title: seedling at T6, exp. to volatiles Sp. HRO-C48, biological rep1

status: Public on Jan 25 2012

city: Tuebingen

first: Joachim

last: Kilian

address: Auf der Morgenstelle 1

department: ZMBP Plant Physiology

country: Germany

institute: University of Tuebingen

description:
Seedlings_HRO-C48_6h_A
Gene expression data from 4 days old seedlings, 6 hours after start of the experiment; volatile-treated from Serratia plymuthica HRO-C48

hyb_protocol: After fragmentation of cRNA using the RNA Fragmentation Reagents (Ambion), 14,25 µg of cRNA was hybridized to Affymetrix Arabidopsis ATH1 Genome Array (ATH1-121501; GEO accession GPL198) according to manufacturers manual. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the protocol 'EukGE-WS2V4'.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® scanner GS3000 7G according to manufacturers manual.

data_processing: The data was anylysed with GeneSpring GX (vers. 7.3) from Agilent. Preprocessing was performed with included RMA Plugin.

source_name: Arabidopsis seedlings exp. To volatiles 4Rx13 6h

label_protocol: 1 µg of total RNA were used to synthesize amplified labeled cRNA (MessageAmp™ II aRNA Amplification Kit; Ambion).

growth_protocol: Surface sterilized seeds from Arabidopsis thaliana Col-0 (by ethanol (2 min 70 %), calcium hypochloride(5 min 1 %), washed 4 times with steril dH2O) were plated on 0.5 MS 0.8 % Agar split-dish plates. Plated seeds were stratified for  3 days at 4°C. Seed/Seedlings were grown under  22°C +/-2°C; 100 +/-10 µE/m-2/s-1; 16 h light/ 8 h dark; 50 +/-10 % humidity.

extract_protocol: For RNA extraction RNeasy Plant Mini kit was used ( according instructions from Quiagen).  Extracted RNA was precipitated: 96 µl RNA;  8 µl 3 M Sodium acetate (pH 5.2); 2 µl Glycogen(5 mg/ml); Ethanol 250 µl. Stored at -80°C for 15 days, than 30 min 13000 rpm 4°C. 2 times washing with 500 µl 70 % ethanol. Resuspended in 50 µl DEPC water. RNA quantity and integrity were assessed using RNA 6000 Nano LabChip Kit and the BioAnalyzer software (Agilent).

treatment_protocol: After 3 days seedlings of the same developmental stage were selected (seedlings not meeting the dev. stage were removed from the plates). After 4 days seedlings were exposed to volatiles of bacteria (Serratia plymuthica HRO-C48 or Stenotrophomonas maltophilia R3089) by applying a bacteria culture of 10^7 CFU to the other half of the split-dish plates. Mock treated (with bacteria growth media) plates were also kept. For both mock treated and volatile-treated samples, pooled seedlings (from 5 diff. plates) from the respective time points were used for RNA extraction. Two biological replicates were performed.

tag: ecotype

value: whole seedling

value: 4 days

tag: agent

value: volatiles from Serratia plymuthica HRO-C48

tag: time

value: 6 hrs


title: seedling at T12, exp. to volatiles Sm. R3089, biological rep1

type: RNA

description:
Seedlings_R3089_12h_A
Gene expression data from 4 days old seedlings, 12 hours after start of the experiment; volatile-treated from Stenotrophomonas maltophilia R3089

label: biotin

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings exp. To volatiles R3089 12h

tag: tissue

tag: age

value: volatiles from Stenotrophomonas maltophilia R3089

value: 12 hrs


title: seedling at T12, exp. to volatiles Sm. R3089, biological rep2

description:
Seedlings_R3089_12h_B
Gene expression data from 4 days old seedlings, 12 hours after start of the experiment; volatile-treated from Stenotrophomonas maltophilia R3089


title: seedling at T24, exp. to volatiles Sm. R3089, biological rep1

description:
Seedlings_R3089_24h_A
Gene expression data from 5 days old seedlings, 24 hours after start of the experiment; volatile-treated from Stenotrophomonas maltophilia R3089

source_name: Arabidopsis seedlings exp. To volatiles R3089 24h

value: 5 days

value: 24 hrs


title: seedling at T12, exp. to volatiles Sp. HRO-C48, biological rep1

description:
Seedlings_HRO-C48_12h_A
Gene expression data from 4 days old seedlings, 12 hours after start of the experiment; volatile-treated from Serratia plymuthica HRO-C48

source_name: Arabidopsis seedlings exp. To volatiles 4Rx13 12h


title: seedling at T24, exp. to volatiles Sp. HRO-C48, biological rep2

description:
Seedlings_HRO-C48_24h_B
Gene expression data from 5 days old seedlings, 24 hours after start of the experiment; volatile-treated from Serratia plymuthica HRO-C48

source_name: Arabidopsis seedlings exp. To volatiles 4Rx13 24h


title: seedling at T6, exp. to volatiles Sp. HRO-C48, biological rep2

description:
Seedlings_HRO-C48_6h_B
Gene expression data from 4 days old seedlings, 6 hours after start of the experiment; volatile-treated from Serratia plymuthica HRO-C48


title: seedling at T12, untreated, biological rep2

description:
Seedlings_untreated_12h_B
Gene expression data from 4 days old seedlings, 12 hours after start of the experiment; mock treated

source_name: Arabidopsis seedlings untreated after 12h

value: untreated


title: seedling at T6, exp. to volatiles Sm. R3089, biological rep2

description:
Seedlings_R3089_6h_B
Gene expression data from 4 days old seedlings, 6 hours after start of the experiment; volatile-treated from Stenotrophomonas maltophilia R3089

source_name: Arabidopsis seedlings exp. To volatiles R3089 6h


title: seedling at T6, exp. to volatiles Sm. R3089, biological rep1

description:
Seedlings_R3089_6h_A
Gene expression data from 4 days old seedlings, 6 hours after start of the experiment; volatile-treated from Stenotrophomonas maltophilia R3089


title: seedling at T12, exp. to volatiles Sp. HRO-C48, biological rep2

description:
Seedlings_HRO-C48_12h_B
Gene expression data from 4 days old seedlings, 12 hours after start of the experiment; volatile-treated from Serratia plymuthica HRO-C48


title: seedling at T24, untreated, biological rep2

description:
Seedlings_untreated_24h_B
Gene expression data from 5 days old seedlings, 24 hours after start of the experiment; mock treated

source_name: Arabidopsis seedlings untreated after 24h


title: GFP-positive cells from twi-GAL4 UAS-2EGFP/UAS-jumu embryos, replicate 2

status: Public on Jan 30 2012

city: Bethesda

first: Shaad

middle: M.

last: Ahmad

state: MD

address: Building 10, Room 7N311, 10 Center Drive MSC 1654

department: Systems Biology Center

country: USA

institute: National Heart Lung and Blood Institute

description: FACS-sorted GFP positive cells from single cell suspensions of late stage 11/early stage 12 embryos with twi-GAL4 and UAS-2EGFP insertions that target GFP fluorescence to Twist expressing mesodermal cells, as well as a UAS-jumu insertion that constitutively expresses Jumu within these Twist expressing cells.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: The data were analyzed with the Bioconductor affy package, using the mas5 command with default settings, and log2 transformed.

organism: Drosophila melanogaster

source_name: FACS-sorted Drosophila cells

label_protocol: Approximately 2-5 µg of total RNA was processed to produce biotinylated cRNA targets

growth_protocol: Embryos were aged to late stage 11-early stage 12 at 29°C.

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

tag: cell type

value: FACS-sorted GFP positive cells

tag: cell derivation

tag: genotype/variation


title: seedling at T6, untreated, biological rep2

description:
Seedlings_untreated_6h_B
Gene expression data from 4 days old seedlings, 6 hours after start of the experiment; mock treated

source_name: Arabidopsis seedlings untreated after 6h


title: seedling at T24, exp. to volatiles Sp. HRO-C48, biological rep1

description:
Seedlings_HRO-C48_24h_A
Gene expression data from 5 days old seedlings, 24 hours after start of the experiment; volatile-treated from Serratia plymuthica HRO-C48


title: seedling at T24, exp. to volatiles Sm. R3089, biological rep2

description:
Seedlings_R3089_24h_B
Gene expression data from 5 days old seedlings, 24 hours after start of the experiment; volatile-treated from Stenotrophomonas maltophilia R3089


title: seedling at T6, untreated, biological rep1

description:
Seedlings_untreated_6h_A
Gene expression data from 4 days old seedlings, 6 hours after start of the experiment; mock treated


title: GFP-positive cells from twi-GAL4 UAS-2EGFP/UAS-jumu embryos, replicate 1

value: single cell suspensions of late stage 11/early stage 12 embryos

value: twi-GAL4 and UAS-2EGFP insertions that target GFP fluorescence to Twist expressing mesodermal cells, as well as a UAS-jumu insertion that constitutively expresses Jumu within these Twist expressing cells


title: seedling at T0, untreated, biological rep1

description:
Seedlings_untreated_0h_A
Gene expression data from 4 days old seedlings, at start of the experiment; mock treated

source_name: Arabidopsis seedlings untreated

value: 0 hrs


title: seedling at T12, untreated, biological rep1

description:
Seedlings_untreated_12h_A
Gene expression data from 4 days old seedlings, 12 hours after start of the experiment; mock treated


title: seedling at T24, untreated, biological rep1

description:
Seedlings_untreated_24h_A
Gene expression data from 5 days old seedlings, 24 hours after start of the experiment; mock treated


title: affy_larvae_jarid2-mb_1

status: Public on Feb 23 2012

city: Kansas CIty

first: Alexander

middle: (Garrett)

last: Garruss

state: Missouri

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 hr at 45C on Affymetrix Drosophila Genome 2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned with GeneChip 3000.

data_processing: Affymetrix Drosophila Genome 2 arrays were analyzed in R, version 2.11.1, using the packages affy (Gautier et al., 2004), version 1.26.1, and limma (Smyth et al., 2005), version 3.4.3. Normalization was done using rma. Annotation information for the probes was taken from Ensembl 63.

label_protocol: Biotin labelling was done with 200 ng total RNA with the Ambion MessageAmp III kit.

growth_protocol: Flies were raised at 25 degrees celsius.  Eye imaginal discs were dissected from late 3rd instar larvae.

extract_protocol: Eye imaginal discs (~500) were dissected as quickly as possible in cold SFX medium and transferred into a microcentrifuge tube containing 500 ul SFX medium followed by centrifugation for 3 min, 300 x g at 4ºC in a microcentrifuge. The supernatant was carefully removed and 0.5 ml of 0.25% Trypsin solution with EDTA (solution needs to be at 37ºC) added. After preincubating the discs for 1 min at 37ºC they were mechanically disrupted with a needle (size 25G1) by sucking the solution up and down 9 times without creating bubbles. The resulting cell clumps were then incubated for another min (maximum 4 min) at 37ºC and the trypsinization stopped by adding 1 ml of cold medium. The cells were centrifuged for 5 min, 300 x g at 4ºC in a microcentrifuge and the supernatant carefully removed. The resulting cell pellet was resuspended in 1 ml of Schneider medium with 10% FBS and submitted for cytometry.Dissociated cells (eye-antenna imaginal discs) were separated based on their GFP fluorescing properties and sorted directly into TRIZOL (100,000 cells per 1 ml of TRIZOL). RNA (from dissociated cells) was purified based on a standard protocol from DGRC (Indiana University). The RNA pellet was suspended in 30 ul of RNAse free water. RNA from third instar larvae was purified by grinding 20 larvae with a plastic pestle in RLT buffer (Qiagen, RNeasy Kit). After passing the suspension over a QIAshredder column (Qiagen) samples were processed as described in the manual. The RNA was analyzed with an RNA nano chip from Agilent.

treatment_protocol: E(z) RNAi utilized UAS-E(z)-RNAi (Bloomington 27993).  The Jarid2 mutant (mb) is Jarid2MB00996/TM3 (Bloomington 22958).

value: 3rd instar larvae

value: jarid2 mutant


title: seedling at T0, untreated, biological rep2

description:
Seedlings_untreated_0h_B
Gene expression data from 4 days old seedlings, at start of the experiment; mock treated


title: tbf1-elf-3

status: Public on Jan 17 2012

city: Birmingham

first: Karolina

last: Pajerowska-Mukhtar

state: Alabama

address: 1300 University Blvd

department: Department of Biology

institute: University of Alabama at Birmingham

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on Affymetrix ATH1 GeneChip (Santa Clara, CA, U.S.A) for 16 hours at 45C with rotation at 60rpm.

scan_protocol: Immediately following hybridization, the hybridized probe arrays undergo an automated washing and staining protocol on the GeneChip® FS450 fluidic station and are then scanned on the GeneChip® Scanner 3000 7G Plus where patterns of hybridization are detected.

