title: A/J_Lung_12h


title: B6_Lung_12h

status: Public on Dec 30 2007

type: RNA

city: Chiba

first: Shuhei

last: Noda

state: Chiba

address: Anagawa 4-9-1

department: Frontier research center

country: Japan

institute: National institute of radiological sciences

description: In channel 1, total RNA was purified and pooled from 3 mice

hyb_protocol: cDNA Microarray Kit Protocol (Double barcoded slide) Version 7.0, Publication Number:  G4100-98000

scan_protocol: Agilent Microarray Scanner User Manual (6.3, 5th edition, December 2003), Publication Number:  G2566-90009 10µm resolution, 100% PMT

data_processing: Feature Extraction Software (Agilent Technologies)

molecule: total RNA

organism: Mus musculus

label_protocol: Agilent Fluorescent Direct Label Kit Protocol (June 2003 Rev 2.1), Publication Number:  G2555-98003_JUNE_2003

treatment_protocol: Twelve hour after local irrradiation (thorax, 10Gy)

tag: 'Strain

value: C57BL6/J', 'Gender:female', 'Age:12~13 week'

source_name: control RNA mixture

tag: Ten of First Choice total RNA (Ambion, Inc.) derived from ten organs(midterm embryo, thymus, ovary, testicle, spleen, lung, heart, liver, kidney, brain) were equally mixed.


title: C3H_Lung_1h

treatment_protocol: One hour after local irrradiation (thorax, 10Gy)

value: C3H/HeMs', 'Gender:female', 'Age:12~13 week'


title: ORF I040F#12 swm1 H3K4Me2 C2

type: genomic

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

description: chip on chip

hyb_protocol: Robyr et al Methods 31 (2003)

scan_protocol: chip reader

data_processing: genespring

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: wt

label_protocol: Robyr et al Methods 31 (2003)

extract_protocol: Robyr et al Methods 31 (2003)

tag: wt sample

tag: swm1 sample


title: A/J_Lung_1h

value: A/J', 'Gender:female', 'Age:12~13 week'


title: A/J_Skin_NoIrradiation

description: In channel 2, total RNA was purified and pooled from 3 mice. Skin was taken as full layers.

treatment_protocol: No treatment


title: A/J_Lung_72h

treatment_protocol: Seventy two hour after local irrradiation (thorax, 10Gy)


title: A/J_Lung_NoIrradiation


title: IGR I040F #3 swm1 H3K4Me2 C1

description: Chip on chip

scan_protocol: Chip Reader

extract_protocol: chip on chip


title: B6_Lung_NoIrradiation


title: IGR I040F #12 swm1 H3K4Me2 C2

description: Chip on chip


title: ORF I040F#11 swm1 H3K9Me2 B2

description: chip on chip


title: ORF I040F#3 swm1 H3K4Me2 C1

description: chip on chip


title: IGR I040F #11 swm1 H3K9Me2 B2

description: Chip on chip


title: Expression in swm1D (E020F#29)

description: We carried out expression profiling experiments in which gene expression in logarithmically growing cultures of swm1 mutant cells was compared to that in wt controls.

hyb_protocol: Xue Y. et al Yeast (2004)

data_processing: GeneSpring

label_protocol: Xue Y. et al Yeast (2004)

extract_protocol: Xue Y. et al Yeast (2004)


title: IGR I040F #2 swm1 H3K9Me2 B1

description: chip on chip

scan_protocol: Chip reader

data_processing: geneSpring


title: ORF I040F#2 swm1 H3K9Me2 B1

description: chip on chip


title: Expression swm1 (E020F #19)


title: E73_CD8_48h_IL2_rep2

status: Public on Dec 29 2007

city: Newark

first: Eleftherios

middle: Terry

last: Papoutsakis

state: DE

address: 15 Innovation Way

department: Chemical Engineering

country: USA

institute: University of Delaware

description: primary T-cell activaiton in CD4+ and CD8+ subsets

hyb_protocol: Followed Agilent 60-mer oligo microarray processing protocol v 4.1, using SSC wash protocol and forced nitrogen drying

scan_protocol: Scanned using Agilent Microarray Scanner (G2565BA) at 10um resolution

data_processing: Agilent Feature Extraction software (v.7.2) was used to assess spot quality and extract feature intensity statistics; duplicate spots were averaged; background-subtracted data were normalized using SNNLERM (Yang et al., PNAS 2003; 100:1122-1127)

organism: Homo sapiens

label_protocol: Agilent Low RNA Input Fluorescent Linear Amplification kit (v2.0) (reverse transcription with oligo-dT primers, in vitro transcription with direct incorporation of fluorescently labeled CTP analogs)

growth_protocol: Grown in AIM V with 2% Human AB Serum, 37degC, 5% CO2

extract_protocol: Agilent RNA isolation mini-kit

treatment_protocol: activated with CD3/CD28 supplemented with IL2 for 48 hours

tag: primary T cells, donor 3

organism: Thymus

source_name: Human Thymus Total RNA

extract_protocol: The material purchased was RNA and its extraction was performed by the manufacturer.

tag: Human Thymus Total RNA


title: E73_CD8_48h_rep2

treatment_protocol: activated with CD3/CD28 for 48 hours


title: E73_CD8_72h_IL2_rep1

treatment_protocol: activated with CD3/CD28 supplemented with IL2 for 72 hours


title: E73_CD8_24h_rep2

treatment_protocol: activated with CD3/CD28 for 24 hours


title: E73_CD8_24h_rep1


title: E73_CD4_72h_IL2_rep1


title: E73_CD4_72h_rep1

treatment_protocol: activated with CD3/CD28 for 72 hours


title: E73_CD8_06h_rep1

treatment_protocol: activated with CD3/CD28 for 06 hours


title: E73_CD8_72h_rep1


title: E73_CD4_24h_rep2


title: E73_CD4_48h_rep1


title: E73_CD4_12h_IL2_rep1

treatment_protocol: activated with CD3/CD28 supplemented with IL2 for 12 hours


title: E73_CD8_24h_IL2_rep2

treatment_protocol: activated with CD3/CD28 supplemented with IL2 for 24 hours


title: E73_CD4_12h_rep1

treatment_protocol: activated with CD3/CD28 for 12 hours


title: E73_CD8_24h_IL2_rep1


title: E73_CD8_48h_IL2_rep1


title: E73_CD4_48h_IL2_rep1


title: E73_CD4_24h_IL2_rep2


title: E73_CD8_48h_rep1


title: E73_CD8_12h_rep1


title: E73_CD4_24h_IL2_rep1


title: E73_CD8_06h_IL2_rep1

treatment_protocol: activated with CD3/CD28 supplemented with IL2 for 06 hours


title: E73_CD8_12h_IL2_rep1


title: E73_CD8_00h_rep1


title: E73_CD4_06h_rep1


title: E73_CD4_00h_rep1


title: E73_CD4_06h_IL2_rep1


title: E64_CD8_72h_rep2

tag: primary T cells, donor 2


title: E64_CD8_72h_IL2_rep1


title: E64_CD8_48h_IL2_rep1


title: E64_CD8_72h_IL2_rep2


title: E64_CD8_48h_rep1


title: E64_CD8_00h_rep1


title: E64_CD4_72h_rep2


title: E64_CD4_48h_IL2_rep2


title: E64_CD4_72h_IL2_rep1


title: E64_CD4_48h_IL2_rep1


title: E64_CD4_12h_rep1


title: E64_CD4_06h_IL2_rep2


title: E64_CD8_06h_rep1


title: E64_CD4_12h_IL2_rep1


title: E64_CD8_12h_IL2_rep1


title: E64_CD4_72h_IL2_rep2


title: E64_CD8_06h_IL2_rep1


title: E64_CD8_12h_rep1


title: E64_CD8_24h_rep1


title: E64_CD8_72h_rep1


title: E64_CD8_24h_IL2_rep1


title: E64_CD4_06h_IL2_rep1


title: E64_CD4_24h_rep1


title: E64_CD4_72h_rep1


title: E64_CD4_24h_IL2_rep1


title: E64_CD4_48h_rep1


title: E64_CD4_00h_rep1


title: E64_CD4_06h_rep1


title: E52_CD8_72h_IL2_rep1

tag: primary T cells, donor 1


title: E52_CD8_48h_IL2_rep1


title: E52_CD8_72h_IL2_rep2


title: E52_CD8_12h_IL2_rep2


title: E52_CD8_00h_rep2


title: E52_CD8_12h_IL2_rep1


title: E52_CD4_72h_IL2_rep2


title: E52_CD4_24h_IL2_rep2


title: E52_CD4_12h_IL2_rep2


title: E52_CD4_24h_IL2_rep1


title: E52_CD8_24h_IL2_rep1


title: E52_CD4_12h_IL2_rep1


title: E52_CD4_00h_rep1


title: E52_CD8_00h_rep1


title: E52_CD8_24h_IL2_rep2


title: Brain_BrB3b

status: Public on Dec 01 2007

city: Foster City

first: Yongming

last: Sun

state: CA

address: 850 Lincoln Center Dr

institute: Applied Biosystems

description: Background strain

hyb_protocol: Hybridization was performed according to Applied Biosystems Chemiluminescence Detection Kit Protocol (PN 4339627) using 10 ug fragmented cRNA

scan_protocol: Image was captured using CCD camera came with AB1700 Microarray Analyzer

data_processing: Quantle normalization was performed

label: digioxigenin

source_name: Mouse Brain Strain C57BL/6J

label_protocol: Digoxigenin labeled cRNA was prepared according to Applied Biosystems nanoamp RT-IVT protocol

extract_protocol: TRIzol extraction

tag: C57BL/6J. Male mice at about 120 days


title: Brain_BrB1b

description: Background strain


title: E52_CD4_72h_IL2_rep1


title: Brain_BrB5b

description: Background strain


title: E52_CD4_48h_IL2_rep1


title: E52_CD4_00h_rep2


title: Brain_Br353C1b

description: Lean congenic homozygote strain

source_name: Mouse Brain Strain B6.C-D7Mit353

tag: B6.C-D7Mit353. Male mice at about 120 days


title: Brain_Br353C5b

description: Lean congenic homozygote strain


title: Gastrocnemius_Gas615

description: Background strain

data_processing: Quantile normalization was performed

source_name: Mouse Gastrocnemius Strain C57BL/6J


title: Gonadal white adipose_GWAT572

description: Background strain

source_name: Mouse Gonadal white adipose Strain C57BL/6J


title: Gonadal white adipose_GWAT615

description: Background strain


title: Gonadal white adipose_GWAT411

description: Background strain


title: Gastrocnemius_Gas570

description: Background strain


title: Gastrocnemius_Gas552

description: Lean congenic homozygote strain

source_name: Mouse Gastrocnemius Strain B6.C-D7Mit353


title: Gastrocnemius_Gas408

description: Background strain


title: Liver_Lb573

description: Background strain

source_name: Mouse Liver Strain C57BL/6J


title: E73_CD4_24h_rep1


title: Gastrocnemius_Gas407

description: Lean congenic homozygote strain


title: Gastrocnemius_Gas409

description: Lean congenic homozygote strain


title: Brain_Br353C5a

description: Lean congenic homozygote strain


title: Liver_L409

description: Lean congenic homozygote strain

source_name: Mouse Liver Strain B6.C-D7Mit353


title: Expression in sim3-143 A170F#4

status: Public on Nov 10 2007

description: We carried out expression profiling experiments in which gene expression in logarithmically growing cultures of sim3-143 cells was compared to that in wt controls.

tag: sim3-143 sample

source_name: Wt


title: Liver_Lb570

description: Background strain


title: Liver_L571

description: Lean congenic homozygote strain

tag: B6.C-D7Mit353 Male mice at about 120 days


title: Gonadal white adipose_GWAT571

description: Lean congenic homozygote strain

source_name: Mouse Gonadal white adipose Strain B6.C-D7Mit353


title: Brain_Br353C4a

description: Lean congenic homozygote strain


title: Liver_Lb572

description: Background strain


title: Liver_L552

description: Lean congenic homozygote strain


title: Expression in sim3-205 vs wt A170F#12

description: We carried out expression profiling experiments in which gene expression in logarithmically growing cultures of sim3-205 mutant cells was compared to that in wt controls.

