title: Dhr96 over-expression (line 35), females, biological rep 2 (DS004009)

description:
Gene expression data from adults
DS004009

source_name: 0-3 day old adults cultured on diet made on 25/1/06

value: Females

value: experiment 2


title: Dhr96 knockdown (line 3), males, biological rep 2 (DS004016)

status: Public on Feb 17 2011

type: RNA

city: RTP

first: Sheetal

last: Shah

state: NC

address: 3054E Cornwallis Road

country: USA

institute: Syngenta

description:
Gene expression data from adults
DS004016

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

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: data was processed using RMA in GeneData Refiner.

label: biotin

molecule: total RNA

organism: Drosophila melanogaster

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

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

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

tag: gender

value: Males

tag: developmental stage

value: 0-3 day old adults

tag: tissue

value: whole animal

tag: number

tag: genotype/variation


title: Dhr96 knockdown (line 3), females, biological rep 1 (DS004007)

description:
Gene expression data from adults
DS004007

source_name: 0-3 day old adults cultured on diet made on 19/1/06

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

value: experiment 1


title: Genetic Control for Dhr96 over-expression, males, biological rep 2 (DS004012)

description:
Gene expression data from adults
DS004012


title: Genetic Control for Dhr96 knockdown, males, biological rep 1 (DS004006)

description:
Gene expression data from adults
DS004006


title: Dhr96 over-expression (line 35), females, biological rep 3 (DS004017)

description:
Gene expression data from adults
DS004017

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

value: experiment 3


title: Dhr96 knockdown (line 3), females, biological rep 2 (DS004015)

description:
Gene expression data from adults
DS004015


title: Genetic Control for Dhr96 knockdown, males, biological rep 2 (DS004014)

description:
Gene expression data from adults
DS004014


title: Dhr96 over-expression (line 35), males, biological rep 1 (DS004002)

description:
Gene expression data from adults
DS004002


title: Genetic Control for Dhr96 over-expression, males, biological rep 1 (DS004004)

description:
Gene expression data from adults
DS004004


title: Genetic Control for Dhr96 knockdown, males, biological rep 3 (DS004022)

description:
Gene expression data from adults
DS004022


title: Genetic Control for Dhr96 knockdown, females, biological rep 2 (DS004013)

description:
Gene expression data from adults
DS004013


title: Dhr96 knockdown (line 3), females, biological rep 3 (DS004023)

description:
Gene expression data from adults
DS004023


title: Dhr96 over-expression (line 35), females, biological rep 1 (DS004001)

description:
Gene expression data from adults
DS004001


title: Dhr96 knockdown (line 3), males, biological rep 3 (DS004024)

description:
Gene expression data from adults
DS004024


title: Genetic Control for Dhr96 over-expression, females, biological rep 1 (DS004003)

description:
Gene expression data from adults
DS004003


title: Genetic Control for Dhr96 over-expression, females, biological rep 3 (DS004019)

description:
Gene expression data from adults
DS004019


title: Genetic Control for Dhr96 knockdown, females, biological rep 1 (DS004005)

description:
Gene expression data from adults
DS004005


title: Dhr96 knockdown (line 3), males, biological rep 1 (DS004008)

description:
Gene expression data from adults
DS004008


title: Genetic Control for Dhr96 knockdown, females, biological rep 3 (DS004021)

description:
Gene expression data from adults
DS004021


title: Dhr96 over-expression (line 35), males, biological rep 2 (DS004010)

description:
Gene expression data from adults
DS004010


title: siliques AtHb1, hypoxia, biological rep1

status: Public on Feb 15 2011

city: Gatersleben

first: Johannes

last: Thiel

address: Corrensstrasse 3

country: Germany

institute: IPK-Gatersleben

description: Gene expression data after treatment

hyb_protocol: After fragmentation, cRNA was hybridized to GeneChip Arabidopsis ATH1 Genome Array according to Affymetrix standard protocol at RZPD. Gene Chips were washed and stained using fluidics protocol EUKGE-WS2V4_450.

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

data_processing: Data were processed with the Affymetrix MicroArray Suite software package (MAS 5.0) and analyzed using Bioconductor packages in R. Data were normalized using the Robust Multi-array Average (RMA) method.

organism: Arabidopsis thaliana

source_name: Arabidopsis siliques after hypoxia treatment (1h)

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, Affymetrix) at the RZPD Deutsches Ressourcenzentrum für Genomforschung GmbH (Berlin, Germany).

growth_protocol: Plants were grown at 22°C under 16/8-h photoperiod, a relative air humidity of 60% and an approximate light intensity of 100-150 µmol photons m-2 second-1.

extract_protocol: Total RNA was isolated from siliques using GENTRA kit (Biozym, Germany) according to the manufacturer´s instructions. RNA was further purified using RNeasy Kit (Quiagen) and subjected to DNAse digestion (Quiagen) according to the manufacturer´s instructions.

treatment_protocol: Complete plants (45 DPG) were aerated with a gas mixture containing 10.5% oxygen (composed of a 1:1 mixture of ambient gas and N2) or ambient gas containing 21% oxygen for control samples in darkness for 1 hour. Plants were decapitated and immediately frozen in liquid nitrogen. About 70-80 siliques were dissected in liquid nitrogen for one biological replicate.

tag: genotype

tag: age

value: 11/12 days after pollination corresponding to mid phase of seed maturation

value: silique

tag: treatment

value: hypoxia


title: siliques AtHb1, hypoxia, biological rep3

description: Gene expression data after treatment


title: siliques AtHb1, hypoxia, biological rep2

description: Gene expression data after treatment


title: siliques AtHb1, control, biological rep1

description: Gene expression data after treatment

source_name: Arabidopsis siliques after control treatment (1h)

value: control


title: siliques AtHb1, control, biological rep2

description: Gene expression data after treatment


title: siliques AtHb1, control, biological rep3

description: Gene expression data after treatment


title: siliques WT, hypoxia, biological rep3

description: Gene expression data after treatment


title: wildtype larvae at mid-L2, biological rep3

status: Public on Feb 02 2011

city: Richmond

first: Keith

middle: D

last: Baker

state: VA

address: 1220 E. Broad St.

department: Biochemistry & Molecular Biology

institute: VCU School of Medicine

description:
Gene expression data from wild type animals hand sorted under a light microscope
w1118 sample3

hyb_protocol: [Fluidics]  Protocol Midi_euk2v3_450  Wash A1 Recovery Mixes 0  Wash A1 Temperature (C) 30  Number of Wash A1 Cycles 10  Mixes per Wash A1 Cycle 2  Wash B Recovery Mixes 0  Wash B Temperature (C) 50  Number of Wash B Cycles 6  Mixes per Wash B Cycle 15  Stain Temperature (C) 35  First Stain Time (seconds) 300  Wash A2 Recovery Mixes 0  Wash A2 Temperature (C) 30  Number of Wash A2 Cycles 10  Mixes per Wash A2 Cycle 4  Second Stain Time (seconds) 300  Third Stain Time (seconds) 300  Wash A3 Recovery Mixes 0  Wash A3 Temperature (C) 35  Number of Wash A3 Cycles 15  Mixes per Wash A3 Cycle 4  Holding Temperature (C) 25 Standard Affymetrix protocol.

scan_protocol: Pixel Size 1.56  Filter 570  Scan Temperature 0  Scan date Aug 15 2007  Scanner ID 50211020  Number of Scans 1  Scanner Type M10

data_processing: Raw data were normalized using MAS5.0

source_name: Drosophila larvae at mid-L2 grown at 25C on yeast paste

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol by the University of Maryland Biotechnology Institute Microarray Core facility

growth_protocol: Larvae were grown on egg caps at 25C and reared on yeast paste.

extract_protocol: Tripure (Roche) extraction of total RNA was performed according to the manufacturer's instructions followed by additional cleaning of the RNA using the RNAeasy kit (Qiagen).

treatment_protocol: Larvae at ~36 hours after hatching were manually selected for size, vitality, and appropriate spiracle formation under a fluorescent or light dissecting scope. Selected larvae were were rinsed with water and frozen at -80C until further processing.

value: whole larvae

value: wild type

tag: lineage

value: w1118 parents

value: middle of second instar

value: ~36 hours after hatch


title: Genetic Control for Dhr96 over-expression, females, biological rep 2 (DS004011)

description:
Gene expression data from adults
DS004011


title: wildtype larvae at mid-L2, biological rep2

description:
Gene expression data from wild type animals hand sorted under a light microscope
w1118 sample2


title: err mutant larvae at mid-L2, biological rep3

description:
Gene expression data from transhet mutant animals hand sorted under a fluorescent microscope
err1/err2 sample3

value: err1/err2 transhet mutant

value: product of the cross of parents err1/TM3,tw-GFP x err2/TM3,twGFP


title: Drosophila_SZ_Mated_To_Male_SZ_biological_rep1

status: Public on Feb 05 2011

city: Uppsala

first: Richard

middle: Ian

last: Bailey

address: Norbyvägen 18 D

department: Animal Ecology

country: Sweden

institute: Uppsala University

description: Gene expression data from whole adult virgin females 7 days post eclosion

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

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

data_processing: Gene expression data were analyzed using R 2.8.1 [34] and BioConductor 2.3 [35]. Background correction, between-array normalization and transformation were carried out using the VSN method for variance stabilization and calibration of microarray data. Summarization employed the Robust Multichip Average (RMA) algorithm as implemented in the Affy package. Filtering involved removal of probe sets with no Entrez Gene ID annotation and, where multiple probe sets mapped to the same Entrez Gene ID, the probe set with the largest variance across samples was retained and others removed. Probe sets showing low variability (variance interquartile range < 0.5) were also removed. To account for differences in reliability between individual arrays, each array was weighted according  to how well its expression values followed the linear model using the REML scoring method.

source_name: Adult female; line SZ; mated to SZ male

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

growth_protocol: The composite line SZ was produced by crossing 6 strong Z lines from Sengwa and Harare [15] (ZS2, ZS11, ZS53, ZS56, ZH12, ZH32). Lines were crossed sequentially for 2 generations before being thoroughly mixed to produce a single population, which was then maintained as a 14-vial culture (population size = 448). LHM has been maintained as a large, outbred population for over 400 non-overlapping generations. All flies were maintained using the standard protocol for LHM. Flies were reared on standard cornmeal/yeast medium and kept on a 12 h: 12 h light: dark cycle.  Rearing and experimentation were carried out at 25° C and 60% relative humidity.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by Qiagen purification.

treatment_protocol: All flies were virgin and 7 days post-eclosion on the day of experimentation. Eight SZ females were individually  mated to LHM (SZ mated to M treatment) and eight to SZ (SZ mated to SZ treatment) males in each of four replicates, and subsequently flashfrozen in liquid nitrogen 30 minutes after copulation had ceased, prior to RNA extraction.

value: Whole fly

value: SZ  composite of Z lines ZS2, ZS11, ZS53, ZS56, ZH12, ZH32

value: 7 days post adult eclosion

value: mated to SZ male


title: Drosophila_SZ_Mated_To_Male_SZ_biological_rep3


title: wildtype larvae at mid-L2, biological rep1

description:
Gene expression data from wild type animals hand sorted under a light microscope
w1118 sample1


title: siliques WT, hypoxia, biological rep2

description: Gene expression data after treatment


title: Drosophila_SZ_Mated_To_Male_M_biological_rep4

source_name: Adult female; line SZ; mated to LHM male

value: mated to LHM male


title: Drosophila_SZ_Mated_To_Male_M_biological_rep2


title: Drosophila_SZ_Mated_To_Male_M_biological_rep3


title: err mutant larvae at mid-L2, biological rep2

description:
Gene expression data from transhet mutant animals hand sorted under a fluorescent microscope
err1/err2 sample2


title: Drosophila_SZ_Mated_To_Male_M_biological_rep1


title: Drosophila_SZ_Mated_To_Male_SZ_biological_rep2


title: Drosophila_SZ_Mated_To_Male_SZ_biological_rep4


title: adult head RNA from EP1306 mutant, replicate 2

status: Public on Feb 01 2011

city: Emeryville

first: Amy

last: Lasek

state: CA

address: 5858 Horton Street, Suite 200

department: Neurology

institute: Ernest Gallo Clinic and Research Center/UCSF

hyb_protocol: performed by Partners HealthCare Center for Personalized Genetic Medicine (Harvard University)

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: adult fly head from EP1306 mutants, untreated

growth_protocol: RNA was isolated from 200 adult male flies, aged 2-3 days. Flies were collected from 3 different bottles grown on the same day and then combined to form a single pool of 600 flies for RNA isolation. RNA was divided into triplicates for hybridization.

