title: 8 hr after ammonium addition, biological rep2

status: Public on May 28 2011

city: San Marcos

first: Matthew

last: Escobar

address: 333 S. Twin Oaks Valley Rd.

department: Biological Sciences

institute: California State University San Marcos

description: Gene expression data

hyb_protocol: aRNA was hybridized to an Affymetrix ATH1-121501 chip according to Lockhart et al. (1996) (Nature Biotech 14, 1675)

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 3000

data_processing: The raw expression values were normalized using RMA or Robust Multichip Average expression summary (http://rmaexpress.bmbolstad.com/). All further processing of the data was performed within the Bioconductor project and the R program software (R is available as Free Software under the terms of the Free Software Foundation's GNU General Public License). The limma package implemented within Bioconductor was used to perform the linear modeling and the empirical Bayes statistics for differential expression analysis. The fold changes and standard errors were estimated by fitting a linear model for each gene and empirical Bayes smoothing was applied to the standard errors. Results are presented between two experimental conditions as a log2-fold change in expression level, the p-value, and the adjusted p-value. The adjusted p-value is the p-value adjusted for multiple testing using the Benjamini and Hochberg’s method to control the false discovery rate. The meaning of the BH q-values is as follows. If all genes with q-value below a threshold of 0.05 are selected as differentially expressed, then the expected proportion of false discoveries in the selected group is controlled to be less than the threshold value of 5%. Transcripts with pvalue less than 0.05 and greater than 1.4 fold change were called as significantly differentially expressed genes.

source_name: Arabidopsis roots harvested 8 hr after ammonium addition

label_protocol: Biotin-labelled aRNA was synthesized from 1 ug of total RNA using a Message Amp II-Biotin Enhanced aRNA sythesis kit.

growth_protocol: Plants were grown hydroponically using Araponics system according to manufacturer's specifications. Plant were grown until they reached stage 5.10 (Boyes et al., 2001; Plant Cell 13,1499)

extract_protocol: For each sample, roots from at least five individual plants were harvested, pooled, and frozen in liquid nitrogen. Total RNA was isolated using a Qiagen Rneasy Plant Kit according to the manufacturer's specifications

treatment_protocol: Plants at growth stage 5.10 were transferred to medium lacking nitrogen for 26 hr. Either 1 mM nitrate or 1 mM ammonium was then added to the media. Plants were harvested just before nitrate/ammonium addition, or at 1.5 hr or 8 hr post-nitrate/ammonium addition.

value: roots from hydroponically grown plants

value: Growth stage 5.10 (Boyes et al. 2001, Plant Cell 13, 1499)


title: seedlings + TSA rep2

status: Public on Jun 03 2011

type: RNA

city: West Lafayette

first: Karen

middle: A

last: Hudson

state: IN

address: 915 West State Street

department: Crop Production and Pest Control

country: USA

institute: USDA-ARS

description: Gene expression data from 10day old seedlings treated with TSA

hyb_protocol: According to Affymetrix protocol

scan_protocol: According to Affymetrix protocol

data_processing: Data for the matrix was normalized using the threestep method from Bioconductor: GCRMA background correction, scaling normalization, and median polish for summarization, for all probes on the array.

label: biotin

molecule: total RNA

organism: Arabidopsis thaliana

source_name: seedlings + 2.5 mg/L trichostatin A

label_protocol: According to Affymetrix protocol

growth_protocol: Plants were germinated in liquid 0.5X MS media with 1% sucrose in 15cm petri plates in constant light at 21C.

extract_protocol: 10 days after germination, RNA was extracted from whole seedlings using the Qiagen Plant Rneasy kit.

treatment_protocol: After 24 hours, 5-AC (20mg/L)  and TSA (2.5mg/L) in DMSO were added to chemically-treated samples, control and ddm1 seedlings received DMSO alone.  After 5 days, media was drained and fresh media including supplements was added.

tag: tissue

value: 10-day old whole seedling

tag: genotype

value: wildtype

tag: ecotype

value: Ws


title: ddm1 mutant seedlings rep1

description: Gene expression data from 10day old ddm1 mutant seedlings

source_name: ddm1 mutant seedlings

value: ddm1 mutant


title: control seedlings rep1

description: Gene expression data from 10day old Ws seedlings grown in contiuous light in 0.5X MS + sucrose.

source_name: untreated, wild-type seedlings


title: ddm1 mutant seedlings rep3


title: 8 hr after nitrate addition, biological rep3

state: CA

description: Gene expression data

source_name: Arabidopsis roots harvested 8 hr after nitrate addition

tag: age


title: 1.5 hr after nitrate addition, biological rep2

description: Gene expression data

source_name: Arabidopsis roots harvested 1.5 hr after nitrate addition


title: 1.5 hr after ammonium addition, biological rep3

description: Gene expression data

source_name: Arabidopsis roots harvested 1.5 hr after ammonium addition


title: seedlings +5AC rep2

description: Gene expression data from 10day old seedlings treated with 5-AC

source_name: seedlings + 20mg/L 5-aza-2’deoxycytidine


title: 1.5 hr after ammonium addition, biological rep1

description: Gene expression data


title: 1.5 hr after nitrate addition, biological rep3

description: Gene expression data


title: 8 hr after ammonium addition, biological rep3

description: Gene expression data


title: 1.5 hr after ammonium addition, biological rep2

description: Gene expression data


title: immediately prior to nitrogen addtion, biological rep3

description: Gene expression data

source_name: Arabidopsis roots harvested just before nitrogen addition


title: 8 hr after nitrate addition, biological rep2

description: Gene expression data


title: ddm1 mutant seedlings rep2


title: immediately prior to nitrogen addtion, biological rep1

description: Gene expression data


title: immediately prior to nitrogen addtion, biological rep2

description: Gene expression data


title: 8 hr after ammonium addition, biological rep1

description: Gene expression data


title: 8 hr after nitrate addition, biological rep1

description: Gene expression data


title: 1.5 hr after nitrate addition, biological rep1

description: Gene expression data


title: Drosophila heads 0-3 days_elavII>4x rCUG_independent line 2

status: Public on Apr 28 2011

city: Brisbane

first: Gareth

last: Price

state: Queensland

address: Carmody Road

country: Australia

institute: Queensland Facility for Advanced Bioinformatics

hyb_protocol: 10ug of fragmented biotinylated cRNA was hybridised for 16hrs at 45oC on a Drosophila Genome 2.0 GeneChip. After 16hrs GeneChips were washed on a FS_450 Fluidics Station using the Midi_euk_2 v3 script.

scan_protocol: Data was acquired on a 7G GeneChip Scanner 3000 and data extraction performed in GCOS v1.2.

data_processing: CHP files were generated in GCOS 1.2 and normalised by global scaling to a value of 100 or 500 depending on the experimental cohort. Samples on the elav c155 background were scaled to 100, samples on the elavII background were scaled to 500.

organism: Drosophila melanogaster

source_name: Heads, Drosophila, newly eclosed, male

label_protocol: Biotinylated cRNA were prepared using the One-Cycle Target Labelling and Control Reagents Kit, according to manufacturers protocol from 2ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: All the Drosophila stocks and flies were maintained in vials containing Fortified (FI) medium and kept at 25°C. The FI medium was composed of 1% agar, 18.75% compressed yeast, 10% polenta, 10% treacle, 1.5% acid mix and 2.5% tegosept.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen), according to manufacturer's protocol. Total RNA was further purified using RNeasy Mini Kit (Qiagen)

treatment_protocol: Samples were frozen in liquid nitrogen and homogenised in Trizol reagent (Invitrogen).

tag: gender

value: male

value: head

value: 0 -3 days

tag: genetic background

value: elavII

value: elavII>4x rCUG_independent line 2


title: Drosophila heads 0-3 days_elavII>4x rCAA_independent line 1

value: elavII>4x rCAA_independent line 1


title: Drosophila heads 0-3 days_elavII>4x rAUUCU_independent line 1

value: elavII>4x rAUUCU_independent line 1


title: Drosophila heads 0-3 days_elavII>4x rCAG_independent line 1

value: elavII>4x rCAG_independent line 1


title: Drosophila heads 0-3 days_elavII>4x rCAA_independent line 2

value: elavII>4x rCAA_independent line 2


title: Drosophila heads 0-3 days_elavII>4x rCAG_independent line 2

value: elavII>4x rCAG_independent line 2


title: Drosophila heads 0-3 days_elav c155>2x rCAG_independent line 3

value: elav c155

value: elav c155>2x rCAG_independent line 3


title: Drosophila heads 0-3 days_elav c155>2x rCAA_independent line 2

value: elav c155>2x rCAA_independent line 2


title: Drosophila heads 0-3 days_elav c155>2x rCUG_independent line 2

value: elav c155>2x rCUG_independent line 2


title: Drosophila heads 0-3 days_elav c155>2x rCAG_independent line 1

value: elav c155>2x rCAG_independent line 1


title: Drosophila heads 0-3 days_elavII>+_rep1

value: elavII>+


title: Drosophila heads 0-3 days_elav c155>2x rCAA_independent line 1

value: elav c155>2x rCAA_independent line 1


title: Drosophila heads 0-3 days_elavII>+_rep2

value: male


title: Drosophila heads 0-3 days_elav c155>2x rCAA_independent line 3

value: head

value: elav c155>2x rCAA_independent line 3


title: Drosophila heads 0-3 days_elavII>4x rCUG_independent line 1

value: 0 -3 days

value: elavII

value: elavII>4x rCUG_independent line 1


title: WT_HN_3

status: Public on Apr 27 2011

city: Montpellier

first: Gabriel

last: Krouk

address: 2 Place Pierre Viala

department: Biology

country: France

institute: CNRS

hyb_protocol: Affymetrix recommendations.

scan_protocol: Affymetrix recommendations.

data_processing: Mas5 [R]

label: Biotin

source_name: Roots, WT, HN

label_protocol: Affymetrix recommendations.

growth_protocol: Plants were grown on basal media supplemented by different nitrogen sources.

extract_protocol: Trizol RNA.

treatment_protocol: Steady state on 0.3 mM KNO3 (low nitrogen) or 10 mM NH4NO3 (high nitrogen).

value: roots

value: WT

tag: environment

value: high nitrogen


title: Drosophila heads 0-3 days_elav c155>2x rCAG_independent line 2

value: elav c155>2x rCAG_independent line 2


title: Drosophila heads 0-3 days_elav c155>2x rCUG_independent line 1

value: elav c155

value: elav c155>2x rCUG_independent line 1


title: hni9_LN_3

source_name: Roots, hni9, LN

value: low nitrogen


title: WT_LN_3

source_name: Roots, WT, LN


title: hni9_HN_3

source_name: Roots, hni9, HN


title: Drosophila heads 0-3 days_elav c155>2x rCUG_independent line 3

value: elav c155>2x rCUG_independent line 3


title: Drosophila heads 0-3 days_elav c155>+_rep2

value: elav c155>+


title: Drosophila heads 0-3 days_elav c155>+_rep1


title: Penfield_2-12_Ler-10-degrees-long-day_Rep3_ATH1

status: Public on Apr 21 2011

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

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

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

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

source_name: Landsberg erecta (Ler-0)

