title: S2-cells_untreated_1 vs S2_cells_no methoxyfenozide_1

description: no extra information to be added

growth_protocol: Schneider 2 (S2) cells (S2-Mt-Dl) were cultured in HyQ SFX-Insect™ medium (Perbio Science, Erembodegem, Belgium).

treatment_protocol:
Cells were exposed to increasing concentrations of methoxyfenozide starting from 0.1 µM up to 100 µM. Gradually increasing amounts of methoxyfenozide (until the highest concentration, 100 µM) were applied for over 4 months. Methoxyfenozide-caused cessation of cell proliferation was used as a critrerium to select resistant S2 cells (as previously described in Mosallanejad, H., Soin, T. and Smagghe, G. (2008) Selection for resistance to methoxyfenozide and 20-hydroxyecdysone in cells of the beet armyworm, Spodoptera exigua. Archives of Insect Biochemistry and Physiology 67, 36-49).
The cell susceptibility of obtained methoxyfenozide-resistant cells was determined by an in vitro bioassay by using the MTT technique. After reaching the highest exposure concentration, we continued subculturing the resistant cells under this pressure.
In order to determine the stability of the observed resistance, the resistant cells were propagated for four passages in the absence of methoxyfenozide.


title: S2-cells_no methoxyfenoside_2 vs S2_cells_untreated_1

status: Public on Nov 08 2010

type: RNA

city: Ghent

first: Guy

last: Smagghe

address: Coupure Links

department: Crop Protection

country: Belgium

institute: Ghent University

description: no extra information to be added

hyb_protocol: Prehybridisation: The slides were incubated in pre-warmed prehybridisation solution (5x SSC, 0.1% SDS, 1% BSA) at 42°C for 1hr. Next, they were washed five times in MilliQ water and once in isopropanol. The slides were dried by centrifugation and hybridization of the samples was performed immediately afterwards. Hybridisation: 75ul of pre-warmed (42°C) hybridisation buffer (50% formamide, 10x SSC, 0.2% SDS) was added to each Alexa Fluor 647 sample, which was dissolved by gently pipetting. Subsequently, the dissolved sample was added to the corresponding Alexa Fluor 555 sample, which was also dissolved by gently pipetting. Next, the samples were denaturated at 95°C during 3min. Immediately afterwards, the samples were applied onto the microarray slides. Hybridisation was performed in a SlideBooster System (Advalytix) at 42°C for 20hr. Wash: The slides were successively washed in 1x SSC, 0.2% SDS (42°C, 5min), 0.1x SSC, 0.2% SDS (room temperature, 5min) and 0,1x SSC (room temperature, 5min), and dried by centrifugation.

scan_protocol: Scanning of the microarray slides was performed at wavelengths of 635nm and 532nm by means of a Genepix Personal 4100A confocal scanner (MDS Analytical Technologies). The photomultiplier tube (PMT) voltage gain was adjusted for each array in order to obtain a count ratio close to one. Image analysis was performed by using the Genepix Pro 6.0 software (MDS Analytical Technologies) and consisted of spot identification and extraction of the fluorescent intensity data.

data_processing: Data were imported in a MIAME (Minimum Information About a Microarray Experiment)-compliant database (www.islab.ua.ac.be/base/), developed by the Intelligent Systems Laboratory (University of Antwerp, Antwerp, Belgium). For each spot the median intensity was calculated (which is the median of intensities measured for each pixel within the spot) and background (BG) corrected. Spots for which the median foreground (FG) signal was smaller than that of the median BG + 2SD (SD: standarddeviation of the background signal) were filtered out. The Cy5/Cy3-ratio was calculated for each spot, log2-transformed and normalized by using the 'variation stabilization normalization' (vsn) method.

label: Alexa Fluor 647 (Invitrogen)

molecule: total RNA

organism: Drosophila melanogaster

source_name: methoxyfenozide treated - again cultured without methoxyfenozide

label_protocol:
The samples were labeled in an indirect manner: aminoallyl-dUTPs were incorporated during the reverse transcription step and subsequently, amine-reactive Alexa Fluor 647 or 555 carboxylic acid succinimidyl ester dyes (Invitrogen) were coupled to the aminoallyl groups. Aminoallyl-dUTPs (aa-dUTPs, Sigma Aldrich) were dissolved in 0,1M KPO4 (pH 7.5) to a final concentration of 100mM. 5ul dATP, 5ul dCTP, 5ul dGTP, 3ul dTTP and 2ul aa-dUTP (each 100mM) were mixed together to obtain the 50x aminoallyl-dNTP mix with a 2:3 aa-dUTP:dTTP ratio. For each sample, 10ug of total RNA was used. 2ug poly-dT oligo (dT18, Sigma Aldrich) and 3ug random hexamers (Sigma Aldrich) were added to the total RNA and the volume was adjusted to 18.5ul with di-methyl-propyl carbonate (DMPC)-treated MilliQ water. Subsequently, the mix was incubated at 70°C during 10min, and immediately afterwards placed on ice. 0.6ul 50x aminoallyl-dNTP mix, 6ul 5x first strand buffer, 3ul DTT (0,1 M), 400U SuperScript III RT (SuperScript III Reverse Transcriptase kit, Invitrogen) and 20U RNaseOut Recombinant Ribonuclease Inhibitor (Invitrogen) were added and the mix was incubated at 46°C for 2hr. Upon reverse transcription the RNA was hydrolized by adding 10ul NaOH (1M) and 10ul EDTA (0.5M). In order to obtain a neutral pH 10ul HCl (1M) and 10ul NaAc (3M) were added. The resulting aminoallyl-labeled cDNA was purified by means of the QIAQuick PCR Purification Kit (Qiagen) as described by the manufacturer, except that not the wash and elution buffers from the kit were used as these contain free amines which interfere with the dye coupling reaction. Instead phosphate wash buffer (5mM KPO4, pH 8.0; 80% EtOH) and elution buffer (4mM KPO4, pH 8.5) were used. Subsequently, the samples were dried by evaporation in a SpeedVac.
Each portion of Alexa Fluor 647 or 555 carboxylic acid succinimidyl ester dye was dissolved in 9ul Na2CO3 (0.1M, pH 9.0) and added to the dry cDNA. The mix was then incubated at room temperature for 1hr. The Alexa Fluor labeled samples were purified by means of the QIAQuick PCR Purification Kit (Qiagen) as described by the manufacturer. Quantification and quality control of the labeled samples were performed with the ND-1000 UV-Vis Spectrophotometer (Thermoscientific, NanoDrop Products). Subsequently, the samples were dried by evaporation in a SpeedVac.

growth_protocol: Schneider 2 (S2) cells (S2-Mt-Dl) were cultured in HyQ SFX-Insect™ medium (Perbio Science, Erembodegem, Belgium). A subpopulation of these untreated S2 cells was cultured in HyQ SFX-Insect™ medium to which increasing amounts of methoxyfenozide were added (cfr. Treatment Protocol). A subpopulation of the methoxyfenozide-resistant S2 was again cultured in normal medium.

extract_protocol: RNeasy Mini Kit (Qiagen)

treatment_protocol:
Cells were exposed to increasing concentrations of methoxyfenozide starting from 0.1 µM up to 100 µM. Gradually increasing amounts of methoxyfenozide (until the highest concentration, 100 µM) were applied for over 4 months. Methoxyfenozide-caused cessation of cell proliferation was used as a critrerium to select resistant S2 cells (as previously described in Mosallanejad, H., Soin, T. and Smagghe, G. (2008) Selection for resistance to methoxyfenozide and 20-hydroxyecdysone in cells of the beet armyworm, Spodoptera exigua. Archives of Insect Biochemistry and Physiology 67, 36-49).
The cell susceptibility of obtained methoxyfenozide-resistant cells was determined by an in vitro bioassay by using the MTT technique. After reaching the highest exposure concentration, we continued subculturing the resistant cells under this pressure.
In order to determine the stability of the observed resistance, a subpopulation of the resistant cells was propagated for four passages in the absence of methoxyfenozide.

tag: cell line

value: Schneider 2 cells (S2-Mt-Dl)

tag: tissue

value: embryo

label: Alexa Fluor 555 (Invitrogen)

source_name: untreated

treatment_protocol: untreated


title: Ume1.1

status: Public on Nov 09 2010

city: Leicester

first: Eran

last: Tauber

address: University Road

department: Genetics

country: United Kingdom

institute: University of Leicester

hyb_protocol: Affymetrix Eukaryotic Target Hybridization protocol

scan_protocol: Affymetrix protocol.

data_processing: R/Bioconductor affylmGUI package (version 1.8.0)

label: Biotin

organism: Saccharomyces cerevisiae

label_protocol: Affymetrix GeneChip® IVT Labeling Kit, according to manufacturer's protocol

growth_protocol: SC –Ura GAL (2%) cultures (12 ml) were inoculated at OD600 0.2 and incubated with shaking at 30º C until reaching an OD600 of ~1.0.

extract_protocol: Cells were harvested and lysed with acid-washed glass beads. Total RNA was isolated with Qiagen RNeasy Midi kit

treatment_protocol: Htt103Q is a galactose (GAL)-inducible,

tag: genotype/variation

tag: strain

value: MATa (BY4741)


title: S2-cells_methoxyfenozide_1 vs S2_cells_untreated_2

description: no extra information to be added

source_name: methoxyfenozide treated

growth_protocol: Schneider 2 (S2) cells (S2-Mt-Dl) were cultured in HyQ SFX-Insect™ medium (Perbio Science, Erembodegem, Belgium). A subpopulation of these untreated S2 cells was cultured in HyQ SFX-Insect™ medium to which increasing amounts of methoxyfenozide were added (cfr. Treatment Protocol).

treatment_protocol:
Cells were exposed to increasing concentrations of methoxyfenozide starting from 0.1 µM up to 100 µM. Gradually increasing amounts of methoxyfenozide (until the highest concentration, 100 µM) were applied for over 4 months. Methoxyfenozide-caused cessation of cell proliferation was used as a critrerium to select resistant S2 cells (as previously described in Mosallanejad, H., Soin, T. and Smagghe, G. (2008) Selection for resistance to methoxyfenozide and 20-hydroxyecdysone in cells of the beet armyworm, Spodoptera exigua. Archives of Insect Biochemistry and Physiology 67, 36-49).
The cell susceptibility of obtained methoxyfenozide-resistant cells was determined by an in vitro bioassay by using the MTT technique. After reaching the highest exposure concentration, we continued subculturing the resistant cells under this pressure.


title: S2-cells_methoxyfenozide_2 vs S2_cells_untreated_1

description: no extra information to be added


title: S2-cells_untreated_2 vs S2_cells_no methoxyfenozide_2

description: no extra information to be added


title: S2-cells_untreated_1 vs S2_cells_methoxyfenozide_1

description: no extra information to be added

growth_protocol: Schneider 2 (S2) cells (S2-Mt-Dl) were cultured in HyQ SFX-Insect™ medium (Perbio Science, Erembodegem, Belgium). A subpopulation of these treatment S2 cells was cultured in HyQ SFX-Insect™ medium to which increasing amounts of methoxyfenozide were added (cfr. Treatment Protocol).


title: Saanen, 1st animal

type: genomic

city: Bologna

first: Pier Luigi

last: Martelli

address: via Irnerio 42

country: Italy

institute: University of Bologna

hyb_protocol: NimbleGen Hybridization Kit

scan_protocol: NimbleGen MS 200 Microarray Scanner with default parameters

data_processing: Data normalization was conducted using the normalize.qsline method from the Bioconductor package in R. Then data were analysed for each hybridization using normalized log2 ratios using the CGHweb server.