scan_protocol: ChipReader

tag: sim3-205 sample


title: Expression in sim3-205 vs wt (E020F)


title: Gonadal white adipose_GWAT409

description: Lean congenic homozygote strain


title: Expression in sim3-143 A170F#15

description: We carried out expression profiling experiments in which gene expression in logarithmically growing cultures of sim-143 mutant cells was compared to that in wt controls.

tag: Xue Y. et al Yeast (2004)


title: 13483872 - drv1 vs Ws

status: Public on Nov 07 2007

city: Evry

first: Frederique

last: Bitton

address: 2 rue Gaston Cremieux

country: France

institute: INRA

description: The impact of cell wall alterations on global gene expression.

hyb_protocol: Ws Cy5 / drv1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 620V,laser power 100%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

source_name: Ws

label_protocol: labelling Cy3 and Cy5 indirect, amplification=yes, DNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: stem - Media 		soil	 hygrometry 	70%	 Temperature 	22 light / 20 dark	 Light 		16h light / 8h dark

tag: Arabidopsis thaliana (wassilewskija)  - dev.stage (Boyes et al. Plant Cell 2001):boyes,6.50


title: Gonadal white adipose_GWAT407

description: Lean congenic homozygote strain


title: ChIP_LNCaP_SUZ12

status: Public on Nov 01 2007

city: Chicago

first: Jindan

last: Yu

state: IL

address: 303 E. Superior St.

department: Medicine - Hem/Onc

institute: Northwestern University

description: A total of 200ng of either whole cell extract DNA or immunoenriched DNA was labeled and purified using BioPrime array CGH genomic labeling kits (Invitrogen, Carlsbad, CA). Whole cell extract DNA was labeled with Cy3 dye whereas immunoenriched DNA was labeled with Cy5 dye (Perkin Elmer, Wellesley, MA). A total of 2.5 μg each of Cy3- or Cy5-labeled DNA were combined and hybridized to hu6k human proximal promoters (Aviva Systems Biology, San Diego, CA) at 65oC for 40 hours

hyb_protocol: Li, Z., S. Van Calcar, et al. (2003). "A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells." Proc Natl Acad Sci U S A 100(14): 8164-9.

scan_protocol: The hybridized promoter chips were scanned using the GenePix 4000B scanner (Axon, Foster City, CA) and analyzed with the GenePix Pro3.0 to extract intensity values and other quality-control parameters.

data_processing: Spot intensity was adjusted by subtraction of the background signal. Features of low intensity (<1000) and bad spots were flagged and excluded from further analysis. Non-flagged features with intensity of 1 standard deviation over background in both channels were included for normalization. The Cy5 and Cy3 channels were normalized by making the mean of the medians-of-Ratios of the normalization features to 1. For all non-flagged features, the normalized median of ratio was taken for further analysis

source_name: Suz12-ChIP chromatin, Cy5

tag: LNCaP cells, ChIP by SUZ12 antibody, LM-PCR amplified, 2.5ug

source_name: whole cell extract DNA, Cy3

tag: LNCaP cells, whole cell extract DNA, LM-PCR amplified, 2.5ug


title: 13483871 - Ws vs drv1

hyb_protocol: drv1 Cy5 / Ws Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Gene expression changes in human colorectal cell line HCT116 DICER Exon5 knockout cells (dye-swap)

status: Public on Oct 26 2007

city: Baltimore

first: Wayne

state: MD

address: 417 N. Caroline St.

department: Cancer Center

institute: Johns Hopkins University

hyb_protocol: Fragmented targets are added an Oligo Microarray, assembled into a hybridization chamber (Agilent Technologies) and hybridized at 65ºC for 17 hours in a hybridization oven with rotation. Hybridized microarrays are washed and dried according to the Agilent microarray processing protocol.

scan_protocol: Microarrays are scanned with Agilent G2565BA microarray scanner under default settings recommended by Agilent Technologies for expression microarrays with 100% PMT and 10 um resolutions.

data_processing:
Data are extracted using Feature Extraction Software v8.5 (Agilent Technologies) under default settings for expression microarrays with linear & lowess normalization.
VALUEs represent log10 (test/reference) ratios, after linear and loess normalization.

source_name: Human coloretal HCT116 cells

label_protocol: Sample amplification and labeling procedures are carried out by using Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). ). 0.4 microgram of total RNA is reverse transcribed into first strand and second strand cDNA by MMLV-RT using an oligo dT primer (System Biosciences) that incorporates a T7 promoter sequence. The cDNA is then used as a template for in vitro transcription in the presence of T7 RNA polymerase and Cyanine labeled CTPs. The labeled cRNA is purified using RNeasy mini kit (Qiagen) and followed by quantification on both concentrations of cRNA and dye labeled. RNA spike-in controls (Agilent Technologies) are added to RNA samples before amplification and labeling according to manufacturer’s protocol.

growth_protocol: Cells were grown in McCoy's 5A medium supplimented with 10% fetal bovine serum.

extract_protocol: RNA was isolated by using TriZol reagent followed by clean-up with RNeasy mini kit plus on-column DNease treatment.

treatment_protocol: There were no specific treatments for cells during growth.

tag: Human coloretal HCT116 cells

source_name: Human coloretal HCT116 DICER exon5 knockout cells


title: 13483873 - Col vs 35S-DRV1

hyb_protocol: 35S-DRV1 Cy5 / Col Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: stem - Media 		soil	 hygrometry 		70%	 Temperature 		22 light / 20 dark	 Light 		16h light / 8h dark

tag: Arabidopsis thaliana (columbia)  - dev.stage (Boyes et al. Plant Cell 2001):6.50,boyes

source_name: Col


title: ChIP_PC3_IgG

data_processing: Spot intensity was adjusted by subtraction of the background signal. Features of low intensity (<1000) and bad spots were flagged and excluded from further analysis. Non-flagged features with intensity of 1 standard deviation over background in both channels were included for normalization.  The Cy5 and Cy3 channels were normalized by making the mean of the medians-of-Ratios of the normalization features to 1. For all non-flagged features, the normalized median of ratio was taken for further analysis

source_name: IgG-ChIP chromatin,  Cy5

label_protocol: Bioprime array CGH genomic labeling kits

tag: PC3 cells, ChIP by rabbit IgG, LM-PCR amplified, 2.5ug

source_name: whole cell extract DNA, cy3

tag: PC3 cells, whole cell extract DNA, LM-PCR amplified, 2.5ug


title: Gene expression changes in human colorectal cell line HCT116 DICER Exon5 knockout cells

source_name: Human colorectal HCT116 DICER Exon5 knockout cells

tag: Human colorectal HCT116 DICER exon5 knockout cells

source_name: Human colorectal HCT116

tag: Human colorectal HCT116 cells


title: Nitrosomonas europaea_exposure to 3.4 uM ZnCl2_60min_biological rep2.

status: Public on Oct 24 2007

city: Corvallis

first: Sunhwa

last: Park

state: OR

address: 116 Gilmore

department: Biological & Ecological Eng.

institute: Oregon State University

description: the activity of nitrosomonas europaea was inhibited about 60% by 3.4 uM ZnCl2.

hyb_protocol: 0.16 ug/ul of six cDNA samples (three controls and three treatments) were hybridized at 60 rpm for 16 h to zebrafish genome array.

scan_protocol: The arrays were scanned using Affymetrix GeneChip Scanner 3000 at 570 nm.

data_processing: The data were analyzed with single array analysis in GeneChip Operating Software (GCOS)

label: biotin

organism: Nitrosomonas europaea

source_name: N. europaea cultured in batch reactor with 50 mM HEPES buffer, exposure to 3.4 uM ZnCl2, 60 min

label_protocol: The 3’termini of the cDNA fragmentation were labeled with 7.5 mM GeneChip DNA labeling reagent (Affymetrix).

growth_protocol: (NH4)2SO4 (5 mM) in 50 mM HEPES buffer, 700rpm, in gas-tight 1.67 L reactor vessels, injection of 3.4 uM zinc

extract_protocol: Total cellular RNA was extracted using 1 ml of Trizol (Ambion Inc., Austin, TX) following the manufacturer’s instructions. The extracted RNA was purified with RNeasy Mini kit (Qiagen Inc., Valencia, CA.) and treated with RNase-free DNase ? (Qiagen) to digest residual chromosomal DNA.

treatment_protocol: Injection of 3.4 uM ZnCl2, 60min

tag: N. europaea cells were cultured in 25 mM (NH4)2SO4 (50 mM of total NH4+) and harvested in mid to late exponential phase. The cells (OD600  0.07) were washed twice with 40 mM NaHPO4 (pH 7.8) to remove residual ammonia and were resuspended in 1000 ml of 50 mM HEPES buffer. The cells (500 ml) were then placed in gas-tight 1.67 L reactor vessels (Wheaton Double-sidearm Cell stir). HEPES buffer was used to prevent zinc precipitates and complexes that can form in phosphate or carbonate buffers. (NH4)2SO4 (5 mM) was injected in the reactor vessels and the cultures were stirred with a magnetic stirring bar rotati


title: Nitrosomonas europaea_exposure to 3.4 uM ZnCl2_60min_biological rep3.


title: TERA_TSA_vs_mock_2

hyb_protocol: Agilent Gene Expression Hybridization Kit using manufecturer's recommended protocol

scan_protocol: Microarrays are scanned with Agilent G2565BA microarray scanner under default settings recommended by Agilent Technologies for expression microarrays with 100% PMT and 10 micrometer resolutions. Data are extracted using Feature Extraction Software v8.1 (Agilent Technologies) under default settings for expression microarrays

data_processing: log2 Ratio of background subtracted TSA intensity to background subtracted Mock treated intensity after loess normalization with Bioconductor

source_name: TSA-treated TERA2

label_protocol: Agilent Low RNA Input Linear Amplification Kit using manufacturer's recommended protocol

growth_protocol: McCoy's 5A medium with 10% BCS and 1x P/S

extract_protocol: TriZol extraction followed by RNeasy clean-up with on-column DNase treatment

treatment_protocol: 300 nanomolar TSA for 18 hours

tag: TERA2 human embryonal carcinoma cell line

source_name: Mock-treated TERA2


title: TERA_TSA_vs_mock


title: TERA_ATRA_vs_mock_2

data_processing: log2 Ratio of background subtracted ATRA intensity to background subtracted Mock treated intensity after loess normalization with Bioconductor

source_name: ATRA-treated TERA2

treatment_protocol: 2 micromolar all_trans retinoic acid for 12 days


title: TERA_Aza_vs_mock

data_processing: log2 Ratio of background subtracted Aza intensity to background subtracted Mock treated intensity after loess normalization with Bioconductor

source_name: Aza-treated TERA2

treatment_protocol: 5 micromolar Aza for 72 hours

source_name: mock-treated TERA2


title: ChIP_PC3_SUZ12

source_name: SUZ12-ChIP chromatin, Cy5

tag: PC3 cells, ChIP by SUZ12 antibody, LM-PCR amplified, 2.5ug


title: Nitrosomonas europaea_exposure to 3.4 uM ZnCl2_60min_biological rep1.


title: Nitrosomonas europaea_control condition_60min_biological rep2.

description: showed 100 % activity of nitrosomonas europaea, control condition(no inhibition), psuedo-steady state

source_name: N. europaea cultured in Batch reactor with 50 mM HEPES buffer, 60 min

growth_protocol: (NH4)2SO4 (5 mM) in 50 mM HEPES buffer, 700rpm, in gas-tight 1.67 L reactor vessels, no injection of zinc

treatment_protocol: No injection of zinc, 60min


title: TERA_Aza_vs_mock_2


title: Nitrosomonas europaea_control condition_60min_biological rep3.


title: 13483874 - 35S-DRV1 vs Col

hyb_protocol: Col Cy5 / 35S-DRV1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: TERA_ATRA_vs_mock

treatment_protocol: 2 micromolar All-trans retinoic acid for 12 days


title: Nitrosomonas europaea_control condition_60min_biological rep1.


