title: AdV-IL4d2_mouse_3

city: Baltimore

first: Sergei

middle: P

last: Atamas

state: MD

address: 10 S. Pine St., MSTF 834

department: Department of Medicine

institute: University of Maryland School of Medicine

description: 14 days after tntratracheal infection with replication-deficient adenovirus encoding: mouse Interleukin-4d2

hyb_protocol: Labeled cRNA (15.0 ug) was fragmented by ion-mediated hydrolysis and hybridized for 16hr at 45oC to Affymetrix Mouse Genome 430 2.0 short oligomer arrays.

scan_protocol: Fluorescence intensities were determined using a GCS 3000 7G high-resolution confocal laser scanner and AGCC software (Affymetrix)

data_processing: The scanned images were analyzed using Expression Console v2.0 software (Affymetrix). Quality control metrics for cRNA integrity, sample loading, and variations in staining were determined after background correction and signal summarization by MAS 5.0 statistical algorithms resident in GCOS and standardization of each array by global scaling the average of the fluorescent intensities of all genes on an array to a constant target intensity (TGT) of 250. Expression data were analyzed following background correction, probe set signal summarization and normalization by MAS5.0 with global scaling (TGT = 250). (Lockhart et al, 1996, Nat. Biotechnol. 14:1675-1680; Liu et al, 2002, Bioinformatics 18:1593-9; Hubbell et al, 2002, Bioinformatics 18(12):1585-92, Irizarry et al, 2006, Bioinformatics 22(7):789-94, and references therein). Probe sets exhibiting significant differential expression were identified using GeneMaths XT (Applied Maths, Austin TX), based on the following criteria: 1) MAS5.0 detection p-values ≤ 0.05 for all samples in at least one experimental group, 2) ANOVA p-value ≤ 0.05, 3) Absolute Signal log ratio ≥ 1.0 and independent t-test p-value ≤ 0.05 for at least one pairwise comparison versus the control group. Unsupervised hierarchical clustering and heat map generation were performed in GeneMaths XT following row mean centering of log2 transformed MAS5.0 signal values; probe set clustering was performed by the UPGMA method (Unweighted Pair Group Method using Arithmetic averages) using Pearson correlation as the similarity metric. Gene annotation, gene ontology information and biochemical pathway information were obtained from the National Center for Biotechnology Information (www.ncbi.nlm.nih.gov), NetAffx (ww.affymetrix.com), the Gene Ontology Consortium (http://amigo.geneontology.org), the Kyoto Encyclopedia of Genes and Genomes (www.genome.jp/kegg), and WebGestalt (http://bioinfo.vanderbilt.edu/webgestalt). Significant enrichment of specific GO categories or KEGG pathways in each comparison is estimated by hypergeometric tests.

source_name: lung

label_protocol: RNA was processed and labeled according to standard RT-IVT methods. First and second strand cDNA were synthesized from 200 ng of total RNA using oligo-dT24-T7 (5’-GGC CAG TGA ATT GTA ATA CGA CTC ACT ATA GGG AGG CGG-3’) as primer and and cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription for 16hr at 37oC, using the 3’ IVT Express cDNA/cRNA Synthesis and Labeling Kit (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions.

growth_protocol: Sterile rodent microisolator caging, with filtered cage top.

extract_protocol: Extraction of total RNA was performed using Trizol (Invitrogen) according to the manufacturer's instructions. Immediately prior to cDNA synthesis, the purity and concentration of RNA samples were determined from OD260/280 readings using a dual beam UV spectrophotometer and RNA integrity was determined by capillary electrophoresis using the RNA 6000 Nano Lab-on-a-Chip kit and the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) as per the manufacturers instructions.

treatment_protocol: After euthanasia, mouse lungs were collected, homogenized, and total RNA isolated using Trizol (Invitrogen).

tag: gender

value: female

value: 14 weeks

value: lung


title: Primary Breast Tumour AS (Methylation)

status: Public on Mar 07 2011

type: genomic

city: Edinburgh

first: Duncan

last: Sproul

state: Mid Lothian

address: Crewe Road South

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

hyb_protocol: Standard Illumina Hybridisation Protocols

scan_protocol: Standard Illuminina Scanning Protocols

data_processing: Data were exported from Illumina Genome Studio (BeadStudio Methylation Analysis Module) and analysed using R.  Submitted data are those exported from Genome Studio.

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Human Breast Tumour Sample

label_protocol: Genomic DNA (500 ng) from each sample was bisulfite converted using the EZ-96 DNA Methylation Kit (Zymo research Corporation, Orange, US) before being amplified and enzymatically fragmented (standard Illumina protocols)

extract_protocol: Genomic DNA was extracted using standard molecular biology protocols (pK digestion, phenol-chloroform extraction and ethanol precipitation)

tag: tissue

value: Primary Breast Tumour

tag: cell line

value: Fresh Frozen Primary Breast Tumour  Sample


title: Primary Breast Tumour AM (Methylation)


title: AdV-IL4d2_mouse_2

type: RNA

country: USA

label: biotin

molecule: total RNA

organism: Mus musculus

tag: strain

tag: age


title: F80

city: Cambridge

first: Bernardo

last: Lemos

state: MA

address: 16 Divinity Avenue, Room 2105

institute: Harvard University

description: Biological replicate

hyb_protocol: 3DNA procedure

scan_protocol: Scanned on an Axon 4000B scanner. Images were quantified using Genepix.

data_processing: LOESS normalized, VALUE data obtained from log of processed Red signal/processed Green signal.

organism: Drosophila melanogaster

source_name: Total RNA from male flies.

label_protocol: 3DNA procedure

extract_protocol: TriZol procedure

tag: genotype

tag: sex

value: male

value: 2 days old


title: Primary Breast Tumour AD (Methylation)


title: Primary Breast Tumour AQ (Methylation)


title: Primary Breast Tumour AC (Methylation)


title: Primary Breast Tumour AJ (Methylation)


title: Primary Breast Tumour AI (Methylation)


title: AdV-IL4_mouse_2

description: 14 days after tntratracheal infection with replication-deficient adenovirus encoding: mouse Interleukin-4


title: AdV-NULL_mouse_3

description: 14 days after tntratracheal infection with replication-deficient adenovirus encoding: NULL


title: Primary Breast Tumour AB (Methylation)


title: Primary Breast Tumour AH (Methylation)


title: Primary Breast Tumour AG (Methylation)


title: AdV-NULL_mouse_1


title: Primary Breast Tumour AF (Methylation)


title: A4_tumor

city: Hannover

first: Astrid

last: Rohrbeck

state: Niedersachsen

address: Carl-Neuberg-Straße 1

department: Department of Toxicology

country: Germany

institute: Medizinische Hochschule Hannover

description:
Lung samples were derived from SP-C/c-raf mice in the C57BL/6 background for at least five generations (aged 5 – 14 months); tumor cells were isolated from 11 – 14 month old mice, unaltered lung tissue were isolated from the dysplasia-bearing transgenic mouse (aged 5 – 7 months). Endogenous normal lung tissue was studied of non-transgenic mice (aged 7 – 10 months). The non-transgenic littermates (wild-type) served as control for transgenic effects.
Mice were sacrificed and the lung tissues were immediately frozen on dry ice and stored at -80°C until further analysis.

hyb_protocol: Following fragmentation, labeled cRNA of each sample was hybridized to Affymetrix GeneChip® Mouse Genome 430 2.0 Arrays covering over 34.000 genes and stained according to the manufacturer's instructions. The hybridization was performed for 16 hours at 60 rpm and 45°C in the GeneChip® Hybridization Oven 640 (Affymetrix). Washing and staining of the arrays were done on the Gene Chip® Fluidics Station 400 (Affymetrix) according to the manufacturers recommendation. The antibody signal amplification, washing and staining protocol (Affymetrix) was used to stain the arrays with streptavidin R-phycoerythrin (SAPE). To amplify staining, SAPE solution was added twice with a biotinylated anti-streptavidin antibody (Vector Laboratories, CA) staining step in between

scan_protocol: The arrays were scanned using the Affymetrix GeneChip® Scanner 7G. Scanned image files was visually inspected for artefacts and then analyzed, each image being scaled to the same target value for comparison between chips. The GeneChip® Operating Software (GCOS) was used to control the fluidics station and the scanner, to capture probe array data and to analyze hybridization intensity data.

data_processing:
Array data was normalized using scaling or per-chip normalization to adjust the total or average intensity of each array to be approximately the same.
Microarray chips were analyzed by the GCOS (GeneChip Operating Software) from Affymetrix with the default settings except that the target signal was set to 500 and used to generate a microarray quality control and data report.
CEL files exported from GCOS were uploaded into ArrayTrack software (National Center for Toxicological Research, U.S. FDA, Jefferson, AR, USA (NCTR/FDA)) and normalized using Total Intensity Normalization after subtracting backgrounds for data management and analysis. ArrayTrack software includes some tools common to other bioinformatics software (e.g., ANOVA, T-test and SAM).To compare the normalized data from dysplasia, normal lung tissue from transgenic mouse, tumor cells and non-transgenic of different mice, we used the Significance Analysis of Microarrays (SAM) algorithm (ArrayTrack), which contains a sliding scale for false discovery rate (FDR) of significantly up- and down-regulated genes. All data were permuted 100 cycles by using the two classes, unpaired data mode of the algorithm. As cut-off for significance an estimated FDR of 0.001 was chosen. Moreover, a cut-off for fold-change of differential expression of 2 was used.
Two clustering approaches were used to determine components of variation in the data in this study as follows.
A) Principal-component analysis (PCA) that was used to obtain a simplified visualization of entire datasets. PCA is a useful linear approach to obtain a simplified visualization of entire datasets, without losing experimental information (variance). PCA allowed the dimension of complex data to be reduced and highlights the most relevant features of a given dataset to be highlighted.
B) Hierarchical gene clustering (HCA) where the data points were organized in a phylogenetic tree in which the branch lengths represent the degree of similarity between the values.

label: Biotin

source_name: A4_tumor, lung tissue

label_protocol: Total RNA (175ng) was used to generate biotin-labeled cRNA (10 µg) by means of Message Amp aRNA Premium Amplification Kit (Ambion, Austin, TX). Quality control of cRNA was performed using a bioanalyzer (Agilent 2001 Biosizing, Agilent Technologies).

extract_protocol:
From each frozen lung tissue 10-µm thick sections were prepared and transferred on polyethylene napthalate foil-covered slides (Zeiss, P.A.L.M. Microlaser Technologies GmbH, Bernried, Germany).
The sections were fixed in methanol / acetic acid and stained in hematoxylin. The desired cells were microdissected using the PALM MicroLaser systems (Zeiss, P.A.L.M. Microlaser Technologies GmbH, Bernried, Germany) and collected in an adhesive cap (Zeiss, P.A.L.M. Microlaser Technologies GmbH, Bernried, Germany). Microdissected cells were resuspended in a guanidine isothiocyanate-containing buffer (RLT buffer from RNeasy MikroKit, Qiagen, Santa Clarita, CA, USA) with 10 µl/ml β-mercaptoethanol to ensure isolation of intact RNA. Approximately an area of 6 x 106 µm2 were pooled from a specific layer of interest in the same animal and used for RNA extraction.
Following microdissection, total RNA-extraction was performed with the RNeasy Micro Kit (RNeasy MicroKit Qiagen, Santa Clarita, CA, USA) according to the manufacturer’s instruction. A standard quality control of the total RNA was performed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

tag: SPC-c-raf transgenic mice, 12 month old, female, tumor


title: AdV-IL4_mouse_3


title: Primary Breast Tumour Z (Methylation)


title: Primary Breast Tumour AA (Methylation)


title: Primary Breast Tumour AE (Methylation)


title: AdV-NULL_mouse_2


title: Primary Breast Tumour U (Methylation)


title: Primary Breast Tumour W (Methylation)


title: A5_tumor

source_name: A5_tumor, lung tissue

tag: SPC-c-raf transgenic mice, 14 month old, male, tumor


title: A3_tumor

source_name: A3_tumor, lung tissue

tag: SPC-c-raf transgenic mice, 10 month old, female, tumor


title: AdV-IL4_mouse_1


title: Primary Breast Tumour Q (Methylation)


title: A1_tumor

source_name: A1_tumor, lung tissue

tag: SPC-c-raf transgenic mice, 10 month old, male, tumor


title: Primary Breast Tumour Y (Methylation)


