title: Leaves at IV (time 0), biological rep2

city: Lisboa

first: Luisa

middle: C

last: Carvalho

address: Tapada da Ajuda

department: DRAT-CBAA

country: Portugal

institute: Instituto Superior de Agronomia, Univarsidade Técnica de Lisboa

description: Gene expression data from leaves of in vitro grown plants

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

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner 3000.

data_processing: Scanned arrays were analyzed first with Affymetrix MAS 5.0 software to obtain Absent/Present calls and for subsequent analysis with DNA-Chip Analyzer (dChip) Version Release (Apr 15, 2005) (http://www.dchip.org, Wong Lab, Harvard).

organism: Vitis vinifera

source_name: Vits leaves from in vitro grown plants, prior to transfer

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Explants were micropropagated in Murashige and Skoog (1962), MS (Duchefa Biochemie, Haarlem, NL) basal medium supplemented with 0.5 µM α-naphthaleneacetic acid (NAA) and 5.0 µM 6-benzylaminopurine (BA). Before root induction, shoots were elongated for two weeks in the same medium but with 1.67 µM BA. For root induction, explants from the elongation phase received a supplement of 2 µM α-naphthaleneacetic acid (NAA) for four days. Cultures were maintained at 16/8h photoperiod and 45 ± 5 µmol m-2 s-1 of photosynthetic photon flux density (PPFD). Temperature was 25 ± 1ºC (light) and 22 ± 1ºC (dark).

extract_protocol: Total RNA from leaves was extracted using a modification of the method described by Geuna et al. (1998).

treatment_protocol: Microcuttings were transplanted to 6 cm diameter pots containing a sterilised mixture of hydrated peat and perlite (1:1, v/v) and placed in 450 L glass chambersunder a PPFD of 200 ± 10 µmol m-2 s-1 with a photoperiod of 16/8h. RH  was 98% and temperature was kept between 25 ± 2ºC (light) and 22 ± 1ºC (dark). Leaves were harvested into 0.5g samples from in vitro material at the moment of transplant (time zero) and after 48h.

tag: variety

value: Touriga Nacional

value: in vitro grown

tag: tissue

value: leaf


title: ls1034.rpmi.1

status: Public on Feb 10 2011

type: RNA

city: Goettingen

first: Melanie

last: Spitzner

address: Robert-Koch-Str. 40

department: Department of General and Visceral Surgery

country: Germany

institute: Georg-August-University Goettingen

description: Cell line: LS1034; Medium: RPMI; SF2: 0.59

hyb_protocol: Subsequently, 1.65 µg of labeled cRNA per sample was fragmentized and hybridized overnight to a 4x44k gene expression microarray (Agilent Technologies).  After a washing step the arrays were scanned on an Agilent DNA microarray scanner G2505B (Agilent Technologies) at 5 micron resolution.  Scanned image files were visually inspected for artifacts and subsequently analyzed.

scan_protocol: Agilent DNA microarray scanner G2505B, 5 micron resolution

data_processing: Median signal intensities from the Feature Extraction Software were converted to log2 and quantile normalized using the R package “limma”.

molecule: total RNA

organism: Homo sapiens

source_name: colorectal cancer cell line

label_protocol: 800 ng of total RNA were reverse-transcribed, amplified and labeled with Cy3 using the Low RNA Input Linear Amplification Kit, PLUS (Agilent Technologies).  After purification, the cRNA yield and integration of cyanine 3-CTP was measured using a spectrophotometer.  cRNA with a specific activity > 9.0 pmol/µg was excluded from further experiments.

growth_protocol: Twelve human colorectal cancer cell lines were obtained from the American Type Culture Collection (ATCC, Manassas, VA): Caco-2, HT-29, LS411N, LS513, LS1034, SW403, SW480, SW620, SW837, SW1116, SW1463, and WiDr.  All lines were cultured in their recommended medium (Invitrogen, Karlsruhe, Germany), supplemented with fetal bovine serum (Pan, Aidenbach, Germany) and 2mM L-glutamine (BioWhittaker, Verviers, Belgium).  Periodically, mycoplasma contamination was excluded by PCR, and cell line cross-contamination was excluded by short tandem repeat profiling.

extract_protocol: Total RNA was isolated using the RNeasy Mini kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions, including a DNase treatment step.  Nucleic acid quantity, quality and purity were determined using NanoDrop ND-1000 spectrophotometer (Peqlab, Erlangen, Germany) and a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).  Only RNA samples with a RNA integrity number > 9.5 were considered for further analysis.

treatment_protocol: No treatment prior to expression profiling analysis.

tag: cell line

tag: medium

value: RPMI

tag: rep


title: ls411n.rpmi.2

description: Cell line: LS411N; Medium: RPMI; SF2: 0.28


title: caco2.mem.3

description: Cell line: Caco-2; Medium: MEM; SF2: 0.58

value: MEM


title: Leaves at IV (time 0), biological rep1

label: biotin

tag: treatment


title: Leaves at 48hours, biological rep1

description: Gene expression data from leaves of plants grown  ex vitro for 48h

source_name: Vits leaves from plants  grown ex vitro for 48h

value: ex vitro for 48 h


title: Primary tumor 7

city: Uppsala

first: Katarina

last: Edfeldt

address: Akademiska Sjukhuset

department: Surgical Sciences

country: Sweden

institute: Uppsala University

hyb_protocol: The hybridizations were done manually and Standard Operation Procedure; SOP 003 Hybridization onto oligo or cDNA Microarrays were followed. http://www.biotech.kth.se/molbio/microarray/protocols.html

scan_protocol: The slides were scanned in the Aglient DNA Microarray Scanner and in GenePix 5.1, Axon Instruments, were used for image analysis. (http://www.moleculardevices.com/Products/Software/GenePix-Pro.html)

data_processing: After removal of bad quality spots (if less than 70% of foreground pixels were below background intensity plus 2 SDs in both channels or if the difference between ratio of medians and regression ratio exceeded 20% in one of the channels), analysis of the gene expression data was carried out in the freely available statistical computing language R (http://www.r-project.org) using a package available from the Bioconductor project (www.bioconductor.org). The raw data was normalized using the LOWESS method (Yang, Dudoit et al. 2002). In order to search for differentially expressed genes between groups, an empirical Bayes moderated t test was applied, using the Limma package (Smyth 2004). To address the problem of multiple testing, the p-values were adjusted using the Benjamini and Hochberg method (Benjamini 1995).

source_name: Primary tumor

label_protocol: For labeling of the total RNA samples a Standard Operation Procedure; SOP 002 Indirect labeling of cDNA using aminoallyl modified nucleotides was used. http://www.biotech.kth.se/molbio/microarray/protocols.html

extract_protocol: Total RNA was extracted using TriZol Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. Sections from all the tumors were stained with Mayer´s hematoxylin and histopathologically evaluated, and the tissue used contained at least 80 % of neoplastic cells. When needed, the tumor was macroscopically resected from excessive stroma tissue, blood vessels, bowel mucosa, lymphoid and liver tissue. Quality and quantity of the extracted RNA was assessed by Aglient 2100 Bioanalyzer (Aglient Technologies, Santa Clara, CA, USA). One lymph node metastases were contaminated with < 5 % of lymphatic tissue (LNmet9181).

treatment_protocol: Tumors were snap frozen in liquid nitrogen and kept at -70°C until used.

tag: gender

value: Female

tag: carcinoid syndrome

value: No

tag: ki67 proliferation index

tag: age at diagnosis

tag: radically operated

value: Yes

tag: disease status

value: Stable

source_name: Universal Human Reference RNA, Agilent Technologies, USA. A mix of 10 human cell lines.

tag: sample type

value: reference


title: Leaves at 48hours, biological rep2


title: Lung_infected_3days_rep3

city: Herston

first: Melissa

middle: Louise

last: Burke

state: QLD

address: 300 Herston Road

department: Division of Infectious Diseases and Immunology

country: Australia

institute: Queensland Institute of Medical Research

description: Gene expression in the lung of C57BL/6 mice 3 days post infection with 500 Schistosoma japonicum cercariae

hyb_protocol: cRNA was hybridised to Illumina mouse-6 v2 expression beadchips according to the manufacturers instructions

scan_protocol: Microarrays were scanned using a Beadstation 500 at Green factor level 2

data_processing: Data was analysed using GenomeStudio version 1.1.1 and Genespring GX 11

organism: Mus musculus

source_name: Lung homogenate, infected

label_protocol: cRNA was synthesised from total RNA with an Illumina Total Prep RNA Amplification Kit (Ambion Inc., USA) according to the manufacturers instructions

extract_protocol: Total RNA was extracted from lung tissue by phase separation with Trizol (Invitrogen, USA) and column chromatography using an Rneasy Mini kit (Qiagen Inc, USA), RNA quantity was measured using a Nanodrop (Nanodrop Technologies, USA) and quality was assessed using an Agilent Bioanalyzer Nanochip (Agilent Technologies, USA)

treatment_protocol: Mice were euthanized and lung tissue was collected and stored in RNAlater for microarray analysis

tag: strain

tag: age

value: 6 weeks

value: Lung

tag: infection

value: Schistosoma japonicum cercariae


title: Primary tumor 6

value: Deceased


title: sw1116.l15.3

description: Cell line: SW1116; Medium: L-15; SF2: 0.68


title: ArcA- mutant vs. WT (dye swap-3)

city: St. Cloud

first: Ryan

middle: Cristiano

last: Fink

state: MN

address: 720 4th Ave S

department: Biology

country: USA

institute: St. Cloud State University

hyb_protocol: The slides were washed at increasing stringencies (2x SSC [1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate], 0.1% sodium dodecyl sulfate [SDS], 42°C; 0.1% SSC, 0.1% SDS, room temperature; 0.1% SSC, room temperature).

scan_protocol: the microarrays were scanned for the Cy3 and Cy5 fluorescent signals with a ScanArray 4000 microarray scanner from GSI Lumonics (Watertown, MA). The intensity of every spot was codified as the sum of the intensities of all the pixels within a circle positioned over the spot itself and the background as the sum of the intensities of an identical number of pixels in the immediate surroundings of the circled spot.

data_processing:
The signal intensity at each spot from the FNR mutant and the WT were background subtracted, normalized, and used to calculate the ratio of gene expression between the two strains. All replicas were combined, and the median expression ratios and standard deviations were calculated for open reading frames (ORFs) showing 2.5-fold change.
VALUE column reports log2 (mutant/wt) ratios.

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: ArcA null mutant

label_protocol: The labelling of the total RNA was performed using indirect labelling with AA-dUTP and subsequent coupling.

growth_protocol: OD600=0.3, anaerobic, LB medium, 20 mM Xylose

extract_protocol: Total RNA was extracted with the RNeasy RNA extraction kit (QIAGEN), and the samples were treated with RNase-free DNase (Invitrogen, Carlsbad, CA). The absence of contaminating DNA and the quality of the RNA was confirmed by using agarose gel electrophoresis.

tag: genotype

value: ArcA null mutant

tag: genetic background

value: ATCC 14028s

source_name: WT


title: Lung_infected_3days_rep2

tag: tissue


title: ls1034.rpmi.3

tag: cell line


title: Primary tumor 4

value: Male


title: sw837.rpmi.1

description: Cell line: SW837; Medium: RPMI

tag: medium


title: ArcA- mutant vs. WT (dye swap-1)


title: Primary tumor 8


title: ArcA- mutant vs. WT (dye swap-2)


title: Lung_infected_3days_rep1


title: Lung_uninfected_control_rep3

description: Gene expression in the lung of normal C57BL/6 mice

source_name: Lung homogenate, uninfected

value: uninfected


title: Lung_uninfected_control_rep2


title: Lymph node metastasis 14

source_name: Lymph node metastasis

tag: associated primary tumor no


title: Primary tumor 3


title: ArcA- mutant vs. WT (3)


title: caco2.mem.1

tag: rep


title: Primary tumor 1

tag: gender


title: Primary tumor 2

tag: carcinoid syndrome

value: 3%, 7 % in hot spots


title: Lung_uninfected_control_rep1


title: sw480.l15.3

description: Cell line: SW480; Medium: L-15; SF2: 0.55


title: ht29.mccoy.3

description: Cell line: HT-29; Medium: McCoy's; SF2: 0.81

value: McCoy's


title: Tregs purified from IIKO-CD3KO chimera, Biological Rep4

status: Public on Feb 09 2011

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

description: Gene expression data from CD4 Tregs lacking TCR / MHC class II interactions in periphery (CD4+ TCRβ+ CD25+ cells purified from IIKO-CD3KO chimeras)

