title: AHY122a vs reference (normalized high intensity scan)


title: VCN_P3

status: Public on May 01 2013

type: RNA

city: Lausanne

first: Nicolas

last: Michalski

address: AI 2104 (Bâtiment AI) Station 19

department: BMI

country: Switzerland

institute: EPFL

hyb_protocol: Affymetrix microarrays 430 2.0 arrays were hybridized with 5 micrograms of labeled, amplified cDNA , washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0001).

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G.

data_processing: Gene level normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003) for each experiment separately.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: VCN from P3 mice

label_protocol: The tissue from six and three male animals was pooled for the analysis at P3 and at P14, respectively. For all samples described, 20 ng of total RNA was used and were amplified using a WT ovation Pico RNA amplification (Nugen, CA, USA).

extract_protocol: Total RNA from the different mouse brainstem regions were extracted using RNeasy mini kit (Qiagen). All RNA samples were DNase-treated and quantified on a NanoDrop spectrophotometer.

treatment_protocol: Tissues were dissected in an ice cold, oxygenated bicarbonate buffered solution.

tag: strain/background

tag: gender

value: male

tag: age

tag: tissue

value: ventral cochlear nucleus


title: AHY121b vs reference (normalized high intensity scan)

city: San Francisco

first: Aaron

last: Hernday

state: Ca

country: USA

institute: UC San Francisco

hyb_protocol: A pooled reference was created from the Cy5 labelled fractions. Equal amounts of Cy3 labelled sample and Cy5 labelled reference were hybridized overnight to custom designed Agilent-020166 Ca21_GE_plus_tiling_2.0 arrays (PMID20735781)

scan_protocol: Following hybridization, slides were processed and then scanned on a Genepix 4000A or 4000B Axon Instrument Scanner (Axon/Molecular Devices, Sunnyvale, CA USA) (PMID20735781).

data_processing: Arrays were gridded using GenePix Pro version 5.1. Global Lowess normalization analysis was performed for each array using a Goulphar script (Lemoine et al., 2006) for R (The R Foundation for Statistical Computing) (PMID20735781).

organism: Candida albicans

source_name: C. albicans white wor2 delete a/a cells

label_protocol: Following cDNA synthesis, samples were dye coupled to both Cy3 and Cy5 in separate reactions (PMID20735781).

growth_protocol: log phase, synthetic complete, 25 degrees

extract_protocol: RNA was extracted using the RiboPure-Yeast RNA kit (Ambion, number AM1926) according to the manufacturer's instruction (PMID 19529758).

tag: genotype/variation

value: wor2 delete a/a cells

tag: cell phenotype

value: white cells

source_name: Mixed reference

tag: sample type

value: mixed white and opaque, wild-type and mutant


title: LSO_P3

source_name: LSO from P3 mice

value: lateral superior olive


title: RZY219 vs reference (normalized high intensity scan)

source_name: C. albicans white wor1 delete a/a cells

value: wor1 delete a/a cells


title: VCN_P14

source_name: VCN from P14 mice


title: RZY235 vs reference (normalized high intensity scan)


title: WT embryo at E16.5 rep 4

city: Detroit

first: Katherine

last: Gurdziel

state: MI

address: 275 E. Hancock

institute: Wayne State University

description:
WT_E16.5-4
Hammer_015_(Mouse430_2).CEL
Gene expression data from WT mouse adrenals at E16.5

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Microarray data were normalized using the robust multiarray average (RMA) algorithm (limma R package).

source_name: WT mouse adrenals at E16.5

label_protocol: standard Affymetrix protocol

growth_protocol: Sf1-Cre/Dicerlox/lox mice, Sf1-Cre/Dicer+/lox and Dicerlox/lox mice were mated together.  Females from each mating pair were monitored for seminal plugs, and the morning of detection was designated as E0.5.

extract_protocol: Total RNA was isolated using the RNAqueous Micro kit (Life Technologies, Carlsbad, CA) in accordance with the manufacturer’s protocol.

tag: strain background

value: WT

tag: developmental stage

value: adrenals


title: MNTB_P3

source_name: MNTB from P3 mice

value: medial nucleus of the trapezoid body


title: -Dox / -PI-103, replicate 3

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

description:
NB942
No pre-treatment doxycycline, DMSO treatment for 6 hours.

hyb_protocol: 10 µg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to the manufacturer's protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to the manufacturer's protocol.

data_processing: Expression data (CEL files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix).

organism: Homo sapiens

source_name: SY5Y-TetR-FOXO3A cells, -Dox, -PI-103

label_protocol: 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with the One-Cycle cDNA synthesis Kit (Affymetrix) according to the manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior to and after fragmentation.

growth_protocol: SY5Y-TetR-HA-FOXO3A cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to the manufacturer's protocol. RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Cells were treated with 0.1 ug/ml doxycycline for 24 hours (or left untreated) to induce over-expression of HA-tagged FOXO3A, and then treated with either 1 uM PI-103 or an equivalent volume of DMSO for 6 additional hours. Each condition was performed in triplicate across three months.

tag: cell line

tag: cell type

value: SY5Y-TetR-FOXO3A neuroblastoma cells

tag: pre-treatment

tag: treatment

value: DMSO


title: +Dox / -PI-103, replicate 3

description:
NB944
24 hour pre-treatment 0.1 ug/ml doxycycline, DMSO treatment for 6 hours.

source_name: SY5Y-TetR-FOXO3A cells, +Dox, -PI-103

value: doxycycline


title: AHY121a vs reference (normalized high intensity scan)


title: -Dox / +PI-103, replicate 2

description:
NB915
No pre-treatment doxycycline, 1 uM PI-103 treament for 6 hours.

source_name: SY5Y-TetR-FOXO3A cells, -Dox, +PI-103


title: KO embryo at E16.5 rep 4

description:
KO_E16.5-4
Hammer_016_(Mouse430_2).CEL
Gene expression data from KO mouse adrenals at E16.5

source_name: KO mouse adrenals at E16.5

value: KO Sf1-Cre/Dicer lox/lox


title: +Dox / -PI-103, replicate 2

description:
NB916
24 hour pre-treatment 0.1 ug/ml doxycycline, DMSO treatment for 6 hours.


title: +Dox / +PI-103, replicate 2

description:
NB917
24 hour pre-treatment 0.1 ug/ml doxycycline, 1 uM PI-103 treatment for 6 hours.

source_name: SY5Y-TetR-FOXO3A cells, +Dox, +PI-103


title: AHY136b vs reference (normalized high intensity scan)

source_name: C. albicans opaque a/a cells

value: a/a cells

value: opaque cells


title: -Dox / -PI-103, replicate 2

description:
NB914
No pre-treatment doxycycline, DMSO treatment for 6 hours.


title: +Dox / +PI-103, replicate 1

description:
NB909
24 hour pre-treatment 0.1 ug/ml doxycycline, 1 uM PI-103 treatment for 6 hours.


title: +Dox / +PI-103, replicate 3

description:
NB945
24 hour pre-treatment 0.1 ug/ml doxycycline, 1 uM PI-103 treatment for 6 hours.


title: -Dox / +PI-103, replicate 3

description:
NB943
No pre-treatment doxycycline, 1 uM PI-103 treament for 6 hours.


