title: S_pombe_StandardConditionPolyA_rep1&2_slide1

description: This sample is PolyA selected RNA extracted from wildtype S.pombe grown under standard conditions and treatment

hyb_protocol: RNA samples (1 ug polyA RNA) were fragmented and combined with Agilent Hi-RPM GE Hybridization kit (cat#5190-0403) reagents.  These samples were hybridized to the array slides at 65C for 17 hr.  The slides were washed in 6x SSPE, 0.005% N-lauroylsarcosine for one min at room temperature and in 0.06x SSPE, 0.005% N-lauroylsarcosine for 1 min at 31C.  The slides were then incubated with 0.025mg/mL primary monoclonal mouse anti-RNA DNA hybrid antibody available in a hybridoma cell line from ATCC (HB-8730).  This was diluted in 500uL of SB+BSA (100mM MES, pH 6.6, 1M NaCl, 0.05% Tween 20, and 1 mg/mL BSA).  The 60 min incubation was at 25C.  After this incubation the slides were washed four times for three min in NSWB (6xSSPE, 0.01% Tween 20).  The secondary Cy3-labeled goat anti-mouse antibody (KPL, cat#078-18-061) was used at a concentration of 3ug/mL in 500uL of SB+BSA.  The slides were incubated with the secondary antibody for 60 min at 25C.  Finally the slides were washed four times for three min in NSWB at room temperature.

molecule: polyA RNA

source_name: PolyA selected RNA extracted from S.pombe grown under standard conditions hybridized to slide 1

extract_protocol: Yeast cells were harvested and after mechanical pulverization, the cell material was stored at -80C. PolyA RNA was selected using the Qiagen Oligotex PolyA Purification kit.


title: subject 12

status: Public on Jun 30 2008

type: RNA

city: Farmington

first: Winfried

last: Krueger

state: CT

address: 263 Farmington Aveneu

department: Genetics & Developmental Biology

country: USA

institute: University of Connecticut Health Center

description: Gene Expression Data from Umbilical Cord

hyb_protocol: the arrays were hybridized for 16 hours at 42 0C and stained in an Affymetrix Fluidics Station using a two-stage signal amplification protocol based on detection of the biotinylated targets by streptavidin-phycoeritherin (SAPE) according to Affymetrix instructions.

scan_protocol: The signal was quantified by detection of bound phycoerythericin using an Affymetrix GeneChip Scanner 3000.

data_processing: scaled data  were RMA normalized using the MAANOVA inherent algorithm.  Genes demonstrating significant regulation were determined by trivariate ANOVA analysis with the variables Smoker status, gender and blood contamination (Erythro ContaminationGroup:  grouping according to their absorbtion at 418 nm into Erythrocyte group 1 (OD418 <1.5, Erythrocyte group 2 (OD418 <2.5 and Erythrocyte group 3 (OD418 >2.5,

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Umbiilical Cord from_smk

label_protocol: The RNA was further amplified as recommended by the manufacturer (Affymetrix, Santa Clara, CA). For each sample, 1.5 ug of RNA was converted into biotinylated targets. Briefly, the RNA was used for first and second strand cDNA synthesis, and the double-stranded cDNA was amplified in the presence of biotinylated ribonucleotides to generate biotinylated cRNA, which was then purified by ion exchange column chromatography.

growth_protocol: Biopsy

extract_protocol: Umbilical cord (UC) tissue midway between infant and placenta was collected within 10 minutes postpartum, cut into 1.5-cm pieces, flash frozen by immersion in liquid nitrogen and stored at -80oC. A random sample of UC tissue (~300 mg) was selected and RNA was isolated using a modified guanidinium isothiocyanate/CsCl procedure (6). Briefly, tissue was cooled with liquid nitrogen, ground to a fine powder, and transferred into a tube containing 1 ml of GTC lysis buffer (4M guanidinium isothiocyanate in 50 mM sodium citrate, TrisHCl or HEPES, 0.1 % sodium sarcosyl). Extracellular matrix was dissociated from the cells, the cells were lysed, and the genomic DNA was sheared using a Polytron mixer. For estimation of blood contamination, an aliquot was analyzed spectrophotometrically at a wavelength of 418 nm. The homogenate was then layered on top of a 1.5 ml cushion of CsCl buffer (5.7 M CsCl/10 mM sodium citrate pH7.0 and 1 mM EDTA), and centrifuged at 45,000 rpm, at 22oC, in a SW50 rotor for 23 hours. RNA sediment was dissolved in 100 ul H2O (RNAsefree), concentrated by overnight precipitation at -20oC in the presence of 0.3M NaOAc and 75% ethanol (final concentration) and sedimented for 10 min at 15,000 rpm, at 4oC,

treatment_protocol: exposure to cigarette smoke

tag: ErythroCountgroup 2, gender = m


title: subject 23

source_name: Umbiilical Cord from_nonsm

tag: ErythroCountgroup 1, gender = m


title: subject 17

tag: ErythroCountgroup 1, gender = f


title: subject 10


title: S_pombe_StandardCondition_rep1&2_slide2

city: Salt Lake City

first: Timothy

middle: J

last: Parnell

state: UT

address: 2000 Circle of Hope

institute: Huntsman Cancer Institute

description: This sample is total RNA extracted from wildtype S.pombe grown under standard conditions

hyb_protocol: RNA samples (15 ug total RNA) were fragmented and combined with Agilent Hi-RPM GE Hybridization kit (cat#5190-0403) reagents.  These samples were hybridized to the array slides at 65C for 17 hr.  The slides were washed in 6x SSPE, 0.005% N-lauroylsarcosine for one min at room temperature and in 0.06x SSPE, 0.005% N-lauroylsarcosine for 1 min at 31C.  The slides were then incubated with 0.025mg/mL primary monoclonal mouse anti-RNA DNA hybrid antibody available in a hybridoma cell line from ATCC (HB-8730).  This was diluted in 500uL of SB+BSA (100mM MES, pH 6.6, 1M NaCl, 0.05% Tween 20, and 1 mg/mL BSA).  The 60 min incubation was at 25C.  After this incubation the slides were washed four times for three min in NSWB (6xSSPE, 0.01% Tween 20).  The secondary Cy3-labeled goat anti-mouse antibody (KPL, cat#078-18-061) was used at a concentration of 3ug/mL in 500uL of SB+BSA.  The slides were incubated with the secondary antibody for 60 min at 25C.  Finally the slides are washed four times for three min in NSWB at room temperature.

scan_protocol: Arrays were scanned in an Agilent G2505B Microarray Scanner using extended dynamic range software. Feature extraction of the scanned images was performed using Agilent Feature Extraction Software Version 9.5.1.