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

growth_protocol: Plants were grown to flowering in long 16h days at 20 degrees celcius under white fluorescent light at 80-100umol m-2 sec-2. After flowering the temperature was changed to 10 degrees celcius until maturity, other parameters were maintained. Mature seed was collected from dehisced siliques.  Levington seed compost  Intercept  I plant per P40 insert daily 10 °C average, 10 °C day, 10 °C night 80 % average, unknown % day, unknown % night

extract_protocol: Qiagen RNAeasy kit protocol

value: wild type Ler

tag: developmental stage

value: seeds

tag: stock code


title: Penfield_2-11_Ler-10-degrees-long-day_Rep2_ATH1

institute: Nottingham Arabidopsis Stock Centre (NASC)


title: Penfield_2-8_Ler-20-degrees-short-day_Rep2_ATH1

growth_protocol: Plants were grown in short 8h days at 20 degrees celcius under white fluorescent light at 80-100umol m-2 sec-2. Mature seed was collected from dehisced siliques.  Levington seed compost  Intercept  I plant per P40 insert daily 20 °C average, 20 °C day, 20 °C night 80 % average, unknown % day, unknown % night


title: Penfield_2-9_Ler-20-degrees-short-day_Rep3_ATH1


title: Penfield_2-10_Ler-10-degrees-long-day_Rep1_ATH1


title: Penfield_2-5_ft1-20-degrees-long-day_Rep2_ATH1

source_name: Glabra

growth_protocol: Plants were grown in long 16h days at 20 degrees celcius under white fluorescent light at 80-100umol m-2 sec-2. Mature seed was collected from dehisced siliques.  Levington seed compost  Intercept  I plant per P40 insert daily 20 °C average, 20 °C day, 20 °C night 80 % average, unknown % day, unknown % night

value: ft-1 mutant

value: N65 Genetic background:Ler Genetic variation:Single marker


title: Penfield_2-4_ft1-20-degrees-long-day_Rep1_ATH1


title: Penfield_2-7_Ler-20-degrees-short-day_Rep1_ATH1


title: colptobis_3 with array type ATH1 from Affymetrix

status: Public on Apr 20 2011

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

institute: inra

description: - Pseudomonas syringae is a plant pathogenic bacterium that relies on a type III secretion system (T3SS) to cause disease in susceptible hosts and to trigger defence in resistant plants. The T3SS translocates effector proteins directly inside the plant cell. Some P. syringae pathovars translocate the effector HopZ1a, which is recognized in Arabidopsis, triggering the hypersensitive response (HR). This resistance does not depend on the usual defence pathways involved in resistance against other avirulence effectors, so it would be very helpful to know the transcriptomic events that take place in the context of a hypersensitive response triggered by HopZ1a. ULP genes codifies for plant SUMO-proteases. Recent studies by our group revealed that they could be involved in plant defense against microorganisms.

hyb_protocol: labelled extract quantity: 15ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003) using R-2.6.2 version and AFFYMETRIX bioconductor packages (Gentleman and Carey, 2002).

label_protocol: labelling Biotin direct, amplification=yes, cRNA 20 ug.

growth_protocol: caulin leaf - -Grown in rich substrate in growth chambers at 21 ºC with 8h light / 16h dark.

extract_protocol: colpto_3:7.5ng. Qiagen_RNeasy kit

treatment_protocol: Name:ColPto - environmental treatment - pathogen infection,inoculation with bacteria pto wild type.:quantity 10cfu/ml time 6hour . - Leaves were infiltrated with bacterial suspension containing 108 cfu/ml of Pseudomonas syringae pv. tomato (Pto) wild type, using a blunt syringae.

value: columbia

tag: developmental stage (boyes et al. plant cell 2001)

value: 1-5 rosette leaf


title: ulppto_2 with array type ATH1 from Affymetrix

growth_protocol: caulin leaf - -Grown in rich substrate in growth chambers at 21 ºC with 8h light / 16h dark

extract_protocol: ulppto_2:7.5ng. Qiagen_RNeasy kit

treatment_protocol: Name:UlpPto - environmental treatment - pathogen infection,inoculation with bacteria pto wild type.:quantity 10cfu/ml time 6hour . - Leaves were infiltrated with bacterial suspension containing 108 cfu/ml of Pseudomonas syringae pv. tomato (Pto) wild type, using a blunt syringae.

tag: genotype/variation

value: mutant (ulp1c/ulp1d)


title: colmock_2 with array type ATH1 from Affymetrix

extract_protocol: colmock_2:7.5ng. Qiagen_RNeasy kit

treatment_protocol: Name:ColMock - environmental treatment - mock infiltration,mock infiltration:quantity 10mM time 6hour . - Leaves were infiltrated with 10mM Magnesium chloride using a blunt syringae.


title: ulppto_1 with array type ATH1 from Affymetrix

extract_protocol: ulppto_1:7.5ng. Qiagen_RNeasy kit


title: Penfield_2-3_Ler-20-degrees-long-day_Rep3_ATH1


title: Penfield_2-2_Ler-20-degrees-long-day_Rep2_ATH1


title: colmock_1 with array type ATH1 from Affymetrix

extract_protocol: colmock_1:7.5ng. Qiagen_RNeasy kit

tag: harvest date


title: Penfield_2-1_Ler-20-degrees-long-day_Rep1_ATH1


title: col_3 with array type ATH1 from Affymetrix

extract_protocol: col_3:7.5ng. Qiagen_RNeasy kit

treatment_protocol: no treatment


title: col_2 with array type ATH1 from Affymetrix

extract_protocol: col_2:7.5ng. Qiagen_RNeasy kit


title: ulppto_3 with array type ATH1 from Affymetrix

extract_protocol: ulppto_3:7.5ng. Qiagen_RNeasy kit


title: colmut_1 with array type ATH1 from Affymetrix

extract_protocol: colmut_1:7.5ng. Qiagen_RNeasy kit

treatment_protocol: Name:ColMut - environmental treatment - pathogen infection,inoculation with bacteria pto expressing the mutant effector hopz1ac216a.:quantity 10cfu/ml time 6hour . - Leaves were infiltrated with bacterial suspension containing 108 cfu/ml of Pseudomonas syringae pv. tomato (Pto) expressing the effector HopZ1a carrying a mutation that inactivates its catalytic site (C216A), using a blunt syringae


title: ulpmock_2 with array type ATH1 from Affymetrix

extract_protocol: ulpmock_2:7.5ng. Qiagen_RNeasy kit

treatment_protocol: Name:UlpMock - environmental treatment - mock infiltration,: mock with magnesium chloride:quantity 10mM time 6hour . Leaves were infiltrated with 10mM Magnesium chloride using a blunt syringae


title: col_1 with array type ATH1 from Affymetrix

extract_protocol: col_1:7.5ng. Qiagen_RNeasy kit


title: ulpmock_1 with array type ATH1 from Affymetrix

extract_protocol: ulpmock_1:7.5ng. Qiagen_RNeasy kit


title: colptobis_2 with array type ATH1 from Affymetrix

extract_protocol: colpto_2:7.5ng. Qiagen_RNeasy kit


title: colptobis_1 with array type ATH1 from Affymetrix

extract_protocol: colpto_1:7.5ng. Qiagen_RNeasy kit


title: colhop_3 with array type ATH1 from Affymetrix

extract_protocol: colhop_3:7.5ng. Qiagen_RNeasy kit

treatment_protocol: Name:ColHop - environmental treatment - pathogen infection,: inoculation with bacteria pto expressing the effector hopz1a:quantity 10cfu/ml time 6hour . - Leaves were infiltrated with bacterial suspension containing 108 cfu/ml of Pseudomonas syringae pv. tomato (Pto) expressing the effector HopZ1a, using a blunt syringae.


title: ulp_3 with array type ATH1 from Affymetrix

extract_protocol: ulp_3:7.5ng. Qiagen_RNeasy kit


title: ulp_2 with array type ATH1 from Affymetrix

extract_protocol: ulp_2:7.5ng. Qiagen_RNeasy kit


title: ulpmock_3 with array type ATH1 from Affymetrix

extract_protocol: ulpmock_3:7.5ng. Qiagen_RNeasy kit


title: colmut_2 with array type ATH1 from Affymetrix

extract_protocol: colmut_2:7.5ng. Qiagen_RNeasy kit


title: colhop_1 with array type ATH1 from Affymetrix

extract_protocol: colhop_1:7.5ng. Qiagen_RNeasy kit


title: ulp_1 with array type ATH1 from Affymetrix

extract_protocol: ulp_1:7.5ng. Qiagen_RNeasy kit


title: colhop_2 with array type ATH1 from Affymetrix

extract_protocol: colhop_2:7.5ng. Qiagen_RNeasy kit


title: colmock_3 with array type ATH1 from Affymetrix

extract_protocol: colmock_3:7.5ng. Qiagen_RNeasy kit


title: colmut_3 with array type ATH1 from Affymetrix

extract_protocol: colmut_3:7.5ng. Qiagen_RNeasy kit


title: C94

status: Public on Apr 10 2011

city: Berlin

first: Dido

last: Lenze

address: Hindenburgdamm 30

department: Pathologie, Campus Benjamin Franklin

country: Germany

institute: Charité-Universitätsmedizin Berlin

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133 Plus 2.0 arrays (Affymetrix). GeneChips were washed and stained with standard protocols in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scanner G3000

data_processing: Data were normalized with VSN (Bioconductor package vsn 3.2.1) and summarized with the median polish method. Data analysis and statistical computing were performed with R (2.6.0).

organism: Homo sapiens

source_name: colon

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3ug total RNA

extract_protocol: For microarray analyses, snap frozen tissue specimens were cut into 7 µm-thick sections that were stained with haematoxylin & eosin (H&E). Stained sections were reviewed by a pathologist to identify areas of vital tumor cells and to ensure a tumor content of 80-90%. Corresponding tumor areas were macrodissected by vertical 3 mm incision into the frozen tissue specimens with a sterile blade. Incision was followed by a series of ten 20 μm frozen sections. Separated tumor areas were harvested by sterile micropipette tip and collected in a buffer (RLT buffer, RNeasy Mini Kit; Qiagen, Hilden, Germany). Each series of ten sections was followed by a 7 µm H&E stained section to control tissue composition. The number of tissue sections used to extract RNA was dependent on the expanse of the area of individual tumor tissue.  Total RNA was isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions and quantified using the Nanodrop ND-1000 UV-vis spectrophotometer (Nanodrop Technologies, USA). The quality of the RNA was controlled using the BioAnalyzer (Agilent Technologies, USA) and exclusively high quality RNA was used for further analysis.

tag: localization

value: distal

value: male

tag: relapse

value: no

tag: microsatellite status

value: MSS

tag: age at diagnosis, years

tag: grading

tag: pt


title: C113

value: female

value: yes

value: MSI-high


title: C71


title: C80


title: C39

value: proximal


title: C83


title: C58


title: C51


title: C102


title: C42


title: C70


title: C65


title: C82


title: C66


title: C68


title: C44


title: C69


title: C46


title: C43


title: C57


title: C60


title: C67


title: C63


title: C52


title: C64


title: C74


title: C48


title: C40


title: C81


title: C38


title: C32


title: C34


title: C29


title: C26


title: C28


title: C24


title: C27


title: C25


title: C23


title: C13


title: C10


title: C33


title: C11


title: C20


title: C6


title: C3


title: C2


title: C8


title: C31


title: C7


title: C30_2


title: mutant_rdo2_siliques_18-19DAP_rep3

status: Public on Apr 08 2011

city: Freiburg im Breisgau

first: Annaick

last: Carles

address: Habsburgerstrasse 49

institute: University of Freiburg

description: Gene expression data from Arabidopsis nearly ripe siliques (18-19 DAP) of mutant rdo2, rep3

hyb_protocol: After fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45 degrees Celsius on GeneChip ATH1 Genome Array. GeneChips were washed and stained with Fluidics Script FS450_004 in the Affymetrix Fluidics Station 450.