title: MNTB_P14

source_name: MNTB from P14 mice


title: KO embryo at E16.5 rep 3

description:
KO_E16.5-3
Hammer_014_(Mouse430_2).CEL
Gene expression data from KO mouse adrenals at E16.5


title: WT embryo at E16.5 rep 3

description:
WT_E16.5-3
Hammer_013_(Mouse430_2).CEL
Gene expression data from WT mouse adrenals at E16.5


title: +Dox / -PI-103, replicate 1

description:
NB908
24 hour pre-treatment 0.1 ug/ml doxycycline, DMSO treatment for 6 hours.


title: LSO_P14

source_name: LSO from P14 mice


title: -Dox / +PI-103, replicate 1

description:
NB907
No pre-treatment doxycycline, 1 uM PI-103 treament for 6 hours.


title: AHY135b vs reference (normalized high intensity scan)

source_name: C. albicans white a/a cells


title: WT embryo at E16.5 rep 2

description:
WT_E16.5-2
Hammer_011_(Mouse430_2).CEL
Gene expression data from WT mouse adrenals at E16.5


title: KO embryo at E16.5 rep 2

description:
KO_E16.5-2
Hammer_012_(Mouse430_2).CEL
Gene expression data from KO mouse adrenals at E16.5


title: AHY136a vs reference (normalized high intensity scan)


title: CIN (cy5) vs. AMA (cy3)- [Mutant cy5 , Control Cy3]_Rep3

city: Bangalore

first: Mainak

last: Das Gupta

state: Karnataka

address: C.V. Raman Avenue

department: Microbiology and Cell Biology

country: India

institute: Indian Institute of Science

description:
Mutant vs WT
RNA extracted from 3-5 mm long (young) cin and wild type leaves

hyb_protocol: Agilent Arabidopsis  thaliana Gene expression Microarray 22k (AMADID: 013324): 750ng of each Cyanine-3 and Cyanine-5 labeled cRNA were combined with 50μl of 10x Blocking agent. The volume is made upto 240 ul using Nuclease free water. 10μl of 25x Fragmentation buffer (Agilent) were added and incubated at 60°C for 30 minutes in dark. The fragmented cRNA were mixed with 250μl of 2x Hybridization Buffer (Agilent). About 490μl of the resulting mixture was applied to the Gene Expression Microarray (Agilent Technologies), and hybridized at 65°C for 17 hours in an Agilent Microarray Hybridization Chamber (SureHyb: G2534A) with Hybridization Oven. After hybridization, slides were washed with Agilent Gene expression Wash Buffer-I for 1 minute at room temperature followed by a 1 min wash with Agilent Gene expression Wash Buffer-II at 37ºC. Slides were finally rinsed with Acetonitrile for cleaning up and drying.Agilent Custom Arabidopsis thaliana 4x44k Gene Expression (AMADID: 015226)& Agilent custom Antirrhinum 4x44k Gene expression (AMADID: 016341) : 825ng of cy3 labeled  samples and 825ng of cy5 labeled samples were pooled, fragmented and hybridized and data from these channels were used for comparison to test hybridizations of respective channels.  Fragmentation of labeled aRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327) and scanned using the Agilent Microarray Scanner G Model G2565BA at 5 micron resolution.

scan_protocol: scanned using the Agilent Microarray Scanner G2505C at 5 micron resolution. Data extraction from Images was done using Agilent Feature Extraction software v 10.5.1.1

data_processing: Data Analysis was performed using Genespring GX Software using LOWESS normalization.

organism: Arabidopsis thaliana

source_name: Leaf 3-5 mm

label_protocol: Agilent Arabidopsis  thaliana Gene expression Microarray 22k (AMADID: 013324):Low RNA Input Linear Amplification Kit (Agilent, Santa Clara, CA) was used for labeling. Briefly, both first and second strand cDNA were synthesized by incubating 500ng of total RNA with 1.2μl of oligo dT-T7 Promoter Primer in nuclease-free water at 65ºC for 10 min followed by incubation with 4.0μl of 5× First strand buffer, 2μl of 0.1M DTT, 1 μl of 10mM dNTP mix, 1μl of 200 U/μl MMLV RT, and 0.5μl of 40U/μl RNaseOUT, at 40ºC for 2 hour. Immediately following cDNA synthesis, the reaction mixture was incubated with 2.4 μl of 10 mM Cyanine-3 CTP or 2.4 μl of 10 mM Cyanine-5 CTP (Perkin-Elmer, Boston, MA), 20μl of 4X Transcription buffer, 8 μl of NTP mixture, 6 μl of 0.1M DTT, 0.5 μl of RNaseOUT, 0.6μl of Inorganic pyrophosphatase, 0.8 μl of T7 RNA polymerase, and 15.3μl of nuclease-free water at 40 ºC for 2 hour. Qiagen’s RNeasy mini spin columns were used for purifying amplified aRNA samples. The quantity and specific activity of cRNA was determined by using NanoDrop ND-1000 UV-VIS Spectrophotometer version3.2.1. Samples with specific activity >8 were used for hybridization.Agilent Custom Arabidopsis thaliana 4x44k Gene Expression (AMADID: 015226)& Agilent custom Antirrhinum 4x44k Gene expression (AMADID: 016341) : The samples for Gene expression were labeled using Agilent Low RNA Input Linear amplification Kit (Part number:5184-3523).  Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 42°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dyes Cy3 CTP(Agilent) for control samples and Cy5 CTP(Agilent) for test samples were incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: Wild type Antirrhinum plants (stock JI-98) and cin-756 mutants were grown in continuous light or 16/8 hrs light/dark regime at 25 ºC.  Third and fourth leaves were used for all the experimental analysis.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: leaf

tag: leaf length


title: WT embryo at E15.5 rep 4

description:
WT_E15.5-4
Hammer_007_(Mouse430_2).CEL
Gene expression data from WT mouse adrenals at E15.5

source_name: WT mouse adrenals at E15.5


title: KO embryo at E16.5 rep 1

description:
KO_E16.5-1
Hammer_010_(Mouse430_2).CEL
Gene expression data from KO mouse adrenals at E16.5


title: KO embryo at E15.5 rep 2

description:
KO_E15.5-2
Hammer_004_(Mouse430_2).CEL
Gene expression data from KO mouse adrenals at E15.5

source_name: KO mouse adrenals at E15.5


title: CIN (cy3) vs. AMA (cy5)  Dye Swap-[Mutant cy3 , Control Cy5]_Rep1


title: LLC-kB OVA_IKKb rep2

city: Tampa

first: Amer

last: Beg

state: FL

address: 12902 Magnolia Drive

institute: Moffitt Cancer Center

description: MiG IKK

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C to the Affymetrix U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 scaner.

data_processing: The data were analyzed with the Affymetrix GCOS 1.4 software using the MAS 5.0 alorighthm with default analysis settings and global scaling as the normalization method. The trimmed mean target intensity of each array was set to 500.

source_name: lung carcinoma

label_protocol: Biotinylated cRNA were prepared according to the Ambion Message Amp Premier protocl using 100 ng of total RNA (Ambion).

growth_protocol: LLC grown in DMEM+10% FBS. Human lines grown in RPMI+10% FBS.

extract_protocol: Isolation of total RNA was performed using the Qiagen RNEasy column according to the manufacturer's instructions.

treatment_protocol: Cells were transduced with control retrovirus (MiG) or MiG retrovirus expressing IkB alpha super-repressor (SR) mutant or activated IKK beta (S177, S181 to E mutations). Cells were FACS sorted by GFP expression.

