title: liver_sesamolin_rep5

city: Niiza

first: Takashi

last: Ide

address: 2-1-28 Sugasawa

institute: Jumonji University

description: Gene expression data from liver of a rat fed a diet containing 0.2% sesamolin for 15 days.

hyb_protocol: Fragmented biotin-labeled cRNA was synthesized from the total RNA of each mouse using One-Cycle Target Labeling and Control Reagents (Affymetrix) and then hybridized to an array (Rat Genome 230 2.0 Array; Affymetrix) at 45°C for 16 hours.

scan_protocol: After hybridization, the gene chips were washed and stained using a GeneChip Fluidics Station 450 (Affymetrix) and then scanned (GeneChip Scanner; Affymetrix) with the GeneChip Operation Software Ver. 1.4 (Affymetrix).

data_processing: Data analysis was performed with a GeneChip Operating Software (Ver. 1.4) using Affymetrix default analysis settings and global scaling as normalization method..

organism: Rattus norvegicus

source_name: liver from a rat fed a diet containing 0.2% sesamolin for 15 days

label_protocol: Double-stranded cDNA was synthesized from the total RNA of each rat using the One-Cycle cDNA Synthesis Kit (Affymetrix Japan KK, Tokyo, Japan) with a T7-(dT)24 primer. Biotin-labeled cRNA was then synthesized using an IVT Labeling Kit (Affymetrix). The biotin-labeled cRNA was further purified and fragmented using the Sample Cleanup Module (Affymetrix).

growth_protocol: Male Sprague-Dawley rats obtained from Charles River Japan, Kanagawa, Japan, at 4 weeks of age were housed individually in animal cages in a room with controlled temperature (20-22 ºC), humidity (55-65%), and lighting (lights on from 7:00 to 19:00 h), and fed a commercial non-purified diet (Type NMF, Oriental Yeast Co., Tokyo, Japan) for 7 d. After this acclimatization period, animals were divided into 4 groups with equal mean body weights consisting of 7 animals each and fed experimental diets.

extract_protocol: Upon termination of the experimental period, animals were anesthetized using diethyl ether and killed by bleeding from the abdominal aorta, after which livers were excised. Hepatic RNA was extracted using the acid guanidium thiocyanate-phenol-chloroform method  (Chomczynski & Sacchi,  Anal. Biochem. 162, 156-159 (1987))

treatment_protocol: Rats were fed either a diet free of lignan or diets containing 0.2% lignan (sesamin, episesamin or sesamolin) for 15 d.

tag: Sex

value: male

tag: strain

value: Sprague‐Dawley

value: liver


title: HTEC-d21_NT-30

status: Public on Dec 04 2012

type: RNA

city: St. Louis

first: Anand

middle: Champak

last: Patel

state: MO

address: Campus Box 8116, 660 S. Euclid Ave.

department: Pulmonary/Critical Care Medicine

country: USA

description:
d21 NT rep 2
NT_504_30

hyb_protocol: Hybridization was performed according to the manufacturer’s instructions at the Washington University School of Medicine Genome Sequencing Center Microarray Core Facility.

scan_protocol: Scanning, including background correction, was performed per manufacturer's instructions using BeadStudio 3.0 software (Illumina) at the Washington University School of Medicine Genome Sequencing Center Microarray Core Facility.

data_processing: Microarray normalization and statistical analysis was performed using packages from the Bioconductor project executed in the R programming environment. Raw image data were imported into Bioconductor using readIllumina as implemented in the beadarray package with background subtraction and image sharpening. The resulting bead-level data was then normalized for intensity at the bead level using the HULK algorithm, to adjust for local spatial effects (i.e. cross-array gradients). The data were then summarized for each bead type. A model-based variance stabilizing transformation was applied to the bead-type summaries, followed by quantile normalization across the experiment using functions in the beadarray package. Bead-types not detected on at least 1 array (detection p<0.01) were then filtered to improve power to detect differentially expressed genes. We assessed differential expression after 21 days of IL-13 treatment (IL-13 versus control) using linear models and empirical Bayes moderated F statistics as implemented in the LIMMA package. We considered differences in gene expression significant if P values were <0.05 after adjustment for multiple testing, so that false discovery rate was <5%. Bead-types were annotated to genes using a combination of the manufacturer’s annotation, transcript level annotations obtained from AceView, and annotations from the University of Cambridge Computational Biology Group in order to optimize interpretation of the gene expression data.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: primary culture airway epithelial cells d21, no IL-13 rep 2

label_protocol: RNA was amplified and biotinylated using the Ambion Illumina TotalPrep Kit.

growth_protocol: Human tracheal epithelial cells (hTECs) were isolated and placed into culture in growth factor enriched medium as described previously. For the present experiments, cells were seeded at 2 x 105 cells per well (24-well Transwell, Corning, Corning, NY) and cultured under submerged conditions until confluence. Cultures were then maintained in DMEM-Ham’s F12 medium with 2% NuSerum (BD, Franklin, NJ), Primocin (100 µg/ml, InvivoGen, San Diego, CA), and retinoic acid (1 x 10–8 M, Sigma), and were switched to air-liquid interface conditions for 3 weeks.  Media was changed twice weekly, cells were fed from the bottom reservoir.

extract_protocol: Total RNA was isolated from hTECs using the Qiagen RNEasy kit (Qiagen)

treatment_protocol: IL-13 (50 ng/ml) was added starting day -2 (two days before ALI), and twice weekly for 21 days thereafter.

tag: day

tag: agent

value: No Treatment

tag: cell type

value: primary culture airway epithelial cell, tracheal


title: LPA_M_14

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

country: Germany

institute: Leibniz Institute for Farm Animal Biology (FBN)

description:
trait 1: Fat area [cm2]: fat area on M. longissimus dorsi at 13th/14th rib
trait 2: Drip loss (%): percentage of weight loss of M. longissimus dorsi samples collected at 24 hours post mortem that was weighted, suspended in a plastic bag, held at 4 °C for 48 h, and thereafter re-weighed

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42C on Affymetrix GeneChip Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500. Affymetrix 'ExpressionConsole' was used to generate the PLIER data.

organism: Sus scrofa

source_name: muscle taken at slaughter, mean end weight of 110 kg

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer's protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

tag: herd

value: commercial pig of crosbred Pix(DLxDE)

tag: trait 1 (see description below)

tag: trait 2 (see description below)

tag: tissue

value: muscle


title: LZ-CLL9-DXM

city: Barcelona

first: Maria Joao

last: Baptista

address: Pg de la Vall d’Hebron 119-129

department: Department of Hematology

country: Spain

institute: Hospital Vall d’Hebron, Institut Recerca Vall d’Hebron

description: Low ZAP-70 chronic lymphocytic leukemia sample 9_treated cells

hyb_protocol: Biotin-labeled cRNA was cleanup and quantified and subsequently it was fragmented by metal-induced hydrolysis (GeneChip Sample Cleanup Module, Affymetrix Inc). Hybridization was performed with GeneChip® Hybridization Wash and Stain Kit (Affymetrix Inc) according to manufactures instructions.

scan_protocol: GeneChips were scanned using the GeneChip®Scanner 3000 7G (Affymetrix Inc).

data_processing: Expression measures were normalized and summarized using the frozen robust multiarray analysis (fRMA) methodology

source_name: peripheral blood mononuclear cells, 6 hours dexamethasone treated

label_protocol: cRNA amplification and biotin labeling was synthesized from 2ug cDNA by means of an in vitro transcription reaction in the presence of T7 RNA Polymerase and of biotinylated nucleotide analog/ribonucleotide mix (GeneChip IVT labeling Kit, Affymetrix Inc, Santa Clara, CA)

growth_protocol: Peripheral blood mononuclear cells from CLL patients were thawed at 37ºC and resuspended in standard culture medium (RPMI-1640 medium (Gibco, Paisley, Scotland, UK) supplemented with 10% heat-inactivated FBS (Gibco), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Lonza, Viviers, Belgium), 2 mM L-glutamine and 1 mM sodium pyruvate (Gibco)) and cultured at 37ºC in a 5% CO2 atmosphere at a density of 1 x 106 cells/ml. Peripheral blood mononuclear cells were allowed to recover from the thawing process for one hour before manipulation

extract_protocol: RNA was extracted from 5x105 cells with Trizol reagent (Invitrogen Life Tecnologies, Paisley, Scotland, UK) according to the manufactures instructions.

treatment_protocol: Samples were split in two for control and incubation with dexamethasone (Merck KGaA, Darmstadt, Germany) at a pharmacological active concentration of 13.25 µM.

value: chronic lymphocytic leukemia

tag: ighv/zap-70 status

value: Mutated IGHV gene / low ZAP-70 expresssion


title: LPA_M_16


title: LZ-CLL13-DXM

description: Low ZAP-70 chronic lymphocytic leukemia sample 13_treated cells


title: liver_sesamolin_rep2

country: Japan


title: LPA_M_19


title: WtPMC_G1

city: Boston

first: Bruce

last: Spiegelman

state: MA

address: DFCI, Dept of Cancer Biology, 450 Brookline Ave. CLSB, 11115

institute: Dana Farber Cancer Institute

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

scan_protocol: The label, hyb and scan were performed by the Dana-Farber Cancer Institute Core facility using affymetrix Gene Chip Mouse Genome 430 2.0 arrays according to established methods

data_processing: The data were normalized using the DNA-chip Analyzer (dChip) software

organism: Mus musculus

source_name: Skeletal Muscle

label_protocol: biotin

growth_protocol: Primary myoblast were isolated from ~2 week old pups and maintained in 10% FBS/bFGF

extract_protocol: Total RNA was isolated by TRIzol extraction and purification using QIAGEN Rneasy mini columns according to the manufacturer's instructions.

treatment_protocol: Myoblasts were differentiated with 2% horse serum for 2 days and infected with an MOI of 100 overnight

tag: celltype

value: Primary Muscle Cells

tag: pgc-1 alpha isoform expression

value: GFP control

tag: muscle hypertrophy

value: no observed hypertrophy


title: WtPMC_G3


title: WtPMC_G2


title: liver_sesamolin_rep3


title: LZ-CLL20-DXM

description: Low ZAP-70 chronic lymphocytic leukemia sample 20_treated cells


title: LZ-CLL21-DXM

description: Low ZAP-70 chronic lymphocytic leukemia sample 21_treated cells


title: LZ-CLL21-UNT

description: Low ZAP-70 chronic lymphocytic leukemia sample 21_untreated cells

source_name: peripheral blood mononuclear cells, untreated


title: liver_episesamin_rep5

description: Gene expression data from liver of a rat fed a diet containing 0.2% episesamin for 15 days.

source_name: liver from a rat fed a diet containing 0.2% episesamin for 15 days


title: liver_episesamin_rep4


title: WtPMC_A4_2

value: myotube hypertrophy observed


title: LZ-CLL9-UNT

description: Low ZAP-70 chronic lymphocytic leukemia sample 9_untreated cells


title: liver_episesamin_rep1


title: WtPMC_A3_3


title: liver_sesamolin_rep4


title: WtPMC_A4_3


title: liver_episesamin_rep2


title: LZ-CLL3-DXM

description: Low ZAP-70 chronic lymphocytic leukemia sample 3_treated cells


title: WtPMC_A3_2


title: WtPMC_A4_1


title: liver_episesamin_rep3


title: HZ-CLL26-DXM

description: High ZAP-70 chronic lymphocytic leukemia sample 26_treated cells

value: Unmutated IGHV gene / high ZAP-70 expresssion


title: Tomato-5G_rep3

city: Ghent

first: Wannes

last: Dermauw

address: Coupure Links 653

department: Crop Protection

country: Belgium

institute: University Ghent

description: Biological replicate 3 of 4, Tomato-5G vs. London

hyb_protocol: Cy3 and Cy5 labeled cRNAs were pooled and hybridized using the Gene Expression Hybridization Kit (Agilent Technologies) for 17h in a rotating hybridization oven at 20 r.p.m. and 65°C; Slides were washed using the Gene Expression Wash Buffer Kit (Agilent Technologies)

scan_protocol: Hybridized arrays were scanned using an Agilent Microarray High Resolution Scanner.

data_processing: Data were extracted and normalized using Agilent Feature Extraction Software 10.5 with default parameter settings for gene expression two-color microarrays (protocol GE2_105_Dec08). Further processed 'fold change' data are generated using Genespring.

organism: Tetranychus urticae

label_protocol: 100 ng of total RNA (+ RNA-spike in control) was used to generate Cy3 or Cy5 labeled cRNAs, using the Agilent Low Input Quick Amp Labeling Kit (version 6.5 Agilent Technologies)

growth_protocol: T. urticae strains, London, MAR-AB and MR-VP, were grown on potted kidney bean (Phaseolus vulgaris cv. "Prelude") plants at 26+-0.5°C and a 16/8h light/dark photoperiod. For the host change experiment, female adut mites from the London strain were grown for 2h, 12h, and 5 generations on tomato (Solanum lycopersicon cv. "Moneymaker") at 26°+-0.5°C and a 16/8 light/dark photoperiod.