title: ambient vs. ambient, o.rep2

status: Public on Oct 15 2007

city: Brisbane

first: Karin

middle: Sonja

last: Kassahn

state: QLD

address: Queensland Bioscience Precinct

department: Institute for Molecular Bioscience

country: Australia

institute: University of Queensland

description: Biological replicate 2 of 2

hyb_protocol: Prior to hybridisation, each microarray slide was immersed in distilled water at 60ºC for 5min and dried by centrifugation at 650 x g for 5min. The purified fluorescently labelled cDNA samples were mixed with 5µg human Cot-1 and 8µg poly A, dried under reduced pressure, resuspended in 14µl formamide and 14µl of 6.25 × SSC, denatured by heating to 100ºC for 3min and transferred directly to ice. Finally, 0.6µl of 10%(w/v) SDS was added to each sample. The probes were applied to the arrays and incubated at 42ºC overnight in a humidified chamber. The arrays were washed in 0.5 × SSC containing 0.01%(w/v) SDS for 1min, 0.5 × SSC for 3min and 0.2 × SSC for 3min.

scan_protocol: The slides were scanned using an Axon 4000B microarray scanner. Single image .tif files were saved for data analysis.

data_processing: Fluorescent signal intensities were extracted using SPOT software (CSIRO Mathematical and Information Sciences, Australia). The data were background corrected using the Spot morphological close/open method. Spot weights were calculated on the basis of the number of pixels in the spot, with spot areas between 30 and 300 pixels given full weight. The ratio of the resultant signal intensities (Cy5/Cy3) was log2-transformed. Statistical analyses were performed using the software package LIMMA, implemented in the R statistical software environment. The transformed signal intensities of each grid on the array and global signal intensity were print-tip Loess normalised, and scale normalised between arrays. 985 of the 16,897 array spots were excluded from analysis because these spots showed poor cross-hybridisation between P. moluccensis and the D. rerio microarray.

label: Alexa Fluor® 647

organism: Pomacentrus moluccensis

source_name: Total RNA from liver, ambient

label_protocol: Forty µg of total RNA were reverse transcribed and labelled using the SuperScript Plus Indirect cDNA Labeling System (Invitrogen) according to the manufacturer’s instructions. Both, oligo dT and random hexamers were used for priming of the reverse transcription reaction and Alexa Fluor® 555/647 dyes were used for labelling.

growth_protocol: Adult Pomacentrus moluccensis were collected around Lizard Island, northern Great Barrier Reef, Australia (14º40’S, 145º28’E) and housed in groups of up to 20 individuals in aquaria supplied with flow-through seawater at ambient temperature (approximately 28ºC). Sections of PVC pipes and dead branching coral were provided for shelter. After two days of acclimation to these conditions, animals were transferred to individual aquaria of 31ºC for five days or remained at ambient temperature (28ºC) for five days. We exposed additional P. moluccensis individuals to severe heat shock (34ºC), moderate heat shock (31ºC), cold shock (22ºC), hypoxia (23-36% air saturation), or hyposmotic conditions (20ppt salinity) for three hours.

extract_protocol: Total RNA from liver tissue of stressed P. moluccensis and P. moluccensis kept at ambient conditions was extracted using TRIzol® (Invitrogen) according to the manufacturer’s instructions and purified using RNeasy™ columns (Qiagen), ethanol-precipitated and subsequently resuspended in nuclease-free water. The concentration and purity of RNA was determined by spectrophotometer readings at 260 and 280nm. The integrity of the RNA was confirmed by agarose gel electrophoresis.

treatment_protocol: Hypoxic conditions were created by applying a constant flow of nitrogen to the tanks. Hyposmotic conditions were created by mixing seawater with distilled water, reducing the salinity of the seawater from 36ppt to 20ppt. On any one day, an equal number of fish were subjected to either one of the stress treatments or transferred to aquaria at ambient conditions, in order to provide time-matched controls.

tag: Sample ID

tag: Age

value: Adult

tag: Gender

value: Male

tag: Tissue

value: Liver

label: Alexa Fluor®555


title: ambient vs. ambient, n.rep2

description: Biological replicate 2 of 2


title: ambient vs. ambient, n.rep1

description: Biological replicate 1 of 2


title: hypoxic shock (~23-36% air saturatioin) vs. ambient, m.rep5

description: Biological replicate 5 of 6

source_name: Total RNA from liver, hypoxic shock, 23-36% air saturatioin, 3hrs


title: hypoxic shock (~23-36% air saturatioin) vs. ambient, m.rep6

description: Biological replicate 6 of 6


title: ambient vs. ambient, o.rep1

description: Biological replicate 1 of 2


title: hypoxic shock (~23-36% air saturatioin) vs. ambient, m.rep2

description: Biological replicate 2 of 6


title: hypoxic shock (~23-36% air saturatioin) vs. ambient, m.rep4

description: Biological replicate 4 of 6


title: hypoxic shock (~23-36% air saturatioin) vs. ambient, m.rep3

description: Biological replicate 3 of 6


title: heat shock (34C, 3hrs) vs. hypoxic shock (~23-36% air saturatioin, 3hrs), l.rep1

description: Biological replicate 1 of 3

source_name: Total RNA from liver, heat shock, 34C, 3hrs


title: heat shock (34C, 3hrs) vs. hypoxic shock (~23-36% air saturatioin, 3hrs), l.rep3

description: Biological replicate 3 of 3


title: hypoxic shock (~23-36% air saturatioin) vs. ambient, m.rep1

description: Biological replicate 1 of 6


title: hyposmotic shock (20ppt, 3hrs) vs. ambient, I.rep3

description: Biological replicate 3 of 6

source_name: Total RNA from liver, hyposmotic shock, 20ppt, 3hrs


title: heat shock (34C, 3hrs) vs. ambient, k.rep5

description: Biological replicate 5 of 5


title: heat shock (34C, 3hrs) vs. ambient, k.rep3

description: Biological replicate 3 of 5


title: heat shock (34C, 3hrs) vs. ambient, k.rep1

description: Biological replicate 1 of 5


title: hyposmotic shock (20ppt, 3hrs) vs. ambient, I.rep5

description: Biological replicate 5 of 6


title: cold shock (22C, 3hrs) vs. ambient, h.rep4

description: Biological replicate 4 of 4

source_name: Total RNA from liver, cold shock, 22C, 3hrs


title: heat shock (34C, 3hrs) vs. hypoxic shock (~23-36% air saturatioin, 3hrs), l.rep2

description: Biological replicate 2 of 3


title: heat shock (34C, 3hrs) vs. ambient, k.rep2

description: Biological replicate 2 of 5


title: hyposmotic shock (20ppt, 3hrs) vs. ambient, I.rep2

description: Biological replicate 2 of 6


title: hyposmotic shock (20ppt, 3hrs) vs. ambient, I.rep4

description: Biological replicate 4 of 6


title: hyposmotic shock (20ppt, 3hrs) vs. ambient, I.rep6

description: Biological replicate 6 of 6


title: heat shock (34C, 3hrs) vs. hyposmotic shock (20ppt, 3hrs), j.rep3

description: Biological replicate 3 of 3


title: hyposmotic shock (20ppt, 3hrs) vs. ambient, I.rep1

description: Biological replicate 1 of 6


title: heat shock (34C, 3hrs) vs. ambient, k.rep4

description: Biological replicate 4 of 5


title: cold shock (22C, 3hrs) vs. ambient, h.rep1

description: Biological replicate 1 of 4


title: heat shock (34C, 3hrs) vs. hyposmotic shock (20ppt, 3hrs), j.rep1

description: Biological replicate 1 of 3


title: heat shock (34C, 3hrs) vs. hyposmotic shock (20ppt, 3hrs), j.rep2

description: Biological replicate 2 of 3


title: cold shock (22C, 3hrs) vs. ambient, h.rep2

description: Biological replicate 2 of 4


title: heat shock (31C, 3hrs) vs. hypoxic shock (~23-36% air saturatioin, 3hrs), g.rep2

description: Biological replicate 2 of 2

source_name: Total RNA from liver, heat shock, 31C, 3hrs


title: heat shock (31C, 3hrs) vs. hypoxic shock (~23-36% air saturatioin, 3hrs), g.rep1

description: Biological replicate 1 of 2


title: heat shock (31C, 3hrs) vs. ambient, f.rep3

description: Biological replicate 3 of 4


title: ambient vs. ambient, e.rep2

description: Biological replicate 2 of 4


title: ambient vs. ambient, e.rep3

description: Biological replicate 3 of 4


title: heat shock (31C, 3hrs) vs. ambient, f.rep4

description: Biological replicate 4 of 4


title: ambient vs. ambient, e.rep4

description: Biological replicate 4 of 4


title: cold shock (22C, 3hrs) vs. ambient, h.rep3

description: Biological replicate 3 of 4


title: heat shock (31C, 3hrs) vs. heat shock (31C, 5days), c.rep2

description: Biological replicate 2 of 2

source_name: Total RNA from liver, heat shock, 31C, 5days


title: heat shock (31C, 3hrs) vs. ambient, f.rep1

description: Biological replicate 1 of 4


title: heat shock (31C, 5days) vs. ambient, d.rep2

description: Biological replicate 2 of 8


title: heat shock (31C, 5days) vs. ambient, d.rep1

description: Biological replicate 1 of 8


title: heat shock (31C, 3hrs) vs. ambient, f.rep2

description: Biological replicate 2 of 4


title: heat shock (31C, 3hrs) vs. cold shock (22C, 3hrs) , a.rep6

description: Biological replicate 6 of 6


title: heat shock (31C, 5days) vs. ambient, d.rep8

description: Biological replicate 8 of 8


title: heat shock (31C, 5days) vs. ambient, d.rep4

description: Biological replicate 4 of 8


title: heat shock (31C, 5days) vs. ambient, d.rep7

description: Biological replicate 7 of 8


title: ambient vs. ambient, e.rep1

description: Biological replicate 1 of 4


title: cold shock (22C, 3hrs) vs. hyposmotic shock (20ppt, 3hrs), b.rep1

description: Biological replicate 1 of 2


title: cold shock (22C, 3hrs) vs. hyposmotic shock (20ppt, 3hrs), b.rep2

description: Biological replicate 2 of 2


title: heat shock (31C, 5days) vs. ambient, d.rep5

description: Biological replicate 5 of 8


title: heat shock (31C, 3hrs) vs. cold shock (22C, 3hrs) , a.rep2

description: Biological replicate 2 of 6


title: heat shock (31C, 5days) vs. ambient, d.rep6

description: Biological replicate 6 of 8


title: heat shock (31C, 3hrs) vs. cold shock (22C, 3hrs) , a.rep3

description: Biological replicate 3 of 6


title: heat shock (31C, 3hrs) vs. cold shock (22C, 3hrs) , a.rep5

description: Biological replicate 5 of 6


title: heat shock (31C, 3hrs) vs. cold shock (22C, 3hrs) , a.rep4

description: Biological replicate 4 of 6


title: heat shock (31C, 3hrs) vs. heat shock (31C, 5days), c.rep1

description: Biological replicate 1 of 2


title: heat shock (31C, 5days) vs. ambient, d.rep3

description: Biological replicate 3 of 8


title: heat shock (31C, 3hrs) vs. cold shock (22C, 3hrs) , a.rep1

description: Biological replicate 1 of 6


title: RCC_G3_no-meta

status: Public on Oct 01 2007

city: Nagoya

first: Shinya

last: Toyokuni

state: Aichi

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

institute: Nagoya University

description: Original sample number: FB28-7

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Affymetrix GCOS 1.0, scaled to 100

organism: Rattus norvegicus

source_name: Renal cell carcinoma, enlarged nuclei, with no metastasis

label_protocol: standard Affymetrix protocol

extract_protocol: RNA was extracted using Isogen (Nippon Gene Co. Ltd., Tokyo).

