title: 0.6% METH_treated 2

status: Public on Oct 31 2010

city: Urbana

first: Hongmei

last: LI

state: IL

address: 505 S. Goodwin Ave

department: Entomology

institute: University of Illinois at Urbana-Champaign

description: Gene expression data from the virgin male Drosophila whole body

hyb_protocol: Amplified cRNA was hybridized to Affymetrix Drosophila Genome 2.0 Arrays (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000

data_processing: Gene chip-operating software (GCOS 1.4) was used to quantify the images.

source_name: whole body

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Flies are reared on the Formula 24® Drosophila diet (Carolina Biological Supply, Burlington, NC) at 22-23 °C and 60-70 % humidity.

extract_protocol: Total RNA were extracted using Trizol reagent for each replicate (Invitrogen Life Technologies, Carlsbad, CA). Three replicated were used for control and methamphetamine treated flies separately. DNA contamination were removed by DNaseI set (Qiagen Inc., Valencia, CA) followed by another step of Trizol extraction to remove DNase.

treatment_protocol: Virgin male flies were collected at the 6th-7th hour of eclosion from the pupa (Ashburner, 1989). These virgin male flies were cultured for 5 days. The 5 days old virgin male flies were place on the following diet for 24 h to feed by themselves: 0.6% methamphetamine fly diet. A total of 20 flies were placed on each replicate diet. A total of three biological replicates were performed for each experiment. At the end of the 24 h feeding period the 20 flies were collected, flash-frozen in liquid nitrogen, and stored at -80 oC. These samples were subsequently used perform the DNA oligo array experiment or metabolite analyses.

tag: strain

tag: gender

value: virgin male

value: 5 days old

value: whole body, 20 flies

tag: feeding diet

value: :0.6% methamphetamine + blue diet


title: 0.6% METH_treated 3

type: RNA

country: USA

label: biotin

molecule: total RNA

organism: Drosophila melanogaster

tag: age

tag: tissue


title: 0.6% METH_Control2

treatment_protocol: Virgin male flies were collected at the 6th-7th hour of eclosion from the pupa (Ashburner, 1989). These virgin male flies were cultured for 5 days. The 5 days old virgin male flies were place on one of the two following diets for 24 h to feed by themselves: (i) standard fly diet (control) or (iii) 0.6% (w/v) methamphetamine (meth) mixed into the standard fly diet. A total of 20 flies were placed on each replicate diet for each treatment. A total of three biological replicates were performed for each experiment (for a total of six samples). At the end of the 24 h feeding period the 20 flies were collected, flash-frozen in liquid nitrogen, and stored at -80 oC. These samples were subsequently used perform the DNA oligo array experiment or metabolite analyses.

value: :0% methamphetamine + blue diet


title: 0.6% METH_treated 1

treatment_protocol: Virgin male flies were collected at the 6th-7th hour of eclosion from the pupa (Ashburner, 1989). These virgin male flies were cultured for 5 days. The 5 days old virgin male flies were place on one of the following diet for 24 h to feed by themselves: 0.6% methamphetamine fly diet. A total of 20 flies were placed on each replicate diet. A total of three biological replicates were performed for each experiment. At the end of the 24 h feeding period the 20 flies were collected, flash-frozen in liquid nitrogen, and stored at -80 oC. These samples were subsequently used perform the DNA oligo array experiment or metabolite analyses.


title: 0.6% METH_Control1

extract_protocol: Total RNA were extracted using Trizol reagent for each replicate (Invitrogen Life Technologies, Carlsbad, CA).  Three replicated were used for control and methamphetamine treated flies separately.  DNA contamination were removed by DNaseI set (Qiagen Inc., Valencia, CA) followed by another step of Trizol extraction to remove DNase.

treatment_protocol: Virgin male flies were collected at the 6th-7th hour of eclosion from the pupa (Ashburner, 1989).  These virgin male flies were cultured for 5 days.  The 5 days old virgin male flies were place on one of the two following diets for 24 h to feed by themselves: (i) standard fly diet (control) or (iii) 0.6% (w/v) methamphetamine (meth) mixed into the standard fly diet.   A total of 20 flies were placed on each replicate diet for each treatment.  A total of three biological replicates were performed for each experiment (for a total of six samples).  At the end of the 24 h feeding period the 20 flies were collected, flash-frozen in liquid nitrogen, and stored at -80 oC.  These samples were subsequently used perform the DNA oligo array experiment or metabolite analyses.

value: 0% methamphetamine + blue diet


title: SND1_12h_rep2

status: Public on Oct 28 2010

city: tokyo

first: Kyoko

last: Ohashi-Ito

address: 7-3-1 hongo bunkyo-ku

department: biological sciences

country: Japan

institute: the university of tokyo

description: Estrogen-inducible SND1 transformed cells with 12h estrogen treatment

hyb_protocol: Hybridization, washing, staining procedures were conducted with Fluidics Station 450 as described in the GeneChip Expression Analysis Technical Manual (Affymetrix).

scan_protocol: Scanning procedure was conducted with GeneChip Scanner 3000 7G as described in the GeneChip Expression Analysis Technical Manual (Affymetrix).

data_processing: GCOS, ExpressionStat 5.0

organism: Arabidopsis thaliana

source_name: SND1 culture cell, 12h

label_protocol: Biotinylated cRNA was prepared from total RNA with GeneChip One-Cycle Target Labeling and Control Reagents (Arab-0018 to Arab-0054) or GeneChip 3' IVT Expression Kit (Arab-113-2 to Arab-124) (Affymetrix).

extract_protocol: Total RNA was extracted with TRIzol (Invitrogen) and purified with Rneasy Micro Kit (QIAGEN)

treatment_protocol: cultured cells were treated with 2 μM estrogen for 0h and 12h

tag: cultured cell type

value: SND1 culture cell

tag: time point


title: VND6_0h_rep3

description: Estrogen-inducible VND6 transformed cells with 0h estrogen treatment

source_name: VND6 culture cell, 0h

value: VND6 culture cell


title: SND1_0h_rep2

description: Estrogen-inducible SND1 transformed cells with 0h estrogen treatment

source_name: SND1 culture cell, 0h


title: SND1_12h_rep3


title: SND1_0h_rep1


title: VND6_12h_rep2

description: Estrogen-inducible VND6 transformed cells with 12h estrogen treatment

source_name: VND6 culture cell, 12h


title: SND1_0h_rep3


title: 0.6% METH_Control3

treatment_protocol: Virgin male flies were collected at the 6th-7th hour of eclosion from the pupa (Ashburner, 1989). These virgin male flies were cultured for 5 days. The 5 days old virgin male flies were place on one of the two following diets for 24 h to feed by themselves: (i) standard fly diet (control). A total of 20 flies were placed on each replicate diet. A total of three biological replicates were performed for each experiment (for a total of six samples). At the end of the 24 h feeding period the 20 flies were collected, flash-frozen in liquid nitrogen, and stored at -80 oC. These samples were subsequently used perform the DNA oligo array experiment or metabolite analyses.


title: VND6_12h_rep3


title: VND6_12h_rep1


title: wt_12h_rep3

description: Arabidopsis cultured cells with 12h estrogen treatment

source_name: wt culture cell, 12h

value: wt culture cell


title: VND6_0h_rep2


title: wt_12h_rep2


title: VND6_0h_rep1


title: wt_0h_rep3

description: Arabidopsis cultured cells with 0h estrogen treatment

source_name: wt culture cell, 0h


title: wt_0h_rep1


title: eto1-4 + AVG_3-day-old_rep1

status: Public on Oct 18 2010

city: Taipei

first: Kevin Long-Chi

last: WANG

address: 128 Section 2, Academia Road

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

hyb_protocol: Standard Affymetrix GeneChip hybridization protocol

scan_protocol: Standard Affymetrix GeneChip scanning protocol

data_processing: MAS5.0 using default settings

source_name: eto1-4 + AVG_3-day-old_rep1

label_protocol: Standard Affymetrix GeneChip labeling protocol

growth_protocol: Seedling were growth on 0.5x MS medium contain 10 μM compound AVG

extract_protocol:
Pine Tree method, for preparation of total RNA from etiolated seedlingss
Plant Molecular Biology Reporter (1993) 11: 113-116

tag: ecotype

tag: genome/variation

value: ethylene mutant (eto1-4)

tag: developmental stage

value: whole seedling

tag: growth condition

value: dark


title: wt_0h_rep2


title: eto1-4 + 7303_3-day-old_rep2

growth_protocol: Seedling were growth on 0.5x MS medium contain 10 μM compound 7303


title: eto1-4_3-day-old_rep1

growth_protocol: Seedling were growth on 0.5x MS medium


title: eto1-4 + 9393_3-day-old_rep2

growth_protocol: Seedling were growth on 0.5x MS medium contain 10 μM compound 9393


title: eto1-4 + 7303_3-day-old_rep1


title: eto1-4 + 9370_3-day-old_rep1

growth_protocol: Seedling were growth on 0.5x MS medium contain 10 μM compound 9370


title: Col-0_3-day-old_rep2

value: WT


title: eto1-4 + 9370_3-day-old_rep2


title: eto1-4 + AVG_3-day-old_rep2

source_name: eto1-4 + AVG_3-day-old_rep2


title: SND1_12h_rep1


title: NELF-depleted DGRC S2 Cells, Replicate 1

city: Boston

first: Karen

last: Adelman

state: MA

address: 45 Shattuck St. LHRRB-201a

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

description: Gene expression analysis was conducted using Drosophila Genome 2.0 Genechip® arrays (Affymetrix, Santa Clara, CA). Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3’ Amplification One-Cycle Target labeling kit according to manufacturer’s protocol. For each array, 10ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.

hyb_protocol: 15ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.

scan_protocol: Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450.  Arrays were then scanned with an Affymetrix Scanner 3000 and data was obtained using the Genechip Operating Software (Version 1.2.0.037).

data_processing:
Affymetrix GeneChip Command Console (V. 1.1), Algorithm: ExpressionStat 5.0
The resulting files (.dat, .cel and .chp) were imported into the Rosetta Resolver system (Version 6.0).  This system performs data pre-processing and error modeling as described in Weng (2006).  Resolver generated fold-changes and p values, based on ratios built in the system, were exported for further analysis.

source_name: DGRC S2 Cells, NELF-depleted

label_protocol: Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3' Amplification One-Cycle Target labeling kit according to manufacturer's protocol.

growth_protocol: S2(DGRC) cells were grown in M3 media (Sigma) supplemented with bacto-peptone and yeast extract + 10% FBS (GIBCO).

extract_protocol: The RNeasy RNA extraction kit (QIAGEN), with on-column DNAse digestion, was used according to manufacturer’s protocol

treatment_protocol: For RNAi experiments, S2 cells (DGRC) were harvested  96 hours after addition of dsRNA targeting NELF (NELF-B and NELF-E subunits; NELF-depleted),  β-galactosidase (Mock-treated), or no addition (Untreated), as described in Armknecht, S. et al. (2005) Methods in Enzymology, 392: pp. 55-73.

tag: cell type

value: S2 cells (DGRC)


title: CrebA sorted 2

city: Baltimore

first: Deborah

middle: J

last: Andrew

state: MD

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

department: Cell Biology

institute: Johns Hopkins University School of Medicine

description: CrebA mutant embryos st. 11-17 isolated based on lack of GFP balancer expression, sorted using a COPAS biosorter

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

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

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

source_name: St 11-15 embryos

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

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

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

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

value: embryo

tag: genotype/variation

value: CrebA null mutant


title: CrebA sorted 3


title: Untreated DGRC S2 Cells, Replicate 2

source_name: DGRC S2 Cells, untreated


title: NELF-depleted DGRC S2 Cells, Replicate 2


title: Col-0_3-day-old_rep1


title: eto1-4 + 9393_3-day-old_rep1


title: wt_12h_rep1


title: dnClk_fatbody_ZT28

status: Public on Oct 05 2010

city: Philadelphia

first: Michael

last: Hughes

state: PA

address: 421 Curie Bvd, Brb 835

institute: UPenn

hyb_protocol: The cRNA products were fragmented to 200 nucleotides or less, heated at 99 degrees C for 5 min and hybridized for 16 h at 45 degrees C. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.