extract_protocol: Total RNA was extracted from about 100 adult female spider mites using RNEasy Mini Kit (Qiagen) following manufacturer's instructions.

tag: age

value: adult

source_name: London


title: HZ-CLL35-DXM

description: High ZAP-70 chronic lymphocytic leukemia sample 35_treated cells


title: liver_sesamin_rep4

description: Gene expression data from liver of a rat fed a diet containing 0.2% sesamin for 15 days.

source_name: liver from a rat fed a diet containing 0.2% sesamin for 15 days


title: LZ-CLL3-UNT

description: Low ZAP-70 chronic lymphocytic leukemia sample 3_untreated cells


title: LZ-CLL13-UNT

description: Low ZAP-70 chronic lymphocytic leukemia sample 13_untreated cells


title: Tomato-5G_rep4

description: Biological replicate 4 of 4, Tomato-5G vs. London


title: liver_sesamin_rep5


title: HZ-CLL43-DXM

description: High ZAP-70 chronic lymphocytic leukemia sample 43_treated cells


title: liver_sesamin_rep2


title: LZ-CLL20-UNT

description: Low ZAP-70 chronic lymphocytic leukemia sample 20_untreated cells


title: Tomato-5G_rep1

description: Biological replicate 1 of 4, Tomato-5G vs. London


title: WtPMC_A3_1


title: WtPMC_A1_3


title: Tomato-5G_rep2

description: Biological replicate 2 of 4, Tomato-5G vs. London


title: LPA_M_628

description:
trait 1: Fat area [cm2]: fat area on M. longissimus dorsi at 13th/14th rib
trait 2: Drip loss (%): percentage of weight loss of M. longissimus dorsi samples collected at 24 hours post mortem that was weighted, suspended in a plastic bag, held at 4 °C for 48 h, and thereafter re-weighed


title: Tomato-12h_rep3

description: Biological replicate 3 of 4, Tomato-12h vs. London


title: WtPMC_A1_2


title: WtPMC_A2_1


title: WtPMC_A2_2


title: WtPMC_A2_3


title: Tomato-12h_rep4

description: Biological replicate 4 of 4, Tomato-12h vs. London


title: HZ-CLL35-UNT

description: High ZAP-70 chronic lymphocytic leukemia sample 35_untreated cells


title: HZ-CLL27-DXM

description: High ZAP-70 chronic lymphocytic leukemia sample 27_treated cells


title: liver_sesamin_rep3


title: liver_sesamin_rep1


title: liver_control diet_rep3

description: Gene expression data from liver of a rat fed a diet free of lignan for 15 days.

source_name: liver from a rat fed a lignan-free diet for 15 days


title: liver_control diet_rep4


title: Tomato-12h_rep1

description: Biological replicate 1 of 4, Tomato-12h vs. London


title: Tomato-12h_rep2

description: Biological replicate 2 of 4, Tomato-12h vs. London


title: HZ-CLL34-DXM

description: High ZAP-70 chronic lymphocytic leukemia sample 34_treated cells


title: HZ-CLL30-DXM

description: High ZAP-70 chronic lymphocytic leukemia sample 30_treated cells


title: liver_control diet_rep5


title: Intensity measures in wild type strain, replicate 2

city: paris

first: gilbert

last: richarme

state: ile de france

address: 15 rue helene brion

country: France

institute: Institut Jacques Monod

description: mRNA

hyb_protocol: The labeled double-strand DNA was used for hybridization to the array. The arrays were washed and stained in the Affymetrix Fluidics Station 400 using the antibody amplification protocol and streptavidin phycoerythrin.

scan_protocol: Arrays were scanned with the Affymetrix Gene Array Scanner.

data_processing: The CEL files generated for each array were analyzed using Affymetrix Expression Console software.

organism: Escherichia coli

source_name: wild type MG1655

label_protocol: cDNA was prepared using total RNA, random primers and SuperScript II (Invitrogen) reverse transcriptase. Second strand cDNA synthesis was carried out using DNA polymerase I and RNase H. cDNA was fragmented to get 50-100 bp fragments, and end labeled with bio-ddATP using terminal deoxy transferase.

growth_protocol: Luria broth (LB) medium under aeration, exponential phase OD600 = 0.3.

extract_protocol: RNA extraction was performed using phenol treatment.

treatment_protocol: Untreated wild type versus untreated yajL mutant.

tag: strain/background

tag: genotype

value: wild type

tag: growth phase

value: exponential

tag: treatment


title: Intensity measures in yajL mutant strain, replicate 2

description: mRNA

source_name: yajL mutant (genetic background MG1655)

value: yajL mutant


title: WtPMC_A1_1

tag: strain


title: Tomato-2h_rep3

description: Biological replicate 3 of 4, Tomato-2h vs. London


title: MAR-AB_rep5

description: Biological replicate 5 of 5, MAR-AB vs. London

source_name: MAR-AB


title: Intensity measures in wild type strain, replicate 1

description: mRNA


title: Intensity measures in yajL mutant strain, replicate 1

description: mRNA


title: liver_control diet_rep2

tag: Sex

value: male

value: Sprague‐Dawley


title: GT_Female3

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

description:
Amplification protocol
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:20731

hyb_protocol: Affymetrix standard protocol Amount labeled  target hybridization to array: 10 µg

data_processing: Analysis method: Affymetrix GCOS and Gene Spring and Avadis programs. GCOS Tgt value: 1500

label: Biotin

source_name: E14 Genital tubercle of female

extract_protocol: Qiagen: RNeasy

treatment_protocol:
Pooled sample: no
Dissection method: Genital tubercle region microdissected

value: FVB/N

value: Female

tag: developmental stage

value: 14 dpc

tag: theiler stage

tag: developmental landmark


title: liver_control diet_rep1

value: liver


title: Tomato-2h_rep4

description: Biological replicate 4 of 4, Tomato-2h vs. London


title: GT_Male4

description:
Amplification protocol
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:20727

source_name: E14 Genital tubercle of Male

value: Male


title: Tomato-2h_rep2

description: Biological replicate 2 of 4, Tomato-2h vs. London


title: MAR-AB_rep3

description: Biological replicate 3 of 5, MAR-AB vs. London


title: GT_Female4

description:
Amplification protocol
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:20732


title: liver_sesamolin_rep1

description: Gene expression data from liver of a rat fed a diet containing 0.2% sesamolin for 15 days.


title: GT_Male3

description:
Amplification protocol
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:20726


title: MAR-AB_rep4

description: Biological replicate 4 of 5, MAR-AB vs. London


title: GT_Female2

description:
Amplification protocol
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:20730


title: HZ-CLL43-UNT

description: High ZAP-70 chronic lymphocytic leukemia sample 43_untreated cells

tag: cell type

value: chronic lymphocytic leukemia


title: HZ-CLL31-DXM

description: High ZAP-70 chronic lymphocytic leukemia sample 31_treated cells


title: HZ-CLL30-UNT

description: High ZAP-70 chronic lymphocytic leukemia sample 30_untreated cells


title: HZ-CLL26-UNT

description: High ZAP-70 chronic lymphocytic leukemia sample 26_untreated cells


title: GT_Male2

description:
Amplification protocol
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:20725


title: Tomato-2h_rep1

description: Biological replicate 1 of 4, Tomato-2h vs. London


title: HZ-CLL27-UNT

description: High ZAP-70 chronic lymphocytic leukemia sample 27_untreated cells


title: MAR-AB_rep2

description: Biological replicate 2 of 5, MAR-AB vs. London


title: HZ-CLL34-UNT

description: High ZAP-70 chronic lymphocytic leukemia sample 34_untreated cells


title: HZ-CLL31-UNT

description: High ZAP-70 chronic lymphocytic leukemia sample 31_untreated cells


title: MR-VP_rep6

description: Biological replicate 6 of 6, MR-VP vs. London

source_name: MR-VP


title: GT_Male1

description:
Amplification protocol
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:20728


title: GT_Female1

description:
Amplification protocol
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:20729


title: G9C8 clone, replicate 3

city: Chicago

first: Alexander

last: Chervonsky

state: IL

address: 924 E 57th Street

department: Pathology

institute: University of Chicago

description: Gene expression from activated and rested in vitro cultured G9C8 clone cells

hyb_protocol: 12ug of labeled and fragmented cRNA were hybridized to Affymetrix Mouse 430v2.0 GeneChips.GeneChips were washed and stained in the Affymetrix Fluidics station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Affymetrix GCOS software was used to run the Comparison analysis method using default parameters, with signal scaling (target value=150) to normalize signal from each chip. Resulting files were subjected to further analysis using GeneSpring GX7.3 (Agilent Technologies) and Ingenuity pathway analysis softwares.

source_name: vial of frozen G9C8 clone cells

label_protocol: Biotinylated cRNA were prepared from 8 ug total RNA  according to the standard Affymetrix  (Affymetrix, Santa Clara, CA) protocol and protocols provided by the Functional Genomics Core facility (University of Chicago).

growth_protocol: 3 separate vials of frozen G9C8 clone T cells or 2 separate (4-8 wk old) transgenic mouse splenocytes were used for in vitro antigenic stimulation with 10ug/ml Insulin B peptide(LYLVCGERG).

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

treatment_protocol: Samples were peptide stimulated for 3 days and rested in IL2 (5 IU/ml) for 2 days. Cells were then harvested, washed with PBS and RNA was extracted.

value: activated CD8 T cells

tag: sample type

value: in vitro cultured G9C8 clone cells


title: 4_MTG16_DOX-I minus 0hr_I

city: Lund

first: Ram

last: Ajore

address: Klinikgatan 26

department: Hematology

country: Sweden

institute: Lund University

hyb_protocol: 200 ng cDNA was used for hybridization-

scan_protocol: Gene array scanner

data_processing: Basic Affymetrix chip and Experimental Quality Analyses were performed using the Expression Console Software v1.1.2.

source_name: MTG16_DOX-I minus 0hr

label_protocol: cDNA were Labelled with Biotin at  37 degree according to standard protocol by Affymetrix.

growth_protocol: Cells were collected after 8 hours of incubation with Doxycycline.

extract_protocol: RNAeasy kit was used for RNA extraction.

treatment_protocol: Cells were treated with 1 mg/ml Doxycycline.

value: Raji cell lines


title: MAR-AB_rep1

description: Biological replicate 1 of 5, MAR-AB vs. London


title: MR-VP_rep5

description: Biological replicate 5 of 6, MR-VP vs. London


title: MR-VP_rep4

description: Biological replicate 4 of 6, MR-VP vs. London


title: 5_MTG16_DOX-II minus 0hr_I_4


title: 6_MTG16_DOX-III minus 0hr_II


title: 1_MTG16_DOX plus 8hr_I

source_name: MTG16_DOX plus 8hr


title: 2_MTG16_DOX plus 8hr_II


title: Embryo_21 DAF_rep1

status: Public on Dec 03 2012

city: Tsukuba

first: Yutaka

last: Sato

state: Ibaraki

address: 2-1-2 Kannondai

institute: National Institute of Agrobiological Sciences

description: Gene expression of embryo at 21 days after flowering

hyb_protocol: For microarray hybridization, 1650 ng of cyanine 3-labeled cRNA were fragmented and hybridized with the rice 4x44K microarray RAP-DB (G2519F#15241) at 65°C for 17 hours using the Agilent Gene Expression Hybridization Kit.

scan_protocol: Slides were scanned on an Agilent G2505B DNA microarray scanner using one-color scan setting for 4x44K array slides (Scan Area 61x21.6 mm, Scan resolution 5um,  Dye channel is set to Green PMT: XDR Hi 100%; XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 and 10.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended processed signal intensities. The processed signal intensities were used for 75 percentile normalization and log2 transformation with GenespringGX11(Agilent).

organism: Oryza sativa Japonica Group

source_name: Embryo at 21 days after flowering, replicate 1

label_protocol: One-color spike-mix was added to the RNA prior to labeling reaction. Labeling was performed using Quick Amp Labeling Kit, One-Color (Agilent Technologies) in the presence of cyanine-3-CTP according to the manufacturer’s protocol. The cyanine-3-labeled cRNA was purified by RNeasy Mini Kit (QIAGEN) and quantified using NanoDrop ND-1000 UV-VIS spectrophotometer.

growth_protocol: All plants were grown in paddy field in Tsukuba, Japan (~36o N latitude) during normal rice growing season in 2008.