value: LLC

tag: cell line type

value: lung carcinoma

value: IKK


title: AHY135a vs reference (normalized high intensity scan)

value: white cells

source_name: Mixed reference


title: -Dox / -PI-103, replicate 1

description:
NB906
No pre-treatment doxycycline, DMSO treatment for 6 hours.


title: Mature tentacles versus mature body columns, replicate 1

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

description: Biological replicate 1 of 2.

hyb_protocol: Hybridizations were performed at 65C for 17 hours under standard conditions (1X Agilent blocking agent, and 1X Agilent hybridization buffer) and slides were washed successively with Agilent GE wash buffer 1, at room temperature and with Agilent GE wash buffer 2, at 31C, prior to scanning.

scan_protocol: Microarray scans were acquired with an Agilent High-Resolution DNA Microarray Scanner (G2505C) and features were quantified with Agilent’s Feature Extraction Software (Version 10.5.1.1).  Hybridization, array washing, scanning and probe information extraction were all performed according to Agilent’s Two-Color Microarray-Based Gene Expression Analysis Protocol, Version 5.7, March 2008 (Quick Amp Labeling).

data_processing: Data was processed using the R environment (November, 2009) and the Limma library. Data was normalized with the normalizeWithinArrays function using loess, and all other options left at default.

organism: Nematostella vectensis

source_name: pooled sections of the oral end of primary polyps with mature tentacles

label_protocol: RNA was amplified and labeled with Cyanine 3-CTP or Cyanine 5-CTP (Quick AMP Labeling Kit; Agilent).

growth_protocol: Animals were raised at 16°C in 12 parts per thousand (ppt) artificial seawater (Sea Salt; Instant Ocean).

extract_protocol: Total RNA was extracted from pools consisting of several hundred dissected animals using the miRNeasy kit (Qiagen) with Trizol (Invitrogen).

treatment_protocol: Animals were microdissected with a sharp tungsten needle to isolate tentacle tissue from the rest of the larval body.  Each animal was bisected perpendicular to the main body axis at the base of the tentacles, generating cognate body column and oral-tentacle fragments.

value: day 30

value: primary polyp

source_name: pooled body columns of primary polyps with mature tentacles removed


title: WT embryo at E15.5 rep 1

description:
WT_E15.5-1
Hammer_001R_(Mouse430_2).CEL
Gene expression data from WT mouse adrenals at E15.5


title: Primary polyp growing tentacles versus body columns, replicate 1

description: Biological replicate 1 of 2.

source_name: pooled sections of the oral end of primary polyps with growing tentacles

value: day 14

value: primary polyp with growing tentacles

source_name: pooled body columns of primary polyps with growing tentacles removed


title: WT embryo at E15.5 rep 2

description:
WT_E15.5-2
Hammer_003_(Mouse430_2).CEL
Gene expression data from WT mouse adrenals at E15.5

value: WT

value: adrenals


title: CIN (cy3) vs. WT (cy5)  Dye Swap-[Mutant cy3 , Control Cy5]_Rep2 (US45102821_251522610005_S01_GE2-v4_91_1_2.txt)


title: CIN (cy3) vs. AMA (cy5)  Dye Swap-[Mutant cy3 , Control Cy5]_Rep3


title: WT embryo at E16.5 rep 1

description:
WT_E16.5-1
Hammer_009_(Mouse430_2).CEL
Gene expression data from WT mouse adrenals at E16.5

source_name: WT mouse adrenals at E16.5


title: KO embryo at E15.5 rep 1

description:
KO_E15.5-1
Hammer_002R_(Mouse430_2).CEL
Gene expression data from KO mouse adrenals at E15.5


title: CIN (cy5) vs. WT (cy3)- [Mutant cy5 , Control Cy3]_Rep2


title: WT embryo at E15.5 rep 3

description:
WT_E15.5-3
Hammer_005_(Mouse430_2).CEL
Gene expression data from WT mouse adrenals at E15.5


title: Primary polyp growing tentacles versus body columns, replicate 2

description: Biological replicate 2 of 2.


title: Mature tentacles versus mature body columns, replicate 2

description: Biological replicate 2 of 2.


title: KO embryo at E15.5 rep 4

description:
KO_E15.5-4
Hammer_008_(Mouse430_2).CEL
Gene expression data from KO mouse adrenals at E15.5


title: KO embryo at E15.5 rep 3

description:
KO_E15.5-3
Hammer_006_(Mouse430_2).CEL
Gene expression data from KO mouse adrenals at E15.5


title: LLC-kB OVA_IKKb rep1

description: MiG IKK


title: Gene expression of S. pombe genome-reduced strain in logarithmic phase, replicate 2

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description:
CP01D10
Comparison between control strain ASP3880 and genome-reduced strain ASP3894 at logarithmic phase in EMM medium.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shaking (250 rpm). Hybridization buffer and washing protocol were according to the protocol supplied by TORAY Industries, Inc.

scan_protocol: GenePix 4000B (Molecular Devices) was used for scanning. Images were quantified using GenePix Pro version 6.0 (Molecular Devices).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global-normalized, background-subtracted data were obtained from log2 of processed Red signal/processed Green signal. Microsoft Excel was used for normalization.

organism: Schizosaccharomyces pombe

source_name: ASP3880 growing cells

label_protocol: cDNA and Amino Allyl aRNA were synthesized using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion #1753). Cy dye coupling and fragmentation were performed according to the protocol supplied by TORAY Industries, Inc.

growth_protocol: S. pombe cells in YES pre-culture medium were inoculated into EMM liquid medium after washing twice with sterile purified water. Cells were harvested after growing to 5x10^7 cell/ml at 32 C.

extract_protocol: Total RNA was isolated from S. pombe cells using the RNeasy mini kit (Qiagen). Manipulation of RNA extraction was performed according to the manufacturer's instructions.

tag: strain

tag: background

tag: genotype

value: leu1 int::EGFP

tag: growth phase

value: logarithmic

source_name: ASP3894 genome-reduced growing cells

value: ALT-D1684 ART-D1554 BLT-D2117 BRT-D1216 leu1 int::EGFP


title: Gene expression of S. pombe genome-reduced strain in logarithmic phase, replicate 3

description:
CP01D11
Comparison between control strain ASP3880 and genome-reduced strain ASP3894 at logarithmic phase in EMM medium.


title: A2AR_KO_LPS_24h_rep4

city: Gold Coast

first: Kevin

middle: John

last: Ashton

state: QLD

address: University Drive

department: Health Sciences & Medicine

country: Australia

institute: Bond University

description: replicate 4

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse Genome Array Mouse430_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000

data_processing: Raw expression data were background corrected, normalized and log2 transformed using the Robust Multichip Average (RMA) method in BioConductor/R.

source_name: ventricular myocardium, A2AR knockout, LPS, 24h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: A2AR KO mice and WT littermates were obtained from a sub-colony of the original lines generated and characterized by Ledent et al (Nature 388: 674-8, 1997).  Mice were bred and maintained on-site at St. Jude Children’s Research Hospital, with standard laboratory food and water available ad libitum. Animal genotype was confirmed by PCR analysis of tail snips.  All animals originated from the same breeding series.

extract_protocol: Total RNA was extracted with Trizol reagent, DNase treated, followed by clean-up with QIAGEN RNeasy mini kit in accordance with manufacturers protocols. Quality control was performed with Agilent 2100 BioAnalyzer.

