL in the darkness for 4 days

value: dark-grown seedlings

value: axr2 mutant

value: BR


title: WT-BR-rep2

description: Gene expression data

source_name: BR-treated seedlings of WT

value: wild type

value: Columbia


title: WT-mock-rep1

description: Gene expression data

source_name: mock-treated seedlings of WT


title: 4C_0h_rep3

city: Thuwal

first: Katsuhiko

last: Mineta

address: 4700 KAUST

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

hyb_protocol: All procedures were carried out following the Affymetrix GeneChip Expression Analysis Technical Manual.

data_processing: Data were analyzed by Bioconductor of R. To extract the expression level of the probe set, the Robust Multichip Average (RMA) method implemented in the Affy package was used. Log-transformed RMA value was delogged and then normalized with the average expression level of poly(A) RNA controls derived from Bacillus subtilis genes.

source_name: T87 cultured cell

growth_protocol: Arabidopsis T87 suspension cells derived from Col-0 ecotype were grown in JPL media (Axelos et al.,Plant Physiol. Biochem. 30, p123-128, 1992) at 22°C under constant light (80 umolm-2s-1) with orbital shaking (120 rpm).

extract_protocol: Total RNA was extracted from the cells by using RNeasy Plant Mini kit (Qiagen), and purified and concentrated with RNeasy MinElute Cleanup kit (Qiagen).

treatment_protocol: Cells at seven days after subculturing were used as control cells. Cold treated cells were then exposed to cold stress by transferring into a growth chamber at 4°C under dim lights (40 umolm-2s-1) for 24 hours.

tag: cell line


title: axr2-mock-rep1

description: Gene expression data

source_name: mock-treated seedlings of axr2


title: 4C_6h_rep3

scan_protocol: All procedures were carried out following the Affymetrix GeneChip Expression Analysis Technical Manual.


title: 22C_1h_rep2

label_protocol: All procedures were carried out following the Affymetrix GeneChip Expression Analysis Technical Manual.


title: 4C_3h_rep3


title: 4C_1h_rep2


title: msg2-BR-rep1

description: Gene expression data

source_name: BR-treated seedlings of msg2

value: msg2 mutant


title: WT-BR-rep1

description: Gene expression data


title: msg2-BR-rep2

description: Gene expression data


title: 22C_0h_rep3


title: 4C_6h_rep2


title: 22C_0h_rep2


title: 4C_3h_rep1


title: 4C_0h_rep2


title: 4C_3h_rep2


title: 22C_3h_rep3


title: axr2-mock-rep2

description: Gene expression data


title: 4C_1h_rep3


title: 22C_1h_rep3


title: 22C_3h_rep2


title: msg2-mock-rep2

description: Gene expression data

source_name: mock-treated seedlings of msg2


title: 4C_6h_rep1


title: WT-mock-rep2

description: Gene expression data


title: 4C_1h_rep1


title: 4C_0h_rep1


title: 22C_3h_rep1


title: axr2-BR-rep2

description: Gene expression data


title: 22C_1h_rep1


title: 22C_0h_rep1


title: msg2-mock-rep1

description: Gene expression data


title: rgs1 treated with no sugars, biological replicate 1

status: Public on Nov 26 2012

city: Tallahassee

first: George

middle: W.

last: Bates

state: FL

address: 89 Cheiftain Way

department: Department of Biological Science

country: USA

institute: Florida State University

description: RNA was amplified twice with T7 RNA polymerase

hyb_protocol: Biotin-labeled RNA was fragmented, and hybridized to ATH1 GeneChips according to Affymetrix’s instructions (see Affymetrix user manuals P/N 702232 and P/N 702731).  The arrays were washed and stained with R-phycoerythrin streptavidin in the GeneChip Fluidics Station 400.

scan_protocol: Arrays were scanned with a Hewlett Packard GeneArray Scanner.

