title: CR20_H016

source_name: Cold treatment for 24hrs(biological repeat 2-technical repeat 2)


title: CR20_H015

status: Public on Oct 15 2014

type: RNA

city: Taipei

first: Men-Chi

last: Chang

address: No. 1, Section 4, Roosevelt Road

department: Agronomy

country: Taiwan

institute: National Taiwan University

hyb_protocol: Fluorescent targets were hybridized to the Mouse Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization at 50 ℃, non-speciﬁc binding targets were washed away by three different washing steps (WashⅠ 42 ℃ 5 mins；Wash Ⅱ 42 ℃, 5 mins, 25 ℃ 5 mins; Wash Ⅲ rinse 20 times)

scan_protocol: The arrays were scanned by GenePix 4200A 01 Autoloader (635nm power 100 PMT 520 ; 532nm power 10, PMT 460) and quantify the fluoresence intensity.

data_processing:
The signal intensity of each spot was loaded into Rosetta Resolver System® (Rosetta Biosoftware) to process data analysis. The error model of Rosetta Resolver System® could remove both systematic and random errors form the data. We ﬁltered out spots that the ﬂag is less than 0. Spots that passed the criteria were normalized by 50% media scaling normalization method. Normalize intensities: Median scaling performed on data set without flagged and control data. Merge technical replicate data: Average intensity values calculated on technical replicates.
Calculate average ratios of the hybridization replicates and find significant values for each gene by pairwise comparision (Ranking and hypothesis testing).

molecule: total RNA

organism: Oryza sativa Indica Group

source_name: Cold treatment for 24hrs(biological repeat 2-technical repeat 1)

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dyes (Amersham Pharmacia, Piscataway, NJ, USA).

growth_protocol: Seeds were immersed in water for germination and then hydroponically cultivated in Kimura B solution at pH 5.0. These seedlings were grown in phytotron under 30oC day/25oC night and 70~80% relative humidity condition.

extract_protocol: RNA extraction by Trizol. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧7).

treatment_protocol: Until growing to three-leaf stage, these plants were transferred into 4oC growth chamber for cold treatment. After 3-hr or 24-hr of cold treatment or recovery to normal growth condition for 24 hrs, rice roots and shoots were harvested and immediately freezed in liquid nitrogen for RNA extraction.

tag: sample name

tag: cultivar

tag: tissue

value: Root

tag: Stage

value: 3-leaf seedlings


title: CR22_H019

source_name: Recovery for 24hrs after cold treatment for 24hrs(biological repeat 1-technical repeat 1)


title: CR18_H012

source_name: Cold treatment for 3hrs(biological repeat 3-technical repeat 2)


title: Caco-2 S1400-1

status: Public on Feb 05 2016

city: Aberdeen

first: Denise

last: Kelly

address: Institute of Medical Sciences

country: United Kingdom

institute: University of Aberdeen

description: Caco-2 cells were treated with Salmonella enteritidis strains S1400 or EAV9 or recombinant flagellin, and their gene expression profile was compared to non-stimulated cells.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

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

data_processing: Initial data analysis was performed using Affymetrix GCOS 1.2 software. Data were further analyzed using Bioconductor (http://www.bioconductor.org) from the R Project for Statistical Computing (http://www.r-project.org). Normalization was performed with gcRMA, p-values were adjusted using the Benjamini-Hochberg method.

label: Biotin

molecule: polyA RNA

organism: Homo sapiens

label_protocol: Fragmented and biotin-labelled cRNA was synthesized from 1 ug purified mRNA using the One-Cycle Target Labeling Kit (Affymetrix) according to the manufacturer's protocol.

growth_protocol: Caco-2 cells were grown in culture flasks in DMEM (Sigma) containing 10% FCS, L-glutamine and antibiotics.

extract_protocol: Total RNA was extracted with an RNeasy kit (Qiagen) and included a DNAse I step (Qiagen). Poly (A)+ RNA was purified using an Oligotex mRNA mini kit (Qiagen).

treatment_protocol: Caco-2 cells were grown in 100-mm culture dishes to 3 days post-confluence in DMEM (Sigma) containing 10% FCS, L-glutamine and antibiotics. Cells were washed twice with HBSS (Sigma) and incubated for 24 h in DTS medium containing DMEM, L-glutamine, transferrin and sodium selenite before incubation for 2 h with 1x10E8 S. enteritidis strain S1400.

value: human, Caucasian, colon, adenocarcinoma


title: Caco-2 S1400-3

source_name: 2 h with 1x10E8 S. enteritidis strain S1400


title: Caco-2 Flagellin-2

source_name: 2 h with 100 ng recombinant flagellin

treatment_protocol: Caco-2 cells were grown in 100-mm culture dishes to 3 days post-confluence in DMEM (Sigma) containing 10% FCS, L-glutamine and antibiotics. Cells were washed twice with HBSS (Sigma) and incubated for 24 h in DTS medium containing DMEM, L-glutamine, transferrin and sodium selenite before incubation for 2 h with 100 ng recombinant flagellin.


title: Caco-2 Control-1

source_name: medium alone

treatment_protocol: Caco-2 cells were grown in 100-mm culture dishes to 3 days post-confluence in DMEM (Sigma) containing 10% FCS, L-glutamine and antibiotics. Cells were washed twice with HBSS (Sigma) and incubated for 24 h in DTS medium containing DMEM, L-glutamine, transferrin and sodium selenite before treatment with the different conditions.


title: Caco-2 Flagellin-3


title: CR17_H010

source_name: Cold treatment for 3hrs(biological repeat 2-technical repeat 2)


title: CR17_H009

source_name: Cold treatment for 3hrs(biological repeat 2-technical repeat 1)


title: Caco-2 EAV9-3

treatment_protocol: Caco-2 cells were grown in 100-mm culture dishes to 3 days post-confluence in DMEM (Sigma) containing 10% FCS, L-glutamine and antibiotics. Cells were washed twice with HBSS (Sigma) and incubated for 24 h in DTS medium containing DMEM, L-glutamine, transferrin and sodium selenite before incubation for 2 h with 1x10E8 S. enteritidis strain EAV9.


title: CR15_H005

source_name: Control(biological repeat 3-technical repeat 1)


title: CR16_H008

source_name: Cold treatment for 3hrs(biological repeat 1-technical repeat 2)


title: CR15_H006

source_name: Control(biological repeat 3-technical repeat 2)


title: CR16_H007

source_name: Cold treatment for 3hrs(biological repeat 1-technical repeat 1)


title: Caco-2 EAV9-1

source_name: 2 h with 1x10E8 S. enteritidis strain EAV9


title: Caco-2 EAV9-2


title: Caco-2 Control-3


title: Caco-2 Flagellin-1


title: Caco-2 Control-2


title: CR14_H004

source_name: Control(biological repeat 2-technical repeat 2)


title: CR14_H003

source_name: Control(biological repeat 2-technical repeat 1)


title: CR13_H002

source_name: Control(biological repeat 1-technical repeat 2)


title: CR13_H001

source_name: Control(biological repeat 1-technical repeat 1)


title: CS24_H024

source_name: Recovery for 24hrs after cold treatment for 24hrs(biological repeat 3-technical repeat 2)

value: Shoot


title: CS24_H023

source_name: Recovery for 24hrs after cold treatment for 24hrs(biological repeat 3-technical repeat 1)


title: CR19_H013

source_name: Cold treatment for 24hrs(biological repeat 1-technical repeat 1)


title: CS23_H021

source_name: Recovery for 24hrs after cold treatment for 24hrs(biological repeat 2-technical repeat 1)


title: CS23_H022

source_name: Recovery for 24hrs after cold treatment for 24hrs(biological repeat 2-technical repeat 2)


title: CR18_H011

source_name: Cold treatment for 3hrs(biological repeat 3-technical repeat 1)


title: CS22_H020

source_name: Recovery for 24hrs after cold treatment for 24hrs(biological repeat 1-technical repeat 2)


title: CS22_H019

source_name: Recovery for 24hrs after cold treatment for 24hrs(biological repeat 1-technical repeat 1)


title: CS21_H017

source_name: Cold treatment for 24hrs(biological repeat 3-technical repeat 1)


title: CS20_H015

source_name: Cold treatment for 24hrs(biological repeat 2-technical repeat 1)


title: CS19_H014

source_name: Cold treatment for 24hrs(biological repeat 1-technical repeat 2)


title: CS18_H012

source_name: Cold treatment for 3hrs(biological repeat 3-technical repeat 2)


title: CS20_H016

source_name: Cold treatment for 24hrs(biological repeat 2-technical repeat 2)


title: CS18_H011


title: CS16_H008

source_name: Cold treatment for 3hrs(biological repeat 1-technical repeat 2)


title: CS17_H009

source_name: Cold treatment for 3hrs(biological repeat 2-technical repeat 1)


title: CS15_H005

source_name: Control(biological repeat 3-technical repeat 1)


title: CS13_H002

source_name: Control(biological repeat 1-technical repeat 2)


title: CS14_H003

source_name: Control(biological repeat 2-technical repeat 1)


title: CS16_H007

source_name: Cold treatment for 3hrs(biological repeat 1-technical repeat 1)


title: CS15_H006

source_name: Control(biological repeat 3-technical repeat 2)


title: CS17_H010

source_name: Cold treatment for 3hrs(biological repeat 2-technical repeat 2)


title: CR11_H021

organism: Oryza sativa Japonica Group

source_name: Recovery for 24hrs after cold treatment for 24hrs(biological repeat 2-technical repeat 1)


title: CS14_H004

source_name: Control(biological repeat 2-technical repeat 2)


title: CR12_H024

source_name: Recovery for 24hrs after cold treatment for 24hrs(biological repeat 3-technical repeat 2)


title: CR10_H020

source_name: Recovery for 24hrs after cold treatment for 24hrs(biological repeat 1-technical repeat 2)


title: CR11_H022

source_name: Recovery for 24hrs after cold treatment for 24hrs(biological repeat 2-technical repeat 2)


title: CR10_H019

source_name: Recovery for 24hrs after cold treatment for 24hrs(biological repeat 1-technical repeat 1)


title: CR9_H017

source_name: Cold treatment for 24hrs(biological repeat 3-technical repeat 1)


title: CS13_H001

source_name: Control(biological repeat 1-technical repeat 1)


title: CR8_H016

source_name: Cold treatment for 24hrs(biological repeat 2-technical repeat 2)


title: CR8_H015

source_name: Cold treatment for 24hrs(biological repeat 2-technical repeat 1)


title: CS21_H018

source_name: Cold treatment for 24hrs(biological repeat 3-technical repeat 2)


title: CR9_H018


title: CR7_H014

source_name: Cold treatment for 24hrs(biological repeat 1-technical repeat 2)


title: CR6_H012

source_name: Cold treatment for 3hrs(biological repeat 3-technical repeat 2)


title: CR5_H009

source_name: Cold treatment for 3hrs(biological repeat 2-technical repeat 1)


title: CR5_H010


title: CR7_H013

source_name: Cold treatment for 24hrs(biological repeat 1-technical repeat 1)


title: CS19_H013


title: CR4_H008

source_name: Cold treatment for 3hrs(biological repeat 1-technical repeat 2)


title: CR3_H006

source_name: Control(biological repeat 3-technical repeat 2)


title: CR6_H011

source_name: Cold treatment for 3hrs(biological repeat 3-technical repeat 1)


title: CR3_H005

source_name: Control(biological repeat 3-technical repeat 1)


title: CR12_H023

source_name: Recovery for 24hrs after cold treatment for 24hrs(biological repeat 3-technical repeat 1)


title: CR1_H002

source_name: Control(biological repeat 1-technical repeat 2)


title: CR1_H001


title: CR2_H004

source_name: Control(biological repeat 2-technical repeat 2)


title: CR2_H003

source_name: Control(biological repeat 2-technical repeat 1)


title: CS11_H022

source_name: Recovery for 24hrs after cold treatment for 24hrs(biological repeat 2-technical repeat 2)