treatment_protocol: Both A2AR KO and WT littermate mice received either a single intraperitoneal injection of 20 mg/kg LPS isolated from E. coli (Sigma-Aldrich, St. Louis, MO), or an equal volume of sterile saline vehicle.

tag: genetic background

value: A2AR KO

tag: Sex

value: male

tag: age

value: 14 weeks

value: ventricular myocardium

value: 20 mg/kg LPS isolated from E. coli


title: LLC-kB OVA_MiG rep2

description: MiG Control

value: LLC

value: lung carcinoma

tag: genotype/variation

value: Control


title: A2AR_KO_LPS_24h_rep3

description: replicate 3

tag: tissue


title: TAK1LPC-KO_RIP3-_- 1

type: genomic

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

country: Germany

institute: LMU University Hospital

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.10.1.1).

data_processing: Bioconductor package MANOR was used for loess normalisation and quality filtering of data

molecule: genomic DNA

source_name: liver cells

label_protocol: 250 ng of genomic DNA were labelled using the Enzo Oligo Array CGH Labelling Kit

extract_protocol: genomic DNA was extracted from FFPE sections using the Qiagen Dneasy FFPE kit

value: liver cells

source_name: pooled normal liver tissue (n=4)

value: liver


title: Tentacle buds versus larval body columns, replicate 1

description: Biological replicate 1 of 2.

source_name: pooled sections of planula larvae tentacle buds

value: day 8

value: budded late planula larvae

source_name: pooled body columns of planula larvae with tentacle buds removed


title: Gene expression of S. pombe genome-reduced strain in logarithmic phase, replicate 1

description:
CP01R11
Comparison between control strain ASP3880 and genome-reduced strain ASP3894 at logarithmic phase in EMM medium.


title: LLC-kB OVA_MiG rep1

description: MiG Control


title: TAK1LPC-KO_RIP3-_- 2


title: TAK1LPC-KO_RIP3-_- 4


title: Tentacle buds versus larval body columns, replicate 2

description: Biological replicate 2 of 2.


title: F4sH12vsDd2_rep1_RNA

city: Seattle

first: Pradipsinh

middle: K

last: Rathod

state: WA

address: Campus Box 351700

department: Chemistry

institute: University of Washington

hyb_protocol: Purified labelled cDNAs were hybridized on microarray slides in hybridization solution containing 3X SSC, 0.2% SDS, 0.025 M HEPES and 0.75 µg/µl of poly A (Sigma) for 16 h at 62oC.

scan_protocol: Slides were scanned in an Axon GenePix 4000B microarray scanner and the intensity of spots was quantified using GenePix Pro 4.0 Software (Axon Instruments, Inc.).

data_processing: The ratio of intensity of the two channels was log2 transformed and normalized for print-tip variability and for slide to slide variability in order to correct the systematic biases in the data set using Aroma package version 0.93 [Bengtsson H: aroma – An R Object-oriented Microarray Analysis environment. [http://www.maths.lth.se/publications/]. 2004] run in R project environment (http://cran.r-project.org).

organism: Plasmodium falciparum Dd2

source_name: F4sH12 clone

label_protocol: 12 µg of total RNA was annealed with 5 µg pd(N)6 random primers (Operon) and reverse transcribed to produce aminoallyl-dUTP (Sigma)-labelled cDNA using Superscript II RT (Invitrogen). cDNA samples were purified on Microcon YM-30 (Millipore) and labelled with either monoreactive-Cy3 or -Cy5 (Amersham Biosciences) in 0.05 M sodium bicarbonate buffer (pH 9.0) in dark at room temperature for 1 hour. Unincorporated dyes were removed using QIAquick PCR purification column (Qiagen).

growth_protocol: P. falciparum clone Dd2 and DSM1 resistant cell-lines (C12sC8, D9sD5, E10sD6, and F4sH12) were cultured by established method of Trager and Jensen [Science 1976, 193(4254):673-675]

extract_protocol: Total RNA was extracted using RNAqueous kit (Ambion) following manufacturer's instructions

treatment_protocol: DSM1 resistant cell culture was maintained under DSM1 at 333 nM. The trophozoite stage parasites were collected and extracted from erythrocytes by saponin lysis.  Parasites were flash-frozen in liquid nitrogen and kept at -80oC until genomic DNA samples were required.

value: clone F4sH12 synchronous parasites

tag: clone type

value: under DSM1 pressure

source_name: Dd2 parasites

value: Dd2 synchronous parasites

value: parental Dd2 clone


title: A2AR_KO_saline_24h_rep3

description: replicate 3

source_name: ventricular myocardium, A2AR knockout, saline, 24h

value: saline


title: A2AR_KO_LPS_24h_rep2

description: replicate 2

value: A2AR KO


title: E10sD6vsDd2_rep3_RNA

source_name: E10sD6 clone

value: clone E10sD6 synchronous parasites


title: E10sD6vsDd2_rep2_RNA


title: F4sH12vsDd2_rep2_RNA


title: F4sH12vsDd2_rep3_RNA


title: Ovcar_silencedRNASET2_rep1_human

city: Varese (VA)

first: Marco

last: Fabbri

address: via dunant 5

country: Italy

institute: Università dell'Insubria

description:
Ovcar_silencedRNASET2_rep1
Gene expression of RNASET2-silenced OVCAR3 injected into mice

hyb_protocol: standard Agilent protocol

scan_protocol: Scanned with the Agilent G2565BA Microarray Scanner (Agilent)

data_processing: The fluorescence intensities on scanned images were extracted and preprocessed by Agilent Feature Extraction Software (v10.5.1.1).

source_name: RNASET2-silenced OVCAR3

label_protocol: standard Agilent protocol

growth_protocol: 6-weeks-old male nude mice were challenged subcutaneously in the left flank with parental or RNASET2-silenced OVCAR3 cells. Animals were monitored twice a week for weight and tumor growth (measuring three perpendicular diameters), and killed at day 39. Separate experiments were performed with three different clones of both control (parental cells) and RNASET2-silenced cells.

extract_protocol: Mice were killed at day 39 and tumors were frozen for RNA extraction.Total RNA extracted using RNeasy Plus kit (Qiagen) according to the manufacturer's instructions

tag: transfection

value: silnced RNASET2


title: A2AR_KO_LPS_24h_rep1

description: replicate 1

value: male

value: 14 weeks

value: ventricular myocardium


title: E10sD6vsDd2_rep1_RNA

tag: cell line


title: Ovcar_control_rep2_human

description:
Ovcar_control_rep2
Gene expression of OVCAR3 injected into mice

source_name: Control OVCAR3

tag: cell type

value: empty vector


title: Ovcar_control_rep3_human

description:
Ovcar_control_rep3
Gene expression of OVCAR3 injected into mice


title: Ovcar_silencedRNASET2_rep2_human

description:
Ovcar_silencedRNASET2_rep2
Gene expression of RNASET2-silenced OVCAR3 injected into mice


title: A2AR_KO_saline_24h_rep1

description: replicate 1


title: A2AR_WT_LPS_24h_rep4

description: replicate 4

source_name: ventricular myocardium, wild-type, LPS, 24h

value: WT

value: 20 mg/kg LPS isolated from E. coli


title: A2AR_KO_saline_24h_rep4

description: replicate 4


title: A2AR_KO_saline_24h_rep2

description: replicate 2


title: Ovcar_silencedRNASET2_rep3_human

description:
Ovcar_silencedRNASET2_rep3
Gene expression of RNASET2-silenced OVCAR3 injected into mice


