title: Cy5: Sa-Low-5206

value: resistant


title: FH 05003-11803-OCT-Carotid-Section-24

status: Public on Oct 01 2011

type: RNA

city: Rahway

first: Oscar

last: Puig

state: NJ

address: 126 East Lincoln Ave

department: Molecular Profiling Research Informatics

country: USA

institute: Merck Research Laboratories

description: Gene expression profiling of carotid plaque. 6 subjects from OCT6 study. Plaques were sectioned in 1 mm slices. Half of the slices were profiled, and the other half, adjacent slices, were processed by IHC

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques.  Arrays are hybridized for 18 hours at 45?C with vigorous mixing.   Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed.  Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Data were loaded into the Rosetta Resolver? system (Rosetta Biosoftware, Seattle, WA) and processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260).  Intensities were calculated based on RMA, a Rosetta-developed error, and a MAS-5 p-value.  The Rosetta-developed error is used in the calculation of xdev for the ratio p-values as described in section 2.2 (http://bioinformatics.oxfordjournals.org/cgi/content/full/22/9/1111).

label: Biotin is incorporated during the amplification.  This binds a streptavidin-conjugated phycoerythrin during the post-hybridization staining process that provides the measurable signal.

molecule: total RNA

organism: Homo sapiens

source_name: carotid plaque

label_protocol: The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin.  After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency.  The labeled molecules are biotinylated-cRNA.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation.  Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.

tag: tissue

value: carotid plaque

tag: patient

tag: sample id

value: FH 05003-11803-OCT-Carotid-Section-24


title: US 8

city: Tokyo

first: Tatsuyuki

last: Chiyoda

address: 35 Shinanomachi Shinjuku-ku

department: Obstetrics and Gynecology

country: Japan

institute: Keio University School of Medicine

description: Gene expression data from frozen tumor samples

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 25x fragmentation buffer and 10x blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2xGE hybridization buffer(HI-RPM) was added to the fragmentation mixture and hybridized to Agilent Whole Human Gene Expression Microarray 4×44K (#014850) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with at room temperature GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10% ).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.1.1.1 (Agilent) using default parameters (GE1-v5_10_Apr08 protocol) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
The algorithm used to normalize data: Threshold raw signals to 1.0. Normalization algorithm 75% Percentile shift. Baseline to median of all samples.

source_name: frozen tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1ug RNA using the One-Color One-Color Quick Amp Labering kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. And RNA was prepared using the RNeasy mini kit (Qiagen, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: sarcoma


title: US 7


title: Cy5: Sa-Low-5064  ##2

city: CASTANET TOLOSAN CEDEX

first: Cécile

last: Bonnefont

address: Auzeville B.P. 52627

country: France

institute: INRA

hyb_protocol: Three ovine 019921 slides (Agilent Technologies), with eight microarrays each containing 15,008 probes were used. The chips were hybridised with labelled RNA at 65°C during 17h and then washed according to the manufacturer's protocol.

scan_protocol: Intensity values were collected with a 4000B Axon scanner. Two channel images were imported into the Agilent's Feature Extraction software for feature (spot) finding and alignment. Features were flagged as present/absent, saturated/unsaturated, uniform/non-uniform and pixel intensities for feature and background were recorded.

data_processing: Output Feature Extraction results (.txt) files were transferred into GeneSpring GX 11. LOESS-normalized data were imported as a single channel data to perform probe by probe analysis and a percentile shift to the median was performed for normalization across arrays.  Data were filtered to remove spots with very low intensity, saturated or not uniform. Only genes for which all data were flagged as present in 100% of one out of the six conditions (resistant line at T0, T3, and T8, and susceptible line at T0, T3, and T8) were conserved for the analysis to focus the analysis on genes that are representative of a condition.

organism: Ovis aries

source_name: Milk somatic cells (MSC)

label_protocol: They were labelled with Cy3 and Cy5 for hybridisation in a two-colour dye-swap experimental design.

extract_protocol: Total RNA was extracted using classical extraction method with Phenol/chloroform with (Trizol, Invitrogen). Extracted RNAs were further purified on RNeasy column (Qiagen). Quantification was performed using a spectrophotometer (NanoDrop Technologies) and RNA quality was assessed using Agilent bioanalyzer 2100 slide.  RNA Integrity Number (RIN) index above 9 was measured for all samples.Two hundred ng of RNA were converted to double-stranded cDNA and amplified with the Amino Allyl Message Amp II aRNA amplification procedure (Ambion kit).

tag: line

tag: challenge

value: S. aureus

tag: cell type

value: Milk somatics cells (MSC) 12h after challenge


title: Cy5: Se-High-5183

value: susceptible

value: S. epidermidis


title: Embryo PBS injected rep2

city: Amsterdam

first: Oliver

last: Stockhammer

state: NH

address: Meibergdreef 15

department: Medical Microbiology

country: Netherlands

institute: AMC

description:
The CR (common reference) was composed by combining RNA of excess embryos from the caudal vein injection experiment
Biological replicate 2 of 3: Zebrafish embryos injected in the caudal vein with phosphate buffered saline (PBS)

hyb_protocol: 825 ng for each channel were combined and made to 55 μl with 10x Blocking Agent and 25x Fragmentation Buffer. 55 μl of 2x Hi-RPM Hybridization Buffer was added (Gene Expression Hybridization Kit, Agilent Technologies). 100 μl of hybridization mixture was loaded onto each array and allowed to hybridize at 65°C (10 RPM) for 17h. The slides were washed with Gene Expression Wash Buffers I and II (Gene Expression Wash Buffer Kit, Agilent Technologies).

scan_protocol: Slides were scanned on an Agilent G2505B scanner at 5 μm resolution and data was extracted with Feature Extraction version 9.3.1.1. (Protocol GE2-v5_95).

data_processing: Microarray data was processed from raw data image files with Feature Extraction Software 9.5.3.1 (Agilent Technologies). The XDR function was used to extend the dynamic range. Processed data were subsequently imported into Rosetta Resolver 7.0 (Rosetta Biosoftware, Seattle, Washington) and subjected to default ratio error modelling.

organism: Danio rerio

label_protocol: Amino Allyl modified aRNA was synthesized in one amplification round from 500 ng of total RNA using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion). Subsequently, 6 ug of Amino Allyl modified aRNA was used for coupling of monoreactive Cy3 or Cy5 dye (GE Healthcare) and column purified.

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5°C in egg water (60µg/ml Instant Ocean sea salts).

extract_protocol: Embryos were individually snap-frozen in liquid nitrogen and subsequently stored at -80°C. A frozen embryo was crushed with a chilled pestle and homogenized in 300 µl of TRI reagent (Ambion). 60 µl chloroform was added and the mixture was transferred to a 1.5 ml reaction tube containing 50 mg phase lock gel (Eppendorf) and incubated at room temperature for 5 minutes. The mixture was centrifuged at 12000 g at 4°C for 15 minutes, after which the aqueous phase was transferred to a fresh tube. 1 volume of 70 % ethanol was added and the mixture transferred to a RNeasy MinElute Cleanup kit (Qiagen) column which was centrifuged 15 seconds at 8000 g. 500 µl RPE buffer from the kit was applied to the column and centrifuged 15 seconds at 8000 g. 500 µl 80 % ethanol was applied to the column and centrifuged 2 minutes at 8000 g. The collection tube was replaced and the column centrifuged 5 minutes at 14000 g. 14 µl H2O was applied to the column and centrifuged 1 minute at 14000 g. The average amount of RNA isolated from a single embryo was 500 ng.

treatment_protocol: Zebrafish were dechorionated manually at 24 hpf. After onset of bloodflow embryos were injected with 200 CFUs of E. tarda or with sterile PBS (phosphate buffered saline). At 8 hpi the embryos were quenched in liquid nitrogen and stored at -80°C.

tag: comment

value: 24 hpf embryos were manually dechorionated and directly after onset of bloodflow injected in the caudal vein with 200 CFUs of E. tarda or with PBS. At 8 hpi the embryos were quenched in liquid nitrogen and stored at -80˚C. This sample is a mixture of embryos from the same experiment but not used as a sample on the microarray.

tag: sample type

value: pooled common reference

value: embryo

tag: time point

value: 36 hpi

tag: infection


title: FH 05003-11803-OCT-Carotid-Section-20

value: FH 05003-11803-OCT-Carotid-Section-20


title: US 6


title: FH 05003-11803-OCT-Carotid-Section-16

value: FH 05003-11803-OCT-Carotid-Section-16


title: Embryo E. tarda injected rep1

description:
The CR (common reference) was composed by combining RNA of excess embryos from the caudal vein injection experiment
Biological replicate 1 of 3: Zebrafish embryos infected by caudal vein injection with 200 CFUs of E. tarda

source_name: D.rerio_embryo_e.tarda_8 hpi_1

value: 200 CFUs of Edwardsiella tarda (strain FL6-60)


title: US 5


title: FH 05003-11803-OCT-Carotid-Section-22

value: FH 05003-11803-OCT-Carotid-Section-22


title: Embryo PBS injected rep1

description:
The CR (common reference) was composed by combining RNA of excess embryos from the caudal vein injection experiment
Biological replicate 1 of 3: Zebrafish embryos injected in the caudal vein with phosphate buffered saline (PBS)


title: Embryo E. tarda injected rep3

description:
The CR (common reference) was composed by combining RNA of excess embryos from the caudal vein injection experiment
Biological replicate 3 of 3: Zebrafish embryos infected by caudal vein injection with 200 CFUs of E. tarda


title: Embryo E. tarda injected rep2

description:
The CR (common reference) was composed by combining RNA of excess embryos from the caudal vein injection experiment
Biological replicate 2 of 3: Zebrafish embryos infected by caudal vein injection with 200 CFUs of E. tarda

source_name: D.rerio_embryo_e.tarda_8 hpi_2


title: Cy5: Se-High-5173


title: Cy5: Se-High-5174


title: EC G3 7

value: endometrioid adenocarcinoma


title: FH 05003-11803-OCT-Carotid-Section-12

value: FH 05003-11803-OCT-Carotid-Section-12


title: FH 05003-11803-OCT-Carotid-Section-18

value: carotid plaque

value: FH 05003-11803-OCT-Carotid-Section-18


title: GB2-shPTN

first: Tetsu

last: Akiyama

address: 1-1-1, Yayoi, Bunkyo-ku

department: Institute of Molecular and Cellular Biosciences

institute: Tokyo University

hyb_protocol: Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data sets were imported into Gene Spring for normalization and statistical analysis.

