title: Sun leaves_2xozone_091006_rep3

source_name: Sun leaves_1xozone_091006_rep.2

source_name: Sun leaves_2xozone_091006_rep.2


title: Sun leaves_2xozone_091006_rep4

status: Public on Oct 21 2011

type: RNA

city: Neuherberg

first: Maren

last: Olbrich

address: Ingolstädter Landstr. 1

country: Germany

institute: Helmholtz Zentrum München

description: A coefficient of variation about all microarrays of one time point was calculated using Acuity 4.0 microarray informatics software [Axon Instruments]. We used only those spots that had a coefficient of variation < 50 and were present on at least half of identical slides. We express the median values as log2 ratios.

hyb_protocol: Blocking: 1. 0.1 % SDS for 2 minutes shaking, 2. 0.1 % SDS for 2 minutes shaking, 3. H2Obidest. for 2 minutes shaking, 4. washing of slides in H2Obidest., 5. washing another time with water for 2 minutes, 6. for 2 minutes in cooking water, 7. for 5 minutes in fresh sodium-boric-solution (0.75 g NaBH4 in 200 ml PBS and 75 ml 100% Ethanol p.a.), 8. 1 minutes washing in 0.1 % SDS, 9. another time washing in 0.1 % SDS for 1 minute, 10. 1 minute washing in H2Obidest, 11. incubating in 100% EtOH for about 20 seconds. Hybridization for 16h up to 20h at 42°C in a hybridization furnace. Washing: in wash buffer (1x SSC/0.2% SDS) for 4 minutes at 42 °C, 4 minutes in wash buffer (0.1x SSC und 0.2% SDS), 2 minutes in wash buffer (0.1x SSC), 2 minutes in wash buffer (0.1x SSC), 2 minutes in Millipore water.

scan_protocol: Hardware: GenePix 4000A (Axon Instruments, Sunnyvale, USA), simultaneous scanning of both wavelengths (532nm, 635nm). Software: GenePix Pro 6.0 (Axon Instruments (Sunnyvale, USA) FLA 8000 Version 1.3.

data_processing:
Normalization via GenePix Pro 4.0.
For normalization, only spots were used which (1) were not marked with "bad", "absent", or "not found"; (2) spots that had for both wavelengths more than 55% of pixel above background one standard deviation; (3) spots with a pixel intensity for both wavelengths above 500; (4) coefficient of determination of actual regression of both wavelengths was above 0.5; (5) light saturation of pixel was under 3%. On the basis of these values, all genes of the array were normalized.

molecule: total RNA

organism: Fagus sylvatica

label_protocol: Cy5 Mono-Reactive Dye Pack dissolved in 85 µl DMSO, dried cDNA dissolved in 4.5µl Na2CO3, 4.5µl dissolved Cy5 dye was added and incubated for about 2 hours at room temperature and in the dark. Precipitate with 35 µl 100 mM NaAc (pH 5,2), purified with QIAquick PCR Purification Kit, Qiagen, Hilden. Dried and dissolved in 62 µl hybridization buffer (50% formamide, 5-fach SSC, 0.1% SDS, 2% salmon sperm DNA (w/w), then for 3 minutes at 90°C, centrifuged and put on array.

extract_protocol: According to Kiefer et al. 2000.

tag: age

value: about 60 years

tag: tissue

value: five pooled sun leaves

tag: tree

tag: exposition

value: 2x ambient ozone, restricted to 150 ppm

tag: sampling

value: 9th of October 2006

label_protocol: Cy3 Mono-Reactive Dye Pack dissolved in 85 µl DMSO, dried cDNA dissolved in 4.5µl Na2CO3, 4.5µl dissolved Cy3 dye was added and incubated for about 2 hours at room temperature and in the dark. Precipitate with 35 µl 100 mM NaAc (pH 5,2), purified with QIAquick PCR Purification Kit, Qiagen, Hilden. Dried and dissolved in 62 µl hybridization buffer (50% formamide, 5-fach SSC, 0.1% SDS, 2% salmon sperm DNA (w/w), then for 3 minutes at 90°C, centrifuged and put on array.

value: 1x ambient ozone


title: IDC29

city: Madrid

first: Gema

last: Moreno-Bueno

state: Madrid

address: Arturo Duperier

department: Biochemistry

country: Spain

institute: IIB

hyb_protocol: The arrays hybridization was performed using In Situ Hybridization Kit Plus (Agilent technologies) according to Peinado et al, Cancer Research 2008.

scan_protocol: After hybridization and washing, the slides were scanned in an Axon GenePix Scanner (Axon Instruments), according to manufacturer´s protocol.

data_processing: The slides were analyzed using Feature Extraction Software 10.0 (Agilent technologies), following manufacturer’s protocol. A hierarchical clustering method was applied to group the genes and samples on the basis of the similarities in expression and the unsupervised analyses were visualized using the SOTA and TreeView software assuming euclidean distances between genes (http://bioinfo.cnio.es/cgi-bin/tools/clustering/sotarray). Genes with potentially significant changes in expression were identified using the POMELO program (http://www.genoma.wi.mit.edu/MPR/software). We tested the null hypothesis of equal means among groups using T-test, computing p-values using a permutation test. To select differentially expressed genes, we adjusted for multiple testing using the False Discovery Rate (FDR) method (Chung et al, 2004)

organism: Homo sapiens

source_name: Total RNA from breast tumor biopsies

label_protocol: 1mg from tRNA was labelled and array hybridized using the Low RNA Linear Amplification Kit (Agilent) following manufacturer’s protocol.

extract_protocol: 1mg of total RNA from each independent tumours were labelled with Cy5-dUTP and as control a pooled RNA obtained from equal concentration of each RNA tumor sample labelled with Cy3-dUTP was used. The amplification and labelling of mRNA were performed using   Low RNA Linear Amplification Kit (Agilent technologies),  following manufacturer’s protocol

tag: gender

value: Female

tag: cell type

value: infiltrative breast ductal carcinoma

source_name: Pool from the analysed samples


title: IDC26


title: Sun leaves_2xozone_091006_rep6


title: Sun leaves_2xozone_091006_rep5

source_name: Sun leaves_1xozone_091006_rep.3

source_name: Sun leaves_2xozone_091006_rep.3


title: Sun leaves_2xozone_091006_rep7

source_name: Sun leaves_1xozone_091006_rep.4

source_name: Sun leaves_2xozone_091006_rep.4


title: IDC30


title: IDC31


title: IDC27


title: IDC24


title: IDC18


title: IDC25


title: Sun leaves_2xozone_091006_rep1

source_name: Sun leaves_1xozone_091006_rep.1

source_name: Sun leaves_2xozone_091006_rep.1


title: Sun leaves_2xozone_091006_rep2


title: IDC22


title: IDC20


title: Shade leaves_2xozone_091006_rep9

source_name: Shade leaves_1xozone_091006_rep.5

value: five pooled shade leaves

source_name: Shade leaves_2xozone_091006_rep.5


title: IDC19


title: Shade leaves_2xozone_091006_rep10


title: Shade leaves_2xozone_091006_rep8

value: 1x ambient ozone, restricted to 150 ppm


title: IDC23


title: IDC21


title: IDC15


title: Shade leaves_2xozone_091006_rep7

source_name: Shade leaves_1xozone_091006_rep.4

value: 1x ambient ozone, restricted

source_name: Shade leaves_2xozone_091006_rep.4


title: Shade leaves_2xozone_091006_rep6


title: Shade leaves_2xozone_091006_rep2


title: Shade leaves_2xozone_120906_rep10

value: 12th of September 2006


title: Shade leaves_2xozone_091006_rep5

source_name: Shade leaves_1xozone_091006_rep.3

source_name: Shade leaves_2xozone_091006_rep.3


title: IDC13


title: Shade leaves_2xozone_091006_rep1

source_name: Shade leaves_1xozone_091006_rep.1

source_name: Shade leaves_2xozone_091006_rep.1


title: IDC14


title: IDC16


title: Shade leaves_2xozone_120906_rep9

source_name: Shade leaves_1xozone_120906_rep.5

source_name: Shade leaves_2xozone_120906_rep.5


title: Shade leaves_2xozone_091006_rep3

source_name: Shade leaves_1xozone_091006_rep.2

source_name: Shade leaves_2xozone_091006_rep.2


title: IDC12

source_name: Total RNA from breast tumor biopsies

source_name: Pool from the analysed samples


title: Shade leaves_2xozone_091006_rep4


title: IDC17


title: Shade leaves_2xozone_120906_rep8


title: IDC11


title: IDC10


title: Shade leaves_2xozone_120906_rep7

source_name: Shade leaves_1xozone_120906_rep.4

source_name: Shade leaves_2xozone_120906_rep.4


title: IDC6


title: IDC7


title: IDC4


title: Sun leaves_2xozone_020806_rep6

value: 2nd of August 2006


title: Sun leaves_2xozone_020806_rep2


title: Sun leaves_2xozone_020806_rep9

source_name: Sun leaves_1xozone_020806_rep.5

source_name: Sun leaves_2xozone_020806_rep.5


title: IDC8


title: Shade leaves_2xozone_120906_rep5

source_name: Shade leaves_1xozone_120906_rep.3

source_name: Shade leaves_2xozone_120906_rep.3


title: IDC5


title: Shade leaves_2xozone_120906_rep1

source_name: Shade leaves_1xozone_120906_rep.1

source_name: Shade leaves_2xozone_120906_rep.1

value: 2x ambient ozone


title: Sun leaves_2xozone_020806_rep8


title: IDC3


title: IDC1


title: Shade leaves_2xozone_020806_rep7

source_name: Shade leaves_1xozone_020806_rep.4

source_name: Shade leaves_2xozone_020806_rep.4


title: IDC9


title: Shade leaves_2xozone_020806_rep8


title: cells treated with the shRNA control, biological replicate 3

first: Jon

last: Gil-Ranedo

address: C/ Nicolás Cabrera nº1, CBMSO, lab 224

institute: CBMSO

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 16 hr at 45ºC on GeneChip® Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix GeneChip® Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G and the AGCC software (Affymetrix).

data_processing: The data were analyzed with GeneChip® Expression Console (Affymetrix) and normalized with the RMA algorithm.

label: biotin

source_name: cells treated with the shRNA control

label_protocol: Biotinylated cRNA were prepared from 250 ng total RNA with the “Ambion ® WT Expression kit” (Applied Biosystems), according to the manufacturer.

growth_protocol: Neurosphere culture was initiated by seeding cells at density of 1x105  viable cells/ml in proliferation medium consist of DMEM:F12 (1:1)  supplemented with glutamax (Gibco), 0,5% Albumax I (Gibco), N2 (1x,Invitrogen), 2 μg/ml heparin (Sigma), 20 ng/ml of both EGF and FGF-2  (Peprotech).

extract_protocol: Total RNA was extracted with the RNAqueous® Kit (Ambion Inc.), according to the manufacturer.

treatment_protocol: For infections, 6x104 viable cells/cm2 were seeded into optimem medium and incubated 6 h. Then, the lentiviral particles expressing the shRNAs  and 4 μg/ml polybrene were added and incubated overnight.