extract_protocol: For the embryo samples, total RNA was extracted using RNeasy Plant Minikit (QIAGEN). For endosperm samples, total RNA was extracted with phenol and purified using the RNeasy mini spin column of the RNeasy plant mini kit. The extracted RNA was quantified using NanoDrop ND-1000 UV-VIS spectrophotometer (NanoDrop) and quality-checked using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

tag: cultivar

value: Nipponbare

tag: organ/tissue

value: Embryo

tag: growth/development stage

value: 21 days after flowering

tag: sampling time


title: Embryo_21 DAF_rep3

source_name: Embryo at 21 days after flowering, replicate 3


title: Endosperm_21 DAF_rep1

description: Gene expression of endosperm at 21 days after flowering

source_name: Endosperm at 21 days after flowering, replicate 1

value: Endosperm


title: 3_MTG16_DOX plus 8hr_III


title: Shoot_JA_6 hr_rep1

description: Gene expression profile of shoot at 6 hr after jasmonic acid treatment

hyb_protocol: For microarray hybridization, 825 ng of Cy3-labeled cRNA and 825 ng of Cy5-labeled cRNA were mixed and fragmented and hybridized with the rice 4x44K microarray RAP-DB (G2519F#15241) at 65°C for 17 hours using the Agilent Gene Expression Hybridization Kit. Hybridization and washing of the hybridized slide were performed according to the manufacture’s instruction.

scan_protocol: Slides were scanned on an Agilent G2505B DNA microarray scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 and 10.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended processed Cy3 signal intensities and Cy5 signal intensities.

source_name: Shoot, 100  μM JA, 6 hr, replicate 1

label_protocol: Two-color spike-mix was added to the total RNA prior to the labeling reaction and labeling was performed using a Quick Amp Labeling Kit, Two-Color (Agilent Technologies) in the presence of cyanine-3 (Cy3)-CTP and cyanine-5 (Cy5)-CTP according to the modified manufacturer’s protocol. The Cy3-labeled cRNA and Cy5-labeled cRNA were purified by RNeasy Mini Kit (Qiagen) and the cRNA yield was determined using the NanoDrop ND-1000 UV-VIS spectrophotomer (NanoDrop).

growth_protocol: Rice (Oryza sativa L. japonica cv. Nipponbare) seeds were sterilized with 70% Et-OH and 1% hypochlorous acid, and imbibed in distilled water. The germinated seeds were transplanted in a mesh floating in distilled water and grown in a growth chamber at 28ºC, 24 h light and 60% humidity. After 3 days of germination, the seedlings were transferred in culture medium consisting of Yoshida’s nutrient solution diluted 5x and adjusted and maintained to pH5.5 using 1mM-MES and 1N-NaOH. The seedlings were allowed to grow for another 4 days. The culture medium was renewed every 2 days.

extract_protocol: Total RNA was extracted from the each sample with RNeasy Plant Minikit (QIAGEN) according to the manufacturer’s protocol. The quantity and quality of the obtained RNAs were checked with Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: Seven-day old seedlings were transferred in culture solution containing the plant hormone and in culture solution without plant hormone to serve as control (mock treatment). We collected shoot samples at 0 min (pretreatment), and at 1 h, 3 h, 6 h and 12 h of incubation after hormone treatment and root samples at 0 min (pretreatment), and at 15 min, 30 min, 1 h, 3 h and 6 h of incubation after hormone treatment, respectively.

value: Seven days after germination

tag: organ

value: Shoot

tag: hormone

value: Jasmonic acid

value: 100 μM (±) Jasmonic acid

tag: elapsed time

value: 6 hr

source_name: Shoot, Mock, 6 hr, replicate 1

tag: mock treatment


title: Shoot_JA_3 hr_rep1

description: Gene expression profile of shoot at 3 hr after jasmonic acid treatment

source_name: Shoot, 100  μM JA, 3 hr, replicate 1

tag: age

value: 3 hr

source_name: Shoot, Mock, 3 hr, replicate 1


title: Shoot_JA_12 hr_rep2

description: Gene expression profile of shoot at 12 hr after jasmonic acid treatment

source_name: Shoot, 100  μM JA, 12 hr, replicate 2

tag: treatment

value: 12 hr

source_name: Shoot, Mock, 12 hr, replicate 2


title: Shoot_JA_1 hr_rep1

description: Gene expression profile of shoot at 1 hr after jasmonic acid treatment

source_name: Shoot, 100  μM JA, 1 hr, replicate 1

value: 1 hr

source_name: Shoot, Mock, 1 hr, replicate 1


title: G9C8 clone, replicate 2


title: Endosperm_21 DAF_rep2

source_name: Endosperm at 21 days after flowering, replicate 2


title: Shoot_JA_3 hr_rep2

source_name: Shoot, 100  μM JA, 3 hr, replicate 2

source_name: Shoot, Mock, 3 hr, replicate 2


title: NOD.G9C8 tg, replicate 1

description: Gene expression from activated and rested transgenic CD8 T cells

source_name: mouse spleen

value: transgenic CD8 T cells from NOD mice

tag: host genetic background

value: NOD/LtJ


title: Endosperm_21 DAF_rep3

source_name: Endosperm at 21 days after flowering, replicate 3


title: Root_JA_6 hr_rep3

description: Gene expression profile of root at 6 hr after jasmonic acid treatment

source_name: Root, 100 μM JA, 6 hr, replicate 3

value: Root

source_name: Root, Mock, 6 hr, replicate 3


title: Root_JA_3 hr_rep2

description: Gene expression profile of root at 3 hr after jasmonic acid treatment

source_name: Root, 100 μM JA, 3 hr, replicate 2

source_name: Root, Mock, 3 hr, replicate 2


title: NOD.G9C8 tg, replicate 2

value: activated CD8 T cells


title: Shoot_JA_6 hr_rep2

source_name: Shoot, 100  μM JA, 6 hr, replicate 2

source_name: Shoot, Mock, 6 hr, replicate 2


title: Embryo_21 DAF_rep2

source_name: Embryo at 21 days after flowering, replicate 2


title: G9C8 clone, replicate 1

source_name: vial of frozen G9C8 clone cells

value: in vitro cultured G9C8 clone cells


title: Root_JA_3 hr_rep3

source_name: Root, 100 μM JA, 3 hr, replicate 3

value: Nipponbare

source_name: Root, Mock, 3 hr, replicate 3


title: Root_JA_6 hr_rep1

source_name: Root, 100 μM JA, 6 hr, replicate 1

source_name: Root, Mock, 6 hr, replicate 1


title: Root_JA_3 hr_rep1

source_name: Root, 100 μM JA, 3 hr, replicate 1

source_name: Root, Mock, 3 hr, replicate 1


title: Shoot_JA_1 hr_rep2

source_name: Shoot, 100  μM JA, 1 hr, replicate 2

source_name: Shoot, Mock, 1 hr, replicate 2


title: Shoot_JA_12 hr_rep1

source_name: Shoot, 100  μM JA, 12 hr, replicate 1

source_name: Shoot, Mock, 12 hr, replicate 1


title: Root_JA_30 min_rep3

description: Gene expression profile of root at 30 min after jasmonic acid treatment

source_name: Root, 100 μM JA, 30 min, replicate 3

value: 30 min

source_name: Root, Mock, 30 min, replicate 3


title: Root_JA_6 hr_rep2

source_name: Root, 100 μM JA, 6 hr, replicate 2

source_name: Root, Mock, 6 hr, replicate 2


title: Root_JA_1 hr_rep3

description: Gene expression profile of root at 1 hr after jasmonic acid treatment

source_name: Root, 100 μM JA, 1 hr, replicate 3

source_name: Root, Mock, 1 hr, replicate 3


title: Root_JA_1 hr_rep2

source_name: Root, 100 μM JA, 1 hr, replicate 2

source_name: Root, Mock, 1 hr, replicate 2


title: Root_JA_1 hr_rep1

source_name: Root, 100 μM JA, 1 hr, replicate 1

source_name: Root, Mock, 1 hr, replicate 1


title: Root_JA_30 min_rep2

source_name: Root, 100 μM JA, 30 min, replicate 2

source_name: Root, Mock, 30 min, replicate 2


title: Root_JA_30 min_rep1

source_name: Root, 100 μM JA, 30 min, replicate 1

source_name: Root, Mock, 30 min, replicate 1


title: Root_JA_15 min_rep1

description: Gene expression profile of root at 15 min after jasmonic acid treatment

source_name: Root, 100 μM JA, 15 min, replicate 1

value: 15 min

source_name: Root, Mock, 15 min, replicate 1


title: Shoot_tZ_6 hr_rep2

description: Gene expression profile of shoot at 6 hr after cytokinin treatment

source_name: Shoot, 1 μM tZ, 6 hr, replicate 2

value: Cytokinin

value: 1 μM trans-Zeatin

source_name: Shoot, Mock, 6 hr, replicate 2


title: Root_JA_15 min_rep3

source_name: Root, 100 μM JA, 15 min, replicate 3

value: Seven days after germination

source_name: Root, Mock, 15 min, replicate 3


title: Shoot_tZ_3 hr_rep1

description: Gene expression profile of shoot at 3 hr after cytokinin treatment

source_name: Shoot, 1 μM tZ, 3 hr, replicate 1

value: Shoot

source_name: Shoot, Mock, 3 hr, replicate 1


title: Shoot_tZ_12 hr_rep1

description: Gene expression profile of shoot at 12 hr after cytokinin treatment

source_name: Shoot, 1 μM tZ, 12 hr, replicate 1

source_name: Shoot, Mock, 12 hr, replicate 1


title: Root_JA_15 min_rep2

source_name: Root, 100 μM JA, 15 min, replicate 2

value: Jasmonic acid

value: 100 μM (±) Jasmonic acid

source_name: Root, Mock, 15 min, replicate 2


title: Shoot_tZ_6 hr_rep1

source_name: Shoot, 1 μM tZ, 6 hr, replicate 1

value: 6 hr

source_name: Shoot, Mock, 6 hr, replicate 1


title: Shoot_tZ_1 hr_rep2

description: Gene expression profile of shoot at 1 hr after cytokinin treatment

source_name: Shoot, 1 μM tZ, 1 hr, replicate 2

source_name: Shoot, Mock, 1 hr, replicate 2


title: Shoot_tZ_3 hr_rep2

source_name: Shoot, 1 μM tZ, 3 hr, replicate 2

value: 3 hr

source_name: Shoot, Mock, 3 hr, replicate 2


title: Shoot_tZ_12 hr_rep2

source_name: Shoot, 1 μM tZ, 12 hr, replicate 2

value: 12 hr

source_name: Shoot, Mock, 12 hr, replicate 2


title: Shoot_tZ_1 hr_rep1

source_name: Shoot, 1 μM tZ, 1 hr, replicate 1

value: 1 hr

source_name: Shoot, Mock, 1 hr, replicate 1


title: Root_tZ_30 min_rep3

description: Gene expression profile of root at 30 min after cytokinin treatment

source_name: Root, 1 μM tZ, 30 min, replicate 3

source_name: Root, Mock, 30 min, replicate 3


title: Root_tZ_6 hr_rep3

description: Gene expression profile of root at 6 hr after cytokinin treatment

source_name: Root, 1 μM tZ, 6 hr, replicate 3

source_name: Root, Mock, 6 hr, replicate 3


title: Root_tZ_1 hr_rep2

description: Gene expression profile of root at 1 hr after cytokinin treatment

source_name: Root, 1 μM tZ, 1 hr, replicate 2

source_name: Root, Mock, 1 hr, replicate 2


title: Root_tZ_3 hr_rep3

description: Gene expression profile of root at 3 hr after cytokinin treatment

source_name: Root, 1 μM tZ, 3 hr, replicate 3

source_name: Root, Mock, 3 hr, replicate 3


title: Root_tZ_30 min_rep1

source_name: Root, 1 μM tZ, 30 min, replicate 1

source_name: Root, Mock, 30 min, replicate 1


title: Root_tZ_3 hr_rep2

source_name: Root, 1 μM tZ, 3 hr, replicate 2

source_name: Root, Mock, 3 hr, replicate 2


title: Root_tZ_1 hr_rep3

source_name: Root, 1 μM tZ, 1 hr, replicate 3

source_name: Root, Mock, 1 hr, replicate 3


title: Root_tZ_15 min_rep2

description: Gene expression profile of root at 15 min after cytokinin treatment

source_name: Root, 1 μM tZ, 15 min, replicate 2

source_name: Root, Mock, 15 min, replicate 2


title: Root_tZ_15 min_rep3

source_name: Root, 1 μM tZ, 15 min, replicate 3

source_name: Root, Mock, 15 min, replicate 3


title: Shoot_BL_12 hr_rep2

description: Gene expression profile of shoot at 12 hr after brassinosteroid treatment

source_name: Shoot, 1 μM BL, 12 hr, replicate 2

value: Brassinosteroid

value: 1 μM Brassinolide

source_name: Shoot, Mock, 12 hr, replicate 2

value: 0.1% Ethanol


title: Shoot_BL_6 hr_rep2

description: Gene expression profile of shoot at 6 hr after brassinosteroid treatment