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

treatment_protocol: untreated

value: EP1306 mutant

value: head

value: male


title: adult head RNA from w;iso control flies, replicate 3

scan_protocol: performed by Partners HealthCare Center for Personalized Genetic Medicine (Harvard University)

source_name: adult fly head from w;iso control flies, untreated

value: w;iso control


title: adult head RNA from BxJ mutant, replicate 3

source_name: adult fly head from BxJ mutants, untreated

label_protocol: performed by Partners HealthCare Center for Personalized Genetic Medicine (Harvard University)

value: BxJ mutant


title: adult head RNA from w;iso control flies, replicate 2


title: adult head RNA from w;iso control flies, replicate 1


title: adult head RNA from EP1306 mutant, replicate 3


title: adult head RNA from EP1306 mutant, replicate 1


title: err mutant larvae at mid-L2, biological rep1

description:
Gene expression data from transhet mutant animals hand sorted under a fluorescent microscope
err1/err2 sample1

value: whole larvae


title: adult head RNA from BxJ mutant, replicate 1


title: WT_3

city: Barcelona

first: David

last: Rossell

address: Baldiri Reixac 10

country: Spain

institute: IRB Barcelona

hyb_protocol: Hybridization of the samples to Affymetrix GeneChip® Drosophila Genome 2.0 Array were performed according to the manufacturer’s instructions (http://www.affymetrix.com).

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

data_processing: Gene expression data was pre-processed and normalized with R/Bioconductor. The data was quantile normalized, and the summarization was obtained via GC-RMA. In order to remove the bias due to the experimentation site, from all expression values for a given gene we subtracted the average expression of that gene in the wild type samples obtained at the same experimentation site.

label_protocol: Labeling was carried out following Affymetrix instructions (http://www.affymetrix.com)

growth_protocol: Drosophila larvae were raised in standard Drosophila medium. Immortalised tumours were maintained by serial transplantation into adult hosts

extract_protocol: Total RNA was prepared using Trizol (Invitrogen). Purity and integrity of the purified RNA was assessed on the Agilent Bioanalyzer 2100. Concentration was determined with a Nanodrop ND-1000 Spectrophotometer.

treatment_protocol: No additional treatment was used prior to RNA extraction

tag: group

tag: experimentation site

value: IRB BARCELONA


title: WT_5

value: EMBL


title: MBT_TS1_17_3

source_name: MBT TS1 17ºC


title: MBT_TS1_29_2

source_name: MBT TS1 29ºC


title: MBT_T5_2

source_name: MBT TS1 FIFTH ROUND


title: WT_2


title: MBT_TS1_29_4


title: MBT_T5_3


title: MBT_TS1_ME2_29_3

source_name: MBT TRANSHETEROZYGOUS TS1/ME2 29ºC


title: MBT_T5_1


title: MBT_TS1_17_1


title: adult head RNA from BxJ mutant, replicate 2


title: MBT_TS1_ME2_29_1


title: MBT_TS1_ME2_29_2


title: MBT_TS1_29_1


title: WT_6


title: MBT_TS1_29_6


title: WT_4


title: MBT_TS1_17_2


title: MBT_TS1_29_3


title: WT_1


title: MBT_T10_3

source_name: MBT TS1 TENTH ROUND


title: MBT_T1_1

source_name: MBT TS1 FIRST ROUND


title: MBT_T1_3


title: MBT_T10_2


title: MBT_E2_29_2

source_name: MBT E2 29ºC


title: MBT_T10_1


title: MBT_E2_29_3


title: MBT_E2_29_1


title: MBT_E2_17_3

source_name: MBT E2 17ºC


title: MBT_E2_17_1


title: mutant, biological rep2

city: Singapore

first: Jishy

last: Varghese

address: 1 Research Link

country: Singapore

institute: TLL, Singapore

description:
Gene expression data from adult male mutant flies.
COHEDRO_04

hyb_protocol: Using standard protocols, the cRNA was hybridized on Affymetrix Drosophila Genome 2.0 array. Washes were done using the Fluidics Station 400.

data_processing: The data were analyzed using CARMAweb 1.4, a comprehensive R- and Bioconductor-based web service for microarray data analysis, using settings specific for Affymetrix using RMA method.

source_name: Drosophila 5-day-old adult male head, mutant sample

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

growth_protocol: 5-day-old male flies reared in similar growth and feeding conditions.

extract_protocol: Trizol extraction of total RNA was done.

treatment_protocol: Head tissue was separated by snap freezing flies in liquid nitrogen and then vortexing.

value: 5-day-old adult

value: homozygous dme-miR-14 mutant


title: MBT_TS1_29_5


title: mutant, biological rep1

description:
Gene expression data from adult male mutant flies.
COHEDRO_03


title: control, biological rep2

description:
Gene expression data from adult male control flies.
COHEDRO_02

source_name: Drosophila 5-day-old adult male head, control sample

value: wild-type


title: rescue, biological rep2

description:
Gene expression data from adult male rescue flies.
COHEDRO_06

source_name: Drosophila 5-day-old adult male head, rescue sample

value: homozygous mutant expressing dme-miR-14 microRNA in insulin-producing cells (IPCs)


title: control, biological rep1

description:
Gene expression data from adult male control flies.
COHEDRO_01


title: rescue, biological rep1

description:
Gene expression data from adult male rescue flies.
COHEDRO_05


title: MBT_E2_17_2


title: MBT_T1_2


title: JIL-1 RNAi, rep4

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

description: Gene expression after JIL-1 RNAi

hyb_protocol: Hybridization was performed by ImaGenes (http://www.imagenes-bio.de)

scan_protocol: Scanning was performed by ImaGenes (http://www.imagenes-bio.de)

data_processing: Raw data was processed using R/Bioconductor. Normalization and probeset expression values were calculated using GCRMA.

source_name: S2 cell line

label_protocol: RNA labelling was performed by ImaGenes (http://www.imagenes-bio.de)

growth_protocol: Cells were grown in 6-well plates in Schneider Medium supplemented with 10% FCS, penicillin and streptomycin.

extract_protocol: Total RNA was extracted using either Qiagen RNAEasy Mini kits including Qiagen DNAse on-column digestion or Qiazol according to manufacturer's instructions.

treatment_protocol: 2x10e6 cells were incubated with 10 µg dsRNA in serum-free medium for 1 hour after which serum-containing medium was added. Cells were splitted after 3 days and harvested after 7 days.

tag: cell type

value: Schneider line2 (S2) cells

tag: rnai type

tag: rnai target

value: JIl-1 3prime

tag: batch

value: B


title: 1h_-Pi_3 rep

city: Berlin

first: Thomas

middle: J.

last: Buckhout

address: Invalidenstrasse 42

department: Biology

institute: Humboldt University Berlin

hyb_protocol: Gene chips were hybridized with 15 μg of fragmented cRNA.

scan_protocol: Hybridization, washing, staining, and scanning procedures were performed as described in the Affymetrix technical manual.

data_processing: Preprocessing and statistical analysis of data was performed using the Bioconductor packages AffylmGUI and Limma (Wettenhall et al., 2006; http://www.bioconductor.org/). Arrays were normalized using the Robust Probe-level Linear Model (PLM) provided in the AffylmGUI package using the default parameters.

source_name: root

label_protocol: cRNA synthesis was performed by use of the Gene chip One-Cycle Target Labeling Kit (Affymetrix).

growth_protocol: Arabidopsis thaliana was grown hydroponically in a growth chamber at a constant relative humidity of 75%, under a 10/14 h light/dark cycle (300 µmol cm-2 s-1) at 21° C (day) or 18° C (night). Plants were grown hydroponically and constantly aerated. The nutrient solution was replaced weekly and at 24 h prior to beginning the experiment. The nutrient solution was composed of KNO3 (3 mM), MgSO4 (0.5 mM), CaCl2 (1.5 mM), K2SO4 (1.5 mM), NaH2PO4 (1.5 mM), H3BO3 (25 µM), MnSO4 (1 µM), ZnSO4 (0.5 µM), (NH4)6Mo7O24 (0.05 µM) CuSO4 (0.3 µM), Fe-EDTA (40 µM) with pH adjusted to 6.0 with KOH (Schmidt, 1994).

extract_protocol: Following transfer, the roots were harvested after 0, 1, 6 and 24 h into RNALater® (Applied Biosystems). Total RNA from roots of control and Pi-deficient plants was isolated with the RNeasy Plant Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: At 30 days after sowing, the plants were washed briefly in a 0.1 mM EDTA solution and transferred into either Pi-free or Pi-replete (controls) nutrient solutions. The experiment was initiated 1 h into the light cycle. For each time-point analyzed, approximately 20 plants were harvested. The total processing time was approximately 15 s. Control plants were treated similarly but were grown in the presence of Pi. Short-term Pi-starvation experiments were conducted with 14-d-old plants by exposing them to liquid Pi-free media for the 10, 30 and 60 min.

value: root

tag: time (h)

tag: [pi]

value: 0 mM

tag: experiment


title: 6h_+Pi_3 rep


title: JIL-1 RNAi, rep3

description: Gene expression after JIL-1 RNAi


title: JIL-1 RNAi, rep5

description: Gene expression after JIL-1 RNAi


title: 0h_-Pi_3 rep


title: JIL-1 RNAi, rep1

description: Gene expression after JIL-1 RNAi

value: JIl-1 5prime

value: A


title: JIL-1 RNAi, rep2

description: Gene expression after JIL-1 RNAi


title: 6h_-Pi_3 rep


title: CTR RNAi, rep1

description: Gene expression after control RNAi

value: control

value: GST


title: 24h_+Pi_3 rep


title: 24h_-Pi_3 rep


title: CTR RNAi, rep3

description: Gene expression after control RNAi


title: CTR RNAi, rep4

description: Gene expression after control RNAi

value: EGFP


title: CTR RNAi, rep5

description: Gene expression after control RNAi


title: CTR RNAi, rep2

description: Gene expression after control RNAi


title: 1h_+Pi_3 rep


title: 0h_+Pi_3 rep


title: 24h_-Pi_2 rep


title: 24h_+Pi_2 rep


title: 0h_-Pi_2 rep


title: 6h_-Pi_2 rep


title: 6h_+Pi_2 rep


title: 1h_-Pi_2 rep


title: 1h_+Pi_2 rep


title: 24h_-Pi_1 rep


title: 6h_+Pi_1 rep


title: 6h_-Pi_1 rep


title: 1h_-Pi_1 rep


title: 0h_+Pi_2 rep


title: 24h_+Pi_1 rep


title: 0h_-Pi_1 rep


title: 1h_+Pi_1 rep


title: 0h_+Pi_1 rep


title: COL2_741

status: Public on Jan 28 2011

city: Marseille

first: Sylviane

last: Olschwang

address: 232 boulevard Sainte-Marguerite

department: Centre de Recherches en Cancérologie de Marseille

country: France

institute: Institut Paoli-Calmettes

description: gene expression data from stage II primary colon adenocarcinoma after surgery only

hyb_protocol: Expression profiles were established with Affymetrix U133 Plus 2.0 human oligonucleotide microarrays

scan_protocol: Scanning was done with an Affymetrix GeneArray scanner and quantification with the Affymetrix GeneChip Operating Software (Affymetrix, Paris France).