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

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

growth_protocol: Arabidopsis plants (Columbia-0 and tbf1 mutant) were grown on soil (Metro Mix 360) at 22˚C under a 16/8 hr light/dark cycle for 3 weeks

extract_protocol: The RNA was extracted with TRIzol (Ambion)

treatment_protocol: Treated with 1 mM SA for 6 hrs (spray) or 10 µM elf18 for 2 hrs (infiltration into leaves). Mock treatments with water were included for both spray and infiltration.

value: mature leaf

tag: genotype

value: tbf1 mutant

tag: treatment

tag: biological replicate


title: tbf1-SA-2

value: 1 mM SA for 6 hrs (spray)


title: tbf1-elf-1

value: 10 µM elf18 for 2 hrs (infiltration into leaves)


title: WT-melf-2

source_name: WT-melf

value: wild type

value: water for 2 hrs (infiltration into leaves)


title: WT-melf-3


title: tbf1-SA-1


title: WT-mSA-3

source_name: WT-mSA

value: water for 6 hrs (spray)


title: tbf1-melf-2


title: WT-SA-3

source_name: WT-SA


title: WT-elf-3

source_name: WT-elf


title: tbf1-elf-2


title: tbf1-melf-3


title: WT-mSA-2


title: WT-melf-1


title: Col_LD_2_EtOH

status: Public on Jan 15 2012

city: Raleigh

first: Colleen

middle: J

last: Doherty

state: NC

address: 128 Polk Hall CB7622

department: Biochemistry

institute: North Carolina State University

hyb_protocol: Affymetrix Eukaryotic Target Hybridization protocol (GeneChip® Expression Analysis Technical Manual) processed at the Veteran's Medical Research Foundation core microarray facility (http://www.vmrf.org/researchcenters/gene-chip/gene-chip.html)

scan_protocol: Affymetrix® GeneChip® Scanner 3000 with GCOS software according to manufactuer's protocol (GeneChip® Expression Analysis Technical Manual) processed at the Veteran's Medical Research Foundation core microarray facility (http://www.vmrf.org/researchcenters/gene-chip/gene-chip.html)

data_processing: Probe set summarization and normalization was performed by robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) using the R/Bioconductor package affy.

label: Biotin

source_name: seedlings, 13 days old, Col-0 ecotype

label_protocol: Affymetrix GeneChip® IVT Labeling Kit, according to manufactuer's protocol (GeneChip® Expression Analysis Technical Manual) processed at the Veteran's Medical Research Foundation core microarray facility (http://www.vmrf.org/researchcenters/gene-chip/gene-chip.html)

extract_protocol: Plant RNA prep using RNeasy (Qiagen) using the manufacturers protocols with RLT buffer

value: wildtype

tag: growth protocol (before start of expt)

value: Entrained in 12:12, Retained in 12:12 (LD)

value: 2.5% ethanol-treated, treated with 20mM MG132

tag: time (of harvest)


title: WT-mSA-1


title: WT-SA-1


title: Col_LD_1_EtOH


title: ALC_Toc1_LD_3_Mock

value: Mock-treated, treated with 20mM MG132


title: ALC_Toc1_LD_1_EtOH


title: Col_LD_3_Mock


title: Col_LD_2_Mock


title: ALC_Toc1_LD_2_Mock


title: ALC_Toc1_LD_1_Mock


title: Col_LD_3_EtOH


title: ALC_Toc1_LD_2_EtOH


title: tbf1-melf-1


title: tbf1-SA-3


title: ALC_Toc1_LD_3_EtOH


title: Col_LD_1_Mock


title: Col_LL_3_EtOH

value: Entrained in 12:12, Shifted to Constant Light(LL)


title: ALC_Toc1_LL_1_EtOH


title: ALC_Toc1_LL_1_Mock


title: Col_LL_3_Mock


title: Col_LL_2_EtOH


title: ALC_Toc1_LL_2_Mock


title: Col_LL_1_Mock


title: ALC_Toc1_LL_3_EtOH


title: ALC_Toc1_LL_3_Mock


title: Col_LL_1_EtOH


title: Col_LL_2_Mock


title: WT-SA-2


title: ALC_Toc1_LL_2_EtOH


title: wild type seedlings at R18, biological rep1

status: Public on Jan 03 2012

city: Bellaterra- Cerdanyola del Valles

first: Elena

last: Monte

state: Barcelona

address: Campus UAB-Edifici CRAG

country: Spain

institute: CRAG

description: Gene expression data from seedlings grown in dark for 4 days+18h in Red.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on ATH1 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using an Agilent Scanner.

data_processing:
The dara were analyzed with Rosetta Resolver platform performing a Benjamini Hochberg FDR error-corrected analysis of variance (ANOVA) followed by a Ratio Error Model as described in Weng et al. 2006 (Bioinformatics 22: 1111)
The matrix table consists of sequence (probe set) intensity values following normalisation with the Rosetta Affymetrix Error Model Normalisation Method, as described in Weng et al (2006), Bioinformatics 22, pp1111-1121, and as implemented in the Rosetta Resolver system, version 7.2.

source_name: Arabidopsis seedlings grown for 4 days  in darkness and 18 hour  in Red continuous light

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

growth_protocol: Seeds were surface-sterilized and plated on GM medium without sucrose, stratified at 4C in the dark for 4 days, exposed to white light for 3 hours to induce germination, and placed in a growth chamber at 21C in darkness for 4 days (D0h) and 4 days and 1 hour (D1h). For Rc treatments seedlings were moved to Rc growth chambers at 21ºC for 1 (R1h) and 18 (R18h) hours.

extract_protocol: Total RNA was prepared using the method of Chang et al.1993 (Plant Mol. Biol. Rep. 11: 113) followed by further purification using RNeasy columns (Qiagen, Valencia,CA).

value: deetiolated seedling

value: Wild type

value: Seedlings grown  for 4 days in darkness and 18 hours in red continuous light


title: pif3 seedlings at D1, biological rep2

description: Gene expression data from seedlings grown in dark for 4 days+1h.

source_name: Arabidopsis seedlings grown for 4 days and 1 hour  in darkness

value: etiolated seedling

value: pif3 mutant

value: Seedlings grown  for 4 days and 1 hour in darkness


title: pif3 seedlings at D0, biological rep2

description: Gene expression data from seedlings grown in dark for 4 days.

source_name: Arabidopsis seedlings grown for 4 days in darkness

value: Seedlings grown  for 4 days in darkness


title: wild type seedlings at D1, biological rep3


title: wild type seedlings at R18, biological rep2


title: wild type seedlings at D18, biological rep1

description: Gene expression data from seedlings grown in dark for 4 days+18h.

source_name: Arabidopsis seedlings grown for 4 days and 18 hour  in darkness

value: Seedlings grown  for 4 days and 18 hour in darkness


title: pif3 seedlings at D1, biological rep1


title: pif3 seedlings at D1, biological rep3


title: wild type seedlings at R1, biological rep3

description: Gene expression data from seedlings grown in dark for 4 days+1h in Red.

source_name: Arabidopsis seedlings grown for 4 days  in darkness and 1 hour  in Red continuous light

value: Seedlings grown  for 4 days in darkness and 1 hour in red continuous light


title: wild type seedlings at D18, biological rep2


title: wild type seedlings at R18, biological rep3


title: wild type seedlings at R1, biological rep2


title: wild type seedlings at D18, biological rep3


title: pif3 seedlings at D0, biological rep3


title: pif3 seedlings at D0, biological rep1


title: wild type seedlings at D0, biological rep3


title: wild type seedlings at D1, biological rep1


title: wild type seedlings at D1, biological rep2


title: wild type seedlings at R1, biological rep1


title: wild type seedlings at D0, biological rep1


title: wild type seedlings at D0, biological rep2


title: arabidopsis nhx5-2/nhx6-2 3

status: Public on Jan 01 2012

city: davis

first: elias

last: bassil

state: CA

address: 1 shields ave

department: plant sciences

institute: university of california

description: Gene expression data from Arabidopsis rosette leaf RNA hybridized to Affymetrix Arabidopsis Genome Array

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

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

data_processing: The data were normalized using JMPGenomics (ver 3.0) with STD normalization and background correction feature.

source_name: double knockout of AtNHX5-2 / AtNHX6-2, biological rep3

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

growth_protocol: Plants were grown in Metromix300 soil in 18-pot trays in a growth chamber with 8h L/16h D and fertilized weekly beginning week 2.

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

value: Rosette leaf

tag: strain/ecotype

value: colombia


title: arabidopsis nhx5-2/nhx6-2 2

source_name: double knockout of AtNHX5-2 / AtNHX6-2, biological rep2


title: arabidopsis nhx5-2 3

source_name: single knockout of AtNHX5, T-DNA line GABI-09H405, biological rep3


title: arabidopsis nhx5-2 2

source_name: single knockout of AtNHX5, T-DNA line GABI-09H405, biological rep2


title: arabidopsis nhx5-2/nhx6-2 1

source_name: double knockout of AtNHX5-2 / AtNHX6-2, biological rep1


title: arabidopsis nhx6-2 3

source_name: single knockout of AtNHX6, T-DNA line SALK_100042, biological rep3


title: arabidopsis nhx5-1/nhx6-1 2

source_name: double knockout of AtNHX5-1 (WiscDsLox345-348M8/ AtNHX6-1 (SALK_113129), biological rep2


title: arabidopsis nhx6-2 2

source_name: single knockout of AtNHX6, T-DNA line SALK_100042, biological rep2


title: arabidopsis wild type 3

source_name: wild type, control, biological rep3


title: arabidopsis wild type 2

source_name: wild type control, biological rep2


title: arabidopsis nhx5-1/nhx6-1 1

source_name: double knockout of AtNHX5-1 (WiscDsLox345-348M8/ AtNHX6-1 (SALK_113129), biological rep1


title: arabidopsis nhx6-2 1

source_name: single knockout of AtNHX6, T-DNA line SALK_100042, biological rep1


title: arabidopsis wild type 1

source_name: wild type control, biological rep1


title: RNAi-Root-+Zn-3

status: Public on Dec 31 2011

city: Bayreuth

first: Stephan

last: Clemens

address: Universitaetsstrasse 30

department: Plant Physiology

institute: University of Bayreuth

description: Hydroponically grown 5-weeks old plants

hyb_protocol: cRNA products were hybridized to the array for 16 h at 45C in a rotating chamber.

scan_protocol: Hybridized arrays were washed and stained in an Affymetrix Fluidics Station FS450, and the fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000.

data_processing: CEL files from the Affymetrix microarray hybridization were processed by use of the R program and Bioconductor packages (Gentleman et al., 2004). The Robust Multi-chip Average (RMA) normalization was performed using the default settings of the corresponding R function (Irizarry et al., 2003). To estimate the amount of expressed mRNAs, the present call information of the non-parametric Wilcoxon signed rank test (PMA values) was computed with the 'affy' package (Gautier et al., 2004). Hybridization data from three biological replicates were generated for each Langelsheim wild-type and RNAi line 1-2.

organism: Arabidopsis halleri

source_name: RNAi_Root_+10 µM Zn2+ medium

label_protocol: 250 ng of total RNA, purified with RNeasy Mini columns (Qiagen, Hilden, Germany) according to the manufacturer's directions, were used to generate double-stranded cDNA and subsequently biotin-labeled cRNA. The length of the cRNA products was assessed using an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, USA)

extract_protocol: RNA was extracted from homogenized A. halleri root tissue with Trizol (Invitrogen Life Technologies) according to the manufacturer’s instructions.

value: 5 weeks old

value: Root


title: WT-Root-+Zn-3

description: Hydroponically grown 5-weeks old plants

source_name: WT_Root_+10 µM Zn2+ medium

value: Langelsheim wild-type


title: RNAi-Root-+Zn-2

description: Hydroponically grown 5-weeks old plants


title: WT-Root-+Zn-2

description: Hydroponically grown 5-weeks old plants


title: RNAi-Root-+Zn-1

description: Hydroponically grown 5-weeks old plants


title: RNAi-Root-Control-1

description: Hydroponically grown 5-weeks old plants

source_name: RNAi_Root_control medium


title: WT-Root-Control-1

description: Hydroponically grown 5-weeks old plants

source_name: WT_Root_control medium


title: RNAi-Root-Control-2

description: Hydroponically grown 5-weeks old plants


title: RNAi-Root-Control-3

description: Hydroponically grown 5-weeks old plants


title: WT-Root-Control-2

description: Hydroponically grown 5-weeks old plants


title: WT-Root-Control-3

description: Hydroponically grown 5-weeks old plants


title: WT-Root-+Zn-1

description: Hydroponically grown 5-weeks old plants


title: ABADFPM_1

city: La Jolla

first: Julian

last: Schroeder

address: 9500 Gilman Drive #0116

department: Division of Biological Sciences

institute: UCSD

description: Plate grown 12-day-old seedlings were transferred into 6 well plates with 30 μM DFPM and 10 μM ABA in water as a treatment for 6 hours. DFPM was added 30 min prior to ABA treatment.

