title: genomic DNA from cord blood sample 24AB-429B

description:
Cord Blood DNA
24AB-429B

source_name: cord blood sample 24AB-429B


title: genomic DNA from cord blood sample 21AB-347B

status: Public on Mar 29 2012

type: genomic

city: Philadelphia

first: Nahid

last: Turan

state: PA

address: 3307 North Broad Street, AHB

department: Fels Institute

country: USA

institute: Temple University School of Medicine

description:
Cord Blood DNA
21AB-347B

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: cord blood sample 21AB-347B

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions. The Zymo Bisulphite Conversion Kit was used to convert the DNA samples.

tag: birth weight (g)

tag: gestational age (wks)

tag: birth weight (%)

tag: tissue

value: Cord Blood


title: Reverb alpha/beta DKO liver_ZT12_rep 1

type: RNA

city: La Jolla

first: Ruth

middle: T

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

description:
6033102040-G
technical replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using cubic spline in Illumina GenomeStudio and also using the VAMPIRE Bayesian model with a 2-sided Bonferroni-corrected threshold of 0.05.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Reverb alpha/beta DKO liver_ZT12

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

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

tag: background strain

tag: strain

value: Reverbalpha/beta Alb Cre+

tag: genotype/variation

value: Reverb alpha/beta DKO

tag: gender

value: male

tag: age

value: 20 week-old

value: liver


title: TEPM-0h LPS-rep1

city: Brisbane

first: Kate

last: Schroder

state: QLD

address: University of Queensland, St Lucia

country: Australia

institute: Institute for Molecular Bioscience

description: TEPM-0h LPS-rep1

hyb_protocol: Samples were hybridised according to Agilent's One-colour Microarray-Based Gene Expression Analysis (Quick Amp Labelling) protocol, V5.7 March 2008.

scan_protocol: Samples were scanned according to Agilent's One-colour Microarray-Based Gene Expression Analysis (Quick Amp Labelling) protocol, V5.7 March 2008, using an Agilent Microarray Scanner G2565BA.

data_processing: Features (including processed signal and flags) were extracted using the Feature Extraction 9.5.3 (Agilent Technologies) software, with default settings and no background subtraction. Processed signal intensities were quantile normalized in R using the Affymetrix package in Bioconductor.

source_name: Mouse thioglycollate-elicited peritoneal macrophages stimulated with 10ng/ml S. minnesota lipopolysaccharide for 0h

label_protocol: Labelling was performed using the Agilent Quick-Amp Labelling Kit (one colour) according to manufacturer's instructions.

growth_protocol: BMM were derived from femurs of 6-8 week-old, male C57Bl/6 mice. Femurs were flushed with medium and bone marrow cells were plated out in complete medium (RPMI 1640 containing 10% FCS, 20U/ml penicillin, 20 µg/ml streptomycin and 2mM L-glutamine) supplemented with 104U/ml (100ng/ml) recombinant human CSF-1 (Chiron) on bacteriological plastic plates (Bibby Sterilin) for 7 days, with refeeding on day 5 and reseeding on day 6 at 1x105 cells/cm2. TEPM were elicited by injecting 6-8 week-old male, mice with 1ml sterile thioglycollate broth (10% in pyrogen-free water, Becton Dickinson) intraperitoneally. 5 days post-injection, peritoneal cells were collected by PBS lavage, plated on tissue culture plastic as for BMM in media without CSF-1 and stimulated the following day. >90% TEPM were F4/80+ macrophages, as assessed by surface staining and flow cytometry (not shown). All cells were cultured at 37˚C with 5% CO2.

extract_protocol: Total RNA was prepared using the Qiagen RNeasy Mini kit with on-column DNaseI treatment, according to the manufacturer’s instructions.

treatment_protocol: BMM and TEPM were treated for various times with lipopolysaccharide (LPS) from Salmonella minnesota (Sigma-Aldrich), at a final concentration of 10 ng/ml.

value: peritoneal

tag: cell type

value: macrophages

tag: treatment

value: untreated

tag: treatment time

value: 0 hours


title: Reverb alpha/beta DKO liver_ZT8_rep 1

description:
6033102040-E
technical replicate 1

source_name: Reverb alpha/beta DKO liver_ZT8


title: Reverb alpha/beta DKO liver_ZT16_rep 1

description:
6033102043-A
technical replicate 1

source_name: Reverb alpha/beta DKO liver_ZT16


title: genomic DNA from cord blood sample 22AB-390B

description:
Cord Blood DNA
22AB-390B

source_name: cord blood sample 22AB-390B


title: Reverb alpha/beta DKO liver_ZT4_rep 1

description:
6033102040-C
technical replicate 1

source_name: Reverb alpha/beta DKO liver_ZT4


title: BMM-24h LPS-rep2

description: BMM-24h LPS-rep2

source_name: Mouse bone marrow-derived macrophages stimulated with 10ng/ml S. minnesota lipopolysaccharide for 24h

value: bone marrow

value: LPS

value: 24 hours


title: BMM-0h LPS-rep3

description: BMM-0h LPS-rep3

source_name: Mouse bone marrow-derived macrophages stimulated with 10ng/ml S. minnesota lipopolysaccharide for 0h


title: genomic DNA from cord blood sample 23AB-399B

description:
Cord Blood DNA
23AB-399B

source_name: cord blood sample 23AB-399B


title: Reverb alpha/beta DKO liver_ZT4_rep 2

description:
6033102040-D
technical replicate 2


title: genomic DNA from cord blood sample 20AB-342B

description:
Cord Blood DNA
20AB-342B

source_name: cord blood sample 20AB-342B


title: genomic DNA from cord blood sample 19AB-335B

description:
Cord Blood DNA
19AB-335B

source_name: cord blood sample 19AB-335B


title: BMM-2h LPS-rep3

description: BMM-2h LPS-rep3

source_name: Mouse bone marrow-derived macrophages stimulated with 10ng/ml S. minnesota lipopolysaccharide for 2h

value: 2 hours


title: genomic DNA from cord blood sample 17AB-271B

description:
Cord Blood DNA
17AB-271B

source_name: cord blood sample 17AB-271B


title: Reverb alpha/beta DKO liver_ZT0_rep 1

description:
6033102040-A
technical replicate 1

source_name: Reverb alpha/beta DKO liver_ZT0


title: Reverb alpha/beta DKO liver_ZT0_rep 2

description:
6033102040-B
technical replicate 2


title: BMM-2h LPS-rep2

description: BMM-2h LPS-rep2


title: DR0199-deletion strains vs. wildtype strains (Cy5/Cy3) rep 3

city: Hangzhou

first: Yuejin

last: Hua

state: Zhejiang

address: 268 KaiXuan Road

department: Institute of Nuclear-Agricultural Sciences

country: China

institute: Zhejiang University

description: Biological replicate 3 of 3.

hyb_protocol: Samples were applied to microarrays enclosed in  hybridization chambers. After hybridization, slides were washed sequential. Dye-swap is carried out.

scan_protocol: Scanned on an Genepix 4000B scanner. Images were quantified using Genepix (version 5.0).

data_processing: Prior to channel normalization, microarray outputs were fitered to remove spots of poor signal quality by excluding those data points with a signal mean intensity less than two standard deviations above background in both channels.  LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Limma software was used. Furthemore, the replicate spots on each array were merged to one value using lmFit function within Limma (this step is not done in this submission).

organism: Deinococcus radiodurans

source_name: Total RNA from DR0199-deletion strains labeled with Cyanine-5 (red).

label_protocol: 16 µg of total RNA were primed with 9 µg of Hexadeoxyribonucleotide mixture at 70°C for 10 min, then reversed transcribed at 42°C for 3 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-labe

growth_protocol: Cells were grown in an normal condition.

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

tag: phenotype

value: growth delay

source_name: Total RNA from wildtype strains labeled with Cyanine-3 (green).

value: Wildtype

value: normal growth rate


title: E. coli O157:H7 interacted with lettuce rhizosphere biological rep 3 slide 5

city: st. paul

first: zhe

last: hou

state: MN

address: 1334 Eckles Ave

department: Food Science and nutrition

institute: University of Minnesota

hyb_protocol: Total RNA was converted to cDNA using the Superscript II Reverse transcriptase and directly labeled with Cy3 or Cy5 dyes (invitrogen) prior to hybridization. The labeled cDNA was applied to microarray slides. Following prehybridization, microarrays were hybridized with labeled cDNAs for 48 hours at 42°C in a water bath under dark

scan_protocol: Image analysis was carried out with the corresponding software program using a file that lists the corresponding gene to each spot. Signal intensities for each spot on scanned image files were determined using GenePix® Pro 6.0 software

data_processing: Signal intensities were normalized for spot and slide abnormalities with the spatial Lowess algorithm and analyzed by mixed-effect ANOVA (MAANOVA) (Kerr et al. 2000). Both Lowess and MAANOVA are part of the R/MAANOVA microarray statistical package, available at (http://www.jax.org/staff/churchill/labsite/). The resulting variety-by-gene interaction (VG) values of the control and experimental spot intensities were combined with the residual noise from each spot to obtain the filtered and adjusted expression values (Cui. et. al). Duplicate expression values from each array were combined, averaged and values from MAANOVA were subsequently subjected to significance analysis of microarray (SAM) data with the SAM package (Tusher. et.al). Significantly up- and down-regulated genes were identified based on a 1.5 cutoff threshold, a global false discovery rate lower than 5% (p<0.05). Six arrays representing a total of 12 replicates were analyzed between a treatment and a control.

organism: Escherichia coli

source_name: Escherichia coli EDL 933 cells interacted with the lettuce rhizosphere for 3 days

label_protocol: The total nucleic acid samples was precipitated and treated with DNase I for 30 min to remove contaminating DNA. The concentration of RNA was measured spectrophotometrically and RNA samples were electrophoresed in 0.8% agarose gels prior to use to ensure RNA integrity. The cDNA was synthesized from 10 µg of total RNA template.

growth_protocol: Escherichia coli EDL 933 were grown in 10 ml of LB medium until stationary phase, collected by centrifugation at 8,000 ×g for 10 min, and washed twice with sterilized, plant growth medium (Caspersen et al. 1999). The resultant cells were re-suspended in 10 ml of the same plant growth medium to a final concentration of approximately 10E9 cells/ml. Germinated lettuce seedlings  were each aseptically transferred into holes in the growth boxes filled with 300 ml of plant growth medium, and 3 ml washed bacterial suspension was added to provide approximately 10E7 cells/ml of growth medium. Seedling boxes were germinated for a week and  transferred to a plant growth chamber, and the aeration pump (Luft Pump; Oceanic systems Inc. Dallas, TX) was immediately started. Each pump supplied aeration of three growth boxes, at a rate of 1.3 L /min. The seedling boxes were incubated under 80% RH at 25°C with a photoperiod of 16 h for 3 days

extract_protocol: Standard hot-phenol method

treatment_protocol: Following incubation, roots had been gently rinsed to remove loosely attached bacteria and roots were cut directly into 100 ml ice cold stop solution (5 % H2O-saturated phenol, pH 4.3, in 95% ethanol).  Root extracts were filtered using 0.5 µm filters to separate bacteria cells from plant cells in order to prevent interference of the cDNA labeling. Qiagen RNA protect solution was used to stabilize RNA during extraction. Bacteria had been collected by shaking and washing and stored in -80°C until using for RNA isolation.

value: EDL 933

value: grown in lettuce rhizosphere

source_name: Escherichia coli EDL 933 cells grown in the hydroponic system without interacting with the lettuce rhizosphere for 3 days

value: grown without lettuce rhizosphere


title: E. coli O157:H7 interacted with lettuce rhizosphere biological rep 2 slide 4


title: E. coli O157:H7 interacted with lettuce rhizosphere biological rep 3 slide 6


title: BMM-6h LPS-rep1

description: BMM-6h LPS-rep1

source_name: Mouse bone marrow-derived macrophages stimulated with 10ng/ml S. minnesota lipopolysaccharide for 6h

value: male

value: 6 hours


title: genomic DNA from cord blood sample 16AB-172B

description:
Cord Blood DNA
16AB-172B

source_name: cord blood sample 16AB-172B

value: Cord Blood


title: BMM-6h LPS-rep2

description: BMM-6h LPS-rep2


title: DR0199-deletion strains vs. wildtype strains (Cy5/Cy3) rep 1

description: Biological replicate 1 of 3.