data_processing:
CEL files were processed in the R/Bioconductor environment. Pre-processing steps (background adjustment, normalization and summarization) were performed with the GCRMA package
Expression measures were handled on log2 scale for statistical computations as well as for display purposes. Genes with overall low intensity were removed from further analysis. All remaining genes had an expression value greater than log2 (100) in at least 10% of the samples. As tumor samples and/or RNA samples were provided by 4 different centres, genes were then median-centred within each centre individually.

organism: Homo sapiens

source_name: colon adenocarcinoma stage II

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

extract_protocol: Enriched tumor zones were selected from frozen material on HE-stained cryosections to ensure a 60% minimum of tumor cells. Nucleic acids were extracted using QIAamp and RNeasy kits (Qiagen, Courtaboeuf France) according to the manufacturer's instructions. Quantification of samples was done with a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Illkirch France). RNA integrity was controlled on an Agilent Bioanalyzer (Agilent Technologies, Massy France).

treatment_protocol: Tissue samples were collected on fresh surgical specimens by pathologists within one hour after surgery from patients who underwent curative colonic resection, then flash frozen in liquid nitrogen and stored at -80°C until nucleic acids extraction.

value: colon adenocarcinoma stage II

tag: age at diagnosis

tag: gender

value: F

tag: localisation

value: Left

tag: metastasis

tag: first apc mutation

tag: second apc mutation

tag: 5q loh


title: COL2_744

tag: tissue


title: COL2_7610

value: M


title: COL2_735


title: COL2_733

value: BONE


title: COL2_743

value: Right


title: COL2_739


title: COL2_9749


title: COL2_9848


title: COL2_9304

value: LUNG


title: COL2_79

value: LIVER


title: COL2_9736


title: COL2_JM_HS_1411

value: LIVER/LUNG


title: COL2_9607


title: COL2_725


title: COL2_8196


title: COL2_726


title: COL2_737


title: COL2_729

value: CNS


title: COL2_720


title: COL2_724


title: COL2_722


title: COL2_731


title: COL2_9243


title: COL2_727


title: COL2_732


title: COL2_723


title: COL2_730


title: COL2_738


title: COL2_721


title: COL2_716


title: COL2_718


title: COL2_719


title: COL2_715


title: COL2_713

value: LIVER/BONE


title: COL2_714


title: COL2_711


title: COL2_708


title: COL2_704


title: COL2_712


title: COL2_705

value: deletion


title: COL2_707


title: COL2_706


title: COL2_701


title: COL2_510


title: COL2_709


title: COL2_534


title: COL2_702


title: COL2_11538


title: COL2_11060


title: COL2_14604


title: COL2_10228


title: COL2_10411


title: COL2_10602


title: COL2_11196


title: COL2_10937


title: COL2_44


title: COL2_244


title: canton-s_dietary_restriction_day40_rep3

status: Public on Jan 20 2011

city: Providence

first: Michael

last: Antosh

state: RI

address: Brown University Box 1843

institute: Michael Antosh

description:
A60_rpd_lc_ctrl_40d_C
gene expression from whole body female; canton-s dietary restriction at day 40

hyb_protocol: The arrays are hybed overnight (16 hr) at 45C 60 rpm. Fluidics protocol is FS450_0002

scan_protocol: Arrays were scanned on a Affymetrix Gene Chip Scanner 3000 7G

data_processing: R/Bioconductor, normalized using GCRMA

source_name: female, canton-s dietary restriction, day 40

label_protocol: Standard Affymetrix protocol.

extract_protocol: Total RNA was isolated from at least 75 females using Trizol (Invitrogen) and further purified using RNeasy columns (QIAGEN). 5 μg total RNA was used with Affymetrix One Cycle DNA conversion Kit (Cat # 900431) and all steps were carried out according to the Affymetrix manual

value: female

value: whole body

tag: genetic background

value: Canton-S

tag: diet

value: restricted

tag: age

value: 40 days


title: yw_w1118_dietary_restriction_day40_rep2

description:
A38_elav_sir2_lc_ru486_minus_40d_B
gene expression from whole body female; yw, w1118 dietary restriction at day 40

source_name: female, yw, w1118 dietary restriction, day 40


title: canton-s_control_day10_rep3

description:
A51_rpd_hc_ctrl_C
gene expression from whole body female; canton-s control at day 10

source_name: female, canton-s control, day 10

value: normal

value: 10 days


title: canton-s_control_day40_rep2

description:
A62_rpd_hc_ctrl_40d_B
gene expression from whole body female; canton-s control at day 40

source_name: female, canton-s control, day 40


title: canton-s_control_day10_rep1

description:
A49_rpd_hc_ctrl_A
gene expression from whole body female; canton-s control at day 10


title: canton-s_control_day40_rep1

description:
A61_rpd_hc_ctrl_40d_A
gene expression from whole body female; canton-s control at day 40


title: canton-s_control_day40_rep3

description:
A63_rpd_hc_ctrl_40d_C
gene expression from whole body female; canton-s control at day 40


title: canton-s_control_day10_rep2

description:
A50_rpd_hc_ctrl_B
gene expression from whole body female; canton-s control at day 10


title: canton-s_dietary_restriction_day40_rep2

description:
A59_rpd_lc_ctrl_40d_B
gene expression from whole body female; canton-s dietary restriction at day 40


title: sir2_control_day40_rep3

description:
A36_elav_sir2_hc_ru486_minus_40d_C
gene expression from whole body female; sir2 control at day 40

source_name: female, sir2 control, day 40

tag: genetic manipulation

value: sir2 control


title: canton-s_dietary_restriction_day10_rep2

description:
A47_rpd_lc_ctrl_B
gene expression from whole body female; canton-s dietary restriction at day 10

source_name: female, canton-s dietary restriction, day 10


title: canton-s_dietary_restriction_day10_rep3

description:
A48_rpd_lc_ctrl_C
gene expression from whole body female; canton-s dietary restriction at day 10


title: yw_w1118_dietary_restriction_day40_rep1

description:
A37_elav_sir2_lc_ru486_minus_40d_A
gene expression from whole body female; yw, w1118 dietary restriction at day 40


title: yw_w1118_dietary_restriction_day40_rep3

description:
A39_elav_sir2_lc_ru486_minus_40d_C
gene expression from whole body female; yw, w1118 dietary restriction at day 40


title: canton-s_dietary_restriction_day40_rep1

description:
A58_rpd_lc_ctrl_40d_A
gene expression from whole body female; canton-s dietary restriction at day 40


title: canton-s_dietary_restriction_day10_rep1

description:
A46_rpd_lc_ctrl_A
gene expression from whole body female; canton-s dietary restriction at day 10


title: sir2_overexpression_day40_rep1

description:
A31_elav_sir2_hc_ru486_plus_40d_A
gene expression from whole body female; sir2 overexpression at day 40

source_name: female, sir2 overexpression, day 40

value: sir2 overexpression


title: sir2_overexpression_day40_rep2

description:
A32_elav_sir2_hc_ru486_plus_40d_B
gene expression from whole body female; sir2 overexpression at day 40


title: sir2_control_day40_rep2

description:
A35_elav_sir2_hc_ru486_minus_40d_B
gene expression from whole body female; sir2 control at day 40


title: p53_control_day40_rep2

description:
A26_elav_dnp53_hc_ru486_minus_40d_B
gene expression from whole body female; p53 control at day 40

source_name: female, p53 control, day 40

value: p53 control


title: yw_w1118_dietary_restriction_day10_rep3

description:
A24_elav_sir2_lc_ru486_minus_C
gene expression from whole body female; yw, w1118 dietary restriction at day 10

source_name: female, yw, w1118 dietary restriction, day 10


title: p53_knockdown_day40_rep2

description:
A29_elav_dnp53_hc_ru486_plus_40d_B
gene expression from whole body female; p53 knockdown at day 40

source_name: female, p53 knockdown, day 40

value: p53 knockdown


title: p53_knockdown_day40_rep3

description:
A30_elav_dnp53_hc_ru486_plus_40d_C
gene expression from whole body female; p53 knockdown at day 40


title: sir2_overexpression_day40_rep3

description:
A33_elav_sir2_hc_ru486_plus_40d_C
gene expression from whole body female; sir2 overexpression at day 40


title: yw_w1118_dietary_restriction_day10_rep1

description:
A22_elav_sir2_lc_ru486_minus_A
gene expression from whole body female; yw, w1118 dietary restriction at day 10


title: sir2_control_day40_rep1

description:
A34_elav_sir2_hc_ru486_minus_40d_A
gene expression from whole body female; sir2 control at day 40


title: p53_control_day40_rep3

description:
A27_elav_dnp53_hc_ru486_minus_40d_C
gene expression from whole body female; p53 control at day 40


title: yw_w1118_dietary_restriction_day10_rep2

description:
A23_elav_sir2_lc_ru486_minus_B
gene expression from whole body female; yw, w1118 dietary restriction at day 10


title: p53_knockdown_day40_rep1

description:
A28_elav_dnp53_hc_ru486_plus_40d_A
gene expression from whole body female; p53 knockdown at day 40


title: p53_control_day40_rep1

description:
A25_elav_dnp53_hc_ru486_minus_40d_A
gene expression from whole body female; p53 control at day 40


title: sir2_control_day10_rep2

description:
A20_elav_sir2_hc_ru486_minus_B
gene expression from whole body female; sir2 control at day 10

source_name: female, sir2 control, day 10


title: sir2_control_day10_rep3

description:
A21_elav_sir2_hc_ru486_minus_C
gene expression from whole body female; sir2 control at day 10


title: sir2_overexpression_day10_rep3

description:
A18_elav_sir2_hc_ru486_plus_C
gene expression from whole body female; sir2 overexpression at day 10

source_name: female, sir2 overexpression, day 10


title: sir2_overexpression_day10_rep2

description:
A17_elav_sir2_hc_ru486_plus_B
gene expression from whole body female; sir2 overexpression at day 10


title: sir2_control_day10_rep1

description:
A19_elav_sir2_hc_ru486_minus_A
gene expression from whole body female; sir2 control at day 10


title: p53_knockdown_day10_rep1

description:
A13_elav_dnp53_hc_ru486_plus_A
gene expression from whole body female; p53 knockdown at day 10

source_name: female, p53 knockdown, day 10


title: p53_knockdown_day10_rep2

description:
A14_elav_dnp53_hc_ru486_plus_B
gene expression from whole body female; p53 knockdown at day 10


title: p53_control_day10_rep2

description:
A11_elav_dnp53_hc_ru486_minus_B
gene expression from whole body female; p53 control at day 10

source_name: female, p53 control, day 10


title: p53_knockdown_day10_rep3

description:
A15_elav_dnp53_hc_ru486_plus_C
gene expression from whole body female; p53 knockdown at day 10


title: sir2_overexpression_day10_rep1

description:
A16_elav_sir2_hc_ru486_plus_A
gene expression from whole body female; sir2 overexpression at day 10


title: p53_control_day10_rep3

description:
A12_elav_dnp53_hc_ru486_minus_C
gene expression from whole body female; p53 control at day 10


title: Drosophila-sens-control-2

city: Los Angeles

first: S

middle: Lawrence

last: Zipursky

state: California

address: 675 Charles E. Young Drive South

department: Biological Chemistry

institute: Howard Hughes Medical Institute

description: Gene expression data from 3rd instar eye discs (antennae removed)

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and were normalized using the GCRMA algorithm implemented in the affy package using Bioconductor and R

source_name: Eye Discs

growth_protocol: Crosses were reared at room temperature and wandering 3rd instar larvae were dissection to obtain eye imaginal discs