hyb_protocol: UCSD GeneChip Microarray Core; Affymetrix Eukaryotic Target Hybridization protocol (GeneChip Expression Analysis Technical Manual)

scan_protocol: UCSD GeneChip Microarray Core; Affymetrix GeneChip Scanner 3000 with GCOS software according to manufactuer's protocol (GeneChip Expression Analysis Technical Manual)

data_processing: Probe set summarization and normalization was performed by robust multi-array averaging (gcrma, including background subtraction, summarization by median polish and quantile normalization) using the R/Bioconductor package affy.

source_name: whole seedling treated with abscisic acid and DFPM

label_protocol: UCSD GeneChip Microarray Core; Affymetrix GeneChip IVT Labeling Kit, according to manufactuer's protocol (GeneChip Expression Analysis Technical Manual)

extract_protocol: Trizol (Invitrogen, Carlsbad, CA, USA) and further purified using RNeasy Plant RNA purification kit (QIAgen, Valencia, CA, USA)

value: 12 day old plate grown seedling


title: ABADFPM_3


title: DFPM_2

description: Plate grown 12-day-old seedlings were transferred into 6 well plates with  30 μM DFPM for 6 hours. DFPM was added 30 min prior to ABA treatment.

source_name: whole seedling treated with [5-(3,4-Dichlorophenyl)Furan-2-yl]-Piperidin-1-ylMethanethione (DFPM)


title: DFPM_3


title: WT treated with chitooctaose, biological rep2

city: Columbia

first: Gary

last: Stacey

state: MO

address: 1201 Rollins Road

department: Plant Sciences

institute: University of Missouri-Columbia

description:
WT-chitooctaose-2
Gene expression data from WT whole seedlings after treatment with chitooctaose for 30 minutes.

hyb_protocol: Hybridization solution containing 50 ng/ul of fragmented aRNA was hybridized to the genome array GeneChip (Affymetrix, Santa Clara, CA) at 45 C for 18 hrs.  After hybridization, the chips were washed and stained with R-phycoerythrin-streptavidin on Affymetrix fluidics station 450 using fluidics protocol FS450_0004.

scan_protocol: The image data was acquired by the Affymetrix GeneChip scanner 3000 and Affymetrix AGCC software.

data_processing: The data were analyzed with dChip (DNA-Chip Analyzer), Build date: Mar 31 2010. The default settings were employed for normalization and calculation of expression values.

source_name: WT treated with chitooctaose for 30 minutes

label_protocol: 0.5 microgram of total RNA was used to make the biotin-labeled antisense RNA (aRNA) target using the MessageAmp Premier RNA amplification kit (Ambion, Austin, TX) by following the manufacturer’s procedures.  Briefly, the total RNA was reverse transcribed to first strand cDNA with a oligo(dT) primer bearing a 5’-T7 promoter using ArrayScript reverse transcriptase.  The first strand cDNA then underwent second-strand synthesis to convert into double-stranded cDNA template for in vitro transcription.  The biotin-labeled aRNA was synthesized using T7 RNA transcriptase with biotin-NTP mix.  After purification, the aRNA was fragmented in 1X fragmentation buffer at 94 C for 35 min.

growth_protocol: Plants were grown in 1/2 MS medium plus vitamin B5 and 2% glucose in a growth chamber with constant light and a temperature of 23 C.

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

treatment_protocol: Seedlings were treated with chitooctaose at a final concentration of 1 uM for 30 minutes. The controls were similarly treated with an equivalent amount of ddH2O.

value: wild-type

value: seedlings

value: 14 days

value: chitooctaose


title: WT treated with water, biological rep1

description:
WT-water-1
Gene expression data from WT whole seedlings after treatment with water for 30 minutes.

source_name: WT treated with water for 30 minutes

value: water


title: ABA_2

description: Plate grown 12-day-old seedlings were transferred into 6 well plates with 10 μM ABA in water as a treatment for 6 hours

source_name: whole seedling treated with abscisic acid


title: ABA_3


title: WT treated with water, biological rep2

description:
WT-water-2
Gene expression data from WT whole seedlings after treatment with water for 30 minutes.


title: Mutant treated with chitooctaose, biological rep3

description:
Mutant-chitooctaose-3
Gene expression data from erf5/6 whole seedlings after treatment with chitooctaose for 30 minutes.

source_name: erf5/6 mutant treated with chitooctaose for 30 minutes

value: ERF5 and 6 double mutant


title: Mutant treated with chitooctaose, biological rep2

description:
Mutant-chitooctaose-2
Gene expression data from erf5/6 whole seedlings after treatment with chitooctaose for 30 minutes.


title: WT treated with water, biological rep3

description:
WT-water-3
Gene expression data from WT whole seedlings after treatment with water for 30 minutes.


title: ABADFPM_2


title: Mutant treated with water, biological rep3

description:
Mutant-water-3
Gene expression data from erf5/6 whole seedlings after treatment with water for 30 minutes.

source_name: erf5/6 mutant treated with water for 30 minutes


title: WT treated with chitooctaose, biological rep3

description:
WT-chitooctaose-3
Gene expression data from WT whole seedlings after treatment with chitooctaose for 30 minutes.


title: WT treated with chitooctaose, biological rep1

description:
WT-chitooctaose-1
Gene expression data from WT whole seedlings after treatment with chitooctaose for 30 minutes.


title: DFPM_1


title: control_2

description: Plate grown 12-day-old seedlings were transferred into 6 well plates with 1:5000 (V/V) DMSO in water as a control

source_name: whole seedling


title: control_3


title: Mutant treated with chitooctaose, biological rep1

description:
Mutant-chitooctaose-1
Gene expression data from erf5/6 whole seedlings after treatment with chitooctaose for 30 minutes.


title: Mutant treated with water, biological rep2

description:
Mutant-water-2
Gene expression data from erf5/6 whole seedlings after treatment with water for 30 minutes.


title: Mutant treated with water, biological rep1

description:
Mutant-water-1
Gene expression data from erf5/6 whole seedlings after treatment with water for 30 minutes.


title: control_1


title: ABA_1


title: WT_CO1_rep3_SK35_sample224

city: Yokohama

first: Miyako

last: Kusano

state: Kanagawa

address: 1-7-22, Suehiro, Tsurumi

country: Japan

institute: RIKEN CSRS

description: The control (wild-type) in CO1 experiment, aerial region, 18-day-old sample grown on solid MS- medium containing 1% sucrose, a single plant was used in each hybridization. The sample was grown under highly controlled growth conditions, under two independent environmental regimes. The chosen conditions were; (i) growth for 17 days under typical long day conditions with 24 h ultraviolet light on day 18 (ultraviolet light 1; UV1)and (ii) growth for 17 days under typical long day conditions with 8 h additional light on day 18 (continuous light 1; CO1). Plants were cultivated in controlled growth chambers (SANYO; MLR-350) at 22°C in 16-h light and 8-h dark conditions for 17 days. The aerial region was harvested, 6 h after the onset of the bright phase under each light treatment.

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

source_name: Arabidopsis thaliana accession Col-0 by the 24-h light treatment (CO1), replicate 3

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

growth_protocol: 16 h light, 8 h dark, 22°C

extract_protocol: Total RNA was prepared using RNeasy Plant Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: two different light treatments

value: 18 days

value: aerial region

tag: genetic background

tag: stress

value: continuous light (control)

value: 1 day


title: sng1_CO1_rep1_SK39_sample242

description: Arabidopsis mutants impaired in sinapoyl-malate (sinapoylglucose accumulator 1 [sng1]) biosynthesis in CO1 experiment, aerial region, 18-day-old sample grown on solid MS- medium containing 1% sucrose, a single plant was used in each hybridization. The sample was grown under highly controlled growth conditions, under two independent environmental regimes. The chosen conditions were; (i) growth for 17 days under typical long day conditions with 24 h ultraviolet light on day 18 (ultraviolet light 1; UV1)and (ii) growth for 17 days under typical long day conditions with 8 h additional light on day 18 (continuous light 1; CO1). Plants were cultivated in controlled growth chambers (SANYO; MLR-350) at 22°C in 16-h light and 8-h dark conditions for 17 days. The aerial region was harvested, 6 h after the onset of the bright phase under each light treatment.

source_name: Arabidopsis thaliana accession sng1 by the 24-h light treatment (CO1), replicate 1


title: WT_CO1_rep2_SK34_sample220

source_name: Arabidopsis thaliana accession Col-0 by the 24-h light treatment (CO1), replicate 2


title: tt4_CO1_rep2_SK37_sample228

description: Arabidopsis mutants impaired in flavonoid (TRANSPARENT TESTA4 [tt4]) biosynthesis in CO1 experiment, aerial region, 18-day-old sample grown on solid MS- medium containing 1% sucrose, a single plant was used in each hybridization. The sample was grown under highly controlled growth conditions, under two independent environmental regimes. The chosen conditions were; (i) growth for 17 days under typical long day conditions with 24 h ultraviolet light on day 18 (ultraviolet light 1; UV1)and (ii) growth for 17 days under typical long day conditions with 8 h additional light on day 18 (continuous light 1; CO1). Plants were cultivated in controlled growth chambers (SANYO; MLR-350) at 22°C in 16-h light and 8-h dark conditions for 17 days. The aerial region was harvested, 6 h after the onset of the bright phase under each light treatment.

source_name: Arabidopsis thaliana accession tt4 by the 24-h light treatment (CO1), replicate 2


title: tt4_CO1_rep1_SK36_sample226

source_name: Arabidopsis thaliana accession tt4 by the 24-h light treatment (CO1), replicate 1


title: sng1_CO1_rep2_SK40_sample244

source_name: Arabidopsis thaliana accession sng1 by the 24-h light treatment (CO1), replicate 2


title: sng1_UV1_rep1_SK30_sample207

description: Arabidopsis mutants impaired in sinapoyl-malate (sinapoylglucose accumulator 1 [sng1]) biosynthesis in UV1 experiment, aerial region, 18-day-old sample grown on solid MS- medium containing 1% sucrose, a single plant was used in each hybridization. The sample was grown under highly controlled growth conditions, under two independent environmental regimes. The chosen conditions were; (i) growth for 17 days under typical long day conditions with 24 h ultraviolet light on day 18 (ultraviolet light 1; UV1)and (ii) growth for 17 days under typical long day conditions with 8 h additional light on day 18 (continuous light 1; CO1). Plants were cultivated in controlled growth chambers (SANYO; MLR-350) at 22°C in 16-h light and 8-h dark conditions for 17 days. The aerial region was harvested, 6 h after the onset of the bright phase under each light treatment.

source_name: Arabidopsis thaliana sng1 by UV-1-day radiation (UV1), replicate 1

value: UV


title: tt4_CO1_rep3_SK38_sample233

source_name: Arabidopsis thaliana accession tt4 by the 24-h light treatment (CO1), replicate 3


title: tt4_UV1_rep1_SK27_sample191

description: Arabidopsis mutants impaired in flavonoid (TRANSPARENT TESTA4 [tt4]) biosynthesis in UV1 experiment, aerial region, 18-day-old sample grown on solid MS- medium containing 1% sucrose, a single plant was used in each hybridization. The sample was grown under highly controlled growth conditions, under two independent environmental regimes. The chosen conditions were; (i) growth for 17 days under typical long day conditions with 24 h ultraviolet light on day 18 (ultraviolet light 1; UV1)and (ii) growth for 17 days under typical long day conditions with 8 h additional light on day 18 (continuous light 1; CO1). Plants were cultivated in controlled growth chambers (SANYO; MLR-350) at 22°C in 16-h light and 8-h dark conditions for 17 days. The aerial region was harvested, 6 h after the onset of the bright phase under each light treatment.

source_name: Arabidopsis thaliana tt4 by UV-1-day radiation (UV1), replicate 1


title: WT_UV1_rep3_SK26_sample188

description: The control (wild-type) in UV1 experiment, aerial region, 18-day-old sample grown on solid MS- medium containing 1% sucrose, a single plant was used in each hybridization. The sample was grown under highly controlled growth conditions, under two independent environmental regimes. The chosen conditions were; (i) growth for 17 days under typical long day conditions with 24 h ultraviolet light on day 18 (ultraviolet light 1; UV1)and (ii) growth for 17 days under typical long day conditions with 8 h additional light on day 18 (continuous light 1; CO1). Plants were cultivated in controlled growth chambers (SANYO; MLR-350) at 22°C in 16-h light and 8-h dark conditions for 17 days. The aerial region was harvested, 6 h after the onset of the bright phase under each light treatment.