data_processing: All of the software used in this analysis is open source and available from the TiMAT2 project site, http://sourceforge.net/projects/timat2. Processing of the Agilent microarray transcriptome data was performed in three basic steps:  data normalization, sliding window summaries, and enriched region identification.  For each condition (growth and or RNA fraction) and strand, the median unadjusted signal intensities from the cy3 channel were extracted. Probes were then mapped to the April 2007 build and those with < 100 exact matches were retained. The two biological replicas for each condition were quantile normalized and scaled in two different ways.  The first was to scale the data such that the median of the zebrafish control probes was one. The second was to scale the data such that the median of the trimmed intergenic region probes was one. Trimmed intergenic probes were defined as those  > 240 bp (4 probes) from any known annotation.  Probe level oligo summaries were calculated by taking the log2 of the mean of the two biological replica probes for each condition.

organism: Schizosaccharomyces pombe

source_name: S.pombe grown under standard conditions hybridized to slide 2

label_protocol: See Sample_hyb_protocol

growth_protocol: Yeast growth, manipulations, and molecular biology were performed according to standard protocols. For rich medium, the strain was grown on yeast extract with glucose (2%) supplemented with histidine, uracil, leucine, and adenine at 32C to an optical density at 600 nm of 1.0.

extract_protocol: Yeast cells were harvested and after mechanical pulverization, the cell material was stored at -80C. Total RNA was extracted using the Ambion mirVanaTM kit.

tag: Strain

tag: Genotype

value: wildtype

tag: Mating type


title: S_pombe_MinimalMediaCondition_rep1&2_slide2

description: This sample is total RNA extracted from wildtype S.pombe grown under minimal media conditions and treatment

source_name: S.pombe grown under minimal media conditions hybridized to slide 2

growth_protocol: Yeast growth, manipulations, and molecular biology were performed according to standard protocols. For the minimal medium transcriptome, cells were cultured as described in media lacking amino acids and containing 2% glucose at 32C to an optical density at 600 nm of 1.0


title: subject 13

tag: ErythroCountgroup 2, gender = f


title: subject 11

tag: ErythroCountgroup 3, gender = m


title: S_pombe_MMSCondition_rep1&2_slide1

description: This sample is total RNA extracted from wildtype S.pombe grown under MMS conditions and treatment

data_processing: All of the software used in this analysis is open source and available from the TiMAT2 project site, http://sourceforge.net/projects/timat2. Processing of the Agilent microarray transcriptome data was performed in three basic steps:  data normalization, sliding window summaries, and enriched region identification.  For each condition (growth and or RNA fraction) and strand, the median unadjusted signal intensities from the cy3 channel were extracted. Probes were then mapped to the April 2007 build and those with < 100 exact matches were retained. The two biological replicas for each condition were quantile normalized and scaled in two different ways.  The first was to scale the data such that the median of the zebrafish control probes was one. The second was to scale the data such that the median of the trimmed intergenic region probes was one. Trimmed intergenic probes were defined as those  > 240 bp (4 probes) from any known annotation.  Probe level  Oligo  summaries were calculated by taking the log2 of the mean of the two biological replica probes for each condition.

source_name: S.pombe grown under MMS conditions  hybridized to slide 1

growth_protocol: Yeast growth, manipulations, and molecular biology were performed according to standard protocols. Cells were cultured to an optical density at 600 nm of 0.6 and then treated as described.

treatment_protocol: For the methyl methane-sulfonate transcriptome, cells were treated with MMS (0.02%) for 1hr.


title: subject 8


title: subject 9

tag: ErythroCountgroup 3, gender = f


title: S_pombe_StandardConditionPolyA_rep1&2_slide2

source_name: PolyA selected RNA extracted from S.pombe grown under standard conditions hybridized to slide 2


title: subject 3


title: subject 7


title: subject 6


title: 16000508001614_UT 120min vs KDO 8BR(EYC060228A41) 120min_A02.txt

status: Public on Jun 28 2008

city: Pasadena

first: Sangdun

last: Choi

state: CA

address: 1200 E. California Blvd

department: Biology

institute: California Institute of Technology

description: RAW 264.7 cells were stimulated with KDO (100 ng/ml), IFN-β (300 pM) and/or 8-Br 100 μM. These ligands were applied individually or in combination with KDO for 60 min and 120 min.

hyb_protocol: The hybridization experiment and analysis were performed as previously described 6,31. Cy5-labeled cRNA (RNA of ligand treated cells) and Cy3-labeled cRNA (RNA of time matched controls) were hybridized in the array. Dye-swap labeling was performed for each pair of samples.

scan_protocol: The arrays were scanned with Agilent Scanner G2505A (Agilent Technologies) and image files were extracted with background subtraction and dye-normalization using Agilent G2566AA Extraction Software version A.6.1.1 (Agilent Technologies).

organism: Mus musculus

source_name: RAW264.7 cells

label_protocol: 16 K mouse oligonucleotide arrays were fabricated with 15,631 oligomers of 65-bp or 70-bp long. The oligomers were purchased from Operon and Sigma-Genosys and were inkjet-printed onto glass slides by Agilent Technologies. The list of genes is available through the GEO (Gene Expression Omnibus - http://www.ncbi.nlm.nih.gov/geo) as an accession number GPL254.

extract_protocol: Total RNA was extracted using TriPure (Roche) following its protocol. The detailed procedure is available at http://www.signaling-gateway.org/data/ProtocolLinks.html (AfCS Procedure Protocol PP00000009). Duplicate experiments were done for each treatment.

