title: 1-8_Columbia-control_Rep2_ATH1

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

description: 4 days at 4oC, Growth chamber, Commercial soil - 50% Farfard 50% MetroMix, 22oC average, 75% average humidity.

hyb_protocol: Biotin Labelled cRNA using "Affymetrix GeneChip Hybridization, Wash and Stain Kit", according to guidelines set out by Affymetrix, Santa Clara, CA

scan_protocol: Scanned according to guidelines set out by Affymetrix, Santa Clara, CA.

data_processing: Raw data from the microarrays was normalized at probe-level using MAS5 algorithm. The detection calls (present, marginal, absent) for each probe set was obtained using the GCOS system

organism: Arabidopsis thaliana

label_protocol: Labelled using protocol described in manual "Affymetrix GeneChip Expression Analysis Technical Manual", One-Cycle target labelling

growth_protocol: Plant were grown for 10 days under 16hr light, 8 hr dark cycles (110 uE m-2 s-1) at constant 22C on a 50/50 mix of Farfard and Metromix. Bottom watered with 0.5g/L Peter's 20-20-20 fertilizer. Soil treated with Marathon pesticide at 40g/36quarts of soil. All above ground plant tissue was collected on day 10, 14 hours after lights on.

extract_protocol: Qiagen RNAeasy kit protocol

tag: developmental stage

value: 10 days

value: above-ground whole plant

tag: ecotype

tag: genotype

value: wild-type

tag: stock code


title: 1-8_curly-leaf-swinger_Rep2_ATH1

status: Public on Apr 20 2010

type: RNA

country: United Kingdom

institute: Nottingham Arabidopsis Stock Centre (NASC)

description: Seeds were stratified for 3 days at 4 degrees Celsius. Greenhouse, Agar, Murashige and Skoog basal salt mixture, 23oC average temperature, 70% humidity.

label: biotin

molecule: total RNA

source_name: swn-7 clf-28 double mutant

growth_protocol: Seeds were sterilized in 70% ethanol 0.0125% Triton then washed in 90% ethanol. Seeds were plated on 9 cm 0.5g/l ms plates for 10 days for col, swn-7, and clf-28, and 12 days for the swn-7 clf-28 double mutant

tag: tissue

value: whole plant

tag: genetic background

value: T-DNA insertion mutant

value: clf-28 swn-7


title: 1-6_Constans-mutant_Rep3_ATH1

source_name: co-SAIL

tag: age

value: Constans mutant


title: 1-4_Constans-mutant_Rep1_ATH1


title: 1-7_Columbia-control_Rep1_ATH1


title: 1-1_HAP5-triple-mutant_Rep1_ATH1

value: T-DNA gene knock out

value: HAP5 triple-mutant

tag: genetic variation


title: 1-5_Col_Rep2_ATH1

value: Columbia (Col-0)


title: 1-9_Columbia-control_Rep3_ATH1


title: 1-2_HAP5-triple-mutant_Rep2_ATH1


title: 1-6_curly-leaf_Rep2_ATH1


title: 1-5_Constans-mutant_Rep2_ATH1


title: 1-4_curly-leaf-swinger_Rep1_ATH1


title: 1-1_Col_Rep1_ATH1


title: NA12813/NA15510

type: genomic

city: Santa Clara

first: Nick

last: Sampas

state: CA

address: 5301 Stevens Creek Blvd

department: Life Science and Nanotechnology Department

country: USA

institute: Agilent Technologies

hyb_protocol: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis ULS Labeling for Blood, Cells, Tissues or FFPE Protocol

scan_protocol: Scanned on an Agilent G2505A Scanner

data_processing: Agilent Feature Extraction v9.1, default CGH parameters. This data represents probes not in the reference assembly (novel probe sequences).  All filtering of novel probes begins with those 54,931 sequences represented in the Sample data tables.

molecule: genomic DNA

organism: Homo sapiens

extract_protocol: Performed by the Coriell Cell Repository

tag: cell line

value: Coriell Lymphoblastoid

tag: coriell sample

tag: population

value: CEU Female

value: Unknown Female Fosmid library:G248


title: RA-1 passage 1 vs. passage 3 b cancer array

city: Bad Nauheim

first: Elena

last: Neumann

address: Benekestr. 2-8

department: Internal Medicine and Rheumatolgy

country: Germany

description: Array comparison evaluation using BD AtlasImageTM 2.7 Software providing data of differentially regulated genes (equally expressed genes are not provided by the software)

hyb_protocol: The PCR products were purified from unincorporated nucleotides and small cDNA fragments by column chromatography. The filters were prehybridized in prewarmed hybridization solution with 100 µg/ml fragmented denatured salmon sperm DNA. The labeled cDNA probe was denatured and 1 µg/µl sheared human genomic DNA was added with an equal volume of neutralizing solution (1M NaH2PO4, pH 7.0). The mixture was added to the filters and hybridized over night.

scan_protocol: The filters were exposed to a Phosphor-Imager-Screen for 3-5 days depending on the intensity of radiation. Data analysis was performed using the Ambis software.

data_processing:
Evaluation was performed using the AtlasImageTM 2.7 software, developed specifically for analysis of the AtlasTM cDNA Expression Arrays. Background and signal intensity was normalized. The default signal threshold was kept constant for all analyses. After background correction, the median signal intensity for all spots on an array were used to calculate the correction coefficient (global normalization). Comparison of the arrays was performed using the “Compare two arrays” setting and resulting .txt-files were saved as .xls-files. Genes spotted on both arrays were evaluated on the GLP139 array only.
*********Only differentially expressed genes are reported in the Sample data tables. Complete data tables were requested and reported to be unavailable by the submitter.*********

source_name: Rheumatoid arthritis synovial fibroblasts from Patient #1 (RA-1)

label_protocol: RAP-PCR of total cellular RNA was performed using 250 ng RNA. First strand synthesis was carried out using MuLV reverse transcriptase (Promega) and 2 µM first strand arbitary primer. Second strand synthesis was performed using AmpliTaq Stoffel Fragment 2.8 µl [32P]dATP (3,000 Ci/mmol, 10 mCi/ml), and 4 µM arbitrary second primer. The reaction was cycled through 30 low stringency cycles 94°C, 35°C, 72°C). Primer combination: OPN23 (5'- CAG GGG CAC C-3') and OPN21 (5'-ACC AGG GGC A-3').

growth_protocol: Synovial tissues were obtained from synovial biopsies of RA patients undergoing joint surgery. Following enzymatic digestion, fibroblasts were seeded in culture flasks (= passage 0) and grown in DMEM containing 10% heat inactivated fetal calf serum and cultured at 37°C in 10% CO2. At 85-95% confluency, cells were passaged 1:2 and a part of the cells was harvested and total RNA was extracted and stored at -70°C.

extract_protocol: Total cellular RNA was extracted using the RNeasy spin column purification kit. To remove contaminating genomic DNA, total RNA was treated with DNase I (0.2 U/µl for 40 minutes at 37°C. RNA concentrations were measured, adjusted to 200 ng/µl and stored at -70°C.

treatment_protocol: Culture conditions were kept constant during the experiments.

tag: passage

value: passage 1

value: passage 3


title: 1-3_HAP5-triple-mutant_Rep3_ATH1


title: 1-7_swinger_Rep2_ATH1


title: 3-6_ASL9-ox3_Rep3_ATH1

description: Sterilized by treatment with bleach. Growth chamber, Agar, Murashige and Skoog basal salt mixture.

growth_protocol: Arabidopsis were grown vertically on MS agar plates for 2 weeks.

extract_protocol: Seedlings were harvested and snap-frozen in liquid nitrogen. RNA was extracted as described in the Qiagen RNAeasy kit.

value: seedlings

value: 2 weeks

value: aerial parts of seedlings

tag: line

value: transgenic overexpressing ASL9


title: 3-4_ASL9-ox1_Rep1_ATH1


title: 3-3_wildtype3_Rep3_ATH1

value: wild-type


title: 1-3_swinger_Rep1_ATH1

value: whole plant


title: 1-5_Temporal-induction_Rep1_ATH1

description: Seeds on lehle plates were placed in the dark at 4C for three days. Seeds were sterilised by soaking in 10% bleach for 10 minutes and then washed five times with water. Growth Room, agar, substrate was autoclaved at 121 centigrade for 15 minutes, average temperature 21oC. Plants were harvested at 14 days old and had 4 rosette leaves.

source_name: Temporal-induction

growth_protocol: Seedlings were grown on lehle plates in constant light

extract_protocol: Standard Affymetrix extraction protocol

treatment_protocol: Seeds were sown on lehle plates, sprayed at 13 days old with 2uM 7-B-estradiol and harvested 24 hours later.

value: 14 days

value: T-DNA


title: 3-5_ASL9-ox2_Rep2_ATH1


title: 1-2_Control_Rep2_ATH1

source_name: Control

treatment_protocol: Empty vector control seedlings (transformed with PER-10 only) were sown onto lehle, sprayed at 13 days old with 2uM 17-B-estradiol and harvested 24 hours later.


title: 3-1_wildtype1_Rep1_ATH1


title: 1-4_Prolonged-induction_Rep2_ATH1

source_name: Prolonged-induction

treatment_protocol: Seeds were sown on lehle containing 2uM 7-B-estradiol and sprayed every 24 hours with 2uM 7-B-estradiol until harvested at 14 days old.


title: 23-Si8LE

city: yokohama

first: kenjiro

last: ikuta

state: kanagawa

address: 10-1, Daikoku-cho, Tsurumi-ku

country: Japan

institute: MITSUBISHI RAYON CO.,LTD

hyb_protocol: Biotinylated RNA (5 mg) was fragmented using fragmentation  reagents (Applied Biosystems Japan) and then incubated at 70 °C for 7.5 min.  The fragmentation reaction was terminated by the addition of stop solution.  Hybridization was carried out with a DNA microarray (Genopal, Mitsubishi  Rayon, Tokyo, Japan) in 150 ml of hybridization buffer (0.12 M Tris-HCl/0.12  M NaCl/0.05% Tween-20) and 5 mg of fragmented biotinylated RNA at 65 °C  overnight. After hybridization, the DNA microarray was washed twice in 0.12  M Tris-HCl/0.12 M NaCl/0.05% Tween-20 at 65 °C for 20 min followed by  washing in 0.12 M Tris-HCl/0.12 M NaCl for 10 min. The DNA microarray was  then labeled with streptavidin-Cy5 (GE Healthcare Bio-Science KK, Tokyo,  Japan). The fluorescent labeled-DNA microarray was washed for 5 min four  times in 0.12 M Tris-HCl/0.12 M NaCl/0.05% Tween-20 at room temperature.

scan_protocol: Microarray was scanned at multiple exposure times ranging from 0 to 40s by DNA microarray reader (Yokogawa Electric Corporation). The intensity values with the best exposure condition for each spot were selected. Fluorescent intensity of images was quantified automatically with the software supplied with the microarray reader.

data_processing: All data were subtracted by background signal intensity of each array and normalized between arrays by constants calculated from signal raitio of internal control probes (GAPDH).

organism: Mus musculus

source_name: RAW264.7 cells

label_protocol: RNA was then amplified using the MessageAmpII biotin-enhanced amplification kit (Applied Biosystems Japan, Tokyo, Japan), according to the manufacturer’s instructions, and column purified.

growth_protocol: RAW264.7 cells were cultured in DMEM supplemented with antibiotics (100 U/ml penicillin and 100 U/ml streptomycin), and 10% (v/v) fetal bovine serum (Intergen, Purchase, NY). The cells were maintained at 37 °C in a humidified incubator containing 5% CO2.