data_processing: The CEL files were imported in the R environment and analyzed by Bioconductor packages.  Quality assessment for evaluation of the overall data coherence was performed with the Affy and AffyQCReport packages, and the raw data were background-corrected, and normalized by GCRMA

source_name: guard cells from Arabidopsis rosette leaves

label_protocol: RNA was amplified twice with the MessageAmp II aRNA Amplification Kit (Ambion) according to the manufacturer's instructions, biotin-11-UTP was included in the second round of amplification.

growth_protocol: rosette leaves from 8-10 week old plants grown at 22 degrees C, 60% RH, 150 microE per meter per sec fluorescent light, 8h light/16h dark diurnal cycles

extract_protocol: RNA was isolated from samples of 50 to 100 guard cell pairs with the PicoPure RNA Isolation Kit (Arcturus) according to the manufacturer's instructions including treatment with DNase during the isolation.

treatment_protocol: 1 mm wide leaf strips were floated on 150 mM sucrose or mannitol solutions containing 50 mM KCl and 0.1 mM CaCl2, vacuum inflitrated (25kPa for 30 sec), and incubated for 5 h at 22 degrees C, under fluorscent lights (30 microE per meter per sec).  Leaf strips were blotted dry, frozen on liquid nitrogen, freeze dried for 4 days, and stored under vacuum at -20 degrees C.  Guard cell pairs were manually dissected from the leaf strips under a dissecting microscope at 50X magnification.

value: rosette leaves

tag: cell type

value: guard cells

value: rgs1 mutant

value: no sugars


title: wild type treated with sucrose, biological replicate 1

value: sucrose


title: wild type treated with sucrose, biological replicate 2


title: wild type treated with mannitol, biological replicate 1

value: mannitol


title: wild type treated with mannitol, biological replicate 2


title: rgs1 treated with no sugars, biological replicate 2


title: rgs1 treated with sucrose, biological replicate 1


title: wild type treated with no sugars, biological replicate 1


title: rgs1 treated with mannitol, biological replicate 1


title: 561-11_high-R:FR-bud-n-2_Rep2_ATH1

status: Public on Nov 21 2012

city: Loughborough

first: nasc

last: nasc

address: Sutton bonington Campus

department: Plant&Crop Sciences

country: United Kingdom

institute: NASC

description: Plants were grown individually in 26 by 60 mm tubes and watered and fertilized optimally. Plants were grown in a split growth chamber (providing uniform temperature and PPFD but allowing for differential R:FR) with 18 h photoperiods (185 microMoles m-2 s-1 PPFD provided by T12 VHO CW fluorescent lamps) and 24oC/18oC day/night temperatures. 3 days at 4oC. 22.5°C average, 24°C day, 18°C night 50% average, 50% day, 50% night Hoagland ampapos;s No.2 basal salt mixture.

hyb_protocol: Biotin-labelled cRNA using the "Affymetrix GeneChip Hybridization, Wash and Stain Kit" according to the guidelines set out by Affymetrix, Santa Clara, CA.

scan_protocol: Scanned according to the guidelines set out by Affymetrix, Santa Clara, CA.

data_processing: Raw data from the microarrays was normalized at probe-level using the MAS5 algorithm. The detection calls (present, marginal, absent) for each probe set was obtained using the GCOS system.

source_name: Col-8, bud n-2, high R:FR

label_protocol: Labelled using the protocol described in the Affymetrix manual "3' IVT Express Kit User Manual".

extract_protocol: Qiagen RNeasy kit protocol.