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

value: Eye Discs

value: 3rd instar larvae

tag: genotype

value: w; sensDF2RES/+; sensE1/+


title: Drosophila-sens-mutant-1

value: w; sensDF2RES/sensDF2RES; sensE1/sensE1


title: Drosophila-ro-Gal4xUAS-runt{G163R]-3

value: w; ro-Gal4/UAS-Run[G163R]


title: Drosophila-sens-mutant-3


title: Drosophila-ro-Gal4xUAS-runt-3

value: w; ro-Gal4/UAS-Run


title: Drosophila-sens-control-1


title: p53_control_day10_rep1

description:
A10_elav_dnp53_hc_ru486_minus_A
gene expression from whole body female; p53 control at day 10

value: female


title: Drosophila-ro-Gal4xUAS-runt-2


title: Drosophila-sens-control-3


title: Drosophila-ro-Gal4xUAS-runt-1


title: Drosophila-sens-mutant-2


title: Drosophila-ro-Gal4xUAS-runt{G163R]-1


title: Drosophila-ro-Gal4xUAS-runt{G163R]-2


title: edr1, 96 hrs, bio rep 4

status: Public on Jan 19 2011

city: Bloomington

first: Roger

last: Innes

state: IN

address: 915 East Third Street

institute: Indiana University

hyb_protocol: Fifteen µg of biotinylated cRNA is added to a total hybridization cocktail of 300 µl, and 200 µl is hybridized to a GeneChip® after adding control oligonucleotides. Hybridization is at 45°C for 17 h with constant rotation. The hybridization mixture is then removed and the GeneChips® are washed, stained with phycoerythrin-labeled Streptavidin, washed, incubated with biotinylated anti-streptavidin, and then restained with phycoerythrin-labeled Streptavidin to amplify the signals; these steps are carried out using the Affymetrix Fluidics Station.

scan_protocol: Arrays were scanned using the dedicated scanner, controlled by Affymetrix GCOS software.  The data was analyzed with Affymetrix MAS5 and the average intensity on each array is normalized by global scaling to a target intensity of 1000.

data_processing: MAS5.0, GCRMA

source_name: edr1 rosettes, 96 hpi with Golovinomyces cichoracearum

label_protocol: Biotinlylated cRNA was made using the Affymetrix IVT kit.

growth_protocol: Arabidopsis thaliana Col-0 and edr1 seeds were sown on Metromix soil and placed at 4ºC for three days.  Plants were then transferred to a growth room and grown under 9 hour days at a temperature of 23ºC for four weeks.

extract_protocol: Tissue was collected for each time point (0, 18, 36, and 96 hours) by harvesting four full rosettes per genotype per biological replicate.  Four biological replicates were collected and placed in liquid nitrogen.  Tissue was ground with a mortar and pestle and used for RNA preparations.  High quality RNA was prepared using the Spectrum Plant Total RNA Kit (Sigma) and concentrated to >0.75 μg/μl with the RNEasy MinElute Cleanup Kit (Qiagen). A total of 6 µg RNA was used.

treatment_protocol: Plants were inoculated with Golovinomyces cichoracearum using a settling tower ~1 meter tall.  Plants to be inoculated were placed at the bottom of the tower, which contained a Nytex mesh screen at the top.  Four pad4 mutants with heavy powder growth were passed over the mesh 20 times each to transfer the spores to the plants below.  Spores were allowed to settle for 30 minutes and the plants were transferred to growth chambers.


title: edr1, 18 hrs, bio rep 1

source_name: edr1 rosettes, 18 hpi with Golovinomyces cichoracearum


title: edr1, 36 hrs, bio rep 4

source_name: edr1 rosettes, 36 hpi with Golovinomyces cichoracearum


title: edr1, 0 hrs, bio rep 4

source_name: edr1 rosettes, 0 hpi with Golovinomyces cichoracearum


title: edr1, 36 hrs, bio rep 2


title: edr1, 18 hrs, bio rep 4


title: edr1, 96 hrs, bio rep 3


title: edr1, 0 hrs, bio rep 2


title: edr1, 18 hrs, bio rep 3


title: edr1, 0 hrs, bio rep 1


title: Col-0, 96 hrs, bio rep 3

source_name: Col-0 rosesttes, 96 hpi with Golovinomyces cichoarcearum


title: edr1, 18 hrs, bio rep 2


title: edr1, 96 hrs, bio rep 1


title: Col-0, 96 hrs, bio rep 2


title: edr1, 96 hrs, bio rep 2


title: Col-0, 36 hrs, bio rep 4

source_name: Col-0 rosettes, 36 hpi with Golovinomyces cichoracearum


title: edr1, 0 hrs, bio rep 3


title: Col-0, 18 hrs, bio rep 4

source_name: Col-0 rosettes, 18 hpi with Golovinomyces cichoracearum


title: Col-0, 36 hrs, bio rep 1


title: Col-0, 96 hrs, bio rep 4


title: TSC 2

city: Amsterdam

first: Floyd

last: Wittink

address: Kruislaan 318

department: MAD

country: Netherlands

institute: Universiteit van Amsterdam

description: Gene expression data from cortical tuber of TSC-diagnosed patients.

hyb_protocol: Following fragmentation, 10 ug cRNA were hybridized for 16 hours at 45C on GeneChip Human Genome U133 Plus 2.0 Array. Genechips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 G7 scanner.

data_processing: The data were analyzed with MicroArray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and Robust Multi-Array Average (RMA) analysis as normalization method. The trimmed mean target intensity of each array was set arbitrarily to 100.

source_name: cortical tuber, TSC

label_protocol: Biotinylated cRNA were prepared according to standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical manual, 2005  Affymetrix).

growth_protocol: Cortical tuber specimens were obtained during epilepsy surgery from 4 patients diagnosed for TSC with perituberal tissue as surgical control samples.

extract_protocol: Trizol LS extraction was perfomed according to manufacturer's instructions.

treatment_protocol: Fixed in liquid nitrogen.

value: surgical

tag: disease

value: tuberous sclerosis complex

value: brain

tag: sub-brain

value: cortical tuber

tag: patient

value: TSC 2


title: Col-0, 0 hrs, bio rep 2

source_name: Col-0 rosettes, 0 hpi with Golovinomyces cichoracearum


title: Col-0, 36 hrs, bio rep 3


title: Col-0, 36 hrs, bio rep 2


title: Col-0, 0 hrs, bio rep 1


title: Col-0, 0 hrs, bio rep 3


title: Col-0, 0 hrs, bio rep 4


title: Col-0, 96 hrs, bio rep 1


title: Col-0, 18 hrs, bio rep 1


title: Col-0, 18 hrs, bio rep 3


title: jap2-F-1

status: Public on Jan 09 2011

first: Paolo

last: Innocenti

address: Norbyvägen 18D

department: Dept. of Animal Ecology

institute: Uppsala university

hyb_protocol: Affymetrix Eukaryotic Target Hybridization protocol

scan_protocol: Affymetrix GeneChip Scanner 3000 with GCOS software

data_processing: Probesets pre-processed with vsnrma separately in the two sexes, as implemented in R/Bioconductor package vsn (Variance Stabilization background subtraction and normalization, median-polish summarization)

source_name: Adult w1118, whole fly

label_protocol: Affymetrix GeneChip IVT Labeling Kit, standard manufacturer's protocol

extract_protocol: Trizol (Invitrogen) extraction and RNeasy (Qiagen) purification

tag: Sex

value: F

tag: strain

value: japan

tag: batch


title: jap1-F-1


title: mys1-F-2

value: mysore


title: mys1-F-1


title: jap1-F-2


title: dah2-F-1

value: dahomey


title: bro1-F-1

value: brownsville


title: mys2-M-2

value: M


title: bro2-F-1


title: mys2-F-1


title: jap2-F-2


title: jap1-M-2


title: mys2-F-2


title: jap2-M-1


title: bro1-F-2


title: jap2-M-2


title: dah1-F-1


title: dah2-F-2


title: als1-F-1

value: alstonville


title: als1-F-2


title: als2-F-2


title: als2-F-1


title: dah1-F-2


title: mys1-M-2


title: dah2-M-2


title: mys1-M-1


title: jap1-M-1


title: bro2-F-2


title: mys2-M-1


title: dah2-M-1


title: dah1-M-2


title: dah1-M-1


title: bro1-M-2


title: bro2-M-1


title: bro2-M-2


title: als1-M-2


title: als1-M-1


title: als2-M-2


title: bro1-M-1


title: als2-M-1


title: Pupa, 19˚C, eGFP, Biol. Repl. 4

status: Public on Dec 31 2010

city: Cambridge

first: Anastasios

middle: Tassos

last: Pavlopoulos

address: Downing Street

department: Department of Zoology

country: United Kingdom

institute: University of Cambridge

description: Control pupal wings developed at the permissive low temperature

hyb_protocol: 10µg of fragmented cRNA were hybridized in 160μl Hyb buffer for 16hrs at 45˚C on the GeneChip Drosophila Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 using standard Affymetrix protocols.

scan_protocol: GeneChips were scanned using a GeneChip Scanner 3000, and array images were analyzed with the GCOSv1.4 software.

data_processing: Gene expression data were analyzed with R/Bioconductor (packages: affy, simpleaffy, genefilter and RankProd). We pre-processed and normalized data by RMA, we filtered out the Affymetrix quality control probe-sets and genes that are not expressed above 5 log2 units, and identified the up- and down-regulated genes using the Rank Products non-parametric method. The False Discovery Rate for each Affymetrix probe-set was computed from 1000 permutations, and a significance cut-off of 0.05 was selected.

source_name: Pupal wings from the control eGFP line grown at 19˚C

label_protocol: For each sample, biotinylated cRNA was prepared from 2µg total RNA  according to standard Affymetrix protocols.

growth_protocol:
For sample collection, animals were grown on standard cornmeal-agar medium, strictly in uncrowded conditions. We used three different temperature-controlled incubators (LMS) at 19˚C, 25˚C and 29˚C. In all temperature shift experiments, crosses were kept at 19˚C and were shifted at the appropriate stage to 29˚C via a one-hour-incubation at 25˚C to minimize any heat-shock responses.
Specific protocol: White prepupae developing at 19˚C were collected and aged for 33.5hrs before dissection.

extract_protocol: From each sample, total RNA was extracted with Trizol (Invitrogen) followed by purification with the RNeasy Micro Kit (Qiagen), both performed according to the manufacturer's instructions.

treatment_protocol: About 15-20 animals per sample were transferred on a silicone rubber plate for dissection in 1xPBS within 20min. Dissected wings were transferred with a pipette tip (pre-coated with BSA) to a clean drop of 1xPBS. Intact wings were transferred to a 1.5ml RNAse-free tube, lysed in 300µl Trizol reagent (Invitrogen), flash frozen in liquid nitrogen and stored at -80 ºC.

tag: developmental stage

value: Pupae

tag: collection parameters

value: 33.5hrs APF at 19˚C

tag: growth temperature

value: Exclusively at 19˚C

value: w; UAS-eGFP / + ; nabGal4NP3537 / Tub-Gal80ts


title: Pupa, 29˚C, eGFP, Biol. Repl. 1

description: Control pupal wings developed at the restrictive high temperature

source_name: Pupal wings from the control eGFP line collected 16hrs after temperature shift from 19 to 29˚C

growth_protocol:
For sample collection, animals were grown on standard cornmeal-agar medium, strictly in uncrowded conditions. We used three different temperature-controlled incubators (LMS) at 19˚C, 25˚C and 29˚C. In all temperature shift experiments, crosses were kept at 19˚C and were shifted at the appropriate stage to 29˚C via a one-hour-incubation at 25˚C to minimize any heat-shock responses.
Specific protocol: White prepupae developing at 19˚C were collected, temperature shifted to 29˚C, and aged for 16hrs before dissection.

value: 16hrs APF at 29˚C

value: 19˚C and then temperature shifted to 29˚C for 16hrs


title: Pupa, 19˚C, eGFP, Biol. Repl. 1


title: Pupa, 29˚C, eGFP, Biol. Repl. 3


title: Pupa, 29˚C, Ubx, Biol. Repl. 4

description: Experimental pupal wings developed at the restrictive high temperature

source_name: Pupal wings from the experimental Ubx line collected 16hrs after temperature shift from 19 to 29˚C

value: w; UAS-UbxIa / + ; nabGal4NP3537 / Tub-Gal80ts


title: Starch sheath at 2 days NAA treatment, biological rep3

city: Wien

first: Javier

last: Agusti

address: Dr. Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute

description:
Gene expression data from stem starch sheath treated for 2 days with NAA in-vitro
2dNAA-SS3_Rep3