extract_protocol: Total RNA was isolated using the Trizol reagent (InvitroGen, Carlsbad, CA) according to the manufacturer’s instructions.

treatment_protocol: The cells were maintained at 37 °C in a humidified incubator containing 5% CO2. RAW264.7 cells were pretreated with 1 micro M EGCG for 1 h, and then stimulated with LPS (50 ng/ml) for 6 h.

tag: cell type

value: 67LR-downregulated RAW264.7 cells treated with EGCG and LPS-stimulated


title: 24-Si8LE


title: 1-7_At-Pp-10.5-hai_Rep1_ATH1

description:
Stratification was performed 2 days at 4C. Seeds were surface sterilised 5 min with sodium hypochlorite (20% commercial bleach; NaOCl, 2.5% active ingredient) and rinsed twice in a 95% ethanol solution.
20% agarose, 110C for 20 min, 10 plants per Petri dish, 25C average, 25C day, 25C night, 100% humidity average, 100% humidity day, 100% humidity night, Murashige & Skoog basal salt mixture.

growth_protocol: Seeds were grown on 1x Murashige and Skoog agar medium (MS; 4.4 gL-1, Sigma Chemical Compagny, MO, USA) supplemented with 10 gL-1 saccharose (Prolabo) and 20 gL-1 agar (difco Agar, Dedon, Dickinson and compagnie, MD, USA). 15-day-old plants were transferred to new square Petri dishes containing a strip of 1 x MS agar Medium and underneath 10 ml of 0.1 x MS medium. Plants were grown under 8h photoperiod at 25C for 1 month.

treatment_protocol: A. thaliana roots were inoculated with Phytophthora parasitica 310 strain (10^6 zoospores per Petri dish).

value: roots

value: Col-0 (Columbia)

value: ecotype

tag: time

value: 10.5 hours after infection


title: 1-6_Temporal-induction_Rep2_ATH1


title: 1-3_Prolonged-induction_Rep1_ATH1


title: 1-9_At-Pp-30-hai_Rep1_ATH1

source_name: Col-8, 30 hai

value: 30 hours after infection


title: 1-10_At-Pp-30-hai_Rep2_ATH1


title: 1-1_Control_Rep1_ATH1


title: 22-Si8LE


title: 1-5_At-Pp-6-hai_Rep1_ATH1

source_name: Col-8, 6 hai

value: 6 hours after infection


title: 1-3_At-Pp-2.5-hai_Rep1_ATH1

source_name: Col-8, 2.5 hai

value: 2.5 hours after infection


title: CadA-D398A under 1uM Cadmium exposure S3

city: Gif-sur-Yvette cedex

first: Jean-Christophe

last: AUDE

address: CEA Saclay Bâtiment 142 - PC 21

department: IBITEC-S

country: France

institute: CEA

description: W303-1A cells expressing CadA or D398A were grown to exponential phase (OD600 = 0.4) in SD minimal medium + all amino acids plus adenine at 30°C. After the addition of cadmium (1 µM), the cells were further incubated for 1 Hour. RNA were extracted from cells, reverse-transcript to cDNA, fluorescently labelled and competitively hybridized to DNA microarrays harbouring yeast ORF.

hyb_protocol: Total RNA were reverse-transcript to cDNA, fluorescently labelled and competitively hybridized to DNA microarrays as previously described (Fauchon et al., 2006).

scan_protocol: Hybridized arrays were scanned using a GenePix 4000A scanner (Axon Instruments, Inc.) and fluorescence ratio measurements were determined with the GenePix Pro 6.0 software (Axon Instruments, Inc.).

data_processing: Analyses were undertaken using the Limma package version 3.2.1 (Smyth, 2005) from the R/Bioconductor software version 2.10.1 (R-Development-Core-Team, 2007). Spot intensities have been processed by subtracting the background measurements and normalized using the LOESS regression. Normalized data served to compute the log2-ratios for each probe.

organism: Saccharomyces cerevisiae

source_name: Strain W303-1A CadA

label_protocol: indirect via aa-dUTP

extract_protocol: Total RNA extraction were performed as previously described (Fauchon et al., 2006)

tag: strain

value: W303-1A CadA

tag: genome/variation

value: Saccharomyces cerevisiae expressing the prokaryotic P-type ATPase CadA from Listeria monocytogenes (Wu et al., 2004).

source_name: Strain W303-1A D398A

extract_protocol: Total RNA extraction were performed as previously described (Laferte et al., 2006)

value: Saccharomyces cerevisiae expressing the mutant D398A of the prokaryotic P-type ATPase from Listeria monocytogenes (Wu et al., 2004).


title: 1-4_At-Pp-2.5-hai_Rep2_ATH1


title: 1-2_At-Control_Rep2_ATH1

source_name: Col-8, control

treatment_protocol: Mock-inoculated roots.

value: 0 hours after infection


title: 21-Si8L

value: 67LR-downregulated RAW264.7 cells LPS-stimulated


title: 1-6_At-Pp-6-hai_Rep2_ATH1


title: 3-2_wildtype2_Rep2_ATH1

tag: developmental stage

value: seedlings

value: 2 weeks

value: aerial parts of seedlings

value: wild-type


title: 1-2_curly-leaf_Rep1_ATH1

value: whole plant

value: T-DNA insertion mutant


title: Pusa Basmati 1 (Low grain number) replicate 1

city: New Delhi

first: Rupesh

middle: Kailasrao

last: Deshmukh

state: Delhi

address: Libraryavenue, PUSA

department: Rice Genome Laboratory

country: India

institute: National Research Center on Plant Biotechnology

description: Gene expression profile of  rice cultivar bearing low grain number in panicle

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: GCOS 1.2

organism: Oryza sativa

source_name: Panicle primordia stage '0'

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated using TRIzol Reagent (Sigma).  RNA samples were processed as recommended by Affymetrix (Affymetrix geneChip Expression Analysis Technical manual; Affymetrix)

tag: grain number

value: Low grain number per panicle

value: Indica Group


title: Pusa Basmati 1 (Low grain number) replicate 2


title: CadA-D398A under 1uM Cadmium exposure S4


title: 20-Si8L


title: Pusa1266 (Low grain number) replicate 1

description: Gene expression profile of  rice cultivar bearing high grain number in panicle

value: High grain number per panicle


title: CadA-D398A under 1uM Cadmium exposure S2


title: 1-1_At-Control_Rep1_ATH1

value: roots

value: Col-0 (Columbia)

value: ecotype


title: CadA-D398A under 1uM Cadmium exposure S1

value: W303-1A CadA


title: 16-Si8E

value: 67LR-downregulated RAW264.7 cells treated with EGCG


title: Pusa1266 (Low grain number) replicate 2


title: 2-5_Col-TF2_Rep1_ATH1

description: Growth Room, Natural soil, 21oC, 75% humidity.

growth_protocol: Plants were grown in compost in a growth room as described (Honys and Twell, Plant Physiology 132: 640-652, 2003).

value: mature pollen


title: 2-6_Col-TF2_Rep2_ATH1


title: 17-Si8E


title: 13-Si8

value: 67LR-downregulated RAW264.7 cells


title: 14-Si8


title: 15-Si8


title: 2-4_Col-TF1_Rep2_ATH1


title: 2-3_Col-TF1_Rep1_ATH1


title: 1-6_AtGA120.2_Rep2_ATH1

description: Seeds were imbibed in water for 3 days at 4C. Seeds were sterilsed for 3 minutes in 70% ethanol, 3 minutes in 10% bleach/0.1% Tween-20 and rinsed three times in water. Growth Room Phytagar 90% 22

source_name: GA2oxOE1I, 120 min

growth_protocol: Roots were grown on 100mm x 100mm square plates stood at an angle of 70º from the horizontal. Plants were grown on 0.7% Gelrite (Duchefa), 0.05% MES (Sigma), 1x Murashige and Skoog (Duchefa), 1% Sucrose (Duchefa) at pH 5.8. Plants were grown in continuous light and harvested when they were 7 days old.

value: 7 days

value: root tips

value: gene knock out

tag: treatment

value: GA

tag: treatment time


title: 1-5_AtCON120.2_Rep2_ATH1

source_name: Col-0, 120 min

tag: tissue

value: untreated


title: 2-1_Col-WT_Rep1_ATH1

tag: genetic background

tag: stock code


title: 2-2_Col-WT_Rep2_ATH1


title: 19-Si8L

value: 67LR-downregulated RAW264.7 cells LPS-stimulated


title: 18-Si8E


title: 11-ScrLE

value: RAW264.7 cells treated with EGCG and LPS-stimulated


title: 1-4_AtCON0.2_Rep2_ATH1

source_name: Col-0, 0 min

value: 0 min.


title: 9-ScrL

value: RAW264.7 cells LPS-stimulated


title: 1-3_AtGA120.1_Rep1_ATH1

tag: genetic variation


title: 8-ScrL


title: 12-ScrLE


title: 7-ScrL


title: 1-8_At-Pp-10.5-hai_Rep2_ATH1

value: 10.5 hours after infection


title: 1-2_AtCON120.1_Rep1_ATH1


title: 5-ScrE

value: RAW264.7 cells treated with EGCG


title: 3-Scr

value: RAW264.7 cells


title: 4-ScrE


title: 1-1_AtCON0.1_Rep1_ATH1


title: 2-8_cngc19_Rep2_ATH1

description: Seeds were washed in 70 % (v/v) ethanol/water, rinsed in distilled water and surface sterilised using NaOCl (1 % active chlorine). Seeds were rinsed again and imbibed for 3-6 days in sterile distilled water at 4 C to break dormancy. Growth Room Hydroponics: In the hydroponics system, plants were supported on polycarbonate discs over 450 mL of aerated nutrient solution contained in a light-proof 500 mL plastic beaker. 80% 22C KH2PO4 0.25mM KOH 0.5mM MgSO4.7H2O 0.75mM CaCl2.2H2O 0.03mM FeNaEDTA 0.1mM Ca(NO3)2.4H2O 4mM H3BO3 30uM MnSO4.4H2O 10uM ZnSO4.7H2O 1uM CuSO4.5H2O 3uM Na2MoO4.2H2O 0.5uM.  Plants had fully formed rosettes but no flowerng stem. Root material from twenty to thirty plants from each treatment were bulked into 1.5 mL colourless, sterile, screw-cap polypropylene tubes and snap-frozen in liquid nitrogen. Tissue samples were stored at -70 C prior to the extraction of total RNA.

growth_protocol: Following imbibation, seeds were sown into 10 cm (length) x 10 cm (width) x 9.5 cm (depth), unvented, polycarbonate culture boxes (Sigma-Aldrich, Dorset, UK). Approximately 35 seeds were sown on perforated polycarbonate discs (diameter 91 mm; thickness 5 mm) placed over 75 mL agar containing a full strength MS basal salt mix at full strength (Murashige and Skoog 1962). Roots grew into the agar, but shoots remained on the opposite side of the disc. Boxes were placed in a growth room and transferred on their polycarbonate discs to a hydroponics system situated in a Saxcil growth cabinet 18 days after germination. In the hydroponics system, plants were supported on polycarbonate discs over 450 mL of aerated nutrient solution contained in a light-proof 500 mL plastic beaker. Plants were grown in these solutions for 7 days before they were harvested (a total of 25 days after germination). Root material from twenty to thirty plants from each treatment was bulked into 1.5 mL colourless, sterile, screw-cap polypropylene tubes and snap-frozen in liquid nitrogen. Tissue samples were stored at -70 C prior to the extraction of total RNA.