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

data_processing: Processing and statistical analysis of the microarray data were done in Expressionist Pro v5.1 (Genedata AG, Basel, Switzerland). We used the GC-RMA algorithm for background correction, normalization and probe summarization. Various quality metrics were examined to exclude quality problems.

label_protocol: Biotinylated cRNA was prepared according to the standard Ambion protocol from 1 ug total RNA (MessageAmp II-Biotin Enhanced Kit, 2008, Ambion).

growth_protocol: Plants were grown on soil containing a mixture of substrate and vermiculite (3:1) in Elbanton growth cabinets (Elbanton BV, Kerkdriel, the Netherlands) under long day conditions (16 h light at 22oC and 8 h dark at 16oC).

extract_protocol: Extraction of RNA was performed using RNAqueous columns (Ambion, Austin, TX, USA).

treatment_protocol: Siliques were harvested from the plants at 18-19 days after pollination and immediately frozen until RNA extraction

value: Ler

tag: genotype


title: mutant_rdo4_siliques_18-19DAP_rep1

description: Gene expression data from Arabidopsis nearly ripe siliques (18-19 DAP) of mutant rdo4, rep1

tag: ecotype


title: mutant_rdo2_siliques_18-19DAP_rep2

description: Gene expression data from Arabidopsis nearly ripe siliques (18-19 DAP) of mutant rdo2, rep2


title: wildtype_Ler_siliques_18-19DAP_rep2

description: Gene expression data from Arabidopsis nearly ripe siliques (18-19 DAP) of wild type Ler, rep2

value: wild type


title: wildtype_Ler_siliques_18-19DAP_rep3

description: Gene expression data from Arabidopsis nearly ripe siliques (18-19 DAP) of wild type Ler, rep3


title: mutant_rdo3_siliques_18-19DAP_rep2

description: Gene expression data from Arabidopsis nearly ripe siliques (18-19 DAP) of mutant rdo3, rep2


title: mutant_rdo2_siliques_18-19DAP_rep1

description: Gene expression data from Arabidopsis nearly ripe siliques (18-19 DAP) of mutant rdo2, rep1


title: mutant_rdo3_siliques_18-19DAP_rep3

description: Gene expression data from Arabidopsis nearly ripe siliques (18-19 DAP) of mutant rdo3, rep3


title: mutant_rdo3_siliques_18-19DAP_rep1

description: Gene expression data from Arabidopsis nearly ripe siliques (18-19 DAP) of mutant rdo3, rep1


title: C22


title: wildtype_Ler_siliques_18-19DAP_rep1

description: Gene expression data from Arabidopsis nearly ripe siliques (18-19 DAP) of wild type Ler, rep1


title: C1


title: mutant_rdo4_siliques_18-19DAP_rep3

description: Gene expression data from Arabidopsis nearly ripe siliques (18-19 DAP) of mutant rdo4, rep3


title: DMTU,rep2

status: Public on Apr 07 2011

city: La Jolla

first: Maik

last: Boehmer

address: 9500 Gilman Dr 0116

institute: University of Caifornia, San Diego

hyb_protocol: Arabidopsis ATH1 oligonucleotide-based genome arrays were used, and hybridization and washing were performed by using the standard Affymetrix protocol for RNA analyses (www.affymetrix.com/products/arrays/specific/arab.affx).

scan_protocol: Affymetrix 7G scanner

data_processing: RMA (Limma)

source_name: T87 suspension cells

label_protocol: Affymetrix 3' IVT labeling kit

growth_protocol: Arabidopsis thaliana (Columbia ecotype) T87 suspension cells were obtained from RIKEN BioResource Center (Tsukuba, Japan) and were cultured at 20 °C under 16 h light, 8h dark illumination (24 μE s−1 m−2) with shaking at 120 rpm. Cells were subcultured every 7 days by adding 10 ml of the cell suspension to a 500 ml flask containing 90 ml of Gamborg B5 medium with 3% sucrose and 0.5 µM 1-naphthaleneacetic acid (NAA). Experiments were carried out in the exponential phase of growth at about 120 h of cell cultivation.

extract_protocol: RNA was isolated with the RNeasy Plant Mini Kit (Qiagen) following the manufacturer's instructions.

treatment_protocol: ABA and DMTU were added to the medium containing the suspension cells to the final required concentrations of 50 µM and 5mM, respectively. Treatments were continued for 20 h before RNA extraction

tag: cell type

value: suspension cells

tag: age

value: 5 days

tag: time

value: 20 hours

tag: hormone

value: ethanol (control)

tag: inhibitor

value: Dimethylthiourea (DMTU)

tag: cell line


title: control,rep2

tag: genetic background


title: ABA+DMTU,rep3

value: abscisic acid (ABA)


title: mutant_rdo4_siliques_18-19DAP_rep2

description: Gene expression data from Arabidopsis nearly ripe siliques (18-19 DAP) of mutant rdo4, rep2


title: ABA,rep1


title: DMTU,rep1


title: ABA,rep2


title: ABA+DMTU,rep1


title: ABA+DMTU,rep2


title: DMTU,rep3


title: Skipsey_1-14_CMP_4hr_Rep2_ATH1

status: Public on Apr 06 2011

description: Wildtype arabidopsis thaliana Col-0 root cultures were grown in the dark at 25oC in Gamborg's B5 medium and used 14 days after initiation.

extract_protocol: Qiagen RNAeasy kit protocol

tag: tissue

value: root


title: Skipsey_1-12_Fenclorim_24hr_Rep3_ATH1


title: Skipsey_1-15_CMP_4hr_Rep3_ATH1


title: Skipsey_1-10_Fenclorim_24hr_Rep1_ATH1


title: Skipsey_1-2_Acetone_4hr_Rep2_ATH1


title: Skipsey_1-17_CMP_24hr_Rep2_ATH1


title: Skipsey_1-13_CMP_4hr_Rep1_ATH1


title: Skipsey_1-5_Acetone_24hr_Rep2_ATH1


title: control,rep3


title: Skipsey_1-11_Fenclorim_24hr_Rep2_ATH1


title: Skipsey_1-1_Acetone_4hr_Rep1_ATH1


title: Skipsey_1-16_CMP_24hr_Rep1_ATH1


title: Skipsey_1-3_Acetone_4hr_Rep3_ATH1


title: Skipsey_1-9_Fenclorim_4hr_Rep3_ATH1


title: Skipsey_1-6_Acetone_24hr_Rep3_ATH1


title: Skipsey_1-4_Acetone_24hr_Rep1_ATH1


title: Skipsey_1-8_Fenclorim_4hr_Rep2_ATH1


title: Skipsey_1-7_Fenclorim_4hr_Rep1_ATH1


title: Skipsey_1-18_CMP_24hr_Rep3_ATH1


title: leaf 20%Inhibition rep3 [Arabidopsis]

status: Public on Apr 01 2011

city: Oak Ridge

first: David

middle: J

last: Weston

state: TN

department: Environmental Sciences Division

institute: David Weston

description: Gene expression data from the first fully expanded leaf of Arabidopsis thaliana at 20% inhibition from optimum

hyb_protocol: Following fragmentation, cRNA was hybridized to the ATH1 Affymetrix slide according to standard protocols (#PM702232; www.affymetrix.com).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 according to standard protocol #PM702232; www.affymetrix.com.

data_processing: All data were analyzed using the limma package in the Bioconductor software (v.2.4). Gene level information for RMA normalized expression values are presented within the matrix for all samples analyzed.

source_name: Arabidopsis thaliana leaf, 20% inhibition

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

growth_protocol: Seeds of Arabidopsis thaliana (ecotype Col-0) were imbibed at 4 °C with distilled water for 4d to facilitate uniform germination.  The seeds were resuspended in 0.05% agarose after the cold treatment and planted in pots containing Fafard 3B mix (Conrad Fafard, Agawam, MA).  Plants were grown in a Conviron BDW80 walk-in growth chamber under the following growth conditions: 22 °C, 60% relative humidity, a 10 h photoperiod, and 350 μmol m-2s-1 light intensity. Plants were watered as needed and fertilized weekly using 125 ppm N of Jack's Professional

extract_protocol: Total RNA was isolated from 100 mg of tissue using an RNeasy® Mini Kit (Qiagen Inc., CA) according to the manufacturer’s instructions.  An on-column DNase 1 treatment (Sigma-Aldrich) was used during RNA extraction to remove any potential genomic DNA contamination.

treatment_protocol: For the microarray analysis, fully expanded leaf samples from 4 randomly collected plants per species were harvested at 4 physiological states as determined from prior gas exchange measurements (growth temperature - baseline, photosynthetic optimum, 20% inhibition of optimum and 30% inhibition of optimum). The temperature response curves were created by increasing temperature step-wise (2 °C per 10 mins) from 22 to 42 °C to the desired physiological state and waiting 20-30 mins for photosynthesis to stabilize before sampling. Each curve took 3-4 h to complete.

value: leaf, first fully expanded

tag: line

value: Columbia

tag: treatment

value: Photosynthesis at 20% inhibition from optimum


title: leaf 30%Inhibition rep2 [Arabidopsis]

description: Gene expression data from the first fully expanded leaf of Arabidopsis thaliana at 30% inhibition from optimum

source_name: Arabidopsis thaliana leaf, 30% inhibition

value: Photosynthesis at 30% inhibition from optimum


title: leaf 20%Inhibition rep4 [Arabidopsis]


title: leaf baseline rep3 [Arabidopsis]

description: Gene expression data from the first fully expanded leaf of Arabidopsis thaliana at growth temperature

source_name: Arabidopsis thaliana leaf, baseline

value: Photosynthesis at growth temperature


title: leaf baseline rep4 [Arabidopsis]


title: leaf optimum rep4 [Arabidopsis]

description: Gene expression data from the first fully expanded leaf of Arabidopsis thaliana at optimum temperature

source_name: Arabidopsis thaliana leaf, optimum

value: Photosynthesis at optimum temperature


title: leaf optimum rep1 [Arabidopsis]


title: leaf optimum rep3 [Arabidopsis]


title: leaf optimum rep2 [Arabidopsis]


title: leaf 30%Inhibition rep4 [Arabidopsis]


title: leaf baseline rep2 [Arabidopsis]


title: leaf 30%Inhibition rep3 [Arabidopsis]


title: leaf 30%Inhibition rep1 [Arabidopsis]


title: leaf 20%Inhibition rep2 [Arabidopsis]


title: leaf baseline rep1 [Arabidopsis]


title: 10d seedlings harboring empty vector treated with CHX, rep4

city: Tsukuba

first: Nobutaka

last: Mitsuda

state: Ibaraki

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

description: Total RNA from 10d whole seedlings expressing 35S:VP16-GR (empty vector) treated with 10mM CHX for 6hrs was isolated to use for control. Replicate 4 of 5.

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. All signals were divided by median value of all probe sets.

source_name: 10d whole seedlings harboring empty vector treated with 10mM CHX for 6hrs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.

growth_protocol: Seedlings were grown in MS agar medium in 16 hrs light at 23 centigrade degree.

extract_protocol: Total RNA was extracted using Nucleospin RNA Plant System (Macherey-Nagel) following instruction.

treatment_protocol: Ten-day-old seedlings grown on a medium were soaked with sterilized water containing 10 µM cycloheximide (CHX), a protein synthesis inhibitor, for 2 hours. After removal of the solution, the seedlings were soaked with sterilized water containing CHX and with or without 10 µM DEX for 4 hours.

value: whole seedlings

value: 10 day old

value: 35S:VP16-GR:NOS homozygous, single insertion

value: 10mM cycloheximide (CHX) 6hrs


title: 10d seedlings harboring empty vector treated with DEX plus CHX, rep2

description: Total RNA from 10d whole seedlings expressing 35S:VP16-GR (empty vector) treated with 10mM CHX for 2hrs followed by 10mM DEX for 4hrs was isolated to identify induced genes by DEX without new protein synthesis. Replicate 2 of 5.

source_name: 10d whole seedlings harboring empty vector treated with 10mM CHX for 2hrs followed by 10mM DEX for 4hrs

value: 10mM cycloheximide (CHX) 2hrs followed by 10mM dexamethazone (DEX) 4hrs


title: 10d seedlings harboring empty vector treated with CHX, rep3

description: Total RNA from 10d whole seedlings expressing 35S:VP16-GR (empty vector) treated with 10mM CHX for 6hrs was isolated to use for control. Replicate 3 of 5.


title: 10d seedlings expressing 35S:VND7-VP16-GR treated with CHX, rep3

description: Total RNA from 10d whole seedlings expressing 35S:VND7-VP16-GR treated with 10mM CHX for 6hrs was isolated to use control. Replicate 3 of 5.

value: 35S:VND-VP16-GR:NOS homozygous, single insertion


title: 10d seedlings expressing 35S:VND7-VP16-GR treated with CHX, rep5

description: Total RNA from 10d whole seedlings expressing 35S:VND7-VP16-GR treated with 10mM CHX for 6hrs was isolated to use control. Replicate 5 of 5.


title: 10d seedlings expressing 35S:VND7-VP16-GR treated with CHX, rep4

description: Total RNA from 10d whole seedlings expressing 35S:VND7-VP16-GR treated with 10mM CHX for 6hrs was isolated to use control. Replicate 4 of 5.


title: 10d seedlings harboring empty vector treated with DEX plus CHX, rep5

description: Total RNA from 10d whole seedlings expressing 35S:VP16-GR (empty vector) treated with 10mM CHX for 2hrs followed by 10mM DEX for 4hrs was isolated to identify induced genes by DEX without new protein synthesis. Replicate 5 of 5.