tag: RAW264.7 Cell line treated with KDO and 8-BR for 120 minutes

source_name: Total RNA from untreated RAW 264.7 cells

tag: RAW264.7 Cell line untreated


title: subject 2


title: 16000508001618_UT 120min vs KDO IFN-B 8BR(EYC060228A44) 120min_A02.txt

tag: RAW264.7 Cell line treated with KDO, IFN-B and 8-BR for 120 minutes


title: 16000508001630_KDO IFN-B(EYC060228A38) 120min vs UT 120min_A02.txt

tag: RAW264.7 Cell line treated with KDO and IFN-B for 120 minutes


title: 16000508001618_KDO IFN-B 8BR(EYC060228A44) 120min vs UT 120min_A01.txt


title: subject 4


title: subject 1


title: 16000508001627_UT 120min vs IFN-B(EYC060228A34) 120min_A01.txt

tag: RAW264.7 Cell line treated with IFN-B for 120 minutes


title: subject 5


title: 16000508001605_UT 120min vs KDO(EYC060228A32) vs 120min_A02.txt

tag: RAW264.7 Cell line treated with KDO for 120 minutes


title: 16000508001629_UT 120min vs 8BR(EYC060228A37) 120min_A01.txt

tag: RAW264.7 Cell line treated with 8-BR for 120 minutes


title: 16000508001629_8BR(EYC060228A37) 120min vs UT 120min_A02.txt


title: 16000508001512_UT 120min vs KDO(EYC060227A33) 120min_A02.txt


title: 16000508001502_KDO IFN-B 8BR(EYC060227A18) 60min vs UT 60min_A01.txt

tag: RAW264.7 Cell line treated with KDO, IFN-B and 8-BR for 60 minutes


title: 16000508001633_KDO 8BR(EYC060228A41) 120min vs UT 120min_A02.txt


title: 16000508001606_UT 120min vs KDO(EYC060228A33) 120min_A02.txt


title: 16000508000644_KDO IFN-B (EYC060227A12) 60min vs UT 60min_A01.txt

tag: RAW264.7 Cell line treated with KDO and IFN-B for 60 minutes


title: 16000508001605_KDO(EYC060228A32) 120min vs UT 120min_A01.txt


title: 16000508000643_UT 60min vs 8BR (EYC060227A11) 60min_A02.txt

tag: RAW264.7 Cell line treated with 8-BR for 60 minutes


title: 16000508001627_IFB(EYC060228A34) 120min vs UT 120min_A02.txt


title: 16000508001502_UT 60min vs KDO IFN-B 8BR(EYC060227A18) 60min_A02.txt


title: 16000508000647_KDO 8BR (EYC060227A15) 60min vs UT 60min_A01.txt

tag: RAW264.7 Cell line treated with KDO and 8-BR for 60 minutes

source_name: Total RNA from untreated RAW 264.7 cells was labeled with Cy5


title: 16000508000638_UT 60min vs IFN-B (EYC060227A08) 60min_A02.txt

tag: RAW264.7 Cell line treated with IFN-B for 60 minutes


title: 16000508000636_UT 60min vs KDO (EYC060227A06) 60min_A02.txt

tag: RAW264.7 Cell line treated with KDO for 60 minutes


title: 16000508000647_UT 60min vs KDO 8BR (EYC060227A15) 60min_A02.txt


title: 16000508000636_KDO (EYC060227A06) 60min vs UT 60min RAW 264.7 cells


title: 16000508001611_UT 120min vs KDO IFN-B(EYC060228A38) 120min_A02.txt


title: 16000508000625_UT 60min_1 vs UT 60min_2_A01 Untreated RAW264.7 cells

source_name: Total RNA from untreated RAW264.7 cells


title: subject 14


title: 16000508000638_IFB (EYC060227A08) 60min vs UT 60min_A01.txt


title: 16000508000625_UT 60min_2 vs UT 60min_1_A02


title: Prostate_AI-Cancer-Met, Rep 2

status: Public on Jun 27 2008

city: New York

first: Cory

last: Abate-Shen

state: NY

address: 1130 St. Nicholas Ave

department: Urology

institute: Columbia University

description: no additional information

hyb_protocol: Hybridization was carried out at 45°C for 16 hours in 200 µl of cocktail containing 20 µg of biotinilated RNA probe according to the Affymetrix Standard Protocol; post hybridization washing and antibody enhancement staining were performed using EukGE-WS2v4 protocol on Affymetrix Fluidics Station.

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

data_processing: GeneChip CEL files underwent normalization using GeneChip Robust Multichip Analysis (RMA) in Bioconductor/R. Differential regulation was defined as probe sets that passed an ANOVA (P<0.1, variances assumed equal; False Detection Rate P<0.1 using Benjamani and Hochberg multiple testing correction) between classes (Normal, Dyplasia/LGPIN, HGPIN/Cancer, AI-HGPIN, AI-Cancer-Met). Functional annotation was performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) 2007 at the National Institute of Allergy and Infectious Diseases (NIAID), NIH, to identify over-represented GO Biological Processes as well as KEGG and BioCarta pathways (p<0.05).

source_name: Primary Prostate Cancer in Castrated Group with Detectable Metastatic Lesions

label_protocol: The RNA was labelied using Small Sample Labeling Protocol VII (Affymetrix).Samples were labeled using a BioArray High Yield RNA transcript labeling kit (Enzo Life Scientific).

growth_protocol: Mutant animals were bred on a mixed 129xC57Bl/6 background. Double heterozgotes (Nkx 3.1+/—; Pten+/—) were mated to obtain desired genotypic combinations.

extract_protocol: Total RNA was prepared from the LCM samples using the PicoPure RNA isolation kit (Arcturus), followed by RNA linear amplification.

treatment_protocol: To obtain androgen-independent lesions, mice were castrated at 7 to 14 months of age.

tag: Strain

value: mixed 129XC57Bl/6, Gender:male, Tissue:prostate

tag: Age (Months)

value: 15, castrated at 13M

tag: Genotyping


title: Prostate_AI-Cancer-Met, Rep 1

description: no additional information

value: 16, castrated at 14M


title: Prostate_AI-HGPIN, Rep 4

description: high-grade prostate intraepithelial neoplasia

source_name: HGPIN in Castrated Group

value: 10, castrated at 7M


title: Prostate_AI-Cancer-Met, Rep 4

description: no additional information

value: 12.5, castrated at 11M


title: Prostate_AI-HGPIN, Rep 3


title: 16000508000643_8BR (EYC060227A11) 60min vs UT 60min_A01.txt


title: Prostate_HGPIN/Cancer, Rep 2

source_name: HGPIN/Cancer Lesion


title: Prostate_HGPIN/Cancer, Rep 1


title: 16000508000644_UT 60min vs KDO IFN-B (EYC060227A12) 60min_A02.txt


title: Prostate_AI-HGPIN, Rep 2


title: Prostate_HGPIN, Rep 4

source_name: Prostate HGPIN Lesion


title: Prostate_HGPIN, Rep 3


title: Prostate_LGPIN, Rep 3

description: low-grade prostate intraepithelial neoplasia

source_name: Prostate LGPIN Lesion


title: Prostate_HGPIN, Rep 2


title: Prostate_AI-HGPIN, Rep 1


title: Prostate_LGPIN, Rep 2


title: Prostate_LGPIN, Rep 4


title: Prostate_LGPIN, Rep 1


title: Prostate_Dysplasia, Rep 2

description: no additional information

source_name: Dysplasia Mouse Prostate


title: Prostate_Dysplasia, Rep 3

description: no additional information


title: Prostate_Dysplasia, Rep 4

description: no additional information


title: Prostate_HGPIN, Rep 1


title: Prostate_Normal, Rep 4

description: no additional information

source_name: Normal Mouse Prostate Gland


title: Prostate_Dysplasia, Rep 1

description: no additional information


title: Prostate_AI-Cancer-Met, Rep 3

description: no additional information

value: 13.8, castrated at 11M


title: Alum Ovalbumin (OVA)-specific CD4 (OTII) T cells 1

city: Birmingham

first: Karine

last: Serre

state: West Midland

address: Wolfson drive, Edgbaston

department: Infection and Immunity

country: United Kingdom

institute: University of Birmingham

description: mRNA in a final volume of 100ul to which 660ul of a mix containing the Quantitect enzyme RT-PCR master mix (Qiagen Quantitect Probe RT-PCR kit) was added. 95ul of this mix was loaded onto each of the 8 channels of the 384 wells cards. Reverse transcription and real-time PCR were performed sequentially onto the microfluidic cards. Standard reaction conditions for the TaqMan RT-PCR were used on the ABI 7900.

hyb_protocol: Gene expression was quantified by RT-PCR using TaqMan technology.

