title: Healthy Control Sample PAX_CONT_3_A1

description: Healthy Control Sample PAX_CONT_3_A1


title: Celiac Disease Sample 3_CAP162639

status: Public on Oct 01 2008

type: RNA

city: London

first: Graham

last: Heap

address: 4 Newark Street

country: United Kingdom

institute: QMUL

description: Celiac Disease Sample 3_CAP162639

hyb_protocol: Complementary RNA was hybridized to Illumina HumanRef-8 v2 Whole Genome BeadChips

scan_protocol: Illumina BeadArray Reader, data was handled through Illumina BeadStudio Gene Expression module v3

data_processing: Quantile-quantile normalization.

molecule: total RNA

organism: Homo sapiens

source_name: Total RNA from peripheral blood RNA.

label_protocol: 2.5 ml of peripheral blood was collected into a PAXgene tube (Becton Dickinson, UK, 762165). PAXgene vials were chosen to prevent density gradient centrifugation, immortalization or in vitro cell culture artifacts changing mRNA profiles. PAXgene tubes were mixed gently and incubated at room temperature for two hours. After collection, tubes were frozen at -20 degrees Celsius for at least 24 hours followed by storage at -80 degrees Celsius. RNA was isolated using the PAXgene Blood RNA isolation kit (Qiagen, UK, 762174). RNA was quantified using the Nanodrop (Nanodrop Technologies, USA). Total RNA integrity was analyzed using an Agilent Bioanalyzer (Agilent Technologies, USA).

extract_protocol: PAXgene Blood RNA isolation kit protocol (Qiagen, UK, 762174)