value: glioblastoma-derived cancer stem cells


title: Shade leaves_2xozone_020806_rep9

source_name: Shade leaves_1xozone_020806_rep.5

source_name: Shade leaves_2xozone_020806_rep.5


title: cells treated with the shRNA control, biological replicate 2


title: Shade leaves_2xozone_020806_rep10


title: cells treated with the shRNA22, biological replicate 2

source_name: cells treated with the shRNA22


title: Shade leaves_2xozone_020806_rep4


title: cells treated with the shRNA control, biological replicate 1


title: Shade leaves_2xozone_020806_rep6


title: Sun leaves_2xozone_020806_rep1

source_name: Sun leaves_1xozone_020806_rep.1

source_name: Sun leaves_2xozone_020806_rep.1


title: Shade leaves_2xozone_020806_rep2


title: IDC2

source_name: Total RNA from breast tumor biopsies

source_name: Pool from the analysed samples


title: cells treated with the shRNA22, biological replicate 1


title: Shade leaves_2xozone_020806_rep3

source_name: Shade leaves_1xozone_020806_rep.2

source_name: Shade leaves_2xozone_020806_rep.2


title: Shade leaves_2xozone_020806_rep1

source_name: Shade leaves_1xozone_020806_rep.1

source_name: Shade leaves_2xozone_020806_rep.1


title: Sun leaves_2xozone_190905_rep10

value: 19th of September 2005


title: Sun leaves_2xozone_020806_rep10


title: cells treated with the shRNA22, biological replicate 3


title: Shade leaves_2xozone_020806_rep5

source_name: Shade leaves_1xozone_020806_rep.3

source_name: Shade leaves_2xozone_020806_rep.3


title: Sun leaves_2xozone_190905_rep5

source_name: Sun leaves_1xozone_190905_rep.3

source_name: Sun leaves_2xozone_190905_rep.3


title: Sun leaves_2xozone_190905_rep4


title: Sun leaves_2xozone_190905_rep9

source_name: Sun leaves_1xozone_190905_rep.5

source_name: Sun leaves_2xozone_190905_rep.5


title: Sun leaves_2xozone_190905_rep6


title: Sun leaves_2xozone_190905_rep8


title: Sun leaves_2xozone_190905_rep3

source_name: Sun leaves_1xozone_190905_rep.2

source_name: Sun leaves_2xozone_190905_rep.2


title: C2C12 infected with Smad3 retrovirus; 24hr TGF-beta; replicate 1

city: Madison

first: Michael

last: Hoffmann

state: WI

address: 1400 University Ave

country: USA

institute: University of Wisconsin-Madison

description:
WTS3__1_01272011.mdp_LEVEL
C2C12 infected with Smad3 retrovirus; 24hr TGF-beta.

hyb_protocol: The Affymetrix GeneChip® Analysis System uses application-specific high-density GeneChip® oligonucleotide probe arrays to efficiently acquire and analyze genetic information for gene expression, genotyping and nucleotide variant detection. This multi-component system includes two GC450 Fluidics Stations, a Hybridization Oven 640, a GC3000 7G scanner, computer workstation, and GeneChip® Command Console® Software v2.0 (AGCC). Affymetrix Command Console® software automates control of the GC450 Fluidics Stations and the GC3000 7G scanner.

scan_protocol: Affymetrix GeneChip GC3000 7G scanner.

data_processing: To identify genes with altered expression between duplicated empty vector controls and wild-type Smad3, we first pre-processed the four arrays using robust multiarray averaging as implemented in the R software package ‘xps’, version 1.10.2 (http://www.bioconductor.org/packages/release/bioc/html/xps.html). This preprocessing corrects for background noise and array effects, and aggregates probe data to 28,836 genes. Duplicates were averaged on the base-2 logarithm scale, and then we took differences between the averages to obtain logarithm-scale fold changes. Genes were selected which showed at least a two-fold change (raw scale) between wild-type Smad3- and empty vector-expressing cells. Due to the limited sample size, we did not apply any statistical tests to estimate false-discovery rate.

organism: Mus musculus

source_name: C2C12 myoblasts, Smad3 overexpression

label_protocol: The Ambion® WT Expression Kit  was used to make amplified sense-strand cDNA ready for fragmentation and labeling using the Affymetrix® GeneChip® WT Terminal Labeling Kit to add the biotinylated, GeneChip® DNA Labeling Reagent.

extract_protocol: Qiagen RNeasy plus kit following the manufacturer's instructions.

treatment_protocol: 24 hours of 100pM TGF-beta.

tag: cell line

value: myoblasts

tag: retroviral infection

value: wild-type Smad3

tag: treatment

value: TGF-β

tag: treatment duration

value: 24 hrs


title: C2C12 infected with control EV; 24hr TGF-beta; replicate 2

description:
EV__2_01272011.mdp_LEVEL
C2C12 infected with control EV retrovirus; 24hr TGF-beta.

source_name: C2C12 myoblasts, control

value: empty vector


title: Shade leaves_2xozone_190905_rep10

value: about 60 years

value: 2x ambient ozone, restricted to 150 ppm


title: Sun leaves_2xozone_190905_rep1

source_name: Sun leaves_1xozone_190905_rep.1

value: five pooled sun leaves

value: 1x ambient ozone

source_name: Sun leaves_2xozone_190905_rep.1


title: Shoots of 6h Root-Flooded Arabidopsis (ein2) Replicate 3

city: Taipei

first: Fu-Chiun

last: Hsu

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

department: Agricultural Biotechnology Research Center

country: Taiwan

institute: Academia Sinica

description: Biological replicate 3 of 4.

hyb_protocol: Hybridyzation experiments were performed at the DNA Microarray Core facility, Institute of Plant and Microbial Biology, Academia Sinica, as described on http://ipmb.sinica.edu.tw/microarray/protocol.htm.

scan_protocol: Array signals were detected and analyzed with Axon GenePix 4000B and GenePix 6.0 (Axon Instruments, Inc., Union City, CA, USA), respectively.

data_processing: The exported GenePix Result (GPR) files that were imported into GeneSpring 7.3 (Silicon Genetics, Redwood, CA, USA) via LOWESS Normalization.

organism: Arabidopsis thaliana

label_protocol: 10 µg of total RNA were primed with 1.25 µl of 100 µM Oligo dTV DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 500 µM each dATP, dCTP, dGTP, with 100 µM dTTP, 400 µM aminoallyl-dUTP. The aminoallyl-labeled cDNA was hydrolyzed to obtain single stranded labeled DNA with addition of 10 µl of 0.5 M EDTA and 10 µl of 1 N NaOH at 65℃ for 15 min followed by neutralization with 25 µl of 1 M HEPES, pH 7.4.  The labed DNA was then purified with Microcon-30 concentrator by washing with water for three times.  NHS-ester Cy dyes were used to couple with the aminoally-cDNA at room temperature for 1 h.  Unreacted NHS-ester Cy dyes were quenched with addition of 4.5 µl of 4 M hydroxylamine and removed by PCR clean up kit (QIAGEN).  For details, see http://ipmb.sinica.edu.tw/microarray/protocol.htm.

growth_protocol: Experiments were carried out on Arabidopsis thaliana ecotype Columbia-0.  The ethylene-signaling mutant, ein2-5 was obtained from the Arabidopsis Biological Resource Center, Ohio State University, USA.  Seeds were surface-sterilized for 20 min in 0.5% of sodium hypochloride and washed at least five times with sterilized water.  Seeds were sown on plates with 0.55% of phytagel (Sigma-Aldrich, St. Louis, MO, USA) in half-strength Murashige and Skoog (MS) medium (Duchefa Biochemie BV, Haarlem, Netherlands) containing 0.5% sucrose, and kept at 4 oC in the dark for 3 days.  Plates were then transferred to a growth chamber, placed vertically, and grown at 22 C under a long photoperiod with 16 h of light (~81 μmol s-1 m-2) and 8 h of darkness for 5 days.  The 5-day-old seedlings were transplanted onto fresh plates, and the plates were placed vertically to prevent roots from growing into medium.  The transplanted seedlings were grown in the growth chamber until they were 14 days old.

extract_protocol: Total RNA was isolated from shoots or roots using TRIZOL reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacture’s description using a 1:2 ratio of sample:TRIZOL reagent.  Total RNA was subjected to DNase treatment using the TURBO RNA free kit (Ambion) according to the manufacture’s instructions. Genomic DNA contamination and RNA integrity were tested on an Agilent 2100 Bioanalyzer.

treatment_protocol: For flooding treatment, 14-day-old plants were placed between two foamed plastic strips as a floating platform. To minimize the effects of mechanical stress, the platforms with plants were put on filter papers that were wetted with half-strength MS for 1 h as pre-treatment.  The platforms were then transferred to liquid half-strength MS that was bubbled with 3% oxygen balanced with nitrogen for the indicated times.  The liquid MS medium was pretreated with 3% oxygen for one hour before use.  For submergence treatment, the plates with 14-day-old plants were submerged into half-strength MS that was bubbled with 3% oxygen balanced with nitrogen for the time indicated.

tag: background ecotype

value: Columbia

tag: genotype/variation

value: ein2-5 mutant

value: Shoots

tag: time under flooding (h)

source_name: Shoots of Arabidopsis (ein2) without flooding treatment

tag: tag


title: C2C12 infected with Smad3 retrovirus; 24hr TGF-beta; replicate 2

description:
WTS3__2_01272011.mdp_LEVEL
C2C12 infected with Smad3 retrovirus; 24hr TGF-beta.


title: C2C12 infected with control EV; 24hr TGF-beta; replicate 1

description:
EV__1_01272011.mdp_LEVEL
C2C12 infected with control EV retrovirus; 24hr TGF-beta.


title: Shoots of 6h Root-Flooded Arabidopsis (ein2) Replicate 4

description: Biological replicate 4 of 4. Dye-swap.


title: Shade leaves_2xozone_190905_rep7

source_name: Shade leaves_1xozone_190905_rep.4

value: five pooled shade leaves

source_name: Shade leaves_2xozone_190905_rep.4


title: Shoots of 6h Root-Flooded Arabidopsis (ein2) Replicate 2

description: Biological replicate 2 of 4. Dye-swap.


title: Shade leaves_2xozone_190905_rep8


title: Sun leaves_2xozone_190905_rep7

source_name: Sun leaves_1xozone_190905_rep.4

source_name: Sun leaves_2xozone_190905_rep.4


title: Shoots of 6h Root-Flooded Arabidopsis (ein2) Replicate 1

description: Biological replicate 1 of 4.


title: Shoots of 3h Root-Flooded Arabidopsis (ein2) Replicate 3

description: Biological replicate 3 of 4.


title: Shoots of 3h Root-Flooded Arabidopsis (ein2) Replicate 4

description: Biological replicate 4 of 4. Dye-swap.


title: Shoots of 3h Root-Flooded Arabidopsis (ein2) Replicate 2

description: Biological replicate 2 of 4. Dye-swap.


title: Shoots of 3h Root-Flooded Arabidopsis (ein2) Replicate 1

description: Biological replicate 1 of 4.


title: Shade leaves_2xozone_190905_rep5

source_name: Shade leaves_1xozone_190905_rep.3

source_name: Shade leaves_2xozone_190905_rep.3


title: Shoots of 0.5h Root-Flooded Arabidopsis (ein2) Replicate 4

description: Biological replicate 4 of 4. Dye-swap.


title: Shade leaves_2xozone_190905_rep6


title: Shade leaves_2xozone_190905_rep3

source_name: Shade leaves_1xozone_190905_rep.2

source_name: Shade leaves_2xozone_190905_rep.2


title: Shade leaves_2xozone_190905_rep9

source_name: Shade leaves_1xozone_190905_rep.5

source_name: Shade leaves_2xozone_190905_rep.5


title: Shade leaves_2xozone_190905_rep4


title: Roots of 6h Root-Flooded Arabidopsis (ein2) Replicate 4

description: Biological replicate 4 of 4. Dye-swap.

value: Roots

source_name: Roots of Arabidopsis (ein2) without flooding treatment


title: Shoots of 0.5h Root-Flooded Arabidopsis (ein2) Replicate 3

description: Biological replicate 3 of 4.


title: Sun leaves_2xozone_120505_rep7

source_name: Sun leaves_1xozone_120505_rep.4

value: 12th of May 2005

source_name: Sun leaves_2xozone_120505_rep.4


title: Sun leaves_2xozone_190905_rep2


title: Shoots of 0.5h Root-Flooded Arabidopsis (ein2) Replicate 2

description: Biological replicate 2 of 4. Dye-swap.


title: Sun leaves_2xozone_120505_rep8


title: Roots of 6h Root-Flooded Arabidopsis (ein2) Replicate 1

description: Biological replicate 1 of 4.


title: Shade leaves_2xozone_190905_rep2


title: Sun leaves_2xozone_120505_rep9


title: Roots of 3h Root-Flooded Arabidopsis (ein2) Replicate 4

description: Biological replicate 4 of 4. Dye-swap.


title: Roots of 6h Root-Flooded Arabidopsis (ein2) Replicate 2

description: Biological replicate 2 of 4. Dye-swap.