data_processing: mRNA transcript level of each gene was analyzed by using SDS applied biosystems software by setting thresholds within the phase of the PCR determining the cycle number at which the threshold was reached (Ct). For a given gene, the threshold value was kept constant in all 9 samples. The Ct of the b2-microglobulin was subtracted from the Ct of the target gene and the relative amount was calculated as 2-DCt.

source_name: Ovalbumin (OVA)-specific CD4 (OTII) T cells were transferred into C57BL/6.

extract_protocol: After various immunization ovalbumin (OVA)-specific CD4 (OTII) T cells were FACS sorted and mRNA extraction was perfomed using Rneasy Micro Spin from QIAGEN.

treatment_protocol: alum-precipitated OVA (alum) = Th2

tag: Ovalbumin (OVA)-specific CD4 (OTII) T cells were transferred into C57BL/6 and then immunized either with live attenuated OVA-expressing Salmonella (Sal) or with alum-precipitated OVA (alum), or not (Naïve).

tag: Gene expression assay was performed on FACS sorted OTII cells (Naïve, Sal, Alum).


title: Salmonella Ovalbumin (OVA)-specific CD4 (OTII) T cells 3

scan_protocol: Gene expression was quantified by RT-PCR using TaqMan technology.

treatment_protocol: Live attenuated OVA-expressing Salmonella (Sal) = Th1


title: Alum Ovalbumin (OVA)-specific CD4 (OTII) T cells 3

label_protocol: Gene expression was quantified by RT-PCR using TaqMan technology.


title: Salmonella Ovalbumin (OVA)-specific CD4 (OTII) T cells 1


title: Salmonella Ovalbumin (OVA)-specific CD4 (OTII) T cells 2

tag: Gene expression assay was performed on FACS sorted OTII cells (Naïve, Sal, Alum


title: Naive Ovalbumin (OVA)-specific CD4 (OTII) T cells 3

treatment_protocol: Non Immunized = Naive


title: Prostate_Normal, Rep 2

description: no additional information


title: Prostate_Normal, Rep 3

description: no additional information


title: Naive Ovalbumin (OVA)-specific CD4 (OTII) T cells 2


title: Prostate_Normal, Rep 1

description: no additional information


title: Alum Ovalbumin (OVA)-specific CD4 (OTII) T cells 2


title: Naive Ovalbumin (OVA)-specific CD4 (OTII) T cells 1

treatment_protocol: Ovalbumin (OVA)-specific CD4 (OTII) T cells were activated in vivo and then kept at -80C until mRNA extraction.


title: T-cell lymphoma_NRH5-2

status: Public on Jun 26 2008

city: Madrid

first: Marcos

last: Malumbres

address: Melchor Fernandez Almagro 3

department: Molecular Oncology

country: Spain

institute: Centro Nacional de Investigaciones Oncológicas (CNIO)

description: gamma-irradiation-induced T-cell lymphoma

hyb_protocol: Hybridizations were performed at 55°C for 17 h using the SlideHyb Microarray Hybridization buffer (Ambion).

scan_protocol: the slides were scanned in an Agilent G2565BA scanner.

data_processing: Images were then analyzed with GenePix 5.1 (Axon Instruments, Inc., Union City, CA) and the TM4 software

source_name: Total RNA from tumoral thymus

label_protocol: Five micrograms of the test RNAs was labeled with fluorescent Cy3 (Amhersam, Sunnyvale), respectively using the SuperScript II RNase H Reverse Transcriptase KIT (Invitrogen,  USA).

growth_protocol: Tumors develop in vivo after irradiation of animals

extract_protocol: Total RNA was extracted by combination of Trizol reagent (Invitrogen) without further purification. The quality of the RNA was evaluated using the BioAnalyzer system (Agilent).

treatment_protocol: 4-week-old mice of both sexes were exposed to four weekly doses of 1.75 Gy/dose of ionizing gamma

tag: T-cell lymphoma


title: T-cell lymphoma_16CG63


title: Illum_Monocyte_28

city: Paris

first: Francois

last: Cambien

state: France

address: 91 Bd de l'Hôpital

department: Cardiovascular Genomics

country: France

institute: INSERM

description: All RNA preparation were checked with Agilent Bioanalyser (RNA 6000 nano-kit) and only RNA with RNA integrity number (RIN) > 8 were accepted for RNA amplification.

hyb_protocol: 1.5 µg were hybridized to human 6 beadarrays (Illumina, CA, USA) for 16 hours at 55°C. Following hybridization, beadarrays were washed and stained with streptavidin-Cy3 (GE Healthcare, UK).

scan_protocol: Fluorescent images were obtained with a Beadarray reader and processed with the BeadScan software (Illumina, CA, USA).

data_processing:
Data were background subtracted using BeadStudio software. (Illumina).
Quality control and pre-processing were performed in the statistical environment R using the Bioconductor packages BeadArray and BeadExplorer Bead-averaged data was normalized using a quantile normalization method Detection scores were calculated in BeadStudio software.

source_name: whole blood, monocyte_28

label_protocol: Refer to the Illumina Gene Expression System Manual

growth_protocol: The human monocytes CD14+ obtained after MACS separation were cultured at a concentration of 1x 106 cells/ml in pure RPMI 1640 medium in P6 Petri dishes. After 1h of incubation at 37°C, non adherent cells were removed and the medium was replaced with RPMI 1640 Glu+ medium supplemented with 100U/ml penicillin, 100 µg/ml streptomycin and 10 % FCS, together with 10 ng/ml of macrophage colony stimulating-factor (M-CSF, SIGMA). Cells were incubated for 6 days at 37°C/5% CO2 to induce the phagocytic differentiation.

extract_protocol: RNA extraction was done using RNAeasy minikit (Qiagen).

treatment_protocol: Blood was drawn under standardized conditions in EDTA tubes: 40 ml samples were collected immediately after coronary angiography and stored at 4°C. Monocytes isolation was performed within 2 hours after Blood drawing. After density gradient centrifugation and washing, PMBC were mixed with CD14 coated beads (MACS, Miltenyi Biotec). To induce phagocytic differentiation, a fraction of the monocytes was incubated for 6 days with macrophage colony stimulating factor (M-CSF, SIGMA).

tag: Age

tag: Gender

value: male

tag: Tissue

value: whole blood

tag: Cell type

value: monocyte

tag: Patient with symptoms of acute coronary syndrome who had

tag: undergone coronary angiography (who had one stenosis >50 % diagnosed in at least one major coronary artery)


title: T-cell lymphoma_NRH7-5


title: T-cell lymphoma_H3-36


title: T-cell lymphoma_H4-11


title: T-cell lymphoma_NRH11-2


title: Illum_Macrophage_28

source_name: whole blood, macrophage_28

value: macrophage


title: Illum_Monocyte_21

source_name: whole blood, monocyte_21


title: Illum_Macrophage_21

source_name: whole blood, macrophage_21


title: Illum_Monocyte_20

source_name: whole blood, monocyte_20


title: Illum_Monocyte_26

source_name: whole blood, monocyte_26


title: Illum_Macrophage_26

source_name: whole blood, macrophage_26


title: T-cell lymphoma_19CG149


title: T-cell lymphoma_H7H-43


title: Illum_Monocyte_16

source_name: whole blood, monocyte_16


title: Illum_Macrophage_16

source_name: whole blood, macrophage_16


title: Wild-type_thymus_C2

description: Normal thymus-control

source_name: Total RNA from wild-type thymus

tag: Wild-type


title: Wild-type_thymus_C1

description: Normal thymus-control


title: subtilis_ccpNexp_ccpN3

city: Thiverval-Grignon

first: Thierry

last: Doan

address: INRA

department: Microbiologie

institute: INRA

description:
Global transcriptional profiling of Bacillus subtilis cells comparing wild-type to a ccpN (yqzB) non polar mutant.
Two-condition experiment, wt vs. ccpN mutant. 4 experiments with 3 independent RNA preparations and 3 sets of macroarrays.