title: TAK1LPC-KO_RIP3-_- 3

value: liver cells

value: liver


title: A2AR_WT_LPS_24h_rep2

description: replicate 2


title: A2AR_WT_saline_24h_rep4

description: replicate 4

source_name: ventricular myocardium, wild-type, saline, 24h


title: C12sC8vsDd2_rep 2_RNA

description: C12sC8vsDd2_rep 2

source_name: C12sC8 clone

value: clone C12sC8 synchronous parasites


title: D9sD5vsDd2_rep3_RNA

source_name: D9sD5 clone

value: clone D9sD5 synchronous parasites


title: A2AR_WT_saline_24h_rep3

description: replicate 3


title: MB 08

city: Nottingham

first: Hazel

middle: Anne

last: Rogers

address: Medical School

department: Clinical Sciences

country: United Kingdom

institute: University of Nottingham

description: no additional information

hyb_protocol: Labeled RNA was hybridized for 16 hours at 45 oC on the U133 plus 2 array. GeneChips were washed and stained in the fluidics station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner 8000 with autoloader

data_processing: Raw data was analysed using Expression console. RMA was used to generate data for analysis. Processed data was analysed in Spotfire DecisionSite for Functional Genomics (TIBCO Software Inc.) for hierarchical clustering and priniciple component analysis. BRB Array Tools Software ver 3.7 (http://linus.nci.nih.gov/BRB-ArrayTools.html) was used for t-tests.

source_name: Tumor material, snap frozen during surgery

label_protocol: Biotinylated cRNA was prepared from 5 mg RNA using the Affymetrix HT IVT labeling method (one cycle)

growth_protocol: Tumor material was removed during surgery then snap frozen

extract_protocol: RNA was extracted using the mirVana miRNA isolation kit (Ambion)

tag: tumour type

value: Medulloblastoma


title: A2AR_WT_LPS_24h_rep3

description: replicate 3

tag: treatment


title: D9sD5vsDd2_rep2_RNA

value: under DSM1 pressure

value: Dd2 synchronous parasites


title: Ovcar_control_rep1_human

description:
Ovcar_control_rep1
Gene expression of OVCAR3 injected into mice


title: C12sC8vsDd2_rep 3_RNA

description: C12sC8vsDd2_rep 3

value: parental Dd2 clone


title: A2AR_WT_saline_24h_rep2

description: replicate 2

value: saline


title: A2AR_WT_LPS_24h_rep1

description: replicate 1


title: B_23

city: Düsseldorf

first: Boris

last: Goerg

address: Moorenstrasse 5

department: Clinic for Gastroenterology, Hepatology and Infectiology

institute: Heinrich-Heine Universität Düsseldorf

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to Agilent Whole Human Genome Oligo Microarrays (8x60K) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C and a final wash step with acetonitrile for 30 sec at RT

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files. FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware, Rosetta error model; Lee Weng et al 2006).

source_name: brain tissue

label_protocol: 100 ng of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

extract_protocol: The RNA was isolated by using standard RNA extraction protocols (RNeasy Mini Kit, Qiagen, Hilden Germany) and the RNA quality checked via the Agilent 2100 Bioanalyzer platform (Agilent Technologies). Only RNAs with calculated RNA Integrity Numbers (RIN) higher than 6 were accepted.

tag: sample source

value: post mortem biopsy

tag: disease state

value: non-cirrhotic control


title: MB 03R

description: no additional information


title: A_19

value: cirrhosis without HE


title: MB 02

description: no additional information


title: Fetal Brain

description: no additional information

source_name: Commercial fetal brain RNA sample (Clontech)

value: Normal fetal brain


title: MB 06

description: no additional information


title: A_18


title: D9sD5vsDd2_rep1_RNA


title: MB 05

description: no additional information


title: MB 01

description: no additional information


title: B_24


title: F4sH12vsDd2_rep3_DNA

hyb_protocol: Purified Dye-labelled DNAs were hybridized on microarray slides in hybridization solution containing 3X SSC, 0.2% SDS and 0.025 M HEPES for 16 h at 62oC.

label_protocol: Genomic DNA was sheared by sonication to generate fragment sizes between 0.5 and 1 kb. 5 µg of sheared gDNA per microarray experiment was labeled with aminoallyl-dUTP (Sigma) by Klenow (NEB) using random primers (Operon). Klenow reactions were cleaned up with DNA Clean and Concentrate-5 kit (Zymo Research). DSM1 -resistant clone and parental strain were then labelled with Cy5 (Amersham Biosciences)  and Cy3 (Amersham Biosciences), respectively. Unincorporated dyes were removed using  DNA Clean and Concentrate-5 kit  (Zymo Research).

extract_protocol: Genomic DNA was extracted using Qiagen Dneasy Kit following manufacturer's instructions

treatment_protocol: DSM1 resistant cell culture was maintained under DSM1 at 333 nM. Predominantly trophozoite stage parasites were collected and extracted from erythrocytes by saponin lysis.  Parasites were flash-frozen in liquid nitrogen and kept at -80oC until genomic DNA samples were required.

value: clone F4sH12 non-synchronous parasites

tag: reference

value: Dd2 non-synchronous parasites


title: MB 04

description: no additional information


title: MB 07

description: no additional information


title: A_21


title: A2AR_WT_saline_24h_rep1

description: replicate 1

value: WT

value: male

value: 14 weeks

value: ventricular myocardium


title: B_22


title: E10sD6vsDd2_rep3_DNA

value: clone E10sD6 non-synchronous parasites


title: F4sH12vsDd2_rep2_DNA


title: F4sH12vsDd2_rep1_DNA


title: C12sC8vsDd2_rep 1_RNA

description: C12sC8vsDd2_rep 1

value: clone C12sC8 synchronous parasites


title: E10sD6vsDd2_rep1_DNA


title: ATRT 01

description: no additional information

value: atypical teratoid/rhabdoid tumour (ATRT)


title: CNS PNET 10

description: no additional information

value: CNS PNET


title: B_17


title: EX6DEL_AT_3

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

description: 4h after treatment

hyb_protocol: Affymetrix standard

scan_protocol: Affymetrix standard

data_processing: The data were analyzed with GCRMA as background correction, summarization & normalization method.

source_name: Granulosa cells pooled from 5 Snfl2 Ex6DEL mice treated with PMSG followed by hCG and  collected at 4h post-hCG

label_protocol: Whole transcript sense target labeling assay

growth_protocol: The Snf2l Ex6DEL transgenic mouse line and the appropriate wild-type (WT) littermate control mice were generously provided by David J. Picketts (Ottawa Hospital Research Institute, Ottawa, Ontario, Canada).  The mice are a hybrid strain resulting from the cross between the ubiquitously expressing Gata-1 Cre transgenic line in a CD-1 background provided by Dr. S. Orkin (Howard Hughes Medical Institute, Chevy Chase MD, USA) and mice with loxP-flanked Snf2l exon 6 developed by Dr. D.J. Picketts in a 129Sv background. The resulting Ex6DEL line was bred to the germline and maintained independently of CRE on a 129SV background. Granulosa cells were harvested by puncturing individual follicles using a 25G needle and applying light pressure with tweezers.

extract_protocol: RNA was extracted using the RNeasy kit (Qiagen, Valencia, CA, USA) according to the manufacturer's instructions.