title: CS10_H019

source_name: Recovery for 24hrs after cold treatment for 24hrs(biological repeat 1-technical repeat 1)


title: CS9_H018


title: CS10_H020

source_name: Recovery for 24hrs after cold treatment for 24hrs(biological repeat 1-technical repeat 2)


title: CS11_H021

source_name: Recovery for 24hrs after cold treatment for 24hrs(biological repeat 2-technical repeat 1)


title: CS8_H015

source_name: Cold treatment for 24hrs(biological repeat 2-technical repeat 1)


title: CS7_H013


title: CS7_H014

source_name: Cold treatment for 24hrs(biological repeat 1-technical repeat 2)


title: CS6_H012

source_name: Cold treatment for 3hrs(biological repeat 3-technical repeat 2)


title: CS6_H011


title: CS9_H017

source_name: Cold treatment for 24hrs(biological repeat 3-technical repeat 1)


title: CR4_H007

source_name: Cold treatment for 3hrs(biological repeat 1-technical repeat 1)


title: CS5_H010

source_name: Cold treatment for 3hrs(biological repeat 2-technical repeat 2)


title: CS12_H024

source_name: Recovery for 24hrs after cold treatment for 24hrs(biological repeat 3-technical repeat 2)


title: CS3_H006

source_name: Control(biological repeat 3-technical repeat 2)


title: CS4_H008

source_name: Cold treatment for 3hrs(biological repeat 1-technical repeat 2)


title: CS3_H005

source_name: Control(biological repeat 3-technical repeat 1)


title: CS5_H009

source_name: Cold treatment for 3hrs(biological repeat 2-technical repeat 1)


title: CS1_H001

source_name: Control(biological repeat 1-technical repeat 1)


title: CS2_H004

source_name: Control(biological repeat 2-technical repeat 2)


title: CS12_H023

source_name: Recovery for 24hrs after cold treatment for 24hrs(biological repeat 3-technical repeat 1)


title: CS2_H003

source_name: Control(biological repeat 2-technical repeat 1)


title: CS8_H016

source_name: Cold treatment for 24hrs(biological repeat 2-technical repeat 2)


title: CS4_H007


title: CS1_H002

source_name: Control(biological repeat 1-technical repeat 2)


title: 6 h SL WT 2

status: Public on Jul 31 2014

city: Umeå

first: Simon

middle: R.

last: Law

state: Västerbotten

address: Umeå University

country: Sweden

institute: Umeå Plant Science Centre

description: Gene expression data from seed during stratification

hyb_protocol: Following fragmentation, 12.5 µg of the labelled aRNA was hybridised rotating at 60 rpm, 16 hr at 45 °C on GeneChip ATH1 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned individually using a GeneChip Scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. Additionally, GC RMA normalisation was carried out using Partek Genomics Suite.

organism: Arabidopsis thaliana

source_name: Col-0 seed germinating in continuous light (SL)

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

growth_protocol: 80 mg of Col-0 and Attim17-1 Arabidopsis thaliana seeds were surface steralized and plated on MS media. Stratification was carried out at 4 °C in darkness, light conditions were 100 µE m -2 sec-1 at 22 °C.

extract_protocol: RNA isolation was carried out using the Sigma-Aldrich® Spectrum™ Plant Total RNA Kit.

treatment_protocol: Dry seed was collected 14 days after collection from the maternal plant (0 h), after 48 h of stratification and after 6 and 24 h in continuous light.

tag: time

value: 6 h

tag: genotype

value: wild type

value: seed

tag: genetic background


title: 24 h SL Attim 17-1 1

description: Gene expression data from germinating seed

source_name: Attim17-1 seed germinating in continuous light (SL)


title: 6 h SL Attim 17-1 1


title: 24 h SL Attim 17-1 2


title: 6 h SL Attim 17-1 2


title: 24 h SL Attim 17-1 3


title: 6 h SL WT 3


title: 6 h SL Attim 17-1 3


title: 24 h SL WT 1


title: 48 h S Attim 17-1 2

source_name: Attim17-1 seed during stratification (S)


title: 48 h S WT 3

source_name: Col-0 seed during stratification (S)


title: 48 h S Attim 17-1 1


title: 0 h WT 3

description: Gene expression data from freshly harvested seed

source_name: Col-0 dry seed (0 h)

value: 0 h


title: 0 h WT 1


title: 0 h Attim 17-1 3

description: Gene expression data from dry seed

source_name: Attim17-1 dry seed (0 h)


title: 24 h SL WT 3


title: 24 h SL WT 2


title: 48 h S WT 1


title: 6 h SL WT 1


title: 0 h Attim 17-1 1

description: Gene expression data from dry seed


title: 48 h S Attim 17-1 3


title: 0 h Attim 17-1 2

description: Gene expression data from dry seed


title: 48 h S WT 2


title: 0 h WT 2


title: 27 1h unlabelled rep2

status: Public on Dec 07 2013

city: Exeter

first: Steven

last: Penfield

address: Stocker Raod

department: Biosciences

institute: University or Exeter

description: 1.5mM 4SU added at 0h

hyb_protocol: GeneChip® Hybridization, Wash, and Stain Kit standard protocol

scan_protocol: GeneChip® Scanner 3000, ACOS

data_processing: MAS 5.0

label: biotin

source_name: 10 day old seedlings

label_protocol: Affymetrix GeneChip IVT labelling kit

growth_protocol: Plants were germinated at 22°C  for three days, grown at the experimental temperature for 7 days on 0.9% MS agar plates in 12 hour white light 12 hour dark cycles. Plants were floated on MS medium 12 hours before the expeimental start time (time 0h).

extract_protocol: RNA was extracted uding Qiagen Plant Rneasy mini kit

treatment_protocol: 1.5mM 4SU was added to indicated samples at time 0h.

value: whole seedlings floating on MS medium

tag: experimental temperature

tag: treatment

value: 1.5mM 4SU added at 0h


title: 27 1h unlabelled rep3

description: 1.5mM 4SU added at 0h


title: Caco-2 S1400-2

source_name: 2 h with 1x10E8 S. enteritidis strain S1400


title: 27 1h labelled rep3

description: 1.5mM 4SU added at 0h


title: 27 1h unlabelled rep1

description: 1.5mM 4SU added at 0h


title: 27 0h total rep3


title: 27 1h total rep3

description: 1.5mM 4SU added at 0h


title: 27 0h total rep2


title: 27 1h total rep2

description: 1.5mM 4SU added at 0h


title: 27 1h labelled rep1

description: 1.5mM 4SU added at 0h


title: 17 2h total rep2

description: 1.5mM 4SU added at 0h


title: 17 2h unlabelled rep2

description: 1.5mM 4SU added at 0h


title: 27 1h labelled rep2

description: 1.5mM 4SU added at 0h


title: 27 0h total rep1


title: 27 1h total rep1

description: 1.5mM 4SU added at 0h


title: T3395A

status: Public on Jan 01 2014

city: Tampa

first: Dung-Tsa

last: Chen

state: FL

address: 12902 Magnolia Drive

department: Biostatistics and Bioinformatics

country: USA

institute: Moffitt Cancer Center

description: frozen colon tissue

hyb_protocol: Hybridization was carried out according to the standard Affymetrix protocol

scan_protocol: According to the Affymetrix standard protocol. (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array)

data_processing: Expression values were calculated using the robust multi-array average (RMA) algorithm using R software.

source_name: frozen colon tissue

label_protocol: Labeling was done according to the standard Affymetrix protocol

extract_protocol: RNA was extracted using the Qiagen RNeasy kit.

tag: corresponding to gse17536

tag: gender

value: FEMALE

tag: t stage

tag: n stage

value: X

tag: m stage (0

value: no; 1:metastasis):X

tag: histologic grade

value: POORLY DIFF

tag: ajcc staging

value: Stage 2

tag: adjuvant chemo

value: N

tag: preoperative chemo

tag: overall survival (os)

tag: os event

value: alive

tag: disease-free survival time (dfs)

tag: dfs event

value: no recurrence


title: 17 2h unlabelled rep3

description: 1.5mM 4SU added at 0h

tag: tissue

tag: time


title: 17 2h labelled rep1

description: 1.5mM 4SU added at 0h

tag: experimental temperature


title: 17 0h total rep2


title: 17 2h unlabelled rep1

description: 1.5mM 4SU added at 0h

tag: treatment


title: 17 0h total rep3


title: 17 2h total rep1

description: 1.5mM 4SU added at 0h


title: 17 2h total rep3

description: 1.5mM 4SU added at 0h


title: 17 0h total rep1


title: 17 2h labelled rep3

description: 1.5mM 4SU added at 0h


title: BLM+INA_rep3

status: Public on Nov 14 2013

city: Durham

first: Shunping

last: Yan

state: North Carolina

address: 127 Science Dr.

institute: Duke University

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 default analysis settings

source_name: seedling

label_protocol: RNA probes were labelled using MessageAmp Premier RNA Amplification Kit (Ambion).

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

extract_protocol: Total RNA was isolated  using  RNeasy Mini Kit (Qiagen)

treatment_protocol: Seedlings were treated with 4 μg/ml BLM and/or low INA (10 μM)

value: seedling

tag: genotype

value: WT

value: BLM and INA


title: BLM_rep3

value: BLM


title: BLM+INA_rep2


title: BLM+INA_rep1


title: BLM_rep1


title: CK_rep3


title: INA_rep2

value: INA


title: INA_rep1


title: INA_rep3


title: BLM_rep2


title: CK_rep2


title: CK_rep1


title: Arabidopsis root 100 µM boron rep1_MH176

status: Public on Nov 13 2013

city: Bunkyo-ku

first: Mayuki

last: Tanaka

state: Tokyo

address: 1-1-1 Yaoyoi

department: Graduate School of Agricultural and Life Sciences

country: Japan

institute: The University of Tokyo

description: gene expression data from root treated with 100 µM boric acid for 2 days

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

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

source_name: Arabidopsis root in 100 µM boron treatment for 2 days (nip5;1 and bor1double mutant)

extract_protocol: Total RNA was extracted from the cells by using RNeasy Plant Mini kit (Qiagen)

treatment_protocol: Plants were grown on solid medium containing 100 µM boron for 10 days and then transferred to 0.3 and 100 µM boric acid for 2 days.

tag: ecotype

tag: genotype/variation

value: nip5;1 and bor1 double mutant

tag: phenotype

value: Inhibition of root and shoot that is similar to nip5;1-1 single mutant under limiting boron conditions.

value: 100 µM boric acid

tag: age

value: 12 days old

value: root


title: Arabidopsis root 0.3 µM boron rep1_MH171

description: gene expression data from root treated with 0.3 µM boric acid for 2 days

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

source_name: Arabidopsis root in 0.3 µM boron treatment for 2 days (nip5;1 and nip6;1double mutant)

value: nip5;1 and nip6;1 double mutant

value: 0.3 µM boric acid


title: Arabidopsis root 0.3 µM boron rep1_MH166

source_name: Arabidopsis root in 0.3 µM boron treatment for 2 days (nip5;1single mutant)

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

value: nip5;1 single mutant

value: Inhibition of root, shoot, flowers and siliques growth when boron was supplied at concentrations of less than10 microM.


title: Arabidopsis root 100 µM boron rep1_MH175

source_name: Arabidopsis root in 100 µM boron treatment for 2 days (bor2single mutant)

value: bor2 single mutant

value: Requires a high level of B. When the B concentration in the medium was reduced to 3 microM, the root length was severely affected in bor2-1 but not in wild-type plants.


title: Arabidopsis root 100 µM boron rep1_MH174

source_name: Arabidopsis root in 100 µM boron treatment for 2 days (bor1single mutant)

value: bor1 single mutant

value: Requires a high level of B. When the B concentration in the medium was reduced to 3 microM, the expansion of rosette leaves was severely affected in bor1-1 but not in wild-type plants.