title: Primary Breast Tumour R (Methylation)


title: Primary Breast Tumour X (Methylation)


title: Primary Breast Tumour V (Methylation)


title: Primary Breast Tumour P (Methylation)


title: Primary Breast Tumour O (Methylation)


title: Primary Breast Tumour D (Methylation)


title: Primary Breast Tumour F (Methylation)


title: Primary Breast Tumour M (Methylation)


title: Primary Breast Tumour I (Methylation)


title: Primary Breast Tumour S (Methylation)


title: Primary Breast Tumour L (Methylation)


title: Primary Breast Tumour N (Methylation)


title: Primary Breast Tumour C (Methylation)


title: Primary Breast Tumour E (Methylation)


title: Primary Breast Tumour T (Methylation)


title: Primary Breast Tumour H (Methylation)


title: Primary Breast Tumour B (Methylation)


title: Primary Breast Tumour G (Methylation)


title: Primary Breast Tumour K (Methylation)


title: Primary Breast Tumour A (Methylation)


title: Normal Colon (Methylation)

description: colon

source_name: Commercial Normal Tissue Sample

value: Normal Colon


title: Normal Liver (Methylation)

description: liver

value: Normal Liver


title: Normal Blood (Methylation)

description: blood

value: Normal Blood


title: Normal Placenta (Methylation)

description: placenta

value: Normal Placenta


title: Normal Testis (Methylation)

description: testis

value: Normal Testis


title: Normal Spleen (Methylation)

description: spleen

value: Normal Spleen


title: ZR751 (Methylation)

source_name: Human Cancer Cell Line

growth_protocol: Standard culture conditions

value: breast


title: T47D (Methylation)


title: SUM159PT (Methylation)


title: Primary Breast Tumour J (Methylation)


title: Normal Fetal Brain (Methylation)

description: brain.fetal

value: Normal Fetal Brain


title: MDAMB468 Biological Replicate 1 (Methylation)


title: Normal Breast (Methylation)

value: Normal Breast


title: MDAMB468 Biological Replicate 2 (Methylation)


title: SUM1315MO2 (Methylation)


title: MCF7 Biological Replicate 5 (Methylation)


title: MDAMB361 (Methylation)


title: SKBR3 (Methylation)


title: MDAMB453 (Methylation)


title: MCF7 Biological Replicate 6 (Methylation)


title: MCF7 Biological Replicate 4 (Methylation)


title: MDAMB231 Biological Replicate 1 (Methylation)


title: HS578T (Methylation)


title: Primary Breast Tumour AL (Methylation)


title: HCT116 (Methylation)

value: colon

value: wild-type HCT116 Cells


title: MDAMB231 Biological Replicate 2 (Methylation)


title: MCF7 Biological Replicate 7 (Methylation)


title: HMEC (Methylation)

description: hmec

source_name: Human Cell Line

value: Human Mammary Epithelial Cells (HMEC)


title: MCF10A (Methylation)


title: MCF7 Biological Replicate 2 (Methylation)


title: MDAMB231 Biological Replicate 3 (Methylation)


title: HCT116DKO (Methylation)

value: DNA methyltransferase deficient HCT116 cells


title: MDAMB157 (Methylation)


title: MCF7 Biological Replicate 3 (Methylation)


title: HCC1954 (Methylation)


title: gene expression of C2C12 siBAF60c cells, in differentiation media replicate 2

city: La Jolla

first: Roy

middle: M

last: Williams

state: CA

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

hyb_protocol: As recommended by illumina

scan_protocol: As suggested by illumina using the illumina scanner

data_processing: Raw data filtered on P value for <0.05 with the remaining data normalised using the affy tools R bioconductor normalize.quantiles routine

source_name: C2C12 cells

label_protocol: As suggested by illumina

growth_protocol: growing C2C12 cells (15% FBS) were transfected with siRNA oligonucleotides specifically targeting Baf60b, baf60c, Brg1 and a scrambled sequence (control) (Smart Pool siRNA, Dharmacon).

extract_protocol: total RNA was purified with TRIZOL Reagent (Invitrogen) and labeled cRNA was prepared from 500 ng RNA using the Illumina® RNA Amplification Kit from Ambion (San Digo, USA).

treatment_protocol: 36h after transfection cells were shifted in differentiation medium (ITS) and harvested after 18h for gene expression analysis.

value: Muscle

tag: cell  line

value: C2C12 myoblast cell line

tag: transfection


title: MCF7 Biological Replicate 1 (Methylation)


title: gene expression of C2C12 siBAF60b cells, in differentiation media replicate 2


title: gene expression of C2C12-siScramble cells in differentiation media replicate 2

value: siScramble


title: gene expression of C2C12 siBRG1 cells in differentiation media replicate 2


title: gene expression of C2C12 siBAF60c cells, in differentiation media replicate 1


title: gene expression of wild type C2C12 cells in differentiation media replicate 2

value: control


title: BT549 (Methylation)


title: HCC1569 (Methylation)


title: SHEF-6  hES  (Methylation)

description: hes

value: embryo

value: SHEF-6 human ES Cells


title: HBL100 (Methylation)


title: gene expression of wild type C2C12 cells in growth media replicate 2


title: C1q-treated neurons C1q 2

city: Irvine

first: Marie

middle: Emeline

last: Benoit

address: 2419 McGaugh Hall

department: Molecular Biology and Biochemistry

institute: UC Irvine

description: gene expression data from C1q-treated neurons

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr on Rat Gene 1.0 ST array. GeneChips were washed in the Affymetrix Fluidics Station 400.

scan_protocol: Affymetrix GCOS software

data_processing: JMP genomics v4.0 software, median based inter-array normalization

organism: Rattus norvegicus

source_name: C1q-treated neurons

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: cortical neurons were isolated from d18 Sprague-Dawley rat embryos and grown for 3 days in NB-N2

extract_protocol: total RNA extraction using the QIAGEN Rneasy Mini Kit was performed according to manufacturer's instructions

treatment_protocol: stimulation with 10 nM C1q for 3h

tag: agent

tag: cell type

value: cortical neurons


title: BT474 Biological Replicate 1 (Methylation)


title: gene expression of wild type C2C12 cells in differentiation media replicate 1


title: C1q-treated neurons C1q 1


title: untreated neurons UT 3

description: gene expression data from untreated neurons

source_name: untreated neurons

treatment_protocol: untreated

value: untreated (control)


title: BT20 (Methylation)


title: BT474 Biological Replicate 2 (Methylation)


title: C1q-treated neurons C1q 3


title: Internode13_vs_Internode9_rep5

status: Public on Mar 06 2011

city: Aberystwyth

first: Maurice

last: Bosch

address: Gogerddan

department: Institute of Biological, Environmental & Rural Sciences

institute: Aberystwyth University

description: Plant 5.

hyb_protocol: Labeled targets were mixed in hybridization buffer (2XSSC, Liquid Block, and 0.08% SDS). Arrays were hybridized at 55C for 8-12 hrs. The full hybridization protocol can be found at: http://ag.arizona.edu/microarray/Microarraymethod1.doc.

scan_protocol: Slides were scanned using a GenePix 4000 microarray scanner. Images were quantified using the Feature Extraction software GenePix Pro 6.0.

data_processing: LOESS normalizatizion was applied to log2 of processed Cy5/Cy3 signal. Bioconductor library limma was used.

organism: Zea mays

source_name: Internode 13

label_protocol: 1 μg RNA samples were used to make Cy3- and Cy5-labeled targets with a three-step protocol as follows: 1) cDNA was synthesized using an oligo-(d)T primer that incorporated the T7 promoter; 2) targets were amplified using in vitro transcription to produce aminoallyl-labeled cRNA; and 3) aminoallyl-labeled cRNA was coupled to Cy-labeled dyes. Details of these protocols can be found at: http://ag.arizona.edu/microarray/Microarraymethod1.doc

growth_protocol: Maize inbred line B73 plants were grown in a greenhouse. Daylight was supplemented with overhead lighting using 400 W high-pressure sodium lamps for 16 h daily. Minimum temperatures were maintained at 25°C (day) and 18°C (night). Internode development was assessed using the vegetative identification system (Ritchie et al., 2005). At stage V13, the plants were harvested, the leaves and leaf sheath were removed and internodes 9 to 13 were excised, avoiding 1 cm either side of the node. The samples were frozen in liquid nitrogen and stored at -80°C.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, Ca, USA) and purified using RNeasy MinElute Cleanup Kit columns (Qiagen, Valencia, CA, USA) according to a protocol recommended at www.maizearray.org.

treatment_protocol: No specific treatments.

tag: line

tag: developmental stage

value: internode 13

tag: cell wall synthesis

value: primary

source_name: Internode 9

value: internode 9

value: secondary


title: untreated neurons UT 1


title: Internode13_vs_Internode9_rep6

description: Plant 6.

tag: tissue


title: gene expression of wild type C2C12 cells in growth media replicate 1


title: Internode13_vs_Internode9_rep4

description: Plant 4.


title: Internode9_vs_Internode13_rep3

description: Plant 3.


title: untreated neurons UT 2


title: Internode9_vs_Internode13_rep1

description: Plant 1.


title: Internode9_vs_Internode13_rep2

description: Plant 2.


title: gene expression of C2C12-siScramble cells in differentiation media replicate 1


title: Il10 Colon Green Aqueous Replicate 6

status: Public on Mar 05 2011

city: Palmerston North

first: Helge

last: Dzierzon

address: Bachelar Road

department: Bioinformatics

country: New Zealand

institute: Plant and Food Research Ltd.

hyb_protocol: Microarray hybridization was performed according to a reference design without dye swap. The in situ hybridization kit-plus (Agilent Technologies Inc., Palo Alto, California, USA) was used to hybridize cRNA samples to Agilent Technologies Mouse G4121A - 44k 60mer oligonucleotide arrays. Cy3-labelled cRNA (sample, 0.75 µg) and Cy5-labelled cRNA (reference, 0.75 µg) were hybridised onto the microarray according to the manufacturer’s protocol. After hybridisation the slides were washed following the supplemental procedures for preventing ozone related problems using (in this order) Gene Expression Wash Buffers 1 and 2, Acetonitrile, and Stabilisation and Drying Solution (Agilent Technologies Inc.).

scan_protocol: Immediately after washing, slides were scanned using an Agilent Microarray Scanner (Agilent Technologies Inc.) with the following settings: 5 µm scan resolution, eXtended Dynamic range selected, XDR Hi 100% and XDR Lo 10% selected for both Red and Green channels. Spot alignment and feature extraction was performed using Feature Extract 9.5.1 software (Agilent) using the GE2-v5_95_Feb07 protocol. After scanning, slides were stored at room temperature in airtight containers away from light.

data_processing: Statistical analysis was performed using Linear models for microarray analysis (Limma) from the Bioconductor project. Blank rows, dark corners, negative controls, landing lights, and positive controls were filtered out before normalization. Data were log transformed before analysis and the mean difference between treatments calculated on this scale, resulting in a log ratio for each probe. The normalized values in the database consist of these log ratios. Quality of the microarray data was assessed on diagnostic plots (boxplots and density plots) and spatial images generated from the raw (non-processed) data. MA plots of the microarray data were drawn in order to check that there was no dependence of the log ratio on the intensity for any slide. Intensity ratio values for all microarray spots were normalized using a global loess smoothing procedure to remove the effect of systematic variation in the microarrays and no background correction was necessary due to homogeneous hybridisation. For each experimental comparison, a candidate list of differentially expressed probe sets was generated by calculating a moderated t-statistic for each probe set using the Limma package. The Limma library implements an empirical Bayes approach to assign differential gene expression. The significance of the log ratio for each probe was determined by calculating one modified t-statistic per probe. Probe sets that satisfied the criterion of ≥ 1.5 fold change (FC) with a moderated p < 0.01 were considered to be significantly different. The normalization used for both experiments was a single print tip global loess with slide normalization with no background correction. There was one slide removed from each experiment (C57BL6J_Gold EthylAcetate_Rep4,T117 Slide6_4 and C57BL6J_Green Control_Rep6,T126 Slide9_4);

source_name: Il10-/- mouse fed Green Kiwifruit Aqueous Extract diet, colon tissue

label_protocol: The Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies Inc., Palo Alto, California, USA) was used to synthesize cDNA and fluorescent cRNA. Labelled cRNA was made on the same day for all sample pools, including the reference sample. cDNA was synthesized from 500 ng of purified total RNA from each pool using T7 promotor primer and Moloney Murine Leukemia Virus Reverse Transcriptase according to the manufacturer’s protocol.