value: root

value: T-DNA gene knock out


title: 2-Scr


title: 1-Scr


title: 2-5_cngc1-3_Rep2_ATH1


title: 2-7_cngc19_Rep1_ATH1


title: 2-3_Col-0_Rep3_ATH1


title: 2-4_cngc1-3_Rep1_ATH1


title: 10-ScrLE


title: 2-6_cngc1-3_Rep3_ATH1


title: 6-ScrE


title: 2-9_cngc19_Rep3_ATH1


title: 2-2_Col-0_Rep2_ATH1


title: 1-9_Heterozygous-AtcesA6_Rep1_ATH1

status: Public on Apr 19 2010

description: Room chamber, untreated 4-week-old heterozygous irx6-1 plants, 50% humidity, 22oC

source_name: Col-0, heterozygous AtCesA6

tag: ecotype

tag: genotype

value: heterozygous AtCesA6

tag: age

value: 4 weeks

value: rosette


title: 1-8_Homozygous-AtcesA6_Rep2_ATH1

description: Room chamber, untreated 4-week-old homozygous irx6-1 plants, 50% humidity, 22oC

source_name: Col-0, homozygous AtCesA6

value: homozygous AtCesA6


title: 1-10_Heterozygous-AtcesA6_Rep2_ATH1


title: 1-5_Heterozygous-AtcesA4_Rep2_ATH1

description: Room chamber, untreated 4-week-old heterozygous irx5-2 plants, 50% humidity, 22oC

source_name: Col-0, heterozygous AtCesA4

value: heterozygous AtCesA4


title: 1-7_Homozygous-AtcesA6_Rep1_ATH1


title: 1-4_Heterozygous-AtcesA4_Rep1_ATH1


title: 2-1_Col-0_Rep1_ATH1


title: 1-6_Heterozygous-AtcesA4_Rep3_ATH1


title: 1-3_Homozygous-AtcesA4_Rep3_ATH1

description: Room chamber, untreated 4-week-old homozygous irx5-2 plants, 50% humidity, 22oC

source_name: Col-0, homozygous AtCesA4

value: homozygous AtCesA4


title: 1-2_Homozygous-AtcesA4_Rep2_ATH1


title: Stage II colorectal cancer  tissue samples 7 (expr)

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

hyb_protocol: Hybridization protocol available via www.agilent.com

scan_protocol: Slides were scanned using the Agilent microarray scanner version G2505B, protocol according to Agilent scanner and feature extraction version A.7.5.1

data_processing: The R-package LIMMA was used for background correction according to the Edward method and within array Lowess and between array quantile normalization according to Smyth and Speed.

source_name: colorectal cancer

label_protocol: DNA labeling protocol available via www.agilent.com

extract_protocol: DNA isolation protocol according to Ambion Inc., Austin, Texas, USA

value: colorectal cancer

tag: tumor stage

value: stage II

source_name: universal human reference RNA, Stratagene

value: comprised of 10 cell lines for human giving broad gene coverage


title: Stage II colorectal cancer  tissue samples 10 (expr)


title: 1-1_Homozygous-AtcesA4_Rep1_ATH1


title: Stage II colorectal cancer  tissue samples 43 (expr)


title: Stage II colorectal cancer  tissue samples 46 (expr)


title: Stage II colorectal cancer  tissue samples 32 (expr)


title: Stage II colorectal cancer  tissue samples 11 (expr)


title: Stage II colorectal cancer  tissue samples 8 (expr)


title: Stage II colorectal cancer  tissue samples 9 (expr)


title: Stage II colorectal cancer  tissue samples 6 (expr)


title: Stage II colorectal cancer  tissue samples 12 (expr)


title: Stage II colorectal cancer  tissue samples 42 (expr)


title: Stage II colorectal cancer  tissue samples 31 (expr)


title: Stage II colorectal cancer  tissue samples 29 (expr)


title: Stage II colorectal cancer  tissue samples 30 (expr)


title: Stage II colorectal cancer  tissue samples 44 (expr)


title: Integrative genomics of ovarian cancer P4684 [HuGene-1_0-st]

city: Melbourne

first: Manasa

last: Ramakrishna

state: Victoria

address: St Andrew's Pl

country: Australia

institute: Peter MacCallum Cancer Centre

description: Gene Expression Data from Epithelial ovarian cancers

hyb_protocol: According to Affymetrix protocol using recommended instrumentation

scan_protocol: According to Affymetrix protocol and using GeneChip Operating Software

data_processing: QC measures using Affymetrix Genotyping Conole and “affyPLM” package in the R open-source environment. Arrays were normalised using robust multichip average (rma) in the aroma.affymetrix package. All gene expression analyses were performed in the R environment using limma package.

source_name: Ovarian tumours at the time of diagnosis

label_protocol: According to Affymetrix protocol, Biotin labelled

extract_protocol: 10uM slices of tumour were hand-microdissected to obtain regions with >80% epithelial cells and reduce contamination from fibroblasts, blood vessels etc. Following this, for DNA extraction, slides containing sections were stained with Haematoxylin and Eosin and DNA was extracted using the Qiagen DNEasy kit. For RNA, identical slides were stained with Cresyl violet and total RNA was extracted using the Ambion mirVana kit according to manufacturer's instructions.

treatment_protocol: All tumours were fresh-frozen and OCT embedded. Lymphocytic DNA was extracted from stored blood samples.

tag: histological subtype

value: serous

tag: grade

tag: stage

tag: batch


title: Control Clone B4-17

city: New Haven

first: Vince

last: Schulz

state: CT

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

description: Control Clone B4-17

hyb_protocol: Performed by NimbleGen using standard protocol

data_processing: The chip signal was log2 transformed.  Desmudged chip signal was obtained by using the SmudgeKit version 2.4 method from J. Emerson. The desmudged data for each channel was processed by the Tilescope software (see http://genomebiology.com/2007/8/5/R81) which identifies bound regions.

source_name: Control Clone B4-17

growth_protocol: EML cells were maintained in Iscove’s modified Dulbecco’s medium (IMDM) containing 20% heat-inactivated horse serum (Invitrogen, Carlsbad, CA, USA) and supplemented with 15% conditioned medium from the BHK/MKL cell line containing rat stem cell factor.  Cells were incubated with antibodies (phycoerythrin conjugated (PE)-anti-c-Kit, PE-anti-Sca-1, PE-anti-Mac-1, PE-anti-Gr-1, PE-anti-B220, PE-anti-Ter119 (eBioscience, San Diego, CA, USA) ) for 20 minutes at 4 degrees C in antibody dilution solution (PBS with 2mM EDTA + 0.5% BSA + 2% rat serum + 2% mouse serum + 0.1% sodium azide).  KLS (c-Kit+, Lin-, Sca-1+) cells were isolated using a FACS Calibur machine (BD Bioscience, San Jose, CA, USA).

extract_protocol: EML-HOXB4 #4 cells (1.5x10^9 – 2x10^9) were lineage depleted to isolate KLS-EML-HOXB4 cells (1.5x10^8 – 2x10^8).  A modified version of the ChIP-chip procedure provided by Roche NimbleGen was used to prepare the ChIP samples for hybridization to the MM8 Refseq promoter genechip array from Roche NimbleGen (Madison, WI, USA), that contains sequences corresponding to 2 kb 5’ and 0.5 kb 3’ to the transcription start site of annotated genes.  Formaldehyde cross-linked chromatin was prepared from KLS-EML-HOXB4 cells. Chromatin was treated with Proteinase K, phenol and chloroform extracted, and DNA was purified using a MinElute column.  Processing and microarray hybridization of the DNA samples was carried out by Roche NimbleGen.

treatment_protocol: Total DNA was extracted from sonicated chromatin.

tag: antibody

value: No antibody,  Total Input Control


title: Stage II colorectal cancer  tissue samples 28 (expr)


title: Integrative genomics of ovarian cancer P5390 [HuGene-1_0-st]

value: clearcell


title: Integrative genomics of ovarian cancer P4616 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer P4093 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer P7820 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer P4178 [HuGene-1_0-st]


title: Stage II colorectal cancer  tissue samples 18 (expr)


title: Integrative genomics of ovarian cancer P4075 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer P2506 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer P2808 [HuGene-1_0-st]

value: mucinous


title: Integrative genomics of ovarian cancer P2803 [HuGene-1_0-st]


title: Control Clone B-4

description: Control Clone B-4

scan_protocol: Performed by NimbleGen using standard protocol

source_name: Control Clone B-4


title: Stage II colorectal cancer tissue samples (FFPE) 26 NimbleGen 135K

description: Normal colon mucosa from each patient was used as reference in the oaCGH experiments

hyb_protocol: Hybridization protocol available via http://www.nimblegen.com/

scan_protocol: Slides were scanned using the Agilent microarray scanner, protocol according to Agilent.

data_processing: Median Signal intensity minus median Background intensity; excluding negative values

label_protocol: DNA labeling protocol according to Enzo Life Sciences

extract_protocol: DNA isolation protocol available via www.vumc.nl/microarrays. Also described in Buffart et al, J Pathol. 2007 Jan;211(1):45-51

value: tumor

tag: disease state

value: colorectal cancer stage II

source_name: normal colorectum mucosa

value: colorectal mucosa (same patient as ch1)

value: normal


title: Integrative genomics of ovarian cancer P4219 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer P2712 [HuGene-1_0-st]


title: Stage II colorectal cancer  tissue samples 17 (expr)


title: Integrative genomics of ovarian cancer P2125 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer P2205 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer P1977 [HuGene-1_0-st]

value: endometrioid


title: Control Clone B-11

description: Control Clone B-11

source_name: Control Clone B-11

label_protocol: Performed by NimbleGen using standard protocol


title: HOXB4 chIP clone B-11

description: HOXB4 Clone B-11

source_name: HOXB4 chIP clone B-11

extract_protocol: EML-HOXB4 #4 cells (1.5x10^9 – 2x10^9) were lineage depleted to isolate KLS-EML-HOXB4 cells (1.5x10^8 – 2x10^8).  A modified version of the ChIP-chip procedure provided by Roche NimbleGen was used to prepare the ChIP samples for hybridization to the MM8 Refseq promoter genechip array from Roche NimbleGen (Madison, WI, USA), that contains sequences corresponding to 2 kb 5’ and 0.5 kb 3’ to the transcription start site of annotated genes.  Formaldehyde cross-linked chromatin was prepared from KLS-EML-HOXB4 cells and incubated with the I12 anti-human HOXB4 rat monoclonal antibody (Developmental Studies Hybridoma Bank, University of Iowa) that had been previously bound to Dynabeads magnetic beads (Invitrogen) conjugated to sheep-anti-rat IgG2a antibody.  ChIP was performed using the Dynabeads magnet system (Invitrogen).  The immunoprecipitate (IP) was serially washed eight times using the Dynabeads magnet system (Invitrogen).  Processing and microarray hybridization of the IP samples was carried out by Roche NimbleGen.