molecule: genomic DNA

organism: Capra hircus

source_name: Reference Goat (Camosciata delle Alpi, animal 1)

label_protocol: NimbleGen Dual-Color DNA Labeling Kit

extract_protocol: Wizard® Genomic DNA Purification kit (Promega Corporation, Madison, WI) extraction protocol

tag: breed

value: Camosciata delle Alpi

tag: gender

value: female

source_name: Test Goat (Saanen, animal 1)

value: Saanen


title: Saanen, 2nd animal

source_name: Test Goat (Saanen, animal 2)


title: Girgentana, 1st animal

source_name: Test Goat (Girgentana, animal 1)

value: Girgentana


title: Girgentana, 2nd animal

source_name: Test Goat (Girgentana, animal 2)


title: mammary_49days_DES1μg_rep2

status: Public on Nov 06 2010

city: sakuragaoka

first: souda

last: masakazu

state: kagoshima/kagoshima

department: tumor pathology, field of oncology

country: Japan

institute: kagoshima university graduate school of medical and dental sciences

description: gene expression after DES1μg-treated within 24 hr after birth

hyb_protocol: The hybridization solution was prepared using the gene expression hybridization kit (Agilent). The Agilent 60-mer array (G4130B) contains 20600 rat probe sequence. 1.5 µg of labeled cRNA and 10 µl of 25×fragmentation buffer were incubated at 60℃ for 30 minutes. Hybridization was carried out in 490 µl of a hybridization mixture at 60℃ for 17 hours in Agilent’s microarray hybridization chambers according to the Agilent protocol. The microarray slides were washed for approximately 1 minute each in gene expression wash buffer 1, wash buffer 2 and Acetonitrile according to the Agilent protocol. The Cy3 fluorescence intensities were determined by an Agilent DNA Microarray Scanner and then were analyzed by Feature Extraction software 9.1 (Agilent).

scan_protocol: Sufficient annotation of the array design  GPL2882.    1) Essential experimental and data processing protocols scanning protocol of raw data (one-color ) by Agilent microarray scanner  1. scan area : 61×21.6mm,  2. scan resolution : 10µm,  3. dye channel : green,  4. green PMT : 100%.    2) Image analysis and digitalization  1. software : Agilent’s Feature Extraction Ver. 9.1,  2. File for spot finding using the Agilent scanner and Agilent’s Feature Extraction software : File name 013328_D_20060331.xml.zip,  3. Grid : 013328_D_20060331,  Image : US22502707_SLOT……,  Protocol : GE1-v1_91.

data_processing:
1. The scanned images were analyzed with Feature Extraction Software 9.1.3.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 013328_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. All values calculated by the Feature Extraction were imported into the GeneSpring GX7.3.1(Agilent). The expression value less than 0.01 were set to 0.01 and the data per chip were normalized to 50 percentile, the data per gene were normalized to control sample (mammary_35days_oil)
2. Procedure of data analysis  2-1. Genes from all genes whose flags in NEO-DES are Present or Marginal in at least 10 of 12 samples.  2-2. Genes from Flags are Present or Marginal with expression normalized data in NEO-DES from 0.5 to 2 in at least 6 of 6 conditions.  2-3. base: [Gene List(2-1)] AND NOT [Gene List (2-2)]          Notes from the individual filter steps follow.          1. Gene List (2-1)              Genes matching Flags are Present or Margina2. Gene List (2-2)              Genes matching Normalized Data between 0.5 and 2   2-4. Genes selected from condition Experiment Type Group II , Treatment type DES1μg(35)  that have Normalized Data values that are greater or less than those in condition(s) Experiment Type Group I , Treatment type Oil(35)  by a factor of 2 fold. Starting gene list: base.  2-5. Genes selected from condition Experiment Type Group III , Treatment type DES100μg(35)  that have Normalized Data values that are greater or less than those in condition(s) Experiment Type Group I , Treatment type Oil(35)  by a factor of 2 fold. Starting gene list: base.                                                   2-6. Genes selected from condition Experiment Type Group II , Treatment type DES1μg(49)  that have Normalized Data values that are greater or less than those in condition(s) Experiment Type Group I , Treatment type Oil(49)  by a factor of 2 fold. Starting gene list: base.  2-7. Genes selected from condition Experiment Type Group III , Treatment type DES100μg(49)  that have Normalized Data values that are greater or less than those in condition(s) Experiment Type Group I , Treatment type Oil(49)  by a factor of 2 fold. Starting gene list: base.

organism: Rattus norvegicus

source_name: mammary(TEBs), 49days, DES1μg, replicate 2

label_protocol: Equal quantities of total RNA from each sample were labeled using Agilent low RNA input linear amplification kit, and hybridized to Agilent oligonucleotide probe sequence. Briefly, total RNA (<100ng) was reverse transcribed into cDNA, using Moloney murine leukemia virus reverse transcriptase with T7 promoter primer, and incubated at 40℃ for 2 hours. Fluorescent cRNA were synthesized by in vitro transcription using T7 RNA polymerase and labeled with cyanine 3 (Cy3). Labeled cRNA were further purified using RNase mini purification columns (Qiagen) to remove unlabeled products. 1.5 µg of the fluorescently labeled cRNA were used for each of the microarray hybridization. The purity and concentration of amplified RNA were determined by Agilent 2100 Bioanalyzer.

growth_protocol: The animals were female inbred Sprague-Dawley rats, maintained in a filtered air laminar flow at the Division of Laboratory Animal Science, Research Center for Life Science Resources, Kagoshima University. They were given a commercial diet (CE-2, CLEA Inc., Tokyo, Japan) and tap water ad libitum. The use of animals in this research complied with all relevant guidelines set by the Japanese government and Kagoshima University.

extract_protocol: For frozen sampling, the abdominal mammary glands (numbers 4-6) in the rat were quickly excised with a sharp scissor and were immediately embedded in a Tissue Tek OTC compound medium (Sakura, Tokyo, Japan) containing RNase-free water (1:1) and stored at－80℃ until LMD.   For LMD, the Application Solutions Laser Microdissection System (Leica Microsystems, Wetzlar, Germany) were used. Serial 6 µm-thick sections were prepared with a cryostat and were mounted onto a foil-coated glass slide (Matsunami Glass Ind., Ltd., Osaka, Japan). The section were then fixed in 5% acetic acid/ethanol for 3 minutes and stained with 0.05% to toluidine blue O (Merck KGaA, Darmstadt, Germany) for 10 second to maintain the morphologic quality required for accurate microdissection. The section was then washed, dehydrated, cleared in xylene. After careful drying, the sections were laser microdissected according to the manufacture’s instructions (Leica Microsystems).   Total RNA were extracted from each sample of laser microdissected cells into 350 µL of buffer RLT (Qiagen, Hilden, Germany) added β-mercaptoethanol to a concentration of 1%. Next, total RNA were purified with the RNeasy Mini kit (Qiagen) following by DNase treatment according to the manufacture’s protocol. The integrity of intact total RNA was verified by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Newborn rats were divided into 3 groups (each 4 animals) and given a single subcutaneous injection of either 0 (group I), 1 (group II) and 100 (group III) DES dissolved in 0.05 ml sesame oil within 24 hr birth. Animal were weaned at 21 days of birth and each group of rats was autopsied at 35 days of birth (group I: n=2, group II: n=2, group III: n=2) and 49 days of birth (group I: n=2, group II: n=2, group III: n=2). We used all animals for microarrays analysis.

value: Sprague-Dawley

value: mammary

tag: age

value: 49 days after birth

tag: agent

value: 1μg diethlstilbestrol


title: mammary_49days_oil_rep2

description: gene expression after oil-treated within 24 hr after birth

source_name: mammary(TEBs), 49days, oil, replicate 2

value: oil


title: mammary_35days_DES1μg_rep1

source_name: mammary(TEBs), 35days, DES1μg, replicate 1

value: 35 days after birth


title: mammary_35days_DES100μg_rep1

description: gene expression after DES100μg-treated within 24 hr after birth

source_name: mammary(TEBs), 35days, DES100μg, replicate 1

value: 100μg diethlstilbestrol


title: mammary_35days_DES100μg_rep2

source_name: mammary(TEBs), 35days, DES100μg, replicate 2


title: mammary_35days_DES1μg_rep2

source_name: mammary(TEBs), 35days, DES1μg, replicate 2


title: Murciano-Granadina, 1st animal

source_name: Test Goat (Murciano-Granadina, animal 1)

value: Murciano-Granadina


title: mammary_49days_DES100μg_rep1

source_name: mammary(TEBs), 49days, DES100μg, replicate 1


title: S2-cells_untreated_2 vs S2_cells_methoxyfenozide_2

description: no extra information to be added


title: mammary_49days_DES1μg_rep1

source_name: mammary(TEBs), 49days, DES1μg, replicate 1


title: Saanen, 3rd animal

source_name: Test Goat (Saanen, animal 3)


title: mammary_49days_oil_rep1

source_name: mammary(TEBs), 49days, oil, replicate 1


title: Murciano-Granadina, 2nd animal

source_name: Test Goat (Murciano-Granadina, animal 2)


title: mammary_49days_DES100μg_rep2

source_name: mammary(TEBs), 49days, DES100μg, replicate 2


title: mammary_35days_oil_rep2

source_name: mammary(TEBs), 35days, oil, replicate 2


title: Aureococcus anophagefferens, -P (phosphorus deficient cells)

status: Public on Nov 05 2010

type: SAGE

anchor: NlaIII

city: Woods Hole

first: Sonya

last: Dyhrman

state: MA

address: 266 Woods Hole Road

department: Biology

country: USA

institute: Woods Hole Oceanographic Institution

data_processing: The sequences collected were analyzed with software created at the Marine Biological Laboratory specifically for SAGE analysis and used in the context of previous work (Dyhrman et al. 2006).  The SAGE software extracts ditag sequences from the ABI 3730xl results according to the Long-SAGE sequence grammar, parses out individual Long-SAGE tags, excludes tags with sequence ambiguities, and reduces all Long-SAGE tags to a look-up table of unique Long-SAGE tag sequences and their observed frequencies among all of the A. anophagefferens Long-SAGE libraries.

molecule: polyA RNA

organism: Aureococcus anophagefferens

source_name: Aureococcus anophagefferens phosphorus-deficient cells harvested at onset of stationary phase

extract_protocol: Long-SAGE libraries were constructed using approximately 30 μg RNA isolated from extractions of replete (control), –P, and –N A. anophagefferens cells following the I-SAGE Long kit protocol (Invitrogen, Carlsbad, CA). Recombinant pZEro1 clones produced by Long-SAGE were purified using GeneMachines RevPrep Orbit (Genomic Solutions, Ann Arbor, MI) and were sequenced on an ABI 3730xl DNA sequencer (Applied Biosystems, Foster City, CA).


title: Aureococcus anophagefferens, -N (nitrogen deficient cells)

source_name: Aureococcus anophagefferens nitrogen-deficient cells harvested at onset of staitionary phase of growth

value: CCMP 1984


title: Camosciata delle Alpi, 2nd animal

source_name: Reference Goat (Camosciata delle Alpi, animal 1)

source_name: Test Goat (Camosciata delle Alpi, animal 2)


title: Girgentana, 3rd animal

source_name: Test Goat (Girgentana, animal 3)


title: Prostate cancer primary tumor PR73

city: Orlando

first: Steve

last: Goodison

address: 6900 Lake Nona Blvd

department: Cancer Research Institute

institute: M. D. Anderson Cancer Center Orlando

description:
PR73
Prostate cancer primary tumor

hyb_protocol: Following fragmentation, cRNA was hybridized to one U133A Affymetrix GeneChip.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

organism: Homo sapiens

source_name: Human prostate cancer

label_protocol: Biotinylated cRNA was prepared according to standard Affymetrix protocols

extract_protocol: RNeasy kit

value: Prostate cancer primary tumor

tag: recurrence status

value: Recurrent


title: Prostate cancer primary tumor PR74

description:
PR74
Prostate cancer primary tumor


title: Aureococcus anophagefferens, Control (nutrient replete growing cells)

source_name: Aureococcus anophagefferens replete growing cells harvested mid-exponential phase of growth


title: mammary_35days_oil_rep1

source_name: mammary(TEBs), 35days, oil, replicate 1


title: Prostate cancer primary tumor PR72

description:
PR72
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR7

description:
PR7
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR68

description:
PR68
Prostate cancer primary tumor

value: Non-Recurrent


title: Prostate cancer primary tumor PR70

description:
PR70
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR8

description:
PR8
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR64

description:
PR64
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR66

description:
PR66
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR69

description:
PR69
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR63

description:
PR63
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR65

description:
PR65
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR6

description:
PR6
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR59

description:
PR59
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR61

description:
PR61
Prostate cancer primary tumor


title: Cripps Pink week -4_rep1

city: Wenatchee

first: Yanmin

last: Zhu

state: WA

address: 1104 N. Western Ave

institute: USDA ARS

description: Pool of fruit flesh tissues from 5 Cripps Pink apples at -4 week stage in relation to the arrival of physiological maturity.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, using NimbleScan version 2.4.31 following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Malus domestica

source_name: Cripps Pink fruit flesh tissue, week -4

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Fruits were harvested from trees about 15 years old in established commercial apple orchards with normal horticulture management. Each fruit sample had maturity data collected by physiological and biochemical methods.