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

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

data_processing: The data were analyzed with the RMA method using limma and affy libraries in the Bioconductor statiscal package (R2.9.0).

source_name: Arabidopsis stem starch sheath after 2 days NAA in vitro treatment

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

growth_protocol: Plants were grown for 3 weeks on short days (8 hours light 16 hours dark)under standard conditions and then switched to lond days (16 hours light 8 hours dark)

extract_protocol: Total RNA extraction was performed using the RNeasy Plus Micro Kit (QIAGEN) following the manufacturer´s instructions.Two RNA amplification rounds were performed using the TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit (EPICENTRE Biotechnologies, Madison, WI, USA) following the manufacturer’s instructions.

treatment_protocol: Stem fragments of 1.5 cm in length located 2.5 cm apically from the base were excised with a scalpel and transferred to MS split-plates considering the original apical to basal orientation. After 2 or 5 days incubation, the central area (3 mm) of these samples, which had no direct contact with the media, was collected for snap-frozen embeding in OCT.Transversal 5 µm sections were cut with a cryostat and mounted in slides that were used to capture the appropriate tissue utilizing Laser Capture Microdissection.

value: starch sheath

tag: tissue collection method

value: laser capture microdissection

value: wild type

tag: treatment

value: NAA treatment

tag: time

value: 2 days

tag: biological rep

tag: protocol

value: Stem starch sheath under NAA in vitro treatment before cell divission


title: Pupa, 19˚C, Ubx, Biol. Repl. 2

description: Experimental pupal wings developed at the permissive low temperature

source_name: Pupal wings from the experimental Ubx line grown at 19˚C


title: Pupa, 19˚C, eGFP, Biol. Repl. 2


title: Pupa, 19˚C, Ubx, Biol. Repl. 4


title: Pupa, 19˚C, eGFP, Biol. Repl. 3


title: Pupa, 29˚C, Ubx, Biol. Repl. 2


title: Pupa, 19˚C, Ubx, Biol. Repl. 3


title: Stem tissue at 2 days NAA treatment, biological rep3

description:
Gene expression data from stem tissue treated with NAA for 2 days in vitro not containing starch sheath or vascular bundles
2dNAA-C3_Rep3

source_name: Arabidopsis stem tissue except the starch sheath and the vascular bundles after 2 days of NAA in vitro treatment

tag: tissue

value: stem tissue

value: Stem tissue with NAA treatment


title: Pupa, 29˚C, eGFP, Biol. Repl. 4


title: Cambium at 5 days NAA treatment, biological rep2

description:
Gene expression data from induced cambium after 5 days NAA in vitro treatment
5dNAA-CAM2_Rep2

source_name: Arabidopsis established interfascicular cambium after 5 daysNAA in vitro treatment

value: cambium

value: 5 days

value: Interfascicular cambium induced after 5 days NAA in vitro treatment


title: Pupa, 29˚C, Ubx, Biol. Repl. 3

value: Pupae


title: Pupa, 29˚C, eGFP, Biol. Repl. 2


title: Starch sheath at 2 days NAA treatment, biological rep2

description:
Gene expression data from stem starch sheath treated for 2 days with NAA in-vitro
2dNAA-SS2_Rep2


title: Starch sheath at 5 days MS incubation, biological rep2

description:
Gene expression data from stem starch sheath incubated for 5 days in MS media in-vitro
5dMS-SS2_Rep2

source_name: Arabidopsis stem starch sheath after 5 days MS incubation

value: MS incubation

value: Stem starch sheath incubated in MS media in vitro


title: Pupa, 19˚C, Ubx, Biol. Repl. 1

value: 33.5hrs APF at 19˚C

value: Exclusively at 19˚C


title: Prepupa, 29˚C, eGFP, Biol. Repl. 4

description: Control prepupal wings developed at the restrictive high temperature

source_name: Prepupal wings from the control eGFP line collected 16hrs after temperature shift from 19 to 29˚C

growth_protocol:
For sample collection, animals were grown on standard cornmeal-agar medium, strictly in uncrowded conditions. We used three different temperature-controlled incubators (LMS) at 19˚C, 25˚C and 29˚C. In all temperature shift experiments, crosses were kept at 19˚C and were shifted at the appropriate stage to 29˚C via a one-hour-incubation at 25˚C to minimize any heat-shock responses.
Specific protocol: Vials with wandering third instar larvae were temperature shifted from 19 to 29˚C, and 10hrs later white prepupae were collected and aged for 6hrs before dissection.

value: Prepupae

value: 6hrs APF at 29˚C

value: 19˚C and then temperature shifted to 29˚C for 16hrs

value: w; UAS-eGFP / + ; nabGal4NP3537 / Tub-Gal80ts


title: Prepupa, 29˚C, eGFP, Biol. Repl. 2


title: Prepupa, 29˚C, Ubx, Biol. Repl. 4

description: Experimental prepupal wings developed at the restrictive high temperature

source_name: Prepupal wings from the experimental Ubx line collected 16hrs after temperature shift from 19 to 29˚C

value: w; UAS-UbxIa / + ; nabGal4NP3537 / Tub-Gal80ts


title: Prepupa, 29˚C, Ubx, Biol. Repl. 2


title: Prepupa, 29˚C, eGFP, Biol. Repl. 3


title: Pupa, 29˚C, Ubx, Biol. Repl. 1

value: 16hrs APF at 29˚C


title: Prepupa, 29˚C, eGFP, Biol. Repl. 1


title: Prepupa, 29˚C, Ubx, Biol. Repl. 1


title: Prepupa, 19˚C, eGFP, Biol. Repl. 4

description: Control prepupal wings developed at the permissive low temperature

source_name: Prepupal wings from the control eGFP line grown at 19˚C

growth_protocol:
For sample collection, animals were grown on standard cornmeal-agar medium, strictly in uncrowded conditions. We used three different temperature-controlled incubators (LMS) at 19˚C, 25˚C and 29˚C. In all temperature shift experiments, crosses were kept at 19˚C and were shifted at the appropriate stage to 29˚C via a one-hour-incubation at 25˚C to minimize any heat-shock responses.
Specific protocol: White prepupae developing at 19˚C were collected and aged for 12.5hrs before dissection.

value: 12.5hrs APF at 19˚C


title: Prepupa, 19˚C, eGFP, Biol. Repl. 2


title: Prepupa, 19˚C, eGFP, Biol. Repl. 1


title: Prepupa, 19˚C, eGFP, Biol. Repl. 3


title: Prepupa, 19˚C, Ubx, Biol. Repl. 3

description: Experimental prepupal wings developed at the permissive low temperature

source_name: Prepupal wings from the experimental Ubx line grown at 19˚C


title: Larva, 29˚C, eGFP, Biol. Repl. 4

description: Control larval wing discs developed at the restrictive high temperature

source_name: Third instar larval wing discs from the control eGFP line collected 16hrs after temperature shift from 19 to 29˚C

growth_protocol:
For sample collection, animals were grown on standard cornmeal-agar medium, strictly in uncrowded conditions. We used three different temperature-controlled incubators (LMS) at 19˚C, 25˚C and 29˚C. In all temperature shift experiments, crosses were kept at 19˚C and were shifted at the appropriate stage to 29˚C via a one-hour-incubation at 25˚C to minimize any heat-shock responses.
Specific protocol: Flies were reared on standard medium supplemented with bromophenol blue (1.5g/l) at 19˚C and then shifted to 29˚C for 16 hrs. Wandering third instar larvae were staged by selecting for a medium blue gut colour intensity.

value: Wandering third instar larvae (staged by gut colour intensity)


title: Prepupa, 19˚C, Ubx, Biol. Repl. 1

value: 12.5hrs after puparium formation (APF) at 19˚C


title: Larva, 29˚C, eGFP, Biol. Repl. 3


title: Larva, 29˚C, Ubx, Biol. Repl. 1

description: Experimental larval wing discs developed at the restrictive high temperature

source_name: Third instar larval wing discs from the experimental Ubx line collected 16hrs after temperature shift from 19 to 29˚C


title: Prepupa, 19˚C, Ubx, Biol. Repl. 4


title: Larva, 19˚C, eGFP, Biol. Repl. 4

description: Control larval wing discs developed at the permissive low temperature

source_name: Third instar larval wing discs from the control eGFP line grown at 19˚C

growth_protocol:
For sample collection, animals were grown on standard cornmeal-agar medium, strictly in uncrowded conditions. We used three different temperature-controlled incubators (LMS) at 19˚C, 25˚C and 29˚C. In all temperature shift experiments, crosses were kept at 19˚C and were shifted at the appropriate stage to 29˚C via a one-hour-incubation at 25˚C to minimize any heat-shock responses.
Specific protocol: Flies were reared on standard medium supplemented with bromophenol blue (1.5g/l) at 19˚C. Wandering third instar larvae were  staged by selecting for a medium blue gut colour intensity.


title: Prepupa, 29˚C, Ubx, Biol. Repl. 3


title: Larva, 19˚C, eGFP, Biol. Repl. 2


title: Larva, 29˚C, eGFP, Biol. Repl. 1


title: Larva, 29˚C, Ubx, Biol. Repl. 2


title: Larva, 29˚C, Ubx, Biol. Repl. 4


title: Larva, 29˚C, eGFP, Biol. Repl. 2


title: Prepupa, 19˚C, Ubx, Biol. Repl. 2


title: Larva, 29˚C, Ubx, Biol. Repl. 3


title: Larva, 19˚C, eGFP, Biol. Repl. 3


title: Larva, 19˚C, Ubx, Biol. Repl. 3

description: Experimental larval wing discs developed at the permissive low temperature

source_name: Third instar larval wing discs from the experimental Ubx line grown at 19˚C


title: Larva, 19˚C, Ubx, Biol. Repl. 4


title: Larva, 19˚C, Ubx, Biol. Repl. 2


title: Larva, 19˚C, Ubx, Biol. Repl. 1


title: Anti-microbial peptides increase tolerance to oxidant stress in Drosophila melanogaster (GAL4xUAS1)

status: Public on Dec 21 2010

city: La Jolla

first: Dan

last: Zhou

address: CMG 103, 9500 Gilman Drive, MC0735

department: Pediatrics

institute: University of California, San Diego, School of Medicine

description: Adult flies from da-GAL4xUAS-AMP cross; AMP over-expression sample

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GCOS1.4 using Affymetrix default analysis settings and global scaling as normalization method.

label: Biotin

source_name: Adult flies from da-GAL4xUAS-AMP cross

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix)

extract_protocol: Total RNA was extracted using RNeasy Micro kit (Invitrogen) according to the manufacturer's instructions.

value: adult

tag: sample composition

value: 25 male + 25 female

value: Whole Organism

tag: genotype/variation

value: AMP over-expression


title: 0-2 day old D. melanogaster CG3875 Knockout flies testes-1

city: Kunming

first: Yun

last: Ding

state: Yunnan

address: #32 Jiaochang Road

country: China

institute: Chinese Academy of Sciences

description: Hybridized to Affymetrix Drosophila genome 2.0 array.

hyb_protocol: GeneChip microarrays are pre-hybridized, loaded with the fragmented target sample and hybridization buffer mix (Hybridization, Wash and Stain Kit, Affymetrix) using standard manual techniques. Arrays are hybridized for 18 hours at 45℃ with 60 rpm rotation. Washing and staining steps (Hybridization, Wash and Stain Kit, Affymetrix)  are performed by the Affymetrix Fluidics Station 450 using standard protocols.

scan_protocol: Arrays are scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The data is analyzed using Affymetrix GeneChip Operating Software Version1.4.

source_name: testes of 0-2 day old CG3875 knockout flies

label_protocol: Biotin-labeled cRNA is synthesized by in vivo transcription reaction at 37℃ for 16 hours and then subjected to purification and fragmentation (MessageAmp II-Biotin, Ambion).

extract_protocol: Total RNA is extracted with Trizol reagent (Invitrogen) following manufacturer's instructions and purified using RNeasy MinElute Cleanup Kit (Qiagen).