growth_protocol: Mice were weighed six times a week throughout the experiment to determine body weight changes. To minimize variation in the time interval between the last food intake and tissue sampling, mice were fasted overnight on the night before sampling. On the morning of sampling, food was returned for two hours, followed by a further two hour fast immediately prior to tissue sampling. Mice were euthanased by CO2 asphyxiation/cervical dislocation. The intestine was removed, cut open lengthwise and flushed with 0.9 % NaCl to remove digesta residues. The proximal half of the colon was cut in three pieces, one for histological evaluation, one for gene expression studies and one backup sample. Samples of the colon tissue for gene expression analysis were frozen in liquid nitrogen and stored at - 80 ºC. Samples for histological analysis were stored in formalin solution (10 % neutral buffered) at room temperature.

extract_protocol: Total RNA was extracted from the colon tissues using Trizol (Invitrogen, Carlsbad, CA, USA) as described by the manufacturer, with a subsequent purification step using RNeasy columns (Qiagen, San Diego, CA, USA). RNA was quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and RNA quality was examined using a RNA 6000 LabChip Kit and a 2100 Bioanalyser (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: Il10-/- and C57BL/6J control mice were received from The Jackson Laboratories (Bar Harbor, Maine, USA) at four or six weeks of age. All mice were housed singly in shoebox-style cages containing Alpha-Dri bedding material (Shepherd Specialty Papers), a clean sheet of tissue paper, and a plastic tube for environmental enrichment. The animal room was maintained at a temperature of ~22°C and humidity of ~50% with a 12 hour light/dark cycle. All mice had ad libitum access to water, which was refreshed twice a week. Mice were offered fresh food 6 days per week and food intake was estimated at each feeding by weighing food remaining from the previous feeding. The food offered to all groups was adjusted weekly to match the intake of C57BL/6J mice in the control diet group. Mice were weighed three times per week and carefully monitored for disease symptoms (weight loss, soft faeces, inactivity).

tag: gender

value: Male

value: 12 weeks

tag: colon histology injury score

source_name: Reference RNA of healthy growing Swiss Mice

growth_protocol: Healthy adult male Swiss mice were maintained on a 12 h:12 h light:dark cycle and were given food and water ad libitum.

treatment_protocol: No treatment prior to tissue collection.

tag: sample type

value: Pooled RNA from small intestine, colon, kidney, liver and fetuses


title: Il10 Colon Green Control Replicate 5

source_name: Il10-/- mouse fed Green Control (AIN-76A) diet, colon tissue

tag: strain

tag: age

value: colon


title: Il10 Colon Green Aqueous Replicate 5


title: gene expression of C2C12 siBRG1 cells in differentiation media replicate 1


title: C57BL6J Colon GreenAqueous Replicate 5

source_name: C57BL/6J mouse fed Green Kiwifruit Aqueous Extract diet, colon tissue


title: Il10 Colon Green Control Replicate 4


title: Il10 Colon Green Aqueous Replicate 4


title: C57BL6J Colon Green EthylAcetate Replicate 4

source_name: C57BL/6J mouse fed Green Kiwifruit Ethyl Acetate Extract diet, colon tissue


title: C57BL6J Colon GreenAqueous Replicate 4


title: Il10 Colon Green Control Replicate 3


title: C57BL6J Colon Green Control Replicate 5

source_name: C57BL/6J mouse fed Green Control (AIN-76A) diet, colon tissue


title: Il10 Colon Green Control Replicate 6


title: Il10 Colon Green EthylAcetate Replicate 6

source_name: Il10-/- mouse fed Green Kiwifruit Ethyl Acetate Extract diet, colon tissue


title: C57BL6J Colon GreenAqueous Replicate 3


title: C57BL6J Colon Green EthylAcetate Replicate 6


title: C57BL6J Colon Green EthylAcetate Replicate 2


title: Il10 Colon Green EthylAcetate Replicate 4


title: C57BL6J Colon GreenAqueous Replicate 6


title: Il10 Colon Green EthylAcetate Replicate 3


title: Il10 Colon Green Control Replicate 2


title: C57BL6J Colon Green EthylAcetate Replicate 3


title: C57BL6J Colon Green EthylAcetate Replicate 5


title: Il10 Colon Green EthylAcetate Replicate 5


title: C57BL6J Colon Green Control Replicate 3


title: C57BL6J Colon Green Control Replicate 2


title: Il10 Colon Green EthylAcetate Replicate 2


title: Il10 Colon Green Aqueous Replicate 3


title: C57BL6J Colon Green Control Replicate 4


title: Il10 Colon Green Aqueous Replicate 2


title: C57BL6J Colon Green Control Replicate 1


title: Il10 Colon Green Control Replicate 1


title: Il10 Colon Green EthylAcetate Replicate 1


title: Il10 Colon Green Aqueous Replicate 1


title: gene expression of C2C12 siBAF60b cells, in differentiation media replicate 1


title: C57BL6J Colon Green EthylAcetate Replicate 1


title: C57BL6J Colon GreenAqueous Replicate 1


title: C57BL6J Colon Gold EthylAcetate Replicate 6

source_name: C57BL/6J mouse fed Gold Kiwifruit Ethyl Acetate Extract diet, colon tissue

value: 10.5 weeks


title: Il10 Colon Gold EthylAcetate Replicate 6

source_name: Il10-/- mouse fed Gold Kiwifruit Ethyl Acetate Extract diet, colon tissue


title: Il10 Colon Gold Control Replicate 6

source_name: Il10-/- mouse fed Gold Control (AIN-76A) diet, colon tissue


title: C57BL6J Colon Gold Aqueous Replicate 6

source_name: C57BL/6J mouse fed Gold Kiwifruit Aqueous Extract diet, colon tissue


title: Il10 Colon Gold EthylAcetate Replicate 5


title: C57BL6J Colon GreenAqueous Replicate 2


title: C57BL6J Colon Gold Aqueous Replicate 5


title: CellLine_CASKI_aCGH

first: Ian

last: Roberts

address: Hills Road

department: Cancer Cell Unit

institute: Hutchison MRC Research Centre

description: Ref gDNA pool contains 10-15 male samples

hyb_protocol: Hybridisation and stringency washing was conducted acording to Agilents' own protocols.

scan_protocol: Arrays were scanned on an Axon 41000 B using GenePix Pro 6.0

data_processing:
Data was processed in R using snapCGH Bioconductor packages and in house scripts.
The aCGH ratio is taken as log 2 {(median Ch1 foreground - median Ch1 background) / (median Ch2 foreground - mediumn Ch2 background)}

label: Alexa 532 dUTP

source_name: Squamous cell carcinoma

label_protocol: gDNA was labelled using Invitrogen Bioprime aCGH labelling kit, according manufacturers recommendations

growth_protocol: Cell lines were cultured in 10% FCS + 90% GMEM + antibiotics, according to standard maintenance procedures

extract_protocol: gDNA was extracted by mechanical disaggregation, followed by 2 hr incubtaion in 1 mg / ml proteinase K at 55oC.  gDNA recovery involved phenol chloroform extraction, ethanol precipitation and RNAse A digestion.  gDNA was quality chked and quantified by Nanodrop spectophotometric assessment and Invitrogen picogreen measurement

value: Cell line

tag: histology

value: High grade, late stage

tag: ID

value: CASKI

label: Alex 635 dUTP

source_name: Peripheral blood lymphocytes

tag: reference

value: pooled random donor blood sample


title: C57BL6J Colon Gold EthylAcetate Replicate 5


title: C57BL6J Colon Gold Control Replicate 6

source_name: C57BL/6J mouse fed Gold Control (AIN-76A) diet, colon tissue


title: Il10 Colon Gold Aqueous Replicate 6

source_name: Il10-/- mouse fed Gold Kiwifruit Aqueous Extract diet, colon tissue


title: CellLine_C33A_aCGH


title: CellLine_SW756_aCGH


title: C57BL6J Colon Gold Control Replicate 5


title: Il10 Colon Gold Aqueous Replicate 5


title: Il10 Colon Gold Control Replicate 4


title: SCC_G16_aCGH

value: Uterine cervix


title: CellLine_HT3_aCGH


title: CellLine_MS751_aCGH


title: CellLine_ME180_aCGH


title: CellLine_C4I_aCGH


title: C57BL6J Colon Gold Control Replicate 4


title: Il10 Colon Gold EthylAcetate Replicate 4


title: Il10 Colon Gold Control Replicate 5


title: CellLine_DOTC2_aCGH


title: SCC_N55_aCGH


title: CellLine_C4II_aCGH


title: SCC_87_aCGH


title: C57BL6J Colon Gold EthylAcetate Replicate 3


title: DM1 pooled 1

city: Singapore

first: Kandiah

last: Jeyaseelan

address: 8 Medical Drive

department: Biochemistry

country: Singapore

institute: National University of Singapore

description: replicate 10

hyb_protocol: hybridized on miRCURY LNA™ Arrays, using MAUI® hybridization system

scan_protocol: Chips were scanned on Innopsys Scan 700, microarray scanner at 532 nm

data_processing: miRNA microarray data were analyzed by subtracting the background signal (B532nm) from the test signal (F532nm)

source_name: DM1 pooled 1

label_protocol: LNA-modified oligonucleotide (Exiqon) probes for human, mouse and rat miRNAs annotated in miRBase version 11.0 were used in the microarray. Total RNA (1 μg) was 3’-end –labeled with Cy3 dye using the miRCURY LNA ™ Power Labeling Kit (Exiqon)

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

value: blood

tag: phenotype

value: unknown

tag: disease state

value: male


title: DM1 pooled 2

description: replicate 11

source_name: DM1 pooled 2


title: SCC_22_04_aCGH


title: DM1-7

description: replicate 7


title: DM1-9

description: replicate 9


title: DM1-8

description: replicate 8


title: SCC_G1_aCGH


title: DM1-6

description: replicate 6


title: DM1-4

description: replicate 4


title: DM1-5

description: replicate 5


title: SCC_N14_aCGH


title: SCC_N98_aCGH


title: CellLine_SIHA_aCGH

value: SIHA


title: SCC_N12_aCGH


title: Il10 Colon Gold EthylAcetate Replicate 3


title: Il10 Colon Gold Aqueous Replicate 4


title: C57BL6J Colon Gold Aqueous Replicate 4


title: DM1-3

description: replicate 3


title: DM1-2

description: replicate 2


title: Obese DM2-5

description: replicate 5

source_name: Obese DM2-5

value: Obese


title: Obese DM2-2

description: replicate 2

source_name: Obese DM2-2


title: Obese DM2-3

description: replicate 3

source_name: Obese DM2-3


title: SCC_88_05_aCGH


title: Obese DM2-6

description: replicate 6

source_name: Obese DM2-6


title: Obese pooled

description: replicate 5

source_name: Obese pooled


title: Obese DM2-4

description: replicate 4

source_name: Obese DM2-4


title: Obese DM2-1

description: replicate 1

source_name: Obese DM2-1


title: SCC_54_05_aCGH


title: AdV-IL4d2_mouse_1

source_name: lung

value: female

value: 14 weeks

value: lung


title: DM1-1

description: replicate 1


title: Obese DM2 pooled

description: replicate 7

source_name: Obese DM2 pooled


title: Il10 Colon Gold Control Replicate 3

source_name: Il10-/- mouse fed Gold Control (AIN-76A) diet, colon tissue

value: Male

source_name: Reference RNA of healthy growing Swiss Mice


title: SCC_G14_aCGH

source_name: Squamous cell carcinoma


title: Il10 Colon Gold Aqueous Replicate 2

value: Pooled RNA from small intestine, colon, kidney, liver and fetuses


title: C57BL6J Colon Gold Aqueous Replicate 3

source_name: C57BL/6J mouse fed Gold Kiwifruit Aqueous Extract diet, colon tissue

value: colon


title: SCC_K7_aCGH

source_name: Peripheral blood lymphocytes


title: C57BL6J Colon Gold Aqueous Replicate 2

value: 10.5 weeks


title: SCC_G18_aCGH


title: Il10 Colon Gold Aqueous Replicate 3

source_name: Il10-/- mouse fed Gold Kiwifruit Aqueous Extract diet, colon tissue


title: SCC_N21_aCGH


title: Obese 6

description: replicate 4

source_name: Obese 6


title: Obese 2

description: replicate 2

source_name: Obese 2


title: C57BL6J Colon Gold EthylAcetate Replicate 2

source_name: C57BL/6J mouse fed Gold Kiwifruit Ethyl Acetate Extract diet, colon tissue