treatment_protocol: Chromatin was immunoprecipitated using I12 anti-rat human HOXB4 antibody


title: Integrative genomics of ovarian cancer P1921 [HuGene-1_0-st]


title: HOXB4 chIP clone B-17

description: HOXB4 Clone B4-17

source_name: HOXB4 chIP clone B-17


title: Integrative genomics of ovarian cancer P1953 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer P1680 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer P1428 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer P1436 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer P1555 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer P1348 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer P1556 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer P1049 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer P4085 [HuGene-1_0-st]


title: Stage II colorectal cancer  tissue samples 5 (expr)


title: Integrative genomics of ovarian cancer P0933 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer P0985 [HuGene-1_0-st]

value: unknown


title: Integrative genomics of ovarian cancer P1246 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer P1768 [HuGene-1_0-st]


title: HOXB4 chIP clone B-4

description: HOXB4 Clone B-4

source_name: HOXB4 chIP clone B-4


title: Integrative genomics of ovarian cancer P0706 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer IC580 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer IC579 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer IC549 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer P1094 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer IC511 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer IC557 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer IC504 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer IC594 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer IC493 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer IC448 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer IC487 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer IC419 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer IC434 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer IC499 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer IC413 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer IC382 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer IC328 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer IC407 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer IC548 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer IC325 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer IC349 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer IC321 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer IC318 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer IC300 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer IC293 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer P5390 [GenomeWideSNP_6]

data_processing: primary data description: Partek's copy number workflow generates copy number ratios relative to matching normal samples or a pooled baseline and then converts and presents these values as whole copy numbers. The file titled SNP6_Normalised-Copy-number.csv contains these values for each sample. In this file, probes on Chromosome Y and the Mitochondrion (MT) have been removed and the probesets are organised first by Chromosome and then by start position. Annotations for this were mapped in Partek using the Affymetrix GenomewideSNP6, CN and SNP annotation files, release number 23. This data was then used for Segmentation using the CBS algorithm in the DNAcopy package in R open-source software.

tag: tissue type (t=tumour; n= normal blood lymphocyte)

value: T

value: clear cell

tag: scandate(batch)

tag: source


title: Integrative genomics of ovarian cancer IC288 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer IC258 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer IC257 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer P2808 [GenomeWideSNP_6]

value: T&N


title: Integrative genomics of ovarian cancer IC315 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer IC201 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer IC179 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer IC220 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer P1768 [GenomeWideSNP_6]


title: Integrative genomics of ovarian cancer IC138 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer IC594 [GenomeWideSNP_6]

value: Campbell


title: Integrative genomics of ovarian cancer IC128 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer P1389 [GenomeWideSNP_6]


title: Integrative genomics of ovarian cancer P2506 [GenomeWideSNP_6]


title: Integrative genomics of ovarian cancer P1680 [GenomeWideSNP_6]


title: Integrative genomics of ovarian cancer IC121 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer IC026 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer P1921 [GenomeWideSNP_6]


title: Integrative genomics of ovarian cancer IC557b [GenomeWideSNP_6]


title: Integrative genomics of ovarian cancer IC022 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer P1977 [GenomeWideSNP_6]


title: Integrative genomics of ovarian cancer IC549 [GenomeWideSNP_6]


title: Integrative genomics of ovarian cancer P2125 [GenomeWideSNP_6]


title: Integrative genomics of ovarian cancer P1436 [GenomeWideSNP_6]


title: Integrative genomics of ovarian cancer IC511 [GenomeWideSNP_6]


title: Integrative genomics of ovarian cancer P1428 [GenomeWideSNP_6]


title: Integrative genomics of ovarian cancer P1094 [GenomeWideSNP_6]


title: Integrative genomics of ovarian cancer IC095 [HuGene-1_0-st]


title: Integrative genomics of ovarian cancer IC580 [GenomeWideSNP_6]


title: Integrative genomics of ovarian cancer P1556 [GenomeWideSNP_6]


title: Blood pool XX Cy5

description: protocols according to manufacturer (Enzo Life Sciences)

label_protocol: Sample_label_protocol_ch1 = DNA labeling protocol according to Enzo Life Sciences

extract_protocol: DNAzol (Invitrogen) according to manufacturer's protocol

tag: gender

value: female

tag: tissue

value: blood

tag: sample type

value: Blood of 18 healthy persons

value: healthy


title: Stage I colorectal cancer tissue samples (FFPE) 50

value: colorectal cancer stage I


title: Integrative genomics of ovarian cancer IC419 [GenomeWideSNP_6]


title: Stage I colorectal cancer tissue samples (Frozen) 50_Cy3

extract_protocol: Wizard® Genomic DNA Purification Kit (Promega, Benelux, Leiden, The Netherlands)

value: colorectal cancer stage 1


title: Stage II colorectal cancer tissue samples (FFPE) 10

value: colorectal cancer

value: stage II

value: normal colon mucosa obtained from the same patient as Channel 1


title: Stage II colorectal cancer tissue samples (FFPE) 12


title: Integrative genomics of ovarian cancer IC434 [GenomeWideSNP_6]


title: Integrative genomics of ovarian cancer IC321 [GenomeWideSNP_6]

value: mucinous


title: BJ fibroblast cell, ELR, rep 2

city: Boston

first: Kevin

last: Struhl

state: MA

address: 240 Longwood Ave.

department: Biological Chemistry and Molecular Pharamcology

institute: Harvard Medical School

description: Expression data from ELR Fibroblast cells

hyb_protocol: RNA samples were processed and hybridized to arrays at the Dana Farber Microarray Facility. RNA was fragmented and 6.5 ug cRNA was hybridized to Affymetrix Human U133 2.0 A expression arrays for 16 to 18 hours at 45 degrees celsius and subsequently washed on fluidics station.

scan_protocol: Arrays were scanned using Affymetrix Gene Chip Scanner 3000

data_processing: All gene expression data was normalized and summarized with RMA algorithm with an updated Entrez gene probeset definition. ComBat was used to remove non-biological experimental variation or batch effects between batches of microarray experiments.

label: Biotin

source_name: Cultured Cells

label_protocol: Biotinylated cRNA were prepared according to T.R. Golub et al, (1999) Science 286:531-537.

growth_protocol: MCF-10A ER-Src and MCF-10A pBABE cells were grown in DMEM/F12 medium supplemented with 5% horse serum, 20ng/ml EGF, 0.5ug/ml hydrocortisone, 100ng/ml cholera toxin and10ug/ml insulin with the addition of puromycin. Extensive description of MCF10A culture conditions are presented in Debnath et al study. The Src oncogene was induced by the addition of 1 uM Tamoxifen (Sigma) to confluent cell cultures for times indicated in the text. All BJ fibroblast cell lines (described previously in Hahn et al) were cultured on KO/DMEM media, 10% FBS, 15% Medium 199, glutamine and Pen/strep.

extract_protocol: RNA was extracted from MCF10A and BJ fibroblast cells using standard Trizol method following purification through RNeasy columns (RNeasy Clean- Up Kit, Qiagen).

treatment_protocol: Er-Src and pBABE control cells were treated with 1 micromolar tamoxifen or equivalent volume of EtOH for the indicated times.

tag: cell line

value: human foreskin fibroblast cell line (BJ)

tag: tranfected molecules

value: hTERT + SV40 early region + hRAS v12


title: Stage II colorectal cancer tissue samples (FFPE) 9


title: Integrative genomics of ovarian cancer IC349 [GenomeWideSNP_6]


title: BJ fibroblast cell, ELR, rep 3


title: BJ fibroblast cell, ELR, rep 1


title: Stage II colorectal cancer tissue samples (FFPE) 6


title: Stage II colorectal cancer tissue samples (FFPE) 8


title: Stage II colorectal cancer tissue samples (FFPE) 7


title: Stage II colorectal cancer tissue samples (FFPE) 11


title: BJ fibroblast cell, EL, rep 3

description: Expression data from EL Fibroblast cells

value: hTERT + SV40 early region


title: Stage II colorectal cancer tissue samples (FFPE) 5


title: Stage II colorectal cancer tissue samples (FFPE) 46


title: Stage II colorectal cancer tissue samples (FFPE) 44


title: BJ fibroblast cell, EH, rep 2

description: Expression data from EH Fibroblast cells

value: hTERT


title: BJ fibroblast cell, EL, rep 1


title: Stage II colorectal cancer tissue samples (FFPE) 40


title: BJ fibroblast cell, EH, rep 1


title: BJ fibroblast cell, EH, rep 3


title: Stage II colorectal cancer tissue samples (FFPE) 39


title: Stage II colorectal cancer tissue samples (FFPE) 43


title: Stage II colorectal cancer tissue samples (FFPE) 42


title: Integrative genomics of ovarian cancer IC300 [GenomeWideSNP_6]

value: endometrioid


title: Stage II colorectal cancer tissue samples (FFPE) 36


title: Integrative genomics of ovarian cancer IC413 [GenomeWideSNP_6]

value: T&N

value: serous


title: Integrative genomics of ovarian cancer P0985 [GenomeWideSNP_6]

value: T

value: other


title: Integrative genomics of ovarian cancer IC504 [GenomeWideSNP_6]

value: Campbell


title: MCF-10A, pBabe, TAM, 24 hour, biological rep 1

description: Gene expression From 24 hour tamoxifen treated

value: human mammary epithelial cell line (MCF10A)

value: pBABE

tag: agent

value: tamoxifen

tag: time

value: 24 hours


title: MCF-10A, pBabe, TAM, 12 hour, biological rep 1

description: Gene expression From 12 hour tamoxifen treated

value: 12 hours


title: MCF-10A, pBabe, TAM, 12 hour, biological rep 2


title: MCF-10A, pBabe, TAM, 24 hour, biological rep 2


title: Stage II colorectal cancer tissue samples (FFPE) 33

value: colorectal cancer

tag: tumor stage

value: stage II

value: normal colon mucosa obtained from the same patient as Channel 1


title: Stage II colorectal cancer tissue samples (FFPE) 31


title: Stage II colorectal cancer tissue samples (FFPE) 34


title: MCF-10A, pBabe, TAM, 0 hour, biological rep 1

description: Gene expression From Untreated

value: untreated

value: 0 hour


title: Stage II colorectal cancer tissue samples (FFPE) 30


title: Integrative genomics of ovarian cancer IC257 [GenomeWideSNP_6]

tag: histological subtype

value: mucinous

tag: age


title: shaking biological rep 6

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from_shaking

hyb_protocol: ~1ug label and fragmented applied for 16hrs 40OC

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus.

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis with a scale filter for Ft genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: shaking

label_protocol: Enzo BioArray Terminal Labeling Kit with Biotin-ddUTP (Affymetrix) was used to label the 3′ termini of the fragmented cDNA products. Labeled cDNA (1 µg) was hybridized to custom Affymetrix GeneChips

growth_protocol: Bacteria were initially streaked on Luria-Bertani (LB) agar supplemented with streptomycin (100 µg/ml), kanamycin (50 µg/ml), chloramphenicol (30 µg/ml), carbenicillin (50 µg/ml) and/or tetracycline (10 µg/ml), and then cultured in LB-Miller broth. ST bacteria were prepared by inoculating one colony from a fresh plate (no more than one week old) into 3 ml of LB-Miller broth and then incubating at 37°

extract_protocol: Total RNA from each sample was stabilized with RNAProtect (Qiagen), extracted and purified using the 96-well plate RNAeasy kit (Qiagen) with slight modifications. RNA samples were treated with DNA-free DNase I (Ambion) and the quality of DNA-free RNAs were monitored on Agilent RNA Pico II LabChips (Agilent Technologies). Additionally, possible DNA contamination was tested by qPCR (see below). 10 mg of total RNA from each sample was reverse-transcribed to cDNA using random hexamer primers (Invitrogen) and SuperScript III reverse transcriptase (Invitrogen). RNA was removed and cDNA was purified using a QiaQuick 96 PCR purification kit (Qiagen), quantified and fragmented with DNase I (Roche)

treatment_protocol: without aeration (no shaking) for 18 h. LL bacteria were prepared by inoculating one colony from a fresh plate into 2 ml of LB-Miller broth, incubating at 37°C with aeration (shaking at 225 rpm) for 18 h. An aliquot of this culture (300 ml) was subcultured into 10 ml of fresh LB-Miller broth in a 150 ml Ehrlenmeyer flask and incubated at 37°C for 3.5 h with aeration.