source_name: Shoot, 1 μM BL, 6 hr, replicate 2

source_name: Shoot, Mock, 6 hr, replicate 2


title: Shoot_BL_12 hr_rep1

source_name: Shoot, 1 μM BL, 12 hr, replicate 1

source_name: Shoot, Mock, 12 hr, replicate 1


title: Root_tZ_6 hr_rep2

source_name: Root, 1 μM tZ, 6 hr, replicate 2

value: Root

source_name: Root, Mock, 6 hr, replicate 2


title: Root_tZ_3 hr_rep1

source_name: Root, 1 μM tZ, 3 hr, replicate 1

value: Nipponbare

source_name: Root, Mock, 3 hr, replicate 1


title: Root_tZ_6 hr_rep1

source_name: Root, 1 μM tZ, 6 hr, replicate 1

source_name: Root, Mock, 6 hr, replicate 1


title: Shoot_BL_3 hr_rep2

description: Gene expression profile of shoot at 3 hr after brassinosteroid treatment

source_name: Shoot, 1 μM BL, 3 hr, replicate 2

source_name: Shoot, Mock, 3 hr, replicate 2


title: Root_BL_6 hr_rep3

description: Gene expression profile of root at 6 hr after brassinosteroid treatment

source_name: Root, 1 μM BL, 6 hr, replicate 3

source_name: Root, Mock, 6 hr, replicate 3


title: Root_tZ_1 hr_rep1

source_name: Root, 1 μM tZ, 1 hr, replicate 1

source_name: Root, Mock, 1 hr, replicate 1


title: Root_tZ_30 min_rep2

source_name: Root, 1 μM tZ, 30 min, replicate 2

value: 30 min

source_name: Root, Mock, 30 min, replicate 2


title: Shoot_BL_1 hr_rep2

description: Gene expression profile of shoot at 1 hr after brassinosteroid treatment

source_name: Shoot, 1 μM BL, 1 hr, replicate 2

source_name: Shoot, Mock, 1 hr, replicate 2


title: Shoot_BL_1 hr_rep1

source_name: Shoot, 1 μM BL, 1 hr, replicate 1

source_name: Shoot, Mock, 1 hr, replicate 1


title: Root_BL_3 hr_rep3

description: Gene expression profile of root at 3 hr after brassinosteroid treatment

source_name: Root, 1 μM BL, 3 hr, replicate 3

source_name: Root, Mock, 3 hr, replicate 3


title: Root_BL_6 hr_rep1

source_name: Root, 1 μM BL, 6 hr, replicate 1


title: Root_BL_3 hr_rep2

source_name: Root, 1 μM BL, 3 hr, replicate 2

source_name: Root, Mock, 3 hr, replicate 2


title: Shoot_BL_3 hr_rep1

source_name: Shoot, 1 μM BL, 3 hr, replicate 1

source_name: Shoot, Mock, 3 hr, replicate 1


title: Shoot_BL_6 hr_rep1

source_name: Shoot, 1 μM BL, 6 hr, replicate 1

source_name: Shoot, Mock, 6 hr, replicate 1


title: Root_tZ_15 min_rep1

source_name: Root, 1 μM tZ, 15 min, replicate 1

value: 15 min

source_name: Root, Mock, 15 min, replicate 1


title: Root_BL_6 hr_rep2

source_name: Root, 1 μM BL, 6 hr, replicate 2

source_name: Root, Mock, 6 hr, replicate 2


title: Root_BL_1 hr_rep3

description: Gene expression profile of root at 1 hr after brassinosteroid treatment

source_name: Root, 1 μM BL, 1 hr, replicate 3

source_name: Root, Mock, 1 hr, replicate 3


title: Shoot_IAA_12 hr_rep2

description: Gene expression profile of shoot at 12 hr after auxin treatment

source_name: Shoot, 10 μM IAA, 12 hr, replicate 2

value: Auxin

value: 10 μM Indole-3-acetic acid

source_name: Shoot, Mock, 12 hr, replicate 2


title: Shoot_IAA_6 hr_rep2

description: Gene expression profile of shoot at 6 hr after auxin treatment

source_name: Shoot, 10 μM IAA, 6 hr, replicate 2

value: Seven days after germination

source_name: Shoot, Mock, 6 hr, replicate 2


title: Root_BL_30 min_rep3

description: Gene expression profile of root at 30 min after brassinosteroid treatment

source_name: Root, 1 μM BL, 30 min, replicate 3

source_name: Root, Mock, 30 min, replicate 3


title: Shoot_IAA_6 hr_rep1

source_name: Shoot, 10 μM IAA, 6 hr, replicate 1

value: Shoot


title: Root_BL_30 min_rep1

source_name: Root, 1 μM BL, 30 min, replicate 1

source_name: Root, Mock, 30 min, replicate 1


title: Root_BL_15 min_rep1

description: Gene expression profile of root at 15 min after brassinosteroid treatment

source_name: Root, 1 μM BL, 15 min, replicate 1


title: Root_BL_15 min_rep2

source_name: Root, 1 μM BL, 15 min, replicate 2

source_name: Root, Mock, 15 min, replicate 2


title: Shoot_IAA_3 hr_rep2

description: Gene expression profile of shoot at 3 hr after auxin treatment

source_name: Shoot, 10 μM IAA, 3 hr, replicate 2

source_name: Shoot, Mock, 3 hr, replicate 2


title: Root_BL_30 min_rep2

source_name: Root, 1 μM BL, 30 min, replicate 2

source_name: Root, Mock, 30 min, replicate 2


title: Shoot_IAA_12 hr_rep1

source_name: Shoot, 10 μM IAA, 12 hr, replicate 1

source_name: Shoot, Mock, 12 hr, replicate 1


title: Root_BL_1 hr_rep2

source_name: Root, 1 μM BL, 1 hr, replicate 2

source_name: Root, Mock, 1 hr, replicate 2


title: Root_BL_15 min_rep3

source_name: Root, 1 μM BL, 15 min, replicate 3

source_name: Root, Mock, 15 min, replicate 3


title: Root_BL_1 hr_rep1

source_name: Root, 1 μM BL, 1 hr, replicate 1

source_name: Root, Mock, 1 hr, replicate 1


title: Shoot_IAA_1 hr_rep1

description: Gene expression profile of shoot at 1 hr after auxin treatment

source_name: Shoot, 10 μM IAA, 1 hr, replicate 1

source_name: Shoot, Mock, 1 hr, replicate 1


title: Shoot_IAA_3 hr_rep1

source_name: Shoot, 10 μM IAA, 3 hr, replicate 1

source_name: Shoot, Mock, 3 hr, replicate 1


title: Root_IAA_6 hr_rep2

description: Gene expression profile of root at 6 hr after auxin treatment

source_name: Root, 10 μM IAA, 6 hr, replicate 2

source_name: Root, Mock, 6 hr, replicate 2


title: Shoot_IAA_1 hr_rep2

source_name: Shoot, 10 μM IAA, 1 hr, replicate 2

source_name: Shoot, Mock, 1 hr, replicate 2


title: Root_IAA_3 hr_rep3

description: Gene expression profile of root at 3 hr after auxin treatment

source_name: Root, 10 μM IAA, 3 hr, replicate 3

source_name: Root, Mock, 3 hr, replicate 3


title: Root_IAA_1 hr_rep2

description: Gene expression profile of root at 1 hr after auxin treatment

source_name: Root, 10 μM IAA, 1 hr, replicate 2


title: Root_IAA_6 hr_rep3

source_name: Root, 10 μM IAA, 6 hr, replicate 3

source_name: Root, Mock, 6 hr, replicate 3


title: Root_IAA_30 min_rep3

description: Gene expression profile of root at 30 min after auxin treatment

source_name: Root, 10 μM IAA, 30 min, replicate 3

source_name: Root, Mock, 30 min, replicate 3


title: Root_IAA_1 hr_rep1

source_name: Root, 10 μM IAA, 1 hr, replicate 1


title: Root_IAA_3 hr_rep2

source_name: Root, 10 μM IAA, 3 hr, replicate 2

source_name: Root, Mock, 3 hr, replicate 2


title: Root_IAA_3 hr_rep1

source_name: Root, 10 μM IAA, 3 hr, replicate 1

source_name: Root, Mock, 3 hr, replicate 1


title: Root_IAA_15 min_rep3

description: Gene expression profile of root at 15 min after auxin treatment

source_name: Root, 10 μM IAA, 15 min, replicate 3

source_name: Root, Mock, 15 min, replicate 3


title: Root_BL_3 hr_rep1

source_name: Root, 1 μM BL, 3 hr, replicate 1


title: Shoot_GA3_12 hr_rep2

description: Gene expression profile of shoot at 12 hr after gibberellin treatment

source_name: Shoot, 10 μM GA3, 12 hr, replicate 2

value: Gibberelin

value: 10 μM Gibberellic acid 3

source_name: Shoot, Mock, 12 hr, replicate 2


title: Root_IAA_30 min_rep1

source_name: Root, 10 μM IAA, 30 min, replicate 1

source_name: Root, Mock, 30 min, replicate 1


title: Root_IAA_15 min_rep1

source_name: Root, 10 μM IAA, 15 min, replicate 1

source_name: Root, Mock, 15 min, replicate 1


title: Shoot_GA3_3 hr_rep1

description: Gene expression profile of shoot at 3 hr after gibberellin treatment

source_name: Shoot, 10 μM GA3, 3 hr, replicate 1

source_name: Shoot, Mock, 3 hr, replicate 1


title: Root_IAA_15 min_rep2

source_name: Root, 10 μM IAA, 15 min, replicate 2

source_name: Root, Mock, 15 min, replicate 2


title: Shoot_GA3_1 hr_rep2

description: Gene expression profile of shoot at 1 hr after gibberellin treatment

source_name: Shoot, 10 μM GA3, 1 hr, replicate 2

source_name: Shoot, Mock, 1 hr, replicate 2


title: Shoot_GA3_12 hr_rep1

source_name: Shoot, 10 μM GA3, 12 hr, replicate 1

source_name: Shoot, Mock, 12 hr, replicate 1


title: Shoot_GA3_6 hr_rep2

description: Gene expression profile of shoot at 6 hr after gibberellin treatment

source_name: Shoot, 10 μM GA3, 6 hr, replicate 2

value: 6 hr

source_name: Shoot, Mock, 6 hr, replicate 2


title: Root_GA3_6 hr_rep3

description: Gene expression profile of root at 6 hr after gibberellin treatment

source_name: Root, 10 μM GA3, 6 hr, replicate 3

source_name: Root, Mock, 6 hr, replicate 3


title: Shoot_GA3_3 hr_rep2

source_name: Shoot, 10 μM GA3, 3 hr, replicate 2

value: 3 hr

source_name: Shoot, Mock, 3 hr, replicate 2


title: Shoot_GA3_6 hr_rep1

source_name: Shoot, 10 μM GA3, 6 hr, replicate 1

source_name: Shoot, Mock, 6 hr, replicate 1


title: Shoot_GA3_1 hr_rep1

source_name: Shoot, 10 μM GA3, 1 hr, replicate 1

source_name: Shoot, Mock, 1 hr, replicate 1


title: Root_GA3_6 hr_rep2

source_name: Root, 10 μM GA3, 6 hr, replicate 2

source_name: Root, Mock, 6 hr, replicate 2


title: Root_IAA_6 hr_rep1

source_name: Root, 10 μM IAA, 6 hr, replicate 1

source_name: Root, Mock, 6 hr, replicate 1


title: Root_IAA_1 hr_rep3

source_name: Root, 10 μM IAA, 1 hr, replicate 3

source_name: Root, Mock, 1 hr, replicate 3


title: Root_GA3_3 hr_rep2

description: Gene expression profile of root at 3 hr after gibberellin treatment

source_name: Root, 10 μM GA3, 3 hr, replicate 2

source_name: Root, Mock, 3 hr, replicate 2


title: Root_GA3_3 hr_rep3

source_name: Root, 10 μM GA3, 3 hr, replicate 3

source_name: Root, Mock, 3 hr, replicate 3


title: Root_IAA_30 min_rep2

source_name: Root, 10 μM IAA, 30 min, replicate 2

source_name: Root, Mock, 30 min, replicate 2


title: Root_GA3_1 hr_rep2

description: Gene expression profile of root at 1 hr after gibberellin treatment

source_name: Root, 10 μM GA3, 1 hr, replicate 2

source_name: Root, Mock, 1 hr, replicate 2


title: Root_GA3_1 hr_rep1

source_name: Root, 10 μM GA3, 1 hr, replicate 1

source_name: Root, Mock, 1 hr, replicate 1


title: Root_GA3_3 hr_rep1

source_name: Root, 10 μM GA3, 3 hr, replicate 1

source_name: Root, Mock, 3 hr, replicate 1


title: Root_GA3_30 min_rep3

description: Gene expression profile of root at 30 min after gibberellin treatment

source_name: Root, 10 μM GA3, 30 min, replicate 3

source_name: Root, Mock, 30 min, replicate 3


title: Root_GA3_15 min_rep2

description: Gene expression profile of root at 15 min after gibberellin treatment