source_name: Arabidopsis thaliana accession Col-0 by UV-1-day radiation (UV1), replicate 3


title: tt4_UV1_rep2_SK28_sample195

source_name: Arabidopsis thaliana tt4 by UV-1-day radiation (UV1), replicate 2


title: sng1_UV1_rep3_SK32_sample213

source_name: Arabidopsis thaliana sng1 by UV-1-day radiation (UV1), replicate 3


title: WT_UV1_rep1_SK24_sample183

source_name: Arabidopsis thaliana accession Col-0 by UV-1-day radiation (UV1), replicate 1


title: sng1_UV1_rep2_SK31_sample211

source_name: Arabidopsis thaliana sng1 by UV-1-day radiation (UV1), replicate 2


title: tt4_UV1_rep3_SK29_sample197

source_name: Arabidopsis thaliana tt4 by UV-1-day radiation (UV1), replicate 3


title: sng1_CO1_rep3_SK41_sample246

source_name: Arabidopsis thaliana accession sng1 by the 24-h light treatment (CO1), replicate 3


title: WT_CO1_rep1_SK33_sample218

source_name: Arabidopsis thaliana accession Col-0 by the 24-h light treatment (CO1), replicate 1


title: WT_UV1_rep2_SK25_sample185

source_name: Arabidopsis thaliana accession Col-0 by UV-1-day radiation (UV1), replicate 2


title: Fork head_Stage11_rep3

city: Baltimore

first: Deborah

last: Andrew

address: 725 N. Wolfe St., Hunterian G-1

department: Cell Biology

institute: Johns Hopkins University School of Medicine

hyb_protocol: Samples and controls were prepared using the Affymetrix GeneChip hybridization, wash and stain kit (P/N 900720). Arrays were prehybridized for 10 minutes prior to sample addition. Following sample addition, arrays were hybridized for 16 hours at 45 Celsius, and shaken at 60 rpm. Arrays were stained and washed using the Affymetrix GeneChip Fluidics Station 450 and FS450_002 fluidics script.

scan_protocol: Arrays were scanned with the Affymetrix GeneChip Scanner 3000 and raw analysis was performed with Affymetrix Command Console and Expression Console.

data_processing: Data was normalized by RMA and statistical analysis was performed using Partek software. Further analysis was performed using Spotfire software.

source_name: Drosophila St. 11 fork head mutant embryos

label_protocol: Amplification and labeling were performed using the Affymetrix GeneChip3' IVT express kit (P/N 901229) following the manufacturer's protocol.

growth_protocol: Embryos were collected and aged at 25 C.

extract_protocol: RNA was isolated by TriZol extraction and cleaned up using the Qiagen Rneasy kit.

treatment_protocol: Embryos were sorted on a COPAS biosorter prior to RNA extraction.

tag: developmental stage

value: embryonic stage 11

tag: strain

value: Oregon R

value: fkh[6] mutant


title: Fork head_Stage11_rep1


title: Fork head_Stage11_rep2


title: Wild type_Stage11_rep2

source_name: Drosophila St. 11 Oregon R embryos

value: wild type


title: Wild type_Stage11_rep3


title: Wild type_Stage11_rep1


title: young adult_24hr Benzene exposure_rep1

city: seoul

first: jinhee

last: choi

address: 90 Jeonnong-dong, Dongdaemun-gu

department: College of Urban Science

country: South Korea

institute: University of Seoul

description:
Gene expression data from Drosophila melanogaster young adults.
Drosophila-Benzene

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

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

data_processing: Affymetrix data were normalized, and summarized with the robust multi-average (RMA) method implemented in the Affymetrix Expression Console 1.1. To reduce noise for the significance analysis, the probesets called Absent by the MAS5 detection call on all arrays were filtered out.

source_name: mRNA isolated from wildtype (Canton-S) young adult, benzene

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA (GeneChip® 3’ IVT Express Kit User Manual Affymetrix, P/N 702646 Rev. 1).

growth_protocol: Drosophila melanogaster were grown on standard cornmeal–agar medium and young adults (1-2 days) were used in all of the experiments.

extract_protocol: The total RNA was prepared from the exposed and control flies according to the standard protocol of the RNeasy Mini kit (Qiagen, Hilden, Germany).

treatment_protocol: Young adult flies were transferred into fly vials with standard medium. The vials were closed with a fine mesh. The vials containing the flies were placed into the exposure bottle where they were exposed to the vapours of benzene, toluene, or formaldehyde.

value: Canton-S

value: wildtype

tag: gender

value: male

value: young adult

value: benzene

tag: treatment time

value: 24 hours


title: leaf_AB mutant_ozone_2d_biological rep3

status: Public on Dec 24 2011

first: Fitzgerald

middle: Lewis

last: Booker

address: 3127 Ligon Street

department: Plant Science Research

institute: USDA-ARS

hyb_protocol: Fragmented aRNA (15 µg) was added to a hybridization cocktail (0.05 µg µl-1 fragmented cRNA, 50 pM control oligonucleotide B2, BioB, BioC, BioD and cre hybridization controls, 0.1 mg ml-1 herring sperm DNA, 0.5 mg ml-1 acetylated BSA, 100 mM MES, 1 M [Na+], 20 mM EDTA and 0.01% Tween 20).  aRNA (10 µg) was used for hybridization in a volume of 200 µl per slide.  Affymetrix arrays were hybridized for 16 h at 45 °C in a GeneChip Hybridization Oven 640 (Affymetrix).

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

data_processing: Affymetrix GeneChip Operating Software was used for washing, scanning and basic analysis. Affymetrix Expression Console software processed the CEL files. The software uses the RMA algorithm.

source_name: Arabidopsis leaf, G-protein null mutant genotype, 125 ppb ozone, treated for 2 d

label_protocol: The MessageAmp II-Biotin Enhanced Kit (Ambion, Invitrogen Corp, Carlsbad, CA) was used to generate biotinylated aRNA from the cDNA reaction.

growth_protocol: Columbia wild-type and G-protein null mutant gpa1-4/agb1-2 plants sown in Metro-Mix were germinated under a photosynthetic photon flux density (PPFD) of 400 µmol m-2 s-1  (9 h light/15 h dark cycle) at 23 °C in a growth chamber in the North Carolina State University Phytotron.  Plants were grown for 4-5 weeks in the growth chamber.  Plants were fertilized with Phytotron nutrient solution (Downs & Thomas, 1983) once per week.

extract_protocol: Extraction of total RNA was performed using  Qiagen RNeasy mini kits according to the manufacturer's instructions.

treatment_protocol: For ozone treatments, plants were transferred to four chambers located in a walk-in growth chamber in the North Carolina State University Phytotron.  Temperature, relative humidity (RH) and PPFD in the chambers were 24 °C, 53% and 362 μmol m-2 s-1, respectively.   Plants were treated with either 5 or 125 ppb ozone for 7 h per day for two days.  Leaf tissue samples from mid-whorl leaves were taken after ozone exposure for 3 h and 2 d, and then frozen in liquid nitrogen for later analysis.

value: ozone

tag: sampling time

value: 2 days


title: leaf_AB mutant_ozone_2d_biological rep4


title: young adult_24hr Toluene exposure_rep1

description:
Gene expression data from Drosophila melanogaster young adults.
Drosophila-Toluene

source_name: mRNA isolated from wildtype (Canton-S) young adult, toluene

value: toluene


title: young adult_not exposed_rep1

description:
Gene expression data from Drosophila melanogaster young adults.
Drosophila-Control

source_name: mRNA isolated from wildtype (Canton-S) young adult, not exposed


title: young adult_24hr Formaldehyde exposure_rep1

description:
Gene expression data from Drosophila melanogaster young adults.
Drosophila-Formaldehyde

source_name: mRNA isolated from wildtype (Canton-S) young adult, formaldehyde

value: formaldehyde


title: leaf_AB mutant_clean-air_2d_biological rep3

source_name: Arabidopsis leaf, G-protein null mutant genotype, clean-air control, treated for 2 d

value: clean-air


title: leaf_AB mutant_ozone_2d_biological rep2


title: leaf_Col_ozone_2d_biological rep1

source_name: Arabidopsis leaf, Col-0 genotype, 125 ppb ozone, treated for 2 d


title: leaf_AB mutant_clean-air_2d_biological rep1


title: leaf_Col_ozone_2d_biological rep2


title: leaf_Col_ozone_2d_biological rep3


title: leaf_AB mutant_ozone_2d_biological rep1


title: leaf_Col_clean-air_2d_biological rep2

source_name: Arabidopsis leaf, Col-0 genotype, clean-air control, treated for 2 d


title: leaf_Col_clean-air_2d_biological rep3


title: leaf_Col_ozone_2d_biological rep4


title: leaf_Col_clean-air_2d_biological rep4


title: leaf_AB mutant_ozone_3h_biological rep1

source_name: Arabidopsis leaf, G-protein null mutant genotype, 125 ppb ozone, treated for 3 h

value: 3 hours


title: leaf_Col_clean-air_2d_biological rep1


title: leaf_AB mutant_ozone_3h_biological rep2


title: leaf_AB mutant_clean-air_2d_biological rep2


title: leaf_AB mutant_clean-air_3h_biological rep2

source_name: Arabidopsis leaf, G-protein null mutant genotype, clean-air control, treated for 3 h


title: leaf_AB mutant_ozone_3h_biological rep3


title: leaf_AB mutant_clean-air_3h_biological rep3


title: leaf_Col_ozone_3h_biological rep3

source_name: Arabidopsis leaf, Col-0 genotype, 125 ppb ozone, treated for 3 h


title: leaf_Col_ozone_3h_biological rep1


title: leaf_Col_ozone_3h_biological rep2


title: leaf_Col_clean-air_3h_biological rep3

source_name: Arabidopsis leaf, Col-0 genotype, clean-air control, treated for 3 h


title: leaf_AB mutant_clean-air_3h_biological rep1


title: leaf_Col_clean-air_3h_biological rep1


title: leaf_Col_clean-air_3h_biological rep2


title: 5905-20d repeat 5

status: Public on Dec 23 2011

city: Philadelphia

first: Bonini

last: Nancy

state: PA

address: 415 S University Ave

institute: University of Pennsylvania

description:
3082_11742_E2_Drosophila_2.mas5.CHP
3082_11742_E2_Drosophila_2.CEL

hyb_protocol: Affymetrix Drosophila 2.0 chips. Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing:
Affymetrix .cel (probe intensity) files were exported from GeneChip Operating Software (Affymetrix). The .cel files were imported to ArrayAssist Lite (Agilent) in which GCRMA probeset expression levels and Affymetrix absent/present/marginal flags were calculated.
MAS5.0-generated data are presented in the tables below.