title: BMM-24h LPS-rep1

description: BMM-24h LPS-rep1


title: BMM-0h LPS-rep2

description: BMM-0h LPS-rep2


title: genomic DNA from cord blood sample 18AB-329B

description:
Cord Blood DNA
18AB-329B

source_name: cord blood sample 18AB-329B


title: wildtype strains vs. DR0199-deletion strains (Cy5/Cy3) rep 2

description: Biological replicate 2 of 3 with dye-swap.

source_name: Total RNA from wildtype strains labeled with Cyanine-5 (red).

source_name: Total RNA from DR0199-deletion strains labeled with Cyanine-3 (green).


title: E. coli O157:H7 interacted with lettuce rhizosphere biological rep 1 slide 2


title: E. coli O157:H7 interacted with lettuce rhizosphere biological rep 2 slide 3


title: genomic DNA from cord blood sample 15AB-168B

description:
Cord Blood DNA
15AB-168B

source_name: cord blood sample 15AB-168B


title: BMM-0h LPS-rep1

description: BMM-0h LPS-rep1

source_name: Mouse bone marrow-derived macrophages stimulated with 10ng/ml S. minnesota lipopolysaccharide for 0h


title: E. coli O157:H7 interacted with lettuce rhizosphere biological rep 1 slide 1


title: genomic DNA from cord blood sample 12AB-151B

description:
Cord Blood DNA
12AB-151B

source_name: cord blood sample 12AB-151B


title: BMM-2h LPS-rep1

description: BMM-2h LPS-rep1


title: genomic DNA from cord blood sample 14AB-166B

description:
Cord Blood DNA
14AB-166B

source_name: cord blood sample 14AB-166B


title: genomic DNA from cord blood sample 13AB-162B

description:
Cord Blood DNA
13AB-162B

source_name: cord blood sample 13AB-162B


title: HMDM-24h LPS-rep4

description: HMDM-24h LPS-rep4

source_name: Human monocyte-derived macrophages stimulated with 10ng/ml S. minnesota lipopolysaccharide for 24h

growth_protocol: HMDM were differentiated in vitro from CD14+ monocytes that were isolated from PBMC. PBMC were separated from buffy coat (obtained from blood donations to the Australian Red Cross Blood Service) by Ficoll-Paque density centrifugation and CD14+ monocytes were isolated by positive selection using MACS magnetic beads (Miltenyi Biotech), yielding >95% CD14+ monocytes, as assessed by surface staining and flow cytometry (data not shown). Monocyte-derived macrophages were differentiated in complete media (IMDM containing 10% FCS, 20U/ml penicillin, 20 µg/ml streptomycin and 2mM L-glutamine), containing 104U/ml (100ng/ml) recombinant human CSF-1 (Chiron) on tissue culture plastic at density of 1.5x106 monocytes/ml. HMDM were supplemented with 50% fresh medium containing CSF-1 on day 5 after seeding, replated on day 6 and used on day 7 at 1x105 HMDM/cm2. Cells were cultured at 37˚C with 5% CO2.

treatment_protocol: HMDM were treated for various times with lipopolysaccharide (LPS) from Salmonella minnesota (Sigma-Aldrich), at a final concentration of 10 ng/ml.

value: blood

value: monocyte-derived macrophages


title: genomic DNA from cord blood sample 11AB-135B

description:
Cord Blood DNA
11AB-135B

source_name: cord blood sample 11AB-135B


title: HMDM-6h LPS-rep4

description: HMDM-6h LPS-rep4

source_name: Human monocyte-derived macrophages stimulated with 10ng/ml S. minnesota lipopolysaccharide for 6h


title: Macrophage_150k Pa_18 hrs_replicate c

city: Boston

first: Alvin

middle: T.

last: Kho

state: MA

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

description:
microarray hybridization data 06/14/2010
Koziel_21.CEL

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

scan_protocol: Scanning is carried out on a Affymetrix GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System.

data_processing: All 21 sample CEL files were input into Bioconductor/R (version 2.11.10) to derive Robust Multi-Array Average (RMA) normalized output using the rma function in the affy library.

label: Biotin

source_name: Macrophage_150k Pa_18 hrs

label_protocol: In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.

growth_protocol: Cells were cultured on polyacrylamide gels of specific stiffnesses that were coated with poly-L-lysine to facilitate cellular attachment.

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

treatment_protocol: RAW 264.7 mouse macrophage cells were cultured in complete DMEM medium(10% heat-inactivated FCS), lifted off with trypsin-EDTA (GIBCO) and transferred to polyacrylamide gels for 24 hours before use. Polyacrylamide gel substrates were prepared according to previously described protocol(Krishnan et al., 2009). Concentrations for 1.2 kPa:5% Acrylamide and 0.03% Bis-acrylamide and for 150 kPa:20% Acrylamide and 0.2% Bis-acrylamide. Following gelation, the surface was activated with 200ul of a solution containing 1mM Sulfosuccinimidyl-6-[4-azido-2-nitrophenylamino] hexanoate (Sulfo-SANPAH; Pierce, Rockford, IL), coated with poly-L-lysine. Cells were allowed to adhere overnight on gels before performance of downstream experiments.

value: RAW 267.4 macrophages

tag: matrix stiffness

value: 150K Pascals

tag: duration

value: 18 hrs


title: HMDM-6h LPS-rep3

description: HMDM-6h LPS-rep3

value: LPS


title: HMDM-24h LPS-rep3

description: HMDM-24h LPS-rep3

value: 24 hours


title: HMDM-0h LPS-rep4

description: HMDM-0h LPS-rep4

source_name: Human monocyte-derived macrophages stimulated with 10ng/ml S. minnesota lipopolysaccharide for 0h

value: untreated

value: 0 hours


title: Panc-1 Gli3T 1

city: Worcester

first: Mihir

last: Rajurkar

address: 364 Plantation st, 470Q LRB

department: Cancer Biology

institute: UMASS Medical School

description: SAMPLE 4

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Cocktails were heated  at 99° for 5 minutes, then 45° for 5 minutes, and centrifuge at max speed for 1 minute. 200μl of hyb solution transfered to each array. Hybridize 16 hours at 45° at 60rpm. Fluidics washing is FS450

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Statistical analyses were performed using R, a system for statistical computation and graphics (Ihaka and Gentleman 1996; http://www.r-project.org). The RMA method in the oligo package from Bioconductor was used in R to summarize probe level data and to normalize the dataset to remove across array variation (Irizarry et al. 2003a,b;Bolstad et al., 2003). Log transformed data were used in subsequent analysis and plotting. To determine differentially expressed genes between control and knockdown, moderated T Statistics in limma (Smyth2004) was used. To adjust for multiple comparisons, p-values were adjusted using B-H method (Benjamini & Hochberg 1995) and genes with adjusted p-value <0.05 and absolute fold change >1.5 were considered potential targets for further investigation ['differentially_expressed.txt' on Series record].

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Cells were cultutured in DMEM with 10% Fetal Bovine Serum

extract_protocol: RNA was isolated from FACS sorted cells using Qiagen RNAeasy kit according to manufacturer protocol

treatment_protocol: Cells were transfected with the control vector or Gli3T expressing vector using Lipofectamine 2000 reagent.

tag: cell line

tag: transfected with

value: pCIG-Gli3T (expressing Gli3T)


title: genomic DNA from cord blood sample 9AB-102B

description:
Cord Blood DNA
9AB-102B

source_name: cord blood sample 9AB-102B

tag: birth weight (g)


title: genomic DNA from cord blood sample 10AB-104B

description:
Cord Blood DNA
10AB-104B

source_name: cord blood sample 10AB-104B

tag: gestational age (wks)


title: Macrophage_1.2k Pa_18 hrs_replicate b

description:
microarray hybridization data 06/14/2010
Koziel_17.CEL

source_name: Macrophage_1.2k Pa_18 hrs

value: 1.2K Pascals


title: HMDM-2h LPS-rep4

description: HMDM-2h LPS-rep4

source_name: Human monocyte-derived macrophages stimulated with 10ng/ml S. minnesota lipopolysaccharide for 2h

value: 2 hours


title: Macrophage_150k Pa_18 hrs_replicate b

description:
microarray hybridization data 06/14/2010
Koziel_20.CEL


title: genomic DNA from cord blood sample 8AB-101B

description:
Cord Blood DNA
8AB-101B

source_name: cord blood sample 8AB-101B

tag: birth weight (%)


title: Panc-1 Ctrl 3

description: SAMPLE 3

value: pCIG (empty vector)


title: genomic DNA from cord blood sample 6AB-A13B

description:
Cord Blood DNA
6AB-A13B

source_name: cord blood sample 6AB-A13B

tag: tissue


title: Panc-1 Gli3T 3

description: SAMPLE 6


title: HMDM-2h LPS-rep3

description: HMDM-2h LPS-rep3


title: genomic DNA from cord blood sample 7AB-A14B

description:
Cord Blood DNA
7AB-A14B

source_name: cord blood sample 7AB-A14B


title: Macrophage_1.2k Pa_18 hrs_replicate c

description:
microarray hybridization data 06/14/2010
Koziel_18.CEL


title: Panc-1 Ctrl 2

description: SAMPLE 2


title: HMDM-0h LPS-rep3

description: HMDM-0h LPS-rep3


title: Macrophage_1.2k Pa_18 hrs_replicate a

description:
microarray hybridization data 06/14/2010
Koziel_16.CEL


title: Macrophage_150k Pa_18 hrs_replicate a

description:
microarray hybridization data 06/14/2010
Koziel_19.CEL


title: Panc-1 Gli3T 2

description: SAMPLE 5


title: Panc-1 Ctrl 1

description: SAMPLE 1


title: HMDM-24h LPS-rep2

description: HMDM-24h LPS-rep2


title: Macrophage_150k Pa_6 hrs_replicate c

description:
microarray hybridization data 06/14/2010
Koziel_15.CEL

source_name: Macrophage_150k Pa_6 hrs

value: 6 hrs


title: genomic DNA from cord blood sample 4AB-A9B

description:
Cord Blood DNA
4AB-A9B

source_name: cord blood sample 4AB-A9B


title: HMDM-2h LPS-rep2

description: HMDM-2h LPS-rep2


title: genomic DNA from cord blood sample 3AB-A7B

description:
Cord Blood DNA
3AB-A7B

source_name: cord blood sample 3AB-A7B


title: control-5

city: Essen

first: Andrea

last: Kindler-Röhrborn

address: Hufeland Str. 55

department: Patholpgy & Neuropathology

country: Germany

institute: University of Essen

data_processing: The data were normalized using average normalization with Beadstudio 3.0. The average data from untreated trigeminal nerve samples is available as a Series supplementary file [control1-6_average_data.txt]

organism: Rattus norvegicus

source_name: rat trigeminal nerve

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

extract_protocol: Total RNA was extracted with TRIZOL reagent according to the manufcturers instructions. Quality control was performed with an Agilent Bioanalyser.

treatment_protocol: Newborn rats were injected sc. with N-ethyl-N-nitrosourea (ENU) (80 µg/g body weight) within postnatale day 1.

value: BDIV

value: male

value: 85 days

value: untreated trigeminal nerves (normal)


title: control-6

value: female


title: genomic DNA from cord blood sample 5AB-A12B

description:
Cord Blood DNA
5AB-A12B

source_name: cord blood sample 5AB-A12B

value: Cord Blood


title: HMDM-0h LPS-rep2

description: HMDM-0h LPS-rep2

value: blood

value: monocyte-derived macrophages


title: control-3

value: BDIX


title: Macrophage_1.2k Pa_6 hrs_replicate c

description:
microarray hybridization data 06/14/2010
Koziel_12.CEL

source_name: Macrophage_1.2k Pa_6 hrs

value: RAW 267.4 macrophages


title: genomic DNA from cord blood sample 1AB-A1B

description:
Cord Blood DNA
1AB-A1B

source_name: cord blood sample 1AB-A1B


title: HMDM-6h LPS-rep2

description: HMDM-6h LPS-rep2

source_name: Human monocyte-derived macrophages stimulated with 10ng/ml S. minnesota lipopolysaccharide for 6h

value: LPS

value: 6 hours


title: control-2

tag: parental strain

value: BDIV and BDIX

value: untreated


title: control-4

tag: strain


title: Macrophage_150k Pa_6 hrs_replicate b

description:
microarray hybridization data 06/14/2010
Koziel_14.CEL

value: 150K Pascals


title: HMDM-2h LPS-rep1

description: HMDM-2h LPS-rep1

value: 2 hours


title: HMDM-6h LPS-rep1

description: HMDM-6h LPS-rep1


title: Macrophage_1.2k Pa_6 hrs_replicate a

description:
microarray hybridization data 06/14/2010
Koziel_10.CEL

value: 1.2K Pascals

value: 6 hrs


title: Macrophage_150k Pa_6 hrs_replicate a

description:
microarray hybridization data 06/14/2010
Koziel_13.CEL


title: MT_micro tumor

description:
MT
The tumors are induced on postnatal day one with ENU. There is a latency time of several months until malignant peripheral system tumors develop after ENU treatment in the adult rat.