tag: F1 from Fischer344 and Brown-Norway, male, Fe-NTA induced renal cell carcinoma, enlarged nuclei, with no metasiasis


title: RCC_G3_meta-lung

description: Original sample number: FB45-4

source_name: Renal cell carcinoma, enlarged nuclei, with metastasis to lung

tag: F1 from Fischer344 and Brown-Norway, male, Fe-NTA induced renal cell carcinoma, enlarged nuclei, with metastasis to lung


title: Kidney_Fe-NTA_3wk_1

description: Original sample number: YL1-4

source_name: Rat kidney, Fe-NTA 3wk

tag: Wistar, male, intraperitoneal injection of Fe-NTA for 3 weeks, kidney


title: RCC_G1_no-meta

description: Original sample number: FB48-5

source_name: Renal cell carcinoma, small nuclei, with no metastasis

tag: F1 from Fischer344 and Brown-Norway, male, Fe-NTA induced renal cell carcinoma, small nuclei, with no metasiasis


title: RCC_G2_meta-lung

description: Original sample number: FB7-7

source_name: Renal cell carcinoma, regular-sized nuclei, with metastasis to lung

tag: F1 from Fischer344 and Brown-Norway, male, Fe-NTA induced renal cell carcinoma, regular-sized nuclei, with metastasis to lung


title: whole ovary-0ppb TCDD-1

status: Public on Sep 01 2007

city: Milwaukee

first: Craig

last: Struble

state: WI

department: Math, Stat, and Comp Sci

institute: Marquette University

description: This study describes the molecular targets of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) within the zebrafish ovary and insights into TCDD’s ovarian toxicity. More details on the reproductive and physiological endpoints can be found in Toxicological Sciences 87(2) 497-507 (2005) and Toxicological Sciences 90(2) 490-499 (2006).

hyb_protocol: Biotin-labeled cRNAs were hybridized to the zebrafish genome array, washed, and stained with phycoerithrin conjugated to streptavidin (Molecular Probes, Eugene, OR) in accordance with standard Affymetrix protocols (Affymetrix, Santa Clara, CA).

scan_protocol: Scanned at 10µM using an Affymetrix scanner. Images were analyzed using Microarray Suite 5.0 (MAS5.0).

label: Biotin with streptavidin phycoerythrin

organism: Danio rerio

source_name: whole ovary 0ppb TCDD

label_protocol: First- and second-strand cDNA was synthesized from 15 µg pooled total RNA (3 µg from each of 5 females), and cRNA was synthesized, labeled and fragmented  in accordance with standard Affymetrix protocols (Affymetrix, Santa Clara, CA). Following hybridization biotin-labeled cRNAs were stained with phycoerithrin conjugated to streptavidin (Molecular Probes, Eugene, OR).

growth_protocol: Male and female zebrafish were housed separately, and acclimated prior to the initiation of experiments for several weeks at the UWM Marine and Freshwater Biomedical Sciences Center (Milwaukee, WI).  Fish were maintained at 26-28ºC on a 14-hour light and 10-hour dark cycle in a flow-through buffered, de-chlorinated water system of the UWM Great Lakes Wisconsin Aquaculture Technology and Environmental Research (WATER) Institute.  Fish were spawned once weekly during the experiment.  All experimental procedures were approved by the University of Wisconsin-Milwaukee Animal Care and Use Committee.

extract_protocol: Following 15 days of dietary exposure, five females from each treatment group were anesthetized in ice-cold water, and fish were killed by cervical spinal cord transection.  Using scissors and forceps cleaned with 0.5M NaOH to reduce RNase contamination, ovaries were removed and immediately frozen in liquid nitrogen and stored at -80C.  Total RNA was isolated from individual ovaries homogenized in Trizol reagent (Invitrogen) and further purified using an RNeasy MinElute cleanup kit (Qiagen) as per manufacturers’ protocols.  Samples were separated by electrophoresis and stained with ethidium bromide to confirm the integrity of the 18s and 28s ribosomal RNAs, and were quantified by UV spectrophotometry at 260nm using a Nanodrop ND-1000 Spectorphotometer (Nanodrop Technologies, Wilmington, DE).

treatment_protocol: The dietary exposure regimen was designed to expose adult female zebrafish to non-lethal concentrations of TCDD that would yield TCDD egg concentrations ranging from 0 – 13.5 ng TCDD/g egg, which are within the range expected to be toxic to embryos based on the LD50 of 2.5 ng TCDD/g egg (Elonen et al., 1998; Henry et al., 1997).  The nominal TCDD concentrations were chosen based on the desired target TCDD concentrations in the eggs following a protocol described by Tietge et al (1998).  Tritium-labeled TCDD was synthesized and purified to >99% by the manufacturer (Eagle-Picher, Lenexa, KS, specific activity 47 Ci/mmol).  Food yielding a final concentration of 272 ng 3H-TCDD/g food was prepared following a protocol described by Fernandez et al. (1998), with modifications.  In brief, the 3H-TCDD stock solution was diluted in acetone, added to trout chow ( Zeigler, Gardner, PA), swirled to ensure homogeneous distribution, and the acetone evaporated from the food in a fume hood overnight.  This food was then mixed with uncontaminated trout chow to achieve appropriate concentrations, which were confirmed by liquid scintillation counting to be 0 (acetone only), 10, 40, 100, and 270 ng 3H-TCDD/g food.

tag: Strain

value: AB

value: Female

value: 6-8 months

value: Whole Ovary


title: whole ovary-0ppb TCDD-2


title: Kidney_Fe-NTA_1wk_2

description: Original sample number: YL1-2

source_name: Rat kidney, Fe-NTA 1wk

tag: Wistar, male, intraperitoneal injection of Fe-NTA for 1 week, kidney


title: whole ovary-40ppb TCDD-1

source_name: whole ovary 40ppb TCDD


title: Kidney_Control_2

description: Original sample number: YL1-13

source_name: Rat kidney, normal

tag: Wistar, male, control (untreated), kidney


title: whole ovary-100ppb TCDD-1

source_name: whole ovary 100ppb TCDD


title: Kidney_Fe-NTA_3wk_2

description: Original sample number: YL1-5


title: whole ovary-10ppb TCDD-1

source_name: whole ovary 10ppb TCDD


title: whole ovary-40ppb TCDD-2


title: Kidney_Fe-NTA_1wk_1

description: Original sample number: YL1-1


title: mock-3

status: Public on Jul 30 2007

city: Tsukuba

first: Hiroshi

last: Takatsuji

state: Ibaraki

address: 2-1-2 Kannondai

department: Division of Plant Sciences

institute: National Institute of Agrobiological Sciences

description: 400 ng RNAs were labeled and 1µg Cy3-labeled cRNAs were used.

hyb_protocol: Agilent protocol G4140-90040

scan_protocol: Agilent scanner model G2505B, software G2565BA

data_processing: Data was analyzed by Fearure Extraction software (version 9.1, Agilent) and normalized by GeneSpringX

organism: Oryza sativa

source_name: leaf, mock-treated, 24 h

label_protocol: Low RNA inout Lineat Amplification/Labeling Lit (Agilent)

extract_protocol: RNeasy Plant Mini Kit (Qiagen)

tag: cultivar

value: Nipponbare,

tag: stage

tag: sample

value: 4th leaf

tag: mock-treated


title: whole ovary-100ppb TCDD-2

data_processing: MAS 5.0


title: Kidney_Control_1

description: Original sample number: YL1-12


title: mock-4


title: whole ovary-10ppb TCDD-2


title: BTH-4

source_name: leaf, BTH-treated, 24 h

tag: treated with 5 mM BTH


title: BTH-3


title: Gene expression profile in the cortex of mouse lens

status: Public on Aug 01 2007

city: Kyoto

first: Shigekazu

last: Nagata

address: Yoshida. Sakyo-ku

department: Department of Medical Chemistry

institute: Graduate School of Medicine, Kyoto University

description: Total RNA was prepared from the fetal liver using an ISOGEN RNA extraction kit (Nippon Gene), and poly(A) RNA was selected using an mRNA Purification Kit (Amersham Biosciences). The gene array analysis was carried out using a Uniset Mouse 20K Codelink Bioarray (Amersham Biosciences) that displays probe DNAs for about 20,000 mouse genes/ESTs. Double-stranded cDNA was prepared with RNA from the fetal livers of the wild-type mouse embryos (E14.5), and transcribed in vitro using biotin-labeled dUTP as a substrate. The complementary RNA was used as probe for hybridizing the array, and the hybridized RNA was detected with Cy5-conjugated streptavidin. The arrays were scanned using an arrayWoRx Biochip Reader (Applied Precision), and the array image was analyzed using CodeLinkTM System Software (Amersham Biosciences).

scan_protocol: Total RNA was prepared from the fetal liver using an ISOGEN RNA  The arrays were scanned using an arrayWoRx Biochip Reader (Applied Precision), and the array image was analyzed using CodeLinkTM System Software (Amersham Biosciences).

data_processing: Data were normalized by Spot-Based Median-Normalization

molecule: polyA RNA

source_name: Cortex of mouse lens

label_protocol: in vitro transcription using biotin-UTP as a substrate

extract_protocol: Total RNA was prepared using RNase Mini kit (Qiagen), and poly(A) RNA was selected using an mRNA Purification KIt (GE Healthcare Bioscience).

tag: Strain, C57BL/6, Age, 13 days; Tissue, cells in the lens cortex;


title: mock-1


title: RA, rep1, post-treatment

status: Public on Jul 07 2007

city: Cork

first: Fergal

last: O'Gara

address: College Road

department: Microbiology

country: Ireland

institute: University College Cork

description: RA, rep1, post-treatment. Rheumatoid Arthritis patient, rep1, post-treatment.

label: Biotin

source_name: RA, rep1, post-treatment


title: BTH-2


title: BTH-1


title: Gene expression profile in the epithelium of mouse eye lens

hyb_protocol: The complementary RNA was used as probe for hybridizing the array, and the hybridized RNA was detected with Cy5-conjugated streptavidin.

source_name: Epithelium of mouse lens

tag: Strain, C57/BL6; Age, 13 days; Tissue, cells in the lens epithelium


title: mock-2


title: RA, rep2, post-treatment.

description: RA, rep2, post-treatment. Rheumatoid Arthritis patient, rep2, post-treatment.

source_name: RA, rep2, post-treatment.


title: HepG2 FA2

status: Public on Jul 01 2007

city: Charleston

first: Stephen

middle: A

last: Duncan

state: SC

address: 173 Ashley Avenue, BSB 6th Floor, Room 657A

department: Regenerative Medicine and Cell Biology

institute: Medical University South Carolina

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: D-Chip, PM/MM model with defaults

source_name: HepG2 cells

label_protocol: Affymetrix kit

extract_protocol: Rneasy kit

tag: HepG2 cells with stable lentiviral knockdown of JAM-A


title: F11rA2

tag: HepG2 cells stably transduced with lentiviral JAM-A knockdown


title: RA, rep2, pre-treatment.

description: RA, rep2, pre-treatment. Rheumatoid Arthritis patient, rep2, pre-treatment.

source_name: RA, rep2, pre-treatment.


title: HepG2 Vector

tag: HepG2 cells with stable lentiviral empty vector


title: NormalControl, rep1

description: NormalControl, rep1. Non-Rheumatoid Arthritis patient, rep1.

source_name: NormalControl, rep1


title: HepG2 FA4

source_name: HepG2 Cells

tag: HepG2 cells stably transduced with lentiviral knockdown of JAM-A


title: Vector2

tag: HepG2 cells stably transduced with empty lentiviral vector


title: NormalControl,rep2

description: NormalControl, rep2. Non-Rheumatoid Arthritis patient, rep2.

tag: Non-Rheumatoid Arthritis patient, rep2.


title: HepG2 V3 U133A


title: HepG2 FA


title: HepG2 V4


title: HepG2 FA5


title: RA, rep1, pre-treatment

description: RA, rep1, pre-treatment. Rheumatoid Arthritis patient, rep1, pre-treatment.