title: Lean DM2-6

description: replicate 6

source_name: Lean DM2-6

value: Lean


title: Lean DM2 pooled

description: replicate 7

source_name: Lean DM2 pooled


title: SCC_11_04_aCGH

value: High grade, late stage


title: Obese 4

description: replicate 3

source_name: Obese 4


title: Il10 Colon Gold Control Replicate 2


title: SCC_K6_aCGH


title: Lean DM2-3

description: replicate 3

source_name: Lean DM2-3


title: Il10 Colon Gold EthylAcetate Replicate 1

source_name: Il10-/- mouse fed Gold Kiwifruit Ethyl Acetate Extract diet, colon tissue


title: Lean DM2-5

description: replicate 5

source_name: Lean DM2-5


title: Il10 Colon Gold EthylAcetate Replicate 2


title: SCC_26_04_aCGH


title: C57BL6J Colon Gold Control Replicate 2

source_name: C57BL/6J mouse fed Gold Control (AIN-76A) diet, colon tissue


title: SCC_81_05_aCGH


title: SCC_21_04_aCGH


title: C57BL6J Colon Gold EthylAcetate Replicate 1


title: Lean DM2-2

description: replicate 2

source_name: Lean DM2-2


title: Obese 1

description: replicate 1

source_name: Obese 1


title: Lean pooled

description: replicate 5

source_name: Lean pooled


title: SCC_8_04_aCGH

source_name: Squamous cell carcinoma


title: SCC_73_05_aCGH


title: Lean 4

description: replicate 3

source_name: Lean 4


title: SCC_71_05_aCGH

source_name: Peripheral blood lymphocytes


title: Lean 2

description: replicate 2

source_name: Lean 2


title: Lean DM2-1

description: replicate 1

source_name: Lean DM2-1


title: C57BL6J Colon Gold Control Replicate 3

source_name: Reference RNA of healthy growing Swiss Mice


title: Lean 1

description: replicate 1

source_name: Lean 1


title: C57BL6J Colon Gold Control Replicate 1


title: Lean 6

description: replicate 4

source_name: Lean 6


title: Il10 Colon Gold Aqueous Replicate 1

source_name: Il10-/- mouse fed Gold Kiwifruit Aqueous Extract diet, colon tissue


title: Il10 Colon Gold Control Replicate 1

source_name: Il10-/- mouse fed Gold Control (AIN-76A) diet, colon tissue


title: C57BL6J Colon Gold Aqueous Replicate 1

source_name: C57BL/6J mouse fed Gold Kiwifruit Aqueous Extract diet, colon tissue


title: SCC_76_05_aCGH


title: Lean DM2-4

description: replicate 4

source_name: Lean DM2-4


title: SCC_G31_aCGH


title: SCC_G22_aCGH


title: SCC_K3_aCGH


title: HGOSC431

status: Public on Mar 04 2011

city: Houston

first: Kwong-Kwok

last: Wong

state: TX

address: T4-3900, 1515 Holcombe Boulevard

department: Gynecologic Oncology and Reproductive Medicine

institute: UT M. D. Anderson Cancer Center

description: high-grade ovarian serous carcinoma

hyb_protocol: Biotin-labeled cDNA was hybridized to Affymetrix GeneChip U133A Plus 2.0 arrays according to manufacturer's instructions.

scan_protocol: Slides were scanned using the Affymetrix 7G scanner, and CEL files generated using the GeneChip Operating System (GCOS).

data_processing: All CEL files were imported into dChip2008, quantiles normalized and expression values were obtained using Model-based expression with PM signal only.

source_name: Laser-capture microdissected tumor cells

label_protocol: The two-cycle Affymetrix amplification method was used with a starting material of 25 ng total RNA. For first round synthesis of double-stranded cDNA, total RNA (25 ng) was reverse transcribed using the Two-Cycle cDNA Synthesis kit (Affymetrix) and oligo(dT)24-T7 (5V-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-3V) primer according to the manufacturer’s instructions followed by amplification with the MEGAscript T7 kit (Ambion, Inc., Austin, TX). After cleanup of the cRNA with a GeneChip Sample Cleanup Module IVT Column (Affymetrix), second-round doublestranded cDNA was amplified using the IVT Labeling kit (Affymetrix).

extract_protocol: Laser capture microdissection was used to isolate epithelial cells from snap-frozen surgical specimens. Total RNA was then isolated using the Stratagene Absolutely RNA MicroPrep kit.

value: high-grade ovarian serous carcinoma


title: SBOT06-102T Braf

description: Laser capture microdissected tumor cells

hyb_protocol: Biotin-labeled cDNA was hybridized to Affymetrix GeneChip U133A plus 2.0 arrays according to manufacturer's instructions.

scan_protocol: Slides : scanned using the Affymetrix 7G scanner, and CEL files generated using the GeneChip Operating System (GCOS).

source_name: ovarian serous borderline tumor with Braf V600E mutation

label_protocol: The 2-cycle Affymetrix amplification method was used with a starting material of 25 ng total RNA.

extract_protocol: Laser capture micordissection was used to isolate epithelial cells from snap-frozen surgical specimens. Total RNA was then isolated using the Stratagene Absolutely RNA MicroPrep kit.

value: Serous borderline tumor of the ovary

tag: braf genotype

value: V600E mutation


title: SBOT02-005T Braf


title: HOSE2085

description: normal human ovarian surface epithelials cells

value: normal ovarian surface epithelials cells


title: SBOT05-074T Braf


title: SBOT03-285T Braf


title: HOSE2061


title: Genotyping data from one patient with unexplained mental retardation and a deletion in 15q13 (patient 2)

city: Tuebingen

first: Michael

last: Bonin

state: BW

address: CAlwerstr. 7

department: Medical Genetics

institute: University Tuebingen

description: Genotyping data from patients with unexplained mental retardation

hyb_protocol: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol

scan_protocol: Standard Agilent Scanner protocol

data_processing:
Data Anaylsis was performed with DNA Analytics 4.0.76 (www.agilent.com) and the integrated  ADM-2 algorithmn (Lipson et al. 2006). The DLRS-Value (derivative log ratio spread) is 0.17.
Minimum number of probes in a region: 4.0; Minimum absolute average log ratio for region 0.0; maximum number of aberrant regions: 1.000.000.0; percent penetrance per feature  0;

source_name: whole blood from patient

extract_protocol: Standard DNA isolation Kit from whole blood (Qiagen)

value: whole blood from patient

source_name: control blood

value: control blood


title: SBOT05-160T wt

source_name: ovarian serous borderline tumor without mutation

value: wildtype


title: SBOT05-052T wt


title: HOSE2008


title: SBOT03-128T wt


title: HOSE2237


title: HOSE2230


title: SBOT06-003T Braf


title: SBOT01-067T wt


title: HGOSC872

description: high-grade ovarian serous carcinoma

scan_protocol: Slides were scanned using the Affymetrix 7G scanner, and CEL files generated using the GeneChip Operating System (GCOS)

label_protocol: The two-cycle Affymetrix amplification method was used with a starting material of 25 ng total RNA. For first round synthesis of double-stranded cDNA, total RNA (25 ng) was reverse transcribed using the Two-Cycle cDNA Synthesis kit (Affymetrix) and oligo(dT)24-T7 (5V-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-3V) primer according to the manufacturer’s instructions followed by amplification with the MEGAscript T7 kit (Ambion, Inc., Austin, TX). After cleanup of the cRNA with a GeneChip Sample Cleanup Module IVT Column (Affymetrix), second-round doublestranded cDNA was amplified using the IVT Labeling kit (Affymetrix)


title: SCC_72_05_aCGH

source_name: Squamous cell carcinoma

value: Uterine cervix

value: pooled random donor blood sample


title: SBOT06-112T wt


title: HGOSC423

description: high-grade ovarian serous carcinoma


title: HOSE2064


title: HGOSC645

description: high-grade ovarian serous carcinoma


title: HGOSC778

description: high-grade ovarian serous carcinoma


title: HGOSC692

description: high-grade ovarian serous carcinoma


title: HGOSC461

description: high-grade ovarian serous carcinoma


title: HGOSC631

description: high-grade ovarian serous carcinoma


title: HGOSC486

description: high-grade ovarian serous carcinoma


title: mESC derived somatic motoneurons, 8 days in differentiation conditions, SHH;RA, biological replicate 3

city: Stockholm

first: Lia

last: Panman

address: Nobelsvag 3

country: Sweden

institute: LICR

description: Gene experssion data from somatic motoneurons

hyb_protocol: cRNA was hybridized to Affymetric GeneChip Mouse Genome 430 2.0 arrays and washed and stained in Fluidics Station FS-450 according to standard Affymetrix protocal

scan_protocol: Arrays were scanned on Affymetrix GeneChip Scanner 3000 7G

data_processing: GeneChip CEL files were analyzed with Genespring GX11.0, processed with the GC-RMA algorithm and normalized by performing baseline transformation to the median expression level of all samples

source_name: NesE-Olig2 ESC line derived somatic motoneurons after 8 days of differentiation in the presence of SHH and RA

label_protocol: Biotinylated cRNA was obtained from 2 ug of total RNA using the Affymetrix 3' IVT Express kit

extract_protocol: Total RNA was extracted from purified post-mitotic neurons using Qiagen Rneasy micro kit (Qiagen)

value: mESC derived post-mitotic neurons

tag: cell-line


title: HGOSC380

description: high-grade ovarian serous carcinoma


title: HGOSC702

description: high-grade ovarian serous carcinoma


title: HGOSC765

description: high-grade ovarian serous carcinoma


title: HGOSC324C

description: high-grade ovarian serous carcinoma


title: HGOSC1214

description: high-grade ovarian serous carcinoma


title: HGOSC389C

description: high-grade ovarian serous carcinoma


title: HGOSC718

description: high-grade ovarian serous carcinoma


title: Genotyping data from one patient with unexplained mental retardation and a deletion in 15q13 (patient 1)

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: We identified genome-wide CNV using Affymetrix Genotyping Console (GTC), which uses a Hidden Markov Model (HMM) algorithm to calculate copy numbers.

label_protocol: Standard Affymetrix protocol

extract_protocol: Standard DNA isolation Kit from whole blood with promega maxwell-technology.

tag: cell type


title: HGOSC317A

description: high-grade ovarian serous carcinoma


title: HGOSC377

description: high-grade ovarian serous carcinoma


title: HGOSC358

description: high-grade ovarian serous carcinoma


title: mESC derived postmitotic neurons, 8 days in differentiation conditions, SHH;RA, biological replicate 2

description: Gene experssion data from neurons located in dorsal hindbrain

source_name: Wild-type ESC line derived neurons after 8 days of differentiation in the presence of RA

value: Wild-type


title: LGOSC131

description: low-grade ovarian serous carcinoma

value: low-grade ovarian serous carcinoma


title: HGOSC1109

description: high-grade ovarian serous carcinoma


title: mESC derived postmitotic neurons, 10 days in differentiation conditions, SHH;FGF8 biological replicate 1

description: Gene experssion data from neurons located in dorsal midbrain

source_name: Wild-type ESC line derived neurons after 10 days of differentiation in the presence of FGF8


title: HGOSC1933

description: high-grade ovarian serous carcinoma


title: mESC derived postmitotic neurons, 10 days in differentiation conditions, SHH;FGF8 biological replicate 3


title: mESC derived visceral motoneurons, 8 days in differentiation conditions, SHH;RA, biological replicate 3

description: Gene experssion data from caudally located visceral motoneurons

source_name: NesE-Phox2b ESC line derived visceral motoneurons after 8 days of differentiation in the presence of SHH and RA


title: LGOSC218

description: low-grade ovarian serous carcinoma


title: LGOSC333

description: low-grade ovarian serous carcinoma


title: LGOSC231

description: low-grade ovarian serous carcinoma


title: LGOSC226

description: low-grade ovarian serous carcinoma


title: mESC derived visceral motoneurons, 8 days in differentiation conditions, SHH;RA, biological replicate 2


title: mESC derived somatic motoneurons, 8 days in differentiation conditions, SHH;RA, biological replicate 1