title: Arabidopsis root 0.3 µM boron rep1_MH169

source_name: Arabidopsis root in 0.3 µM boron treatment for 2 days (nip5;1 and bor1double mutant)


title: Arabidopsis root 0.3 µM boron rep1_MH170

source_name: Arabidopsis root in 0.3 µM boron treatment for 2 days (nip5;1 and bor2 double mutant)

value: nip5;1 and bor2 double mutant


title: Arabidopsis root 100 µM boron rep1_MH177

source_name: Arabidopsis root in 100 µM boron treatment for 2 days (nip5;1 and bor2 double mutant)


title: Arabidopsis root 0.3 µM boron rep1_MH165

source_name: Arabidopsis root in 0.3 µM boron treatment for 2 days (Col-0)

value: wild-type


title: Arabidopsis root 100 µM boron rep1_MH173

source_name: Arabidopsis root in 100 µM boron treatment for 2 days (nip5;1single mutant)


title: Arabidopsis root 100 µM boron rep1_MH172

source_name: Arabidopsis root in 100 µM boron treatment for 2 days (Col-0)


title: Arabidopsis root 100 µM boron rep1_MH178

source_name: Arabidopsis root in 100 µM boron treatment for 2 days (nip5;1 and nip6;1double mutant)


title: Arabidopsis root 0.3 µM boron rep1_MH168

source_name: Arabidopsis root in 0.3 µM boron treatment for 2 days (bor2 single mutant)


title: Arabidopsis root 0.3 µM boron rep1_MH167

source_name: Arabidopsis root in 0.3 µM boron treatment for 2 days (bor1single mutant)


title: Wild type (Col-0) inflorescence, drought-treated, day 3, replicate 2

status: Public on Nov 06 2013

city: University Park

first: Zhao

last: SU

state: PA

address: 354 N. Frear

department: Biology

institute: The Penn State University

description: Gene expression data from Arabidopsis unopen flower buds sampled 3 days later from drought-treated plant

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: The data were analyzed by using robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) with the R/Bioconductor package affy. and then converted to logarithm base 2.

source_name: Arabidopsis inflorescence sampled 3 days later from drought-treated plant

label_protocol: Standard Affymetrix protocol.

growth_protocol: Seeds were directly sown into pots containing 100g soil mixture of Metro-Mix 360 soil (Sun Gro Horticulture Canada Ltd) and Turface profile greens grade (Profile Products LLC) in 3:2 ratio by volume, with a maximum water-holding capacity of 100g (defined as 100% soil moisture). Seeds were stratified in a cold room for 2 d at 4 ℃ in the dark. After stratification, the pots with seeds were transferred into a Conviron growth chamber (Conviron Inc), which was set at our normal conditions (22 ℃, 16h day/8h night photoperied, ~300 μmol m-2 s-1 photon flux, 60% humidity) until just after flowering (bolting) when some of the plants were subjected to drought stress.

extract_protocol: Total RNA was isolated from unopened flower buds using RNeasy columns following instructions from the manufacturer (Qiagen, Valencia, CA, USA).

treatment_protocol: Arabidopsis were well-watered until after just bolting (after 24 days growth with the main stem about 1 cm high) when drought treatment was started by withholding water (defined as day 0 for drought treatment). The relative soil moisture content decreased sharply and, after about 80 hours (defined as day 3 for drought treatment), the relative soil moisture content was near 35% of the soil water-holding capacity. The soil water condition was maintained by daily watering until almost all the fruits were mature and ready to harvest (about 50 days). For well-watered (control) plants, 90% of the soil water-holding capacity was maintained until tissue harvest or after seed maturation (pots were weighed and watered twice per day). Unopened flower samples were collected, from both treated and control plants, at day 0, 3, 4, 5, 10.

value: Unopen flower buds

value: Arabidopsis at day 28 after seed germination

tag: sample date

value: 3 days later

tag: stress

value: drought-treated


title: Wild type (Col-0) inflorescence, drought-treated, day 10, replicate 3

description: Gene expression data from Arabidopsis unopen flower buds sampled 10 days later from drought-treated plant

source_name: Arabidopsis inflorescence sampled 10 days later from drought-treated plant

value: Arabidopsis at day 34 after seed germination

value: 10 days later


title: Wild type (Col-0) inflorescence, well-watered, day 4, replicate 2

description: Gene expression data from Arabidopsis unopen flower buds sampled 4 days later from well-watered plant

source_name: Arabidopsis inflorescence sampled 4 days later from well-watered plant

value: Arabidopsis at day 29 after seed germination

value: 4 days later

value: well-watered


title: Wild type (Col-0) inflorescence, well-watered, day 0, replicate 2

description: Gene expression data from Arabidopsis unopen flower buds sampled from well-watered control

source_name: Arabidopsis inflorescence sampled from well-watered control

value: Arabidopsis at day 24 after seed germination


title: Wild type (Col-0) inflorescence, well-watered, day 5, replicate 1

description: Gene expression data from Arabidopsis unopen flower buds sampled 5 days later from well-watered plant

source_name: Arabidopsis inflorescence sampled 5 days later from well-watered plant

value: Arabidopsis at day 30 after seed germination

value: 5 days later


title: Wild type (Col-0) inflorescence, drought-treated, day 3, replicate 1


title: Wild type (Col-0) inflorescence, drought-treated, day 10, replicate 2


title: Wild type (Col-0) inflorescence, well-watered, day 0, replicate 1


title: Wild type (Col-0) inflorescence, well-watered, day 4, replicate 1


title: Wild type (Col-0) inflorescence, well-watered, day 10, replicate 3

description: Gene expression data from Arabidopsis unopen flower buds sampled 10 days later from well-watered plant

source_name: Arabidopsis inflorescence sampled 10 days later from well-watered plant


title: Wild type (Col-0) inflorescence, well-watered, day 3, replicate 2

description: Gene expression data from Arabidopsis unopen flower buds sampled 3 days later from well-watered plant

source_name: Arabidopsis inflorescence sampled 3 days later from well-watered plant


title: Wild type (Col-0) inflorescence, well-watered, day 10, replicate 2


title: Wild type (Col-0) inflorescence, well-watered, day 3, replicate 1


title: Ambient_CO2_AMPLE_N_DAY_Rep3

status: Public on Oct 15 2013

city: Urbana

first: Robert

middle: John Cody

last: Markelz

state: IL

address: 1206 W Gregory Dr

department: Plant Biology

institute: University of Illinois

description: Ambient CO2, Ample nitrogen (N) availability, Midday timepoint, replicate 3

hyb_protocol: Labeling was performed by the Keck Center University of Illinois Urbana-Champaign Following manufacturers protocols using the 3' IVT Express Kit User Manual

scan_protocol: Wash and Scanning were performed by the Keck Center University of Illinois Urbana-Champaign Following manufacturers protocols using the Expression Wash, Stain, Scan User Manual for Cartridge Arrays Manual on an Affymetrix model 3000 scanner

data_processing: The data were analyzed using JMP Genomics Version 5.1 (SAS Institute, Inc., Cary NC, USA) using the Basic Expression Workflow Option with the median intensity normalization method option. Probesets not called present in at least 3 biological replicates for each treatment combination were considered insufficiently replicated and were dropped,  leaving 12826 remaining for the analysis.

growth_protocol: Arabidopsis thaliana (Col) seeds were surface sterilized with 70% ethanol solution for 2 minutes and a 15% Clorox solution for 15 minutes with occasional shaking. Clorox was removed by and seeds were rinsed 5 times in sterile DI water. Seeds were plated on sterilized 0.5% gellan gum containing 0.5x MS and 0.3% sucrose (pH 5.7) in a sterile hood where the plates were wrapped in aluminum foil and stored at 4 °C for 48 hours to synchronize emergence. Plates were removed from foil and placed in growth chambers vertically to allow for downward root growth. 5 days after emergence, seedlings were transplanted to 514 cm3 pots containing LC1 sunshine mixed homogeneously with 20% v/v of small grain vermiculite. Conviron (company name) growth chamber conditions were 10/14 hour day/night cycle with 21 °C/18 °C temperatures, 70% RH, and 250 µmol m-2/s-1 for PPFD levels.

extract_protocol: Youngest most fully expanded leaves were excised at midday and midnight on day 35, wrapped in aluminum foil, immediately plunged into liquid N, and stored at -80°C until total RNA was isolated using a Spectra Plant RNA Isolation Kit (Sigma) following manufacturers instructions

treatment_protocol: Pots were watered passively by adding 1L of 40% Long Ashton solution per tray once per week until week 4 when trays were watered every five days. NH4+ and NO3- concentrations were varied in the Long Ashton solution to establish the N treatments as limiting (0.25 mM NH4NO3) and ample (6 mM NH4NO3). CO2 concentration was precisely maintained at either 370 ppm (ambient) or 750 ppm (elevated) by retrofitting the chambers with CO2 source/scrub capabilities. With the exception of final biomass, which involved all aboveground tissue, the following analyses were preformed on the youngest most fully expanded leaves 35 days after germination.

value: Youngest Most Fully Expanded Leaf

value: 35 Days after germination


title: Ambient_CO2_LIMITING_N_DAY_Rep3

description: Ambient CO2, Limiting nitrogen (N) availability, Midday timepoint, replicate 3

label_protocol: Labeling was performed by the Keck Center University of Illinois Urbana-Champaign Following manufacturers protocols using the 3' IVT Express Kit User Manual


title: Elevated_CO2_LIMITING_N_DAY_Rep4

description: Elevated CO2, Limiting nitrogen (N) availability, Midday timepoint, replicate 4


title: Elevated_CO2_AMPLE_N_DAY_Rep3

description: Elevated CO2, Ample nitrogen (N) availability, Midday timepoint, replicate 3


title: Ambient_CO2_LIMITING_N_DAY_Rep4

description: Ambient CO2, Limiting nitrogen (N) availability, Midday timepoint, replicate 4


title: Ambient_CO2_LIMITING_N_DAY_Rep2

description: Ambient CO2, Limiting nitrogen (N) availability, Midday timepoint, replicate 2


title: Ambient_CO2_AMPLE_N_DAY_Rep4

description: Ambient CO2, Ample nitrogen (N) availability, Midday timepoint, replicate 4


title: Elevated_CO2_LIMITING_N_DAY_Rep2

description: Elevated CO2, Limiting nitrogen (N) availability, Midday timepoint, replicate 2


title: Elevated_CO2_AMPLE_N_DAY_Rep2

description: Elevated CO2, Ample nitrogen (N) availability, Midday timepoint, replicate 2


title: Ambient_CO2_AMPLE_N_DAY_Rep2

description: Ambient CO2, Ample nitrogen (N) availability, Midday timepoint, replicate 2


title: Elevated_CO2_LIMITING_N_DAY_Rep3

description: Elevated CO2, Limiting nitrogen (N) availability, Midday timepoint, replicate 3


title: Elevated_CO2_LIMITING_N_DAY_Rep1

description: Elevated CO2, Limiting nitrogen (N) availability, Midday timepoint, replicate 1


title: Ambient_CO2_AMPLE_N_DAY_Rep1

description: Ambient CO2, Ample nitrogen (N) availability, Midday timepoint, replicate 1


title: Elevated_CO2_AMPLE_N_NIGHT_Rep3

description: Elevated CO2, Ample nitrogen (N) availability, Midnight timepoint, replicate 3


title: Elevated_CO2_AMPLE_N_DAY_Rep1

description: Elevated CO2, Ample nitrogen (N) availability, Midday timepoint, replicate 1


title: Ambient_CO2_LIMITING_N_DAY_Rep1

description: Ambient CO2, Limiting nitrogen (N) availability, Midday timepoint, replicate 1


title: Ambient_CO2_AMPLE_N_NIGHT_Rep4

description: Ambient CO2, Ample nitrogen (N) availability, Midnight timepoint, replicate 4


title: Ambient_CO2_AMPLE_N_NIGHT_Rep3

description: Ambient CO2, Ample nitrogen (N) availability, Midnight timepoint, replicate 3


title: Ambient_CO2_LIMITING_N_NIGHT_Rep2

description: Ambient CO2, Limiting nitrogen (N) availability, Midnight timepoint, replicate 2