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

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix)

data_processing: The data were analizing with affy R package (RMA) and statistical analysis were then performed with MeV software (TIGR, Rockville MD)

source_name: Tregs purified from IIKO-CD3KO chimera

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Following the GeneChip whole transcript (WT) Sense Target labelling assay kit Affymetrix)

extract_protocol: Total RNA was extracted using the Rneasy Mini kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: CD4+ TCRβ+ CD25+ cells were isolated by magnetic bead enrichment followed by fluorescence activated cell sorting.

value: 6-8 weeks of age

tag: genotype/variation

value: IIKO-CD3KO chimera

tag: origin tissue

value: Peripheral lymph nodes and spleen

tag: cell type

value: CD4 Tregs lacking TCR


title: Tregs purified from IIKO-CD3KO chimera, Biological Rep3


title: Tregs purified from IIKO-CD3KO chimera, Biological Rep2


title: ArcA- mutant vs. WT (1)


title: ArcA- mutant vs. WT (2)


title: 001_HuCCT1_untreated

city: Tokushima

first: Shuichi

last: Iwahashi

address: Kuramoto 3-18-15

department: Department of Surgery

country: Japan

institute: Institute of Health Biosciences, The University of Tokushima Graduate School

hyb_protocol: Approximately 5.5μg of fragmented and labeled DNA target was hybridized to the Affymetrix GeneChip○R Human Gene 1.0 ST Array at 45°C for 17h on a GeneChip○R Hybridization Oven 640  (Affymetrix) according to the manufacturer’s recommendation.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip○R Fluidics Station 450 and scanned on a GeneChip○R Scanner 3000 7G (Affymetrix), and then generated CEL files for each array.

data_processing: The microarray data was normalized by RMA using GeneSpring GX 11.5 software (Agilent). The cut-off value was set at 0.5 to 2.0 for the ratio (more than 2.0: up-regulation, 0.5-2.0: no change, less than 0.5: down-regulation).

source_name: Human cancer cell

label_protocol: First standard cDNA was synthesized from 300 ng of total RNA by using GeneChip○R Whole Transcript (WT) cDNA Synthesis and Amplification Kit (Affymetrix) according to the manufacturer’s instructions. 10 μg of cRNA were input into the second-cycle cDNA reaction. cDNA was fragmented and end-labeled with the GeneChip○R WT Terminal Labeling Kit (Affymetrix).

extract_protocol: Total RNA was isolated from both the stimulated and unstimulated cells (HuCCT-1) using RNeasy Mini kit (Qiagen, Valencia, CA). Relative purity was examined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

value: cholangiocarcinoma cell line HuCCT1

tag: agent

value: control (untreated)


title: 003_HuCCT1_GEM

value: GEM


title: dmyc_vs_cd2-48h-rep6

city: Madrid

first: Eduardo

last: Moreno

address: Melchor Fernandez-Almagro

department: Molecular Oncology

country: Spain

institute: CNIO

hyb_protocol: Slides were Pre-hybridized in 5X SSC 0.1% SDS 0.5 ml 0.1% solution at 55°C for at least 1 hour. Arrays were hybridized simultaneously with Cy5- and Cy3-labeled probes under a cover slip in sealed humid chamber with 60 μl of hybridization buffer (0.5 M NaPO4, pH 7.0, 1.0% SDS, 2 mM EDTA, 2 x SSC, 4 x Denhardt’s Solution) at 55°C for 10-15 hours. After incubation, slides were washed three times in 1X SSC, 0.1% SDS at 55°C for 10 minutes each, once in 1X SSC at room temperature for 30 seconds and finally one time in 0.1X SSC at room temperature for 30 seconds. Slides were dried by centrifugation at 500 rcf for 1 minute.

scan_protocol: The slides were scanned at a resolution of 10 µm with Agilent G2565BA Microarray Scanner (Agilent Technologies) and Cy3 and Cy5 fluorescent signals were quantified using GenePix Pro 4.0 software (Axon Instruments Inc.).

data_processing: GPR files with raw data were introduced in GEPAS v1.0 Preprocessor tool (http://www.transcriptome.ens.fr/cgi-bin/gepas/preprocess) to remove patterns with more than 20% missing data and to average replicated genes after removing inconsistent ones (with a maximum distance to median of replicates equal to 1). Filtered data was then Print_tip_group_Lowess normalized with the web application DNMAD (http://dnmad.bioinfo.cnio.es/).

organism: Drosophila melanogaster

source_name: tub>dmyc>Gal4 transgene cells

label_protocol: The amplification procedure is based on themethod described by Eberwine in 1996. Briefly, double-stranded cDNA was synthesized from total RNA isolated from imaginal discs. The cDNA was used as a template for in vitro transcription, routinely generating an aRNA product that represented an amplification of approximately 1,000 fold. This aRNA was subjected to a second round of RT and IVT. The yield from the second round represented an approximately 100-fold amplification, resulting in an overall amplification of 1 to 5.10E5. Probes for hybridization were synthesized by RT and labeled with either Cy5 (red) or Cy3 (green) by swaping fluorochromes in 3 of the 6 replicated experiments for each time point.

growth_protocol: All Drosophila strains were grown at 25º on fly medium (5,5% yeast, 7,12% glucose, 0.8% agar , 2.5 % corn meal, 1.1% soy meal, 0.003% propionic acid, Methyl 4-hydroxybenzonate)

extract_protocol: Total RNA was extracted from wing discs undergoing competition (tub>dmyc>Gal4) and control discs (tub>cd2>Gal4) at different time points (0, 12, 24 and 48 hours) using with Trizol reagent (Invitrogen, Carlsbad, CA) and RNeasy Mini Kit (Quiagen Inc., Hilden, Germany). Following extraction, RNA was treated with RNase free DNase (Ambion Inc, Austin, TX). Quality of the RNA was determined with a 2100 Bioanalyzer (Agilent Technologies, Carlsbad, CA) and RNA amount was established by using a NanoDrop spectrophotometer (NanoDrop, Wilmington, DE).

treatment_protocol: Flies were subjected to a 15 min heat-shock at 37º to produce the maximum amount of boundaries where GFP and non-GFP clones contact each other.

tag: developmental stage

value: 3rd instar larvae

value: tub>dmyc>Gal4 transgene cells

tag: time point

value: 48 hr

source_name: tub>cd2>Gal4 control cells

value: tub>cd2>Gal4 control cells


title: Tregs purified from IIKO-CD3KO chimera, Biological Rep1

tag: strain

tag: age


title: 004_HuCCT1_GEM_VPA

value: GEM_VPA combination


title: Tregs purified from WT-CD3KO chimera, Biological Rep4

description: Gene expression data from CD4 Tregs NOT lacking TCR / MHC class II interactions in periphery (CD4+ TCRβ+ CD25+ cells purified from WT-CD3KO chimeras)

source_name: Tregs purified from WT-CD3KO chimera

value: WT-CD3KO chimera

value: CD4 Tregs NOT lacking TCR


title: dmyc_vs_cd2-48h-rep5


title: 002_HuCCT1_VPA

value: VPA


title: dmyc_vs_cd2-48h-rep4


title: Tregs purified from WT-CD3KO chimera, Biological Rep3


title: Tregs purified from WT-CD3KO chimera, Biological Rep1


title: Primary tumor 5

value: Female

value: No

tag: ki67 proliferation index

value: Varying 10 %

tag: age at diagnosis

tag: radically operated

value: Yes

tag: disease status

value: Deceased

tag: sample type

value: reference


title: Tregs purified from WT-CD3KO chimera, Biological Rep2

value: 6-8 weeks of age

value: Peripheral lymph nodes and spleen


title: dmyc_vs_cd2-12h-rep3

value: 12 hr


title: dmyc_vs_cd2-24h-rep5

value: 3rd instar larvae

value: 24 hr


title: dmyc_vs_cd2-12h-rep4

value: tub>dmyc>Gal4 transgene cells


title: dmyc_vs_cd2-24h-rep6

value: tub>cd2>Gal4 control cells


title: dmyc_vs_cd2-48h-rep1

value: 48 hr


title: dmyc_vs_cd2-24h-rep4


title: dmyc_vs_cd2-24h-rep3


title: dmyc_vs_cd2-24h-rep2


title: dmyc_vs_cd2-24h-rep1


title: dmyc_vs_cd2-12h-rep5


title: dmyc_vs_cd2-48h-rep3


title: dmyc_vs_cd2-48h-rep2


title: dmyc_vs_cd2-0h-rep6

value: 0 hr


title: dmyc_vs_cd2-12h-rep2


title: dmyc_vs_cd2-0h-rep5


title: dmyc_vs_cd2-12h-rep6


title: dmyc_vs_cd2-12h-rep1


title: dmyc_vs_cd2-0h-rep4


title: dmyc_vs_cd2-0h-rep3


title: dmyc_vs_cd2-0h-rep2


title: Papillary Thyroid Carcinoma Thy185

city: Ann Arbor

first: Rork

last: Kuick

state: MI

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

institute: University of Michigan

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Ann Arbor quantile-normalized trimmed-mean method, PMID: 15705192.

source_name: Papillary Thyroid Carcinoma

label_protocol: 3-5 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Total RNA was extracted from the tissue lysate using Trizol (Invitrogen) and cleanup performed with an RNeasy kit (Qiagen)

tag: tissue

value: Papillary Thyroid Carcinoma

tag: morphology of papillary carcinomas

value: follicular variant of papillary carcinoma

tag: ret/ptc translocation

value: N

tag: braf t1799a mutation

tag: pax8/pparg translocation

tag: kras, nras, or hras mutation

tag: comment

value: no comment


title: dmyc_vs_cd2-0h-rep1

tag: genotype/variation


title: Anaplastic Thyroid Carcinoma Thy187

source_name: Anaplastic Thyroid Carcinoma

value: Anaplastic Thyroid Carcinoma


title: Anaplastic Thyroid Carcinoma Thy022


title: Medullary Thyroid Carcinoma Thy153

source_name: Medullary Thyroid Carcinoma

value: Medullary Thyroid Carcinoma


title: Anaplastic Thyroid Carcinoma Thy182_2

value: Y


title: Anaplastic Thyroid Carcinoma Thy001


title: Papillary Thyroid Carcinoma Thy149


title: Medullary Thyroid Carcinoma Thy236


title: Papillary Thyroid Carcinoma Thy006

value: classical type of papillary carcinoma


title: Papillary Thyroid Carcinoma Thy073


title: Papillary Thyroid Carcinoma Thy140


title: Papillary Thyroid Carcinoma Thy048


title: Papillary Thyroid Carcinoma Thy098


title: Papillary Thyroid Carcinoma Thy237

value: tall cell variant of papillary carcinoma


title: Papillary Thyroid Carcinoma Thy196


title: Papillary Thyroid Carcinoma Thy182_1


title: Papillary Thyroid Carcinoma Thy191


title: Papillary Thyroid Carcinoma Thy181


title: Papillary Thyroid Carcinoma Thy186


title: Papillary Thyroid Carcinoma Thy158


title: Papillary Thyroid Carcinoma Thy049


title: Papillary Thyroid Carcinoma Thy183


title: Papillary Thyroid Carcinoma Thy105


title: Papillary Thyroid Carcinoma Thy194


title: Papillary Thyroid Carcinoma Thy180


title: Papillary Thyroid Carcinoma Thy099


title: Papillary Thyroid Carcinoma Thy120


title: Papillary Thyroid Carcinoma Thy101


title: Papillary Thyroid Carcinoma Thy077


title: Papillary Thyroid Carcinoma Thy092


title: Papillary Thyroid Carcinoma Thy074


title: Papillary Thyroid Carcinoma Thy035


title: Papillary Thyroid Carcinoma Thy045


title: Papillary Thyroid Carcinoma Thy141


title: Papillary Thyroid Carcinoma Thy026


title: Papillary Thyroid Carcinoma Thy009


title: Papillary Thyroid Carcinoma Thy152

value: Tricky RET/PTC. Discussed in PMID:16007166.


