title: HEK293-siSET8-Wnt-1

first: Zhenfei

last: li

address: No.320 Yueyang Road

institute: Institute of Biochemistry and Cell Biology

hyb_protocol: Labeled cDNA was hybridized in NimbleGen Hybridization System following their standard operating protocol.

scan_protocol: Slides were scanned with the Axon GenePix 4000B microarray scanner following their standard operating protocol.

data_processing: Raw data were extracted as pair files by NimbleScan software (version 2.5). NimbleScan software’s implementation of RMA offers quantile normalization and background correction. The Probe level (*_norm_RMA.pair) files and Gene summary (*_RMA.calls) files were produced. The 6 gene summary files were imported into Agilent GeneSpring Software (version11.0) for further analysis. The positive effect of normalization is illustrated in Box-plot (see example in figure 1 below). Genes that have values greater than or equal to lower cut-off: 50.0 in all samples (“All Targets Value”) were chosen for data analysis. Differentially expressed genes were identified through Fold-change screening. P-value was calculated from TTest.

source_name: HEK293 cells transfected with SET8 shRNA and treatd with Wnt3a meidum for 7 hours

label_protocol: cDNA was labeled using a NimbleGen One-Color DNA Labeling Kit following their standard operating protocol.

growth_protocol: HEK293 cell lines were cultured with DMEM containing 10% FBS at 37°C,5% CO2.

extract_protocol: Total RNAs are harvested using TRIzol (Invitrogen) and the RNeasy kit (Qiagen) according to manufacturer’s instructions, including a DNase digestion step.RNA was measured on the Nanodrop ND-1000.

treatment_protocol: HEK293 cells were transfected with control or SET8 shRNA for about 40 hours and then stimulated with Control or Wnt3a CM for 7 hours.

value: HEK293 cells

tag: treatment group


title: vector-LoVo (2)

status: Public on Dec 29 2010

type: RNA

city: Philadelphia

first: Catrina

last: King

state: PA

address: 415 Curie Blvd

department: Gastroenterology

country: USA

institute: University of Pennsylvania

description: Gene expression data from additional vector-LoVo cell line

hyb_protocol: The resulting cDNA was fragmented, assessed by Bioanalyzer, and biotinylated. cDNA yields were added to Affymetrix hybridization cocktails, heated at 99ºC for 2 min and hybridized for 16 h at 45ºC

scan_protocol: A confocal scanner was used to collect fluorescence signal after excitation at 570 nm

data_processing: Significance Analysis of Microarrays (SAM v3.0, www-stat.stanford.edu/~tibs/SAM/) was used to generate lists of statistically significant differentially expressed genes in pairwise comparisons of replicate averages between conditions

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: LoVo colon cancer cell line transduced with MSCV-PIG (2)

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

growth_protocol: Cells cultured in DMEM + 10% FBS

extract_protocol: RNA isolated using a mirVana RNA isolation kit (Ambion, Austin, TX)

treatment_protocol: Cells were trypsinized to remove from plate, then lysed in RIPA buffer (Tris 50mM, NaCl 150 mM, SDS 0.1%, Na.Deoxycholate 0.5%, Triton X 100 1%) + protease inhibitor cocktail (Roche Diagnostics, Manheim Germany).

tag: sample type

value: modified ATCC cell line (#CCL-229)

tag: cell line

value: LoVo

tag: transduction

value: MSCV-PIG (2)


title: TPO+Dox_rep1

city: Hong Kong

first: Kathy

middle: YY

last: Chan

address: Rm84041, 6/F, Clinical Science Building, Prince of Wales Hospital, Shatin, N.T.

department: Paediatrics

country: Hong Kong

institute: The Chinese University of Hong Kong

description: Gene expression of the rat heart tissue after exposure to DOX+TPO

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B US45102920) using one color scan setting for 4x44k array slides.

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid:014879_D_F_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities.
GeneSpring data process settings:
Threshold: 1
Logbase: 2
Technology: Agilent.SingleColor.14879
Normalization: Shift to 75.0 percentile
Baseline Transformation: Median of all samples
FlagSettings:  Feature is not Uniform:A
Feature is a population outlier:A
Feature is Saturated:A
Feature is not positive and significant:A
Feature is not above background:A

organism: Rattus norvegicus

source_name: TPO+Dox-treated heart_day 6_replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).

growth_protocol: Doxorubicin-induced cardiomyopathy in rat acute model

extract_protocol: RNA was prepared using the Trizol Reagent (Invitrogen, Carlsbad, CA) and Rneasy Mini kit (Qiagen, Valencia, CA) following the manufacturer's recommendations. The RNA quality and integrity were analyzed with Nanodrop ND 1000 spectrophotometer (Rockland, DE) and Bioanalyzer (Agilent, Cheshire, UK).

treatment_protocol: Thrombopoietin treatment at day-1, day 1, 3 and 5 (10 ug/Kg TPO per dose).  A single dose of DOX was adminstrated at day 0 (17.5mg/ Kg body weight).

tag: tissue

value: Whole Heart


title: Manisopliae_RootExudate_1h-0h_R2

city: College Park

first: Monica

last: Pava-Ripoll

state: MD

address: 4112 Plant Sciencies Bldg

department: Entomology

institute: University of Maryland

description: Hybridization using Loop design where every time point is compared to the next one (Time1h-Rep2/Time0h-Rep2).

hyb_protocol: Hybridization of 5 mg labeled cDNA to Metarhizium anisopliae arrays was conducted following the recommendations of the array manufacturer (http://www.umbi.umd.edu/carb/core-facilities/microarray-services/facility.php).

scan_protocol: Axon 4200 microarray scanner (Molecular Devices).

data_processing: Intensity of spots was extracted by Spotfinder program (http://www.pfgrc.tigr.org/tools.shtml, JCVI, Rockville, MD) as MEV files. Data of the MEV files were normalized using LOWESS (LOcally WEighted Scatterplot Smoothing) technique using the software MIDAS (http://www.pfgrc.tigr.org/tools.shtml, JCVI, Rockville, MD).  MIDAS output files project included standard deviation regularization, low intensity filter and in-slide replicate analysis. Normalized files were analized using Bayesian Analysis of Time Series microarray experiments (BATS) (http://www.na.iac.cnr.it/bats/).

organism: Metarhizium anisopliae

source_name: Fungal mycellium, root exudate, time 1 h

label_protocol: Direct labeling of mRNA/cDNA was performed with Cy3 (green) and Cy5 (red) cyanine dyes using the Ovation™ Aminoallyl system (Nugen, San Carlos, CA), according to manufacturer's instructions.

growth_protocol: Samples were incubated in a shaker/incubator at 27°C/220 rpm (New Brunswick Scientific, Edison, NJ).

extract_protocol: Total RNA was immediately extracted from the samples using the Qiagen RNeasy Mini kit, according to manufacturer's instructions.

treatment_protocol: 5 ml of Metarhizium anisopliae mycelium suspension (previously grown for 30 hours on Saboreaud dextrose broth (SDB) at 27C, collected through vacuum filtration and washed three times with sterile distilled water) were transferred for a final concentration of 5 mg/mL of bean RE. Samples were incubated in a shaker/incubator at 27°C/220 rpm (New Brunswick Scientific, Edison, NJ) and mycelium was collected from individual flasks before (time 0) and after 1, 4, 8 and 12 hours of incubation

tag: strain

value: ARSEF 2575

value: Fungal Mycellium grown for 30 h at 27C

tag: bean root exudate concentration (mg/ml)

tag: time (hours)

source_name: Fungal mycellium, root exudate, time 0 h


title: Dox_rep2

description: Gene expression of the rat heart tissue after exposure to DOX

source_name: Dox-treated heart_day 6_replicate 2


title: tumor_33, expression

city: StLouis

first: Nobish

last: Varghese

state: MO

address: 4444 Forest Park Ave.

institute: Washington University in St.Louis

hyb_protocol: Labeled targets were then hybridized to Mouse Exon 1.0S T arrays (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned using Affymetrix GeneArray scanner GS 3000.

data_processing:
Raw data were processed with the RMA algorithm in Affymetrix Expression ConsoleTM version1.1 (Affymetrix Inc., USA).

This analysis included core exons.
Probe-group file: MoEx-1_0-st-v1.r2.pgf
Meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.core.mps

organism: Mus musculus

source_name: spleen, APL

label_protocol: Amplified cDNA was biotin labeled using the Encore Biotin Module (NuGen Technologies, San Carlos, CA) according to the manufacturer’s instructions.

extract_protocol: Total cellular RNA was purified using Trizol reagent, quantified using UV spectroscopy (Nanodrop Technologies, Wilmington,DE) and qualitatively assessed using an Experian Bioanalyzer (Hercules,CA). Amplified cDNA was prepared from 20ng of total RNA using the whole transcript WT-Ovation TM RNA Amplification System.

value: Bl/6 Taconic

value: spleen

tag: disease state

value: acute promyelocytic leukemia (APL)


title: HEK293-sictr-Wnt-2

city: Shanghai

country: China

source_name: HEK293 cells transfected with control shRNA and treatd with Wnt3a meidum for 7 hours


title: tumor_9500, expression


title: E. coli BL21(DE3) cells expressing catalytically inactive mutant of  M.HpyAVIB

city: BANGALORE

first: RITESH

last: KUMAR

address: DEPARTMENT OF BIOCHEMISTRY, INDIAN INSTITUTE OF SCIENCE

country: India

institute: INDIAN INSTITUTE OF SCIENCE

description: Gene expression after 1hr of induction with 0.5 Mm IPTG

hyb_protocol: The labeled cRNA samples were hybridized on to a Custom Gene Expression E. coli  8x15k (AMADID: 19439). 600 ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours.

scan_protocol: The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327) and scanned using the Agilent Microarray Scanner G Model G2565BA at 5 micron resolution.

data_processing: Data extraction from Images was done using Feature Extraction software v 9.5.1 of Agilent. Feature extracted raw data was analyzed using GeneSpring GX V 7.3.1 software from Agilent. Normalization of the data was done in GeneSpring GX using the recommended one color Per Chip and Per Gene Data Transformation: Set measurements less than 0.01 to 0.01, Per Chip: Normalize to 50th percentile, Per Gene: Normalize to Specific Samples. Significant genes up and down regulated showing one fold and above among the samples was identified.

organism: Escherichia coli BL21(DE3)

source_name: mutant

label_protocol: Five hundred nanograms each of the samples were incubated with reverse trancription mix at 42°C and converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step.

growth_protocol: Cells were grown to an OD of 0.4 and then 0.5 mM IPTG was added to induce the protein expression

extract_protocol: Bacterial RNA was stabilized in vivo, by using RNA protect Bacteria Reagent (Qiagen). Total RNA was isolated by using RNeasy Kits for RNA purification (Qiagen) as per the manufacturer’s protocol.

tag: genotype/variation

value: mutant M.HpyAVIB


title: tumor_31, expression


title: HEK293-siSET8-Wnt-2

value: transfected with SET8 shRNA and treatd with Wnt3a meidum for 7 hours


title: tumor_9504, expression


title: HEK293-sictr-ctr-2

source_name: HEK293 cells transfected with control shRNA and treatd with control meidum for 7 hours


title: tumor_9523, expression


title: Control_rep2

description: Gene expression of the rat heart tissue

source_name: Control heart_day 6_ replicate 2


title: TPO+Dox_rep2

source_name: TPO+Dox-treated heart_day 6_replicate 2


title: tumor_9514, expression


title: tumor_26, expression


title: tumor_29, expression


title: Dox_rep1

source_name: Dox-treated heart_day 6_replicate 1


title: HEK293-sictr-Wnt-1

value: transfected with control shRNA and treatd with Wnt3a meidum for 7 hours


title: tumor_9529, expression


title: E. coli BL21(DE3) cells expressing wild-type M.HpyAVIB

source_name: wild type

value: wild type M.HpyAVIB


title: tumor_9520, expression


title: tumor_36, expression


title: tumor_9492, expression


title: tumor_9495, expression


title: tumor_9509, expression


title: Manisopliae_RootExudate_0h-1h_R1

description: Hybridization using Loop design where every time point is compared to the next one (Time0h-Rep1/Time1h-Rep1).