source_name: Root, 10 μM GA3, 15 min, replicate 2

source_name: Root, Mock, 15 min, replicate 2


title: Root_GA3_6 hr_rep1

source_name: Root, 10 μM GA3, 6 hr, replicate 1

source_name: Root, Mock, 6 hr, replicate 1


title: Root_GA3_15 min_rep3

source_name: Root, 10 μM GA3, 15 min, replicate 3

source_name: Root, Mock, 15 min, replicate 3


title: Shoot_ABA_12 hr_rep2

description: Gene expression profile of shoot at 12 hr after abscisic acid treatment

source_name: Shoot, 50 μM ABA, 12 hr, replicate 2

value: Abscisic acid

value: 50 μM (±) Abscisic acid

value: 12 hr

source_name: Shoot, Mock, 12 hr, replicate 2


title: Root_GA3_30 min_rep1

source_name: Root, 10 μM GA3, 30 min, replicate 1

source_name: Root, Mock, 30 min, replicate 1


title: Root_GA3_1 hr_rep3

source_name: Root, 10 μM GA3, 1 hr, replicate 3

value: 1 hr

source_name: Root, Mock, 1 hr, replicate 3


title: Shoot_ABA_12 hr_rep1

source_name: Shoot, 50 μM ABA, 12 hr, replicate 1

source_name: Shoot, Mock, 12 hr, replicate 1

value: 0.1% Ethanol


title: Root_GA3_15 min_rep1

source_name: Root, 10 μM GA3, 15 min, replicate 1

value: Root

source_name: Root, Mock, 15 min, replicate 1


title: Root_GA3_30 min_rep2

source_name: Root, 10 μM GA3, 30 min, replicate 2

value: Nipponbare

source_name: Root, Mock, 30 min, replicate 2


title: Root_ABA_6 hr_rep3

description: Gene expression profile of root at 6 hr after abscisic acid treatment

source_name: Root, 50 μM ABA, 6 hr, replicate 3

source_name: Root, Mock, 6 hr, replicate 3


title: Shoot_ABA_1 hr_rep1

description: Gene expression profile of shoot at 1 hr after abscisic acid treatment

source_name: Shoot, 50 μM ABA, 1 hr, replicate 1

source_name: Shoot, Mock, 1 hr, replicate 1


title: Shoot_ABA_1 hr_rep2

source_name: Shoot, 50 μM ABA, 1 hr, replicate 2

source_name: Shoot, Mock, 1 hr, replicate 2


title: Root_ABA_3 hr_rep2

description: Gene expression profile of root at 3 hr after abscisic acid treatment

source_name: Root, 50 μM ABA, 3 hr, replicate 2

source_name: Root, Mock, 3 hr, replicate 2


title: Shoot_ABA_6 hr_rep2

description: Gene expression profile of shoot at 6 hr after abscisic acid treatment

source_name: Shoot, 50 μM ABA, 6 hr, replicate 2

source_name: Shoot, Mock, 6 hr, replicate 2


title: Root_ABA_3 hr_rep1

source_name: Root, 50 μM ABA, 3 hr, replicate 1

source_name: Root, Mock, 3 hr, replicate 1


title: Shoot_ABA_3 hr_rep1

description: Gene expression profile of shoot at 3 hr after abscisic acid treatment

source_name: Shoot, 50 μM ABA, 3 hr, replicate 1

source_name: Shoot, Mock, 3 hr, replicate 1


title: Root_ABA_6 hr_rep2

source_name: Root, 50 μM ABA, 6 hr, replicate 2

source_name: Root, Mock, 6 hr, replicate 2


title: Root_ABA_3 hr_rep3

source_name: Root, 50 μM ABA, 3 hr, replicate 3

source_name: Root, Mock, 3 hr, replicate 3


title: Root_ABA_6 hr_rep1

source_name: Root, 50 μM ABA, 6 hr, replicate 1

source_name: Root, Mock, 6 hr, replicate 1


title: Root_ABA_1 hr_rep3

description: Gene expression profile of root at 1 hr after abscisic acid treatment

source_name: Root, 50 μM ABA, 1 hr, replicate 3

source_name: Root, Mock, 1 hr, replicate 3


title: Shoot_ABA_6 hr_rep1

source_name: Shoot, 50 μM ABA, 6 hr, replicate 1

source_name: Shoot, Mock, 6 hr, replicate 1


title: Root_ABA_30 min_rep3

description: Gene expression profile of root at 30 min after abscisic acid treatment

source_name: Root, 50 μM ABA, 30 min, replicate 3

value: 30 min

source_name: Root, Mock, 30 min, replicate 3


title: Root_ABA_1 hr_rep2

source_name: Root, 50 μM ABA, 1 hr, replicate 2

source_name: Root, Mock, 1 hr, replicate 2


title: Root_Pretreatment_0 min_rep1

description: Gene expression profile of root at 0 min (pretreatment)

source_name: Root, Pretreatment, 0 min, replicate 1

value: Pretreatment

value: 0 min

source_name: Root, Pretreatment, 0 min, replicate 4


title: Root_ABA_1 hr_rep1

source_name: Root, 50 μM ABA, 1 hr, replicate 1

source_name: Root, Mock, 1 hr, replicate 1


title: Embryo_10 DAF_rep2

description: Gene expression of embryo at 10 days after flowering

hyb_protocol: For microarray hybridization, 1650 ng of cyanine 3-labeled cRNA (or entire labeled cRNA for samples with low yield) were fragmented and hybridized with the rice 4x44K microarray RAP-DB (G2519F#15241) at 65°C for 17 hours using the Agilent Gene Expression Hybridization Kit.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended processed signal intensities. The processed signal intensities were used for 75 percentile normalization and log2 transformation with GenespringGX11(Agilent).

source_name: Embryo at 10 days after flowering, replicate 2

extract_protocol: Total RNA was extracted using RNeasy Plant Minikit (QIAGEN). The extracted RNA was quantified using NanoDrop ND-1000 UV-VIS spectrophotometer (NanoDrop) and quality-checked using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

value: Embryo

value: 10 days after flowering


title: Root_ABA_30 min_rep1

source_name: Root, 50 μM ABA, 30 min, replicate 1

value: Seven days after germination

source_name: Root, Mock, 30 min, replicate 1


title: Root_Pretreatment_0 min_rep2

source_name: Root, Pretreatment, 0 min, replicate 2

source_name: Root, Pretreatment, 0 min, replicate 5


title: Shoot_Pretreatment_0 min_rep1

description: Gene expression profile of shoot at 0 min (pretreatment)

source_name: Shoot, Pretreatment, 0 min, replicate 1

value: Shoot

source_name: Shoot, Pretreatment, 0 min, replicate 3


title: Root_ABA_15 min_rep1

description: Gene expression profile of root at 15 min after abscisic acid treatment

source_name: Root, 50 μM ABA, 15 min, replicate 1

value: 15 min

source_name: Root, Mock, 15 min, replicate 1


title: Root_ABA_15 min_rep3

source_name: Root, 50 μM ABA, 15 min, replicate 3

source_name: Root, Mock, 15 min, replicate 3


title: Shoot_Pretreatment_0 min_rep2

source_name: Shoot, Pretreatment, 0 min, replicate 2

source_name: Shoot, Pretreatment, 0 min, replicate 4


title: Root_ABA_30 min_rep2

source_name: Root, 50 μM ABA, 30 min, replicate 2

source_name: Root, Mock, 30 min, replicate 2


title: Embryo_08 DAF_rep2

description: Gene expression of embryo at 8 days after flowering

source_name: Embryo at 8 days after flowering, replicate 2

value: 8 days after flowering


title: Embryo_09 DAF_rep1

description: Gene expression of embryo at 9 days after flowering

source_name: Embryo at 9 days after flowering, replicate 1

value: 9 days after flowering


title: Shoot_ABA_3 hr_rep2

source_name: Shoot, 50 μM ABA, 3 hr, replicate 2

value: Abscisic acid

value: 3 hr

source_name: Shoot, Mock, 3 hr, replicate 2


title: Embryo_08 DAF_rep1

source_name: Embryo at 8 days after flowering, replicate 1


title: Embryo_10 DAF_rep1

source_name: Embryo at 10 days after flowering, replicate 1


title: Root_Pretreatment_0 min_rep3

source_name: Root, Pretreatment, 0 min, replicate 3

source_name: Root, Pretreatment, 0 min, replicate 6


title: Root_ABA_15 min_rep2

source_name: Root, 50 μM ABA, 15 min, replicate 2

value: 50 μM (±) Abscisic acid

source_name: Root, Mock, 15 min, replicate 2


title: Embryo_09 DAF_rep2

source_name: Embryo at 9 days after flowering, replicate 2


title: Embryo_07 DAF_rep2

description: Gene expression of embryo at 7 days after flowering

source_name: Embryo at 7 days after flowering, replicate 2

value: 7 days after flowering


title: Embryo_05 DAF_rep2

description: Gene expression of embryo at 5 days after flowering

source_name: Embryo at 5 days after flowering, replicate 2

value: 5 days after flowering


title: Embryo_06 DAF_rep1

description: Gene expression of embryo at 6 days after flowering

source_name: Embryo at 6 days after flowering, replicate 1

value: 6 days after flowering


title: Embryo_06 DAF_rep2

source_name: Embryo at 6 days after flowering, replicate 2

value: Nipponbare


title: Embryo_04 DAF_rep2

description: Gene expression of embryo at 4 days after flowering

source_name: Embryo at 4 days after flowering, replicate 2

value: 4 days after flowering


title: Embryo_04 DAF_rep1

source_name: Embryo at 4 days after flowering, replicate 1


title: Embryo_05 DAF_rep1

source_name: Embryo at 5 days after flowering, replicate 1


title: Ovary_10 DAF_rep2

description: Gene expression of ovary at 10 days after flowering

source_name: Ovary at 10 days after flowering, replicate 2

value: Ovary

value: Daytime 10:00


title: Ovary_09 DAF_rep1

description: Gene expression of ovary at 9 days after flowering

source_name: Ovary at 9 days after flowering, replicate 1


title: Ovary_10 DAF_rep1

source_name: Ovary at 10 days after flowering, replicate 1


title: Ovary_09 DAF_rep2

source_name: Ovary at 9 days after flowering, replicate 2


title: Ovary_08 DAF_rep2

description: Gene expression of ovary at 8 days after flowering

source_name: Ovary at 8 days after flowering, replicate 2


title: Embryo_07 DAF_rep1

source_name: Embryo at 7 days after flowering, replicate 1

value: Embryo


title: Ovary_04 DAF_rep2

description: Gene expression of ovary at 4 days after flowering

source_name: Ovary at 4 days after flowering, replicate 2


title: Inflorescence_4.0-5.0 mm_rep2

description: Gene expression of 4.0-5.1 mm inflorescence

hyb_protocol: For microarray hybridization, 1650 ng of cyanine 3-labeled cRNA  were fragmented and hybridized with the rice 4x44K microarray RAP-DB (G2519F#15241) at 65°C for 17 hours using the Agilent Gene Expression Hybridization Kit.

source_name: 4.0-5.0 mm inflorescence, replicate 2

value: Inflorescence

value: Daytime


title: Ovary_06 DAF_rep1

description: Gene expression of ovary at 6 days after flowering

source_name: Ovary at 6 days after flowering, replicate 1


title: Inflorescence_2.0-2.5 mm_rep2

description: Gene expression of 2.0-2.5 mm inflorescence

source_name: 2.0-2.5 mm inflorescence, replicate 2


title: Inflorescence_4.0-5.0 mm_rep1

description: Gene expression of 4.0-5.0 mm inflorescence

source_name: 4.0-5.0 mm inflorescence, replicate 1


title: Inflorescence_2.5-3.0 mm_rep2

description: Gene expression of 2.5-3.0 mm inflorescence

source_name: 2.5-3.0 mm inflorescence, replicate 2


title: Ovary_02 DAF_rep2

description: Gene expression of ovary at 2 days after flowering

source_name: Ovary at 2 days after flowering, replicate 2

value: 2 days after flowering


title: Root_83DAT_24:00

description: Gene expression of root at nighttime 83 days after transplanting

hyb_protocol: For hybridization, 1650 ng of cyanine 3-labeled cRNA is fragmented and hybridized on the slide of rice 4x44K microarray RAP-DB (G2519F#15241) at 65°C for 17 hours using the Agilent Gene Expression Hybridization Kit.

source_name: Root, 83 days after transplanting, 24:00

growth_protocol: All plants were grown in paddy field in Tsukuba, Japan (~36o N latitude) during a normal rice growing season in 2008.