hyb_protocol: Panorama B. subtilis gene macroarrays (Sigma-Genosys) containing full-length PCR products of all 4107 B. subtilis protein-coding genes in duplicate were prehybridized for 2h at 65C with 100 µg/mL herring sperm DNA, and then hybridized for 20h at 65C with the denatured radiolabelled cDNA

scan_protocol: The arrays were then exposed for 24 hours to an Imaging Plate and scanned with a STORM phosphoimager (GE Lifesciences), images of the hybridized arrays were processed and signal intensities quantified using the Array Vision software (Imaging Research, Canada)

data_processing: Data analysis was performed using Array Vision software (Imaging Research, Canada) for signals and background quantitations. The raw data were re-scaled to account for the differences in individual hybridization intensities.

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: Bacillus subtilis cells, ccpN mutant, glucose medium

label_protocol: cDNA labelling kit were provided by Sigma-Genosys and used as recommended. 2µg total RNA was used for labeled cDNA preparation in the presence of 2,5 µL [a-33P]-dCTP (10 µCi/µL).

growth_protocol: Cells pellet for RNA extraction were obtained from cultures grown up to exponential growth phase (OD600=0.5) in TSS miminal medium (Fouet and Sonenshein, 1990) supplemented with 10g/L glucose.

extract_protocol: High-quality RNA preparation, radiolabelled cDNA synthesis and hybridization were performed as previously described (Hauser et al., 1998; Eymann et al., 2002). Cells pellet for RNA extraction were obtained from cultures grown up to exponential growth phase (OD600=0.5).

treatment_protocol: no particular treatment was performed on cells prior to extract preparation.

tag: ccpN mutant strain strain GM1560, whole cells grown in glucose medium, exponential phase (OD600 0.5)


title: Wild-type_thymus_C4

description: Normal thymus-control


title: subtilis_ccpNexp_ccpN4


title: Wild-type_thymus_C3

description: Normal thymus-control


title: subtilis_ccpNexp_ccpN2


title: Thymic lymphoma RB90

description: Thymic lymphoma versus control

source_name: Total RNA from several cell lines

label_protocol: Twenty-five micrograms of the test or reference amplified RNAs were labeled with fluorescent Cy5 and Cy3 (Amhersam, Sunnyvale), respectively using the SuperScript II RNase H Reverse Transcriptase KIT (Invitrogen,  USA).

extract_protocol: Total RNA was extracted by combination of Trizol reagent (Invitrogen) and purification using the RNeasy Protect kit (Qiagen, Hilden). The quality of the RNA was evaluated using the BioAnalyzer system (Agilent).

source_name: Normal Thymus RB90


title: Thymic lymphoma RB48

description: Thymic lymphoma versus control

source_name: Normal Thymus RB48


title: Thymic lymphoma RB53

description: Thymic lymphoma versus control

source_name: Normal Thymus MRB53


title: Thymic lymphoma RB42

description: Thymic lymphoma versus control

source_name: Normal Thymus RB42


title: subtilis_ccpNexp_ccpN1


title: Thymic lymphoma RB2

description: Thymic lymphoma versus control

source_name: Normal Thymus RB2


title: subtilis_ccpNexp_wt4

source_name: Bacillus subtilis cells, wild-type, glucose medium

tag: wild-type strain 168 CA, whole cells grown in glucose medium, exponential phase (OD600 0.5)


title: Thymic lymphoma RB15

description: Thymic lymphoma versus control

source_name: Normal Thymus RB15


title: subtilis_ccpNexp_wt1

tag: wild-type strain 168 CA, whole cells

tag: grown in glucose medium, exponential phase (OD600 0.5)


title: subtilis_ccpNexp_wt2


title: Thymic lymphoma RB40

description: Thymic lymphoma versus control

source_name: Normal Thymus RB40


title: subtilis_ccpNexp_wt3


title: Thymic lymphoma RB37

description: Thymic lymphoma versus control

source_name: Normal Thymus RB37


title: Thymic lymphoma 16CG63

description: Thymic lymphoma versus control

source_name: Normal Thymus 16CG63


title: Thymic lymphoma 19CG1

description: Thymic lymphoma versus control

source_name: Normal Thymus 19CG1


title: Thymic lymphoma 19CG9

description: Thymic lymphoma versus control

source_name: Normal Thymus 19CG9


title: Wild-type_thymus_M1

description: Normal thymus-control

source_name: Normal Thymus M1


title: Wild-type_thymus_M3

description: Normal thymus-control

source_name: Normal Thymus M3


title: Thymic lymphoma H3-36

description: Thymic lymphoma versus control

source_name: Normal Thymus H3-36


title: Thymic lymphoma H4-11

description: Thymic lymphoma versus control

source_name: Normal Thymus H4-11


title: Thymic lymphoma 16CG149

description: Thymic lymphoma versus control

source_name: Total RNA from several cell lines

source_name: Normal Thymus 16CG149


title: Thymic lymphoma NRH7-5

description: Thymic lymphoma versus control

source_name: Normal Thymus NRH7-5


title: Wild-type_thymus_H3

description: Normal thymus-control

source_name: Normal Thymus H3


title: Wild-type_thymus_H2

description: Normal thymus-control

source_name: Normal Thymus H2


title: Thymic lymphoma 19CG1

type: genomic

description: Tumor DNA versus wild-type DNA

molecule: genomic DNA

source_name: Total cDNA from wild-type thymus

label_protocol: One microgram of test and reference DNA were labeled with fluorescent Cy5 and Cy3 (Amhersam, Sunnyvale), respectively.

extract_protocol: Total DNA was extracted by routine phenol extraction. The quality of the DNA was evaluated by gel electrophoresis.