title: Healthy Control CD8 Memory HC-8

status: Public on Dec 28 2010

city: Bethesda

first: Marta

last: Catalfamo

state: Maryland

address: 9000 Rockville Pike

department: Laboratory of Immunoregulation

institute: NIAID, NIH

scan_protocol: standard SAB protocol

data_processing: Quantification of transcript levels was determined by normalizing to 5 housekeeping genes from each individual sample.

label: RT² SYBR Green

source_name: CD8 T cells

label_protocol: RT² SYBR Green as performed by SAB

growth_protocol: Sorted human Naïve and Memory CD4 and CD8 T cell subsets from healthy controls and HIV infected individuals

extract_protocol: Briefly, total RNA was harvested from each individual T cell subset from each patient or healthy control and contaminating DNA was digested with DNase. Messenger RNA was converted to cDNA and loaded onto PCR array plates for quantitative real-time PCR.

value: HIV infected

tag: cell type

value: CD8 T cells


title: Healthy Control CD8 Naïve HC-8


title: Healthy Control CD8 Memory HC-7


title: Healthy Control CD8 Naïve HC-7


title: Healthy Control CD8 Memory HC-6


title: tumor_9508, expression


title: 81176 E64_CY5_W_slide 18

city: Ames

first: Haihong

last: Hao

state: IA

address: 1600 Christensen Drive

institute: Iowa State University

description: macrolide susceptible strain C. jejuni 81176

hyb_protocol: equal amounts of labeled cDNA of the wild-type and the mutant were mixed and dried in a speed vacuum concentrator. After resuspension with hybridization buffer provided by the slide manufacturer, the mixture was denatured by heating at 95 ◦C for 10 min. The hybridization mixture was loaded onto a microarray slide and hybridized in a shaking incubator at 42 ºC for 24 h. Slides were washed as the manufacture’s recommendations and dried by centrifugation.

scan_protocol: Using a ScanArray Express laser scanner (Applied Biosystem Inc., Foster City, CA) each dye channel of each slide was scanned at a 10 μm resolution using three predetermined laser power and photomultiplier gain settings. Thus for each slide six scans were performed, three separate scans at different settings of each of the two dye channels.

data_processing: ImaGene software (BioDiscovery, El Segundo, CA) was used for spot finding and to measure the spot-specific mean signal strength  of each spot. The fluorescentc intensities of all spots were log2 transformed. The median of the three log2-transformed spot signals was determined and this value was used as spot signal for all further calculations. As an additional measure against intensity dependent dye bias the data was then subjected to LOWESS normalization.

organism: Campylobacter

source_name: C. jejuni 81-176

label_protocol: cDNA was synthesized using aminoallyl-dNTP according to the manufacturer’s instruction. After purification, aminoallyl labeled cDNA was fluorescently labeled with Cy-3/cy-5 mono-Reactive Dye Pack (Amersham Biosciences, Piscataway, NJ)

extract_protocol: Total RNA was isolated using RNAprotectTM bacteria reagent (Qiagen) and an RNeasy kit (Qiagen) according to the manufacturer’s protocol with an optional step of on-column DNase treatment with RNase-Free DNase (Qiagen). RNA concentration was measured with a NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, DE)

value: macrolide susceptible strain C. jejuni 81-176


title: 81176 E64_CY5_W_slide 40


title: 81176 E8_CY5_W_slide 16


title: 81176 E8_CY3_R_slide 16

description: Intermedial-level macrolide resistant strain 76 E8 which was selected from c.jejuni 81176 by erythromycin  and contains A2074C mutation in  two copies of 23S rRNA gene.

source_name: C. jejuni 81-176 E8

value: intermedial-level macrolide resistant strain 76 E8


title: 81176 E8_CY3_R_slide 38


title: 81176 E64_CY3_W_slide 39


title: Healthy Control CD8 Memory HC-5


title: 81176 E64_CY3_R_slide 40

description: high-level macrolide resistant strain 76 E64 which was selected from c.jejuni 81176 by erythromycin  and contains A2074C mutation in  three copies of 23S rRNA gene.


title: 81176 E64_CY5_R_slide 39

value: high-level macrolide resistant strain 76 E64


title: Control_rep1

description: Gene expression of the rat heart tissue

source_name: Control heart_day 6_ replicate 1


title: 81176 E8_CY5_R_slide 37


title: HEK293-sictr-ctr-1

value: HEK293 cells

value: transfected with control shRNA and treatd with control meidum for 7 hours


title: 81176 E64_CY5_R_slide 17


title: Healthy Control CD4 Memory HC-4

source_name: CD4 T cells

value: CD4 T cells


title: 81176 E2_CY3_R_slide 36

description: Intermedial-level macrolide resistant strain 76 E2  selected from c.jejuni 81176 by erythromycin  did not contain mutation in 23S rRNA gene.

source_name: C. jejuni 81-176 E2

value: intermedial-level macrolide resistant strain 76 E2


title: 81176 E8_CY3_W_slide 37


title: 81176 E2_CY5_W_slide 36


title: 81176 E8_CY5_W_slide 38


title: 81176 E64_CY3_R_slide 18


title: 81176 E2_CY5_R_slide 35


title: Healthy Control CD4 Naïve HC-4


title: 81176 E2_CY3_W_slide 35


title: Healthy Control CD8 Naïve HC-6


title: Healthy Control CD4 Memory HC-3


title: Healthy Control CD4 Naïve HC-3


title: 81176 E2_CY5_W_slide 14


title: 81176 E2_CY3_R_slide 14


title: Healthy Control CD4 Memory HC-2


title: Healthy Control CD4 Naïve HC-2


title: HIV infected CD8 Memory HIV-7

value: Healthy


title: 81176 E2_CY3_W_slide 13


title: 11168 E64_CY3_W_slide 30

organism: Campylobacter jejuni

source_name: C. jejuni NCTC-11168

value: macrolide susceptible strain NCTC 11168


title: 11168 E64_CY3_R_slide 33

value: high-level macrolide resistant strain 68 E64


title: HIV infected CD8 Naïve HIV-6


title: HIV infected CD8 Memory HIV-5


title: 11168 E64_CY5_R_slide 24


title: Healthy Control CD4 Memory HC-1


title: 11168 E64_CY5_W_slide 25


title: 11168 E64_CY3_W_slide 24


title: HIV infected CD8 Memory HIV-1


title: 11168 E8_CY5_W_slide 23


title: Healthy Control CD4 Naïve HC-1


title: 11168 E8_CY3_R_slide 32

value: Intermedial-level macrolide resistant strain 68 E8


title: 11168 E64_CY3_R_slide 25


title: 11168 E8_CY3_R_slide 23


title: HIV infected CD8 Naïve HIV-7


title: 11168 E8_CY5_R_slide 21


title: HIV infected CD8 Naïve HIV-1


title: 11168 E8_CY5_W_slide 32


title: 81176 E2_CY5_R_slide 13


title: HIV infected CD8 Memory HIV-6


title: 11168 E64_CY5_W_slide 33


title: 11168 E8_CY5_R_slide 29


title: 11168 E8_CY3_W_slide 21


title: HIV infected CD8 Naïve HIV-5


title: HIV infected CD4 Memory HIV-4


title: 11168 E64_CY5_R_slide 30


title: 11168 E8_CY3_W_slide 29


title: HIV infected CD4 Naïve HIV-4


title: HIV infected CD4 Memory HIV-3


title: HIV infected CD4 Naïve HIV-3


title: 11168 E1_CY5_W_slide 31

hyb_protocol: After purification, the fluorescent labeling of the DNA was quantitated, and equal amounts of labeled cDNA of the wild-type and the mutant were mixed and dried in a speed vacuum concentrator. After resuspension with hybridization buffer provided by the slide manufacturer, the mixture was denatured by heating at 95 ◦C for 10 min. The hybridization mixture was loaded onto a microarray slide and hybridized in a shaking incubator at 42 ºC for 24 h. Slides were washed as the manufacture’s recommendations and dried by centrifugation.


title: HIV infected CD4 Naïve HIV-2


title: HIV infected CD4 Memory HIV-2


title: Rat_SINFH_1

city: Hangzhou

first: Qiang

last: Mao

state: Zhejiiang Province

address: Binjiang District

institute: Zhejiang Chinese Medical University

description: Gene expression data from rat femoral head in Steroid Induced Necrosis of Femoral Head group.

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

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 7G.

data_processing: The data were analyzed with PARTEK genomic suit 6.4 using RMA normalization.

source_name: Rat femoral head in Steroid Induced Necrosis of Femoral Head group

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA (3_ivt_express_kit_manual  Affymetrix).

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

value: Femoral head

tag: gender

value: male

tag: developmental stage

value: adult


title: 11168 E1_CY3_R_slide 31

value: Low-level macrolide resistant strain 68 E1


title: U251 glioma cells treated with G-TPP

city: Weehawken

first: Markus

middle: D

last: Siegelin

state: NJ

address: 963 Boulevard E

institute: Markus Siegelin

description: Gene expression data from G-TPP traeted glioma cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed using RMA normalization (Affymetrix Expression Console Software (ver 1.1.2)).

source_name: U251 glioma cells treated with G-TPP

growth_protocol: U251 glioblastoma cells were grown in DMEM/High Glucose

treatment_protocol: U251 Glioblastoma cells were treated either with a DMSO control or 5 um of Gamitrinib, G-TPP, for 6 hours

tag: agent

value: G-TPP


title: U251 glioma cells treated with DMSO

description: Gene expression data from DMSO traeted glioma cells

source_name: U251 glioma cells treated with DMSO

value: DMSO


title: 11168 E1_CY3_R_slide 20


title: Rat_SINFH_2


title: 11168 E1_CY5_R_slide 28


title: Rat_SINFH_3


title: HIV infected CD4 Memory HIV-1


title: THz irradiated group vs. Control group

city: Los Alamos

first: Boian

middle: S

last: Alexandrov

state: NM

address: Bikini Atoll Road

department: Theoretical Division

institute: LANL

description:
ch1: Mouse mesenchymal stem cells after 9 hours of THz irradiation
ch2: Mouse mesenchymal stem cells control group
ch1 CEL file: 19_Mouse430_2.CEL
ch2 CEL file: 29_Mouse430_2.CEL

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

data_processing:
Statistically significant differentially expressed genes in the Affymetrix GeneChip® microarray data were identified via the Bioconductor software framework and the Significance Score (S-Score) algorithm version 1.20.0.
SScore is an R package that facilitates the comparison of gene expression between Affymetrix GeneChips using the S-score algorithm. The S-score algorithm uses probe level data directly to assess differences in gene expression, without preliminary separate step of probe set expression summary estimation. Therefore, the algorithm avoids introduction of error associated with the expression summary estimation process and has been demonstrated to improve the accuracy of identifying differentially expressed genes. The S-score produces accurate results even when few or no replicates are available.
Reference: Kennedy RE, Kerns RT, Kong X, Archer KJ, Miles MF. SScore: an R package for detecting differential gene expression without gene expression summaries. Bioinformatics. 2006;22:1272–1274

source_name: Mouse mesenchymal stem cells

growth_protocol: Mouse mesenchymal stem cells were cultured on tissue-culture treated flasks. Once the cells reached 80–90% confluence, they were sub-cultured in supplemented medium (95% α-MEM, 5% FBS, and antibiotics) for THz irradiation treatment. Roziglitazone (1µM), insulin (5 µg/ml), 3-Isobutyl-1-methylxanthine (100µM), and dexamethasone (1µM) were added to the medium 24 hours before irradiation. Roziglitazone (1µM), insulin (5 µg/ml), 3-Isobutyl-1-methylxanthine (100µM), and dexamethasone (1µM) were added to the medium 24 hours before irradiation.

extract_protocol: Cellular RNA was extracted using the RNeasy Mini kit (Qiagen) following the manufacturer's instructions.

treatment_protocol: Cells are irradiated for 9 hours with high-energy (~1 µJ, pulsewidth 35 fsi.e. high peak power per pulse ~30 MW), average density power 1mW/cm2, broadband THz radiation(~10 THz) at a high repetition rate (1 kHz)

value: mesenchymal stem cells

value: 9 hours of THz irradiation

value: control


title: Rat_control_3

description: Gene expression data from rat femoral head in control group.