title: Sun leaves_2xozone_120505_rep6

value: 1x ambient ozone, restricted to 150 ppm


title: Sun leaves_2xozone_120505_rep4


title: Sun leaves_2xozone_120505_rep5

source_name: Sun leaves_1xozone_120505_rep.3

source_name: Sun leaves_2xozone_120505_rep.3


title: Shade leaves_2xozone_190905_rep1

source_name: Shade leaves_1xozone_190905_rep.1

value: 19th of September 2005

source_name: Shade leaves_2xozone_190905_rep.1


title: Roots of 6h Root-Flooded Arabidopsis (ein2) Replicate 3

description: Biological replicate 3 of 4.


title: Roots of 3h Root-Flooded Arabidopsis (ein2) Replicate 3

description: Biological replicate 3 of 4.


title: Roots of 3h Root-Flooded Arabidopsis (ein2) Replicate 1

description: Biological replicate 1 of 4.


title: Roots of 0.5h Root-Flooded Arabidopsis (ein2) Replicate 4

description: Biological replicate 4 of 4. Dye-swap.


title: Roots of 0.5h Root-Flooded Arabidopsis (ein2) Replicate 3

description: Biological replicate 3 of 4.


title: Sun leaves_2xozone_120505_rep2


title: Roots of 0.5h Root-Flooded Arabidopsis (ein2) Replicate 1

description: Biological replicate 1 of 4.


title: Roots of 0.5h Root-Flooded Arabidopsis (ein2) Replicate 2

description: Biological replicate 2 of 4. Dye-swap.


title: Shoots of 12h Root-Flooded Arabidopsis (Columbia) Replicate 4

description: Biological replicate 4 of 4. Dye-swap.

value: wild type

source_name: Shoots of Arabidopsis (Columbia) without flooding treatment


title: Shade leaves_2xozone_120505_rep10


title: Sun leaves_2xozone_120505_rep3

source_name: Sun leaves_1xozone_120505_rep.2

source_name: Sun leaves_2xozone_120505_rep.2


title: Shoots of 0.5h Root-Flooded Arabidopsis (ein2) Replicate 1

description: Biological replicate 1 of 4.

source_name: Shoots of Arabidopsis (ein2) without flooding treatment


title: Shoots of 12h Root-Flooded Arabidopsis (Columbia) Replicate 3

description: Biological replicate 3 of 4.


title: Shade leaves_2xozone_120505_rep9

source_name: Shade leaves_1xozone_120205_rep.5

source_name: Shade leaves_2xozone_120505_rep.5


title: Shade leaves_2xozone_120505_rep8


title: Shade leaves_2xozone_120505_rep7

source_name: Shade leaves_1xozone_120205_rep.4

source_name: Shade leaves_2xozone_120505_rep.4


title: Shoots of 12h Root-Flooded Arabidopsis (Columbia) Replicate 2

description: Biological replicate 2 of 4. Dye-swap.


title: Roots of 3h Root-Flooded Arabidopsis (ein2) Replicate 2

description: Biological replicate 2 of 4. Dye-swap.


title: Shade leaves_2xozone_120505_rep6


title: Sun leaves_2xozone_120505_rep1

source_name: Sun leaves_1xozone_120505_rep.1

source_name: Sun leaves_2xozone_120505_rep.1


title: Shade leaves_2xozone_120505_rep5

source_name: Shade leaves_1xozone_120205_rep.3

source_name: Shade leaves_2xozone_120505_rep.3


title: Shoots of 6h Root-Flooded Arabidopsis (Columbia) Replicate 4

description: Biological replicate 4 of 4. Dye-swap.


title: Shoots of 12h Root-Flooded Arabidopsis (Columbia) Replicate 1

description: Biological replicate 1 of 4.


title: Shoots of 6h Root-Flooded Arabidopsis (Columbia) Replicate 2

description: Biological replicate 2 of 4. Dye-swap.


title: Shade leaves_2xozone_120505_rep4


title: hN2_10 μM_72 h_4

city: Silver Spring

first: Xiugong

last: Gao

state: MD

address: 503 Robert Grant Ave

institute: Walter Reed Army Institute of Research

description:
hN2_10 μM_72 h_4
gene expression data of hN2 human neural cells exposed to 10 μM VX 72 h after exposure

hyb_protocol: Hybridization was carried out using the Affymetrix GeneChip Hybridization, Wash, and Stain Kit following the manufacturer's protocols.

scan_protocol: The chips were scanned using an Affymetrix GeneChip Instrument System and the image (.DAT) files were processed using the Affymetrix GeneChip Operating Software (GCOS) to generate cell intensity (.CEL) files.

data_processing: The data were averaged and normalized in Partek Genomics Suite 6.5 (Partek, St. Louis, MO) using the robust multiarray analysis (RMA) algorithm.

label_protocol: ~0.1 μg of total RNA were labeled using the Affymetrix (Santa Clara, CA) GeneChip 3' IVT Express Kit following the manufacturer's protocol.

growth_protocol: Human hN2 neural cells were seeded in 12-well plates in media formulated by the manufacturer (Neuromics, Edina, MN) and cultured at 37 °C under humidified 5% CO2 for 48 h (without changing media) before VX exposure.

extract_protocol: Total RNA was isolated using the RNeasy Plus Mini Kit from Qiagen (Valencia, CA) following the manufacturer’s protocol, including an on-column DNase digestion.

treatment_protocol: VX was added to cell culture at the specified concentrations and maintained for 1 h. Then VX was removed and the culture was washed 3X with fresh medium. The culture was then maintained at 37 °C with 5% CO2 until the indicated time points.

value: hN2 neural cells derived from WA09 human embryonic stem cells


title: Shoots of 6h Root-Flooded Arabidopsis (Columbia) Replicate 1

description: Biological replicate 1 of 4.


title: Shoots of 6h Root-Flooded Arabidopsis (Columbia) Replicate 3

description: Biological replicate 3 of 4.


title: hN2_10 μM_24 h_1

description:
hN2_10 μM_24 h_1
gene expression data of hN2 human neural cells exposed to 10 μM VX 24 h after exposure


title: hN2_10 μM_24 h_3

description:
hN2_10 μM_24 h_3
gene expression data of hN2 human neural cells exposed to 10 μM VX 24 h after exposure


title: hN2_10 μM_6 h_4

description:
hN2_10 μM_6 h_4
gene expression data of hN2 human neural cells exposed to 10 μM VX 6 h after exposure


title: Shoots of 3h Root-Flooded Arabidopsis (Columbia) Replicate 4

description: Biological replicate 4 of 4. Dye-swap.


title: hN2_10 μM_72 h_1

description:
hN2_10 μM_72 h_1
gene expression data of hN2 human neural cells exposed to 10 μM VX 72 h after exposure


title: hN2_10 μM_24 h_4

description:
hN2_10 μM_24 h_4
gene expression data of hN2 human neural cells exposed to 10 μM VX 24 h after exposure


title: hN2_10 μM_24 h_2

description:
hN2_10 μM_24 h_2
gene expression data of hN2 human neural cells exposed to 10 μM VX 24 h after exposure


title: Shade leaves_2xozone_120505_rep1

source_name: Shade leaves_1xozone_120205_rep.1

source_name: Shade leaves_2xozone_120505_rep.1


title: hN2_10 μM_72 h_3

description:
hN2_10 μM_72 h_3
gene expression data of hN2 human neural cells exposed to 10 μM VX 72 h after exposure


title: hN2_10 μM_6 h_3

description:
hN2_10 μM_6 h_3
gene expression data of hN2 human neural cells exposed to 10 μM VX 6 h after exposure


title: Shade leaves_2xozone_120505_rep2


title: hN2_10 μM_6 h_2

description:
hN2_10 μM_6 h_2
gene expression data of hN2 human neural cells exposed to 10 μM VX 6 h after exposure


title: Shade leaves_2xozone_210605_rep10

value: 21st of June 2005


title: hN2_10 μM_6 h_1

description:
hN2_10 μM_6 h_1
gene expression data of hN2 human neural cells exposed to 10 μM VX 6 h after exposure


title: hN2_0.1 μM_72 h_2

description:
hN2_0.1 μM_72 h_2
gene expression data of hN2 human neural cells exposed to 0.1 μM VX 72 h after exposure


title: Shoots of 3h Root-Flooded Arabidopsis (Columbia) Replicate 3

description: Biological replicate 3 of 4.


title: Shade leaves_2xozone_120505_rep3

description: A coefficient of variation about all microarrays of one time point was calculated using Acuity 4.0 microarray informatics software [Axon Instruments]. We used only those spots that had a coefficient of variation < 50 and were present on at least half of identical slides. We express the median values as log2 ratios.

source_name: Shade leaves_1xozone_120205_rep.2

source_name: Shade leaves_2xozone_120505_rep.2


title: hN2_10 μM_72 h_2

description:
hN2_10 μM_72 h_2
gene expression data of hN2 human neural cells exposed to 10 μM VX 72 h after exposure


title: Shoots of 3h Root-Flooded Arabidopsis (Columbia) Replicate 1

description: Biological replicate 1 of 4.


title: hN2_0.1 μM_72 h_4

description:
hN2_0.1 μM_72 h_4
gene expression data of hN2 human neural cells exposed to 0.1 μM VX 72 h after exposure


title: Shade leaves_2xozone_210605_rep8


title: Shade leaves_2xozone_210605_rep9

source_name: Shade leaves_1xozone_210605_rep.5

source_name: Shade leaves_2xozone_210605_rep.5


title: Shoots of 1h Root-Flooded Arabidopsis (Columbia) Replicate 4

description: Biological replicate 4 of 4. Dye-swap.

source_name: Shoots of Arabidopsis (Columbia) without flooding treatment


title: Shade leaves_2xozone_210605_rep7

source_name: Shade leaves_1xozone_210605_rep.4

source_name: Shade leaves_2xozone_210605_rep.4


title: hN2_0.1 μM_72 h_3

description:
hN2_0.1 μM_72 h_3
gene expression data of hN2 human neural cells exposed to 0.1 μM VX 72 h after exposure


title: Shoots of 3h Root-Flooded Arabidopsis (Columbia) Replicate 2

description: Biological replicate 2 of 4. Dye-swap.


title: hN2_0.1 μM_24 h_3

description:
hN2_0.1 μM_24 h_3
gene expression data of hN2 human neural cells exposed to 0.1 μM VX 24 h after exposure


title: Shade leaves_2xozone_210605_rep6


title: hN2_0.1 μM_24 h_2

description:
hN2_0.1 μM_24 h_2
gene expression data of hN2 human neural cells exposed to 0.1 μM VX 24 h after exposure


title: hN2_0.1 μM_6 h_4

description:
hN2_0.1 μM_6 h_4
gene expression data of hN2 human neural cells exposed to 0.1 μM VX 6 h after exposure


title: hN2_0.1 μM_72 h_1

description:
hN2_0.1 μM_72 h_1
gene expression data of hN2 human neural cells exposed to 0.1 μM VX 72 h after exposure


title: Shade leaves_2xozone_210605_rep5

source_name: Shade leaves_1xozone_210605_rep.3

source_name: Shade leaves_2xozone_210605_rep.3


title: Shoots of 1h Root-Flooded Arabidopsis (Columbia) Replicate 2

description: Biological replicate 2 of 4. Dye-swap.


title: hN2_0.1 μM_6 h_3

description:
hN2_0.1 μM_6 h_3
gene expression data of hN2 human neural cells exposed to 0.1 μM VX 6 h after exposure


title: hN2_0.1 μM_24 h_4

description:
hN2_0.1 μM_24 h_4
gene expression data of hN2 human neural cells exposed to 0.1 μM VX 24 h after exposure


title: Shade leaves_2xozone_210605_rep4


title: hN2_control_72 h_rep4

description:
hN2_0 μM_72 h_4
gene expression data of hN2 human neural cells not exposed to VX at 72 h


title: Shoots of 1h Root-Flooded Arabidopsis (Columbia) Replicate 3

description: Biological replicate 3 of 4.


title: Shoots of 1h Root-Flooded Arabidopsis (Columbia) Replicate 1

description: Biological replicate 1 of 4.