tag: genetic background

tag: stock code

tag: developmental stage

value: rosette axillary bud n-2

value: high R:FR


title: rgs1 treated with sucrose, biological replicate 2

tag: agent


title: 561-2_low-R:FR-bud-n_Rep2_ATH1

source_name: Col-8, bud n, low R:FR

value: rosette axillary bud n

value: low R:FR


title: 561-1_low-R:FR-bud-n_Rep1_ATH1


title: rgs1 treated with mannitol, biological replicate 2


title: wild type treated with no sugars, biological replicate 2


title: wild type treated with sucrose, biological replicate 3


title: rgs1 treated with mannitol, biological replicate 3


title: 561-4_high-R:FR-bud-n_Rep1_ATH1

source_name: Col-8, bud n, high R:FR


title: wild type treated with mannitol, biological replicate 3


title: rgs1 treated with no sugars, biological replicate 3


title: wild type treated with no sugars, biological replicate 3


title: 561-7_low-R:FR-bud-n-2_Rep1_ATH1

source_name: Col-8, bud n-2, low R:FR


title: rgs1 treated with sucrose, biological replicate 3


title: 561-5_high-R:FR-bud-n_Rep2_ATH1


title: 561-6_high-R:FR-bud-n_Rep3_ATH1


title: 561-8_low-R:FR-bud-n-2_Rep2_ATH1


title: 561-9_low-R:FR-bud-n-2_Rep3_ATH1


title: 561-10_high-R:FR-bud-n-2_Rep1_ATH1


title: 561-3_low-R:FR-bud-n_Rep3_ATH1


title: 561-12_high-R:FR-bud-n-2_Rep3_ATH1


title: nia1nia2 biological rep4

status: Public on Nov 01 2012

city: Valencia

last: Leon

address: CPI Edificio 8E, Ingeniero Fausto Elio s/n

institute: IBMCP (CSIC-UPV)

description: Gene expression data from 15 day-old whole seedlings

hyb_protocol: Three biological replicates and their corresponding negative controls were independently hybridized to ATH1 microarrays (Affymetrix), containing 22 500 transcript variants from 24 000 well-characterized Arabidopsis genes. Each sample was added to a hybridization solution containing 100 mM 2-(N-morpholino) ethanesulfonic acid, 1 M Na+, and 20 mM of EDTA in the presence of 0.01% Tween-20. Hybridization was performed for 16 h at 45°C.

scan_protocol: Each microarray was washed and stained with streptavidin–phycoerythrin in a Fluidics station 450 (Affymetrix) and scanned at 2.5-μm resolution in a GeneChip® Scanner 3000 7G system (Affymetrix). Data analyses were performed using genechip operating software (GCOS), to generate the corresponding CEL files.

data_processing: Linear model methods (LiMMA) were used for determining differentially expressed genes. To control the false-discovery rate, P-values were corrected using the method of Benjamini and Hochberg (1995). Criteria for selection of genes were fold value >1.9 and false-discovery rate ≤ 0.05. Statistical analysis and graphical visualization of data were performed with the interactive tool fiesta (http://bioinfogp.cnb.csic.es/tools/FIESTA/).

source_name: 15 day-old seedlings

label_protocol: RNAs were ligated to an RNA oligonucleotide adaptor (Invitrogen) using T4 RNA ligase (Ambion, http://www.ambion.com/). The RNAs were extracted once with phenol-chloroform and non-ligated adapter was removed by chromatography with MicroSpin S-300 HR columns (GE Healthcare, http://www.gehealthcare.com/). Purified ligation products were precipitated in ethanol and used as templates for reverse transcription with Superscript III (Invitrogen) for 3 h at 46°C, using oligonucleotide oligo(dT) as primer. Template RNA was removed by alkaline hydrolysis and first-strand cDNA purified with S.N.A.P. columns (Invitrogen). Second-strand synthesis was performed with Taq DNA polymerase (Roche, http://www.roche.com/) for 5 min at 94°C, 5 min; 58°C, 1 min; 72°C, 10 min. A forward oligonucleotide T7-Adap primer, which was complementary to the RNA adapter and contained the sequence of bacteriophage T7 promoter, was used. Double-stranded cDNA was then purified with MinElute columns (Qiagen) and in vitro transcribed with T7 RNA polymerase, using a MessageAmp aRNA kit (Ambion). Amplified RNA was treated with DNase I (Roche) to remove cDNA templates, purified with an aRNA Purification Module (Ambion) and then used as template for single-stranded cDNA synthesis, according to Affymetrix instructions (http://www.affymetrix.com/) as dolows: aRNA was reverse transcribed with SuperScript II (Invitrogen) for 1 h at 42°C with oligo(dT) as primer. After alkaline hydrolysis of aRNA and purification (MinElute columns, Qiagen), cDNA was fragmented with 1.5 units of DNase I (GE Healthcare) into fragments in the 50–200 bp range. Finally, 3' ends of fragmented cDNA were biotin-ddUTP labeled with terminal deoxynucleotidyl transferase (Promega, http://www.promega.com/) and GeneChip DNA labeling reagent (Affymetrix).