tag: disease state

value: Celiac Disease

tag: tissue

value: Peripheral blood


title: Celiac Disease Sample 2_CAP152902

description: Celiac Disease Sample 2_CAP152902


title: Celiac Disease Sample 1_CAP152795

description: Celiac Disease Sample 1_CAP152795


title: Celiac Disease Sample 2_CAP152618

description: Celiac Disease Sample 2_CAP152618


title: Celiac Disease Sample 1_CAP152694

description: Celiac Disease Sample 1_CAP152694


title: Celiac Disease Sample 3_CAP152615

description: Celiac Disease Sample 3_CAP152615


title: Celiac Disease Sample 1_CAP152793

description: Celiac Disease Sample 1_CAP152793


title: Celiac Disease Sample 1_CAP152758

description: Celiac Disease Sample 1_CAP152758


title: Celiac Disease Sample 1_CAP152610

description: Celiac Disease Sample 1_CAP152610


title: Celiac Disease Sample 2_CAP152851

description: Celiac Disease Sample 2_CAP152851


title: Celiac Disease Sample 1_CAP152695

description: Celiac Disease Sample 1_CAP152695


title: Celiac Disease Sample 1_CAP152788

description: Celiac Disease Sample 1_CAP152788


title: Healthy Control Sample PAX_CONT_3_B2

description: Healthy Control Sample PAX_CONT_3_B2

value: Healthy Control


title: Healthy Control Sample PAX_CONT_3_A8

description: Healthy Control Sample PAX_CONT_3_A8


title: Celiac Disease Sample 1_CAP152708

description: Celiac Disease Sample 1_CAP152708


title: Celiac Disease Sample 3_CAP162349

description: Celiac Disease Sample 3_CAP162349


title: Healthy Control Sample PAX_CONT_3_A2

description: Healthy Control Sample PAX_CONT_3_A2


title: Celiac Disease Sample 2_CAP152908

description: Celiac Disease Sample 2_CAP152908


title: Celiac Disease Sample 1_CAP152789

description: Celiac Disease Sample 1_CAP152789


title: Celiac Disease Sample 1_CAP152598

description: Celiac Disease Sample 1_CAP152598


title: Celiac Disease Sample 1_CAP152664

description: Celiac Disease Sample 1_CAP152664


title: Celiac Disease Sample 2_CAP152604

description: Celiac Disease Sample 2_CAP152604


title: Celiac Disease Sample 2_CAP153241

description: Celiac Disease Sample 2_CAP153241


title: Celiac Disease Sample 1_CAP152784

description: Celiac Disease Sample 1_CAP152784


title: Celiac Disease Sample 2_CAP152894

description: Celiac Disease Sample 2_CAP152894


title: Celiac Disease Sample 1_CAP152780

description: Celiac Disease Sample 1_CAP152780


title: Celiac Disease Sample 1_CAP152777

description: Celiac Disease Sample 1_CAP152777


title: Celiac Disease Sample 1_CAP152693

description: Celiac Disease Sample 1_CAP152693


title: Celiac Disease Sample 3_CAP152640

description: Celiac Disease Sample 3_CAP152640


title: Celiac Disease Sample 3_CAP162337

description: Celiac Disease Sample 3_CAP162337


title: Celiac Disease Sample 2_CAP152843

description: Celiac Disease Sample 2_CAP152843


title: Celiac Disease Sample 1_CAP152690

description: Celiac Disease Sample 1_CAP152690


title: Celiac Disease Sample 2_CAP152882

description: Celiac Disease Sample 2_CAP152882


title: Celiac Disease Sample 1_CAP152661

description: Celiac Disease Sample 1_CAP152661


title: Celiac Disease Sample 1_CAP152689

description: Celiac Disease Sample 1_CAP152689


title: Celiac Disease Sample 2_CAP152891

description: Celiac Disease Sample 2_CAP152891


title: Celiac Disease Sample 1_CAP152773

description: Celiac Disease Sample 1_CAP152773


title: Celiac Disease Sample 2_CAP153245

description: Celiac Disease Sample 2_CAP153245


title: Celiac Disease Sample 1_CAP152662

description: Celiac Disease Sample 1_CAP152662


title: Celiac Disease Sample 1_CAP153113

description: Celiac Disease Sample 1_CAP153113


title: Celiac Disease Sample 1_CAP152778

description: Celiac Disease Sample 1_CAP152778


title: Celiac Disease Sample 2_CAP152893

description: Celiac Disease Sample 2_CAP152893


title: Celiac Disease Sample 2_CAP152918

description: Celiac Disease Sample 2_CAP152918


title: Celiac Disease Sample 2_CAP152575

description: Celiac Disease Sample 2_CAP152575


title: Celiac Disease Sample 1_CAP152770

description: Celiac Disease Sample 1_CAP152770


title: Celiac Disease Sample 2_CAP152585

description: Celiac Disease Sample 2_CAP152585


title: Celiac Disease Sample 2_CAP152580

description: Celiac Disease Sample 2_CAP152580


title: Celiac Disease Sample 3_CAP152834

description: Celiac Disease Sample 3_CAP152834


title: Celiac Disease Sample 1_CAP152765

description: Celiac Disease Sample 1_CAP152765


title: Celiac Disease Sample 2_CAP152901

description: Celiac Disease Sample 2_CAP152901


title: Celiac Disease Sample 2_CAP152873

description: Celiac Disease Sample 2_CAP152873


title: Celiac Disease Sample 2_CAP152879

description: Celiac Disease Sample 2_CAP152879


title: Celiac Disease Sample 1_CAP153120

description: Celiac Disease Sample 1_CAP153120


title: Celiac Disease Sample 1_CAP152769

description: Celiac Disease Sample 1_CAP152769


title: Celiac Disease Sample 2_CAP153219

description: Celiac Disease Sample 2_CAP153219


title: Celiac Disease Sample 3_CAP152715

description: Celiac Disease Sample 3_CAP152715


title: Celiac Disease Sample 2_CAP152888

description: Celiac Disease Sample 2_CAP152888


title: Celiac Disease Sample 2_CAP153212

description: Celiac Disease Sample 2_CAP153212


title: Celiac Disease Sample 1_CAP153115

description: Celiac Disease Sample 1_CAP153115


title: Celiac Disease Sample 1_CAP152757

description: Celiac Disease Sample 1_CAP152757


title: Celiac Disease Sample 1_CAP152706

description: Celiac Disease Sample 1_CAP152706


title: Celiac Disease Sample 1_CAP152713

description: Celiac Disease Sample 1_CAP152713


title: Celiac Disease Sample 1_CAP152714

description: Celiac Disease Sample 1_CAP152714


title: Celiac Disease Sample 2_CAP153222

description: Celiac Disease Sample 2_CAP153222


title: Celiac Disease Sample 3_CAP152564

description: Celiac Disease Sample 3_CAP152564


title: Celiac Disease Sample 1_CAP152705

description: Celiac Disease Sample 1_CAP152705


title: Celiac Disease Sample 3_CAP152569

description: Celiac Disease Sample 3_CAP152569


title: Celiac Disease Sample 2_CAP152558

description: Celiac Disease Sample 2_CAP152558


title: Celiac Disease Sample 2_CAP152896

description: Celiac Disease Sample 2_CAP152896


title: Celiac Disease Sample 1_CAP152752

description: Celiac Disease Sample 1_CAP152752


title: Celiac Disease Sample 3_CAP152559

description: Celiac Disease Sample 3_CAP152559


title: Celiac Disease Sample 3_CAP152556

description: Celiac Disease Sample 3_CAP152556


title: Celiac Disease Sample 1_CAP153018

description: Celiac Disease Sample 1_CAP153018


title: Celiac Disease Sample 2_CAP153217

description: Celiac Disease Sample 2_CAP153217


title: Celiac Disease Sample 2_CAP152871

description: Celiac Disease Sample 2_CAP152871


title: Celiac Disease Sample 2_CAP152898

description: Celiac Disease Sample 2_CAP152898


title: Celiac Disease Sample 2_CAP152832

description: Celiac Disease Sample 2_CAP152832


title: Celiac Disease Sample 1_CAP152678

description: Celiac Disease Sample 1_CAP152678


title: Celiac Disease Sample 2_CAP152627

description: Celiac Disease Sample 2_CAP152627


title: Celiac Disease Sample 1_CAP152749

description: Celiac Disease Sample 1_CAP152749


title: Celiac Disease Sample 1_CAP152750

description: Celiac Disease Sample 1_CAP152750


title: Celiac Disease Sample 2_CAP152547

description: Celiac Disease Sample 2_CAP152547


title: Celiac Disease Sample 1_CAP152799

description: Celiac Disease Sample 1_CAP152799


title: Celiac Disease Sample 2_CAP152626

description: Celiac Disease Sample 2_CAP152626


title: Celiac Disease Sample 1_CAP152798

description: Celiac Disease Sample 1_CAP152798


title: Celiac Disease Sample 1_CAP152747

description: Celiac Disease Sample 1_CAP152747


title: Celiac Disease Sample 3_CAP152538

description: Celiac Disease Sample 3_CAP152538


title: Celiac Disease Sample 2_CAP152543

description: Celiac Disease Sample 2_CAP152543


title: Celiac Disease Sample 2_CAP152842

description: Celiac Disease Sample 2_CAP152842


title: Celiac Disease Sample 3_CAP152698

description: Celiac Disease Sample 3_CAP152698


title: Celiac Disease Sample 2_CAP152892

description: Celiac Disease Sample 2_CAP152892


title: Celiac Disease Sample 1_CAP152736

description: Celiac Disease Sample 1_CAP152736


title: Celiac Disease Sample 1_CAP152740

description: Celiac Disease Sample 1_CAP152740


title: Celiac Disease Sample 2_CAP153292

description: Celiac Disease Sample 2_CAP153292


title: Celiac Disease Sample 1_CAP152735

description: Celiac Disease Sample 1_CAP152735


title: Celiac Disease Sample 2_CAP152872

description: Celiac Disease Sample 2_CAP152872


title: Celiac Disease Sample 2_CAP152912

description: Celiac Disease Sample 2_CAP152912


title: Celiac Disease Sample 3_CAP152544

description: Celiac Disease Sample 3_CAP152544


title: Celiac Disease Sample 2_CAP152886

description: Celiac Disease Sample 2_CAP152886


title: Celiac Disease Sample 2_CAP152621

description: Celiac Disease Sample 2_CAP152621


title: Celiac Disease Sample 1_CAP152733

description: Celiac Disease Sample 1_CAP152733


title: Celiac Disease Sample 3_CAP152542

description: Celiac Disease Sample 3_CAP152542


title: Celiac Disease Sample 2_CAP152553

description: Celiac Disease Sample 2_CAP152553


title: Celiac Disease Sample 1_CAP152730

description: Celiac Disease Sample 1_CAP152730


title: Celiac Disease Sample 1_CAP152731

description: Celiac Disease Sample 1_CAP152731


title: Celiac Disease Sample 2_CAP152904

description: Celiac Disease Sample 2_CAP152904


title: Celiac Disease Sample 2_CAP162542

description: Celiac Disease Sample 2_CAP162542


title: Celiac Disease Sample 1_CAP152700

description: Celiac Disease Sample 1_CAP152700


title: Celiac Disease Sample 1_CAP152701

description: Celiac Disease Sample 1_CAP152701


title: Celiac Disease Sample 3_CAP153242

description: Celiac Disease Sample 3_CAP153242


title: IL10-/- mice OA diet colon tissue (Pool 1)

status: Public on Jul 10 2008

city: Puddle Alley

first: Alan

middle: Francis

last: McCulloch

state: Mosgiel

address: Invermay

country: New Zealand

institute: AgResearch NZ

description: The histological scoring of the inflammation was done with no prior knowledge of the treatments. Scoring of stained sections was based on: 1) inflammatory lesions (mononuclear cell, neutrophil, eosinophil and plasmocyte infiltration, fibrin exudation and lymphangiectasis); 2) tissue destruction (enterocyte loss, ballooning degeneration, oedema and mucosal atrophy); 3) tissue repair (hyperplasia, angiogenesis, granulomas and fibrosis). A score between 0 (no change from normal tissue) and 3 (lesions present in most areas and all layers of the intestinal section including mucosa, muscle and omental fat) was given for each aspect of inflammatory lesions, tissue destruction and tissue repair. The histological injury score (HIS) was calculated as: HIS = [(inflammatory lesions score) x 2] + tissue destruction score + tissue repair score. The concentrations of serum amyloid A in the plasma were measured to gain information on systemic inflammation levels and to complement HIS. Fifty μl of diluted plasma was used to assess the plasma concentration of SAA using the serum amyloid A kit (Tridelta Development Limited, Maynooth, County Kildare, Ireland), as described by the manufacturer. Total RNA was extracted from 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).