extract_protocol: Total RNAs were isolated using the cetyltrimethylammonium bromide (CTAB)-based protocol, basically following Gasic et al. (2004). RNA was quantified by a photospectometer (nino-drop), and RNA integrity was verified by agarose gel electophoresis.

treatment_protocol: Apple fruit peel and core were removed. The fruit flesh tissues were cut into smaller pieces and immediately frozen in liquid nitrogen. Tissues were stored in a -80oC freezer before RNA isolation.

tag: cultivar

value: Cripps Pink

tag: developmental stage

value: week -4 relative to physiological maturity

value: cortex


title: Prostate cancer primary tumor PR62

description:
PR62
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR60

description:
PR60
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR58

description:
PR58
Prostate cancer primary tumor


title: Cripps Pink week -2_rep2

description: Pool of fruit flesh tissues from 5 Cripps Pink apples at -2 week stage in relation to the arrival of physiological maturity.

source_name: Cripps Pink fruit flesh tissue, week -2

value: week -2 relative to physiological maturity


title: Cripps Pink week -2_rep3


title: Cripps Pink week -2_rep4


title: Cripps Pink week -4_rep4


title: Prostate cancer primary tumor PR54

description:
PR54
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR55

description:
PR55
Prostate cancer primary tumor


title: Cripps Pink week -4_rep2


title: Prostate cancer primary tumor PR52

description:
PR52
Prostate cancer primary tumor


title: Cripps Pink week 0_rep3

description: Pool of fruit flesh tissues from 5 Cripps Pink apples at week 0 stage in relation to the arrival of physiological maturity.

source_name: Cripps Pink fruit flesh tissue, week 0

value: week 0 relative to physiological maturity


title: Prostate cancer primary tumor PR56

description:
PR56
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR9

description:
PR9
Prostate cancer primary tumor


title: Cripps Pink week -4_rep3


title: Honeycrisp week -4_rep3

description: Pool of fruit flesh tissues from 5 Honeycrisp apples at -4 week stage in relation to the arrival of physiological maturity.

source_name: Honeycrisp fruit flesh tissue, week -4

value: Honeycrisp


title: Prostate cancer primary tumor PR53

description:
PR53
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR57

description:
PR57
Prostate cancer primary tumor


title: Cripps Pink week 0_rep2


title: Cripps Pink week -2_rep1


title: Cripps Pink week 0_rep4


title: Cripps Pink week 0_rep1


title: Honeycrisp week -4_rep4


title: Prostate cancer primary tumor PR50

description:
PR50
Prostate cancer primary tumor


title: Honeycrisp week -4_rep2


title: Prostate cancer primary tumor PR71

description:
PR71
Prostate cancer primary tumor


title: Honeycrisp week -2_rep2

description: Pool of fruit flesh tissues from 5 Honeycrisp apples at -2 week stage in relation to the arrival of physiological maturity.

source_name: Honeycrisp fruit flesh tissue, week -2


title: Honeycrisp week 0_rep4

description: Pool of fruit flesh tissues from 5 Honeycrisp apples at week 0 stage in relation to the arrival of physiological maturity.

source_name: Honeycrisp fruit flesh tissue, week 0


title: Honeycrisp week -4_rep1


title: Prostate cancer primary tumor PR48

description:
PR48
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR45

description:
PR45
Prostate cancer primary tumor


title: Honeycrisp week -2_rep4


title: Honeycrisp week -2_rep1


title: Prostate cancer primary tumor PR43

description:
PR43
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR5

description:
PR5
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR41

description:
PR41
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR42

description:
PR42
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR49

description:
PR49
Prostate cancer primary tumor


title: Honeycrisp week -2_rep3


title: Prostate cancer primary tumor PR37

description:
PR37
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR44

description:
PR44
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR40

description:
PR40
Prostate cancer primary tumor


title: Honeycrisp week 0_rep3


title: Prostate cancer primary tumor PR39

description:
PR39
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR32

description:
PR32
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR31

description:
PR31
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR33

description:
PR33
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR4

description:
PR4
Prostate cancer primary tumor


title: Honeycrisp week 0_rep2


title: Honeycrisp week 0_rep1


title: SC5314 vs SC5314

city: Shanghai

first: Feng

last: Yang

address: Guohe Road

country: China

institute: Second Military Medical University

description: control experiment for the array CGH

hyb_protocol: standard CapitalBio Methods

scan_protocol: Luxscan 10K (CapitalBio)

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed. For each test and control sample, one hybridization strategy was perfomed, the geometric mean of lowess normalized log2 ratio (test/control) was calculated.

organism: Candida albicans

source_name: normal cells as control sample

label_protocol: the genomic DNA was sonicated to generate fragments 50–2000 bp in size,then the DNA fragment was labeled by fluorescent dye (Cy5 and Cy3-dCTP) with random primer and Klenow enzyme.

growth_protocol: C.albicans strains were cultivated overnight in 5 ml YEPD medium, at 30℃, with 200 rpm agitation, until cell density reached 108-109 cells/ml, harvested and washed three times with distilled water by centrifugation for 5 minutes at 3000 g, resuspended in 200μl lysis buffer (2% Triton Ⅹ-100, 1% SDS, 100 mM NaCl, 1 mM EDTA, 10 mM Tris,pH 8.0), and stored at -80℃ until used for DNA extraction.

extract_protocol: For DNA extraction, 200μl of 25:24:1 phenol/chloroform/isoamyl alcohol were added to the cells resuspended in lysis buffer, together with 300 mg of acid-washed glass beads. The mixture was vortexed for 3 minutes before the addition of 200μl of TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH8.0). Following a 5 minutes centrifugation at 9300 g and 4℃ for phase separation (Eppendorf centrifuge 5415D), the DNA in the aqueous phase was precipitated with 1 ml ethanol (96%, v/v) at room temperature, resuspended in 400μl of TE containing 60 mg RNaseA (GE healthcare), and incubated at 37℃ for 6 hours, the DNA was precipitated with 40μl of 3 M ammonium acetate and 1 ml of cold absolute ethanol at -20℃ for 15 minutes, followed by a 5 minutes centrifugation at 9300 g at 4℃. The DNA pellet was carefully washed with 1 ml ethanol (70%, v/v), left to dry at room temperature, and resuspended in 50μl of TE buffer.   DNA was purified using the PCR Clean-up NucleoSpin Extract Ⅱ Kit (Macherey-Nagel, Germany) according to manufacturer’s directions.


title: Prostate cancer primary tumor PR3

description:
PR3
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR29

description:
PR29
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR26

description:
PR26
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR27

description:
PR27
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR28

description:
PR28
Prostate cancer primary tumor


title: strain P546 vs SC5314

description: analysis used genomic contents of SC5314 as control samples for comparison to experimental samples

hyb_protocol: Standard CapitalBio Methods

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed. For each test and control sample, two hybridizations were performed by using a reversal fluorescent strategy,the geometric mean  of lowess normalized log2 ratio (test/control) of two dye-swap slides was calculated.

source_name: clinical strain cells as test samples

label_protocol: The genomic DNA was sonicated to generate fragments 50–2000 bp in size,then the DNA fragment was labeled by fluorescent dye (Cy5 and Cy3-dCTP) with random primer and Klenow enzyme.


title: Prostate cancer primary tumor PR24

description:
PR24
Prostate cancer primary tumor


title: strain S904 vs SC5314


title: strain S197 vs SC5314


title: strain S727 vs SC5314


title: Prostate cancer primary tumor PR47

description:
PR47
Prostate cancer primary tumor


title: strain U885 vs SC5314


title: strain S204 vs SC5314


title: Prostate cancer primary tumor PR25

description:
PR25
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR51

description:
PR51
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR35

description:
PR35
Prostate cancer primary tumor


title: strain F32 vs SC5314


title: Prostate cancer primary tumor PR22

description:
PR22
Prostate cancer primary tumor


title: strain S241 vs SC5314


title: Prostate-specific Pten and p53 deletion anterior prostate tumor 11527A0-REDO

city: Boston

first: Zhihu

last: Ding

address: 44 Binney Street

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Gene expression data from prostate-specific Pten and p53 deletion anterior prostate tumor

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

organism: Mus musculus

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

extract_protocol: Trizol extraction of total RNA followed by Rneasy column cleanup was performed according to the manufacturer's instructions.

value: Anterior prostate tumor

tag: genotype

value: Prostate-specific Pten and p53 deletion

value: 15 weeks of age

tag: genetic background

value: FVB/n, C57BL/6, and 129/Sv mixed background


title: Prostate-specific Pten and p53 deletion anterior prostate tumor 11452A0


title: shBAP1 #2 cells, rep2

city: Montreal

first: El Bachir

last: Affar

state: Quebec

address: 5415 boul. De l'Assomption

country: Canada

institute: Maisonneuve-Rosemont Hospital, University of Montreal

hyb_protocol: The hybridizations to Human genome Hu133 plus 2.0 arrays (Affymetrix) were conducted following the One-Cycle target Labeling Protocol of the GeneChip ® Expression Analysis Technical Manual from Affymetrix (Genome Québec Innovation Centre, Montréal, Canada).

scan_protocol: Probe arrays have been scanned using the Affymetrix® GeneChip® Scanner 3000.

data_processing: Gene expression levels from shControl and shRNAs were subjected to comparative analysis using the expression analysis software Flex Array V1.1 (Michal Blazejczyk, Mathieu Miron, Robert Nadon (2007), Genome Quebec, Montreal, Canada, URL http://genomequebec.mcgill.ca/FlexArray). Data were normalized with Robust Multi-Array Average (RMA) and the algorithm EB (Wright and Simon) was used for statistical analysis.

source_name: U2OS osteosarcoma cell line transfected with shBAP1 #2 construct

label_protocol: The generation of cDNA and biotinylated cRNA were conducted following the One-Cycle target Labeling Protocol of the GeneChip ® Expression Analysis Technical Manual from Affymetrix (Genome Québec Innovation Centre, Montréal, Canada).

growth_protocol: U2OS osteosarcoma cells were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum and penicillin/streptomycin.

extract_protocol: RNA was prepared using Trizol reagent (Invitrogen) and the RNeasy kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: Cells were transfected with either a non-targeting control (shControl) or BAP1 RNA interference (shBAP1) plasmid using Lipofectamine 2000 and were  selected with puromycin containing medium. Then, the cells were synchronized at the G1/S border using a thymidine double block protocol.

tag: treatment

value: shBAP1 #2


title: Prostate-specific Pten and Smad4 deletion anterior prostate tumor A7907

description: Gene expression data from prostate-specific Pten and Smad4 deletion anterior prostate tumor


title: Prostate-specific Pten and Smad4 deletion anterior prostate tumor A5755


title: shBAP1 #2 cells, rep1


title: Prostate-specific Pten and p53 deletion anterior prostate tumor 11526A0-REDO


title: shBAP1 #2 cells, rep3


title: shBAP1 #1 cells, rep3

source_name: U2OS osteosarcoma cell line transfected with shBAP1 #1 construct

value: shBAP1 #1


title: Prostate cancer primary tumor PR2

description:
PR2
Prostate cancer primary tumor


title: Prostate-specific Pten and Smad4 deletion anterior prostate tumor A6296


title: Prostate cancer primary tumor PR19

description:
PR19
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR21

description:
PR21
Prostate cancer primary tumor


title: Prostate-specific Pten and Smad4 deletion anterior prostate tumor A6291


title: Prostate-specific Pten and Smad4 deletion anterior prostate tumor A6295


title: Prostate cancer primary tumor PR18

description:
PR18
Prostate cancer primary tumor


title: shBAP1 #1 cells, rep2


title: shControl cells, rep2

source_name: U2OS osteosarcoma cell line transfected with an shControl construct

value: shControl


title: shControl cells, rep3


title: Prostate-specific Pten deletion anterior prostate tumor M5853

description: Gene expression data from prostate-specific Pten deletion anterior prostate tumor

value: Prostate-specific Pten deletion


title: Prostate cancer primary tumor PR16

description:
PR16
Prostate cancer primary tumor

value: Prostate cancer primary tumor


title: Prostate cancer primary tumor PR20

description:
PR20
Prostate cancer primary tumor

value: Recurrent


title: Gene expression: MCF7

city: Vancouver

first: Raj

last: Chari

state: BC

address: 675 West 10th Avenue

department: Cancer Genetics and Developmental Biology

institute: BC Cancer Research Centre

description:
Data obtained from caBIG (https://cabig.nci.nih.gov)
Breast cancer cell line, ATCC# HTB-22