label: biotin

source_name: Glioblastoma stem cell, shRNA targeting pleiotrophin

label_protocol: Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.

extract_protocol: total RNA was extracted using the NucleoSpin RNA Clean-up kit (Macherey-Nagel) according to manufacturer's instruction.

tag: cell line

value: Glioblastoma stem cell


title: GB2-shALK

source_name: Glioblastoma stem cell, shRNA targeting ALK


title: FH 05003-11803-OCT-Carotid-Section-08

value: FH 05003-11803-OCT-Carotid-Section-08


title: GB2-siCont

source_name: Glioblastoma stem cell, Control shRNA


title: Cy5: Sa-Low-5136

value: resistant

value: S. aureus

value: Milk somatics cells (MSC) 12h after challenge


title: CS 14

value: carcinosarcoma

tag: carcinosarcoma status

value: :heterologous


title: Cy5: Sa-Low-5179


title: FH 05003-11803-OCT-Carotid-Section-14

value: FH 05003-11803-OCT-Carotid-Section-14


title: Cy5: Se-Low-5064

value: S. epidermidis


title: Cy5: Sa-High-5019

value: susceptible


title: Cy5: Sa-High-5173


title: EC G1 8


title: CS 13

value: :homologous


title: CS 12


title: Cy5: Sa-Low-5064


title: FH 05003-11803-OCT-Carotid-Section-10

value: FH 05003-11803-OCT-Carotid-Section-10


title: FH 05003-11803-OCT-Carotid-Section-06

value: FH 05003-11803-OCT-Carotid-Section-06


title: OPM2 len 24h

city: Scottsdale

first: Esteban

last: Braggio

state: AZ

address: 13208 East Shea Boulevard, MCRB 3-024

department: Biochemistry

institute: Mayo Clinic

description: Gene expression data from multiple myeloma cell line

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on HG-U133A Plus2.0 GeneChip.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings  as normalization method.

source_name: OPM2 cell line treated with lenalidomide (30uM) for 24h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA.

extract_protocol: Total RNA extraction was performed according to the manufacturer's instructions (Qiagen).

tag: protocol


title: FH 05003-11821-OCT-Carotid-Section-34

value: FH 05003-11821-OCT-Carotid-Section-34


title: Cy5: Se-High-5019


title: OPM2 Len 72h

source_name: OPM2 cell line treated with lenalidomide (30uM) for 72h


title: FH 05003-11821-OCT-Carotid-Section-32

value: FH 05003-11821-OCT-Carotid-Section-32


title: OPM2 len 48h

source_name: OPM2 cell line treated with lenalidomide (30uM) for 48h


title: EC G1 7

value: endometrioid adenocarcinoma


title: EC G1 6


title: CS 11


title: Cy3: Sa-Low-5073  ##2


title: Cy3: Sa-High-5183  ##2


title: OPM2 control 48h

source_name: OPM2 cell line treated with vehicle for 48h

value: treated with vehicle for 48h


title: OPM2 control 72h

source_name: OPM2 cell line treated with vehicle for 72h

value: treated with vehicle for 72h


title: US 4

value: sarcoma


title: FH 05003-11821-OCT-Carotid-Section-28

value: carotid plaque

value: FH 05003-11821-OCT-Carotid-Section-28


title: Cy3: Sa-Low-5009  ##2

value: resistant

value: S. aureus

value: Milk somatics cells (MSC) 12h after challenge


title: EC G3 8


title: Cy3: Sa-Low-5073


title: FH 05003-11821-OCT-Carotid-Section-24

value: FH 05003-11821-OCT-Carotid-Section-24


title: FH 05003-11821-OCT-Carotid-Section-30

value: FH 05003-11821-OCT-Carotid-Section-30


title: Cy3: Sa-Low-5136


title: OPM2 NT sorted

source_name: OPM2 cell line stably expressing NT (non-targeting) shRNA (sensitive to lenalidomide) treated with vehicle for 48h


title: Cy3: Se-High-5067

value: susceptible

value: S. epidermidis


title: FH 05003-11821-OCT-Carotid-Section-26

value: FH 05003-11821-OCT-Carotid-Section-26


title: OPM2 NT sorted Len 48h

source_name: OPM2 cell line stably expressing NT (non-targeting) shRNA (sensitive to lenalidomide)  treated with lenalidomide for 48h


title: CS 10

value: carcinosarcoma

value: :homologous


title: OPM2 #13 sorted len 48h

source_name: OPM2 cell line stably expressing CRBN shRNA (resistant to lenalidomide) treated with lenalidomide for 48h


title: CS 9

value: :heterologous


title: CS 8


title: OPM2 #13 sorted

source_name: OPM2 cell line stably expressing CRBN shRNA (resistant to lenalidomide) treated with vehicle for 48h


title: US 3


title: CS 7


title: Cy3: Se-High-5006


title: Cy3: Se-High-5019


title: OPM2 NT 72h

source_name: OPM2 cell line infected by NT shRNA expressing lentivirus for 72h


title: FH 05003-11821-OCT-Carotid-Section-22

source_name: carotid plaque

value: FH 05003-11821-OCT-Carotid-Section-22


title: US 1

source_name: frozen tissue


title: FH 05003-11821-OCT-Carotid-Section-20

value: FH 05003-11821-OCT-Carotid-Section-20


title: Cy3: Sa-High-5183

source_name: Milk somatic cells (MSC)


title: Cy3: Sa-High-5174  ##2


title: FH 05003-11821-OCT-Carotid-Section-16

value: FH 05003-11821-OCT-Carotid-Section-16


title: FH 05003-11821-OCT-Carotid-Section-12

value: FH 05003-11821-OCT-Carotid-Section-12


title: Cy3: Sa-Low-5009


title: US 2

value: sarcoma


title: MM.1S

source_name: MM1.S cell line, sensitive to Lenolidomide


title: OPM2 #13 72h

source_name: OPM2 cell line infected by CRBN shRNA expressing lentivirus for 72h


title: MM1.S Res

source_name: Derived from MM1.S cell line, Resistant to Lenolidomide


title: FH 05003-11821-OCT-Carotid-Section-18

value: carotid plaque

value: FH 05003-11821-OCT-Carotid-Section-18


title: OPM2 #13 48h

source_name: OPM2 cell line infected by CRBN shRNA expressing lentivirus for 48h


title: OPM2 NT 48h

source_name: OPM2 cell line infected by NT shRNA expressing lentivirus for 48h


title: FH 05003-11821-OCT-Carotid-Section-10

value: FH 05003-11821-OCT-Carotid-Section-10


title: CS 5


title: CS 6


title: FH 05003-11821-OCT-Carotid-Section-14

value: FH 05003-11821-OCT-Carotid-Section-14


title: FH 05003-11821-OCT-Carotid-Section-08

value: FH 05003-11821-OCT-Carotid-Section-08


title: EC G3 6

value: endometrioid adenocarcinoma


title: Cy3: Sa-High-5173

value: susceptible

value: S. aureus

value: Milk somatics cells (MSC) 12h after challenge


title: Cy3: Sa-High-5174


title: EC G3 5


title: CD140aNeg_5

city: Buffalo

first: Fraser

middle: James

last: Sim

state: NY

address: 3435 Main Street

department: Pharmacology

institute: University at Buffalo

hyb_protocol: Standard Affymetrix protocol for U133 Plus 2.0 Arrays

data_processing: Affymetrix .cel raw data files were normalized using RMA. All data processing was performed using R and the Bioconductor package.

source_name: PDGFRAneg

label_protocol: Nugen Ovation biotin labeling system using manufacturer's protocol

growth_protocol: Fetal brain was dissociated and FACS sorting performed for CD140a/PDGFRA antigen expression. RNA was extracted immediately post-sort.

extract_protocol: Total RNA was extracted using RNeasy (Qiagen) and amplified using 3 -biased ribo-SPIA (NuGen Ovation), according to the manufacturer's instructions.

tag: developmental stage

value: 22.5wk fetus

value: brain

value: glial progenitor


title: Cy3: Se-Low-5206

value: resistant

value: S. epidermidis


title: FH 05003-11821-OCT-Carotid-Section-04

value: FH 05003-11821-OCT-Carotid-Section-04


title: FH 05003-11821-OCT-Carotid-Section-06

value: FH 05003-11821-OCT-Carotid-Section-06


title: EC G3 4


title: CD140aPos_5

scan_protocol: Standard Affymetrix protocol for U133 Plus 2.0 Arrays

source_name: PDGFRApos


title: Cy3: Se-Low-5179


title: FH 05003-11821-OCT-Carotid-Section-02

value: FH 05003-11821-OCT-Carotid-Section-02


title: Cy3: Se-Low-5064


title: EC G3 3


title: CD140aNeg_4

value: 20wk fetus


title: Cy3: Sa-Low-5179


title: Cy3: Se-Low-5009


title: CD140aPos_4


title: EC G3 2


title: Cy3: Se-High-5183


title: EC G2 7


title: EC G2 5


title: EC G2 8


title: CE5-014-OCT-Carotid-Section-31

value: carotid plaque


title: Cy3: Se-High-5174


title: CD140aNeg_3

value: 21wk fetus


title: CD140aNeg_2

value: 21.1wk fetus


title: CD140aPos_1

value: 20.3wk fetus


title: CE5-014-OCT-Carotid-Section-20


title: CE5-014-OCT-Carotid-Section-27


title: EC G3 1

value: endometrioid adenocarcinoma


title: EC G2 6


title: Cy3: Sa-High-5067

value: susceptible


title: CD140aPos_3


title: CE5-014-OCT-Carotid-Section-29


title: Cy3: Se-Low-5073


title: CE5-014-OCT-Carotid-Section-14


title: CE5-014-OCT-Carotid-Section-18


title: CE5-014-OCT-Carotid-Section-22


title: CD140aPos_2


title: CD140aNeg_1


title: EC G1 5


title: CE5-014-OCT-Carotid-Section-12


title: EC G2 4


title: Cy3: BMDC 5009-Low-T8

source_name: Bone marrow derived dendritic cells (BMDC)

value: bone marrow-derived dendritic cells

tag: s. aureus stimulation time (hours)

value: CCS- (S. aureus resistant)


title: EC G2 3


title: GBMC29_XG

type: genomic

city: Baltimore

first: Michael

middle: F

last: Ochs

state: MD

address: 550 North Broadway, Ste 1103

department: Oncology Biostatistics

institute: Johns Hopkins University

hyb_protocol: Chip process and data analysis were performed by using reagents provided in the kit and following manufacturer's manual.