source_name: rat trigeminal nerve micro tumor

value: male

value: adult

value: ENU-induced malignant peripheral nerve sheath tumors (MPNSTs)

value: ENU 80 µg/g body weight on postnatal day 1


title: Macrophage_150k Pa_2 hrs_replicate c

description:
microarray hybridization data 06/14/2010
Koziel_09.CEL

source_name: Macrophage_150k Pa_2 hrs

value: 2 hrs


title: control-1

value: 85 days

value: untreated trigeminal nerves (normal)


title: T12_tumor

description:
T12
The tumors are induced on postnatal day one with ENU. There is a latency time of several months until malignant peripheral system tumors develop after ENU treatment in the adult rat.

source_name: rat trigeminal nerve tumor

value: BDIV


title: HMDM-0h LPS-rep1

description: HMDM-0h LPS-rep1

source_name: Human monocyte-derived macrophages stimulated with 10ng/ml S. minnesota lipopolysaccharide for 0h

value: blood

value: monocyte-derived macrophages

value: 0 hours


title: Macrophage_150k Pa_2 hrs_replicate a

description:
microarray hybridization data 06/14/2010
Koziel_07.CEL

value: RAW 267.4 macrophages


title: BMM_rep2_24

description: no additional information

data_processing: The scanned microarrays were  processed using Illumina Beadstudio software (no background subtraction or normalisation).  Data was normalised using Genespring.  Values below 0.01  were set to 0.01.  Each measurement was divided by the  50.0th percentile of all measurements in that sample  (per-chip normalisation). Specific samples were  normalized to one another (per-gene normalisation):  all  replica one samples were were normalized against the mean  of the replica one unstimulated control sample; and all  replica two samples were were normalized against the mean  of the replica two unstimulated control samples (which  were hybridised in technical duplicate ie. the same RNA hybridised  twice).

source_name: Mouse bone marrow-derived macrophages stimulated with 10ng/ml S. minnesota lipopolysaccharide for 24h.

label_protocol: Biotin-labelled cRNA.  Refer to the Illumina Gene Expression System Manual for details.

growth_protocol: BMM were derived from femurs of 6-8 week old, male C57Bl/6 mice. Femurs were flushed with medium and bone marrow cells were plated out in complete medium (RPMI 1640 containing 10% FCS, 20U/ml penicillin, 20 µg/ml streptomycin and 2mM L-glutamine) supplemented with 104U/ml (100ng/ml) recombinant human CSF-1 (Chiron) on bacteriological plastic plates (Bibby Sterilin) for 7 days, with refeeding on day 5 and reseeding on day 6 at 1x105 cells/cm2. All cells were cultured at 37˚C with 5% CO2.

treatment_protocol: BMM  were treated for various times with lipopolysaccharide (LPS) from Salmonella minnesota (Sigma-Aldrich), at a final concentration of 10 ng/ml.

value: bone marrow-derived macrophages

tag: lps treatment (time)

value: 24 hours


title: BMM_rep2_2

description: no additional information

hyb_protocol: Refer to the Illumina Gene Expression System Manual for details.

source_name: Mouse bone marrow-derived macrophages stimulated with 10ng/ml S. minnesota lipopolysaccharide for 2h.

value: 2 hours


title: BMM_rep2_6

description: no additional information

scan_protocol: Refer to the Illumina Gene Expression System Manual for details.

source_name: Mouse bone marrow-derived macrophages stimulated with 10ng/ml S. minnesota lipopolysaccharide for 6h.

value: 6 hours


title: Rosi-treated diabetic-5

city: Stanford

first: Kitchener

middle: D.

last: Wilson

address: S140 Grant Bldg

institute: Stanford University

hyb_protocol: cRNA was hybridized to 4×44K whole human genome microarray slides from Agilent (Part G4112F) according to the manufacturer's instructions. The hybridization was carried in a rotating hybridization chamber in the dark at 65°C for 17 h.

scan_protocol: Slides were washed with Gene Expression Wash Buffer 1 and 2 (Agilent Technologies, Santa Clara, CA) followed by Acetonitrile. A final wash in Stabilization and Drying Solution was performed to prevent Cy-5 degradation by ozone. The array was scanned using an Agilent G2505B DNA microarray scanner under extended Dynamic range.

data_processing: The image files were extracted using the Agilent Feature Extraction software version 9.5.1 applying LOWESS background subtraction and dye-normalization.

source_name: Rosi-treated diabetic

label_protocol: Using Low RNA Input Fluorescent Linear Amplification Kits (Agilent Technologies, Santa Clara, CA, USA), cDNA was reverse transcribed from each RNA sample, and cRNA was then transcribed and fluorescently labeled from each cDNA sample. The mouse heart tissue cRNA samples were labeled with Cy5 and the Universal Mouse reference cRNA was labeled with Cy3. The resulting cRNA was purified using an RNeasy kit (Qiagen, Valencia, CA, USA) followed by quantification of the cRNA by spectroscopy using an ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). 825 ng Cy3- and Cy5- labeled and amplified cRNA was mixed and fragmented according to the Agilent technology protocol.

extract_protocol: Total RNA was isolated separately from five heart samples for each condition using TRIzol reagent (Invitrogen, San Diego, CA) according to the manufacturer's instructions. Total RNA was purified using RNeasy columns (Qiagen, Chatsworth, CA). RNA concentration was measured by spectrophotometry, and RNA integrity assessed with an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA) with 6000 Nano Chips according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to 18S and 28S ribosomal RNA subunits and had a RNA Integrity Number (RIN) greater than six.

treatment_protocol: Please see our publication Wilson et al PLoS One 2008, PMID: 18648539

tag: genotype/variation

value: C57BL/KLS-leprdb/leprdb (db/db)

source_name: Universal control (Stratagene)

tag: reference

value: Universal mouse reference


title: Macrophage_150k Pa_2 hrs_replicate b

description:
microarray hybridization data 06/14/2010
Koziel_08.CEL

tag: cell type

value: 150K Pascals


title: T10_tumor

description:
T10
The tumors are induced on postnatal day one with ENU. There is a latency time of several months until malignant peripheral system tumors develop after ENU treatment in the adult rat.

value: BDIV and BDIX

tag: gender

value: male

tag: age

value: adult

value: ENU-induced malignant peripheral nerve sheath tumors (MPNSTs)

tag: treatment


title: T11_tumor

description:
T11
The tumors are induced on postnatal day one with ENU. There is a latency time of several months until malignant peripheral system tumors develop after ENU treatment in the adult rat.

value: female

value: ENU 80 µg/g body weight on postnatal day 1


title: Macrophage_1.2k Pa_6 hrs_replicate b

description:
microarray hybridization data 06/14/2010
Koziel_11.CEL

tag: matrix stiffness

value: 1.2K Pascals

value: 6 hrs


title: T9_tumor

description:
T9
The tumors are induced on postnatal day one with ENU. There is a latency time of several months until malignant peripheral system tumors develop after ENU treatment in the adult rat.


title: Macrophage_1.2k Pa_2 hrs_replicate c

description:
microarray hybridization data 06/14/2010
Koziel_06.CEL

source_name: Macrophage_1.2k Pa_2 hrs

tag: duration

value: 2 hrs


title: genomic DNA from cord blood sample 2AB-A3B

description:
Cord Blood DNA
2AB-A3B

source_name: cord blood sample 2AB-A3B

value: Cord Blood


title: Macrophage_1.2k Pa_2 hrs_replicate b

description:
microarray hybridization data 06/14/2010
Koziel_05.CEL

value: RAW 267.4 macrophages


title: BMM_rep1_24

description: no additional information

value: bone marrow-derived macrophages

value: 24 hours


title: Macrophage_1.2k Pa_2 hrs_replicate a

description:
microarray hybridization data 06/14/2010
Koziel_04.CEL


title: T8_tumor

description:
T8
The tumors are induced on postnatal day one with ENU. There is a latency time of several months until malignant peripheral system tumors develop after ENU treatment in the adult rat.


title: Macrophage_Control_0 hrs_replicate c

description:
microarray hybridization data 06/14/2010
Koziel_03.CEL

source_name: Macrophage_Control_0 hrs

value: Control

value: 0 hrs


title: BMM_rep2_0F

description: no additional information

source_name: Mouse bone marrow-derived macrophages stimulated with 10ng/ml S. minnesota lipopolysaccharide for 0h.

value: untreated


title: Rosi-treated diabetic-4

value: C57BL/KLS-leprdb/leprdb (db/db)

value: Universal mouse reference


title: T7_tumor

description:
T7
The tumors are induced on postnatal day one with ENU. There is a latency time of several months until malignant peripheral system tumors develop after ENU treatment in the adult rat.

value: BDIV and BDIX

value: male


title: BMM_rep2_0A

description: no additional information


title: BMM_rep2_0.5

description: no additional information

source_name: Mouse bone marrow-derived macrophages stimulated with 10ng/ml S. minnesota lipopolysaccharide for 0.5h.

value: 30 minutes


title: Rosi-treated diabetic-1


title: Rosi-treated diabetic-3


title: BMM_rep1_6

description: no additional information

value: 6 hours


title: Rosi-treated diabetic-2


title: BMM_rep1_2

description: no additional information

value: 2 hours


title: T5_tumor

description:
T5
The tumors are induced on postnatal day one with ENU. There is a latency time of several months until malignant peripheral system tumors develop after ENU treatment in the adult rat.

value: female

value: adult

value: ENU-induced malignant peripheral nerve sheath tumors (MPNSTs)

value: ENU 80 µg/g body weight on postnatal day 1


title: Macrophage_Control_0 hrs_replicate b

description:
microarray hybridization data 06/14/2010
Koziel_02.CEL

value: RAW 267.4 macrophages


title: BMM_rep1_0

description: no additional information

value: bone marrow-derived macrophages


title: Untreated diabetic-4

source_name: Untreated diabetic


title: T3_tumor

description:
T3
The tumors are induced on postnatal day one with ENU. There is a latency time of several months until malignant peripheral system tumors develop after ENU treatment in the adult rat.

value: BDIX


title: Untreated diabetic-2


title: Untreated diabetic-5


title: Untreated diabetic-3


title: Macrophage_Control_0 hrs_replicate a

description:
microarray hybridization data 06/14/2010
Koziel_01.CEL

value: Control


title: T6_tumor

description:
T6
The tumors are induced on postnatal day one with ENU. There is a latency time of several months until malignant peripheral system tumors develop after ENU treatment in the adult rat.


title: BMM_rep1_0.5

description: no additional information


title: Rep2 24h LPS

description: no additional information

data_processing: The scanned microarrays were  processed using Illumina Beadstudio software (no background subtraction or normalisation).  Data was normalised using Genespring.  Values below 0.01  were set to 0.01.  Each measurement was divided by the  50.0th percentile of all measurements in that sample  (per-chip normalisation). Each gene was divided by the median of its measurements in all samples.

source_name: Human monocyte-derived macrophages stimulated with 10ng/ml S. minnesota lipopolysaccharide for 24h.

value: monocyte-derived macrophages

value: 24 hours


title: T4_tumor

description:
T4
The tumors are induced on postnatal day one with ENU. There is a latency time of several months until malignant peripheral system tumors develop after ENU treatment in the adult rat.


title: Rep2 6h LPS

description: no additional information

source_name: Human monocyte-derived macrophages stimulated with 10ng/ml S. minnesota lipopolysaccharide for 6h.


title: 3T3-L1 cells 6h after hormonal induction (6h), polysomal fraction pool of RNA, replicate 2

city: Göttingen

first: Silvia

last: von der Heyde

address: Humboldtalle 32

department: Medical Statistics

institute: University Medical Center Göttingen

description:
6h_F9.10.11_AV2
3T3-L1 cells, mouse embryonic fibroblasts (preadipocytes), inducible to mature adipocytes
total + viral RNA
RNA extracted from polysomal (highly translated) fractions after sucrose gradient centrifugation

hyb_protocol: After a two-hour reaction, 1.5 μg of purified, Cy3-labeled cRNA were hybridized to an oligonucleotide M.musculus Microarray (014868, 4x44K, Agilent Technologies) for 17 hours at 65˚C, then washed according to manufacturer's protocol.

scan_protocol: Slides were scanned using an Agilent G2505C scanner, and data were extracted using Agilent's Feature Extraction software version 10.7.1.1 (Agilent Technologies).

data_processing: Signal intensities were converted to a log2 scale. Normalisation was based on the spike-ins, i.e. adjusting the signal intensities so that the means of the spike-ins in all samples have a constant value. In case of multiple probeIDs the related values were averaged.