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA normalized

label: standard Affymetrix protocol

source_name: RNA from breast cancer cell line

label_protocol: standard Affymetrix protocol

extract_protocol: standard Affymetrix protocol

tag: catalog number

value: ATCC# HTB-22


title: shControl cells, rep1


title: Prostate-specific Pten deletion anterior prostate tumor M6167


title: Prostate cancer primary tumor PR17

description:
PR17
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR15

description:
PR15
Prostate cancer primary tumor


title: Prostate-specific Pten deletion anterior prostate tumor M7802


title: wild-type anterior prostate Q6516AP

description: Gene expression data from wild-type anterior prostates

source_name: wild-type anterior prostates Q6516AP

value: Anterior prostate tissue

value: wild-type


title: shBAP1 #1 cells, rep1


title: Gene expression: MCF10A (from GSM254525)

description:
MCF10A_Monolayer_3
FS450_0001 protocol is used for staining and washing the GeneChips using the Affymetrix Fluidics Station 450 (P/N 00-0079).

hyb_protocol: The hybridization, staining, and washing are carried out using the Affymetrix GeneChip Hybridization Wash and Stain Kit following the manufacturer’s protocols, and the arrays were hybridized for 16 hr at 45oC.   FS450_0001 protocol is used for staining and washing the GeneChips using the Affymetrix Fluidics Station 450 (P/N 00-0079).

scan_protocol: The GeneChips are scanned with Affymetrix GeneChip Scanner 3000 7G using GCOS and software and Affymetrix preset settings.

source_name: monolayer

label_protocol: Quality of total RNA was first analyzed by Agilent Bioanalyzer 2100, and RNA samples with RIN (RNA Integrity Number) greater than 7.0 are acceptable for microarray analysis.  Total RNA samples were amplified one round, and the amplified RNA (aRNA) biotinylated using Ambion Biotin-Enhanced Message Amp II kit (#1791, Ambion, Austin, Texas), following the manufacturer’s protocols.

growth_protocol: Normal growth media for MCF10As is DMEM:F12 (Cellgro) w/ 2mM glutamine, containing 5% horse serum, insulin (10 µg ml-1) (Gibco), hydrocortisone (0.5 µg ml-1) (Sigma), EGF (20 ng ml-1) (Upstate) and 1 I.U. ml-1 penicillin, 0.1 µg ml-1 streptomysin, 0.25 µg ml-1 amphotericin B (Cellgro).

extract_protocol: Total RNA from cells grown in monolayer and Transwell® cultures were extracted using Tri reagent (MRC, Cincinnati, OH) and cleaned using DNaseI (Promega, Madison, WI) followed by standard phenol/chloroform precipitation and extraction method.

value: ATCC# CRL-10317


title: Prostate cancer primary tumor PR14

description:
PR14
Prostate cancer primary tumor

source_name: Human prostate cancer


title: Prostate cancer primary tumor PR13

description:
PR13
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR11

description:
PR11
Prostate cancer primary tumor


title: wild-type anterior prostate Q6424AP_redo

source_name: wild-type anterior prostates Q6424AP_redo


title: Gene expression: BT474

description:
Data obtained from caBIG (https://cabig.nci.nih.gov)
Breast cancer cell line, ATCC# HTB-20

value: ATCC# HTB-20


title: wild-type anterior prostate Q6515AP

source_name: wild-type anterior prostates Q6515AP


title: Prostate-specific Pten deletion anterior prostate tumor M5852


title: Prostate-specific Pten deletion anterior prostate tumor M7805


title: Prostate cancer primary tumor PR10

description:
PR10
Prostate cancer primary tumor


title: Gene expression: HCC1937

description: Breast cancer cell line, ATCC# CRL-2336

data_processing: RMA Normalized

label: Affymetrix

source_name: RNA from cell line

extract_protocol: Qiagen Mini prep

value: ATCC# CRL-2336


title: Prostate cancer primary tumor PR1

description:
PR1
Prostate cancer primary tumor


title: Prostate cancer primary tumor PG53

description:
PG53
Prostate cancer primary tumor

value: Non-Recurrent


title: LUNG_2_0

city: East Lansing

first: juan

middle: p

last: steibel

state: MI

address: 1205 I Anthony Hall

institute: Michigan State University

hyb_protocol: Labeled aRNAs were purified, fragmented and denatured at 95°C for 10 min., combined according to the experimental design, and mixed with 50 µl of SlideHyb Buffer (SlideHybTM Glass Array Hybridization Buffer #1, Ambion Inc.). Pigoligoarray hybridizations were performed in sealed hybridization cassettes (ArrayIt, TeleChem International, Inc.) for 18 h at a humid 43°C . Following hybridization, microarray slides were washed with low (2xSSC and 0.5% SDS) and high (0.2xSSC and 0.2% SDS) stringency wash buffers for 10 minutes each.

scan_protocol: Fluorescent images were detected by an Axon GenePix® 4000B scanner (Molecular Devices, Sunnyvale, CA, USA) and fluorescence intensity data were collected using GenePix® Pro 6 software (Molecular Devices) after spot alignment.

data_processing: Median intensities were extracted and normalized using a within print-tip lowess location normalization and an overall scale normalization. The resulting normalized data were expressed in the log2 scale.

organism: Sus scrofa

label_protocol: For each sample, 1 µg of total RNA was subjected to the first strand cDNA synthesis with a T7 oligo(dT) primer using Amino Allyl MessageAmpTM II aRNA Amplification Kit (Ambion Inc.) according to the manufacturer’s instructions. For second-strand synthesis, the cDNAs were in vitro transcribed to synthesize multiple copies of amino allyl-modified aRNAs (aRNAs). After purification 10 µg of aRNAs were labeled with Alexa Fluor®555 and Alexa Fluor®647 dyes (Invitrogen). The measurement of the final dye incorporation in labeled, purified samples was carried out using NanoDrop.

extract_protocol: Frozen 3-mm3 tissue sections were rapidly homogenized in TRIzol® (Invitrogen) using a mortar and pestle. RNA was extracted from homogenized samples (PureLinkTM kit, Invitrogen). All RNA samples were DNAse-treated, evaluated for RNA quantity using Nanodrop Spectrophotometer 2000c (Peqlab) and for RNA quality using Bioanalyzer (Agilent) which results in an RNA Integrity Number (RIN) higher than 8.5.

treatment_protocol: Hampshire by Duroc (HD) cross pigs were used in this study (Petry et al., 2005, 2007). Animals were inoculated intranasally (1 cc per nostril) with 105 cell culture infectious dose 50% (CCID50) of PRRSV strain 97-7985 (Osorio et al., 2002). Lung and bronchial lymph node (BLN) tissues were collected at necropsy (day 14) and stored in –80°C.

value: lung

tag: sample type

value: low (L) PRRSV buden pigs

value: pooled reference


title: LUNG_1_0


title: LUNG_3_0

value: high (H) PRRSV buden pigs


title: LUNG_4_0


title: Prostate cancer primary tumor PG52

description:
PG52
Prostate cancer primary tumor


title: LUNG_0_8


title: Gene expression: HCC1395

description: Breast cancer cell line, ATCC# CRL-2324

value: ATCC# CRL-2324


title: Occlusion-Thalamus-3, Anesthetized

city: Gainesville

first: Vipa

last: Bernhardt

state: FL

address: 1600 Archer Rd

institute: University of Florida

description: US22502637_251487912063_S01_GE2-v5_95_Feb07_1_2

hyb_protocol: Standard Agilent two-color protocol (Agilent 60-mer oligo microarray processing protocol) was used.

scan_protocol: The microarrays were washed and scanned with a laser-based detection system (Agilent, Palo Alto, CA).

data_processing: The intensity of each spot was summarized by the median pixel intensity. A log transformed signal ratio between the experimental (Cy5) channel and the reference (Cy3) channel was calculated for each spot, followed by within-array lowess transformation and between array scale normalization on median intensities (Zahurak et al., 2007). Probes that did not hybridize were removed from consideration.

source_name: Medial thalamus from rat that received tracheal occlusions

label_protocol: Complementary cDNA synthesis, cRNA labeling, and hybridizations were performed following the manufacturer’s kits and protocols (QuickAmp Labeling Kit; Agilent Technologies, Palo Alto, CA).

growth_protocol: Male Sprague-Dawley rats were housed two per cage in a temperature-controlled room (72°F) on a 12:12 light:dark cycle, and with free access to food and water. All animal experiments were approved by the Institutional Animal Care and Use Committee of the University of Florida.

extract_protocol: Total RNA was isolated using the RNA Stat-60 reagent (Tel-test, Friendswood, TX).

treatment_protocol: Eight male Sprague-Dawley rats (277g) were anesthetized by intraperitoneal injection of urethane and instrumented with an inflatable cuff placed around the trachea; inflation of the cuff results in obstruction of trachea, deflation reverses process. For 4 experimental group animals, the cuff was inflated to obstruct  2-4 breaths, then deflated for a minimum of 15 breaths. The obstructions were repeated for 10 minutes. For 4 control group animals, the cuff was not inflated. Brains were removed immediately after the obstructions in the experimental group, or 70 min after surgical setup for control animals

value: Sprague-Dawley

value: Medial thalamus

value: Occlusions

source_name: Reference

value: Medial thalamus from all 8 (treated and control) animals


title: Gene expression: HCC1143

description: Breast cancer cell line, ATCC# CRL-2321

value: ATCC# CRL-2321


title: Control-Thalamus-4, Anesthetized

description: US22502637_251487912062_S01_GE2-v5_95_Feb07_1_4

source_name: Medial thalamus from surgical control rat

value: Control


title: Control-Thalamus-3, Anesthetized

description: US22502637_251487912062_S01_GE2-v5_95_Feb07_1_2


title: Control-Thalamus-1, Anesthetized

description: US22502637_251487912063_S01_GE2-v5_95_Feb07_1_1


title: Gene expression: HCC38

description: Breast cancer cell line, ATCC# CRL-2314

value: ATCC# CRL-2314


title: Occlusion-Thalamus-4, Anesthetized

description: US22502637_251487912063_S01_GE2-v5_95_Feb07_1_4


title: DNA methylation: HCC1937

description: Breast cancer cell line, ATCC# CRL-2336

hyb_protocol: Illumina Infinium HM27 Assay

scan_protocol: Illumina Infinium HM27 Assay

data_processing: default Illumina BeadStudio method

label: Illumina Infinium HM27 Assay

source_name: DNA from breast cancer cell line

label_protocol: Illumina Infinium HM27 Assay

extract_protocol: performed as recommended by the Illumina


title: Control-Thalamus-2, Anesthetized

description: US22502637_251487912063_S01_GE2-v5_95_Feb07_1_3


title: Occlusion-Thalamus-1, Anesthetized

description: US22502637_251487912062_S01_GE2-v5_95_Feb07_1_1


title: LUNG_0_7


title: Gene expression: HCC1008

description: Breast cancer cell line, ATCC# CRL-2320

value: ATCC# CRL-2320


title: DNA methylation: MCF7

description: Breast cancer cell line, ATCC# HTB-22

data_processing: Illumina BeadStudio

extract_protocol: Standard DNA extraction protocol

value: ATCC# HTB-22


title: Prostate cancer primary tumor PG42

description:
PG42
Prostate cancer primary tumor

value: Prostate cancer primary tumor

value: Recurrent


title: Gene expression: HCC2218

description: Breast cancer cell line, ATCC# CRL-2343

value: ATCC# CRL-2343


title: Prostate cancer primary tumor PG41

description:
PG41
Prostate cancer primary tumor


title: Occlusion-Thalamus-2, Anesthetized

description: US22502637_251487912062_S01_GE2-v5_95_Feb07_1_3


title: LUNG_0_6

value: lung


title: Prostate cancer primary tumor PG46

description:
PG46
Prostate cancer primary tumor


title: Prostate cancer primary tumor PG50

description:
PG50
Prostate cancer primary tumor

value: Non-Recurrent


title: DNA methylation: HCC1008

description: Breast cancer cell line, ATCC# CRL-2320


title: Prostate cancer primary tumor PG45

description:
PG 45
Prostate cancer primary tumor


title: Prostate cancer primary tumor PR12

description:
PR12
Prostate cancer primary tumor


title: Control-Thalamus-4, Conscious

hyb_protocol: Sample cRNA synthesis, labeling, hybridization and microarray processing were performed according to manufacturer’s protocol One-Color Microarray-Based Gene Expression Analysis (version 1.0). 1ug of total RNA was used. The labeling reactions were performed using the Agilent Low RNA Input Linear Amplification Kit in the presence of cyanine 3-CTP.