extract_protocol: Total RNA was extracted using RNeasy Plant Mini Kit (QIAGEN) according to the manufacturer's protocol, quantitied using NanoDrop ND-1000 UV-VIS spectrophotometer (NanoDrop) and quality-checked using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

value: Root

value: 83 days after transplanting

value: nighttime 24:00


title: Ovary_04 DAF_rep1

source_name: Ovary at 4 days after flowering, replicate 1


title: Inflorescence_1.5-2.0 mm_rep1

description: Gene expression of 1.5-2.0 mm inflorescence

source_name: 1.5-2.0 mm inflorescence, replicate 1


title: Root_97DAT_24:00

description: Gene expression of root at nighttime 97 days after transplanting

source_name: Root, 97 days after transplanting, 24:00

value: 97 days after transplanting


title: Inflorescence_2.5-3.0 mm_rep1

source_name: 2.5-3.0 mm inflorescence, replicate 1


title: Root_55DAT_24:00

description: Gene expression of root at nighttime 55 days after transplanting

source_name: Root, 55 days after transplanting, 24:00

value: 55 days after transplanting


title: Ovary_06 DAF_rep2

source_name: Ovary at 6 days after flowering, replicate 2


title: Ovary_08 DAF_rep1

source_name: Ovary at 8 days after flowering, replicate 1

value: 8 days after flowering


title: Inflorescence_1.0-1.5 mm_rep2

description: Gene expression of 1.0-1.5 mm inflorescence

source_name: 1.0-1.5 mm inflorescence, replicate 2


title: Inflorescence_2.0-2.5 mm_rep1

source_name: 2.0-2.5 mm inflorescence, replicate 1


title: Root_69DAT_24:00

description: Gene expression of root at nighttime 69 days after transplanting

source_name: Root, 69 days after transplanting, 24:00

value: 69 days after transplanting


title: Inflorescence_1.0-1.5 mm_rep1

source_name: 1.0-1.5 mm inflorescence, replicate 1


title: Inflorescence_1.5-2.0 mm_rep2

source_name: 1.5-2.0 mm inflorescence, replicate 2


title: Root_90DAT_24:00

description: Gene expression of root at nighttime 90 days after transplanting

source_name: Root, 90 days after transplanting, 24:00

value: 90 days after transplanting


title: Root_104DAT_24:00

description: Gene expression of root at nighttime 104 days after transplanting

source_name: Root, 104 days after transplanting, 24:00

value: 104 days after transplanting


title: Root_48DAT_24:00

description: Gene expression of root at nighttime 48 days after transplanting

source_name: Root, 48 days after transplanting, 24:00

value: Nipponbare

value: 48 days after transplanting


title: Ovary_02 DAF_rep1

source_name: Ovary at 2 days after flowering, replicate 1

value: Ovary


title: Root_13DAT_24:00

description: Gene expression of root at nighttime 13 days after transplanting

source_name: Root, 13 days after transplanting, 24:00

value: 13 days after transplanting


title: Root_62DAT_24:00

description: Gene expression of root at nighttime 62 days after transplanting

source_name: Root, 62 days after transplanting, 24:00

value: 62 days after transplanting


title: Root_34DAT_24:00

description: Gene expression of root at nighttime 34 days after transplanting

source_name: Root, 34 days after transplanting, 24:00

value: 34 days after transplanting


title: Root_97DAT_12:00

description: Gene expression of root at daytime 97 days after transplanting

source_name: Root, 97 days after transplanting, 12:00

value: Daytime 12:00


title: Root_41DAT_24:00

description: Gene expression of root at nighttime 41 days after transplanting

source_name: Root, 41 days after transplanting, 24:00

value: 41 days after transplanting


title: Root_83DAT_12:00

description: Gene expression of root at daytime 83 days after transplanting

source_name: Root, 83 days after transplanting, 12:00

value: Root


title: Root_104DAT_12:00

description: Gene expression of root at daytime 104 days after transplanting

source_name: Root, 104 days after transplanting, 12:00


title: Root_62DAT_12:00

description: Gene expression of root at daytime 62 days after transplanting

source_name: Root, 62 days after transplanting, 12:00


title: Root_69DAT_12:00

description: Gene expression of root at daytime 69 days after transplanting

source_name: Root, 69 days after transplanting, 12:00


title: Root_20DAT_24:00

description: Gene expression of root at nighttime 20 days after transplanting

source_name: Root, 20 days after transplanting, 24:00

value: 20 days after transplanting


title: Root_34DAT_12:00

description: Gene expression of root at daytime 34 days after transplanting

source_name: Root, 34 days after transplanting, 12:00


title: Root_41DAT_12:00

description: Gene expression of root at daytime 41 days after transplanting

source_name: Root, 41 days after transplanting, 12:00


title: Root_45DAT_10:00

description: Gene expression of Root at 45 days after transplanting, 10:00

source_name: Root, 45 days after transplanting, 10:00

value: 45 days after transplanting


title: Root_45DAT_02:00

description: Gene expression of Root at 45 days after transplanting, 02:00

source_name: Root, 45 days after transplanting, 02:00


title: Root_48DAT_12:00

description: Gene expression of root at daytime 48 days after transplanting

source_name: Root, 48 days after transplanting, 12:00


title: Root_45DAT_08:00

description: Gene expression of Root at 45 days after transplanting, 08:00

source_name: Root, 45 days after transplanting, 08:00


title: Root_45DAT_04:00

description: Gene expression of Root at 45 days after transplanting, 04:00

source_name: Root, 45 days after transplanting, 04:00


title: Root_44DAT_16:00

description: Gene expression of Root at 44 days after transplanting, 16:00

source_name: Root, 44 days after transplanting, 16:00

value: 44 days after transplanting


title: Root_90DAT_12:00

description: Gene expression of root at daytime 90 days after transplanting

source_name: Root, 90 days after transplanting, 12:00


title: Root_44DAT_24:00

description: Gene expression of Root at 44 days after transplanting, 24:00

source_name: Root, 44 days after transplanting, 24:00


title: Root_13DAT_12:00

description: Gene expression of root at daytime 13 days after transplanting

source_name: Root, 13 days after transplanting, 12:00


title: Root_44DAT_18:00

description: Gene expression of Root at 44 days after transplanting, 18:00

source_name: Root, 44 days after transplanting, 18:00


title: Root_55DAT_12:00

description: Gene expression of root at daytime 55 days after transplanting

source_name: Root, 55 days after transplanting, 12:00

value: 55 days after transplanting


title: Root_44DAT_20:00

description: Gene expression of Root at 44 days after transplanting, 20:00

source_name: Root, 44 days after transplanting, 20:00


title: Root_20DAT_12:00

description: Gene expression of root at daytime 20 days after transplanting

source_name: Root, 20 days after transplanting, 12:00


title: Root_45DAT_06:00

description: Gene expression of Root at 45 days after transplanting, 06:00

source_name: Root, 45 days after transplanting, 06:00


title: Root_44DAT_22:00

description: Gene expression of Root at 44 days after transplanting, 22:00

source_name: Root, 44 days after transplanting, 22:00


title: Root_44DAT_10:00

description: Gene expression of Root at 44 days after transplanting, 10:00

source_name: Root, 44 days after transplanting, 10:00


title: Root_44DAT_12:00

description: Gene expression of Root at 44 days after transplanting, 12:00

source_name: Root, 44 days after transplanting, 12:00


title: Root_44DAT_14:00

description: Gene expression of Root at 44 days after transplanting, 14:00

source_name: Root, 44 days after transplanting, 14:00


title: Root_44DAT_04:00

description: Gene expression of Root at 44 days after transplanting, 04:00

source_name: Root, 44 days after transplanting, 04:00


title: Root_44DAT_02:00

description: Gene expression of Root at 44 days after transplanting, 02:00

source_name: Root, 44 days after transplanting, 02:00


title: Root_43DAT_20:00

description: Gene expression of Root at 43 days after transplanting, 20:00

source_name: Root, 43 days after transplanting, 20:00

value: 43 days after transplanting


title: Root_43DAT_22:00

description: Gene expression of Root at 43 days after transplanting, 22:00

source_name: Root, 43 days after transplanting, 22:00


title: Root_44DAT_08:00

description: Gene expression of Root at 44 days after transplanting, 08:00

source_name: Root, 44 days after transplanting, 08:00


title: Root_44DAT_06:00

description: Gene expression of Root at 44 days after transplanting, 06:00

source_name: Root, 44 days after transplanting, 06:00


title: Root_43DAT_12:00

description: Gene expression of Root at 43 days after transplanting, 12:00

source_name: Root, 43 days after transplanting, 12:00


title: Root_43DAT_16:00

description: Gene expression of Root at 43 days after transplanting, 16:00

source_name: Root, 43 days after transplanting, 16:00


title: Root_16DAT_24:00

description: Gene expression of Root at 16 days after transplanting, 24:00

source_name: Root, 16 days after transplanting, 24:00

value: 16 days after transplanting


title: Root_17DAT_02:00

description: Gene expression of Root at 17 days after transplanting, 02:00

source_name: Root, 17 days after transplanting, 02:00

value: 17 days after transplanting


title: Root_43DAT_18:00

description: Gene expression of Root at 43 days after transplanting, 18:00

source_name: Root, 43 days after transplanting, 18:00


title: Root_43DAT_14:00

description: Gene expression of Root at 43 days after transplanting, 14:00

source_name: Root, 43 days after transplanting, 14:00


title: Root_43DAT_24:00

description: Gene expression of Root at 43 days after transplanting, 24:00

source_name: Root, 43 days after transplanting, 24:00


title: Root_43DAT_10:00

description: Gene expression of Root at 43 days after transplanting, 10:00

source_name: Root, 43 days after transplanting, 10:00


title: Root_17DAT_06:00

description: Gene expression of Root at 17 days after transplanting, 06:00

source_name: Root, 17 days after transplanting, 06:00


title: Root_16DAT_12:00

description: Gene expression of Root at 16 days after transplanting, 12:00

source_name: Root, 16 days after transplanting, 12:00


title: Root_17DAT_04:00

description: Gene expression of Root at 17 days after transplanting, 04:00

source_name: Root, 17 days after transplanting, 04:00


title: Root_16DAT_22:00

description: Gene expression of Root at 16 days after transplanting, 22:00

source_name: Root, 16 days after transplanting, 22:00


title: Root_17DAT_10:00

description: Gene expression of Root at 17 days after transplanting, 10:00

source_name: Root, 17 days after transplanting, 10:00


title: Root_17DAT_08:00

description: Gene expression of Root at 17 days after transplanting, 08:00

source_name: Root, 17 days after transplanting, 08:00


title: Root_16DAT_16:00

description: Gene expression of Root at 16 days after transplanting, 16:00

source_name: Root, 16 days after transplanting, 16:00


title: Root_16DAT_18:00

description: Gene expression of Root at 16 days after transplanting, 18:00

source_name: Root, 16 days after transplanting, 18:00


title: Root_16DAT_06:00

description: Gene expression of Root at 16 days after transplanting, 06:00

source_name: Root, 16 days after transplanting, 06:00


title: Root_15DAT_24:00

description: Gene expression of Root at 15 days after transplanting, 24:00

source_name: Root, 15 days after transplanting, 24:00

value: 15 days after transplanting


title: Root_16DAT_10:00

description: Gene expression of Root at 16 days after transplanting, 10:00

source_name: Root, 16 days after transplanting, 10:00

value: Nipponbare


title: Root_15DAT_16:00

description: Gene expression of Root at 15 days after transplanting, 16:00

source_name: Root, 15 days after transplanting, 16:00


title: Root_16DAT_02:00

description: Gene expression of Root at 16 days after transplanting, 02:00

source_name: Root, 16 days after transplanting, 02:00


title: Root_15DAT_14:00

description: Gene expression of Root at 15 days after transplanting, 14:00

source_name: Root, 15 days after transplanting, 14:00


title: Root_16DAT_20:00

description: Gene expression of Root at 16 days after transplanting, 20:00

source_name: Root, 16 days after transplanting, 20:00


title: Root_15DAT_22:00

description: Gene expression of Root at 15 days after transplanting, 22:00

source_name: Root, 15 days after transplanting, 22:00


title: Root_16DAT_14:00

description: Gene expression of Root at 16 days after transplanting, 14:00

source_name: Root, 16 days after transplanting, 14:00


title: Root_16DAT_04:00

description: Gene expression of Root at 16 days after transplanting, 04:00

source_name: Root, 16 days after transplanting, 04:00


title: Root_15DAT_20:00

description: Gene expression of Root at 15 days after transplanting, 20:00

source_name: Root, 15 days after transplanting, 20:00


title: Root_15DAT_12:00

description: Gene expression of Root at 15 days after transplanting, 12:00

source_name: Root, 15 days after transplanting, 12:00


title: Root_16DAT_08:00

description: Gene expression of Root at 16 days after transplanting, 08:00

source_name: Root, 16 days after transplanting, 08:00


title: LeafBlade_78DAT_19:20

description: Gene expression of leaf blade at 78 days after transplanting, 19:20

source_name: Leaf blade, 78 days after transplanting, 19:20

label_protocol: 400 ng of total RNA was added with one-color spike-mix and labeling was performed using Quick Amp Labeling Kit, One-Color (Agilent) in the presence of cyanine-3-CTP accoring to the manufacturer's protocol. The cyanine-3-labeled cRNA was purified by RNeasy Mini Kit (QIAGEN), and quantified using NanoDrop ND-1000 UV-VIS spectrophotometer.