scan_protocol: Data were extracted and summarized using BeadStudio v3.0 software.

data_processing: Data were preprocessed using a custom R script to retain only methylation probes containing ≥3 CpG sites per probe.  There were 12,023 probes retained for 3 tumors, 3 xenografts, 7 UPPPs, 5 cancer cell lines, and 2 normal mucosa-derived cell lines.  Empirical Bayes comparisons were made between different tissues and cell lines using the limma package in R/Bioconductor to determine the difference in methylation between these groups.

molecule: genomic DNA

source_name: Xenograft of HNSCC

label_protocol: Illumina Infinium Human Methylation27 Beadchip Kit (WG-311-1202)

extract_protocol: DNA was extracted from all samples by digestion with 50 µg/mL proteinase K (Boehringer, Mannheim, Germany) in the presence of 1% SDS at 48°C overnight, followed by phenol/chloroform extraction and ethanol precipitation. Bisulfite conversion of genomic DNA was done with the EZ DNA methylation Kit (Zymo Research, D5002) by following manufacturer’s protocol with modifications for Illumina Infinium Methylation Assay.

value: Fresh HNSCC tissue direct xenograft from GBMC29_PT

tag: class

value: xenograft


title: CE5-014-OCT-Carotid-Section-10


title: EC G2 2


title: GBMC12_XG

value: Fresh HNSCC tissue direct xenograft from GBMC12_PT


title: Cy3: BMDC 5206-Low-T8


title: CE5-014-OCT-Carotid-Section-06


title: EC G2 1


title: GBMC29_PT

source_name: HNSCC

value: Greater Baltimore Medical Center HNSCC Patient Ref 29

value: HNSCC


title: Cy3: BMDC 5025-High-T0

value: CCS+ (S. aureus susceptible)


title: EC G1 2


title: Cy3: BMDC 5067-High-T0


title: EC G1 4


title: Cy3: BMDC 5006-High-T8


title: UPPP64

source_name: Normal mucosa

value: Normal mucosa Ref 64

value: normal


title: GBMC12_PT

value: Greater Baltimore Medical Center HNSCC Patient Ref 12


title: Cy3: BMDC 5136-Low-T0


title: CE11-001-OCT-Carotid-Section-28

value: carotid plaque


title: CE5-014-OCT-Carotid-Section-02


title: CE5-014-OCT-Carotid-Section-04


title: UPPP46

value: Normal mucosa Ref 46


title: CE11-001-OCT-Carotid-Section-26


title: UPPP65

value: Normal mucosa Ref 65


title: EC G1 3


title: UPPP61

value: Normal mucosa Ref 61


title: CE11-001-OCT-Carotid-Section-21


title: EC G1 1

value: endometrioid adenocarcinoma


title: Cy3: BMDC 5073-Low-T0


title: Cy3: BMDC 5067-High-T8


title: UPPP32

value: Normal mucosa Ref 32


title: NOK-SI

source_name: Normal mucosa cells

value: NOK-SI normal oral keratinocytes that spontaneously immortalized, provided by Dr. Silvio Gutkind (National Institutes of Health, Bethesda, MD)

value: normal cell line


title: CS 4

value: carcinosarcoma

value: :homologous


title: Cy3: BMDC 5025-High-T8

value: bone marrow-derived dendritic cells


title: PT2

value: Johns Hopkins HNSCC Patient Ref2


title: Cy3: BMDC 5009-Low-T0

value: CCS- (S. aureus resistant)


title: CS 2

value: :heterologous


title: Cy3: BMDC 5073-Low-T8


title: CS 3


title: CE11-001-OCT-Carotid-Section-17


title: CE11-001-OCT-Carotid-Section-11


title: OKF6

value: OKF6 minimally transformed oral keratinocyte line from Dr. James Rheinwald (Department of Dermatology, Brigham and Women's Hospital and Harvard Skin Disease Research Center)


title: Cy3: BMDC 5019-High-T0

value: CCS+ (S. aureus susceptible)


title: CE11-001-OCT-Carotid-Section-19


title: CS 1


title: CE11-001-OCT-Carotid-Section-13


title: XG2

value: Fresh HNSCC tissue direct xenograft from PT2

value: xenograft


title: UM22A

source_name: HNSCC cells

value: UM22A cell line provided by Ajay Verma (Merck & Co., North Wales, PA)

value: HNSCC cell line


title: Cy3: BMDC 5206-Low-T0


title: CE11-001-OCT-Carotid-Section-05

value: carotid plaque


title: Mouse_embryo_e16_3

city: Boston

first: Vishal

middle: S

last: Vaidya

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Brigham and Women's Hospital. Harvard Medical School

description: Replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: Biotin

organism: Mus musculus

source_name: Embryo e16

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

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

tag: strain

value: Balb/c

tag: age

value: embryonic day 16

value: Kidney


title: Mouse_embryo_e16_5

description: Replicate 5

tag: tissue


title: Cy3: BMDC 5206-Low-T3


title: Cy3: BMDC 5006-High-T0


title: CE11-001-OCT-Carotid-Section-09

source_name: carotid plaque

tag: patient

tag: sample id


title: UM22B

value: UM22B cell line provided by Ajay Verma (Merck & Co., North Wales, PA)


title: Mouse_embryo_e16_4

description: Replicate 4


title: Cy3: BMDC 5136-Low-T3

tag: line


title: Cy3: BMDC 5073-Low-T3

tag: cell type


title: CE11-001-OCT-Carotid-Section-01


title: JHU022

value: Johns Hopkins 022 HNSCC cell line from primary cells


title: FADU

value: FADU cells from American Type Culture Collection


title: Mouse_embryo_e16_2

description: Replicate 2


title: Mice_p7-5

description: Replicate 5

source_name: Posnatal day7

value: 7 days


title: JHU011

value: Johns Hopkins 011 HNSCC cell line from primary cells


title: CE11-001-OCT-Carotid-Section-03


title: UPPP25

value: Normal mucosa Ref 25

value: normal


title: UPPP30

value: Normal mucosa Ref 30


title: CE11-001-OCT-Carotid-Section-15


title: Mouse_embryo_e16_1

description: Replicate 1


title: CE11-001-OCT-Carotid-Section-23-24


title: Mice_p7-4

description: Replicate 4


title: Cy3: BMDC 5019-High-T3

value: bone marrow-derived dendritic cells

value: CCS+ (S. aureus susceptible)


title: NonMeth_DKO

source_name: HCT116 DNA methyltransferase double knock-out

value: Fully demethylated cell line

value: negative control


title: Mice_p7-3

description: Replicate 3


title: Cy3: BMDC 5025-High-T3


title: CE5-014-OCT-Carotid-Section-24-25


title: Cy3: BMDC 5006-High-T3


title: Cy3: BMDC 5067-High-T3


title: Mice_p7-2

description: Replicate 2


title: P494_OCT_Carotid_Section_22


title: Cy3: BMDC 5009-Low-T3

value: CCS- (S. aureus resistant)


title: P494_OCT_Carotid_Section_20

value: carotid plaque


title: P494_OCT_Carotid_Section_21


title: BreastTumorTissue-HEL_183

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

data_processing:
The data were log base 2 transformed and normalised using quantile normalisation with R.
Data table below does not report controls.  For complete tables of normalized and non-normalized data, see supplementary files on Series record.

source_name: BreastTumorTissue

growth_protocol: Fresh frozen human mammary tumor samples stored in liquid nitrogen

extract_protocol: RNA was isolated using miRvana miRNA isolation kit (Applied Biosystems) according to manufacturers protocol.

treatment_protocol: samples were homogenized with Precellys MK28-R Kit (6800Rpm, 3 x 25 s)

tag: 10years followup time (months)

tag: 10years vital status

value: 0 (alive or censored)

tag: bddm followup time (months)

tag: bddm status

value: 0 (no event or censored)


title: BreastTumorTissue-HEL_182


title: FullMeth_HCT116

source_name: HCT116 cells

value: Fully methylated cell line

value: positive control


title: CE11-001-OCT-Carotid-Section-07


title: BreastTumorTissue-HEL_180


title: CE5-014-OCT-Carotid-Section-16


title: P494_OCT_Carotid_Section_18


title: Cy5: BMDC 5067-High-T8


title: P494_OCT_Carotid_Section_19


title: Cy5: BMDC 5025-High-T8


title: Mice_p1-3

description: Replicate 3

source_name: Posnatal day 1

value: Balb/c

value: 1 day

value: Kidney


title: BreastTumorTissue-HEL_181

value: 2 (breast cancer death)

value: 1 (breast cancer death or distant metastasis)


title: Mice_p1-2

description: Replicate 2


title: BreastTumorTissue-HEL_178

value: 1 (death from any cause but breast cancer)


title: Cy5: BMDC 5009-Low-T0


title: Cy5: BMDC 5206-Low-T0


title: Mice_p7-1

description: Replicate 1

value: 7 days


title: P494_OCT_Carotid_Section_16


title: Cy5: BMDC 5073-Low-T8

value: bone marrow-derived dendritic cells


title: BreastTumorTissue-HEL_179


title: Mice_p1-5

description: Replicate 5


title: control_mouse6

city: amsterdam

first: Martijn

last: Bakker

address: meibergdreef 15

department: heart failure research center

institute: academic medical center

description: control

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Beadarray v1.3 probe summarization; vsn normalization. Matrix non-normalized: Two columns per sample. First column contains intensity values; second column contains detection p-value, is low when intensity value is above background threshold. Matrix normalized: Two columns per sample. First column contains vsn normalized intensity values; second column contains same detection p-values as non-normalized data

source_name: left atrial appendage

extract_protocol: mice sacrificed on day 5, RNA extracted using the Machery Nagel total RNA isolation kit

treatment_protocol: 4 days of intraperitoneal Tamoxifen-injections

value: FVB

tag: development stage

value: adult

tag: gender

value: male

tag: genotype


title: P494_OCT_Carotid_Section_17


title: P494_OCT_Carotid_Section_15


title: Mice_p1-1

description: Replicate 1


title: Cy5: BMDC 5019-High-T0

value: CCS+ (S. aureus susceptible)


title: Mice_p1-4

description: Replicate 4


title: Cy5: BMDC 5006-High-T0


title: Cy5: BMDC 5009-Low-T8

value: CCS- (S. aureus resistant)