title: Elevated_CO2_AMPLE_N_NIGHT_Rep1

description: Elevated CO2, Ample nitrogen (N) availability, Midnight timepoint, replicate 1


title: Elevated_CO2_LIMITING_N_NIGHT_Rep4

description: Elevated CO2, Limiting nitrogen (N) availability, Midnight timepoint, replicate 4


title: Ambient_CO2_LIMITING_N_NIGHT_Rep3

description: Ambient CO2, Limiting nitrogen (N) availability, Midnight timepoint, replicate 3


title: Elevated_CO2_LIMITING_N_NIGHT_Rep3

description: Elevated CO2, Limiting nitrogen (N) availability, Midnight timepoint, replicate 3


title: Ambient_CO2_AMPLE_N_NIGHT_Rep2

description: Ambient CO2, Ample nitrogen (N) availability, Midnight timepoint, replicate 2


title: Elevated_CO2_AMPLE_N_NIGHT_Rep2

description: Elevated CO2, Ample nitrogen (N) availability, Midnight timepoint, replicate 2


title: Ambient_CO2_LIMITING_N_NIGHT_Rep4

description: Ambient CO2, Limiting nitrogen (N) availability, Midnight timepoint, replicate 4


title: Ambient_CO2_AMPLE_N_NIGHT_Rep1

description: Ambient CO2, Ample nitrogen (N) availability, Midnight timepoint, replicate 1


title: Elevated_CO2_AMPLE_N_NIGHT_Rep4

description: Elevated CO2, Ample nitrogen (N) availability, Midnight timepoint, replicate 4


title: Elevated_CO2_AMPLE_N_NIGHT_Rep5

description: Elevated CO2, Ample nitrogen (N) availability, Midnight timepoint, replicate 5


title: Ambient_CO2_AMPLE_N_NIGHT_Rep5

description: Ambient CO2, Ample nitrogen (N) availability, Midnight timepoint, replicate 5


title: Ambient_CO2_LIMITING_N_NIGHT_Rep1

description: Ambient CO2, Limiting nitrogen (N) availability, Midnight timepoint, replicate 1


title: Elevated_CO2_LIMITING_N_NIGHT_Rep1

description: Elevated CO2, Limiting nitrogen (N) availability, Midnight timepoint, replicate 1


title: Elevated_CO2_LIMITING_N_NIGHT_Rep2

description: Elevated CO2, Limiting nitrogen (N) availability, Midnight timepoint, replicate 2


title: WOX1-2_3

status: Public on Sep 27 2013

city: Yokohama

first: Ryo

last: Nakabayashi

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

institute: RIKEN CSRS

hyb_protocol: Affymetrix ATH1 GeneChip (24K) was conducted according to the manufacturer’s instructions.

data_processing: R package in Bioconductor (http://www.bioconductor.org/) was used for normalization (MAS5) of the CELL files.

source_name: aerial parts of 3-week old plants

growth_protocol: Sterilized seeds were kept for 2 days at 4°C in the dark and were sown on plates of growth medium (GM) agar containing 1% sucrose. All plates were set in a growth chamber at 22°C and relative humidity (approximately 60%) under a 16 h light (approximately 40 mols−1m−2)/8 h dark cycle. The drought stress experiment was conducted at 21°C and 40% ± 5% relative humidity under 16 h/8 h light/dark conditions in a plant growth room. Harvested plant samples were immediately frozen in liquid nitrogen and stored at −80°C until use.

value: crossing of MYB12OX and pap1-D (homogygous)

value: aerial part

value: 3-week old plants


title: pap1-D/tt4_1

scan_protocol: Affymetrix ATH1 GeneChip (24K) was conducted according to the manufacturer’s instructions.

value: crossing of pap1-D and tt4 (homogygous)


title: tt4_2

label_protocol: Affymetrix ATH1 GeneChip (24K) was conducted according to the manufacturer’s instructions.

value: CHS mutant (Col-0 background)


title: WOX1-2_2

extract_protocol: Affymetrix ATH1 GeneChip (24K) was conducted according to the manufacturer’s instructions.


title: pap1-D/tt4_2


title: pap1-D/tt4_3


title: MYB12OX/tt4_3

value: crossing of MYB12OX and tt4 (homogygous)


title: WOX1-1_3


title: tt4_3


title: MYB12OX/tt4_2


title: WOX1-1_2


title: WOX1-2_1


title: pap1-D_2

value: MYB75/PAP1 overexpressor (Col-0 background, homogygous)


title: MYB12OX_2

value: MYB12 overexpressor (Col-0 background, homogygous)


title: MYB12OX/tt4_1


title: Col-0_2

value: Col-0 (wild-type)


title: MYB12OX_3


title: WOX1-1_1


title: pap1-D_3


title: Col-0_3


title: tt4_1


title: pap1-D_1


title: MYB12OX_1


title: Col-0_1


title: Leafminer damaged A.thaliana seedlings rep3

status: Public on Sep 24 2013

city: Beijing

first: Sufang

last: Zhang

address: No.2 Dong Xiao Fu, Wan Shou Shan, Haidian District

country: China

institute: Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry

description:
Arabidopsis-L-3
Gene expression data from leafminer directly damaged Arabidopsis leaves

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome 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 with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: leafminer damaged A.thaliana seedling

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 surface-sterilized for 15 min in 10% bleach, washed five times with sterile water, and plated on half-strength Murashige and Skoog medium. Plants were stratified at 4C for 2 days in darkness and then transferred to an environmental chamber set at 22C with a 16-h-light/8-h-dark cycle (light intensity 120 mmol m-2 s-1).  After 2 to 3 weeks, seedlings were also potted in a mixed potting medium of peat and vermiculite (1:2), and placed in a growth room at 22C with a 16-h-light/8-h-dark cycle (light intensity 120 mmol m-2 s-1).

extract_protocol: Total RNAs were isolated using the RNeasy Plant Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer's instructions.

treatment_protocol: A. thaliana plants were frozen in liquid nitrogen. Each sample contained tissues from at least 8 plants

tag: genotype/ecotype

value: leaves

value: 4-week old


title: Leafminer damaged A.thaliana seedlings rep2

description:
Arabidopsis-L-2
Gene expression data from leafminer directly damaged Arabidopsis leaves


title: Healthy A.thaliana seedlings rep2

description:
Arabidopsis-H-2
Gene expression data from control healthy Arabidopsis leaves

source_name: healthy A.thaliana seedling


title: Healthy A.thaliana seedlings rep3

description:
Arabidopsis-H-3
Gene expression data from control healthy Arabidopsis leaves


title: Healthy A.thaliana seedlings rep1

description:
Arabidopsis-H-1
Gene expression data from control healthy Arabidopsis leaves


title: Leafminer damaged A.thaliana seedlings rep1

description:
Arabidopsis-L-1
Gene expression data from leafminer directly damaged Arabidopsis leaves


title: A.thaliana seedlings treated by volatiles from leafminer damaged Lima bean plants for 48h rep3

description:
Arabidopsis-LH-48h-3
Gene expression data from leaves treated by volatiles from leafminer damaged lima bean for 48h


title: A.thaliana seedlings treated by volatiles from leafminer damaged Lima bean plants for 48h rep1

description:
Arabidopsis-LH-48h-1
Gene expression data from leaves treated by volatiles from leafminer damaged lima bean for 48h


title: A.thaliana seedlings treated by volatiles from leafminer damaged Lima bean plants for 24h rep2

description:
Arabidopsis-LH-24h-2
Gene expression data from leaves treated by volatiles from leafminer damaged lima bean for 24h


title: A.thaliana seedlings treated by volatiles from leafminer damaged Lima bean plants for 48h rep2

description:
Arabidopsis-LH-48h-2
Gene expression data from leaves treated by volatiles from leafminer damaged lima bean for 48h


title: A.thaliana seedlings treated by volatiles from healthy Lima bean plants for 24h rep2

description:
Arabidopsis-HH-24h-2
Gene expression data from leaves treated by volatiles from healthy lima bean for 24h, control

source_name: A.thaliana seedling_priming control_24h


title: A.thaliana seedlings treated by volatiles from leafminer damaged Lima bean plants for 24h rep1

description:
Arabidopsis-LH-24h-1
Gene expression data from leaves treated by volatiles from leafminer damaged lima bean for 24h


title: A.thaliana seedlings treated by volatiles from healthy Lima bean plants for 48h rep1

description:
Arabidopsis-HH-48h-1
Gene expression data from leaves treated by volatiles from healthy lima bean for 48h, control

source_name: A.thaliana seedling_priming control_48h


title: A.thaliana seedlings treated by volatiles from healthy Lima bean plants for 48h rep3

description:
Arabidopsis-HH-48h-3
Gene expression data from leaves treated by volatiles from healthy lima bean for 48h, control


title: A.thaliana seedlings treated by volatiles from healthy Lima bean plants for 48h rep2

description:
Arabidopsis-HH-48h-2
Gene expression data from leaves treated by volatiles from healthy lima bean for 48h, control


title: GRX-overexpression seedlings, MV treatment, rep2

status: Public on Sep 23 2013

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

description: Gene expression data from MV-treated GRX overexpression Arabidopsis seedlings

hyb_protocol: Following fragmentation, 10 microgram of cRNA were hybridized for 16 h at 45 degree C on the rice Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChip were scanned using Affymetrix scanner

data_processing: CEL files wer imported into Genespring software and probe summarization and normalization was performed using RMA algorithm

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

growth_protocol: Wild-type and transgenic Arabidopsis seedlings were grown on MS medium for 14-days in a culture room with a daily photoperiodic cycle of 16h light and 8h dark

extract_protocol: Total RNA was extracted using TRI reagent according to the manufacturer's instructions

treatment_protocol: Seedlings were incubated in water (control) or 100 µM solution of indole-3-acetic acid (auxin, IAA), 200 mM sodium chloride (salt, NaCl) and 25 µM solution of methyl viologen (MV)for 3h

value: GRX-overexpression

tag: agent

value: MV

value: Columbia

value: Seedlings

tag: Stage


title: Wild-type seedlings, MV treatment, rep1

description: Gene expression data from MV-treated wild-type Arabidopsis seedlings

source_name: Wild-type seedlings, MV treatment, rep1

value: Wild-type


title: GRX-overexpression seedlings, IAA treatment, rep1

description: Gene expression data from IAA-treated GRX overexpression Arabidopsis seedlings

value: IAA


title: Wild-type seedlings, NaCl treatment, rep2

description: Gene expression data from NaCl-treated wild-type Arabidopsis seedlings

value: NaCl


title: GRX-overexpression seedlings, control, rep2

description: Gene expression data from control GRX overexpression Arabidopsis seedlings

value: control


title: GRX-overexpression seedlings, MV treatment, rep1


title: Wild-type seedlings, IAA treatment, rep1

description: Gene expression data from IAA-treated wild-type Arabidopsis seedlings


title: Wild-type seedlings, NaCl treatment, rep1


title: Wild-type seedlings, control, rep1

description: Gene expression data from control wild-type Arabidopsis seedlings

source_name: Wild-type seedlings, control, rep1


title: A.thaliana seedlings treated by volatiles from healthy Lima bean plants for 24h rep1

description:
Arabidopsis-HH-24h-1
Gene expression data from leaves treated by volatiles from healthy lima bean for 24h, control


title: dde2-2 at 24 hpi with A. brassicicola, biological rep 3

status: Public on Sep 03 2013

city: Saint Paul

first: Jane

last: Glazebrook

state: MN

address: 1500 Gortner Avenue

institute: University of Minnesota

hyb_protocol: Biotin Labelled cRNA using Affymetrix GeneChip Hybridization, Wash and Stain Kit, according to guidelines set out by Affymetrix, Santa Clara, CA

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

data_processing: Col-0.24R3 (Col-0 at 24 hpi with A. brassicicola, biological rep 3) was removed from data processing because the data did not pass a QC based on affyPML of Bioconducter. The data from the remaining .CEL files were processed using gcrma of Bioconductor (v.2.32.0), using the default parameters.