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

growth_protocol: 3T3-L1 cells were ordered from HPACC and cultured in Dulbecco’s modified Eagle’s medium (DMEM; PAN) supplemented with 10 % newborn bovine serum (c•c•pro), 25 mM HEPES (PAN) and 1 % antibiotics (Penicillin/Streptomycin, c•c•pro) in 5 % CO2 at 37 °C. Absence of Mycoplasm was assessed by DAPI method on a regular basis.

extract_protocol: Cells were lysed mechanically in polysome buffer (300 mM KCl, 5 mM MgCl2, 10 mM PIPES pH 7.4), 0,5 % NP40, 12U RNase Inhibitor (Roche) and 100 ng/ml Cycloheximide (Sigma). To separate polysomal RNA from non-polysomal RNA, linear sucrose gradients were built from polysome buffer with 0 % to 50 % sucrose concentration (10). Cell lysate was cooled on ice and layered onto gradients which were subjected to centrifugation at 37,500 rpm (28,000 x g) in a SW40 rotor (Beckmann Optima™ L Preparative Ultracentrifuge) at 4 °C for 120 min. 13 fractions of 1 ml were collected from the top of the gradient. From 600 µl of each fraction RNA was isolated with Trizol protocol and the ratio of 18S and 28S rRNA was measured to obtain the polysome profile on Agilent 2100 Bioanalyzer. Based on the polysome profile. 200 µl of gradient fractions 5 to 7 was used for pooling samples into non-polysomal part and from fractions  9  to 11 for pooling samples into polysomal part. An appropriate amount of viral RNA (One Color Spike-In Kit; Agilent Technologies; Cat. No. 5188-5279) for 1 µg of test-RNA was added to allow for the comparison of relative RNA amounts in later analysis. The mRNA from pools was extracted by Trizol precipitation.

treatment_protocol: For differentiation, 3T3-L1 cells were cultured to confluence (day 0) and exposed to the differentiation mixture (DMEM, 10 % fetal bovine serum, 25 mM HEPES, 1 % antibiotics, 0.5 mM isobutylmethylxanthine, 1 µM dexamethasone, 5 µg/ml insulin; all from Sigma). 3T3-L1 cells were harvested at day 0 (T0, without hormonal induction) and 6 h after hormonal induction (T6).

tag: cell line

tag: time

value: 6 h

tag: fraction

value: polysomal


title: Untreated diabetic-1

value: C57BL/KLS-leprdb/leprdb (db/db)

value: Universal mouse reference


title: T2_tumor

description:
T2
The tumors are induced on postnatal day one with ENU. There is a latency time of several months until malignant peripheral system tumors develop after ENU treatment in the adult rat.

value: BDIV and BDIX

value: male


title: 3T3-L1 cells 6h after hormonal induction (6h), polysomal fraction pool of RNA, replicate 3

description:
6h_F9.10.11_AV3
3T3-L1 cells, mouse embryonic fibroblasts (preadipocytes), inducible to mature adipocytes
total + viral RNA
RNA extracted from polysomal (highly translated) fractions after sucrose gradient centrifugation

value: DMEM, 10 % fetal bovine serum, 25 mM HEPES, 1 % antibiotics, 0.5 mM isobutylmethylxanthine, 1 µM dexamethasone, 5 µg/ml insulin


title: T1_tumor

description:
T1
The tumors are induced on postnatal day one with ENU. There is a latency time of several months until malignant peripheral system tumors develop after ENU treatment in the adult rat.

value: female


title: Nondiabetic-5

source_name: Nondiabetic

value: C57BL/KLS-leprdb/lepr+ (db/+)


title: 3T3-L1 cells 6h after hormonal induction (6h), polysomal fraction pool of RNA, replicate 1

description:
6h_F9.10.11_AV1
3T3-L1 cells, mouse embryonic fibroblasts (preadipocytes), inducible to mature adipocytes
total + viral RNA
RNA extracted from polysomal (highly translated) fractions after sucrose gradient centrifugation


title: Nondiabetic-4


title: 3T3-L1 cells 6h after hormonal induction (6h), non-polysomal fraction pool of RNA, replicate 2

description:
6h_F5.6.7_AV2
3T3-L1 cells, mouse embryonic fibroblasts (preadipocytes), inducible to mature adipocytes
total + viral RNA
RNA extracted from non-polysomal (untranslated) fractions after sucrose gradient centrifugation

value: non-polysomal


title: 3T3-L1 cells 6h after hormonal induction (6h), non-polysomal fraction pool of RNA, replicate 3

description:
6h_F5.6.7_AV3
3T3-L1 cells, mouse embryonic fibroblasts (preadipocytes), inducible to mature adipocytes
total + viral RNA
RNA extracted from non-polysomal (untranslated) fractions after sucrose gradient centrifugation


title: Rep2 2h LPS

description: no additional information

source_name: Human monocyte-derived macrophages stimulated with 10ng/ml S. minnesota lipopolysaccharide for 2h.

value: 2 hours


title: Nondiabetic-1


title: 3T3-L1 cells 6h after hormonal induction (6h), non-polysomal fraction pool of RNA, replicate 1

description:
6h_F5.6.7_AV1
3T3-L1 cells, mouse embryonic fibroblasts (preadipocytes), inducible to mature adipocytes
total + viral RNA
RNA extracted from non-polysomal (untranslated) fractions after sucrose gradient centrifugation


title: Nondiabetic-2


title: 3T3-L1 cells harvested at day 0 without hormonal induction (0h), polysomal fraction pool of RNA, replicate 3

description:
0h_F9.10.11_AV3
3T3-L1 cells, mouse embryonic fibroblasts (preadipocytes), inducible to mature adipocytes
total + viral RNA
RNA extracted from polysomal (highly translated) fractions after sucrose gradient centrifugation

value: untreated


title: Rep2 0.5h LPS

description: no additional information

source_name: Human monocyte-derived macrophages stimulated with 10ng/ml S. minnesota lipopolysaccharide for 0.5h.

value: 30 mins


title: Rep1 24h LPS

description: no additional information


title: Rep2 0h LPS

description: no additional information

source_name: Human monocyte-derived macrophages stimulated with 10ng/ml S. minnesota lipopolysaccharide for 0h.


title: Nondiabetic-3


title: Rep1 6h LPS

description: no additional information

value: 6 hours


title: 3T3-L1 cells harvested at day 0 without hormonal induction (0h), polysomal fraction pool of RNA, replicate 1

description:
0h_F9.10.11_AV1
3T3-L1 cells, mouse embryonic fibroblasts (preadipocytes), inducible to mature adipocytes
total + viral RNA
RNA extracted from polysomal (highly translated) fractions after sucrose gradient centrifugation


title: Rep1 0.5h LPS

description: no additional information


title: 3T3-L1 cells harvested at day 0 without hormonal induction (0h), non-polysomal fraction pool of RNA, replicate 3

description:
0h_F5.6.7_AV3
3T3-L1 cells, mouse embryonic fibroblasts (preadipocytes), inducible to mature adipocytes
total + viral RNA
RNA extracted from non-polysomal (untranslated) fractions after sucrose gradient centrifugation


title: HMDM-24h LPS-rep1

description: HMDM-24h LPS-rep1

source_name: Human monocyte-derived macrophages stimulated with 10ng/ml S. minnesota lipopolysaccharide for 24h

value: blood

value: LPS

tag: treatment time


title: Endothelial MP-rep1

city: Suita

first: Hisamichi

last: Naito

state: Osaka

address: Yamada-oka 3-1

department: Signal Transduction

country: Japan

institute: The Research Institute for Microbial Diseases

description: EC-MP (MP1)

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr on Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with AGCC (Affymetrix GeneChip Command Console), Affymetrix expression console and GeneSpring GX 10.0.

source_name: mouse CD31+CD45- main population

label_protocol: Biotinylated cRNA were prepared with Two-cycle Target Labeling Protocol according to the standard Affymetrix protocol from 10 ng total RNA

growth_protocol: Wild type mice were bred conventionally

extract_protocol: RNA was extracted using an RNeasy Mini Kit (Qiagen)

treatment_protocol: Hindlimb muscle were minced and dispersed with dispase and collagenase

value: endothelial cells from hindlimb

value: 8 weeks


title: Endothelial MP-rep2


title: Rep1 2h LPS

description: no additional information

value: monocyte-derived macrophages


title: 3T3-L1 cells harvested at day 0 without hormonal induction (0h), non-polysomal fraction pool of RNA, replicate 2

description:
0h_F5.6.7_AV2
3T3-L1 cells, mouse embryonic fibroblasts (preadipocytes), inducible to mature adipocytes
total + viral RNA
RNA extracted from non-polysomal (untranslated) fractions after sucrose gradient centrifugation


title: Rep1 0h LPS

description: no additional information


title: Endothelial SP-rep1

description: EC-SP (SP1)

source_name: mouse CD31+CD45- side population


title: CRSwNP UT-2

status: Public on Mar 28 2012

city: Chicago

first: Atsushi

last: Kato

state: IL

address: 240 E. Huron St.

department: Allergy-Immunology Division

institute: Northwestern University Feinberg School of Medicine

description: Sinonasal and nasal polyp tissues were obtained from routine Functional Endoscopic Sinus Surgery in patients with CRS. Sinus tissues from disease-free control subjects were obtained during endoscopic skull base brain tumor excisions as well as intranasal

hyb_protocol: Started from 100ng total RNA, 3.75ug labeled cDNA was hybridized on Affymetrix U133 Plus 2.0 arrays. GeneChips were washed and stained using the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned on an Affymetrix 7G GeneChip Scanner.

data_processing: Normalized data was generated by GeneSpring software version 7.2 (Agilent). To normalize the variations in staining intensity among chips, the 'Average Difference' values for all genes on a given chip were divided by the median value for expression of all genes on the chip. ABS_CALL was calculated by GeneChip Command Console Software version 3.2 and Average Difference value of microarray was generated by  MAS5.

source_name: Uncinate tissue from patient with CRSwNP

label_protocol: NuGEN Ovation RNA Amplification System V2 was used for cDNA amplification and Biotin Labeling Module to prepare cDNA for hybridization (using manufacturer’s protocol).

extract_protocol: Total RNA from sinus tissue was extracted using QIAzol (Qiagen, Valencia, CA) and was cleaned and treated with DNase I using RNeasy according to the manufacturer's instructions.

tag: disease

value: Chronic rhinosinusitis (CRS)

tag: crs type

value: CRS with nasal polyps (CRSwNP)

value: uncinate tissue (UT)


title: 3T3-L1 cells harvested at day 0 without hormonal induction (0h), non-polysomal fraction pool of RNA, replicate 1

description:
0h_F5.6.7_AV1
3T3-L1 cells, mouse embryonic fibroblasts (preadipocytes), inducible to mature adipocytes
total + viral RNA
RNA extracted from non-polysomal (untranslated) fractions after sucrose gradient centrifugation


title: MRS4012

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

country: Netherlands

institute: NIZO food research

description: Biological replicate 2 of 2, technical replicate 1 of 3.

hyb_protocol: Hybridization buffer (Agilent In Situ Hybridization Kit Plus) was added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers at 65 degrees Celsius for 17 h. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5).

data_processing: Signals of the scanned slides were corrected for background signal, log2 transformed and subsequently normalised using quantile normalization as described in Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64.