growth_protocol: MS media plus 1 % sucrose, 15 days

extract_protocol: Total RNA from wild type and NO-deficient plants was isolated and purified by the Micro-to-Midi Total RNA Purification System from Invitrogen (Carlsbad, CA, USA).

treatment_protocol: Samples were harvested 5 h after dawn of day 15 after sowing and seedlings were grown under long days (16 h light / 8 h darkness) photoperiodic conditions.

value: whole seedlings

value: 15 day-old (after transition to flowering)

value: double nia1nia2 mutant


title: nia1nia2noa1-2 biological rep1

value: triple nia1nia2noa1-2 mutant


title: nia1nia2noa1-2 biological rep3


title: noa1-2 biological rep3

value: noa1-2 mutant


title: noa1-2 biological rep2


title: noa1-2 biological rep1


title: nia1nia2 biological rep3


title: nia1nia2 biological rep2


title: Col-0 biological rep3

value: Col-0 wild-type


title: nia1nia2noa1-2 biological rep2


title: Col-0 biological rep1


title: Col-0 biological rep2


title: shoots of WT 100uM Fe, biological rep3

status: Public on Sep 30 2012

city: Hanover

first: Alicia

last: Sivitz

state: NH

address: 78 College St

institute: Dartmouth College

description: Gene expression data from shoots of 10-day-old plants grown on 0.5X MS supplemented with 100uM iron added

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on ATH1 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed using simpleAffy from Bioconductor and RMA normalization.

source_name: shoots of WT 100uM Fe

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

growth_protocol: 10-day-old plants grown on 0.5X MS plates without or with (100 micromolar) iron.

extract_protocol: Qiagen RNAeasy extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Plants were grown either in the absence of iron or in the presence of 100uM Fe.

value: shoots

tag: genotype

value: WT (Col 0)

value: 10 days old

value: 100uM Fe


title: roots of WT 100uM Fe, biological rep3

description: Gene expression data from roots of 10-day-old plants grown on 0.5X MS supplemented with 100uM iron added

source_name: roots of WT 100uM Fe

value: roots


title: roots of bhlh100/101 100uM Fe, biological rep3

source_name: roots of bhlh100/101 100uM Fe


title: roots of WT 0uM Fe, biological rep3

description: Gene expression data from roots of 10-day-old plants grown on 0.5X MS without any iron added

source_name: roots of WT 0uM Fe

value: 0uM Fe


title: roots of bhlh100/101 100uM Fe, biological rep2


title: roots of WT 100uM Fe, biological rep2


title: roots of WT 0uM Fe, biological rep1


title: roots of bhlh100/101 0uM Fe, biological rep3

source_name: roots of bhlh100/101 0uM Fe


title: shoots of WT 0uM Fe, biological rep3

description: Gene expression data from shoots of 10-day-old plants grown on 0.5X MS without any iron added