hyb_protocol: Labeled cRNAs were hybridised using an In Situ Hybridization Plus Kit (Agilent Technologies, Santa Clara, CA, USA), following the manufacturer’s protocols, using 750 ng of sample cRNA and 750 ng of reference cRNA onto 44k mouse oligonucleotide arrays (Agilent Technologies, Santa Clara, CA, USA). After hybridisation, slides were washed in solutions I, II and III (Agilent Technologies, Santa Clara, CA, USA) and air-dried.

scan_protocol: Slides were scanned after washing using a GenePix Professional 4200A scanner (Molecular Devices, Sunnyvale, CA, USA), at photomultiplier tube voltages of 585 (red) and 600 (green). Spot identification and quantification was performed using GenePix 6.0 software (Molecular Devices). All slides were individually checked and manually flagged for abnormalities.

data_processing: Statistical analysis was performed using Linear models for microarray analysis (Limma) from the Bioconductor project. Data with bad flags (-50 = poor or irregular spots, automatically flagged by the GenePix 4200A scanner; and -100, flagged by hand after visual inspection of the images) were not included in the analysis. Control probes (eQC, Bright corners, E1A and Pro25G) were also removed 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 ≥ 1.3 fold change (FC) with a moderated p < 0.01 were considered to be significantly different. This fold change was chosen because recent studies show that a FC above 1.6 can underestimate the number of differentially expressed genes regulated by dietary treatment.

organism: Mus musculus

source_name: IL10-/- mice EPA diet colon tissue

label_protocol: cDNA and cRNA were synthesised using the Low RNA Input Linear Amplification kit (Agilent Technologies, Santa Clara, CA, USA), following the manufacturer’s instructions. Briefly, 500 ng of purified total RNA from each pool was amplified and reverse transcribed in vitro to cDNA using T7-polymerase, which was subsequently labelled with either cyanine 3-CTP (sample) or cyanine 5-CTP (reference pool) dyes. A reference design was used. The Nanodrop ND-1000 was used to monitor dye incorporation; sample and reference were between 9 and 22 pmol/μg cRNA.

growth_protocol: Throughout the experimental period, food intake was estimated by collecting and weighing uneaten food. Animals were not fed ad libitum; the food given was adjusted daily to equal the mean amount of feed consumed by Il10-/- mice on the previous day. Water was provided ad libitum and refreshed twice a week. All mice were weighed three times a week and carefully monitored for disease symptoms (weight loss, soft faeces, inactivity). After 77 days of age, all mice were randomly divided into two sampling days and three staggered groups of four mice within each day. This time was selected based on a previous study, where Il10-/- mice inoculated with EF and CIF showed an acceptable and consistent level of colon inflammation by 77 days of age. Randomisation of the mice into sampling days and groups was done to minimize any bias of food intake for the EPA or OA diet groups. On the last day, mice were fasted overnight for 14 hours, food was reoffered for 2 hours and again removed for the two hours immediately before sampling. This was done to minimize the variation in time between the last food intake and tissue sampling. Animals were euthanized by CO2 asphyxiation and cervical dislocation. Blood was sampled via cardiac puncture (0.5 to 1 ml) and centrifuged. The plasma was frozen in liquid nitrogen and stored at -85°C for serum amyloid A analysis. The intestine was quickly removed, cut open lengthwise, flushed with 0.9% NaCl to remove digesta and divided into duodenum, jejunum, ileum and colon. A piece of each section was stored at room temperature in 10% phosphate buffered formalin for histological analysis. Tissue samples were also frozen in liquid nitrogen and stored at -85°C for gene and protein profiling.

extract_protocol: Total RNA was extracted from 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). An equimolar pool of colon RNA extracts from 2 to 3 mice per treatment was made to minimize individual variation. A reference RNA was used for microarray hybridization.

treatment_protocol: Twenty-four male IL10-/- and twenty-four male C57 mice, four weeks of age were used for the experiment. All mice were between 28 to 35 days of age at the start of the trial, and were purchased from the Jackson Laboratory (Bar Harbor, Maine, USA). Mice were individually housed in standard shoebox size cages (332 mm x 150 mm x 130 mm) containing untreated wood shavings and a plastic tube for environmental enrichment, and maintained under conventional conditions with a temperature of approximately 22°C, 50% relative humidity and a 12 hour light-dark cycle. After 4 days, all mice were inoculated orally with bacteria commonly found in the intestinal lumen to obtain a more consistent and reproducible intestinal inflammation. Briefly, a mixture of Enterococcus faecalis and E. faecium (EF) strains and complex intestinal flora (CIF) was administrated via oral gavage. Mice were randomly assigned to one of four AIN-76A based diets made in-house with six Il10-/- and six C57 mice in each group. Mice were randomly assigned to four treatment groups of 12 animals each. Each treatment group received one of the following diets: 1) AIN-76A diet 2) AIN-76A (fat-free) + 1% corn oil + 3.7% oleic acid (OA, control) 3) AIN-76A (fat-free) + 1% corn oil + 3.7% eicosapentaenoic acid (EPA,n-3) 4) AIN-76A (fat-free) + 1% corn oil + 3.7% arachidonic acid (AA, n-6). Corn oil supplemented with purified linoleic and alpha-linolenic acid to meet the nutritional requirements of mice for these essential fatty acids. Diets fed for 6 weeks. The diets were isocaloric, contained equal amounts of protein and varied only in lipid composition, containing 5% fat (w/w) as in the AIN-76A base diet. The experimental diets met the nutritional requirements of laboratory mice. The extraction and analysis of fatty acids in the EPA and OA diets were performed before the start of the experiment to confirm fatty acid composition. The diets were aliquoted in daily portions and stored at -85°C until used. Fresh diet (3.5 to 4.0 g/mouse) was provided daily to reduce lipid oxidation. EPA (98% purity, ethyl ester form) was obtained from Brainfats Biotechnology Limited, (Auckland, NZ). The AA, OA, linoleic and alpha-linolenic acid (all 99% purity, ethyl ester form) were purchased from NuCheck, Inc. (Elysian, MN, USA).

tag: strain

source_name: Reference RNA of healthy growing Swiss Mice

label_protocol: As for channel 1 (but Cy5)

growth_protocol: Reference

extract_protocol: as for Channel 1

treatment_protocol: Reference

tag: reference

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


title: Celiac Disease Sample 2_CAP152890

description: Celiac Disease Sample 2_CAP152890


title: C57 mice OA diet colon tissue (Pool 1)

source_name: C57 mice OA diet colon tissue

value: C57 mice (C57BL/6J)

tag: gender

value: male

tag: age

value: 5 weeks

value: colon tissue


title: IL10-/- mice EPA diet colon tissue (Pool 1)


title: IL10-/- mice EPA diet colon tissue (Pool 2)


title: C57 mice OA diet colon tissue (Pool 2)


title: IL10-/- mice OA diet colon tissue (Pool 2)

source_name: IL10-/- mice OA diet colon tissue


title: miR - MM - RB deletion - p831

status: Public on Mar 18 2010

city: Salamanca

first: Norma

middle: Carmen

last: Gutierrez

department: Hematology

country: Spain

institute: University Hospital

description: miR - MM - RB deletion - p831

data_processing:
The SDS files are the raw files for real-time PCR data and are readable by Applied Biosystems SDS Software v2.3. SDS Software is available for download from the Applied Biosystems website.
Normalization was performed with the mean of RNU44 and RNU48.
CT = threshold cycle value
dCT = CT_(miRNA) - CT_(control miRNA) for comparisons between MM samples and normal PC.
ddCT = dCT_(MM) - dCT_(average normal PC) for comparisons between MM samples.
The dCT and ddCT data are presented as log10 of the relative quantity of each miRNA.