organism: Lactiplantibacillus plantarum WCFS1

source_name: bacterial cells

label_protocol: Annealing Mix x µl RNA preparation (=5µg) y µl nuclease-free water 1 µl Random Nonamers 11 µl TOTAL 1. mix Annealing Mix in a 200 µl PCR tube gently by pipetting up and down 2. incubate for 5' 70°C 3. cool at room temperature for 10' (annealing) 4. spin down the mixture to the bottom of the tube 5. place on ice Reverse transcription Reverse Transcription Mix 4 µl 5x buffer 2 µl 0.1 M DTT 1 µl dNTP-mix 1 µl AA-dUTP 1 µl TMIII (keep only briefly outside 20°C) 20 µl TOTAL 1. Mix by very gently by pipetting up and down (vigorous pipetting will denature the enzyme!) 2. Incubate for 3 hrs at 42°C (in PCR-machine) 3. Cool on ice for immediate purification or place at 20°C for storage Degradation of mRNA 1. Add 2 µl 2,5 M NaOH 2. Mix (vortex) and spin down 3. Incubate for 15 min. at 37°C 4. Add 10 µl 2 M HEPES free acid 5. Mix (vortex) and spin down 6. Ready for purification or store at 20°C Labelling and purification of cDNA with cyanine dyes Followed GE Healthcare kit Amersham CyDye (Cy3/Cy5) Reactive Dye Protocols for Post Labelling Aminoallyl-cDNA and Aminoallyl-aRNA code RPN5661 Labelling of amino allyl-modified cDNA with CyDye 1. Add the amino allyl modified cDNA (in 0.1 M sodium bicarbonate) directly into one aliquot of CyDye NHS Ester. Resuspend the ester completely by pipetting several times and transfer the solution to an amber 1.5 ml tube 2. Incubate at room temperature, in the dark for 60 to 90 minutes 3. Add 15 µl 4 M Hydroxylamine to each coupling reaction 4. Mix by stirring and incubate at room temperature, in the dark, for 15 minutes 5. Proceed directly to purification of CyDye-labelled cDNA Purification of CyDye labelled cDNA Followed GE Healthcare kit Amersham CyDye (Cy3/Cy5) Reactive Dye Protocols for Post Labelling Aminoallyl-cDNA and Aminoallyl-aRNA code RPN5661.

growth_protocol: Cultures were grown in MRS at 37˚C without agitation.

extract_protocol: Cultures were lysed by beat-beating, and total RNA was isolated by subsequent phenol-chloroform extraction.

treatment_protocol: Harvested cultures were immediately pelleted at 4570xg and 4˚C.


title: CRSwNP polyp-6

source_name: Nasal polyp tissue from patient with CRSwNP

tag: tissue

value: nasal polyp (NP) tissue


title: CRSwNP UT-4


title: Endothelial SP-rep2

tag: strain


title: MRS4013

description: Biological replicate 2 of 2, technical replicate 2 of 3.


title: CRSwNP UT-6


title: CRSwNP UT-5


title: CRSwNP polyp-1


title: CRSwNP polyp-3


title: CRSwNP UT-3


title: CRSwNP polyp-4


title: CRSwNP polyp-5


title: CRSwNP UT-1


title: MRS4014

description: Biological replicate 2 of 2, technical replicate 3 of 3.


title: CRSwNP polyp-2


title: CRSsNP UT-5

source_name: Uncinate tissue from patient with CRSsNP

value: CRS without nasal polyps (CRSsNP)


title: CRSsNP UT-3


title: CRSsNP UT-6


title: CRSsNP UT-2


title: Control UT-6

source_name: Uncinate tissue from control subject


title: Control UT-3


title: CRSsNP UT-4


title: Control UT-5


title: Control UT-4


title: Control UT-2


title: Control UT-1


title: 3T3-L1 cells harvested at day 0 without hormonal induction (0h), polysomal fraction pool of RNA, replicate 2

description:
0h_F9.10.11_AV2
3T3-L1 cells, mouse embryonic fibroblasts (preadipocytes), inducible to mature adipocytes
total + viral RNA
RNA extracted from polysomal (highly translated) fractions after sucrose gradient centrifugation

value: polysomal


title: MMRC0206_1_GEP

city: Phoenix

first: Jonathan

middle: J

last: Keats

state: Arizona

address: 445 N. Fifth Street

department: Integrated Cancer Genomics

institute: Translational Genomics Research Institute (TGen)

description: Single sample standard labeling and hybridization

hyb_protocol: Labeled cRNA was hybridized to U133Plus2.0 GeneChips in a GeneChip Hybridization Oven 640 and washed using a GeneChip Fluidics Station 450 as per the manufacturers protocol

scan_protocol: Arrays were scanned using a GeneChip Scanner 3000 following the recommendations of the manufacturer

data_processing: Signal estimates were generated in Expression Console (Affymetrix) using the MAS5 algorithm with default settings

source_name: MMRC0206_1 RNA

label_protocol: 2 ug of Total RNA was labeled using the One-Cycle Target Labeling kit from Affymetrix as per the manufacturers suggestion

growth_protocol: Bone marrow aspirates were attained from patients after they signed informed consent documetnation

extract_protocol: RNA was extracted from cells using  TRIzol (Invitrogen) in combination with PureLink Micro-to-Midi RNA columns (Invitrogen) using the manufacturers protocol. RNA samples were tested for purity and concentration on a Nanodrop spectrophotometer and quality checked on an Agilent Bioanalyzer

treatment_protocol: CD138 positive tumor cells were isolated from bone marrow aspirates using magnetic sorting, both Miltenyi and Stem Cell Technologies

value: CD138 Positive Myeloma Cells

tag: sample order

tag: tc class

tag: cyto risk

value: high

tag: 17p13 deletion

value: biallelic

tag: ploidy

value: non-hyperdiploid

tag: uams 70gene index

value: good

tag: copy number abnormalities

tag: time since sample1 months


title: MMRC0161_2_GEP

source_name: MMRC0161_2 RNA

tag: cell type

value: low

value: no

value: hyperdiploid


title: MMRC0161_1_GEP

source_name: MMRC0161_1 RNA


title: MC1484_MCA0436_BM_CD138pos_GEP

source_name: MC1484_MCA0436_BM_CD138pos RNA

value: maf


title: MMRC0154_1_GEP

source_name: MMRC0154_1 RNA


title: MC1472_MCA0658_BM_CD138pos_GEP

source_name: MC1472_MCA0658_BM_CD138pos RNA


title: MMRC0191_1_GEP

source_name: MMRC0191_1 RNA


title: MMRC0035_1_GEP

source_name: MMRC0035_1 RNA

value: poor


title: MMRC0155_2_GEP

source_name: MMRC0155_2 RNA


title: MMRC0191_2_GEP

source_name: MMRC0191_2 RNA


title: MC1059_MCA0433_BM_CD138pos_GEP

source_name: MC1059_MCA0433_BM_CD138pos RNA


title: MMRC0124_1_GEP

source_name: MMRC0124_1 RNA


title: MMRC0206_2_GEP

source_name: MMRC0206_2 RNA

value: monoallelic


title: MMRC0359_2_GEP

source_name: MMRC0359_2 RNA


title: MC1130_MCA0798_PB_CD138pos_U133P2

source_name: MC1130_MCA0798_PB_CD138pos RNA


title: MMRC0395_2_GEP

source_name: MMRC0395_2 RNA


title: MC1130_MCA0119_BM_CD138pos_GEP

source_name: MC1130_MCA0119_BM_CD138pos RNA


title: MC1472_MCA0404_BM_CD138pos_GEP

source_name: MC1472_MCA0404_BM_CD138pos RNA


title: MC0678_PreTx_GEP

source_name: MC0678_PreTx RNA


title: MMRC0359_1_GEP

source_name: MMRC0359_1 RNA


title: MC0678_PostTx_GEP

source_name: MC0678_PostTx RNA


title: MC0474_MCA0491_BM_CD138pos_GEP

source_name: MC0474_MCA0491_BM_CD138pos RNA


title: MMRC0395_1_GEP

source_name: MMRC0395_1 RNA


title: CRSsNP UT-1

source_name: Uncinate tissue from patient with CRSsNP

value: Chronic rhinosinusitis (CRS)


title: MMRC0154_2_GEP

source_name: MMRC0154_2 RNA


title: MC0506_MCA0147_BM_CD138pos_GEP

source_name: MC0506_MCA0147_BM_CD138pos RNA


title: MMRC0155_1_GEP

source_name: MMRC0155_1 RNA


title: MC1272_MCA0123_BM_CD138pos_GEP

source_name: MC1272_MCA0123_BM_CD138pos RNA


title: MC0391_MCAxxx1_BM_CD138pos_GEP

source_name: MC0391_MCAxxx1_BM_CD138pos RNA


title: MC0005_MCRxxx3_BM_CD138pos_GEP

source_name: MC0005_MCRxxx3_BM_CD138pos RNA


title: MC0134_MCRxxx5_BM_CD138pos_GEP

source_name: MC0134_MCRxxx5_BM_CD138pos RNA


title: MC0007_MCRxxx4_BM_CD138pos_GEP

source_name: MC0007_MCRxxx4_BM_CD138pos RNA


title: MC0004_MCR1470_BM_CD138pos_GEP

source_name: MC0004_MCR1470_BM_CD138pos RNA


title: No_cluster  rep C4.1 (ONH)

city: Mount Desert

first: Gareth

middle: Rhys

last: Howell

address: 600 Main Street

institute: The Jackson Laboratory

hyb_protocol: 2.5 μg of each biotin-labeled and fragmented cDNA sample was then hybridized onto Mouse Genome 430 v2.0 GeneChip™ arrays (Affymetrix, Santa Clara, CA). Post-hybridization staining and washing were performed according to the manufacturer's protocols using the Fluidics Station 450 instrument (Affymetrix).

scan_protocol: the arrays were scanned with a GeneChipTM Scanner 3000 laser confocal slide scanner.

data_processing: The images were quantified using GeneChipTM Operating Software (GCOS) v1.2. Probe level data were imported into the R statistical software environment and expression values for each probe set on the array were summarized using the Robust MultiChip Average (RMA) method with quantile normalization in the R/affy package

source_name: Optic nerve head

label_protocol: For RNA labeling and microarray processing, Biotin-labeled cDNA was synthesized separately from 20ng of each total RNA sample per the manufacturer’s protocols (Ovation™ Biotin System (NuGEN, San Carlos, CA).

extract_protocol: For RNA preparation, total RNA was isolated using the RNeasy Micro Kit (Qiagen, Valencia, CA).

treatment_protocol: the optic nerve head was excised using a sharpened 1 mm glass capillary centered over the optic nerve. The punched out nerve head was immediately placed in RNAlater® (Ambion, Austin TX).

tag: glaucoma

value: glaucoma

tag: radiation

value: Radiation treatment

tag: mouse strain

tag: gender

value: Female

tag: age (mos)


title: No_cluster  rep B3.3 (ONH)

value: No radiation treatment


title: MC0002_MCA0122_BM_CD138pos_GEP

source_name: MC0002_MCA0122_BM_CD138pos RNA


title: No_cluster  rep B1.8 (ONH)

value: control


title: No_cluster  rep B2.7 (ONH)


title: MC0004_MCR2845_BM_CD138pos_GEP

source_name: MC0004_MCR2845_BM_CD138pos RNA

value: CD138 Positive Myeloma Cells


title: MC0391_MCA0479_BM_CD138pos_GEP

source_name: MC0391_MCA0479_BM_CD138pos RNA


title: MC0134_MCR1312_BM_CD138pos_GEP

source_name: MC0134_MCR1312_BM_CD138pos RNA


title: No_cluster  rep C5.2 (ONH)


title: No_cluster  rep C5.7 (ONH)


title: MC0474_MCA0142_BM_CD138pos_GEP

source_name: MC0474_MCA0142_BM_CD138pos RNA


title: No_cluster  rep C5.8 (ONH)


title: No_cluster  rep B3.8 (ONH)


title: No_cluster  rep C3.8 (ONH)


title: MC0007_MCR3642_BM_CD138pos_GEP

source_name: MC0007_MCR3642_BM_CD138pos RNA


title: No_cluster  rep B3.7 (ONH)


title: No_cluster  rep C5.3 (ONH)


title: No_cluster  rep B1.1 (ONH)


title: No_cluster  rep C3.2 (ONH)


title: MC0391_MCA0375_BM_CD138pos_GEP

source_name: MC0391_MCA0375_BM_CD138pos RNA


title: MC0003_MCA0650_PB_CD138pos_GEP

source_name: MC0003_MCA0650_PB_CD138pos RNA


title: MC0005_MCRxxx2_BM_CD138pos_GEP

source_name: MC0005_MCRxxx2_BM_CD138pos RNA

value: high


title: No_cluster  rep C4.5 (ONH)


title: No_cluster  rep C5.6 (ONH)


title: No_cluster  rep B2.8 (ONH)


title: No_cluster  rep C5.1 (ONH)


title: MC0002_MCA0061_BM_CD138pos_GEP

source_name: MC0002_MCA0061_BM_CD138pos RNA


title: HF+CR_2

city: Beijing

first: Bing

last: Zhou

address: Datun Road

department: Center for Molecular Systems Biology

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hours at 45℃, 60 rpm on GeneChip mouse 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene array Scanner7000.

data_processing: Signal intensity was normalized using quantile algorithm.

source_name: High-fat diet, calorie restriction

label_protocol: Biotinylated cRNA were prepared according to the manufacturer's instructions.