source_name: shoots of WT 0uM Fe


title: roots of WT 100uM Fe, biological rep1


title: roots of bhlh100/101 100uM Fe, biological rep1


title: roots of bhlh100/101 0uM Fe, biological rep2


title: shoots of WT 0uM Fe, biological rep2


title: shoots of WT 100uM Fe, biological rep2


title: roots of bhlh100/101 0uM Fe, biological rep1


title: shoots of WT 0uM Fe, biological rep1


title: roots of WT 0uM Fe, biological rep2


title: shoots of WT 100uM Fe, biological rep1


title: shoots of bhlh100/101 100uM Fe, biological rep3

source_name: shoots of bhlh100/101 100uM Fe


title: shoots of bhlh100/101 100uM Fe, biological rep1


title: shoots of bhlh100/101 100uM Fe, biological rep2


title: Kas_-Fe_48h_Shoots_r3

city: Columbia

first: Samuel

middle: Alonzo

last: McInturf

state: Missouri

address: 1201 Rollins Street

department: Plant Sciences

institute: University of Missouri - Columbia

description: gene expression data from Kas shoots on minus iron media for 48h

hyb_protocol: Done according the manufacturer’s protocol

data_processing: R/Bioconductor.  Normalized with rma

source_name: Kas shoots on minus iron media for 48h

growth_protocol: Seeds of Arabidopsis thaliana ecotypes Kas-1 and Tsu-1 were imbibed in 0.1% agar at 4°C for 72 h, planted onto rockwool, and grown on hydroponic solution. Lighting was provided at a photoperiod of 16 h of 150 µmol m-2 s-1  4,100K fluorescent light. The ecotypes used are Kas-1 and Tsu-1 for our study, the citation of Schuler (2011) used Columbia-0.

extract_protocol: Total RNA was isolated from whole rosettes using the RNeasy Plant Kit (Qiagen), and quality was assessed using the Agilent Bioanalyzer 2100.

treatment_protocol: 24 d old plants were transferred to treatments of +Fe (50 µM Fe(III)-EDDHA) or -Fe for 24 or 48 h.

value: Kas

tag: time

tag: iron

value: Minus


title: Kas_+Fe_24h_Shoots_r3

description: gene expression data from Kas shoots on complete media for 24h

scan_protocol: Done according the manufacturer’s protocol

source_name: Kas shoots on complete media for 24h

value: Plus


title: Kas_-Fe_48h_Shoots_r2

label_protocol: Done according the manufacturer’s protocol


title: Kas_+Fe_24h_Shoots_r2


title: shoots of bhlh100/101 0uM Fe, biological rep3

source_name: shoots of bhlh100/101 0uM Fe

tag: tissue


title: Kas_-Fe_24h_Shoots_r2

description: gene expression data from Kas shoots on minus iron media for 24h

source_name: Kas shoots on minus iron media for 24h


title: Tsu_-Fe_48h_Shoots_r2

description: gene expression data from Tsu shoots on minus iron media for 48h

source_name: Tsu shoots on minus iron media for 48h

value: Tsu


title: shoots of bhlh100/101 0uM Fe, biological rep2


title: Tsu_-Fe_24h_Shoots_r3

description: gene expression data from Tsu shoots on minus iron media for 24h

source_name: Tsu shoots on minus iron media for 24h


title: Kas_-Fe_48h_Shoots_r1


title: Kas_-Fe_24h_Shoots_r3


title: Tsu_-Fe_24h_Shoots_r1


title: Tsu_-Fe_24h_Shoots_r2


title: Kas_-Fe_24h_Shoots_r1


title: Tsu_-Fe_48h_Shoots_r1


title: Kas_+Fe_24h_Shoots_r1


title: Tsu_+Fe_24h_Shoots_r1

description: gene expression data from Tsu shoots on complete media for 24h

source_name: Tsu shoots on complete media for 24h


title: shoots of bhlh100/101 0uM Fe, biological rep1


title: osmotic_11day_leaf_rep1

status: Public on Sep 19 2012

city: No.12 Zhongguancun South Street, Haidian

first: Jun

last: Liu

state: Beijing

address: 1230 York Avenue

department: Chinese Academy of Agricultural Sciences

institute: Institute of Crop Science

hyb_protocol: Probe synthesis, hybridization and scanning of all arrays were carried out at the Genomics Resource Center in the Rockefeller University following the manufacturer’s manual (Affymetrix).

data_processing: Background correction was performed as described by Irizarry et al. (2003). Quantile normalization was performed as described by Bolstad et al (2003). Finally, probes were summarized into single gene expression (probe-set) values on a per chip basis using the medianpolish algorithm (Tukey, 1977).

source_name: osmotic 11day leaf replicate1

growth_protocol: Arabidopsis thaliana ecotype Columbia-0 was used as Wild-type.For hydroponic culture, WT seeds  after a 3-day cold treatment at 4°C were sowed on rock wool (Grodan Inc.) pre-soaked  in MGRL media. In short, plants were  grown at 22°C with a 150 μmol m-2 S-1 fluorescence rate and under 12 hour / 12 hour  light dark cycle in MGRL hydroponic medium.