label: FAM

source_name: Bone marrow, MM

label_protocol: Standard Taqman Assay

extract_protocol: Total RNA was extracted from normal and tumor plasma cells using miRNEasy Mini Kit (Qiagen, Valencia, USA) following manufacturer's protocol. The RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

value: bone marrow

tag: cell type

value: CD138-positive plasma cell

tag: disease

value: multiple myeloma


title: NSCB_CGH_390K_H9.DE_3153302

status: Public on Jul 18 2008

type: genomic

city: Madison

first: Melodee

last: Patterson

state: WI

address: 510 Charmany Dr Ste 58 & 59

country: USA

institute: WiCell

description: This CGH experiment is designed to detect deletion, insertation, amplication, etc. in the sample relative to the reference.

hyb_protocol: 1. Incubate at 95°C (in heat block), 5 min., spin briefly 2. Place at 42°C (in Maui machine), 5-15 min. 3. Prepare microarray: A)pre-heat array on Maui station B) put array into array-holder (with number facing up going in first) carefully remove glue-sticker from lid and put lid onto array C) take array w/ lid out of array-holder thoroughly attach lid using thick slide place array onto Maui station, approx. 2 min. make sure lid is completely attached D) Add 40 µl hyb solution onto microarray and allow to settle (approx. 15 sec.), dry lid thoroughly 4. Place stickers onto lid, press down on both at the same time, make sure are thoroughly attached 5. Squeeze bubbles away from center of array 6. Wet humid cover and place on Maui station 7. Incubate on Maui at 42°C overnight (17 hours) 8. Remove microarray w/lid from Maui and put in array-holder in Wash 1 (at 42°C) 9. Peel lid off chip while submerged 10. Incubate 10-15 sec. w/ gentle agitation 11. Transfer slide into a slide rack in a new container of Wash 1 (r.t.) Incubate 2 min. w/ gentle agitation 12. Transfer to Wash 2 13. Incubate 1 min. w/ gentle agitation 14. Transfer to Wash 3 15. Incubate 15 sec. w/ gentle agitation 16. Spin approx. 1 min. in Array-Go-Round (place arrays such that numbers are facing to the right when rack is placed in front part of wheel) (the rod on slide holder should be on the inside) 17. Blow off any residual liquid 18. Keep slides protected from light and scan as soon as possible

scan_protocol: NimbleGen scan protocol

data_processing:
1. Image extraction:
NimbleScan provided by NimbleGen is used to extract signal data from image files
(*.TFF). Signals from the scan for Cy3 (green channel) are saved in a file named as chipID_532.pair while signals from the scan for Cy5 (red channel) are saved in a file named as chipID_635.pair.
2. Normalization:
Signals from Cy3/Cy5 channels are transformed by logarithms to base 2 and normalized with loess or qspline (Workman et al., 2002) algorithms by R to resolve the systematic errors and bias introduced by the microarray experimental platform. The log ratios of the signals are obtained by subtracting the log transformed signals from one channel by the corresponding ones from another channel.
3. Data smoothing and break-points identification:
Ratios of the normalized data are plotted by the corresponding genome locations. The data are smoothed by an adaptive weights smoothing algorithm (GLAD R-package, Wang et al., 2005), break-points are identified by a binary segmentation algorithm (DNAcopy R-package, Olshen et al., 2004) or by the segmentation algorithm available within Nimbelgen’s Nimblescan software.
4. Data visualization:
CGH results can be saved as SignalMap GFF files and can be visualized by SignalMap provided by NimbleGen. CGH results can also be visualized by other software, such as aCGHViewer (Shankar et al., 2006), CHARMView (Myers et al., 2005), etc. However, different software requires different input format.

molecule: genomic DNA

label_protocol:
1. Dry the sample in the Speed Vac set at 30°C.
2. Resuspend the sample in 4.5μl 0.1 M Na2CO3, pH 9.0.
3. Resuspend the Cy3 NHS ester in 4.5μl DMSO
4. Add Cy3 NHS ester to sample
5. Incubate at 22°C in a heat block for 1 hour. Protect the heat block and sample from light.
6. Purify the sample using a Qiaquick PCR purification Kit:
A) Add 35μl 100 mM NaOAc, pH 5.2 to the sample.
B) Add 250μl PB buffer to the sample and load the sample on the column.
C) Spin at 13.000 rpm for 1 minute and remove the flow through.
D) Add 750μl PE buffer to the column.
E) Spin at 13.000 rpm for 1 minute and remove the flow through.
F) Spin at 13.000 rpm for 1 minute.
G) Transfer the column to new tube.
H) Add 30μl H20 and incubate for 1 minute on the column.
I) Elute once by centrifuging at 13.000 rpm for 1 minute.