title: 10d seedlings harboring empty vector treated with DEX plus CHX, rep3

description: Total RNA from 10d whole seedlings expressing 35S:VP16-GR (empty vector) treated with 10mM CHX for 2hrs followed by 10mM DEX for 4hrs was isolated to identify induced genes by DEX without new protein synthesis. Replicate 3 of 5.


title: 10d seedlings harboring empty vector treated with CHX, rep1

description: Total RNA from 10d whole seedlings expressing 35S:VP16-GR (empty vector) treated with 10mM CHX for 6hrs was isolated to use for control. Replicate 1 of 5.


title: 10d seedlings harboring empty vector treated with CHX, rep5

description: Total RNA from 10d whole seedlings expressing 35S:VP16-GR (empty vector) treated with 10mM CHX for 6hrs was isolated to use for control. Replicate 5 of 5.


title: 10d seedlings harboring empty vector treated with DEX plus CHX, rep4

description: Total RNA from 10d whole seedlings expressing 35S:VP16-GR (empty vector) treated with 10mM CHX for 2hrs followed by 10mM DEX for 4hrs was isolated to identify induced genes by DEX without new protein synthesis. Replicate 4 of 5.


title: 10d seedlings harboring empty vector treated with DEX plus CHX, rep1

description: Total RNA from 10d whole seedlings expressing 35S:VP16-GR (empty vector) treated with 10mM CHX for 2hrs followed by 10mM DEX for 4hrs was isolated to identify induced genes by DEX without new protein synthesis. Replicate 1 of 5.


title: 10d seedlings expressing 35S:VND7-VP16-GR treated with CHX, rep1

description: Total RNA from 10d whole seedlings expressing 35S:VND7-VP16-GR treated with 10mM CHX for 6hrs was isolated to use control. Replicate 1 of 5.


title: 10d seedlings expressing 35S:VND7-VP16-GR treated with CHX, rep2

description: Total RNA from 10d whole seedlings expressing 35S:VND7-VP16-GR treated with 10mM CHX for 6hrs was isolated to use control. Replicate 2 of 5.


title: 10d seedlings expressing 35S:VND7-VP16-GR treated with DEX plus CHX, rep4

description: Total RNA from 10d whole seedlings expressing 35S:VND7-VP16-GR treated with 10mM CHX for 2hrs followed by 10mM DEX for 4hrs was isolated to identify induced genes by VND7 without new protein synthesis. Replicate 4 of 5.


title: 10d seedlings expressing 35S:VND7-VP16-GR treated with DEX plus CHX, rep5

description: Total RNA from 10d whole seedlings expressing 35S:VND7-VP16-GR treated with 10mM CHX for 2hrs followed by 10mM DEX for 4hrs was isolated to identify induced genes by VND7 without new protein synthesis. Replicate 5 of 5.


title: 10d seedlings expressing 35S:VND7-VP16-GR treated with DEX plus CHX, rep2

description: Total RNA from 10d whole seedlings expressing 35S:VND7-VP16-GR treated with 10mM CHX for 2hrs followed by 10mM DEX for 4hrs was isolated to identify induced genes by VND7 without new protein synthesis. Replicate 2 of 5.


title: 10d seedlings expressing 35S:VND7-VP16-GR treated with DEX plus CHX, rep3

description: Total RNA from 10d whole seedlings expressing 35S:VND7-VP16-GR treated with 10mM CHX for 2hrs followed by 10mM DEX for 4hrs was isolated to identify induced genes by VND7 without new protein synthesis. Replicate 3 of 5.


title: 10d seedlings expressing 35S:VND7-VP16-GR treated with DEX plus CHX, rep1

description: Total RNA from 10d whole seedlings expressing 35S:VND7-VP16-GR treated with 10mM CHX for 2hrs followed by 10mM DEX for 4hrs was isolated to identify induced genes by VND7 without new protein synthesis. Replicate 1 of 5.


title: pif4 pil5 3160min rep2

status: Public on Mar 31 2011

city: Davis

first: Julin

middle: N

last: Maloof

address: One Shields Ave

department: Plant Biology

institute: University of California, Davis

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 05.02.07 30 ATH1.CEL
Sample name: D10

hyb_protocol: Hybridization was performed according to the EukGE-WS2v4_450 protocol

scan_protocol: Scanning was performed on a GCS3000 scanner

data_processing: Data was normalized using the rma function of the affy package in R/Bioconductor

source_name: pif4 pil5 seedlings, dark, 3160 minutes after dawn day 4

label_protocol: Biotinolyated cRNA was obtained using the protocol described by Schmid, M. et al. Nat. Genet. 37, 501-506 (2005)

growth_protocol: Plants were grown on 1X MSMO media supplemented with 3% sucrose

extract_protocol: total RNA was extracted using Qiagen RNeasy Plant Mini kit and manufactuer's instructions

value: pif4 pil5

tag: days after germination

tag: minutes after dawn day 4

tag: light

value: dark

tag: growth

value: not growing


title: pif4 pil5 1720min rep2

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 05.02.07 29 ATH1.CEL
Sample name: D6

source_name: pif4 pil5 seedlings, dark, 1720 minutes after dawn day 4


title: CCA1OX 1080min rep2

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 04.27.07 15 ATH1.CEL
Sample name: B15

source_name: CCA1OX seedlings, light, 1080 minutes after dawn day 4

value: light


title: CCA1OX 280min rep2

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 04.24.07 14 ATH1.CEL
Sample name: B14

source_name: CCA1OX seedlings, dark, 280 minutes after dawn day 4

value: growing


title: pif4 pil5 280min rep1

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 05.02.07 25 ATH1.CEL
Sample name: C2

source_name: pif4 pil5 seedlings, dark, 280 minutes after dawn day 4


title: CCA1OX 3160min rep2

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 05.02.07 22 ATH1.CEL
Sample name: B22

source_name: CCA1OX seedlings, dark, 3160 minutes after dawn day 4


title: CCA1OX 1240min rep2

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 04.27.07 16 ATH1.CEL
Sample name: B16

source_name: CCA1OX seedlings, dark, 1240 minutes after dawn day 4


title: CCA1OX 3960min rep2

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 05.02.07 23 ATH1.CEL
Sample name: B23

source_name: CCA1OX seedlings, light, 3960 minutes after dawn day 4


title: Col 2680min rep2

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 05.02.07 08 ATH1.CEL
Sample name: B8

source_name: Col seedlings, dark, 2680 minutes after dawn day 4

value: Col


title: Col 1720min rep2

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 04.27.07 06 ATH1.CEL
Sample name: B6

source_name: Col seedlings, dark, 1720 minutes after dawn day 4


title: Col 1560min rep2

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 04.27.07 05 ATH1.CEL
Sample name: B5

source_name: Col seedlings, light, 1560 minutes after dawn day 4


title: CCA1OX 120min rep2

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 04.24.07 13 ATH1.CEL
Sample name: B13

source_name: CCA1OX seedlings, light, 120 minutes after dawn day 4


title: pif4 pil5 3160min rep1

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 05.02.07 27 ATH1.CEL
Sample name: C10


title: pif4 pil5 1720min rep1

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 05.02.07 26 ATH1.CEL
Sample name: C6


title: CCA1OX 1720min rep2

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 04.27.07 18 ATH1.CEL
Sample name: B18

source_name: CCA1OX seedlings, dark, 1720 minutes after dawn day 4


title: CCA1OX 2680min rep2

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 05.02.07 20 ATH1.CEL
Sample name: B20

source_name: CCA1OX seedlings, dark, 2680 minutes after dawn day 4


title: Col 3160min rep2

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 05.02.07 10 ATH1.CEL
Sample name: B10

source_name: Col seedlings, dark, 3160 minutes after dawn day 4


title: Col 3960min rep2

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 05.02.07 11 ATH1.CEL
Sample name: B11

source_name: Col seedlings, light, 3960 minutes after dawn day 4


title: CCA1OX 1560min rep2

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 04.27.07 17 ATH1.CEL
Sample name: B17

source_name: CCA1OX seedlings, light, 1560 minutes after dawn day 4


title: Col 280min rep2

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 04.24.07 02 ATH1.CEL
Sample name: B2

source_name: Col seedlings, dark, 280 minutes after dawn day 4


title: Col 1080min rep2

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 04.27.07 03 ATH1.CEL
Sample name: B3

source_name: Col seedlings, light, 1080 minutes after dawn day 4


title: pif4 pil5 280min rep2

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 05.02.07 28 ATH1.CEL
Sample name: D2


title: Col 1240min rep2

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 04.27.07 04 ATH1.CEL
Sample name: B4

source_name: Col seedlings, dark, 1240 minutes after dawn day 4


title: CCA1OX 3960min rep1

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 07.12.05 23 ATH1.CEL
Sample name: A23


title: CCA1OX 3000min rep1

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 07.12.05 21 ATH1.CEL
Sample name: A21

source_name: CCA1OX seedlings, light, 3000 minutes after dawn day 4


title: CCA1OX 1560min rep1

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 07.12.05 17 ATH1.CEL
Sample name: A17


title: leaf 20%Inhibition rep1 [Arabidopsis]

description: Gene expression data from the first fully expanded leaf of Arabidopsis thaliana at 20% inhibition from optimum

source_name: Arabidopsis thaliana leaf, 20% inhibition

value: leaf, first fully expanded

value: Columbia


title: Col 120min rep2

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 04.24.07 01 ATH1.CEL
Sample name: B1

source_name: Col seedlings, light, 120 minutes after dawn day 4


title: CCA1OX 2520min rep1

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 07.12.05 19 ATH1.CEL
Sample name: A19

source_name: CCA1OX seedlings, light, 2520 minutes after dawn day 4


title: Col 3000min rep1

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 07.12.05 09 ATH1.CEL
Sample name: A9

source_name: Col seedlings, light, 3000 minutes after dawn day 4


title: Col 120min rep1

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 06.24.05 01 ATH1.CEL
Sample name: A1


title: Col 2520min rep1

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 07.12.05 07 ATH1.CEL
Sample name: A7

source_name: Col seedlings, light, 2520 minutes after dawn day 4


title: CCA1OX 120min rep1

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 06.24.05 13 ATH1.CEL
Sample name: A13


title: Col 3960min rep1

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 07.12.05 11 ATH1.CEL
Sample name: A11


title: Col 1560min rep1

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 07.12.05 05 ATH1.CEL
Sample name: A5


title: polysome mRNA eif3k-1

status: Public on Mar 29 2011

city: Knoxville

first: Albrecht

last: von Arnim

address: M407 Walters Life Sciences Building

department: Biochemistry, Cellular and Molecular Biology

institute: the University of Tennessee

description:
08-AVA021_3K4_PL1
eif3k: Locus ID: At4g33250, T-DNA insertion line GK-274H04-015098, AL943500 (Vector: pAC161); confirmed insertion site: intron #6.

Based on our analysis, the data from replicates #1 and #2  more closely resemble each other than replicate #3. Microarray data were generated on the following dates:  replicate 1 and replicate 2:  5/13/2009, replicate 3: 12/2/2009.

hyb_protocol: cDNA samples were hybridized to the Affymetrix ATH1 array (July 01, 2002) according to the manufacturer's protocol (Affymetrix) by the  Affymetrix Microarry Core Facility of the University of Tennessee. Probe set ID, Locus and Description refer to the Arabidopsis thaliana genome release TAIR 9 (June 19, 2009).

scan_protocol: Array scanning was performed according to the manufacturer's instructions (Affymetrix) by the  Affymetrix Microarray Core Facility of the University of Tennessee.

data_processing: Data were GCRMA normalized. TL states (Log(2)[PL/NP]) were calculated (=Log(2)PL - Log(2)NP).

source_name: eif3k, polysome mRNA

label_protocol: cDNA were generated and labeled according to the standard protocol by the  Affymetrix Microarray Core Facility of the University of Tennessee, Knoxville.

growth_protocol: Medium: GM medium with 1% sucrose and 0.8% agar, in petri plates wrapped with parafilm that was pierced to allow gas exchange; Light: 16 h long day, from fluorescent bulbs at ~80umole/m2/second; Temperature: 22oC.

extract_protocol:
Harvest method: Under room light, flood seedlings with liquid Nitrogen and scrape off into liquid nitrogen with spatula; Timing: 4 hours after light on.