title: mESC derived visceral motoneurons, 10 days in differentiation conditions, SHH;FGF8 biological replicate 1

description: Gene experssion data from rostrally located visceral motoneurons

source_name: NesE-Phox2b ESC line derived visceral motoneurons after 10 days of differentiation in the presence of SHH and FGF8


title: mESC derived postmitotic neurons, 10 days in differentiation conditions, SHH;FGF8 biological replicate 2


title: mESC derived serotonergic neurons, 10 days in differentiation conditions, SHH;RA, biological replicate 3

description: Gene experssion data from caudal hindbrain serotonergic neurons

source_name: NesE-Nkx2.2 ESC line derived serotonergic neurons after 10 days of differentiation in the presence of SHH and RA


title: HGOSC957

description: high-grade ovarian serous carcinoma


title: LGOSC279

description: low-grade ovarian serous carcinoma


title: mESC derived somatic motoneurons, 8 days in differentiation conditions, SHH;RA, biological replicate 2


title: mESC derived visceral motoneurons, 10 days in differentiation conditions, SHH;FGF8 biological replicate 2


title: mESC derived serotonergic neurons, 10 days in differentiation conditions, SHH;RA, biological replicate 2


title: mESC derived visceral motoneurons, 8 days in differentiation conditions, SHH;RA, biological replicate 1


title: LGOSC136

description: low-grade ovarian serous carcinoma


title: LGOSC150

description: low-grade ovarian serous carcinoma


title: mESC derived visceral motoneurons, 10 days in differentiation conditions, SHH;FGF8 biological replicate 3


title: LGOSC183

description: low-grade ovarian serous carcinoma


title: LGOSC627

description: low-grade ovarian serous carcinoma


title: mESC derived serotonergic neurons, 10 days in differentiation conditions, SHH;FGF8, biological replicate 2

description: Gene experssion data from rostral hindbrain serotonergic neurons

source_name: NesE-Nkx2.2 ESC line derived serotonergic neurons after 10 days of differentiation in the presence of SHH and FGF8


title: mESC derived serotonergic neurons, 10 days in differentiation conditions, SHH;RA, biological replicate 1


title: LGOSC94

description: low-grade ovarian serous carcinoma


title: P0_Ovary_AMH_biological rep 2

city: Pullman

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description:
Gene expression data from rat P0 Ovary incubated in the presence of 50 ng/ml AMH for 24 hours
Marina-PO-Ovary-AMH-2_6-052710-5.CEL

hyb_protocol: Following fragmentation, ssDNA were hybridized  on Affymetrix Rat Gene 1.0 ST Array according to standard Affymetrix protocol. Chips were washed and stained in the   Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Partek Genomic Suite 6.5 beta software (Partek Inc., St. Louis, MO) on 6.21.2010, using RMA, GC-content adjusted algorithm background correction, quantile normalization, median polish methods for probesets summarization, and log values of probes signals using base 2.  Organ culture date batch effect was removed.

label_protocol: Biotin-labeled ssDNA were prepared according to the standard Affymetrix protocol from at least 300 ng total RNA (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual, 2005-2209, Affymetrix).

growth_protocol: Zero-day old (< 8 hour old) female Sprague-Dawley rats (Harlan Laboratories, Inc., USA) were euthanized according to Washington State University IACUC approved protocols and the ovaries removed and cultured whole as described previously [Dole, G., et al., 2008].

extract_protocol: RNA was isolated from whole rat ovaries (2-3 ovaries per each sample) after homogenization in 1 ml Trizol™ reagent (Sigma-Aldritch, USA), according to manufacturer’s instructions.

treatment_protocol: For each ovary sample from which RNA was collected for microarrays, 1-3 ovaries per filter/well were cultured for 24 hours in the absence  (controls) or presence (treated) AMH (human Anti-Mullerian Hormone)(50 ng/mL, PeproTech Inc., NJ USA).   Two or three ovaries from the same culture well (from different rat pups out of the same litter) and receiving the same treatment were pooled and homogenized together.

value: Sprague-Dawley

value: Female

value: ovary

tag: organ culture date batch

value: day P0

tag: agent

value: AMH


title: P0_Ovary_Control_biological rep 1

description:
Gene expression data from rat P0 Ovary incubated for 24 hours with no treatment
Marina-PO-Ovary-Con-1_1-052710-1.CEL

tag: developmental stage

value: untreated


title: LGOSC70

description: low-grade ovarian serous carcinoma

tag: tissue


title: P0_Ovary_Control_biological rep 3

description:
Gene expression data from rat P0 Ovary incubated for 24 hours with no treatment
Marina-PO-Ovary-Con-3_3-052710-3.CEL

tag: gender


title: P0_Ovary_AMH_biological rep 1

description:
Gene expression data from rat P0 Ovary incubated in the presence of 50 ng/ml AMH for 24 hours
Marina-PO-Ovary-AMH-1_5-052710-4.CEL


title: ES cells_OE_rep3

first: Qiang

last: Wu

description:
Gene expression data from Prmt6 overexpressed embryonic stem cells
P+6 OE 03

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Robust Multi-array Analysis (RMA) as normalization method.

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

growth_protocol: HM1 mouse ES cells were cultured in GMEM (GIBCO) supplemented with 15% ES qualified fetal bovine serum (FBS; Hyclone), 1mM sodium pyruvate (GIBCO), 0.1mM β-mercaptoethanol, 0.1mM MEM non-essential amino acids (NEAA; GIBCO) and 1000U/ml of leukemia inhibitory factor (LIF; Millipore) at 37°C and 5% CO2.

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

treatment_protocol: Mouse Prmt6 was cloned into pCAGIP.puro and transfected into HM1 cells with Lipofectamine 2000 (Invitrogen). Cells were subjected to 3 days of selection by puromycin (1μg/ml).

tag: cell line

value: HM1 embryonic stem cell line

tag: genotype/variation

value: Prmt6 overexpression


title: mESC derived serotonergic neurons, 10 days in differentiation conditions, SHH;FGF8, biological replicate 1

description: Gene experssion data from rostral hindbrain  serotonergic neurons


title: LMP2082

description: low-malignant tumors of the ovary

value: low-malignant tumors of the ovary


title: P0_Ovary_AMH_biological rep 3

description:
Gene expression data from rat P0 Ovary incubated in the presence of 50 ng/ml AMH for 24 hours
Marina-PO-Ovary-AMH-3_7-052710-6.CEL

tag: strain


title: P0_Ovary_Control_biological rep 2

description:
Gene expression data from rat P0 Ovary incubated for 24 hours with no treatment
Marina-PO-Ovary-Con-2_2-052710-2.CEL


title: ES cells_OE_rep2

description:
Gene expression data from Prmt6 overexpressed embryonic stem cells
P+6 OE 02


title: mESC derived mesencephalic dopaminergic neurons, 10 days in differentiation conditions, SHH;FGF8, biological replicate 3

description: Gene experssion data from immature mesencephalic dopamine neurons

source_name: NesE-Lmx1a ESC line derived mesencephalic dopamine neurons after 10 days of differentiation in the presence of SHH and FGF8


title: mESC derived mesencephalic dopaminergic neurons, 10 days in differentiation conditions, SHH;FGF8, biological replicate 2


title: ES cells_control_rep3

description:
Gene expression data from control embryonic stem cells
Control RNA 03

source_name: Control mouse embryonic stem cells

value: control


title: ES cells_OE_rep1

description:
Gene expression data from Prmt6 overexpressed embryonic stem cells
P+6 OE 01


title: mESC derived postmitotic neurons, 8 days in differentiation conditions, SHH;RA, biological replicate 3

description: Gene experssion data from neurons located in dorsal hindbrain


title: LMP1102

description: low-malignant tumors of the ovary


title: mESC derived serotonergic neurons, 10 days in differentiation conditions, SHH;FGF8, biological replicate 3


title: ES cells_control_rep1

description:
Gene expression data from control embryonic stem cells
Control RNA 01


title: LGOSC129

description: low-grade ovarian serous carcinoma


title: mESC derived mesencephalic dopaminergic neurons, 14 days in differentiation conditions, SHH;FGF8, biological replicate 3

description: Gene experssion data from mature mesencephalic dopamine neurons

source_name: NesE-Lmx1a ESC line derived mesencephalic dopamine neurons after 14 days of differentiation in the presence of SHH and FGF8


title: LMP459

description: low-malignant tumors of the ovary


title: LMP1911

description: low-malignant tumors of the ovary


title: A296

status: Public on Mar 03 2011

first: Jun

last: Zhou

address: 16 Divinity Ave. Rm2112

department: Organismic and Evolutionary Biology

description: Biological replicate

hyb_protocol: Genisphere 3DNA system

data_processing: Sequential spatial and intensity normalization.

source_name: Genomic DNA from PS1 male genotype.

label_protocol: Genisphere 3DNA system

extract_protocol: QIAGEN DNeasy blood and tissue kit

value: male (XY)

value: adult

source_name: Genomic DNA from CS male genotype.

value: CS


title: LMP494

description: low-malignant tumors of the ovary

source_name: Laser-capture microdissected tumor cells


title: A294

description: Biological replicate


title: A249

description: Biological replicate

source_name: Genomic DNA from PS2/CS heterozygous male genotype.


title: mESC derived mesencephalic dopaminergic neurons, 14 days in differentiation conditions, SHH;FGF8, biological replicate 1


title: mESC derived postmitotic neurons, 8 days in differentiation conditions, SHH;RA, biological replicate 1


title: mESC derived mesencephalic dopaminergic neurons, 14 days in differentiation conditions, SHH;FGF8, biological replicate 2


title: A280

description: Biological replicate

source_name: Genomic DNA from PS5/CS heterozygous male genotype.


title: A248

description: Biological replicate


title: ES cells_control_rep2

description:
Gene expression data from control embryonic stem cells
Control RNA 02


title: LMP1779

description: low-malignant tumors of the ovary


title: A245

description: Biological replicate

source_name: Genomic DNA from PS2 male genotype.


title: mESC derived mesencephalic dopaminergic neurons, 10 days in differentiation conditions, SHH;FGF8, biological replicate 1


title: A239

description: Biological replicate

source_name: Genomic DNA from PS5 male genotype.


title: A297

description: Biological replicate


title: A240

description: Biological replicate


title: A244

description: Biological replicate


title: A235

description: Biological replicate


title: A236

description: Biological replicate


title: LMP1868

description: low-malignant tumors of the ovary


title: Dunn

city: Tokyo

first: Takeshi

middle: G

last: Kashima

address: Hongo 7-3-1

department: Pathology

country: Japan

institute: University of Tokyo

description: Parental line

hyb_protocol: 100 ug of cRNA were hybridizedon GeneChip Mouse Genome 430 2.0 Array.