source_name: Rat femoral head in control group


title: 11168 E1_CY3_W_slide 28


title: 11168 E1_CY5_R_slide 19


title: Rat_control_2


title: HIV infected CD4 Naïve HIV-1


title: 11168 E1_CY5_W_slide 20


title: Rat_control_1


title: 81176 E64_CY3_W_slide 17

value: macrolide susceptible strain C. jejuni 81-176


title: Patient3, CD133+ CD44-

first: Ying

last: Hou

address: Yueyang Road 320

institute: Institute of Neuroscience, China Academy of Science

description: Gene expression of CD133+CD44- tumors in patient 3.

hyb_protocol: 875ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

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

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

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Tumor cells were dissected and prepared from operating HCC specimens by enzyme digestion. CD133+CD44+ and CD133+CD44- subgroups of tumor cells were then isolated using a flow cytometer.

extract_protocol: RNA was prepared using Trizol (Invitrogen) following the manufacturer's recommendations. Crude RNA were further purified by Qiagen RNeasy Kit. RNA was quantified using a NanoDrop-1000 spectrophotometer, and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: operating resected hepatocellular carcinoma (HCC)

tag: subpopulation

tag: age

value: 45 years

tag: tumor stage

value: TNM stage III

tag: patient


title: Patient2, CD133+ CD44-

description: Gene expression of CD133+CD44- tumors in patient 2.

value: 32 years


title: Patient3, CD133+ CD44+

description: Gene expression of CD133+CD44+ tumors in patient 3.


title: Patient2, CD133+ CD44+

description: Gene expression of CD133+CD44+ tumors in patient 2.


title: Patient1, CD133+ CD44+

description: Gene expression of CD133+CD44+ tumors in patient 1.

value: 58 years

value: TNM stage II


title: 11168 E1_CY3_W_slide 19

value: macrolide susceptible strain NCTC 11168


title: str.wt.cntr.2

status: Public on Dec 27 2010

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing: BeadStudio, quantile normalization. 1 sample (cb.wt.cntr.3 [4068838009_C]) was a technical outlier and was excluded from the analysis.

label: Biotin

source_name: striatum RNA

label_protocol: Biotin

extract_protocol: Trizol

treatment_protocol: HDACi 4b (1 mg/ml) was administered for 67 days in solutions that replaced drinking water beginning at 4 months of age.

value: CBA x C57BL/6

value: brain

tag: brain region

value: str

tag: genotype

value: wt

tag: treatment

value: cntr

value: f


title: str.wt.cntr.1

tag: tissue

value: m


title: Patient1, CD133+ CD44-

description: Gene expression of CD133+CD44- tumors in patient 1.

value: male


title: str.tg.cntr.4

tag: strain

value: tg


title: str.wt.4b.1

value: HDACi 4b


title: str.tg.4b.4


title: str.wt.4b.2


title: str.wt.cntr.3


title: str.tg.cntr.3


title: cx.wt.cntr.4

source_name: cortex RNA

value: cx


title: str.wt.cntr.4


title: str.wt.4b.3


title: str.wt.4b.4


title: cx.wt.cntr.2


title: cx.tg.cntr.4


title: str.tg.cntr.1


title: cx.wt.4b.3


title: str.tg.4b.1


title: cx.wt.4b.4


title: cx.wt.4b.2


title: str.tg.cntr.2


title: cx.tg.cntr.2


title: cx.wt.4b.1


title: cx.wt.cntr.3


title: str.tg.4b.2


title: str.tg.4b.3


title: cx.wt.cntr.1


title: cx.tg.cntr.3


title: cx.tg.4b.4


title: cx.tg.4b.2


title: cb.wt.cntr.4

source_name: cerebellum RNA

value: cb


title: cb.wt.4b.4


title: cx.tg.4b.1


title: cx.tg.4b.3


title: cb.wt.cntr.2


title: cb.wt.cntr.1


title: cb.wt.4b.2


title: cx.tg.cntr.1


title: cb.tg.cntr.3


title: cb.tg.cntr.4


title: cb.tg.cntr.2


title: cb.wt.4b.1


title: cb.tg.cntr.1


title: Scerevisiae_D12_rep2

city: Gothenburg

first: wanwipa

last: vongsangnak

address: Kemivägen 10

department: Department of Chemical and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

hyb_protocol: Hybridization was done according to the Affymetrix GeneChip Expression Analysis Technical Manual on a GeneChip Fluidics Station FS-400.

scan_protocol: Scanning was done according to the Affymetrix GeneChip Expression Analysis Technical Manual on a GeneChip Scanner 3000.

data_processing: Affymetrix CEL-data files were preprocessed using the statistical language and environment R Language version 2.5. The probe intensities were normalised for background using the robust multiarray average (RMA) method (Irizarry, 2003) using only perfect match (PM) probes. Normalization was performed subsequently using the qspline algorithm (Workman, 2002). Gene expression values were calculated from the PM probes with the medianpolish summary method (Irizarry, 2003). All statistical preprocessing methods were used by invoking them through the affy package (Gautier, 2004).

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae grown on glucose-limited medium

label_protocol: Labeled was done according to the Affymetrix GeneChip Expression Analysis Technical Manual.

extract_protocol: Total RNA was isolated from frozen yeast using the Qiagen RNeasy Mini Kit.

tag: growth medium

value: glucose-limited condition

tag: growth condition

value: chemostat cultivation, D=0.1 h-1

tag: sampling time

value: steady-state culture for at least 5 residence times


title: Scerevisiae_D12_rep3


title: TCP3-SRDX induced 10d cuc1 seedling replicate 4

city: Tsukuba

first: Nobutaka

last: Mitsuda

state: Ibaraki

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

description: Biological replicate 4 of 4. 10 day cuc1 seedling harboring pXVE:TCP3-SRDX, treated with estradiol or DMSO, harvested after 24 hr treatment

hyb_protocol: Fragmented 0.825µg-each labeled cRNAs with hybridization buffer (Agilent GE hybridization buffer HI-PRM) were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed.

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version 9.1.3.1).

data_processing: Agilent Feature Extraction Software (v 9.1.3.1) was used for background subtraction and LOWESS normalization.

organism: Arabidopsis thaliana

source_name: 10d cuc1 seedling harboring pXVE:TCP3-SRDX treated with estradiol

label_protocol: 1 µg of total RNA were used for reverse transcription at 40°C for 2 h, and labeled cRNA were prepared using T7 RNA polymerase with Cy3/5-labeled CTP at 40°C for 2 h following manufacture's instructions (Agilent Quick Amp Labeling kit).

growth_protocol: 10 day seedlings were transferred into a liquid medium that contained half-strength MS salts, 5 g/L sucrose 0.5 g/L MES for 24 hr with DMSO or 5µM estradiol

extract_protocol: Total RNA was extracted using Trizol or Plant RNeasy kit (QIAGEN).

value: cuc1 pXVE:TCP3-SRDX

value: T2 mixture of no. 4

value: 10 day after germination

value: whole seedling

value: 5µM estradiol in DMSO for 24 hr

tag: ecotype

source_name: 10d cuc1 seedling harboring pXVE:TCP3-SRDX treated with DMSO

value: DMSO for 24 hr


title: Toxoplasma gondii, Intracellular 2hr, 2

city: St Louis

first: Michael

middle: Sean

last: Behnke

address: 660 S. Euclid Ave

department: Molecular Microbiology

institute: Washington University School of Medicine

description: Type I RH intracellular 2hr expression using the Affymetrix Toxoplasma gondii Genechip.

hyb_protocol: Standard Affymetrix protocol with 5ug labeled cRNA.

scan_protocol: Standard Affymetrix protocol

data_processing: GeneSpring 7.2 RMA, Data transformation: Set measurements less than 0.01 to 0.01, Per Chip and Per Gene: Median Polishing

organism: Toxoplasma gondii

source_name: Intracellular, 2hr

label_protocol: Affymetrix One Cycle: 3ug starting RNA - Standard One Cycle protocol

growth_protocol: grown in human foreskin fibroblasts

extract_protocol: Parasites were harvested and RNA was extracted using the Qiagen RNeasy kit (b-mercaptoethanol and DNase I treatment).

value: type I strain RH

value: tachyzoite


title: Toxoplasma gondii, Intracellular 0hr, 1

description: Type I RH intracellular 0hr expression using the Affymetrix Toxoplasma gondii Genechip.

source_name: Intracellular, 0hr


title: Scerevisiae_D12_rep1


title: Toxoplasma gondii, Intracellular 2hr, 1


title: Scerevisiae_D126_rep1


title: cb.tg.4b.4

value: CBA x C57BL/6

value: brain

value: f


title: Scerevisiae_D126_rep3


title: Scerevisiae_D126_rep2


title: TCP3-SRDX induced 10d cuc1 seedling replicate 1

description: Biological replicate 1 of 4. 10 day cuc1 seedling harboring pXVE:TCP3-SRDX, treated with estradiol or DMSO, harvested after 24 hr treatment

growth_protocol: 10 day seedlings were transferred into a liquid medium that contained half-strength MS salts, 5 g/L sucrose 0.5 g/L MES for 24 hr with DMSO or 5mM estradiol

value: T2 mixture of no. 1


title: Toxoplasma gondii, Extracellular, 1

description: Type I RH extracellular expression using the Affymetrix Toxoplasma gondii Genechip.

source_name: Extracellular


title: Toxoplasma gondii, Intracellular 0hr, 2


title: cb.tg.4b.2

value: tg

value: HDACi 4b


title: cb.tg.4b.3

value: cb


title: Scerevisiae_REF_rep3

value: REF

value: glucose-limited condition

value: chemostat cultivation, D=0.1 h-1


title: TCP3-SRDX induced 10d cuc1 seedling replicate 3

description: Biological replicate 3 of 4. 10 day cuc1 seedling harboring pXVE:TCP3-SRDX, treated with estradiol or DMSO, harvested after 24 hr treatment

value: cuc1 pXVE:TCP3-SRDX

value: T2 mixture of no. 3

value: 5µM estradiol in DMSO for 24hr


title: Scerevisiae_REF_rep2

value: steady-state culture for at least 5 residence times


title: Toxoplasma gondii, Extracellular, 2


title: cb.tg.4b.1

value: m


title: TCP3-SRDX induced 10d seedling replicate 1

description: Biological replicate 1 of 3. 10 day seedling harboring pXVE:TCP3-SRDX, treated with estradiol or DMSO, harvested after 24 hr treatment

source_name: 10d seedling harboring pXVE:TCP3-SRDX treated with DMSO

value: 10 day after germination

value: whole seedling

value: DMSO for 24 hr

source_name: 10d seedling harboring pXVE:TCP3-SRDX treated with estradiol

value: 5µM estradiol in DMSO for 24 hr


title: TCP3-SRDX induced 10d cuc1 seedling replicate 2

description: Biological replicate 2 of 4. 10 day cuc1 seedling harboring pXVE:TCP3-SRDX, treated with estradiol or DMSO, harvested after 24 hr treatment

value: T2 mixture of no. 2


title: cb.wt.4b.3

value: CBA x C57BL/6

value: brain

value: wt


title: Day2_Dox_rep3

status: Public on Dec 26 2010

city: Research Triangle Park

first: Deepak

last: Mav

state: NC

address: 2 Davis Drive

institute: Sciome LLC

description: Replicate 3 of 4.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scan protocol using the Illumina iScan scanner.

data_processing: The raw data were background corrected using the MBCB method (Nucleic Acids Research, 2008, Vol. 36, No. 10), quantile normalized using R software (normalize.quantiles function from preProcessCore package) and log2 transformed.

source_name: C4-2B/Rx2dox cells, doxycycline, day 2

label_protocol: Standard Illumina labelling protocol using biotin.

growth_protocol: The C4-2B/Rx2dox cells were grown in RPMI 1640 medium supplemented with 10% Tet System Approved FBS from Clontech, CA, USA. The incubator was maintained at 37 degree Celcius with 5% carbon dioxide.

extract_protocol: Total RNA was isolated using the Aurum Total RNA kit (Bio-Rad Laboratories Inc., Hercules, CA, USA) following the manufacturer’s recommendations, and 1 µg was reverse transcribed using the Superscript III kit (Invitrogen, CA, USA). The cDNA was subjected to real-time PCR amplification using iQ SYBR Green Supermix and a Opticon™2 real time PCR machine from Bio-Rad, Hercules, CA.