extract_protocol: Each array probe for Arabidopsis Genechip ATH1 was synthesized from 1 μg total RNA extracted by RNA easy extraction kit (Qiagen). Eighteen individual Genechip probes with three biological replicates for CL (Col Leaf), CR (Col Root), OL (Osmotic stressed Leaf), OR (Osmotic stressed Root), RL (Recovery Leaf), and RR (Recovery Root).

treatment_protocol: Thirty-day-old plants were then subjected to high osmotic stress by adding 0.3M mannitol to the basal MGRL medium for 3 hr in the light. Recovery plants were transfer back to the MGRL medium for 1 day after stress treatment and sampled.  to high osmotic stress by adding 0.3M mannitol to the basal MGRL medium for 3 hr in  the light. Recovery plants were transfer back to the MGRL medium for 1 day after stress  treatment and sampled.

value: leaves

value: osmotic

tag: time point


title: Tsu_+Fe_24h_Shoots_r3


title: Tsu_-Fe_48h_Shoots_r3


title: osmotic_11day_root_rep3

scan_protocol: Probe synthesis, hybridization and scanning of all arrays were carried out at the Genomics Resource Center in the Rockefeller University following the manufacturer’s manual (Affymetrix).

source_name: osmotic 11day root replicate3


title: osmotic_11day_root_rep2

source_name: osmotic 11day root replicate2

label_protocol: Probe synthesis, hybridization and scanning of all arrays were carried out at the Genomics Resource Center in the Rockefeller University following the manufacturer’s manual (Affymetrix).


title: osmotic_11day_leaf_rep3

source_name: osmotic 11day leaf replicate3


title: osmotic_11day_root_rep1

source_name: osmotic 11day root replicate1


title: Tsu_+Fe_24h_Shoots_r2


title: osmotic_10day_root_rep3

source_name: osmotic 10day root replicate3


title: osmotic_11day_leaf_rep2

source_name: osmotic 11day leaf replicate2


title: osmotic_10day_root_rep2

source_name: osmotic 10day root replicate2


title: osmotic_10day_leaf_rep3

source_name: osmotic 10day leaf replicate3


title: osmotic_10day_leaf_rep1

source_name: osmotic 10day leaf replicate1


title: osmotic_10day_root_rep1

source_name: osmotic 10day root replicate1


title: mock_10day_leaf_rep2

source_name: mock 10day leaf replicate2

value: mock


title: osmotic_10day_leaf_rep2

source_name: osmotic 10day leaf replicate2


title: Flies on 5mM paraquat and 0.1 mg/ml nicotine, biological rep1

status: Public on Sep 05 2012

city: Albany

first: Haydeh

last: Payami

state: NY

address: 150 New Scotland Ave.

department: Wadsworth Center

institute: NY State Department of Health

description:
dmel_PQNic_1
Gene expression data from heads of flies exposed to food with 0.1 mg/ml nicotine for 10 days, followed by food with 5 mM paraquat and 0.1 mg/ml nicotine for 6 days.

hyb_protocol: The labeled cDNA was hybridized overnight to the GeneChip Drosophila 2.0 array (Affymetrix).

scan_protocol: The arrays were scanned on a GeneChip Scanner 30007G using standard protocols, and raw data were obtained using Affymetrix Command Console Software.

data_processing: The data were analyzed and normalized using the Bioconductor R packages affy and GCRMA (using the default options of quantile normalization, pmonly correction, and median polish summarization).

organism: Drosophila melanogaster

source_name: Drosophila adult female heads, 10 days on food with nicotine and 6 days on food with paraquat and nicotine

label_protocol: The cDNA was fragmented and biotin labeled using the Encore Biotin module according to standard protocols (NuGEN).

growth_protocol: Female D. melanogaster w1118 flies were collected up to 24 hours after eclosion and placed into food vials for pretreatment.