title: hN2_0.1 μM_6 h_1

description:
hN2_0.1 μM_6 h_1
gene expression data of hN2 human neural cells exposed to 0.1 μM VX 6 h after exposure


title: hN2_control_72 h_rep2

description:
hN2_0 μM_72 h_2
gene expression data of hN2 human neural cells not exposed to VX at 72 h


title: hN2_0.1 μM_24 h_1

description:
hN2_0.1 μM_24 h_1
gene expression data of hN2 human neural cells exposed to 0.1 μM VX 24 h after exposure


title: Shade leaves_2xozone_210605_rep2


title: hN2_control_24 h_rep3

description:
hN2_0 μM_24 h_3
gene expression data of hN2 human neural cells not exposed to VX at 24 h


title: hN2_0.1 μM_6 h_2

description:
hN2_0.1 μM_6 h_2
gene expression data of hN2 human neural cells exposed to 0.1 μM VX 6 h after exposure


title: hN2_control_72 h_rep3

description:
hN2_0 μM_72 h_3
gene expression data of hN2 human neural cells not exposed to VX at 72 h


title: Shoots of 0.5h Root-Flooded Arabidopsis (Columbia) Replicate 4

description: Biological replicate 4 of 4. Dye-swap.


title: Shade leaves_2xozone_210605_rep1

description: A coefficient of variation about all microarrays of one time point was calculated using Acuity 4.0 microarray informatics software [Axon Instruments]. We used only those spots that had a coefficient of variation < 50 and were present on at least half of identical slides. We express the median values as log2 ratios.

source_name: Shade leaves_1xozone_210605_rep.1

source_name: Shade leaves_2xozone_210605_rep.1


title: Shoots of 0.5h Root-Flooded Arabidopsis (Columbia) Replicate 3

description: Biological replicate 3 of 4.


title: hN2_control_24 h_rep4

description:
hN2_0 μM_24 h_4
gene expression data of hN2 human neural cells not exposed to VX at 24 h


title: hN2_control_72 h_rep1

description:
hN2_0 μM_72 h_1
gene expression data of hN2 human neural cells not exposed to VX at 72 h


title: hN2_control_24 h_rep1

description:
hN2_0 μM_24 h_1
gene expression data of hN2 human neural cells not exposed to VX at 24 h


title: hN2_control_6 h_rep3

description:
hN2_0 μM_6 h_3
gene expression data of hN2 human neural cells not exposed to VX at 6 h


title: Sun leaves_2xozone_210605_rep10

value: 20th of June 2005


title: hN2_control_6 h_rep1

description:
hN2_0 μM_6 h_1
gene expression data of hN2 human neural cells not exposed to VX at 6 h


title: hN2_control_24 h_rep2

description:
hN2_0 μM_24 h_2
gene expression data of hN2 human neural cells not exposed to VX at 24 h


title: Sun leaves_2xozone_210605_rep9

source_name: Sun leaves_1xozone_210605_rep.5

source_name: Sun leaves_2xozone_210605_rep.5


title: Shoots of 0.5h Root-Flooded Arabidopsis (Columbia) Replicate 1

description: Biological replicate 1 of 4.


title: Shade leaves_2xozone_210605_rep3

source_name: Shade leaves_1xozone_210605_rep.2

source_name: Shade leaves_2xozone_210605_rep.2


title: Roots of 12h Root-Flooded Arabidopsis (Columbia) Replicate 4

description: Biological replicate 4 of 4. Dye-swap.

source_name: Roots of Arabidopsis (Columbia) without flooding treatment


title: hN2_control_0 h_rep3

description:
hN2_0 μM_0 h_3
gene expression data of hN2 human neural cells not exposed to VX at the beginning of experiment


title: Roots of 12h Root-Flooded Arabidopsis (Columbia) Replicate 3

description: Biological replicate 3 of 4.


title: Shoots of 0.5h Root-Flooded Arabidopsis (Columbia) Replicate 2

description: Biological replicate 2 of 4. Dye-swap.


title: Roots of 6h Root-Flooded Arabidopsis (Columbia) Replicate 4

description: Biological replicate 4 of 4. Dye-swap.


title: Roots of 12h Root-Flooded Arabidopsis (Columbia) Replicate 1

description: Biological replicate 1 of 4.


title: Sun leaves_2xozone_210605_rep8


title: Roots of 12h Root-Flooded Arabidopsis (Columbia) Replicate 2

description: Biological replicate 2 of 4. Dye-swap.


title: hN2_control_6 h_rep2

description:
hN2_0 μM_6 h_2
gene expression data of hN2 human neural cells not exposed to VX at 6 h


title: hN2_control_0 h_rep2

description:
hN2_0 μM_0 h_2
gene expression data of hN2 human neural cells not exposed to VX at the beginning of experiment


title: Roots of 6h Root-Flooded Arabidopsis (Columbia) Replicate 3

description: Biological replicate 3 of 4.


title: Slug at D4, rep 3

city: Durham

first: Dhiral

last: Phadke

state: NC

address: Research Triangle Park

institute: SRA International Inc

description: RNA isolated from MCF-7 cells treated with Slug Adenovirus for 4 days

hyb_protocol: 12.5 μg of amplified biotin-cRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.

scan_protocol: Arrays were stained with streptavidin/phycoerythrin, washed and then scanned in an Affymetrix Scanner 3000 and data obtained using the GeneChip® Operating Software (GCOS; Version 1.4.0.036).

data_processing: The cel files were normalized using RMA

source_name: Slug at D4, rep 3

label_protocol: One μg of total RNA was amplified as directed in the Affymetrix One-Cycle cDNA Synthesis protocol.

growth_protocol: MCF-7 cells were grown in DMEM/F-12 with 10% FBS in a humid incubator under 5% carbondioxide

extract_protocol: Total RNA was extracted using Trizol, precipitated with isopropanol and purified using Qiagen columns. The samples were resuspended in DEPC-treated water.

treatment_protocol: Cells were untreated, or treated with control, Snail or Slug adenovirus for 1,2 or 4 days before RNA isolation

value: Slug

tag: duration

tag: replicate


title: Slug at D2, rep 3

description: RNA isolated from MCF-7 cells treated with Slug Adenovirus for 2 days

source_name: Slug at D2, rep 3


title: hN2_control_0 h_rep4

description:
hN2_0 μM_0 h_4
gene expression data of hN2 human neural cells not exposed to VX at the beginning of experiment


title: Sun leaves_2xozone_210605_rep7

source_name: Sun leaves_1xozone_210605_rep.4

tag: age

value: about 60 years

source_name: Sun leaves_2xozone_210605_rep.4


title: Slug at D4, rep 2

source_name: Slug at D4, rep 2


title: Sun leaves_2xozone_210605_rep3

source_name: Sun leaves_1xozone_210605_rep.2

tag: tissue

source_name: Sun leaves_2xozone_210605_rep.2

value: 2x ambient ozone, restricted to 150 ppm


title: Sun leaves_2xozone_210605_rep6

value: five pooled sun leaves

tag: tree


title: Slug at D2, rep 2

source_name: Slug at D2, rep 2


title: Slug at D1, rep 2

description: RNA isolated from MCF-7 cells treated with Slug Adenovirus for 1 day

source_name: Slug at D1, rep 2


title: Slug at D4, rep 1

source_name: Slug at D4, rep 1


title: hN2_control_0 h_rep1

description:
hN2_0 μM_0 h_1
gene expression data of hN2 human neural cells not exposed to VX at the beginning of experiment


title: Slug at D2, rep 1

source_name: Slug at D2, rep 1


title: Snail at D2, rep 2

description: RNA isolated from MCF-7 cells treated with Snail Adenovirus for 2 days

source_name: Snail at D2, rep 2

value: Snail


title: Sun leaves_2xozone_050805_rep10

tag: exposition

value: 5th of August 2005

value: 1x ambient ozone


title: Roots of 6h Root-Flooded Arabidopsis (Columbia) Replicate 1

description: Biological replicate 1 of 4.

value: Columbia


title: Snail at D4, rep 1

description: RNA isolated from MCF-7 cells treated with Snail Adenovirus for 4 days

source_name: Snail at D4, rep 1


title: Roots of 3h Root-Flooded Arabidopsis (Columbia) Replicate 3

description: Biological replicate 3 of 4.


title: Slug at D1, rep 3

source_name: Slug at D1, rep 3


title: Snail at D2, rep 1

source_name: Snail at D2, rep 1


title: Sun leaves_2xozone_210605_rep5

description: A coefficient of variation about all microarrays of one time point was calculated using Acuity 4.0 microarray informatics software [Axon Instruments]. We used only those spots that had a coefficient of variation < 50 and were present on at least half of identical slides. We express the median values as log2 ratios.

source_name: Sun leaves_1xozone_210605_rep.3

tag: sampling

source_name: Sun leaves_2xozone_210605_rep.3


title: Roots of 6h Root-Flooded Arabidopsis (Columbia) Replicate 2

description: Biological replicate 2 of 4. Dye-swap.

source_name: Roots of Arabidopsis (Columbia) without flooding treatment


title: Sun leaves_2xozone_210605_rep4


title: Roots of 3h Root-Flooded Arabidopsis (Columbia) Replicate 1

description: Biological replicate 1 of 4.


title: Snail at D4, rep 3

source_name: Snail at D4, rep 3


title: Snail at D2, rep 3

source_name: Snail at D2, rep 3


title: Snail at D4, rep 2

source_name: Snail at D4, rep 2


title: Slug at D1, rep 1

source_name: Slug at D1, rep 1


title: Roots of 3h Root-Flooded Arabidopsis (Columbia) Replicate 4

description: Biological replicate 4 of 4. Dye-swap.


title: Roots of 3h Root-Flooded Arabidopsis (Columbia) Replicate 2

description: Biological replicate 2 of 4. Dye-swap.


title: Round spermatis_control_purified_rep3

city: New York

first: Binyamin

middle: David

last: Berkovits

state: NY

address: 1130 St. Nicholas Ave. Room 611

department: Genetics and Development

institute: Columbia University

description: Gene expression data from control round spermatids

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

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

data_processing: Signal intensities were ascertained and statistical analysis was performed within the R\Bioconductor statistical framework . We used the limma package to pre-process the raw data and perform the quality controls. Expression intensities were background corrected, normalized, and summarized using the Gene Chip Robust Multiarray Algorithm (GC-RMA)

label: Biotin

source_name: Purified control round spermatids

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. This RNA was then purified and concentrated using the RNeasy MinElute Cleanup kit (Qiagen).

treatment_protocol: Pure populations of round spermatids were separated on a 4%-2% BSA in DPBS gradient.

value: Purified round spermatids

tag: strain

value: 129 Sv/Ev

value: Adults, 2-4 months old


title: Sun leaves_2xozone_210605_rep1

source_name: Sun leaves_1xozone_210605_rep.1

source_name: Sun leaves_2xozone_210605_rep.1


title: Sun leaves_2xozone_210605_rep2


title: Round spermatis_control_purified_rep4


title: Snail at D1, rep 1

description: RNA isolated from MCF-7 cells treated with Snail Adenovirus for 1 day

source_name: Snail at D1, rep 1


title: Round spermatis_control_purified_rep2


title: Sun leaves_2xozone_050805_rep9

source_name: Sun leaves_1xozone_050805_rep.5

source_name: Sun leaves_2xozone_050805_rep.5


title: Round spermatis_control_purified_rep1


title: Roots of 1h Root-Flooded Arabidopsis (Columbia) Replicate 4

description: Biological replicate 4 of 4. Dye-swap.

value: Roots


title: Roots of 1h Root-Flooded Arabidopsis (Columbia) Replicate 2

description: Biological replicate 2 of 4. Dye-swap.


title: Sun leaves_2xozone_050805_rep7

source_name: Sun leaves_1xozone_050805_rep.4

source_name: Sun leaves_2xozone_050805_rep.4


title: Snail at D1, rep 2

source_name: Snail at D1, rep 2


title: Round spermatids_BrdtΔBD1 mutant _purified_ rep4

description: Gene expression data from mutant round spermatids

source_name: Purified BrdtΔBD1 mutant round spermatids

value: Purified round spermatids from BrdtΔBD1 mutant


title: Sun leaves_2xozone_050805_rep8


title: Roots of 0.5h Root-Flooded Arabidopsis (Columbia) Replicate 4

description: Biological replicate 4 of 4. Dye-swap.