treatment_protocol: Doxycycline was added to the growth medium (250 nanogram per mL) and samples were harvested following 24 hours and 48 hours.

tag: cell line

tag: cell type

value: prostate cancer

value: doxycycline

tag: treatment time

value: 2 days


title: Day2_Dox_rep1

description: Replicate 1 of 4.


title: TCP3-SRDX induced 10d seedling replicate 2

description: Biological replicate 2 of 3. 10 day seedling harboring pXVE:TCP3-SRDX, treated with estradiol or DMSO, harvested after 24 hr treatment


title: Day2_Dox_rep2

description: Replicate 2 of 4.


title: Day2_veh_rep1

description: Replicate 1 of 4.

source_name: C4-2B/Rx2dox cells, control, day 2

value: vehicle control


title: Day2_Dox_rep4

description: Replicate 4 of 4.


title: Day1_Dox_rep4

description: Replicate 4 of 4.

source_name: C4-2B/Rx2dox cells, doxycycline, day 1

value: 1 day


title: Day1_veh_rep2

description: Replicate 2 of 4.

source_name: C4-2B/Rx2dox cells, control, day 1


title: Scerevisiae_REF_rep1

value: REF

value: glucose-limited condition

value: chemostat cultivation, D=0.1 h-1


title: Day1_veh_rep4

description: Replicate 4 of 4.


title: Day1_veh_rep3

description: Replicate 3 of 4.


title: Day2_veh_rep4

description: Replicate 4 of 4.


title: Day2_veh_rep3

description: Replicate 3 of 4.


title: Day1_Dox_rep3

description: Replicate 3 of 4.


title: Day1_Dox_rep2

description: Replicate 2 of 4.


title: Day2_veh_rep2

description: Replicate 2 of 4.


title: Day1_Dox_rep1

description: Replicate 1 of 4.


title: PBS followed by PBS (P+P)

status: Public on Dec 25 2010

city: Abiko

first: Minori

last: Dateki

state: Chiba

department: Environmental Science Laboratory

institute: Central Research Institute of Electric Power Industry

hyb_protocol: Following fragmentation, the synthesized cRNA was hybridized for 16 hr at 45C on Affymetrix Mouse 430 2.0 Arrays. The arrays were washed and stained using an Affymetrix Fluidics Station 450

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

data_processing: Cel files were analyzed with Affymetrix GeneChip Operating Software (version 1.3). All probe sets were scaled to a target signal of 500.

source_name: Mouse liver received PBS injection followed by PBS injection (P+P)

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

growth_protocol: Mice were fed in isolate chamber maintained at 23C with a cycle of 12 h light and shade.

extract_protocol: Total RNA was purified using an RNeasy mini kit (Qiagen). The RNA integrity number (RIN) was determined using an Agilent Technologies 2100 bioanalyzer and A2100 expert software (ver. B0202SI238; Agilent).

treatment_protocol: Four animal groups received the following treatments: phosphate-buffered saline (PBS) followed by PBS (P+P), ethylbenzene followed by PBS (E+P), PBS followed by ethylbenzene (P+E), and ethylbenzene followed by ethylbenzene (E+E).  For the first exposure, ethylbenzene (7 mmol kg-1) or PBS (equivalent volume to ethylbenzene) was intraperitoneally injected twice at a 24 h interval. After 7 days of normal feeding, each animal group was treated with ethylbenzene (7 mmol kg-1) or PBS as the secondary exposure. The mice were sacrificed 5 h after the secondary exposure

value: 2 months old

value: liver


title: Day1_veh_rep1

description: Replicate 1 of 4.


title: Ad-control infected

source_name: Mouse liver infected with Ad-control

treatment_protocol: Mice were infected with Ad-control (empty adenovirus vector) or Ad-PDK4 (PDK4 overexpressing adenovirus vector) at a dose of 10^9 PFU/mouse by tail vein injection. 3 days after the infection, mice were sacrificed for RNA preparation from the liver. Ad-control infected = 4, Ad-PDK4 infected = 3. Specimens from mice of each group were pooled, and 10 ug RNA from each pool was used for cRNA synthesis.


title: ethylbenzene followed by PBS (E+P)

source_name: Mouse liver received ethylbenzene injection followed by PBS injection (E+P)


title: untreated rep1

city: Bronx

first: Giulia

last: Calenda

state: NY

address: 1300 Morris Park Avenue

department: Urology

institute: Albert Einstein College of Medicine

hyb_protocol: Labeling, hybridization and scanning were performed by the Affymetrix facility at Albert Einstein College of Medicine following standard Affymetrix protocols

data_processing: Gene expression in the silenced cells was compared with controls using AffylmGUI software, from www.bioconductor.org

source_name: human corporal smooth muscle cells, untreated

growth_protocol: Penile tissue was obtained from patients undergoing surgery for implantation of prostheses. Explant cell cultures were grown in DMEM, 10% fetal bovine serum (Invitrogen)

extract_protocol: Cells were harvested 48h after transfection and RNA was isolated using RNeasy Mini Kit (Quiagen). Efficacy of silencing (>90%) was confirmed by quantitative RT-PCR.

treatment_protocol: Silencing of MaxiK expression was obtained using Stealth Select RNAi (Invitrogen). Cultured cells were transfected with 30nM siRNA using Lipofectamine RNAiMAX transfection reagent (Invitrogen) following the instructions of the manufacturer.

value: corpus cavernosum smooth muscle cell


title: ethylbenzene followed by ethylbenzene (E+E)

source_name: Mouse liver received ethylbenzene injection followed by ethylbenzene injection (E+E)


title: Ad-PDK4 infected

source_name: Mouse liver infected with Ad-PDK4


title: PBS followed by ethylbenzene (P+E)

source_name: Mouse liver received PBS injection followed by ethylbenzene injection (P+E)


title: untreated rep3

scan_protocol: Labeling, hybridization and scanning were performed by the Affymetrix facility at Albert Einstein College of Medicine following standard Affymetrix protocols


title: untreated rep2

label_protocol: Labeling, hybridization and scanning were performed by the Affymetrix facility at Albert Einstein College of Medicine following standard Affymetrix protocols


title: 48h siRNA rep4

source_name: human corporal smooth muscle cells, MaxiK expression silenced for 48h


title: Sorted positive cells at E17.5 rep2

city: Suita

first: Takahisa

last: Furukawa

state: Osaka

address: 6-2-4 Furuedai

department: Developmental Biology

institute: Osaka Bioscience Institute

description: Gene expression data from sorted EGFP positive cells

hyb_protocol: cRNA was hybridized to GeneChip mouse genome 430 2.0 arrayin Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: Signal intensity was determined using GeneChip Operating Software 1.4. MoEx-1_0-st-v1.r2.pgf. MoEx-1_0-st-v1.r2.dt1.mm8.mps. Quantile normalized gene expression values were obtained with GeneSpring software. The normalization method is RMA algorithm. We adoptated a threshold  at signal intensity 20.

source_name: BAC-Crx-EGFP-positive-retina

label_protocol: Biotin-labeled cRNA was prepared using IVT labeling kit.

growth_protocol: Mice were housed in a temperature-controlled room with a 12 h light/dark cycle.  Fresh water and rodent diet were available at all times.

extract_protocol: Total RNA (100ng) of the sorted positive or negative cells were isolated using TRIzol reagent (Invitrogen). The whole taranscript cDNA synthesis and amplification kit (Affymetrix) conform to the manufacture’s instruction.

treatment_protocol: The mouse retinas were dissected using forceps.

value: EGFP positive retinal cells

value: BAC-Crx-EGFP

tag: genetic background


title: Sorted negative cells at E17.5 rep2

description: Gene expression data from sorted EGFP negative cells

source_name: BAC-Crx-EGFP-negative-retina

value: EGFP negative retinal cells


title: Sorted negative cells at E17.5 rep1


title: 48h siRNA rep2


title: Sorted positive cells at E17.5 rep1


title: 48h siRNA rep3


title: 48h siRNA rep1


title: IgG control replicate 3 array A

status: Public on Dec 24 2010

type: genomic

city: Barcelona

first: Luciano

last: Di Croce

address: Dr. Aiguader, 88

country: Spain

institute: Centre for Genomic Regulation

description: Biological replicate 2 of 3, IgG versus treated reference (1h), array A

hyb_protocol: Three biological replicate experiments were performed for each hybridisation of IP sample versus reference

scan_protocol: Fluorescent images were obtained using an Agilent G2565BA scanner at 100% PMT 100% laser power settings and quantified through the Featrue Extraction software (Agilent Technology) version 9.5.3.1

data_processing: Absolute foreground and background readings from channels were used as input to the chipper program. Default parameters were used as defined in the original paper. Chipper calculates q-values (corrected p-values) thus accounting for multiple testing corrections per probe. Probes with q-values < 0.05 were accepted as significant. Probes, which are significantly bound by ZRF1, were compared to those significantly bound by IgG to subtract IgG targets. ZRF1 targets were mapped to genes according to the information provided by Agilent.

molecule: genomic DNA

source_name: NTERA2 (NT2/D1) cells lines, IgG

label_protocol: 2000ng of DNA were labelled using random primers and exo-Klenow fragments wiht the Agilent Genomic DNA Labeling Kit PLUS (Agilent p/n 5188-5309), and hybridized following the manufacturer’s instructions (Agilent Mammalian ChIP-on-chip protocol, version 10.0, December 2007).

growth_protocol: The embryonic carcinoma cell line NTERA2 (NT2/D1) were cultured in DMEM medium supplemented with 10 % FBS at 37 ºC and 5% CO2.

extract_protocol: Cells were either kept untreated or were treated with RA at 0.01 µM for 1 and 3hours. Immunoprecipitated material was amplified following the modified WGA Sigma protocol as described by O'Geen et al., 2006.

value: IgG

source_name: NTERA2 (NT2/D1) cells lines, reference


title: WT, Rep1

city: Blacksburg

first: Andy

last: Pereira

state: VA

address: Washington Street MC0477

department: Virginia Bioinformatics Institute

institute: Virginia Tech

description: Rice WT control plants

hyb_protocol: 4 µg RNA samples were hybridized to the Affymetrix Rice Genome Array. Hybridization was done using the GeneChip Hybridization, Wash, and Stain kit. The cocktail included 12.5 μg aRNA, control oligo B2, 20x hyb controls of bioB, bioC, bioD, and cre, 2X hyb mix, and DMSO. The hybe mix is heated at 99C for 5 min, 45C for 5 min, and then hybridized for 16h at 45C.

scan_protocol: Arrays were stained using the Affymetrix FS450 fluidics station with FS450_0001 fluidics protocol. Afterwards, arrays were scanned with the Affymetrix Gene Chip Scanner 3000 with HR (high resolution).

data_processing: Raw data were background corrected, normalized and summarized according to the custom CDF using RMA (Irizarry et al., 2003). The custom CDF was built by uniquely mapping 442,810 probe sequences to 35,161 rice gene-based probe sets in the following manner: (i) probes that have perfect sequence identity with a single target gene were selected, (ii) probes mapping to reverse complements of genes were annotated separately as antisense probes (not used in the above counts), and finally, (iii) probes were grouped into probe sets, each corresponding to a single gene, and probe sets having at least 3 unique sequences were retained (>98% probe sets have >=5 probes). Note that these stringent criteria used to construct the CDF make it possible to reliably measure expression values of members of multigene families (free from cross-hybridization between paralogs showing high sequence similarity).

organism: Oryza sativa Japonica Group

source_name: Leaf tissue samples from WT rice plants

label_protocol: RNA preparation/labeling was done using the Affymetrix 3' IVT Express kit, with biotin as label. The cRNA (or aRNA) is purified via by beads and fragmented before hybridization.

growth_protocol: Regenerated transgenic plantlets (see 'treatment protocol') were transferred to the greenhouse in hydroponic culture with a regime of 12 hours light, 28°C, 85% relative humidity and 12 hours dark, 21°C, 60% humidity.