scan_protocol: An Axon GenePix®4000B Microarray Scanner (Molecular Deviced Inc., Concord, Ontario, Canada) was used to scan the microarrays.

data_processing: Data were extracted from microarray images using Agilent Feature Extraction software (Agilent Technologies, Palo Alto, CA). A log2 transformed signal ratio between the experimental channel and the reference channel was calculated for each spot, followed by within-array lowess transformation and between array scale normalization on median intensities (Zahurak et al., 2007). Linear models were firstly used to assess differential expression (Smyth, Michaud, & Scott, 2005), then an empirical Bayes method was used to moderate the standard errors. T-test for the samples was performed on normalized log2 transformed signal ratios of each probe individually, followed by multiple testing correction using a Benjamini-Hochberg approach (Benjamini and Hochberg, 1995).

label_protocol: One microgram of total RNA was used for all hybridizations. Complementary cDNA synthesis, cRNA labeling, and hybridizations were performed following the manufacturer’s kits and protocols (QuickAmp Labeling Kit; Agilent Technologies, Palo Alto, CA).

treatment_protocol: During the experimental session the rats underwent repeated trials of 3-10 breath occlusions followed by approximately 30 s of recovery. Control animals did not receive occlusions. Occlusion and control sessions were performed daily for 10 days. On day 10, within 10 min of completing the ITTO trial, the rats were sacrificed via overdose of anesthetic.


title: LUNG_0_5

value: pooled reference

value: low (L) PRRSV buden pigs


title: Gene expression: HCC1599

description: Breast cancer cell line, ATCC# CRL-2331

value: ATCC# CRL-2331


title: Control-Thalamus-3, Conscious

value: Sprague-Dawley


title: DNA methylation: HCC1395

description: Breast cancer cell line, ATCC# CRL-2324

value: ATCC# CRL-2324


title: BLN_0_7

value: bronchial lymph node

value: high (H) PRRSV buden pigs


title: BLN_0_8


title: BLN_5_0


title: Prostate cancer primary tumor PG15

description:
PG15
Prostate cancer primary tumor


title: Control-Thalamus-2, Conscious

value: Medial thalamus


title: BLN_6_0


title: BLN_4_0


title: DNA methylation: BT474

description: Breast cancer cell line, ATCC# HTB-20

value: ATCC# HTB-20


title: Prostate cancer primary tumor PG37

description:
PG37
Prostate cancer primary tumor


title: Control-Thalamus-1, Conscious

value: Control


title: BLN_3_0


title: Prostate cancer primary tumor PG13

description:
PG13
Prostate cancer primary tumor


title: DNA methylation: MCF10A

description: Breast cancer cell line, ATCC# CRL-10317

value: ATCC# CRL-10317


title: Prostate cancer primary tumor PG12

description:
PG12
Prostate cancer primary tumor


title: Occlusion-Thalamus-4, Conscious

value: Occlusions


title: Prostate cancer primary tumor PG8

description:
PG8
Prostate cancer primary tumor

value: Prostate cancer primary tumor


title: DNA methylation: HCC1599

description: Breast cancer cell line, ATCC# CRL-2331


title: JiOV vs JiTT

status: Public on Nov 04 2010

city: Pathumthani

first: nitsara

last: karoonuthaisiri

state: Pathumthani

address: Paholyothin

department: Central

country: Thailand

institute: BIOTEC

hyb_protocol: The probe was resuspended in hybridization solution (50% Formamide; 5x SSC; 0.1% SDS; 1 mg/ml Human Placental DNA; 10mM Tris, pH 7.5) and placed onto the post-processed slides.  The slides were hybridized at 420C for 16 hrs before they were washed according to Corning’s protocol.

scan_protocol: The slides were scanned with GenePix 4000B (Molecular Devices, Sunnyvale, CA).  Microarray spots on scanned images are located using GenePix Pro version 6.1.

data_processing: All “empty” and “bad” spots were removed from the analysis.  “Empty” spots were failed PCR products whereas “bad” spots were flagged by visual inspection of the spot images.  From the remaining spots, only the spots with intensities more than one standard deviation above the background intensity were further analyzed.  The processed data were normalized within each array by the median-nomalization method, and across arrays, using the Aroma package (Bengtsson, available from: http://www.maths.lth.se/help/R/aroma/) run in R project environment (http://cran.r-project.org).  Data from replicated spots were averaged before clustering.  Logarithmic base 2 values of intensities from both Cy3- and Cy5- samples (M values) were used as inputs for clustering.  Cluster program was used to perform hierarchical clustering and Treeview program was used to visualized the clustered results (Eisen et al., 1998)

organism: Penaeus monodon

source_name: ovary

label_protocol: The RNA from ovary was labeled with Cy3 dye as a reference and that from testes was labeled with Cy5 dye.  The Cy3- and Cy5-samples were mixed together and hybridized onto the arrays overnight. The hybridized slides were washed according to Corning’s instruction.

extract_protocol: RNA samples were extracted from testes and ovaries of juveniles (4 month-old, pooled from n=112 and n=98 for testes and ovaries, respectively) and broodstocks from Andaman Sea. Contaminated genomic DNA was removed by treatment with DNase I at 0.15 U/μg total RNA at 37°C for 30 min.

value: Individual juvenile shrimp

value: ovary

source_name: testis

value: testis


title: DNA methylation: HCC2218

description: Breast cancer cell line, ATCC# CRL-2343

value: ATCC# CRL-2343


title: JpOV vs JpTT

value: Pooled juvenile shrimps


title: Occlusion-Thalamus-3, Conscious


title: WBOV vs WBTT

value: Individual wild-caught broodstock shrimp, female shrimp stage 4, GSI = 12.55

tag: gonadosomatic index

value: Individual wild-caught broodstock shrimp, male shrimp, GSI = 1.549


title: DNA methylation: HCC38

description: Breast cancer cell line, ATCC# CRL-2314

tag: cell line

value: ATCC# CRL-2314


title: DNA methylation: HCC1143

description: Breast cancer cell line, ATCC# CRL-2321

value: ATCC# CRL-2321


title: Occlusion-Thalamus-2, Conscious

value: Sprague-Dawley

tag: tissue


title: Occlusion-Thalamus-1, Conscious


title: BLN_0_1

value: bronchial lymph node

value: pooled reference

value: low (L) PRRSV buden pigs


title: normal diet and normal water H43

city: Athens

first: Ken

last: Jones

state: GA

address: 150 E. Green St.

department: Environmental Health Science

institute: University of Georgia

description:
S805368.J22.CEL
Control

hyb_protocol: standard Affymetrix protocols

scan_protocol: standard Affymetrix protocols

data_processing: Data from the CHP file (from Affymetrix GCOS software) was statistically analyzed in GeneSpring

source_name: thyroid after 2 months 14 day of experiment (control)

label_protocol: Labeling, hybing, and scanning of the chips followed standard Affymetrix protocols for gene expression assay

growth_protocol: Adult rats were housed in standard rat cages in the Uiversity of Georgia's animal care facility for 2 months and one day, or 2 months and 14 days, respectively.

extract_protocol: RNA was extracted from thyroids using a Trizol procedure, and subsecuently cleaned using a Qiagen Rneasy column

treatment_protocol: Adult rats were either fed a normal diet and normal water (controls), normal diet and perchlorate treated water, iodine-deficient diet and normal water, or iodine-deficient diet and perchlorate treated water

value: male

value: thyroid

tag: protocol

value: normal diet and normal water (control)

tag: time

value: 14 days


title: BLN_0_2

value: high (H) PRRSV buden pigs


title: normal diet and normal water H47

description:
S805368.J24.CEL
Control

tag: strain


title: iodine-deficient diet and normal water F33

description:
S805368.J17.CEL
iodine deficiency

source_name: thyroid after 2 months 14 day iodine deficient diet

tag: gender

value: iodine-deficient diet and normal water


title: normal diet and perchlorate water G40

description:
S805368.J20.CEL
95 mg potassium perchlorateper liter drinking water

source_name: thyroid after 2 months 14 day normal diet + 14 day of perchlorate exposure

value: normal diet and perchlorate water


title: normal diet and normal water D21

description:
S805368.J11.CEL
Control

source_name: thyroid after 2 months 1 day of experiment (control)

value: 1 day


title: iodine-deficient diet and normal water B9

description:
S805368.J05.CEL
iodine deficiency

source_name: thyroid after 2 months 1 day iodine deficient diet


title: iodine-deficient diet and perchlorate water E29

description:
S805368.J14.CEL
iodine deficiency + 95 mg potassium perchlorateper liter drinking water

source_name: thyroid after 2 months 14 day iodine deficient diet + 14 day perchlorate exposure


title: normal diet and perchlorate water C15

description:
S805368.J07.CEL
95 mg potassium perchlorateper liter drinking water

source_name: thyroid after 2 months 1 day normal diet + 1 day of perchlorate exposure


title: iodine-deficient diet and perchlorate water A3

description:
S805368.J02.CEL
iodine deficiency + 95 mg potassium perchlorateper liter drinking water

source_name: thyroid after 2 months 1 day iodine deficient diet + 1 day perchlorate exposure


title: iodine-deficient diet and normal water F34

description:
S805368.J18.CEL
iodine deficiency


title: iodine-deficient diet and normal water B8

description:
S805368.J04.CEL
iodine deficiency


title: normal diet and perchlorate water G39

description:
S805368.J19.CEL
95 mg potassium perchlorateper liter drinking water


title: normal diet and perchlorate water C16

description:
S805368.J08.CEL
95 mg potassium perchlorateper liter drinking water


title: iodine-deficient diet and perchlorate water A2

description:
S805368.J01.CEL
iodine deficiency + 95 mg potassium perchlorateper liter drinking water


title: normal diet and perchlorate water G42

description:
S805368.J21.CEL
95 mg potassium perchlorateper liter drinking water


title: iodine-deficient diet and normal water F32

description:
S805368.J16.CEL
iodine deficiency


title: iodine-deficient diet and perchlorate water E27

description:
S805368.J13.CEL
iodine deficiency + 95 mg potassium perchlorateper liter drinking water


title: iodine-deficient diet and perchlorate water E30

description:
S805368.J15.CEL
iodine deficiency + 95 mg potassium perchlorateper liter drinking water


title: normal diet and normal water D24

description:
S805368.J12.CEL
Control


title: normal diet and normal water D22

description:
S805368.J10.CEL
Control


title: normal diet and perchlorate water C18

description:
S805368.J09.CEL
95 mg potassium perchlorateper liter drinking water


title: iodine-deficient diet and normal water B12

description:
S805368.J06.CEL
iodine deficiency


title: iodine-deficient diet and perchlorate water A6

description:
S805368.J03.CEL
iodine deficiency + 95 mg potassium perchlorateper liter drinking water


title: normal diet and normal water H44

description:
S805368.J23.CEL
Control


title: breast nontumor part_N_rep1 5999

city: Taipei

first: Fon-Jou

last: Hsieh

address: No. 7, Chung-Shan South Rd

department: Department of obstetrics and gynecology

country: Taiwan

institute: National Taiwan University

description: breast nontumor part_N_rep1

scan_protocol: Agilent Oligo Microarray Kit, hybridization protocol version 5.0 with Agilent scanner and Feature Extraction 6.0.

data_processing: Agilent Two-Color Microarray-Based Gene Expression Analysis, version 4.0. The log2 ratio for each gene was centered by subtracting the median across all samples to discriminate the subclass of the dataset.

source_name: non-tumor part, Buffer 1

label_protocol: Agilent Low RNA Input Fluorescent Linear Amplification Kit, protocol version 2.0

growth_protocol: The fresh samples used for this study were immediately frozen by liquid nitrogen without any additional growth procedure applied before RNA extraction.