title: Papillary Thyroid Carcinoma Thy072


title: Papillary Thyroid Carcinoma Thy179


title: Papillary Thyroid Carcinoma Thy043


title: Papillary Thyroid Carcinoma Thy008


title: Papillary Thyroid Carcinoma Thy004


title: Papillary Thyroid Carcinoma Thy174


title: Papillary Thyroid Carcinoma Thy178


title: Papillary Thyroid Carcinoma Thy176


title: Papillary Thyroid Carcinoma Thy171


title: Papillary Thyroid Carcinoma Thy190


title: Papillary Thyroid Carcinoma Thy175


title: Papillary Thyroid Carcinoma Thy164


title: Papillary Thyroid Carcinoma Thy038


title: L1 vs L3i - repeat 1 - rev. label - mAdbID:103423

city: Bethesda

first: Roshan

last: Ramanathan

state: MD

address: 4 Center Drive

department: NIAID

institute: National Institutes of Health

description: mAdb experiment ID: 103423

hyb_protocol: Hybridization Protocol Other: Labeled samples were combined with blocking buffer composed of poly(dA), yeast tRNA, and human Cot-1, with 25% formamide/5× SSC/0.2% SDS to a total volume of 60 ul. After heating the sample (95°C for 3 minutes), it was centrifuged (12,000 rpm × 3 minutes) and 58 ul of the sample (1.6 micrograms of labeled cDNA) was loaded onto the microarray chip. The microarray chips were hybridized overnight at 45°C using the microarray user interface hybridization system (MAUI; BioMicro Systems, Inc., Salt Lake City, UT). The following day, the chips were washed twice in 1× SSC/0.05% SDS buffer (3 minutes each wash) and twice in 0.1× SSC buffer (5 minutes each wash).

scan_protocol: Scan_MicronsPerPixelX: 5 Scan_MicronsPerPixelY: 5 Scan_ScannerName: Axon Instruments (V1.00) GenePix 4000B [83871] unknown Scanning Protocol Other: The microarray chips were imaged using a 4000 B scanner (Axon Instruments, Sunnyvale, CA).

data_processing:
Data Processing Protocol - rev. label
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. Spot values were calculated using a linear lowess dye normalization. Further, the 50th percentile of a subset of all the ribosomal genes in the array was applied to all spot values. Within array multiple occurences of Gene Symbol were reduced to a single instance by averaging ratios (Cy3/Cy5) in log2 space.

organism: Strongyloides stercoralis

source_name: L1 stage larvae - Cy5

label_protocol:
Cy5 Labeling Protocol
Other: RNA samples from L1- or L3i-stage S. stercoralis were co-hybridized using Cy5 label to discriminate the relative level of target bound to the microarray probe. Fluorescent-labeled cDNA targets were prepared from total RNA using the Ovations amino-allyl kit (NuGEN, San Carlos, CA) according to the manufacturer's protocol.

extract_protocol:
Sample Extraction Protocol
Other: Total RNA was extracted by thawing samples at 37°C in a warm water bath and centrifuging at 4°C (805 X g) for 10 minutes to obtain a pellet. The pellet was frozen in liquid nitrogen and ground thoroughly with an autoclaved mortar and pestle and subsequently purified using an RNeasy mini kit (Qiagen, Valencia, CA) following the manufacturer's protocol.

tag: developmental stage

value: L1 stage larvae

tag: other

value: Sample Pooling Protocol:All larvae used in this analysis were obtained from laboratory dogs infected with S. stercoralis, UPD strain. Post parasitic L1 larvae were recovered from freshly deposited stool samples. Fecal samples from dogs were processed using the charcoal coproculture followed by Baermann funnel technique. S. stercoralis L1 were decontaminated by three washes with PBS containing antibiotic cocktail. Decontaminated parasites were subsequently stored in Trizol reagent (Invitrogen, San Diego, CA) at –80°C. Using this method, 30,700 post-parasitic L1 larvae were collected. Pooled samples were thawed at 37°C in a warm water bath and centrifuged at 4°C (805 X g) for 10 minutes to obtain a pellet. The pellet was frozen in liquid nitrogen and ground thoroughly with an autoclaved mortar and pestle.

source_name: L3i stage larvae - Cy3

label_protocol:
Cy3 Labeling Protocol
Other: RNA samples from L1- or L3i-stage S. stercoralis were co-hybridized using Cy3 label to discriminate the relative level of target bound to the microarray probe. Fluorescent-labeled cDNA targets were prepared from total RNA using the Ovations amino-allyl kit (NuGEN, San Carlos, CA) according to the manufacturer's protocol.

value: L3i stage larvae

value: Sample Pooling Protocol:All larvae used in this analysis were obtained from laboratory dogs infected with S. stercoralis, UPD strain. L3i larvae were recovered after 3–5 days of incubation of stool at 22°C. Fecal samples from dogs were processed using the charcoal coproculture followed by Baermann funnel technique. S. stercoralis L3i underwent surface decontamination by migration through low-melting-point agarose. Decontaminated parasites were subsequently stored in Trizol reagent (Invitrogen, San Diego, CA) at –80°C. Using this method, 50,000 L3i S. stercoralis larvae were collected. Pooled samples were thawed at 37°C in a warm water bath and centrifuged at 4°C (805 X g) for 10 minutes to obtain a pellet. The pellet was frozen in liquid nitrogen and ground thoroughly with an autoclaved mortar and pestle.


title: L3i vs L1- repeat 4 - mAdbID:103422

description: mAdb experiment ID: 103422

data_processing:
Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. Spot values were calculated using a linear lowess dye normalization. Further, the 50th percentile of a subset of all the ribosomal genes in the array was applied to all spot values. Within array multiple occurences of Gene Symbol were reduced to a single instance by averaging ratios (Cy5/Cy3) in log2 space.

source_name: L1 stage larvae - Cy3

source_name: L3i stage larvae - Cy5


title: L3i vs L1- repeat 3 - mAdbID:103421

description: mAdb experiment ID: 103421


title: L3i vs L1- repeat 2 - mAdbID:103420

description: mAdb experiment ID: 103420


title: Papillary Thyroid Carcinoma Thy177


title: Papillary Thyroid Carcinoma Thy169


title: Papillary Thyroid Carcinoma Thy189


title: Papillary Thyroid Carcinoma Thy132


title: Papillary Thyroid Carcinoma Thy135


title: Papillary Thyroid Carcinoma Thy137


title: Papillary Thyroid Carcinoma Thy040


title: Oncocytic Thyroid Carcinoma Thy139

source_name: Oncocytic Thyroid Carcinoma

value: Oncocytic Thyroid Carcinoma


title: Oncocytic Thyroid Carcinoma Thy145


title: Oncocytic Thyroid Carcinoma Thy233


title: Oncocytic Thyroid Carcinoma Thy234


title: Oncocytic Thyroid Carcinoma Thy197


title: Oncocytic Thyroid Carcinoma Thy094


title: Oncocytic Thyroid Carcinoma Thy235


title: Oncocytic Thyroid Adenoma Thy232

source_name: Oncocytic Thyroid Adenoma

value: Oncocytic Thyroid Adenoma


title: Oncocytic Thyroid Carcinoma Thy039


title: Oncocytic Thyroid Adenoma Thy231


title: Oncocytic Thyroid Adenoma Thy226


title: Oncocytic Thyroid Adenoma Thy227


title: Oncocytic Thyroid Adenoma Thy229


title: Oncocytic Thyroid Adenoma Thy230


title: Oncocytic Thyroid Adenoma Thy228


title: Follicular Thyroid Adenoma Thy224

source_name: Follicular Thyroid Adenoma

value: Follicular Thyroid Adenoma


title: EM.P2.C30.A

city: Paris

first: Edi

last: Prifti

state: IDF

address: 15, rue de l'école de Médecine

institute: INSERM UMRS-U872

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with lumi-package in R statistical language

source_name: human adipose tissue

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

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

value: subcutaneous adipose tissue

tag: patient id

value: EM

tag: period

tag: diet

value: LC-CONV

tag: time

value: 120 days


title: PA.P1.K5.A

value: PA

value: LC-P-LGI

value: 5 days


title: Follicular Thyroid Adenoma Thy223

value: no comment


title: NO.P1.C5.A

value: NO


title: EM.P1.K30.A

value: 30 days


title: PA.P1.K30.A


title: MA.P2.K30.A

value: MA


title: NO.P2.K30.A


title: NO.P1.C30.A


title: NO.P1.C0.A

value: 0 days


title: PA.P2.C30.A


title: MA.P2.K0.A

value: 90 days


title: EM.P2.C5.A

value: 95 days


title: MA.P1.C5.A


title: NO.P2.K0.A


title: MA.P1.C0.A


title: PA.P2.C0.A


title: EM.P1.K5.A


title: MA.P1.C30.A


title: EM.P2.C0.A


title: PA.P1.K0.A


title: NO.P2.K5.A


title: Follicular Thyroid Adenoma Thy222


title: Follicular Thyroid Adenoma Thy221


title: YV.P2.K30.A

value: YV


title: YV.P2.K5.A


title: Follicular Thyroid Adenoma Thy219


title: YV.P2.K0.A


title: YV.P1.C30.A


title: YV.P1.C0.A


title: VA.P2.C30.A

value: VA


title: Follicular Thyroid Adenoma Thy220

value: Follicular Thyroid Adenoma


title: Follicular Thyroid Adenoma Thy042

value: N

value: Y


title: YV.P1.C5.A

value: subcutaneous adipose tissue

value: LC-CONV


title: Follicular Thyroid Adenoma Thy030


title: EM.P1.K0.A

value: EM


title: Follicular Thyroid Adenoma Thy024


title: Follicular Thyroid Adenoma Thy023


title: VA.P2.C5.A


title: VA.P1.K0.A

value: LC-P-LGI


title: GE.P2.C30.A

value: GE

value: 120 days


title: VA.P2.C0.A


title: GE.P2.C5.A


title: VA.P1.K5.A

value: 5 days


title: GE.P1.K30.A

value: 30 days


title: GE.P1.K5.A


title: GE.P2.C0.A


title: Brain_Anaplastic-Oligodendroglioma-gradeIII_1017

city: TOLEDO

first: Barbara

last: Melendez

address: AVDA. BARBER 30

department: UNIDAD DE INVESTIGACION DE PATOLOGIA MOLECULAR

institute: HOSPITAL VIRGEN DE LA SALUD

hyb_protocol: 1 μg of tumoral and reference RNA was reverse transcribed into cDNA using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). Test and reference cDNA was transcribed into cRNA by using T7 RNA polymerase, and labeled with either cyanine 5 (Cy5)- or cyanine 3 (Cy3)-CTP, respectively (Perkin Elmer, Wellesley, MA). Fluorescent cRNA was purified with RNeasy Mini columns (Qiagen, Valencia, CA). The quality of each cRNA sample was verified by total yield and its specificity calculated based on NanoDrop ND-1000 spectrophotometer measurements (NanoDrop Technologies). Hybridization was carried out at 65ºC for 17 h in a humidified chamber.

scan_protocol: Arrays were scanned using an Axon GenePix 4100A confocal scanner. Images were analyzed using GenePix Pro 6.0 software (Axon Instruments Inc., Union City, CA).

data_processing: Fluorescence ratios of Cy5/Cy3 were normalized for each oligo microarray by the print-tip loess method and background subtraction with the Diagnosis and Normalization Array Data (DNMAD) tool. After normalizing and filtering the data, replicates were averaged using the Gene Expression Pattern Analysis Suite (GEPAS, version 4. 0).

label_protocol: 1 μg of tumoral RNA was reverse transcribed into cDNA using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). Test cDNA was transcribed into cRNA by using T7 RNA polymerase, and labeled with cyanine 5 (Cy5 (Perkin Elmer, Wellesley, MA).

extract_protocol: Total RNA was extracted from frozen tissue by the Trizol RNA isolation method (Life Technologies, Grand Island, NY).

value: brain

tag: disease state

value: oligodendroglioma (anaplastic)

tag: who grade

value: iii

tag: sample id

tag: tumor grade

value: High grade oligodendroglial tumor

source_name: Universal Human RNA_Pool of cell lines_Comercially purchased from Stratagene

label_protocol: 1 μg of tumoral RNA was reverse transcribed into cDNA using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). Test cDNA was transcribed into cRNA by using T7 RNA polymerase, and labeled with cyanine 3 (Cy3 (Perkin Elmer, Wellesley, MA).

extract_protocol: Universal Human RNA is comercially purchased from Stratagene, La Jolla, CA.