extract_protocol: For RNA isolation, two biological replicate samples of 6 pooled plants each were obtained for the transgenic rice AtSHN lines and WT. RNA was isolated using RNeasy Kit (Qiagen, USA).  Following that, genomic DNA was eliminated using DNase I digestion. RNA quantity/quality measured by the Agilent 2100 Bioanalyzer (Agilent Technolgies, USA)

treatment_protocol: An Arabidopsis SHINE (SHN) gene overexpression construct was made by assembling the individual fragments (promoter, SHN gene, terminator) with appropriate compatible cohesive ends and ligated into the binary vector. The promoter comprised a CaMV 35S promoter fragment extending from -526 to the transcription start site, obtained as a 0.55 Kb HindIII-BamHI fragment from a pBS-SK+ derivative of pDH51 (Pietrzak et al., 1986) . The full length coding region of Arabidopsis SHN2 (At5g11190) was obtained as a BamHI-NotI fragment (Aharoni et al., 2004) and a CaMV 35S terminator fragment was obtained as a 0.21 Kb NotI-EcoRI fragment from a pBS-SK+ derivative of pDH51 (Pietrzak et al., 1986). The construct was made in the binary vector pMOG22 (ZENECA-MOGEN, NL), which contains a chimeric CaMV 35S-hygromycin phosphotransferase-tNos for selection during transformation. Agrobacterium-mediated transformation of Oryza sativa ssp. japonica cv. Nipponbare, plant regeneration and growth were performed (Greco et al., 2001), using the Agrobacterium strain AGL-1.

value: Leaf

value: WT


title: NT2 RA treated 1h replicate 3 array A

description: Biological replicate 3 of 3, ZRF1 IP versus reference, treated with Retinoic Acid 1h, array A

source_name: NTERA2 (NT2/D1) cells lines, ZRF1 IP, RA treated 1h

treatment_protocol: Cells were either kept untreated or were treated with RA at 0.01 µM for 1 and 3hours. Immunoprecipitated material was amplified following the modified WGA Sigma protocol as described by O'Geen et al., 2006.

value: treated with RA (1h)

source_name: NTERA2 (NT2/D1) cells lines, reference, RA treated 1h


title: Rice AtSHN line, Rep2

description: Rice plants transformed with Arabidopsis SHN (AtSHN) gene

source_name: Leaf tissue samples from rice AtSHN lines

value: Rice AtSHN


title: NT2 RA treated 3h replicate 2 array A

description: Biological replicate 2 of 3, ZRF1 IP versus reference, treated with Retinoic Acid 3h, array A

source_name: NTERA2 (NT2/D1) cells lines, ZRF1 IP, RA treated 3h

value: treated with RA (3h)

source_name: NTERA2 (NT2/D1) cells lines, reference, RA treated 3h


title: NT2 RA treated 1h replicate 1 array A

description: Biological replicate 1 of 3, ZRF1 IP versus reference, treated with Retinoic Acid 1h, array A


title: IgG control replicate 2 array A


title: NT2 untreated 0h replicate 1 array A

description: Biological replicate 1 of 3, ZRF1 IP versus reference, untreated 0h, array A

source_name: NTERA2 (NT2/D1) cells lines, ZRF1 IP, untreated

value: untreated (0h)

source_name: NTERA2 (NT2/D1) cells lines, reference, untreated


title: WT, Rep2

description: Rice WT control plants


title: Rice AtSHN line, Rep1


title: NT2 untreated 0h replicate 3 array A

description: Biological replicate 3 of 3, ZRF1 IP versus reference, untreated 0h, array A


title: NT2 RA treated 3h replicate 3 array A

description: Biological replicate 3 of 3, ZRF1 IP versus reference, treated with Retinoic Acid 3h, array A


title: IgG control replicate 1 array A

description: Biological replicate 1 of 3, IgG versus treated reference (1h), array A


title: NT2 RA treated 3h replicate 1 array A

description: Biological replicate 1 of 3, ZRF1 IP versus reference, treated with Retinoic Acid 3h, array A


title: NT2 RA treated 1h replicate 2 array A

description: Biological replicate 2 of 3, ZRF1 IP versus reference, treated with Retinoic Acid 1h, array A


title: NT2 untreated 0h replicate 2 array A

description: Biological replicate 2 of 3, ZRF1 IP versus reference, untreated 0h, array A


title: IDC-56

city: Montreal

first: Sean

last: Cory

state: QC

address: 3649 Promenade Sir William Osler

department: Goodman Cancer centre

country: Canada

institute: McGill

hyb_protocol: 750ng of labelled cDNA was hybridised onto Agilent Whole Genome Oligo Microarrays

scan_protocol: Scanned on an Agilent G2565A scanner.

data_processing: Agilent Feature Extraction Software (v 9.1) was used for background subtraction and LOWESS normalization and RMA

label_protocol: Total RNA was amplified and labelled using Agilent LOW RNA Input Fluorescent Linear Amplification Kit

extract_protocol: Total RNA was extracted from each sample using the Rneasy Mini Kit (Qiagen, Hilden, Germany)

tag: serialnumber

tag: diagnosis

value: IDC

tag: diagnosisyr

tag: death

tag: deathmonths

tag: eortc

tag: elston

tag: grade

tag: size

tag: xray

tag: chemo

tag: hormonetreatment

tag: er

tag: pr

tag: lymph

value: NORMAL


title: DCIS-6

value: DCIS

tag: age

value: LUMINAL A


title: MIXED-39

value: MIXED

value: BASAL


title: IDC-68

value: HER 2


title: DCIS-8


title: IDC-45


title: IDC-25

value: LUMINAL B


title: MIXED-65


title: MIXED-96


title: MIXED-74


title: MIXED-36


title: MIXED-48


title: IDC-11


title: IDC-43


title: IDC-9


title: DCIS-2


title: TCP3-SRDX induced 10d seedling replicate 3

description: Biological replicate 3 of 3. 10 day seedling harboring pXVE:TCP3-SRDX, treated with estradiol or DMSO, harvested after 36 hr treatment

source_name: 10d seedling harboring pXVE:TCP3-SRDX treated with DMSO

tag: genotype

tag: strain

value: T2 mixture of no. 3

value: 10 day after germination

tag: tissue

value: whole seedling

tag: treatment

value: DMSO for 24 hr

tag: ecotype

source_name: 10d seedling harboring pXVE:TCP3-SRDX treated with estradiol

value: 5µM estradiol in DMSO for 24 hr


title: MIXED-86

tag: serialnumber

tag: diagnosis

tag: diagnosisyr

tag: death

tag: deathmonths


title: MIXED-87

tag: eortc

tag: elston

tag: grade

tag: size

tag: xray


title: DCIS-23

tag: chemo

tag: hormonetreatment

tag: er

tag: pr

tag: lymph


title: IDC-46

tag: age


title: DCIS-41


title: MIXED-88


title: DCIS-55


title: MIXED-30


title: IDC-12


title: MIXED-78


title: MIXED-49


title: DCIS-67


title: MIXED-33


title: MIXED-29


title: MIXED-76


title: IDC-57


title: MIXED-53


title: DCIS-7


title: DCIS-5


title: DCIS-1


title: MIXED-21


title: MIXED-3


title: MIXED-13


title: MIXED-204


title: DCIS-24


title: IDC-188


title: IDC-26


title: IDC-113


title: IDC-198


title: DCIS-192


title: NORMAL-303


title: NORMAL-305


title: NORMAL-306


title: NORMAL-302


title: MIXED-136


title: DCIS-120


title: MIXED-162


title: NORMAL-304


title: DCIS-102


title: IDC-151


title: IDC-169


title: DCIS-143


title: IDC-209


title: DCIS-194rep2


title: IDC-137


title: MIXED-167


title: DCIS-153


title: DCIS-222


title: MIXED-129


title: MIXED-208


title: IDC-141


title: IDC-174


title: MIXED-164


title: MIXED-238


title: IDC-232


title: MIXED-112


title: DCIS-177


title: DCIS-220


title: IDC-218


title: DCIS-100


title: DCIS-142


title: IDC-145


title: NORMAL-301rep2


title: IDC-148


title: MIXED-117


title: DCIS-116


title: DCIS-115


title: IDC-122


title: IDC-221


title: MIXED-229


title: MIXED-219


title: Canine epithelial cells, monolayer stage, rep3

city: San Francisco

first: SH

last: Kwon

address: 600 16th St./N214 Mostov lab

institute: University of California San Francisco

description:
Monolayer-T0_3
Before co-culture with MRC-5 fibroblasts.

hyb_protocol: Labeled cRNA was assessed using the Nandrop ND-100, and equal amounts of Cy3-labeled target were hybridized to Agilent Whole Genome Canine arrays. Hybridizations were performed for 14 hrs, according to the manufacturer's protocol.

scan_protocol: Arrays were scanned using the Agilent microarray scanner (Agilent).

data_processing: Raw signal intensities were extracted with Feature Extraction v9.1 software (Agilent). The dataset was normalized using the quantile normalization method. The median feature pixel intensity was used as the raw signal before normalization and no background subtraction was performed.

organism: Canis lupus familiaris

source_name: epithelial cells, monolayer stage

label_protocol: 400ng of RNA was amplified and labeled with Cy3 using the One-Color Agilent Low RNA Input Linear Amplification Kit.

growth_protocol: To induce tubule formation, MDCK monolayer grown on the top of thick collagen matrix was co-cultured with MRC-5 fibroblasts.

extract_protocol: Total RNA was extracted using Trizol and further purified and concentrated with Rneasy MinElute (Qiagen).

tag: cell type

value: epithelial cells

tag: morphological stage

value: monolayer


title: IDC-130

tag: serialnumber

tag: diagnosis


title: IDC-247

tag: diagnosisyr

tag: death


title: MIXED-51rep2

tag: deathmonths

tag: eortc


title: Canine epithelial cells, tubule stage, rep4

description:
Tubule-T2_4
144 hr after co-culture with MRC-fibroblasts.

source_name: epithelial cells, tubule stage

value: tubule


title: Canine epithelial cells, monolayer stage, rep2

description:
Monolayer-T0_2
Before co-culture with MRC-5 fibroblasts.


title: Canine epithelial cells, tubule stage, rep2

description:
Tubule-T2_2
144 hr after co-culture with MRC-fibroblasts.


title: Canine epithelial cells, tubule stage, rep3

description:
Tubule-T2_3
144 hr after co-culture with MRC-fibroblasts.


title: Canine epithelial cells, extension stage, rep4

description:
Extension-T1_4
72 hr after co-culture with MRC-5 fibroblasts.

source_name: epithelial cells, extension stage

value: extension


title: Canine epithelial cells, extension stage, rep3

description:
Extension-T1_3
72 hr after co-culture with MRC-5 fibroblasts.


title: Canine epithelial cells, monolayer stage, rep4

description:
Monolayer-T0_4
Before co-culture with MRC-5 fibroblasts.


title: Canine epithelial cells, extension stage, rep2

description:
Extension-T1_2
72 hr after co-culture with MRC-5 fibroblasts.


title: shZRF1 vs shRandom 3h replicate 3 dye swap

description: Biological replicate 3 of 3, Technical replicate 2 of 2, ZRF1 knockdown versus control cells, treated with Retinoic Acid 3 h

hyb_protocol: Three biological replicate experiments were performed for analyzing differences between ZRF1 knockdown cells and control cells, once untreated and once treated with Retinoic Acid. For all three three biological replicates each experimental pair of labelled samples was co-hybridized on two separate microarrays with dye swapping to correct for dye bias effects. Thus, up to six microarray hybridizations were processed for each of the two comparisons shZRF1 untreated vs shRandom untreated and shZRF1 treated vs shRandom treated, totalling 12 array datasets.

scan_protocol: Fluorescent images were obtained using an Agilent G2565BA scanner at 110% PMT 110% laser power settings and quantified through the GenePix 6.0 software (Axon, Molecular Devices, Sunnywale, CA) using the irregular feature finding option.

data_processing: Raw data was analysed using the Limma package. The median background intensity was subtracted from median foreground intensity. Values less that 20 were set to 20. Then all the triplicates from the two experiments were normalised together using vsn normalisation. Vsn returns log2-transformed intensities.

source_name: NTERA2 (NT2/D1) control cells treated (3h)

label_protocol: 500 ng of total RNA were labelled by in vitro transcription using the Quick Am Labeling Kit Two color (Agilent 5190-0444), and hybridized following the manufacturer’s instructions (Two-Color Microarray-Based Gene Expression Analysis-Quick Amp Labeling protocol, version 5.7, March 2008).