source_name: wildtype 5905 flies

label_protocol: FL-Ovation™ cDNA Biotin Module V2 (Ovation)

growth_protocol: Fly were grown in standard cornmeal molasses agar medium with dry yeast, at 25°C

extract_protocol: Trizol reagent

treatment_protocol: natural aging; 3d vs. 20d

tag: tissue

value: dissected brain

tag: time


title: 5905-3d repeat 3

description:
3082_11733_C1_Drosophila_2.mas5.CHP
3082_11733_C1_Drosophila_2.CEL


title: 5905-20d repeat 4

description:
3082_11738_D2_Drosophila_2.mas5.CHP
3082_11738_D2_Drosophila_2.CEL


title: 0110-3d repeat 3

description:
3082_11735_C3_Drosophila_2.mas5.CHP
3082_11735_C3_Drosophila_2.CEL

source_name: miR-34 null flies

value: miR-34 null


title: 5905-20d repeat 3

description:
3082_11734_C2_Drosophila_2.mas5.CHP
3082_11734_C2_Drosophila_2.CEL


title: 0110-3d repeat 4

description:
3082_11739_D3_Drosophila_2.mas5.CHP
3082_11739_D3_Drosophila_2.CEL


title: 0110-3d repeat 5

description:
3082_11743_E3_Drosophila_2.mas5.CHP
3082_11743_E3_Drosophila_2.CEL


title: 0110-20d repeat 1

description:
3082_11728_A4_Drosophila_2.mas5.CHP
3082_11728_A4_Drosophila_2.CEL


title: 5905-3d repeat 4

description:
3082_11737_D1_Drosophila_2.mas5.CHP
3082_11737_D1_Drosophila_2.CEL


title: 0110-20d repeat 2

description:
3082_11732_B4_Drosophila_2.mas5.CHP
3082_11732_B4_Drosophila_2.CEL


title: 60d replicate 2 (mRNA)

description:
HHMI (640) 60 days #2 Drosophila_2.CEL
HHMI (640) 60 days #2 Drosophila_2.CHP

scan_protocol: Standard Affymetrix protocol

source_name: dissected brain tissue

treatment_protocol: natural aging


title: 5905-3d repeat 5

description:
3082_11741_E1_Drosophila_2.mas5.CHP
3082_11741_E1_Drosophila_2.CEL


title: 0110-20d repeat 3

description:
3082_11736_C4_Drosophila_2.mas5.CHP
3082_11736_C4_Drosophila_2.CEL


title: 0110-20d repeat 5

description:
3082_11744_E4_Drosophila_2.mas5.CHP
3082_11744_E4_Drosophila_2.CEL


title: 0110-3d repeat 1

description:
3082_11727_A3_Drosophila_2.mas5.CHP
3082_11727_A3_Drosophila_2.CEL


title: 60d replicate 1 (mRNA)

description:
HHMI (639) 60 days #1 Drosophila_2.CEL
HHMI (639) 60 days #1 Drosophila_2.CHP


title: 5905-3d repeat 1

description:
3082_11725_A1_Drosophila_2.mas5.CHP
3082_11725_A1_Drosophila_2.CEL


title: 60d replicate 3 (mRNA)

description:
HHMI (641) 60 days #3 Drosophila_2.CEL
HHMI (641) 60 days #3 Drosophila_2.CHP


title: 3d replicate 3 (mRNA)

description:
HHMI (635) 3 days #3 Drosophila_2.CEL
HHMI (635) 3 days #3 Drosophila_2.CHP


title: 30d replicate 1 (mRNA)

description:
HHMI (636) 30 days #1 Drosophila_2.CEL
HHMI (636) 30 days #1 Drosophila_2.CHP


title: 5905-20d repeat 1

description:
3082_11726_A2_Drosophila_2.mas5.CHP
3082_11726_A2_Drosophila_2.CEL


title: 0110-20d repeat 4

description:
3082_11740_D4_Drosophila_2.mas5.CHP
3082_11740_D4_Drosophila_2.CEL


title: 5905-3d repeat 2

description:
3082_11729_B1_Drosophila_2.mas5.CHP
3082_11729_B1_Drosophila_2.CEL


title: 0110-3d repeat 2

description:
3082_11731_B3_Drosophila_2.mas5.CHP
3082_11731_B3_Drosophila_2.CEL


title: 5905-20d repeat 2

description:
3082_11730_B2_Drosophila_2.mas5.CHP
3082_11730_B2_Drosophila_2.CEL


title: 3d replicate 2 (mRNA)

description:
HHMI (634) 3 days #2 Drosophila_2.CEL
HHMI (634) 3 days #2 Drosophila_2.CHP


title: Ctrl-rnai affy rep2

status: Public on Dec 22 2011

data_processing: Affymetrix Drosophila Genome 2 arrays were analyzed in R, version 2.11.1, using the packages affy (Gautier et al., 2004), version 1.26.1, and limma (Smyth et al., 2005), version 3.4.3. Normalization was done using rma. Annotation information for the probes was taken from Ensembl 62.

label_protocol: Biotin labeling was done starting with 1 ug of total RNA using Ambion's MessageAmp II-Biotin Enhanced Kit (cat#1791).

growth_protocol: S2 cells were grown in Schneider's media with 10% FBS at room temperature.

extract_protocol: Two micrograms of DNase-treated total RNA was depleted of Ribosomal RNA with the Ribo-Zero kit from Epicentre (catalog #RZH1046), followed by use of the TruSeq RNA Sample Prep Kit (catalog #FC-122-1001) following manufacturer instructions.

treatment_protocol: Drosophila RNAi was performed by feeding S2 cells with dsRNA prepared with the Megascript T7 dsRNA synthesis kit from Ambion (catalog #1626.) Cells at a density of 2e6 cells/ml were serum starved treated with 10 µg of dsRNA. Additional boosts of 10 µg dsRNA were added at 48 and 96 hours. Cells were harvested at 120 hours. RNAi was performed with the ELL-A dsRNA. A region of the B-lactamase gene was used as a nontargeting control.

tag: knockdown

value: control

tag: cell line


title: 30d replicate 2 (mRNA)

description:
HHMI (637) 30 days #2 Drosophila_2.CEL
HHMI (637) 30 days #2 Drosophila_2.CHP


title: 30d replicate 3 (mRNA)

description:
HHMI (638) 30 days #3 Drosophila_2.CEL
HHMI (638) 30 days #3 Drosophila_2.CHP


title: 3d replicate 1 (mRNA)

description:
HHMI (633) 3 days #1 Drosophila_2.CEL
HHMI (633) 3 days #1 Drosophila_2.CHP


title: ELL-rnai affy rep1

value: ELL


title: trh sorted 3

status: Public on Dec 21 2011

description:
trh mutant embryos st. 11-16 isolated based on lack of GFP balancer expression, sorted using a COPAS biosorter
trh3-DG2_(Drosophila_2).CEL

hyb_protocol: Samples and controls were prepared using the Affymetrix GeneChip hybridization, wash and stain kit (P/N 900720).  Arrays were prehybridized for 10 minutes prior to sample addition.  Following sample addition, arrays were hybridized for 16 hours at 45 Celsius, and shaken at 60 rpm.  Arrays were stained and washed using the Affymetrix GeneChip Fluidics Station 450 and FS450_002 fluidics script.

data_processing: Data was normalized by RMA and statistical analysis was performed using Partek software.  Further analysis was performed using Spotfire software.

source_name: St 11-16 embryos

label_protocol: Amplification and labeling were performed using the Affymetrix GeneChip 3' IVT Express kit (P/N 901229) following the manufacturer's protocol.

growth_protocol: Embryos were collected for eight hours and aged an additional 11 hours by the time of RNA extraction.

tag: genotype/variation

value: trh null mutant

value: embryo (stage 11-16)


title: S2 cells dKDM2 RNAi, biological rep2

status: Public on Dec 13 2011

city: Rotterdam

first: Yuri

last: Moshkin

address: Dr. Molewaterplein 50

country: Netherlands

institute: Erasmus University Medical Center

description: S2 dKDM2 KD #2

hyb_protocol: Hybridization was performed by the microarray core facility of the Erasmus MC Center for Biomics according to Affymetrix specifications (Expression Analysis Technical Manual, 2001, Affymetrix).

scan_protocol: Scanning was performed by the microarray core facility of the Erasmus MC Center for Biomics.

data_processing: Statistical analysis of the microarray data was performed using the R and Bioconductor free software (http://www.bioconductor.org). Gene expression values were calculated using the robust multichip average (gcRMA) algorithm implemented in gcrma package.

source_name: S2 cells_dKDM2 RNAi

label_protocol: One cycle labeling was performed according to the standard  Affymetrix protocol from 7 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Drosophila S2 cells were cultured in Schneider's media (Invitrogen 21720-024) supplied with 10% FBS and Penicillin/Streptomycin mixture at 25°C

extract_protocol: RNA was extracted using the SV Total RNA Isolation System (Promega) and tested on an Agilent BioAnalyzer (Agilent). Samples with RNA integrity numbers of >8 were selected.

treatment_protocol: Drosophila S2 cells were treated with double-stranded RNA (dsRNA) for 4 days as described (Worby, C. A., N. Simonson-Leff, and J. E. Dixon. 2001. RNA interference of gene expression (RNAi) in cultured Drosophila cells. Sci. STKE 2001:PL1). Double-stranded RNA was synthesized using an Ambion Megascript T7 kit according to the manufacturer's protocol.

value: Drosophila S2

value: RNAi depleted (KD) for dKDM2


title: S2 cells PC RNAi, biological rep3

description: S2 PC KD #3

source_name: S2 cells_PC RNAi

value: RNAi depleted (KD) for PC


title: Wild type 1

description:
Wild type embryos st. 11-17 isolated following passage through a COPAS biosorter
WT1-DG2_(Drosophila_2).CEL

value: wild type


title: Wild type 3

description:
Wild type embryos st. 11-17 isolated following passage through a COPAS biosorter
WT3-DG2_(Drosophila_2).CEL


title: S2 cells PC RNAi, biological rep2

description: S2 PC KD #2


title: trh sorted 1

description:
trh mutant embryos st. 11-16 isolated based on lack of GFP balancer expression, sorted using a COPAS biosorter
trh1-DG2_(Drosophila_2).CEL


title: S2 cells dRING RNAi, biological rep2

description: S2 dRING KD #2

source_name: S2 cells_dRING RNAi

value: RNAi depleted (KD) for dRING


title: S2 cells PH RNAi, biological rep2

description: S2 PH KD #2

source_name: S2 cells_PH RNAi

value: RNAi depleted (KD) for PH


title: trh sorted 2

description:
trh mutant embryos st. 11-16 isolated based on lack of GFP balancer expression, sorted using a COPAS biosorter
trh2-DG2_(Drosophila_2).CEL


title: S2 cells PH RNAi, biological rep1

description: S2 PH KD #1


title: S2 cells PH RNAi, biological rep3

description: S2 PH KD #3


title: Control discs, biological rep2

status: Public on Dec 20 2011

city: Los Angeles

first: Shubha

last: Gururaja Rao

address: 5032 Terasaki Life Sciences Building, 621 Charles E. Young Drive South

department: MCDB

institute: UCLA

description: Gene expression data from GMR Gal4 pupae

hyb_protocol: Following fragmentation, 11 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 Affymetrix 3G scanner

data_processing: The data were analyzed with Expression console using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Drosophila pupal eye discs of GMR Gal4 genotype

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The genotypes were grown at 29 deg C until about 40 hrs after pupariation

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Qiagen RNAeasy kit)

treatment_protocol: The pupae were dissected in PBS

value: Pupal Eye Discs

tag: genotype

value: GMR Gal4

tag: age

value: 40 hrs after pupariation


title: S2 cells PSC RNAi, biological rep3

description: S2 PSC KD #3

source_name: S2 cells_PSC RNAi

value: RNAi depleted (KD) for PSC


title: Control discs, biological rep1


title: S2 cells dRING RNAi, biological rep3

description: S2 dRING KD #3


title: S2 cells dKDM2 RNAi, biological rep3

description: S2 dKDM2 KD #3


title: S2 cells PSC RNAi, biological rep1

description: S2 PSC KD #1


title: S2 cells dRING RNAi, biological rep1

description: S2 dRING KD #1


title: Yorkie overexpressing discs, biological rep1

description: Gene expression data from GMR Gal4, UAS Yki pupal eye discs

source_name: Drosophila pupal eye discs of GMR Gal4, UAS Yki genotype

value: GMR Gal4 crossed to UAS Yki


title: S2 cells PC RNAi, biological rep1

description: S2 PC KD #1


title: ELL-rnai affy rep2


title: S2 cells PSC RNAi, biological rep2

description: S2 PSC KD #2


title: S2 cells, biological rep14

description: S2 Mock #14

source_name: untreated S2 cells_Mock

value: untreated S2 cells (Mock)


title: S2 cells, biological rep13

description: S2 Mock #13


title: Yorkie overexpressing discs, biological rep2


title: S2 cells, biological rep12

description: S2 Mock #12


title: S2 cells dKDM2 RNAi, biological rep1

description: S2 dKDM2 KD #1


title: S2 cells, biological rep11

description: S2 Mock #11


title: S2 cells, biological rep8

description: S2 Mock #8


title: S2 cells, biological rep9

description: S2 Mock #9


title: S2 cells, biological rep6

description: S2 Mock #6


title: S2 cells, biological rep2

description: S2 Mock #2


title: S2 cells, biological rep5

description: S2 Mock #5


title: S2 cells, biological rep10

description: S2 Mock #10


title: S2 cells, biological rep3

description: S2 Mock #3


title: S2 cells, biological rep7

description: S2 Mock #7


title: S2 cells, biological rep4

description: S2 Mock #4


title: S2 cells, biological rep1

description: S2 Mock #1


title: Wild type stage 13 rep C

status: Public on Dec 10 2011

city: Chapel Hill

first: Jason

last: Reed

address: CB #3280, Coker Hall

department: Biology

institute: University of North Carolina at Chapel Hill

description: Wild type stage 13 rep C

hyb_protocol: Fragmented aRNA (15 µg) was then added to a hybridization cocktail (0.05 µg/µl fragmented aRNA, 50 pM control oligonucleotide B2, BioB, BioC, BioD and cre hybridization controls, 0.1 mg/ml herring sperm DNA, 0.5 mg/ml acetylated BSA, 100 mM MES, 1 M [Na+], 20 mM EDTA, 0.01% Tween 20).  aRNA (10 µg) was used for hybridization in a volume of 200 µl per slide.  ATH1 arrays (Redman et al., 2004)(Affymetrix, Santa Clara, CA) were hybridized for 16 hours at 45°C in the GeneChip Hybridization Oven 640 (Affymetrix).