data_processing:
Cel to text file condensation was performed using the MAS5.0 algorithm using Affymertrix software
values were visualized using GenSpring (Silicon Genetics) software package

source_name: fatbody, ZT28

label_protocol: Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.

growth_protocol: Newly eclosed adult male flies were entrained for 5 days to a 12L:12D cycle at 25 degrees.

extract_protocol: abdominal fatbody was dissected as previously described (DiAngelo and Birnbaum); 10 fatbodies were pooled per timepoint and total RNA was extracted using Trizol (Invitrogen) according to the manufacturer's protocol

treatment_protocol: On the 6th day, dnClk flies were collected every 4 hours for 2 consecutive days

value: adult

tag: Sex

value: male

value: dnClk

value: abdominal fatbody

tag: timepoint


title: dnClk_fatbody_ZT44

source_name: fatbody, ZT44


title: dnClk_fatbody_ZT32

source_name: fatbody, ZT32


title: Mock-treated DGRC S2 Cells, Replicate 1

source_name: DGRC S2 Cells, mock-treated


title: dnClk_fatbody_ZT36

source_name: fatbody, ZT36


title: dnClk_fatbody_ZT24

source_name: fatbody, ZT24


title: Untreated DGRC S2 Cells, Replicate 1


title: dnClk_fatbody_ZT40

source_name: fatbody, ZT40


title: dnClk_fatbody_ZT8

source_name: fatbody, ZT8


title: CrebA sorted 1


title: dnClk_fatbody_ZT0

source_name: fatbody, ZT0


title: WT_fatbody_ZT28

treatment_protocol: On the 6th day, wildtype flies (w; UAS-dnClk/+) were collected every 2 hours for 2 consecutive days

value: wildtype (w; UAS-dnClk/+)


title: WT_fatbody_ZT44


title: dnClk_fatbody_ZT16

source_name: fatbody, ZT16


title: WT_fatbody_ZT46

source_name: fatbody, ZT46


title: WT_fatbody_ZT30

source_name: fatbody, ZT30


title: dnClk_fatbody_ZT4

source_name: fatbody, ZT4


title: WT_fatbody_ZT32


title: WT_fatbody_ZT38

source_name: fatbody, ZT38


title: WT_fatbody_ZT20

source_name: fatbody, ZT20


title: dnClk_fatbody_ZT12

source_name: fatbody, ZT12


title: WT_fatbody_ZT34

source_name: fatbody, ZT34


title: dnClk_fatbody_ZT20


title: WT_fatbody_ZT40


title: Mock-treated DGRC S2 Cells, Replicate 2


title: WT_fatbody_ZT42

source_name: fatbody, ZT42


title: WT_fatbody_ZT22

source_name: fatbody, ZT22


title: WT_fatbody_ZT36


title: WT_fatbody_ZT24


title: WT_fatbody_ZT16


title: WT_fatbody_ZT14

source_name: fatbody, ZT14


title: WT_fatbody_ZT18

source_name: fatbody, ZT18


title: WT_fatbody_ZT12


title: WT_fatbody_ZT10

source_name: fatbody, ZT10


title: WT_fatbody_ZT2

source_name: fatbody, ZT2


title: WT_fatbody_ZT4


title: WT_fatbody_ZT6

source_name: fatbody, ZT6


title: WT_fatbody_ZT0


title: WT_fatbody_ZT26

source_name: fatbody, ZT26


title: Roots-oas-a1.1-18h-REP3

status: Public on Oct 01 2010

city: Sevilla

first: Cecilia

last: Gotor

address: Avda. Américo Vespucio, 49

country: Spain

institute: Instituto de Bioquímica Vegetal y Fotosíntesis

description: Gene expression data from 18h-treated root cells (oas-a1.1 mutant)

hyb_protocol: Following fragmentation, 15 µg of biotinylated cRNA were hybridized to Affymetrix chips (GeneChip Arabidopsis ATH1 Genome Array). Each sample was added to a hybridization solution containing 100mM 2-(N-morpholino)ethanesulfonic acid, 1 M Na+, and 20mM of EDT

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

data_processing: GeneChip intensities were background-corrected, normalized and sumarized by RMA method, using the “Affy” package from Bioconductor.

source_name: Roots, oas-a1.1, 18h

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 4 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Arabidopsis thaliana (accession Col-0) and the oas-a1.1 mutant (SALK_072213) seeds were grown on Petri dishes on MS medium containing 2.5 g L-1 Phytagel (Sigma-Aldrich) and 1% (w/v) Suc for two weeks and then seedlings were transferred to hydroponic culture. The nutrient solution contained 2 mM Ca(NO3)2, 0.5 mM KH2PO4, 0.75 mM MgSO4, 10 mM KNO3, 1.5 µM CuSO4, 2 µM ZnSO4, 10 µM MnSO4, 50 µM H3BO3, 0.1 µM MoO3, 50 µM KCl, and 50 µM Fe-Na-EDTA, and was replaced once a week. The Cd treatment of hydroponically-grown plants was performed by adding 50 mM of CdCl2 to the above-described nutrient solution after a two-week period of acclimation to the hydroponic conditions. Plants were grown under a photoperiod of 16 h of white light (120 mE m-2 s-1) at 20ºC / 8 h dark at 18ºC.

extract_protocol: Hydroponically-grown plants were cultured in the absence and presence of 50 mM CdCl2 for 18 and 24 h. The untreated-roots, 18 h treated-roots, untreated-shoots and 24h treated-shoots were collected and RNA extracted from each sample. Total RNA was isolated with Trizol reagent (Invitrogen) followed by cleaning with the RNeasy Plant Mini Kit (Qiagen).

tag: genotype

value: oas-a1.1 mutant

value: Root


title: Roots-WildType-18h-REP1

description: Gene expression data from 18h-treated root cells (wild type)

source_name: Roots, Wild Type, 18h

value: Wild Type


title: Shoots-oas-a1.1-24h-REP1

description: Gene expression data from 24h-treated shoot cells (oas-a1.1 mutant)

source_name: Shoots, oas-a1.1, 24h

value: Shoot


title: Shoots-oas-a1.1-Untreated-REP3

description: Gene expression data from untreated shoot cells (oas-a1.1 mutant)

source_name: Shoots, oas-a1.1, Untreated


title: Shoots-WildType-24h-REP3

description: Gene expression data from 24h-treated shoot cells (wild type)

source_name: Shoots, Wild Type, 24h


title: Shoots-WildType-Untreated-REP3

description: Gene expression data from untreated shoot cells (wild type)

source_name: Shoots, Wild Type, Untreated


title: Shoots-oas-a1.1-24h-REP2


title: Roots-oas-a1.1-18h-REP2


title: Roots-WildType-Untreated-REP1

description: Gene expression data from untreated root cells (wild type)

source_name: Roots, Wild Type, Untreated


title: Shoots-WildType-Untreated-REP2


title: Roots-WildType-Untreated-REP2


title: Roots-oas-a1.1-18h-REP1


title: Shoots-oas-a1.1-Untreated-REP1


title: Shoots-oas-a1.1-24h-REP3


title: Shoots-oas-a1.1-Untreated-REP2


title: Shoots-WildType-24h-REP2


title: Roots-oas-a1.1-Untreated-REP1

description: Gene expression data from untreated root cells (oas-a1.1 mutant)

source_name: Roots, oas-a1.1, Untreated


title: Shoots-WildType-24h-REP1


title: Shoots-WildType-Untreated-REP1


title: wild-type roots - Fe, biological rep2

status: Public on Sep 25 2010

city: Saarbrücken

first: Mara

last: Schuler

address: Campus SB, Geb.A2 4

country: Germany

institute: Saarland University

description: Roots of wild-type, ecotype Columbia, grown under Fe deficiency

hyb_protocol: (see label protocol)

scan_protocol: Affymetrix GeneChip scanner 3000

data_processing: Data were processed by Affymetrix GeneChip Operating software (GCOS) and quantile normalized using R.

label: Biotin

source_name: wild-type, Roots grown under - Fe, ecotype Columbia

label_protocol: 5 µg RNA of each sample were processed into biotin-labeled cRNA and hybridized to Affymetrix GeneChip Arabidopsis ATH1 Genome Arrays (Affymetrix, High Wycombe, U.K.), using the Affymetrix One-Cycle Labeling and Control (Target) kit

growth_protocol: Wild-type and nas4x-1 plants were grown in hydroponic solution containing a quarter strength of Hoagland salts supplied with 10µM FeNa-EDTA. The medium was exchanged weekly. Four weeks after germination, plants were divided into two groups, one of them was kept in the same conditions as mentioned above (10µM FeNa-EDTA, + Fe) while the other group was transferred to Hoagland solution without Fe (0 µM FeNa-EDTA, - Fe). Cultivation took place at 21°C/19°C and 16-h-light, 8-h-dark cycles and a light intensity of 150 µmol x m-2 x s-1.

extract_protocol: Total RNA was extracted from 100 mg of root and leaf material with the Quiagen RNeasy Plant Mini Prep Kit.

treatment_protocol: No special treatment has been applied

value: Roots


title: wild-type roots + Fe, biological rep3

description: Roots of wild-type, ecotype Columbia, grown under Fe supply

source_name: wild-type, Roots grown under + Fe, ecotype Columbia


title: nas4x-1 roots - Fe, biological rep2

description: Roots of quadruple nasT-DNA insertionmutant in background of ecotype Columbia, grown under Fe deficiency

source_name: nas4x-1, Roots grown under - Fe


title: wild-type roots - Fe, biological rep1


title: nas4x-1 roots - Fe, biological rep3


title: wild-type roots + Fe, biological rep2


title: nas4x-1 roots + Fe, biological rep3

description: Roots of quadruple nasT-DNA insertionmutant in background of ecotype Columbia, grown under Fe supply

source_name: nas4x-1, Roots grown under + Fe


title: nas4x-1 roots - Fe, biological rep1


title: nas4x-1 roots + Fe, biological rep2


title: WT_fatbody_ZT8

source_name: fatbody, ZT8


title: nas4x-1 leaves - Fe, biological rep2

description: leaves of quadruple nasT-DNA insertionmutant in background of ecotype Columbia, grown under Fe deficiency

source_name: nas4x-1, leaves grown under - Fe

value: Leaves


title: nas4x-1 roots + Fe, biological rep1


title: wild-type leaves - Fe, biological rep1

description: leaves of wild-type, ecotype Columbia, grown under Fe deficiency

source_name: wild-type, leaves grown under - Fe, ecotype Columbia


title: nas4x-1 leaves + Fe, biological rep3

description: leaves of quadruple nasT-DNA insertionmutant in background of ecotype Columbia, grown under Fe supply

source_name: nas4x-1, leaves grown under + Fe


title: nas4x-1 leaves - Fe, biological rep1


title: wild-type leaves - Fe, biological rep2


title: wild-type leaves + Fe, biological rep2

description: leaves of wild-type, ecotype Columbia, grown under Fe supply

source_name: wild-type, leaves grown under + Fe, ecotype Columbia


title: wild-type leaves - Fe, biological rep3


title: wild-type leaves + Fe, biological rep3


title: wild-type leaves + Fe, biological rep1


title: nas4x-1 leaves + Fe, biological rep2


title: nas4x-1 leaves + Fe, biological rep1


title: AR52Q + limpet duplication, DHT-treated, replicate 4, expt 2

status: Public on Sep 23 2010

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

description:
nbn056
Experiment 2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Affymetrix Drosophila Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneChip Operating Software version 1.4 using the default MAS 5.0 algorithm settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Head expressing AR52Q in genetic background of limpet duplication, treated with DHT

label_protocol: Biotinylated cRNA was prepared according to the Affymetrix 3' IVT Express protocol from 100 ng total RNA (Affymetrix Technical Manual, 2008).

growth_protocol: UAS-AR flies were crossed to GMR-GAL4 flies at 29°C on food containing either 1 mM DHT (Steraloids) or 1% ethanol (vehicle).

extract_protocol: Heads of 15 female offspring were collected and frozen, and RNA was extracted using TRIzol (Invitrogen).