extract_protocol: Trizol reagent combined with RNAeasy mini kit

treatment_protocol: The surgical removed tumors and non-tumor part of breast specimens were excised, collected and snap-frozen in liquid nitrogen immediately before RNA extraction.

value: female

value: non tumor part of breast tissue.

source_name: Commercially available.

value: Stratagene's human common reference RNA


title: breast nontumor part_N_rep1 5425

description: breast nontumor part_N_rep1

hyb_protocol: Agilent Oligo Microarray Kit, hybridization protocol version 5.0


title: breast nontumor part_N_rep1 5423

description: breast nontumor part_N_rep1


title: Normal control 12

city: Woolloongabba

first: Gethin

last: Thomas

state: QLD

address: Princess Alexandra Hospital

country: Australia

institute: University of Queensland Diamantina Institute

scan_protocol: Scanned on Illumina Beadscan according to Direct Hyb protocol

data_processing:
Data processed using Lumi - data were transformed by variance stabilization transformation and normalized by robust spline normalization. In the intial study 18 patients and 18 controls were used but 2 patients and 2 controls were excluded from analysis due to samples drying out on the chip during hybridisationa dn giving aberrant fluoresence signals. This was verified during clustering analysis where these samples were clear outliers. Probes that were not expressed above background in any of the samples were removed.
ID ref = Illumina probe ID, sample values = normalised, log transformed signal intensities

source_name: Whole blood, control

label_protocol: cRNA generated an amplified according to Illumina® TotalPrep™ RNA Amplification Kit (Ambion). 500ng of total RNA was used as starting material. A 14hr incubation was used for the in vitro transcription stage.

extract_protocol: RNA extracted from PAXgene tubes according to manufacturers protocol. Excess globin mRNA transcripts were removed using the Ambion GLOBINclear kit according to the manufacturer's protocol.

value: Whole blood

tag: cell type

value: PBMC

tag: disease status

value: Normal control


title: Normal control 13


title: breast nontumor part_N_rep1 5429

description: breast nontumor part_N_rep1


title: Normal control 10


title: Normal control 8


title: Normal control 6


title: breast nontumor part_N_rep1 5431

description: breast nontumor part_N_rep1


title: breast nontumor part_N_rep1 5405

description: breast nontumor part_N_rep1


title: breast nontumor part_N_rep1 5421

description: breast nontumor part_N_rep1


title: breast nontumor part_N_rep1 5415

description: breast nontumor part_N_rep1


title: Ankylosing spondylitis patient 16

source_name: Whole blood, affected

value: Ankylosing spondylitis patient


title: Normal control 15


title: Normal control 7


title: Normal control 1


title: breast nontumor part_N_rep1 5411

description: breast nontumor part_N_rep1


title: Normal control 3


title: breast nontumor part_N_rep1 5413

description: breast nontumor part_N_rep1


title: Normal control 14


title: breast nontumor part_N_rep1 5407

description: breast nontumor part_N_rep1


title: Normal control 4


title: Normal control 2


title: Normal control 11


title: Normal control 5


title: breast nontumor part_N_rep1 5419

description: breast nontumor part_N_rep1


title: Normal control 16


title: Ankylosing spondylitis patient 15


title: breast nontumor part_N_rep1 5403

description: breast nontumor part_N_rep1


title: breast nontumor part_N_rep1 5293

description: breast nontumor part_N_rep1


title: Ankylosing spondylitis patient 13


title: Ankylosing spondylitis patient 10


title: Ankylosing spondylitis patient 12


title: Ankylosing spondylitis patient 14


title: Normal control 9


title: Ankylosing spondylitis patient 7


title: Ankylosing spondylitis patient 9


title: Ankylosing spondylitis patient 8


title: MAVS_KO_16h

first: Jonathan

last: Kagan

address: 300 Longwood Ave, Enders 649

institute: Children's Hospital Boston

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina BeadStudio version 3 software

source_name: MAVS-KO MEFs

label_protocol: Total RNA was reversely transcribed in cDNA, in vitro transcribed into biotin-labeled cRNA

growth_protocol: Cell were cultured in DMEM+10% FBS in 6 well tissue culture plates overnight.

extract_protocol: RNA was purified using QIAShredder and the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Cells were infected with reovirus.  At the indicated times, RNA was isolated as described below.

value: mouse embryonic fibroblasts

tag: genotype/variation

value: Stable line expressing the indicated MAVS allele


title: Ankylosing spondylitis patient 5


title: Ankylosing spondylitis patient 1


title: Ankylosing spondylitis patient 6


title: MAVS_Pex_16h

source_name: MAVS-Pex MEFs


title: MAVS_WT_16h

source_name: MAVS-WT MEFs


title: MAVS_Mito_16h

source_name: MAVS-Mito MEFs


title: MAVS_KO_9h


title: Ankylosing spondylitis patient 3


title: Ankylosing spondylitis patient 2


title: MAVS_Cyto_16h

source_name: MAVS-Cyto MEFs


title: wild type (Hwayoung), biological rep3

city: paris

first: yongfeng

last: hu

address: univercite paris-sud Bat 630

country: France

institute: IBP

description:
HY3
Gene expression data from 11-day-old wild-type seedlings.

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

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Oryza sativa

source_name: rice, 11-day-old seedling, wild type

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

growth_protocol: Seeds of both wild type and CHR729 mutant were surface-sterilized and germinated on media containing 0.8% agar supplemented with 3% (w/v) sucrose at 28°C (in light) and 24°C (in dark) with a 14-h-light/10-h-dark cycle.

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

tag: cultivar

value: Hwayoung

value: wild type

value: seedling

tag: age

value: 11 days


title: isolate UUPA38, microarray rep 2

city: Belfast

first: Sally

middle: Helene

last: Pattison

address: MBC 97 Lisburn Road

department: Centre for Infection & Immunity

institute: Queen's University Belfast

description: Comparative genomic hybridisation data from P. aeruginosa isolate UUPA38.

hyb_protocol: All labelled product was added to the hybridisation cocktail as required for a 100 Format (midi) array and hybridised to a GeneChip® P. aeruginosa Genome Array for 16 h at 50˚C.  The array was washed and stained according to the pre-defined fluidics script on a GeneChip® Fluidics Station 450

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip® Scanner 3000.

data_processing: Gene presence indicated by consistently present calls in microarray replicates.

organism: Pseudomonas aeruginosa

label_protocol: Fragmented genomic DNA was labelled according to the standard Affymetrix protocol for cDNA (Affymetrix GeneChip® Expression Analysis Technical Manual 701021 Rev. 5) using GeneChip® DNA Labeling Reagent (Affymetrix).

extract_protocol: Genomic DNA was extracted using PureLink Genomic DNA Mini Kit (Invitrogen) and fragmented with DNase I (Ambion).

value: bacterial cells

tag: quorum sensing (qs) phenotype

value: QS+


title: CHR729 T-DNA mutant, biological rep3

description:
CH3
Gene expression data from 11-day-old CHR729 mutant seedlings.

source_name: rice, 11-day-old seedling, CHR729 mutant

tag: genotype

value: CHR729 T-DNA mutation


title: CHR729 T-DNA mutant, biological rep1

description:
CH1
Gene expression data from 11-day-old CHR729 mutant seedlings.


title: wild type (Hwayoung), biological rep2

description:
HY2
Gene expression data from 11-day-old wild-type seedlings.


title: Ankylosing spondylitis patient 4


title: wild type (Hwayoung), biological rep1

description:
HY1
Gene expression data from 11-day-old wild-type seedlings.


title: Ankylosing spondylitis patient 11


title: MAVS_Mimic_16h

source_name: MAVS-Mimic MEFs


title: isolate UUPA85, microarray rep 2

description: Comparative genomic hybridisation data from P. aeruginosa isolate UUPA85.

value: QS-


title: CHR729 T-DNA mutant, biological rep2

description:
CH2
Gene expression data from 11-day-old CHR729 mutant seedlings.


title: MAVS_Mimic_9h


title: isolate UUPA85, microarray rep 1


title: planktonic grown QS- strain UUPA85, biological rep 3

description: Gene expression data from QS- P. aeruginosa strain UUPA85 grown as biofilm.

data_processing: Data were normalised per-chip to the median and per-gene to the QS+ isolate in GeneSpring GX. Hierarchical clustering of genes present or marginal in all samples, using Spearman correlation as the similarity measure and Average Linkage as the clustering algorithm, showed clustering of the samples first by isolate, and then based on mode of growth.  Principle components analysis was performed by Partek Pro 5.1. Genes consistently present or marginal were analysed by Student’s t-test to determine the significance of expression ratios.

source_name: UUPA85 planktonic culture 3

label_protocol: cDNA was labelled according to the standard Affymetrix protocol (Affymetrix GeneChip® Expression Analysis Technical Manual 701021 Rev. 5) using GeneChip® DNA Labeling Reagent (Affymetrix).

growth_protocol: Planktonic cultures were grown to stationary phase in 2 l Luria Bertani broth shaken at 220 rpm at 37°C .

extract_protocol: Total RNA was extracted using the RNeasy Mini Purification Kit (Qiagen) with lysozyme being applied at 1 mg/ml rather than the recommended 400 µg/ml.  10 mg of total RNA was used for cDNA synthesis.

tag: culture

value: planktonic


title: isolate UUPA38, microarray rep 1


title: planktonic grown QS+ strain UUPA38, biological rep 2

description: Gene expression data from QS+ P. aeruginosa strain UUPA38 grown as biofilm.

source_name: UUPA38 planktonic culture 2


title: planktonic grown QS+ strain UUPA38, biological rep 3

source_name: UUPA38 planktonic culture 3


title: MAVS_Pex_9h


title: planktonic grown QS+ strain UUPA38, biological rep 1

source_name: UUPA38 planktonic culture 1


title: MAVS_Mito_9h


title: planktonic grown QS- strain UUPA85, biological rep 2

source_name: UUPA85 planktonic culture 2


title: biofilm grown QS- strain UUPA85, biological rep 3

source_name: UUPA85 biofilm culture 3

growth_protocol: Biofilms were grown for 5 days in Luria Bertani broth at 22°C as 1 m flow-through tube cultures (bore=5 mm; flow rate=0.5 ml/min)

value: biofilm


title: biofilm grown QS+ strain UUPA38, biological rep 3

source_name: UUPA38 biofilm culture 3


title: planktonic grown QS- strain UUPA85, biological rep 1

source_name: UUPA85 planktonic culture 1


title: MAVS_Mimic_3h


title: MAVS_WT_9h


title: biofilm grown QS+ strain UUPA38, biological rep 2

source_name: UUPA38 biofilm culture 2


title: MAVS_Cyto_9h


title: MAVS_KO_3h

source_name: MAVS-KO MEFs


title: biofilm grown QS- strain UUPA85, biological rep 2

source_name: UUPA85 biofilm culture 2


title: biofilm grown QS- strain UUPA85, biological rep 1

source_name: UUPA85 biofilm culture 1


title: MAVS_Mito_3h

source_name: MAVS-Mito MEFs


title: MAVS_Pex_3h

source_name: MAVS-Pex MEFs


title: MAVS_Cyto_3h

source_name: MAVS-Cyto MEFs


title: MAVS_Pex_Control


title: MAVS_Mimic_Control


title: MAVS_Mito_Control


title: MAVS_WT_3h

source_name: MAVS-WT MEFs


title: MAVS_WT_Control


title: MAVS_KO_Control


title: Transcription profile of WT cells array3

city: Philadelphia

first: Louise

middle: C

last: Showe

state: PA

address: 3601 Spruce St

institute: The Wistar Institute

description: Affymetrix standard protocol

hyb_protocol: Affymetrix standard protocol (16hr)

scan_protocol: Affymetrix standard protocol

organism: Schizosaccharomyces pombe

source_name: wild type cells

label_protocol: Affymetrix standard protocol

growth_protocol: Liquid culture in YEA

extract_protocol: Phenol extraction followed by DNase I treatment

treatment_protocol: 30 degrees

value: wt:h+ leu1-32 ade6-210 ura4-DS/E


title: MAVS_Cyto_Control


title: biofilm grown QS+ strain UUPA38, biological rep 1

source_name: UUPA38 biofilm culture 1


title: WT-mannose

city: Norman

first: Tyrrell

last: Conway

state: OK

address: 101 David L. Boren Blvd.