title: control_mouse4

description: control


title: Cy5: BMDC 5206-Low-T8


title: control_mouse5

description: control


title: Cy5: BMDC 5067-High-T0


title: P494_OCT_Carotid_Section_12

value: carotid plaque


title: BreastTumorTissue-HEL_176

value: 0 (alive or censored)

value: 0 (no event or censored)


title: Cy5: BMDC 5006-High-T8


title: P494_OCT_Carotid_Section_14


title: P494_OCT_Carotid_Section_13


title: BreastTumorTissue-HEL_177


title: Cy5: BMDC 5025-High-T0


title: BreastTumorTissue-HEL_171


title: T3up_mouse6


title: BreastTumorTissue-HEL_172


title: BreastTumorTissue-HEL_173


title: control_mouse3

description: control


title: BreastTumorTissue-HEL_174


title: BreastTumorTissue-HEL_175


title: P494_OCT_Carotid_Section_11


title: P494_OCT_Carotid_Section_10


title: control_mouse1

description: control


title: Cy5: BMDC 5136-Low-T0


title: T3up_mouse4


title: control_mouse2

description: control


title: Cy5: BMDC 5019-High-T3


title: BreastTumorTissue-HEL_169


title: T3up_mouse3


title: BreastTumorTissue-HEL_170


title: P494_OCT_Carotid_Section_09


title: BreastTumorTissue-HEL_168


title: T3up_mouse1


title: P494_OCT_Carotid_Section_08


title: P494_OCT_Carotid_Section_07


title: T3up_mouse2


title: P494_OCT_Carotid_Section_06


title: Cy5: BMDC 5006-High-T3


title: Cy5: BMDC 5073-Low-T0


title: BreastTumorTissue-HEL_167


title: Cy5: BMDC 5025-High-T3


title: Cy5: BMDC 5206-Low-T3


title: P494_OCT_Carotid_Section_05


title: BreastTumorTissue-HEL_165


title: Rat male fetal pituitary TCDD T5 MP

city: Fukuoka

first: Tomoki

last: Takeda

address: 3-1-1 Maidashi, Higashi-ku

department: Pharmaceutical sciences

institute: Kyushu University

description: replicate 5

hyb_protocol: The biotinylated-cRNA (total amount, 1,500 ng) prepared from each sample was overlaid onto an individual array spot of the rat microarray chip (RatRef12-v1 BeadChip; Illumina), according to the hybridization protocol. The chip was hybridized at 58°C for 19 hours.

scan_protocol: Standard Illumina scanning protocol (BeadArray Reader; Illumina)

data_processing: The data were normalized by quantile normalization using lumi and preprocess package in R. This series includes two dataset; hypothalamic and pituitary samples (each case; N=3x2). The normalization applied each dataset.

organism: Rattus norvegicus

source_name: Rat male fetal pituitary TCDD

label_protocol: The total RNA (250 ng) was converted to its biotinylated-cRNA according to the manufacturer’s procedures (Illumina TotalPrep RNA Amplification Kit). Briefly, reverse transcription to synthesize the first-strand cDNA was performed for 2 hours at 42°C, using an oligo (dT) primer bearing a T7 promoter and reverse transcriptase (ArrayScript; Ambion). The second strand cDNA was synthesized by incubating the first strand for 2 hours at 16°C in the presence of DNA polymerase I and ribonuclease H. After cDNA purification by a short column, the eluted cDNA was used for in vitro transcription with T7 RNA polymerase. In vitro transcription was performed at 37°C for 14 hours, yielding the multiple copies of the biotinylated antisense RNA originated from respective mRNAs in the sample.

extract_protocol: The total RNA was extracted from the fetal pituitary and hypothalamus at GD20 according to the manufacturer's protocol (Rneasy Mini Kits).

treatment_protocol: Pregnant Wistar rats were orally treated with TCDD (1 mg/kg in corn oil) at GD15.

value: Wistar

value: Male

value: Pituitary

value: Embronic day 20

tag: treatment

value: TCDD


title: Rat male fetal pituitary TCDD T2 MP

description: replicate 2


title: Rat male fetal pituitary Control C2 MP

description: replicate 2

source_name: Rat male fetal pituitary Control

value: control


title: BreastTumorTissue-HEL_166

value: 1 (breast cancer death or distant metastasis)


title: P494_OCT_Carotid_Section_04


title: Cy5: BMDC 5009-Low-T3

tag: s. aureus stimulation time (hours)


title: Cy5: BMDC 5067-High-T3


title: BreastTumorTissue-HEL_162

value: 2 (breast cancer death)


title: BreastTumorTissue-HEL_163


title: Cy5: BMDC 5073-Low-T3

value: bone marrow-derived dendritic cells


title: P494_OCT_Carotid_Section_03


title: BreastTumorTissue-HEL_164


title: P493_OCT_Carotid_Section_19


title: Rat male fetal pituitary TCDD T1 MP

description: replicate 1


title: P493_OCT_Carotid_Section_20


title: P494_OCT_Carotid_Section_01


title: Rat male fetal pituitary Control C1 MP

description: replicate 1


title: P494_OCT_Carotid_Section_02


title: Rat male fetal hypothalamus TCDD MH T4

description: replicate 4

source_name: Rat male fetal hypothalamus TCDD

value: Hypothalamus


title: Cy5: BMDC 5136-Low-T3

source_name: Bone marrow derived dendritic cells (BMDC)


title: Tri6 KO vs WT BR3 cy3

city: Ottawa

first: Linda

middle: J

last: Harris

state: Ontario

address: 960 Carling Ave.

department: Eastern Cereal & Oilseed Research Centre

country: Canada

institute: Agriculture & Agri-Food Canada (AAFC)

description: Tri6 KO vs WT BioRep3. Cy3 test. Grown in 1st stage media for 24h and then 5h in 2nd stage media

hyb_protocol: Hybridizations were incubated overnight at 65ºC in a Robbins 400 oven outfitted with a Hybridization Oven Rotator (Agilent G2530-60029). Slides were washed as recommended by Agilent: Wash with Stabilization and Drying Solution.

scan_protocol: Slides were scanned on the Genepix 4200a (Molecular Devices) at 5µ resolution. Images were quantified using Genepix Pro 6.0 (Molecular Devices)

data_processing: Array results files (.gpr) were imported in Acuity 4.0 and Lowess M log ratio normalized. A dataset was formed with all arrays. Features that had Lowess A intensities lower that 7.5 in at least 50% of the arrays were removed. Spike-in controls were removed. Cy3 test array data were swapped to Cy5.

organism: Fusarium graminearum

source_name: WT BR3

label_protocol: 500ng of total RNA was labelled using reagents and procedure described in the Two-color Quick Amp Labeling protocol version 5.7 (Agilent Technologies) except only half the amounts of reagents were used in Step 2 of the labelling reaction.

growth_protocol: Two strains of Fusarium graminearum were grown under nitrogen-limiting conditions in a two stage media protocol, modified from Miller and Blackwell [1986. Biosynthesis of 3-acetyldeoxynivalenol and other metabolites by Fusarium culmorum HLX 1503 in a stirred jar fermenter. Can J Bot 64:1–5]. 20,000 spores were inoculated into 4 mL of first stage growth media and incubated in Falcon Multiwell 6-well culture trays. The culture trays were affixed to an orbital shaker and the spores were grown for 24 hr at 28˚C in the dark with constant shaking at 170 rpm. Following 24 hr growth, the mycelial solids were washed with water and resuspended in 4 mL of second stage media (pH 4.0) and then transferred to the 6-well culture trays. The mycelium was grown in second stage media for 5 hrs at 28˚C in the dark with constant shaking at 170 rpm.

extract_protocol: The mycelial pellet was ground to a powder in liquid nitrogen. Total RNA was isolated from 0.25 g of ground mycelia with 1mL of Trizol (Invitrogen, USA) according to manufacturer’s instructions. The InviTrap Spin Cell RNA mini kit (Invitek, Germany) was used, according to the manufacture’s instructions, to further purify the RNA. Integrity of RNA was confirmed by an Agilent 2100 Bioanalyzer (Agilent, Canada).

treatment_protocol: Fusarium graminearum wildtype strain GZ3639 (NRRL 38155) and a transgenic tri6∆ mutant derived from GZ3639 were compared under the same mycotoxin-inducing growth conditions.

source_name: Tri6 KO BR3


title: BreastTumorTissue-HEL_161


title: Rat male fetal pituitary Control C3 MP

description: replicate 3


title: BreastTumorTissue-HEL_160


title: P493_OCT_Carotid_Section_18


title: BreastTumorTissue-HEL_159


title: Rat male fetal hypothalamus TCDD MH T3

description: replicate 3


title: BreastTumorTissue-HEL_158


title: P493_OCT_Carotid_Section_16


title: Tri6 KO vs WT BR3 cy5

description: Tri6 KO vs WT BioRep3. Cy5 test. Grown in 1st stage media for 24h and then 5h in 2nd stage media


title: P493_OCT_Carotid_Section_17


title: Rat male fetal hypothalamus Control MH C5

description: replicate 5

source_name: Rat male fetal hypothalamus Control


title: Rat male fetal hypothalamus TCDD MH T1

description: replicate 1


title: BreastTumorTissue-HEL_157


title: P493_OCT_Carotid_Section_13


title: Rat male fetal hypothalamus Control Mhy C1

description: replicate 1


title: Rat male fetal hypothalamus Control MH C3

description: replicate 3


title: Tri6 KO vs WT BR1 cy5

description: Tri6 KO vs WT BioRep1. Cy5 test. Grown in 1st stage media for 24h and then 5h in 2nd stage media

source_name: Tri6 KO BR1

source_name: WT BR1


title: BreastTumorTissue-HEL_155


title: BreastTumorTissue-HEL_154


title: Tri6 KO vs WT BR2 cy3

description: Tri6 KO vs WT BioRep2. Cy3 test. Grown in 1st stage media for 24h and then 5h in 2nd stage media

source_name: WT BR2

source_name: Tri6 KO BR2


title: Tri6 KO vs WT BR2 cy5

description: Tri6 KO vs WT BioRep2. Cy5 test. Grown in 1st stage media for 24h and then 5h in 2nd stage media


title: BreastTumorTissue-HEL_156


title: P493_OCT_Carotid_Section_12

source_name: carotid plaque


title: P493_OCT_Carotid_Section_14


title: Tri6 KO vs WT BR1 cy3

description: Tri6 KO vs WT BioRep1. Cy3 test. Grown in 1st stage media for 24h and then 5h in 2nd stage media


title: P493_OCT_Carotid_Section_11


title: P493_OCT_Carotid_Section_09


title: P493_OCT_Carotid_Section_10


title: BreastTumorTissue-HEL_153


title: 24 hpf 300 mM ethanol rep 3 [mRNA]

city: Corvallis

first: Robert

middle: L

last: Tanguay

state: OR

department: EMT

institute: Oregon State University

description:
This sample is of 75 pooled embryos exposed to 300 mM ethanol from 4-24 hpf. It is the third of four biological replicates used in this experiment, each from pools of embryos.
Raw data file: 300 mM ethanol rep 3_395174genepixA09_2010-08-06_7092010_532-alligned.pair

hyb_protocol: cDNA synthesis, labeling and hybridization were performed by the University of Idaho Initiative for Bioinformatics and Evolutionary Studies core facility according to NimbleGen microarray protocol v.5.0 with the exception of the first-strand synthesis step in which 50µM oligo (dT) per reaction and 400 ng of random hexamers per µL of reaction were used.