title: Stage II colorectal cancer tissue samples (FFPE) 35


title: Stage II colorectal cancer tissue samples (FFPE) 32


title: Stage II colorectal cancer tissue samples (FFPE) 29


title: Stage II colorectal cancer tissue samples (FFPE) 28


title: MCF-10A, pBabe, EtOH, 24 hour, biological rep 3

description: Gene expression From 24 hour EtOH treated

value: EtOH (control)


title: MCF-10A, pBabe, TAM, 36 hour, biological rep 1

description: Gene expression From 36 hour tamoxifen treated

value: 36 hours


title: Integrative genomics of ovarian cancer IC179 [GenomeWideSNP_6]

value: T&N

value: endometrioid

tag: grade

tag: stage


title: shaking biological rep 3

description: Gene expression data from_shaking


title: Integrative genomics of ovarian cancer IC258 [GenomeWideSNP_6]


title: shaking biological rep 2

description: Gene expression data from_shaking


title: shaking biological rep 1

description: Gene expression data from_shaking


title: shaking biological rep 5

description: Gene expression data from_shaking


title: static biological rep 6

description: Gene expression data from_static

source_name: static


title: MCF-10A, pBabe, EtOH, 24 hour, biological rep 2


title: MCF-10A, pBabe, TAM, 24 hour, biological rep 3


title: BJ fibroblast cell, EL, rep 2

value: human foreskin fibroblast cell line (BJ)

value: hTERT + SV40 early region


title: Stage II colorectal cancer tissue samples (FFPE) 25


title: static biological rep 4

description: Gene expression data from_static


title: Integrative genomics of ovarian cancer IC151 [GenomeWideSNP_6]

value: Campbell


title: Stage II colorectal cancer tissue samples (FFPE) 27


title: Integrative genomics of ovarian cancer IC448 [GenomeWideSNP_6]


title: MCF-10A, pBabe, EtOH, 24 hour, biological rep 1

value: human mammary epithelial cell line (MCF10A)

value: pBABE


title: static biological rep 3

description: Gene expression data from_static


title: MCF-10A, pBabe, EtOH, 12 hour, biological rep 3

description: Gene expression From 12 hour EtOH treated


title: MCF-10A, pBabe, EtOH, 36 hour, biological rep 1

description: Gene expression From 36 hour EtOH treated


title: Integrative genomics of ovarian cancer IC095 [GenomeWideSNP_6]


title: Stage II colorectal cancer tissue samples (FFPE) 24


title: Integrative genomics of ovarian cancer IC128 [GenomeWideSNP_6]


title: MCF-10A, pBabe, EtOH, 12 hour, biological rep 2


title: static biological rep 2

description: Gene expression data from_static


title: Integrative genomics of ovarian cancer IC121 [GenomeWideSNP_6]


title: Integrative genomics of ovarian cancer IC138 [GenomeWideSNP_6]


title: static biological rep 1

description: Gene expression data from_static


title: MCF-10A, pBabe, EtOH, 12 hour, biological rep 1


title: MCF-10A, Er-src, EtOH, 36 hour, biological rep 1

description: Gene expression From 36 hour EtOH treated MCF10A ER-Src Cells

value: pBABE-ER-Src


title: MCF-10A, Er-src, EtOH, 12 hour, biological rep 3

description: Gene expression From 12 hour EtOH treated MCF10A ER-Src Cells

value: 12 hours


title: static biological rep 5

description: Gene expression data from_static


title: shaking biological rep 4

description: Gene expression data from_shaking


title: MCF-10A, Er-src, EtOH, 24 hour, biological rep 1

description: Gene expression From 24 hour EtOH treated MCF10A ER-Src Cells

value: 24 hours


title: MCF-10A, Er-src, EtOH, 12 hour, biological rep 2


title: MCF-10A, Er-src, EtOH, 24 hour, biological rep 2


title: Stage II colorectal cancer tissue samples (FFPE) 17

value: colorectal cancer

value: stage II


title: Stage II colorectal cancer tissue samples (FFPE) 21

value: normal colon mucosa obtained from the same patient as Channel 1


title: Stage II colorectal cancer tissue samples (FFPE) 16


title: Stage II colorectal cancer tissue samples (FFPE) 18


title: Stage II colorectal cancer tissue samples (FFPE) 15


title: MCF-10A, Er-src, EtOH, 12 hour, biological rep 1


title: Stage II colorectal cancer tissue samples (FFPE) 13


title: MCF-10A, pBabe, TAM, 12 hour, biological rep 3

value: tamoxifen


title: young_shock_red_Rep3

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

description: 1h after shock-context-exposure

hyb_protocol: After a two-hour reaction, 1.5 μg of purified, Cy3-labeled cRNA were hybridized to an oligonucleotide Whole Mouse Genome Microarray (4x44K, Agilent Technologies) for 17 hours at 65˚C. Post processing washes were done according to the Agilent Technologies SSPE protocol (v2.1), replacing wash solution 3 by acetonitril, followed by immediate scanning.

scan_protocol: Slides were scanned using an Agilent G2565BA scanner, and data were extracted using the Feature Extraction software version 9.5.3.1 (Agilent Technologies).

data_processing: Median signal intensities from the Feature Extraction Software were normalized using the VSN method from R package “limma”.

source_name: Shock 3

label_protocol: 600 ng of total RNA were reverse-transcribed and amplified, thereby incorporating Cyanine 3-CTP nucleotides, using the Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer's recommendations (Agilent One-Color Microarray-Based Gene Expression Analysis, protocol version 5.5, February 2007; Agilent Technologies).

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen, Gaithersburg, MD).  Nucleic acid quantity, quality and purity were determined using a spectrophotometer (Nanodrop, Rockland, DE) and a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).  Only RNA samples with a RNA integrity number between 9.0 and 10.0 were considered for further analysis.

treatment_protocol: To measure associative learning we employed the contextual fear conditioning paradigm. We subjected mice  to fear conditioning. The training consisted of a single exposure to the conditioning context (3 min) followed by a single electric foot shock (0.7 mA, constant current, 2s). Explorative behavior during the training and the response to the foot-shock was similar among groups. Animals that were not subjected to fear conditioning but otherwise treated identically served as control. Hippocampi from mice were isolated 1h after treatment and were flash frozen into liquid nitrogen and stored in -80 ºC for subsequent extraction of nucleic acids.

tag: strain

value: hippocampus

value: 3 months


title: MCF-10A, Er-src, TAM, 36 hour, biological rep 2

description: Gene expression From 36 hour tamoxifen treated MCF10A ER-Src Cells

value: 36 hours


title: young_shock_red_Rep4

description: 1h after shock-context-exposure

source_name: Shock 4


title: young_shock_red_Rep2

description: 1h after shock-context-exposure

source_name: Shock 2


title: Stage II colorectal cancer tissue samples (FFPE) 4


title: Stage II colorectal cancer tissue samples (FFPE) 14


title: young_context_Rep4

description: 1h after context-exposure

source_name: Context 4


title: MCF-10A, Er-src, TAM, 24 hour, biological rep 1

description: Gene expression From 24 hour tamoxifen treated MCF10A ER-Src Cells


title: MCF-10A, Er-src, TAM, 36 hour, biological rep 1


title: young_context_Rep1

description: 1h after context-exposure

source_name: Context 1


title: young_shock_red_Rep1

description: 1h after shock-context-exposure

source_name: Shock 1


title: old_fear_Rep4

description: 1h after fear conditioning (FC) (context-shock exposure)

source_name: 16 month old after FC 4

value: 16 months


title: cyclo 30-2 tech 2

city: Brummeria

first: John

middle: van Wyk

last: Becker

state: Gauteng

address: Meiring Naude Road

department: Biosciences

country: South Africa

institute: Council for Scientific and industrial Research

description: Biological replicate 2, technical replicate 2

hyb_protocol: Probe labelling was estimated on a Nanodrop. Similar amounts of labelled probe (typically 100 picomoles) were hybridized to the microarray slides. Slides were prehybridized with a solution containing 5X SSC (from 20X SSC: 3 M NaCl, 1.5 M sodium citrate, pH 7.0), 0.1% SDS and 0.1 mg/mL BSA, prewarmed to 42ºC. Prehybridization proceeded in 50 mL Falcon tubes, incubated at 42ºC for 45-60 min. Following prehybridization, the slides were washed in three washes of 0.1X SSC before centrifugation for 5 min at 200 xg. The combined Cy-labelled probes (4 µl) were mixed with 36 µl of Operon hybridization buffer for a total volume of 40 µl. The probes were denatured at 95ºC for 5 min, and subsequently applied to the slide under Lifterslips (Erie Scientific Company). The microarray slides were enclosed in ArrayIt (Telechem International) hybridization chambers and submersed in a heated water bath and incubated for 16-20 h at 42ºC. The slides were successively washed in low stringency (2X SSC, 0.5% SDS; heated to 42ºC), medium stringency (1X SSC) and high stringency (0.1X SSC) wash buffers for 5 min each. Slides were then centrifuged (5 min, 200X g). Scanning was performed with an Axon GenePix 4000B scanner (Molecular Devices).

scan_protocol: Washed slides were scanned with a Genepix™ 4000B scanner (Axon Instruments, Foster City, CA, USA).  Separate images were acquired for each fluorophore at a resolution of 10 μm per pixel.

data_processing: GenePix results (gpr) files were generated using GenePix 6.0 (Molecular Devices) software, without normalization. For clustering analyses, results files were normalized with DNMAD using print-tip loess. The normalized values were subsequently downloaded and analyzed with the Multiexperiment Viewer (MeV) in the TM4 software suite. Hierarchical Clustering (HCL, average linkage was performed to estimate technical and biological variation between samples and at which point cytostasis most likely occurred for comparative purposes in downstream analyses. Intensity data for individual slides were imported into LIMMA (linear models for microarray data) in the R computing environment (www.bioconductor.org). Pre- and post-normalization diagnostic plots were performed using MARRAY. Data from each microarray slide was normalized using print-tip loess. Data between microarrays was normalized using rquantile normalisation. Results from biological and slide replicates within each of the time points was collated, and linear models were computed to contrast gene expression between time points.  A two-fold change in gene expression was used as cut-off, in conjunction with correction for false discovery (FDR = 5%). Analysis of differentially expressed genes was performed in MADIBA (Micro Array Data Interface for Biological Annotation; http://www.bi.up.ac.za/MADIBA/index.php).

organism: Plasmodium falciparum

source_name: Cyclohexylamine treated P. falciparum 30 hpi

label_protocol: cDNA synthesis reactions of 12 µg each were set up for each sample or reference RNA in a total of 50 µl. Before denaturation at 70ºC for 10 min, 2 µl of oligo d(T) primer (2 µg/µl) and 8 µl of random nanomer primer (0.5 µg/µl) (both New England Biolabs) were added. cDNA synthesis proceeded overnight at 42ºC after the addition of an aminoallyl-dNTP mix (Fermentas), DTT, reaction buffer and 200 U of SuperScript III Reverse Transcriptase (Invitrogen). RNA was hydrolyzed by the addition of 10 µl each of 1 M NaOH and 0.5 M EDTA solutions and incubated at 65ºC for 10 min. Unincorporated aminoallyl dUTP was removed by purification using the Macherey-Nagel NucleoSpin Extract II Kit. The eluted cDNA was quantified using a Nanodrop and similar quantities of test and reference cDNA (typically 2 µg) were dried down to a volume of 2.5 µl in a vacuum drier. Five microliters of a 0.2 M Na2CO3 buffer, pH 9.0, was added to the cDNA and mixed well. Cy3 (sample) or Cy5 (reference) (2.5 µl) (GE Healthcare) ester was added and the coupling allowed to proceed for 2 h in the dark at room temperature. Uncoupled dyes were removed by purification with the RNeasy Mini Kit (Qiagen).