treatment_protocol: Flies were bred on food containing either 1mM DHT or 1% ethanol (vehicle).

value: GMR-GAL4; UAS-AR x limpet duplication

tag: androgen receptor (ar) status

value: 52 polyglutamine

tag: sex

value: female

value: 5 days

value: head

tag: treatment

value: DHT


title: AR52Q + limpet duplication, vehicle-treated, replicate 3, expt 2

description:
nbn051
Experiment 2

source_name: Head expressing AR52Q in genetic background of limpet duplication, treated with ethanol

tag: strain

value: adult

value: ethanol


title: AR52Q + limpet duplication, DHT-treated, replicate 3, expt 2

description:
nbn055
Experiment 2

tag: age


title: AR52Q + limpet duplication, DHT-treated, replicate 2, expt 2

description:
nbn054
Experiment 2

tag: tissue


title: AR52Q + limpet duplication, vehicle-treated, replicate 1, expt 2

description:
nbn049
Experiment 2


title: AR52Q, DHT-treated, replicate 2, expt 2

description:
nbn046
Experiment 2

source_name: Head expressing AR52Q, treated with DHT

value: GMR-GAL4 x UAS-AR


title: AR52Q + limpet duplication, DHT-treated, replicate 1, expt 2

description:
nbn053
Experiment 2


title: AR52Q, vehicle-treated, replicate 3, expt 2

description:
nbn043
Experiment 2

source_name: Head expressing AR52Q, treated with ethanol


title: AR52Q + limpet duplication, vehicle-treated, replicate 4, expt 2

description:
nbn052
Experiment 2


title: AR52Q, vehicle-treated, replicate 4, expt 2

description:
nbn044
Experiment 2


title: AR52Q, DHT-treated, replicate 4, expt 2

description:
nbn048
Experiment 2


title: AR52Q, DHT-treated, replicate 1, expt 2

description:
nbn045
Experiment 2


title: AR52Q + limpet duplication, vehicle-treated, replicate 2, expt 2

description:
nbn050
Experiment 2


title: AR52Q, DHT-treated, replicate 3, expt 2

description:
nbn047
Experiment 2


title: AR52Q, vehicle-treated, replicate 2, expt 2

description:
nbn042
Experiment 2


title: nas4x-1 leaves - Fe, biological rep3


title: AR52Q A574D, vehicle-treated, replicate 4

description:
nbn036
Experiment 1

source_name: Head expressing AR52Q A574D mutant, treated with ethanol

value: 52 polyglutamine, A574D mutation


title: AR52Q A574D, DHT-treated, replicate 2

description:
nbn039
Experiment 1

source_name: Head expressing AR52Q A574D mutant, treated with DHT


title: AR72Q K720A, DHT-treated, replicate 3

description:
nbn031
Experiment 1

source_name: Head expressing AR72Q K720A mutant, treated with DHT

value: 72 polyglutamine, K720A mutation


title: AR72Q K720A, DHT-treated, replicate 1

description:
nbn029
Experiment 1


title: AR52Q A574D, vehicle-treated, replicate 1

description:
nbn033
Experiment 1


title: AR72Q K720A, vehicle-treated, replicate 4

description:
nbn028
Experiment 1

source_name: Head expressing AR72Q K720A mutant, treated with ethanol


title: AR72Q K720A, vehicle-treated, replicate 3

description:
nbn027
Experiment 1


title: AR52Q A574D, vehicle-treated, replicate 2

description:
nbn034
Experiment 1


title: AR52Q A574D, DHT-treated, replicate 1

description:
nbn038
Experiment 1


title: AR52Q A574D, DHT-treated, replicate 3

description:
nbn040
Experiment 1


title: AR72Q K720A, vehicle-treated, replicate 2

description:
nbn026
Experiment 1


title: AR52Q A574D, vehicle-treated, replicate 3

description:
nbn035
Experiment 1


title: AR72Q K720A, DHT-treated, replicate 2

description:
nbn030
Experiment 1


title: AR66Q E897K, DHT-treated, replicate 3

description:
nbn024
Experiment 1

source_name: Head expressing AR66Q E897K mutant, treated with DHT

value: 66 polyglutamine, E897K mutation


title: AR66Q E897K, vehicle-treated, replicate 4

description:
nbn020
Experiment 1

source_name: Head expressing AR66Q E897K mutant, treated with ethanol


title: AR52Q, vehicle-treated, replicate 1, expt 2

description:
nbn041
Experiment 2


title: AR66Q E897K, DHT-treated, replicate 2

description:
nbn023
Experiment 1


title: AR66Q E897K, vehicle-treated, replicate 2

description:
nbn018
Experiment 1


title: AR52Q, DHT-treated, replicate 1

description:
nbn013
Experiment 1


title: AR52Q, DHT-treated, replicate 3

description:
nbn015
Experiment 1


title: AR72Q K720A, vehicle-treated, replicate 1

description:
nbn025
Experiment 1


title: AR66Q E897K, vehicle-treated, replicate 3

description:
nbn019
Experiment 1


title: AR66Q E897K, vehicle-treated, replicate 1

description:
nbn017
Experiment 1


title: AR52Q, vehicle-treated, replicate 4

description:
nbn012
Experiment 1


title: AR66Q E897K, DHT-treated, replicate 1

description:
nbn022
Experiment 1


title: AR52Q, DHT-treated, replicate 2

description:
nbn014
Experiment 1


title: AR52Q, DHT-treated, replicate 4

description:
nbn016
Experiment 1


title: AR52Q, vehicle-treated, replicate 3

description:
nbn011
Experiment 1


title: AR52Q, vehicle-treated, replicate 1

description:
nbn009
Experiment 1


title: AR52Q, vehicle-treated, replicate 2

description:
nbn010
Experiment 1


title: AR72Q K720A, DHT-treated, replicate 4

description:
nbn032
Experiment 1


title: AR12Q, DHT-treated, replicate 2

description:
nbn006
Experiment 1

source_name: Head expressing AR12Q, treated with DHT

value: 12 polyglutamine


title: AR12Q, DHT-treated, replicate 3

description:
nbn007
Experiment 1


title: AR12Q, DHT-treated, replicate 1

description:
nbn005
Experiment 1


title: AR12Q, vehicle-treated, replicate 2

description:
nbn002
Experiment 1

source_name: Head expressing AR12Q, treated with ethanol


title: AR12Q, vehicle-treated, replicate 4

description:
nbn004
Experiment 1


title: AR12Q, vehicle-treated, replicate 3

description:
nbn003
Experiment 1


title: AR12Q, DHT-treated, replicate 4

description:
nbn008
Experiment 1


title: AR12Q, vehicle-treated, replicate 1

description:
nbn001
Experiment 1


title: wnk 8-1 untreated, biological rep2

status: Public on Sep 21 2010

city: Riverside

first: Tokuji

last: Tsuchiya

state: CA

address: 3220 Batchelor Hall, University of California at Riverside

department: Botany and Plant Sciences

institute: University of California at Riverside

description: Gene expression data from 2-week-old seedlings grown under short day conditions

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 450.

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

data_processing: Data was processed in the statistical programming environment R using Bioconductor packages. Raw expression values were normalized using the robust multichip averaging algorithm.

source_name: wnk8-1 mutant

label_protocol: Biotinylated cRNA were prepared according to the standard 1 cycle Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manua, REV3, Affymetrix).

growth_protocol: Arabidopsis plants were grown at 22 °C under short day conditions (8 hr light/16 hr dark)

extract_protocol: Total RNA was isolated from seedlings using TRIzol Reagenet (Invitrogen) and further purified with RNeasy Plant mini kit columns (Qiagen) according to the protocols supplied by the manufacturers.

treatment_protocol: Untreated.

value: seedlings

value: wnk8-1 mutant


title: Col-0 untreated, biological rep3

source_name: Col-0 wildtype

value: Col-0 wildtype


title: wnk 8-3 untreated, biological rep2

source_name: wnk8-3 mutant

value: wnk8-3 mutant


title: edm2-2 untreated, biological rep2

source_name: edm2-2 mutant

value: edm2-2 mutant


title: edm2-2 untreated, biological rep3


title: pXVE:HA-EDM2-a untreated, biological rep3

source_name: pXVE:HA-EDM2-a, an edm2-2 complementation line


title: wnk 8-2 untreated, biological rep3

source_name: wnk8-2 mutant

value: wnk8-2 mutant


title: wnk 8-1 untreated, biological rep3


title: wnk 8-3 untreated, biological rep3


title: wnk 8-2 untreated, biological rep2


title: pXVE:HA-EDM2-a untreated, biological rep2

value: pXVE:HA-EDM2-a, an edm2-2 complementation line


title: wnk 8-1 untreated, biological rep1


title: edm2-2 untreated, biological rep1


title: pXVE:HA-EDM2-a untreated, biological rep1


title: At_PR_OZ2_39

status: Public on Sep 12 2010

city: Durham

first: Miguel

middle: Angel

last: Moreno-Risueno

state: NC

address: 124 Science Dr

department: Biology

institute: Duke University

description: Gene expression data the OZ2 (upper half) under standard conditions for 5 days

hyb_protocol: see Affymetrix standard protocols

scan_protocol: see Affymetrix standard protocols

data_processing: MAS 5.0

label_protocol: see Affymetrix standard protocols

extract_protocol: see Affymetrix standard protocols

value: Columbia

value: 5 days after germination

value: lower half of seedling root

tag: growth media

value: Standard media for 5 days

tag: periodic order


title: Col-0 untreated, biological rep2


title: At_PR_OZ2_23

tag: ecotype


title: wnk 8-3 untreated, biological rep1


title: At_PR_OZ2_38


title: At_PR_OZ2_40


title: At_PR_OZ2_15


title: wnk 8-2 untreated, biological rep1


title: At_PR_OZ2_14


title: At_PR_OZ2_21


title: Col-0 untreated, biological rep1


title: At_PR_OZ2_4


title: At_PR_OZ1_33

description: Gene expression data the OZ1 (lower half) under standard conditions for 5 days

value: upper half of seedling root


title: At_PR_OZ2_1


title: At_PR_OZ1_23


title: At_PR_OZ2_10


title: At_PR_OZ1_17


title: At_PR_OZ1_14


title: At_PR_OZ2_6


title: At_PR_OZ1_13


title: At_PR_OZ1_22


title: At_PR_OZ1_20


title: At_PR_OZ1_9


title: At_PR_OZ1_19


title: At_PR_OZ1_4


title: At_PR_OZ1_2


title: At_PR_OZ1_1


title: 2xX2x cross, biological replicate 2

status: Public on Aug 26 2010

city: London

first: Reiner

last: Schulz

address: 8th floor Guy's Tower

department: Medical & Molecular Genetics

country: United Kingdom

institute: King's College London

description: 2xX2x_2: biological replicate of 2xX2x_1

hyb_protocol: Labelled cRNA was hybridised according to manufacturer’s protocols (done at NASC: http://affymetrix.arabidopsis.info/)

scan_protocol: Standard manufacturer's protocol (done at NASC: http://affymetrix.arabidopsis.info/)

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: Siliques

label_protocol: Biotin labelling of cRNA using Affymetrix Enzo Kit according to manufacturer’s protocols (done at NASC: http://affymetrix.arabidopsis.info/)

growth_protocol: Plants were grown at 18hr day cycles at 60% humidity. Male sterile lines were pollinated by the appropriate pollen depending on the cross, and siliques harvested in liquid nitrogen at 5 days after pollination (DAP). For the msi1 sample, the msi1 mutation was introgressed in a A9 barnase male sterile line, siliques were left to elongate in absence of fertilization and were harvested 7 days after flower opening.

extract_protocol: Total RNA from siliques was extracted using the RNeasy Plant Mini Kit (Qiagen) and concentrated using an RNeasy MinElute Cleanup Kit (Qiagen).