source_name: Thymic lymphoma 19CG1


title: Wild-type_thymus_H1

description: Normal thymus-control

source_name: Normal Thymus H1


title: Thymic lymphoma H3-36

description: Tumor DNA versus wild-type DNA

source_name: Thymic lymphoma H3-36


title: Thymic lymphoma NRH5-2

description: Tumor DNA versus wild-type DNA

source_name: Thymic lymphoma NRH5-2


title: Thymic lymphoma NRH5-4

description: Tumor DNA versus wild-type DNA

source_name: Thymic lymphoma NRH5-4


title: Thymic lymphoma NRH7-5

description: Tumor DNA versus wild-type DNA

source_name: Thymic lymphoma NRH7-5


title: Thymic lymphoma NRH12-26

description: Tumor DNA versus wild-type DNA

source_name: Thymic lymphoma NRH12-26


title: Thymic lymphoma NRH5-10

description: Tumor DNA versus wild-type DNA

source_name: Thymic lymphoma NRH5-10


title: Illum_Macrophage_20

source_name: whole blood, macrophage_20


title: Thymic lymphoma NRH11-2

description: Tumor DNA versus wild-type DNA

source_name: Thymic lymphoma NRH11-2


title: Thymic lymphoma H7H-L-43

description: Tumor DNA versus wild-type DNA

source_name: Thymic lymphoma H7H-L-43


title: Thymic lymphoma 16CG63

description: Tumor DNA versus wild-type DNA

source_name: Thymic lymphoma 16CG63


title: Thymic lymphoma H4-11

description: Tumor DNA versus wild-type DNA

source_name: Thymic lymphoma H4-11


title: Thymic lymphoma 16CG149

description: Tumor DNA versus wild-type DNA

source_name: Thymic lymphoma 16CG149


title: p53+/+ ctrl. 1

city: Bures-sur-Yvette

first: Arndt

last: Benecke

address: 35 route des Chartres

department: Integrative Biology

institute: Institut des Hautes Etudes Scientifiques & I.R.I.-CNRS

description: ctrl AS treated HCT-116 p53+/+ cells

hyb_protocol: Array hybridization was performed for 16 hrs at 55 oC. Pre-Hybridization, Hybridization, antibody binding and Chemiluminescence reaction were performed using Applied Biosystems Chemiluminescence Detection Kit (P/N 4342142) following the manufacturer’s protocol (P/N 4339627).

scan_protocol: image acquisition and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit (P/N 4342142) and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer (P/N 4338036) following the manufacturer’s protocol (P/N 4339629).

data_processing: Images were auto-gridded and the chemiluminescent signals were quantified, corrected for background, and finally, spot- and spatially-normalized using the Applied Biosystems 1700 Chemiluminescent Microarray Analyzer software v 1.1 (P/N 4336391). Median normalization and Probabilty for a gene to be expressed(A) were calculated with proprietary software.

label: DIG-UTP

source_name: HCT-116 p53 +/+ cell line

label_protocol: Digoxigenin-UTP labeled cRNA was generated and amplified from 2 µg of total RNA from each sample using Applied Biosystems NanoAmp RT-IVT Labeling Kit (P/N 4365715) according to the manufacturer’s protocol(P/N 4365710).

extract_protocol: RNA was extracted from the cell lines using RNeasy Midi Kit (Quiagen) according to the instructions provided by the manufacturer

tag: HCT-116  p53 +/+ cells + Control antisense RNA oligo


title: p53-/- ctrl. 3

description: ctrl AS treated HCT-116 p53-/- cells

source_name: HCT-116 p53 -/- cell line

tag: HCT-116  p53-/- cells + Control antisense RNA oligo


title: p53+/+ TAF6 AS2 3

description: TAF6 AS2 treated HCT-116 p53+/+ cells

tag: HCT-116  p53 +/+ cells + Taf6 RNA oligo


title: p53-/- TAF6 AS2 1

description: TAF6 AS2 treated HCT-116 p53-/- cells

tag: HCT-116  p53-/- cells + Taf6 RNA oligo


title: p53+/+ ctrl. 2

description: ctrl AS treated HCT-116 p53+/+ cells


title: p53+/+ TAF6 AS2 1

description: TAF6 AS2 treated HCT-116 p53+/+ cells


title: 60-N3-4_v_67-N3-4 (array 2of2)

city: Ames

first: Patrick

middle: S.

last: Schnable

state: IA

address: 2035B Roy J Carver Co-Lab

institute: Iowa State University

description: 60 days node3 vs 67 days node3 replication number 4. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.

hyb_protocol: Fluorescent targets were hybridized as described in the cDNA microarray protocol file at http://schnablelab.plantgenomics.iastate.edu/resources/protocols/.

scan_protocol: Each microarray chip (134 total) was scanned four times in ascending amounts of laser power and PMT gain settings using a ProScanArray scanner (PerkinElmer, Boston, MA). Two scans (one scan for each channel) from each chip were selected based on the median value of the natural log of the signal median for all spots on the slide.

data_processing: The lowess normalization method of Dudoit, Yang, Callow, and Speed (2002) was applied to the log of background-corrected raw signal intensities to remove signal-intensity-dependent dye effects from each slide.  Normalization was carried out separately for each slide to avoid introducing dependencies among biological replications. Following lowess normalization, the normalized data for each slide/dye combination were median centered so that expression measures would be comparable across slides.  Median-centering involves subtracting the median value for a particular slide/dye combination from each individual value associated with the particular slide/dye combination. The lowess normalized data from each scan was used for a mixed linear model analysis (Wolfinger et al., 2001).

organism: Oryza sativa

source_name: Node 3 of 67 day old seedlings

label_protocol: Targets were synthesized and hybridized as described at http://schnablelab.plantgenomics.iastate.edu/resources/protocols/

growth_protocol: Seeds were incubated in water at 42C for 24hrs prior to planting. Initial watering contained a mixture of 1 to 1 Scotts Excel 21-5-20 All Purpose Water Soluble Fertilizer and Scotts Excel 15-5-15 Cal-Mg Water Soluble Fertilizer. Subsequent watering contained no fertilizer mix and was applied to maintain water levels high enough to submerse the seed. Seedlings were grown in a Percival PGC-105 growth chamber with settings of 12hrs light at 28C with 85% humidity and 12hrs dark at 22C with 60% humidity.

extract_protocol: RNA was isolated using RNeasy Plant Mini kit (Qiagen), following the manufacturer's protocol.

tag: Genotype

value: Nipponbare

tag: Developmental Stage

value: 67 days

value: node 3

tag: Replicate

source_name: Node 3 of 60 day old seedlings

value: 60 days


title: p53+/+ ctrl. 3

description: ctrl AS treated HCT-116 p53+/+ cells


title: p53-/- TAF6 AS2 2

description: TAF6 AS2 treated HCT-116 p53-/- cells


title: p53-/- ctrl. 1

description: ctrl AS treated HCT-116 p53-/- cells

tag: HCT-116 p53-/- cells + Control antisense RNA oligo


title: 67-N2-2_v_46-N2-2 (array 2of2)

description: 67 days node2 vs 46 days node2 replication number 2. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.

source_name: Node 2 of 46 day old seedlings

value: 46 days

tag: Tissue

value: node 2

source_name: Node 2 of 67 day old seedlings


title: 67-N3-2_v_53-N3-2 (array 2of2)

description: 67 days node3 vs 53 days node3 replication number 2. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.