source_name: dde2-2 at 24 hpi with A. brassicicola

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

growth_protocol: Arabidopsis plants were grown at 22°C with relative humidity of 75% with a 12h-light/12h-dark cycle (dawn at 8 am and dusk at 8 pm). The 3rd to 5th true leaves of 3-week old plants were used. The A. brassicicola strain ATCC96836 was grown on 1/2 x potato dextrose agar for 7 days before spores were suspended in water. The density of spore suspension was adjusted to 1xE5 spores/ml, based on the counting with a hemocytometer.

extract_protocol: Qiagen RNeasy kit protocol

treatment_protocol: 10 ul droplet of the spore suspension was placed on adaxial side of each leaf. The inoculated plants were placed in relative humidity of 100% for the course of the experiment. Inoculation was performed at 10 am.

value: 3-week old plants

value: 3rd-5th true leaves

tag: inoculant

value: A. brassicicola

tag: hpi

value: 24 hpi


title: GRX-overexpression seedlings, control, rep1


title: Wild-type seedlings, control, rep2

source_name: Wild-type seedlings, control, rep2


title: ein2-1 at 9 hpi with A. brassicicola, biological rep 3

source_name: ein2-1 at 9 hpi with A. brassicicola

value: 9 hpi


title: Col-0 at 24 hpi with mock, biological rep 3

source_name: Col-0 at 24 hpi with mock

value: wild type

value: mock


title: ein2-1 at 24 hpi with A. brassicicola, biological rep 3

source_name: ein2-1 at 24 hpi with A. brassicicola


title: sid2-2 at 9 hpi with A. brassicicola, biological rep 3

source_name: sid2-2 at 9 hpi with A. brassicicola


title: Col-0 at 9 hpi with A. brassicicola, biological rep 3

source_name: Col-0 at 9 hpi with A. brassicicola


title: Col-0 at 9 hpi with A. brassicicola, biological rep 2


title: Col-0 at 24 hpi with mock, biological rep 2


title: sid2-2 at 24 hpi with A. brassicicola, biological rep 2

source_name: sid2-2 at 24 hpi with A. brassicicola


title: ein2-1 at 9 hpi with A. brassicicola, biological rep 2


title: sid2-2 at 24 hpi with A. brassicicola, biological rep 3


title: Col-0 at 24 hpi with A. brassicicola, biological rep 2

source_name: Col-0 at 24 hpi with A. brassicicola


title: dde2-2 at 9 hpi with A. brassicicola, biological rep 2

source_name: dde2-2 at 9 hpi with A. brassicicola


title: ein2-1 at 24 hpi with A. brassicicola, biological rep 2


title: dde2-2 at 9 hpi with A. brassicicola, biological rep 3


title: Col-0 at 9 hpi with mock, biological rep 3

source_name: Col-0 at 9 hpi with mock


title: sid2-2 at 9 hpi with A. brassicicola, biological rep 2


title: dde2-2 at 24 hpi with A. brassicicola, biological rep 2


title: sid2-2 at 24 hpi with A. brassicicola, biological rep 1


title: ein2-1 at 24 hpi with A. brassicicola, biological rep 1


title: Col-0 at 9 hpi with mock, biological rep 2


title: sid2-2 at 9 hpi with A. brassicicola, biological rep 1


title: Col-0 at 24 hpi with mock, biological rep 1


title: dde2-2 at 9 hpi with A. brassicicola, biological rep 1


title: ein2-1 at 9 hpi with A. brassicicola, biological rep 1


title: Col-0 at 9 hpi with A. brassicicola, biological rep 1


title: dde2-2 at 24 hpi with A. brassicicola, biological rep 1


title: Arabidopsis, root cells, stele, 140mM NaCl for 8 hours, replicate 2

status: Public on Sep 01 2013

city: Stanford

first: Jose

middle: Ramon

last: Dinneny

state: United States

address: 260 Panama St

institute: Carnegie Institution for Science, Department of Plant Biology

description: Gene expression data from isolated stele cells after roots were treated with 140 mM NaCl for 8 hour

hyb_protocol: Arrays were washed using a GeneChip® Fluidics Station 450 and GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix), and performed in the microarray facilities located at the Biopolis Shared Facilities, Agency of Science and Technology Research, Singapore

scan_protocol: Data acquisition was on a GeneChip® Scanner (Affymetrix), and performed in the microarray facilities located at the Biopolis Shared Facilities, Agency of Science and Technology Research, Singapore

data_processing: Data quality was examined using the signal distribution of Affymetrix built-in controls (Spike-in and hybridization controls) using Expression Console software (Affymetrix) and AffyQCReport. GCRMA in R/Bioconductor was used for data normalization.

source_name: Protoplasted and FACS sorted root cells

label_protocol: Fragmented cRNA probes were prepared using the one-cycle amplification protocol by Affymetrix.

growth_protocol: Seeds were surface sterilized with 20% Bleach and 0.1% Tween for 5 minutes and then rinsed 3 times with sterile water.  Seeds were stratified at 4˚C for 2 days before being planted on standard media.  Standard media is 1X concentration Murashige and Skoog salt mixture (Caisson laboratories), 0.5g/L MES, 1% sucrose, 1% agar and adjusted to pH 5.7 with KOH.  Salt media is standard media with 140mM NaCl added.  Nylon mesh was placed on top of the solidified media and seeds were evenly placed on the mesh at a density of ~20 seeds/cm in two rows.

extract_protocol: RNA was extracted using the RNAeasy Micro Kit (Qiagen GmbH).

treatment_protocol: Samples were prepared as in Birnbaum et al. (2005) Nat. Methods for roots grown under standard conditions for 1hr and 48hrs before protoplasting.  For salt treated samples, roots were transferred to 140 mM NaCl for 1hr, 3hrs, 8hrs, 20hrs, 32hrs, and 48hrs before protoplasting.

value: Seedling roots, 5-7 days after germination

tag: gfp-reporter

tag: growth media

value: Standard media for 5 days, transferred to media supplemented with 140mM NaCl for 8 hour before protoplasting

tag: cell type

value: stele


title: Col-0 at 24 hpi with A. brassicicola, biological rep 1

tag: tissue


title: Col-0 at 9 hpi with mock, biological rep 1


title: Arabidopsis, root cells, stele, 140mM NaCl for 32 hours, replicate 3

description: Gene expression data from isolated stele cells after roots were treated with 140 mM NaCl for 32 hour

value: Standard media for 5 days, transferred to media supplemented with 140mM NaCl for 32 hour before protoplasting


title: Arabidopsis, root cells, stele, 140mM NaCl for 32 hours, replicate 2

value: Columbia


title: Arabidopsis, root cells, stele, 140mM NaCl for 8 hours, replicate 1


title: Arabidopsis, root cells, stele, 140mM NaCl for 20 hours, replicate 2

description: Gene expression data from isolated stele cells after roots were treated with 140 mM NaCl for 20 hour

value: Standard media for 5 days, transferred to media supplemented with 140mM NaCl for 20 hour before protoplasting


title: Arabidopsis, root cells, stele, 140mM NaCl for 48 hours, replicate 3

description: Gene expression data from isolated stele cells after roots were treated with 140 mM NaCl for 48 hour

value: Standard media for 5 days, transferred to media supplemented with 140mM NaCl for 48 hour before protoplasting


title: Arabidopsis, root cells, stele, 140mM NaCl for 3 hours, replicate 2

description: Gene expression data from isolated stele cells after roots were treated with 140 mM NaCl for 3 hour

value: Standard media for 5 days, transferred to media supplemented with 140mM NaCl for 3 hour before protoplasting


title: Arabidopsis, root cells, stele, 140mM NaCl for 20 hours, replicate 3


title: Arabidopsis, root cells, stele, 140mM NaCl for 3 hours, replicate 1


title: Arabidopsis, root cells, stele, 140mM NaCl for 1 hour, replicate 2

description: Gene expression data from isolated stele cells after roots were treated with 140 mM NaCl for 1 hour

value: Standard media for 5 days, transferred to media supplemented with 140mM NaCl for 1 hour before protoplasting


title: Arabidopsis, root cells, stele, 140mM NaCl for 32 hours, replicate 1


title: Arabidopsis, root cells, stele, 140mM NaCl for 8 hours, replicate 3


title: Arabidopsis, root cells, stele, 140mM NaCl for 48 hours, replicate 1


title: Arabidopsis, root cells, stele, standard conditions for 48 hours, replicate 1

description: Gene expression data from isolated stele cells

value: Standard media


title: Arabidopsis, root cells, stele, 140mM NaCl for 1 hour, replicate 1


title: Arabidopsis, root cells, stele, 140mM NaCl for 1 hour, replicate 3


title: Arabidopsis, root cells, stele, 140mM NaCl for 20 hours, replicate 1


title: Arabidopsis, root cells, stele, 140mM NaCl for 3 hours, replicate 3


title: Arabidopsis, root cells, stele, standard conditions for 48 hours, replicate 2


title: Arabidopsis, root cells, stele, standard conditions for 1 hour, replicate 3


title: Arabidopsis, root cells, stele, standard conditions for 48 hours, replicate 3


title: Arabidopsis, root cells, stele, standard conditions for 1 hour, replicate 2


title: Arabidopsis, root cells, endodermis, 140mM NaCl for 48 hours, replicate 3

description: Gene expression data from isolated endodermal cells after roots were treated with 140 mM NaCl for 48 hour

value: endodermis


title: Arabidopsis, root cells, endodermis, 140mM NaCl for 32 hours, replicate 3

description: Gene expression data from isolated endodermal cells after roots were treated with 140 mM NaCl for 32 hour


title: Arabidopsis, root cells, endodermis, 140mM NaCl for 48 hours, replicate 1


title: Arabidopsis, root cells, stele, standard conditions for 1 hour, replicate 1


title: Arabidopsis, root cells, endodermis, 140mM NaCl for 20 hours, replicate 1

description: Gene expression data from isolated endodermal cells after roots were treated with 140 mM NaCl for 20 hour


title: Arabidopsis, root cells, endodermis, 140mM NaCl for 20 hours, replicate 2


title: Arabidopsis, root cells, endodermis, 140mM NaCl for 48 hours, replicate 2


title: Arabidopsis, root cells, endodermis, 140mM NaCl for 8 hours, replicate 2

description: Gene expression data from isolated endodermal cells after roots were treated with 140 mM NaCl for 8 hour


title: Arabidopsis, root cells, endodermis, 140mM NaCl for 1 hour, replicate 2

description: Gene expression data from isolated endodermal cells after roots were treated with 140 mM NaCl for 1 hour


title: Arabidopsis, root cells, stele, 140mM NaCl for 48 hours, replicate 2


title: Arabidopsis, root cells, endodermis, standard conditions for 48 hours, replicate 2

description: Gene expression data from isolated endodermal cells


title: Arabidopsis, root cells, endodermis, standard conditions for 1 hour, replicate 1


title: Arabidopsis, root cells, endodermis, standard conditions for 48 hours, replicate 3


title: Arabidopsis, root cells, endodermis, standard conditions for 1 hour, replicate 3


title: Arabidopsis, root cells, endodermis, 140mM NaCl for 8 hours, replicate 3


title: Arabidopsis, root cells, endodermis, 140mM NaCl for 8 hours, replicate 1


title: Arabidopsis, root cells, endodermis, 140mM NaCl for 3 hours, replicate 1

description: Gene expression data from isolated endodermal cells after roots were treated with 140 mM NaCl for 3 hour


title: Arabidopsis, root cells, endodermis, standard conditions for 48 hours, replicate 1


title: Arabidopsis, root cells, endodermis, 140mM NaCl for 1 hour, replicate 3


title: Arabidopsis, root cells, cortex, 140mM NaCl for 48 hours, replicate 3

description: Gene expression data from isolated cortical cells after roots were treated with 140 mM NaCl for 48 hour