extract_protocol: RNA was extracted by the RNeasy extraction kit from Qiagen.

treatment_protocol: Cells were either kept untreated or were treated with RA at 0.01 µM for 3hours.

tag: cell line

value: NTERA2 (NT2/D1) shRandom

tag: treatment

value: treated with RA (3h)

source_name: NTERA2 (NT2/D1) ZRF1 knockdown cells treated (3h)

value: NTERA2 (NT2/D1) shZRF6


title: IDC-190

value: IDC

tag: elston

tag: grade

tag: size

tag: xray


title: IDC-241

tag: chemo

tag: hormonetreatment

tag: er

tag: pr


title: Canine epithelial cells, tubule stage, rep1

description:
Tubule-T2_1
144 hr after co-culture with MRC-fibroblasts.

tag: cell type

tag: morphological stage


title: shZRF1 vs shRandom 3h replicate 2 dye swap

description: Biological replicate 2 of 3, Technical replicate 2 of 2, ZRF1 knockdown versus control cells, treated with Retinoic Acid 3 h

value: NTERA2 (NT2/D1) shZRF5


title: DCIS-183

tag: serialnumber

tag: diagnosis

value: DCIS

tag: age

tag: lymph

value: NORMAL


title: DCIS-228

tag: diagnosisyr

tag: death

tag: deathmonths

tag: eortc


title: shZRF1 vs shRandom 3h Replicate 3

description: Biological replicate 3 of 3, Technical replicate 1 of 2, ZRF1 knockdown versus control cells, treated with Retinoic Acid 3 h

tag: cell line

tag: treatment


title: Canine epithelial cells, monolayer stage, rep1

description:
Monolayer-T0_1
Before co-culture with MRC-5 fibroblasts.


title: Canine epithelial cells, extension stage, rep1

description:
Extension-T1_1
72 hr after co-culture with MRC-5 fibroblasts.


title: IDC-111

tag: elston

tag: grade

tag: size

tag: xray

value: BASAL


title: IDC-4

tag: chemo

tag: hormonetreatment

tag: er

tag: pr


title: shZRF1 vs shRandom 3h Replicate 2

description: Biological replicate 2 of 3, Technical replicate 1 of 2, ZRF1 knockdown versus control cells, treated with Retinoic Acid 3 h


title: shZRF1 vs shRandom 0h replicate 3 dye swap

description: Biological replicate 3 of 3, Technical replicate 2 of 2, ZRF1 knockdown versus control cells, untreated 0h

source_name: NTERA2 (NT2/D1) control cells untreated (0h)

value: untreated (0h)

source_name: NTERA2 (NT2/D1) ZRF1 knockdown cells untreated (0h)

value: NTERA2 (NT2/D1) shZRF3


title: MIXED-106

tag: serialnumber

tag: diagnosis

value: MIXED


title: MIXED-59

tag: age

tag: lymph

value: HER 2


title: IDC-44

tag: diagnosisyr

tag: death

value: LUMINAL A


title: shZRF1 vs shRandom 3h replicate 1 dye swap

description: Biological replicate 1 of 3, Technical replicate 2 of 2, ZRF1 knockdown versus control cells, treated with Retinoic Acid 3 h

value: NTERA2 (NT2/D1) shZRF4


title: MIXED-89

tag: deathmonths

tag: eortc

value: LUMINAL B


title: MIXED-239


title: shZRF1 vs shRandom 0h Replicate 1

description: Biological replicate 1 of 3, Technical replicate 1 of 2, ZRF1 knockdown versus control cells, untreated 0h

tag: cell line

value: NTERA2 (NT2/D1) shZRF1

tag: treatment


title: MIXED-72

tag: elston

tag: grade


title: MIXED-69

tag: size

tag: xray


title: shZRF1 vs shRandom 0h replicate 1 dye swap

description: Biological replicate 1 of 3, Technical replicate 2 of 2, ZRF1 knockdown versus control cells, untreated 0h


title: npr1-7 mock 1

first: Hiroshi

last: Takatsuji

address: 2-1-2 Kannondai

department: Division of Plant Sciences

institute: National Institute of Agrobiological Sciences

hyb_protocol: Agilent protocol G4140-90040

scan_protocol: Slides were scanned immediately after washing on Agilent Scanner model G2505B and software G2565BA using default parameters

data_processing: The scanned images were analyzed with Feature Extraction software (version 9.1; Agilent Technologies) using default parameters. We used GeneSpring software and processed the data with the setting of Per Gene: normalize to specific samples.

organism: Oryza sativa

source_name: WRKY45-knockdown rice npr1-7 treated with 0.01%  DMSO

label_protocol: The RNAs (400-ng aliquots) were labeled with a Low RNA Input Linear Amplification/Labeling Kit (Agilent Technologies)

extract_protocol: Total RNA was isolated using an RNeasy plant mini kit (Qiagen).

treatment_protocol: seedlings at the four-leaf stage were excised around 5 mm above the soil surface and held in a solution containing 10 μM BTH or 0.01% DMSO (mock) for 24 h

tag: tissue

value: 4th leaves at 4-leaf stage

tag: line

value: WRKY45-knockdown npr1-7


title: MIXED-38

tag: chemo

tag: hormonetreatment

tag: er

tag: pr


title: DCIS-250

tag: serialnumber

tag: diagnosis

tag: age

tag: lymph


title: DCIS-42

tag: diagnosisyr

tag: death

tag: deathmonths

tag: eortc


title: shZRF1 vs shRandom 0h Replicate 2

description: Biological replicate 2 of 3, Technical replicate 1 of 2, ZRF1 knockdown versus control cells, untreated 0h

tag: cell line

value: NTERA2 (NT2/D1) shZRF2

tag: treatment

value: NTERA2 (NT2/D1) shRandom


title: DCIS-104

tag: elston

tag: grade

tag: size

tag: xray


title: npr1-7 mock 3

tag: tissue

tag: line


title: IDC-256

value: IDC

tag: chemo

tag: hormonetreatment

tag: er

tag: pr


title: npr1-7 mock 2


title: shZRF1 vs shRandom 3h Replicate 1

description: Biological replicate 1 of 3, Technical replicate 1 of 2, ZRF1 knockdown versus control cells, treated with Retinoic Acid 3 h

value: treated with RA (3h)


title: shZRF1 vs shRandom 0h Replicate 3

description: Biological replicate 3 of 3, Technical replicate 1 of 2, ZRF1 knockdown versus control cells, untreated 0h


title: npr1-7 BTH 4

source_name: WRKY45-knockdown rice npr1-7 treated with 10 µM BTH


title: IDC-107

tag: serialnumber

tag: diagnosis

tag: age

tag: lymph


title: DCIS-123

value: DCIS

tag: diagnosisyr

tag: death

tag: deathmonths

tag: eortc


title: shZRF1 vs shRandom 0h replicate 2 dye swap

description: Biological replicate 2 of 3, Technical replicate 2 of 2, ZRF1 knockdown versus control cells, untreated 0h

tag: cell line

tag: treatment


title: MIXED-135

tag: elston

tag: grade

tag: size

tag: xray


title: npr1-7 BTH 3

tag: tissue

tag: line


title: MIXED-214

tag: chemo

tag: hormonetreatment

tag: er

tag: pr

value: NORMAL


title: npr1-7 mock 4


title: npr1-14 mock 4

source_name: WRKY45-knockdown rice npr1-14 treated with 0.01%  DMSO

value: WRKY45-knockdown npr1-14


title: npr1-14 mock 1


title: aneurysm_ruptured_rep7

city: Kuopio

first: Mitja

last: Kurki

address: Yliopistonranta 1 E

country: Finland

institute: University of Eastern Finland

description: no additional information

hyb_protocol: Twenty micrograms of purified cRNA was hybridized to Human Genome U133 Plus 2.0 GeneChips (Affymetrix Inc., Santa Clara, CA). The chips were stained and washed using Affymetrix Fluidics Station 400 according to manufacturers instruction

scan_protocol: GeneChips where scanned using Affymetrix GeneChip Scanner 3000 according to manufacturers instructions

data_processing: GeneSpring implementation of RMA algorithm was used for background correction, normalization across arrays, and summarizing probe values

source_name: ruptured aneurysm

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix two-cycle amplification protocol from 100 ng of RNA

extract_protocol: Total RNA exrtaction was performed using Trizol Reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions

treatment_protocol: The samples were snap frozen in liquid nitrogen after surgical clipping from patients

tag: ruptured aneurysm


title: npr1-14 mock 3


title: npr1-14 BTH 3

source_name: WRKY45-knockdown rice npr1-14 treated with 10 µM BTH


title: MIXED-200

tag: serialnumber

tag: diagnosis

tag: diagnosisyr

tag: age

tag: lymph


title: DCIS-210

tag: death

tag: deathmonths

tag: eortc

value: BASAL


title: aneurysm_ruptured_rep10

description: no additional information


title: aneurysm_ruptured_rep11

description: no additional information


title: npr1-14 mock 2

source_name: WRKY45-knockdown rice npr1-14 treated with  0.01%  DMSO


title: npr1-14 BTH 4


title: NB mock 4

source_name: Nipponbare wild-type rice treated with  0.01%  DMSO

tag: genotype

value: Nipponbare


title: NB mock 3

source_name: Nipponbare wild-type rice treated with 0.01%  DMSO


title: npr1-14 BTH 1


title: npr1-7 BTH 1


title: aneurysm_ruptured_rep8

description: no additional information


title: aneurysm_ruptured_rep9

description: no additional information


title: IDC-211

tag: elston

tag: grade

tag: size

tag: xray


title: npr1-14 BTH 2

tag: tissue

tag: line


title: aneurysm_unruptured_rep7

description: no additional information

source_name: unruptured aneurysm

tag: unruptured aneurysm


title: aneurysm_unruptured_rep8

description: no additional information


title: NT2 RA treated 1h replicate 3 array B

description: Biological replicate 3 of 3, ZRF1 IP versus reference, treated with Retinoic Acid 1h, array B

source_name: NTERA2 (NT2/D1) cells lines, ZRF1 IP, RA treated 1h

tag: treatment

value: treated with RA (1h)

source_name: NTERA2 (NT2/D1) cells lines, reference, RA treated 1h


title: NT2 RA treated 3h replicate 1 array B

description: Biological replicate 1 of 3, ZRF1 IP versus reference, treated with Retinoic Acid 3h, array B

source_name: NTERA2 (NT2/D1) cells lines, ZRF1 IP, RA treated 3h

source_name: NTERA2 (NT2/D1) cells lines, reference, RA treated 3h


title: IgG control replicate 2 array B

description: Biological replicate 2 of 3, IgG versus treated reference (1h), array B

source_name: NTERA2 (NT2/D1) cells lines, IgG

value: IgG

source_name: NTERA2 (NT2/D1) cells lines, reference


title: IgG control replicate 3 array B


title: NB mock 1


title: IgG control replicate 1 array B

description: Biological replicate 1 of 3, IgG versus treated reference (1h), array B


title: NB BTH 3

source_name: Nipponbare wild-type rice treated with 10 µM BTH


title: NT2 RA treated 3h replicate 2 array B

description: Biological replicate 2 of 3, ZRF1 IP versus reference, treated with Retinoic Acid 3h, array B


title: NT2 RA treated 3h replicate 3 array B

description: Biological replicate 3 of 3, ZRF1 IP versus reference, treated with Retinoic Acid 3h, array B


title: aneurysm_unruptured_rep5

description: no additional information


title: aneurysm_unruptured_rep2

description: no additional information


title: NB BTH 2


title: NB BTH 4


title: aneurysm_unruptured_rep1

description: no additional information


title: aneurysm_ruptured_rep6

description: no additional information

tag: ruptured aneurysm


title: aneurysm_ruptured_rep4

description: no additional information


title: aneurysm_unruptured_rep4

description: no additional information


title: aneurysm_ruptured_rep5

description: no additional information


title: aneurysm_ruptured_rep3

description: no additional information


title: aneurysm_unruptured_rep3

description: no additional information


title: NB mock 2


title: aneurysm_unruptured_rep6

description: no additional information


title: NT2 RA treated 1h replicate 2 array B

description: Biological replicate 2 of 3, ZRF1 IP versus reference, treated with Retinoic Acid 1h, array B


title: aneurysm_ruptured_rep2

description: no additional information


title: NT2 RA treated 1h replicate 1 array B

description: Biological replicate 1 of 3, ZRF1 IP versus reference, treated with Retinoic Acid 1h, array B


title: CGH_QUIGLEY_T9

status: Public on Dec 23 2010

first: David

last: Quigley

address: 1450 Third St. Room 207

department: Helen Diller Comprehensive Cancer Center

institute: UCSF

hyb_protocol: The test and reference DNAs were hybridized to the BAC arrays for ~48 hrs at 37C. After post-hybridization washes, the arrays were mounted in a solution containing 90% glycerol, 10% PBS and 1 uM DAPI and sealed with a cover slip.