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

data_processing: MAS5.0, scaled to 100

source_name: osteosarcoma cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA

growth_protocol: Dunn and LM8 cells were grown in Minimum Essential Medium Eagle supplemented with 10% heat-incubated FBS, L-glutamine, antibiotics and 1% non-essential amino acid.

treatment_protocol: not applicable

value: Non-metastatic

value: Dunn


title: A242

description: Biological replicate

scan_protocol: Scanned on an Axon 4000B scanner. Images were quantified using Genepix.


title: A295

description: Biological replicate


title: LMP834

description: low-malignant tumors of the ovary


title: A234

description: Biological replicate


title: A281

description: Biological replicate


title: LM8

description: Subline

value: Highly metastatic


title: A279

description: Biological replicate


title: A276

description: Biological replicate

source_name: Genomic DNA from PS3 male genotype.


title: A278

description: Biological replicate


title: A277

description: Biological replicate


title: A274

description: Biological replicate


title: A233

description: Biological replicate

source_name: Genomic DNA from PS4 male genotype.


title: A231

description: Biological replicate


title: A275

description: Biological replicate


title: A232

description: Biological replicate


title: A246

description: Biological replicate


title: A241

description: Biological replicate


title: A243

description: Biological replicate


title: A230

description: Biological replicate


title: liver-old LA-8

city: Corvallis

first: Tory

last: Hagen

state: OR

address: 110 Weniger Hall

department: Linus Pauling Institute

institute: Oregon State University

hyb_protocol: Following fragmentation 10ug of cRNA were hybridized on Rat Expression 230 2.0 Genechips.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned with an Affymetrix GeneChip® Scanner 3000 at 570nm.

data_processing: Processing of  Cel files was performed by GC-RMA.

source_name: liver-old LA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3ug total RNA (Expression Analysis Technical Manual 701021 Rev. 5.)

extract_protocol: Total RNA was extracted using RNeasy minikit (Qiagen) according to manufacturer's protocols for liver tissue.

treatment_protocol: 2-week modified pair-feeding with or without 0.2% R-alpha-lipoic acid.

value: Fischer 344

value: male

value: liver

tag: age

tag: diet

value: lipoic acid supplemented


title: liver-old LA-1


title: A238

description: Biological replicate


title: liver-old LA-2


title: A237

description: Biological replicate


title: A247

description: Biological replicate


title: liver-old LA-7


title: liver-old control-8

source_name: liver-old control


title: A229

description: Biological replicate

source_name: Genomic DNA from PS1 female genotype.

value: female (XX)


title: 144h 5ng/mL BMP4-FGF2 (144hr_fgf_147883)

type: mixed

city: madison

first: James

last: Thomson

state: Wisconsin

address: 425 Henry Mall

department: Regenerative Biology

institute: Mogridge Institute for Research

description: the second channel (genomic DNA) serve as common reference across the experiments

hyb_protocol: Array hybridization, wash were performed according to NimbleGen’s recommended protocol

scan_protocol: Arrays were scanned using a GenePix 4000B scanner and the PMT settings were followed by NimbleGen array manual

data_processing: 1. Image extraction:  NimbleScan provided by NimbleGen is used to extract signal data from image files  (*.TFF). Signal meansurements were saved in .pair files.  2. Normalization:  Signal intensities from RNA and gDNA samples are normalized with Robust Multiple-chip Analysis (RMA) algorithm (Irizarry et al., 2003) separately. A median-adjusted ratio is calculated for each gene by dividing its signal intensity from the RNA sample by the sum of the corresponding signal intensity from the gDNA sample and median signal intensity of all genes from the gDNA channel.

source_name: H1 cells treated in -FGF2+BMP4(5ng/mL) medium for 144h

label_protocol: Amino Allyl labeling method

growth_protocol: H1 ES cells were maintained in defined TeSR1 medium on Matrigel plates.

extract_protocol: Total RNA was extracted using RNeasy kit (Qiagen) with on-column DNAse (Qiagen).

treatment_protocol: Cells were dissociated by TrpLE (Invitrogen) and plated into TeSR1 medium +BMP4 or TeSR1 medium -FGF2 +BMP4 to initiate differentiation. Different concentrations of BMP4 were used according to expreimental descriptions. Cells were collected at various time points during time course experiments.

tag: passage

value: differentiated human embryonic stem cell

tag: treatment

value: 144h 5ng/mL BMP4-FGF2

source_name: undifferentiated H1

value: undifferentiated H1


title: A227

description: Biological replicate


title: A228

description: Biological replicate


title: liver-old LA-5


title: liver-old LA-3


title: liver-old control-5


title: liver-old control-3


title: A226

description: Biological replicate


title: liver-young LA-7

source_name: liver-young LA

value: 3 months


title: 36h 5ng/mL BMP4-FGF2 (36hr_fgf_147781)

source_name: H1 cells treated in -FGF2+BMP4(5ng/mL) medium for 36h

value: 36h 5ng/mL BMP4-FGF2


title: liver-old control-7

value: control


title: 48h 5ng/mL BMP4-FGF2 (48hr_fgf_147783)

source_name: H1 cells treated in -FGF2+BMP4(5ng/mL) medium for 48h

value: 48h 5ng/mL BMP4-FGF2


title: 72h 5ng/mL BMP4-FGF2 (72hr_fgf_147785)

source_name: H1 cells treated in -FGF2+BMP4(5ng/mL) medium for 72h

value: 72h 5ng/mL BMP4-FGF2


title: 120h 5ng/mL BMP4-FGF2 (120hr_fgf_229688)

source_name: H1 cells treated in -FGF2+BMP4(5ng/mL) medium for 120h

value: 120h 5ng/mL BMP4-FGF2


title: liver-young LA-6


title: liver-old control-4


title: liver-old control-2


title: 96h 5ng/mL BMP4-FGF2 (96hr_fgf_147793)

source_name: H1 cells treated in -FGF2+BMP4(5ng/mL) medium for 96h

value: 96h 5ng/mL BMP4-FGF2


title: 24h 5ng/mL BMP4-FGF2 (24hr_fgf_229684)

source_name: H1 cells treated in -FGF2+BMP4(5ng/mL) medium for 24h

value: partially differentiated human embryonic stem cell

value: 24h 5ng/mL BMP4-FGF2


title: liver-old control-1

value: Fischer 344


title: liver-old control-6

value: male


title: liver-young LA-8

value: liver


title: 12h 5ng/mL BMP4-FGF2 (12hr_fgf_147770)

source_name: H1 cells treated in -FGF2+BMP4(5ng/mL) medium for 12h

value: 12h 5ng/mL BMP4-FGF2


title: liver-young LA-4

value: lipoic acid supplemented


title: liver-young LA-3


title: liver-young LA-5


title: 6h 5ng/mL BMP4-FGF2 (6hr_fgf_147767)

source_name: H1 cells treated in -FGF2+BMP4(5ng/mL) medium for 6h

value: 6h 5ng/mL BMP4-FGF2


title: TeSR1 144h control (144hr_TeSR_ctrl_147903)

source_name: H1 cells cultured in TeSR1 medium for 144h

value: human embryonic stem cell

value: TeSR1 144h control


title: liver-young LA-2

value: 3 months


title: 18h 5ng/mL BMP4-FGF2 (18hr_fgf_147777)

source_name: H1 cells treated in -FGF2+BMP4(5ng/mL) medium for 18h

value: 18h 5ng/mL BMP4-FGF2

value: undifferentiated H1


title: 144h 5ng/mL BMP4+FGF2 (144hr_149705)

source_name: H1 cells treated in +FGF2+BMP4(5ng/mL) medium for 144h

value: differentiated human embryonic stem cell

value: 144h 5ng/mL BMP4+FGF2


title: liver-young LA-1


title: liver-young control-8

source_name: liver-young control

value: control


title: 72h 5ng/mL BMP4+FGF2 (72hr_148050)

source_name: H1 cells treated in +FGF2+BMP4(5ng/mL) medium for 72h

value: 72h 5ng/mL BMP4+FGF2


title: 96h 5ng/mL BMP4+FGF2 (96hr_229682)

source_name: H1 cells treated in +FGF2+BMP4(5ng/mL) medium for 96h

value: 96h 5ng/mL BMP4+FGF2


title: 120h 5ng/mL BMP4+FGF2 (120hr_149718)

source_name: H1 cells treated in +FGF2+BMP4(5ng/mL) medium for 120h

value: 120h 5ng/mL BMP4+FGF2


title: liver-young control-6

value: Fischer 344


title: liver-young control-7

value: male


title: 24h 5ng/mL BMP4+FGF2 (24hr_147916)

source_name: H1 cells treated in +FGF2+BMP4(5ng/mL) medium for 24h

value: partially differentiated human embryonic stem cell

value: 24h 5ng/mL BMP4+FGF2

source_name: undifferentiated H1


title: 18h 5ng/mL BMP4+FGF2 (18hr_147914)

source_name: H1 cells treated in +FGF2+BMP4(5ng/mL) medium for 18h

value: 18h 5ng/mL BMP4+FGF2


title: liver-young control-4

value: liver


title: liver-young control-5


title: liver-young control-3


title: liver-young control-1


title: 36h 5ng/mL BMP4+FGF2 (36hr_147921)

source_name: H1 cells treated in +FGF2+BMP4(5ng/mL) medium for 36h

value: 36h 5ng/mL BMP4+FGF2


title: 12h 5ng/mL BMP4+FGF2 (12hr_147913)

source_name: H1 cells treated in +FGF2+BMP4(5ng/mL) medium for 12h

value: 12h 5ng/mL BMP4+FGF2


title: 6h 5ng/mL BMP4+FGF2 (6hr_147904)

source_name: H1 cells treated in +FGF2+BMP4(5ng/mL) medium for 6h

value: 6h 5ng/mL BMP4+FGF2


title: TeSR1 0h control (0hr_TeSR_ctrl_147898)

source_name: Undifferentiated H1 cells cultured in TeSR1 medium. The starting point of this experiment.

value: human embryonic stem cell

value: TeSR1 0h control


title: IPF AEx broncoalveolar lavage Viro3P29-050

city: San Francisco

first: Sharon

middle: Chao

last: Wootton

address: Byers Hall, Rm s403c 1700 4th St.

department: Joint Graduate Group in Bioengineering

institute: UC Berkeley and UC San Francisco

description: BAL collected from IPF patients experiencing acute exacerbations

hyb_protocol: 65 degree incubation overnight in standard microarray hybridization chamber

scan_protocol: microarray scanned with GenePix scanner

data_processing: Median feature intensity minus median background intensity generated. The sum-normalization was just done as part of the E-Predict program, and the data was analyzed using Cluster and E-Predict.

organism: Viruses

source_name: total nucleic acid from BAL of acute exacerbations of IPF

label_protocol:
labeling of aminoallyl dNTP with Cy3/Cy5; Cy3 for amplified sample, Cy5 for Probe70 (internal reference for GenePix oligo recognition)
Probe 70 is a spiked-in control that is not used for normalization.  Because our microarrays are printed in-house, there are slight variations in location of the oligo on the array relative to previous print sets.  The Probe-70 allows Gene-pix to locate the oligos on every array independent of the hybridization of the sample in the Cy3 channel.

extract_protocol: Total nucleic acid extraction

tag: sample medical procedure

value: BAL

value: acute exacerbations IPF

tag: volume


title: 48h 5ng/mL BMP4+FGF2 (48hr_148049)

source_name: H1 cells treated in +FGF2+BMP4(5ng/mL) medium for 48h

value: differentiated human embryonic stem cell

value: 48h 5ng/mL BMP4+FGF2

value: undifferentiated H1


title: IPF AEx broncoalveolar lavage Viro3P29-044

tag: disease state


title: IPF AEx broncoalveolar lavage Viro3P29-034


title: Normal skin from Tgfbeta_control mouse, biological replicate 3

city: Boston

first: William

middle: R

last: Swindell

address: 77 Avenue Louis Pasteur

department: Genetics

description: Normal skin without psoriasiform phenotype

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray TM Scanner 3000.

data_processing: Robust Multichip Average (RMA)

source_name: Normal skin from Tgfbeta_control mouse

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

growth_protocol: Laboratory animals were maintained under standard conditions in accordance with protocols approved by animal welfare committees at each participating institution

extract_protocol: RNA was extracted using QIAGEN RNeasy mini kits

treatment_protocol: For all experiments involving transgenic mice, experimental and control animals were genotyped at weaning using PCR, and development of psoriasiform lesions was spontaneous and not induced by wounding (e.g., tape stripping). For the IMQ-generated phenotype, the treatment protocol was to apply a daily topical dose of 62.5 mg IMQ cream (5% Aldara; 3M Pharmaceuticals) to the shaved back region of 8-10 week old C57BL/6 mice. This treatment was carried out for six consecutive days, and during this time, control animals were treated with a vehicle cream (Vaseline Lanette cream; Fagron). In all experiments, adult mice were euthanized at 10-20 weeks of age at which time ear, tail or back skin samples were flash frozen and stored at -80C prior to the isolation of total RNA.