source_name: RA, rep1, pre-treatment


title: aedes_aegypti_hemolymph-mlut-1hr-br1-tr1

city: Madison

first: Bruce

middle: M

last: Christensen

address: 1656 Linden Drive

department: Pathobiological Sciences

institute: University of Wisconsin-Madison

description: Biological replicate 1, Technical replicate 1

hyb_protocol: Slides were prehybridized using the reagents from the Corning/Pronto Hybridization Kit (Corning P/N:40026). A target of 50pmoles per label was suspended in Pronto hybridization buffer and deposited on a 24x60mm cover slip.  A prepared slide was lowered onto the cover slip and then placed into a Corning hybridization chamber and incubated in a level water bath at 42 degrees C overnight (14-16 hours).

scan_protocol: Slides were washed using reagents from the Corning/Pronto Hybridization Kit (Corning P/N:40026) and dried via centrifugation at 2400rpm (NEED G-force) for 2 minutes.  Slides were then scanned in an Axon 4000B scanner at 635nm and 532nm.  PMT voltages were adjusted to balance fluorescence in each channel.  Intensity values were exported as GPR files.

data_processing: Sample values were generated using the DNMAD software from the GEPAS (Gene Expression Pattern Analysis Suite) website at CNIO (Centro Nacional de Investigaciones Oncologicas).

organism: Aedes aegypti

source_name: Perfused hemolymph, 1 hour post inoculation with approximately 500,000 bacteria from an overnight culture of M. luteus.

growth_protocol: Mosquitoes were maintained as described in Bartholomay, et. al., 2004 (PMID:15213157)

extract_protocol: RNA was purified from hemolymph tissue as described by Chomczynski and Sacchi, 1987 (PMID:2440339)

treatment_protocol: Bacteria were inoculated and hemolymph material extracted 1 hour post-inoculation, as described in as described in Bartholomay, et. al., 2004 (PMID:15213157).

tag: Species

value: Aedes aegypti, Strain:Liverpool. Sex:Females, Age:2-3 days, Tissue:hemolymph

source_name: perfused hemolymph from naïve adult females

label_protocol: Purified total RNA was labeled using the Amersham CyScribe cDNA post-labeling kit (P/N:RPN5660).  Labeled cDNA was purified with Amersham GFX columns (P/N:27-9606-02) and quantified via absorbance.

treatment_protocol: Hemolymph material was extracted from naïve mosquitoes as described in as described in Bartholomay, et. al., 2004 (PMID:15213157).

value: Aedes aegypti, Strain:Liverpool. Sex:Females, Age:, Tissue:hemolymph


title: aedes_aegypti_hemolymph-mlut-1hr-br2-tr1

description: Biological replicate 2, Technical replicate 1

label_protocol: Purified total RNA was labeled using the Amersham CyScribe cDNA post-labeling kit (P/N:RPN5660).  Labeled cDNA was purified with Amersham GFX columns (P/N:27-9606-02)


title: aedes_aegypti_hemolymph-mlut-8hr-br1-tr1-ds

description: Biological replicate 1, Technical replicate 1 Dye-Swap

source_name: Perfused hemolymph, 8 hours post inoculation with approximately 500,000 bacteria from an overnight culture of M. luteus

treatment_protocol: Bacteria were inoculated and hemolymph material extracted 8 hours post-inoculation, as described in as described in Bartholomay, et. al., 2004 (PMID:15213157).


title: aedes_aegypti_hemolymph-mlut-8hr-br1-tr2-ds

description: Biological replicate 1, Technical replicate 2 Dye-Swap


title: aedes_aegypti_hemolymph-mlut-1hr-br1-tr2

description: Biological replicate 1, Technical replicate 2


title: aedes_aegypti_hemolymph-ecoli-1hr-br1-tr1

source_name: Perfused hemolymph, 1 hour post inoculation with approximately 500,000 bacteria from an overnight culture of E. coli, MG1655.


title: aedes_aegypti_hemolymph-ecoli-8hr-br1-tr2-ds

description: Biological replicate 1, Technical replicate 2, Dye-Swap

source_name: Perfused hemolymph, 8 hours post inoculation with approximately 500,000 bacteria from an overnight culture of E. coli, MG1655.


title: NHM2-E6_GEO

city: Morrisville

first: Tong

last: Zhou

state: NC

address: 133 Southcenter Court, Suite 400

department: Clincial Genetics

institute: Gentris Corperation

description: The gene expression level was presented as ratio of sample intensity against reference intensity.

hyb_protocol: The Cy3- and Cy5-labeled samples were quantified, combined and then hybridized overnight at 65°C to a  44,000 element human genome 60mer oligonucleotide microarray (G4112A, Agilent Technologies, Palo Alto, CA).

scan_protocol: Arrays were scanned using a GenePix 4000B scanner (Axon Instruments, Foster City, CA).

data_processing: Images were gridded and quantified using GenePix Pro 5.1 software (Molecular Devices Corp, Sunnyvale, CA). Significance analysis of microarrays (SAM)  and Bayesian statistical theory was also applied to identify signifcant genes.

source_name: reference RNA

label_protocol: 1 µg of global reference RNA (Stratagene) was converted to cDNA with reverse transcriptase then amplified using T7 RNA polymerase while labeling with Cy3-dUTP (Agilent’s Low RNA Input Linear Amplification Kit). The quality of each labeled cRNA was evaluated using an Agilent 2100 Bioanalyzer prior to hybridization.

extract_protocol: Stratagene protocol for preparation of reference RNA

tag: global reference RNA

source_name: Sample RNA

label_protocol: 1 µg of sample RNA was converted to cDNA with reverse transcriptase then amplified using T7 RNA polymerase while labeling with Cy5-dUTP (Agilent’s Low RNA Input Linear Amplification Kit). The quality of each labeled cRNA was evaluated using an Agilent 2100 Bioanalyzer prior to hybridization.

growth_protocol: Cells were cultured in Medium 254 containing PMA-free Human Melanocyte Growth Supplement (HMGS-2; Cascade Biologics, Portland, OR).

extract_protocol: Qiagen RNeasy kit

treatment_protocol: Expression of  HPV16E6 by retroviral gene transfer

tag: Melanoma cell line


title: aedes_aegypti_hemolymph-ecoli-1hr-br2-tr1-ds

description: Biological replicate 2, Technical replicate 1, Dye-Swap

source_name: Perfused hemolymph from naïve adult females


title: aedes_aegypti_hemolymph-ecoli-1hr-br1-tr2


title: aedes_aegypti_hemolymph-ecoli-8hr-br1-tr1-ds

description: Biological replicate 1, Technical replicate 1, Dye-Swap


title: HPV18-positive Hela cell line, siRNA 18E6E7 mediated knockdown_dyeswap_rep2

city: Heidelberg

first: Ruprecht

last: Kuner

address: Im Neuenheimer Feld 460

department: Molecular Genetics

country: Germany

institute: German Cancer Research Center and National Center of Tumor Diseases

description: siRNA18E6E7_DKFZ Replicate 2_dyeswap

hyb_protocol: ch1 and ch2 together are solved in 50 µl 1x DIG-Easy hybridization buffer (Roche Diagnostics, Mannheim, Germany), containing 10x Denhardt’s solution and 2 ng/µl Cot1-DNA (Invitrogen); sample was denaturated at 65°C for 2min, hybridzation of arrays were performed in Corning chambers 14h at 37°C; slides were washed twice in 1xSSC+0.1SDS and once in 0.1xSSC+ 0.1SDS before air pressure drying and scanning.

scan_protocol: arrays were scanned with the GenePix 4000B microarray scanner and analyzed using GenePix Pro 4.1 software (Axon Instruments)

data_processing: raw data processing was performed using ArrayMagic (Buness et al., 2005) including VSN normalization method; after removal of bad quality clones, generalized log ratios from 26629 cDNA clones were given in the data table

source_name: cell line Hela siRNA siControl Rep2

label_protocol: direct fluorescent labelling of 2 µg amplified RNA, anneling of 0.5µg Random Primer and reverse-transcribed into cDNA with Superscript III reverse transcriptase for 1h at 42°C in the presence of 0.4 mM dGTP, 0.4 mM dATP, 0.4 mM dTTP, 0.24 mM dCTP, 0.125 mM Cy3-dCTP. After hydrolysis of RNA in 0.2 M NaOH, Cy3-labeled probes were purified with Microcon YM-30 column.

growth_protocol: cells were cultivated in Dulbecco’s minimal essential medium (D-MEM, pH 7,2, Gibco BRL, Gaithersburg, MD, USA), supplemented with 10 % fetal calf serum (FCS), 50 U/ml penicillin, and 50 µg/ml streptomycin sulfate

extract_protocol: total RNA was extracted using the acid guanidinium thiocyanate-phenol-chloroform method (Chomczynski and Sacchi, 1987); 2µg total RNA was amplified one round based on T7 RNA Polymerase (Agilent low RNA Input Amplification Kit) according to the manufacturer’s instructions

treatment_protocol: Synthetic siRNAs (Dharmacon Research, Lafayette, USA) were transfected with Oligofectamine (Invitrogen, Karlsruhe, Germany)

tag: siRNA siControl, target sequence 5’-UAGCGACUAAACACAUCAA-3’ (Dharmacon Research, Lafayette, USA), cell culture replicate 2

source_name: cell line Hela siRNA 18E6E7_3.5 Rep2

tag: construct siRNA 18E6E7_3.5, target sequence 5’-CCACAACGUCACACAAUGU-3’ (HPV18 nt 755-773), cell culture replicate 2


title: HPV18-positive Hela cell line, siRNA 18E6E7 mediated knockdown_dyeswap_rep1

description: siRNA18E6E7_DKFZ Replicate 1_dyeswap

source_name: cell line Hela siRNA siControl Rep1

tag: siRNA siControl, target sequence 5’-UAGCGACUAAACACAUCAA-3’ (Dharmacon Research, Lafayette, USA), cell culture replicate 1

source_name: cell line Hela siRNA 18E6E7_3.5 Rep1

tag: construct siRNA 18E6E7_3.5, target sequence 5’-CCACAACGUCACACAAUGU-3’ (HPV18 nt 755-773), cell culture replicate 1


title: aedes_aegypti_hemolymph-mlut-1hr-br2-tr2

description: Biological replicate 2, Technical replicate 2


title: HPV18-positive Hela cell line, siRNA 18E6E7 mediated knockdown_rep2

description: siRNA18E6E7_DKFZ Replicate 2


title: HPV18-positive Hela cell line, siRNA 18E6E7 mediated knockdown_rep3

description: siRNA18E6E7_DKFZ Replicate 3

source_name: cell line Hela siRNA 18E6E7_3.5 Rep3

tag: construct siRNA 18E6E7_3.5, target sequence 5’-CCACAACGUCACACAAUGU-3’ (HPV18 nt 755-773), cell culture replicate 3

source_name: cell line Hela siRNA siControl Rep3

tag: siRNA siControl, target sequence 5’-UAGCGACUAAACACAUCAA-3’ (Dharmacon Research, Lafayette, USA), cell culture replicate 3


title: HPV18-positive Hela cell line, siRNA 18E6E7 mediated knockdown_dyeswap_rep3

description: siRNA18E6E7_DKFZ Replicate 3_dyeswap


title: WT_Mel8322_GEO

growth_protocol: Cells were cultured in PRMI 1640 (Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS, Sigma Chemical Co, St. Louis, MO, USA) and pen/strep.

treatment_protocol: wild type in B-raf and N-ras


title: WT_PMWK_GEO

growth_protocol: Cells were cultured in MEM  (Invitrogen, Carlsbad, CA, USA) supplemented with 0.5 x Non-essentail Amino Acids, 10% fetal bovine serum (FBS, Sigma Chemical Co, St. Louis, MO, USA) and pen/strep.


title: WT_SKMel187_GEO

growth_protocol: Cell were cultured in DMEM high-glucose medium (Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS, Sigma Chemical Co, St. Louis, MO, USA) and pen/strep.