value: wild type


title: Sun leaves_2xozone_050805_rep4


title: Round spermatids_BrdtΔBD1 mutant _purified_ rep3


title: Sun leaves_2xozone_050805_rep5

source_name: Sun leaves_1xozone_050805_rep.3

source_name: Sun leaves_2xozone_050805_rep.3


title: Round spermatids_BrdtΔBD1 mutant _purified_ rep1


title: Sun leaves_2xozone_050805_rep6


title: Roots of 0.5h Root-Flooded Arabidopsis (Columbia) Replicate 3

description: Biological replicate 3 of 4.

source_name: Roots of Arabidopsis (Columbia) without flooding treatment


title: Roots of 1h Root-Flooded Arabidopsis (Columbia) Replicate 3

description: Biological replicate 3 of 4.


title: Round spermatids_BrdtΔBD1 mutant _purified_ rep2


title: Control at D4, rep 1

description: RNA isolated from MCF-7 cells treated with Control Adenovirus for 4 days

source_name: Control at D4, rep 1

value: Control


title: Control at D4, rep 2

source_name: Control at D4, rep 2


title: Control at D4, rep 3

source_name: Control at D4, rep 3


title: Roots of 1h Root-Flooded Arabidopsis (Columbia) Replicate 1

description: Biological replicate 1 of 4.


title: Snail at D1, rep 3

source_name: Snail at D1, rep 3


title: Sun leaves_2xozone_050805_rep2


title: Sun leaves_2xozone_050805_rep3

source_name: Sun leaves_1xozone_050805_rep.2

source_name: Sun leaves_2xozone_050805_rep.2


title: Control at D2, rep 3

description: RNA isolated from MCF-7 cells treated with Control Adenovirus for 2 days

source_name: Control at D2, rep 3


title: Control at D1, rep 3

description: RNA isolated from MCF-7 cells treated with Control Adenovirus for 1 day

source_name: Control at D1, rep 3


title: Control at D2, rep 2

source_name: Control at D2, rep 2


title: Shade leaves_2xozone_050805_rep10

value: five pooled shade leaves


title: DU145 miR203

city: Ann Arbor

first: Christopher

last: Maher

state: MI

address: 1500 E. Medical Center Drive

institute: Michigan Center for Translational Pathology

hyb_protocol: According to the manufacturer's protocol

scan_protocol: Scanned on Agilent Technologies Scanner G2505B Images were quantified using Agilent Feature Extraction Software

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

tag: overexpression

source_name: DU145 miR203 Control overexpression

value: control scrambled small RNA


title: DU145 miR200a

source_name: DU145 miR200a

label_protocol: According to the manufacturer's protocol

tag: cell line

source_name: DU145 miR200a Control overexpression


title: DU145 miR200b

source_name: DU145 miR200b

extract_protocol: According to the manufacturer's protocol

source_name: DU145 miR200b Control overexpression


title: Sun leaves_2xozone_050805_rep1

source_name: Sun leaves_1xozone_050805_rep.1

source_name: Sun leaves_2xozone_050805_rep.1


title: Shade leaves_2xozone_050805_rep9

source_name: Shade leaves_1xozone_050805_rep.5

source_name: Shade leaves_2xozone_050805_rep.5


title: Shade leaves_2xozone_050805_rep6

value: 60 years

value: 2x ambient ozone


title: Control at D2, rep 1

source_name: Control at D2, rep 1


title: Shade leaves_2xozone_050805_rep7

source_name: Shade leaves_1xozone_050805_rep.4

source_name: Shade leaves_2xozone_050805_rep.4


title: Control at D1, rep 1

source_name: Control at D1, rep 1


title: Roots of 0.5h Root-Flooded Arabidopsis (Columbia) Replicate 2

description: Biological replicate 2 of 4. Dye-swap.

source_name: Roots of Arabidopsis (Columbia) without flooding treatment


title: Roots of 0.5h Root-Flooded Arabidopsis (Columbia) Replicate 1

description: Biological replicate 1 of 4.


title: DU145 miR200c

source_name: DU145 miR200c

source_name: DU145 miR200c Control overexpression


title: umbilical_cord_normal_primip_male_sample_24

city: Singapore

first: Emilia

last: Tng

address: 30 Medical Drive

country: Singapore

institute: Singapore Institute for Clinical Sciences

description: Gene expression in human umbilical cord (at birth)

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Umbilical Cord, normal birth weight

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Umbilical cord tissue was first placed in sterile Dispomix tubes and homogenized for 30 s in Trizol using the Dispomix (Medic Tools, AG, Switzerland). RNA was subsequently purified by Trizol, followed by precipitation with isopropanol. The RNA pellet was washed in 70% (v/v) ethanol, air-dried and resuspended in RNase-free water. The isolated RNA was then purified using the RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions. The purified RNA was then eluted in 30 µl of RNase-free water and stored at -80C. RNA concentration and purity were measured using a nanodrop ND-8000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA), and RNA integrity was determined using the Agilent 2100 Bioanalyzer (Agilent Technologies) using RNA 6000 Nano Labchips (Agilent).

tag: births

value: primiparous

value: umbilical cord

tag: gender

value: male

value: 0yr (neonate)


title: DU145 miR181a

source_name: DU145 miR181a

source_name: DU145 miR181a Control overexpression


title: Shade leaves_2xozone_050805_rep8

value: about 60 years

value: 2x ambient ozone, restricted to 150 ppm

value: 5th of August 2005

value: 1x ambient ozone


title: MCF-7 (no treatment) at D0, rep 2

description: RNA isolated on Day 0 from MCF-7 cells (untreated)

source_name: MCF-7 (no treatment) at D0, rep 2

tag: treatment


title: umbilical_cord_normal_primip_male_sample_22


title: MCF-7 (no treatment) at D0, rep 3

source_name: MCF-7 (no treatment) at D0, rep 3


title: umbilical_cord_LBW_primip_male_sample_1

source_name: Umbilical Cord, low birth weight


title: umbilical_cord_LBW_multip_male_sample_1

value: multiparous


title: Shade leaves_2xozone_050805_rep5

source_name: Shade leaves_1xozone_050805_rep.3

source_name: Shade leaves_2xozone_050805_rep.3


title: DU145 miR101

source_name: DU145 miR101 Control overexpression


title: umbilical_cord_LBW_primip_male_sample_2c


title: DU145 miR181b

source_name: DU145 miR181b

source_name: DU145 miR181b Control overexpression


title: umbilical_cord_LBW_primip_male_sample_2a


title: Shade leaves_2xozone_050805_rep4


title: umbilical_cord_LBW_multip_male_sample_3


title: Shade leaves_2xozone_050805_rep3

source_name: Shade leaves_1xozone_050805_rep.2

source_name: Shade leaves_2xozone_050805_rep.2


title: Shade leaves_2xozone_050805_rep1

source_name: Shade leaves_1xozone_050805_rep.1

source_name: Shade leaves_2xozone_050805_rep.1


title: MCF-7 (no treatment) at D0, rep 1

source_name: MCF-7 (no treatment) at D0, rep 1


title: BT549 miR-181b Rep1

source_name: BT549 miR-181b Overexpression Rep1

source_name: BT549 miR-181b Control Overexpression Rep1


title: BT549 miR-181a Rep2

source_name: BT549 miR-181a Overexpression Rep2

source_name: BT549 miR-181a Control Overexpression Rep2


title: Shade leaves_2xozone_050805_rep2


title: BT549 miR200c Rep2

source_name: BT549 miR200c Overexpression Rep2

source_name: BT549 miR200c Control Overexpression Rep2


title: BT549 miR-181b Rep2

source_name: BT549 miR-181b Overexpression Rep2

source_name: BT549 miR-181b Control Overexpression Rep2


title: umbilical_cord_LBW_multip_female_sample_5

source_name: Umbilical Cord, low birth weight

value: female


title: umbilical_cord_LBW_multip_male_sample_2


title: umbilical_cord_LBW_primip_male_sample_2b


title: ICM of whole embryo derived hESC line SG4-WED2

city: Reno

first: Gnanaratnam

last: Giritharan

state: Nevada

address: 645 Sierra Rose Drive, Suite 205

institute: Nevada Center for Reproductive Medicine

description: Frozen hESC pellets were sent to Expression Analysis (Expression Analysis, Inc., Durham, NC, USA) for analysis.

hyb_protocol: According to the Affymetrix standard protocol. (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array).

data_processing: MAS 5.0

growth_protocol: Samples from 3 of the blastomere derived hESC lines (SAB-113B, SAB-113D and W10), and 2 of the whole embryo derived hESC lines (SG4 and SG7) established in our laboratory were collected for microarray analysis. All the selected hESC lines were adjusted to growth under feeder-free defined culture conditions on defined human matrix (CellStart, Invitrogen)-coated dishes in StemPro SFM serum-free hESC medium (Invitrogen) containing FGF (10 ng/ml), and passaged using accutase (Millipore, Temecula, CA, USA) for enzymatic cell separation. For each hESC line, cells were collected when the colonies showed 70-80% confluency in three biological replicates for SAB-113B and SAB-113D lines and 2 replicates for W10, SG4 and SG7 lines.

extract_protocol: Trizol

treatment_protocol: hESC line derived from ICM of whole embryo

tag: cell type

value: ICM of whole embryo derived hESC line


title: Clontech human universal reference total RNA ref-RNA-2

description: Frozen ref-RNA samples from 2 different lot numbers were sent to Expression Analysis (Expression Analysis, Inc., Durham, NC, USA) for analysis.

scan_protocol: According to the Affymetrix standard protocol. (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array).

data_processing: Protocol used by Expression Analysis (Expression Analysis, Inc., Durham, NC, USA).

growth_protocol:
Clontech human universal reference total RNA - Catalog No. 636538
These commercially available RNA samples were made by pooling total RNA extracts from a collection of different whole tissue sources, thus providing the broadest coverage of expressed genes.

extract_protocol: purchased from Clontech

tag: sample type

value: clontech human universal reference total rna

tag: catalog #


title: BT549 miR-181a Rep1

source_name: BT549 miR-181a Overexpression Rep1

source_name: BT549 miR-181a Control Overexpression Rep1


title: Single blastomere derived hESC line SAB-113D-SBD8

label_protocol: According to the Affymetrix standard protocol. (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array).

treatment_protocol: hESC line derived from single blastomere of 8-cell stage embryo

value: single blastomere derived hESC line


title: BT549 miR200c Rep1

source_name: BT549 miR200c Overexpression Rep1

source_name: BT549 miR200c Control Overexpression Rep1


title: umbilical_cord_LBW_primip_male_sample_4


title: BT549 miR200a Rep2

source_name: BT549 miR200a Overexpression Rep2

source_name: BT549 miR200a Control Overexpression Rep2


title: ICM of whole embryo derived hESC line SG7-WED3


title: ERR KO, stimulated, rep. 3

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

state: CA

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

hyb_protocol: GeneChip Mouse Genome 430A 2.0

scan_protocol: Axon Genepix 4000B Scanner

data_processing: GC-RMA, JMP Genomics 4.1

source_name: ERR KO_stimulated by anti-CD3 and anti-CD28

label_protocol: Ambion MessageAmp Premier Labeling

growth_protocol: CD4+ T cells from 6-8 week old mice were negatively selected (Miltenyi), resulting in > 95% purity and cultured in RPMI 1640 (Mediatech) with 10% FBS (Gemini Bio-Products).

extract_protocol: RNA was harvested using the RNeasy Plus Kit from Qiagen.

treatment_protocol: Isolated CD4+ T cells from wild-type (WT) or ERRa-/- (ERRKO) mice were harvested ex vivo or stimulated with 10ug of anti-CD3 and ant-CD28 antibodies for 12 hours in the presence or absence of 20uM XCT790 or 20uM compound A.