tag: tissue type

value: back skin


title: IPF AEx broncoalveolar lavage Viro3P29-036


title: IPF AEx broncoalveolar lavage Viro3P29-037


title: liver-young control-2

value: Fischer 344

value: 3 months

value: control


title: IPF AEx broncoalveolar lavage Viro3P29-015


title: IPF AEx broncoalveolar lavage Viro3P27-075


title: IPF AEx broncoalveolar lavage Viro3P29-016


title: IPF AEx broncoalveolar lavage Viro3P29-041


title: IPF AEx broncoalveolar lavage Viro3P29-019


title: IPF AEx broncoalveolar lavage Viro3P29-004


title: IPF AEx broncoalveolar lavage Viro3P27-060


title: IPF AEx broncoalveolar lavage Viro3P27-058


title: IPF AEx broncoalveolar lavage Viro3P29-002


title: IPF AEx broncoalveolar lavage Viro3P27-061


title: IPF AEx broncoalveolar lavage Viro3P29-013


title: Normal skin from Tgfbeta_control mouse, biological replicate 2


title: IPF AEx broncoalveolar lavage Viro3P29-026


title: Normal skin from Tgfbeta_control mouse, biological replicate 1


title: IPF AEx broncoalveolar lavage Viro3P29-006


title: IPF AEx broncoalveolar lavage Viro3P27-064


title: IPF AEx broncoalveolar lavage Viro3P27-042


title: Lesional skin from K5-Tgfbeta mouse, biological replicate 3

description: Psoriasiform skin

source_name: Lesional skin from K5-Tgfbeta mouse


title: IPF AEx broncoalveolar lavage Viro3P27-043


title: IPF AEx broncoalveolar lavage Viro3P29-033


title: IPF AEx broncoalveolar lavage Viro3P27-065


title: IPF AEx broncoalveolar lavage Viro3P27-069


title: IPF AEx broncoalveolar lavage Viro3P27-053


title: IPF AEx broncoalveolar lavage Viro3P29-047


title: Lesional skin from K5-Tgfbeta mouse, biological replicate 2

description: Psoriasiform skin


title: IPF AEx broncoalveolar lavage Viro3P29-011


title: IPF AEx broncoalveolar lavage Viro3P27-049


title: IPF AEx broncoalveolar lavage Viro3P27-040


title: Normal skin from Stat3c_control mouse, biological replicate 2

source_name: Normal skin from Stat3c_control mouse

value: FVB/NHsd


title: IPF AEx broncoalveolar lavage Viro3P27-041


title: Lesional skin from K5-Stat3c mouse, biological replicate 1

description: Psoriasiform skin

source_name: Lesional skin from K5-Stat3c mouse


title: Normal skin from Stat3c_control mouse, biological replicate 1


title: IPF AEx broncoalveolar lavage Viro3P27-039


title: Normal tail skin from control mouse, biological replicate 3

source_name: Normal tail skin from control mouse

value: FVB/NCrIBR

value: tail skin


title: Normal tail skin from control mouse, biological replicate 2


title: Normal tail skin from control mouse, biological replicate 1


title: IPF AEx broncoalveolar lavage Viro3P27-012


title: Lesional tail skin from K14-Areg mouse, biological replicate 3

description: Psoriasiform skin

source_name: Lesional tail skin from K14-Areg mouse


title: Lesional skin from K5-Stat3c mouse, biological replicate 2

description: Psoriasiform skin


title: Lesional skin from K5-Tgfbeta mouse, biological replicate 1

description: Psoriasiform skin


title: IPF AEx broncoalveolar lavage Viro3P27-008


title: IPF AEx broncoalveolar lavage Viro3P27-007


title: IPF AEx broncoalveolar lavage Viro3P27-009


title: Lesional tail skin from K14-Areg mouse, biological replicate 1

description: Psoriasiform skin


title: Lesional tail skin from K14-Areg mouse, biological replicate 2

description: Psoriasiform skin


title: IPF AEx broncoalveolar lavage Viro3P27-037


title: Normal ear skin from control mouse, biological replicate 2

source_name: Normal ear skin from control mouse

value: ear skin


title: IPF AEx broncoalveolar lavage Viro3P27-010


title: Normal ear skin from control mouse, biological replicate 3


title: Normal ear skin from control mouse, biological replicate 1


title: IPF AEx broncoalveolar lavage Viro3P27-011


title: IPF AEx broncoalveolar lavage Viro3P27-001


title: IPF AEx broncoalveolar lavage Viro3P29-052


title: Lesional ear skin from K14-Areg mouse, biological replicate 3

description: Psoriasiform skin

source_name: Lesional ear skin from K14-Areg mouse


title: IPF AEx broncoalveolar lavage Viro3P27-006


title: IPF AEx broncoalveolar lavage Viro3P27-003


title: Lesional ear skin from K14-Areg mouse, biological replicate 1

description: Psoriasiform skin


title: IPF AEx broncoalveolar lavage Viro3P29-051


title: IPF AEx broncoalveolar lavage Viro3P29-045


title: IPF AEx broncoalveolar lavage Viro3P29-046


title: Normal skin from lmq_control mouse, biological replicate 3

source_name: Normal skin from lmq_control mouse


title: Normal skin from lmq_control mouse, biological replicate 2


title: 72h 50ng/mL BMP4-FGF2 (bmp4_fgf_72h_110673)

source_name: H1 cells treated in -FGF2+BMP4(50ng/mL) medium for 72h

tag: cell type

value: 72h 50ng/mL BMP4-FGF2

source_name: undifferentiated H1


title: IPF AEx broncoalveolar lavage Viro3P27-004


title: Normal skin from lmq_control mouse, biological replicate 1


title: IPF AEx broncoalveolar lavage Viro3P29-049


title: 24h 50ng/mL BMP4-FGF2 (bmp4_fgf_24h_110671)

source_name: H1 cells treated in -FGF2+BMP4(50ng/mL) medium for 24h

value: 24h 50ng/mL BMP4-FGF2


title: 120h 50ng/mL BMP4-FGF2 (bmp4_fgf_120h_103526)

source_name: H1 cells treated in -FGF2+BMP4(50ng/mL) medium for 120h

value: 120h 50ng/mL BMP4-FGF2


title: IPF AEx broncoalveolar lavage Viro3P29-043


title: IPF AEx broncoalveolar lavage Viro3P29-039


title: IPF AEx broncoalveolar lavage Viro3P29-048


title: IPF AEx broncoalveolar lavage Viro3P29-032

description: BAL collected from stable IPF patients

source_name: total nucleic acid from BAL of stable IPF

value: stable IPF


title: 12h 50ng/mL BMP4-FGF2 (bmp4_fgf_12h_110818)

source_name: H1 cells treated in -FGF2+BMP4(50ng/mL) medium for 12h

value: partially differentiated human embryonic stem cell

value: 12h 50ng/mL BMP4-FGF2


title: IPF AEx broncoalveolar lavage Viro3P29-035

description: BAL collected from stable IPF patients

value: BAL


title: IPF AEx broncoalveolar lavage Viro3P27-002

source_name: total nucleic acid from BAL of acute exacerbations of IPF

value: acute exacerbations IPF


title: IPF AEx broncoalveolar lavage Viro3P29-040


title: 48h 50ng/mL BMP4-FGF2 (bmp4_fgf_48h_103375)

source_name: H1 cells treated in -FGF2+BMP4(50ng/mL) medium for 48h

value: differentiated human embryonic stem cell

value: 48h 50ng/mL BMP4-FGF2

value: undifferentiated H1


title: Lesional skin from imiquimod-treated mouse, biological replicate 2

description: Psoriasiform skin

value: back skin


title: IPF AEx broncoalveolar lavage Viro3P29-038


title: IPF AEx broncoalveolar lavage Viro3P29-030

description: BAL collected from stable IPF patients


title: Lesional skin from imiquimod-treated mouse, biological replicate 3

description: Psoriasiform skin


title: IPF AEx broncoalveolar lavage Viro3P29-031

description: BAL collected from stable IPF patients


title: Normal skin from Tie2_control mouse, biological replicate 3

source_name: Normal skin from Tie2_control mouse


title: IPF AEx broncoalveolar lavage Viro3P29-025

description: BAL collected from stable IPF patients


title: TeSR1 120h control (Control_120h_110678)

source_name: H1 cells cultured in TeSR1 medium for 120h

value: human embryonic stem cell

value: TeSR1 120h control


title: IPF AEx broncoalveolar lavage Viro3P29-029

description: BAL collected from stable IPF patients


title: Normal skin from Tie2_control mouse, biological replicate 2


title: IPF AEx broncoalveolar lavage Viro3P29-027

description: BAL collected from stable IPF patients


title: IPF AEx broncoalveolar lavage Viro3P29-023

description: BAL collected from stable IPF patients


title: Lesional ear skin from K14-Areg mouse, biological replicate 2

description: Psoriasiform skin

value: FVB/NCrIBR


title: IPF AEx broncoalveolar lavage Viro3P29-028

description: BAL collected from stable IPF patients


title: Lesional skin from imiquimod-treated mouse, biological replicate 1

description: Psoriasiform skin


title: Normal skin from Tie2_control mouse, biological replicate 1


title: 6h 50ng/mL BMP4-FGF2 (bmp4_fgf_6h_110665)

source_name: H1 cells treated in -FGF2+BMP4(50ng/mL) medium for 6h

value: 6h 50ng/mL BMP4-FGF2


title: 48h 50ng/mL BMP4+FGF2 (bmp4_48h_102557_R1)

source_name: H1 cells treated in +FGF2+BMP4(50ng/mL) medium for 48h

value: 48h 50ng/mL BMP4+FGF2


title: Lesional skin from K5-Tie2 mouse, biological replicate 3

description: Psoriasiform skin

source_name: Lesional skin from K5-Tie2 mouse


title: 72h 50ng/mL BMP4+FGF2 (bmp4_72h_103557)

source_name: H1 cells treated in +FGF2+BMP4(50ng/mL) medium for 72h

value: 72h 50ng/mL BMP4+FGF2


title: 120h 50ng/mL BMP4+FGF2 (bmp4_120h_103374)

source_name: H1 cells treated in +FGF2+BMP4(50ng/mL) medium for 120h

value: 120h 50ng/mL BMP4+FGF2


title: Lesional skin from K5-Tie2 mouse, biological replicate 2

description: Psoriasiform skin


title: IPF AEx broncoalveolar lavage Viro3P29-017

description: BAL collected from stable IPF patients


title: Lesional skin from K5-Tie2 mouse, biological replicate 1

description: Psoriasiform skin


title: IPF AEx broncoalveolar lavage Viro3P29-024

description: BAL collected from stable IPF patients


title: IPF AEx broncoalveolar lavage Viro3P29-008

description: BAL collected from stable IPF patients


title: IPF AEx broncoalveolar lavage Viro3P29-018

description: BAL collected from stable IPF patients


title: IPF AEx broncoalveolar lavage Viro3P29-014

description: BAL collected from stable IPF patients


title: IPF AEx broncoalveolar lavage Viro3P29-021

description: BAL collected from stable IPF patients


title: IPF AEx broncoalveolar lavage Viro3P29-007

description: BAL collected from stable IPF patients


title: 100ng/mL BMP4 - FGF2 (100ng_fgf_104256)

source_name: Day 5 differentiated H1 cells with 100ng/mL BMP4 - FGF2 treatment

value: 100ng/mL BMP4 - FGF2


title: IPF AEx broncoalveolar lavage Viro3P27-074

description: BAL collected from stable IPF patients

value: stable IPF


title: IPF AEx broncoalveolar lavage Viro3P29-020

description: BAL collected from stable IPF patients


title: IPF AEx broncoalveolar lavage Viro3P29-009

description: BAL collected from stable IPF patients


title: MOSE Late Cells, biological replicate 1

city: Blacksburg

first: Eva

last: Schmelz

state: VA

address: Virginia Tech

department: HNFE

institute: Virginia Tech

description:
13_p2.136.CEL
Gene Expression of MOSE cells at different transformation stages

hyb_protocol: The RNA samples were processed using Affymetrix's GeneChip WT cDNA Synthesis and Amplification Kit (900672). Hybridization was done using Affymetrix Hybridization, Wash, and Stain Kit (part # 900720). Arrays were hybed for 16 hr at 45C. Samples were stained and washed using the Genechip Fluidics 450 station

scan_protocol: GeneChips were scanned using the GCS 3000 HR scanner.

data_processing: We utilized MicroArray Suite 5.0 (Affymetrix, Santa Clara, CA) to process raw microarray data.   Data values were globally scaled to an average target intensity to allow inter-GeneChip comparisons.

source_name: mouse ovarian surface epithelial cells in culture

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

growth_protocol: MOSE cell lines were routinely maintained in DMEM high glucose medium supplemented with 4% fetal bovine serum, 100 mg/ml each of penicillin and streptomycin, 5 mg/ml insulin, 5 mg/ml transferrin, and 5 ng/ml sodium selenite.

extract_protocol: RNA samples for early (passage 13, 14, and 15), intermediate (63, 71, and 73), and late (136, 142, and 143) passages were isolated using the RNeasy Kit according to the manufacturers instructions and treated with ribonuclease-free deoxyribonuclease I.  RNA samples were assayed on the Agilent 2100 BioAnalyzer for qualitative assessment and quantification.