department: Advanced Center for Genome Technology

institute: University of Oklahoma

hyb_protocol: Hybridization was at 60 degrees C for 16 h according to Affymetrix protocol ProkGE_WS2v2-450.

scan_protocol: Affymetrix GCOS scanner software and GeneChip Scanner 3000.

data_processing: RMA with quartile normalization according to method of Irizarry et al, 2003. The raw .cel files were processed in RMA using Bioconductor R package: affy Version:1.8.1 Date:2005-09-03, with the option Filter.genes containing a subset of probesets corresponding to MG1655 genes and intergenic regions listed in the matrix data. Replicates were averaged for ratio calculations.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli wild-type, A600=0.4 on mannose

label_protocol: RNA converted to cDNA by random-hexamer primed first strand synthesis with Superscript II and biotinylated with Roche Enzo kit according to Affymetrix protocol.

growth_protocol: Cells were grown at 37oC without shaking in 18 mm test tubes containing 5 ml of the MOPS-based culture medium designed by Neidhardt. Mouse cecal mucus was prepared from streptomycin-treated CD-1 mice (not colonized with E. coli). Cultures were grown to A600 = 0.4 in MOPS medium containing glucose or mannose (0.2%) and also in 10 mg/ml of lyophilized mucus at A600=0.2 (P1) or 0.5 (P2).

extract_protocol: Cultures were diluted into DNA-RNA Protect (Sierra Diagnostics) to inhibit RNA degradation and the RNA was purified using RNeasy minkits with the optional DNase treatment (Qiagen).

value: wild-type


title: flhD-glucose

source_name: E. coli flhD, A600=0.4 on glucose

value: flhD


title: MG1655star-glucose

source_name: E. coli MG1655star, A600=0.4 on glucose


title: WT-mucus-P1

source_name: E. coli wild-type, A600=0.2 on mucus


title: MG1655star-mannose

source_name: E. coli MG1655star, A600=0.4 on mannose


title: flhD-mannose

source_name: E. coli flhD, A600=0.4 on mannose


title: WT MEFs with IFNa 1000 U/ml treatment for 2 h

first: Chien-Kuo

last: Lee

address: No. 1, Jen-Ai Road, Section 1, Rm 513

department: Graduate Institute of Immunology

institute: National Taiwan University College of Medicine

data_processing: The data were normalised using Illumina Inc. BeadStudio version 3.2.3, normalization = cubic spline.

source_name: WT Mouse Embryonic Fibroblasts (MEFs) with IFNa 1000 U/ml treatment for 2 h

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

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

value: MEF cell line

value: WT

tag: agent

value: IFNa


title: flhD-mucus-P2

source_name: E. coli flhD, A600=0.5 on mucus


title: flhD-mucus-P1

source_name: E. coli flhD, A600=0.2 on mucus


title: MG1655star-mucus-P1

source_name: E. coli MG1655star, A600=0.2 on mucus


title: WT-mucus-P2

source_name: E. coli wild-type, A600=0.5 on mucus


title: Transcription profile of WT cells array1

description: Affymetrix standard protocol


title: MG1655star-mucus-P2

source_name: E. coli MG1655star, A600=0.5 on mucus


title: STAT3KO MEFs without IFNa treatment

source_name: STAT3KO Mouse Embryonic Fibroblasts (MEFs) without IFNa treatment

value: no IFNa treatment


title: STAT3KO MEFs with IFNa 1000U/ml treatment for 2h

source_name: STAT3KO Mouse Embryonic Fibroblasts (MEFs) with IFNa 1000U/ml treatment for 2h


title: WT-glucose-Rep1

source_name: E. coli wild-type, A600=0.4 on glucose


title: WT-glucose-Rep2


title: ID4+/-TCL1-tg spleen CD19+ B cells collected from 3 mice 3

city: Columbus

first: Lianbo

last: Yu

state: OH

address: 1800 Cannon Drive

department: Center for Biostatistics

institute: The Ohio State University

description: Gene expression data from ID4+/-TCL1-tg spleen CD19+ B cells

hyb_protocol: Samples were hybridized using Herring sperm DNA, Acetylated BSA (50mg/mL), BioArray Eukaryotic Hybridization Controls (Enzo Life Sciences). Heat 65 degree C for 5 minutes, 99 degree C for 5 minutes, 45 degree C for 5 minutes. Centrifuge top speed for 5 minutes. Hybridize 16 hours at 45 degree C at 60rpm. Fluidics script EukGE-WS2v4_450.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G using Command Console.

data_processing: The data were analyzed through Bioconductor package, RMA method was used as the background-correction, normalization, and probe summarization method.

label: enzymatically labeled

source_name: ID4+/-TCL1-tg spleen CD19+ B cells

label_protocol: Samples were enzymatically labeled using BioArray HighYield RNA Transcript Labeling kit (Enzo)

extract_protocol: Total RNA was prepared from CD19-positive splenic B cells isolated from 1-month old ID4+/-TCL1-tg and ID4+/+TCL1-tg mice, using the RNEasy column purification Kit (Qiagen).

value: F1 littermate of TCL1 (C3H/B6) and ID4+/- (CD1) mice

tag: tissue type

value: spleen

value: CD19+ B

tag: age of the mice

value: 1 month old


title: ID4+/+TCL1-tg spleen CD19+ B cells collected from 3 mice 3

description: Gene expression data from ID4+/+ TCL1-tg spleen CD19+ B cells

source_name: ID4+/+TCL1-tg spleen CD19+ B cells

value: F1 littermate of TCL1 (C3H/B6) and ID4+/+ (CD1) mice


title: ID4+/-TCL1-tg spleen CD19+ B cells collected from 3 mice 2


title: ID4+/+TCL1-tg spleen CD19+ B cells collected from 3 mice 2


title: WT E2+Tamoxifen 24h, 2

status: Public on Nov 03 2010

city: Yokohama

first: Mariko

last: Okada

address: W518, 1-7-22, Suehiro-cho, Tsurumi-ku

institute: RIKEN RCAI

description:
Gene expression in E2+Tamoxifen-stimulated WT cells.
wt4.E2_Tam.24h

hyb_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual) was used. Complete protocol can be found on the manufacturer's web site (http://www.affymetrix.com/support/technical/manual/expression_manual.affx) (section2, 2.2.p3-8 & 2.3.p3-14).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 with default parameters.

data_processing: The data were preprocessed with RMA. Signal intensity was calculated for RefSeq mRNA by using a CustomCDF (HGU133Plus2_Hs_REFSEQ ver.11).

source_name: breast epithelial cell, adherent, E2+Tamoxifen, 24h

label_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual) was used. Complete protocol can be found on the manufacturer's web site (http://www.affymetrix.com/support/technical/manual/expression_manual.affx) (section2, chapter1-p13-18, & 2.1.p32-33,p36-40).

growth_protocol: Prior to the growth factor (GF) treatment, cells were serum starved for 16-18 hours with serum-free RPMI medium and incubated at 37C/5% CO2. The medium was again changed 2 hr prior to the GF treatment.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen) and then purified using the QIAGEN Rneasy kit.

treatment_protocol: Following the incubation in serum-free medium, the ligand was added and incubated for the indicated time.

tag: cell line

tag: tissue origination

value: mammary gland, breast

value: epithelial

tag: disease

value: adenocarcinoma

value: female

tag: ethnicity

value: Caucasian

tag: tamoxifen phenotype

value: sensitive

tag: treatment

value: E2, tamoxifen


title: Transcription profile of WT cells array2

description: Affymetrix standard protocol

source_name: wild type cells

value: wt:h+ leu1-32 ade6-210 ura4-DS/E


title: ID4+/+TCL1-tg spleen CD19+ B cells collected from 3 mice 1

tag: strain

tag: cell type


title: ID4+/-TCL1-tg spleen CD19+ B cells collected from 3 mice 1

tag: genotype/variation


title: WT E2+Tamoxifen 48h

description:
Gene expression in E2+Tamoxifen-stimulated WT cells.
wt4.E2_Tam.48h

source_name: breast epithelial cell, adherent, E2+Tamoxifen, 48h

tag: gender

tag: time


title: WT E2+Tamoxifen 12h

description:
Gene expression in E2+Tamoxifen-stimulated WT cells.
wt4.E2_Tam.12h

source_name: breast epithelial cell, adherent, E2+Tamoxifen, 12h

tag: age


title: WT E2+Tamoxifen 6h

description:
Gene expression in E2+Tamoxifen-stimulated WT cells.
wt4.E2_Tam.06h

source_name: breast epithelial cell, adherent, E2+Tamoxifen, 6h


title: WT E2+Tamoxifen 2h

description:
Gene expression in E2+Tamoxifen-stimulated WT cells.
wt4.E2_Tam.02h

source_name: breast epithelial cell, adherent, E2+Tamoxifen, 2h


title: WT E2+Tamoxifen 1h

description:
Gene expression in E2+Tamoxifen-stimulated WT cells.
wt4.E2_Tam.01h

source_name: breast epithelial cell, adherent, E2+Tamoxifen, 1h


title: WT E2 3h

description:
Gene expression in E2-stimulated WT cells.
wt4.E2.03h

source_name: breast epithelial cell, adherent, E2, 3h


title: WT E2 24h, 2

description:
Gene expression in E2-stimulated WT cells.
wt4.E2.24h

source_name: breast epithelial cell, adherent, E2, 24h


title: WT E2+Tamoxifen 3h

description:
Gene expression in E2+Tamoxifen-stimulated WT cells.
wt4.E2_Tam.03h

source_name: breast epithelial cell, adherent, E2+Tamoxifen, 3h


title: WT E2 6h

description:
Gene expression in E2-stimulated WT cells.
wt4.E2.06h

source_name: breast epithelial cell, adherent, E2, 6h


title: WT E2 12h

description:
Gene expression in E2-stimulated WT cells.
wt4.E2.12h

source_name: breast epithelial cell, adherent, E2, 12h


title: WT E2 2h

description:
Gene expression in E2-stimulated WT cells.
wt4.E2.02h

source_name: breast epithelial cell, adherent, E2, 2h


title: WT E2 1h

description:
Gene expression in E2-stimulated WT cells.
wt4.E2.01h

source_name: breast epithelial cell, adherent, E2, 1h


title: WT Tamoxifen 0h, 2

description:
Gene expression in Tamoxifen-stimulated WT cells.
wt3.Tam.00h

source_name: breast epithelial cell, adherent, without stimulus

value: tamoxifen


title: WT E2 48h

description:
Gene expression in E2-stimulated WT cells.
wt4.E2.48h

source_name: breast epithelial cell, adherent, E2, 48h


title: WT E2+Tamoxifen 0h

description:
Gene expression in E2+Tamoxifen-stimulated WT cells.
wt4.E2_Tam.00h

source_name: breast epithelial cell, adherent, E2+Tamoxifen, 0h


title: WT HRG+Tamoxifen 24h

description:
Gene expression in HRG+Tamoxifen-stimulated WT cells.
wt2.HRG_Tam.24h

source_name: breast epithelial cell, adherent, HRG+Tamoxifen, 24h

value: HRG, tamoxifen


title: WT E2 0h

description:
Gene expression in E2-stimulated WT cells.
wt4.E2.00h

source_name: breast epithelial cell, adherent, E2, 0h


title: WT Tamoxifen 0h

description:
Gene expression in Tamoxifen-stimulated WT cells.
wt2.Tam.00h

source_name: breast epithelial cell, adherent, Tamoxifen, 0h


title: WT Tamoxifen 2h

description:
Gene expression in Tamoxifen-stimulated WT cells.
wt2.Tam.02h

source_name: breast epithelial cell, adherent, Tamoxifen, 2h


title: WT Tamoxifen 6h

description:
Gene expression in Tamoxifen-stimulated WT cells.
wt2.Tam.06h

source_name: breast epithelial cell, adherent, Tamoxifen, 6h


title: WT E2 24h

description:
Gene expression in E2-stimulated WT cells.
wt3.E2.24h

source_name: breast epithelial cell, adherent, E2+Tamoxifen, 24h


title: WT Control

description:
Gene expression in unstimulated WT cells.
wt3.Ctrl

value: untreated


title: WT Tamoxifen 1h

description:
Gene expression in Tamoxifen-stimulated WT cells.
wt2.Tam.01h

source_name: breast epithelial cell, adherent, Tamoxifen, 1h


title: WT E2+Tamoxifen 24h

description:
Gene expression in E2+Tamoxifen-stimulated WT cells.
wt3.E2_Tam.24h

source_name: breast epithelial cell, adherent, Tamoxifen, 24h


title: WT HRG+Tamoxifen 12h

description:
Gene expression in HRG+Tamoxifen-stimulated WT cells.
wt2.HRG_Tam.12h