extract_protocol:
1. Determine When to Harvest hES cells for DNA Extraction
A) At least 1x10^6 hES cells should be harvested for DNA extraction, depending on the quantity
required.
B) Yields of genomic DNA will vary from sample to sample depending on the amount and type of cells processed. In addition, the quality of starting material will affect DNA yield.
C) Estimated yield for hES cells: 5pg of DNA per cell (5μg DNA per 10^6 cells). One well of a 6-well plate will normally have between 1-4x106 hES cells by day 5 after passage.
2. Trypsinize the Cells
A) The following steps should be performed in a sterile biosafety cabinet while wearing personal protective equipment.
B) Add 1.5ml of 1X trypsin-EDTA working solution (pre-warmed to 37oC) to each well of a 6- well plate.
C) Return the plate to the 37C incubator for 2-3 minutes.
D) Remove the plate from the incubator and observe cell detachment with an inverted phase contrast microscope. Proceed to next step when colony edges begin to lift off the plate.
E) Using a sterile glass serological pipet, gently pipet up and down to detach the cells and break up the cell clumps.
F) Pool the detached cells in a 15ml centrifuge tube containing 5ml of trypsin stop solution within 5-7 minutes of adding the trypsin-EDTA solution.
G) Gently pipet the solution up and down to mix thoroughly.
H) Centrifuge the tube for 5 minutes at 1000 RPM.
3. RNA Digestion
A) Aspirate the supernatant and gently flick the tube until the pellet is resuspended.
B) Slowly add 200μl PBS to the cells while tapping gently on the tube to ensure good mixing.
C) Add 4μl RNase A (100mg/ml) and incubate at room temperature (RT) for 2 minutes.
4. Protein Digestion
A) Add 20μl Proteinase K and 200μl Buffer AL to the sample, mixing thoroughly by
vortexing. It is important that the solution is immediately and thoroughly mixed by
vortexing and pipetting to yield a homogenous solution.
NOTE: Do not add proteinase K directly to buffer AL.
B) Incubate the cell solution in a 70°C waterbath for 10 minutes.
5. DNA Precipitation and Separation of Cellular Components
A) Add 200μl ethanol (96-100%) to the sample, and mix thoroughly by vortexing.
B) A white precipitate may form on addition of ethanol. This precipitate does not interfere with the DNeasy procedure.
C) Pipet the mixture (including all of the precipitate) into the DNeasy Mini spin column placed in a 2ml collection tube. Centrifuge at ≥6000 x g (8000 rpm) for 1 minute. Discard flowthrough and collection tube.
NOTE: In order to obtain optimum DNA yield and quality, it is important not to overload
the spin column. The maximum number of hES cells that should be used in a DNA
extraction is 5x106 (normally, 2 wells of a 6-well plate). For larger amounts of starting material use multiple spin columns.
6. Wash the DNA
A) Place the DNeasy spin column in a new collection tube and add 500μl of Buffer AW1.
B) Centrifuge at ≥6000 x g (8000rpm) for 1 minute. Discard flow-through and collection tube.
C)Place the DNeasy spin column in a new collection tube and add 500μl of buffer AW2.
D) Centrifuge at 20,000 x g (14,000 rpm) for 3 minutes to dry the DNeasy membrane. Discard flow-through and collection tube.
NOTE: It is important to dry the membrane of the DNeasy Mini spin column, since
residual ethanol may interfere with subsequent reactions. This centrifugation step ensures that no residual ethanol will be carried over during the following elution.
E) Following the centrifugation step, remove the DNeasy Mini spin column carefully so the column does not come into contact with the flow-through, since this will result in carryover of ethanol. If carryover of ethanol occurs, place the spin column in a new collection tube and centrifuge again for 1 minute at 20,000 x g (14,000 rpm). Again discard the flow-through and collection tube.
7. Elution
A) Place the DNeasy Mini spin column in a clean 1.5ml or 2ml microcentrifuge tube and pipet 50-200μl Buffer AE directly onto the DNeasy membrane. Incubate the column at room temperature for 1 minute and then centrifuge for 1 minute at ≥6000 x g (8000rpm) to elute.
NOTE: Elution with less than 200μl of Buffer AE increases the final DNA concentration in the elute, but also decreases the overall DNA yield.
B) Repeat elution step as described in 7 A).
NOTE: A new microcentrifuge tube can be used for the second elution step to prevent dilution of the first elute. Alternatively, to combine the two elutes, the microcentrifuge tube from step 4.7.1 can be reused for the second elution step.
NOTE: More than 200μl should not be eluted into a 1.5 ml microcentrifuge tube because the DNeasy spin column will come into contact with the elute.

tag: cell line

value: human embryonic stem (hES) cell line H1 [reference]


title: IL10-/- mice control diet colon tissue (Pool 1)

source_name: IL10-/- mice control diet colon tissue


title: NSCB_CGH_390K_#6

status: Public on Jul 26 2008

value: WiCell #6

value: Promega Std


title: IL10-/- mice control diet colon tissue (Pool 2)


title: C57 mice EPA diet colon tissue (Pool 2)

source_name: C57 mice EPA diet colon tissue


title: C57 mice AA diet colon tissue (Pool 2)

description:
The histological scoring of the inflammation was done with no prior knowledge of the treatments. Scoring of stained sections was based on: 1) inflammatory lesions (mononuclear cell, neutrophil, eosinophil and plasmocyte infiltration, fibrin exudation and lymphangiectasis); 2) tissue destruction (enterocyte loss, ballooning degeneration, oedema and mucosal atrophy); 3) tissue repair (hyperplasia, angiogenesis, granulomas and fibrosis). A score between 0 (no change from normal tissue) and 3 (lesions present in most areas and all layers of the intestinal section including mucosa, muscle and omental fat) was given for each aspect of inflammatory lesions, tissue destruction and tissue repair. The histological injury score (HIS) was calculated as: HIS = [(inflammatory lesions score) x 2] + tissue destruction score + tissue repair score.
The concentrations of serum amyloid A in the plasma were measured to gain information on systemic inflammation levels and to complement HIS. Fifty μl of diluted plasma was used to assess the plasma concentration of SAA using the serum amyloid A kit (Tridelta Development Limited, Maynooth, County Kildare, Ireland), as described by the manufacturer.
Total RNA was extracted from 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).

data_processing:
Statistical analysis was performed using Linear models for microarray analysis (Limma) from the Bioconductor project. Data with bad flags (-50 = poor or irregular spots, automatically flagged by the GenePix 4200A scanner; and -100, flagged by hand after visual inspection of the images) were not included in the analysis. Control probes (eQC, Bright corners, E1A and Pro25G) were also removed 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 ≥ 1.3 fold change (FC) with a moderated p < 0.01 were considered to be significantly different. This fold change was chosen because recent studies show that a FC above 1.6 can underestimate the number of differentially expressed genes regulated by dietary treatment.

source_name: C57 mice AA diet colon tissue

label_protocol:
cDNA and cRNA were synthesised using the Low RNA Input Linear Amplification kit (Agilent Technologies, Santa Clara, CA, USA), following the manufacturer’s instructions. Briefly, 500 ng of purified total RNA from each pool was amplified and reverse transcribed in vitro to cDNA using T7-polymerase, which was subsequently labelled with either cyanine 3-CTP (sample) or cyanine 5-CTP (reference pool) dyes.
A reference design was used. The Nanodrop ND-1000 was used to monitor dye incorporation; sample and reference were between 9 and 22 pmol/μg cRNA.

growth_protocol:
Throughout the experimental period, food intake was estimated by collecting and weighing uneaten food. Animals were not fed ad libitum; the food given was adjusted daily to equal the mean amount of feed consumed by Il10-/- mice on the previous day. Water was provided ad libitum and refreshed twice a week. All mice were weighed three times a week and carefully monitored for disease symptoms (weight loss, soft faeces, inactivity). After 77 days of age, all mice were randomly divided into two sampling days and three staggered groups of four mice within each day. This time was selected based on a previous study, where Il10-/- mice inoculated with EF and CIF showed an acceptable and consistent level of colon inflammation by 77 days of age. Randomisation of the mice into sampling days and groups was done to minimize any bias of food intake for the EPA or OA diet groups.
On the last day, mice were fasted overnight for 14 hours, food was reoffered for 2 hours and again removed for the two hours immediately before sampling. This was done to minimize the variation in time between the last food intake and tissue sampling. Animals were euthanized by CO2 asphyxiation and cervical dislocation. Blood was sampled via cardiac puncture (0.5 to 1 ml) and centrifuged. The plasma was frozen in liquid nitrogen and stored at -85°C for serum amyloid A analysis. The intestine was quickly removed, cut open lengthwise, flushed with 0.9% NaCl to remove digesta and divided into duodenum, jejunum, ileum and colon. A piece of each section was stored at room temperature in 10% phosphate buffered formalin for histological analysis. Tissue samples were also frozen in liquid nitrogen and stored at -85°C for gene and protein profiling.