extract_protocol: Heads were dissected from 20 females per vial and pooled. Total RNA was extracted using Tri Reagent and the associated protocol, and RNA was cleaned using the Qiagen RNeasy Cleanup Kit and the associated protocol. Total RNA (50ng) was used to generate cDNA and amplified using a NuGEN 3'-Applause amplification system according to the manufacturer's instructions (NuGEN).

treatment_protocol: Flies were pretreated on food containing either 0 or 0.1 mg/ml nicotine for 10 days, and then treated on food containing either 0 or 5 mM paraquat plus the pretreatment dose of nicotine for 6 days. Flies were transferred to fresh food vials every other day.

tag: Sex

value: female

value: adult

value: head

tag: nicotine exposure

value: 0.1 mg/ml

tag: paraquat exposure

value: 5 mM


title: Flies on plain food, biological rep3

description:
dmel_control_3
Gene expression data from heads of flies exposed to plain food for 16 days.

source_name: Drosophila adult female heads, 16 days on plain food

value: 0 mg/ml

value: 0 mM


title: Flies on 0.1 mg/ml nicotine, biological rep2

description:
dmel_Nic_2
Gene expression data from heads of flies exposed to food with 0.1 mg/ml nicotine for 16 days.

source_name: Drosophila adult female heads, 16 days on food with nicotine


title: Flies on 5mM paraquat, biological rep3

description:
dmel_PQ_3
Gene expression data from heads of flies exposed to plain food for 10 days, followed by food with 5 mM paraquat for 6 days.

source_name: Drosophila adult female heads, 10 days on plain food and 6 days on food with paraquat


title: Flies on plain food, biological rep2

description:
dmel_control_2
Gene expression data from heads of flies exposed to plain food for 16 days.


title: Flies on 5mM paraquat and 0.1 mg/ml nicotine, biological rep3

description:
dmel_PQNic_3
Gene expression data from heads of flies exposed to food with 0.1 mg/ml nicotine for 10 days, followed by food with 5 mM paraquat and 0.1 mg/ml nicotine for 6 days.


title: 0-24 Hrs dMyc+ embryos, biological rep3

status: Public on Sep 15 2012

city: Charlotte

first: Kaveh

last: Daneshvar

address: 9201 University City Blvd.

institute: University of North Carolina at Charlotte

description: Gene expression data from embryos between 0 t0 24 hours old

hyb_protocol: Affymetrix hybridization protocol. Done by Expression Analysis (Durham, NC, USA)

scan_protocol: Affymetrix GeneChip Scannerl. Done by Expression Analysis (Durham, NC, USA)

data_processing: The data were analyzed using Affymetrix default analysis settings and global scaling as normalization method. Done by Expression Analysis (Durham, NC, USA)

source_name: 0-24 hour old embryos

label_protocol: 3” IVT Express kit was used. Done by Expression Analysis (Durham, NC, USA)

growth_protocol: For both genotypes (Control and dMyc+) 0-24 hours embryos were collected on a grape juice agar at 25C.

extract_protocol: Total RNA was extracted using Trizol solution (Invitrogen), according to manufacturer’s recommendation.

treatment_protocol: Embryos were dechorionated with 100% bleach, and washed with D.I. water several times. Washed and drained embryos were placed in the Trizol solution (Invitrogen).

value: dechorionated embryo

tag: age

value: 0-24 hour old

tag: genotype/variation

value: Myc+ (flies over-expressing dMyc under UAS enhancer)


title: Flies on 5mM paraquat and 0.1 mg/ml nicotine, biological rep2

description:
dmel_PQNic_2
Gene expression data from heads of flies exposed to food with 0.1 mg/ml nicotine for 10 days, followed by food with 5 mM paraquat and 0.1 mg/ml nicotine for 6 days.


title: 0-24 Hrs dMyc+ embryos, biological rep1


title: Flies on 0.1 mg/ml nicotine, biological rep1

description:
dmel_Nic_1
Gene expression data from heads of flies exposed to food with 0.1 mg/ml nicotine for 16 days.