treatment_protocol: Female mice were injected intra-peritoneally (ip) at 24-26 days of age with 5 IU pregnant mares' serum gonadotropin (PMSG; Folligon; Intervet, Boxmeer, The Netherlands) to stimulate follicle growth. For the PMSG only treated group, granulosa cells were collected after 48h in both WT and Ex6DEL littermates (5 mice per group). For the PMSG and hCG treated, the PMSG injection was followed 48h later  by a single intra-peritoneal (ip) injection of 5 IU human chorionic gonadotropin (hCG; Sigma, St. Louis, MO) and granulosa cells were collected after 4h in both WT and Ex6DEL mice (5 mice per group).

value: granulosa

value: Snfl2 Ex6DEL


title: PB 01

description: no additional information

value: Pineoblastoma


title: B_18

value: post mortem biopsy


title: E10sD6vsDd2_rep2_DNA

value: under DSM1 pressure

value: parental Dd2 clone


title: EX6DEL_AT_1

description: 4h after treatment


title: B_20

value: non-cirrhotic control


title: CNS PNET 09

description: no additional information


title: B_21


title: EX6DEL_BT_2

description: before treatment

source_name: Granulosa cells pooled from 5 Snfl2 Ex6DEL mice treated with PMSG


title: D9sD5vsDd2_rep3_DNA

value: clone D9sD5 non-synchronous parasites


title: B_12-1

value: cirrhosis with HE


title: EX6DEL_AT_2

description: 4h after treatment


title: B_29


title: B_31


title: WT_BT_3

description: before treatment

source_name: Granulosa cells pooled from 5 WT mice treated with PMSG

value: wild type


title: B-3-1


title: EX6DEL_BT_3

description: before treatment


title: WT_BT_2

description: before treatment


title: EX6DEL_BT_1

description: before treatment


title: D9sD5vsDd2_rep1_DNA

value: Dd2 non-synchronous parasites


title: CNS PNET 06

description: no additional information


title: D9sD5vsDd2_rep2_DNA


title: WT_AT_3

description: 4h after treatment

source_name: Granulosa cells pooled from 5 WT mice treated with PMSG followed by hCG and  collected at 4h post-hCG


title: CNS PNET 07R

description: no additional information


title: B_32


title: WT_AT_2

description: 4h after treatment


title: CNS PNET 07

description: no additional information


title: C12sC8vsDd2_rep 1_DNA

description: C12sC8vsDd2_rep 1

value: clone C12sC8 non-synchronous parasites


title: CNS PNET 05R

description: no additional information


title: WT_BT_1

description: before treatment


title: B_30


title: CNS PNET 03R

description: no additional information


title: C12sC8vsDd2_rep 3_DNA

description: C12sC8vsDd2_rep 3


title: C12sC8vsDd2_rep 2_DNA

description: C12sC8vsDd2_rep 2


title: CNS PNET 04

description: no additional information


title: CNS PNET 06R

description: no additional information


title: CNS PNET 08

description: no additional information


title: B_27


title: CNS PNET 05

description: no additional information


title: Prostate Cancer 198

status: Public on Apr 01 2013

city: San Diego

first: Yi

last: Zhang

state: CA

address: 9640 Towne Centre Drive, Suite 200

institute: bioTheranostics

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R007_C002

hyb_protocol: Standard DASL (Illumina) hybridization protocol

scan_protocol: Standard DSL (Illumina) scanning protocol

data_processing: loess normalized and log2 transformed

label: Cy3 and Cy5

source_name: Prostate cancer

extract_protocol: Total RNA was isolated and purified using The High Pure RNA Isolation kit (Roche) and cDNA was generated using the Single-Use cDNA Synthesis Kit (Illumina).

tag: gleason score

tag: biochemical failure (y/n)

tag: pathologic tumor stage


title: Prostate Cancer 199

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R007_C003


title: B_25


title: Prostate Cancer 205

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R007_C009


title: Prostate Cancer 206

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R007_C010


title: Prostate Cancer 200

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R007_C004


title: Prostate Cancer 201

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R007_C005

value: 3a, +margin


title: Prostate Cancer 202

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R007_C006


title: Prostate Cancer 208

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R007_C012


title: Prostate Cancer 207

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R007_C011


title: Prostate Cancer 203

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R007_C007


title: Prostate Cancer 209

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R008_C001


title: Prostate Cancer 210

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R008_C002


title: Hom E14.5 agonadal urogenital ridges

city: Boston

first: Jose

last: Teixeira

state: MA

address: 55 Fruit St.

department: VCRB

institute: Massachusetts General Hospital

description: Gene expression data from urogenital ridges that are not responsive to MIS

hyb_protocol: Hybridization is carried out in an Affymetrix Model 640 hybridization chamber according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays.  Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.

scan_protocol: Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station.  Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.  Scanning is carried out on a GeneChip® Model 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System. Chip library files specific to each array and necessary for scan interpretation are stored on the computer workstation controlling the scanner and are updated regularly as necessary when updates are made available from Affymetrix.

data_processing:
GCOS was used with MAS5 algorithm
GenePattern pipeline run requested on server http://genepattern.hpcgg.partners.org/ by user system@portal.hpcgg.org at Wed Nov 14 10:33:56 EST 2007
Pipeline [name=AffxToFold; version=1.0; desc=Automated bioinformatics analysis for two class fold comparison; author=Eugene Clark, HPCGG; param-count=5]
Input Parameters:
AffxToFold1.classes = control:1170B;case:1170A
AffxToFold1.comparisons = control,case
AffxToFold1.input.filename = /udd/gigpad/research/Facilities/Affymetrix Microarrays_61/Batches/15223039-7_Teixeira_Teixeira/Project1170_ScaledTo500_no_rows_with_absent_calls_for_all_samples.xls
AffxToFold1.foldLevel = 2
AffxToFold1.sortOrder = ascending
Result download directory: /udd/gigpad/research/Facilities/Affymetrix Microarrays_61/Batches/15223039-7_Teixeira_Teixeira/AffxToFold_case_vs_control
Task 0 done at Wed Nov 14 10:34:11 EST 2007: AffxToFold
Download AffxToFold output files done at Wed Nov 14 10:34:11 EST 2007
All done at Wed Nov 14 10:34:11 EST 200

source_name: mouse urogenital ridges (approximately 100)

label_protocol: For each experimental sample, RNA quality was assessed by RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100. Concentrations may also be determined using a NanoDrop 1000 spectrophotometer. Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed.   Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols using the Affymetrix GeneChip Cleanup Module (Affymetrix Catalog # 900371). In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.

growth_protocol: Embryos were collected from dams at E14.5

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

treatment_protocol: urogenital ridges were scored by using a YFP reporter for genotype

value: agonadal urogenital ridges

tag: strain

value: mix of C57Bl/6 and 129SVEV

tag: genotype


title: Prostate Cancer 204

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R007_C008


title: WT_AT_1

description: 4h after treatment


title: Spinal cord_lewis female_MBP EAE_218

status: Public on Apr 03 2013

city: Brisbane

first: Hayley

middle: Ruth

last: Inglis

state: Queensland

address: Building 71/918, Royal Brisbane & Women’s Hospital Campus,Herston, QLD, 4029

department: Clinical Neurosciences

institute: University of Queensland , Centre for Clinical Research

description: Total snap frozen spinal cord ,Lewis rat # 218

hyb_protocol: 5ug of fragmented biotinylated ssDNA was hybridised for 16hrs at 45oC, 60rpm on a Rat Exon 1.0 ST Array. After 16hrs GeneChips were washed on a FS_450 Fluidics Station using the washing script FS450_0001 with buffers and stains supplied with the GeneChip Hybridization, Wash, and Stain Kit from Affymetrix.