scan_protocol: Labeled cDNA samples were hybridized to a zebrafish 12x135K Nimblegen array and arrays were scanned at 532 pmt. NimbleScan software was used for image analysis.

data_processing: NimbleScan software was used for image analysis and quality control.  Raw intensity data were quantile normalized by RMA summarization and outliers were identified by correlation analysis based on Pearson correlation coefficient.  A single replicate was removed from the 100mM treatment group and resulting data were subject to both pairwise analysis of variance with Tukey's post hoc test and 5% false discovery rate calculation.

source_name: whole embryo 24 hpf

growth_protocol: Adult Tropical 5D strain zebrafish (Danio rerio) were raised according to Institutional Animal Care and Use Committee protocols in the Sinnhuber Aquatic Research Laboratory at Oregon State University. Adults were maintained on a 14 h light/10 h dark schedule on a recirculating system in which water was maintained at 28±1 °C with a pH of 7.0±0.2. Following adult spawns, embryos were collected, rinsed, and housed at 28±1 °C in pools of 75 embryos until the start of the experiment.

extract_protocol: mRNA was isolated using TRIzol Reagent from pools of 75 embryos at 24 hpf that were exposed to 100-300 mM ethanol or embryo medium control from 4-24 hpf (n=4). Sample clean-up was performed using MinElute columns.

treatment_protocol: Groups of embryos were waterborne exposed to 0-300 mM ethanol (absolute ethyl alcohol USP, 200 proof) in buffered embryo mediumor embryo medium alone in 20-ml glass vials sealed with Teflon-lined lids to prevent volatilization. Each exposure group was considered a single replicate. Based on previous studies, embryos were exposed to ethanol from 4-24 hpf, rinsed and embryo homogenate was collected.

value: Tropical 5D

tag: agent

value: ethanol

tag: dose

tag: locomotion phenotype

value: Abnormal

tag: collection time

value: 24 hpf


title: 120 hours medulla 3

description: Replicate 3

source_name: Renal medulla

treatment_protocol: Bilateral renal ischemia reperfusion

tag: strain

tag: age

value: 3 months

tag: tissue

value: Kidney medulla

value: 120hr after ischemic-reperfusion injury


title: 120 hours medulla 2

description: Replicate 2

value: Wistar


title: 120 hours cortex 3

description: Replicate 3

source_name: Renal cortex

value: Kidney cortex


title: 120 hours medulla 1

description: Replicate 1


title: BreastTumorTissue-HEL_151

source_name: BreastTumorTissue

value: 0 (alive or censored)

value: 0 (no event or censored)


title: BreastTumorTissue-HEL_152


title: 120 hours cortex 2

description: Replicate 2


title: 120 hours cortex 1

description: Replicate 1


title: 24 hpf 300 mM ethanol rep 4 [mRNA]

description:
This sample is of 75 pooled embryos exposed to 300 mM ethanol from 4-24 hpf. It is the fourth of four biological replicates used in this experiment, each from pools of embryos.
Raw data file: 300 mM ethanol rep 4_395174genepixA12_2010-08-06_7092010_532-alligned.pair

label_protocol: cDNA synthesis, labeling and hybridization were performed by the University of Idaho Initiative for Bioinformatics and Evolutionary Studies core facility according to NimbleGen microarray protocol v.5.0 with the exception of the first-strand synthesis step in which 50µM oligo (dT) per reaction and 400 ng of random hexamers per µL of reaction were used.


title: BreastTumorTissue-HEL_148


title: 24 hpf 100 mM ethanol rep 2 [mRNA]

description:
This sample is of 75 pooled embryos exposed to 100 mM ethanol from 4-24 hpf. It is the second of four biological replicates used in this experiment, each from pools of embryos.
Raw data file: 100 mM ethanol rep 2_395174genepixA05_2010-08-06_7092010_532-alligned.pair


title: 24 hpf 300 mM ethanol rep 1 [mRNA]

description:
This sample is of 75 pooled embryos exposed to 300 mM ethanol from 4-24 hpf. It is the first of four biological replicates used in this experiment, each from pools of embryos.
Raw data file: 300 mM ethanol rep 1_395174genepixA03_2010-08-06_7092010_532-alligned.pair


title: 24 hpf 300 mM ethanol rep 2 [mRNA]

description:
This sample is of 75 pooled embryos exposed to 300 mM ethanol from 4-24 hpf. It is the second of four biological replicates used in this experiment, each from pools of embryos.
Raw data file: 300 mM ethanol rep 2_395174genepixA06_2010-08-06_7092010_532-alligned.pair


title: BreastTumorTissue-HEL_149


title: P493_OCT_Carotid_Section_08

description: Gene expression profiling of carotid plaque. 6 subjects from OCT6 study. Plaques were sectioned in 1 mm slices. Half of the slices were profiled, and the other half, adjacent slices, were processed by IHC

value: carotid plaque

tag: patient

tag: sample id


title: P493_OCT_Carotid_Section_07


title: BreastTumorTissue-HEL_150

tag: 10years followup time (months)

tag: 10years vital status


title: P493_OCT_Carotid_Section_05


title: P493_OCT_Carotid_Section_06


title: 24 hpf 100 mM ethanol rep 3 [mRNA]

description:
This sample is of 75 pooled embryos exposed to 100 mM ethanol from 4-24 hpf. It is the third of four biological replicates used in this experiment, each from pools of embryos.
Raw data file: 100 mM ethanol rep 3_395174genepixA08_2010-08-06_7092010_532-alligned.pair


title: 24 hpf 100 mM ethanol rep 4 [mRNA]

description:
This sample is of 75 pooled embryos exposed to 100 mM ethanol from 4-24 hpf. It is the fourth of four biological replicates used in this experiment, each from pools of embryos.
Raw data file: 100 mM ethanol rep 4_395174genepixA11_2010-08-06_7092010_532-alligned.pair


title: BreastTumorTissue-HEL_146

tag: bddm followup time (months)

tag: bddm status


title: BreastTumorTissue-HEL_147


title: 24 hours medulla 2

description: Replicate 2

value: 24hr after ischemic-reperfusion injury


title: 24 hpf 100 mM ethanol rep 1 [mRNA]

description:
This sample is of 75 pooled embryos exposed to 100 mM ethanol from 4-24 hpf. It is the first of four biological replicates used in this experiment, each from pools of embryos.
Raw data file: 100 mM ethanol rep 1_395174genepixA02_2010-08-06_7092010_532-alligned.pair


title: 24 hours medulla 3

description: Replicate 3


title: 24 hours medulla 1

description: Replicate 1


title: P493_OCT_Carotid_Section_04


title: P490_OCT_Carotid Section_172-180

value: P490_OCT_Carotid Section_172-180


title: 24 hours cortex 2

description: Replicate 2


title: BreastTumorTissue-HEL_144


title: P490_OCT_Carotid Section_162-170

value: P490_OCT_Carotid Section_162-170


title: 24 hours cortex 1

description: Replicate 1


title: 24 hpf control rep 3 [mRNA]

description:
This sample is of 75 pooled embryos exposed to embryo medium control from 4-24 hpf. It is the third of four biological replicates used in this experiment, each from pools of embryos.
Raw data file: control rep 3_395174genepixA07_2010-08-06_7092010_532-alligned.pair

value: control

value: Normal


title: BreastTumorTissue-HEL_143


title: 24 hpf control rep 4 [mRNA]

description:
This sample is of 75 pooled embryos exposed to embryo medium control from 4-24 hpf. It is the fourth of four biological replicates used in this experiment, each from pools of embryos.
Raw data file: control rep 4_395174genepixA10_2010-08-06_7092010_532-alligned.pair

value: Tropical 5D


title: 6 hours medulla 2

description: Replicate 2

value: 6hr after ischemic-reperfusion injury


title: BreastTumorTissue-HEL_145


title: 24 hpf control rep 2 [mRNA]

description:
This sample is of 75 pooled embryos exposed to embryo medium control from 4-24 hpf. It is the second of four biological replicates used in this experiment, each from pools of embryos.
Raw data file: control rep 2_395174genepixA04_2010-08-06_7092010_532-alligned.pair


title: P490_OCT_Carotid Section_142-150

value: P490_OCT_Carotid Section_142-150


title: 24 hours cortex 3

description: Replicate 3


title: 24 hpf control rep 1 [mRNA]

description:
This sample is of 75 pooled embryos exposed to embryo medium control from 4-24 hpf. It is the first of four biological replicates used in this experiment, each from pools of embryos.
Raw data file: control rep 1_395174genepixA01_2010-08-06_7092010_532-alligned.pair

value: 24 hpf


title: P490_OCT_Carotid Section_152-160

value: P490_OCT_Carotid Section_152-160


title: BreastTumorTissue-HEL_142


title: 6 hours medulla 3

description: Replicate 3

value: 3 months

value: Kidney medulla


title: P490_OCT_Carotid Section_132-140

value: P490_OCT_Carotid Section_132-140


title: BreastTumorTissue-HEL_141


title: 6 hours cortex 3

description: Replicate 3

value: Wistar

value: Kidney cortex


title: 6 hours medulla 1

description: Replicate 1


title: BreastTumorTissue-HEL_140

value: 1 (death from any cause but breast cancer)

value: 0 (no event or censored)


title: BreastTumorTissue-HEL_139

value: 0 (alive or censored)


title: KO-mock, biological rep2

city: Durham

first: Feng

last: Feng

state: NC

address: 127 Jone Building, 207 Research Drive

department: Biostatistics&Bioinformatics

institute: Duke University

description: gene expression data from miR-17-92 deficient CD4 T cells transduced with empty vetor

hyb_protocol: Labeled cRNAs were hybridized to GeneChip mouse Genome 430A2.0 Arrays in Affymetrix GeneChip hybridization oven 645, washed in Affymetrix GeneChip Fluidics Station 450

scan_protocol: GeneChips were scaned with Affymetrix GeneChip Scanner 7G accroding to standard Affymetrix GeneChip Hybridization, Wash, and stain protocols

data_processing: Probe intensities were background- adjusted, normalized, and probeset-summarized using the Robust Multi-chip Average (RMA) method using the software Bioconductor. For differential expression analysis, an empirical Bayes statistical analysis was carried out using the software Bioconductor.