Polysome gradient and RNA purification were carried out essentially as decribed in Kim et al. (2007) Genome Biology 8:R60 (PMID 17439654). The top 6 fractions were pooled as non-polysomal (NP), and the bottom 6 fractions were pooled as polysomal (PL).

value: eif3k mutant

value: 11 days

value: aerial part

tag: rna

value: polysome mRNA


title: non-polysome mRNA eif3k-3

description:
11-AVA034_3k3_NP3
eif3k: Locus ID: At4g33250, T-DNA insertion line GK-274H04-015098, AL943500 (Vector: pAC161); confirmed insertion site: intron #6.

Based on our analysis, the data from replicates #1 and #2  more closely resemble each other than replicate #3. Microarray data were generated on the following dates:  replicate 1 and replicate 2:  5/13/2009, replicate 3: 12/2/2009.

source_name: eif3k, non-polysome mRNA

tag: genotype

value: non-polysome mRNA


title: total mRNA WT-1

description:
04-AVA017_WT_T1

Based on our analysis, the data from replicates #1 and #2  more closely resemble each other than replicate #3. Microarray data were generated on the following dates: replicate 1 and replicate 2:  5/13/2009, replicate 3: 12/2/2009.

data_processing: Data were GCRMA normalized.

source_name: wild type, total mRNA

tag: ecotype

value: wild type

value: total mRNA


title: polysome mRNA eif3k-3

description:
12-AVA033_3k3_PL3
eif3k: Locus ID: At4g33250, T-DNA insertion line GK-274H04-015098, AL943500 (Vector: pAC161); confirmed insertion site: intron #6.

Based on our analysis, the data from replicates #1 and #2  more closely resemble each other than replicate #3. Microarray data were generated on the following dates:  replicate 1 and replicate 2:  5/13/2009, replicate 3: 12/2/2009.


title: CCA1OX 1080min rep1

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 06.24.05 15 ATH1.CEL
Sample name: A15

source_name: CCA1OX seedlings, light, 1080 minutes after dawn day 4


title: non-polysome mRNA WT-2

description:
15-AVA026_WT5_NP2

Based on our analysis, the data from replicates #1 and #2  more closely resemble each other than replicate #3. Microarray data were generated on the following dates:  replicate 1 and replicate 2:  5/13/2009, replicate 3: 12/2/2009.

source_name: wild type, non-polysome mRNA


title: non-polysome mRNA eif3k-2

description:
09-AVA028_3K5_NP2
eif3k: Locus ID: At4g33250, T-DNA insertion line GK-274H04-015098, AL943500 (Vector: pAC161); confirmed insertion site: intron #6.

Based on our analysis, the data from replicates #1 and #2  more closely resemble each other than replicate #3. Microarray data were generated on the following dates:  replicate 1 and replicate 2:  5/13/2009, replicate 3: 12/2/2009.


title: total mRNA WT-2

description:
05-AVA023_WT_T2

Based on our analysis, the data from replicates #1 and #2  more closely resemble each other than replicate #3. Microarray data were generated on the following dates: replicate 1 and replicate 2:  5/13/2009, replicate 3: 12/2/2009.


title: non-polysome mRNA eif3k-1

description:
07-AVA022_3K4_NP1
eif3k: Locus ID: At4g33250, T-DNA insertion line GK-274H04-015098, AL943500 (Vector: pAC161); confirmed insertion site: intron #6.

Based on our analysis, the data from replicates #1 and #2  more closely resemble each other than replicate #3. Microarray data were generated on the following dates:  replicate 1 and replicate 2:  5/13/2009, replicate 3: 12/2/2009.


title: total mRNA eif3k-1

description:
01-AVA018_3K_T1
eif3k: Locus ID: At4g33250, T-DNA insertion line GK-274H04-015098, AL943500 (Vector: pAC161); confirmed insertion site: intron #6.

Based on our analysis, the data from replicates #1 and #2  more closely resemble each other than replicate #3. Microarray data were generated on the following dates: replicate 1 and replicate 2:  5/13/2009, replicate 3: 12/2/2009.

source_name: eif3k, total mRNA


title: total mRNA WT-3

description:
06-AVA029_WT_T3

Based on our analysis, the data from replicates #1 and #2  more closely resemble each other than replicate #3. Microarray data were generated on the following dates: replicate 1 and replicate 2:  5/13/2009, replicate 3: 12/2/2009.


title: total mRNA eif3k-3

description:
03-AVA032_3k3_T3
eif3k: Locus ID: At4g33250, T-DNA insertion line GK-274H04-015098, AL943500 (Vector: pAC161); confirmed insertion site: intron #6.

Based on our analysis, the data from replicates #1 and #2  more closely resemble each other than replicate #3. Microarray data were generated on the following dates: replicate 1 and replicate 2:  5/13/2009, replicate 3: 12/2/2009.


title: Col 1080min rep1

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
K Nozue 06.24.05 03 ATH1.CEL
Sample name: A3


title: total mRNA eif3k-2

description:
02-AVA024_3K4_T2
eif3k: Locus ID: At4g33250, T-DNA insertion line GK-274H04-015098, AL943500 (Vector: pAC161); confirmed insertion site: intron #6.

Based on our analysis, the data from replicates #1 and #2  more closely resemble each other than replicate #3. Microarray data were generated on the following dates: replicate 1 and replicate 2:  5/13/2009, replicate 3: 12/2/2009.


title: polysome mRNA WT-2

description:
16-AVA025_WT5_PL2

Based on our analysis, the data from replicates #1 and #2  more closely resemble each other than replicate #3. Microarray data were generated on the following dates:  replicate 1 and replicate 2:  5/13/2009, replicate 3: 12/2/2009.

source_name: wild type, polysome mRNA


title: sid2-2, mock treated, biological replicate 1

status: Public on Mar 27 2011

city: Freising

first: Carina

last: Behringer

address: Emil-Ramann-Str. 4

department: Institute of plant systems biology

institute: TU München

description:
sid2-2 mutant (Nawrath and Metraux, 1999 [PMID 10449575]).
Gene expression data from rosette leaves of 4-week-old Arabidopsis thaliana plants.

hyb_protocol: Arrays were hybridized at 45°C with 19 µg of the labelled and fragmented cRNAs, and washed and developed in a GeneChip Fluidics Station 450/250 (Affimetrix).

scan_protocol: Arrays were scanned using an Affymetrix scanner, and CEL files were generated using Affymetrix GCOS software.

data_processing: The Genedata Expressionist software package (Genedata, Basel, Switzerland) was used for data analysis. Raw chip data (CEL files) were loaded into the Genedata Expressionist Refiner module. Data were condensed and expression levels for individual chips were calculated after background correction and normalization using the RMA algorithm (Irizarry et al., 2003). All chips were normalized to a median expression value of 200 with a quality criteria p-value set at 0.04.

source_name: rosette leaves, sid2-2 mutant, mock treated

label_protocol: Labelled cRNA was prepared and hybridized to Affymetrix ATH1 GeneChips following the manufacturer’s guidelines (Affymetrix, Santa Clara, CA). Briefly, a Microarray cDNA Synthesis Kit (Roche Diagnostics) was used for oligo-dT-primed cDNA synthesis from 10 µg of total RNA. Biotinylated cRNA was obtained with the BioArray High Yield RNA Transcript Labeling Kit (Enzo Life Science Inc., Farmingdale).

growth_protocol: Arabidopsis thaliana plants were grown on soil for 4 weeks under long day conditions (16h light, 23°C 40% humidity, 8 h dark 17°C, 50% humidity).

extract_protocol: Total RNA was extracted using the Qiagen RNeasy midi kit following the manufacturer’s (Qiagen) instructions.

treatment_protocol: Arabidopsis thaliana plants grown in 12 cm pots were treated with 875 µL/pot of a formulation containing safeners (5 mM mefenpyr and 7.2 mM isoxadifen) in 1 ml of 0.2 % agrotin (Bayer AG; Leverkusen, Germany) supplemented with 25 µL emulsifier (5 % phenylsulfonate CA 70 (Clariant; Muttenz, Switzerland), 7 % Emulsogen EL360 (Clariant), 40 % Isophoron (Dow Chemical Co.; Midland, MI). Mock treatments contained an equal volume of the solvent (DMSO) used for safeners stock solutions. The formulation was applied using an airbrush pistol (Grafo model T1, Fisher Airbrush und Künstlerbedarf; Naumburg-Meyhen, Germany). The effective concentrations of safeners responded to a field application rate of 1500 g/ha, respectively.

value: sid2-2 mutant

value: 4 weeks

value: rosette leaves

value: DMSO control


title: sid2-2, mock treated, biological replicate 2


title: sid2-2, safener treated, biological replicate 3

source_name: rosette leaves, sid2-2 mutant, safener treated

value: safener (mefenpyr and isoxadifen)


title: 4tga, mock treated, biological replicate 2

description:
tga2tga3tga5tga6 mutant (Kesarwani et al., 2007 [PMID 17369431]).
Gene expression data from rosette leaves of 4-week-old Arabidopsis thaliana plants.

source_name: rosette leaves, tga2tga3tga5tga6 mutant, mock treated

value: tga2tga3tga5tga6 mutant


title: sid2-2, mock treated, biological replicate 3


title: 4tga, safener treated, biological replicate 1

source_name: rosette leaves, tga2tga3tga5tga6 mutant, safener treated


title: sid2-2, safener treated, biological replicate 1


title: sid2-2, safener treated, biological replicate 2


title: 4tga, mock treated, biological replicate 1


title: 4tga, safener treated, biological replicate 2


title: polysome mRNA eif3k-2

description:
10-AVA027_3K5_PL2
eif3k: Locus ID: At4g33250, T-DNA insertion line GK-274H04-015098, AL943500 (Vector: pAC161); confirmed insertion site: intron #6.

Based on our analysis, the data from replicates #1 and #2  more closely resemble each other than replicate #3. Microarray data were generated on the following dates:  replicate 1 and replicate 2:  5/13/2009, replicate 3: 12/2/2009.


title: Col0, mock treated, biological replicate 3

description: Gene expression data from rosette leaves of 4-week-old Arabidopsis thaliana plants.

source_name: rosette leaves, wild type, mock treated


title: 4tga, mock treated, biological replicate 3


title: Col0, safener treated, biological replicate 3

source_name: rosette leaves, wild type, safener treated


title: 4tga, safener treated, biological replicate 3


title: Col0, safener treated, biological replicate 1


title: Col0, mock treated, biological replicate 2


title: Col0, mock treated, biological replicate 1


title: SL2 cells treated with GFP dsRNA only, biological rep. 2

status: Public on Mar 25 2011

city: Heidelberg

first: Milan

last: Spasic

address: Im Neuenheimer Feld 280

institute: German Cancer Research Centre

hyb_protocol: Fragmentation of cRNA and subsequent hybridization (16 hours) was performed according to Affymetrix GeneChip Expression Analysis Technical Manual (P/N 702232 Rev. 2), using a Hyb Oven 640 and a Fluidics Station FS450.