value: cortex


title: Arabidopsis, root cells, endodermis, 140mM NaCl for 3 hours, replicate 3


title: Arabidopsis, root cells, cortex, 140mM NaCl for 48 hours, replicate 2


title: Arabidopsis, root cells, endodermis, 140mM NaCl for 32 hours, replicate 1


title: Arabidopsis, root cells, endodermis, 140mM NaCl for 3 hours, replicate 2


title: Arabidopsis, root cells, endodermis, 140mM NaCl for 32 hours, replicate 2


title: Arabidopsis, root cells, cortex, 140mM NaCl for 32 hours, replicate 3

description: Gene expression data from isolated cortical cells after roots were treated with 140 mM NaCl for 32 hour


title: Arabidopsis, root cells, endodermis, 140mM NaCl for 20 hours, replicate 3


title: Arabidopsis, root cells, endodermis, standard conditions for 1 hour, replicate 2


title: Arabidopsis, root cells, endodermis, 140mM NaCl for 1 hour, replicate 1


title: Arabidopsis, root cells, cortex, 140mM NaCl for 32 hours, replicate 2


title: Arabidopsis, root cells, cortex, 140mM NaCl for 48 hours, replicate 1


title: Arabidopsis, root cells, cortex, 140mM NaCl for 20 hours, replicate 2

description: Gene expression data from isolated cortical cells after roots were treated with 140 mM NaCl for 20 hour


title: Arabidopsis, root cells, cortex, 140mM NaCl for 20 hours, replicate 3


title: Arabidopsis, root cells, cortex, 140mM NaCl for 32 hours, replicate 1


title: Arabidopsis, root cells, cortex, 140mM NaCl for 20 hours, replicate 1


title: Arabidopsis, root cells, cortex, 140mM NaCl for 8 hours, replicate 3

description: Gene expression data from isolated cortical cells after roots were treated with 140 mM NaCl for 8 hour


title: Arabidopsis, root cells, cortex, 140mM NaCl for 3 hours, replicate 3

description: Gene expression data from isolated cortical cells after roots were treated with 140 mM NaCl for 3 hour


title: Arabidopsis, root cells, cortex, 140mM NaCl for 8 hours, replicate 1


title: Arabidopsis, root cells, cortex, 140mM NaCl for 8 hours, replicate 2


title: Arabidopsis, root cells, cortex, standard conditions for 1 hour, replicate 3

description: Gene expression data from isolated cortical cells


title: Arabidopsis, root cells, cortex, 140mM NaCl for 3 hours, replicate 2


title: Arabidopsis, root cells, cortex, standard conditions for 48 hours, replicate 1


title: Arabidopsis, root cells, cortex, 140mM NaCl for 3 hours, replicate 1


title: Arabidopsis, root cells, cortex, 140mM NaCl for 1 hour, replicate 2

description: Gene expression data from isolated cortical cells after roots were treated with 140 mM NaCl for 1 hour


title: Arabidopsis, root cells, cortex, 140mM NaCl for 1 hour, replicate 1


title: Arabidopsis, root cells, epidermis, 140mM NaCl for 48 hours, replicate 1

description: Gene expression data from isolated epidermal cells after roots were treated with 140 mM NaCl for 48 hour

value: epidermis


title: Arabidopsis, root cells, epidermis, 140mM NaCl for 32 hours, replicate 3

description: Gene expression data from isolated epidermal cells after roots were treated with 140 mM NaCl for 32 hour


title: Arabidopsis, root cells, cortex, standard conditions for 48 hours, replicate 3


title: Arabidopsis, root cells, epidermis, 140mM NaCl for 20 hours, replicate 3

description: Gene expression data from isolated epidermal cells after roots were treated with 140 mM NaCl for 20 hour


title: Arabidopsis, root cells, epidermis, 140mM NaCl for 32 hours, replicate 2


title: Arabidopsis, root cells, epidermis, 140mM NaCl for 20 hours, replicate 1


title: Arabidopsis, root cells, cortex, standard conditions for 48 hours, replicate 2


title: Arabidopsis, root cells, cortex, standard conditions for 1 hour, replicate 2


title: Arabidopsis, root cells, epidermis, 140mM NaCl for 48 hours, replicate 2


title: Arabidopsis, root cells, cortex, standard conditions for 1 hour, replicate 1


title: Arabidopsis, root cells, epidermis, 140mM NaCl for 32 hours, replicate 1


title: Arabidopsis, root cells, epidermis, 140mM NaCl for 48 hours, replicate 3


title: Arabidopsis, root cells, epidermis, 140mM NaCl for 20 hours, replicate 2


title: Arabidopsis, root cells, cortex, 140mM NaCl for 1 hour, replicate 3


title: Arabidopsis, root cells, epidermis, 140mM NaCl for 8 hours, replicate 2

description: Gene expression data from isolated epidermal cells after roots were treated with 140 mM NaCl for 8 hour


title: Arabidopsis, root cells, epidermis, 140mM NaCl for 8 hours, replicate 3


title: Arabidopsis, root cells, epidermis, 140mM NaCl for 3 hours, replicate 3

description: Gene expression data from isolated epidermal cells after roots were treated with 140 mM NaCl for 3 hour


title: Arabidopsis, root cells, epidermis, 140mM NaCl for 3 hours, replicate 1


title: Arabidopsis, root cells, epidermis, 140mM NaCl for 1 hour, replicate 3

description: Gene expression data from isolated epidermal cells after roots were treated with 140 mM NaCl for 1 hour


title: Arabidopsis, root cells, epidermis, 140mM NaCl for 3 hours, replicate 2


title: Arabidopsis, root cells, epidermis, 140mM NaCl for 1 hour, replicate 2


title: Arabidopsis, root cells, epidermis, 140mM NaCl for 1 hour, replicate 1


title: Arabidopsis, root cells, epidermis, standard conditions for 48 hours, replicate 3

description: Gene expression data from isolated epidermal cells


title: Arabidopsis, root cells, epidermis, standard conditions for 48 hours, replicate 2


title: Arabidopsis, root cells, epidermis, standard conditions for 48 hours, replicate 1


title: Arabidopsis, root cells, epidermis, standard conditions for 1 hour, replicate 2


title: Arabidopsis, root cells, epidermis, standard conditions for 1 hour, replicate 3


title: Arabidopsis, root cells, epidermis, standard conditions for 1 hour, replicate 1


title: Arabidopsis, root cells, epidermis, 140mM NaCl for 8 hours, replicate 1


title: IAA 12h rep3

city: WINSTON SALEM

first: Gloria

middle: Kressin

last: Muday

address: 1834 Wake Forest Road

institute: Wake Forest University

description: 6 day old arabidopsis roots

hyb_protocol: Following fragmentation, 20 ug of labeled cRNA was hybridized for 16 hr at 45 degrees C on the Affymetrix GeneChips. GeneChips were washed and stained using the GeneChip 450 Fluidics Station according to standard Affymetrix operating procedures

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G system according to the standard Affymetrix protocol

data_processing: Raw data were normalized using systematic variation normalization, and the log2 of the signal intensity is reported.

source_name: 6 day old roots placed on auxin medium for 12 hours

label_protocol: Approximately 5ug of purified total RNA was processed to produce biotinylated cRNA targets followed by streptavidin-phycoerythrin fluorescent staining according to the standard Affymetrix 3’-IVT labeling protocol

growth_protocol: 6 days of growth in 100 umol/m2sec2 continuous cool white light on a nylon screen (03-100/32; Sefar Filtration) pressed tigghtly against 1xMS 1% sucrose media (pH 5.6)

extract_protocol: Root samples were ground in liquid nitrogen and the RNA was extracted using the Qiagen Plant RNeasy kit.  The RNA was then precipitated from the eluate with isopropanol

treatment_protocol: Nylon mesh with seedlings grown on the surface was transferred to control media or media containing 1 uM IAA at time 0

value: root


title: control 2h rep3

description: 6 day old arabidopsis roots

source_name: 6 day old roots placed on control medium for 2 hours


title: control 4h rep3

description: 6 day old arabidopsis roots

source_name: 6 day old roots placed on control medium for 4 hours


title: IAA 4h rep3

description: 6 day old arabidopsis roots

source_name: 6 day old roots placed on auxin medium for 4 hours


title: control 8h rep2

description: 6 day old arabidopsis roots

source_name: 6 day old roots placed on control medium for 8 hours


title: control 12h rep3

description: 6 day old arabidopsis roots

source_name: 6 day old roots placed on control medium for 12 hours


title: IAA 2h rep2

description: 6 day old arabidopsis roots

source_name: 6 day old roots placed on auxin medium for 2 hours


title: IAA 24h rep2

description: 6 day old arabidopsis roots

source_name: 6 day old roots placed on auxin medium for 24 hours


title: IAA 24h rep3

description: 6 day old arabidopsis roots


title: control 0.5h rep3

description: 6 day old arabidopsis roots

source_name: 6 day old roots placed on control medium for 30 minutes


title: IAA 0.5h rep2

description: 6 day old arabidopsis roots

source_name: 6 day old roots placed on auxin medium for 30 minutes


title: IAA 8h rep3

description: 6 day old arabidopsis roots

source_name: 6 day old roots placed on auxin medium for 8 hours


title: IAA 4h rep2

description: 6 day old arabidopsis roots


title: IAA 1h rep3

description: 6 day old arabidopsis roots

source_name: 6 day old roots placed on auxin medium for 1 hour


title: IAA 0.5h rep3

description: 6 day old arabidopsis roots


title: IAA 0h rep2

description: 6 day old arabidopsis roots

source_name: 6 day old roots placed on auxin medium for < 5 minutes


title: control 1h rep3

description: 6 day old arabidopsis roots

source_name: 6 day old roots placed on control medium for 1 hour


title: IAA 8h rep2

description: 6 day old arabidopsis roots


title: IAA 12h rep2

description: 6 day old arabidopsis roots


title: control 4h rep2

description: 6 day old arabidopsis roots


title: control 8h rep3

description: 6 day old arabidopsis roots


title: control 2h rep2

description: 6 day old arabidopsis roots


title: IAA 1h rep2

description: 6 day old arabidopsis roots


title: IAA 2h rep3

description: 6 day old arabidopsis roots


title: control 24h rep2

description: 6 day old arabidopsis roots

source_name: 6 day old roots placed on control medium for 24 hours


title: control 0h rep2

description: 6 day old arabidopsis roots

source_name: 6 day old roots placed on control medium for <5 minutes


title: control 24h rep3

description: 6 day old arabidopsis roots


title: control 12h rep2

description: 6 day old arabidopsis roots


title: control 0.5h rep2

description: 6 day old arabidopsis roots


title: control 1h rep2

description: 6 day old arabidopsis roots


title: IAA 0h rep1

description: 6 day old arabidopsis roots


title: IAA 4h rep1

description: 6 day old arabidopsis roots


title: IAA 8h rep1

description: 6 day old arabidopsis roots


title: control 12h rep1

description: 6 day old arabidopsis roots


title: IAA 24h rep1

description: 6 day old arabidopsis roots


title: IAA 0.5h rep1

description: 6 day old arabidopsis roots


title: control 1h rep1

description: 6 day old arabidopsis roots


title: IAA 12h rep1

description: 6 day old arabidopsis roots


title: control 8h rep1

description: 6 day old arabidopsis roots


title: control 4h rep1

description: 6 day old arabidopsis roots


title: control 0h rep1

description: 6 day old arabidopsis roots


title: control 2h rep1

description: 6 day old arabidopsis roots


title: control 0.5h rep1

description: 6 day old arabidopsis roots


title: Var2-1 roots 2hr KCl control treated, biological rep2

city: New York

first: Kenneth

middle: David

last: Birnbaum

state: NY

address: 12 Waverly Place

institute: New York University

description: 2 Var2-1 C.CEL

hyb_protocol: Following fragmentation, 8 ug of cRNA were hybridized for 16 hr at 45C on an Affymetrix ATH1 GeneChip Arabidopsis Whole Genome Array in the Affymetrix Hybridization oven 640 following standard Affymetrix protocols. GeneChips were washed and stained using the 'EukGE-WS2v4_450' protocol in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 Scanner according to standard Affymetrix protocols.