source_name: breast epithelial cell, adherent, HRG+Tamoxifen, 12h


title: WT Tamoxifen 3h

description:
Gene expression in Tamoxifen-stimulated WT cells.
wt2.Tam.03h

source_name: breast epithelial cell, adherent, Tamoxifen, 3h


title: WT HRG+Tamoxifen 3h

description:
Gene expression in HRG+Tamoxifen-stimulated WT cells.
wt2.HRG_Tam.03h

source_name: breast epithelial cell, adherent, HRG+Tamoxifen, 3h


title: WT HRG+Tamoxifen 1h

description:
Gene expression in HRG+Tamoxifen-stimulated WT cells.
wt2.HRG_Tam.01h

source_name: breast epithelial cell, adherent, HRG+Tamoxifen, 1h


title: WT HRG+Tamoxifen 2h

description:
Gene expression in HRG+Tamoxifen-stimulated WT cells.
wt2.HRG_Tam.02h

source_name: breast epithelial cell, adherent, HRG+Tamoxifen, 2h


title: WT Tamoxifen 48h

description:
Gene expression in Tamoxifen-stimulated WT cells.
wt2.Tam.48h

source_name: breast epithelial cell, adherent, Tamoxifen, 48h


title: WT Tamoxifen 12h

description:
Gene expression in Tamoxifen-stimulated WT cells.
wt2.Tam.12h

source_name: breast epithelial cell, adherent, Tamoxifen, 12h


title: WT Tamoxifen 24h

description:
Gene expression in Tamoxifen-stimulated WT cells.
wt2.Tam.24h


title: WT HRG+Tamoxifen 6h

description:
Gene expression in HRG+Tamoxifen-stimulated WT cells.
wt2.HRG_Tam.06h

source_name: breast epithelial cell, adherent, HRG+Tamoxifen, 6h


title: WT HRG+Tamoxifen 48h

description:
Gene expression in HRG+Tamoxifen-stimulated WT cells.
wt2.HRG_Tam.48h

source_name: breast epithelial cell, adherent, HRG+Tamoxifen, 48h


title: WT HRG 12h

description:
Gene expression in HRG-stimulated WT cells.
wt2.HRG.12h

source_name: breast epithelial cell, adherent, HRG, 12h

value: HRG


title: WT HRG 3h

description:
Gene expression in HRG-stimulated WT cells.
wt2.HRG.03h

source_name: breast epithelial cell, adherent, HRG, 3h


title: WT HRG 1h

description:
Gene expression in HRG-stimulated WT cells.
wt2.HRG.01h

source_name: breast epithelial cell, adherent, HRG, 1h


title: WT HRG 0h

description:
Gene expression in HRG-stimulated WT cells.
wt2.HRG.00h

source_name: breast epithelial cell, adherent, HRG, 0h


title: WT HRG 48h

description:
Gene expression in HRG-stimulated WT cells.
wt2.HRG.48h

source_name: breast epithelial cell, adherent, HRG, 48h


title: WT HRG 2h

description:
Gene expression in HRG-stimulated WT cells.
wt2.HRG.02h

source_name: breast epithelial cell, adherent, HRG, 2h


title: WT HRG+Tamoxifen 0h

description:
Gene expression in HRG+Tamoxifen-stimulated WT cells.
wt2.HRG_Tam.00h

source_name: breast epithelial cell, adherent, HRG+Tamoxifen, 0h


title: WT HRG 24h

description:
Gene expression in HRG-stimulated WT cells.
wt2.HRG.24h

source_name: breast epithelial cell, adherent, HRG, 24h


title: WT HRG 48h rep2

description:
Gene expression in HRG-stimulated WT cells.
wt1.HRG.48h.r2


title: WT HRG 24h rep1

description:
Gene expression in HRG-stimulated WT cells.
wt1.HRG.24h.r1


title: WT HRG 24h rep2

description:
Gene expression in HRG-stimulated WT cells.
wt1.HRG.24h.r2


title: WT HRG 6h rep2

description:
Gene expression in HRG-stimulated WT cells.
wt1.HRG.06h.r2

source_name: breast epithelial cell, adherent, HRG, 6h


title: WT HRG 3h rep1

description:
Gene expression in HRG-stimulated WT cells.
wt1.HRG.03h.r1


title: WT HRG 1h rep1

description:
Gene expression in HRG-stimulated WT cells.
wt1.HRG.01h.r1


title: WT HRG 2h rep2

description:
Gene expression in HRG-stimulated WT cells.
wt1.HRG.02h.r2


title: WT HRG 2h rep1

description:
Gene expression in HRG-stimulated WT cells.
wt1.HRG.02h.r1


title: WT HRG 1h rep2

description:
Gene expression in HRG-stimulated WT cells.
wt1.HRG.01h.r2


title: WT HRG 3h rep2

description:
Gene expression in HRG-stimulated WT cells.
wt1.HRG.03h.r2


title: WT HRG 6h

description:
Gene expression in HRG-stimulated WT cells.
wt2.HRG.06h


title: WT E2 12h rep1

description:
Gene expression in E2-stimulated WT cells.
wt1.E2.12h.r1

source_name: breast epithelial cell, adherent, E2, 12h


title: WT HRG 0h rep2

description:
Gene expression in HRG-stimulated WT cells.
wt1.HRG.00h.r2


title: WT HRG 0h rep1

description:
Gene expression in HRG-stimulated WT cells.
wt1.HRG.00h.r1


title: WT E2 24h rep1

description:
Gene expression in E2-stimulated WT cells.
wt1.E2.24h.r1

source_name: breast epithelial cell, adherent, E2, 24h


title: WT HRG 12h rep2

description:
Gene expression in HRG-stimulated WT cells.
wt1.HRG.12h.r2


title: WT E2 48h rep2

description:
Gene expression in E2-stimulated WT cells.
wt1.E2.48h.r2

source_name: breast epithelial cell, adherent, E2, 48h


title: WT E2 12h rep2

description:
Gene expression in E2-stimulated WT cells.
wt1.E2.12h.r2


title: WT E2 24h rep2

description:
Gene expression in E2-stimulated WT cells.
wt1.E2.24h.r2


title: WT E2 3h rep2

description:
Gene expression in E2-stimulated WT cells.
wt1.E2.03h.r2

source_name: breast epithelial cell, adherent, E2, 3h


title: WT E2 48h rep1

description:
Gene expression in E2-stimulated WT cells.
wt1.E2.48h.r1


title: WT E2 3h rep1

description:
Gene expression in E2-stimulated WT cells.
wt1.E2.03h.r1


title: WT E2 6h rep2

description:
Gene expression in E2-stimulated WT cells.
wt1.E2.06h.r2

source_name: breast epithelial cell, adherent, E2, 6h


title: WT E2 2h rep2

description:
Gene expression in E2-stimulated WT cells.
wt1.E2.02h.r2

source_name: breast epithelial cell, adherent, E2, 2h


title: WT E2 1h rep2

description:
Gene expression in E2-stimulated WT cells.
wt1.E2.01h.r2

source_name: breast epithelial cell, adherent, E2, 1h


title: WT E2 0h rep2

description:
Gene expression in E2-stimulated WT cells.
wt1.E2.00h.r2

source_name: breast epithelial cell, adherent, E2, 0h


title: WT HRG 48h rep1

description:
Gene expression in HRG-stimulated WT cells.
wt1.HRG.48h.r1


title: TamR#6 E2 24h

description:
Gene expression in E2-stimulated TamR cells.
TamR6.E2.24h

value: resistant


title: WT E2 6h rep1

description:
Gene expression in E2-stimulated WT cells.
wt1.E2.06h.r1


title: WT E2 2h rep1

description:
Gene expression in E2-stimulated WT cells.
wt1.E2.02h.r1


title: WT E2 1h rep1

description:
Gene expression in E2-stimulated WT cells.
wt1.E2.01h.r1


title: WT E2 0h rep1

description:
Gene expression in E2-stimulated WT cells.
wt1.E2.00h.r1


title: TamR#6 E2+Tamoxifen 24h

description:
Gene expression in E2+Tamoxifen-stimulated TamR cells.
TamR6.E2_Tam.24h

source_name: breast epithelial cell, adherent, E2+Tamoxifen, 24h


title: TamR#6 Control

description:
Gene expression in unstimulated TamR cells.
TamR6.Ctrl

source_name: breast epithelial cell, adherent, without stimulus


title: TamR#3 E2+Tamoxifen 24h

description:
Gene expression in E2+Tamoxifen-stimulated TamR cells.
TamR3.E2_Tam.24h


title: TamR#4 Tamoxifen 0h

description:
Gene expression in Tamoxifen-stimulated TamR cells.
TamR4.Tam.00h

source_name: breast epithelial cell, adherent, Tamoxifen, 0h


title: TamR#4 E2+Tamoxifen 24h

description:
Gene expression in E2+Tamoxifen-stimulated TamR cells.
TamR4.E2_Tam.24h


title: TamR#2 E2+Tamoxifen 24h

description:
Gene expression in E2+Tamoxifen-stimulated TamR cells.
TamR2.E2_Tam.24h


title: TamR#3 Tamoxifen 0h

description:
Gene expression in Tamoxifen-stimulated TamR cells.
TamR3.Tam.00h


title: TamR#4 Control

description:
Gene expression in unstimulated TamR cells.
TamR4.Ctrl


title: TamR#2 Tamoxifen 0h

description:
Gene expression in Tamoxifen-stimulated TamR cells.
TamR2.Tam.00h


title: TamR#5 E2 24h

description:
Gene expression in E2-stimulated TamR cells.
TamR5.E2.24h


title: TamR#3 Control

description:
Gene expression in unstimulated TamR cells.
TamR3.Ctrl


title: TamR#4 E2 24h

description:
Gene expression in E2-stimulated TamR cells.
TamR4.E2.24h


title: TamR#5 Control

description:
Gene expression in unstimulated TamR cells.
TamR5.Ctrl


title: TamR#1 Control

description:
Gene expression in unstimulated TamR cells.
TamR1.Ctrl


title: TamR Tamoxifen 48h

description:
Gene expression in Tamoxifen-stimulated TamR cells.
TamR.Tam.48h

source_name: breast epithelial cell, adherent, Tamoxifen, 48h


title: TamR#3 E2 24h

description:
Gene expression in E2-stimulated TamR cells.
TamR3.E2.24h


title: TamR#5 E2+Tamoxifen 24h

description:
Gene expression in E2+Tamoxifen-stimulated TamR cells.
TamR5.E2_Tam.24h


title: TamR#1 E2 24h

description:
Gene expression in E2-stimulated TamR cells.
TamR1.E2.24h


title: TamR#2 Control

description:
Gene expression in unstimulated TamR cells.
TamR2.Ctrl


title: TamR#1 E2+Tamoxifen 24h

description:
Gene expression in E2+Tamoxifen-stimulated TamR cells.
TamR1.E2_Tam.24h


title: TamR#2 E2 24h

description:
Gene expression in E2-stimulated TamR cells.
TamR2.E2.24h


title: TamR Tamoxifen 1h

description:
Gene expression in Tamoxifen-stimulated TamR cells.
TamR.Tam.01h

source_name: breast epithelial cell, adherent, Tamoxifen, 1h


title: TamR Tamoxifen 6h

description:
Gene expression in Tamoxifen-stimulated TamR cells.
TamR.Tam.06h

source_name: breast epithelial cell, adherent, Tamoxifen, 6h


title: TamR HRG+Tamoxifen 12h

description:
Gene expression in HRG+Tamoxifen-stimulated TamR cells.
TamR.HRG_Tam.12h

source_name: breast epithelial cell, adherent, HRG+Tamoxifen, 12h


title: TamR Tamoxifen 2h

description:
Gene expression in Tamoxifen-stimulated TamR cells.
TamR.Tam.02h

source_name: breast epithelial cell, adherent, Tamoxifen, 2h


title: TamR Tamoxifen 3h

description:
Gene expression in Tamoxifen-stimulated TamR cells.
TamR.Tam.03h

source_name: breast epithelial cell, adherent, Tamoxifen, 3h