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

data_processing: The RMA algorithm (Robust Multichip Average) was used for normalization of raw data (RMAExpress software, http://rmaexpress.bmbolstad.com/).

source_name: Drosophila melanogaster SL2 cells; GFP-dsRNA

label_protocol: Labeling was performed according to Affymetrix GeneChip Expression Analysis Technical Manual (P/N 702232 Rev. 2), using biotin as label.

extract_protocol: Total RNA was extracted from cells using RNEasy kit from Qiagen (Cat. No. 74106) according to the manufacturer's instructions.

value: GFP dsRNA depletion only


title: SL2 cells treated with Tis11 dsRNA only, biological rep. 1

source_name: Drosophila melanogaster SL2 cells; Tis11-dsRNA

value: Tis11 dsRNA depletion only


title: SL2 cells treated with GFP dsRNA and LPS, biological rep. 3

source_name: Drosophila melanogaster SL2 cells; GFP-dsRNA; LPS

value: GFP dsRNA depletion and LPS


title: SL2 cells treated with Tis11 dsRNA only, biological rep. 3


title: SL2 cells treated with Tis11 dsRNA only, biological rep. 2


title: SL2 cells treated with GFP dsRNA and LPS, biological rep. 1


title: SL2 cells treated with GFP dsRNA only, biological rep. 3


title: SL2 cells treated with Tis11 dsRNA and LPS, biological rep. 1

source_name: Drosophila melanogaster SL2 cells; Tis11-dsRNA; LPS

value: Tis11 dsRNA depletion and LPS


title: SL2 cells treated with Tis11 dsRNA and LPS, biological rep. 2


title: SL2 cells treated with GFP dsRNA and LPS, biological rep. 2


title: SL2 cells treated with GFP dsRNA only, biological rep. 1


title: SL2 cells treated with Tis11 dsRNA and LPS, biological rep. 3


title: pathogen infection: mock inoculated - RNA fraction: total RNA - rep1

status: Public on Mar 11 2011

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description: This sample was grown for 3.5 wks under 12hr days in a growth chamber, then mock-inoculated.  Ten days after infection rosette tissue was sampled.

hyb_protocol: Affymetrix GeneChip Hyb

scan_protocol: Affy- Array Scanning

data_processing: The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.

source_name: rosette leaf (pathogen infection: mock inoculated - RNA fraction: total RNA)

label_protocol: Affymetrix one-cycle target labeling

growth_protocol: Growth Description:  Plants are grown in 12 hr days in a growth chamber, 4 plants per round pot, 10 pots per flat.  Just before the plant sends bolts, they are inoculated.

extract_protocol: Hot Phenol/Guanidine Thiocyanate and RNeasy Clean up

tag: germplasm name

value: Columbia-0 (Col-0)

tag: genome/variation

value: All phenotypes to date of this transgenic line constitutively overexpressing RPL18 fused to his and flag epitopes are equivalent to those of wildtype Columbia-0 ecotype.

value: PO:0000014 rosette leaf

tag: developmental stage

value: PO:0007134 A vegetative growth

value: Plants are approximately 3.5 weeks at time of inoculation. Inoculation lasts 10 days.

tag: growth media

value: LC-1 Soil Mix


title: pathogen infection: TuMV inoculated - RNA fraction: total RNA - rep3

description: This sample was grown for 3.5 wks under 12hr days in a growth chamber, then inoculated with TuMV-GFP.  Ten days after infection green-fluorescing rosette tissue was sampled.  Following immunoprecipitation of RPL18-HF, RNA (translation-initiated) was isolated by a modified trizol method.

source_name: rosette leaf (pathogen infection: TuMV inoculated - RNA fraction: total RNA)

tag: age


title: pathogen infection: mock inoculated - RNA fraction: polysomal RNA - rep3

source_name: rosette leaf (pathogen infection: mock inoculated - RNA fraction: polysomal RNA)

extract_protocol: Isolation of polysomal mRNA by ribosomal immunopurification


title: pathogen infection: mock inoculated - RNA fraction: polysomal RNA - rep1


title: pathogen infection: TuMV inoculated - RNA fraction: total RNA - rep1


title: pathogen infection: mock inoculated - RNA fraction: total RNA - rep3


title: non-polysome mRNA WT-1

description:
13-AVA020_WT4_NP1

Based on our analysis, the data from replicates #1 and #2  more closely resemble each other than replicate #3. Microarray data were generated on the following dates:  replicate 1 and replicate 2:  5/13/2009, replicate 3: 12/2/2009.

value: Columbia

value: wild type

value: 11 days

value: aerial part

value: non-polysome mRNA


title: pathogen infection: TuMV inoculated - RNA fraction: polysomal RNA - rep3

source_name: rosette leaf (pathogen infection: TuMV inoculated - RNA fraction: polysomal RNA)


title: pathogen infection: mock inoculated - RNA fraction: total RNA - rep2


title: pathogen infection: mock inoculated - RNA fraction: polysomal RNA - rep2


title: pathogen infection: TuMV inoculated - RNA fraction: polysomal RNA - rep1


title: pathogen infection: TuMV inoculated - RNA fraction: total RNA - rep2


title: Col0, safener treated, biological replicate 2

value: 4 weeks

value: rosette leaves

value: safener (mefenpyr and isoxadifen)


title: polysome mRNA WT-1

description:
14-AVA019_WT4_PL1

Based on our analysis, the data from replicates #1 and #2  more closely resemble each other than replicate #3. Microarray data were generated on the following dates:  replicate 1 and replicate 2:  5/13/2009, replicate 3: 12/2/2009.

value: polysome mRNA


title: Genotype: PolyQ Atro A75QN, Day: 0, Repl: 3

status: Public on Mar 01 2011

city: London

first: Eric

last: Blanc

address: New Hunt's House

department: MRC Centre for Developmental Neurobiology

institute: King's College London

description:
Replicate 3 for gene expression on log2 scale for adult flies expressing PolyQ Atro A75QN at the outset of ageing at 29 C
A75QN-d0-30

hyb_protocol: The resulting cRNA was Hybridysed on GeneChip Drosophila Genome Array 2.0. The Genechips were washed and stained in the Affimetrix fluidic station.

scan_protocol: GeneChips were scanned at the EMBL Gene Core Facility

data_processing: The data were normalized using a variance stabilisation protocol on perfect matches only, and summarized using median polish. The algorithms were implemented in Bioconductor 2.8.0, packages vsn (3.16.0) and affy (1.26.1), on a machine running R 2.11.0 compiled for x86_64-apple-darwin9.8.0

source_name: Adult flies expressing PolyQ Atro A75QN as they are switched from 18 C to 29 C for ageing

label_protocol: The affymetrix protocol was followed for labelling 5ug of total RNA.

growth_protocol: Flies were allowed to develop at 18°C, and newly eclosed flies (0-48 hours) were collected and sacrificed immediately (0 days) or aged for 2 or 14 days at 29°C. The fly food used was standard cornmeal supplemented with yeast and molass. For ageing flies were flipped in fresh vials every 48 hours.

extract_protocol: RNA was extracted from 20 fly heads using the RNAgents kit (Promega) according to manifacturer instruction; RNA quantity and quality were assessed by Nanodrop 1000 (Thermo Scientific)

treatment_protocol: Flies were anesthetised with CO2, decapitated and heads were immediately snap frozen in liquid N2.

tag: ageing at 29 c in days

value: PolyQ Atro A75QN transgene expressed


title: Genotype: PolyQ Atro A75QN, Day: 14, Repl: 3

description:
Replicate 3 for gene expression on log2 scale for adult flies expressing PolyQ Atro A75QN after 14 days of ageing at 29 C
A75QN-d14-36

source_name: Adult flies expressing PolyQ Atro A75QN after 14 days at 29 C


title: Genotype: PolyQ Atro A75QN, Day: 0, Repl: 2

description:
Replicate 2 for gene expression on log2 scale for adult flies expressing PolyQ Atro A75QN at the outset of ageing at 29 C
A75QN-d0-29


title: Genotype: PolyQ Atro A66QC, Day: 14, Repl: 2

description:
Replicate 2 for gene expression on log2 scale for adult flies expressing PolyQ Atro A66QC after 14 days of ageing at 29 C
A66QC-d14-26

source_name: Adult flies expressing PolyQ Atro A66QC after 14 days at 29 C

value: PolyQ Atro A66QC transgene expressed


title: pathogen infection: TuMV inoculated - RNA fraction: polysomal RNA - rep2

value: Columbia-0 (Col-0)


title: Genotype: PolyQ Atro A66QC, Day: 2, Repl: 3

description:
Replicate 3 for gene expression on log2 scale for adult flies expressing PolyQ Atro A66QC after 2 days of ageing at 29 C
A66QC-d2-24

source_name: Adult flies expressing PolyQ Atro A66QC after 2 days at 29 C


title: Genotype: PolyQ Atro A75QN, Day: 2, Repl: 1

description:
Replicate 1 for gene expression on log2 scale for adult flies expressing PolyQ Atro A75QN after 2 days of ageing at 29 C
A75QN-d2-31

source_name: Adult flies expressing PolyQ Atro A75QN after 2 days at 29 C


title: Genotype: PolyQ Atro A66QC, Day: 2, Repl: 2

description:
Replicate 2 for gene expression on log2 scale for adult flies expressing PolyQ Atro A66QC after 2 days of ageing at 29 C
A66QC-d2-23


title: Genotype: PolyQ Atro A66QC, Day: 14, Repl: 1

description:
Replicate 1 for gene expression on log2 scale for adult flies expressing PolyQ Atro A66QC after 14 days of ageing at 29 C
A66QC-d14-25


title: Genotype: PolyQ Atro A75QN, Day: 14, Repl: 2

description:
Replicate 2 for gene expression on log2 scale for adult flies expressing PolyQ Atro A75QN after 14 days of ageing at 29 C
A75QN-d14-35


title: Genotype: PolyQ Atro A66QC, Day: 2, Repl: 1

description:
Replicate 1 for gene expression on log2 scale for adult flies expressing PolyQ Atro A66QC after 2 days of ageing at 29 C
A66QC-d2-22


title: Genotype: PolyQ Atro A66QC, Day: 0, Repl: 2

description:
Replicate 2 for gene expression on log2 scale for adult flies expressing PolyQ Atro A66QC at the outset of ageing at 29 C
A66QC-d0-20

source_name: Adult flies expressing PolyQ Atro A66QC as they are switched from 18 C to 29 C for ageing


title: Genotype: PolyQ Atro A66QC, Day: 0, Repl: 1

description:
Replicate 1 for gene expression on log2 scale for adult flies expressing PolyQ Atro A66QC at the outset of ageing at 29 C
A66QC-d0-19


title: Genotype: PolyQ Atro A75QN, Day: 2, Repl: 3

description:
Replicate 3 for gene expression on log2 scale for adult flies expressing PolyQ Atro A75QN after 2 days of ageing at 29 C
A75QN-d2-33


title: Genotype: PolyQ Atro A66QC, Day: 14, Repl: 3

description:
Replicate 3 for gene expression on log2 scale for adult flies expressing PolyQ Atro A66QC after 14 days of ageing at 29 C
A66QC-d14-27


title: Genotype: Atro, Day: 14, Repl: 2

description:
Replicate 2 for gene expression on log2 scale for adult flies expressing Atro after 14 days of ageing at 29 C
AWT-d14-17

source_name: Adult flies expressing Atro after 14 days at 29 C

value: Wild type Atro transgene expressed


title: Genotype: Atro, Day: 14, Repl: 3

description:
Replicate 3 for gene expression on log2 scale for adult flies expressing Atro after 14 days of ageing at 29 C
AWT-d14-18


title: Genotype: Atro, Day: 2, Repl: 3

description:
Replicate 3 for gene expression on log2 scale for adult flies expressing Atro after 2 days of ageing at 29 C
AWT-d2-15

source_name: Adult flies expressing Atro after 2 days at 29 C


title: Genotype: Atro, Day: 2, Repl: 1

description:
Replicate 1 for gene expression on log2 scale for adult flies expressing Atro after 2 days of ageing at 29 C
AWT-d2-13


title: Genotype: Atro, Day: 2, Repl: 2

description:
Replicate 2 for gene expression on log2 scale for adult flies expressing Atro after 2 days of ageing at 29 C
AWT-d2-14


title: Genotype: Atro, Day: 0, Repl: 2

description:
Replicate 2 for gene expression on log2 scale for adult flies expressing Atro at the outset of ageing at 29 C
AWT-d0-11

source_name: Adult flies expressing Atro as they are switched from 18 C to 29 C for ageing


title: Genotype: PolyQ Atro A66QC, Day: 0, Repl: 3

description:
Replicate 3 for gene expression on log2 scale for adult flies expressing PolyQ Atro A66QC at the outset of ageing at 29 C
A66QC-d0-21


title: Genotype: Control, Day: 14, Repl: 3

description:
Replicate 3 for gene expression on log2 scale for control adult flies after 14 days of ageing at 29 C
CTRL-d14-09

source_name: Adult flies after 14 days at 29 C

value: GMR-Gal4 and Gal80


title: Genotype: Atro, Day: 0, Repl: 3

description:
Replicate 3 for gene expression on log2 scale for adult flies expressing Atro at the outset of ageing at 29 C
AWT-d0-12


title: Genotype: Atro, Day: 14, Repl: 1

description:
Replicate 1 for gene expression on log2 scale for adult flies expressing Atro after 14 days of ageing at 29 C
AWT-d14-16


title: Genotype: Atro, Day: 0, Repl: 1

description:
Replicate 1 for gene expression on log2 scale for adult flies expressing Atro at the outset of ageing at 29 C
AWT-d0-10