tag: reference

value: Universal human RNA, pool of cell lines (Stratagene)


title: VA.P1.K30.A

tag: tissue

value: VA


title: Normal Thyroid Thy027

source_name: Normal Thyroid

value: Normal Thyroid

tag: morphology of papillary carcinomas

tag: ret/ptc translocation

tag: braf t1799a mutation

value: no comment


title: Brain_Anaplastic-Oligodendroglioma-gradeIII_1765


title: Brain_Anaplastic-Oligodendroglioma-gradeIII_1770


title: Normal Thyroid Thy012

tag: pax8/pparg translocation

tag: kras, nras, or hras mutation

tag: comment


title: Normal Thyroid Thy013


title: Brain_Anaplastic-Oligodendroglioma-gradeIII_1763


title: GE.P1.K0.A

value: 0 days


title: Follicular Thyroid Carcinoma Thy203

source_name: Follicular Thyroid Carcinoma

value: Follicular Thyroid Carcinoma

value: N

value: Tricky PAX8/PPARG.  Discussed in PMID:16609007


title: OU.P2.C5.A

value: subcutaneous adipose tissue

value: OU

value: LC-CONV

value: 95 days


title: Normal Thyroid Thy015

value: A few normal C-cells


title: OU.P2.C0.A

value: 90 days


title: Follicular Thyroid Carcinoma Thy215

value: Y


title: Brain_Anaplastic-Oligodendroglioma-gradeIII_1014

value: brain

value: oligodendroglioma (anaplastic)

value: iii


title: Follicular Thyroid Carcinoma Thy214


title: OU.P2.C30.A

value: 120 days


title: OU.P1.K5.A

value: LC-P-LGI

value: 5 days


title: Brain_Anaplastic-Oligodendroglioma-gradeIII_1518

value: High grade oligodendroglial tumor

value: Universal human RNA, pool of cell lines (Stratagene)


title: AU.P1.K30.A

value: AU

value: 30 days


title: AU.P2.C5.A

value: subcutaneous adipose tissue


title: OU.P1.K0.A

value: OU

value: 0 days


title: AU.P2.C0.A

value: LC-CONV


title: OU.P1.K30.A


title: Brain_Oligodendroglioma-gradeII_939

value: oligodendroglioma

value: ii

value: Low grade oligodendroglial tumor


title: FI.P2.K30.A

value: FI


title: Brain_Oligodendroglioma-gradeII_1768

value: brain


title: Follicular Thyroid Carcinoma Thy211

value: Follicular Thyroid Carcinoma

value: Y

value: no comment


title: AU.P1.K0.A

value: LC-P-LGI


title: AU.P2.C30.A

value: 120 days


title: Brain_Oligodendroglioma-gradeII_1015

value: Universal human RNA, pool of cell lines (Stratagene)


title: AU.P1.K5.A

value: AU

value: 5 days


title: Follicular Thyroid Carcinoma Thy213

value: N


title: Brain_Oligodendroglioma-gradeII_937


title: Follicular Thyroid Carcinoma Thy112


title: Brain_Oligodendroglioma-gradeII_935


title: FI.P1.C30.A

value: subcutaneous adipose tissue

value: 30 days


title: FI.P1.C5.A

value: LC-CONV


title: FI.P2.K5.A

value: 95 days


title: FI.P2.K0.A

value: 90 days


title: Follicular Thyroid Carcinoma Thy204


title: Follicular Thyroid Carcinoma Thy202


title: FI.P1.C0.A

value: 0 days


title: PAI.P2.C0.A

value: PAI


title: Brain_Oligodendroglioma-gradeII_936

value: brain

value: oligodendroglioma

value: ii

value: Low grade oligodendroglial tumor


title: Follicular Thyroid Carcinoma Thy201

value: Follicular Thyroid Carcinoma

value: Y

value: no comment


title: PAI.P2.C30.A

value: 120 days


title: Brain_Oligodendroglioma-gradeII_947

value: Universal human RNA, pool of cell lines (Stratagene)


title: PAI.P2.C5.A


title: JA.P2.K30.A

value: JA

value: LC-P-LGI


title: Brain_Oligodendroglioma-gradeII_938


title: PAI.P1.K0.A

value: subcutaneous adipose tissue


title: Follicular Thyroid Carcinoma Thy150

value: N


title: PAI.P1.K30.A

value: 30 days


title: JA.P2.K5.A

value: 95 days


title: JA.P2.K0.A

value: 90 days


title: Brain_Oligodendroglioma-gradeII_901


title: Brain_Oligodendroglioma-gradeII_902


title: Follicular Thyroid Carcinoma Thy121


title: Infected leaves_14dpi_rep3

city: Thiverval-Grignon

first: Isabelle

last: Fudal

address: avenue Lucien Bretignieres

institute: INRA

hyb_protocol: Hybridization by NimbleGen Company.

scan_protocol: Scanning by NimbleGen Company.

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

organism:
Brassica napus
Plenodomus lingam

source_name: infected oilseed rape leaves 14 days post infection

label_protocol: Labelling by NimbleGen Company.

growth_protocol: Mycelium was grown during one week in Fries liquid medium. Oilseed rape leaves were infected with Leptosphaeria maculans (isolate v23.1.3) spores and harvested 7 and 14 days post inoculation.

extract_protocol: RNA extraction was carried out using TRIzol reagent (Invitrogen) according to the manufacturer’s protocol. Total RNA was treated with DNase I RNase-Free (New England Biolabs).

tag: strain

value: derived from infected Brassica napus leaves

tag: time point

value: 14 days post infection


title: Follicular Thyroid Carcinoma Thy085


title: PAI.P1.K5.A

tag: patient id

value: PAI

tag: period

value: 5 days


title: JA.P1.C30.A

tag: diet

value: LC-CONV

tag: time


title: Brain_Anaplastic-Oligoastrocytoma-gradeIII_1882

value: brain

tag: disease state

value: oligoastrocytoma (anaplastic)

tag: who grade

value: iii

value: High grade oligodendroglial tumor


title: Brain_Oligodendroglioma-gradeII_903

value: oligodendroglioma

value: ii

tag: sample id

tag: tumor grade

value: Low grade oligodendroglial tumor

value: Universal human RNA, pool of cell lines (Stratagene)


title: HUVEC-on matrigel (8hr)

city: seoul

first: Hongryeol

last: Park

address: seodaemun-gu yonsei-ro

department: biochemstry

country: South Korea

institute: yonsei univ.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized to the Affymetrix HG-U133 plus 2.0 chip according to the protocols provided by the manufacturer.

scan_protocol: GeneChips were scanned using the GeneArray Scanner 7GPLUS

data_processing: The data were normalised using GC-RMA method with GCRMA version 2.14.1 in R/Bioconductor package.

source_name: Human umbilical vein endothelial cell on matrigel, 8hr

label_protocol: Biotinylated cRNA were prepared from 2 microg total RNA using the BioArray-High-Yield-RNA-Transcript-Labeling-Kit (Enzo, Farmingdale, NY).

extract_protocol: HUVECs from human umbilical vein were cultured on matrigel coated plate for 0.5hr, 8hr,18hr. RNA was extracted using the Invisorb RNA Kit II (Invitek, Berlin, Germany) according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

tag: cell type

value: Human umbilical vein endothelial cell


title: HUVEC-on matrigel (18hr)

source_name: Human umbilical vein endothelial cell on matrigel, 18hr


title: Follicular Thyroid Carcinoma Thy093

tag: tissue

value: Follicular Thyroid Carcinoma

tag: morphology of papillary carcinomas

value: N

value: Y

value: no comment


title: JA.P1.C0.A

value: subcutaneous adipose tissue

value: JA

value: 0 days


title: Brain_Anaplastic-Oligoastrocytoma-gradeIII_1881

tag: reference


title: JA.P1.C5.A

value: LC-CONV

value: 5 days


title: Infected leaves_14dpi_rep2

value: derived from infected Brassica napus leaves

value: 14 days post infection


title: Infected leaves_14dpi_rep1


title: Brain_Anaplastic-Oligoastrocytoma-gradeIII_1632

value: brain

value: oligoastrocytoma (anaplastic)

value: iii

value: High grade oligodendroglial tumor


title: Brain_Anaplastic-Oligoastrocytoma-gradeIII_1056

value: Universal human RNA, pool of cell lines (Stratagene)


title: Infected leaves_7dpi_rep3

source_name: infected oilseed rape leaves 7 days post infection

value: 7 days post infection


title: HUVEC-on matrigel (0.5hr)

source_name: Human umbilical vein endothelial cell on matrigel, 0.5hr

value: Human umbilical vein endothelial cell


title: Blimp1 gfp/gfp Treg, rep1

city: Clayton

first: Wei

last: Shi

state: Victoria

address: Wellington Rd

institute: Monash University

hyb_protocol: Labeled cRNA (1.5 μg) was prepared for hybridization to Illumina mouseWG-6 V1.1 (R3) BeadChips following the standard Illumina protocol. The bead arrays were washed and blocked in E1 buffer for 10 min in a rocking incubator and 10 additional minutes with 2 ml of E1 buffer. They were then stained with streptavidin-conjugated Cy3 fluorescent dye. The fluorescent reagent was washed away with E1BC solution. The arrays were finally air dried.

scan_protocol: Arrays were scanned by an Illumina BeadArray Reader (Illumina California USA). The default setting was used.

data_processing: Non-normalized summary probe profiles were output from BeadStudio and analyzed using the limma packages of the Bioconductor open-source software project (http://www.bioconductor.org). The raw intensities were normexp background corrected with offset 16, and normalized by the neqc function.

source_name: Bone marrow

label_protocol: We labeled up to 500 ng with Cy3 using the Total Prep RNA amplification kit (Ambion).

extract_protocol: RNA from regulatory T cells were prepared with the RNeasy Micro kit (Qiagen). RNA quality was ascertained using the Agilent Bioanalyser 2100 with the NanoChip protocol.

value: bone marrow

value: regulatory T cells

tag: genotype

value: Blimp1 gfp/gfp

tag: beadchip barcode

tag: beadchip section

value: D


title: Brain_Anaplastic-Oligoastrocytoma-gradeIII_1079


title: Blimp1 +/gfp Treg, rep3

tag: strain

value: Blimp1 +/gfp

value: F


title: Blimp1 gfp/gfp Treg, rep2

value: E


title: Infected leaves_7dpi_rep1

tag: time point


title: Infected leaves_7dpi_rep2


title: SP cell, biological replicate3

city: London

last: Dai

address: Du Cane Road

department: Sugery and Cancer

country: United Kingdom

institute: Imperial College London

description: Gene expression data from IGROV1 SP cell

hyb_protocol: The NuGEN hybtidsation v1.0 protocol was followed for hybridising labelled DNA to standard GeneChips with 11 micron feature size. This hybridisation protocol is derived from the NuGEN FL-Ovation cDNA Biotin Module v2 user guide and the Affymetrix GeneChip Expression Analysis Technical Manual

scan_protocol: The Affymetrix GeneChip scanner 3000 running GCOS software

data_processing: The data were analyzed in R (version 2.8.1) using Affy package and RMA as the normalisation method

source_name: IGROV1, SP cell

label_protocol: The RNA was amplified using the WT-Ovation Pico target pre v 1.0 protocol which was derived from the NuGEN WT-Ovation Pico RNA Amplication system (WTO_Pico_UserGuide) and the NuGEN FL-Ovation cNDA Biotin Module v2 (FLBv2_User_Guide)

growth_protocol: IGROV1 cell line was maintained in RPMI 1640 (Invitrogen, Paisley, UK) containing 10% fetal bovine serum (PAA Laboratories, Yeovil, UK) in humidified 5% CO2 in air incubators at 37 ̊C

extract_protocol: Cells isolated by FACS and RNA isolated using Arcturus Pico Pure Kit

treatment_protocol: Hoechst 33342 cell sorting

value: side population cell

tag: cell line source


title: Mycelium_rep2

organism: Plenodomus lingam

source_name: mycelium grown in in vitro liquid Fries medium

value: mycelium

value: 7 days of growth


title: SP cell, biological replicate2


title: Blimp1 +/gfp Treg, rep1


title: Mycelium_rep3


title: non-SP cell, biological replicate2

description: Gene expression data from IGROV1 non-SP cell

source_name: IGROV1, non-SP cell

value: non-side population cell


title: Brain_Oligoastrocytoma-gradeII_1976

value: brain

value: oligoastrocytoma

value: ii

value: Low grade oligodendroglial tumor


title: Blimp1 gfp/gfp Treg, rep3


title: SP cell, biological replicate1


title: Brain_Oligoastrocytoma-gradeII_1971

value: Universal human RNA, pool of cell lines (Stratagene)


title: Blimp1 +/gfp Treg, rep2


title: Brain_Anaplastic-Oligoastrocytoma-gradeIII_886

value: oligoastrocytoma (anaplastic)

value: iii

value: High grade oligodendroglial tumor


title: Brain_Oligoastrocytoma-gradeII_1967


title: STAT5-deficient T cells, cultured 3 days in Th17 condition (expression)

first: Golnaz

last: Vahedi

address: 9000 Rockville Pike Bldg 10 Rm 13C101A

department: NIAMS

hyb_protocol: aRNA was hybridized to GeneChip Mouse Genome 430 2.0 Arrays from Affymetrix according the manufacturers protocol.