tag: genotype/variation

value: ERRa-/- (ERRKO)

value: 6-8 week old

value: T lymphocytes

tag: stimulation

value: Stimulated

value: No treatment


title: BT549 miR200b Rep2

source_name: BT549 miR200b Overexpression Rep2

source_name: BT549 miR200b Control Overexpression Rep2

value: control scrambled small RNA


title: ERR KO, stimulated, rep. 2


title: Single blastomere derived hESC line SAB-113D-SBD7


title: umbilical_cord_LBW_multip_female_sample_3

value: umbilical cord


title: umbilical_cord_LBW_primip_female_sample_6

value: primiparous

value: 0yr (neonate)


title: Single blastomere derived hESC line SAB-113B-SBD4

extract_protocol: Protocol used by Expression Analysis (Expression Analysis, Inc., Durham, NC, USA).


title: BT549 miR200b Rep1

source_name: BT549 miR200b Overexpression Rep1

source_name: BT549 miR200b Control Overexpression Rep1


title: Single blastomere derived hESC line SAB-113B-SBD5


title: ERR KO, stimulated, rep. 1


title: ERR KO, resting, rep. 2

source_name: ERR KO_resting

value: No stimulation


title: ERR WT, treated with Cmpnd. A, rep. 3

source_name: ERR WT_treated with Cmpnd. A

value: WT

value: Compound A


title: ERR KO, resting, rep. 3


title: umbilical_cord_normal_multip_male_sample_7

source_name: Umbilical Cord, normal birth weight

value: multiparous

value: male


title: umbilical_cord_normal_multip_male_sample_15


title: ERR WT, treated with Cmpnd. A, rep. 2


title: umbilical_cord_LBW_multip_male_sample_4


title: Clontech human universal reference total RNA ref-RNA-1

treatment_protocol: Clontech human universal reference total RNA - Catalog No. 636538


title: Single blastomere derived hESC line SAB-113B-SBD3

growth_protocol: Samples from 3 of the blastomere derived hESC lines (SAB-113B, SAB-113D and W10), and 2 of the whole embryo derived hESC lines (SG4 and SG7) established in our laboratory were collected for microarray analysis.  All the selected hESC lines were adjusted to growth under feeder-free defined culture conditions on defined human matrix (CellStart, Invitrogen)-coated dishes in StemPro SFM serum-free hESC medium (Invitrogen) containing FGF (10 ng/ml), and passaged using accutase (Millipore, Temecula, CA, USA) for enzymatic cell separation. For each hESC line, cells were collected when the colonies showed 70-80% confluency in three biological replicates for SAB-113B and SAB-113D lines and 2 replicates for W10, SG4 and SG7 lines.


title: ERR KO, resting, rep. 1


title: ICM of whole embryo derived hESC line SG7-WED4

value: ICM of whole embryo derived hESC line


title: BT549 miR200a Rep1

source_name: BT549 miR200a Overexpression Rep1

source_name: BT549 miR200a Control Overexpression Rep1


title: Control at D1, rep 2

source_name: Control at D1, rep 2

value: Control

tag: duration

tag: replicate


title: ICM of whole embryo derived hESC line SG4-WED1


title: H16N2 Rep1

description: Illumina Human v1 MicroRNA expression beadchip

scan_protocol: Fluorescent signals were imaged by confocal laser scanning using the Illumina BeadArray Reader.

data_processing: The data was processed with Beadstudio software. Data was average normalized.

source_name: H16N2 Rep1


title: H16N2 Rep2

source_name: H16N2 Rep2


title: RWPE Rep1

source_name: RWPE Rep1

value: RWPE


title: Single blastomere derived hESC line SAB-113D-SBD6

value: single blastomere derived hESC line


title: umbilical_cord_normal_multip_male_sample_8

tag: tissue

tag: age


title: BT549 miR203 Rep1

source_name: BT549 miR203 Overexpression Rep1

source_name: BT549 miR203 Control Overexpression Rep1


title: BT549 miR203 Rep2

source_name: BT549 miR203 Overexpression Rep2

source_name: BT549 miR203 Control Overexpression Rep2


title: umbilical_cord_normal_multip_male_sample_5


title: Prec Rep2

source_name: Prec Rep2

value: Prec


title: umbilical_cord_normal_multip_female_sample_19

value: female


title: umbilical_cord_normal_primip_male_sample_21


title: Prec Rep1

source_name: Prec Rep1


title: HME Rep2

source_name: HME Rep2

value: HME


title: ERR WT, treated with Cmpnd. A, rep. 1

value: 6-8 week old

value: T lymphocytes


title: umbilical_cord_normal_primip_male_sample_16

value: umbilical cord


title: Single blastomere derived hESC line W10-SBD2

source_name: Single blastomere derived hESC line W10


title: ERR WT, treated with XCT790. rep. 3

source_name: ERR WT_treated with XCT790


title: Gene expression profiles in UMRC2 FoxO3 cells with vehicle(ethanol) treatment for 12 hours

city: Houston

first: Sujun

last: Hua

state: Tx

address: 1901 East Rd

institute: MD Anderson Cancer Center

description:
We generated UMRC2 cell lines with stable expression of FoxO3(TA)-ERT2, which expressed a fusion protein consisting of FoxO(TA)ERT2 (containing three Ser/Thr AKT phosphorylation sites mutated to alanine) fused to the T2-modified estrogen receptor (ERT2) moiety (For simplicity, FoxO3(TA)-ERT2 cell lines is referred to as FoxO3 thereafter).
Gene expression profiles on Human Genome U133 Plus 2.0 Array for UMRC2 FoxO3 cells treated with vehicle (ethanol) for 12 hours.

hyb_protocol: Standard Affymetrix procedures.

scan_protocol: Standard Affymetrix procedures.

data_processing:
dChip (Li and wong, 2003) was used to normalize arrays and to compute expression indices. Briefly, raw probe intensities were normalized across profiles. Expression values for each probe set were summarized. Differentially expressed probe sets were selected based on fold change as well as modified t-statistics after adjusting for multiple tests.

The Sample data tables include MAS5.0 data and not dChip data.

source_name: UMRC2 FoxO3 cells, ethanol treatment

label_protocol: Approximately 3 ug of total RNA was processed to produce biotinylated cRNA targets.

growth_protocol: Cells were grown in DMEM + 10%FBS with puromycin selection.

extract_protocol: One 10 cm plate of cells (~5 X 106 cells) were lysed using Trizol (Invitrogen). Total RNA was extracted from cells using RNeasy (Qiagen) per manufacture instruction.

treatment_protocol: UMRC2 FoxO3 cells were treated with vehicle (ethanol) for 12 hours.

tag: stable expression

value: ethanol

tag: treatment duration = 12 hrs


title: umbilical_cord_LBW_primip_male_sample_3

source_name: Umbilical Cord, low birth weight

value: primiparous

value: 0yr (neonate)


title: BT549 miR101

source_name: BT549 miR101 Overexpression

source_name: BT549 miR101 Control Overexpression

value: control scrambled small RNA


title: ERR WT, treated with XCT790, rep. 1

value: WT

value: No stimulation


title: umbilical_cord_normal_primip_female_sample_5

source_name: Umbilical Cord, normal birth weight


title: umbilical_cord_LBW_primip_female_sample_1


title: Gene expression profiles in UMRC2 FoxO3 cells with 100 nM 4OHT treatment for 12 hours

description:
We generated UMRC2 cell lines with stable expression of FoxO3(TA)-ERT2, which expressed a fusion protein consisting of FoxO(TA)ERT2 (containing three Ser/Thr AKT phosphorylation sites mutated to alanine) fused to the T2-modified estrogen receptor (ERT2) moiety (For simplicity, FoxO3(TA)-ERT2 cell lines is referred to as FoxO3 thereafter).
Gene expression profiles on Human Genome U133 Plus 2.0 Array for UMRC2 FoxO3 cells treated with 100 nM 4OHT for 12 hours.

source_name: UMRC2 FoxO3 cells, 4OHT treatment

treatment_protocol: UMRC2 FoxO3 cells were treated with 100 nM 4OHT for 12 hours.


title: ERR WT, treated with XCT790, rep. 2


title: ERR WT, stimulated, rep. 1

source_name: ERR WT_stimulated by anti-CD3 and anti-CD28

value: Stimulated

value: No treatment


title: Gene expression profiles in UMRC2 FoxO1 cells with 100 nM 4OHT treatment for 12 hours

description:
We generated UMRC2 cell lines with stable expression of FoxO1(TA)-ERT2, which expressed a fusion protein consisting of FoxO(TA)ERT2 (containing three Ser/Thr AKT phosphorylation sites mutated to alanine) fused to the T2-modified estrogen receptor (ERT2) moiety (For simplicity, FoxO1(TA)-ERT2 cell lines is referred to as FoxO1 thereafter).
Gene expression profiles on Human Genome U133 Plus 2.0 Array for UMRC2 FoxO1 cells treated with 100 nM 4OHT for 12 hours.

source_name: UMRC2 FoxO1 cells, 4OHT treatment

treatment_protocol: UMRC2 FoxO1 cells were treated with 100 nM 4OHT for 12 hours.


title: EZH2 siRNA (DU145) Rep2

source_name: EZH2 siRNA (DU145) Rep2

tag: knockdown

value: EZH2 siRNA


title: umbilical_cord_normal_multip_female_sample_13

value: multiparous


title: Gene expression profiles in UMRC2 empty vector cells with 100 nM 4OHT treatment for 12 hours

description:
We generated UMRC2 cell lines with stable expression of the T2-modified estrogen receptor (ERT2) moiety (For simplicity, ERT2 cell lines is referred to as EV (empty vector) thereafter).
Gene expression profiles on Human Genome U133 Plus 2.0 Array for UMRC2 EV cells treated with 100 nM 4OHT for 12 hours.

source_name: UMRC2 empty vector cells, 4OHT treatment

treatment_protocol: UMRC2 EV cells were treated with 100 nM 4OHT treatment for 12 hours.


title: ERR WT, stimulated, rep. 2


title: RWPE Rep2

source_name: RWPE Rep2

value: RWPE


title: Gene expression profiles in UMRC2 FoxO1 cells with vehicle (ethanol) treatment for 12 hours

description:
We generated UMRC2 cell lines with stable expression of FoxO1(TA)-ERT2, which expressed a fusion protein consisting of FoxO(TA)ERT2 (containing three Ser/Thr AKT phosphorylation sites mutated to alanine) fused to the T2-modified estrogen receptor (ERT2) moiety (For simplicity, FoxO1(TA)-ERT2 cell lines is referred to as FoxO1 thereafter).
Gene expression profiles on Human Genome U133 Plus 2.0 Array for UMRC2 FoxO1 cells treated with vehicle (ethanol) for 12 hours.

source_name: UMRC2 FoxO1 cells, ethanol treatment

treatment_protocol: UMRC2 FoxO1 cells were treated with vehicle (ethanol) for 12 hours.


title: Single blastomere derived hESC line W10-SBD1

value: single blastomere derived hESC line


title: ERR WT, stimulated, rep. 3


title: EZH2 siRNA-ctrl (DU145) Rep2

source_name: EZH2 siRNA-ctrl (DU145) Rep2

value: EZH2 scrambled siRNA control


title: Gene expression profiles in UMRC2 empty vector cells with vehicle (ethanol) treatment for 12 hours

description:
We generated UMRC2 cell lines with stable expression of the T2-modified estrogen receptor (ERT2) moiety (For simplicity, ERT2 cell lines is referred to as EV (empty vector) thereafter).
Gene expression profiles on Human Genome U133 Plus 2.0 Array for UMRC2 EV cells treated with vehicle (ethanol) for 12 hours.

source_name: UMRC2 empty vector cells, ethanol treatment

treatment_protocol: UMRC2 EV cells were treated with vehicle (ethanol) for 12 hours.


title: HME Rep1

source_name: HME Rep1

value: HME


title: umbilical_cord_normal_primip_male_sample_17

value: male


title: ERR WT, resting, rep. 2

source_name: ERR WT_resting

value: 6-8 week old

value: T lymphocytes


title: ERR WT, resting, rep. 3


title: EZH2 siRNA-ctrl (DU145) Rep1

source_name: EZH2 siRNA-ctrl (DU145) Rep1


title: Blood, rep2

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

description: Peripheral blood sample were obtained, with informed consent, from healthy volunteers. Blood samples were mixed with erythrocyte lysis buffer (Qiagen, Germany) and centrifuged at 400g for 10 min at 4°C. The leukocyte pellet was washed and centrifuged again. The remaining leukocytes were snap-frozen and used for further experiments.