value: Leaf Blade

value: 78 days after transplanting


title: LeafBlade_78DAT_19:50

description: Gene expression of leaf blade at 78 days after transplanting, 19:50

source_name: Leaf blade, 78 days after transplanting, 19:50


title: LeafBlade_78DAT_19:40

description: Gene expression of leaf blade at 78 days after transplanting, 19:40

source_name: Leaf blade, 78 days after transplanting, 19:40


title: LeafBlade_78DAT_19:10

description: Gene expression of leaf blade at 78 days after transplanting, 19:10

source_name: Leaf blade, 78 days after transplanting, 19:10


title: LeafBlade_78DAT_18:30

description: Gene expression of leaf blade at 78 days after transplanting, 18:30

source_name: Leaf blade, 78 days after transplanting, 18:30


title: LeafBlade_78DAT_19:00

description: Gene expression of leaf blade at 78 days after transplanting, 19:00

source_name: Leaf blade, 78 days after transplanting, 19:00


title: Root_15DAT_10:00

description: Gene expression of Root at 15 days after transplanting, 10:00

source_name: Root, 15 days after transplanting, 10:00


title: LeafBlade_78DAT_18:50

description: Gene expression of leaf blade at 78 days after transplanting, 18:50

source_name: Leaf blade, 78 days after transplanting, 18:50


title: LeafBlade_78DAT_18:40

description: Gene expression of leaf blade at 78 days after transplanting, 18:40

source_name: Leaf blade, 78 days after transplanting, 18:40


title: Root_15DAT_18:00

description: Gene expression of Root at 15 days after transplanting, 18:00

source_name: Root, 15 days after transplanting, 18:00


title: LeafBlade_78DAT_19:30

description: Gene expression of leaf blade at 78 days after transplanting, 19:30

source_name: Leaf blade, 78 days after transplanting, 19:30


title: LeafBlade_78DAT_18:10

description: Gene expression of leaf blade at 78 days after transplanting, 18:10

source_name: Leaf blade, 78 days after transplanting, 18:10


title: LeafBlade_78DAT_18:20

description: Gene expression of leaf blade at 78 days after transplanting, 18:20

source_name: Leaf blade, 78 days after transplanting, 18:20


title: LeafBlade_78DAT_17:20

description: Gene expression of leaf blade at 78 days after transplanting, 17:20

source_name: Leaf blade, 78 days after transplanting, 17:20


title: LeafBlade_79DAT_6:00_rep2

description: Gene expression of leaf blade at 79 days after transplanting, 6:00

source_name: Leaf blade, 79 days after transplanting, 6:00, replicate 2

value: 79 days after transplanting


title: LeafBlade_78DAT_17:30

description: Gene expression of leaf blade at 78 days after transplanting, 17:30

source_name: Leaf blade, 78 days after transplanting, 17:30


title: LeafBlade_79DAT_5:10_rep2

description: Gene expression of leaf blade at 79 days after transplanting, 5:10

source_name: Leaf blade, 79 days after transplanting, 5:10, replicate 2


title: LeafBlade_79DAT_5:30_rep1

description: Gene expression of leaf blade at 79 days after transplanting, 5:30

source_name: Leaf blade, 79 days after transplanting, 5:30, replicate 1


title: LeafBlade_79DAT_5:40_rep1

description: Gene expression of leaf blade at 79 days after transplanting, 5:40

source_name: Leaf blade, 79 days after transplanting, 5:40, replicate 1


title: LeafBlade_79DAT_5:40_rep2

source_name: Leaf blade, 79 days after transplanting, 5:40, replicate 2


title: LeafBlade_78DAT_17:00

description: Gene expression of leaf blade at 78 days after transplanting, 17:00

source_name: Leaf blade, 78 days after transplanting, 17:00


title: LeafBlade_79DAT_5:50_rep1

description: Gene expression of leaf blade at 79 days after transplanting, 5:50

source_name: Leaf blade, 79 days after transplanting, 5:50, replicate 1


title: LeafBlade_79DAT_5:30_rep2

source_name: Leaf blade, 79 days after transplanting, 5:30, replicate 2


title: LeafBlade_79DAT_5:10_rep1

source_name: Leaf blade, 79 days after transplanting, 5:10, replicate 1


title: LeafBlade_78DAT_17:40

description: Gene expression of leaf blade at 78 days after transplanting, 17:40

source_name: Leaf blade, 78 days after transplanting, 17:40


title: LeafBlade_78DAT_17:10

description: Gene expression of leaf blade at 78 days after transplanting, 17:10

source_name: Leaf blade, 78 days after transplanting, 17:10


title: LeafBlade_79DAT_5:20_rep1

description: Gene expression of leaf blade at 79 days after transplanting, 5:20

source_name: Leaf blade, 79 days after transplanting, 5:20, replicate 1


title: LeafBlade_79DAT_4:40_rep2

description: Gene expression of leaf blade at 79 days after transplanting, 4:40

source_name: Leaf blade, 79 days after transplanting, 4:40, replicate 2


title: LeafBlade_79DAT_5:50_rep2

source_name: Leaf blade, 79 days after transplanting, 5:50, replicate 2


title: LeafBlade_79DAT_5:00_rep2

description: Gene expression of leaf blade at 79 days after transplanting, 5:00

source_name: Leaf blade, 79 days after transplanting, 5:00, replicate 2


title: LeafBlade_79DAT_5:00_rep1

source_name: Leaf blade, 79 days after transplanting, 5:00, replicate 1


title: LeafBlade_79DAT_4:50_rep2

description: Gene expression of leaf blade at 79 days after transplanting, 4:50

source_name: Leaf blade, 79 days after transplanting, 4:50, replicate 2


title: LeafBlade_79DAT_4:40_rep1

source_name: Leaf blade, 79 days after transplanting, 4:40, replicate 1


title: LeafBlade_79DAT_4:10_rep2

description: Gene expression of leaf blade at 79 days after transplanting, 4:10

source_name: Leaf blade, 79 days after transplanting, 4:10, replicate 2


title: LeafBlade_79DAT_4:50_rep1

source_name: Leaf blade, 79 days after transplanting, 4:50, replicate 1


title: LeafBlade_79DAT_4:00_rep2

description: Gene expression of leaf blade at 79 days after transplanting, 4:00

source_name: Leaf blade, 79 days after transplanting, 4:00, replicate 2


title: LeafBlade_79DAT_4:30_rep1

description: Gene expression of leaf blade at 79 days after transplanting, 4:30

source_name: Leaf blade, 79 days after transplanting, 4:30, replicate 1


title: LeafBlade_79DAT_4:10_rep1

source_name: Leaf blade, 79 days after transplanting, 4:10, replicate 1


title: LeafBlade_79DAT_3:50_rep2

description: Gene expression of leaf blade at 79 days after transplanting, 3:50

source_name: Leaf blade, 79 days after transplanting, 3:50, replicate 2


title: LeafBlade_118DAT_24:00_rep2

description: Gene expression of leaf blade at nighttime 118 days after transplanting

source_name: Leaf blade, 118 days after transplanting, 24:00, replicate 2

value: 118 days after transplanting

value: Nighttime 24:00


title: LeafBlade_104DAT_24:00_rep2

description: Gene expression of leaf blade at nighttime 104 days after transplanting

source_name: Leaf blade, 104 days after transplanting, 24:00, replicate 2

value: 104 days after transplanting


title: LeafBlade_118DAT_24:00_rep1

source_name: Leaf blade, 118 days after transplanting, 24:00, replicate 1


title: LeafBlade_90DAT_24:00_rep2

description: Gene expression of leaf blade at nighttime 90 days after transplanting

source_name: Leaf blade, 90 days after transplanting, 24:00, replicate 2

value: 90 days after transplanting


title: LeafBlade_69DAT_24:00_rep2

description: Gene expression of leaf blade at nighttime 69 days after transplanting

source_name: Leaf blade, 69 days after transplanting, 24:00, replicate 2

value: 69 days after transplanting


title: LeafBlade_111DAT_24:00_rep1

description: Gene expression of leaf blade at nighttime 111 days after transplanting

source_name: Leaf blade, 111 days after transplanting, 24:00, replicate 1

value: 111 days after transplanting


title: LeafBlade_97DAT_24:00_rep2

description: Gene expression of leaf blade at nighttime 97 days after transplanting

source_name: Leaf blade, 97 days after transplanting, 24:00, replicate 2

value: 97 days after transplanting


title: LeafBlade_90DAT_24:00_rep1

source_name: Leaf blade, 90 days after transplanting, 24:00, replicate 1


title: LeafBlade_97DAT_24:00_rep1

source_name: Leaf blade, 97 days after transplanting, 24:00, replicate 1


title: LeafBlade_111DAT_24:00_rep2

source_name: Leaf blade, 111 days after transplanting, 24:00, replicate 2


title: LeafBlade_55DAT_24:00_rep2

description: Gene expression of leaf blade at nighttime 55 days after transplanting

source_name: Leaf blade, 55 days after transplanting, 24:00, replicate 2


title: LeafBlade_83DAT_24:00_rep1

description: Gene expression of leaf blade at nighttime 83 days after transplanting

source_name: Leaf blade, 83 days after transplanting, 24:00, replicate 1

value: 83 days after transplanting


title: LeafBlade_79DAT_3:50_rep1

source_name: Leaf blade, 79 days after transplanting, 3:50, replicate 1


title: LeafBlade_48DAT_24:00_rep1

description: Gene expression of leaf blade at nighttime 48 days after transplanting

source_name: Leaf blade, 48 days after transplanting, 24:00, replicate 1

value: 48 days after transplanting


title: LeafBlade_41DAT_24:00_rep1

description: Gene expression of leaf blade at nighttime 41 days after transplanting

source_name: Leaf blade, 41 days after transplanting, 24:00, replicate 1

value: 41 days after transplanting


title: LeafBlade_83DAT_24:00_rep2

source_name: Leaf blade, 83 days after transplanting, 24:00, replicate 2


title: LeafBlade_62DAT_24:00_rep2

description: Gene expression of leaf blade at nighttime 62 days after transplanting

source_name: Leaf blade, 62 days after transplanting, 24:00, replicate 2

value: 62 days after transplanting


title: LeafBlade_55DAT_24:00_rep1

source_name: Leaf blade, 55 days after transplanting, 24:00, replicate 1

value: 55 days after transplanting


title: LeafBlade_48DAT_24:00_rep2

source_name: Leaf blade, 48 days after transplanting, 24:00, replicate 2


title: LeafBlade_62DAT_24:00_rep1

source_name: Leaf blade, 62 days after transplanting, 24:00, replicate 1


title: LeafBlade_78DAT_17:50

description: Gene expression of leaf blade at 78 days after transplanting, 17:50

source_name: Leaf blade, 78 days after transplanting, 17:50


title: LeafBlade_104DAT_24:00_rep1

source_name: Leaf blade, 104 days after transplanting, 24:00, replicate 1


title: LeafBlade_13DAT_24:00_rep1

description: Gene expression of leaf blade at nighttime 13 days after transplanting

source_name: Leaf blade, 13 days after transplanting, 24:00, replicate 1

value: 13 days after transplanting


title: LeafBlade_34DAT_24:00_rep2

description: Gene expression of leaf blade at nighttime 34 days after transplanting

source_name: Leaf blade, 34 days after transplanting, 24:00, replicate 2

value: Nipponbare

value: 34 days after transplanting


title: LeafBlade_34DAT_24:00_rep1

source_name: Leaf blade, 34 days after transplanting, 24:00, replicate 1

value: Leaf Blade


title: LeafBlade_20DAT_24:00_rep1

description: Gene expression of leaf blade at nighttime 20 days after transplanting

source_name: Leaf blade, 20 days after transplanting, 24:00, replicate 1

value: 20 days after transplanting


title: LeafBlade_69DAT_24:00_rep1

source_name: Leaf blade, 69 days after transplanting, 24:00, replicate 1


title: LeafBlade_114DAT_16:00

description: Gene expression of leaf blade at 114 days after transplanting, 16:00

source_name: Leaf blade, 114 days after transplanting, 16:00

value: 114 days after transplanting


title: LeafBlade_114DAT_08:00

description: Gene expression of leaf blade at 114 days after transplanting, 08:00

source_name: Leaf blade, 114 days after transplanting, 08:00


title: LeafBlade_41DAT_24:00_rep2

source_name: Leaf blade, 41 days after transplanting, 24:00, replicate 2

value: Nighttime 24:00


title: LeafBlade_115DAT_04:00

description: Gene expression of leaf blade at 115 days after transplanting, 04:00

source_name: Leaf blade, 115 days after transplanting, 04:00

value: 115 days after transplanting


title: LeafBlade_114DAT_04:00

description: Gene expression of leaf blade at 114 days after transplanting, 04:00