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

value: male

tag: age

value: 62 weeks

value: liver


title: HF+Ex_2

source_name: High-fat diet, exercise

tag: tissue


title: HF+CR_1

tag: strain


title: LF_8M

data_processing: Signal intensity was normalized using RMA algorithm.

source_name: Low-fat diet, ad libitum, 8 months

value: 8 months


title: LF_4M

source_name: Low-fat diet, ad libitum, 4 months

value: 4 months


title: LF_21M

source_name: Low-fat diet, ad libitum, 21 months

value: 21 months


title: LF+CR_1

source_name: Low-fat diet, calorie restriction


title: LF_13M

source_name: Low-fat diet, ad libitum, 13 months

value: 13 months


title: HF_2

source_name: High-fat diet, ad libitum


title: LF+CR_2


title: HF+Ex_3


title: LF_3

source_name: Low-fat diet, ad libitum


title: HF_3


title: LF+Ex_1

source_name: Low-fat diet, exercise


title: HF+CR_3


title: LF_2


title: LF+CR_3


title: LF+Ex_2


title: HF+Ex_1


title: LF_1


title: HF_1


title: Stg1A rep B2.1 (ONH)

scan_protocol: The arrays were scanned with a GeneChipTM Scanner 3000 laser confocal slide scanner.

source_name: Stg1A rep B2.1 (ONH)


title: Stg1C rep B3.9 (ONH)

source_name: Stg1C rep B3.9 (ONH)


title: Rad-D2 rep C5.9 (ONH)

source_name: Rad-D2 rep C5.9 (ONH)


title: Stg1B rep B2.4 (ONH)

source_name: Stg1B rep B2.4 (ONH)


title: Stg1B rep B2.6 (ONH)

source_name: Stg1B rep B2.6 (ONH)


title: Stg1C rep B3.6 (ONH)

source_name: Stg1C rep B3.6 (ONH)


title: D2-Gp2 rep B1.4 (ONH)

source_name: D2-Gp2 rep B1.4 (ONH)


title: Stg1B rep B2.10 (ONH)

source_name: Stg1B rep B2.10 (ONH)


title: D2-Gp2 rep B1.7 (ONH)

source_name: D2-Gp2 rep B1.7 (ONH)


title: D2-Gp1 rep B6 (ONH)

source_name: D2-Gp1 rep B6 (ONH)


title: Stg1B rep B3.5 (ONH)

source_name: Stg1B rep B3.5 (ONH)


title: D2-Gp2 rep B1.2 (ONH)

source_name: D2-Gp2 rep B1.2 (ONH)


title: Stg1A rep B3.10 (ONH)

source_name: Stg1A rep B3.10 (ONH)


title: Rad-D2 rep C5.4 (ONH)

source_name: Rad-D2 rep C5.4 (ONH)


title: Rad-D2 rep C4.9 (ONH)

source_name: Rad-D2 rep C4.9 (ONH)


title: Stg1B rep B2.5 (ONH)

source_name: Stg1B rep B2.5 (ONH)


title: Rad-D2 rep C3.10 (ONH)

source_name: Rad-D2 rep C3.10 (ONH)


title: D2-Gp2 rep B1.3 (ONH)

source_name: D2-Gp2 rep B1.3 (ONH)


title: D2-Gp1 rep B10 (ONH)

source_name: D2-Gp1 rep B10 (ONH)


title: Stg1B rep B2.9 (ONH)

source_name: Stg1B rep B2.9 (ONH)


title: Stg1A rep B3.1 (ONH)

source_name: Stg1A rep B3.1 (ONH)


title: Stg1B rep B3.2 (ONH)

source_name: Stg1B rep B3.2 (ONH)


title: Rad-D2 rep C3.4 (ONH)

source_name: Rad-D2 rep C3.4 (ONH)


title: Rad-D2 rep C5.10 (ONH)

source_name: Rad-D2 rep C5.10 (ONH)


title: Stg1B rep B2.3 (ONH)

source_name: Stg1B rep B2.3 (ONH)


title: Stg1C rep B3.4 (ONH)

source_name: Stg1C rep B3.4 (ONH)


title: Stg1A rep B2.2 (ONH)

source_name: Stg1A rep B2.2 (ONH)


title: Rad-D2 rep C5.5 (ONH)

source_name: Rad-D2 rep C5.5 (ONH)


title: D2-Gp2 rep B1.5 (ONH)

source_name: D2-Gp2 rep B1.5 (ONH)


title: LF+Ex_3

source_name: Low-fat diet, exercise


title: Myc DMI3 roots early stages biological replicate 1

city: Hannover

first: Helge

last: Küster

address: Herrenhäuser Str. 2

department: Institut für Pflanzengenetik

institute: Leibniz Universität Hannover

description: Gene expression data from Gigaspora margarita-colonized Medicago truncatula root fragments at 5 days post inoculation

hyb_protocol: 12.5 μg of fragmented aRNA was added to a 250 μl hybridization cocktail also containing hybridization controls. 200 μl of the mixture was hybridized on GeneChips for 16 h at 45°C. Standard post hybridization wash and double-stain protocols (FS450_0001; GeneChip HWS kit; Affymetrix, Santa Clara, CA, USA) were used on an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned on an Affymetrix GeneChip scanner 3000 7G.

data_processing: Cel files obtained from Medicago GeneChip hybridizations were analysed using the Robin software (http://mapman.gabipd.org/web/guest/robin). Normalization was performed across all GeneChips using the Robust Multichip Average (RMA) algorithm. Intensity values calculated for each probe set were log2-transformed and averaged across all three biological replicates. Log2 differences between the conditions studied were evaluated statistically by applying a false discovery rate (FDR) correction for p-values implemented in Robin.

organism: Medicago truncatula

label_protocol: RNA was processed for use on Affymetrix (Santa Clara, CA, USA) GeneChip Medicago Genome Arrays, according to the manufacturer’s GeneChip 3’ IVT Express kit user manual. Briefly, 100 ng of total RNA with by a RIN number (Agilent 2100 Bioanalyzer, Agilent, Böblingen, Germany) of at least 8.5 containing spiked-in poly-A+ RNA controls was used in a reverse transcription reaction (GeneChip 3’ IVT Express Kit; Affymetrix) to generate first-strand cDNA. After secondstrand synthesis, double-stranded cDNA was used in a 16 h in vitro transcription (IVT) reaction to generate aRNA (GeneChip 3’ IVT Express Kit; Affymetrix). Size distribution of in vitro transcribed aRNA and fragmented aRNA, respectively, was assessed via an Agilent 2100 Bioanalyzer, using an RNA 6000 Nano Assay.

growth_protocol: Hairy roots of Medicago truncatula Gaertn cv Jemalong genotypes A17 and DMI3 were maintained in Petri dishes containing M medium and covered with Biofolie 25™ (Sartorius).

extract_protocol: Root fragments were taken from frozen stocks, and ground using using a Retsch® ball mill for 2 min. RNA was then extracted using the total RNA isolation system (Promega). Integrity of RNA samples was checked using a Biorad Experion Bioanalyzer, while RNA purity was determined by a NanoDrop, ensuring spectrophotometric ratios of A260nm/A280nm ~ 2 and A260nm/A230nm ≥ 2. Removal of genomic DNA was done via  the Turbo DNA-free™ reagent (Ambion, Austin, TX, USA) following the manufacturer’s instructions. Absence of genomic DNA was verified by RT-PCR using a One-step kit (Qiagen) with specific primer for M. truncatula elongation factor alpha (MtTefalpha).

treatment_protocol: Hairy roots were inoculated with 8 spores of G.margarita BEG 3. Fungal spores originated  from pot cultures of  mycorrhizal  clover, vernalized  at 4°C for 2 weeks and surface sterilized  with 3% (w/v) chloramine and streptomycin.

value: Root

tag: genotype

value: Jemalong DMI3

value: 5 days

tag: treatment

value: Gigaspora margarita-colonized


title: Myc DMI3 roots early stages biological replicate 3

source_name: Gigaspora margarita-colonized Medicago truncatula root fragments at 5 days post inoculation


title: Rad-D2 rep C4.3 (ONH)

source_name: Rad-D2 rep C4.3 (ONH)

value: glaucoma

value: Radiation treatment


title: MC0496_MCR1643

description: Competitive Oligo CGH assay, MC0496_MCR1643 versus Promega Female DNA

hyb_protocol: hybridizations were carried out as suggested in the Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol Version 6.2 (October 2009)

scan_protocol: scans were carried out as suggested in the Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol Version 6.2 (October 2009) with both PMTs at 100%

data_processing: Raw data was extracted from TIFF image files by  Agilent Feature extraction using the 013282_D_20050516 grid file

label_protocol: genomic DNA was digested with AluI and RsaI, digested DNA was labeled using the Invitrogen BioPrime Labeling kit, Test tumor samples were labeled with Cy5 and control DNA were labeled with Cy3

growth_protocol: Bone marrow aspirates were attained from patients after they signed informed consent documentation

extract_protocol: DNA was extracted from cell lysates stored in TRIzol

treatment_protocol: CD138 positive tumor cells were isolated from bone marrow aspirates using magnetic sorting, both Miltenyi and Stemcell Technologies

tag: sample order

tag: tc class

tag: cyto risk

value: low

value: no

value: hyperdiploid

source_name: Promega Female DNA

tag: reference

value: Promega Female DNA


title: MDCK_pH7.4_rep4

city: Los Angeles

first: Thomas

middle: Thong

last: Nguyen

address: 11301 Wilshire Blvd

institute: Sachs Lab

description: Gene expression after 24H incubation in pH 7.4 media

hyb_protocol: To prepare the cRNA for hybridization the Agilent Fragmentation mix was used according to the Quick Amp Protocol. After a 30 minute incubation period at 60º C, 55uL of 2x GE Hybridization Buffer HI-RPM was added to each reaction tube. Samples were then vortexed and briefly spun for 1 minute at 13,000 RPM to collect the sample at the bottom of the tube. Samples were then loaded onto the microarray slides and incubated in a hybridization chamber for 17 hours at 65 º C. The preparation was then washed with Agilent’s Gene Expression Wash Buffer 1 and 2 (with Triton X) according to the protocol and scanned using the DNA Microarray Scanner11.0.2.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014868_D_F_20101102) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Data were filtered by expression (20-100%) using GeneSpring GX Software 11.5.1. All data with at least a two- fold change compared to control were subjected to a T-test. Only those genes whose expression was altered by at least 2 fold with a P-value less than 0.05 were considered to represent significantly regulated genes.

organism: Canis lupus familiaris

source_name: Renal tubule cells, pH 7.4, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0 ug RNA using the One-Color Microarray-Based Gene Expression Analysis Quick Amp Labeling protocol (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 (3.7.1) Spectrophotometer.

growth_protocol: Madin Darby Canine Kidney cells (MDCK) were obtained from the American Type Culture Collection.  Cells were grown to confluence in 5 ml of DMEM with fetal bovine serum (pH 7.3 to 7.4) for 3 to 5 days in an aerobic environment 20% O2, 5% CO2 and 75% N2 at 37ºC. Twenty-four hours prior to the experiment, culture media was switched to serum-free DMEM/Hams-F-12 pH 7.4.

extract_protocol: Total RNA was isolated from the MDCK cells held at pH 7.4 or 7.0 for 24hrs using TRIzol reagent (Invitrogen, Carlsbad, California) combined with RNeasy columns (Qiagen, Valencia, California) and the Qiagen Eukaryotic RNA isolation kit. The cells were collected from the experimental flask and lysed in 1 ml  of TRIzol reagent. To the extract the RNA from the lysed cells, 100mL of chloroform was added per 500ul of cell lysate. The cell extraction mixtures were repeatedly inverted in a microcentrifuge tube for 15 seconds, after which they were centrifuged at 12,000 rpm at 4ºC for 10 min. The clear supernatant was mixed with 250 mL of ethanol, transferred to the RNAeasy Spin column and RNA purification was performed following the manufacturer’s instructions. The RNA concentration was quantified by absorbance at 260nm, and the quality was evaluated by capillary electrophoresis using a model 2100 Bioanalyzer with a RNA 6000 Nano Assay kit (Agilent Technologies).