scan_protocol: Data was acquired on a 7G GeneChip Scanner 3000 and .CEL file generation performed using AGCC

data_processing:
Expression Console with RMA was used initially to extract probe intensity data. This data was used to access Affymetrix supplied PolyA and Eukaryotic Hybridisation controls to confirm consistent processing of the RNA samples. Subsequent analysis was performed in Partek Genomics Suite - Version 6.11.0801. The Affimetrix RaEx-1_0-st-v1.r2.dt.rn4.core.mps was used to filter probe sets.  RMA background correction was applied including pre-background adjustment for CG content and quantile normalization across all chips in the experiment.  Log2 transformation of probe data and mean probeset summarization was used to produce the gene-summary expression values used in the gene expression comparisons.  Two way ANOVA was used to compare gene expression in the spinal cords of rats at the clinical peak of disease to age matched healthy controls.
probe group file: RaEx-1_0-st-v1.r2.pgf
meta-probeset file: RaEx-1_0-st-v1.r2.dt1.rn4.core.mps

organism: Rattus norvegicus

source_name: Lewis female, virgin ,MBP EAE

label_protocol: Samples were enzymatically fragmented and biotinylated using the Encore Biotin Module labelling kit (NuGEN)

growth_protocol: Rat spinal cords extracted by insuflation at the peak of disease in EAE animals and at the same time from healthy control age matched (littermates)

extract_protocol: Spinal cords were excised from the spinal column by insufflation using a large bore blunt ended needle and 60 ml syringe. Tissue was snap frozen in liquid nitrogen prior to being stored at -80˚C. Total RNA was prepared using the Rneasy®Lipid Tissue Midi Kit (QIAGEN) and treated with DNase I to remove all traces of genomic DNA prior to storage at -80˚C . cDNA synthesis and amplification was performed using the Applause WT-Amp Plus ST kit (NuGEN).

treatment_protocol: EAE animals were treated by subcutanious injection with 50 ug of guinea-pig brain MBP (Sigma-Aldrich) in Freund's incomplete adjuvant containing 4.0 mg/ml M.Butiricium, at the base of the tail.  Healthy controls were age matched untreated littermates .

value: Lewis

tag: gender

value: Female

tag: age

value: 16 wks

value: 50 ug MBP

tag: days post injection

value: spinal cord


title: Spinal cord_lewis female_healthy control_195

description: Total snap frozen spinal cord ,Lewis rat # 195

source_name: Lewis female, virgin ,healthy control

tag: tissue


title: B_26

value: post mortem biopsy


title: Het E14.5 agonadal urogenital ridges

description: Gene expression data from urogenital ridges responsive to MIS.


title: Spinal cord_lewis female_MBP EAE_217

description: Total snap frozen spinal cord ,Lewis rat # 217


title: Spinal cord_lewis female_healthy control_196

description: Total snap frozen spinal cord ,Lewis rat # 196


title: Spinal cord_lewis female_healthy control_193

description: Total snap frozen spinal cord ,Lewis rat # 193


title: CNS PNET 02R

description: no additional information

value: CNS PNET


title: Lignified xylem, CB2009304-H, biological rep2

status: Public on Apr 23 2013

city: Canberra

first: xiaohui

last: yang

address: Ross

institute: CSIRO

description: Expression data from two-year-old mature xylem of Populus tomentosa.

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Populus tomentosa

source_name: Populus tomentosa mature xylem from natural condition

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: The seedlings were planted in the field of Xiaotangshan, Beijing, China. After growth for about two years, all the plantation for sampling with approximately the same crown size and equal height were chosen.

extract_protocol: Total RNAs were extracted using the RNeasy Plant Mini Kits (Qiagen, Inc. Valencia, CA, USA).

treatment_protocol: Five trees grew under natural condition.