value: 5 days after pollination

tag: maternal ecotype

tag: paternal ecotype

tag: maternal genetic modification

value: A9-barnase transgene

tag: paternal genetic modification


title: 2xX4x interploidy cross, biological replicate 2

description: 2xX4x_2: biological replicate of 2xX4x_1

tag: developmental stage


title: 6xX2x interploidy cross, biological replicate 2

description: 6xX2x_2: biological replicate of 6xX2x_1


title: 2xX6x interploidy cross, biological replicate 1

description: 2xX6x_1: biological replicate of 2xX6x_2


title: msi1 unfertilised mutant

value: 7 days after flowering

value: msi1-2 homozygous mutant


title: 2xX2x cross, biological replicate 1

description: 2xX2x_1: biological replicate of 2xX2x_2


title: 2xX4x interploidy cross, biological replicate 1

description: 2xX4x_1: biological replicate of 2xX4x_2


title: fis1X2x fis1 mutant cross, biological replicate 1

description: fis1X2x_1: biological replicate of fis1X2x_2

value: Ler

value: fis1-3 (=mea-3/f644) homozygous mutant


title: 6xX2x interploidy cross, biological replicate 1

description: 6xX2x_1: biological replicate of 6xX2x_2


title: 2xX6x interploidy cross, biological replicate 2

description: 2xX6x_2: biological replicate of 2xX6x_1


title: 4xX2x interploidy cross, biological replicate 1

description: 4xX2x_1: biological replicate of 4xX2x_2


title: fis1X2x fis1 mutant cross, biological replicate 2

description: fis1X2x_2: biological replicate of fis1X2x_1


title: bZIP1ko mutant, treatment N+L+, 2 biological rep

status: Public on Aug 25 2010

city: Capital Federal

first: Mariana

last: Obertello

address: Vuelta de Obligado 2490

department: Department of Biology

country: Argentina

institute: INGEBI-CONICET

description: Gene expression data before 2 hours treatment

hyb_protocol: We used 15 µg of labeled cRNA to hybridize the Arabidopsis ATH1 Affymetrix gene chip for 16 h at 42°C. Washing, staining and scanning were performed as recommended by Affymetrix.

scan_protocol: Scanning were performed as recommended by Affymetrix.

data_processing: All microarray data was processed with Microarray Analysis Suite 5.0 software (MASv5.0).  MASv5.0 Affymetrix call (Absent, Marginal or Present) were used to keep only probes having at least a Marginal/Present call in one of the 24 hybridization.  Such a procedure facilitated the elimination of transcripts with very low signals in both treatments (declared “absent”).

source_name: 14 days-old Arabidopsis thaliana

label_protocol: Biotin-labeled cRNA was synthesized using the Enzo BioArray HighYield RNA Transcript Labeling Kit (Enzo, New York, NY).

growth_protocol: Arabidopsis thaliana (var. Columbia Col-0) was used as parental line. The mutant plant with a knock-out in the bZIP1 gene, named bzip1-1, contains a T-DNA insertion in the unique exon of the gene (At5g49450). Arabidopsis seeds were placed for 2 days in the dark at 4°C to synchronize germination. Seeds were surface sterilized and then sowed into plates containing a sterile mesh over the agar surface to facilitate their transfer into the treatment plates. Plates contained basal MS salts (custom-made; GIBCO) with 0.5 mM KNO3, 3 mM sucrose and 0.8% BactoAgar at pH 5.7.

extract_protocol: RNA was isolated from whole plants using Trizol reagent according to the intructions of the manufacturer (15596; Invitrogen).

treatment_protocol: After 14 days under long-day (16 h light: 8 h dark) conditions with light intensity of 50 μE.m-2.s-1 and at 22°C, plants were transferred to new plates containing 20 mM KNO3 and 20 mM NH4NO3 (referred here as 1xN: concentrations in MS media) in the absence or presence of light for 2 h at the start of their light cycle. Control plants were transferred toward a fresh media complemented with KCl, also in the absence or presence of light as a mock treatment.  Light – dark treatment were done by simply leaving the treatment plates in the growth chamber or by covering them with double aluminium foil (dark treatment) for two hours. After treatment, whole seedlings were harvest and immediately frozen in liquid nitrogen.

value: whole plant

tag: genotype variation


title: bZIP1ko mutant, treatment N+L+, 3 biological rep


title: bZIP1ko mutant, treatment N+L+, 1 biological rep


title: 4xX2x interploidy cross, biological replicate 2

description: 4xX2x_2: biological replicate of 4xX2x_1


title: bZIP1ko mutant, treatment N-L+, 3 biological rep


title: bZIP1ko mutant, treatment N-L-, 3 biological rep


title: bZIP1ko mutant, treatment N-L+, 2 biological rep


title: bZIP1ko mutant, treatment N-L-, 2 biological rep


title: bZIP1ko mutant, treatment N+L-, 3 biological rep


title: bZIP1ko mutant, treatment N+L-, 2 biological rep


title: WT-sib, treatment N+L+, 2 biological rep

value: WT


title: bZIP1ko mutant, treatment N+L-, 1 biological rep


title: WT-sib, treatment N+L+, 1 biological rep


title: bZIP1ko mutant, treatment N-L+, 1 biological rep


title: WT-sib, treatment N-L+, 2 biological rep


title: bZIP1ko mutant, treatment N-L-, 1 biological rep

tag: genotype variation:


title: WT-sib, treatment N+L+, 3 biological rep


title: WT-sib, treatment N-L+, 3 biological rep


title: WT-sib, treatment N-L+, 1 biological rep


title: WT-sib, treatment N+L-, 3 biological rep


title: WT-sib, treatment N-L-, 1 biological rep


title: WT-sib, treatment N+L-, 1 biological rep


title: WT-sib, treatment N+L-, 2 biological rep


title: WT-sib, treatment N-L-, 3 biological rep


title: WT-sib, treatment N-L-, 2 biological rep


title: adenocarcinoma_97

status: Public on Aug 01 2010

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed (Fluidics Scripts FS450_001) and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner.

data_processing: Cell intensity files were generated using GCOS (Affymetrix). The probe set data was generated using R/BioConductor (version 2.8.1) packages affy (version 1.20.2), gcrma (version 2.14.1), and FLUSH.LVS.bundle (version 1.2.1, proportion=0.6). For data filtration, we selected the probe sets with signal intensity above the threshold limit in at least 5% of samples. The threshold was established at the 98th percentile of the expression levels from Y-chromosome–linked probe set signals detected detectable in female samples. In addition, the probe sets with signal FC higher than 1.5 (in relation to median) in less than 6 samples were removed.

organism: Homo sapiens

source_name: colon

label_protocol: Biotinylated cRNA were prepared according to the standard one-cycle Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual With Specific Protocols for Using the GeneChip® Hybridization, Wash, and Stain Kit, 2005-2009, Affymetrix)

extract_protocol: Extraction of total RNA was performed using the RNeasy Plus Mini Kit (cat. 74134) according to Qiagen's instructions.

value: adenocarcinoma

tag: Sex

value: female

tag: protocol

value: surgery

tag: localization

value: ascending


title: adenoma_102

value: adenoma

value: male

value: colonoscopy


title: adenoma_105

value: rectum


title: adenoma_100

value: sigmoid


title: normal_colon_96 (macro)

value: normal colon


title: adenoma_103


title: adenoma_104


title: normal_colon_101 (macro)

value: caecum


title: adenocarcinoma_99


title: adenoma_94


title: adenoma_95


title: adenocarcinoma_98


title: adenoma_93


title: adenocarcinoma_89

value: transverse


title: adenoma_82


title: adenocarcinoma_78

value: descending+sigmoid


title: normal_colon_77 (macro)

value: descending


title: adenoma_75


title: adenoma_67


title: adenoma_60


title: normal_colon_88 (macro)


title: adenoma_61


title: adenocarcinoma_90


title: normal_colon_92 (macro)


title: adenocarcinoma_91


title: adenoma_59


title: adenocarcinoma_87


title: adenocarcinoma_63


title: adenocarcinoma_85


title: normal_colon_84 (macro)


title: normal_colon_83 (macro)


title: adenoma_86


title: adenoma_81


title: adenoma_80


title: normal_colon_79 (macro)


title: adenoma_55


title: adenocarcinoma_76


title: adenoma_74


title: adenocarcinoma_44


title: adenocarcinoma_70


title: adenocarcinoma_71


title: adenocarcinoma_69


title: normal_colon_68 (macro)


title: adenocarcinoma_45


title: normal_colon_43 (macro)


title: adenoma_41


title: adenoma_73


title: adenoma_40


title: adenoma_72


title: adenoma_66


title: adenoma_65


title: adenocarcinoma_35


title: normal_colon_33 (macro)


title: normal_colon_62 (macro)


title: adenocarcinoma_37


title: adenocarcinoma_64


title: adenocarcinoma_31


title: adenocarcinoma_36


title: normal_colon_30 (macro)


title: adenocarcinoma_58


title: adenocarcinoma_42

value: rectosigmoid


title: normal_colon_57 (macro)


title: adenoma_54


title: adenoma_48


title: normal_colon_49 (macro)


title: adenocarcinoma_51


title: adenocarcinoma_56


title: adenoma_53


title: adenocarcinoma_50


title: adenoma_46


title: adenoma_52


title: normal_colon_29 (macro)


title: adenocarcinoma_25


title: adenoma_34


title: normal_colon_23 (macro)


title: adenoma_38


title: adenoma_21


title: adenocarcinoma_22


title: adenoma_47


title: adenocarcinoma_17


title: adenocarcinoma_32


title: adenoma_39


title: adenoma_28


title: adenoma_27


title: adenoma_26


title: normal_colon_18 (macro)


title: adenocarcinoma_11


title: adenoma_19


title: adenocarcinoma_24


title: colonic_crypt_epithelial_cells_adenoma_36 (micro)

data_processing: Cell intensity files were generated using GCOS (Affymetrix). The probe set data was generated using R/BioConductor (version 2.8.1) packages affy (version 1.20.2), gcrma (version 2.14.1), and FLUSH.LVS.bundle (version 1.2.1, proportion=0.6). For data filtration, we selected the probe sets with signal intensity above the threshold limit in at least 5% of samples. The threshold was established at the 98th percentile of the expression levels from Y-chromosome–linked probe set signals detected detectable in female samples

label_protocol: Biotinylated cRNA were prepared according to the standard two-cycle Affymetrix protocol from 10-50 ng total RNA (Expression Analysis Technical Manual With Specific Protocols for Using the GeneChip® Hybridization, Wash, and Stain Kit, 2005-2009, Affymetrix)

extract_protocol: Extraction of total RNA was performed using the RNeasy Plus Micro Kit (cat. 74034) according to Qiagen's instructions.