source_name: Leaf blade, 114 days after transplanting, 04:00


title: LeafBlade_20DAT_24:00_rep2

source_name: Leaf blade, 20 days after transplanting, 24:00, replicate 2


title: LeafBlade_79DAT_5:20_rep2

description: Gene expression of leaf blade at 79 days after transplanting, 5:20

source_name: Leaf blade, 79 days after transplanting, 5:20, replicate 2

value: 79 days after transplanting


title: LeafBlade_115DAT_06:00

description: Gene expression of leaf blade at 115 days after transplanting, 06:00

source_name: Leaf blade, 115 days after transplanting, 06:00


title: LeafBlade_114DAT_20:00

description: Gene expression of leaf blade at 114 days after transplanting, 20:00

source_name: Leaf blade, 114 days after transplanting, 20:00


title: LeafBlade_13DAT_24:00_rep2

source_name: Leaf blade, 13 days after transplanting, 24:00, replicate 2


title: LeafBlade_115DAT_02:00

description: Gene expression of leaf blade at 115 days after transplanting, 02:00

source_name: Leaf blade, 115 days after transplanting, 02:00


title: LeafBlade_79DAT_4:20_rep2

description: Gene expression of leaf blade at 79 days after transplanting, 4:20

source_name: Leaf blade, 79 days after transplanting, 4:20, replicate 2


title: LeafBlade_114DAT_22:00

description: Gene expression of leaf blade at 114 days after transplanting, 22:00

source_name: Leaf blade, 114 days after transplanting, 22:00


title: LeafBlade_114DAT_12:00

description: Gene expression of leaf blade at 114 days after transplanting, 12:00

source_name: Leaf blade, 114 days after transplanting, 12:00


title: LeafBlade_113DAT_24:00

description: Gene expression of leaf blade at 113 days after transplanting, 24:00

source_name: Leaf blade, 113 days after transplanting, 24:00

value: 113 days after transplanting


title: LeafBlade_114DAT_24:00

description: Gene expression of leaf blade at 114 days after transplanting, 24:00

source_name: Leaf blade, 114 days after transplanting, 24:00


title: LeafBlade_115DAT_10:00

description: Gene expression of leaf blade at 115 days after transplanting, 10:00

source_name: Leaf blade, 115 days after transplanting, 10:00


title: LeafBlade_79DAT_4:30_rep2

description: Gene expression of leaf blade at 79 days after transplanting, 4:30

source_name: Leaf blade, 79 days after transplanting, 4:30, replicate 2


title: LeafBlade_114DAT_18:00

description: Gene expression of leaf blade at 114 days after transplanting, 18:00

source_name: Leaf blade, 114 days after transplanting, 18:00


title: LeafBlade_114DAT_10:00

description: Gene expression of leaf blade at 114 days after transplanting, 10:00

source_name: Leaf blade, 114 days after transplanting, 10:00


title: LeafBlade_115DAT_08:00

description: Gene expression of leaf blade at 115 days after transplanting, 08:00

source_name: Leaf blade, 115 days after transplanting, 08:00


title: LeafBlade_114DAT_06:00

description: Gene expression of leaf blade at 114 days after transplanting, 06:00

source_name: Leaf blade, 114 days after transplanting, 06:00


title: LeafBlade_114DAT_14:00

description: Gene expression of leaf blade at 114 days after transplanting, 14:00

source_name: Leaf blade, 114 days after transplanting, 14:00


title: LeafBlade_113DAT_18:00

description: Gene expression of leaf blade at 113 days after transplanting, 18:00

source_name: Leaf blade, 113 days after transplanting, 18:00


title: LeafBlade_113DAT_20:00

description: Gene expression of leaf blade at 113 days after transplanting, 20:00

source_name: Leaf blade, 113 days after transplanting, 20:00


title: LeafBlade_113DAT_22:00

description: Gene expression of leaf blade at 113 days after transplanting, 22:00

source_name: Leaf blade, 113 days after transplanting, 22:00


title: LeafBlade_113DAT_12:00

description: Gene expression of leaf blade at 113 days after transplanting, 12:00

source_name: Leaf blade, 113 days after transplanting, 12:00


title: LeafBlade_113DAT_14:00

description: Gene expression of leaf blade at 113 days after transplanting, 14:00

source_name: Leaf blade, 113 days after transplanting, 14:00


title: LeafBlade_101DAT_10:00

description: Gene expression of leaf blade at 101 days after transplanting, 10:00

source_name: Leaf blade, 101 days after transplanting, 10:00

value: 101 days after transplanting


title: LeafBlade_100DAT_24:00

description: Gene expression of leaf blade at 100 days after transplanting, 24:00

source_name: Leaf blade, 100 days after transplanting, 24:00

value: 100 days after transplanting


title: LeafBlade_101DAT_02:00

description: Gene expression of leaf blade at 101 days after transplanting, 02:00

source_name: Leaf blade, 101 days after transplanting, 02:00


title: LeafBlade_101DAT_08:00

description: Gene expression of leaf blade at 101 days after transplanting, 08:00

source_name: Leaf blade, 101 days after transplanting, 08:00


title: LeafBlade_101DAT_06:00

description: Gene expression of leaf blade at 101 days after transplanting, 06:00

source_name: Leaf blade, 101 days after transplanting, 06:00


title: LeafBlade_114DAT_02:00

description: Gene expression of leaf blade at 114 days after transplanting, 02:00

source_name: Leaf blade, 114 days after transplanting, 02:00


title: LeafBlade_100DAT_16:00

description: Gene expression of leaf blade at 100 days after transplanting, 16:00

source_name: Leaf blade, 100 days after transplanting, 16:00


title: LeafBlade_100DAT_18:00

description: Gene expression of leaf blade at 100 days after transplanting, 18:00

source_name: Leaf blade, 100 days after transplanting, 18:00


title: LeafBlade_100DAT_06:00

description: Gene expression of leaf blade at 100 days after transplanting, 06:00

source_name: Leaf blade, 100 days after transplanting, 06:00


title: LeafBlade_100DAT_22:00

description: Gene expression of leaf blade at 100 days after transplanting, 22:00

source_name: Leaf blade, 100 days after transplanting, 22:00


title: LeafBlade_99DAT_22:00

description: Gene expression of leaf blade at 99 days after transplanting, 22:00

source_name: Leaf blade, 99 days after transplanting, 22:00

value: 99 days after transplanting


title: LeafBlade_113DAT_10:00

description: Gene expression of leaf blade at 113 days after transplanting, 10:00

source_name: Leaf blade, 113 days after transplanting, 10:00


title: LeafBlade_100DAT_12:00

description: Gene expression of leaf blade at 100 days after transplanting, 12:00

source_name: Leaf blade, 100 days after transplanting, 12:00


title: LeafBlade_113DAT_16:00

description: Gene expression of leaf blade at 113 days after transplanting, 16:00

source_name: Leaf blade, 113 days after transplanting, 16:00


title: LeafBlade_100DAT_02:00

description: Gene expression of leaf blade at 100 days after transplanting, 02:00

source_name: Leaf blade, 100 days after transplanting, 02:00


title: LeafBlade_99DAT_24:00

description: Gene expression of leaf blade at 99 days after transplanting, 24:00

source_name: Leaf blade, 99 days after transplanting, 24:00


title: LeafBlade_100DAT_04:00

description: Gene expression of leaf blade at 100 days after transplanting, 04:00

source_name: Leaf blade, 100 days after transplanting, 04:00


title: LeafBlade_100DAT_10:00

description: Gene expression of leaf blade at 100 days after transplanting, 10:00

source_name: Leaf blade, 100 days after transplanting, 10:00


title: LeafBlade_101DAT_04:00

description: Gene expression of leaf blade at 101 days after transplanting, 04:00

source_name: Leaf blade, 101 days after transplanting, 04:00


title: LeafBlade_99DAT_20:00

description: Gene expression of leaf blade at 99 days after transplanting, 20:00

source_name: Leaf blade, 99 days after transplanting, 20:00


title: LeafBlade_79DAT_4:20_rep1

description: Gene expression of leaf blade at 79 days after transplanting, 4:20

source_name: Leaf blade, 79 days after transplanting, 4:20, replicate 1


title: LeafBlade_99DAT_18:30

description: Gene expression of leaf blade at 99 days after transplanting, 18:30

source_name: Leaf blade, 99 days after transplanting, 18:30


title: LeafBlade_99DAT_10:00

description: Gene expression of leaf blade at 99 days after transplanting, 10:00

source_name: Leaf blade, 99 days after transplanting, 10:00


title: LeafBlade_100DAT_14:00

description: Gene expression of leaf blade at 100 days after transplanting, 14:00

source_name: Leaf blade, 100 days after transplanting, 14:00


title: LeafBlade_99DAT_14:00

description: Gene expression of leaf blade at 99 days after transplanting, 14:00

source_name: Leaf blade, 99 days after transplanting, 14:00


title: LeafBlade_94DAT_10:00

description: Gene expression of leaf blade at 94 days after transplanting, 10:00

source_name: Leaf blade, 94 days after transplanting, 10:00

value: 94 days after transplanting


title: LeafBlade_99DAT_16:00

description: Gene expression of leaf blade at 99 days after transplanting, 16:00

source_name: Leaf blade, 99 days after transplanting, 16:00


title: LeafBlade_94DAT_02:00

description: Gene expression of leaf blade at 94 days after transplanting, 02:00

source_name: Leaf blade, 94 days after transplanting, 02:00


title: LeafBlade_94DAT_04:00

description: Gene expression of leaf blade at 94 days after transplanting, 04:00

source_name: Leaf blade, 94 days after transplanting, 04:00


title: LeafBlade_93DAT_24:00

description: Gene expression of leaf blade at 93 days after transplanting, 24:00

source_name: Leaf blade, 93 days after transplanting, 24:00

value: 93 days after transplanting


title: LeafBlade_99DAT_12:00

description: Gene expression of leaf blade at 99 days after transplanting, 12:00

source_name: Leaf blade, 99 days after transplanting, 12:00


title: LeafBlade_93DAT_14:00

description: Gene expression of leaf blade at 93 days after transplanting, 14:00

source_name: Leaf blade, 93 days after transplanting, 14:00


title: LeafBlade_94DAT_08:00

description: Gene expression of leaf blade at 94 days after transplanting, 08:00

source_name: Leaf blade, 94 days after transplanting, 08:00


title: LeafBlade_93DAT_12:00

description: Gene expression of leaf blade at 93 days after transplanting, 12:00

source_name: Leaf blade, 93 days after transplanting, 12:00


title: LeafBlade_93DAT_10:00

description: Gene expression of leaf blade at 93 days after transplanting, 10:00

source_name: Leaf blade, 93 days after transplanting, 10:00


title: LeafBlade_94DAT_06:00

description: Gene expression of leaf blade at 94 days after transplanting, 06:00

source_name: Leaf blade, 94 days after transplanting, 06:00


title: LeafBlade_93DAT_22:00

description: Gene expression of leaf blade at 93 days after transplanting, 22:00

source_name: Leaf blade, 93 days after transplanting, 22:00


title: LeafBlade_93DAT_16:00

description: Gene expression of leaf blade at 93 days after transplanting, 16:00

source_name: Leaf blade, 93 days after transplanting, 16:00


title: LeafBlade_93DAT_06:00

description: Gene expression of leaf blade at 93 days after transplanting, 06:00

source_name: Leaf blade, 93 days after transplanting, 06:00


title: LeafBlade_93DAT_18:00

description: Gene expression of leaf blade at 93 days after transplanting, 18:00

source_name: Leaf blade, 93 days after transplanting, 18:00


title: LeafBlade_93DAT_08:00

description: Gene expression of leaf blade at 93 days after transplanting, 08:00

source_name: Leaf blade, 93 days after transplanting, 08:00


title: LeafBlade_100DAT_08:00

description: Gene expression of leaf blade at 100 days after transplanting, 08:00

source_name: Leaf blade, 100 days after transplanting, 08:00


title: LeafBlade_93DAT_20:00

description: Gene expression of leaf blade at 93 days after transplanting, 20:00

source_name: Leaf blade, 93 days after transplanting, 20:00


title: LeafBlade_92DAT_22:00

description: Gene expression of leaf blade at 92 days after transplanting, 22:00

source_name: Leaf blade, 92 days after transplanting, 22:00

value: 92 days after transplanting


title: LeafBlade_92DAT_24:00

description: Gene expression of leaf blade at 92 days after transplanting, 24:00

source_name: Leaf blade, 92 days after transplanting, 24:00


title: LeafBlade_93DAT_04:00

description: Gene expression of leaf blade at 93 days after transplanting, 04:00

source_name: Leaf blade, 93 days after transplanting, 04:00


title: LeafBlade_92DAT_20:00

description: Gene expression of leaf blade at 92 days after transplanting, 20:00

source_name: Leaf blade, 92 days after transplanting, 20:00


title: LeafBlade_92DAT_14:00

description: Gene expression of leaf blade at 92 days after transplanting, 14:00

source_name: Leaf blade, 92 days after transplanting, 14:00


title: LeafBlade_92DAT_12:00

description: Gene expression of leaf blade at 92 days after transplanting, 12:00

source_name: Leaf blade, 92 days after transplanting, 12:00