value: CG3875 Knockout

tag: sex

value: male

tag: age

value: 0-2 day

value: testes


title: 7-day-old seedling of Ws at control condition, biological rep1

status: Public on Dec 23 2010

city: Shulin City, Taipei County

first: Hsiang-chin

last: Liu

address: 9F., No.332, Xuefu Rd.

country: Taiwan

institute: Academia sinica

description: Gene expression data from seedling at control condition

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

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

data_processing: The data were analyzed with GeneChip Operation System 1.4 (GCOS 1.4) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

growth_protocol: Col-0, Ws and QK were grown at 22°C on 0.5x MS plates containing 1% sucrose for 7 days.

extract_protocol: Total RNA was extracted using RNeasy RNA extraction kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: Samples were incubated for 1 h at 37 °C then collected for RNA extraction.

value: seedling

tag: genotype

value: Ws

value: 7 day old


title: Anti-microbial peptides increase tolerance to oxidant stress in Drosophila melanogaster (UAS3)

description: Adult flies from UAS-AMP control

source_name: Adult flies from UAS-AMP stock

value: control


title: dsr1 mock treated  biological rep 1

status: Public on Dec 14 2010

city: Wembley

first: Cynthia

last: Gleason

state: WA

address: Private Bag #5

department: Plant Industry

country: Australia

institute: CSIRO

description: Gene expression data from dsr1 seedlings that contain the GSTF8::LUC reporter treated with water (mock)

hyb_protocol: cRNA was hybridized to the GeneChip® Arabidopsis ATH1 Genome Array using a Genechip instrument system with scanner 3000 7G and autoloader for expression array processing and analysis, following manufacturer's protocol.  Labeling, hybing and scanning were performed at the Australian Genome Research Facility.

scan_protocol: Genechips were scanned Affymetrix GeneChip scanner 3000 7G

data_processing: The raw data files underwent background correction, normalization, probe specific correction, and summary value computation using the Robust Multichip Average (RMA) method in the Bioconductor package.  To find the differentially expressed genes we utilized the limma package for R to calculate the Log2 fold change, the moderate t-statistic, B value, and the adjusted p value (Benjamini–Hochberg FDR) for each array probe.

source_name: whole seedlings, mock treated, 10 hr

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

growth_protocol: WT (a Columbia line containing a -800GSTF8::LUC reporter) and dsr1 (an EMS mutant of the Columbia line containing a -800GSTF8::LUC reporter) Arabidopsis seeds were stratified for 3 days at 4ºC.  They were germinated on MS-media and grown in a  21ºC growth room with a 16 hour light/ 8 hour dark cycle.  4 day old seedlings were used in this experiment.

extract_protocol: Total RNA was extracted using the Qiagen Rneasy kit, following manufacturer's instructions

treatment_protocol: 5 ml of either water (mock) or 1 mM salicylic acid (SA) was poured onto 56 mm Petri dishes containing 4-day old seedlings. After 40 min of incubation at room temperature, the excess liquid was discarded.  Ten hours after treatment, samples were collected.

value: Whole seedling

tag: agent

value: mock

tag: genetic background


title: 0-2 day old D. melanogaster CG3875 Wildtype flies testes-1

source_name: testes of 0-2 day old CG3875 wildtype flies

value: Wildtype


title: 0-2 day old D. melanogaster CG3875 Knockout flies testes-2


title: Larva, 19˚C, eGFP, Biol. Repl. 1

value: Wandering third instar larvae (staged by gut colour intensity)

value: Exclusively at 19˚C

value: w; UAS-eGFP / + ; nabGal4NP3537 / Tub-Gal80ts


title: 7-day-old seedling of Ws at HS condition, biological rep2

description: Gene expression data from seedling at heat shock condition

value: heat shocked


title: Anti-microbial peptides increase tolerance to oxidant stress in Drosophila melanogaster (GAL4xUAS2)

value: adult

value: 25 male + 25 female

value: Whole Organism


title: 7-day-old seedling of Ws at control condition, biological rep2


title: 0-2 day old D. melanogaster CG3875 Wildtype flies testes-2

value: male


title: 7-day-old seedling of Ws at HS condition, biological rep1


title: WT mock treated  biological rep 3

description: Gene expression data from WT seedlings that contain the GSTF8::LUC reporter treated with water (mock)

value: WT


title: WT SA treated  biological rep 3

description: Gene expression data from WT seedlings that contain the GSTF8::LUC reporter treated with salicylic acid

source_name: whole seedlings, SA treated, 10 hr

value: salicylic acid


title: Anti-microbial peptides increase tolerance to oxidant stress in Drosophila melanogaster (GAL4xUAS3)

value: AMP over-expression


title: dsr1 mock treated  biological rep 3


title: WT mock treated  biological rep 2


title: WT SA treated  biological rep 2


title: Anti-microbial peptides increase tolerance to oxidant stress in Drosophila melanogaster (UAS2)

description: Adult flies from UAS-AMP control


title: phr1 phl1 Root-Pi, biological rep1

status: Public on Dec 09 2010

city: Campus de Cantoblanco

first: Regla

last: Bustos

state: Madrid

address: Darwin 3

institute: CNB-CSIC

description: Gene expression data from roots of phr1-phl1 double mutants grown in Johnson solid media lacking Pi.

hyb_protocol: 10µg of fragmented cRNA were hybridized to the Arabidopsis ATH1 Genome array (Affymetrix, SantaClara, CA), containing 22500 transcript variants from 24000 well -characterized Arabidopsis thaliana genes. Each sample was added to a hybridization solution containing 100mM2-(N-morpholino) ethanesulfonic acid, 1M Na+,and 20mM of EDTA in the presence of 0.01% of Tween-20 to a final cRNA concentration of 0.05µg/ml. Hybridization was performed for 16 h at 45ºC . Each microarray was washed and stained with streptavidin-phycoerythrin in a Fluidics station 450 (Affymetrix)

scan_protocol: Each microarray was scanned at 2.5 µm resolution in a GeneChip® Scanner 3000 7G System (Affymetrix)

data_processing: Analysis was performed using the affylmaGUI R package (Wettenhall et al, 2006). Robust Muti-array Analysis (RMA) algorithm was used for background correction, normalization and expression levels summarization (Irizarry et al., 2003).

source_name: roots from phr1-phl1 double mutants grown in media lacking Pi

label_protocol: Each RNA preparation was tested for degradation using the Agilent 2100 Bioanalyzer (Agilent technologies, Palo Alto, CA). cDNA was synthesized from 4 µg of total RNA using One-cycle target labeling and control reagents(Affymetrix, Santa Clara, CA) to produce biotin-labeled cRNA. The cRNA preparations (15 µg) were fragmented at 94ºC for 35 min into 35-200 bases in length.

growth_protocol: Plants were grown for 7 days in solid Johnson medium containing 2% sucrose and either 2mM Pi (KH2PO4) for complete medium (+Pi) or in phosphate-lacking medium (-Pi).

extract_protocol: The RNA from root and shoot samples processed separately was isolated using RNeasy plant mini kit from Quiagen

value: roots

value: phr1-phl1 double mutants


title: phr1 phl1 Shoot-Pi, biological rep3

description: Gene expression data from shoots of phr1-phl1 double mutants grown in Johnson solid media lacking Pi.

source_name: shoots from phr1-phl1 double mutants grown in media lacking Pi

value: shoots


title: phr1 Root-Pi, biological rep1

description: Gene expression data from roots of phr1 mutants grown in Johnson solid media lacking Pi.

source_name: roots from phr1 mutants grown in media lacking Pi

value: phr1 mutants


title: phr1 Root-Pi, biological rep3


title: phr1 phl1 Root-Pi, biological rep3


title: Anti-microbial peptides increase tolerance to oxidant stress in Drosophila melanogaster (UAS1)

description: Adult flies from UAS-AMP control

value: control


title: phr1 phl1 Root-Pi, biological rep2


title: phr1 Shoot-Pi, biological rep3

description: Gene expression data from shoots of phr1 mutants grown in Johnson solid media lacking Pi.

source_name: shoots from phr1 mutants grown in media lacking Pi


title: WT Root-Pi, biological rep2

description: Gene expression data from roots of wild type plants grown in Johnson solid media lacking Pi.

source_name: roots from wild type plants grown in media lacking Pi

value: wild type


title: phr1 Root-Pi, biological rep2


title: WT Root-Pi, biological rep1


title: phr1 phl1 Shoot-Pi, biological rep1


title: WT Root+Pi, biological rep1

description: Gene expression data from roots of wild type plants grown in Johnson solid media in presence of Pi.

source_name: roots from wild type plants grown in presence of Pi


title: phr1 phl1 Shoot-Pi, biological rep2


title: WT Shoot-Pi, biological rep2

description: Gene expression data from shoots of wild type plants grown in Johnson solid media lacking Pi.

source_name: shoots from wild type plants grown in media lacking Pi


title: WT Shoot-Pi, biological rep3


title: phr1 Shoot-Pi, biological rep1


title: WT Shoot-Pi, biological rep1


title: WT Shoot+Pi, biological rep1

description: Gene expression data from shoots of wild type plants grown in Johnson solid media in presence of Pi.

source_name: shoots from wild type plants grown in presence of Pi


title: WT Root+Pi, biological rep2


title: phr1 Shoot-Pi, biological rep2


title: WT Root-Pi, biological rep3


title: WT Root+Pi, biological rep3


title: WT Shoot+Pi, biological rep2


title: WT Shoot+Pi, biological rep3


title: Embryos (4-8hr), w1118, Biological Replicate 3

status: Public on Dec 07 2010

city: Brisbane

first: Gareth

last: Price

state: Queensland

address: Carmody Road

institute: Queensland Facility for Advanced Bioinformatics

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

scan_protocol: GeneChips were scanned on a GeneChip Scanner 3000 with High Resolution (7G) capacity

data_processing: Data was extracted using GCOS 1.4, using Affymetrix supplied default settings with data analysed using Global Scaling for normalisation, set to 100.

source_name: 4-8 hour Drosophila melanogaster embryos

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

growth_protocol: All the Drosophila stocks and flies were maintained in vials containing Fortified (FI) medium and kept at either 18°C or 25°C. The FI medium was composed of 1% agar, 18.75% compressed yeast, 10% polenta, 10% treacle, 1.5% acid mix and 2.5% tegosept.