value: colon tumor

tag: tissue morphology

value: colonic crypt epithelial cells

tag: malignacy


title: normal_colon_16 (macro)

tag: age


title: adenoma_12

tag: tissue


title: adenocarcinoma_4

value: adenocarcinoma


title: colonic_crypt_epithelial_cells_normal_colon_35 (micro)

value: female


title: adenoma_20


title: mucosa_carcinoma_34 (micro)

value: mucosa

value: carcinoma


title: adenoma_14

value: adenoma


title: mucosa_distant_normal_colon_39 (micro)

value: distant normal colon


title: adenocarcinoma_15

value: surgery


title: normal_colon_8 (macro)

value: male

value: ascending


title: normal_colon_9 (macro)

value: normal colon

value: colonoscopy


title: normal_colon_10 (macro)

value: rectum


title: adenoma_7

value: sigmoid


title: adenocarcinoma_3


title: adenoma_6


title: normal_colon_5 (macro)


title: adenoma_13

value: descending


title: colonic_crypt_epithelial_cells_distant_normal_colon_38 (micro)


title: adenocarcinoma_2


title: colonic_crypt_epithelial_cells_carcinoma_37 (micro)


title: normal_colon_1 (macro)


title: mucosa_normal_colon_32 (micro)


title: mucosa_adenoma_40 (micro)


title: colonic_crypt_epithelial_cells_normal_colon_31 (micro)


title: mucosa_normal_colon_33 (micro)


title: mucosa_distant_normal_colon_29 (micro)


title: mucosa_distant_normal_colon_28 (micro)


title: mucosa_distant_normal_colon_30 (micro)


title: colonic_crypt_epithelial_cells_distant_normal_colon_23 (micro)


title: colonic_crypt_epithelial_cells_carcinoma_22 (micro)


title: colonic_crypt_epithelial_cells_distant_normal_colon_24 (micro)


title: colonic_crypt_epithelial_cells_adenoma_18 (micro)


title: mucosa_distant_normal_colon_27 (micro)


title: colonic_crypt_epithelial_cells_distant_normal_colon_26 (micro)


title: colonic_crypt_epithelial_cells_carcinoma_17 (micro)


title: colonic_crypt_epithelial_cells_distant_normal_colon_25 (micro)


title: colonic_crypt_epithelial_cells_carcinoma_21 (micro)


title: mucosa_carcinoma_12 (micro)


title: mucosa_adenoma_10 (micro)


title: mucosa_carcinoma_9 (micro)


title: colonic_crypt_epithelial_cells_adenoma_15 (micro)


title: mucosa_normal_colon_5 (micro)


title: colonic_crypt_epithelial_cells_normal_colon_14 (micro)


title: mucosa_adenoma_11 (micro)


title: colonic_crypt_epithelial_cells_normal_colon_19 (micro)


title: colonic_crypt_epithelial_cells_adenoma_20 (micro)


title: colonic_crypt_epithelial_cells_adenoma_13 (micro)


title: mucosa_adenoma_6 (micro)


title: colonic_crypt_epithelial_cells_normal_colon_4 (micro)


title: mucosa_adenoma_3 (micro)


title: colonic_crypt_epithelial_cells_carcinoma_16 (micro)


title: mucosa_carcinoma_7 (micro)


title: mucosa_normal_colon_1 (micro)


title: mucosa_carcinoma_8 (micro)


title: mucosa_normal_colon_2 (micro)


title: heads at 10d, biological rep2

city: Providence

first: Sara

last: Hillenmeyer

state: RI

address: 60 Olive St

department: MCB

institute: Brown University

description: Gene expression data from 10 day old female heads

hyb_protocol: 10ug of the fragmented and labeled cRNA were hybridized to Drosophila 2.0 arrays overnight at 45 ° C, 60 rpm.

scan_protocol: The array was stained using Affymetrix Hybridization-Wash-Stain kit and Fluidics Script FS450 0002 on the Affymetrix 450 fluidics station. The arrays were scanned using an Affymetrix 3000 G7 scanner.

data_processing: The data were analyzed with gcRMA and drosophila2.db using bioconductor and R

source_name: Female Drosophila heads, 10 days

label_protocol: 150 ng of the RNA was amplified with the 3’ Express kit (Affymetrix).

extract_protocol: Total head mRNA was extracted from 75-100 heads of three independent biological replicates of 10 and 40 day old flies using Qiagen RNeasy total RNA isolation kit

tag: strain

value: Canton S


title: Sox14, rep 3

status: Public on Jul 31 2010

city: Athens

first: Robert

middle: B

last: Beckstead

state: GA

address: 119 Poultry Science Building

department: Poultry Science

institute: The University of Georgia

description: Gene expression data from 0 hour w1118;sox14L1/sox14L1 prepupa.

hyb_protocol: Following fragmentation, 5 ug of aRNA were hybridized for 16 hr at 45C on the Drosophila Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were analyzed within Expression Console 1.1 using Affymetrix default analysis settings and RMA as the normalization method. Differential expression was assessed using Significance Analysis of Microarray (SAM).

source_name: Drosophila w1118; sox14L1/sox14L1 0 hour prepupa

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). The manual that was used has a copyright of 2008-2009.

growth_protocol: Animals were raised at 25C on standard Drosophila media.

extract_protocol: Total RNA was isolated using TriPure (Roche), followed by purification with RNAeasy columns (Qiagen).

value: whole body

value: prepupa

tag: background strain

tag: genotype


title: heads at 40d, biological rep2

description: Gene expression data from 40 day old female heads

source_name: Female Drosophila heads, 40 days


title: heads at 40d, biological rep3


title: W1118, rep 1

description: Gene expression data from 0 hour w1118 prepupa.

source_name: Drosophila w1118 0 hour prepupa

tag: sample type

value: control


title: heads at 40d, biological rep1


title: W1118, rep 2


title: Sox14, rep 1


title: heads at 10d, biological rep1


title: W1118, rep 3


title: Wild_type_Drosophila_normoxia_sample6

city: Heidelberg

first: Matias

last: Mosqueira

state: Baden-Wuttenberg

address: Im Neuenheimer Feld, 326 R414

department: Institute of Physiology and Pathop

institute: Heidelberg University Hospital

description: Each sample was made using single whole fly.

hyb_protocol: cDNA yields ranged from 5000-6000ug, and 3.75ug were added to Affymetrix hybridization cocktails, heated at 99ºC for 2 min and hybridized for 16 h at 45ºC to Drosophila V2.0 GeneChips (Affymetrix Inc., Santa Clara CA). The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.

scan_protocol: The chip was scanned at 6um resolution with Agilent model G2500A GeneArray scanner. A visual quality control measurement was performed to ensure proper hybridization after each chip was scanned.

data_processing: Quality control parameters such as scaling factors used to normalize the chips, average background, and noise were also evaluated. In addition, raw intensities for each probe set were stored in electronic formats by the GeneChip Operating System version 1.1 (GCOS1.1, Affymetrix Inc.) for GC-RMA analysis in GeneSpring Software later on.

source_name: DmWT Nx # 6, normoxia, two weeks

label_protocol: 100ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by a poly(T) oligomer that incorporated a synthetic RNA sequence.  Second-strand cDNA synthesis was followed by ribo-SPIA (Single Primer Isothermal Amplification, NuGEN Technologies Inc. San Carlo, CA) for linear amplification of each transcript, and the resulting cDNA was fragmented, assessed by Bioanalyzer, and biotinylated

extract_protocol: Total RNA was isolated and purified from each fly by RNeasy micro kit (Qiagen, Valencia, CA) as described by manufacturer.

treatment_protocol: In order to understand the chronic hypoxia (CH) effect upon the absence of dystrophin, Drosophila melanogaster wild type and the model for DMD (dmDys), in which all dystrophins expression was knocked out by iRNA, were exposed to high altitude hypoxia (hypobaric hypoxia) during a 16-day climbing period reaching the summit of Mount McKinley (6194 meters above sea level). Furthermore, dmDys and Drosophila wild type were exposed to normobaric hypoxia (hypoxic chamber) following the same oxygen levels observed during the climbing expedition and to normoxic conditions for comparison.

tag: id

value: Sample # 6

value: Adult (3-5 days old)

value: Wild type

tag: treatment

value: Exposed to normoxia at Philadelphia-PA for two weeks.


title: heads at 10d, biological rep3


title: Sox14, rep 2


title: Wild_type_Drosophila_normoxia_sample3

source_name: DmWT Nx # 3, normoxia, two weeks

value: Sample # 3


title: Dystrophic_Drosophila_normoxic_sample8

source_name: DmDys CH # 8, normoxic, two weeks

value: Sample # 8

value: dmDys

value: Exposed to normoxia (room air at Philadelphia-PA) for two weeks.


title: Wild_type_Drosophila_normobaric_hypoxia_sample7

source_name: DmWT CH # 7, normobaric hypoxia, two weeks

value: Sample # 7

value: Exposed to normobaric hypoxia at Philadelphia-PA for two weeks.


title: Wild_type_Drosophila_normobaric_hypoxia_sample6

source_name: DmWT CH # 6, normobaric hypoxia, two weeks


title: Dystrophic_Drosophila_chronic_hypoxia_sample7

source_name: DmDys CH # 7, hypobaric hypoxia, two weeks

label_protocol: 100ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by a poly(T) oligomer that incorporated a synthetic RNA sequence.  Second-strand cDNA synthesis was followed by ribo-SPIA (Single Primer Isothermal Amplification, NuGEN Technologies Inc. San Carlo, CA) for linear amplification of each transcript, and the resulting cDNA was fragmented, assessed by Bioanalyzer, and biotinylated.

treatment_protocol: In order to understand the chronic hypoxia (CH) effect upon the absence of dystrophin, Drosophila melanogaster  wild type and the model for DMD (dmDys), in which all dystrophins expression was knocked out by iRNA, were exposed to high altitude hypoxia (hypobaric hypoxia) during a 16-day climbing period reaching the summit of Mount McKinley (6194 meters above sea level). Furthermore, dmDys and Drosophila wild type were exposed to normobaric hypoxia (hypoxic chamber) following the same oxygen levels observed during the climbing expedition and to normoxic conditions for comparison.

value: Exposed to hypobaric hypoxia (Mount McKinley, Alaska) for two weeks.


title: Dystrophic_Drosophila_chronic_hypoxia_sample6

source_name: DmDys CH # 6, hypobaric hypoxia, two weeks


title: Dystrophic_Drosophila_chronic_hypoxia_sample8

source_name: DmDys CH # 8, hypobaric hypoxia, two weeks


title: Wild_type_Drosophila_normoxia_sample2

source_name: DmWT Nx # 2, normoxia, two weeks

value: Sample # 2


title: Dystrophic_Drosophila_normoxic_sample10

source_name: DmDys CH # 10, normoxic, two weeks

value: Sample # 10


title: Wild_type_Drosophila_normobaric_hypoxia_sample5

source_name: DmWT CH # 5, normobaric hypoxia, two weeks


title: Dystrophic_Drosophila_chronic_hypoxia_sample5

source_name: Exposed to hypobaric hypoxia (Mount McKinley, Alaska) for two weeks

value: Sample # 5

tag: dystrophic Drosophila melanogaster (dmDys)


title: Dystrophic_Drosophila_normoxic_sample6

source_name: DmDys CH # 6, normoxic, two weeks


title: Dystrophic_Drosophila_normoxic_sample7

source_name: DmDys CH # 7, normoxic, two weeks


title: Wild_type_Drosophila_normoxia_sample5

source_name: DmWT Nx # 5, normoxia, two weeks


title: Wild_type_Drosophila_normobaric_hypoxia_sample3

source_name: DmWT CH # 3, normobaric hypoxia, two weeks


title: Arabidopsis ATH1_SCR inducible line_time course_second biological replicate Time 12H after Dex treatment

status: Public on Jul 19 2010

first: Rosangela

last: Sozzani

description: Gene expression data from J0571 sorted cells under standard conditions for 5 days and transferred to dex containing plates

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

source_name: J0571 sorted cells

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

growth_protocol: Seeds were surface sterilized for 2 minutes in 70% ethanol, the ethanol was removed, then replaced with 30% Bleach and 0.02% Triton X-100 for 15 minutes. Seeds were rinsed 3 times with sterile water, stratified at 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.  Dex media is 1X Murashige and Skoog salt mixture in which 1micromolar of Dex is added. Nylon mesh was placed on top of the solidified media and seeds were planted at ~20 seeds/cm in two rows.

extract_protocol: Approximately 1000 roots were collected per replicate, with two biological replicates being performed per time point.  Samples were briefly sonicated to disrupt the tissue.  RNA was extracted using the RNAeasy Plant Mini Kit (Qiagen).

treatment_protocol: Seedlings were grown for 5 days before transfer to Dex media.  Roots were cut with a razor blade 0.5 mm below the root/hypocotyl junction and collected into RNA extraction buffer.

tag: ecotype

value: Columbia

value: Seedling roots, 5 days after germination

value: Dex media for 12 hours


title: Arabidopsis ATH1_SCR inducible line_time course_second biological replicate Time 3H after Dex treatment