scan_protocol: According the manufacturers protocol

data_processing: Affymetrix Power Tools using apt-probeset-summarize & rma-sketch.

source_name: primary naïve CD4+ T cells from spleen and lymph nodes

label_protocol: RNA was biotin-labeled using the MessageAmpII-Biotin Enhanced Kit from Ambion

growth_protocol: Control and STAT-deficient naïve CD4+CD44-CD62L+ T cells were isolated and sorted on the flow cytometer. Cells from STAT3 WT and STAT3 KO were cultured for 72h with platebound anti-CD3, anti-CD28 (10 mg/ml each), IL-6 (20 ng/ml) TGF-beta (2 ng/ml) , anti-IL-2 (10 ug/ml) and anti-IL-4 (10 mg/ml) for 3 days. Cells from STAT5 WT and STAT5 KO were cultured for 72h with platebound anti-CD3, anti-CD28 (10 mg/ml each), IL-6 (20 ng/ml) TGF-beta (2 ng/ml) , IL-2 (100IU/ml) and anti-IL-4 (10 mg/ml) for 3 days.

extract_protocol: Total RNA was extracted using the MirVana RNA Isolation kit from Ambion.

treatment_protocol: After 3 day culture in vitro, cells were harvested and lysised with 300 ul lysis buffer from the MirVana RNA Isolation kit.

tag: genotype/variation

value: CD4-Cre stat5 fl/fl OT2 (STAT5 wild type)


title: STAT3-wild type T cells, cultured 3 days in Th17 condition (expression)

value: stat3 fl/fl OT2 (STAT3 wild type)

value: primary naïve CD4+ T cells from spleen and lymph nodes


title: non-SP cell, biological replicate3


title: STAT5-wild type T cells, cultured 3 days in Th17 condition (expression)

value: stat5 fl/fl OT2 (STAT5 wild type)


title: non-SP cell, biological replicate1


title: Mycelium_rep1


title: STAT3-deficient T cells, cultured 3 days in Th17 condition (expression)

value: CD4-Cre stat3 fl/fl OT2 (STAT3 wild type)


title: CCdl54TT_CCdl67TF_3d

status: Public on Feb 08 2011

city: Stanford

first: Junhee

last: Seok

state: CA

address: 318 Campus Drive W310 - Davis Lab

institute: Stanford University

hyb_protocol: standard Affymetrix procedure

scan_protocol: standard Affymetrix procedure

data_processing: RMA using Affymetrix Expression Console

source_name: Breast

label_protocol: cRNA synthesis was performed with 2 µg of total cellular RNA, and labelled based on the protocol outlined by Affymetrix Inc. (Santa Clara, CA), with few modifications

extract_protocol: total epithelial cell RNA was directly extracted from duplicate wells of each treatment using the Rneasy kit (Qiagen)

tag: sample name

tag: tumor sample id

tag: tumor sample histological grade

value: high, T2

tag: fibroblast sample id

tag: fibroblast sample histological grade

value: low, TF1

value: breat cancer tumor

tag: treatment

value: tumor co-cultured with fibroblast


title: NME2 mock (IgG) 3

type: genomic

city: Delhi

first: Vinod

middle: Kumar

last: Yadav

state: Delhi

address: Mall Road

department: Bioinformatics

country: India

institute: IGIB

description: Chromatin immunoprecipitated DNA

hyb_protocol: The uracil glycosilase treatment, streptavidin/phycoerythrin labeling, hybridization and microarray scanning were performed as per Affymetrix Chromatin Immunoprecipitation Assay Protocol (http://www.affymetrix.com/products/arrays/specific/human_promoter.affx)

data_processing: DTT files obtained were processed by GCOS to generate CEL files which upon processing by TAS gave signal and P-values for each array. The signal intensities obtained were averaged across three experiments. The average was used for ChIP-chip peak generation using ChIPOTle at default settings. The results file are .CHP files. For each array two CHP files are generated; one containing signal and the other containing p values.

molecule: genomic DNA

source_name: NME2 mock (IgG)

growth_protocol: Lung epithelial adenocarcinoma A549 cells were grown in DMEM medium supplemented with 10% FBS. Cells were kept at 37 degrees in a humidified incubator with 5% CO2.

extract_protocol: A549 cells were fixed with 1% formaldehyde for 10 minutes and lysed. Chromatin was sheared to an average size of ~0.5 to 1kb using a Misonix 3000 sonicator and incubated overnight with antibody at 40C. Immune complexes were collected using herring sperm DNA saturated protein –A sepharose in 3 hours and washed extensively. Chelex-100 resin was used to extract DNA from immunoprecipitated chromatin.

treatment_protocol: A549 cells were transfected with pcDNA plasmid to over express NME2 tagged with MYC epitope. After 48 hours of transfection, cells were formaldehyde fixed and processed for chromatin immunoprecipitation assay.

tag: tissue type

value: lung adenocarcinoma

tag: cell line


title: CCdl672TT_CCdl67TF_3d

tag: time

tag: tissue


title: CCdl68TT_CCdl257TF_3d

value: low, T1

value: high, TF2


title: CCdl22TT_CCdl257TF_3d


title: CCdl1797TT_CCdl67TF_3d


title: CCdl257T_CCdl257TF_3d


title: CCdl1797TT_CCdl257TF_3d


title: CCdl672TT_none_3d

tag: treatment class

value: tumor not co-cultured with fibroblast


title: CCdl257T_CCdl67TF_3d


title: CCdl1797TT_none_3d


title: CCdl67TT_CCdl257TF_3d


title: CCdl54TT_none_3d


title: CCdl257T_none_3d


title: CCdl22TT_none_3d


title: NME2 ChIP 2

description: Chromatin immunoprecipitated DNA

scan_protocol: The uracil glycosilase treatment, streptavidin/phycoerythrin labeling, hybridization and microarray scanning were performed as per Affymetrix Chromatin Immunoprecipitation Assay Protocol (http://www.affymetrix.com/products/arrays/specific/human_promoter.affx)

source_name: NME2 ChIP


title: NME2 ChIP 1

description: Chromatin immunoprecipitated DNA

label_protocol: The uracil glycosilase treatment, streptavidin/phycoerythrin labeling, hybridization and microarray scanning were performed as per Affymetrix Chromatin Immunoprecipitation Assay Protocol (http://www.affymetrix.com/products/arrays/specific/human_promoter.affx)


title: NME2 mock (IgG) 1

description: Chromatin immunoprecipitated DNA


title: CCdl68TT_none_3d


title: CCdl67TT_none_3d


title: NME2 Control A549 cell Replicate2

hyb_protocol: Subsequently, 15 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix HU133 plus 2.0 array.

scan_protocol: The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450, followed by scanning on a GeneChip Scanner 3000.

data_processing: The results were quantified and analyzed using GCOS 1.1.1 software (Affymetrix, Inc.) using default values (Scaling, Target Signal Intensity = 500; Normalization, All Probe Sets; Parameters, all set at default values).

source_name: Control A549

label_protocol: Single-stranded, then double-stranded cDNA was synthesized from the poly(A)+ mRNA present in the isolated total RNA (5 ug total RNA starting material each sample reaction) using the one cycle cDNA synthesis kit (Affymetrix, Inc.,Santa Clara CA ). A portion of the resulting ds cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction (IVT), using the Gene Chip IVT labeling kit.20ug of the resulting biotin-tagged cRNA was fragmented to strands of 35-200 bases in length following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual).

extract_protocol: Isolated total RNA samples were processed as recommended by Affymetrix, Inc. (Affymetrix GeneChip Expression Analysis Technical Manual, Affymetric, Inc., Santa Clara, CA). In brief, total RNA was initially isolated using TRI Reagent (Sigma, St. Louis, MO), and passed through an RNeasy spin column (Qiagen, Chatsworth, CA) for further clean up. All starting total RNA samples were quality assessed prior to beginning target preparation/processing steps by running out a small amount of each sample (typically 25-250 ng/well) onto a RNA Lab-On-A-Chip (Caliper Technologies Corp., Mountain View, CA) that was evaluated on an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).


title: CCdl67TT_CCdl67TF_3d


title: NME2 Control A549 cell Replicate1


title: NME2 mock (IgG) 2

description: Chromatin immunoprecipitated DNA


title: NME2 Depleted A549 cell Replicate3

source_name: NME2 Depleted A549

extract_protocol: Isolated total RNA samples were processed as recommended by Affymetrix, Inc. (Affymetrix GeneChip Expression Analysis Technical Manual, Affymetric, Inc., Santa Clara, CA). In brief, total RNA was initially isolated using TRI Reagent (Sigma, St. Louis, MO), and passed through an RNeasy spin column (Qiagen, Chatsworth, CA) for further clean up.  All starting total RNA samples were quality assessed prior to beginning target preparation/processing steps by running out a small amount of each sample (typically 25-250 ng/well) onto a RNA Lab-On-A-Chip (Caliper Technologies Corp., Mountain View, CA) that was evaluated on an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).


title: NME2 Depleted A549 cell Replicate1


title: NME2 depleted A549 cell Replicate2


title: NME2 ChIP 3

description: Chromatin immunoprecipitated DNA


title: Brain_Anaplastic-Oligoastrocytoma-gradeIII_1018

value: brain

tag: disease state

tag: who grade

tag: sample id

tag: tumor grade

source_name: Universal Human RNA_Pool of cell lines_Comercially purchased from Stratagene

tag: reference

value: Universal human RNA, pool of cell lines (Stratagene)


title: NME2 Control A549 cell Replicate3


title: 348161

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

description:
SSEA-1- vs SSEA-1+
Date:2008/05/06

hyb_protocol: Agilent : 2500.0 ng at 48 degree_C during 17 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Interslide norm. : vsn, Intraslide norm. : none, Background norm. : none, Software used : rscript --> VALUE data obtained from log of processed Red signal/processed Green signal.

label_protocol: Ulysis + MirVana

extract_protocol: Chomzynski

tag: cell type

tag: extract

value: H9 CTL

tag: sample

tag: subject


title: HCC70-N

city: Kyoto

first: Akira

last: Myomoto

address: Yoshida-Shimoadachi

institute: Kyoto Univ.

description: Total miRNA was spotted on 934 features. We used only human miRNA in our analysis. Therefore, a total of 68 features were already eliminated from the all features on this array.

hyb_protocol: The labeled samples were individually hybridized onto DNA chip surface, and incubated at 42 ℃ for 16 hours.

scan_protocol: Washed and dried DNA chip in an ozone-removed environment was scanned using a ProScanArray™ microarray scanner. The obtained microarray images were analyzed using the Genepix Pro™ 4.0 software.

data_processing: The median values of the foreground signal minus the local background were represented as feature intensities. All data obtained from microarray experiments were normalized by a quantile normalization method, and filtered.

source_name: Hepatocellular Carcinoma in Milan Criteria Cases with Mild Liver Cirrhosis

label_protocol: For each patient, 500 ng of total RNA derived from tumor and non-tumor samples were labeled using miRCURY LNA™ microRNA Power Labeling Kits Hy5

extract_protocol: Tumor and non-tumor tissues were obtained and frozen in liquid nitrogen immediately after hepatic resection, and stored in liquid nitrogen until RNA extraction. Total RNA samples were extracted by a phenol-chloroform RNA extraction method.