treatment_protocol: On the day of study, cells were divided and placed either in media with a pH of 7.4 or one with a pH of 7.0 produced by reducing media bicarbonate concentration. They were then returned to the incubator for periods of 24 hours.  The pH of the media while residing in the incubator was confirmed by measuring pH with an in situ pH electrode.

value: Madin Darby Canine Kidney cells (MDCK)

tag: ph

value: Physiological


title: MDCK_pH7.0_rep5

description: Gene expression after 24H incubation in pH 7.0 media

source_name: Renal tubule cells, pH 7.0, replicate 5

value: Acidic


title: MDCK_pH7.0_rep1

source_name: Renal tubule cells, pH 7.0, replicate 1


title: Myc DMI3 roots early stages biological replicate 2


title: MC0134_MCR0881

description: Competitive Oligo CGH assay, MC0134_MCR0881 versus Promega Female DNA

value: CD138 Positive Myeloma Cells

tag: 17p13 deletion

tag: ploidy

tag: uams 70gene index

tag: copy number abnormalities

tag: time since sample1 months


title: MC0518_MCR0917

description: Competitive Oligo CGH assay, MC0518_MCR0917 versus Promega Female DNA

tag: cell type

value: high

value: monoallelic

value: non-hyperdiploid


title: MDCK_pH7.4_rep6

source_name: Renal tubule cells, pH 7.4, replicate 6


title: MDCK_pH7.0_rep2

source_name: Renal tubule cells, pH 7.0, replicate 2


title: Rad-D2 rep C4.7 (ONH)

source_name: Rad-D2 rep C4.7 (ONH)

tag: glaucoma

tag: radiation

tag: mouse strain

tag: gender

value: Female

tag: age (mos)


title: MDCK_pH7.4_rep1

source_name: Renal tubule cells, pH 7.4, replicate 1


title: Myc A17 roots early stages biological replicate 2

tag: tissue

value: Root

tag: genotype

value: Jemalong A17

tag: age

tag: treatment


title: MC0453_MCR0198

description: Competitive Oligo CGH assay, MC0453_MCR0198 versus Promega Female DNA

tag: sample order

tag: tc class

tag: cyto risk

tag: reference


title: Rad-D2 rep C3.6 (ONH)

source_name: Rad-D2 rep C3.6 (ONH)


title: MDCK_pH7.0_rep6

source_name: Renal tubule cells, pH 7.0, replicate 6

tag: ph


title: MDCK_pH7.4_rep5

source_name: Renal tubule cells, pH 7.4, replicate 5


title: MC0085_MCR1026

description: Competitive Oligo CGH assay, MC0085_MCR1026 versus Promega Female DNA

tag: 17p13 deletion

tag: ploidy

tag: uams 70gene index

tag: copy number abnormalities


title: MDCK_pH7.4_rep2

source_name: Renal tubule cells, pH 7.4, replicate 2

tag: cell type


title: MC0496_MCR0417

description: Competitive Oligo CGH assay, MC0496_MCR0417 versus Promega Female DNA

tag: time since sample1 months


title: Myc A17 roots early stages biological replicate 3

value: 5 days

value: Gigaspora margarita-colonized


title: Myc A17 roots early stages biological replicate 1


title: MDCK_pH7.4_rep3

source_name: Renal tubule cells, pH 7.4, replicate 3


title: MDCK_pH7.0_rep4

source_name: Renal tubule cells, pH 7.0, replicate 4


title: Control DMI3 roots early stages biological replicate 3

description: Gene expression data from Non-colonized Medicago truncatula root fragments

value: Jemalong DMI3


title: Control A17 roots early stages biological replicate 2

source_name: Non-colonized Medicago truncatula root fragments


title: MC0518_MCR1136

description: Competitive Oligo CGH assay, MC0518_MCR1136 versus Promega Female DNA

value: biallelic


title: Control DMI3 roots early stages biological replicate 2


title: Control A17 roots early stages biological replicate 3


title: Control DMI3 roots early stages biological replicate 1


title: Control A17 roots early stages biological replicate 1


title: MDCK_pH7.0_rep3

source_name: Renal tubule cells, pH 7.0, replicate 3


title: High-grade osteosarcoma pre-chemotherapy biopsy L3536int

city: Oslo

first: Marieke

middle: Lydia

last: Kuijjer

address: Gaustadalléen 21

country: Norway

institute: Centre for Molecular Medicine Norway

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Two supplementary/raw data files are present because each array that represents one Sample consists of 2 chips. The supplementary/raw data files represent the bead level data (2 raw .txt files per sample, containing all intensities per bead).

hyb_protocol: As per manufacturer's instructions.

scan_protocol: As per manufacturer's instructions.

data_processing: Data were analyzed using the statistical language R. As Illumina identifiers are not stable and consistent between different chip versions, raw oligonucleotide sequences were converted to nuIDs. Data were transformed using the variance stabilizing transformation (vst) algorithm and subsequently normalized using robust spline normalization. Conversion to nuIDs, variance stabilizing transformation, and normalization of the data were all carried out using the Bioconductor package lumi. Quality control was performed using the Bioconductor package arrayQualityMetrics. Poor quality arrays were removed from further analyses.

label_protocol: As per manufacturer's instructions.

extract_protocol: RNA isolation, cDNA synthesis, cRNA amplification, Illumina Human-6 v2.0 Expression BeadChip hybridization, qPCR validation, and microarray data analysis were performed as previously described (Buddingh EP, Kuijjer ML, Duim RA, Burger H, Agelopoulos K, Myklebost O, et al. Tumor-infiltrating macrophages are associated with metastasis suppression in high-grade osteosarcoma: a rationale for treatment with macrophage-activating agents. Clin Cancer Res 2011 Apr 15;17(8):2110-2119).

tag: type

value: biopsy

tag: gender

value: M

value: 178 months

tag: histological subtype

value: sclerosing osteosarcoma

tag: tumor location

value: femur

tag: huvos grade

tag: matching copy number data

value: no


title: High-grade osteosarcoma pre-chemotherapy biopsy L3538int

value: unknown

tag: age


title: High-grade osteosarcoma pre-chemotherapy biopsy L3535int

value: 160 months

value: giant cell rich osteosarcoma

value: tibia/fibula

value: yes


title: High-grade osteosarcoma pre-chemotherapy biopsy L3476int

value: 324 months

value: fibroblastic osteosarcoma


title: High-grade osteosarcoma pre-chemotherapy biopsy L3474int

value: 192 months

value: osteoblastic osteosarcoma

value: humerus


title: High-grade osteosarcoma pre-chemotherapy biopsy L3473int

value: 312 months


title: High-grade osteosarcoma pre-chemotherapy biopsy L3533int

value: biopsy

value: 150 months

value: fibroblastic giant cell rich osteosarcoma


title: High-grade osteosarcoma pre-chemotherapy biopsy L3472int

value: M

value: 516 months


title: High-grade osteosarcoma pre-chemotherapy biopsy L3471int

value: F

value: 300 months

value: axial

value: no


title: High-grade osteosarcoma pre-chemotherapy biopsy L3469int

value: 284 months

value: chondroblastic osteosarcoma

value: femur


description:
High-grade osteosarcoma pre-chemotherapy biopsy
Affymetrix SNP 6.0 arrays were used.

hyb_protocol: Genomic DNA preparation, labeling and hybridization were performed according to Affymetrix's recommended protocols (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Arrays were scanned with GeneChip GSC3000 7G Whole-Genome Association System (Affymetrix).

data_processing: Microarray data pre-processing was performed as described in Pansuriya et al. (PMID: 21235737). Hybridization quality was estimated by the genotype call rate using the Birdseed genotype calling algorithm in Genotyping Console (version 4.0, Affymetrix). We performed copy number analysis in Nexus software version 5 using CNCHP log-ratio files generated by genotyping console using 27 controls as a baseline, which is a subset of the reference set of 29 samples which was used in Pansuriya et al (PMID: 21235737, GEO Series accession number GSE22984), because we rejected 2 samples based on results from the quality control analysis in Genotyping Console. We used the following samples for the reference file (GEO accession numbers): GSM566679, GSM566716, GSM566745, GSM566752, GSM566762, GSM566780, GSM566785, GSM566787, GSM566788, GSM566789, GSM566790, GSM566791, GSM566814, GSM566815, GSM567029, GSM567042, GSM567046, GSM567050, GSM567053, GSM567055, GSM567062, GSM567083, GSM567110, GSM567114, GSM567339, GSM567342, GSM567343. Hidden Markov model (HMM) based SNP-FASST segmentation was used to identify aberrant genomic regions. We used an aberration frequency cut-off of 35%.

extract_protocol: DNA from fresh frozen tissue was isolated using the wizard genomic DNA purification kit (Promega, Madison, WI), according to the manufacturer instructions.

value: distal femur

tag: matching expression data

value: yes


title: High-grade osteosarcoma pre-chemotherapy biopsy L3467int

label_protocol: Genomic DNA preparation, labeling and hybridization were performed according to Affymetrix's recommended protocols (Affymetrix, Santa Clara, CA, USA).

value: 168 months

value: osteoblastic osteosarcoma

value: left femur


title: Heat stress - 1h at 42ºC, biological rep2

city: Lisboa

first: Margarida

last: Rocheta

address: Tapada da ajuda

country: Portugal

institute: Instituto Superior de Agronomia

description:
Portugal_ST4
Gene expression data from leaves of greenhouse grown plants

hyb_protocol: Microarrays hybridization were performed according to the Affymetrix GeneChip® expression Analysis Technical Manual.

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 greenhouse grown plants

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

growth_protocol: Plants were transplanted to pots filled with soil placed in the greenhouse under 200 µmol m-2 s-1 light intensity, 16h light / 8h dark photoperiod, temperature of 25ºC day / 23ºC night and irrigation when necessary with nutrient solution [53]. When plants were about 50 to 60 cm high, with 6 to 8 expanded leaves, stresses were applied to groups of six plants,

extract_protocol: Total RNA from leaves was extracted through the method described by Reid et al [PMID 17105665].

treatment_protocol: Vitis vinifera L. variety Aragonês shoots were collected in the field during the winter pruning season. Collected shoots were disinfected with 2g L-1 fungicide (mixture of ciprodinil and fludioxonil), wrapped in absorbent paper and placed at 4ºC for circa two months. Then they were placed in distilled water under controlled conditions (25ºC, 50 mmol m-2 s-1) for two weeks upon which they had developed roots and a few new leaves.

tag: tissue

value: leaves

tag: variety

value: Aragonês

tag: treatment group

value: Heat stress - 1h at 42ºC


title: High-grade osteosarcoma pre-chemotherapy biopsy L3453int

value: M

value: 173 months

value: left distal femur


title: High-grade osteosarcoma pre-chemotherapy biopsy L3658int

value: unknown

value: 143 months

value: 3 or 4


title: High-grade osteosarcoma pre-chemotherapy biopsy L3659int

value: no


title: High-grade osteosarcoma pre-chemotherapy biopsy L3465int

value: F

value: 129 months

value: chondroblastic osteosarcoma


source_name: High-grade osteosarcoma pre-chemotherapy biopsy

value: 160 months

value: giant cell rich osteosarcoma

value: right proximal fibula

value: yes


title: High-grade osteosarcoma pre-chemotherapy biopsy L3438int

value: 220 months

value: osteoblastic osteosarcoma

value: right proximal tibia


title: High-grade osteosarcoma pre-chemotherapy biopsy L3657int

value: 204 months

value: left humerus

value: 1 or 2


title: High-grade osteosarcoma pre-chemotherapy biopsy L3437int

value: M

value: 183 months

value: distal femur


title: High-grade osteosarcoma pre-chemotherapy biopsy L3461int

value: 184 months

value: left distal femur


title: High-grade osteosarcoma pre-chemotherapy biopsy L2613int

value: 181 months


title: High-grade osteosarcoma pre-chemotherapy biopsy L3439int

value: 385 months

value: chondromyxoid fibroma-like osteosarcoma

value: right humerus


title: High-grade osteosarcoma pre-chemotherapy biopsy L3468int

value: biopsy

value: 744 months

value: chondroblastic osteosarcoma

value: other

value: unknown

value: no


title: High-grade osteosarcoma pre-chemotherapy biopsy L2301int

value: 304 months

value: osteoblastic osteosarcoma

value: left proximal tibia

value: yes


title: Heat stress - 1h at 42ºC, biological rep1

description:
Portugal_ST2
Gene expression data from leaves of greenhouse grown plants