source_name: active KO CD4 T cells  transduced with empty vector

label_protocol: Hybridization targets were prepared with MessageAmpTM premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) from total RNA

growth_protocol: CD4+CD25- T cells were FACS sorted, activated with plate bound anti-CD3/CD28, and transduced with indicated retrovirus. 5 days later total RNA were extracted for microarray analysis.

extract_protocol: Total RNAs were extracted by miRVana extraction kit from Ambion according to the manufacturer's instructions.

treatment_protocol: T cells were cultured in RPMI supplemented with 10% FBS with 7% CO2

tag: cell type

value: CD4+CD25- T cells

value: miR-17-92f/f CD4-cre+ B6


title: KO-miR-17, biological rep2

description: gene expression data from miR-17-92 deficient CD4 T cells transduced with miR-17

source_name: active KO CD4 T cells  transduced with miR-17 overexpressing vector

tag: genotype

tag: overexpression


title: KO-miR-17, biological rep1


title: P490_OCT_Carotid Section_122-130

value: carotid plaque

value: P490_OCT_Carotid Section_122-130


title: P490_OCT_Carotid Section_102-110

value: P490_OCT_Carotid Section_102-110


title: 6 hours cortex 2

description: Replicate 2

tag: treatment

value: 6hr after ischemic-reperfusion injury


title: BreastTumorTissue-HEL_138


title: 6 hours cortex 1

description: Replicate 1


title: BreastTumorTissue-HEL_136


title: WT-mock, biological rep2

description: gene expression data from WT CD4 T cells transduced with empty vetor

source_name: active WT CD4 T cells  transduced with empty vector

value: WT B6


title: E19CT22 [group 2]

city: Wuhan

first: Xiaodong

last: Li

state: Hubei Province

address: Luojia Hill, Wuchang District

department: College of Life Sciences

country: China

institute: Wuhan University

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Data from CEL files were normalized in R using the 'affy' package and the gcRMA algorithm. Log transformation of values was reversed and all values of a series of arrays were median normalized to 100

source_name: Fetal mouse liver at E19CT22

label_protocol: Standard Affymetrix protocol

extract_protocol: Trizol extraction followed by Qiagen RNeasy MinElue Cleanup kit

value: liver

tag: developmental stage

value: fetal (late gestation)

tag: timepoint


title: Control medulla 2

description: Replicate 2

value: 3 months

value: sham


title: KO-mock, biological rep1


title: P490_OCT_Carotid Section_112-120

value: P490_OCT_Carotid Section_112-120


title: WT-mock, biological rep1


title: P490_OCT_Carotid Section_72-80

value: P490_OCT_Carotid Section_72-80


title: Control medulla 3

description: Replicate 3

value: Wistar

value: Kidney medulla


title: BreastTumorTissue-HEL_135

value: 0 (no event or censored)


title: Control cortex 3

description: Replicate 3

value: Kidney cortex


title: Control medulla 1

description: Replicate 1


title: P490_OCT_Carotid Section_92-100

value: P490_OCT_Carotid Section_92-100


title: P490_OCT_Carotid Section_62-70

value: P490_OCT_Carotid Section_62-70


title: BreastTumorTissue-HEL_137

value: 0 (alive or censored)


title: E19CT18 [group 2]

source_name: Fetal mouse liver at E19CT18


title: BreastTumorTissue-HEL_133


title: E19CT14 [group 2]

source_name: Fetal mouse liver at E19CT14


title: P490_OCT_Carotid Section_52-60

value: carotid plaque

value: P490_OCT_Carotid Section_52-60


title: P490_OCT_Carotid Section_82-90

value: P490_OCT_Carotid Section_82-90


title: Control cortex 2

description: Replicate 2


title: E19CT6 [group 2]

source_name: Fetal mouse liver at E19CT6


title: Control cortex 1

description: Replicate 1


title: BreastTumorTissue-HEL_132


title: E19CT10 [group 2]

source_name: Fetal mouse liver at E19CT10


title: BreastTumorTissue-HEL_134


title: P490_OCT_Carotid Section_42-50

value: P490_OCT_Carotid Section_42-50


title: BreastTumorTissue-HEL_131


title: P490_OCT_Carotid Section_22-30

value: P490_OCT_Carotid Section_22-30


title: E18CT22 [group 2]

source_name: Fetal mouse liver at E18CT22

value: liver

value: fetal (late gestation)


title: BreastTumorTissue-HEL_130


title: E18CT18 [group 2]

source_name: Fetal mouse liver at E18CT18


title: E18CT10 [group 2]

source_name: Fetal mouse liver at E18CT10


title: Mouse MSC (FGF+)

city: Genova

first: Roberta

last: Tasso

address: Largo Rosanna Benzi 10

country: Italy

institute: University of Genova

description: Gene expression data from MSC (FGF+)

hyb_protocol: Fragmented cRNA, run on the Bioanalyzer to verify the correct electropherogram, was hybridized in a hybridization oven (16 hours, 45°C) to a Human Gene 1.0 ST array (Affymetrix) representing whole-transcript coverage. The washing and staining of the arrays with phycoerythrin-conjugated streptavidin (Molecular Probes, Eugene, OR) was completed in Fluidics Station 450 (Affymetrix).

scan_protocol: The arrays were subsequently scanned using a confocal laser GeneChip Scanner 3000 7G and GeneChip Command Console (Affymetrix).

data_processing: Affymetrix raw data files (CEL files) are used as input files in expression console environment (Affymetrix, Inc., Santa Clara, CA). Briefly, Cel files were processed using Robust Multi-Array Analysis procedure (Irizarry et al., 2003). The RMA method was used, first, to convert the intensities from the multiple probes in a probeset into a single expression value with greater precision and reduced background noise, relying on the perfect match probes only (ignoring the mismatch probes) and, after, to normalize by sketch quantile normalization. Also quality assessement were performed in expression console environment.

source_name: Mouse Mesenchymal Stem Cells (MSC), cultured in presence of basic-Fibroblast Growth Factor (FGF)

label_protocol: Briefly, accordingly to the recommendations of the manufacturer, 100 ng total RNA was used in the first-round synthesis of double-stranded cDNA. The RNA was reverse transcribed using a WT cDNA synthesis and amplification kit (Affymetrix). The resulting biotin-labeled cRNA was purified using an IVT clean-up kit (Affymetrix) and quantified using a UV spectrophotometer (A260/280; Beckman, Palo Alto, CA). An aliquot (15 µg) of cRNA was fragmented by heat and ion-mediated hydrolysis at 94°C for 35 minutes.

growth_protocol: Cells were cultured (15x106 nucleated cells/10 cm Petri dish) in Coon’s modified F12 medium (Biochrom AG, Berlin, Germany) supplemented with 10% fetal calf serum (FCS) (GIBCO, S. Giuliano Milanese, MI, Italy), 2 mM L-glutamine, 50 mg/ml penicillin/streptomycin and 1 ng/ml basic fibroblast growth factor (bFGF) (standard medium). MSC were allowed to adhere to the plastic support for 5 days before the first medium change. The cells were cultured in standard medium, with a medium change every 3 days, and routinely expanded after reaching about 85% confluence using 0.05% trypsin-EDTA (Gibco, MI, Italy). All cultures were maintained in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
miRNeasy Mini Kit (Qiagen) with DNase treatment.
RNA concentration and purity were determined from measuring absorbance at 260 and 280 nm; 2 μg total RNA was run on a 1% denaturing gel and 100 ng were loaded on the 2100 Bioanalyzer (Agilent, Palo Alto, CA) to verify RNA integrity.

treatment_protocol: MSC were obtained from C57Bl/6 mice. Briefly, mice were sacrificed and bone marrow cells were collected by flushing nucleated cells out of the femurs and tibiae with cold phosphate-buffered saline (PBS: 137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, 2mM KH2PO4, pH 7.4).

value: MSC

tag: sample type

value: MSC cultured in presence of bFGF


title: Tomont_whole_P100_rep2

city: Auburn

first: Eric

last: Peatman

state: AL

address: 203 Swingle Hall

department: Fisheries and Allied Aquacultures

institute: Auburn University

description: Tomont life-stage, the second of three biological replicates, isolated at passage 100

hyb_protocol: Hybridization was perfomed by Nimblegen Systems, Inc., Madison, WI, USA using their standard labelling protocol.  See www.nimblegen.com for further details.

scan_protocol: Scanning was perfomed by Nimblegen Systems, Inc., Madison, WI, USA using their standard labelling protocol.  See www.nimblegen.com for further details.

data_processing:
The raw data (.pair file) was subjected to RMA (Robust Multichip Average; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package from Nimblegen.  See www.nimblegen.com for futher details.
The data was quantile normalized and subjected to RMA by Nimblegen.  Final differential expression was determined using the DNA-chip Analyzer (dChip) software (Li C. BMC Bioinformatics 9:231).

organism: Ichthyophthirius multifiliis

source_name: Tomont life-stage

label_protocol: Labeling was perfomed by Nimblegen Systems, Inc., Madison, WI, USA using their standard labelling protocol.  See www.nimblegen.com for further details.

extract_protocol: Total RNA was isolated using the TRIzol reagent from Invitrogen, Carlsbad, CA, USA.  RNA quantity and quality was assessed using a spectrophotometer and denaturing agarose gel electrophoresis containing formaldehyde.