value: Non-tumor


title: HCC69-N


title: HCC72-N


title: HCC73-N


title: 348159

description:
SSEA-1- vs SSEA-1+
Date:2008/05/06

hyb_protocol: Agilent : 3500.0 ng at 48 degree_C during 17 hours

value: H1 CTL


title: 348158

description:
HUESC vs HUESC-POU5F1
Date:2008/05/06

hyb_protocol: Agilent : 5000.0 ng at 48 degree_C during 17 hours

source_name: HUESC

value: HUESC

value: Hues 24 CTL

value: Hues 24 POU5F1


title: HCC67-N


title: HCC71-N


title: HCC61-N


title: HCC62-N


title: HCC65-N


title: HCC63-N


title: HCC64-N


title: HCC66-N


title: 348156

description:
SSEA-1+ vs SSEA-1-
Date:2008/05/06

value: HS 420 CTL


title: HCC60-N


title: 348160

description:
SSEA-1- vs SSEA-1+
Date:2008/05/06


title: 348157

description:
SSEA-1+ vs SSEA-1-
Date:2008/05/06


title: HCC57-N


title: HCC59-N


title: 348154

description:
HUESC-POU5F1 vs HUESC
Date:2008/05/06


title: HCC56-N


title: HCC68-N


title: HCC58-N


title: 348155

description:
SSEA-1+ vs SSEA-1-
Date:2008/05/06


title: ZF4 Repl 3

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

description: Gene expression in ZF4 cells

hyb_protocol: Arrays were hybridized for 17 hours (65 °C) and washed before scanning as per the protocol recommended by Agilent  (One-Color Microarray-Based Gene Expression Analysis (Low input Quick Amp Labeling)).

scan_protocol: The arrays were scanned with GenePix 4000b (Molecular Devices, Sunnyvale, CA, USA).

data_processing: Data processed with Bioconductor package Limma (3.4.4); backgroundCorrect('normexp', offset=50); normalizeBetweenArrays(method='quantile')

organism: Danio rerio

source_name: ZF4 cell line

label_protocol: Total RNA (200 ng) and spike-in control RNA was converted to cDNA, followed by cRNA synthesis and amplification, and then purification of cRNA. We followed the protocol from Agilent: One-Color Microarray-Based Gene Expression Analysis (Low input Quick Amp Labeling). This method uses T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- labeled CTP which generates cy3 labeled fluorescent cRNA.

growth_protocol: The ZF4 zebrafish embryo-derived cell line (Amerian Type Culture Collection) was cultured in vitro as described earlier (Driever W and Rangini Z (1993) In Vitro Cell Dev Biol Anim 0029A: 749-754).

extract_protocol: Cells (10e6) were suspended in 2 ml Trizol, incubated for 5 min, RNA extracted with chloroform, cells were sedimented (10,000 g). The upper phase was collected, glycogen was added and RNA precipitated with isopropanol for 10 min before centrifugation. The RNA pellet was washed with 75% ethanol and dissolved prior to DNase I treatment and clean-up using the RNeasy Kit (Qiagen). RNA samples were stored at -80oC until processed for microarray.


title: ZF4 Repl 4

description: Gene expression in ZF4 cells


title: ZF4 Repl 2

description: Gene expression in ZF4 cells


title: HCC55-N


title: HCC51-N


title: HCC49-N


title: HCC50-N


title: HCC52-N


title: HCC53-N


title: HCC47-N


title: HCC44-N


title: HCC45-N


title: HCC46-N


title: HCC34-N


title: HCC35-N


title: HCC43-N


title: HCC38-N


title: HCC41-N


title: HCC40-N


title: HCC42-N


title: HCC39-N


title: HCC36-N


title: HCC33-N


title: HCC28-N


title: HCC27-N


title: HCC30-N


title: HCC54-N


title: HCC31-N


title: HCC32-N


title: HCC29-N


title: HCC48-N


title: HCC37-N


title: HCC26-N


title: HCC22-N


title: HCC23-N


title: HCC25-N


title: HCC24-N


title: HCC20-N


title: HCC19-N


title: HCC17-N


title: HCC16-N


title: HCC10-N


title: HCC14-N


title: HCC11-N


title: HCC5-N


title: HCC8-N


title: HCC13-N


title: HCC4-N


title: HCC6-N


title: HCC1-N


title: HCC2-N


title: HCC3-N


title: HCC18-N


title: HCC15-N


title: HCC12-N


title: HCC21-N


title: HCC9-N


title: HCC72-T

value: Tumor


title: HCC7-N


title: HCC71-T


title: HCC68-T


title: HCC69-T


title: HCC73-T


title: HCC70-T


title: HCC57-T


title: HCC58-T


title: HCC66-T


title: HCC59-T


title: HCC61-T


title: HCC60-T


title: HCC64-T


title: HCC63-T


title: HCC67-T


title: HCC62-T


title: HCC65-T


title: HCC55-T


title: HCC56-T


title: SKBR3

city: Basel

first: Christian

last: Ruiz

address: Schoenbeinstrasse 40

department: Institute for Pathology

country: Switzerland

institute: University Hospital Basel

hyb_protocol: Labeled DNAs were hybridized in an ozone free environment in a rotisserie oven at 20 rpm for 40 hours then washed according to array supplier's (Agilent)protocol

scan_protocol: All arrays were  scanned using an Agilent 2565C Scanner and default settings for CGH.

data_processing: Data was extracted from the TIFF files using Agilent FE 10.5.  The data quality was assessed using the QC Report output in F.E. 10.5.  All arrays that passed the experimental Q.C. were then visualized and analyzed using DNA Analytics 4.0.85 and the ADM2 step gram algorithm.

source_name: 10q22 amplified tumor cell line

label_protocol: For each hybridization, 1ug of extracted DNA and 1ug of 46XX reference (Promega, Madison, WI) were digested with the restriction enzymes Alu I and RSA I (Promega, Madison, WI). Labeling of the DNA was performed using the BioPrime labeling kit (Invitrogen, Carlsbad, CA): Cy-5 for test sample, Cy-3 for reference.

growth_protocol: Tumor cells were grown as recommended by the supplier.

extract_protocol: One million cells were collected in PBS and DNA was extracted by usage of the DNeasy Blood and Tissue Kit (QIAGEN, Valencia, CA) according to the manufacturer’s protocol.

treatment_protocol: None.

value: 10q22 amplified tumor cell line

source_name: pooled normal (46,XX) reference

value: Normal female genome


title: Brain_Oligodendroglioma-gradeII_940

description: Not additional information

value: oligodendroglioma

value: ii

value: Low grade oligodendroglial tumor


title: ME180


title: ZF control, replicate1

city: Vicksburg

first: Mitchell

last: Wilbanks

state: MS

address: 3909 Halls Ferry Road

department: Environmental Laboratory

institute: US Army Engineer Research and Development Center

description: 251916110149_zebrafish rdx 96h_GE1-v5_95_Feb07_1_4.txt

hyb_protocol: For ZF, 1650 ng of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 30 seconds with Acetonitrile, and dried with Agilent Stabilization and Drying Solution.

scan_protocol: Slides were scanned immediately after washing on a GenePix 4200AL scanner at PMT gain level 420 using default setting (Scan resolution 5um, One channel-Green, Laser power 100%).

data_processing: The scanned images were analyzed with GenePix Pro 6.1  (Molecular Devices, Sunnyvale, CA) using default parameters and an Agilient-provided GEML grid file to obtain signal intensities.  GeneSpring GX (Agilent Technologies) was used to normalize data by 75th percentile shift and conduct baseline transformation to the median of all samples.  Statistical analysis was also performed in GeneSpring utilizing data from all microarray probes and consisted of one-way ANOVA with Benjamini-Hochberg multiple-tests correction to test for significant differential expression of microarray targets.

source_name: whole fish (10 fish/replicate)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.4 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Control and test waters were Vicksburg, MS, USA tap water dechlorinated via activated charcoal filtration.  Exposures were conducted in an environmental chamber at a temperature of 25 °C and light:dark cycle of 16h:8h.  Each replicate was housed in individual beakers where dissolved oxygen concentrations were ensured via slight aeration (approximately one bubble per second) into each beaker with a single glass pipette connected to a constant air flow.  Fish were exposed in 300 ml high-form lipless beakers.  The exposures were static renewal, renewed once after 48-h.  Fish were fed three hours before the 48-h water renewal.  FHM were fed brine shrimp (Artemia sp.) nauplii, and ZF were fed ARTEMAC-0 fish food (20-80 µM diameter, Aquafauna Bio-Marine, Inc., Hawthorne, CA, USA).

extract_protocol: RNA was prepared using the RNeasy mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Four replicates were used per treatment with ten fish per replicate.    Both fathead minnow and zebrafish investigation included control, 0.9, 1.8, 7.0 and 13.8 mg/L treatments.

tag: developmental stage

value: fry

tag: agent

value: control

value: whole fish


title: ZF control, replicate3

description: 251916110149_zebrafish rdx 96h_GE1-v5_95_Feb07_1_1.txt


title: ZF 0.9, replicate3

description: 251916110151_zebrafish rdx 96h_GE1-v5_95_Feb07_1_2.txt

value: RDX

tag: agent dose (mg/l)


title: ZF 15, replicate4

description: 251916110150_zebrafish rdx 96h_GE1-v5_95_Feb07_1_4.txt


title: ZF 15, replicate3

description: 251916110150_zebrafish rdx 96h_GE1-v5_95_Feb07_1_3.txt


title: PC3


title: MFM223


title: ZF 3.8, replicate4

description: 251916110149_zebrafish rdx 96h_GE1-v5_95_Feb07_1_2.txt


title: ZF 1.9, replicate1

description: 251916110149_zebrafish rdx 96h_GE1-v5_95_Feb07_1_3.txt


title: ZF 0.9, replicate4

description: 251916110151_zebrafish rdx 96h_GE1-v5_95_Feb07_1_4.txt


title: ZF 1.9, replicate2

description: 251916110151_zebrafish rdx 96h_GE1-v5_95_Feb07_1_1.txt


title: ZF 1.9, replicate3

description: 251916110150_zebrafish rdx 96h_GE1-v5_95_Feb07_1_2.txt


title: ZF 3.8, replicate3

description: 251916110151_zebrafish rdx 96h_GE1-v5_95_Feb07_1_3.txt


title: ZF 7.5, replicate4

description: 251916110150_zebrafish rdx 96h_GE1-v5_95_Feb07_1_1.txt


title: HCC52-T

tag: tissue type


title: HCC47-T


title: HCC49-T


title: HCC51-T


title: HCC48-T


title: HCC46-T


title: HCC45-T


title: HCC44-T


title: HCC50-T


title: ZF 15, replicate1

description: 251916110148_zebrafish rdx 96h_GE1-v5_95_Feb07_1_1.txt


title: ZF 7.5, replicate2

description: 251916110148_zebrafish rdx 96h_GE1-v5_95_Feb07_1_2.txt


title: ZF 15, replicate2

description: 251916110147_zebrafish rdx 96h_GE1-v5_95_Feb07_1_3.txt


title: ZF 1.9, replicate4

description: 251916110147_zebrafish rdx 96h_GE1-v5_95_Feb07_1_1.txt


title: HCC41-T

description: Total miRNA was spotted on 934 features. We used only human miRNA in our analysis. Therefore, a total of 68 features were already eliminated from the all features on this array.


title: ZF 3.8, replicate1

description: 251916110146_zebrafish rdx 96h_GE1-v5_95_Feb07_1_4.txt


title: ZF control, replicate4

description: 251916110147_zebrafish rdx 96h_GE1-v5_95_Feb07_1_4.txt


title: HCC37-T


title: ZF 7.5, replicate1

description: 251916110148_zebrafish rdx 96h_GE1-v5_95_Feb07_1_3.txt


title: HCC38-T


title: HCC40-T


title: HCC42-T


title: HCC39-T


title: ZF 7.5, replicate3

description: 251916110148_zebrafish rdx 96h_GE1-v5_95_Feb07_1_4.txt


title: ZF 3.8, replicate2

description: 251916110147_zebrafish rdx 96h_GE1-v5_95_Feb07_1_2.txt


title: HCC43-T


title: HCC36-T


title: HCC53-T


title: ZF control, replicate2

description: 251916110146_zebrafish rdx 96h_GE1-v5_95_Feb07_1_2.txt


title: ZF 0.9, replicate2

description: 251916110146_zebrafish rdx 96h_GE1-v5_95_Feb07_1_1.txt


title: HCC35-T


title: HCC32-T


title: HCC33-T


title: HCC34-T


title: HCC31-T


title: HCC30-T


title: HCC29-T


title: ZF 0.9, replicate1

description: 251916110146_zebrafish rdx 96h_GE1-v5_95_Feb07_1_3.txt


title: HCC28-T


title: HCC26-T


title: FHM 15, replicate1 (420PMT)

description: 251959710208_12-8-08 FHM fry 420_GE1-v5_95_Feb07_1_3.txt

hyb_protocol: For FHM, 600 ng of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 30 seconds with Acetonitrile, and dried with Agilent Stabilization and Drying Solution.