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

value: Dex media for 3 hours


title: Arabidopsis ATH1_SCR inducible line_time course_first biological replicate Time 3H after Dex treatment


title: Arabidopsis ATH1_SCR inducible line_time course_first biological replicate Time 12H after Dex treatment


title: Arabidopsis ATH1_SCR inducible line_time course_first biological replicate Time 6H after Dex treatment

value: Dex media for 6 hours


title: Arabidopsis ATH1_SHR inducible line_time course_second biological replicate Time 6H after Dex treatment


title: Arabidopsis ATH1_SCR inducible line_time course_first biological replicate Time 1H after Dex treatment

value: Dex media for 1 hour


title: Arabidopsis ATH1_cortex/endodermis initial cell type_CYCD6 marker GFP line_tird biological replicate

description: Gene expression data from CEI sorted cells under standard conditions for 5 days

source_name: CEI sorted cells

value: Standard media


title: Arabidopsis ATH1_cortex/endodermis initial cell type_CYCD6 marker GFP line_first biological replicate


title: Arabidopsis ATH1_SHR inducible line_time course_first biological replicate Time 12H after Dex treatment


title: Arabidopsis ATH1_SCR inducible line_time course_first biological replicate Time 0H after Dex treatment

value: Dex media for 0 hours


title: Arabidopsis ATH1_SHR inducible line_time course_second biological replicate Time 12H after Dex treatment


title: Arabidopsis ATH1_SHR inducible line_time course_second biological replicate Time 1H after Dex treatment


title: Arabidopsis ATH1_SCR inducible line_time course_second biological replicate Time 6H after Dex treatment


title: Arabidopsis ATH1_SHR inducible line_time course_first biological replicate Time 1H after Dex treatment


title: Arabidopsis ATH1_SHR inducible line_time course_second biological replicate Time 3H after Dex treatment


title: Arabidopsis ATH1_SHR inducible line_time course_first biological replicate Time 6H after Dex treatment


title: Arabidopsis ATH1_SHR inducible line_time course_first biological replicate Time 3H after Dex treatment


title: Arabidopsis ATH1_SHR inducible line_time course_second biological replicate Time 0H after Dex treatment


title: per01:large PDF cells from adult ZT12, biological replicate 1

status: Public on Jul 15 2010

city: Evanston

first: Elzbieta

last: Kula-Eversole

address: 2205 Tech Drive

department: NBP

institute: Northwestern University

description:
Purified cells.
per0large_ZT12_1

hyb_protocol: Following fragmentation, 5-10ug of cRNA were hybridized for 18hrs at 45C on GeneChip Drosophila v2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with the Affymetrix GeneArray Scanner G3000.

data_processing: Data were processed using the GCRMA algorithm in R version 2.6 and Bioconductor version 2.1 with default settings.

source_name: adult brain ZT12, large pdf-GFP positive cells in per01 background

label_protocol: Biotinylated cRNA was prepared using two rounds of T7 in vitro transcription based RNA amplification (Affymetrix Small Sample Target Labeling Assay Version II) from about 0.1 to 0.4 ng of total RNA.

growth_protocol: Flies were grown under standard condtions in 12hrs dark:12hrs light cycles.

extract_protocol: Total RNA was extracted using PicoPure RNA isolation kit (Arcturus) according to the manufacturer's protocol.

treatment_protocol: About 50 adult brains were dissected at ZT0, ZT6, ZT12 or ZT18, digested with protease, and dissociated. GFP-positive cells were collected.

tag: background

value: brain

tag: cell type

value: large PDF circadian neurons

tag: developmental stage

value: adult

tag: gender

value: male

tag: time


title: per01:large PDF cells from adult ZT12, biological replicate 2

description:
Purified cells.
per0large_ZT12_2


title: Arabidopsis ATH1_SHR inducible line_time course_first biological replicate Time 0H after Dex treatment


title: small PDF cells from adult, ZT12, biological replicate 2

description:
Purified cells.
small_ZT12_2

source_name: adult brain ZT12, small pdf-GFP positive cells

value: yw

value: small PDF circadian neurons

value: male and female


title: small PDF cells from adult ZT0, biological replicate 1

description:
Purified cells.
small_ZT0_1

source_name: adult brain ZT0, small pdf-GFP positive cells


title: per01:large PDF cells from adult ZT0, biological replicate 1

description:
Purified cells.
per0large_ZT0_1

source_name: adult brain ZT0, large pdf-GFP positive cells in per01 background


title: large PDF cells from adult ZT18, biological replicate 2

description:
Purified cells.
large_ZT18_2

source_name: adult brain ZT18, large pdf-GFP positive cells


title: large PDF cells from adult ZT18, biological replicate 1

description:
Purified cells.
large_ZT18_1


title: small PDF cells from adult ZT0, biological replicate 2

description:
Purified cells.
small_ZT0_2


title: per01:large PDF cells from adult ZT0, biological replicate 2

description:
Purified cells.
per0large_ZT0_2


title: large PDF cells from adult ZT12, biological replicate 3

description:
Purified cells.
large_ZT12_3

source_name: adult brain ZT12, large pdf-GFP positive cells


title: small PDF cells from adult, ZT12, biological replicate 1

description:
Purified cells.
small_ZT12_1


title: large PDF cells from adult ZT6, biological replicate 1

description:
Purified cells.
large_ZT6_1

source_name: adult brain ZT6, large pdf-GFP positive cells


title: large PDF cells from adult ZT12, biological replicate 1

description:
Purified cells.
large_ZT12_1


title: ELAV cells from adult ZT0, biological replicate 3

description:
Purified cells.
ELAV_ZT0_3

source_name: adult brain ZT0, ELAV-GFP positive cells

value: ELAV neurons


title: large PDF cells from adult ZT6, biological replicate 2

description:
Purified cells.
large_ZT6_2


title: ELAV cells from adult ZT0, biological replicate 2

description:
Purified cells.
ELAV_ZT0_2


title: ELAV cells from adult ZT0, biological replicate 1

description:
Purified cells.
ELAV_ZT0_1


title: large PDF cells from adult ZT0, biological replicate 1

description:
Purified cells.
large_ZT0_1

source_name: adult brain ZT0, large pdf-GFP positive cells


title: large PDF cells from adult ZT12, biological replicate 2

description:
Purified cells.
large_ZT12_2


title: large PDF cells from adult ZT0, biological replicate 2

description:
Purified cells.
large_ZT0_2


title: large PDF cells from adult ZT0, biological replicate 3

description:
Purified cells.
large_ZT0_3


title: ELAV cells from adult ZT12, biological replicate 1

description:
Purified cells.
ELAV_ZT12_1

source_name: adult brain ZT12, ELAV-GFP positive cells


title: ELAV cells from adult ZT12, biological replicate 3

description:
Purified cells.
ELAV_ZT12_3


title: ELAV cells from adult ZT12, biological replicate 2

description:
Purified cells.
ELAV_ZT12_2


title: Columbia.Dry.MN.rep3

status: Public on Jul 01 2010

city: Toronto

first: Malcolm

middle: M.

last: Campbell

state: ON

address: 25 Willcocks Street

department: Cell & Systems Biology

country: Canada

institute: University of Toronto

description:
28 days without water limitation followed by 4 days without further input of water 4 days.
bot0875

hyb_protocol: Affymetrix protocol: Eukaryotic target preparation: Eukaryotic target hybridization.

scan_protocol: Affymetrix protocol: GeneChip Scanner 3000 7G Affymetrix 00-0073.

data_processing: GC-RMA in BioConductor.

source_name: whole rosette, water-limited, midnight

label_protocol: Affymetrix protocol: Eukaryotic target preparation: One-cycle target labeling assay.

growth_protocol: Col-0 seeds were planted on Sunshine mix #1. Seeds were cold stratified for 3 days, then transferred to growth chambers with a 12h photoperiod. Plants were watered every other morning with tap water.

extract_protocol: Trizol, as per manufacturer's instructions.

treatment_protocol: After 28 days of growth without water limitation, no further input of water was given to 50% of plants. The other 50% were watered as before.

value: wild type

value: whole rosette

value: 32 days

value: water-limited

tag: time of day

value: 00h00 (midnight)


title: Columbia.Wet.LD.rep3

description:
32 days without water limitation.
bot0866

source_name: whole rosette, well-watered, late day

value: well-watered

value: 18h00 (late day)


title: Columbia.Dry.LD.rep3

description:
28 days without water limitation followed by 4 days without further input of water 4 days.
bot0869

source_name: whole rosette, water-limited, late day


title: Columbia.Wet.PD.rep3

description:
32 days without water limitation.
bot0854

source_name: whole rosette, well-watered, pre-dawn

value: 06h00 (pre-dawn)


title: Columbia.Wet.MN.rep1

description:
32 days without water limitation.
bot0870

source_name: whole rosette, well-watered, midnight


title: Columbia.Wet.MN.rep3

description:
32 days without water limitation.
bot0872


title: Columbia.Wet.PD.rep1

description:
32 days without water limitation.
bot0852


title: Columbia.Dry.PD.rep3

description:
28 days without water limitation followed by 4 days without further input of water 4 days.
bot0857

source_name: whole rosette, water-limited, pre-dawn


title: Columbia.Dry.MN.rep2

description:
28 days without water limitation followed by 4 days without further input of water 4 days.
bot0874


title: Columbia.Dry.LD.rep2

description:
28 days without water limitation followed by 4 days without further input of water 4 days.
bot0868


title: Columbia.Dry.MD.rep3

description:
28 days without water limitation followed by 4 days without further input of water 4 days.
bot0863

source_name: whole rosette, water-limited, midday

value: 12h00 (midday)


title: Columbia.Dry.PD.rep2

description:
28 days without water limitation followed by 4 days without further input of water 4 days.
bot0856


title: Columbia.Dry.LD.rep1

description:
28 days without water limitation followed by 4 days without further input of water 4 days.
bot0867


title: Columbia.Dry.MN.rep1

description:
28 days without water limitation followed by 4 days without further input of water 4 days.
bot0873


title: Columbia.Dry.MD.rep1

description:
28 days without water limitation followed by 4 days without further input of water 4 days.
bot0861


title: Columbia.Wet.LD.rep1

description:
32 days without water limitation.
bot0864


title: Columbia.Dry.PD.rep1

description:
28 days without water limitation followed by 4 days without further input of water 4 days.
bot0855


title: Columbia.Wet.MN.rep2

description:
32 days without water limitation.
bot0871


title: Columbia.Wet.PD.rep2

description:
32 days without water limitation.
bot0853


title: Columbia.Wet.LD.rep2

description:
32 days without water limitation.
bot0865


title: Columbia.Dry.MD.rep2

description:
28 days without water limitation followed by 4 days without further input of water 4 days.
bot0862


title: Columbia.Wet.MD.rep3

description:
32 days without water limitation.
bot0860

source_name: whole rosette, well-watered, midday


title: gir_flower_33d_rep4

city: Taipei

first: Wan-Hsing

last: Cheng

address: 128, Section 2, Academia Road, Nankang

institute: Academia Sinica

hyb_protocol: Standard hybridization protocol of Affymetrix expression array

scan_protocol: Standard scanning protocol of Affymetrix expression array

source_name: gir mutant, 33-day-old, excised flower

label_protocol: Standard labeling protocol of Affymetrix expression array

growth_protocol: Soil-grown plants

extract_protocol: QIAGEN RNease Plant Kit

value: gir mutant

value: 33 days old

value: flower


title: Columbia.Wet.MD.rep2

description:
32 days without water limitation.
bot0859


title: Columbia.Wet.MD.rep1

description:
32 days without water limitation.
bot0858


title: gir_root_4%glc_rep1

hyb_protocol: Standard hybridization protocal of Affymetrix expression array

source_name: gir mutant, 4% glucose treatment, excised root

label_protocol: Standard labeling protocal of Affymetrix expression array

growth_protocol:
1. Plants were grown on 0% glucose + 1/2 MS agar plate for 7 days.
2. Then, transfer seedlings to 0% glucose + 1/2 MS vertical agar plate
3. Then, transfer seedlings to 4% glucose + 1/2 MS vertical agar plate
4. The root tissues were excised for GeneChip analysis

extract_protocol: QIAGEN RNeasy Plant Kit

value: 21 days old

tag: agent

value: 4% glucose

value: root


title: Col-7_flower_33d_rep2

source_name: Col-7, 33-day-old, excised flower


title: Col-7_root_4%glc_rep3

source_name: Col-7, 4% glucose treatment, excised root


title: gir_flower_33d_rep1


title: gir_root_4%glc_rep2


title: Col-7_root_4%glc_rep2


title: Col-7_root_4%glc_rep1


title: Col-7_flower_33d_rep3


title: gir_flower_33d_rep3


title: gir_flower_33d_rep2

source_name: gir mutant, 33-day-oid, excised flower


title: Col-7_flower_33d_rep1


title: gir_root_4%glc_rep3


title: ea_atoGOF2_rep3

status: Public on Jun 28 2010

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: eye-antennal imaginal discs of third instar larvae of Drosophila melanogaster

hyb_protocol: A mixture of purified and fragmented biotinylated cRNA and added hybridisation controls (Affymetrix) was hybridised on Affymetrix Drosophila 2.0 arrays followed by staining and washing in the GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using the GeneChip scanner 3000 (Affymetrix).