title: N-ras_SKMel147_GEO

treatment_protocol: N-ras mutation


title: N-ras_SKMel119_GEO


title: NHM2-179(p53)_GEO

treatment_protocol: Expression of a dominant-negative p53 allele (p53H179Q) by retroviral gene transfer

tag: Normal human melanocyte


title: N-ras_SKMel103_GEO


title: N-ras_SKMel173_GEO


title: N-ras_Mel224_GEO


title: WT_Mel505_GEO


title: NHM5_GEO

treatment_protocol: Normal cells


title: N-ras_VMM39_GEO


title: HPV18-positive Hela cell line, siRNA 18E6E7 mediated knockdown_rep1

description: siRNA18E6E7_DKFZ Replicate 1


title: NHM4_GEO

growth_protocol: cells were cultured in Medium 254 containing PMA-free Human Melanocyte Growth Supplement (HMGS-2; Cascade Biologics, Portland, OR).


title: B-raf_SKMel257_GEO

treatment_protocol: B-raf mutation


title: NHM1_GEO


title: NHM3_GEO


title: NHM2_GEO


title: B-raf_SKMel28_GEO


title: B-raf_SKMel24_GEO


title: B-raf_A2058_GEO

growth_protocol: Cells were cultured in DMEM high-glucose medium (Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS, Sigma Chemical Co, St. Louis, MO, USA) and pen/strep.


title: aedes_aegypti_hemolymph-mlut-8hr-br3-tr1

description: Biological replicate 3, Technical replicate 1


title: aedes_aegypti_hemolymph-mlut-8hr-br2-tr1


title: aedes_aegypti_hemolymph-mlut-8hr-br4-tr1

description: Biological replicate 4, Technical replicate 1


title: B-raf_A375_GEO


title: aedes_aegypti_hemolymph-mlut-8hr-br4-tr2

description: Biological replicate 4, Technical replicate 2


title: aedes_aegypti_hemolymph-mlut-24hr-br4-tr1

treatment_protocol: Bacteria were inoculated and hemolymph material extracted 24 hours post-inoculation, as described in as described in Bartholomay, et. al., 2004 (PMID:15213157).


title: aedes_aegypti_hemolymph-mlut-8hr-br3-tr2-ds

description: Biological replicate 3, Technical replicate 2, Dye-Swap

source_name: Perfused hemolymph, 8 hours post inoculation with approximately 500,000 bacteria from an overnight culture of M. luteus.


title: aedes_aegypti_hemolymph-mlut-24hr-br3-tr1


title: aedes_aegypti_hemolymph-mlut-24hr-br3-tr2

description: Biological replicate 3, Technical replicate 2


title: aedes_aegypti_hemolymph-mlut-8hr-br2-tr2


title: aedes_aegypti_hemolymph-mlut-1hr-br4-tr1


title: aedes_aegypti_hemolymph-mlut-24hr-br1-tr2


title: aedes_aegypti_hemolymph-mlut-24hr-br4-tr2


title: aedes_aegypti_hemolymph-mlut-1hr-br3-tr1


title: aedes_aegypti_hemolymph-mlut-1hr-br3-tr2


title: aedes_aegypti_hemolymph-mlut-24hr-br2-tr2


title: aedes_aegypti_hemolymph-mlut-24hr-br1-tr2-rpt

description: Biological replicate 1, Technical replicate 2, Technical repetition


title: aedes_aegypti_hemolymph-mlut-24hr-br2-tr1


title: aedes_aegypti_hemolymph-mlut-24hr-br1-tr1


title: aedes_aegypti_hemolymph-ecoli-8hr-br4-tr1


title: aedes_aegypti_hemolymph-ecoli-8hr-br3-tr2-ds


title: aedes_aegypti_hemolymph-ecoli-8hr-br3-tr1


title: aedes_aegypti_hemolymph-ecoli-8hr-br4-tr2


title: aedes_aegypti_hemolymph-ecoli-24hr-br2-tr1

source_name: Perfused hemolymph, 24 hours post inoculation with approximately 500,000 bacteria from an overnight culture of E. coli, MG1655.


title: aedes_aegypti_hemolymph-ecoli-24hr-br3-tr1


title: aedes_aegypti_hemolymph-mlut-1hr-br4-tr2


title: aedes_aegypti_hemolymph-ecoli-24hr-br1-tr1


title: aedes_aegypti_hemolymph-ecoli-24hr-br4-tr1


title: aedes_aegypti_hemolymph-ecoli-24hr-br1-tr2


title: aedes_aegypti_hemolymph-ecoli-24hr-br2-tr2


title: aedes_aegypti_hemolymph-ecoli-8hr-br2-tr2


title: B-raf_WM2644_GEO


title: aedes_aegypti_hemolymph-ecoli-24hr-br4-tr2


title: aedes_aegypti_hemolymph-ecoli-24hr-br1-tr2-rpt


title: aedes_aegypti_hemolymph-ecoli-1hr-br4-tr1


title: aedes_aegypti_hemolymph-ecoli-8hr-br2-tr1


title: imaginal discs

status: Public on Jun 10 2007

type: other

city: San Francisco

first: James

middle: Graham

last: Ruby

address: 1700 4th Street QB3 s404

department: Biochemistry

institute: UCSF

description: small RNAs

data_processing: extraction of sequences flanked by perfect 9mer matches to the expected adjacent adapter sequences

molecule: other

organism: Drosophila melanogaster

source_name: Drosophila melanogaster imaginal discs

extract_protocol: total RNA, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

tag: imaginal discs


title: aedes_aegypti_hemolymph-ecoli-1hr-br5-tr2

description: Biological replicate 5, Technical replicate 2


title: aedes_aegypti_hemolymph-ecoli-1hr-br3-tr1


title: aedes_aegypti_hemolymph-ecoli-1hr-br4-tr2


title: aedes_aegypti_hemolymph-ecoli-1hr-br3-tr2


title: tissue culture cells (S2 only)

description: small RNAs

source_name: Drosophila melanogaster tissue culture cells (S2 only)

tag: tissue culture cells (S2 only)


title: aedes_aegypti_hemolymph-ecoli-1hr-br5-tr1

description: Biological replicate 5, Technical replicate 1

source_name: perfused hemolymph from naïve adult females


title: aedes_aegypti_hemolymph-ecoli-1hr-br2-tr2-ds

description: Biological replicate 2, Technical replicate 2, Dye-Swap


title: pupae: 0-1 day, 0-2 day, 2-4 day

description: small RNAs

source_name: Drosophila melanogaster pupae: 0-1 day, 0-2 day, 2-4 day

tag: pupae


title: larvae: 1st instar and 3rd instars

description: small RNAs

source_name: Drosophila melanogaster larvae: 1st instar and 3rd instars

tag: larvae

value: 1st instar and 3rd instars


title: late embryo (12-24)

description: small RNAs

source_name: Drosophila melanogaster late embryo (12-24)

tag: late embryo (12-24)


title: HUC infected by Enterococcus faecalis, 10 hours post infection

city: Oklahoma City

first: Robert

middle: Evan

last: Hurst

state: OK

address: 920 S. L. Young Blvd

department: Urology

institute: Oklahoma University Health Sciences Center

description: Details about microarray handling/processing techniques can be obtained from platform’s manufacturer.

hyb_protocol: Ventana Discovery 9h, 58 C washed to 0.1xSSC

scan_protocol: scanned on Agilient G2505B scanner Imagene 5.0

data_processing: Data were normalized as was described previously in Dozmorov I et al., Nucleic Acids Res. 2004 Oct 28;32(19). In general, intensities were converted to expression and normalized to low-expressed genes, which provide possible technical noise level. “Control” and “Blank” spots were excluded prior normalization to exclude part of technical noise. The arrays are then adjusted to each other by robust linear regression and this data presented for each sample. Group of low-expressed genes is  selected by normal distribution fitting. This group provides internal standard of measurement noise (ISMN). Genes above 3SD from mean of ISMN were selected as hypervariable yielding 1409 genes. Further filtering by gene variability across time points was done, sorting out genes with standard deviation less than 0.2. This produced 239 genes.

source_name: HUC infected by Enterococcus faecalis

label_protocol: Omniscript reverse-transcriptase, 37 C, 2 hrs

growth_protocol: Cells were grown for 7 days in Ham's F-12 medium containing 10% FCS changed every 2 or 3 days.  At day 6, cells were trypsinized from one membrane to obtain a cell number so that the concentration of Enterococcus bacteria would have a multiplicity of infection (MOI) of 10.  W32944 strain of Enterococcus was layered onto each Huc-BC/SIS membrane and incubations of  0 minutes, 30 minutes, 60 minutes, 90 minutes, 2 hours, 4 hours, 6 hours, 8 hours, 10 hours, and 24 hours were carried out at 37° C in a 5% CO2 incubator.

extract_protocol: RNA was isolated at each time point with RNAeasy kit (QIAGEN Inc.,Valencia, CA) according to manufacturer’s protocol.

treatment_protocol: Small intestine submucosa (SIS) membranes encased in plastic inserts (Cook Biotech, West Lafayette, IN) were equilibrated with 3 washes of Hanks Balanced Salt Solution (Invitrogen – Gibco, Carlsbad, CA).  After washing,  the SIS inserts were incubated in Ham’s F12 ( Invitrogen – Gibco, Carlsbad, CA) with 10% FCS (Invitrogen – Gibco, Carlsbad, CA) for at least 3 hours before cells were placed on membranes. Each SIS insert was placed in an individual well of a 6-well plate (BD Falcon, Bedford, MA) with care taken to ensure air is not captured under the membrane and full contact with the Ham’s F-12 media is made.  All but 2.5 ml of the media removed as well as the media on top of the membrane itself.  GFP expressing HUC–BC cells were typsinized and brought up in media at a concentration of 150,000 cells/50µl.  50µl seeded  onto a membrane surface with area of 50.3 mm2, This cell number is sufficient to cover the membrane with a monolayer of cells and volume enough to keep cells within the membrane insert.

tag: The SV40-immortalized human urothelial cell line HUC-BC (ATCC) was infected with the retrovirus pLEGFP (Clontech, Mountain View, CA) and cells stably expressing  green fluorescent protein (GFP) were selected with flow cytometry.


title: HUC infected by Enterococcus faecalis, 8 hours post infection


title: HUC infected by Enterococcus faecalis, 6 hours post infection


title: mid embryo (6-10)

description: small RNAs

source_name: Drosophila melanogaster mid embryo (6-10)

tag: mid embryo (6-10)


title: HUC infected by Enterococcus faecalis, 1 hour post infection


title: HUC infected by Enterococcus faecalis, 4 hours post infection

source_name: infected by Enterococcus faecalis


title: HUC infected by Enterococcus faecalis, 1.5 hours post infection


description: small RNAs

source_name: Drosophila melanogaster adult bodies (female bodies, male bodies)


title: early embryo (2-6)

description: small RNAs

source_name: Drosophila melanogaster early embryo (2-6)

tag: early embryo (2-6)


title: HUC infected by Enterococcus faecalis, 0 hours post infection


title: adult heads (female heads, male heads)

description: small RNAs

source_name: Drosophila melanogaster adult heads (female heads, male heads)

tag: adult heads (female heads, male heads)


title: very early embryo (0-1)

description: small RNAs

source_name: Drosophila melanogaster very early embryo (0-1)

tag: very early embryo (0-1)


title: Control day 05 sample 1

status: Public on Jun 01 2007

city: Zeist

first: Ashwin

last: Dihal

address: Utrechtseweg 48

department: Business Unit Physiologival Sciences

country: Netherlands

institute: TNO Quality of Life

description: Probe sets with an “absent call” (P ≥ 0.065 for HG-U133A 2.0 GeneChip® arrays) across all 8 arrays (n = 7,285) were considered not to be affected by quercetin treatment and/or incubation time and were therefore excluded from further analyses

hyb_protocol: Hybridization protocol according to Affymetrix® GeneChip® Expression Analysis Technical Manual

scan_protocol: Scan protocol with GeneChip® Scanner 3000 7G, according to Affymetrix® GeneChip® Expression Analysis Technical Manual

data_processing: CEL files were imported in Rosetta Resolver 5.0 (Rosetta Inpharmatics LLC, Seattle, U.S.A.), applying data pre-processing (to estimate and reduce systematic errors) and error modeling (for improvement of accuracy of the present and absent calls for low replicate numbers).