data_processing: The scanned images were analyzed with GenePix Pro 6.1  (Molecular Devices, Sunnyvale, CA) using default parameters and Agilient-provided GEML grid file 021219_G2_D_F_20080811.xml to obtain signal intensities.  GeneSpring GX (Agilent Technologies) was used to normalize data by 75th percentile shift and conduct baseline transformation to the median of all samples.  Statistical analysis was also performed in GeneSpring utilizing data from all microarray probes and consisted of one-way ANOVA with Benjamini-Hochberg multiple-tests correction to test for significant differential expression of microarray targets.

organism: Pimephales promelas


title: HCC25-T


title: FHM 0.9, replicate1 (420PMT)

description: 251959710207_FHM fry @420 12-3-08_GE1-v5_95_Feb07_1_4.txt


title: FHM control, replicate2 (420PMT)

description: 251959710207_FHM fry @420 12-3-08_GE1-v5_95_Feb07_2_4.txt


title: FHM 15, replicate4 (420PMT)

description: 251959710208_12-8-08 FHM fry 420_GE1-v5_95_Feb07_1_1.txt


title: FHM control, replicate1 (420PMT)

description: 251959710208_12-8-08 FHM fry 420_GE1-v5_95_Feb07_1_4.txt


title: Feces, Treated 2

type: other

city: Vancouver

first: L. Caetano

middle: M.

last: Antunes

state: BC

department: Michael Smith Laboratories

country: Canada

institute: The University of British Columbia

description: Each sample was measured twice in negative and twice in positive ionization modes.

hyb_protocol: Not applicable

scan_protocol: Not applicable

data_processing: Raw mass spectrometry data were processed using a custom-developed software package, as described elsewhere (Han et al. 2008. Metabolomics. 4:128-140). First, raw mass spectra acquired from each sample group were batch-processed using the instrument vendor’s data analysis software, DataAnalysis®, but with a home-written VBA script to do automatic internal mass calibration with the reference masses of the spiked calibration standards and a known contaminant, N-butylbenzensulfonamide. Monoisotopic peaks corresponding to the isotopic pattern distributions were then automatically determined and those with a signal/noise ratio above 3 were picked. Their m/z values were converted to neutral masses by subtracting 1.007276 for positive ion mode or adding 1.007276 for negative ion mode. Next, the resulting mass lists from all the mass spectra within each set of untreated or treated groups detected in positive or negative ion modes were further processed with another customized software program developed with LabVIEW® (National Instruments, Austin, USA). Adduct ions were recognized and converted to neutral masses from the mass lists based on the expected mass differences between protonated (M+H)+, (M+Na)+ and/or (M+K)+ ions for positive ion mode or deprotonated (M-H)- and (M+Cl)- ions for negative ion mode, within 2 ppm, to yield a list of unique biochemical component masses together with the sum of their peak intensities. The peak intensities of all the monoisotopic neutral masses are subsequently normalized to the intra-sample total ion intensity. Masses observed in at least three of four samples from one of the sample groups (untreated or treated) were aligned and then combined into unique metabolite features from the masses that matched within 2 ppm across all the data. Finally, a two-dimensional data matrix (mass vs. relative intensity) was generated for each sample group and saved in a format amenable for further data analysis. Heat maps were then created using the freely-available softwares Cluster and Java TreeView (http://rana.lbl.gov/eisensoftware.htm). To identify differences in metabolite composition between untreated and treated samples, we first filtered our list of masses for metabolites that were present on one set of samples (untreated or treated) but not the other. Additionally, we averaged the mass intensities of metabolites in each group and calculated the ratios between averaged intensities of metabolites from untreated and treated samples. To assign possible metabolite identities to the masses present in only one of the sample groups or showing at least a 2-fold change in intensities between the sample groups, the monoisotopic neutral masses of interest were queried against MassTrix (http://masstrix.org), a free-access software designed to incorporate masses into metabolic pathways using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database (http://www.genome.jp/kegg/). Masses were searched against the Mus musculus database within a mass error of 3 ppm.

label: Not applicable

molecule: other

source_name: Feces

label_protocol: Not applicable

extract_protocol: To extract metabolites from feces, acetonitrile was added to samples (approximately 10-25 μL of acetonitrile per 1 mg of tissue), which were then homogenized. The samples were then cleared by centrifugation and the supernatant was collected and dried at room temperature using a centrifuge equipped with a vacuum pump. All extracts were kept at -80 oC until used.

treatment_protocol: 20 mg of streptomycin through oral gavage

tag: strain

tag: gender

value: Female

tag: treatment

value: 20 mg streptomycin

tag: source

value: feces

tag: molecule type

value: metabolites


title: FHM 1.9, replicate3 (420PMT)

description: 251959710207_FHM fry @420 12-3-08_GE1-v5_95_Feb07_2_2.txt

tag: tissue


title: FHM 0.9, replicate4 (420PMT)

description: 251959710208_12-8-08 FHM fry 420_GE1-v5_95_Feb07_2_1.txt


title: FHM 7.5, replicate1 (420PMT)

description: 251959710208_12-8-08 FHM fry 420_GE1-v5_95_Feb07_1_2.txt


title: Feces, Treated 1


title: Feces, Treated 4


title: HCC23-T

description: Total miRNA was spotted on 934 features. We used only human miRNA in our analysis. Therefore, a total of 68 features were already eliminated from the all features on this array.

tag: sample id


title: HCC27-T


title: FHM 1.9, replicate2 (420PMT)

description: 251959710207_FHM fry @420 12-3-08_GE1-v5_95_Feb07_1_3.txt


title: HCC22-T


title: FHM control, replicate3 (420PMT)

description: 251959710208_12-8-08 FHM fry 420_GE1-v5_95_Feb07_2_3.txt


title: FHM 0.9, replicate2 (420PMT)

description: 251959710207_FHM fry @420 12-3-08_GE1-v5_95_Feb07_2_3.txt


title: FHM 0.9, replicate3 (420PMT)

description: 251959710207_FHM fry @420 12-3-08_GE1-v5_95_Feb07_1_1.txt


title: HCC21-T


title: FHM 7.5, replicate2 (420PMT)

description: 251959710207_FHM fry @420 12-3-08_GE1-v5_95_Feb07_1_2.txt


title: FHM 7.5, replicate3 (420PMT)

description: 251959710206_FHM fry @420 12-3-08_GE1-v5_95_Feb07_2_2.txt


title: FHM 15, replicate2 (420PMT)

description: 251959710206_FHM fry @420 12-3-08_GE1-v5_95_Feb07_2_1.txt


title: HCC24-T


title: HCC20-T


title: HCC19-T


title: Feces, Treated 3


title: HCC54-T


title: Feces, Untreated 2

treatment_protocol: No treatment

value: untreated


title: Feces, Untreated 3


title: Feces, Untreated 4


title: Feces, Untreated 1


title: FHM 7.5, replicate4 (420PMT)

description: 251959710206_FHM fry @420 12-3-08_GE1-v5_95_Feb07_2_4.txt


title: FHM 15, replicate3 (420PMT)

description: 251959710206_FHM fry @420 12-3-08_GE1-v5_95_Feb07_1_3.txt


title: HCC18-T


title: Liver,  Infected, 3

description:
L-I-3
Each sample was measured twice.

hyb_protocol: Not applicable.

scan_protocol: Not applicable.

data_processing: Raw mass spectrometry data were processed using a custom-developed software package, as described elsewhere (Han et al. 2008. Metabolomics. 4:128-140 [PMID 19081807]). First, raw mass spectra acquired from each sample group were batch-processed using the instrument vendor’s data analysis software, DataAnalysis®, but with a home-written VBA script to do automatic internal  mass calibration with the reference masses of the spiked calibration standards and a known contaminant, N-butylbenzensulfonamide. Monoisotopic peaks corresponding to the isotopic pattern distributions were then automatically determined and those with a signal/noise ratio above 3 were picked. Their m/z values were converted to neutral masses by subtracting 1.007276 for positive ion mode or adding 1.007276 for negative ion mode. Next, the resulting mass lists from all the mass spectra within each set of uninfected/infected groups detected in positive or negative ion modes were further processed with another customized software program developed with LabVIEW® (National Instruments, Austin, USA). The first step of this software is to remove the adduct ions (M+Na)+ and (M+K)+ in positive ion mode and (M+Cl)- in negative ion mode from the mass lists based on the expected mass differences for these ions within 2 ppm to yield a list of unique biochemical component masses together with their peak intensities. The peak intensities of all the monoisotopic neutral masses are subsequently normalized to the intra-sample total ion intensity. Masses observed in at least three of four samples (feces) or two of three samples (livers) of one of the conditions (infected or uninfected) were aligned and combined into unique metabolite features from the masses that matched within 2 ppm across all the data. Finally, a two-dimensional data matrix (mass vs. relative intensity) was generated for each sample group and saved in a format amenable for further data analysis. To identify differences in metabolite composition between samples from uninfected and infected mice, we first filtered our list of masses for metabolites which were present in one set of samples (uninfected or infected) but not the other. Additionally, we averaged the mass intensities of metabolites in each group and calculated the ratios between averaged intensities of metabolites from uninfected and infected mice. To assign possible metabolite identities to the masses present in only one of the sample groups or showing at least a 2-fold change in intensities between the sample groups, the monoisotopic neutral masses of interest were queried against MassTrix (http://masstrix.org), a software designed to incorporate mass queries into metabolic pathways. Masses were searched against the Mus musculus database within a mass error of 3 ppm.

source_name: Liver, infected

label_protocol: Not applicable.

growth_protocol: Not applicable.

extract_protocol: To extract metabolites from livers and feces, acetonitrile was added to samples (approximately 1 μL of acetonitrile per 1 μg of tissue), which were then homogenized. The samples were then cleared by centrifugation and the supernatant was collected into a new tube and dried at room temperature using a centrifuge equipped with a vacuum pump. All extracts were kept at -80oC until further use.

treatment_protocol: Oral infection with 7.5x10^7 Salmonella enterica serovar Typhimurium SL1344.

value: female

value: liver

tag: infection


title: FHM 1.9, replicate4 (420PMT)

description: 251959710206_FHM fry @420 12-3-08_GE1-v5_95_Feb07_1_1.txt


title: HCC17-T

value: Tumor


title: HCC16-T


title: HCC15-T


title: Liver,  Infected, 1

description:
L-I-1
Each sample was measured twice.

value: Salmonella enterica serovar Typhimurium SL1344


title: HCC14-T


title: Liver,  Uninfected, 3

description:
L-U-3
Each sample was measured twice.

source_name: Liver, uninfected

value: uninfected


title: HCC13-T


title: Liver,  Infected, 2

description:
L-I-2
Each sample was measured twice.


title: FHM control, replicate3 (440PMT)

description: 251959710178_FHM sub-adult RDX challenge 071509 440PMT_GE1-v5_95_Feb07_1_4.txt


title: HCC12-T


title: HCC11-T


title: FHM control, replicate1 (440PMT)

description: 251959710178_FHM sub-adult RDX challenge 071509 440PMT_GE1-v5_95_Feb07_1_1.txt


title: FHM 0.9, replicate4 (440PMT)

description: 251959710178_FHM sub-adult RDX challenge 071509 440PMT_GE1-v5_95_Feb07_1_2.txt


title: FHM 1.9, replicate1 (440PMT)

description: 251959710178_FHM sub-adult RDX challenge 071509 440PMT_GE1-v5_95_Feb07_1_3.txt


title: HCC10-T


title: Feces, Infected, 4

description:
F-I-4
Each sample was measured twice.

source_name: Feces, infected


title: FHM control, replicate2 (440PMT)

description: 251959710177_FHM sub-adult RDX challenge 071509 440PMT_GE1-v5_95_Feb07_2_4.txt


title: HCC9-T


title: HCC8-T


title: FHM 1.9, replicate3 (440PMT)

description: 251959710177_FHM sub-adult RDX challenge 071509 440PMT_GE1-v5_95_Feb07_2_2.txt


title: FHM 15, replicate1 (440PMT)

description: 251959710177_FHM sub-adult RDX challenge 071509 440PMT_GE1-v5_95_Feb07_2_1.txt


title: Feces, Infected, 3

description:
F-I-3
Each sample was measured twice.