data_processing: RMA

source_name: eye-antennal imaginal discs atoGal4 x UASato

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technolgies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 2 µg of total RNA spiked with four bacterial RNA transcripts (Affymetrix) was converted and amplified to double stranded cDNA in a 1-cycle cDNA reverse transcription reaction. Subsequently the sample was converted to antisense cRNA and labeled with biotin through an in vitro transcription reaction according to the manufacturers protocol (Affymetrix).   All amplification and labeling reactions were performed on a Biomek 3000 ArrayPlex Workstation (Beckman Coulter).

growth_protocol: Flies and crosses are kept in standard food at 18 degrees, at early third instar stage shifted for 24 hours at 28 degrees Celcius

extract_protocol: eye-antennal imaginal discs are dissected from 3rd instar larvae in RNAlater (Ambion) and transferred to the RNA extraction buffer, on ice, of the ZymoResearch mini RNA isolation kit.

tag: genotype/variation

value: Atonal gain-of-function (GOF)

tag: replicate

tag: line

value: atoGal4 x UASato

value: third instar larva

value: eye-antennal imaginal discs


title: ea_atoLOF_rep3

source_name: eye-antennal imaginal discs ato-/-

value: Atonal loss-of-function (LOF)

value: ato-/-

tag: tissue


title: ea_atoGOF1_rep3

source_name: eye-antennal imaginal discs Gal47 x UASato

value: Gal4/7 x UASato


title: ea_atoLOF_rep2


title: ea_sensGOF_rep3

source_name: eye-antennal imaginal discs atoGal4 x UASsens

value: Senseless gain-of-function (GOF)

value: atoGal4 x UASsens


title: ea_control3_rep2

source_name: eye-antennal imaginal discs UASato

value: control

value: UASato


title: ea_atoGOF2_rep2


title: ea_atoGOF1_rep2


title: ea_control2_rep2

source_name: eye-antennal imaginal discs atoGal4 (NP6558)


title: ea_sensGOF_rep2


title: ea_atoLOF_rep1


title: ea_sensGOF_rep1


title: ea_control1_rep2

source_name: eye-antennal imaginal discs Gal47


title: ea_control4_rep2

source_name: eye-antennal imaginal discs cantonS wild type

value: cantonS


title: ea_control4_rep1


title: ea_control1_rep1


title: ea_atoGOF1_rep1


title: ea_control3_rep1


title: ea_atoGOF2_rep1


title: MBD-R2 construct M3, rep3

status: Public on Jun 26 2010

city: Munich

first: Christian

last: Feller

address: Schillerstraße 44

department: Molecular Biology

institute: Adolf-Butenandt Institute at the LMU University Munich

hyb_protocol: Performed by imaGenes (www.imagenes-bio.de).

data_processing: Intensity values were normalized, summarized and log2 transformed using the ‘gcrma’ package (Wu and Irizarry, 2005).

source_name: SL2 cells, MBD-R2 RNAi M2

growth_protocol: SL2 cells were cultivated as previously described (Straub et al. 2005).

extract_protocol: RNA was isolated using Trizol (Invitrogen) followed by a purification using RNeasy kit (Quiagen) according to the instructions of the suppliers.

treatment_protocol: RNA interference (RNAi) of target genes were carried out as described previously (Straub et al., 2005). In brief, 1.5 10^6 SL2 cells were incubated with 10 μg dsRNA for 1 hour in serum-free medium. After addition of serum-containing medium, cells were incubated for 7 days at 26°C before RNA extraction.

tag: cell line

tag: rnai target


title: MBD-R2 construct M2, rep1

scan_protocol: Performed by imaGenes (www.imagenes-bio.de).


title: GST RNAi, rep2

source_name: SL2 cells, GST RNAi

label_protocol: Performed by imaGenes (www.imagenes-bio.de).

value: GST


title: MBD-R2 construct M1, rep3

source_name: SL2 cells, MBD-R2 RNAi M1


title: Pre-operation on-pump ADU_ON03_A

status: Public on Jun 22 2010

city: Bristol

first: Mohamed

middle: T.

last: Ghorbel

address: Level 7, BRI, Marlborough street

department: Bristol Heart Institute

institute: University of Bristol

description: Pre-operative human heart

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: RMA normalized.

source_name: Left ventricle biopsy

label_protocol: One microgram of total RNA was processed to produce biotinylated cRNA targets using the Affymetrix protocol

extract_protocol: Five to ten milligrams of frozen left ventricle biopsy was homogenized and total RNA extracted using the Qiagen MiniElute protocol (Qiagen, UK).

tag: Patients with a diagnosis of two or three vessel ischemic heart disease undergoing primary myocardial revascularisation with the use of cardiopulmonary bypass and cardiac arrest.


title: MBD-R2 construct M1, rep2


title: MBD-R2 construct M1, rep1


title: no RNAi treatment

description: control

source_name: SL2 cells, control


title: GST RNAi, rep1


title: ea_control2_rep1


title: Pre-operation on-pump ADU_ON05_A

description: Pre-operative human heart


title: GST RNAi, rep3


title: Pre-operation on-pump ADU_ON06_A

description: Pre-operative human heart


title: MBD-R2 construct M2, rep2


title: Pre-operation on-pump ADU_ON04_A

description: Pre-operative human heart


title: Post operation on-pump ADU_ON06_C

description: Post-operative human heart


title: Post operation off-pump ADU_OF15_C

description: Post-operative human heart

tag: Patients with a diagnosis of two or three vessel ischemic heart disease undergoing primary myocardial revascularisation without the use of cardiopulmonary bypass.


title: Pre-operation on-pump ADU_ON08_A

description: Pre-operative human heart


title: Post operation on-pump ADU_ON05_C

description: Post-operative human heart


title: Post operation off-pump ADU_OF14_C

description: Post-operative human heart


title: Post operation on-pump ADU_ON04_C

description: Post-operative human heart


title: Post operation off-pump ADU_OF12_C

description: Post-operative human heart


title: Post operation on-pump ADU_ON09_C

description: Post-operative human heart


title: Post operation on-pump ADU_ON03_C

description: Post-operative human heart


title: Pre-operation off-pump ADU_OF03_A

description: Pre-operative human heart


title: Post operation off-pump ADU_OF03_C

description: Post-operative human heart


title: Pre-operation off-pump ADU_OF02_A

description: Pre-operative human heart


title: Group B2-IVIG+IVMP-Post-3

status: Public on Jun 17 2010

city: Sagamihara

first: Shohei

last: Ogata

state: Kanagawa

address: 1-15-1, Kitasato

department: Pediatrics

institute: Kitasato University, School of Medicine

description: no additional information

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array in Hybridization Oven 640 (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using GeneChip Hybridization, Wash and Stain Kit (Affymetrix).

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

data_processing: The expression analysis file created from each chip (sample) was imported into GeneSpring GX version 7.3 software (Agilent Technologies, Santa Clara, CA) for further data characterization. Each array was normalized (mean centered) to the median intensity array.

source_name: IVIG-resistant patient, IVMP + IVIG post-treatment

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

extract_protocol: Total RNA was isolated from 2.5 ml of whole blood using a PAXgene tube, according to the manufacturer’s recommended protocol (Paxgene Blood RNA Kit, PreanalytiX, QIAGEN, Valencia, CA). Next alpha-globin and beta-globin mRNA was removed from the total RNA using the globin reduction method according to the manufacturer’s recommended protocol (Affymetrix, Santa Clara, CA).

treatment_protocol:
The six patients who were predicted IVIG-responders by Egami score were randomly selected Group A (KD_GA). Eleven IVIG-resistant patients predicted by Egami score were randomly assigned to the single-IVIG treatment group (Group KD_GB1; n = 6) and IVIG-plus-IVMP combined therapy group (Group KD_GB2; n = 5)
Groups A (Kd_GA) and B1(KD_GB1) patients were administered single-IVIG treatment (2.0 g/kg for 1 day). Group B2 (KD_GB2) patients received IVMP therapy, 30 mg/kg over 2 hours before receiving IVIG treatment (2.0 g/kg for 1 day). All patients received aspirin (30 mg /kg per day) during the acute stage of illness. The dose of aspirin decreased to 5 mg/kg per day after defervescence.

value: whole blood

tag: patient

value: IVIG-resistant patient

tag: treatment

value: methylprednisolone (IVMP) + IVIG

value: post-treatment


title: Group B2-IVIG+IVMP-Post-2

description: no additional information


title: Group B1-IVIG-Pre-1

description: no additional information

source_name: IVIG-resistant patient, single-IVIG pre-treatment

value: IVIG

value: pre-treatment


title: Group B2-IVIG+IVMP-Post-5

description: no additional information


title: Group B1-IVIG-Post-1

description: no additional information

source_name: IVIG-resistant patient, single-IVIG post-treatment


title: Group B1-IVIG-Post-4

description: no additional information


title: Group B2-IVIG+IVMP-Pre-5

description: no additional information

source_name: IVIG-resistant patient, IVMP + IVIG pre-treatment


title: Group B2-IVIG+IVMP-Pre-4

description: no additional information


title: Group B1-IVIG-Pre-5

description: no additional information


title: Group B2-IVIG+IVMP-Post-1

description: no additional information


title: Group B2-IVIG+IVMP-Pre-3

description: no additional information


title: Group B1-IVIG-Pre-6

description: no additional information


title: Pre-operation off-pump ADU_OF15_A

description: Pre-operative human heart


title: Group B1-IVIG-Pre-4

description: no additional information


title: Group B1-IVIG-Pre-3

description: no additional information


title: Group B1-IVIG-Post-6

description: no additional information


title: Group B1-IVIG-Post-3

description: no additional information


title: Group B2-IVIG+IVMP-Pre-1

description: no additional information


title: Group B2-IVIG+IVMP-Pre-2

description: no additional information


title: Group B1-IVIG-Post-2

description: no additional information


title: Group A-IVIG-Post-6

description: no additional information

source_name: IVIG-responsive patient, post-treatment

value: IVIG-responsive patient


title: Group B2-IVIG+IVMP-Post-4

description: no additional information


title: Group B1-IVIG-Post-5

description: no additional information


title: Group B1-IVIG-Pre-2

description: no additional information


title: Pre-operation off-pump ADU_OF14_A

description: Pre-operative human heart


title: Group A-IVIG-Pre-6

description: no additional information

source_name: IVIG-responsive patient, pre-treatment


title: Post operation off-pump ADU_OF02_C

description: Post-operative human heart


title: Group A-IVIG-Post-3

description: no additional information


title: Group A-IVIG-Pre-4

description: no additional information


title: Group A-IVIG-Pre-5

description: no additional information


title: Pre-operation off-pump ADU_OF12_A

description: Pre-operative human heart


title: Arab_GiantCell_Root_Pico_BioRep1_TechRep2

status: Public on May 26 2010

city: Gainesville

first: Lauren

last: McIntyre

state: FL

address: 2033 Mowry Rd

department: Department of Molecular Genetics and Microbiology

institute: University of Florida

description: cDNA amplified from total RNA isolated from giant cells

hyb_protocol: Hybridization mixture was prepared according to NuGEN and Affymetrix procedures and hybridized to GeneChip© Arabidopsis ATH1 Arrays.

scan_protocol: GeneChips were scanned at the University of Pennsylvania School of Medicine Microarray Facility according to standard manufacturer protocols.

data_processing: Data were quantified with the Expression Console (Affymetrix) software application using the MAS5 algorithm

source_name: LCM of Arabidopsis giant cells

label_protocol: NuGEN FL module

growth_protocol: Arabidopsis seedlings  were grown for infestation with Meloidogyne incognita nematodes according to (Hammes et al. Plant J. 2006 48:414-426).  Briefly, Arabidopsis seeds were sterilized and sown, five seeds per plate, 30 plates total, in a medium containing 2% sucrose, 0.3% Gamborg’s basal salts, and 0.6 % Phytagel, pH 6.1.  Plates were placed at a 45o angle in a short-day chamber.