title: Genotype: Control, Day: 2, Repl: 3

description:
Replicate 3 for gene expression on log2 scale for control adult flies after 2 days of ageing at 29 C
CTRL-d2-06

source_name: Adult flies after 2 days at 29 C


title: Genotype: Control, Day: 14, Repl: 1

description:
Replicate 1 for gene expression on log2 scale for control adult flies after 14 days of ageing at 29 C
CTRL-d14-07


title: Genotype: Control, Day: 0, Repl: 2

description:
Replicate 2 for gene expression on log2 scale for control adult flies at the outset of ageing at 29 C
CTRL-d0-02

source_name: Adult flies as they are switched from 18 C to 29 C for ageing


title: Genotype: Control, Day: 0, Repl: 3

description:
Replicate 3 for gene expression on log2 scale for control adult flies at the outset of ageing at 29 C
CTRL-d0-03


title: Genotype: Control, Day: 2, Repl: 1

description:
Replicate 1 for gene expression on log2 scale for control adult flies after 2 days of ageing at 29 C
CTRL-d2-04


title: Genotype: Control, Day: 2, Repl: 2

description:
Replicate 2 for gene expression on log2 scale for control adult flies after 2 days of ageing at 29 C
CTRL-d2-05


title: Genotype: Control, Day: 14, Repl: 2

description:
Replicate 2 for gene expression on log2 scale for control adult flies after 14 days of ageing at 29 C
CTRL-d14-08


title: Genotype: Control, Day: 0, Repl: 1

description:
Replicate 1 for gene expression on log2 scale for control adult flies at the outset of ageing at 29 C
CTRL-d0-01


title: Genotype: PolyQ Atro A75QN, Day: 14, Repl: 1

description:
Replicate 1 for gene expression on log2 scale for adult flies expressing PolyQ Atro A75QN after 14 days of ageing at 29 C
A75QN-d14-34


title: WT_HN_2

description: WT, 10 mM NH4NO3.

source_name: Roots, WT, HN

extract_protocol: Trizol RNA.

value: roots

value: WT

tag: environment

value: high nitrogen


title: WT_LN_2

description: WT, 0.3 mM KNO3.

source_name: Roots, WT, LN

tag: tissue

value: low nitrogen


title: hni9-2_LN_2

description: hni9, 0.3 mM KNO3.

source_name: Roots, hni9, LN


title: hni9-2_HN_2

description: hni9, 10 mM NH4NO3.

source_name: Roots, hni9, HN


title: WT_LN_1

description: WT, 0.3 mM KNO3.


title: hni9-1_LN_1

description: hni9, 0.3 mM KNO3.


title: WT_HN_1

description: WT, 10 mM NH4NO3.


title: 100 H2O2, 1 BL, replicate 1

status: Public on Feb 28 2011

city: Urbana

first: Steven

middle: C.

last: Huber

state: IL

address: 1201 W. Gregory Drive, 197 ERML

description: H2O2 100mM plus BR.

hyb_protocol: Purified, fragmented cRNA was hybridized to Affymetrix's ATH1-121501 Array using Affymetrix's GeneChip Fluidics Station 450, as per Affymetrix's instructions.

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

data_processing: Pre-processing was done using the GCRMA algorithm in R and Bioconductor packages.

source_name: whole seedlings, 100mM H2O2 and BL treated

label_protocol: Biotin-labeled cRNA samples were made using Affymetrix GeneChip  Expression 3'-Amplification Reagents (One-Cycle Target Labeling and Control Reagents package) according to the manufacturer's instructions.

growth_protocol: Arabidopsis seedlings were grown from seeds (pre-treated at 4C for 1 week in water) in standard Petri dishes using liquid media (1/2 strength MS media, pH 5.7 supplemented with 0.25% sucrose) for 12 days in long day conditions (16 hr light, 110 Microeinsteins m-2 sec-1, 22C).

extract_protocol: Total RNA was isolated from whole seedlings using TRIzol reagent (Invitrogen) and purified using the RNeasy Midi Kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: On day 12, seedlings were moved at midday to a darkened room for one hour. After 1hr, seedlings were pretreated with H2O2 diluted in liquid media to the final concentrations shown. Control treatments were media only. After 30min of pretreatment in the dark, the seedlings were additionally treated with epi-BL (Sigma) at 1uM final concentration (again, diluted in liquid media; control was liquid media plus an equal amount of EtOH that was used as the epi-BL solvent in the treatments). The seedlings were treated with the BL for one hour in the dark. The media was not exchanged, so the original H2O2 treatment was still present as well. At this point the seedlings were harvested and flash frozen in liquid nitrogen for RNA extraction.

value: Whole seedling

value: Col

value: Wt

value: 12-day seedlings

tag: h2o2 treatment level

tag: bl treatment level


title: hni9-1_HN_1

description: hni9, 10 mM NH4NO3.


title: 0 H2O2, 1 BL, replicate 1

description: Control BR rep 1.

source_name: whole seedlings, BL treated, control


title: 0 H2O2, 0 BL, replicate 3

description: Control rep 3.

source_name: whole seedlings, control


title: 50 H2O2, 1 BL, replicate 1

description: H2O2 50mM plus BR.

source_name: whole seedlings, 50mM H2O2 and BL treated


title: 5 H2O2, 1 BL, replicate 1

description: H2O2 5mM plus BR.

source_name: whole seedlings, 5mM H2O2 and BL treated


title: 50 H2O2, 0 BL, replicate 1

description: H2O2 alone 50mM.

source_name: whole seedlings, 50mM H2O2 treated


title: 25 H2O2, 1 BL, replicate 1

description: H2O2 25mM plus BR.

source_name: whole seedlings, 25mM H2O2 and BL treated


title: 5 H2O2, 0 BL, replicate 1

description: H2O2 alone 5mM.

source_name: whole seedlings, 5mM H2O2 treated


title: 0 H2O2, 1 BL, replicate 3

description: Control BR rep 3.


title: 0 H2O2, 0 BL, replicate 2

description: Control rep 2.


title: 100 H2O2, 0 BL, replicate 1

description: H2O2 alone 100mM.

source_name: whole seedlings, 100mM H2O2 treated


title: 1 H2O2, 1 BL, replicate 1

description: H2O2 1mM plus BR.

source_name: whole seedlings, 1mM H2O2 and BL treated


title: Genital_disc_P20_male_rep1

status: Public on Feb 25 2011

city: New York

first: Mark

middle: L

last: Siegal

state: NY

address: 100 Washington Sq E

department: Department of Biology, Center for Genomics and Systems Biology

institute: New York University

description: Gene expression data from Drosophlia genital discs of male pupae approximately 20 hours after puparium formation (P20)

hyb_protocol: For each sample, 1.5 µg biotinylated cDNA was hybridized to an Affymetrix GeneChip Drosophila Genome 2.0 Array and washed and stained using the Affymetrix Fluidics Station 450 following manufacturer's protocols.

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

data_processing: The data were background-corrected and normalized using RMA as implemented in the R/Bioconductor package.

label_protocol: Biotinylated cDNA was produced from 20 ng of total RNA using the NuGEN Ovation Biotin System, following the manufacturer's instructions.

growth_protocol: Flies were reared at 25C on standard cornmeal-molasses-agar medium.

extract_protocol: Total RNA was extracted using the Ambion MELT kit then further purified and concentrated using Qiagen RNeasy MinElute columns, following each manufacturer's instructions.

treatment_protocol: Larvae or pupae were dissected in cold PBS and immediately transferred to the RNA extraction protocol's lysis buffer.

value: dissected genital disc

value: esgGAL4.B, UAS-GFP.nls/CyO

value: pupa approximately 20 hours APF (P20)

tag: sex

value: male


title: 0 H2O2, 1 BL, replicate 2

institute: USDA-ARS

description: Control BR rep 2.


title: 1 H2O2, 0 BL, replicate 1

description: H2O2 alone 1mM.

source_name: whole seedlings, 1mM H2O2 treated


title: 25 H2O2, 0 BL, replicate 1

description: H2O2 alone 25mM.

source_name: whole seedlings, 25mM H2O2 treated


title: Genital_disc_P20_male_rep4

source_name: Drosophlia genital discs of male pupae approximately 20 hours after puparium formation (P20)


title: Genital_disc_P20_male_rep3


title: 0 H2O2, 0 BL, replicate 1

description: Control rep 1.


title: Genital_disc_P20_female_rep4

description: Gene expression data from Drosophlia genital discs of female pupae approximately 20 hours after puparium formation (P20)

value: female


title: Genital_disc_P20_female_rep2

source_name: Drosophlia genital discs of female pupae approximately 20 hours after puparium formation (P20)


title: Genital_disc_P20_male_rep2


title: Genital_disc_P20_female_rep3


title: Genital_disc_P6_male_rep2

description: Gene expression data from Drosophlia genital discs of male pupae approximately 6 hours after puparium formation (P6)

value: pupa approximately 6 hours APF (P6)


title: Genotype: PolyQ Atro A75QN, Day: 2, Repl: 2

description:
Replicate 2 for gene expression on log2 scale for adult flies expressing PolyQ Atro A75QN after 2 days of ageing at 29 C
A75QN-d2-32

source_name: Adult flies expressing PolyQ Atro A75QN after 2 days at 29 C

value: PolyQ Atro A75QN transgene expressed


title: Genital_disc_P20_female_rep1


title: Genital_disc_P6_male_rep4

source_name: Drosophlia genital discs of male pupae approximately 6 hours after puparium formation (P6)


title: Genital_disc_P6_male_rep3


title: Genital_disc_P6_male_rep1


title: Genital_disc_P6_female_rep2

description: Gene expression data from Drosophlia genital discs of female pupae approximately 6 hours after puparium formation (P6)


title: Genital_disc_L3_male_rep3

description: Gene expression data from Drosophlia genital discs of male late third-instar larvae (L3)

value: late third-instar larva (L3)


title: Genital_disc_P6_female_rep4

source_name: Drosophlia genital discs of female pupae approximately 6 hours after puparium formation (P6)


title: Genital_disc_L3_male_rep1

source_name: Drosophlia genital discs of male late third-instar larvae (L3)


title: Genital_disc_L3_male_rep2


title: Genital_disc_L3_female_rep4

description: Gene expression data from Drosophlia genital discs of female late third-instar larvae (L3)


title: Genital_disc_P6_female_rep3


title: Genital_disc_L3_female_rep1

source_name: Drosophlia genital discs of female late third-instar larvae (L3)


title: Genital_disc_P6_female_rep1


title: Genital_disc_L3_male_rep4


title: Genotype: PolyQ Atro A75QN, Day: 0, Repl: 1

description:
Replicate 1 for gene expression on log2 scale for adult flies expressing PolyQ Atro A75QN at the outset of ageing at 29 C
A75QN-d0-28

source_name: Adult flies expressing PolyQ Atro A75QN as they are switched from 18 C to 29 C for ageing


title: Genital_disc_L3_female_rep3


title: HRE1-RNAi20 upon normoxia, biological rep3

status: Public on Feb 24 2011

city: Taipei

first: Yang

last: Chin-Ying

address: No. 128, Sec. 2, Academia Road, Nankang

country: Taiwan

institute: Agriculture Biotechnology Research Center Academia Sinica

description: Gene expression data from roots of HRE1-RNAi22 knock-down line in normoxic condition

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

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

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

source_name: AtERF73/HRE1-RNAi20 seedlings upon normoxia 6 hrs

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

growth_protocol: All seeds were sterilized and kept for 3 d at 4ºC in the dark to break dormancy.  Seeds were germinated on 0.8% (w/v) agar plates containing 1/2 Murashige and Skoog (MS) medium supplemented with 0.5% (w/v) sucrose at pH5.7.  The plates were incubated at 22ºC under a 16-h light (81 μmol s-1 m-2)/8-h dark cycle in a growth chamber for 14 d.

extract_protocol: Total RNA samples were isolated from frozen tissue of Arabidopsis using the TRIzol reagent (Invitrogen).