data_processing: The data were analyzed with MAS5.0 as normal for Col0 data but with a modification to the normalisation method to enable a subset of probe sequences within each probe set to be excluded for non-Col0 data.  Probe sequences (within probe sets for each gene) whose signal values were not used were those predicted using our bioinformatic analysis not to hybridise non-Col0 RNA on the Col0 Affymetrix microarray due to sequence differences in the non-Col0 ecotypes; these were excluded to give a more accurate signal value for each gene in the non-Col0 ecotypes.  The probe sequences to be excluded were identified per experiment (i.e. an experiment consisted of the three replicate samples, e.g. Kas2 control, or Kas2 treat). Lists of probe sequences within each gene probeset that were not used for normalisation are supplied in text files (one per experiment) together with a key that denotes the probe numbers given in the experiment files to the Affymetrix probe IDs. On average, 10% of all probe sets were analysed with the complete set of 11 elements and a further 70% analysed with 9 or 10 elements. For example, in Kas2C_Probe_Elements_Removed, the first row is 4,1.  4,1 refers to probe number '4'.  The key for which probe number '4' is, is in the 'key' file and it corresponds to the probe name given on row 4. The same key file is used to interpret all of the other files.  The '1' means that the first element of this probeset was excluded from analysis.  The data was analysed within replicate sets, so for replicates 1, 2, and 3 of Kas2 C the same elements were removed. The reasoning for this is that we used all replicates to identify with best accuracy which elements were not hybridising normally.

source_name: 12 day old Arabidopsis Var2-1 ecotype roots, 2 hr 5mM KCl control treated

label_protocol: Biotinylated cRNA from all isolated root samples were prepared according to the standard one-cycle Affymetrix protocol from 1 ug total RNA.

growth_protocol: Plants were grown for 12 days in long day (16hr light/8hr dark) 22 oC conditions in a Percival (Percival Scientific).  Plants were grown hydroponically in basal MS containing no nitrogen except 0.5mM ammonium succinate and 3mM sucrose.

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA) according to manufacturer's instructions.

treatment_protocol: At dawn on 12th day plants were either nitrogen-treated (KNO3 to 5mM added) or KCl treated (KCl to 5mM added) as a control treatment for 2 hrs. Whole roots were then harvested and frozen using liquid nitrogen.

value: KCl control

value: 12 day old seedling roots


title: Var2-1 roots 2hr KNO3 nitrogen treated, biological rep2

description: 2 Var2-1 T.CEL

source_name: 12 day old Arabidopsis Var2-1 ecotype roots, 2 hr 5mM KNO3 nitrogen treated

value: KNO3 nitrogen


title: TAMM27 roots 2hr KNO3 nitrogen treated, biological rep2

description: 2 TAMM27 T.CEL

source_name: 12 day old Arabidopsis TAMM27 ecotype roots, 2 hr 5mM KNO3 nitrogen treated


title: TAMM27 roots 2hr KCl control treated, biological rep2

description: 2 TAMM27 C.CEL

source_name: 12 day old Arabidopsis TAMM27 ecotype roots, 2 hr 5mM KCl control treated


title: Var2-1 roots 2hr KCl control treated, biological rep3

description: 3 Var2-1 C.CEL


title: Var2-1 roots 2hr KCl control treated, biological rep1

description: 1 Var2-1 C.CEL


title: TAMM27 roots 2hr KCl control treated, biological rep3

description: 3 TAMM27 C.CEL


title: Ts5 roots 2hr KCl control treated, biological rep2

description: 2 Ts5 C.CEL

source_name: 12 day old Arabidopsis Ts5 ecotype roots, 2 hr 5mM KCl control treated


title: Ts5 roots 2hr KCl control treated, biological rep3

description: 3 Ts5 C.CEL


title: IAA 1h rep1

description: 6 day old arabidopsis roots


title: TAMM27 roots 2hr KNO3 nitrogen treated, biological rep3

description: 3 TAMM27 T.CEL


title: SQ8 roots 2hr KNO3 nitrogen treated, biological rep2

description: 2 SQ8 T.CEL

source_name: 12 day old Arabidopsis SQ8 ecotype roots, 2 hr 5mM KNO3 nitrogen treated


title: TAMM27 roots 2hr KNO3 nitrogen treated, biological rep1

description: 1 TAMM27 T.CEL


title: control 24h rep1

description: 6 day old arabidopsis roots


title: TAMM27 roots 2hr KCl control treated, biological rep1

description: 1 TAMM27 C.CEL


title: SQ8 roots 2hr KCl control treated, biological rep1

description: 1 SQ8 C.CEL

source_name: 12 day old Arabidopsis SQ8 ecotype roots, 2 hr 5mM KCl control treated


title: Var2-1 roots 2hr KNO3 nitrogen treated, biological rep1

description: 1 Var2-1 T.CEL


title: NFA8 roots 2hr KCl control treated, biological rep3

description: 3 NFA8 C.CEL

source_name: 12 day old Arabidopsis NFA8 ecotype roots, 2 hr 5mM KCl control treated


title: NFA8 roots 2hr KCl control treated, biological rep2

description: 2 NFA8 C.CEL


title: Var2-1 roots 2hr KNO3 nitrogen treated, biological rep3

description: 3 Var2-1 T.CEL


title: NFA8 roots 2hr KNO3 nitrogen treated, biological rep1

description: 1 NFA8 T.CEL

source_name: 12 day old Arabidopsis NFA8 ecotype roots, 2 hr 5mM KNO3 nitrogen treated


title: Kas2 roots 2hr KNO3 nitrogen treated, biological rep2

description: 2 Kas2 T.CEL

source_name: 12 day old Arabidopsis Kas2 ecotype roots, 2 hr 5mM KNO3 nitrogen treated


title: Kas2 roots 2hr KNO3 nitrogen treated, biological rep1

description: 1 Kas2 T.CEL


title: Kas2 roots 2hr KNO3 nitrogen treated, biological rep3

description: 3 Kas2 T.CEL


title: SQ8 roots 2hr KCl control treated, biological rep2

description: 2 SQ8 C.CEL


title: Kas2 roots 2hr KCl control treated, biological rep3

description: 3 Kas2 C.CEL

source_name: 12 day old Arabidopsis Kas2 ecotype roots, 2 hr 5mM KCl control treated


title: SQ8 roots 2hr KCl control treated, biological rep3

description: 3 SQ8 C.CEL


title: NFA8 roots 2hr KNO3 nitrogen treated, biological rep3

description: 3 NFA8 T.CEL


title: Col0 roots 2hr KNO3 nitrogen treated, biological rep3

description: 3 Col0 T.CEL

source_name: 12 day old Arabidopsis Col0 ecotype roots, 2 hr 5mM KNO3 nitrogen treated


title: NFA8 roots 2hr KNO3 nitrogen treated, biological rep2

description: 2 NFA8 T.CEL


title: Col0 roots 2hr KNO3 nitrogen treated, biological rep2

description: 2 Col0 T.CEL


title: Kas2 roots 2hr KCl control treated, biological rep1

description: 1 Kas2 C.CEL


title: Kas2 roots 2hr KCl control treated, biological rep2

description: 2 Kas2 C.CEL


title: Col0 roots 2hr KCl control treated, biological rep3

description: 3 Col0 C.CEL

source_name: 12 day old Arabidopsis Col0 ecotype roots, 2 hr 5mM KCl control treated


title: Col0 roots 2hr KCl control treated, biological rep2

description: 2 Col0 C.CEL


title: Col0 roots 2hr KNO3 nitrogen treated, biological rep1

description: 1 Col0 T.CEL


title: Evans_2-8_35s-FAD3-cold_Rep1_ATH1

status: Public on Aug 30 2013

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

description: Growth Room 20 oC 16h on  8 h off MS 4 days in fridge after sowing

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

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

label_protocol: labelled using protocol described in manual " Affymetrix Genechip IVT kit"

extract_protocol: Qiagen RNAeasy kit protocol

tag: growth stage (source - paradigm genetics)

value: whole seedling

tag: treatment

value: cold temperature


title: Evans_2-2_col-WT-cold_Rep1_ATH1

institute: Nottingham Arabidopsis Stock Centre (NASC)

tag: genotype

value: whole seedling Stock code:N1092


title: Evans_2-3_fab1-mut-ambient_Rep1_ATH1

tag: genetic variation

value: EMS mutant

value: ambient temperature


title: Evans_2-11_FAD3-7-8-mut-aeq-ambient_Rep1_ATH1

value: single mutants created by EMS mutagenesis. Triple mutant by crossing double mutants together.


title: Evans_2-12_FAD3-7-8-mut-aeq-cold_Rep1_ATH1


title: Evans_2-1_col-WT-ambient_Rep1_ATH1


title: Evans_2-9_col-aeq-ambient_Rep1_ATH1

source_name: Col-aeq

value: Col-aeq


title: Evans_2-4_fab1-mut-cold_Rep1_ATH1


title: Evans_2-10_col-aeq-cold_Rep1_ATH1


title: Evans_2-6_fad2-mut-cold_Rep1_ATH1


title: Evans_2-7_35s-FAD3-ambient_Rep1_ATH1


title: no current injection, Rep 1

status: Public on Aug 21 2013

city: Lausanne

first: Seyed

middle: Ali Reza

last: Mousavi

state: Vaud

address: Route de Sorge

department: DBMV

country: Switzerland

institute: University of Lausanne

hyb_protocol: Affymetrix ATH1 (batch 1211501) arrays (Affymetrix, Santa Clara, CA, USA) were hybridized according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0007).

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix) and raw data was extracted from the scanned images

data_processing: Gene level normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003) împlemented in the Affymetrix Power Tools software package (Affymetrix).

source_name: leaf 8, no current injection

label_protocol: Total RNA (300ng) was amplified using the MessageAmp™ II-Biotin Enhanced Single Round aRNA Amplification Kit (AM1791, Ambion). 12.5µg of the resulting biotinlabelled cRNA was chemically fragmented.

growth_protocol: Arabidopsis thaliana accession Col-0, was soil-grown (one plant per 7 cm diameter pot) for 5 weeks with 10 h light (100 µE sec-1 m-2), 70% humidity; day 22°C, night 18°C.

extract_protocol: Total RNAs from leaves were isolated and purified with RNeasy Plant Mini Kit (Qiagene, Germany) according to the manufacturer's instructions.

treatment_protocol: These were controls for current injection experiments. Platinum wire were placed in the petiole of leaf 8 but no current was injected. The lamina was harvested for analysis.

tag: ecotype


title: current injection, Rep 1

source_name: leaf 8, current injection

treatment_protocol: Current (40 μA, 10 s) injected into the petiole of leaf 8 and the lamina was harvested 1 h later.

value: 40 microampere of electric current for 10 second


title: current injection, Rep 2


title: current injection, Rep 3


title: unwounded leaves, Rep 1

source_name: leaf 13 from unwounded plant

treatment_protocol: The plants were not wounded. These were control samples for wounding experiments.


title: leaf13, Rep1

source_name: leaf 13 when leaf 8 was wounded

treatment_protocol: 40% of the apex of leaf 8 was wounded. 1 h later leaf 13 was harvested.


title: Evans_2-5_fad2-mut-ambient_Rep1_ATH1


title: leaf13, Rep2


title: no current injection, Rep 3


title: unwounded leaves, Rep 2


title: no current injection, Rep 2


title: leaf13, Rep3


title: intact root auxin 1

status: Public on Aug 06 2013

city: La Jolla

first: Bastiaan

middle: Otto Robert

last: Bargmann

state: CA

address: 9500 Gilman Dr

institute: UCSD

hyb_protocol: The labeled cDNA was hybridized, washed and stained on an ATH-121501 Arabidopsis full genome microarray using a Hybridization Control Kit, a GeneChip Hybridization, Wash, and Stain Kit, a GeneChip Fluidics Station 450 and a GeneChip Scanner (Affymetrix).