growth_protocol: P. falciparum isolate 3D7 parasites were cultured in 75cm2 flasks (Nalgene) in human erythrocytes (blood group A+) and RPMI 1640 medium supplemented with 25 mM HEPES, 0.0088% hypoxanthine, 40 ug/ml gentamycin (all Sigma) and 0.5 % Albumax (Invitrogen). Parasites were maintained in continuous culture in a 10 ml volume, and were scaled up to 50 ml for drug treatments. The parasitemia and morphological forms detected in the cultures were determined and estimated by Giemsa (Fluka) stained smears under 1000x light microscopy.

extract_protocol: Erythrocytes from harvested cultures were pelleted, washed once with 1X PBS to remove traces of culture medium, and then frozen at -80ºC until RNA extractions were performed. RNA was isolated from 15 ml culture samples with a Qiagen RNeasy kit, using a modified protocol including Qiazol (Qiagen) in the lysis step.  Contaminating genomic DNA was removed with DNase I (Qiagen).

treatment_protocol: Fresh cultures were scaled up to 50 ml (5% hematocrit, 10% parasitemia), synchronized twice with 5% D-sorbitol for 5 min at 37ºC to select for parasites in the ring stage, and treated with 2 mM cyclohexylamine at invasion. Fifteen milliliters of culture was harvested at late ring/early trophozoite (18 hpi), mid trophozoite (25 hpi) and late trophozoite (30 hpi) stages. Similar volumes were harvested from untreated P. falciparum 3D7 control cultures at the same time points. Parallel drug treatments were conducted, serving as biological replicates.

value: Cyclohexylamine

tag: time point

value: 30 hpi

source_name: Total RNA pooled from mixed stage in vitro Plasmodium falciparum cultures

tag: reference

value: Total RNA pooled from mixed stage in vitro Plasmodium falciparum isolate 3D7 cultured in human erythrocytes


title: old_fear_Rep3

source_name: 16 month old after FC 3


title: Integrative genomics of ovarian cancer IC220 [GenomeWideSNP_6]

source_name: Ovarian tumours at the time of diagnosis

tag: tissue type (t=tumour; n= normal blood lymphocyte)

value: T&N

value: endometrioid

tag: scandate(batch)

value: Campbell


title: MCF-10A, Er-src, TAM, 16 hour, biological rep 2

description: Gene expression From 16 hour tamoxifen treated MCF10A ER-Src Cells

value: human mammary epithelial cell line (MCF10A)

value: pBABE-ER-Src

value: 16 hours


title: young_context_Rep3

description: 1h after context-exposure

source_name: Context 3


title: young_fear_Rep4

source_name: 3 month old after FC 4


title: old_fear_Rep1

source_name: 16 month old after FC 1


title: cyclo 30-2 tech 1

description: Biological replicate 2, technical replicate 1


title: Stage II colorectal cancer tissue samples (FFPE) 1

description: Normal colon mucosa from each patient was used as reference in the oaCGH experiments

source_name: colorectal cancer

value: colorectal cancer

source_name: normal colorectum mucosa


title: Stage II colorectal cancer tissue samples (FFPE) 26

value: stage II


title: young_context_Rep2

description: 1h after context-exposure

source_name: Context 2


title: Stage II colorectal cancer tissue samples (FFPE) 2

value: normal colon mucosa obtained from the same patient as Channel 1


title: MCF-10A, Er-src, TAM, 16 hour, biological rep 1

source_name: Cultured Cells

value: tamoxifen


title: cyclo 30-1

description: Biological replicate 1, technical replicate 1


title: young_fear_Rep3

source_name: 3 month old after FC 3

value: hippocampus


title: old_control_Rep4

description: naive, not subjected to any training (control)

source_name: 16 month old control 4


title: old_fear_Rep2

source_name: 16 month old after FC 2


title: old_control_Rep2

source_name: 16 month old control 2


title: young_fear_Rep1

source_name: 3 month old after FC 1

value: 3 months


title: old_control_Rep3

source_name: 16 month old control 3


title: MCF-10A, Er-src, TAM, 12 hour, biological rep 3

description: Gene expression From 12 hour tamoxifen treated MCF10A ER-Src Cells

value: 12 hours


title: MCF-10A, Er-src, TAM, 12 hour, biological rep 1


title: MCF-10A, Er-src, TAM, 8 hour, biological rep 1

description: Gene expression From 8 hour tamoxifen treated MCF10A ER-Src Cells

value: 8 hours


title: MCF-10A, Er-src, TAM, 12 hour, biological rep 2


title: young_control_Rep2

source_name: 3 month old control 2


title: young_control_Rep3

source_name: 3 month old control 3


title: cyclo 25-2

source_name: Cyclohexylamine treated P. falciparum 25 hpi

value: Cyclohexylamine

value: 25 hpi

source_name: Total RNA pooled from mixed stage in vitro Plasmodium falciparum cultures


title: cyclo 18-2

source_name: Cyclohexylamine treated P. falciparum 18 hpi

value: 18 hpi

value: Total RNA pooled from mixed stage in vitro Plasmodium falciparum isolate 3D7 cultured in human erythrocytes


title: young_control_Rep4

source_name: 3 month old control 4


title: old_control_Rep1

source_name: 16 month old control 1

value: 16 months


title: ctrl 30-2

source_name: Untreated P. falciparum 30 hpi

value: 30 hpi


title: MCF-10A, Er-src, TAM, 8 hour, biological rep 2

value: human mammary epithelial cell line (MCF10A)


title: cyclo 25-1 tech 1


title: cyclo 18-1 tech 1


title: cyclo 18-1 tech 2

description: Biological replicate 1, technical replicate 2


title: Integrative genomics of ovarian cancer IC293 [GenomeWideSNP_6]

source_name: Ovarian tumours at the time of diagnosis

value: T&N

value: endometrioid

tag: source

value: Campbell


title: MCF-10A, Er-src, TAM, 4 hour, biological rep 1

description: Gene expression From 4 hour tamoxifen treated MCF10A ER-Src Cells

value: pBABE-ER-Src

value: 4 hours


title: young_control_Rep1

source_name: 3 month old control 1

tag: tissue


title: Liver_OSe_animal#25

city: Lexington

first: Shengfa

middle: F

last: Liao

state: KY

address: 214 WP Garrigus Bldg

department: Dept of Animal & Food Sciences

institute: University of Kentucky

description: Liver tissue was obtained with aspiration biopsy technique

hyb_protocol: Following fragmentation, 10 μg of labeled cRNA was hybridized to Affymetrix Bovine Genome Array for 16 hr at 45°C using the GeneChip Hybridization Oven 640 (Affymetrix Technical Analysis Manual). GeneChips were washed and stained in the Affymetrix Fluidics Station 450. GeneChips were stained with R-Phycoerythrin Streptavidin, followed by an antibody solution and a second R-Phycoerythrin Streptavidin solution, with all liquid handling performed by a GeneChip Fluidics Station 450.

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

data_processing: The raw data were collected with the GeneChip Operating Software (GCOS, version 1.2). The expression intensity values from the software (i.e., the “.cel” files) were imported into Partek Genomics Suite software (version 6.4; Partek Inc., St. Louis, MO).  The algorithm of Robust Multichip Averaging adjusted with GC oligo content was implemented for background correction.  The background-corrected data were further converted into expression values via the algorithms of Quantile normalization of different chips and then Median Polish summarization of multiple probes.

organism: Bos taurus

source_name: Liver tissue from organic Se supplmented heifers

label_protocol: Biotinylated cRNA was prepared from 4 μg of total RNA as per the standard labeling protocol described in the Affymetrix GeneChip Technical Analysis Manual (2005; Affymetrix, Santa Clara, CA).  Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers.  Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the GeneChip IVT Labeling kit (Affymetrix, Santa Clara, CA) incorporating biotinylated UTP.

growth_protocol: Thirty Angus heifers (Age 261 ± 6 d) obtained from and raised at the University of Kentucky Agricultural Research and Education Center (Princeton, KY) were fed a corn silage-based diet without Se supplementation for 75 d. Then the heifers (BW 393 ± 9 kg) were randomly assigned to 3 dietary treatment groups (Ctrl, ISe, OSe; n = 10) as described in the “overall design” section above. To achieve a growth rate of 0.5 kg/d, heifers were individually fed a basal cracked corn and cottonseed hull-based diet (7.8 kg/d for the first 80 d and 8.2 kg/d for the last 25 to 26 d) using a Calan gate system.  A commercial mineral-vitamin premix (Kentucky Nutrition Service, Lawrenceburg, KY) with or without Se supplementation was administered daily by manually mixing into each individual animal’s basal diet. The basal diet plus the mineral-vitamin premix totally provide intrinsic Se to the animals at 0.48 mg/animal daily.

extract_protocol: TRIzol extraction of total RNA was performed according to the manufacturer's instructions (Invitrogen Corporation, Carlsbad, CA).

treatment_protocol: The treatment protocol (i.e., dietary Se supplementation) has been described in the “overall design” and “growth protocol” sections above.

value: Biopsied liver (right lobe) tissue

value: organic selenium


title: Liver_ISe_animal#29

source_name: Liver tissue from inorganic Se supplmented heifers

value: inorganic selenium


title: Liver_OSe_animal#23


title: ctrl 30-1 tech 2


title: young_fear_Rep2

source_name: 3 month old after FC 2

value: hippocampus

value: 3 months


title: Liver_ISe_animal#22


title: MCF-10A, Er-src, TAM, 2 hour, biological rep 2

description: Gene expression From 2 hour tamoxifen treated MCF10A ER-Src Cells

source_name: Cultured Cells

value: tamoxifen

value: 2 hours


title: MCF-10A, Er-src, TAM, 1 hour, biological rep 2

description: Gene expression From 1 hour tamoxifen treated MCF10A ER-Src Cells

value: 1 hours


title: Liver_Ctrl_animal#21

source_name: Liver tissue from control heifers (without Se supplementation)

value: control


title: Liver_ISe_animal#26


title: MCF-10A, Er-src, TAM, 2 hour, biological rep 1


title: ctrl 30-1 tech 1

value: Total RNA pooled from mixed stage in vitro Plasmodium falciparum isolate 3D7 cultured in human erythrocytes


title: ctrl 25-2 tech 2

source_name: Untreated P. falciparum 25 hpi

value: 25 hpi


title: Liver_ISe_animal#18


title: MCF-10A, Er-src, TAM, 4 hour, biological rep 2

value: human mammary epithelial cell line (MCF10A)


title: Liver_OSe_animal#19


title: MCF-10A, Er-src, TAM, 0 hour, biological rep 2

description: Gene expression From Untreated MCF10A ER-Src Cells

value: untreated

value: 0 hour


title: Stage II colorectal cancer tissue samples (FFPE) 20

source_name: colorectal cancer

value: colorectal cancer

value: stage II

source_name: normal colorectum mucosa

value: normal colon mucosa obtained from the same patient as Channel 1


title: MCF-10A, Er-src, TAM, 1 hour, biological rep 1

value: pBABE-ER-Src


title: Liver_Ctrl_animal#16

value: Biopsied liver (right lobe) tissue


title: Liver_OSe_animal#14

value: organic selenium


title: Liver_Ctrl_animal#17


title: ctrl 18-2

source_name: Untreated P. falciparum 18 hpi

value: 18 hpi


title: ctrl 25-2 tech 1


title: ctrl 25-1


title: Liver_ISe_animal#11

value: inorganic selenium


title: Liver_OSe_animal#12


title: Liver_ISe_animal#7


title: Liver_Ctrl_animal#6


title: Liver_OSe_animal#8


title: ctrl 18-1 tech 1


title: ctrl 18-1 tech 2


title: MBCD/chol R8h

status: Public on Apr 17 2010

city: Namur

first: conny

last: mathay

address: 61, rue de Bruxelles

country: Belgium

institute: FUNDP

description: gene expression data on mock cholesterol-depleted keratinocytes at R8h