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

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

value: Embyros


title: Embryos (4-8hr), Wwox, Biological Replicate 2

description: Wwox1  (for 67-2) (Ref: O’Keefe LV et al (2005) FRA16D common chromosomal fragile site oxido-reductase (FOR/WWOX) protects against the effects of ionizing radiation in Drosophila. Oncogene 29, 6590-6)


title: Embryos (4-8hr), Wwox, Biological Replicate 3


title: Embryos (4-8hr), Wwox, Biological Replicate 1


title: Embryos (4-8hr), w1118, Biological Replicate 2


title: Embryos (4-8hr), Wwoxf04545, Biological Replicate 2

description: Wwoxf04545 (for pBac) (Bloomington Drosophila Stock Centre 2004.11.6)


title: Embryos (4-8hr), Wwoxf04545, Biological Replicate 3


title: Embryos (4-8hr), Wwoxf04545, Biological Replicate 1


title: Embryos (4-8hr), w1118, Biological Replicate 1


title: normal mouse kidney E12.5, biological rep 2

city: Toronto

first: Brian

middle: Joseph

last: Cox

state: Ontario

address: 1 King's College Circle, Rm 3360

department: Physiology

country: Canada

institute: University of Toronto

description: Expression data for normal mousee embryonic day E12.5 kidney

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

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

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

organism: Mus musculus

source_name: normal mouse embryonic kidney day 12.5

label_protocol: one cycle amplification as per Affymetrix protocol from 1ug of total RNA

extract_protocol: Samples were stored in RNAlater RNA stabilization reagent (Qiagen, Canada) and then isolated using the RNeasy Micro kit (Qiagen, Canada).

treatment_protocol: tissue was disected, imaged by digital microscopy and randomly sorted into one of three sample vials

tag: pool of 3 normal E12.5 kidneys


title: gpa1 +ABA LF repl1

status: Public on Dec 06 2010

city: State College

first: Sarah

middle: M.

last: Assmann

state: PA

address: 210 Mueller Laboratory, University Park

institute: Pennsylvania State University

description: Gene expression data from gpa1 mutant leaves treated with ABA (50 μM) for 3 hrs

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: The RMA method implemented in the affy package in the bioconductor project (http://bioconductor.org/packages/release/bioc/html/affy.html) was used to normalize the data for the entire probe sets using default parameters (PMID: 14960456).

source_name: gpa1 mutant leaves, abscisic acid treatment

label_protocol: RNA samples exhibiting a 25S/18S ratio >1.4 and no significant degradation in Bioanalyzer profiles (Agilent Technology, Palo Alto, CA) were used for cDNA and then cRNA synthesis.

growth_protocol: Arabidopsis plants were grown in growth chambers with an 8 hr light/16hr dark, 20oC/18oC cycle, with light intensity of 120 µmol m-2s-1.

extract_protocol: Three hundred Arabidopsis leaves excised from 60-70 five-week-old plants were used as the starting material for each guard cell microarray. Ten mature leaves taken from 3-4 plants grown side-by side with the plants for guard cell isolation were used for each leaf sample. Total RNA was isolated from each sample using Trizol reagent (Invitrogen). Trizol-isolated RNA was further purified using the Plant RNeasy kit (Qiagen, Valencia, CA).

treatment_protocol: Leaves were incubated in ddH2O containing 50 micromolar ABA for 3 hours

tag: ecotype

value: Columbia (Col-0)

value: gpa1-4 mutant

value: Leaves of five week-old plants


title: agb1 gpa1 +ABA LF repl1

description: Gene expression data from agb1 gpa1 mutant leaves treated with ABA (50 μM) for 3 hrs

source_name: agb1 gpa1 mutant leaves, abscisic acid treatment

value: agb1-2 gpa1-4 double mutant


title: agb1 gpa1 -ABA LF repl1

description: Gene expression data from agb1 gpa1 mutant leaves treated with EtOH (solvent control) for 3 hrs

source_name: agb1 gpa1 mutant leaves, no treatment


title: agb1 +ABA LF repl1

description: Gene expression data from agb1 mutant leaves treated with ABA (50 μM) for 3 hrs

source_name: agb1 mutant leaves, abscisic acid treatment

value: agb1-2 mutant


title: Col-0 +ABA LF repl3

description: Gene expression data from wild type (Col) leaves treated with ABA (50 μM) for 3 hrs

source_name: Columbia wild-type leaves, abscisic acid treatment


title: gpa1 -ABA LF repl3

description: Gene expression data from gpa1 mutant leaves treated with EtOH (solvent control) for 3 hrs

source_name: gpa1 mutant leaves, no treatment


title: gpa1 -ABA LF repl1


title: Col-0 +ABA LF repl2


title: Col-0 +ABA LF repl1


title: normal mouse kidney E12.5, biological rep 1


title: agb1 gpa1 +ABA LF repl3


title: gpa1 +ABA LF repl3


title: agb1 gpa1 -ABA LF repl3


title: agb1 +ABA LF repl3


title: normal mouse kidney E12.5, biological rep 3


title: agb1 gpa1 -ABA LF repl2


title: agb1 +ABA LF repl2


title: gpa1 +ABA LF repl2


title: agb1 gpa1 +ABA LF repl2


title: gpa1 -ABA LF repl2


title: agb1 -ABA LF repl3

description: Gene expression data from agb1 mutant leaves treated with EtOH (solvent control) for 3 hrs

source_name: agb1 mutant leaves, no treatment


title: Col-0 -ABA LF repl3

description: Gene expression data from wild type (Col) leaves treated with EtOH (solvent control) for 3 hrs

source_name: Columbia wild-type leaves, no treatment


title: Col-0 -ABA LF repl2


title: agb1 -ABA LF repl1


title: Col-0 -ABA LF repl1


title: agb1 gpa1 +ABA GC repl1

description: Gene expression data from agb1 gpa1 mutant guard cells treated with ABA (50 μM) for 3 hrs

source_name: agb1 gpa1 mutant guard cells, abscisic acid treatment

value: Guard cells taken for mature leaves of five week-old plants


title: agb1 gpa1 +ABA GC repl3


title: gpa1 +ABA GC repl2

description: Gene expression data from gpa1 mutant guard cells treated with ABA (50 μM) for 3 hrs

source_name: gpa1 mutant guard cells, abscisic acid treatment


title: gpa1 -ABA GC repl2

description: Gene expression data from gpa1 mutant guard cells treated with EtOH (solvent control) for 3 hrs

source_name: gpa1 mutant guard cells, no treatment


title: Col-0 +ABA GC repl1

description: Gene expression data from wild type (Col) guard cells treated with ABA (50 μM) for 3 hrs

source_name: Columbia wild-type guard cells, abscisic acid treatment


title: Col-0 +ABA GC repl2


title: gpa1 -ABA GC repl1


title: agb1 -ABA GC repl3

description: Gene expression data from agb1 mutant guard cells treated with EtOH (solvent control) for 3 hrs

source_name: agb1 mutant guard cells, no treatment


title: agb1 -ABA LF repl2


title: agb1 +ABA GC repl3

description: Gene expression data from agb1 mutant guard cells treated with ABA (50 μM) for 3 hrs

source_name: agb1 mutant guard cells, abscisic acid treatment


title: agb1 +ABA GC repl1


title: agb1 gpa1 +ABA GC repl2


title: agb1 +ABA GC repl2


title: agb1 gpa1 -ABA GC repl3

description: Gene expression data from agb1 gpa1 mutant guard cells treated with EtOH (solvent control) for 3 hrs

source_name: agb1 gpa1 mutant guard cells, no treatment


title: agb1 gpa1 -ABA GC repl1


title: Col-0 +ABA GC repl3


title: gpa1 +ABA GC repl3


title: agb1 -ABA GC repl1


title: agb1 gpa1 -ABA GC repl2


title: Col-0 -ABA GC repl3

description: Gene expression data from wild type (Col) guard cells treated with EtOH (solvent control) for 3 hrs

source_name: Columbia wild-type guard cells, no treatment


title: gpa1 -ABA GC repl3


title: Col-0 -ABA GC repl1


title: agb1 -ABA GC repl2


title: Col-0 -ABA GC repl2


title: dTIP60E431Q, Biological Rep2

status: Public on Nov 29 2010

city: Philadelphia

first: Felice

last: Elefant

address: 3141 Chestnut Street, Stratton Hall 226

institute: Drexel University

description: Gene expression data

hyb_protocol: Performed by Seqwright: 10 ug of Biotin-labeled cRNA in 200ul hybridization cocktail was injected onto each array and hybridized at 45°C for 16 hours with rotation of 60 rpm in a GeneChip Hybridization Oven 640 (Affymetrix). Staining and washing of each array was performed on a GeneChip Fluidics Station 450 (Affymetrix) using Streptavidin Phycoerythrin (Invitrogen Cat. No. S866), goat IgG (Sigma Cat. No. I 5256) and Biotinylated anti-streptavidin antibody (Vector Laboratories Cat. No. BA-0500).

scan_protocol: Performed by Seqwright: Each array was scanned with a GeneChip 7G Plus Scanner (Affymetrix) to acquire the raw image and Affymetrix GCOS software was used to process the data.

data_processing: Expression values were generated in dCHIP using model-based expression algorithms and the perfect match/mismatch model (PM/MM). Array intensities were normalized to the array with median intensity. Probe sets were filtered using a Student's t-test and p<0.05, fold change >2, and a 90% confidence bound. Correlation coefficients showed good agreement between duplicate samples.

source_name: Drosophila larvae, ubiquitously expressing dTIP60 HAT mutant

label_protocol: Performed by Seqwright using Affymetrix GeneChip 3' IVT Express Target Amplification, Labeling, and Control kit (Affymetrix Cat. No. 901229): 500 ng of total RNA was used for 1st and 2nd strand cDNA synthesis with oligo-dT containing T7 promoter. This synthesized double-stranded cDNA was used as template to generate Biotin-labeled cRNA, which was fragmented to 35-200 bases in size using fragmentation buffer.

growth_protocol: Virgin female w1118, dTIP60E431Q, and dTIP60WT flies were crossed to 337-GAL4 males that express GAL4 ubiquitously at 25°C. Fertilized embryos were collected in 3-hour intervals and incubated at 25°C for three days.

extract_protocol: Total RNA was isolated from a pool of 35 larvae for each chip using Trizol according to the manufacturer's instructions and was treated twice with Dnase II according to the manufacturer's instructions.

treatment_protocol: Ubiquitous UAS expression with the 337-GAL4 driver.

value: 35 whole larvae

value: GAL4-337 and dTIP60E431Q parents


title: Arabidopsis_npr1 sni1 ssn2 _triple water_3

city: Durham

first: shui

last: wang

address: 124 Science Dr

institute: Duke University

description: 3-week-old soil grown plants

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on Affymetrix ATH1 GeneChip (Santa Clara, CA, U.S.A).

scan_protocol: GeneChips were scanned using the Axon Genepix Scanner (Genepix 4000B).

data_processing: The GSE23617_SSN2_raw_data.txt data refer to the linear data which has been summarized using a summarization algorithm (RMA16, PLIER 16 and Iterative PLIER 16). All summarization algorithms also do variance stabilization by adding 16.The normalized data are generated after the log transformation and baseline transformation step.

label_protocol: RNA probes were labelled using the Ambion MessageAmp Premier.

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

extract_protocol: Total RNA was isolated from the frozen material using Qiagen Rneasy Plant Mini kit

treatment_protocol: 3-week old npr1 sni1 brca2a mutants were treated with 0.5 mM salicylic acid for 16 hours.  Replicates are derived from two (SA treated) or three (water treated) independent biological experiments.

value: seedling

value: npr1 sni1 ssn2

value: water

value: 16 hours


title: Arabidopsis_npr1 sni1 ssn2 _triple water_1

description: 3-week-old soil grown plants

tag: pathogen


title: Arabidopsis_npr1 sni1 ssn2_triple SA_2

description: 3-week-old soil grown plants

value: salicylic acid


title: Control, Biological Rep1

description: Gene expression data

source_name: Drosophila larvae, wild type

value: GAL4-337 and w1118 parents


title: dTIP60WT, Biological Rep1

description: Gene expression data

source_name: Drosophila larvae, ubiquitously expressing dTIP60 wild type

value: GAL4-337 and dTIP60WT parents


title: Triple_SA_rep1

status: Public on Nov 21 2010

description: 3-week-old soil grown plants

scan_protocol: GeneChips were scanned according to Affymetrix protocol.

data_processing: The GSE23617_BRCA2A_raw_data.txt refer to the linear data which has been summarized using a summarization algorithm (RMA16, PLIER 16 and Iterative PLIER 16). All summarization algorithms also do variance stabilization by adding 16. The normalized data are generated after the log transformation and baseline transformation step.

treatment_protocol: 3-week old npr1 sni1 and npr1 sni1 brca2a mutants were treated with 0.5 mM salicylic acid for 16 hours. Replicates are derived from three independent biological experiments.

value: npr1 sni1 brca2a


title: dTIP60WT, Biological Rep2

description: Gene expression data


title: Arabidopsis_npr1 sni1 ssn2 _triple water_2

description: 3-week-old soil grown plants


title: Double_SA_rep1

description: 3-week-old soil grown plants

value: npr1 sni1


title: Control, Biological Rep2

description: Gene expression data


title: Third instar Dm larvae control 6hrs

status: Public on Nov 23 2010

city: New York

first: Shubha

last: Govind

state: NY

address: 160 Convent Avenue

institute: The City College of New York

hyb_protocol: The biotin labeled cRNA was fragmented and hybridized to the Affymetrix Drosophila Genome  2.0 GeneChip arrays (Santa Clara, CA) for analysis of over 18,000 transcripts on a single array.