scan_protocol: Chips were scanned using an Affymetrix GeneChip scanner

data_processing: Data was MAS5.0 normalized using FlexArray software

source_name: intact root auxin 1

label_protocol: RNA was quantified with a Bioanalyzer (Agilent Technologies) and reverse-transcribed, amplified and labeled with WT-Ovation Pico RNA Amplification System and FL-Ovation cDNA Biotin Module V2 (NuGEN).

growth_protocol: Seed from Arabidopsis plant lines (summarized in supplementary methods Table SM1) was sterilized by 5 min incubation with 96% ethanol followed by 20 min incubation with 50% household bleach and rinsing with sterile water and vernalized for 2 days at 4° C in the dark. Seedlings were grown hydroponically, on nylon mesh in phytatrays (Sigma) with growth medium (2.2 g/l Murashige and Skoog Salts [Sigma-Aldrich], 1% [w/v] sucrose, 0.5 g/l MES hydrate [Sigma-Aldrich], pH 5.7 with KOH), or plated on square petri dishes (Fisher Scientific) with growth medium plus 1% (w/v) agar (as in (Bargmann and Birnbaum, 2010)). Phytatrays and plates were placed in an Advanced Intellus environmental controller (Percival) set to 35 µmol/m2*sec-1 and 22° C with an 18h-light/6h-dark regime.

extract_protocol: RNA was extracted using an RNeasy Micro Kit with RNase-free DNase Set according to the manufacturer’s instructions (QIAGEN).

treatment_protocol: One-week-old seedlings were treated with 5 µM indole-3-acetic acid (IAA; Sigma-Aldrich) or mock-treated with solvent alone for the indicated amount of time. A 10 mM IAA stock was dissolved in ethanol and stored at -20° C.

tag: cultivar

value: whole root

value: 5 uM indole-3-acetic acid


title: unwounded leaves, Rep 3


title: intact root auxin 3

source_name: intact root auxin 3


title: columella control 2

source_name: columella control 2

value: columella

value: mock


title: epidermis control 3

source_name: epidermis control 3

value: epidermis


title: intact root control 1

source_name: intact root control 1


title: intact root control 2

source_name: intact root control 2


title: intact root auxin 2

source_name: intact root auxin 2


title: intact root control 3

source_name: intact root control 3


title: columella auxin 3

source_name: columella auxin 3


title: columella control 1

source_name: columella control 1


title: epidermis auxin 3

source_name: epidermis auxin 3


title: epidermis auxin 1

source_name: epidermis auxin 1


title: columella auxin 1

source_name: columella auxin 1


title: columella auxin 2

source_name: columella auxin 2


title: epidermis auxin 2

source_name: epidermis auxin 2


title: epidermis control 2

source_name: epidermis control 2


title: epidermis control 1

source_name: epidermis control 1


title: pericycle control 1

source_name: pericycle control 1

value: pericycle


title: columella control 3

source_name: columella control 3


title: pericycle control 3

source_name: pericycle control 3


title: pericycle auxin 3

source_name: pericycle auxin 3


title: pericycle auxin 1

source_name: pericycle auxin 1


title: pericycle auxin 2

source_name: pericycle auxin 2


title: stele auxin 3

source_name: stele auxin 3

value: stele


title: stele auxin 1

source_name: stele auxin 1


title: stele control 3

source_name: stele control 3


title: stele auxin 2

source_name: stele auxin 2


title: stele control 2

source_name: stele control 2


title: pericycle control 2

source_name: pericycle control 2


title: stele control 1

source_name: stele control 1


title: Day Time Control 1

status: Public on Aug 02 2013

city: Buenos Aires

first: Marcelo

last: Yanovsky

state: Ciudad Autonoma de Buenos Aires

address: Av. Patricias Argentinas 435

country: Argentina

institute: Fundación Instituto Leloir. IIBBA- CONICET

description: Subj Day Cntrl Rep 1

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Arabidopsis Genome ATH1 Array were washed and stained in the Affymetrix Fluidics Station 450.

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

source_name: Aerial Rosete_Day Time Control 1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: 15 days old plant were grown in 12/12 white light/dark cycles and then were transfered to countinuos dark free running conditions.

extract_protocol: Total RNA extraction was performed using RNaeasy Mini kit system according to the manufacturer's instructions.

treatment_protocol: 1hr white light pulse during middle of the night (CT=6) or middle of the subjective day (CT=18). Control samples were collected without light pulse treatment.

tag: developmental stage

value: seedling

value: aerial rosette

tag: genotype/variation

value: WT

value: Columbia

tag: time

value: Control (without light pulse)


title: Day Time Treatment 1

description: Subj Day Rep 1

source_name: Aerial Rosete_Day Time Treatment 1

value: 1hr white light pulse


title: Day Time Treatment 3

description: Subj Day Rep 3

source_name: Aerial Rosete_Day Time Treatment 3


title: RL/LD treated Ler, biological rep2

status: Public on Jul 22 2013

city: Taipei

first: Wen-Ping

last: Hsieh

address: 128 Academia Road, Section 2, Nankang

institute: Academia Sinica

description: 4-day-old etiolated seedlings

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16.5 hr at 45C on GeneChip Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: RL/LD treated Ler

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 701021 Rev. 5, Affymetrix).

growth_protocol: Seeds were surface sterilized and plated on 1/2 MS (0.8% agar, pH 5.7) plates.

extract_protocol: Total RNA was isolated as described previously [(Chang et al, Plant J 54, 205 (2008)]. Polysome RNA was isolated through a sucrose gradient and purified with phenol/chloroform extraction, LiCl precipitation and dissolved in RNase-free H2O.

treatment_protocol: Seedlings were grown under dark or red-light and long-day (0.5 μmole m-2 sec-1) contitions for 4 days.

value: aerial part of seedlings

value: Ler

value: wild type


title: etiolated Ler, biological rep3

description: 4-day-old etiolated seedlings

source_name: etiolated Ler

value: etiolated


title: Day Time Control 3

description: Subj Day Cntrl Rep 3

source_name: Aerial Rosete_Day Time Control 3


title: Day Time Control 2

description: Subj Day Cntrl Rep 2

source_name: Aerial Rosete_Day Time Control 2


title: RL/LD treated atbzip16, biological rep3

description: 4-day-old seedlings grown under RL/LD

source_name: RL/LD treated atbzip16

value: grown under dark or red-light and long-day (0.5 μmole m-2 sec-1)


title: Day Time Treatment 2

description: Subj Day Rep 2

source_name: Aerial Rosete_Day Time Treatment 2


title: RL/LD treated Ler, biological rep1

description: 4-day-old etiolated seedlings


title: Night Time Treatment 1

description: Night Light Rep 1

source_name: Aerial Rosete_Night Time Treatment 1


title: Night Time Treatment 2

description: Night Light Rep 2

source_name: Aerial Rosete_Night Time Treatment 2


title: NFA8 roots 2hr KCl control treated, biological rep1

description: 1 NFA8 C.CEL

source_name: 12 day old Arabidopsis NFA8 ecotype roots, 2 hr 5mM KCl control treated

value: root

tag: agent

value: KCl control

tag: age

value: 12 day old seedling roots


title: Night Time Control 2

description: Night Cntrl Rep 2

source_name: Aerial Rosete_Night Time Control 2


title: Night Time Treatment 3

description: Night Light Rep 3

source_name: Aerial Rosete_Night Time Treatment 3


title: RL/LD treated atbzip16, biological rep2

description: 4-day-old seedlings grown under RL/LD


title: Night Time Control 3

description: Night Cntrl Rep 3

source_name: Aerial Rosete_Night Time Control 3


title: etiolated atbzip16, biological rep3

description: 4-day-old seedlings grown under RL/LD

source_name: etiolated atbzip16


title: RL/LD treated atbzip16, biological rep1

description: 4-day-old seedlings grown under RL/LD


title: RL/LD treated Ler, biological rep3

description: 4-day-old etiolated seedlings


title: etiolated Ler, biological rep1

description: 4-day-old etiolated seedlings


title: Night Time Control 1

description: Night Cntrl Rep 1

source_name: Aerial Rosete_Night Time Control 1


title: etiolated atbzip16, biological rep1

description: 4-day-old seedlings grown under RL/LD


title: etiolated atbzip16, biological rep2

description: 4-day-old seedlings grown under RL/LD


title: etiolated Ler, biological rep2

description: 4-day-old etiolated seedlings


title: vtc2 mature somatic embryo, bio rep1

status: Public on Jul 17 2013

city: Winnipeg

first: Mark

middle: Findlay

last: Belmonte

state: Manitoba

address: 50 Sifton Road

department: Biological Sciences

country: Canada

institute: University of Manitoba

description: gene expression data from mature somatic embryos in a vtc2 mutant

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

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

data_processing: The data were analyzed with the Affymetrix GeneChip Operating system 1.4 (GCOS) using default analysis settings and global scaling as a normalization method.  The mean target intensity of each array was set to 500.

source_name: vtc2 mutant mature somatic embryos at day 14

label_protocol: Amplification and labeling was performed using 3 μg RNA into the Enzo Single-Round RNA Amplification and Biotin Labeling system (Life Technologies).

growth_protocol: plants were grown in a Conviron growth cabinet under long day conditions (16 hour light, 8 hours dark) with fluorescent lamps at 22°C and 50% - 70% relative humidity.

extract_protocol: Total RNA was extracted using Plant RNA reagent (Invitrogen). DNA contamination was removed with the Ambion Turbo DNA-free kit (Life Technologies)

treatment_protocol: bent cotyledon embryos were cultured on modified MS media supplemented with the phytohormone 2,4-D for 14 days to promote callus development. Explants that formed callus were then transferred to MS media lacking 2,4-D for embryos to develop.

tag: ecotype/cultivar

value: mature somatic embryo


title: vtc2 zygotic embryo, bio rep2

description: gene expression data from vtc2 mutant zygotic embryos

source_name: vtc2 mutant bent cotyledon zygotic embryo

value: bent cotyledon zygotic embryo


title: wild type zygotic embryo, bio rep2

description: gene expression data from zygotic embryos

source_name: wild type bent cotyledon zygotic embryo


title: wild type zygotic embryo, bio rep1


title: wild type mature somatic embryo, bio rep2

description: gene expression data from mature somatic embryos

source_name: wild type mature somatic embryos at day 14


title: wild type day 7 induction, bio rep1

description: gene expression data from early induction phase of somatic embryogenesis

source_name: wild type day 7 induction +2,4-D

value: day 7 induction


title: sid2-1 3 week cold, biological rep1

status: Public on Jun 30 2013

city: Beltsville

first: Sunchung

last: Park

state: MD

address: 10300 Baltimore ave, Bldg001

department: ARS-NEA

institute: USDA -ARS

description: Arabidopsis mutant sid2-1 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

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.

source_name: Arabidopsis mutant sid2-1 grown at 22⁰C followed by 3 weeks at 4⁰C

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

value: entire aerial part

tag: cultivar/ecotype

value: mutant sid2-1


title: sid2-1 3 week cold, biological rep3


title: sid2-1 warm, biological rep2

description: Arabidopsis mutant sid2-1 grown at 22⁰C in soil under a 12 h photoperiod for approx 23 d

source_name: Arabidopsis mutant sid2-1 grown at 22⁰C


title: sid2-1 warm, biological rep1


title: sid2-1 warm, biological rep3


title: WT 3 week cold, biological rep1

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: rsa1 salt 0 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 without salt stress

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.

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, 0 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

value: Control

tag: genetic background

value: Columbia gl1 expressing RD29A::LUC transgene

value: Seven-day-old


title: rsa1 salt 12 h rep1

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

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

value: Salt with 120 mM NaCl for 24 h


title: rsa1 salt 0 h rep1


title: rsa1 salt 0 h rep3


title: WT salt 0 h rep3

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

source_name: Arabidopsis wild type, salt, 0 h.


title: WT salt 12 h rep3

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

source_name: Arabidopsis wild type, salt, 24 h.


title: WT salt 12 h rep1


title: WT salt 0 h rep1


title: WT warm, biological rep1 [2]

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

source_name: Arabidopsis Col-0 grown at 22⁰C


title: WT salt 0 h rep2


title: sid2-1 3 week cold, biological rep2