hyb_protocol: Following fragmentation,cRNA was hybridized onto Affymetrix U133 Plus 2.0 GeneChips® at 45º C for 16 h. Subsequent to hybridization, the arrays were washed and stained with streptavidin-phycoerythrin,

scan_protocol: Scan in an Affymetrix GeneChip® Scanner 3000

data_processing:
Alternative CDF from AffyProbeMiner, GCRMA as preprocessing method, probe level ANOVA 2 as processing method, False Discovery Rate analysis as multiple testing adjustment
Probe sets with a fold change higher than 2 or lower than -2 and a p value lower than 0.05 (adjusted for multiple testing) were defined to be differentially regulated

source_name: Mock cholesterol-depleted keratinocyte culture after recovery time of 8h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1.5ug total RNA

growth_protocol: Passage 2 adult normal abdominal keratinocytes are seeded in culture dishes in KGM2 medium, switched the following day to Epilife with HKGS medium. When cell attained 50% confluence, the culture medium is replaced by Epilife without HKGS, a culture medium containg no exogenous peptide factors and which is only supplemented in amino acids and hydrocortisone. In this medium the immerged autocrine cultures grow until cell confluence with medium changes every two days.

extract_protocol: total RNA extraction by mini RNeasy columns Plus (Qiagen) was performed according to the manufacturer's instructions.

treatment_protocol: Parallel confluent culture dishes are left untreated (Ctrl) or treated for 1h with 7.5 mM methyl-beta-cyclodextrin (MBCD) or treated for 1h with 7.5mM cholesterol-charged methyl-beta-cyclodextrin complexes (MBCD/chol). After the treament cell were washed twice with PBS and then cells were either harvested immediately (recovery time 0h =R0h) or were incubated in autocrine culture medium for 1h (recovery time 1h =R1h) or 8h (recovery time 8h =R8h)

tag: tissue type

value: Normal abdominal keratinocytes P2, strain 169

tag: cell type

value: mock cholesterol-depleted keratinocytes


title: MCF-10A, Er-src, TAM, 24 hour, biological rep 2

description: Gene expression From 24 hour tamoxifen treated MCF10A ER-Src Cells

tag: cell line

tag: tranfected molecules

value: tamoxifen

value: 24 hours


title: MDA-MB-231_parental

city: Stockholm

first: Pekka

middle: Juhani

last: Kohonen

address: Nobelsväg 13, Box 210

department: IMM Institute of Environmental Medicine

country: Sweden

institute: Karolinska Institutet

hyb_protocol: Biotin-labeled target cRNAs were fragmented and the quality of labelling procedures was assessed with GeneChip Test3 arrays. Hybridizations to U133 Plus 2.0 arrays were performed for 16 hours at 45°C, followed by automated array washing and staining procedures.

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

data_processing: The simpleaffy_2.20.0 R-package was used to carry out RMA normalization using custom CDF hgu133plus2hsensgcdf_12.1.0. Probe values were mapped to Ensembl genes. The affymetrix controls beginning with AFFX were removed.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA.

growth_protocol: DMEM (1,000 mg/L glucose) with 10% inactivated fetal bovine serum (FBS), 1% nonessential amino acids, 100 U/mL penicillin and 100 µg/mL streptomycin in an incubator with a humidified atmosphere of 95% air and 5% CO2 at 37°C.

extract_protocol: RNA was extracted using the RNeasy kit (Qiagen) according to the manufacturer’s instructions.

value: breast cancer cell line


title: MBCD R1h

description: gene expression data on cholesterol-depleted keratinocytes at R1h

source_name: Cholesterol-depleted keratinocyte culture after recovery time of 1h

value: cholesterol-depleted keratinocytes


title: Liver_Ctrl_animal#1

tag: agent

value: control


title: MBCD R8h

description: gene expression data on cholesterol-depleted keratinocytes at R8h

source_name: Cholesterol-depleted keratinocyte culture after recovery time of 8h


title: MDA-MB-231(SA)

value: MDA-MB-231(SA) variant


title: MBCD/chol R0h

description: gene expression data on mock cholesterol-depleted keratinocytes at R0h

source_name: Mock cholesterol-depleted keratinocyte culture without recovery time


title: Ctrl R1h

description: gene expression data on untreated keratinocytes at R1h

source_name: Control keratinocyte culture after recovery time of 1h

value: untreated keratinocytes


title: Ctrl R8h

description: gene expression data on untreated keratinocytes at R8h

source_name: Control keratinocyte culture after recovery time of 8h


title: Ctrl R0h

description: gene expression data on untreated keratinocytes at R0h

source_name: Control keratinocyte culture without recovery time


title: MBCD/chol R1h

description: gene expression data on mock cholesterol-depleted keratinocytes at R1h

source_name: Mock cholesterol-depleted keratinocyte culture after recovery time of 1h


title: Dupuytren's contracture-derived fibroblasts 1575578014_F

status: Public on Apr 16 2010

city: Pittsburgh

first: Latha

last: Satish

state: PA

address: 320 E North Avenue

department: Center for Genomic Sciences

institute: Allegheny-Singer Research Institute

hyb_protocol: The biotin labeled cRNA (1.5 μg) was hybridized overnight in a temperature controlled shaking incubator at 37°C.

scan_protocol: Post-hybridization processing included a stringent wash to remove unbound and non-specifically hybridized target molecules, a staining step with a Cy™3-streptavidin conjugate followed by several non-stringent washing steps to remove unbound conjugate. Following a final rinse, the bioarrays were dried by centrifugation and scanned. The arrays were read in an Illumina Bead Array Reader.

data_processing: The data were analyzed using the Significance Analysis of Microarrays (SAM) software package. Normalization was performed using MS Excel via median array normalization. The median normalized data for each individual array was obtained by dividing each probe intensity value by the median value of that entire array.

source_name: Fibroblasts

label_protocol: Total RNA was amplified, labeled and hybridized according to the manufacturers' protocols. Biotin labeled cRNA probe was prepared by a linear amplification method. After first and second strand synthesis, the cDNA served as the template for an in vitro transcription (IVT) reaction to produce the target cRNA.

growth_protocol: Fibroblasts from both carpal tunnel and Dupuytren's contracture were grown to confluenced

extract_protocol: RNA was extracted using RNA isolation kit from Qiagen.

treatment_protocol: Once the cells reached 80% confluence RNA was extracted

value: Fibroblasts

tag: disease status

value: Dupuytren's contracture


title: Liver_Ctrl_animal#10


title: Dupuytren's contracture-derived fibroblasts 1575578032_D


title: Dupuytren's contracture-derived fibroblasts 1575578032_E


title: Dupuytren's contracture-derived fibroblasts 1575578032_F


title: Dupuytren's contracture-derived fibroblasts 1575578014_E


title: MBCD R0h

description: gene expression data on cholesterol-depleted keratinocytes at R0h

source_name: Cholesterol-depleted keratinocyte culture without recovery time


title: carpal-tunnel derived fibroblasts 1575578032_B

value: carpal-tunnel


title: carpal-tunnel derived fibroblasts 1575578014_B


title: carpal-tunnel derived fibroblasts 1575578014_C


title: carpal-tunnel derived fibroblasts 1575578032_C


title: Dupuytren's contracture-derived fibroblasts 1575578014_D


title: MCF-10A, Er-src, TAM, 0 hour, biological rep 1

value: human mammary epithelial cell line (MCF10A)

value: pBABE-ER-Src

value: untreated

tag: time

value: 0 hour


title: carpal-tunnel derived fibroblasts 1575578032_A


title: cyclo 25-1 tech 2

source_name: Cyclohexylamine treated P. falciparum 25 hpi

value: Cyclohexylamine

value: 25 hpi

source_name: Total RNA pooled from mixed stage in vitro Plasmodium falciparum cultures

value: Total RNA pooled from mixed stage in vitro Plasmodium falciparum isolate 3D7 cultured in human erythrocytes


title: carpal-tunnel derived fibroblasts 1575578014_A


title: Dupuytren's contracture-derived fibroblasts 4 Codelink

hyb_protocol: The biotin labeled cRNA (10 μg) was hybridized overnight in a temperature controlled shaking incubator at 37°C.

scan_protocol: Post-hybridization processing included a stringent wash to remove unbound and non-specifically hybridized target molecules, a staining step with a Cy™5-streptavidin conjugate followed by several non-stringent washing steps to remove unbound conjugate. Following a final rinse, the bioarrays were dried by centrifugation and scanned. The CodeLink bioarrays were read in a Lumonix-Packard scanner.

data_processing: Data were median-normalized using CodeLink software (available as a supplementary file on the Series record).  Further normalization was performed using MS Excel via median array normalization (provided in Sample data table below). The median normalized data for each individual array was obtained by dividing each probe intensity value by the median value of that entire array. Significance determination was performed using the Significance Analysis of Microarrays (SAM) software package.


title: Dupuytren's contracture-derived fibroblasts 6 Codelink


title: Dupuytren's contracture-derived fibroblasts 5 Codelink


title: Dupuytren's contracture-derived fibroblasts 2 Codelink


title: Dupuytren's contracture-derived fibroblasts 1 Codelink


title: carpal-tunnel derived fibroblasts 6 Codelink


title: carpal-tunnel derived fibroblasts 2 Codelink


title: carpal-tunnel derived fibroblasts 3 Codelink


title: carpal-tunnel derived fibroblasts 4 Codelink


title: Dupuytren's contracture-derived fibroblasts 3 Codelink


title: Neuroblastoma SH-SY5Y cells_cloneB_stably transfected with RNAi against DJ-1_replicate1

city: Trieste

first: Paola

last: Roncaglia

state: TS

address: via Bonomea 265

department: Neurobiology

country: Italy

institute: SISSA/ISAS (International School for Advanced Studies)

hyb_protocol: Labeled cRNA was hybridized on Affymetrix GeneChip Human U133A 2.0 Arrays containing over 14,500 transcripts. Hybridized GeneChips were stained and washed (GeneChip Fluidics Station 450).