treatment_protocol:
Twenty-four male IL10-/- and twenty-four male C57 mice, four weeks of age were used for the experiment. All mice were between 28 to 35 days of age at the start of the trial, and were purchased from the Jackson Laboratory (Bar Harbor, Maine, USA). Mice were individually housed in standard shoebox size cages (332 mm x 150 mm x 130 mm) containing untreated wood shavings and a plastic tube for environmental enrichment, and maintained under conventional conditions with a temperature of approximately 22°C, 50% relative humidity and a 12 hour light-dark cycle. After 4 days, all mice were inoculated orally with bacteria commonly found in the intestinal lumen to obtain a more consistent and reproducible intestinal inflammation. Briefly, a mixture of Enterococcus faecalis and E. faecium (EF) strains and complex intestinal flora (CIF) was administrated via oral gavage.
Mice were randomly assigned to one of four AIN-76A based diets made in-house with six Il10-/- and six C57 mice in each group. Mice were randomly assigned to four treatment groups of 12 animals each. Each treatment group received one of the following diets: 1) AIN-76A diet 2) AIN-76A (fat-free) + 1% corn oil + 3.7% oleic acid (OA, control) 3) AIN-76A (fat-free) + 1% corn oil + 3.7% eicosapentaenoic acid (EPA,n-3) 4) AIN-76A (fat-free) + 1% corn oil + 3.7% arachidonic acid (AA, n-6). Corn oil supplemented with purified linoleic and alpha-linolenic acid to meet the nutritional requirements of mice for these essential fatty acids. Diets fed for 6 weeks. The diets were isocaloric, contained equal amounts of protein and varied only in lipid composition, containing 5% fat (w/w) as in the AIN-76A base diet. The experimental diets met the nutritional requirements of laboratory mice. The extraction and analysis of fatty acids in the EPA and OA diets were performed before the start of the experiment to confirm fatty acid composition. The diets were aliquoted in daily portions and stored at -85°C until used. Fresh diet (3.5 to 4.0 g/mouse) was provided daily to reduce lipid oxidation. EPA (98% purity, ethyl ester form) was obtained from Brainfats Biotechnology Limited, (Auckland, NZ). The AA, OA, linoleic and alpha-linolenic acid (all 99% purity, ethyl ester form) were purchased from NuCheck, Inc. (Elysian, MN, USA).


title: C57 mice control diet colon tissue (Pool 1)

source_name: C57 mice control diet colon tissue


title: C57 mice AA diet colon tissue (Pool 1)

treatment_protocol:
Twenty-four male IL10-/- and twenty-four male C57 mice, four weeks of age were used for the experiment. All mice were between 28 to 35 days of age at the start of the trial, and were purchased from the Jackson Laboratory (Bar Harbor, Maine, USA). Mice were individually housed in standard shoebox size cages (332 mm x 150 mm x 130 mm) containing untreated wood shavings and a plastic tube for environmental enrichment, and maintained under conventional conditions with a temperature of approximately 22°C, 50% relative humidity and a 12 hour light-dark cycle. After 4 days, all mice were inoculated orally with bacteria commonly found in the intestinal lumen to obtain a more consistent and reproducible intestinal inflammation. Briefly, a mixture of Enterococcus faecalis and E. faecium (EF) strains and complex intestinal flora (CIF) was administrated via oral gavage.
Mice were randomly assigned to one of four AIN-76A based diets made in-house with six Il10-/- and six C57 mice in each group. Mice were randomly assigned to four treatment groups of 12 animals each. Each treatment group received one of the following diets: 1) AIN-76A diet 2) AIN-76A (fat-free) + 1% corn oil + 3.7% oleic acid (OA, control)   3) AIN-76A (fat-free) + 1% corn oil + 3.7% eicosapentaenoic acid (EPA,n-3)  4) AIN-76A (fat-free) + 1% corn oil + 3.7% arachidonic acid (AA, n-6). Corn oil supplemented with purified linoleic and alpha-linolenic acid to meet the nutritional requirements of mice for these essential fatty acids. Diets fed for 6 weeks. The diets were isocaloric, contained equal amounts of protein and varied only in lipid composition, containing 5% fat (w/w) as in the AIN-76A base diet. The experimental diets met the nutritional requirements of laboratory mice. The extraction and analysis of fatty acids in the EPA and OA diets were performed before the start of the experiment to confirm fatty acid composition. The diets were aliquoted in daily portions and stored at -85°C until used. Fresh diet (3.5 to 4.0 g/mouse) was provided daily to reduce lipid oxidation. EPA (98% purity, ethyl ester form) was obtained from Brainfats Biotechnology Limited, (Auckland, NZ). The AA, OA, linoleic and alpha-linolenic acid (all 99% purity, ethyl ester form) were purchased from NuCheck, Inc. (Elysian, MN, USA).


title: Whole Blood DDC72

status: Public on Mar 01 2010

first: Andrew

middle: E

last: Teschendorff

address: 72 Huntley Street

department: UCL Cancer Institute/Institute for Women's Health

institute: University College London

description: whole blood from cases and controls, matched for age and sex, were drawn from two irish cohorts. Three replicates labeled with an r are included.

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

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

data_processing: BeadStudio software v3.2

label: Biotin

source_name: genomic DNA from whole blood DDC72

label_protocol: Standard Illumina Protocol for Infinium 27k Chip

extract_protocol: DNA was extracted from whole blood of T1D patients using a salting out method