source_name: Node 3 of 53 day old seedlings

value: 53 days


title: 67-N2-4_v_46-N2-4 (array 2of2)

description: 67 days node2 vs 46 days node2 replication number 4. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: p53-/- TAF6 AS2 3

description: TAF6 AS2 treated HCT-116 p53-/- cells


title: 53-N2-4_v_60-N2-4 (array 2of2)

description: 53 days node2 vs 60 days node2 replication number 4. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.

source_name: Node 2 of 60 day old seedlings

source_name: Node 2 of 53 day old seedlings


title: p53+/+ TAF6 AS2 2

description: TAF6 AS2 treated HCT-116 p53+/+ cells


title: 60-N3-2_v_67-N3-2 (array 2of2)

description: 60 days node3 vs 67 days node3 replication number 2. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: p53-/- ctrl. 2

description: ctrl AS treated HCT-116 p53-/- cells


title: 60-N2-4_v_67-N2-4 (array 2of2)

description: 60 days node2 vs 67 days node2 replication number 4. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 60-N2-2_v_67-N2-2 (array 2of2)

description: 60 days node2 vs 67 days node2 replication number 2. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 60-N2-6_v_67-N2-6 (array 2of2)

description: 60 days node2 vs 67 days node2 replication number 6. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 67-N4-1_v_60-N4-1 (array 2of2)

description: 67 days node4 vs 60 days node4 replication number 1. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.

source_name: Node 4 of 60 day old seedlings

value: node 4

source_name: Node 4 of 67 day old seedlings


title: 46-N2-4_v_53-N2-4 (array 2of2)

description: 46 days node2 vs 53 days node2 replication number 4. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 46-N2-1_v_67-N2-1 (array 2of2)

description: 46 days node2 vs 67 days node2 replication number 1. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 67-N1-2_v_46-N1-2 (array 2of2)

description: 67 days node1 vs 46 days node1 replication number 2. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.

source_name: Node 1 of 46 day old seedlings

value: node 1

source_name: Node 1 of 67 day old seedlings


title: 67-N2-6_v_46-N2-6 (array 2of2)

description: 67 days node2 vs 46 days node2 replication number 6. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 60-N1-2_v_67-N1-2 (array 2of2)

description: 60 days node1 vs 67 days node1 replication number 2. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.

source_name: Node 1 of 60 day old seedlings


title: 53-N3-1_v_67-N3-1 (array 2of2)

description: 53 days node3 vs 67 days node3 replication number 1. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 67-N4-5_v_60-N4-5 (array 2of2)

description: 67 days node4 vs 60 days node4 replication number 5. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 67-N1-1_v_60-N1-1 (array 2of2)

description: 67 days node1 vs 60 days node1 replication number 1. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 46-N1-1_v_67-N1-1 (array 2of2)

description: 46 days node1 vs 67 days node1 replication number 1. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 60-N3-1_v_53-N3-1 (array 2of2)

description: 60 days node3 vs 53 days node3 replication number 1. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 60-N2-1_v_53-N2-1 (array 2of2)

description: 60 days node2 vs 53 days node2 replication number 1. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 67-N3-1_v_60-N3-1 (array 2of2)

description: 67 days node3 vs 60 days node3 replication number 1. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 53-N2-1_v_46-N2-1 (array 2of2)

description: 53 days node2 vs 46 days node2 replication number 1. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 67-N4-3_v_60-N4-3 (array 2of2)

description: 67 days node4 vs 60 days node4 replication number 3. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 67-N2-1_v_60-N2-1 (array 2of2)

description: 67 days node2 vs 60 days node2 replication number 1. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 60-N2-4_v_67-N2-4 (array 1of2)

description: 60 days node2 vs 67 days node2 replication number 4. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 67-N2-4_v_46-N2-4 (array 1of2)

description: 67 days node2 vs 46 days node2 replication number 4. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 60-N3-4_v_67-N3-4 (array 1of2)

description: 60 days node3 vs 67 days node3 replication number 4. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 60-N1-1_v_53-N1-1 (array 2of2)

description: 60 days node1 vs 53 days node1 replication number 1. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.

source_name: Node 1 of 53 day old seedlings


title: 67-N3-3_v_60-N3-3 (array 2of2)

description: 67 days node3 vs 60 days node3 replication number 3. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 67-N1-4_v_46-N1-4 (array 2of2)

description: 67 days node1 vs 46 days node1 replication number 4. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 60-N4-2_v_67-N4-2 (array 1of2)

description: 60 days node4 vs 67 days node4 replication number 2. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 60-N3-2_v_67-N3-2 (array 1of2)

description: 60 days node3 vs 67 days node3 replication number 2. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 60-N3-3_v_53-N3-3 (array 2of2)

description: 60 days node3 vs 53 days node3 replication number 3. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 67-N3-2_v_53-N3-2 (array 1of2)

description: 67 days node3 vs 53 days node3 replication number 2. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 67-N1-2_v_46-N1-2 (array 1of2)

description: 67 days node1 vs 46 days node1 replication number 2. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 67-N2-2_v_46-N2-2 (array 1of2)

description: 67 days node2 vs 46 days node2 replication number 2. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 67-N3-4_v_53-N3-4 (array 2of2)

description: 67 days node3 vs 53 days node3 replication number 4. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 60-N2-2_v_67-N2-2 (array 1of2)

description: 60 days node2 vs 67 days node2 replication number 2. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 67-N2-6_v_46-N2-6 (array 1of2)

description: 67 days node2 vs 46 days node2 replication number 6. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 60-N4-4_v_67-N4-4 (array 2of2)

description: 60 days node4 vs 67 days node4 replication number 4. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 53-N2-4_v_60-N2-4 (array 1of2)

description: 53 days node2 vs 60 days node2 replication number 4. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 60-N4-2_v_67-N4-2 (array 2of2)


title: 46-N2-4_v_53-N2-4 (array 1of2)

description: 46 days node2 vs 53 days node2 replication number 4. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 67-N3-1_v_60-N3-1 (array 1of2)

description: 67 days node3 vs 60 days node3 replication number 1. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 53-N3-4_v_60-N3-4 (array 2of2)

description: 53 days node3 vs 60 days node3 replication number 4. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 53-N3-1_v_67-N3-1 (array 1of2)

description: 53 days node3 vs 67 days node3 replication number 1. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 60-N1-4_v_67-N1-4 (array 2of2)

description: 60 days node1 vs 67 days node1 replication number 4. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 60-N2-6_v_67-N2-6 (array 1of2)

description: 60 days node2 vs 67 days node2 replication number 6. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 60-N1-2_v_67-N1-2 (array 1of2)

description: 60 days node1 vs 67 days node1 replication number 2. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 53-N2-2_v_60-N2-2 (array 2of2)

description: 53 days node2 vs 60 days node2 replication number 2. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 46-N2-1_v_67-N2-1 (array 1of2)

description: 46 days node2 vs 67 days node2 replication number 1. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 53-N1-1_v_46-N1-1 (array 2of2)