source_name: Human colon cancer cell line Caco-2

label_protocol: Labeling protocol according to Affymetrix® GeneChip® Expression Analysis Technical Manual

growth_protocol: Caco-2 cells of passage 37 were seeded (1 : 10 split ratio) in triplicate on polycarbonate membrane transwell® inserts (Corning Life Sciences, Cambridge, U.K.), with a membrane diameter of 75 mm (growth area 44 cm2, 0.4 µm pore size) at a density of approx. 40,000 cells/cm2. After 2 days, cell cultures reached confluency, and this time point was considered experimental day 0 and the initial exposure to quercetin. Cells were exposed for a total number of 9 days

extract_protocol: On days 5 and 10 post-confluency, cells were first rinsed with ice cold phosphate buffered saline without calcium or magnesium (InvitrogenTM Life Technologies, Breda, The Netherlands). Subsequently, cells were harvested in 2 x 0.75 ml of ice-cold TRIzol (Life Technologies, Paisley, U.K.), immediately frozen in liquid nitrogen and stored at -80°C for up to 2 months, until RNA isolation according to the TRIzol protocol. Following isolation, total RNA was purified with RNeasy Midi columns (QIAGEN, Westburg, Leusden, The Netherlands), including a DNAse incubation step. Quality of purified total RNA was determined on a UV-VIS spectrofotometer (Shimadzu Benelux, ‘s Hertogenbosch, The Netherlands) by calculation of the A260/A280 ratio (1.7 - 2.0) and confirmed on a Lab-on-a-Chip on the Agilent 2100 bioanalyser (Agilent Technologies, Palo Alto, California, U.S.A.) by determining the 28S/18S ribosomal RNA ratio

treatment_protocol: Dulbecco’s Modified Eagle Medium supplemented with 10% (v/v) heat inactivated mycoplasma tested fetal calf serum, 2 mM L-glutamine (6 mM final concentration), 1% (v/v) MEM non-essential amino acids and 50 µg/ml gentamicin. As quercetin in DMEM culture medium was stabilized by 1 mM ascorbate, control cells were exposed to 1mM ascorbate-only

tag: The Caco-2 cell line is derived from a male Caucasian with a colon tumor


title: Quercetin day 05 sample 2

treatment_protocol: Dulbecco’s Modified Eagle Medium supplemented with 10% (v/v) heat inactivated mycoplasma tested fetal calf serum, 2 mM L-glutamine (6 mM final concentration), 1% (v/v) MEM non-essential amino acids and 50 µg/ml gentamicin. Quercetin in DMEM culture medium was stabilized by 1 mM ascorbate


title: Quercetin day 05 sample 1

description: Probe sets with an “absent call” (P ≥ 0.065 for HG-U133A 2.0 GeneChip® arrays) across all 8 arrays (n = 7,285) were considered not to be affected by quercetin treatment and/or incubation time and were therefore excluded from further analyses.

growth_protocol: Caco-2 cells of passage 37 were seeded (1 : 10 split ratio) in triplicate on polycarbonate membrane transwell® inserts (Corning Life Sciences, Cambridge, U.K.), with a membrane diameter of 75 mm (growth area 44 cm2, 0.4 µm pore size) at a density of approx. 40,000 cells/cm2. After 2 days, cell cultures reached confluency, and this time point was considered experimental day 0 and the initial exposure to quercetin. Cells were exposed for a total number of 9 days.


title: Control day 10 sample 1

treatment_protocol: Dulbecco’s Modified Eagle Medium supplemented with 10% (v/v) heat inactivated mycoplasma tested fetal calf serum, 2 mM L-glutamine (6 mM final concentration), 1% (v/v) MEM non-essential amino acids and 50 µg/ml gentamicin. As quercetin in DMEM culture medium was stabilized by 1 mM ascorbate, control cells were exposed to 1 mM ascorbate-only


title: Control day 10 sample 2


title: HUC infected by Enterococcus faecalis, 0.5 hours post infection


title: Quercetin day 10 sample 2


title: Quercetin day 10 sample 1


title: Control day 05 sample 2


title: autism with FMR1-FM AU039305

city: Los Angeles

first: Yuhei

last: Nishimura

address: 2309 Gonda 695 Charles E Young Dr. South

department: Neuropsychiatric Institute

institute: University of California Los Angeles

hyb_protocol: The generated cRNAs were mixed and subjected to hybridization to the Agilent Whole Human Genome Array G4112A according to the manufacture's protocol.

scan_protocol: Scanning of the microarray was done by Agilent DNA microarray scanner.

data_processing: Scanner output image file was normalized and filtered using Feature Extraction Software ver 8.5. Normalization was performed so that overall intensity ratio of Cy5 to Cy3 was equal to one.

source_name: pool

label_protocol: cRNA synthesis was performed using a Low RNA Input Fluorescent Linear Amplification Kit (Agilent) according to the manufacture's protocol.

growth_protocol: A total of 9x10(6) of lymphoblastoid cells were seeded in a T75 flask in 30 ml of fresh medium. Medium was RPMI1640 with 2 mM L glutamine and 25 mM HEPES and 10 percent fetal bovine serum and 1x Anitbiotic Antimicotic solution. After 24 hours total RNA was extracted.

extract_protocol: Total RNA was extracted from lymphoblastoid cells of 14 individuals using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

tag: Pooled total RNAs from lymphoblastoid cells of 14 individuals

source_name: Autism with FMR1-FM AU039305

label_protocol: Target preparation was performed using a Low RNA Input Fluorescent Linear Amplification Kit (Agilent) according to the manufacture's protocol.

extract_protocol: Total RNA was extracted from lymphoblastoid cells of AU039305 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

tag: AU039305 is a male with autism and full mutation of FMR1.


title: autism with FMR1-FM AU046703

source_name: Autism with FMR1-FM AU046703

extract_protocol: Total RNA was extracted from lymphoblastoid cells of AU046703 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

tag: AU046703 is a male with autism and full mutation of FMR1.


title: autism with dup(15q) AU010604

source_name: Autism with dup(15q) AU010604

extract_protocol: Total RNA was extracted from lymphoblastoid cells of AU010604 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

tag: AU010604 is a male with autism and duplication of 15q11-13.


title: control AU1348302

source_name: control AU1348302

extract_protocol: Total RNA was extracted from lymphoblastoid cells of AU1348302 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

tag: AU1348302 is a control male without autism.


title: autism with FMR1-FM AU066704

source_name: Autism with FMR1-FM AU066704

extract_protocol: Total RNA was extracted from lymphoblastoid cells of AU066704 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

tag: AU066704 is a male with autism and full mutation of FMR1.


title: control AU081206

source_name: control AU081206

extract_protocol: Total RNA was extracted from lymphoblastoid cells of AU081206 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

tag: AU081206 is a control male without autism.


title: control AU055103

source_name: control AU055103

extract_protocol: Total RNA was extracted from lymphoblastoid cells of AU055103 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

tag: AU055103 is a control male without autism.


title: control AU016804

source_name: control AU016804

extract_protocol: Total RNA was extracted from lymphoblastoid cells of AU016804 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

tag: AU016804 is a control male without autism.


title: control AU0943303

source_name: control AU0943303

extract_protocol: Total RNA was extracted from lymphoblastoid cells of AU0943303 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

tag: AU0943303 is a control male without autism.


title: control AU060003

source_name: control AU060003

extract_protocol: Total RNA was extracted from lymphoblastoid cells of AU060003 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

tag: AU060003 is a control male without autism.


title: HSC_12Months_p53m_A

city: Houston

first: Stuart

last: Chambers

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

description: LT-Hematopoietic stem cell isolated by flow cytometry

hyb_protocol: Standard protocol from manufacturer (Affymetrix)

scan_protocol: Hardware: GeneChip¨ Scanner 3000

data_processing: Normalization was done with the GCRMA package from Bioconductor

source_name: Hematopoietic stem cells from p53+/m mice

label_protocol: Second round of MessageAmp(Ambion) amplification was biotinylated with bio-CTP and bio-UTP per manufature's protocol.

extract_protocol: 25,000- 50,000 cells were FACS sorted, RNA was isolated with RNAqueous Kit (Ambion) per manufacture's protocol, DNAse treated with DNAse1, phenol:chloroform:isoamyl alcohol extracted, and amplified through two rounds of in vitro transcription using MessageAmp (Ambion) per manufacture's protocol

tag: Strain

value: C57Bl/6 p53+/m, Gender:male, Age:2-months-old


title: control AU0995302

source_name: control AU0995302

extract_protocol: Total RNA was extracted from lymphoblastoid cells of AU0995302 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

tag: AU0995302 is a control male without autism.


title: control AU1086301

source_name: control AU1086301

extract_protocol: Total RNA was extracted from lymphoblastoid cells of AU1086301 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

tag: AU1086301 is a control male without autism.


title: HSC_12Months_p53_het_B

source_name: Hematopoietic stem cells from p53+/- mice

value: C57Bl/6 p53+/-, Gender:male, Age:2-months-old


title: HSC_12Months_p53m_B


title: autism with FMR1-FM AU046706

source_name: Autism with FMR1-FM AU046706

extract_protocol: Total RNA was extracted from lymphoblastoid cells of AU046706 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

tag: AU046706 is a male with autism and full mutation of FMR1.


title: control AU1215303

source_name: control AU1215303

extract_protocol: Total RNA was extracted from lymphoblastoid cells of AU1215303 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

tag: AU1215303 is a control male without autism.


title: control AU016703

source_name: pool

source_name: control AU016703

extract_protocol: Total RNA was extracted from lymphoblastoid cells of AU016703 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

tag: AU016703 is a control male without autism.


title: autism with FMR1-FM AU066703

extract_protocol: Total RNA was extracted from lymphoblastoid cells of 14 individuals using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

tag: Pooled total RNAs from lymphoblastoid cells of 14 individuals

source_name: Autism with FMR1-FM AU066703

extract_protocol: Total RNA was extracted from lymphoblastoid cells of AU066703 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

tag: AU066703 is a male with autism and full mutation of FMR1.


title: control AU1157302

source_name: control AU1157302

extract_protocol: Total RNA was extracted from lymphoblastoid cells of AU1157302 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

tag: AU1157302 is a control male without autism.


title: GMPho_02

city: Berlin-Steglitz

first: Dirk

last: Carstanjen

state: Berlin

address: Krahmer Strasse 6

institute: Institute for Molecular Pharmacology

description: GMP from Icsbp-deficient mice were isolated by flow cytometry.

hyb_protocol: 15 µg cRNA was hybridized to Affymetrix mouse expression 430A arrays at 45 °C for 16 h.

scan_protocol: Scanned according to the manufacturer's protocol (GA2500).

data_processing: Scanned GeneChip DAT files were analyzed by the GeneChip Analysis Suite Software (Affymetrix) with global scaling to 500.

source_name: Icsbp (Irf-8) deficient mice

label_protocol: Total RNA (5 µg) was used to generate cDNA according to the technical manual (Affymetrix, Santa Clara, CA). cRNA was generated with the BioArray high-yield transcript labelling kit (ENZO,Farmingdale, NY).

extract_protocol:
Total RNA was isolated from purified progenitor cell populations from 10 –16 week old mice
using the RNeasy Kit including DNase digestion (Qiagen, Hilden, Germany).


title: HSC_12Months_p53_het_A


title: WBM_2Months_A

description: Cells isolated from whole bone marrow

source_name: Whole Bone Marrow

value: C57Bl/6, Gender:male, Age:2-months-old


title: HSC_21Months_B

source_name: Hematopoietic stem cells


title: autism with FMR1-FM AU039304

source_name: Autism with FMR1-FM AU039304

extract_protocol: Total RNA was extracted from lymphoblastoid cells of AU039304 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

tag: AU039304 is a male with autism and full mutation of FMR1.