tag: source

value: bi-sulphite converted genomic whole blood DNA from Control

tag: case/control

value: Control

tag: ageatdiagnosis

tag: sex

value: F

tag: cohort

value: Dublin

value: H

tag: bs conversion c1

tag: bs conversion c2


title: NSCB_CGH_390K_H9.TSF_3618002.1

value: 100% SF cell line

extract_protocol:
1. Determine When to Harvest hES cells for DNA Extraction
A) At least 1x10^6 hES cells should be harvested for DNA extraction, depending on the quantity
required.
B) Yields of genomic DNA will vary from sample to sample depending on the amount and type of cells processed. In addition, the quality of starting material will affect DNA yield.
C) Estimated yield for hES cells: 5pg of DNA per cell (5μg DNA per 10^6 cells). One well of a 6-well plate will normally have between 1-4x106 hES cells by day 5 after passage.
2. Trypsinize the Cells
A) The following steps should be performed in a sterile biosafety cabinet while wearing personal protective equipment.
B) Add 1.5ml of 1X trypsin-EDTA working solution (pre-warmed to 37oC) to each well of a 6- well plate.
C) Return the plate to the 37C incubator for 2-3 minutes.
D) Remove the plate from the incubator and observe cell detachment with an inverted phase contrast microscope. Proceed to next step when colony edges begin to lift off the plate.
E) Using a sterile glass serological pipet, gently pipet up and down to detach the cells and break up the cell clumps.
F) Pool the detached cells in a 15ml centrifuge tube containing 5ml of trypsin stop solution within 5-7 minutes of adding the trypsin-EDTA solution.
G) Gently pipet the solution up and down to mix thoroughly.
H) Centrifuge the tube for 5 minutes at 1000 RPM.
3. RNA Digestion
A) Aspirate the supernatant and gently flick the tube until the pellet is resuspended.
B) Slowly add 200μl PBS to the cells while tapping gently on the tube to ensure good mixing.
C) Add 4μl RNase A (100mg/ml) and incubate at room temperature (RT) for 2 minutes.
4. Protein Digestion
A) Add 20μl Proteinase K and 200μl Buffer AL to the sample, mixing thoroughly by
vortexing. It is important that the solution is immediately and thoroughly mixed by
vortexing and pipetting to yield a homogenous solution.
NOTE: Do not add proteinase K directly to buffer AL.
B) Incubate the cell solution in a 70°C waterbath for 10 minutes.
5. DNA Precipitation and Separation of Cellular Components
A) Add 200μl ethanol (96-100%) to the sample, and mix thoroughly by vortexing.
B) A white precipitate may form on addition of ethanol. This precipitate does not interfere with the DNeasy procedure.
C) Pipet the mixture (including all of the precipitate) into the DNeasy Mini spin column placed in a 2ml collection tube. Centrifuge at ≥6000 x g (8000 rpm) for 1 minute. Discard flowthrough and collection tube.
NOTE: In order to obtain optimum DNA yield and quality, it is important not to overload
the spin column. The maximum number of hES cells that should be used in a DNA
extraction is 5x106 (normally, 2 wells of a 6-well plate). For larger amounts of starting material use multiple spin columns.
6. Wash the DNA
A) Place the DNeasy spin column in a new collection tube and add 500μl of Buffer AW1.
B) Centrifuge at ≥6000 x g (8000rpm) for 1 minute. Discard flow-through and collection tube.
C)Place the DNeasy spin column in a new collection tube and add 500μl of buffer AW2.
D) Centrifuge at 20,000 x g (14,000 rpm) for 3 minutes to dry the DNeasy membrane. Discard flow-through and collection tube.
NOTE: It is important to dry the membrane of the DNeasy Mini spin column, since
residual ethanol may interfere with subsequent reactions. This centrifugation step ensures that no residual ethanol will be carried over during the following elution.
E) Following the centrifugation step, remove the DNeasy Mini spin column carefully so the column does not come into contact with the flow-through, since this will result in carryover of ethanol. If carryover of ethanol occurs, place the spin column in a new collection tube and centrifuge again for 1 minute at 20,000 x g (14,000 rpm). Again discard the flow-through and collection tube.
7. Elution
A) Place the DNeasy Mini spin column in a clean 1.5ml or 2ml microcentrifuge tube and pipet 50-200μl Buffer AE directly onto the DNeasy membrane. Incubate the column at room temperature for 1 minute and then centrifuge for 1 minute at ≥6000 x g (8000rpm) to elute.
NOTE: Elution with less than 200μl of Buffer AE increases the final DNA concentration in the elute, but also decreases the overall DNA yield.
B) Repeat elution step as described in 7 A).
NOTE: A new microcentrifuge tube can be used for the second elution step to prevent dilution of the first elute. Alternatively, to combine the two elutes, the microcentrifuge tube from step 4.7.1 can be reused for the second elution step.
NOTE: More than 200μl should not be eluted into a 1.5 ml microcentrifuge


title: NSCB_CGH_High_density_H9.TSF

value: WiCell #1

value: WiCell #2


title: C57 mice control diet colon tissue (Pool 2)

value: C57 mice (C57BL/6J)

value: male

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


title: IL10-/- mice AA diet colon tissue (Pool 1)

source_name: IL10-/- mice AA diet colon tissue Pool 1


title: IL10-/- mice AA diet colon tissue (Pool 2)

source_name: IL10-/- mice AA diet colon tissue


title: C57 mice EPA diet colon tissue (Pool 1)

value: 5 weeks

value: colon tissue


title: Primary Lung Adenocarcinoma Sample_A48

status: Public on May 01 2007

city: Brisbane

first: Jill

middle: Everland

last: Larsen

state: Queensland

address: Rode Road, Chermside

department: Thoracic Medicine

country: Australia

institute: The Prince Charles Hospital

hyb_protocol: After the purification, the samples were combined for hybridization. The labeled cDNAs were co-hybridized to 22K oligo microarrays.

scan_protocol: Slides were scanned on a GMS418 confocal scanner (Agilent).

data_processing: Raw images were imported into Imagene V5.1 (BioDiscovery, CA, USA) to extract pixel intensities and to flag spots with poor/absent signal. The raw background-subtracted signal median for each probe was imported into GeneSpring GX V7.3 (Agilent Technologies, Inc., CA, USA) for analysis. Data was normalized (Lowess: per spot and per chip; per chip to the 50th percentile) and probe signals filtered on pixel intensity (for both red and green channels any spots less than 20 units or greater than 65,000 units were excluded) and consistent spot morphology. Only spots flagged present in at least 80% of samples were included. For each probe, the logarithm to the base 2 of the ratio between the intensity in the tumor sample (red) channel and the reference (green) channel was used as the expression value for the probe.

source_name: Universal Reference RNA

label_protocol: Synthesis of the labelled first strand cDNA was conducted using Amersham CyScribe Post-Labelling kit with starting material of 20 ug of total RNA. The amino-allyl labeled dNTP mix was added to the reaction to generate amino-allyl labelled second strand cDNA. Following the hydrolysis reaction, single-stranded cDNA probes were purified using Amersham GFX columns. Dye coupling reactions were performed by mixing the cDNA samples with Amersham Cy3 (reference) or Cy5 (tumour) and incubating in the dark. The reactions were purified with Amersham GFX columns to remove the unincorporated/quenched dyes.

extract_protocol: The Universal Reference RNA was commercially available (Stratagene).

value: pool of 10 cell lines

tag: sample type

value: reference

source_name: Tumour sample A48, NARLC-AC

extract_protocol: Total RNA was extracted from fresh-frozen tissue using Trizol (Invitrogen) and RNeasy (Qiagen) clean-up.

value: primary lung adenocarcinoma

tag: lung cancer type

value: non-asbestos-related lung cancer-adenocarcinoma (NARLC-AC)

tag: age (yrs)


title: Primary Lung Adenocarcinoma Sample_A42

source_name: Tumour sample A42, NARLC-AC

tag: tissue


title: Primary Lung Adenocarcinoma Sample_A49

source_name: Tumour sample A49, NARLC-AC


title: Primary Lung Adenocarcinoma Sample_A46

source_name: Tumour sample A46, NARLC-AC


title: Primary Lung Adenocarcinoma Sample_A40

source_name: Tumour sample A40, NARLC-AC


title: NSCB_CGH_390K_ES03_73

status: Public on Mar 11 2008

value: ES03_73 embryonic stem cell

value: human embryonic stem (hES) cell line H1 [reference]


title: NSCB_CGH_390K_ES03_78

status: Public on Feb 01 2008

value: ES03_78 embryonic stem cell


title: Primary Lung Adenocarcinoma Sample_A24

source_name: Tumour sample A24, ARLC-AC

value: asbestos-related lung cancer-adenocarcinoma (ARLC-AC)


title: NSCB_CGH_390K_HSF1_2

value: HSF1 human embryonic stem cell

value: human embryonic stem (hES) cell line H9 [reference]


title: NSCB_CGH_390K_UC01.14_49

value: UC01.14_49 embryonic stem cell


title: Primary Lung Adenocarcinoma Sample_A30

source_name: Tumour sample A30, NARLC-AC


title: MDCC36_Tumor_52

status: Public on Mar 02 2010

city: Philadelphia

first: Jay

last: Johnson

state: PA

address: 422 Curie Blvd

department: Pathology and Laboratory Medicine

institute: University of Pennsylvania

description: This tumor is ALT-positive.