description: 53 days node1 vs 46 days node1 replication number 1. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 67-N4-1_v_60-N4-1 (array 1of2)

description: 67 days node4 vs 60 days node4 replication number 1. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 67-N2-1_v_60-N2-1 (array 1of2)

description: 67 days node2 vs 60 days node2 replication number 1. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 67-N1-1_v_60-N1-1 (array 1of2)

description: 67 days node1 vs 60 days node1 replication number 1. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 53-N3-2_v_60-N3-2 (array 2of2)

description: 53 days node3 vs 60 days node3 replication number 2. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 46-N2-2_v_53-N2-2 (array 2of2)

description: 46 days node2 vs 53 days node2 replication number 2. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 67-N1-4_v_46-N1-4 (array 1of2)

description: 67 days node1 vs 46 days node1 replication number 4. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 60-N2-1_v_53-N2-1 (array 1of2)

description: 60 days node2 vs 53 days node2 replication number 1. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 46-N1-2_v_53-N1-2 (array 2of2)

description: 46 days node1 vs 53 days node1 replication number 2. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 53-N1-2_v_60-N1-2 (array 2of2)

description: 53 days node1 vs 60 days node1 replication number 2. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 67-N4-5_v_60-N4-5 (array 1of2)

description: 67 days node4 vs 60 days node4 replication number 5. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 60-N1-1_v_53-N1-1 (array 1of2)

description: 60 days node1 vs 53 days node1 replication number 1. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 46-N1-1_v_67-N1-1 (array 1of2)

description: 46 days node1 vs 67 days node1 replication number 1. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 60-N3-1_v_53-N3-1 (array 1of2)

description: 60 days node3 vs 53 days node3 replication number 1. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 53-N2-1_v_46-N2-1 (array 1of2)

description: 53 days node2 vs 46 days node2 replication number 1. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 67-N3-3_v_60-N3-3 (array 1of2)

description: 67 days node3 vs 60 days node3 replication number 3. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 53-N3-4_v_60-N3-4 (array 1of2)

description: 53 days node3 vs 60 days node3 replication number 4. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 60-N4-6_v_67-N4-6 (array 2of2)

description: 60 days node4 vs 67 days node4 replication number 6. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 60-N2-5_v_53-N2-5 (array 2of2)

description: 60 days node2 vs 53 days node2 replication number 5. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 46-N2-5_v_67-N2-5 (array 2of2)

description: 46 days node2 vs 67 days node2 replication number 5. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 53-N1-1_v_46-N1-1 (array 1of2)

description: 53 days node1 vs 46 days node1 replication number 1. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 67-N2-5_v_60-N2-5 (array 2of2)

description: 67 days node2 vs 60 days node2 replication number 5. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 53-N2-5_v_46-N2-5 (array 2of2)

description: 53 days node2 vs 46 days node2 replication number 5. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 67-N3-4_v_53-N3-4 (array 1of2)

description: 67 days node3 vs 53 days node3 replication number 4. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 60-N3-3_v_53-N3-3 (array 1of2)

description: 60 days node3 vs 53 days node3 replication number 3. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 60-N4-4_v_67-N4-4 (array 1of2)

description: 60 days node4 vs 67 days node4 replication number 4. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 53-N1-2_v_60-N1-2 (array 1of2)

description: 53 days node1 vs 60 days node1 replication number 2. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 60-N1-4_v_67-N1-4 (array 1of2)

description: 60 days node1 vs 67 days node1 replication number 4. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 46-N2-2_v_53-N2-2 (array 1of2)

description: 46 days node2 vs 53 days node2 replication number 2. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 53-N3-2_v_60-N3-2 (array 1of2)

description: 53 days node3 vs 60 days node3 replication number 2. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 46-N1-2_v_53-N1-2 (array 1of2)

description: 46 days node1 vs 53 days node1 replication number 2. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 53-N2-2_v_60-N2-2 (array 1of2)

description: 53 days node2 vs 60 days node2 replication number 2. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 46-N2-5_v_67-N2-5 (array 1of2)


title: 60-N4-6_v_67-N4-6 (array 1of2)


title: 53-N1-4_v_60-N1-4 (array 2of2)

description: 53 days node1 vs 60 days node1 replication number 4. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 46-N1-5_v_67-N1-5 (array 2of2)

description: 46 days node1 vs 67 days node1 replication number 5. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 67-N2-5_v_60-N2-5 (array 1of2)


title: 67-N1-5_v_60-N1-5 (array 2of2)

description: 67 days node1 vs 60 days node1 replication number 5. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 60-N1-5_v_53-N1-5 (array 2of2)

description: 60 days node1 vs 53 days node1 replication number 5. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 60-N2-5_v_53-N2-5 (array 1of2)

description: 60 days node2 vs 53 days node2 replication number 5. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 53-N1-5_v_46-N1-5 (array 2of2)

description: 53 days node1 vs 46 days node1 replication number 5. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 53-N1-4_v_60-N1-4 (array 1of2)


title: 53-N3-5_v_67-N3-5 (array 2of2)

description: 53 days node3 vs 67 days node3 replication number 5. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 46-N1-5_v_67-N1-5 (array 1of2)


title: 60-N3-5_v_53-N3-5 (array 1of2)

description: 60 days node3 vs 53 days node3 replication number 5. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 53-N3-5_v_67-N3-5 (array 1of2)


title: 60-N2-3_v_53-N2-3 (array 1of2)

description: 60 days node2 vs 53 days node2 replication number 3. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 67-N3-5_v_60-N3-5 (array 2of2)

description: 67 days node3 vs 60 days node3 replication number 5. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 46-N1-4_v_53-N1-4 (array 1of2)

description: 46 days node1 vs 53 days node1 replication number 4. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 53-N3-3_v_67-N3-3 (array 2of2)

description: 53 days node3 vs 67 days node3 replication number 3. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 67-N3-5_v_60-N3-5 (array 1of2)


title: 53-N2-3_v_46-N2-3 (array 1of2)

description: 53 days node2 vs 46 days node2 replication number 3. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 60-N2-3_v_53-N2-3 (array 2of2)


title: 67-N4-3_v_60-N4-3 (array 1of2)

description: 67 days node4 vs 60 days node4 replication number 3. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 53-N2-3_v_46-N2-3 (array 2of2)


title: 67-N1-5_v_60-N1-5 (array 1of2)


title: 60-N3-5_v_53-N3-5 (array 2of2)


title: 53-N3-3_v_67-N3-3 (array 1of2)


title: 67-N1-3_v_60-N1-3 (array 1of2)

description: 67 days node1 vs 60 days node1 replication number 3. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 60-N1-5_v_53-N1-5 (array 1of2)


title: 46-N1-4_v_53-N1-4 (array 2of2)


title: 53-N2-6_v_60-N2-6 (array 1of2)

description: 53 days node2 vs 60 days node2 replication number 6. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 53-N1-5_v_46-N1-5 (array 1of2)


title: 60-N1-6_v_67-N1-6 (array 1of2)

description: 60 days node1 vs 67 days node1 replication number 6. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.