extract_protocol: Total RNA amplified according to NuGEN WT-Ovation Pico kit instructions.

treatment_protocol: Arabidopsis seedlings were infested with Meloidogyne incognita nematodes according to (Hammes et al. Plant J. 2006 48:414-426). Briefly, 3 week old Arabidopsis seedlings, 5 per plate, were inoculated with 1,000 M. incognita stage 2 juveniles and placed at an angle in a clear acrylic humid box in a short-day chamber. Twenty-one days after inoculation, root cells undergoing giant cell formation (~5,000,000 um2 area) were captured from infested regions of the root. Giant cells were catapulted using the AutoLPC method directly to P.A.L.M. Adhesive caps.

value: 21 days post challenge with M. incognita

value: laser captured giant cells

tag: ecotype

value: Columbia ecotype

tag: sample size

value: ~ 80 cells

value: NuGEN WT-Ovation Pico


title: Group A-IVIG-Post-1

description: no additional information


title: Arab_Control_Root_Pico_BioRep1

description: cDNA amplified from total RNA isolated from control root cells

source_name: LCM of Arabidopsis control root cells

treatment_protocol: Arabidopsis seedlings were infested with Meloidogyne incognita nematodes according to (Hammes et al. Plant J. 2006 48:414-426). Briefly, 3 week old Arabidopsis seedlings, 5 per plate, were inoculated with 1,000 M. incognita stage 2 juveniles and placed at an angle in a clear acrylic humid box in a short-day chamber. Twenty-one days after inoculation, control root cells not undergoing giant cell formation (~13,000,000 um2 area) were captured from non-infested regions of the infested root. Control root cells were catapulted using the AutoLPC method directly to P.A.L.M. Adhesive caps.

value: laser captured control root cells

value: ~ 150 cells


title: Arab_GiantCell_Root_OneDirect_BioRep1_TechRep2

extract_protocol: Total RNA amplified according to NuGEN WT-Ovation One-Direct kit instructions.

value: NuGEN WT-Ovation One-Direct


title: Arab_GiantCell_Root_OneDirect_BioRep1_TechRep3


title: Arab_Control_Root_Pico_BioRep2_TechRep2


title: Group A-IVIG-Pre-2

description: no additional information


title: Arab_GiantCell_Root_OneDirect_BioRep3


title: Arab_GiantCell_Root_OneDirect_BioRep2


title: Group A-IVIG-Post-2

description: no additional information


title: Arab_Control_Root_OneDirect_BioRep2_TechRep2


title: Arab_GiantCell_Root_Pico_BioRep1_TechRep3


title: Arab_Control_Root_OneDirect_BioRep2_TechRep1


title: Group A-IVIG-Post-5

description: no additional information


title: Arab_Control_Root_Pico_BioRep2_TechRep1


title: Arab_GiantCell_Root_Pico_BioRep2


title: Arab_Control_Root_OneDirect_BioRep2_TechRep3


title: Arab_GiantCell_Root_Pico_BioRep1_TechRep1


title: Arab_Control_Root_Pico_BioRep2_TechRep3


title: Group A-IVIG-Pre-1

description: no additional information


title: Group A-IVIG-Post-4

description: no additional information


title: Group A-IVIG-Pre-3

description: no additional information


title: Arab_Control_Root_Pico_BioRep3


title: Arab_GiantCell_Root_Pico_BioRep3


title: Root Col(0) replica 2

status: Public on May 25 2010

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

country: Norway

institute: Norwegian University of Science and Technology

description: Gene expression in 18 days old roots

hyb_protocol: 15 µg of labeled cRNA was used for each hybridization. After 16 hours of hybridization at 45C the arrays were processed through the washing and staining procedures according to the manufacturer instructions (Affymetrics).

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

data_processing: The microarray data were preprocessed using the Robust Multichip Average (RMA) package (Irizarry RA et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4:249-264.) using R. The data were normalized using quantile normalization, and expression measures were produced by fitting the RMA robust linear model.

source_name: Col(0), roots

label_protocol: To prepare the samples for microarray experiments the “GeneChip Expression Analysis” procedure of Affymetrix (Santa Clara, USA) was followed. Briefly, 10 µg total RNA was processed through a one-cycle cDNA synthesis procedure, the resulting double-stranded cDNA was cleaned up and submitted to the synthesis of biotin-labelled cRNA. This biotin-labelled cRNA was then cleaned up, quantified and fragmented.

growth_protocol: Wild-type Col-0 and mutant glu1-2 seeds were surface sterilised and sown on solid in vitro cultivation medium consisting of 1x Murashige and Skoog basal salt mixture, 3% sucrose, 0.75% phytoagar (w/v), pH5.7. This medium contains 1650 mg ammonium nitrate/L. Seeds were stratified for 3 days at 4°C before being transferred to a controlled growth chamber under a 16 hour photoperiod (light intensity: 75 µmol.m-2.sec-1) at 21-23°C. Leaves and roots of 18 day old in vitro grown plantlets were harvested separately and immediately flash-frozen in liquid N2. Harvesting of tissue was performed two hours after onset of the 16 hour light period. The harvested tissue was stored at -80°C until further processing.

extract_protocol: Total RNA was extracted from plant tissue (300 mg roots, 500 mg leaves) using the RNeasy Midi kit (Qiagen, Hilden, Germany) following the supplier’s instructions. Total RNA was consentrated using Microcon YM30 columns (Amicon). RNasin (Promega , Madison, USA) was added to the RNA to the final concentration of 1 U/µl. RNA quality was assessed by standard denaturing agarose gel electrophoresis and RNA concentration was measured with a NanoDrop ND-1000 (Nanodrop, Delaware, USA).

value: roots

tag: stage

value: 18 days after germination


title: Root GLU1-KO replica 4

description: Gene expression in 18 days old roots

source_name: GLU1-KO, roots


title: Arab_GiantCell_Root_OneDirect_BioRep1_TechRep1


title: Leaf Col(0) replica 4

description: Gene expression in 18 days old rosette leaves

source_name: Col(0), rosette leaves

value: rosette leaves

value: 18 days after germination, before bolting


title: Root GLU1-KO replica 1

description: Gene expression in 18 days old roots


title: Root Col(0) replica 4

description: Gene expression in 18 days old roots


title: Leaf Col(0) replica 3


title: Leaf Col(0) replica 1


title: Root GLU1-KO replica 2

description: Gene expression in 18 days old roots


title: Leaf GLU1-KO replica 2

source_name: GLU1-KO, rosette leaves


title: Root GLU1-KO replica 3

description: Gene expression in 18 days old roots


title: Root Col(0) replica 1

description: Gene expression in 18 days old roots


title: Leaf Col(0) replica 2


title: Leaf GLU1-KO replica 3


title: Leaf GLU1-KO replica 1


title: Arab_Control_Root_OneDirect_BioRep1


title: Leaf GLU1-KO replica 4


title: VAD-HTx-45

status: Public on May 20 2010

city: Bad Oeynhausen

first: Patrick

last: Schwientek

address: Georgstr. 11

department: Klinik f. Thorax- & Kardiovaskularchirurgie

institute: Herz- & Diabeteszentrum NRW

description: Gene expression data from patients suffering end-stage heart-failure after VAD support

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133 Plus 2.0 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.

source_name: Transplant Sample 27

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: Myocardial tissue was directly taken from non-failing and failing hearts.

extract_protocol: Samples were pruned from the left ventricle near the apex. RNA extraction has been carried out with TRIzol reagent and tissue was homogenized using a rotor-stator homogenizer. Homogenates were transferred to a Phase Lock Gel (PLG) Heavy tube (Eppendorf), chloroform was added, and the mixture was centrifuged. Supernatants were collected, and isopropanol was added to precipitate the RNA. The RNA pellet was washed with 80% ethanol, then air-dried before dissolving in 100  l of RNase-free H2O. RNA was further purified using the RNeasy Mini protocol according to the manufacturer’s directions (Qiagen).

treatment_protocol: The samples were frozen in liquid nitrogen directly after pruning and defrosted only for microarray analysis.

tag: sample pairs

value: Myocard

tag: vad status

value: after VAD support

tag: disease status

value: ischemic cardiomyopathy

tag: vad

value: Heartmate I

tag: age

tag: gender

value: m


title: VAD-HTx-40

source_name: Transplant Sample 24

value: dilated cardiomyopathy


title: VAD-HTx-27

source_name: Transplant Sample 20


title: VAD-HTx-48

source_name: Transplant Sample 28

value: Novacor


title: VAD-HTx-51

source_name: Transplant Sample 29

value: CorAide


title: VAD-HTx-30

source_name: Transplant Sample 23

value: DuraHeart


title: VAD-HTx-57

source_name: Transplant Sample 30


title: VAD-HTx-28

source_name: Transplant Sample 21


title: VAD-HTx-26

source_name: Transplant Sample 19


title: VAD-HTx-29

source_name: Transplant Sample 22


title: VAD-HTx-44

source_name: Transplant Sample 26

value: Thoratec (biVAD)


title: VAD-HTx-42

source_name: Transplant Sample 25

value: dilated cardiomyopathy (VD)


title: Arab_Control_Root_OneDirect_BioRep3

source_name: LCM of Arabidopsis control root cells

tag: time

value: 21 days post challenge with M. incognita

value: laser captured control root cells

value: Columbia ecotype

value: ~ 150 cells


title: VAD-HTx-14

source_name: Transplant Sample 10

tag: tissue

value: f


title: VAD-HTx-21

source_name: Transplant Sample 15


title: VAD-HTx-23

source_name: Transplant Sample 17


title: VAD-HTx-9

source_name: Transplant Sample 7


title: VAD-HTx-3

source_name: Transplant Sample 2

value: Thoratec


title: VAD-HTx-12

source_name: Transplant Sample 9

value: Myocard


title: VAD-HTx-24

source_name: Transplant Sample 18

value: after VAD support


title: VAD-HTx-17

source_name: Transplant Sample 13


title: VAD-HTx-6

source_name: Transplant Sample 4


title: VAD-HTx-8

source_name: Transplant Sample 6

value: ischemic cardiomyopathy


title: VAD-HTx-7

source_name: Transplant Sample 5

value: Thoratec (iVAD)


title: VAD-HTx-15

source_name: Transplant Sample 11

value: Heartmate I

value: m


title: VAD-HTx-10

source_name: Transplant Sample 8

value: Novacor


title: VAD-HTx-22

source_name: Transplant Sample 16

value: Incor


title: VAD-HTx-18

source_name: Transplant Sample 14

value: dilated cardiomyopathy


title: VAD-HTx-16

source_name: Transplant Sample 12


title: VAD-HTx-2

source_name: Transplant Sample 1


title: VAD-HTx-4

source_name: Transplant Sample 3


title: VAD-IP-45

description: Gene expression data from patients suffering end-stage heart-failure

source_name: Implant Sample 27

value: before VAD support


title: VAD-IP-51

source_name: Implant Sample 29

value: CorAide


title: VAD-IP-40

source_name: Implant Sample 24


title: VAD-IP-28

source_name: Implant Sample 21


title: VAD-IP-44

source_name: Implant Sample 26

value: Thoratec (biVAD)


title: VAD-IP-48

source_name: Implant Sample 28


title: VAD-IP-57

source_name: Implant Sample 30

value: DuraHeart


title: VAD-IP-30

source_name: Implant Sample 23


title: VAD-IP-42

source_name: Implant Sample 25

value: dilated cardiomyopathy (VD)


title: VAD-IP-29

source_name: Implant Sample 22


title: VAD-IP-26

source_name: Implant Sample 19


title: VAD-IP-21

source_name: Implant Sample 15


title: VAD-IP-24

source_name: Implant Sample 18


title: VAD-IP-27

source_name: Implant Sample 20


title: VAD-IP-22

source_name: Implant Sample 16


title: VAD-IP-16

source_name: Implant Sample 12