value: Tomont life-stage

tag: lab-passage number

value: serial passage 100


title: BreastTumorTissue-HEL_129


title: BreastTumorTissue-HEL_128


title: Mouse MSC (FGF-)

description: Gene expression data from MSC (FGF-)

source_name: Mouse Mesenchymal Stem Cells (MSC), cultured in absence of basic-Fibroblast Growth Factor (FGF)

growth_protocol: Cells were cultured (15x106 nucleated cells/10 cm Petri dish) in Coon’s modified F12 medium (Biochrom AG, Berlin, Germany) supplemented with 10% fetal calf serum (FCS) (GIBCO, S. Giuliano Milanese, MI, Italy), 2 mM L-glutamine, 50 mg/ml penicillin/streptomycin. MSC were allowed to adhere to the plastic support for 5 days before the first medium change. The cells were cultured in standard medium, with a medium change every 3 days, and routinely expanded after reaching about 85% confluence using 0.05% trypsin-EDTA (Gibco, MI, Italy). All cultures were maintained in a humidified incubator at 37°C with 5% CO2.

tag: strain

value: MSC cultured in absence of bFGF


title: P490_OCT_Carotid Section_32-40

city: Rahway

first: Oscar

last: Puig

address: 126 East Lincoln Ave

institute: Merck Research Laboratories

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques.  Arrays are hybridized for 18 hours at 45?C with vigorous mixing.   Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed.  Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Data were loaded into the Rosetta Resolver? system (Rosetta Biosoftware, Seattle, WA) and processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260).  Intensities were calculated based on RMA, a Rosetta-developed error, and a MAS-5 p-value.  The Rosetta-developed error is used in the calculation of xdev for the ratio p-values as described in section 2.2 (http://bioinformatics.oxfordjournals.org/cgi/content/full/22/9/1111).

source_name: carotid plaque

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation.  Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.

value: P490_OCT_Carotid Section_32-40


title: Tomont_whole_P100_rep3

description: Tomont life-stage, the third of three biological replicates, isolated at passage 100


title: Mouse Osteoblasts

description: Gene expression data from osteoblasts

source_name: Mouse Osteoblasts

growth_protocol: OB obtained from the last two digestions were pooled and plated together in tissue culture dishes. The cells were cultured until confluence in DMEM supplemented with 10% FCS, 2 mM L-Glutamine and 50 mg/ml Penicillin/Streptomycin with a medium change every 3 days, and routinely expanded after reaching about 85% confluence using 0.05% trypsin-EDTA (Gibco, MI, Italy). All cultures were maintained in a humidified incubator at 37°C with 5% CO2.

treatment_protocol: OB were enzymatically isolated from calvariae of newborn C57Bl/6 mice. Briefly, skin and soft connective tissue were removed. Bone was cut and washed two times in Ringer Solution (147 mM NaCl, 4 mM KCl, 1.13 mM CaCl2, pH 7.4). The bone pieces were sequentially digested in a trypsin (25 mg) (Gibco, MI, Italy)/collagenase I (30 mg) (Gibco, MI, Italy)/collagenase II (30 mg) (Gibco, MI, Italy) in 25 ml Ringer Solution at 37  C for 10, 20, 30, 50, 70 min.

value: osteoblasts

value: control


title: E18CT14 [group 2]

source_name: Fetal mouse liver at E18CT14

tag: age


title: BreastTumorTissue-HEL_127

source_name: BreastTumorTissue

value: 0 (no event or censored)


title: Tomont_whole_P100_rep1

description: Tomont life-stage, the first of three biological replicates, isolated at passage 100


title: Tomont_whole_P1_rep3

description: Tomont life-stage, the third of three biological replicates, isolated at passage 1

value: serial passage 1


title: E19CT2 [group 2]

source_name: Fetal mouse liver at E19CT2

tag: tissue


title: BreastTumorTissue-HEL_126

value: 0 (alive or censored)


title: Mouse ES Cells

description: Gene expression data from ES cells

source_name: Mouse ES Cells

value: embryonic stem cells


title: BreastTumorTissue-HEL_125


title: E18CT2 [group 2]

source_name: Fetal mouse liver at E18CT2


title: bone marrow cells, 11 days stimulated with Flt3-L, treated with Cyclosporin A rep2

city: Singapore

first: jinmiao

last: chen

address: Biopolis

country: Singapore

institute: Singapore Immunology Network

hyb_protocol: Fragmented ssDNAs were hybridized to the standard arrays for 17 hours at 45°C; the arrays were then washed and stained using the fluidics station.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000

data_processing: Microarray data handling was mainly done using Bioconductor 2.6 and an R package AMDA. The Robust Multichip Average (RMA) method was employed to calculate probe set intensity.

source_name: Flt3_L stimulation for 11 days in presence of Cyclosporin A

label_protocol: WT Expression Kit (Ambion/Affymetrix) were used. ssDNA was prepared, fragmented and labelled according to the Affymetrix protocol

growth_protocol: Bone marrow cells harvested from femurs and tibiae of 8-12 week old C57BL/6 mice were cultured in Iscove’s modified Dulbecco’s medium (containing 10% heat-inactivated FCS (Life Technologies), penicillin 100U/ml, streptomycin 100 ug/ml and Flt3-L ~200 ng/ml (from transfected B16 tumor cells (51)) at 2.5x 106 cells/ml.

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

treatment_protocol: CsA (Sigma) was added to some cultures at 2 µg/ml for 30 min prior to addition of Flt3-L and was maintained throughout the culture.

value: 8-12 weeks

value: bone marrow cells


title: Tomont_whole_P1_rep2

description: Tomont life-stage, the second of three biological replicates, isolated at passage 1


title: bone marrow cells, 48h stimulated with Flt3-L, treated with Cyclosporin A rep2

source_name: Flt3_L stimulation for 48h in presence of Cyclosporin A


title: Tomont_whole_P1_rep1

description: Tomont life-stage, the first of three biological replicates, isolated at passage 1


title: BreastTumorTissue-HEL_124


title: Trophont_whole_P100_rep3

description: Trophont life-stage, the third of three biological replicates, isolated at passage 100

source_name: Trophont life-stage

value: Trophont life-stage


title: bone marrow cells, 48h stimulated with Flt3-L, treated with Cyclosporin A rep3


title: E18CT6 [group 2]

source_name: Fetal mouse liver at E18CT6

value: liver


title: bone marrow cells, 11 days stimulated with Flt3-L, treated with Cyclosporin A rep3


title: BreastTumorTissue-HEL_123


title: E19CT10 [group 1]

source_name: Fetal mouse liver at E19CT10

value: fetal (late gestation)


title: BreastTumorTissue-HEL_121


title: bone marrow cells, 48h stimulated with Flt3-L, treated with Cyclosporin A rep1


title: Trophont_whole_P100_rep2

description: Trophont life-stage, the second of three biological replicates, isolated at passage 100


title: E19CT14 [group 1]

source_name: Fetal mouse liver at E19CT14


title: bone marrow cells, 24h stimulated with Flt3-L, treated with Cyclosporin A rep3

source_name: Flt3_L stimulation for 24h in presence of Cyclosporin A


title: Trophont_whole_P100_rep1

description: Trophont life-stage, the first of three biological replicates, isolated at passage 100


title: E19CT22 [group 1]

source_name: Fetal mouse liver at E19CT22


title: bone marrow cells, 11 days stimulated with Flt3-L, treated with Cyclosporin A rep1


title: E19CT18 [group 1]

source_name: Fetal mouse liver at E19CT18


title: BreastTumorTissue-HEL_120

value: 2 (breast cancer death)

value: 1 (breast cancer death or distant metastasis)


title: BreastTumorTissue-HEL_122


title: bone marrow cells, 24h stimulated with Flt3-L, treated with Cyclosporin A rep2


title: E19CT6 [group 1]

source_name: Fetal mouse liver at E19CT6


title: Trophont_whole_P1_rep2

description: Trophont life-stage, the second of three biological replicates, isolated at passage 1


title: Trophont_whole_P1_rep3

description: Trophont life-stage, the third of three biological replicates, isolated at passage 1


title: BreastTumorTissue-HEL_119


title: bone marrow cells, 24h stimulated with Flt3-L, treated with Cyclosporin A rep1


title: E19CT2 [group 1]


title: Trophont_whole_P1_rep1

description: Trophont life-stage, the first of three biological replicates, isolated at passage 1


title: bone marrow cells, 12h stimulated with Flt3-L, treated with Cyclosporin A rep3

source_name: Flt3_L stimulation for 12h in presence of Cyclosporin A


title: BreastTumorTissue-HEL_116


title: E18CT22 [group 1]

source_name: Fetal mouse liver at E18CT22


title: E18CT18 [group 1]

source_name: Fetal mouse liver at E18CT18


title: E18CT14 [group 1]

source_name: Fetal mouse liver at E18CT14


title: BreastTumorTissue-HEL_118

source_name: BreastTumorTissue


title: BreastTumorTissue-HEL_115


title: bone marrow cells, 12h stimulated with Flt3-L, treated with Cyclosporin A rep1


title: BreastTumorTissue-HEL_117


title: BreastTumorTissue-HEL_114


title: E18CT10 [group 1]

source_name: Fetal mouse liver at E18CT10


title: bone marrow cells, 11 days stimulated with Flt3-L rep1

source_name: Flt3_L stimulation for 11 days


title: Tomont_whole_rep2

description: Tomont life-stage, the second of three biological replicates

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multichip Average; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package from Nimblegen.  See www.nimblegen.com for futher details.

source_name: Tomont life-stage

value: Tomont


title: Theront_whole_rep3

description: Theront life-stage, the third of three biological replicates

source_name: Theront life-stage

value: Theront


title: E18CT6 [group 1]


title: Theront_whole_rep2

description: Theront life-stage, the second of three biological replicates


title: Theront_whole_rep1

description: Theront life-stage, the first of three biological replicates


title: bone marrow cells, 11 days stimulated with Flt3-L rep2


title: BreastTumorTissue-HEL_113


title: bone marrow cells, 12h stimulated with Flt3-L, treated with Cyclosporin A rep2


title: Tomont_whole_rep3

description: Tomont life-stage, the third of three biological replicates


title: bone marrow cells, 11 days stimulated with Flt3-L rep3


title: bone marrow cells, 48h stimulated with Flt3-L rep3

source_name: Flt3_L stimulation for 48h


title: B. longum and E.coli O157:H7_rep2

city: Tsuruoka

first: Shinji

last: Fukuda

state: Yamagata

address: 246-2 Mizukami, Kakuganji

department: Institute for Advanced Biosciences

institute: Keio University

description: O157 and BL were pre-cultured for overnight anaerobically. In monoculture, BL and O157 were inoculated 1% individually for the labeling medium in 100-mL serum vials and cultured at 37°C. In coculture, pre-cultured O157 was inoculated 1% for the labeling medium and cultured at 37°C. After 1 hr, pre-cultured BL was inoculated 1% for O157 culture medium and cultured at 37°C. These cultures were stopped at the mid-exponential phase (OD600 = 1.0) and centrifuged for 10 min at 15,000 rpm and the supernatants were removed.