treatment_protocol: For hypoxia treatment, 14-d-old Arabidopsis seedlings were pretreatment on the wet filter paper containing 1/2 MS solution supplemented with 0.5% (w/v) sucrose at pH5.7 for 1 hour in the dark then placed into a floating platform with roots dipped into 1/2 MS solution contain 0.5% (w/v) sucrose at pH5.7, which was constantly supplied with 3% (v/v) oxygen and 97% (v/v) nitrogen in the dark for the times indicated.

value: seedling roots

value: 14-d-old seedling

tag: treatment

value: normoxia

tag: knockdown

value: HRE1-RNAi20 knock-down

value: Columbia


title: Col upon normoxia, biological rep2

description: Gene expression data from roots of wild-type Arabidopsis seedling in normoxic condition

source_name: wild-type Arabidopsis seedlings upon normoxia 6 hrs

value: control


title: HRE1-RNAi20 upon hypoxia 6 hrs, biological rep1

description: Gene expression data from roots of HRE1-RNAi21 knock-down line in hypoxic condition

source_name: AtERF73/HRE1-RNAi20 seedlings upon hypoxia 6 hrs

value: hypoxia


title: Col upon hypoxia 6 hrs, biological rep4

description: Gene expression data from roots of wild-type Arabidopsis seedling in hypoxic condition

source_name: wild-type Arabidopsis seedlings upon hypoxia 6 hrs


title: HRE1-RNAi20 upon normoxia, biological rep4

description: Gene expression data from roots of HRE1-RNAi23 knock-down line in normoxic condition


title: Col upon normoxia, biological rep3


title: HRE1-RNAi20 upon hypoxia 6 hrs, biological rep3

description: Gene expression data from roots of HRE1-RNAi23 knock-down line in hypoxic condition


title: Col upon hypoxia 6 hrs, biological rep2


title: HRE1-RNAi20 upon hypoxia 6 hrs, biological rep2

description: Gene expression data from roots of HRE1-RNAi22 knock-down line in hypoxic condition


title: HRE1-RNAi20 upon normoxia, biological rep1

description: Gene expression data from roots of HRE1-RNAi20 knock-down line in normoxic condition


title: Col upon hypoxia 6 hrs, biological rep3


title: HRE1-RNAi20 upon hypoxia 6 hrs, biological rep4

description: Gene expression data from roots of HRE1-RNAi24 knock-down line in hypoxic condition


title: HRE1-RNAi20 upon normoxia, biological rep2

description: Gene expression data from roots of HRE1-RNAi21 knock-down line in normoxic condition


title: Col upon hypoxia 6 hrs, biological rep1


title: Genital_disc_L3_female_rep2


title: Col upon normoxia, biological rep4


title: Canton, biological rep 2

status: Public on Feb 22 2011

city: Charlestown

first: Brandon

last: Nicolay

state: MA

address: Building 149, 13th Street

department: Cancer Center

institute: Massachusetts General Hospital

description:
wt2
Brandon2.CEL
Gene expression data from third intstar larval eye discs.

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

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

data_processing: The total 12 affymatrix (Drosophila 2)*.CEL files were background corrected, normalized using R-Bioconductor package “affy” (http://www.bioconductor.org/packages/2.0/bioc/html/affy.html) and annotation package drosophila2.db (http://www.bioconductor.org/packages/release/data/annotation/html/drosophila2.db.html). Quality of microarray experiment was verified by Bioconductor package “arrayQualityMetrics” (http://www.bioconductor.org/packages/2.4/bioc/html/arrayQualityMetrics.html) (Kauffmann 2009).

source_name: Drosophila third instar larval eye discs

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Samples were then purified using a Qiagen RNeasy kit (cat. 74104)

value: third instar larva

value: eye discs

value: Canton S


title: rbfl120a+wts,  biological rep 1

description:
rbfwarts1
Brandon3.CEL
Gene expression data from third intstar larval eye discs.

value: rbf120a wtsX1Lats


title: Canton, biological rep 1

description:
wt1
Brandon1.CEL
Gene expression data from third intstar larval eye discs.


title: Col upon normoxia, biological rep1


title: rbfl120a, biological rep 3

description:
rbf3
Brandon11redo.CEL
Gene expression data from third intstar larval eye discs.


title: wts , biological rep 1

description:
warts1
Brandon5.CEL
Gene expression data from third intstar larval eye discs.


title: rbfl120a, biological rep 1

description:
rbf1
Brandon7.CEL
Gene expression data from third intstar larval eye discs.


title: wts, biological rep 3

description:
warts3
Brandon9.CEL
Gene expression data from third intstar larval eye discs.


title: rbfl120a+wts, biological rep 3

description:
rbfwarts3
Brandon10.CEL
Gene expression data from third intstar larval eye discs.


title: rbfl120a, biological rep 2

description:
rbf2
Brandon8.CEL
Gene expression data from third intstar larval eye discs.


title: rbfl120a+wts, biological rep 2

description:
rbfwarts2
Brandon4.CEL
Gene expression data from third intstar larval eye discs.


title: atonalmutGFP- t1 rep2

status: Public on Feb 18 2011

city: Edinburgh

first: Ian

last: Simpson

address: 10 Crichton Street

department: Institute for Adaptive and Neural Computation

institute: University of Edinburgh

hyb_protocol: Hybridisation was performed with an Affymetrix Fluidic Station 400 according to the manufacturers recommended protocols.

scan_protocol: Scanning and quality control was performed with an Affymetrix Gene Array scanner 3000 7G according to the manufacturers recommended protocols.

data_processing: Quality control and normalisation of microarray expression data from raw CEL files was performed using the Bioconductor package AffyPLM (Gautier et al., 2004) using the standard RMA method with quantile normalisation.

source_name: Embryonic Drosophila cells isolated as atonal GFP- from atonal mutant embryos by FACS at 5.75-6.75 hours after egg laying.

label_protocol: Total RNA was isolated from frozen samples using the manufacturers recommended protocols using the RNeasy Mini Kit (Qiagen #74104). The quantity of total RNA was assessed using an Agilent 2100 Bioanalyzer and quantity by RT-PCR using a QuantiTect SYBR Green RT-PCR kit (Qiagen #204141) using the rpL32 gene as a control. Labeling was performed with a single round of amplification using the one-cycle target labeling kit (Affymetrix #900493) according to the manufacturers recommended protocols.

growth_protocol: Eggs laid for 1 hour at 25C then embryos matured at 18C for either 11.5, 13.5 or 15.5 hours. Developmental times given as time after egg laying calculated as for development at 25C.

extract_protocol: The embryos were throughly washed in water then transferred to a dounce homogeniser that had been rinsed with S2 medium (Shields and Sang, Sigma #C3652, 5%FBS, Gibco #10500-056). As much water as possible was removed during transfer to the homogeniser using a Pastuer pipette. Embryos were then homogenised in 3ml of S2 medium with 25 gentle strokes of the loose pestle. The resulting cell suspensions were transferred to siliconised 1.5ml plastic tubes that had been rinsed with S2 medium. The rest of the protocol was carried out at room temperature. Cell suspensions were centrifuged at 1000g for 3 minutes, the supernatant was discarded, the pellet re-suspended in 1ml of protease solution (90% Trypsin-EDTA, Sigma #T4174, 10% 10xPBS) by gently pipetting up and down 10 times and was then incubated on a rotating wheel at room temperature for 7 minutes. Cells were pelleted by centrifugation at 1000g at 4C for 3 minutes, resuspended in 200ul S2, 1ml S2 was then added and they were then centrifuged again and resuspended in a final volume of 100um S2 ready for cell sorting. Cells were sorted into GFP+ and GFP- populations using a DakoCytomation MoFlo MLS flow cytometer. Typically between 300,000 GFP+ and 1,000,000 GFP- cells were collected from wild type embryos and 15,000-75,000 GFP+ and 500,000-1,000,000 GFP- cells were collected from mutant embryos. Cells were sorted into S2 medium and immediately spun down, homogenised in RNA extraction buffer (RLT) and snap frozen in liquid Nitrogen.

treatment_protocol: Embryos were dechorinated in 50% bleach for 2m30s.

value: dechorinated embryo, flow sorted cells

value: 5.75-6.75 hours after egg laying


title: atonalGFP+ t3 rep2

source_name: Embryonic Drosophila cells isolated as atonal GFP+ by FACS at 7.75-8.75 hours after egg laying.

value: 7.75-8.75 hours after egg laying


title: atonalmutGFP+ t1 rep2

source_name: Embryonic Drosophila cells isolated as atonal GFP+ from atonal mutant embryos by FACS at 5.75-6.75 hours after egg laying.


title: atonalmutGFP- t1 rep1


title: atonalmutGFP+ t1 rep1


title: atonalGFP+ t3 rep3


title: atonalGFP- t3 rep3

source_name: Embryonic Drosophila cells isolated as atonal GFP- by FACS at 7.75-8.75 hours after egg laying.


title: atonalmutGFP- t1 rep4


title: atonalmutGFP+ t1 rep4


title: atonalGFP+ t3 rep4


title: atonalmutGFP+ t1 rep3


title: atonalGFP- t3 rep1


title: atonalGFP+ t3 rep1


title: atonalmutGFP- t1 rep3


title: atonalGFP- t3 rep2


title: Canton, biological rep 3

description:
wt3
Brandon12.CEL
Gene expression data from third intstar larval eye discs.


title: wts, biological rep 2

description:
warts2
Brandon6.CEL
Gene expression data from third intstar larval eye discs.


title: atonalGFP+ t2 rep4

source_name: Embryonic Drosophila cells isolated as atonal GFP+ by FACS at 6.75-7.75 hours after egg laying.

value: 6.75-7.75 hours after egg laying


title: atonalGFP- t2 rep2

source_name: Embryonic Drosophila cells isolated as atonal GFP- by FACS at 6.75-7.75 hours after egg laying.


title: atonalGFP+ t2 rep2


title: atonalGFP- t2 rep3


title: atonalGFP- t2 rep4


title: atonalGFP- t1 rep3

source_name: Embryonic Drosophila cells isolated as atonal GFP- by FACS at 5.75-6.75 hours after egg laying.


title: atonalGFP+ t2 rep3


title: atonalGFP- t2 rep1


title: atonalGFP- t1 rep4


title: atonalGFP+ t1 rep2

source_name: Embryonic Drosophila cells isolated as atonal GFP+ by FACS at 5.75-6.75 hours after egg laying.


title: atonalGFP+ t1 rep3


title: atonalGFP+ t1 rep4


title: atonalGFP+ t2 rep1


title: atonalGFP- t1 rep2


title: atonalGFP- t1 rep1


title: atonalGFP+ t1 rep1


title: Dhr96 over-expression (line 35), males, biological rep 3 (DS004018)

status: Public on Feb 17 2011

city: RTP

first: Sheetal

last: Shah

state: NC

address: 3054E Cornwallis Road

institute: Syngenta

description:
Gene expression data from adults
DS004018

hyb_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA. 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome 2.0 Array. GeneChips were washed and stained in an Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: data was processed using RMA in GeneData Refiner.

source_name: 0-3 day old adults cultured on diet made on 1/2/06

growth_protocol: Drosophila melanogaster flies were cultured according to standard methods, and  maintained on a rich diet (10L water, 100g agar (USP #7060 Bio-serve), 350g Brewer’s dried yeast (Sunshine Health), 300g black treacle (Lyles), 150g sucrose (Tate & Lyle), 300g Difco dextrose (Becton Dickinson), 150g cornmeal (#1151, Bioserve), 100g wheatgerm (#1659, Bioserve), 200g soya bean flour (#S9633 Sigma Aldrich), 10g methyl-4-hydroxybenzoate (#H3647 Sigma Aldrich) in 10ml ethanol, 50ml proprionic acid (#P5561  Sigma Aldrich)).

extract_protocol: RNA from the frozen flies per treatment was extracted using RNAwiz (Ambion) according to the manufacturer's instructions.

treatment_protocol: 0-3 day old adult flies of appropriate genotype & sex were collected as they emerged from cultures where they were incubated under standard conditions (25oC, 70-75% humidity). The adult flies were transferred into eppendorf tubes and immediately frozen on dry ice and then stored in a -80oC freezer.

tag: gender

value: Males

value: 0-3 day old adults

value: whole animal

tag: number

value: experiment 3

tag: genotype/variation


title: Genetic Control for Dhr96 over-expression, males, biological rep 3 (DS004020)

description:
Gene expression data from adults
DS004020

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