hyb_protocol: As described in webpage: http://www.genomics.agilent.com/GenericA.aspx?PageType=Product&SubPageType=ProductLiterature&PageID=1533

scan_protocol: Agilent Technology G2565BA scanner was used. The scanned images were processed using the Feature Extraction software package version 9.5 (Agilent Technology).

data_processing: For each miRNA, multiple probes were spotted on the array and the average intensity of these probes was calculated to represent the expression value of the miRNA. In addition, multiple spots were included as negative controls. Coefficient of variation (CV) within groups of replicate probes was used as a quality control measure to reflect the intra-array reproducibility. MiRNA microarray results were analyzed using Partek® Genomics Suite software V6.5, Copyright© 2009 (Partek Inc., St. Louis, MO, USA; www.partek.com). Data were normalized and summarized with the robust multi-average method (RMA), using quantile normalization approach.

source_name: Peripheral blood samples were obtained from healthy volunteers.

label_protocol: Cyanine-3 (Cy3) labeling as described in webpage: http://www.genomics.agilent.com/GenericA.aspx?PageType=Product&SubPageType=ProductLiterature&PageID=1533

growth_protocol: All methods employed in this study were in accordance with the Declaration of Helsinki. Peripheral blood sample were obtained, with verbal informed consent, from healthy volunteers. Blood samples were mixed with erythrocyte lysis buffer (Qiagen, Germany) and centrifuged at 400g for 10 min at 4°C. The leukocyte pellet was washed and centrifuged again. The remaining leukocytes were snap-frozen and used for further experiments.K562 cell line (obtained from the German Resource Center for Biological Material [DSMZ], DSMZ no. ACC 10) was cultured in RPMI-1640 medium supplemented with 10% heat-inactivated fetal bovine serum (FBS), 2mM glutamine, 1% penicillin and streptomycin and cultured at 37°C in a humidified incubator with 5% CO2.

extract_protocol: MiRNAs were extracted from each sample using the miRNeasy Mini Kit (Qiagen, Germany) according to manufacturer's protocol.

treatment_protocol: Imatinib mesylate (STI571, Gleevec, Glivec; LC Laboratories, USA) was dissolved in DDW. Imatinib was added to the cells for 48h at a final concentration of 0.15μM. Dasatinib (BMS-354825, Sprycel; LC Laboratories, USA) was dissolved in DDW. Dasatinib was added to the cells for 48h at a final concentration of 1.2nM.

value: Blood

tag: disease state

value: control


title: umbilical_cord_LBW_primip_female_sample_3

source_name: Umbilical Cord, low birth weight

value: primiparous

value: umbilical cord

value: female

value: 0yr (neonate)


title: Blood, rep1


title: EZH2 siRNA (DU145) Rep1

source_name: EZH2 siRNA (DU145) Rep1

tag: cell line


title: umbilical_cord_normal_primip_female_sample_3

tag: births


title: Gene expression profiles in RCC4 FoxO1 cells with 100 nM 4OHT treatment for 12 hours

description:
We generated RCC4 cell lines with stable expression of FoxO1(TA)-ERT2, which expressed a fusion protein consisting of FoxO(TA)ERT2 (containing three Ser/Thr AKT phosphorylation sites mutated to alanine) fused to the T2-modified estrogen receptor (ERT2) moiety (For simplicity, FoxO1(TA)-ERT2 cell lines is referred to as FoxO1 thereafter).
Gene expression profiles on Human Genome U133 Plus 2.0 Array for RCC4 FoxO1 cells treated with 100 nM 4OHT for 12 hours.

source_name: RCC4 FoxO1 cells, 4OHT treatment

treatment_protocol: RCC4 FoxO1 cells were treated with 100 nM 4OHT for 12 hours.


title: Gene expression profiles in RCC4 FoxO3 cells with 100 nM 4OHT treatment for 12 hours

description:
We generated RCC4 cell lines with stable expression of FoxO3(TA)-ERT2, which expressed a fusion protein consisting of FoxO(TA)ERT2 (containing three Ser/Thr AKT phosphorylation sites mutated to alanine) fused to the T2-modified estrogen receptor (ERT2) moiety (For simplicity, FoxO3(TA)-ERT2 cell lines is referred to as FoxO3 thereafter).
Gene expression profiles on Human Genome U133 Plus 2.0 Array for RCC4 FoxO3 cells treated with 100 nM 4OHT for 12 hours.

source_name: RCC4 FoxO3 cells, 4OHT treatment

treatment_protocol: RCC4 FoxO3 cells were treated with 100 nM 4OHT for 12 hours.


title: Gene expression profiles in RCC4 empty vector cells with 100 nM 4OHT treatment for 12 hours

description:
We generated RCC4 cell lines with stable expression of the T2-modified estrogen receptor (ERT2) moiety (For simplicity, ERT2 cell lines is referred to as EV (empty vector) thereafter).
Gene expression profiles on Human Genome U133 Plus 2.0 Array for RCC4 EV cells treated with 100 nM 4OHT for 12 hours.

source_name: RCC4 empty vector cells, 4OHT treatment

treatment_protocol: RCC4 EV cells were treated with 100 nM 4OHT treatment for 12 hours.


title: S12

type: genomic

city: Quebec City

first: Frederic

last: Raymond

state: Quebec

address: 2440 Bd Hochelaga Suite 1710

department: École de nutrition

country: Canada

institute: Université Laval

hyb_protocol: 250-350 pmol of dye per sample in a volume of 8µl for each sample were mixed with 1µl of pre-heated ssDNA (10mg/ml stock), 1µl tRNA (10mg/ml stock), 4.5µl Agilent 10X blocking agent and 22.5µl Agilent 2X hybridization buffer. The 45µl mix were heated at 95°C for 3 min then immediately transfered at 37°C for at least 30 min. The mix were loaded onto the micro-arrays and hybridization were performed during 24h at 65°C at 20 RPM.

scan_protocol: Detection of CY3 and CY5 signals were performed on a G2565CA microarray scanner (Agilent Technologies, Santa Clara, CA USA) at 5 µm resolution.

data_processing: The signal intensity data were extracted from the primary scanned images using GenePix Pro 6.0 software (Axon Instruments, Union City, CA, USA). Normalization and statistical analyses were performed in R 2.2.1 software using the LIMMA (Linear Models for Microarray Data) 2.7.3 package. Background correction was performed using the “edwards” method; within-array normalization was done by loess and between array normalization by the Aquantile method. Multiple testing corrections were done using the false discovery rate method with a threshold p value of 0.05. Only genes statistically significant with an absolute ratio greater than 2 were considered.

label: Alexa Fluor 555

molecule: genomic DNA

organism: Leishmania tarentolae

source_name: F

label_protocol: 8 µg of purified PvuII + MseI digested genomic DNA were labeled by adding 9µg of random hexamers (Roche), 5µl 10X Klenow buffer (provided with the exo-klenow enzyme), 5µl 10X dNTP mix (2mM each dATP, dGTP, dTTP and 0.5 mM dCTP), 1.25µl 100µM DTT, 1.5µl Cy-dCTP (Amersham, 1mM stocks) and 1.5µl exo- Klenow (50U/µl stock, NEB). The reaction were incubated overnight at 37°C. The labeled probes were purified using the Telechem purification kit and the probes were quantified by measuring the absorbance at 260nm, 280nm, 550nm (for Cy3) and 650nm (for Cy5).

growth_protocol: All cells were grown in SDM79 medium supplemented with 10% heat-inactivated fetal bovine serum and 5µg/ml hemin at 25°C.

extract_protocol: Cells are collected and washed in Hepes-NaCl and lysed in 500µl of DNAzol solution. The DNAs were precipitated by adding 500 µl of EtOH 99% and collected with a loop. The DNA were washed, once in 1 ml EtOH 70% and once in 1 ml EtOH 100% at room temperature. The DNAs were dissolved in 700 µl of nuclease-free water then sheared by passing successively through 22Gx1 (4-5 times) and 27G ½ needles (10-15 times). The sheared DNAs were digest with PvuII + MseI enzymes for 1h at 37. The digested DNAs were cleaned up by phenol/chloroforme extraction (Ambion, pH 7.9) and ethanol precipation, followed by resuspension in nuclease free water.

treatment_protocol: There is no treatment protocol.

tag: strain

label: Alexa Fluor 647

organism: Leishmania major

source_name: C


title: umbilical_cord_LBW_primip_female_sample_4

tag: gender


title: S8

organism: Leishmania infantum

source_name: B

source_name: E

value: Parrot-TarII


title: S11

source_name: D

value: Friedlin


title: umbilical_cord_normal_primip_female_sample_13

source_name: Umbilical Cord, normal birth weight


title: K562 + Dasatinib, rep2

description: Dasatinib (BMS-354825, Sprycel; LC Laboratories, USA) was dissolved in DDW. Dasatinib was added to CML cells for 48h at a final concentration of 1.2nM.

source_name: K562 + Dasatinib

value: CML

tag: treatment

value: Dasatinib (1.2nM for 48 h)


title: K562 + Dasatinib, rep1


title: K562 + Imatinib, rep2

description: Imatinib mesylate (STI571, Gleevec, Glivec; LC Laboratories, USA) was dissolved in DDW. Imatinib was added to CML cells for 48h at a final concentration of 0.15μM.

source_name: K562 + Imatinib

value: Imatinib (Gleevec, 0.15μM for 48h)


title: umbilical_cord_normal_primip_female_sample_15

description: Gene expression in human umbilical cord (at birth)


title: umbilical_cord_normal_primip_female_sample_8


title: umbilical_cord_LBW_primip_female_sample_2


title: S10


title: umbilical_cord_normal_primip_female_sample_7


title: ERR WT, resting, rep.1

value: WT

tag: cell type

value: No stimulation

value: No treatment


title: Gene expression profiles in RCC4 FoxO3 cells with vehicle(ethanol) treatment for 12 hours

description:
We generated RCC4 cell lines with stable expression of FoxO3(TA)-ERT2, which expressed a fusion protein consisting of FoxO(TA)ERT2 (containing three Ser/Thr AKT phosphorylation sites mutated to alanine) fused to the T2-modified estrogen receptor (ERT2) moiety (For simplicity, FoxO3(TA)-ERT2 cell lines is referred to as FoxO3 thereafter).
Gene expression profiles on Human Genome U133 Plus 2.0 Array for RCC4 FoxO3 cells treated with vehicle (ethanol) for 12 hours.

source_name: RCC4 FoxO3 cells, ethanol treatment

treatment_protocol: RCC4 FoxO3 cells were treated with vehicle (ethanol) for 12 hours.

value: ethanol


title: umbilical_cord_normal_primip_female_sample_12


title: Gene expression profiles in RCC4 FoxO1 cells with vehicle (ethanol) treatment for 12 hours

description:
We generated RCC4 cell lines with stable expression of FoxO1(TA)-ERT2, which expressed a fusion protein consisting of FoxO(TA)ERT2 (containing three Ser/Thr AKT phosphorylation sites mutated to alanine) fused to the T2-modified estrogen receptor (ERT2) moiety (For simplicity, FoxO1(TA)-ERT2 cell lines is referred to as FoxO1 thereafter).
Gene expression profiles on Human Genome U133 Plus 2.0 Array for RCC4 FoxO1 cells treated with vehicle (ethanol) for 12 hours.

source_name: RCC4 FoxO1 cells, ethanol treatment

treatment_protocol: RCC4 FoxO1 cells were treated with vehicle (ethanol) for 12 hours.


title: Gene expression profiles in RCC4 empty vector cells with vehicle (ethanol) treatment for 12 hours

description:
We generated RCC4 cell lines with stable expression of the T2-modified estrogen receptor (ERT2) moiety (For simplicity, ERT2 cell lines is referred to as EV (empty vector) thereafter).
Gene expression profiles on Human Genome U133 Plus 2.0 Array for RCC4 EV cells treated with vehicle (ethanol) for 12 hours.

source_name: RCC4 empty vector cells, ethanol treatment

treatment_protocol: RCC4 EV cells were treated with vehicle (ethanol) for 12 hours.