scan_protocol: The arrays were washed and stained with R-phycoerythrin streptavidin in the GeneChip Fluidics Station 450 (Affymetrix) using wash protocol EukGE-WS2v4, and arrays were scanned with the GeneChip Scanner 3000 7G Plus with autoloader.

data_processing: Affymetrix MAS 5.0 GeneChip Operating Software was used for washing, scanning and basic analysis.  Data were analyzed using Genespring GX 10.0.1 software.  Raw data were background corrected and normalized using the RMA algorithm with no baseline correction.

source_name: Wild type, stage 13 open flowers

label_protocol: Total RNA (1000ng) was used to synthesize cDNA followed by aRNA.  The MessageAmp™ II-Biotin Enhanced Kit (Ambion) was used to generate biotinylated aRNA from the cDNA reaction.  The aRNA was then fragmented in fragmentation buffer from the Ambion kit at 94°C for 35 minutes before the chip hybridization.

growth_protocol: Wild-type plants were grown in 16 hour days/8 hour nights in a controlled environment growth chamber.  Light intensity was approximately 100 micromoles/m2sec.  Flowers were harvested in the morning between 2 and 4 hours after subjective dawn and frozen directly in liquid nitrogen.

extract_protocol: Frozen tissue was ground in a mortar and pestle.  RNA was isolated with Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA) or with RNeasy plant mini kits (Qiagen) according to manufacturer's instructions.

tag: ecotype

value: columbia

value: Wild type

tag: flower stage


title: arf6 arf8 stage 12 rep C

description: arf6 arf8 stage 12 rep C

source_name: arf6 arf8, stage 12 buds

value: arf6-2 arf8-3


title: myb21 myb24 stage 13 rep B

description: myb21 myb24 stage 13 rep B

source_name: myb21 myb24, stage 13 flowers


title: arf6 arf8 stage 13 rep A

description: arf6 arf8 stage 13 rep A

source_name: arf6 arf8, stage 13 flowers


title: Wild type stage 12 rep B

description: Wild type stage 12 rep B

source_name: Wild type, stage 12 buds


title: myb21 myb24 stage 13 rep A

description: myb21 myb24 stage 13 rep A


title: Wild type stage 12 rep C

description: Wild type stage 12 rep C


title: arf6 arf8 stage 12 rep A

description: arf6 arf8 stage 12 rep A


title: myb21 myb24 stage 12 rep A

description: myb21 myb24 stage 12 rep A

source_name: myb21 myb24, stage 12 buds


title: Wild type stage 13 rep A

description: Wild type stage 13 rep A


title: myb21 myb24 stage 13 rep C

description: myb21 myb24 stage 13 rep C


title: arf6 arf8 stage 13 rep C

description: arf6 arf8 stage 13 rep C


title: Wild type stage 12 rep A

description: Wild type stage 12 rep A


title: 35S:LOB-GR, dexamethasone treated, biological rep 1

status: Public on Dec 07 2011

city: Riverside

first: Patricia

last: Springer

address: 900 University Ave

department: Botany and Plant Sciences

institute: University of California

hyb_protocol: Standard Affymetrix protocol.

data_processing: R/Bioconductor, RMA normalization.

source_name: Arabidopsis seedlings, 9-d-o, 35S:LOB-GR, DEX

label_protocol: Standard Affymetrix protocol.

growth_protocol: Nine-day-old seedlings, grown on MS plates.

extract_protocol: Total RNA was isolated using TRIzol, followed by purification over RNeasy columns (Qiagen).

treatment_protocol: Seedlings were flooded with MS medium with or without 5µM DEX and incubated, with shaking, for 4 hours.

tag: cultivar/background

value: seedling

value: 9 days

tag: treatment

value: dexamethasone


title: 35S:LOB-GR, mock treated, biological rep 3

source_name: Arabidopsis seedlings, 9-d-o, 35S:LOB-GR, mock

value: mock


title: Columbia, dexamethasone treated, biological rep 1

source_name: Arabidopsis seedlings, 9-d-o, WT, DEX

value: wild-type


title: 35S:LOB-GR, dexamethasone treated, biological rep 2


title: Columbia, mock treated, biological rep 1

source_name: Arabidopsis seedlings, 9-d-o, WT, mock


title: Columbia, mock treated, biological rep 3


title: 35S:LOB-GR, mock treated, biological rep 2


title: Columbia, dexamethasone treated, biological rep 2


title: Columbia, mock treated, biological rep 2


title: myb21 myb24 stage 12 rep C

description: myb21 myb24 stage 12 rep C


title: Columbia, dexamethasone treated, biological rep 3


title: 35S:LOB-GR, dexamethasone treated, biological rep 3


title: 35S:LOB-GR, mock treated, biological rep 1


title: MPK6 Over Expression Shoot Hypoxia Biological Rep 2

status: Public on Dec 03 2011

first: Charles

last: Jang

address: 2215 Batchelor Hall

institute: UC Riverside

hyb_protocol: cRNA were hybridized onto ATH1 genechip according to the GeneChip Expression Analysis Technical Manual R.5 (affymetrix)

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Workstation

data_processing: The data were analyzed with the Bioconductor package in R using RMA.

source_name: 10 do MPK6 Over Expression Arabidopsis Shoot 9 h Hypoxia

label_protocol: Biotinylated cRNA were prepared according to the 2-cycle synthesis and labeling kit (Affymetrix)

growth_protocol: Col-0 seedling were grown on 0.5x MS, 1% sucrose, 0.4% phytagel plates grown vertically for 10 days under long day conditions (16 hr light 8 hr darkness)

extract_protocol: Seedlings were disected into root and shoot tissue and frozen in liquid nitrogen.  RNA were extracted using RNeasy plant mini kit (Quiagen).

treatment_protocol: Seedlings were placed into an airtight lucite chamber flooded with 99.998% argon for 2 hrs for hypoxia treatment.  Normoxic treatment required placing seedlings into an open lucite box for 2 hrs (mock).

value: T-DNA insertion 35s::MPK6 Overexpression

value: Shoot

tag: oxygen treatment

value: Hypoxia


title: MPK6 Over Expression Shoot Hypoxia Biological Rep 1


title: MPK6 Over Expression Root Hypoxia Biological Rep 1

source_name: 10 do MPK6 Over Expression Arabidopsis Root 9 h Hypoxia

value: Root


title: mpk6 T-DNA insertion Knockout Shoot Hypoxia Biological Rep 2

source_name: 10 do mpk6 T-DNA insertion Knockout Arabidopsis Shoot 9 h Hypoxia

value: T-DNA insertion mpk6 knockout


title: mpk6 T-DNA insertion Knockout Shoot Normoxia (mock) Biological Rep 2

source_name: 10 do mpk6 T-DNA insertion Knockout Arabidopsis Shoot Normoxia (mock)

value: Normoxia (mock)


title: Wild type 2

description:
Wild type embryos st. 11-17 isolated following passage through a COPAS biosorter
WT2-DG2_(Drosophila_2).CEL

source_name: St 11-16 embryos

value: wild type

tag: developmental stage

value: embryo (stage 11-16)


title: MPK6 Over Expression Root Normoxia (mock) Biological Rep 2

source_name: 10 do MPK6 Over Expression Arabidopsis Root Normoxia (mock)


title: MPK6 Over Expression Root Hypoxia Biological Rep 2


title: MPK6 Over Expression Root Hypoxia Biological Rep 3


title: mpk6 T-DNA insertion Knockout Shoot Normoxia (mock) Biological Rep 1


title: MPK6 Over Expression Root Normoxia (mock) Biological Rep 1


title: MPK6 Over Expression Shoot Normoxia (mock) Biological Rep 2

source_name: 10 do MPK6 Over Expression Arabidopsis Shoot Normoxia (mock)


title: mpk6 T-DNA insertion Knockout Root Hypoxia Biological Rep 2

source_name: 10 do mpk6 T-DNA insertion Knockout Arabidopsis Root 9 h Hypoxia


title: MPK6 Over Expression Shoot Normoxia (mock) Biological Rep 1


title: mpk6 T-DNA insertion Knockout Root Hypoxia Biological Rep 1


title: mpk6 T-DNA insertion Knockout Shoot Hypoxia Biological Rep 1


title: Ctrl-rnai affy rep1

first: Alexander

last: Garruss

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 hr at 45C on Affymetrix Drosophila Genome 2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned with GeneChip 3000.

value: control


title: Wild Type Shoot Hypoxia Biological Rep 1

source_name: 10 do Wild Type Arabidopsis Shoot 9 h Hypoxia

value: Wild Type Col-0


title: Wild Type Shoot Hypoxia Biological Rep 2


title: mpk6 T-DNA insertion Knockout Root Normoxia (mock) Biological Rep 1

source_name: 10 do mpk6 T-DNA insertion Knockout Arabidopsis Root Normoxia (mock)


title: mpk6 T-DNA insertion Knockout Root Normoxia (mock) Biological Rep 2


title: Wild Type Root Hypoxia Biological Rep 2

source_name: 10 do Wild Type Arabidopsis Root 9 h Hypoxia


title: Wild Type Root Hypoxia Biological Rep 1


title: Wild Type Shoot Normoxia (mock) Biological Rep 2

source_name: 10 do Wild Type Arabidopsis Shoot Normoxia (mock)


title: Wild Type Shoot Normoxia (mock) Biological Rep 1


title: Wild Type Root Normoxia (mock) Biological Rep 2

source_name: 10 do Wild Type Arabidopsis Root Normoxia (mock)


title: ABA SA 3h-1

status: Public on Dec 01 2011

city: Kurashiki

first: Takashi

last: Hirayama

state: Okayama

department: Institute of Plant Science and Resources

institute: Okayama University

hyb_protocol: 30 ug cRNA was hybridized to ATH1 GeneChip arrays.

scan_protocol: Arrays were scanned using a GSC3000 scanner according to the manufacturer's recommendations.

data_processing: RMA normalized using Cel file with affllmGUI.

source_name: T87 cultured cell, ABA+JA, 3hr

label_protocol: First-strand of cDNA was synthesized using 16 ug of total RNA and SuperScript Double-stranded cDNA Synthesis kit (Invitrogen). The labeled cRNA was synthesized using BioArray RNA Transcripts Labeling Kit (T7) (ENZO Life Sciences inc.). After labeling, the cRNA was digested partially by incubating in 40 mM Tris-acetate, pH8.0, 100 mM KOAc, 30 mM MgOAc, at 94C for 35 min.

growth_protocol: The cells were incubated and subcultured every seven days in 20 mL of a liquid modified JPL medium (Axelos et al., 1992) in a 100 mL baffled Erlenmeyer flask at 100 rpm on a rotary shake at 24C at a 16 h light and 8 h dark cycle.

extract_protocol: Total RNA was extracted from frozen tissue using TRIzol reagent (Invitrogen) and purified using a RNase MinElute Cleanup Kit (Qiagen).

treatment_protocol: Growing T87 cells were exposed to 25uM ABA and 100 uM MeJA for 3hr.

value: ABA+JA

tag: treatment duration


title: JA 3h-1

source_name: T87 cultured cell, JA, 3hr

treatment_protocol: Growing T87 cells were exposed to 100 uM MeJA for 3hr.

value: JA


title: ABA SA 3h-2


title: ABA JA 24h-1

source_name: T87 cultured cell, ABA+JA, 24hr

treatment_protocol: Growing T87 cells were exposed to 25uM ABA and 100 uM MeJA for 24hr.


title: Wild Type Root Normoxia (mock) Biological Rep 1


title: ABA SA 24h-1

source_name: T87 cultured cell, ABA+SA, 24hr

treatment_protocol: Growing T87 cells were exposed to 25uM ABA and 300 uM SA for 24hr.

value: ABA+SA


title: JA 24h-1

source_name: T87 cultured cell, JA, 24hr

treatment_protocol: Growing T87 cells were exposed to 100 uM MeJA for 24hr.


title: SA 3h-1

source_name: T87 cultured cell, SA, 3hr

treatment_protocol: Growing T87 cells were exposed to 300 uM SA for 3hr.

value: SA


title: SA 24h-1

source_name: T87 cultured cell, SA, 24hr

treatment_protocol: Growing T87 cells were exposed to 300 uM SA for 24hr.