value: leaves

value: Aragonês

value: Heat stress - 1h at 42ºC


title: High-grade osteosarcoma pre-chemotherapy biopsy L3466int

value: F

value: 189 months

value: femur


title: Control, biological rep1

description:
Portugal_C1
Gene expression data from leaves of greenhouse grown plants

value: control


title: High-grade osteosarcoma pre-chemotherapy biopsy L3446int

value: M

value: 174 months

value: giant cell rich osteosarcoma

value: left distal femur


title: Water stress - irrigation withdrawn until ψleaf= -0.9 Mpa, biological rep1

description:
Portugal_SH1
Gene expression data from leaves of greenhouse grown plants


title: High-grade osteosarcoma pre-chemotherapy biopsy L3464int

value: biopsy

value: 144 months

value: tibia/fibula


title: High-grade osteosarcoma pre-chemotherapy biopsy L3435int

value: 200 months

value: osteoblastic osteosarcoma

value: right proximal femur


title: Control, biological rep2

description:
Portugal_C2
Gene expression data from leaves of greenhouse grown plants

value: leaves


title: Water stress - irrigation withdrawn until ψleaf= -0.9 Mpa, biological rep2

description:
Portugal_SH16
Gene expression data from leaves of greenhouse grown plants

value: Aragonês


title: High-grade osteosarcoma pre-chemotherapy biopsy L3434int

value: 181 months

value: sclerosing osteosarcoma

value: right proximal tibia

value: yes


title: High-grade osteosarcoma pre-chemotherapy biopsy L3448int

value: 170 months


title: High-grade osteosarcoma pre-chemotherapy biopsy L3436int

value: M

value: 205 months

value: chondroblastic osteosarcoma


title: High-grade osteosarcoma pre-chemotherapy biopsy L2611int

value: F

value: 242 months

value: right distal femur


title: High-grade osteosarcoma pre-chemotherapy biopsy L3462int

value: biopsy

value: 189 months

value: tibia/fibula

value: no


title: High-grade osteosarcoma pre-chemotherapy biopsy L3461int

value: 184 months

value: osteoblastic osteosarcoma

value: femur


title: High-grade osteosarcoma pre-chemotherapy biopsy L2617int

value: 181 months

value: left proximal tibia


title: High-grade osteosarcoma pre-chemotherapy biopsy L3454int

value: 492 months

value: ilium

value: yes


title: High-grade osteosarcoma pre-chemotherapy biopsy L3458int

value: M

value: 220 months


title: High-grade osteosarcoma pre-chemotherapy biopsy L1376int

value: F

value: 164 months

value: telangiectatic osteosarcoma

value: right proximal tibia


title: High-grade osteosarcoma pre-chemotherapy biopsy L1382int

value: 175 months

value: right distal tibia


title: High-grade osteosarcoma pre-chemotherapy biopsy L3467int

value: biopsy

value: 168 months


title: MMRC0359_2

description: Competitive Oligo CGH assay, MMRC0359_2 versus Promega Female DNA

data_processing: Raw data was extracted from TIFF image files by  Agilent Feature extraction using protocol CGH_107_Sep09 and grid 014693_D_F_20080627

source_name: MMRC0359_2 DNA

label_protocol: genomic DNA was digested with DNaseI for 12 minutes, digested DNA was labeled using the Invitrogen BioPrime Labeling kit, Test tumor samples were labeled with Cy5 and control DNA were labeled with Cy3

extract_protocol: DNA was extracted from cell lysates stored in TRIzol or using Puregene isolations from Dry Cell Pellets

value: CD138 Positive Myeloma Cells

tag: sample order

tag: tc class

tag: cyto risk

value: low

tag: 17p13 deletion

value: no

value: non-hyperdiploid

value: good

source_name: Promega Female DNA

tag: reference

value: Promega Female DNA


title: High-grade osteosarcoma pre-chemotherapy biopsy L2296int

value: 198 months

value: osteoblastic osteosarcoma

value: left proximal tibia

value: yes


title: MMRC0395_2

description: Competitive Oligo CGH assay, MMRC0395_2 versus Promega Female DNA

source_name: MMRC0395_2 DNA

tag: cell type

tag: ploidy

value: hyperdiploid

tag: uams 70gene index

tag: copy number abnormalities

tag: time since sample1 months


title: MMRC0395_1

description: Competitive Oligo CGH assay, MMRC0395_1 versus Promega Female DNA

source_name: MMRC0395_1 DNA

value: poor


title: High-grade osteosarcoma pre-chemotherapy biopsy L3456int

tag: type

tag: gender

value: M

value: 196 months

tag: histological subtype

value: fibroblastic osteosarcoma

tag: tumor location

value: tibia/fibula

tag: huvos grade


title: MMRC0359_1

description: Competitive Oligo CGH assay, MMRC0359_1 versus Promega Female DNA

source_name: MMRC0359_1 DNA


title: High-grade osteosarcoma pre-chemotherapy biopsy L3457int

value: biopsy

value: F

tag: age

value: 115 months

value: humerus

tag: matching copy number data


title: High-grade osteosarcoma pre-chemotherapy biopsy L3459int

value: 180 months

value: no


title: High-grade osteosarcoma pre-chemotherapy biopsy L3455int

value: 237 months

value: chondroblastic osteosarcoma


title: High-grade osteosarcoma pre-chemotherapy biopsy L3453int

value: 173 months

value: osteoblastic osteosarcoma

value: femur


title: MMRC0206_2

description: Competitive Oligo CGH assay, MMRC0206_2 versus Promega Female DNA

source_name: MMRC0206_2 DNA

value: CD138 Positive Myeloma Cells

tag: sample order

value: high

value: monoallelic

value: non-hyperdiploid

value: Promega Female DNA


title: MMRC0191_1

description: Competitive Oligo CGH assay, MMRC0191_1 versus Promega Female DNA

source_name: MMRC0191_1 DNA

tag: tc class

value: low

value: hyperdiploid

value: good


title: MMRC0155_2

description: Competitive Oligo CGH assay, MMRC0155_2 versus Promega Female DNA

source_name: MMRC0155_2 DNA

tag: cyto risk


title: MMRC0206_1

description: Competitive Oligo CGH assay, MMRC0206_1 versus Promega Female DNA

source_name: MMRC0206_1 DNA

tag: 17p13 deletion

value: biallelic


title: MMRC0161_1

description: Competitive Oligo CGH assay, MMRC0161_1 versus Promega Female DNA

source_name: MMRC0161_1 DNA

tag: reference


title: MMRC0191_2

description: Competitive Oligo CGH assay, MMRC0191_2 versus Promega Female DNA

source_name: MMRC0191_2 DNA

tag: cell type


title: MMRC0124_1

description: Competitive Oligo CGH assay, MMRC0124_1 versus Promega Female DNA

source_name: MMRC0124_1 DNA

tag: ploidy


title: MMRC0154_2

description: Competitive Oligo CGH assay, MMRC0154_2 versus Promega Female DNA

source_name: MMRC0154_2 DNA

tag: uams 70gene index


description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Two supplementary/raw data files are present because each array that represents one Sample consists of 2 chips. The supplementary/raw data files represent the bead level data (2 raw .txt files per sample, containing all intensities per bead).

value: biopsy

value: M

value: 492 months

value: other

value: yes


title: MC1484_MCA0680_BM_CD138pos

description: Competitive Oligo CGH assay, MC1484_MCA0680_BM_CD138pos versus Promega Female DNA

source_name: MC1484_MCA0680_BM_CD138pos DNA

value: maf

value: no

tag: copy number abnormalities


title: MMRC0155_1

description: Competitive Oligo CGH assay, MMRC0155_1 versus Promega Female DNA

source_name: MMRC0155_1 DNA

tag: time since sample1 months


title: MC1472_MCA0404_BM_CD138pos

description: Competitive Oligo CGH assay, MC1472_MCA0404_BM_CD138pos versus Promega Female DNA

source_name: MC1472_MCA0404_BM_CD138pos DNA


title: MMRC0161_2

description: Competitive Oligo CGH assay, MMRC0161_2 versus Promega Female DNA

source_name: MMRC0161_2 DNA


description:
High-grade osteosarcoma pre-chemotherapy biopsy
Affymetrix SNP 6.0 arrays were used.

value: 220 months

value: osteoblastic osteosarcoma

value: distal femur

tag: matching expression data


title: MC1387_MCA0653_BM_CD138pos

description: Competitive Oligo CGH assay, MC1387_MCA0653_BM_CD138pos versus Promega Female DNA

source_name: MC1387_MCA0653_BM_CD138pos DNA

value: CD138 Positive Myeloma Cells


title: MMRC0035_1

description: Competitive Oligo CGH assay, MMRC0035_1 versus Promega Female DNA

source_name: MMRC0035_1 DNA

value: poor

source_name: Promega Female DNA


title: MC1484_MCA0436_BM_CD138pos

description: Competitive Oligo CGH assay, MC1484_MCA0436_BM_CD138pos versus Promega Female DNA

source_name: MC1484_MCA0436_BM_CD138pos DNA

value: high

value: non-hyperdiploid

value: Promega Female DNA


title: MMRC0154_1

description: Competitive Oligo CGH assay, MMRC0154_1 versus Promega Female DNA

source_name: MMRC0154_1 DNA

value: low

value: hyperdiploid

value: good


title: MC1272_MCA0595_BM_CD138pos

description: Competitive Oligo CGH assay, MC1272_MCA0595_BM_CD138pos versus Promega Female DNA

source_name: MC1272_MCA0595_BM_CD138pos DNA


title: MC1272_MCA0862_BM_CD138pos

description: Competitive Oligo CGH assay, MC1272_MCA0862_BM_CD138pos versus Promega Female DNA

source_name: MC1272_MCA0862_BM_CD138pos DNA


title: MC1272_MCA0123_BM_CD138pos

description: Competitive Oligo CGH assay, MC1272_MCA0123_BM_CD138pos versus Promega Female DNA

source_name: MC1272_MCA0123_BM_CD138pos DNA


title: MC1472_MCA0658_BM_CD138pos

description: Competitive Oligo CGH assay, MC1472_MCA0658_BM_CD138pos versus Promega Female DNA

source_name: MC1472_MCA0658_BM_CD138pos DNA


title: High-grade osteosarcoma pre-chemotherapy biopsy L1370int

tag: gender

value: M

value: 216 months

value: left distal femur


title: MC1130_MCA0556_BM_CD138pos

description: Competitive Oligo CGH assay, MC1130_MCA0556_BM_CD138pos versus Promega Female DNA

source_name: MC1130_MCA0556_BM_CD138pos DNA


title: MC1130_MCA0119_BM_CD138pos

description: Competitive Oligo CGH assay, MC1130_MCA0119_BM_CD138pos versus Promega Female DNA

source_name: MC1130_MCA0119_BM_CD138pos DNA


title: MC1130_MCA0361_BM_CD138pos

description: Competitive Oligo CGH assay, MC1130_MCA0361_BM_CD138pos versus Promega Female DNA

source_name: MC1130_MCA0361_BM_CD138pos DNA


title: MC1130_MCA0699_BM_CD138pos

description: Competitive Oligo CGH assay, MC1130_MCA0699_BM_CD138pos versus Promega Female DNA

source_name: MC1130_MCA0699_BM_CD138pos DNA

value: biallelic


title: High-grade osteosarcoma pre-chemotherapy biopsy L2292int

value: 136 months

tag: histological subtype

value: left proximal tibia

value: yes


title: MC1059_MCA0619_BM_CD138pos

description: Competitive Oligo CGH assay, MC1059_MCA0619_BM_CD138pos versus Promega Female DNA

source_name: MC1059_MCA0619_BM_CD138pos DNA

value: no


title: High-grade osteosarcoma pre-chemotherapy biopsy L2615int

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Two supplementary/raw data files are present because each array that represents one Sample consists of 2 chips. The supplementary/raw data files represent the bead level data (2 raw .txt files per sample, containing all intensities per bead).

tag: type

value: biopsy

value: 261 months

value: osteoblastic osteosarcoma

tag: tumor location

value: tibia/fibula


title: High-grade osteosarcoma pre-chemotherapy biopsy L2376int

value: F

tag: age

value: 114 months

value: humerus

tag: huvos grade

value: unknown


title: High-grade osteosarcoma pre-chemotherapy biopsy L2347int

value: 170 months

value: telangiectatic osteosarcoma

value: femur

tag: matching copy number data