scan_protocol: After Hybridization, GeneChip arrays was washed, stained, and scanned by GeneChip Scanner 3000 7G according to the Affymetrix Expression Analysis technical Manual.

data_processing: Affymetrix GeneChip Operating Software was used for image acquisition. The target signal intensity from each chip was scaled to 500. The data normalization, statistical analysis, and pattern study were performed with GeneSpring software (Agilent, Redwood City, CA). Gene Ontology analysis using Pathway Express software allows mapping of differently expressed genes to the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways (http://www.genome.jp/kegg)

source_name: Whole body

label_protocol: The cDNA was synthesized with a primer containing oligo (dT) and T7 RNA polymerase promoter sequences. Double-stranded cDNA was then purified and used as a template to generate biotinylated cRNA. The quantity and quality of the amplified cRNA was assessed using NanoDrop ND-1000 Spectrophotometer (Thermo Scientific, Wilmington, DE) and Agilent Bioanalyzer (Santa Clara CA).

growth_protocol: Host y w P1 were placed in vials containing typical fly food (sugar/agar) for a 2-day egglay. P1 were removed and F1 were grown until the third instar. Parasitic wasps P1 were reared on typical household honey diluted with water (4:1 water to honey). For experinmental class, host larvae and parasites were combined in fly food contaning petri-dish for respective time points (3 or 6 hours). Wasps were thereupon removed and dissection/treatment began. For control, same steps were taken except wasps were not introduced to the petri-dish

extract_protocol: Total RNA was isolated by using Qiagen RNeasy mini kit (Valencia, CA) and then Affymetrix a one-round in vitro transcription (IVT) RNA Amplification Kit was used to amplify 1.5 microgram amounts of total RNA.

treatment_protocol: Immediately after wasps were removed and infection was verified, larvae were placed in liquid nitrogen and ground in Trizol. RNA was extracted and checked by agarose gel-electrophoresis to ensure integrity

tag: time point

value: Yellow white

value: Third instar larvae

tag: infection

value: Control


title: Arabidopsis_npr1 sni1 ssn2_triple SA_1

description: 3-week-old soil grown plants

tag: treatment


title: Third instar Dm larvae post Gx infection 3hrs

value: Ganaspis xanthopoda


title: Double_water_rep3

description: 3-week-old soil grown plants

tag: time


title: Third instar Dm larvae post Gx infection 6hrs


title: Double_SA_rep3

description: 3-week-old soil grown plants


title: Triple_water_rep3

description: 3-week-old soil grown plants


title: Triple_SA_rep3

description: 3-week-old soil grown plants


title: Triple_water_rep2

description: 3-week-old soil grown plants


title: Third instar Dm larvae control 3hrs


title: Triple_SA_rep2

description: 3-week-old soil grown plants


title: Triple_water_rep1

description: 3-week-old soil grown plants


title: Double_water_rep2

description: 3-week-old soil grown plants


title: dTIP60E431Q, Biological Rep1

description: Gene expression data


title: Double_SA_rep2

description: 3-week-old soil grown plants


title: Double_water_rep1

description: 3-week-old soil grown plants


title: Root_submergence_7h_rep2

status: Public on Nov 12 2010

city: Riverside

first: Seung Cho

last: Lee

address: 2150 Batchelor Hall

department: Botany & Plant Sciences

institute: University of California Riverside

hyb_protocol: 12 μg labeled cRNA was hybridized against Arabidopsis ATH1 Genome Array (Affymetrix) at 45 °C for 16 h, on a rotating platform.

scan_protocol: GeneChips were scanned by use of the Affymetrix GeneChip Workstation Scanner 3000.

data_processing: CEL files from the Affymetrix Chips were processed by use of the R program (http://cran.at.r-project.org/) and Bioconductor packages (http://www.bioconductor.org/). The Robust Multi-chip Average (RMA) normalization was performed using the default settings of the corresponding R function. Present, Marginal or Absent (P/M/A) calls were computed with the affy package.

source_name: Root tissues at 9-10 leaf developmental stage, 7 h submergence in darkness

label_protocol: Biotin-labeled cRNA was synthesized from 500 ng total RNA with the Affymetrix 3’ IVT Express Labeling kit.

growth_protocol: Arabidopsis thaliana seeds were sown in pots containing soil and perlite in a 1:2 volume mixture supplemented with 0.14 mg MgOCaO (17%; Vitasol BV, Stolwijk, The Netherlands) and 0.14 mg Osmocote (Scotts Europe, Heerlen, The Netherlands) per pot. The seeds were cold treated at 4 °C in the dark for 4 d and then grown for 8 d in a chamber at 20°C, 70% (v/v) relative humidity, with a 9 h photoperiod (200 μmol m-2s-1 photosynthetic active radiation). Individual seedlings were transplanted to a pot and fertilized with a nutrient solution (2.6 mM KNO3, 2.0 mM Ca [NO3]2, 0.6 mM KH2PO4, 0.9 mM MgSO4, 6.6 μM MnSO4, 2.8 μM ZnSO4, 0.5 μM CuSO4, 66 μM H3BO3, 0.8 μM Na2MoO4 and 134 μM Fe-EDTA, pH 5.8). Each pot was covered with a thin mesh fabric secured with a rubber band to limit loss of soil upon submergence. Pots were watered from the bottom every day at the beginning of the photoperiod.

extract_protocol: Total RNA was extracted from frozen pulverized plant tissue using the RNeasy Plant Mini Kit (Qiagen), quantified by detection of A260/A280 ND with NanoDrop ND-1000 UV-Vis spectrophotometer. The quality of the RNA was evaluated using the Agilent 2100 Bioanalyzer with the RNA 6000 Nano reagent kit.

treatment_protocol: Plants were grown in individual pots in soil for 8 d in a chamber at 20 °C, 70% (v/v) relative humidity, with a 9 h photoperiod (200 μmol m-2s-1 photosynthetic active radiation). Plants of uniform size with 9 to 10 leaves were selected the day prior to treatments Two h into the light period, pots were completely submerged in water-filled tanks that had been been left standing for 24 h at 20 oC. Submergence was in complete darkness. Control plants were maintained in the growth chamber (light control, watered every day) or in the dark in the same chamber used for the submergence treatments (dark control, watered every other day).

tag: developmental stage

value: rosette plants with 9-10 leaves

value: whole root

value: 7 h submergence in darkness


title: Shoot_submergence_7h_rep1

source_name: Shoot tissues at 9-10 leaf developmental stage, 7 h submergence in darkness

value: whole shoot


title: Shoot_dark_control_7h_rep2

source_name: Shoot tissues at 9-10 leaf developmental stage, 7 h non-submerged dark condition

value: 7 h non-submerged dark condition


title: Shoot_submergence_7h_rep2


title: Shoot_light_control_rep2

source_name: Shoot tissues at 9-10 leaf developmental stage, non-submerged light condition

value: non-submerged light condition


title: Shoot_submergence_24h_rep1

source_name: Shoot tissues at 9-10 leaf developmental stage, 24 h submergence in darkness

value: 24 h submergence in darkness


title: Shoot_light_control_rep1


title: Shoot_dark_control_24h_rep1

source_name: Shoot tissues at 9-10 leaf developmental stage, 24 h non-submerged dark condition

value: 24 h non-submerged dark condition


title: Root_dark_control_7h_rep2

source_name: Root tissue at 9-10 leaf rosette stage, non-submerged dark condition

value: rosette stage with 9-10 leaves

value: non-submerged dark condition for 7 hours


title: Shoot_submergence_24h_rep2


title: Root_dark_control_7h_rep1


title: Root_submergence_24h_rep2

source_name: Root tissues at 9-10 leaf developmental stage, 24 h submergence in darkness


title: Root_submergence_7h_rep1


title: Root_dark_control_24h_rep2

value: non-submerged dark condition for 24 hours


title: Shoot_dark_control_24h_rep2

value: 24 h non-submerged dark dondition


title: Root_submergence_24h_rep1


title: Shoot_dark_control_7h_rep1


title: Root_dark_control_24h_rep1


title: Root_light_control_rep2

source_name: Root tissue at 9-10 leaf rosette stage, non-submerged light condition


title: Root_light_control_rep1


title: ATH1_upb1-1_meristematic zone_second biological rep

first: HIRONAKA

last: TSUKAGOSHI

address: 4128 FFSC Building

institute: Duke university

description: Gene expression data from root meristem zone of upb1-1 under standard conditions for 6 days

hyb_protocol: Samples were submitted to Duke Microarray Facility (Durham, NC) for hybridization to Affymetrix ATH1 microarrays.

source_name: root meristem zone

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

growth_protocol: Seeds were surface sterilized for 5 minutes in 30% Bleach and 0.02% Triton X-100 for 15 minutes. Seeds were rinsed 3 times with sterile water, stratified for 4˚C for 2 days, then placed on standard media. Standard media is 1X Murashige and Skoog salt mixture, 1% sucrose, 1% agar and adjusted to pH 5.7 with KOH and seeds were planted at 5 seeds/cm in two rows.

extract_protocol: Approximately 60 roots were collected per replicate.  Samples were briefly sonicated to disrupt the tissue.  RNA was extracted using the RNAeasy Micro Kit (Qiagen).

treatment_protocol: Seedlings were grown for 6 days.  Roots were cut into the meristematic and elongation zone with a razor blade under microscope and collected into RNA extraction buffer.  Approximately 60 roots were collected per replicate, with two biological replicates being performed per sample.  Samples were briefly sonicated to disrupt the tissue.

value: Seedling root meristem zone

value: 6 days after germination

tag: growth media

value: Standard media (1xMS, 1% Sucrose, 1% agarose)


title: ATH1_Col-0_meristematic zone_first biological rep

description: Gene expression data from root meristem zone of Col-0 under standard conditions for 6 days

scan_protocol: Samples were submitted to Duke Microarray Facility (Durham, NC) for hybridization to Affymetrix ATH1 microarrays.

tag: tissue


title: ATH1_Col-0_elongation zone_second biological rep

description: Gene expression data from root elongation zone of Col-0 under standard conditions for 6 days

source_name: root elongation zone

value: Seedling root elongation zone


title: ATH1_upb1-1_meristematic zone_first biological rep


title: 15m.KNO3.2

status: Public on Nov 10 2010

city: Montpellier

first: Gabriel

last: Krouk

address: 2 Place Pierre Viala

institute: CNRS

description: replicate:  2

hyb_protocol: Affy

scan_protocol: The Affy ATH1 chips have been processed and scanned according to the manufacturer protocol or as described by Krouk et al. PLoS Comput Biol 2009, 5(3):e1000326.  The Scanner is an Affymetrix GeneChip(R) scanner 3000 7G.

source_name: 14 day old Roots

label_protocol: Affy

growth_protocol: arabidopsis are grown hydroponically for 14 days

extract_protocol: Plants have been extracted by Trizol reagent according to the manufacturer protocol.

treatment_protocol: High resolution NO3 treatments

value: 14 day old Roots

tag: time (minutes)


title: ATH1_upb1-1_elongation zone_second biological rep

description: Gene expression data from root elongation zone of upb1-1 under standard conditions for 6 days


title: 15m.KNO3.1

description: replicate:  1


title: ATH1_upb1-1_elongation zone_first biological rep


title: ATH1_Col-0_meristematic zone_second biological rep


title: 15m.KCl.2

description: replicate:  2

value: KCl


title: 6m.KCl.2

description: replicate:  2


title: 12m.KCl.2

description: replicate:  2


title: 3m.KCl.2

description: replicate:  2


title: 12m.KNO3.2

description: replicate:  2


title: 12m.KNO3.1

description: replicate:  1


title: 3m.KNO3.1

description: replicate:  1


title: 3m.KNO3.2

description: replicate:  2


title: 12m.KCl.1

description: replicate:  1


title: 6m.KNO3.1

description: replicate:  1


title: 3m.KCl.1

description: replicate:  1


title: 15m.KCl.1

description: replicate:  1


title: 6m.KCl.1

description: replicate:  1


title: 6m.KNO3.2

description: replicate:  2