title: ABA 3h-3

source_name: T87 cultured cell, ABA, 3hr

treatment_protocol: Growing T87 cells were exposed to 25 uM ABA for 3hr.

value: ABA


title: ABA SA 24h-2


title: SA 3h-2


title: EtOH 24h-1

source_name: T87 cultured cell, control, 24hr

treatment_protocol: Growing T87 cells were exposed to 0.6% EtOH.

value: control (EtOH)


title: ABA 3h-2


title: ABA JA 24h-2


title: JA 3h-2


title: JA 24h-2


title: SA 24h-2


title: ABA JA 3h-1

source_name: T87 cultured cell, ABA+SA, 3hr

treatment_protocol: Growing T87 cells were exposed to 25uM ABA and 300 uM SA for 3hr.


title: ABA 24h-2

source_name: T87 cultured cell, ABA, 24hr

treatment_protocol: Growing T87 cells were exposed to 25 uM ABA for 24hr.


title: ABA 24h-3


title: EtOH 3h-2

source_name: T87 cultured cell, control, 3hr


title: ABA 24h-1


title: EtOH 24h-2


title: Split KCl roots - 2days - repeat 3

city: NYC

first: Sandrine

last: Ruffel

state: NY

address: 100 Washington Square East. 1009 Main Building

institute: New York University

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Heat cocktails at 99° for 5 minutes, then 42° for 10 minutes centrifuge at max speed for 1 minute. Transfer 200μl of hyb solution to each array. Hybridize 16 hours at 45° at 60rpm. Fluidics washing is EukGE-WS2v4_450.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using MAS5.0v

source_name: Split KCl roots - 2days - repeat 3

label_protocol: Samples were enzymatically fragmented and biotinylated using the IVT - labeling kit (Affymetrix)

growth_protocol: Plants are grown on a custom-made basal Murashige and Skoog solid medium (no nitrogen, no sucrose), supplemented with 0.5 mM NH4-succinate, 0.1mM KNO3 and 3mM sucrose. After 8-10 days, the primary root was cut below the first two lateral roots and roots still grown on these plates for 4 more days. Then, each plant with two main roots was transferred on individual 10x10 cm plates containing the same 40 ml solid medium supplemented with 0.5mM NH4+-succinate as the nitrogen source. The solid medium was divided in two compartments by a trench to allow the physical separation of the two roots.

extract_protocol: RNA extractions were carried out on roots collected at 2 hours, 8 hours and 2 days after the beginning of the split-root treatment with TRIzol (Invitrogen)

treatment_protocol: We selected the 12-14 days old plants with balanced roots on both sides and they were transferred on 12x12cm segmented agar plates containing either 5mM KNO3 or 5mM KCl on both sides for the controls or 5mM KNO3 on one side and 5mM KCl on the other side for the split. These plates contained 60 ml of solid basal MS medium supplemented with 0.3mM sucrose. The KNO3 or KCl compartments were obtained by spreading concentrated KNO3 and KCl solution on the solid medium 24 hr before the experiments to allow diffusion of the solutions

value: roots

value: Columbia

value: 5mM KCl on both sides for 2 days


title: EtOH 3h-1


title: Split KCl roots - 2days - repeat 1

source_name: Split KCl roots - 2days - repeat 1


title: Split KCl roots - 2days - repeat 2

source_name: Split KCl roots - 2days - repeat 2


title: Split KNO3 roots - 2days - repeat 2

source_name: Split KNO3 roots - 2days - repeat 2

value: 5mM KNO3 on ONE side for 2 days


title: Split KCl roots - 8hours - repeat 2

source_name: Split KCl roots - 8hours - repeat 2

value: 5mM KCl on both sides for 8 hours


title: Split KNO3 roots - 8hours - repeat 2

source_name: Split KNO3 roots - 8hours - repeat 2

value: 5mM KNO3 on ONE side for 8 hours


title: Split KNO3 roots - 8hours - repeat 1

source_name: Split KNO3 roots - 8hours - repeat 1


title: Split KNO3 roots - 2days - repeat 1

source_name: Split KNO3 roots - 2days - repeat 1


title: Split KCl roots - 2hours - repeat 1

source_name: Split KCl roots - 2hours - repeat 1

value: 5mM KCl on both sides for 2 hours


title: Control KCl roots - 2days - repeat 1

source_name: Control KCl roots - 2days - repeat 1

value: 5mM KCl on ONE side for 2 days


title: Control KNO3 roots - 2days - repeat 1

source_name: Control KNO3 roots - 2days - repeat 1

value: 5mM KNO3 on both sides for 2 days


title: Control KNO3 roots - 8hours - repeat 1

source_name: Control KNO3 roots - 8hours - repeat 1

value: 5mM KNO3 on both sides for 8 hours


title: Control KCl roots - 2days - repeat 2

source_name: Control KCl roots - 2days - repeat 2


title: Split KCl roots - 8hours - repeat 1

source_name: Split KCl roots - 8hours - repeat 1


title: Split KNO3 roots - 2hours - repeat 1

source_name: Split KNO3 roots - 2hours - repeat 1

value: 5mM KNO3 on ONE side for 2 hours


title: Split KCl roots - 8hours - repeat 3

source_name: Split KCl roots - 8hours - repeat 3


title: Split KNO3 roots - 8hours - repeat 3

source_name: Split KNO3 roots - 8hours - repeat 3


title: Split KNO3 roots - 2days - repeat 3

source_name: Split KNO3 roots - 2days - repeat 3


title: Split KCl roots - 2hours - repeat 3

source_name: Split KCl roots - 2hours - repeat 3


title: Split KNO3 roots - 2hours - repeat 2

source_name: Split KNO3 roots - 2hours - repeat 2


title: Control KNO3 roots - 2days - repeat 3

source_name: Control KNO3 roots - 2days - repeat 3


title: Control KCl roots - 2days - repeat 3

source_name: Control KCl roots - 2days - repeat 3


title: Control KCl roots - 8hours - repeat 3

source_name: Control KCl roots - 8hours - repeat 3

value: 5mM KCl on ONE side for 8 hours


title: Control KNO3 roots - 2days - repeat 2

source_name: Control KNO3 roots - 2days - repeat 2


title: Split KNO3 roots - 2hours - repeat 3

source_name: Split KNO3 roots - 2hours - repeat 3


title: Control KNO3 roots - 8hours - repeat 3

source_name: Control KNO3 roots - 8hours - repeat 3


title: Control KCl roots - 8hours - repeat 1

source_name: Control KCl roots - 8hours - repeat 1


title: Control KCl roots - 2hours - repeat 3

source_name: Control KCl roots - 2hours - repeat 3

value: 5mM KCl on ONE side for 2 hours


title: Control KCl roots - 2hours - repeat 1

source_name: Control KCl roots - 2hours - repeat 1


title: Control KNO3 roots - 8hours - repeat 2

source_name: Control KNO3 roots - 8hours - repeat 2


title: Control KCl roots - 8hours - repeat 2

source_name: Control KCl roots - 8hours - repeat 2


title: Control KCl roots - 2hours - repeat 2

source_name: Control KCl roots - 2hours - repeat 2


title: Control KNO3 roots - 2hours - repeat 3

source_name: Control KNO3 roots - 2hours - repeat 3

value: 5mM KNO3 on both sides for 2 hours


title: Control KNO3 roots - 2hours - repeat 2

source_name: Control KNO3 roots - 2hours - repeat 2


title: wandering L3 control reared biological rep 1

status: Public on Nov 30 2011

city: St. Louis

first: Jennifer

middle: G

last: Duncan

address: 660 S. Euclid, Box 8208

department: Pediatrics

institute: Washington University School of Medicine

description: Gene expression data from wandering L3 larvae, after feeding has ceased but before pupariation.

hyb_protocol: 15 ug of biotinylated cRNAs were hybridized to Affymetrix Drosophila 2.0 oligonucleotide arrays.

scan_protocol: Gene chips were scanned using the GeneChip GS3000.

data_processing: The data were analyzed with dChip (2006 version) and precise match/mismatch probe intensity was used as normalization method.

source_name: whole male w1118 Drosophila mid third instar larvae

label_protocol: Biotinylated cRNA were prepared according tot the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: w1118 were reared at 25C on Bloomington Semi-Defined Food with sucrose substituted for sucrose (0.15M).

extract_protocol: Tripure extraction of total RNA was performed according to the manufacturer's instructions; RNA was DNase-treated and then cleaned on a Qiagen RNeasy column and eluted in RNase-free H2O.

treatment_protocol: Maternal flies were fed either 0.15M (control) or high sucrose Semi-Defined food within 24 hours of eclosion for 7 days, then mated with male flies on control food.

value: whole larva

value: mid third instar larvae

tag: strain

tag: gender

value: male

value: maternal control diet


title: wandering L3 high sugar reared biological rep 1

value: maternal high sucrose diet


title: wandering L3 control reared biological rep 2


title: wandering L3 high sugar reared biological rep 2


title: wandering L3 control reared biological rep 3


title: 4-day-old Arabidopsis plants (Col-0) treated with 200 uM As, biological rep1

status: Public on Nov 26 2011

city: Changhua

first: Shih-Feng

last: Fu

state: Changhua

address: No.1 Jin-De Road

country: Taiwan

institute: National Changhua University of Education

description: Gene expression data from 4-day-old Arabidopsis plants (Col-0) treated with 200 uM As, biological rep 1

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 100.

source_name: 4-day-old seedlings in quarter-strength MS

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).

extract_protocol: Total RNA were extracted using QIAGEN RNeasy kit follwed by DNAse treatment. The RNA samples were further purified and concentrated by RNeasy MinElute Cleanup.

treatment_protocol: Either with or without As (V) treatment (100 and 200 uM) for 1.5 and 3 hr

value: Roots

value: 4-day-old seedlings

value: treated with 200 uM As


title: 4-day-old Arabidopsis plants (Col-0) treated with 100 uM As, biological rep3

description: Gene expression data from 4-day-old Arabidopsis plants (Col-0) treated with 100 uM As, biological rep 3

growth_protocol: 4-day-old seedlings in quarter-strength MS

value: treated with 100 uM As


title: wandering L3 high sugar reared biological rep 3


title: 4-day-old Arabidopsis plants (Ws-2) treated with 0 uM As, biological rep3

description: Gene expression data from 4-day-old Arabidopsis plants (Ws-2) treated with 0 uM As, biological rep 3

value: treated with 0 uM As


title: 4-day-old Arabidopsis plants (Ws-2) treated with 100 uM As, biological rep2

description: Gene expression data from 4-day-old Arabidopsis plants (Ws-2) treated with 100 uM As, biological rep 2


title: 4-day-old Arabidopsis plants (Ws-2) treated with 100 uM As, biological rep1

description: Gene expression data from 4-day-old Arabidopsis plants (Ws-2) treated with 100 uM As, biological rep 1


title: 4-day-old Arabidopsis plants (Col-0) treated with 200 uM As, biological rep2

description: Gene expression data from 4-day-old Arabidopsis plants (Col-0) treated with 200 uM As, biological rep 2


title: 4-day-old Arabidopsis plants (Col-0) treated with 0 uM As, biological rep1

description: Gene expression data from 4-day-old Arabidopsis plants (Col-0) treated with 0 uM As, biological rep 1


title: 4-day-old Arabidopsis plants (Ws-2) treated with 0 uM As, biological rep1

description: Gene expression data from 4-day-old Arabidopsis plants (Ws-2) treated with 0 uM As, biological rep 1


title: 4-day-old Arabidopsis plants (Col-0) treated with 100 uM As, biological rep2

description: Gene expression data from 4-day-old Arabidopsis plants (Col-0) treated with 100 uM As, biological rep 2


title: 4-day-old Arabidopsis plants (Col-0) treated with 100 uM As, biological rep1

description: Gene expression data from 4-day-old Arabidopsis plants (Col-0) treated with 100 uM As, biological rep 1


title: 4-day-old Arabidopsis plants (Ws-2) treated with 100 uM As, biological rep3

description: Gene expression data from 4-day-old Arabidopsis plants (Ws-2) treated with 100 uM As, biological rep 3


title: 4-day-old Arabidopsis plants (Col-0) treated with 200 uM As, biological rep3

description: Gene expression data from 4-day-old Arabidopsis plants (Col-0) treated with 200 uM As, biological rep 3


title: 4-day-old Arabidopsis plants (Col-0) treated with 0 uM As, biological rep2

description: Gene expression data from 4-day-old Arabidopsis plants (Col-0) treated with 0 uM As, biological rep 2


title: 4-day-old Arabidopsis plants (Col-0) treated with 0 uM As, biological rep3

description: Gene expression data from 4-day-old Arabidopsis plants (Col-0) treated with 0 uM As, biological rep 3


title: Arabidopsis root cells, cortex, sulfur deficient media, replicate 3

status: Public on Nov 23 2011

city: Durham

first: Anjali

middle: S

last: Iyer-Pascuzzi

institute: Duke University

description: Expression analysis of cortex cells exposed to sulfur deficient media for 3H

hyb_protocol: hybs with fragmented cRNA were preformed by Expression Analysis (Durham, NC)

scan_protocol: scans were preformed by Expression Analysis (Durham, NC)

data_processing: CHP files contain MAS 5.0 probe set summarizations using Affymetrix default analysis settings and global scaling as normalization method. The mean target intensity of each array was set to 250.