title: HSC_21Months_A


title: autism with dup(15q) AU006504

source_name: Autism with dup(15q) AU006504

extract_protocol: Total RNA was extracted from lymphoblastoid cells of AU006504 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

tag: AU006504 is a male with autism and duplication of 15q11-13.


title: WBM_2Months_B

description: Cells isolated from whole bone marrow


title: autism with dup(15q) AU010603

source_name: Autism with dup(15q) AU010603

extract_protocol: Total RNA was extracted from lymphoblastoid cells of AU010603 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

tag: AU010603 is a male with autism and duplication of 15q11-13.


title: HSC_12Months_B


title: KO_3

city: Jena

first: Christoph

last: Englert

address: Beutenbergstrasse 11

institute: Leibniz-Institute for Age Research

hyb_protocol: CodeLink Expression Assay protocol

scan_protocol: The arrays were scanned using a GenePix 4000B Array scanner

data_processing: Data was analyzed using CodeLink Expression Analysis software.

source_name: urogenital ridges of 5 Wt1-/- mouse embryos with 11-12 tail somites

label_protocol: CodeLink Expression Assay protocol

growth_protocol: Mice were housed under a 12L:12D cycle. Embryos were collected from timed matings, with noon of the day on which the plug was observed designated as E0.5

extract_protocol: Absolute RNA Microprep Kit (Stratagene)

treatment_protocol: urogenital ridges were isolated in PBS and immediately frozen on dry ice

value: Mf1; Genotype:homozygous for deletion of the Wilms tumor gene Wt1; Sex:four female, one male; Age:embryonic day E11.5; Stage:11-12 tail somites; Tissue:urogenital ridges


title: autism with dup(15q) 02-07

source_name: Autism with dup(15q) 02-07

extract_protocol: Total RNA was extracted from lymphoblastoid cells of 02-07 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

tag: 02-07 is a male with autism and duplication of 15q11-13.


title: autism with dup(15q) 03-43

source_name: Autism with dup(15q) 03-43

extract_protocol: Total RNA was extracted from lymphoblastoid cells of 03-43 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

tag: 03-43 is a male with autism and duplication of 15q11-13.


title: control AU1038304

source_name: control AU1038304

extract_protocol: Total RNA was extracted from lymphoblastoid cells of AU1038304 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

tag: AU1038304 is a control male without autism.


title: control AU1327303

source_name: control AU1327303

extract_protocol: Total RNA was extracted from lymphoblastoid cells of AU1327303 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

tag: AU1327303 is a control male without autism.


title: autism with dup(15q) 01-19

source_name: Autism with dup(15q) 01-19

extract_protocol: Total RNA was extracted from lymphoblastoid cells of 01-19 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

tag: 01-19 is a male with autism and duplication of 15q11-13.


title: autism with dup(15q) 98-19

source_name: Autism with dup(15q) 98-19

extract_protocol: Total RNA was extracted from lymphoblastoid cells of 98-19 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

tag: 98-19 is a male with autism and duplication of 15q11-13.


title: KO_1

tag: Strain


title: control AU1165303

source_name: pool

source_name: control AU1165303

extract_protocol: Total RNA was extracted from lymphoblastoid cells of AU1165303 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

tag: AU1165303 is a control male without autism.


title: 768Br_JH1h

status: Public on May 31 2007

city: Alfenas

first: Angel

middle: Roberto

last: Barchuk

state: Minas Gerais

address: Rua Gabriel Monteiro Silva 700, Campus Unifal

department: Cell and Developmental Biology

country: Brazil

institute: Federal University of Alfenas

hyb_protocol: For hybridization, probes (in 90µL 2X SSC) were pre-heated at 50°C during 3 min and placed on microarrays under lifter-slip cover glasses (22x60, 31.25µL).  cDNA microarrays were placed in single slide hybridization chambers which were incubated in a water bath for hybridization for 17h, at 50°C.  Washing procedure included the following steps: 2X SSC and 0.1% SDS; 2X SSC; 0.1X SSC and bidistilled water; 3 min per wash, all at room temperature.  Slides were dried by centrifugation at 750 rpm for 5 min previous scanning.

scan_protocol: Slides were scanned by using Affymetrix 428 Array Scanner and Jaguar 2.0 software; gain 40-68dB, 10 micron resolution, Cy3 with Green Laser (532nm), Filter FM570-10 and Cy5 with Red Laser (635nm), Filter FM665-12.  For images quantitation we used ScanAlyze 2.35 (http://rana.lbl.gov/EisenSoftware.htm) with default parameters.

data_processing: Background correction was performed in a way we could avoid the correction of negative or zero intensities (offset correction) by adding to the background-corrected intensities a positive constant (=50).  It damps spurious variation in log-ratios, particularly at low intensity spots.  The “print-tip loess” normalization was used to correct for within-array dye and spatial effects and single channel normalization was used to facilitate comparison between arrays (Smyth et al., 2005a).  Since our slides had 4 (768Br) and 2 (bEST_9000) within array replicate spots, the normalization procedure also considered the variation among their values (Smyth et al., 2005b).   After normalization we determined a log2 ratio (Queen´s sample intensity/Worker´s sample intensity), for each probe on each array. The fold-change in expression and its standard error for each gene were calculated by fitting a linear regression to the normalized expression data.  A Baysian smoothing procedure was used to shrink the estimated standard errors, with which we calculated the moderated t-statistic for each gene.

organism: Apis mellifera

source_name: A. mellifera workers, larval instar 4, JH1h-Control

label_protocol: cDNA synthesis, RNA amplification and probe synthesis (from 1μg of amplified RNA) were done with and according to Low RNA Input Fluorescent Linear Amplification Kit (Agilent, Cat. 5184-3523).  Probes purification was done using MinElute PCR Purification Kit (QIAGEN, Cat. 28004).

extract_protocol: Total RNA was extracted following Invitrogen’s protocol combined with column purification (RNeasy Mini Kit, QIAGEN, Cat. 74104).  RNA quality was determined by electrophoresis in agarose gels.

treatment_protocol: Acetona (2μL)

tag: Africanized

source_name: A. mellifera workers, larval instar 4, JH1h-Treated

treatment_protocol: To test the effects of exogenous JH on worker larvae gene expression profile, fourth instar larvae received a topical application of 10μg JH III (C16-juvenile hormone, Fluka Biochemika, 59992; diluted in acetone to a stock solution of 2.5 μg/μL). The amount of applied hormone was based on our previous experiments in which we examined the induction of vg and usp expression by JH during post-embryonic development in honeybees (Barchuk et al., 2002, 2004) and on a pioneer work of Goewie and Beetsma (1976) of “artificial” queens development by JH application.


title: WT_3

source_name: urogenital ridges of 5 wild-type mouse embryos with 11-12 tail somites

value: Mf1 wild-type; Sex:four female, one male; Age:embryonic day E11.5; Stage:11-12 tail somites; Tissue:urogenital ridges


title: 768Br_S2

source_name: A. mellifera workers, 5th instar spinning stage larvae (L5S2)

source_name: A. mellifera queens, 5th instar spinning stage larvae (L5S2)


title: HSC_2Months_A

source_name: Hematopoietic stem cells

extract_protocol: 25,000- 50,000 cells were FACS sorted, RNA was isolated with RNAqueous Kit (Ambion) per manufacture's protocol, DNAse treated with DNAse1, phenol:chloroform:isoamyl alcohol extracted, and amplified through two rounds of in vitro transcription using MessageAmp (Ambion) per manufacture's protocol


title: KO_2


title: 768Br_JH24h

source_name: A. mellifera workers, larval instar 4, JH24h-Control

source_name: A. mellifera workers, larval instar 4, JH24h-Treated


title: 768Br_L3

source_name: A. mellifera workers, Larval instar 3

source_name: A. mellifera queens, Larval instar 3


title: HSC_6Months_B


title: WT_1


title: HSC_6Months_A


title: WT_2


title: In vitro angiogenesis at 25hr, biological rep 3

status: Public on May 20 2007

city: Aurora

first: Allan

middle: Ray

last: Albig

state: CO

department: Pharmacology

institute: University of Colorado Health Sciences

description:
no additional information
Angiogenesis on Matrigel 25hr

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

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: MAS 5

source_name: Murine MB114 microvascular Endothelial cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

growth_protocol: MB114 cells were split 1:3 24 hours prior to culture on Matrigel matrix

extract_protocol: Ambion RNAqueus kit, phenol chloroform extraction, Quiagen Rneasy kit

treatment_protocol: Matrigel cultures were harvested after 1, 5, 15, 25 hours on Matrigel

tag: Angiogenesis on Matrigel 25hr


title: In vitro angiogenesis at 5hr, biological rep 3

description:
no additional information
Angiogenesis on Matrigel 5hr

tag: Angiogenesis on Matrigel 5hr


title: In vitro angiogenesis at 15hr, biological rep 1

description:
no additional information
Angiogenesis on Matrigel 15hr

tag: Angiogenesis on Matrigel 15hr


title: HSC_12Months_A


title: In vitro angiogenesis at 25hr, biological rep 1


title: In vitro angiogenesis at 25hr, biological rep 2


title: In vitro angiogenesis at 15hr, biological rep 2


title: bb9000_S2


title: bb9000_L4

source_name: A. mellifera workers, Larval instar 4

source_name: A. mellifera queens, Larval instar 4


title: 768Br_L4


title: bb9000_JH24h

treatment_protocol: Acetone (2μL)


title: In vitro angiogenesis at 15hr, biological rep 3


title: bb9000_JH1h


title: bb9000_L3


title: Profiling RB for miRNAs_RB sample 1451

city: Toronto

first: Tomas

last: Babak

state: ON

address: 112 College St

department: Banting and Best Department of Medical Research

country: Canada

institute: Best Institute

description: Samples GSM169532&GSM169534, GSM169533&GSM170986, and GSM169535&GSM170842 represent sample RNAs cohybridized on the same two-color array.  However, the data were treated as single channel data not as ratio data.

hyb_protocol: miRNA-labeling, reverse transcription, mRNA isolation, cDNA labeling, and hybridization were carried out as described previously (Babak et al., 2004; Zhang et al., 2004). Following labeling, samples were resuspended in 0.5 mL of hybridization buffer (1 M NaCl, 0.5% sodium sarcosine, 50 mM methyl ethane sulfonate, pH 6.5, 33% formamide and 40ug salmon sperm DNA), and hybridized on a rotating platform for 16-24 h at 42°C. Slides were washed (rocking ~30 seconds in 6x SSPE, 0.005% sarcosine, ~30 seconds in 0.06x SSPE).

scan_protocol: Slides were scanned with an Axon 4000A microarray scanner (Axon Instruments, Union City, CA).

data_processing: arcsinh (normalized,spatially detrended absolute intensity)

label: Alexa Fluor 546 or 647

source_name: RB sample 1451

label_protocol: miRNA-labeling, reverse transcription, mRNA isolation, cDNA labeling, and hybridization were carried out as described previously (Babak et al., 2004; Zhang et al., 2004). In brief, for miRNA profiling, 7ug of DNAse treated (Fermentas) total RNA was chemically labeled with Ulysis Alexa Fluor 546/647 kits (Invitrogen) according to manufacturer’s instructions. For mRNA profiling, cDNA was generated and labeled as described (Zhang et al., 2004).

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) according to the manufacturer’s instructions.

tag: RB sample 1451


title: Profiling RB for miRNAs_normal retina_repeat2

source_name: normal retina (2/3)

tag: This is one of three miRNA profiling repeats of human normal retina.


title: In vitro angiogenesis at 5hr, biological rep 2


title: In vitro angiogenesis at 5hr, biological rep 1


title: Profiling RB for miRNAs_normal retina_repeat3

label: direct lablelling

source_name: normal retina (3/3)


title: In vitro angiogenesis at 1hr, biological rep 1

description:
no additional information
Angiogenesis on Matrigel 1hr

tag: Angiogenesis on Matrigel 1hr


title: Profiling RB for miRNAs_RB sample 430

source_name: RB - patient #3 (430)

tag: RB - patient #3 (430)


title: In vitro angiogenesis at 1hr, biological rep 2