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

data_processing: Cell intensity values and probe detection calls were computed from the raw microarray data using the Affymetrix GeneChip Operating Software (GCOS). Further data processing was performed in the R computing environment (http://www.r-project.org/) using packages from the BioConductor software project (http://www.bioconductor.org/). Robust Multi-Array Average (RMA) normalization was applied. Normalized data were then filtered based on the Affymetrix detection call, so that only probes with a Present call in at least one of the arrays were retained. Data were then imported in the MultiExperiment Viewer (MeV) software, and statistical analysis was performed using SAM (Significance Analysis of Microarrays). Additionally, an expression fold-change cutoff of 2 was applied to detect significantly differentially expressed genes.

source_name: Neuroblastoma SH-SY5Y cells, stably transfected with RNAi against DJ-1

label_protocol: 10 micrograms of each total RNA sample was labeled according to the standard one-cycle amplification and labeling protocol developed by Affymetrix (Santa Clara, CA).

growth_protocol: Human neuroblastoma SH-SY5Y cells (ATCC) were maintained in culture as suggested by vendors.

extract_protocol: Total RNA was isolated using the TRIZOL reagent (Invitrogen) following the manufacturer’s instructions, and purified using the RNeasy mini kit (Qiagen). The quality of total RNA was assessed using a bioanalyzer (Agilent 2100; Agilent Technologies) and RNA was quantified using a ND-1000 Nanodrop spectrophotometer.

value: human neuroblastoma cells

tag: clone

value: B

tag: transfectant type


title: carpal-tunnel derived fibroblasts 5 Codelink


title: carpal-tunnel derived fibroblasts 1 Codelink


title: Neuroblastoma SH-SY5Y cells_cloneM_scramble control_replicate1

source_name: Neuroblastoma SH-SY5Y cells, transfected with scramble control

value: M

value: stably transfected with scramble control


title: Neuroblastoma SH-SY5Y cells_cloneH_scramble control_replicate1

value: H


title: Neuroblastoma SH-SY5Y cells_cloneM_scramble control_replicate2


title: Neuroblastoma SH-SY5Y cells_cloneH_scramble control_replicate2


title: Neuroblastoma SH-SY5Y cells_cloneB_stably transfected with RNAi against DJ-1_replicate2


title: Neuroblastoma SH-SY5Y cells_cloneG_stably transfected with RNAi against DJ-1_replicate1

value: G


title: Pterygium, sample 2

status: Public on Apr 15 2010

city: Singapore

first: Silin

last: Chen

address: 11 Third Hospital Avenue

country: Singapore

institute: Singapore Eye Research Institute

description: Half of each sample was taken and mixed to form the common reference pool. Each sample was then hybridized against this common reference, which can then be used as a common factor to which signals from all samples can be normalized, enabling direct comparison.

hyb_protocol: The Hy3™-labeled samples and the Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA array version 11.0 (Exiqon, Denmark), which contains capture probes targeting all miRNAs for human, mouse or rat registered in the miRBASE version 12.0 at the Sanger Institute. The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria).

scan_protocol: After hybridization, the microarray slides were scanned and stored in an ozone-free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA).

data_processing: A technical quality assessment was performed based on results from spike-in controls, flagging of spots, background intensity levels and signal intensity distribution. Image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA). The quantified signals were background corrected (Normexp with offset value 10 – Ritchie et al., 2007) and normalized in Exiqon-R software using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.

source_name: primary pterygium tissue

label_protocol: 0.4 µg total RNA from sample and reference were labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labeling kit (Exiqon, Denmark) following the procedure described by the manufacturer.

extract_protocol: RNA isolation was carried out using TRIzol® Reagent (Invitrogen, Carlsbad, CA) and RNeasy Mini Kit (Qiagen, Valencia, CA) in accordance with the manufacturer’s procedure.

value: pterygium

tag: patient

source_name: Common reference pool

value: pterygium, conjunctiva


title: Pterygium, sample 1


title: Conjunctiva, sample 1

source_name: uninvolved conjunctiva tissue

value: conjunctiva


title: Pterygium, sample 3


title: Conjunctiva, sample 3


title: Conjunctiva, sample 2


title: FAH iPSCs #7

city: Münster

first: Boris

last: Greber

address: Röntgenstraße 20

department: Cell and Developmental Biology

institute: Max Planck Institute for Molecular Biomedicine

hyb_protocol: According to manufacturer's instructions. Hybridization time: 18h

scan_protocol: Illumina iScan system using default settings

data_processing: Cubic Spline normalization with background subtraction in BeadStudio.

source_name: cell culture of FAH iPSCs, line #7

label_protocol: Ambion TotalPrep RNA Amplification Kit. RNA input: 400ng, IVT: 12h

extract_protocol: Trizol, according to manufacturer's instructions

value: induced pluripotent stem cells

tag: genotype


title: Neuroblastoma SH-SY5Y cells_cloneG_stably transfected with RNAi against DJ-1_replicate2


title: FAH iPSCs #4

source_name: cell culture of FAH iPSCs, line #4


title: FAH gene-corrected iPSCs, line 7.2

source_name: cell culture of FAH gene-corrected iPSCs, line 7, subclone 2

value: gene-corrected induced pluripotent stem cells

value: gene-corrected FAH(-/-)


title: 292FW34

city: Bethesda

first: Jennifer

last: Barb

state: MD

address: 12 South Drive Bldg 12A Room 2001

department: DCB

description: Fetal eyes were obtained from Advanced Bioscience Resources (Alameda, CA) based on the availability of the aborted fetuses. RPE cells were collected and RNA was extracted (24-48 hours period following the abortion procedure).

hyb_protocol: Biotin-labeled cRNA was then fragmented at 94oC for 35 min with 5X fragmentation buffer  (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 ug) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45oC

scan_protocol: Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400.  Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).

data_processing: Affymetrix Microarray Suite version 5.0

source_name: native fetal RPE

label_protocol: Ten micrograms of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using T7-(dT) 24  primer (Geneset Oligos, La Jolla, CA, USA) containing T7 RNA polymerase promoter. After synthesis of the second cDNA strand, this product was used in an in vitro transcription reaction to generate biotinylated cRNA using a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). The biotinylated cRNA was cleaned with the RNAeasy Mini Kit (Qiagen, Valencia, CA).

growth_protocol: Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.

extract_protocol: Fetal and adult RPE cells were collected, homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and RNA was subsequently purified using an RNeasy Mini kit (Qiagen Inc, Valencia, CA).  Double-stranded cDNA was synthesized from 6µg of total RNA using the SuperScript Choice system (Invitrogen, Carlsbad, CA) and the T7-Oligo (dT) promoter primer kit (Affymetrix, Santa Clara, CA).  cDNA was purified using Phase Lock Gels (Eppendorf, Westbury, NY).  Concentration and quality of RNA samples was determined on the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA). The integrity of RNA is assessed by looking at 18 & 28s rRNA peaks and though the RIN (RNA integrity number). RNA concentrations were measured using the Nano drop spectrophotometer (Wilmington, DE) and all samples used for the study had 260/280 ratios above 2.0 and 260/230 ratios above 1.7.

value: native fetal RPE

tag: gestational age

value: 17 weeks


title: 292FW35

description: Adult native RPE (anRPE) were collected from donors of Caucasian decent and total RNA was extracted right after.

source_name: adult native RPE

value: adult native RPE from 78 y.o. donor


title: 292FW31

description: ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.

source_name: ARPE-19 cell line


title: 292FW30


title: 292FW29


title: 292FW28


title: FAH MEFs

source_name: cell culture of FAH MEFs

value: mouse embryonic fibroblasts


title: OG2 ESCs

source_name: cell culture of OG2 ESCs

value: mouse embryonic stem cells


title: 292FW24


title: 292FW33


title: FAH gene-corrected iPSCs, line 7.1

source_name: cell culture of FAH gene-corrected iPSCs, line 7, subclone 1


title: 292FW32

value: 16 weeks


title: Donor 6 Control

city: San Francisco

first: Jun

middle: S

last: Song

address: 513 Parnassus Avenue, Box 0794

department: Institute for Human Genetics

institute: UCSF

description: Donor 6 Control

data_processing: Each sample had eight RNU44 and eight RNU48 technical replicate measurements for quality control and reference normalization.  For each sample, we removed any RNU48 outliers by using the Weisberg t-test at a p-value cutoff of 0.05, a method for detecting outliers in small data sets; microRNA CT values were then normalized by subtracting the mean RNU48 CT value of the resulting trimmed set. Some miRNA expression values could not be determined by PCR, and we considered only the miRNAs whose expression could be assayed in at least 3 out of 7 paired samples.  Fold-changes in miRNA expression levels after forskolin treatment in the seven samples were pooled together and ranked.  Highly ranked miRNAs were then found; more precisely, p-values for the rank distribution of  miRNA differential expression were computed using the hypergeometric test, as in the Redundant siRNA Activity (RSA) analysis.  For each miRNA, we also performed a robust paired t-test on a trimmed set obtained by removing at most one outlier sample found by the Weisberg t-test at the 5% significance level. We obtained a final list of miRNAs differentially expressed at the 5% significance level of both hypergeometric test and t-test.

label: FAM

source_name: primary melanocyte

label_protocol: Standard Applied Biosystem's Taqman Protocol

growth_protocol: Primary human melanocytes were isolated from neonatal foreskin as described (McGill et al., 2002). Primary melanocytes between passages 2 and 5 were stimulated with 20 uM forskolin (Sigma Aldrich) or with DMSO (as a vehicle control), for indicated times after an overnight starvation in F10 media supplemented with penicillin/streptomycin/glutamine (PSQ).  Serum starvation conditions did not affect cell viability.

extract_protocol: Total RNA was purified using Trizol reagent (Invitrogen) according to the manufacturer’s instructions, followed by treatment with RNase-free DNase (Qiagen). Dried RNA pellets were resuspended in DEPC/ddH2O. RNA was quantified by measuring OD260/280.

treatment_protocol: Primary human melanocytes were serum depleted for 12 hours, followed by treatment with 20uM forskolin (or DMSO control) for 16 hours.

value: primary melanocyte


title: Donor 6 Forskolin Treated

description: Donor 6 Forskolin Treated


title: 292FW27


title: Donor 7 Forskolin Treated

description: Donor 7 Forskolin Treated


title: Donor 5 Forskolin Treated

description: Donor 5 Forskolin Treated


title: Donor 4 Control

description: Donor 4 Control


title: Donor 5 Control

description: Donor 5 Control


title: Donor 4 Forskolin Treated

description: Donor 4 Forskolin Treated


title: Donor 3 Forskolin Treated

description: Donor 3 Forskolin Treated


title: Donor 2 Control

description: Donor 2 Control


title: Donor 1 Control

description: Donor 1 Control


title: 292FW25


title: Donor 3 Control

description: Donor 3 Control


title: exp 2, control, rep 1

first: Adán

last: Colón-Carmona

address: 100 Morrissey Blvd

department: Biology

institute: University of Massachusetts Boston

description:
Global gene expression.
21d whole plants, >=20 individuals pooled, long-day light, 23C.
batch_2_control_1

hyb_protocol: Chips were hybridized and processed on a Affymetrix Fluidics Station Model 450 per the manufacturer's instructions.

scan_protocol: Hybridized chips were read on a model M10 scanner.

data_processing:
.CEL files were produced by the Affymetrix MAS, and normalization was performed in R/Bioconductor using the just.gcrma function with default parameters.

Values are unmodified outputs from Bioconductor/just.gcrma and represent the log2 transformation of the signal level.

source_name: whole plants, 0 mM phenanthrene

label_protocol: Labeling was performed with the Affymetrix Enzo kit per the manufacturer's instructions.

growth_protocol: 21d whole plants grown from sterilized seeds on 0.5MS + phytoagar, long-day light, 23C +/- 1C.

extract_protocol: RNA was isolated using TRIzol (Molecular Research Center) per the manufacturer's instructions, DNAse treated (Invitrogen), and purified with RNeasy Mini Cleanup (Qiagen) per the manufacturers' instructions.

treatment_protocol: Phenanthrene was thoroughly mixed into sterile media prior to pouring plates.

tag: ecotype

value: Columbia

value: whole plants

tag: age

value: 21 days

tag: treatment


title: exp 2, treated, rep 1

description:
Global gene expression.
21d whole plants, >=20 individuals pooled, long-day light, 23C.
batch_2_treated_1

source_name: whole plants, 0.25 mM phenanthrene

value: phenanthrene