scan_protocol: A custom built CCD camera system was used to acquire 16 bit 1024x1024 pixel DAPI, Cy3 and Cy5 images (Pinkel et al., 1998). Image analysis was carried out using UCSF SPOT software (Jain et al., 2002).

data_processing: The log2ratio of the total integrated Cy3 and Cy5 intensities for each spot after background subtraction was calculated, normalized to the median log2ratio of all the clones on the array and the average of the triplicates calculated using a second custom program, SPROC. Automatic data filtering to reject data points based on low DAPI intensity, low correlation between Cy3 and Cy5 within each segmented spot and low reference/DAPI signal intensity was also carried out using SPROC. Data files were subsequently manually edited by rejecting clones for which only one spot of the triplicate survived after SPROC analysis and for which the standard deviation of the log2ratio of the triplicate was >0.2. For each tumor, the data are plotted as the mean log2ratio of the triplicate spots for each clone normalized to the genome median log2ratio. The clones are ordered by position in the genome (NCBI37) beginning at chromosome 1 and ending with chromosome X.

source_name: Skin Carcinoma from [FVBxSpretus]xSpretus backcross

label_protocol: The tumor genomic DNA and normal individually-matched genomic reference DNA (300 ng each) were labeled by random priming in separate 50 ul reactions to incorporate Cy3-dUTP and Cy5-dUTP, respectively.

growth_protocol: Mice were fed standard chow and allowed water ad libitum.

extract_protocol: DNA was extracted from flash-frozen carcinomas by standard techniques. In addition, genomic DNA was extracted from flash-frozen normal mouse tail from the same mouse that contributed the tumor to be used as a matched reference.

treatment_protocol: Tumors were initiated on dorsal back skin with a single dose of DMBA (25 µg per mouse in 200 µl acetone). Starting one week after the initiation tumors were promoted with TPA (200 µl of 10-4 M solution in acetone) twice weekly for 20 weeks.

tag: strain

value: [FVBxSpretus]xSpretus backcross

source_name: Matched tail epidermis from [FVBxSpretus]xSpretus backcross


title: aneurysm_ruptured_rep1

description: no additional information


title: CGH_QUIGLEY_T10_1


title: npr1-7 BTH 2

source_name: WRKY45-knockdown rice npr1-7 treated with 10 µM BTH


title: CGH_QUIGLEY_T14_2


title: CGH_QUIGLEY_T14_1


title: CGH_QUIGLEY_T7


title: CGH_QUIGLEY_T13


title: CGH_QUIGLEY_T4


title: CGH_QUIGLEY_T10_2


title: CGH_QUIGLEY_T12


title: NB BTH 1


title: NT2 untreated 0h replicate 1 array B

description: Biological replicate 1 of 3, ZRF1 IP versus reference, untreated 0h, array B

source_name: NTERA2 (NT2/D1) cells lines, ZRF1 IP, untreated

value: untreated (0h)

source_name: NTERA2 (NT2/D1) cells lines, reference, untreated


title: NT2 untreated 0h replicate 2 array B

description: Biological replicate 2 of 3, ZRF1 IP versus reference, untreated 0h, array B


title: NT2 untreated 0h replicate 3 array B

description: Biological replicate 3 of 3, ZRF1 IP versus reference, untreated 0h, array B


title: Female A186 vs E17

city: Planegg-Martinsried

first: Stephan

last: Hutter

state: Bavaria

address: Grosshaderner Strasse 2

department: Department of Biology II

country: Germany

institute: University of Munich

description: Competitive hybridization between A186 and E17

hyb_protocol: Hybridizations were performed following CDMC protocols (http://www.flyarrays.com) using Corning microarray hybridization chambers (Corning Incorporated, Corning, NY, USA)

scan_protocol: Scanned on an aQuire microarray scanner (Genetix, New Milton, UK), images were quantified using Genetix QScan software (Version 1.1.8.10)

data_processing: Normalized 647/555 ratios were obtained using CARMAweb (https://carmaweb.genome.tugraz.at/). Dye-swap replicates were normalized as pairs. Local background effects, within-array variation, and between-array variation was corrected using the "minimum", "printtiploess", and "quantile" methods, respectively. Spots passed quality control if they showed mean signal intensities of one standard deviation above background for both channels.

label: Alexa Fluor 647

organism: Drosophila melanogaster

label_protocol: 50 µg of total RNA were reverse transcribed and labeled using the SuperScript Plus Indirect cDNA Labeling System and Alexa Flour dyes (Invitrogen, Carlsbad, CA, USA) following the manufacturer's protocol

growth_protocol: Flies were reared at 22ºC

extract_protocol: TRIzol procedure

tag: sex

value: female

tag: developmental stage

value: adult

value: 4-6 days

value: whole fly

label: Alexa Fluor 555


title: CGH_QUIGLEY_T97


title: CGH_QUIGLEY_T3


title: Female A377 vs E18 dye-swap

description: Competitive hybridization between E18 and A377

tag: age


title: Female A398 vs E16

description: Competitive hybridization between A398 and E16


title: Female A82 vs E20

description: Competitive hybridization between A82 and E20


title: Female A186 vs E17 dye-swap

description: Competitive hybridization between E17 and A186


title: Female A398 vs E16 dye-swap

description: Competitive hybridization between E16 and A398


title: CGH_QUIGLEY_T95_1


title: Female A377 vs E18

description: Competitive hybridization between A377 and E18


title: Female A82 vs E20 dye-swap

description: Competitive hybridization between E20 and A82


title: Female A131 vs E15

description: Competitive hybridization between A131 and E15


title: Female A131 vs E15 dye-swap

description: Competitive hybridization between E15 and A131


title: CGH_QUIGLEY_T89_2


title: CGH_QUIGLEY_T92


title: CGH_QUIGLEY_T93


title: CGH_QUIGLEY_T94


title: CGH_QUIGLEY_T89_1


title: CGH_QUIGLEY_T86


title: Female A95 vs E14 dye-swap

description: Competitive hybridization between E14 and A95


title: Female A384 vs E12 dye-swap

description: Competitive hybridization between E12 and A384


title: Female A384 vs E12

description: Competitive hybridization between A384 and E12


title: CGH_QUIGLEY_T96


title: Female A398 vs A384

description: Competitive hybridization between A398 and A384


title: Female A398 vs A384 dye-swap

description: Competitive hybridization between A384 and A398


title: Female A384 vs A377 dye-swap

description: Competitive hybridization between A377 and A384


title: CGH_QUIGLEY_T85


title: Female A95 vs E14

description: Competitive hybridization between A95 and E14


title: CGH_QUIGLEY_T84


title: CGH_QUIGLEY_T75


title: CGH_QUIGLEY_T82


title: Female A84 vs E01 dye-swap

description: Competitive hybridization between E01 and A84


title: CGH_QUIGLEY_T66


title: CGH_QUIGLEY_T63_star


title: CGH_QUIGLEY_T72


title: CGH_QUIGLEY_T62_star


title: CGH_QUIGLEY_T61_star


title: Female A84 vs E01

description: Competitive hybridization between A84 and E01


title: Female A377 vs A131

description: Competitive hybridization between A377 and A131


title: Female A186 vs A95 dye-swap

description: Competitive hybridization between A95 and A186


title: Female A384 vs A186

description: Competitive hybridization between A384 and A186


title: CGH_QUIGLEY_T63


title: CGH_QUIGLEY_T61


title: Female A384 vs A186 dye-swap

description: Competitive hybridization between A186 and A384


title: CGH_QUIGLEY_T62


title: Female A186 vs A84 dye-swap

description: Competitive hybridization between A84 and A186


title: Female A186 vs A84

description: Competitive hybridization between A186 and A84


title: Female A384 vs A377

description: Competitive hybridization between A384 and A377


title: Female A398 vs A82 dye-swap

description: Competitive hybridization between A82 and A398


title: Female A186 vs A95

description: Competitive hybridization between A186 and A95


title: Female A377 vs A131 dye-swap

description: Competitive hybridization between A131 and A377


title: CGH_QUIGLEY_T55


title: Female A131 vs A84 dye-swap

description: Competitive hybridization between A84 and A131


title: Female A398 vs A82

description: Competitive hybridization between A398 and A82


title: Female A131 vs A84

description: Competitive hybridization between A131 and A84


title: CGH_QUIGLEY_T54


title: CGH_QUIGLEY_T57


title: Spleen_infected_42hpi_rep3

city: Bangi

first: Sheila

last: Nathan

state: Selangor

address: Jalan Universiti

department: Faculty of Science & Technology

country: Malaysia

institute: Universiti Kebangsaan Malaysia

description: Biological replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: BeadStudio version 1.0 (Illumina, USA) software was used to generate signal intensity values from the scans. Then, the standard normalization procedure for one-colour array data in GeneSpring GX7.3.1 Expression Analysis (Agilent Technologies, USA) was used.

source_name: spleen, 42hpi

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification kit for BeadChip arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

value: BALB/c

value: 7-9 weeks old

value: Spleen

tag: time point (hrs post-infection)


title: Spleen_infected_24hpi_rep3

description: Biological replicate 3

source_name: spleen, 24hpi


title: Liver_uninfected_rep3

description: Biological replicate 3

source_name: liver, uninfected

value: Liver


title: CGH_QUIGLEY_T51_2


title: Female A131 vs A82

description: Competitive hybridization between A131 and A82


title: CGH_QUIGLEY_T51_1


title: CGH_QUIGLEY_T49


title: Spleen_infected_16hpi_rep3

description: Biological replicate 3

source_name: spleen, 16hpi


title: Liver_infected_24hpi_rep3

description: Biological replicate 3

source_name: liver, 24hpi


title: Liver_infected_42hpi_rep3

description: Biological replicate 3

source_name: liver, 42hpi


title: CGH_QUIGLEY_T46


title: Spleen_infected_24hpi_rep2

description: Biological replicate 2


title: CGH_QUIGLEY_T44


title: Liver_uninfected_rep2

description: Biological replicate 2


title: Liver_infected_16hpi_rep3

description: Biological replicate 3

source_name: liver, 16hpi


title: Female A95 vs A82 dye-swap

description: Competitive hybridization between A82 and A95


title: Liver_infected_42hpi_rep2

description: Biological replicate 2


title: Female E20 vs E18

description: Competitive hybridization between E20 and E18


title: Spleen_uninfected_rep2

description: Biological replicate 2

source_name: spleen, uninfected


title: Spleen_infected_42hpi_rep2

description: Biological replicate 2


title: Female A131 vs A82 dye-swap

description: Competitive hybridization between A82 and A131


title: High-grade ovarian cancer cell line OVCAR-3

city: Zurich

first: Jean-Philippe

middle: Paul

last: Theurilllat

address: Schafmattstrasse 18

department: Cell Biology

country: Switzerland

institute: ETH Hönggerberg

description: Human ovarian cell line

hyb_protocol: According to the Affimetrix Cytogenetics Copy Number assay protocol (Human SNP Nsp/Sty 6.0)

data_processing:
Affymetrix Genotyping Console using 67 HapMap files as a reference
CHP files for each cell line containg Log2Ratio with HapMap as reference