source_name: Protoplasted and FACS sorted Arabidopsis root cells from the cortex

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle protocol from total RNA isolated from sorted cells

growth_protocol: Seedlings were grown for 5 days (described in Birnbaum et al. 2005) on 1X MS media before transfer to sulfur deficient media for 3 hours prior to protoplasting and FACS sorting

extract_protocol: Total RNA was extracted with Qiagen Rneasy micro kit according to manufacturer's instructions

treatment_protocol: Seeds were surface sterilized with 50% Bleach and 0.1% Tween for 5 minutes and then rinsed 3 times with sterile water. Seeds were stratified at 4˚C for 2 days before being planted on media standard media. At 5 days, seedlings were transferred to sulfur deficient media for 3 hours. Sulfur deficient media is composed of 20.6 mM NH4NO3, 18.8 mM KNO3, 1.25 mM KPO4H2, 5 μM KI, 2.99 mM CaCl2, 0.1 mM H3BO3, 1 μM Na2MoO42H2O, 0.1 μM CoCl26H2O, 0.1 mM Na2EDTA2H20, 1.5 mM MgCl2, 0.1 μM CuCl2, 0.1mM FeCl2, 0.1 mM MnCl2, 0.03 mM ZnCl2, 0.05% MES, 1% sucrose, 1% agar.

value: Columbia

tag: marker line

tag: cell type

value: cortex


title: Arabidopsis root cells, stele, sulfur deficient media, replicate 3

description: Expression analysis of stele cells exposed to sulfur deficient media for 3H

source_name: Protoplasted and FACS sorted Arabidopsis root cells from the stele

value: stele


title: Arabidopsis root cells, stele, sulfur deficient media, replicate 1


title: Arabidopsis root cells, endodermis, sulfur deficient media, replicate 1

description: Expression analysis of endodermal cells exposed to sulfur deficient media for 3H

source_name: Protoplasted and FACS sorted Arabidopsis root cells from the endodermis and quiescent center

value: endodermis and quiescent center


title: Arabidopsis root cells, endodermis, sulfur deficient media, replicate 2


title: Arabidopsis root cells, stele, sulfur deficient media, replicate 2


title: Arabidopsis root cells, cortex, sulfur deficient media, replicate 1


title: 4-day-old Arabidopsis plants (Ws-2) treated with 0 uM As, biological rep2

description: Gene expression data from 4-day-old Arabidopsis plants (Ws-2) treated with 0 uM As, biological rep 2

tag: tissue


title: Arabidopsis root cells, endodermis, sulfur deficient media, replicate 3


title: Arabidopsis root cells, cortex, sulfur deficient media, replicate 2


title: Arabidopsis root cells, epidermis and lateral root cap, sulfur deficient media, replicate 1

description: Expression analysis of epidermal and lateral root cap cells exposed to sulfur deficient media for 3H

source_name: Protoplasted and FACS sorted Arabidopsis root cells from the epidermis and lateral root cap

value: epidermis and lateral root cap


title: Arabidopsis root cells, epidermis and lateral root cap, sulfur deficient media, replicate 2


title: Arabidopsis root cells, columella root cap, sulfur deficient media, replicate 3

description: Expression analysis of columella cells exposed to sulfur deficient media for 3H

source_name: Protoplasted and FACS sorted Arabidopsis root cells from the columella root cap

value: columella root cap


title: Arabidopsis root cells, epidermis and lateral root cap, sulfur deficient media, replicate 3


title: Whole root - S_12H_rep2

description: Expression analysis of roots transferred to sulfur deficient media for 12H

source_name: whole roots transferred to sulfur deficient media, 12H

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

growth_protocol: Seedlings were grown for 5 days on standard MS media before transfer either to standard (0H) or sulfur deficient media for the indicated time

extract_protocol: Total RNA was extracted with Qiagen Rneasy Plant mini kit according to manufacturer's instructions

treatment_protocol: Seeds were surface sterilized with 50% Bleach and 0.1% Tween for 5 minutes and then rinsed 3 times with sterile water. Seeds were stratified at 4˚C for 2 days before being planted on media standard media. At 5 days, seedlings were transferred to fresh standard (0H) or sulfur deficient media for the indicated time. Sulfur deficient media is composed of 20.6 mM NH4NO3, 18.8 mM KNO3, 1.25 mM KPO4H2, 5 μM KI, 2.99 mM CaCl2, 0.1 mM H3BO3, 1 μM Na2MoO42H2O, 0.1 μM CoCl26H2O, 0.1 mM Na2EDTA2H20, 1.5 mM MgCl2, 0.1 μM CuCl2, 0.1mM FeCl2, 0.1 mM MnCl2, 0.03 mM ZnCl2, 0.05% MES, 1% sucrose, 1% agar.

value: whole roots

tag: teatment

value: sulfur deficient media for 12 hr


title: Whole root - S_24H_rep2

description: Expression analysis of roots transferred to sulfur deficient media for 24H

source_name: whole roots transferred to sulfur deficient media, 24H

value: sulfur deficient media for 24 hr


title: Whole root - low pH 6H_rep2

description: Expression profile of whole root exposed to pH 4.6 for 6H

source_name: whole roots transferred to low pH, 6H

growth_protocol: Seedlings were grown for 5 days on standard (pH 5.7) media before transfer either to standard or low pH (pH 4.6) media for the indicated time

treatment_protocol: Seeds were surface sterilized with 50% Bleach and 0.1% Tween for 5 minutes and then rinsed 3 times with sterile water. Seeds were stratified at 4˚C for 2 days before being planted on media containing 1X concentration Murashige and Skoog salt mixture (Caisson laboratories), 0.5g/L MES, 1% sucrose, 1% agar and adjusted to pH 5.7 with KOH. At 5 days, seedlings were transferred to standard pH (pH 5.7) or low pH (pH 4.6) media for the indicated time. Low pH media is 1X concentration Murashige and Skoog salt mixture (Caisson laboratories), 3mM DMG, 1% sucrose, 1% agar and adjusted to pH 4.6 with KOH. Standard pH is the same except pH is adjusted to 5.7.

value: whole root

value: pH 4.6 for 6 hr


title: Whole root - low pH 12H_rep2

description: Expression profile of whole root exposed to pH 4.6 for 12H

source_name: whole roots transferred to low pH, 12H

value: pH 4.6 for 12 hr


title: Whole root - S_12H_rep1


title: Whole root - S_3H_rep1

description: Expression analysis of roots transferred to sulfur deficient media for 3H

source_name: whole roots transferred to sulfur deficient media, 3H

value: sulfur deficient media for 3 hr


title: Whole root - low pH 48H_rep1

description: Expression profile of whole root exposed to pH 4.6 for 48H

source_name: whole roots transferred to low pH, 48H

value: pH 4.6 for 48 hr


title: Whole root - low pH 3H_rep2

description: Expression profile of whole root exposed to pH 4.6 for 3H

source_name: whole roots transferred to low pH, 3H

value: pH 4.6 for 3 hr


title: Arabidopsis root cells, columella root cap, sulfur deficient media, replicate 1


title: Arabidopsis root cells, columella root cap, sulfur deficient media, replicate 2


title: Whole root - S_0H_rep2

description: Expression analysis of roots transferred to fresh MS (i.e. 0H)

source_name: whole roots transferred to std media, 0H

value: MS for 0 hr


title: Whole root - low pH_24H_rep1

description: Expression profile of whole root exposed to pH 4.6 for 24H

source_name: whole roots transferred to low pH, 24H

value: pH 4.6 for 24 hr


title: Whole root - low pH 3H_rep1

value: Columbia


title: Whole root - low pH 48H_rep2


title: Whole root - S_48H_rep1

description: Expression analysis of roots transferred to sulfur deficient media for 48H

source_name: whole roots transferred to sulfur deficient media, 48H

value: sulfur deficient media for 48 hr


title: Whole root - S_24H_rep1


title: Whole root - low pH 6H_rep1


title: Whole root - low pH 12H_rep1


title: Whole root - S_3H_rep2


title: Whole root - S_48H_rep2


title: Whole root - low pH 1H_rep2

description: Expression profile of whole root exposed to pH 4.6 for 1H

source_name: whole roots transferred to low pH, 1H

value: pH 4.6 for 1 hr


title: Whole root - low pH_24H_rep2


title: Whole root - S_0H_rep1


title: Whole root - low pH 1H_rep1


title: Whole root - S_72H_rep1

description: Expression analysis of roots transferred to sulfur deficient media for 72H

source_name: whole roots transferred to sulfur deficient media, 72H

value: sulfur deficient media for 72 hr


title: Whole root - S_72H_rep2


title: Whole root - low pH 30min_rep2

description: Expression profile of whole root exposed to pH 4.6 for 30 min

source_name: whole roots transferred to low pH, 30min

value: pH 4.6 for 30 min


title: Whole root - Std pH 6H_rep2

description: Expression profile of whole root exposed to pH 5.7 for 6H

source_name: whole roots transferred to std pH, 6H

value: pH 5.7 for 6 hr


title: Arabidopsis root section, longitudinal zone 3, pH 5.7, replicate 2

description: Gene expression data from root developmental stage zone 3

source_name: root tissue

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

growth_protocol: Seedlings were grown for 5 days on standard (pH 5.7) media before transfer either to standard or low pH (pH 4.6) media for 24 hours prior to dissection

treatment_protocol: Seeds were surface sterilized with 50% Bleach and 0.1% Tween for 5 minutes and then rinsed 3 times with sterile water. Seeds were stratified at 4˚C for 2 days before being planted on media containing 1X concentration Murashige and Skoog salt mixture (Caisson laboratories), 0.5g/L MES, 1% sucrose, 1% agar and adjusted to pH 5.7 with KOH. At 5 days, seedlings were transferred to standard pH (pH 5.7) or low pH (pH 4.6) media for 24 hours prior to dissection. Low pH media is 1X concentration Murashige and Skoog salt mixture (Caisson laboratories), 3mM DMG, 1% sucrose, 1% agar and adjusted to pH 4.6 with KOH. Standard pH is the same except pH is adjusted to 5.7.

tag: longitudinal zone

value: 6 day old roots


title: Whole root - Std pH 3H_rep1

description: Expression profile of whole root exposed to pH 5.7 for 3H

source_name: whole roots transferred to std pH, 3H

value: pH 5.7 for 3 hr


title: Whole root - Std pH 1H_rep2

description: Expression profile of whole root exposed to pH 5.7 for 1H

source_name: whole roots transferred to std pH, 1H

value: pH 5.7 for 1 hr


title: Whole root - Std pH 6H_rep1

value: whole root


title: Whole root - Std pH 48H_rep2

description: Expression profile of whole root exposed to pH 5.7 for 48H

source_name: whole roots transferred to std pH, 48H

value: pH 5.7 for 48 hr


title: Arabidopsis root section, longitudinal zone 3, pH 4.6, replicate 2


title: Whole root - Std pH 24H_rep1

description: Expression profile of whole root exposed to pH 5.7 for 24H

source_name: whole roots transferred to std pH, 24H

value: pH 5.7 for 24 hr


title: Arabidopsis root section, longitudinal zone 4, pH 5.7, replicate 2

description: Gene expression data from root developmental stage zone 4


title: Arabidopsis root section, longitudinal zone 4, pH 5.7, replicate 1


title: Arabidopsis root section, longitudinal zone 3, pH 5.7, replicate 1


title: Whole root - Std pH 24H_rep2


title: Whole root - Std pH 30min_rep2

description: Expression profile of whole root exposed to pH 5.7 for 30 min

source_name: whole roots transferred to std pH, 30 min

value: pH 5.7 for 30 min


title: Whole root - Std pH 30min_rep1


title: Arabidopsis root section, longitudinal zone 2, pH 5.7, replicate 2

description: Gene expression data from root developmental stage zone 2


title: Whole root - Std pH 12H_rep2

description: Expression profile of whole root exposed to pH 5.7 for 12H

source_name: whole roots transferred to std pH, 12H

value: pH 5.7 for 12 hr


title: Arabidopsis root section, longitudinal zone 4, pH 4.6, replicate 2