title: K562, rep1

description: K562 cell line (CML, obtained from the German Resource Center for Biological Material [DSMZ], DSMZ no. ACC 10) was cultured in RPMI-1640 medium supplemented with 10% heat-inactivated fetal bovine serum (FBS), 2mM glutamine, 1% penicillin and streptomycin and cultured at 37°C in a humidified incubator with 5% CO2.

source_name: K562 cell line


title: K562, rep2


title: S7

source_name: A


title: umbilical_cord_LBW_multip_female_sample_1

source_name: Umbilical Cord, low birth weight

value: multiparous


title: S9


title: S1


title: S6


title: K562 + Imatinib, rep1


title: BL23 bile_2

status: Public on Oct 20 2011

city: Paterna

first: Manuel

last: Zúñiga

state: Valencia

address: Avda. Profesor Agustín Escardino 7

department: Biotecnología

institute: Instituto de Agroquímica y Tecnología de Alimentos

hyb_protocol: SDS based hybridization solution, during 24 hours

scan_protocol: FUJIFILM FLA-3000

data_processing:
The software for image analysis is ArrayVision 7.0 (Imaging Research Inc.). This software yields raw and background substracted data.
The Background Substracted Signals are raw individual data. After considering the three replicates performed in the experiment and after median normalization, first between replicates and after between conditions, we obtain the ratio values for each gene/ORF (see supplementary file on Series record).

organism: Lacticaseibacillus casei

source_name: Cultured cells

label_protocol: First-strand cDNA was synthesized from 45 µg RNA using the Transcriptor first strand cdna synthesis kit (Roche) with random hexamer primers as recommended by the manufacturer. Labelled cDNA was purified with illustra MicroSpin G-50 Columns (GE Healthcare) as recommended by the manufacturer.

growth_protocol: Cells were stored at -80C in MRS medium supplemented with 15% glycerol (stock culture). For the assay, cells from the stock culture were inoculated in MRS agar plates. A single colony was used to inoculate 5 ml of MRS medium and the culture was incubated overnight at 37C. This culture was used to inoculate MRS medium at 0.05 O.D. 595 nm. for the treatment or control assays.

extract_protocol: Total RNA was isolated from L. casei by using TRIZOL reagent (Invitrogen). Cells were collected by centrifugation, washed with cold 50 mM EDTA (pH 8.0), resuspended in 1 ml of TRIZOL reagent, and then mechanically disrupted with glass beads in a cell disrupter (Savant Instruments, Holbrook, N.Y.). Additional steps were performed according to the instructions of the TRIZOL manufacturer. RNA samples purified as described above were treated with the Ambion Turbo DNA-free kit (Applied Biosystems) using the routine DNase I treatment outlined by the supplier in order to remove contaminating DNA. The quality and concentration of the RNA samples were subsequently evaluated by using the Experion automated electrophoresis system (Bio-Rad). Samples with 23S/16S ratios lower than 0.85 were discarded.

treatment_protocol: Cells were grown in MRS medium at 37C without shaking until O.D. 595 nm. reached 0.5. The culture was then two fold diluted with prewarmed MRS medium supplemented with 0.2% bovine bile (Sigma) and incubation continued for 45 min.

tag: agent

value: bile


title: umbilical_cord_normal_primip_female_sample_1


title: S5


title: BL23 bile_1


title: S3


title: Lodderomyces elongisporus Xylose Replicate 2

type: mixed

city: Carlisle

first: Dana

middle: Jasmine

last: Wohlbach

state: PA

institute: Dickinson College

description: Biological replicate 2 of 3. Experimental xylose-grown cells, harvested after 3 generations.

hyb_protocol: Arrays were hybridized in a NimbleGen hybridization system 12 (BioMicro) following the standard NimbleGen operating protocol. See www.nimblegen.com.

scan_protocol: Arrays were scanned using a GenePix 4000B scanning laser (Molecular Devices) following the standard NimbleGen operating protocol. See www.nimblegen.com.

data_processing: Data normalization was performed using custom perl scripts and Bioconductor (Gentleman, R. C. et al.  (2004) Genome Biol 5: R80).  The affy() package (Gautier, L. et al. (2004) Bioinformatics 20: 307-315) was used to apply probe-level quantile normalization to the log2 signal of RNA versus the genomic DNA control (Cy5/Cy3).  Gene-level expression changes were summarized with the median value of each probe set contained completely within each predicted ORF.  See the included file LeloProbeMapping.txt for a mapping of probes to genes.

organism: Lodderomyces elongisporus NRRL YB-4239

source_name: Lodderomyces elongisporus NRRL YB-4239 xylose

label_protocol: Sample labeling was performed as described in Gasch, A. P. (2002) Methods Enzymol 350: 393-414, using cyanine dyes (Amersham), Superscript III (Invitrogen), and amino-allyl-dUTP (Ambion).  RNA collected from cells grown in each sugar condition was labeled with Cy5 dye and was directly compared to a genomic DNA reference sample labeled with Cy3 dye.

growth_protocol: Lodderomyces elongisporus NRRL YB-4239 was grown aerobically at 30˚C for approximately 16 h in YPD (1% yeast extract, 2% peptone, 2% glucose) to early-log phase.  Cells were washed once in YP (1% yeast extract, 2% peptone) and split into two cultures.  Both cultures received the addition of sugar to a final concentration of 2%: glucose was added to one culture; xylose was added to the other culture.  Cells were collected at OD600 0.5-0.6 after 3 generations aerobic growth at 30˚C.

extract_protocol: Cell collection, lysis, and total RNA isolation were performed as previously described in Gasch, A. P. (2002) Methods Enzymol 350: 393-414.  Following total RNA isolation, RNA was further purified with LiCl and RNeasy Mini kit (Qiagen).  RNA concentration was determined by NanoDrop spectrophotometer (Thermo Scientific).

treatment_protocol: One culture was treated with 2% glucose for 3 generations growth; the other culture was treated with 2% xylose for 3 generations growth.

value: 2% xylose for 3 generations growth

source_name: Lodderomyces elongisporus NRRL YB-4239 genomic

value: Genomic DNA was extracted from cells growing in log phase


title: Candida albicans Xylose Replicate 2

data_processing: Data normalization was performed using custom perl scripts and Bioconductor (Gentleman, R. C. et al.  (2004) Genome Biol 5: R80).  The affy() package (Gautier, L. et al. (2004) Bioinformatics 20: 307-315) was used to apply probe-level quantile normalization to the log2 signal of RNA versus the genomic DNA control (Cy5/Cy3).  Gene-level expression changes were summarized with the median value of each probe set contained completely within each predicted ORF.  See the included file CalbProbeMapping.txt for a mapping of probes to genes.

organism: Candida albicans WO-1

source_name: Candida albicans WO-1 xylose

growth_protocol: Candida albicans WO-1 was grown aerobically at 30˚C for approximately 16 h in YPD (1% yeast extract, 2% peptone, 2% glucose) to early-log phase.  Cells were washed once in YP (1% yeast extract, 2% peptone) and split into two cultures.  Both cultures received the addition of sugar to a final concentration of 2%: glucose was added to one culture; xylose was added to the other culture.  Cells were collected at OD600 0.5-0.6 after 3 generations aerobic growth at 30˚C.

source_name: Candida albicans WO-1 genomic


title: S2

source_name: B


title: umbilical_cord_normal_multip_female_sample_11


title: Candida albicans Xylose Replicate 1

description: Biological replicate 1 of 3. Experimental xylose-grown cells, harvested after 3 generations.


title: Candida albicans Glucose Replicate 3

description: Biological replicate 3 of 3. Control glucose-grown cells, harvested after 3 generations.

source_name: Candida albicans WO-1 glucose

value: 2% glucose for 3 generations growth


title: S4

source_name: D

source_name: C


title: umbilical_cord_normal_multip_female_sample_12

source_name: Umbilical Cord, normal birth weight

value: umbilical cord


title: BL23 bile_3


title: Lodderomyces elongisporus Xylose Replicate 1


title: Lodderomyces elongisporus Glucose Replicate 3

source_name: Lodderomyces elongisporus NRRL YB-4239 glucose


title: BL23 MRS_2

treatment_protocol: Cells were grown in MRS medium at 37C without shaking until O.D. 595 nm. reached 0.5. The culture was then two fold diluted with prewarmed MRS medium and incubation continued for 45 min.

value: control


title: BL23 MRS_1


title: BL23 MRS_3


title: Candida albicans Xylose Replicate 3

description: Biological replicate 3 of 3. Experimental xylose-grown cells, harvested after 3 generations.


title: Candida albicans Glucose Replicate 1

description: Biological replicate 1 of 3. Control glucose-grown cells, harvested after 3 generations.


title: Candida albicans Glucose Replicate 2

description: Biological replicate 2 of 3. Control glucose-grown cells, harvested after 3 generations.


title: umbilical_cord_normal_multip_female_sample_14

value: female

value: 0yr (neonate)


title: Lodderomyces elongisporus Glucose Replicate 2


title: Surgical sample O-4-8

city: Chuo-ku

first: Hiroki

last: Sasaki

state: Tokyo

country: Japan

institute: National Cancer Center Reseach Institute

description:
O-4-8
Gene expression data from surgical sample of esophageal cancer.

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

scan_protocol: GeneChips were scanned using the Agilent GeneArray Scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using default settings by Expression Console ver 1.1.

source_name: Esophagus, cancerous portion, surgical

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: All esophageal cancer tissues and non-cancerous tissues were provided by the Central Hospital or East Hospital at the National Cancer Center after obtaining written informed consent from each patient and approval by the Center’s Ethics Committee.

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

treatment_protocol: All surgical samples were obtained from esophageal cancer patients without neoadjuvant therapy, and all biopsy samples were obtained before treatment. For the surgical samples, trained pathologists carefully excised bulk tissue samples from the main tumor, leaving a clear margin from the surrounding normal tissue. Surgical and biopsy samples were immediately frozen at -80 ﾟC until use. Frozen samples were placed in the ISOGEN solution (Nippon Gene, Toyama, Japan) and homogenised befor total RNA extraction.

value: esophageal cancer

value: cancerous portion of esophagus

tag: sample type

value: surgical


title: Lodderomyces elongisporus Glucose Replicate 1


title: Surgical sample O-4-12

description:
O-4-12
Gene expression data from surgical sample of esophageal cancer.


title: Lodderomyces elongisporus Xylose Replicate 3


title: Surgical sample O-3-30

description:
O-3-30
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-4-1

description:
O-4-1
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-4-11

description:
O-4-11
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-4-5

description:
O-4-5
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-4-9

description:
O-4-9
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-3-22

description:
O-3-22
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-3-23

description:
O-3-23
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-4-6

description:
O-4-6
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-4-2

description:
O-4-2
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-4-10

description:
O-4-10
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-3-27

description:
O-3-27
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-4-7

description:
O-4-7
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-3-24

description:
O-3-24
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-3-29

description:
O-3-29
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-4-4

description:
O-4-4
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-3-16

description:
O-3-16
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-3-18

description:
O-3-18
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-4-3

description:
O-4-3
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-3-25

description:
O-3-25
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-3-26

description:
O-3-26
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-3-20

description:
O-3-20
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-3-17

description:
O-3-17
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-3-19

description:
O-3-19
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-3-15

description:
O-3-15
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-3-28

description:
O-3-28
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-3-21

description:
O-3-21
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-3-9

description:
O-3-9
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-3-14

description:
O-3-14
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-3-12

description:
O-3-12
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-3-6

description:
O-3-6
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-3-4

description:
O-3-4
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-3-13

description:
O-3-13
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-3-11

description:
O-3-11
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-3-8

description:
O-3-8
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-3-3

description:
O-3-3
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-2-2

description:
O-2-2
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-3-5

description:
O-3-5
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-2-3

description:
O-2-3
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-3-10

description:
O-3-10
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-1-17

description:
O-1-17
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-2-1

description:
O-2-1
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-1-11

description:
O-1-11
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-1-12

description:
O-1-12
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-2-4

description:
O-2-4
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-1-16

description:
O-1-16
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-1-13

description:
O-1-13
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample O-3-1

description:
O-3-1
Gene expression data from surgical sample of esophageal cancer.