hyb_protocol: Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0 Wash A1 Temperature (C)=30 Number of Wash A1 Cycles=10 Mixes per Wash A1 Cycle=2 Wash B Recovery Mixes=0 Wash B Temperature (C)=50 Number of Wash B Cycles=6 Mixes per Wash B Cycle=15 Stain Temperature (C)=35 First Stain Time (seconds)=300 Wash A2 Recovery Mixes=0 Wash A2 Temperature (C)=30 Number of Wash A2 Cycles=10 Mixes per Wash A2 Cycle=4 Second Stain Time (seconds)=300 Third Stain Time (seconds)=300 Wash A3 Recovery Mixes=0 Wash A3 Temperature (C)=35 Number of Wash A3 Cycles=15 Mixes per Wash A3 Cycle=4< Holding Temperature (C)=25

scan_protocol: The probe array was scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Standard Affymetrix protocol

source_name: Liposarcoma

label_protocol: The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).

extract_protocol: Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.

tag: tumor

value: Liposarcoma

tag: subtype

value: dedifferentiated


title: Primary Lung Adenocarcinoma Sample_A29

source_name: Tumour sample A29, NARLC-AC

tag: gender

value: female


title: Primary Lung Adenocarcinoma Sample_A23

source_name: Tumour sample A23, NARLC-AC

value: male


title: NSCB_CGH_390K_ES04

value: ES04 embryonic stem cell


title: Primary Lung Adenocarcinoma Sample_A34

source_name: Tumour sample A34, NARLC-AC


title: Primary Lung Adenocarcinoma Sample_A37

source_name: Tumour sample A37, ARLC-AC


title: NSCB_CGH_390K_WA09_30

value: WA09 embryonic stem cell


title: Primary Lung Adenocarcinoma Sample_A17

value: pool of 10 cell lines

source_name: Tumour sample A17, NARLC-AC


title: Primary Lung Adenocarcinoma Sample_A39

value: reference

source_name: Tumour sample A39, NARLC-AC


title: NSCB_CGH_390K_WA09_35

value: WA09_35 embryonic stem cell


title: Primary Lung Adenocarcinoma Sample_A28

source_name: Tumour sample A28, ARLC-AC

value: primary lung adenocarcinoma


title: Primary Lung Adenocarcinoma Sample_A12

source_name: Tumour sample A12, NARLC-AC

value: non-asbestos-related lung cancer-adenocarcinoma (NARLC-AC)


title: Primary Lung Adenocarcinoma Sample_A22

source_name: Universal Reference RNA

source_name: Tumour sample A22, NARLC-AC


title: Primary Lung Adenocarcinoma Sample_A19

source_name: Tumour sample A19, NARLC-AC


title: Primary Lung Adenocarcinoma Sample_A36

source_name: Tumour sample A36, NARLC-AC


title: Primary Lung Adenocarcinoma Sample_A11

source_name: Tumour sample A11, NARLC-AC


title: Primary Lung Adenocarcinoma Sample_A8

source_name: Tumour sample A8, NARLC-AC


title: NSCB_CGH_390K_UC01.14

value: UC01.14 embryonic stem cell


title: Primary Lung Adenocarcinoma Sample_A9

source_name: Tumour sample A9, NARLC-AC


title: Primary Lung Adenocarcinoma Sample_A10

source_name: Tumour sample A10, NARLC-AC


title: Peripheral Whole Blood 108269

description: whole blood from cases are from postmenopausal women with ovarian cancer, drawn either before or after treatment

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

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

label: as per Illumina Infinium 27k methylation assay protocol

source_name: genomic DNA from whole blood 108269

label_protocol: A single base extension was performed using labelled DNP- and biotin labelled dNTPs. See the Illumina Infinium 27k methylation assay protocol.

extract_protocol: DNA was extracted at Tepnel (www.tepnel.com) using a chloroform extraction method and 800ng DNA from each sample was bisulphite converted using the EZ DNA Methylation Kit D5008 (Zymo Research, Orange, CA, USA)

value: bi-sulphite converted genomic whole blood DNA from Case

tag: agegroupatsampledraw

tag: ageatrecruitment

tag: histology

value: Serous

tag: stage

value: IIIc

tag: grade

value: Grade 3

tag: pre-treatment sample

value: Yes

tag: post-treatment sample

value: No

tag: batch


title: Monocrotaline 6hr rat Pool Liver vs. Monocrotaline 6hr rat 3233.2 Liver-2

status: Public on Apr 28 2009

city: RTP

first: Pierre

middle: Robert

last: Bushel

state: NC

department: Biostatistics and Computational Biology Branch

institute: NIEHS

description: 10 mg/kg X 6hr

hyb_protocol: Equal amounts of Cy3- or Cy5-labeled cRNA were hybridized to the array for 17 hours prior to washing and scanning.

scan_protocol: Pixel intensity data were extracted from scanned images using the Agilent Technologies Scanner and Feature Extraction Software (Agilent Technologies).  See the header of the Agilent data files for more details of the scanning and data acquisition harware and software versions and parameters.

data_processing: log base 2 ratio of Dye Normalized rProcessedSignal to gProcessedSignal

organism: Rattus norvegicus

source_name: 10 mg/kg Monocrotaline 6hr rat 3233.2 Liver

label_protocol: 1 ug of total RNA was amplified and labeled with a fluorescent dye using the Low RNA Input Linear Amplification Labeling kit (Agilent Technologies, Palo Alto, CA, USA) following the manufacturer's protocol.

extract_protocol: RNA was isolated from the flash frozen portion of the left lateral liver lobe using RNeasy Midi columns (Qiagen, Valencia, CA, USA) according to the manufacturer's protocol.

tag: strain

tag: age

value: 10-12 weeks

value: Liver

source_name: 0 mg/kg Monocrotaline 6hr rat Pool Liver


title: Hepatitis/cirrhotic liver (P.NY516)

status: Public on Oct 15 2008

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

hyb_protocol: Refer to the Illumina DASL Assay System Manual. Hybridization was performed for 4 DASL assay oligo pool (DAP)s, DAP1~4, including 1536 probes each on 4 separate microarrays.

data_processing: For each probe, Red and Green intensities are computed as average of single bead values. The final signal is the sum of the Red and Green intensities. Data were were then normalized using the cubic spline algorithm for each DAP.

label: Cy3 and Cy5

source_name: hepatitis/cirrhotic liver

extract_protocol: Using 10µm sections taken from formalin-fixed paraffin-embeded tissue blocks, total RNA was extracted using TRIzol LS reagent (Invitrogen) with semi-automated robotic extraction.

tag: corresponding tumor sample in gse19977

tag: used for prognostic prediction

tag: clinical data

value: withheld from GEO due to privacy concerns


title: Hepatitis/cirrhotic liver (P.B030)

scan_protocol: Refer to the Illumina DASL Assay System Manual

tag: ethnicity

value: Spanish

tag: egf level

value: Low


title: Hepatitis/cirrhotic liver (P.M278)

label_protocol: Refer to the Illumina DASL Assay System Manual


title: Celiac Disease Sample 2_CAP152889

description: Celiac Disease Sample 2_CAP152889

source_name: Total RNA from peripheral blood RNA.

tag: disease state

value: Celiac Disease

tag: tissue

value: Peripheral blood