value: mouse ovarian surface epithelial (MOSE) cell

tag: malignant potential

value: malignant


title: 12ng/mL BMP4 - FGF2 (12ng_fgf_103718)

source_name: Day 5 differentiated H1 cells with 12ng/mL BMP4 - FGF2 treatment

value: 12ng/mL BMP4 - FGF2


title: TeSR1 0h control (Control_0h_102511)

source_name: Undifferentiated H1 cells cultured in TeSR1 medium. The starting point of this experiment.

value: TeSR1 0h control

source_name: undifferentiated H1


title: 24h 50ng/mL BMP4+FGF2 (bmp4_24h_103553)

source_name: H1 cells treated in +FGF2+BMP4(50ng/mL) medium for 24h

value: partially differentiated human embryonic stem cell

value: 24h 50ng/mL BMP4+FGF2


title: 12h 50ng/mL BMP4+FGF2 (bmp4_12h_102513_R1)

source_name: H1 cells treated in +FGF2+BMP4(50ng/mL) medium for 12h

value: 12h 50ng/mL BMP4+FGF2

value: undifferentiated H1


title: MOSE Intermediate Cells, biological replicate 3

description:
6_p2.73.CEL
Gene Expression of MOSE cells at different transformation stages

value: intermediate


title: 25ng/mL BMP4 - FGF2 (25ng_fgf_104252)

source_name: Day 5 differentiated H1 cells with 25ng/mL BMP4 - FGF2 treatment

value: differentiated human embryonic stem cell

value: 25ng/mL BMP4 - FGF2


title: IPF AEx broncoalveolar lavage Viro3P27-050

description: BAL collected from stable IPF patients

source_name: total nucleic acid from BAL of stable IPF

value: BAL


title: IPF AEx broncoalveolar lavage Viro3P27-052

description: BAL collected from stable IPF patients


title: IPF AEx broncoalveolar lavage Viro3P29-010

description: BAL collected from stable IPF patients


title: IPF AEx broncoalveolar lavage Viro3P29-012

description: BAL collected from stable IPF patients


title: IPF AEx broncoalveolar lavage Viro3P27-077

description: BAL collected from stable IPF patients


title: MOSE Intermediate Cells, biological replicate 1

description:
4_p2.63.CEL
Gene Expression of MOSE cells at different transformation stages


title: IPF AEx broncoalveolar lavage Viro3P29-005

description: BAL collected from stable IPF patients


title: MOSE Late Cells, biological replicate 3

description:
15_p2.143.CEL
Gene Expression of MOSE cells at different transformation stages


title: IPF AEx broncoalveolar lavage Viro3P29-022

description: BAL collected from stable IPF patients


title: 6ng/mL BMP4 - FGF2 (6ng_fgf_103717)

source_name: Day 5 differentiated H1 cells with 6ng/mL BMP4 - FGF2 treatment

value: 6ng/mL BMP4 - FGF2


title: 50ng/mL BMP4 - FGF2 (50ng_fgf_104255)

source_name: Day 5 differentiated H1 cells with 50ng/mL BMP4 - FGF2 treatment

value: 50ng/mL BMP4 - FGF2


title: 6h 50ng/mL BMP4+FGF2 (bmp4_6h_102513)

source_name: H1 cells treated in +FGF2+BMP4(50ng/mL) medium for 6h

value: 6h 50ng/mL BMP4+FGF2


title: IPF AEx broncoalveolar lavage Viro3P29-001

description: BAL collected from stable IPF patients


title: IPF AEx broncoalveolar lavage Viro3P27-046

description: BAL collected from stable IPF patients


title: H1 control in TeSR1 - FGF2 (Control_fgf_103249)

source_name: Day 5 H1 cells cultured in -FGF2 TeSR1medium to show the effect from FGF2 withdrawal only

value: human embryonic stem cell

value: H1 control in TeSR1 - FGF2


title: IPF AEx broncoalveolar lavage Viro3P27-048

description: BAL collected from stable IPF patients

value: stable IPF


title: MOSE Early Cells, biological replicate 3

description:
3_p2.15.CEL
Gene Expression of MOSE cells at different transformation stages

value: mouse ovarian surface epithelial (MOSE) cell

value: non-malignant


title: MOSE Late Cells, biological replicate 2

description:
14_p2.142.CEL
Gene Expression of MOSE cells at different transformation stages

value: malignant


title: IPF AEx broncoalveolar lavage Viro3P29-003

description: BAL collected from stable IPF patients


title: MOSE Early Cells, biological replicate 2

description:
2_p2.14.CEL
Gene Expression of MOSE cells at different transformation stages


title: MOSE Early Cells, biological replicate 1

description:
1_p2.13.CEL
Gene Expression of MOSE cells at different transformation stages


title: MOSE Intermediate Cells, biological replicate 2

description:
5_p2.71.CEL
Gene Expression of MOSE cells at different transformation stages


title: 50ng/mL BMP4 + FGF2 (50ng_102557)

source_name: Day 5 differentiated H1 cells with 50ng/mL BMP4 + FGF2 treatment

value: 50ng/mL BMP4 + FGF2


title: 100ng/mL BMP4 + FGF2 (100ng_102561)

source_name: Day 5 differentiated H1 cells with 100ng/mL BMP4 + FGF2 treatment

value: 100ng/mL BMP4 + FGF2


title: SI3_wk2_HF (high fat diet, low calcium)

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

description:
Pooled total RNA sample of 6 mice.
SI3_wk2_LCa

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip Scanner 3000.

data_processing: Data analysis was performed using Microarray Analysis Suite 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The mean target intensity of each array was set to 500.

source_name: SI3 after 2 wks on a HFD, LCa diet

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (described in the eukaryotic section in the GeneChip Expression Analysis Technical Manual Rev. 3 from Affymetrix).

growth_protocol: Male C57BL/6J mice were purchased from Harlan (Horst, The Netherlands) and were housed in the light- and temperature-controlled animal facility of Wageningen University. They had free access to water and prior to the diet intervention they received standard laboratory chow.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen, Breda, The Netherlands) according to the manufacturer’s instructions. The isolated RNA was further column-purified using the SV total RNA isolation system (Promega, Leiden, The Netherlands). RNA concentration was measured on a NanoDrop ND-1000 UV-Vis spectrophotometer (Isogen, Maarssen, The Netherlands) and analyzed on a bioanalyzer (Agilent Technologies, Amsterdam, the Netherlands) with 6000 Nano Chips according to the manufacturer’s instructions. For each part of small intestine, total RNA was pooled per diet group (n=6).

treatment_protocol: Nine-week-old mice were fed a high-fat purified diet with a low calcium concentration of 50mmol/kg (LCa diet) for 8 weeks.

value: male

value: small intestine, SI 3

tag: dietary fat

value: high

tag: dietary calcium

value: low

value: 9wks old at start of diet intervention

tag: diet intervention time


title: 25ng/mL BMP4 + FGF2 (25ng_102550)

source_name: Day 5 differentiated H1 cells with 25ng/mL BMP4 + FGF2 treatment

value: differentiated human embryonic stem cell

value: 25ng/mL BMP4 + FGF2

value: undifferentiated H1


title: SI2_wk2_HF (high fat diet, low calcium)

description:
Pooled total RNA sample of 6 mice.
SI2_wk2_LCa

source_name: SI2 after 2 wks on a HFD, LCa diet

tag: gender

tag: tissue

value: small intestine, SI 2


title: 6ng/mL BMP4 + FGF2 (6ng_102545)

source_name: Day 5 differentiated H1 cells with 6ng/mL BMP4 + FGF2 treatment

tag: cell line

value: 6ng/mL BMP4 + FGF2


title: SI1_wk2_HF (high fat diet, low calcium)

description:
Pooled total RNA sample of 6 mice.
SI1_wk2_LCa

source_name: SI1 after 2 wks on a HFD, LCa diet

tag: strain

value: small intestine, SI 1


title: 12ng/mL BMP4 + FGF2 (12ng_102546)

source_name: Day 5 differentiated H1 cells with 12ng/mL BMP4 + FGF2 treatment

value: 12ng/mL BMP4 + FGF2


title: H1 control in TeSR1 (Control_102540)

source_name: Undifferentiated H1 cells cultured in TeSR1 medium. The starting point of this experiment.

value: human embryonic stem cell

value: H1 control in TeSR1

source_name: undifferentiated H1


title: F9 teratocarcinoma cells after differentiation with retinoic acid/theophylline/cAMP. Replicate 1

status: Public on Mar 02 2011

first: Steven

last: Head

address: 10550 N Torrey Pines Rd

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the v1 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with RMA Express using the default settings (Background Adjust - Yes, Normalization - Quantile, Summarization Method - Median Polish, Store Residuals - unchecked).

value: F9 teratocarcinoma


title: Nanog immunoprecipitate

type: other

city: Providence

last: Fairbrother

state: RI

address: 70 Ship St

department: MCB

institute: Brown University

description:
MEGAshift protocol:
A complex pool of 60-mer oligonucleotides was synthesized as a custom oligonucletide microarray ('synthesized array') to contains the union of the intersection of ChIP-ChIP fragments of POU5F1 (Oct4), Nanog and Sox2 as found in Core Transcriptional Regulatory Circuitry In Humand Embryonic Stem Cell (Boyer et. Al, 2005). Each oligo was designed as a tiled genomic 30-mer flanked by the common sequence CCAGTAGATCTGCCA and ATGGAGTCCAGGTTG that were used as universal primers.
Oligo pool was liberated from the slide by boiling at 99C for 1 hour. Low cycle PCR was used to amplify the pool. The amplified oligonucleotide pool was then was incubated with embryonic stem cell extract to perform a binding assay.
A 'detection array' (Agilent_BrownUniversity/FairbrotherLab Human 2x105K OSN_Validation tiling array) complimentary to the 'synthesized array' is used to measure the degree to which each oligonucleotide is enriched in the bound fraction. The array returns binding measurements for each oligonucleotide, which can be used to define biologically relevant motifs and to create binding maps.

hyb_protocol: A 2 × 104 k Custom Agilent oligonucleotide detection microarray was designed complimentary to the oligonucleotide pool.  Microarrays were hybridized for 3 hours at 50C using an optimized Agilet gene expression hybridization kit and protocol.

scan_protocol: Microarrays were scanned at 5um using GenePix 400B scanner and analyzed using Feature Extraction Software from Agilent.

data_processing: We obtained the log10 ratio of normalized rProcessedSignal to normalized gProcessedSignal. Signal values were normalized by taking the ratio of each probe to the summed signal of probes on the array. Probes were omitted where Cy3 probes were not well above background.

molecule: other

source_name: [starting] oligo pool that tiles through genomic DNA representing 316 PluCR regions (i.e., regions of simulataneous in vivo Oct4, Sox2 and Nanog ChIP enrichement in human ES cells

label_protocol: RNA target were produced containing amino-allyl UTP using MEGAshortscript™ High-Yield Transcription kit (Ambion) after appending a T7 promoter to the oligonucleotides. Amino-Allyl UTP’s were then coupled to Cy3 and Cy5 dyes, through a labeling procedure. RNA was pelleted and resuspended in 1M NA2CO3, monoreactive dyes were added and reaction was allowed to continue for 1h at room temperature. 4M hydroxylamine was used to quench the reaction followed by phenol:chloroform and ethanol precipitation to remove remaining free nucleotides.

extract_protocol: DNA isolated from four different co-immunoprecipitation reactions (POU5F1(Oct4), POU2F1(Oct1), SOX2, NANOG) was  transcribed into RNA and used to produce targets for array analysis. Starting DNA pool was transcribe similarly.

tag: antibody

source_name: [co-immunoprecipitate] oligo pool that tiles through genomic DNA representing 316 PluCR regions (i.e., regions of simulataneous in vivo Oct4, Sox2 and Nanog ChIP enrichement in human ES cells

value: anti-Nanog

tag: antibody vendor

value: Cosmo Bio Co., LTD.

tag: antibody lot#

tag: antibody catalog#


title: F9 teratocarcinoma cells after differentiation with retinoic acid/theophylline/cAMP. Replicate 3

city: La Jolla

institute: The Scripps Research Institute


title: OCT1 immunoprecipitate

value: Santa Cruz Biotechnology, Inc.


title: 3ng/mL BMP4 - FGF2 (3ng_fgf_103709)

source_name: Day 5 differentiated H1 cells with 3ng/mL BMP4 - FGF2 treatment

tag: passage

tag: treatment

value: 3ng/mL BMP4 - FGF2