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from ovarian cell lines using the Qiagen DNA Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

tag: cell line


title: Female A95 vs A82

description: Competitive hybridization between A95 and A82


title: Female E20 vs E18 dye-swap

description: Competitive hybridization between E18 and E20


title: Female E18 vs E17 dye-swap

description: Competitive hybridization between E17 and E18


title: Liver_infected_24hpi_rep2

description: Biological replicate 2


title: pooled placenta tissues from two GDM women

city: Beijing

first: Dapeng

last: Wang

address: No.7 Beitucheng West Road, Chaoyang District, Beijing 100029, PR China

institute: Beijing Institute of Genomics

data_processing: The data were normalised using cubic spline method with Beadstudio software

source_name: GDM placenta tissues

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays by using 500ng total RNA

extract_protocol: Total RNA of whole blood was obtained using QIAamp RNA Blood Mini Kit (Qiagen) and digested with RNase-Free DNase (Promega) according to the manufacturer’s suggestions. Total RNA of the placenta tissue was obtained using the TRIzol reagent (Invitrogen) according to the manufacturer’s suggestions.

value: placenta


title: Female E18 vs E17

description: Competitive hybridization between E18 and E17


title: High-grade ovarian cancer cell line FU-OV-1

description: Human ovarian cell line

scan_protocol: According to the Affimetrix Cytogenetics Copy Number assay protocol (Human SNP Nsp/Sty 6.0)


title: NAKR1_sample3

city: St. Louis

first: Ivan

last: Baxter

address: 975 North Warson Rd

department: PLant Genetics Research Unit

institute: USDA-ARS

description: NAKR1 mutant array for detection of deletions

hyb_protocol: Affymetrix standard

scan_protocol: Affymetrix standard

source_name: flowers and leaves

label_protocol: Invitrogen Bioprime labelling kit

extract_protocol: Qiagen DNeasy kit

value: mature plants

value: Flowers and Leaves

tag: genetic background

value: nakr1 mutant


title: pooled placenta tissues from two healthy women

source_name: non-GDM placenta tissues


title: NAKR1_sample1

tag: genotype


title: NAKR1_sample2


title: CGH_QUIGLEY_T39


title: CGH_QUIGLEY_T41_1


title: CGH_QUIGLEY_T41_2


title: Spleen_infected_16hpi_rep2

description: Biological replicate 2


title: Col-0_tiling_hyb3

description: Col-0 array control

value: wild type


title: Liver_infected_16hpi_rep2

description: Biological replicate 2


title: CGH_QUIGLEY_T42


title: CGH_QUIGLEY_T38


title: CGH_QUIGLEY_T43


title: Female E17 vs E16

description: Competitive hybridization between E17 and E16


title: Liver_uninfected_rep1

description: Biological replicate 1


title: pooled blood tissues from four GDM women

source_name: GDM blood tissue

value: blood


title: blood tissue from GDM woman


title: Female E20 vs E15

description: Competitive hybridization between E20 and E15


title: Liver_infected_42hpi_rep1

description: Biological replicate 1


title: Spleen_uninfected_rep1

description: Biological replicate 1


title: pooled blood tissues from four healthy women

source_name: non-GDM blood tissue


title: Female E20 vs E15 dye-swap

description: Competitive hybridization between E15 and E20


title: Female E17 vs E16 dye-swap

description: Competitive hybridization between E16 and E17


title: Col-0_tiling_hyb1

description: Col-0 array control


title: Col-0_tiling_hyb2

description: Col-0 array control


title: CGH_QUIGLEY_T69

source_name: Skin Carcinoma from [FVBxSpretus]xSpretus backcross

source_name: Matched tail epidermis from [FVBxSpretus]xSpretus backcross


title: Spleen_infected_24hpi_rep1

description: Biological replicate 1


title: CGH_QUIGLEY_T35


title: Female E16 vs E15 dye-swap

description: Competitive hybridization between E15 and E16


title: CGH_QUIGLEY_T37


title: Liver_infected_24hpi_rep1

description: Biological replicate 1


title: CGH_QUIGLEY_T31


title: Female E15 vs E14 dye-swap

description: Competitive hybridization between E14 and E15


title: CGH_QUIGLEY_T32


title: Spleen_infected_16hpi_rep1

description: Biological replicate 1


title: CGH_QUIGLEY_T29


title: Female E17 vs E12 dye-swap

description: Competitive hybridization between E12 and E17


title: CGH_QUIGLEY_T34


title: Spleen_infected_42hpi_rep1

description: Biological replicate 1


title: Liver_infected_16hpi_rep1

description: Biological replicate 1


title: Female E14 vs E12 dye-swap

description: Competitive hybridization between E12 and E14


title: Female E15 vs E14

description: Competitive hybridization between E15 and E14


title: MSC-BM-Fetal

city: Singapore

first: FAN

last: ZHOU

address: 8A Biomedical Grove

country: Singapore

institute: Institute of Medical Biolog

description: SAMPLE 22

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalization (Illumina BeadStudio 3.2).

source_name: MSC, fetal bone marrow

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

extract_protocol: RNA was extracted with Trizol reagent, followed by the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: group name

value: MSC-BM-Fetal

tag: tissue source

value: fetal bone marrow

tag: cell type

value: mesenchymal stem cells from fetal bone marrow


title: Female E16 vs E15

description: Competitive hybridization between E16 and E15

value: female


title: CGH_QUIGLEY_T28

value: [FVBxSpretus]xSpretus backcross


title: MSC-BM-Adult

description: SAMPLE 23

source_name: MSC, adult bone marrow

value: MSC-BM-Adult

value: adult bone marrow

value: mesenchymal stem cells from adult bone marrow


title: HGPS-iPS-MSC-2

description: SAMPLE 20

source_name: MSC, HPGS-iPS

value: HGPS-iPS-MSC

value: skin

value: mesenchymal stem cells derived from HPGS-iPS


title: Drought treated young panicle at booting stage, biological rep2

first: pan

last: yajiao

address: Zhongguancun South Street No.12

institute: The chinese academy of agriculture sciences

description: DK151, a drought tolerant line from IR64

hyb_protocol: RNA from the three independent replicate samples were used for hybridization to the Affymetrix Genechips® Rice Genome Array chips, which contain probes to query 51,279 transcripts from two rice cultivars, including 48,564 japonica transcripts and 1,260 indica transcripts from Affymetrix (Santa Clara, CA).Hybridization to the arrays and quality control checks were carried out at the Company of CapitalBio Corporation, Beijing. (Affymetrix GeneChip Expression Analysis g of this fragmented target cRNA wasmTechnical Manual).

scan_protocol: Affy- Array Scanning

data_processing: The SAM (Significant Analysis of Microarray) software was applied to identify differentially regulated genes (DRGs) between samples using the two classes unpaired method based on the empirical criterion of more than two-fold change and significant q value (FDR adjusted P value) less than 0.05. A list of known or unknown genes was generated by performing a BLASTn search (http://www.ncbi.nlm.nih.gov/blast/Blast.cgi) from the Affymetrix website

source_name: Oryza DK151, panicle

label_protocol: Biotin labeled cRNA was produced with 5 ug of total RNA as starting material for each sample reaction.

growth_protocol: Rice plants were grown in PVC tubes (size: 75 cm×20 cm, each with a 20 cm hole from the bottom) with Turface and watered with 0.5×Yoshida.

extract_protocol: Total RNA were extracted using TRIzol reagents according to the instruction and then purified and concentrated using RNeasy MinElute Cleanup kit (Qiagen).

treatment_protocol: Drought stress was processed by slowly draining the solution until leaf relative water content was 65%–75%.

value: panicle

value: booting stage


title: Female E20 vs E01 dye-swap

description: Competitive hybridization between E01 and E20

value: adult

value: 4-6 days

value: whole fly


title: HGPS-iPS-MSC-1

description: SAMPLE 19

hyb_protocol: Standard Illumina hybridization protocol.


title: Female E14 vs E12

description: Competitive hybridization between E14 and E12


title: CGH_QUIGLEY_T26


title: hES-MSC

description: SAMPLE 21

source_name: MSC, hESC

value: hES-MSC

value: embryo

value: mesenchymal stem cells derived from hES


title: CGH_QUIGLEY_T25


title: CGH_QUIGLEY_T24


title: Female E17 vs E12

description: Competitive hybridization between E17 and E12


title: Drought treated young panicle at booting stage, biological rep1

value: DK151, a drought tolerant line from IR64


title: Drought treated young panicle at booting stage, biological rep3


title: normal young panicle at booting stage, biological rep3


title: CGH_QUIGLEY_T22


title: Female E20 vs E01

description: Competitive hybridization between E20 and E01

value: female


title: normal young panicle at booting stage, biological rep2


title: Female E12 vs E01

description: Competitive hybridization between E12 and E01


title: N-iPS-MSC-1

description: SAMPLE 17

source_name: MSC, N-iPS

value: N-iPS-MSC

value: mesenchymal stem cells derived from N-iPS


title: N-iPS-MSC-2

description: SAMPLE 18


title: CGH_QUIGLEY_T19

value: [FVBxSpretus]xSpretus backcross


title: Drought treated leaves at booting stage, biological rep3

source_name: Oryza DK151, leaf

value: leaf


title: normal young panicle at booting stage, biological rep1


title: CGH_QUIGLEY_T17


title: PG2-Fib

description: SAMPLE 16

source_name: HGPS skin fibroblasts

value: HGPS-Fib

value: Hutchinson-Gilford Progeria syndrome (HGPS) skin fibroblasts


title: Drought treated leaves at booting stage, biological rep2


title: CGH_QUIGLEY_T30


title: CGH_QUIGLEY_T16


title: Female E12 vs E01 dye-swap

description: Competitive hybridization between E01 and E12


title: CGH_QUIGLEY_T14_3


title: N2-Fib

description: SAMPLE 15

source_name: normal skin fibroblasts

value: N-Fib

value: skin

value: normal skin fibroblasts


title: Drought treated leaves at booting stage, biological rep1

value: booting stage


title: H9-2

description: SAMPLE 13

source_name: hESC

value: HES

value: human embryonic stem cells


title: normal leaves at booting stage, biological rep3


title: MCF10A_rep3

city: Detroit

first: Andrea

last: Baillo

address: 4100 John R

institute: Wayne State University

description: replicate 3

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep-96 RNA Amplification Kit

growth_protocol: MCF10A cells were cultured in Ham's F-12 with 1 μg/ml hydrocortisone, 1 mg/ml bovine serum albumin, 10 mm Hepes, 5 mm ethanolamine, 5 μg/ml transferrin, 10 nm triiodothyronine, 50 nm sodium selenate, 5 μg/ml gentamicin, 2.5 μg/ml fungizone, and 5 μg/ml insulin. MCF10A+AREG cells were supplemented with 20ng/ml AREG and MCF10A cells were supplememnted with 10ng/ml EGF

extract_protocol: RNA was extracted with the QIAGEN Rneasy Plus kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with the Agilent Bioanylizer and the Agilent RNA 6000 Nano Kit.

tag: agent

value: control

value: immortalized human mammary epthelial cells


title: HES3-2

description: SAMPLE 14

value: embryo


title: MCF10A-AREG_rep3

description: replicate 3

value: -AREG


title: MCF10A+AREG_rep3

description: replicate 3

value: +AREG


title: MCF10A-EGF_rep3

description: replicate 3

value: -EGF


title: normal leaves at booting stage, biological rep1

tag: tissue

value: DK151, a drought tolerant line from IR64


title: normal leaves at booting stage, biological rep2


title: MCF10A-AREG_rep2

description: replicate 2


title: N2-iPSC-2

description: SAMPLE 12

source_name: iPSC, normal skin fibroblasts

value: N-iPS

value: iPSC reprogrammed from normal skin fibroblasts


title: N2-iPSC-1

description: SAMPLE 11


title: Drought treated roots at panicle elongation stage, biological rep3

source_name: Oryza DK151, root

value: root

value: panicle elongation stage


title: PG2-iPSC-2

description: SAMPLE 10

source_name: iPSC, HGPS skin fibroblasts

value: HGPS-iPS

value: iPSC reprogrammed from Hutchinson-Gilford Progeria syndrome (HGPS) skin fibroblasts


title: Drought treated roots at panicle elongation stage, biological rep1


title: PG2-iPSC-1

description: SAMPLE 9

value: skin


title: MCF10A+AREG_rep2

description: replicate 2


title: normal roots at panicle elongation stage, biological rep3


title: Drought treated roots at panicle elongation stage, biological rep2