value: two years old

value: lignified xylem


title: Spinal cord_lewis female_MBP EAE_219

description: Total snap frozen spinal cord ,Lewis rat # 219


title: Spinal cord_lewis female_MBP EAE_241

description: Total snap frozen spinal cord ,Lewis rat # 241


title: Prostate Cancer 197

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R007_C001


title: Prostate Cancer 194

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R005_C005


title: Prostate Cancer 195

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R006_C011


title: Prostate Cancer 196

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R006_C012


title: Lignified xylem, CB2009304-G, biological rep1


title: CNS PNET 01

description: no additional information


title: Spinal cord_lewis female_healthy control_194

description: Total snap frozen spinal cord ,Lewis rat # 194


title: Prostate Cancer 173

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R003_C008

value: 3b, +margin


title: Prostate Cancer 174

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R003_C009


title: Prostate Cancer 190

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R005_C001


title: Prostate Cancer 188

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R004_C011


title: Prostate Cancer 189

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R004_C012

value: 2a or 2b


title: Prostate Cancer 175

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R003_C010


title: Prostate Cancer 179

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R004_C002


title: Prostate Cancer 177

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R003_C012


title: Prostate Cancer 176

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R003_C011


title: Prostate Cancer 178

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R004_C001


title: Prostate Cancer 181

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R004_C004


title: Prostate Cancer 180

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R004_C003


title: Prostate Cancer 166

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R003_C001


title: Prostate Cancer 168

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R003_C003


title: Prostate Cancer 172

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R003_C007


title: Prostate Cancer 170

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R003_C005


title: Prostate Cancer 171

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R003_C006


title: Prostate Cancer 167

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R003_C002


title: Prostate Cancer 191

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R005_C002


title: Prostate Cancer 169

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R003_C004


title: Prostate Cancer 182

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R004_C005


title: Prostate Cancer 183

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R004_C006


title: Prostate Cancer 187

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R004_C010


title: Prostate Cancer 186

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R004_C009


title: Prostate Cancer 193

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R005_C004


title: Prostate Cancer 192

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R005_C003


title: Prostate Cancer 184

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R004_C007


title: Prostate Cancer 185

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R004_C008


title: Prostate Cancer 165

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R002_C012


title: Prostate Cancer 162

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R002_C009


title: Prostate Cancer 164

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R002_C011


title: Prostate Cancer 159

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R002_C006


title: Prostate Cancer 163

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R002_C010


title: Prostate Cancer 160

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R002_C007


title: Prostate Cancer 161

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R002_C008


title: Prostate Cancer 158

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R002_C005


title: Prostate Cancer 157

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R002_C004


title: Prostate Cancer 156

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R002_C003


title: Prostate Cancer 154

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R002_C001


title: Prostate Cancer 155

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R002_C002


title: Prostate Cancer 149

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R001_C008


title: Prostate Cancer 148

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R001_C007


title: Prostate Cancer 144

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R001_C003


title: Prostate Cancer 145

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R001_C004


title: Prostate Cancer 146

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R001_C005


title: Prostate Cancer 147

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R001_C006


title: Prostate Cancer 142

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R001_C001


title: Prostate Cancer 143

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R001_C002


title: Prostate Cancer 139

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R008_C008


title: Prostate Cancer 140

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R008_C009


title: Prostate Cancer 141

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R008_C010


title: Prostate Cancer 138

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R008_C007

value: 3ab, +margin


title: Prostate Cancer 127

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R006_C004


title: Prostate Cancer 126

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R006_C003


title: Prostate Cancer 129

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R006_C006


title: Prostate Cancer 128

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R006_C005


title: Prostate Cancer 125

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R006_C002


title: Prostate Cancer 124

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R006_C001


title: Prostate Cancer 150

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R001_C009


title: Prostate Cancer 152

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R001_C011


title: Prostate Cancer 123

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R005_C012


title: Prostate Cancer 136

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R008_C005


title: Prostate Cancer 122

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R005_C011


title: Prostate Cancer 153

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R001_C012


title: Prostate Cancer 131

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R006_C008


title: Prostate Cancer 133

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R006_C010


title: Prostate Cancer 130

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R006_C007


title: Prostate Cancer 135

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R008_C004


title: Prostate Cancer 134

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R008_C003


title: Prostate Cancer 151

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R001_C010


title: Prostate Cancer 132

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R006_C009


title: Prostate Cancer 121

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R005_C010


title: Prostate Cancer 120

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R005_C009


title: Prostate Cancer 137

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R008_C006


title: Prostate Cancer 113

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R008_C007


title: Prostate Cancer 114

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R008_C008


title: Prostate Cancer 112

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R008_C006


title: Prostate Cancer 116

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R008_C010


title: Prostate Cancer 115

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R008_C009


title: Prostate Cancer 117

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R005_C006


title: Prostate Cancer 118

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R005_C007


title: Prostate Cancer 119

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557311004_R005_C008


title: Prostate Cancer 110

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R008_C004


title: Prostate Cancer 111

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R008_C005


title: Prostate Cancer 106

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R007_C012


title: Prostate Cancer 107

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R008_C001


title: Prostate Cancer 109

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R008_C003


title: Prostate Cancer 108

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R008_C002


title: Prostate Cancer 90

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R006_C008


title: Prostate Cancer 103

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R007_C009


title: Prostate Cancer 100

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R007_C006


title: Prostate Cancer 91

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R006_C009


title: Prostate Cancer 101

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R007_C007


title: Prostate Cancer 102

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R007_C008


title: Prostate Cancer 104

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R007_C010


title: Prostate Cancer 105

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R007_C011


title: Prostate Cancer 92

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R006_C010


title: Prostate Cancer 93

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R006_C011


title: Prostate Cancer 88

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R006_C006


title: Prostate Cancer 89

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R006_C007


title: Prostate Cancer 98

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R007_C004


title: Prostate Cancer 95

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R007_C001


title: Prostate Cancer 97

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R007_C003


title: Prostate Cancer 96

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R007_C002


title: Prostate Cancer 94

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R006_C012


title: Prostate Cancer 99

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R007_C005


title: Prostate Cancer 85

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R006_C003


title: Prostate Cancer 78

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R005_C008


title: Prostate Cancer 87

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R006_C005


title: Prostate Cancer 82

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R005_C012


title: Prostate Cancer 77

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R005_C007


title: Prostate Cancer 86

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R006_C004


title: Prostate Cancer 83

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R006_C001


title: Prostate Cancer 84

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R006_C002


title: Prostate Cancer 73

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R005_C003


title: Prostate Cancer 72

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R005_C002


title: Prostate Cancer 68

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R004_C010


title: Prostate Cancer 69

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R004_C011


title: Prostate Cancer 70

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R004_C012


title: Prostate Cancer 76

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R005_C006


title: Prostate Cancer 71

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R005_C001


title: Prostate Cancer 79

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R005_C009


title: Prostate Cancer 80

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R005_C010


title: Prostate Cancer 81

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R005_C011


title: Prostate Cancer 66

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R004_C008


title: Prostate Cancer 65

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R004_C007


title: Prostate Cancer 74

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R005_C004


title: Prostate Cancer 75

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R005_C005


title: Prostate Cancer 67

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R004_C009


title: Prostate Cancer 64

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R004_C006


title: Prostate Cancer 46

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R002_C012


title: Prostate Cancer 48

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R003_C002


title: Prostate Cancer 52

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R003_C006


title: Prostate Cancer 49

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R003_C003


title: Prostate Cancer 53

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R003_C007


title: Prostate Cancer 51

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R003_C005


title: Prostate Cancer 50

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R003_C004


title: Prostate Cancer 56

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R003_C010


title: Prostate Cancer 59

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R004_C001


title: Prostate Cancer 58

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R003_C012


title: Prostate Cancer 54

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R003_C008


title: Prostate Cancer 57

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R003_C011


title: Prostate Cancer 55

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R003_C009


title: Prostate Cancer 42

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R002_C008


title: Prostate Cancer 45

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R002_C011


title: Prostate Cancer 43

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R002_C009


title: Prostate Cancer 44

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R002_C010


title: Prostate Cancer 47

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R003_C001


title: Prostate Cancer 61

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R004_C003


title: Prostate Cancer 60

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R004_C002


title: Prostate Cancer 62

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R004_C004


title: Prostate Cancer 63

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R004_C005


title: Prostate Cancer 38

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R002_C004


title: Prostate Cancer 37

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R002_C003


title: Prostate Cancer 40

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R002_C006


title: Prostate Cancer 36

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R002_C002


title: Prostate Cancer 39

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R002_C005


title: Prostate Cancer 41

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R002_C007


title: Prostate Cancer 32

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R001_C010


title: Prostate Cancer 30

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R001_C008


title: Prostate Cancer 34

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R001_C012


title: Prostate Cancer 31

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R001_C009


title: Prostate Cancer 35

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R002_C001


title: Prostate Cancer 33

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R001_C011


title: Prostate Cancer 5

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1544878014_F1


title: Prostate Cancer 6

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1544878014_F2


title: Prostate Cancer 7

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1544878014_G1


title: Prostate Cancer 8

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1544878014_G2


title: Prostate Cancer 26

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R001_C004


title: Prostate Cancer 25

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R001_C003


title: Prostate Cancer 27

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R001_C005


title: Prostate Cancer 24

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R001_C002


title: Prostate Cancer 28

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R001_C006


title: Prostate Cancer 29

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R001_C007


title: Prostate Cancer 1

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1544878014_D1


title: Prostate Cancer 2

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1544878014_D2


title: Prostate Cancer 10

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1544878015_A2


title: Prostate Cancer 14

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1544878015_C2


title: Prostate Cancer 13

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1544878015_C1


title: Prostate Cancer 12

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1544878015_B2


title: Prostate Cancer 9

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1544878015_A1


title: Prostate Cancer 11

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1544878015_B1


title: Prostate Cancer 3

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1544878014_E1


title: Prostate Cancer 4

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1544878014_E2


title: Prostate Cancer 15

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1544878015_D1


title: Prostate Cancer 17

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1544878015_E1


title: Prostate Cancer 18

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1544878015_E2


title: Prostate Cancer 22

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1544878015_G2


title: Prostate Cancer 21

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1544878015_G1


title: Prostate Cancer 20

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1544878015_F2


title: Prostate Cancer 19

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1544878015_F1


title: Prostate Cancer 16

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1544878015_D2


title: Prostate Cancer 23

description:
cDNA is amplified in a PCR reaction using fluorescently labeled primers to generate target-specific amplicons that are then hybridized to an array
AVG_Signal.1557290034_R001_C001