title: wild type sample 3

city: Sheffield

first: Sarah

middle: Ruth

last: Walmsley

address: Department of Infection and Immunity, The Medical School, Beech Hill Road

institute: University of Sheffield

description: From each individual mouse neutrophils were isolated by negative magnetic selection

hyb_protocol: 15µg of cRNA molecules were heat fragmented and applied to the Mouse Genome 430_2 GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions

scan_protocol: the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files

data_processing: Affymetrix data was MAS 5.0 normalised and log fold change determined using PANTHER software

label_protocol: Biotinylation of antisense RNA carried out according to Affymetrix protocol

extract_protocol: mirVana total RNA extraction was used for RNA extraction according to manufacturers' instructions

tag: genotype

value: wild type mouse

value: neutrophil

value: hypoxia

tag: genetic background


title: HCC7-T

description: Total miRNA was spotted on 934 features. We used only human miRNA in our analysis. Therefore, a total of 68 features were already eliminated from the all features on this array.


title: FHM 0.9, replicate1 (440PMT)

description: 251959710177_FHM sub-adult RDX challenge 071509 440PMT_GE1-v5_95_Feb07_1_4.txt

value: fry


title: FHM 0.9, replicate3 (440PMT)

description: 251959710177_FHM sub-adult RDX challenge 071509 440PMT_GE1-v5_95_Feb07_1_1.txt


title: FHM 1.9, replicate2 (440PMT)

description: 251959710177_FHM sub-adult RDX challenge 071509 440PMT_GE1-v5_95_Feb07_1_3.txt


title: Feces, Infected, 2

description:
F-I-2
Each sample was measured twice.


title: wild type sample 2

tag: cell type


title: Liver,  Uninfected, 2

description:
L-U-2
Each sample was measured twice.


title: phd3 null sample 3

source_name: phd3 null 130608

value: phd3 null


title: wild type sample 1


title: phd3 null sample 2

source_name: phd3 null 120608


title: HCC6-T


title: Feces, Infected, 1

description:
F-I-1
Each sample was measured twice.


title: Feces, Uninfected, 4

description:
F-U-4
Each sample was measured twice.

source_name: Feces, uninfected


title: FHM 7.5, replicate4 (440PMT)

description: 251959710176_FHM sub-adult RDX challenge 071509 440PMT_GE1-v5_95_Feb07_2_4.txt

value: whole fish


title: HCC5-T


title: Liver,  Uninfected, 1

description:
L-U-1
Each sample was measured twice.


title: Feces, Uninfected, 3

description:
F-U-3
Each sample was measured twice.


title: HCC3-T


title: Feces, Uninfected, 1

description:
F-U-1
Each sample was measured twice.


title: HCC4-T


title: FHM 7.5, replicate3 (440PMT)

description: 251959710176_FHM sub-adult RDX challenge 071509 440PMT_GE1-v5_95_Feb07_2_2.txt

value: RDX


title: FHM 15, replicate2 (440PMT)

description: 251959710176_FHM sub-adult RDX challenge 071509 440PMT_GE1-v5_95_Feb07_2_1.txt


title: Astrocyte_control-transfected_rep3

city: Nara City

first: Hiroyuki

last: Tanabe

state: Nara

address: 3327-204 Nakamachi

department: Faculty of Agriculture Department of Advanced Bioscience

institute: Kinki University

hyb_protocol: The dye-labeled target (1.6 μg as cRNA) was fragmented and hybridized on an Agilent Whole Mouse Genome 4X44K microarray at 65°C for 17 hr with a Gene Expression Hybridization Kit. The hybridized slide was washed in Gene Expression Wash Buffer 1 at room temperature for 1 min, which was followed by a wash for 1 min in Gene Expression Wash Buffer 2.

scan_protocol: The processed microarrays were scanned using an Agilent DNA Microarray Scanner.

data_processing: Data extraction from raw image files was done with Agilent Feature Extraction software ver.10.7.

source_name: mus musculus fetal astrocyte, control-transfected

label_protocol: The labeling reaction was carried out separately for the RNA samples using a Quick Amp Labeling Kit one-color, in the presence of cyanine 3-CTP.

growth_protocol: Primary astrocyte cultures prepared from cerebral cortex of fetal C57BL/6 mouse (embryonic 18-day old) were purchased from ScienCell Research Laboratories. Cells were always cultured and maintained in poly-L-lysine-coated plastic wares (AGC) supplied with Astrocyte Medium (ScienCell) following the supplyer’s recommendations.

treatment_protocol: Astrocytes were transfected in six-well plates (AGC Techno Glass, Japan) containing the medium supplemented with 80 nM each of miR-29 (Ambion Pre-miR hsa-miR-29a/b/c Precursors) or control miRNA (Ambion Pre-miR Negative Control1) using RNAiMax (Invitrogen) in accordance with manufacturer’s protocols. miR-29 RNA for the transfection was prepared by mixing the three miR-29 isoforms in a 1:2:1 molar ratio of Pre-miR-29a:-29b:-29c Precursors. The transfection was conducted three weeks after the initial plating. 48 hr posttransfection, cells were harvested and processed for preparation of RNA samples. The transfection efficiency was above 90% as determined using a fluorochrome-conjugated miR-29 precursor (TAKARA BIO, Japan). RNA extraction was performed in triplicate for each cell type. Total RNA was isolated from the transfected astrocyte cells using an RNAiso Plus (TAKARA BIO). The quality of RNA was assessed using an Agilent 2100 Bioanalyzer, which is indicative of integrity of every RNA sample sufficient for downstream assays.

tag: age

value: embryonic day 18

value: astrocyte, primary culture


title: phd3 null sample 1

source_name: phd3 null 110608


title: FHM 15, replicate4 (440PMT)

description: 251959710176_FHM sub-adult RDX challenge 071509 440PMT_GE1-v5_95_Feb07_1_2.txt


title: FHM 7.5, replicate1 (440PMT)

description: 251959710176_FHM sub-adult RDX challenge 071509 440PMT_GE1-v5_95_Feb07_1_4.txt


title: Astrocyte_control-transfected_rep2

extract_protocol: Total RNA was isolated from the transfected astrocyte cells using an RNAiso Plus (TAKARA BIO).


title: Feces, Uninfected, 2

description:
F-U-2
Each sample was measured twice.

value: feces


title: HCC2-T


title: HCC1-T


title: Astrocyte_miR-29-transfected_rep2

source_name: mus musculus fetal astrocyte, miR-29-transfected


title: Tumor sample 74T vs RP

status: Public on Feb 07 2011

city: Leiden

first: Eddy

last: van Roon

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: LUMC

description: Tumor vs Reference panel LogRatios

hyb_protocol: Hybridisation and washing was performed in a GeneTAC hybstation (microgen, Oklahoma City, OK, USA) using a hybsolution containing 66% formamide, 2.5x SSC and 12.5g/100ml dextran sulphate.

scan_protocol: Image analysis was done using GenePix6.0 (Molecular Devices, Union City, CA, USA)

data_processing: Pre-processing was performed using the GenePix error model in Rosetta Resolver version 5.0 (Rosetta Biosoftware, Seattle, WA, USA). Microarray data for the tumour and normal samples were compared using an error-weighted ANOVA model and corrected for multiple testing in Rosetta resolver

source_name: Colon tumor

label_protocol: MseI digestion was performed in a 50 ul sample volume containing  2 ug of genomic DNA. Digests were purified and their sticky-ends ligated with 0.5 nmol of unphosphorylated linkers. Ligated DNA was digested with methylation-sensitive endonucleases BstUI and HpaII. Incorporation of aminoallyl dUTP into amplicons (5 ug) was conducted using the BioPrime DNA labeling system (Life Technologies, Inc.). Cy5 and Cy3 fluorescent dyes were coupled to amino-allyl dUTP-labeled tumor and normal amplicons.

extract_protocol: Total genomic DNA has been isolated using a standard phenol/cholorform and alcohol precipitation extraction

tag: sample type

value: unknown

value: Colon tumor

source_name: Reference panel

value: SW48, RKO, SW480, Caco2, SW837, and LS411


title: Astrocyte_control-transfected_rep1


title: Tumor sample 108T vs RP

description: Tumor vs Reference panel LogRatios

value: Female, 52, ascending colon, MSS

value: Female


title: Tumor sample 97T vs RP

description: Tumor vs Reference panel LogRatios

value: Female, 68, coecum, MSS


title: Tumor sample 57T vs RP

description: Tumor vs Reference panel LogRatios

value: Female, 75, ascending colon, MSI-H


title: Tumor sample 56T vs RP

description: Tumor vs Reference panel LogRatios

value: Male, 75, coecum, MSI-H

value: Male


title: FHM 15, replicate3 (440PMT)

description: 251959710176_FHM sub-adult RDX challenge 071509 440PMT_GE1-v5_95_Feb07_1_3.txt

tag: developmental stage


title: Tumor sample 127T vs RP

description: Tumor vs Reference panel LogRatios

value: Female, 87, ascending colon, MSS


title: Tumor sample 499T vs RP

description: Tumor vs Reference panel LogRatios

value: Female, 69, coecum, MSI-H


title: Tumor sample 39T vs RP

description: Tumor vs Reference panel LogRatios

value: Male, 77, coecum, MSS


title: Tumor sample 49T vs RP

description: Tumor vs Reference panel LogRatios

value: Female, 80, ascending colon, MSI-H


title: Tumor sample 86T vs RP

description: Tumor vs Reference panel LogRatios


title: Tumor sample 184T vs RP

description: Tumor vs Reference panel LogRatios

value: Female, 56, coecum, MSI-H


title: FHM 1.9, replicate1 (420PMT)

description: 251959710172_012009@420_GE1-v5_95_Feb07_2_4.txt

value: fry

tag: agent

value: RDX

value: whole fish


title: Astrocyte_miR-29-transfected_rep1

value: embryonic day 18

value: astrocyte, primary culture


title: Tumor sample 187T vs RP

description: Tumor vs Reference panel LogRatios

value: Female, 61, coecum, MSS

value: Colon tumor

value: SW48, RKO, SW480, Caco2, SW837, and LS411


title: Tumor sample 197T vs RP

description: Tumor vs Reference panel LogRatios

value: Female, 58, transverse colon, MSI-H

value: Female


title: Tumor sample 503T vs RP

description: Tumor vs Reference panel LogRatios

value: Female, 63, coecum, MSS


title: Tumor sample 180T vs RP

description: Tumor vs Reference panel LogRatios

value: Female, 86, ascending colon, MSS


title: Sample 4 / Control 4

city: Rehovot

first: Akhil

last: Rajput

address: 1, Herzl

department: Biological Chemistry

country: Israel

institute: The Weizmann Institute

description: Sample 4 / Control 4

hyb_protocol: Arrays labelled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit and hybridised using the In situ Hybridization Kit. All protocols available from www.agilent.com

scan_protocol: Scanner Model: G2565BA DNA Scanner.

data_processing:
Agilent Feature Extraction Software Version: 9.5. Extraction Protocol: GE2-v5_95_Feb07. Data pre-processing involved normalization (linear lowess) and background subtraction. Data table below represents log10(knockdown/control) ratios, [log(REDsignal/GREENsignal) per feature (processed signals used)].
Data Analysis was performed in GeneSpring (Agilent Technologies) with pathway analysis performed using “Pathway Express” from Wayne State University (http://vortex.cs.wayne.edu/research.htm). This is a free web-based programme.

source_name: SV80 Cells, sample

growth_protocol: SV80 cells were grown in DMEM with 10% FBS and antibiotics

extract_protocol: The RNA was isolated using RNeasy Mini Kit (Cat. No. 74104, QIAGEN) according to manufacturers instructions.

treatment_protocol: The cells were treated with Control or caspase-8 siRNA expressing lenti viruses

tag: cell line

value: fibroblastoid cell line SV80

tag: protocol

value: siRNA-mediated caspase-8 knockdown

source_name: SV80 Cells, control

value: control


title: Tumor sample 131T vs RP

description: Tumor vs Reference panel LogRatios

value: Female, 71, ascending colon, MSS


title: Astrocyte_miR-29-transfected_rep3

tag: strain


title: Sample 3 / Control 3

description: Sample 3 / Control 3

label_protocol: Arrays labelled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit and hybridised using the In situ Hybridization Kit. All protocols available from www.agilent.com


title: Normal mucosa 197N vs RP

description: Normal mucosa vs Reference panel LogRatios

source_name: Colon, normal mucosa

value: Female, 58, transverse colon

tag: gender

value: Colon, normal mucosa


title: Normal mucosa 184N vs RP

value: Female, 56, coecum


title: Normal mucosa 131N vs RP

value: Female, 71, ascending colon