hyb_protocol: Affymetrix standard procedures

scan_protocol: using GeneChip Scanner 3000

data_processing: GeneSpring version 7.3.1 (Agilent software) was used for RMA normalization.

organism: Bifidobacterium longum

source_name: B. longum and E. coli O157:H7 invitro coculture

label_protocol: One-Cycle Target Labeling and Control Reagents

extract_protocol: Total RNA was isolated using the RNAprotect™ Bacteria Reagent Kit, in accordance with the manufacturer’s protocol (Qiagen, Valencia, CA). Aliquots of approximately 10 ug of isolated RNA were treated with 5 units of RNase-free DNase (Ambion, Austin, TX) for 30 min at room temperature. A Qiagen RNeasy MinElute Kit (Qiagen) was used to purify DNase-treated total RNA, removing degraded DNA, tRNA, rRNA, DNase, contaminating proteins, and potential inhibitors of the reverse transcription reaction.

tag: strain(s)

value: B. longum and e. coli o157:H7

tag: culture condition

value: invitro coculture


title: Tomont_whole_rep1

description: Tomont life-stage, the first of three biological replicates


title: BreastTumorTissue-HEL_112

tag: 10years followup time (months)


title: Trophont_whole_rep3

description: Trophont life-stage, the third of three biological replicates

source_name: Trophont life-stage

value: Trophont


title: E18CT2 [group 1]

source_name: Fetal mouse liver at E18CT2


title: bone marrow cells, 24h stimulated with Flt3-L rep2

source_name: Flt3_L stimulation for 24h


title: bone marrow cells, 48h stimulated with Flt3-L rep1


title: PMT_sample11

city: Guelph

first: Roger

middle: A

last: Moorehead

address: 50 Stone Rd East

department: Department of Biomedical Sciences

institute: University of Guelph

description:
Sample name: RJ279
Raw data file: july8_251486819130_S01_GE2-v5_95_Feb07_1_2.txt

hyb_protocol: hybridization was performed using the Agilent In situ Hybridization Kit using the manufacturer's protocol

scan_protocol: scanned on an Agilent G2565BA DNA Scanner

data_processing: Agilent Feature Extraction Software v9.5

source_name: primary mammary tumour

label_protocol: 500ug of total RNA was labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit using the manufacturer's protocol

extract_protocol: Total RNA was extracted using the Rneasy RNA Isolation Kit from Qiagen using the manufacturer's protocol

value: FVB

tag: initial tumour onset (days)

tag: tumor regression (days)

tag: tumor recurrence (days)

tag: age at tissue collection (days)

source_name: universal mouse reference RNA

value: universal mouse reference RNA


title: bone marrow cells, 24h stimulated with Flt3-L rep1


title: B. longum and E.coli O157:H7_rep1

value: b. longum and e. coli o157:H7


title: B. longum_rep2

source_name: B. longum invitro monoculture

value: Bifidobacterium longum

value: invitro monoculture


title: BreastTumorTissue-HEL_111

tag: 10years vital status

value: 0 (alive or censored)

tag: bddm followup time (months)

tag: bddm status

value: 0 (no event or censored)


title: bone marrow cells, 24h stimulated with Flt3-L rep3

value: 8-12 weeks

value: bone marrow cells


title: WT_sample8

description:
Sample name: RM97
Raw data file: july8_251486819130_S01_GE2-v5_95_Feb07_1_4.txt

source_name: wild type mammary glands


title: Trophont_whole_rep1

description: Trophont life-stage, the first of three biological replicates

tag: developmental stage


title: B. longum_rep1


title: Trophont_whole_rep2

description: Trophont life-stage, the second of three biological replicates


title: PMT_sample10

description:
Sample name: RJ286
Raw data file: july8_251486819130_S01_GE2-v5_95_Feb07_1_1.txt


title: bone marrow cells, 12h stimulated with Flt3-L rep3

source_name: Flt3_L stimulation for 12h


title: PMT_sample9

description:
Sample name: RJ236
Raw data file: july8_251486819004_S01_GE2-v5_95_Feb07_1_4.txt


title: WT_sample7

description:
Sample name: RJ10
Raw data file: july8_251486819130_S01_GE2-v5_95_Feb07_1_3.txt


title: BreastTumorTissue-HEL_106


title: RST_sample9

description:
Sample name: RJ422
Raw data file: july8_251486819004_S01_GE2-v5_95_Feb07_1_3.txt

source_name: recurrent spindle tumour


title: BreastTumorTissue-HEL_108


title: BreastTumorTissue-HEL_110


title: BreastTumorTissue-HEL_109


title: BreastTumorTissue-HEL_107


title: bone marrow cells, unstimulated, rep3

source_name: unstimulated control


title: Baseline2 vs. Exp2_Macrophage_Control-3

department: Molecular Profiling Research Informatics

description: human atherosclerotic aortic arch transplanted into a normolipidemic mouse

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

source_name: Macrophages from aortic arch

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: genotype

tag: cell type

value: macrophages from aortic arch

tag: sample id

tag: disease state

value: baseline

value: control


title: WT_sample6

description:
Sample name: RJ1
Raw data file: july8_251486819004_S01_GE2-v5_95_Feb07_1_2.txt

tag: strain

tag: sample type


title: bone marrow cells, 12h stimulated with Flt3-L rep2

tag: age

tag: tissue


title: bone marrow cells, 12h stimulated with Flt3-L rep1


title: bone marrow cells, unstimulated, rep1


title: Baseline2 vs. Exp2_Macrophage_Progression-2

value: atherosclerotic progression


title: Baseline2 vs. Exp2_Macrophage_Regression-2

value: atherosclerotic regression


title: BreastTumorTissue-HEL_102

source_name: BreastTumorTissue

tag: 10years followup time (months)


title: bone marrow cells, unstimulated, rep2


title: BreastTumorTissue-HEL_104


title: BreastTumorTissue-HEL_103


title: Baseline2 vs. Exp2_Macrophage_Regression-3


title: BreastTumorTissue-HEL_105


title: PMT_sample8

description:
Sample name: RJ330
Raw data file: july8_251486819003_S01_GE2-v5_95_Feb07_1_4.txt

tag: initial tumour onset (days)


title: RST_sample8

description:
Sample name: RJ348
Raw data file: july8_251486819004_S01_GE2-v5_95_Feb07_1_1.txt

tag: tumor regression (days)


title: RST_sample6

description:
Sample name: RJ407
Raw data file: july8_251486819003_S01_GE2-v5_95_Feb07_1_2.txt

tag: tumor recurrence (days)


title: BreastTumorTissue-HEL_101


title: RST_sample7

description:
Sample name: RJ307
Raw data file: july8_251486819003_S01_GE2-v5_95_Feb07_1_3.txt

tag: age at tissue collection (days)


title: BreastTumorTissue-HEL_100

tag: 10years vital status


title: BreastTumorTissue-HEL_099

tag: bddm followup time (months)


title: WT_sample5

description:
Sample name: RJ187
Raw data file: july3_251486819145_S01_GE2-v5_95_Feb07_1_4.txt


title: PMT_sample7

description:
Sample name: RJ284
Raw data file: july8_251486819003_S01_GE2-v5_95_Feb07_1_1.txt


title: Baseline2 vs. Exp2_Macrophage_Progression-4


title: Baseline2 vs. Exp2_Macrophage_Progression-3


title: BreastTumorTissue-HEL_098

tag: bddm status


title: MDCKII, 3D, biological rep1

city: Madrid

first: Manuel

last: Galvez-Santisteban

state: Madrid

address: Nicolas Cabrera 1

department: Cell Biology and Immunology

country: Spain

institute: CSIC-CBM Severo Ochoa

description: Gene expression data from cells forming cysts embebded in matrigel

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

scan_protocol: Gene Chips were scanned at 2.5 µm resolution in a GeneChip® Scanner 3000 7G System (Affymetrix)

data_processing: Robust Muti-array Analysis (RMA) algorithm was used for background correction, normalization and expression levels summarization . Differential expression analysis was performed with the Bayes t-statistics from the linear models for Microarray data (LIMMA).Statistical analysis and graphical visualization of data were performed with the interactive tool FIESTA

organism: Canis lupus familiaris

source_name: MDCKII cells, 3D, 36h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA (Affymetrix, Santa Clara, CA)

growth_protocol: MDCK cells were cultured in 60 mm culture dishes in MEM at 37ºC 5% CO2 during 36h. After 36h RNA was extracted.

treatment_protocol: MDCK cells were cultured in absence (2D) or presence (3D) of extracellular matrix (matrigel). 3D cultured cells were plated in a thin layer of matrigel (100 ul per 60 mm culture dish) with MEM containing Matrigel 2%

tag: cell line

value: MDCKII

tag: culture type

value: Three dimensional (Matrigel)

tag: time after plating


title: RST_sample5

description:
Sample name: RJ423
Raw data file: july3_251486819145_S01_GE2-v5_95_Feb07_1_3.txt


title: MDCKII, 3D, biological rep3


title: Baseline2 vs. Exp2_Macrophage_Control-1

tag: genotype

tag: cell type

tag: sample id


title: Baseline2 vs. Exp2_Macrophage_Progression-1

tag: disease state


title: BreastTumorTissue-HEL_095

value: 2 (breast cancer death)

value: 1 (breast cancer death or distant metastasis)


title: Baseline1 vs. Exp1_Macrophage_Progression-3


title: RST_sample4

description:
Sample name: RJ356
Raw data file: july3_251486819144_S01_GE2-v5_95_Feb07_1_4.txt

tag: strain

value: FVB

tag: sample type

value: universal mouse reference RNA


title: BreastTumorTissue-HEL_097

tag: 10years followup time (months)


title: E.coli O157:H7 and B. longum_rep2

description: O157 and BL were pre-cultured for overnight anaerobically. In monoculture, BL and O157 were inoculated 1% individually for the labeling medium in 100-mL serum vials and cultured at 37°C. In coculture, pre-cultured O157 was inoculated 1% for the labeling medium and cultured at 37°C. After 1 hr, pre-cultured BL was inoculated 1% for O157 culture medium and cultured at 37°C. These cultures were stopped at the mid-exponential phase (OD600 = 1.0) and centrifuged for 10 min at 15,000 rpm and the supernatants were removed.

organism: Escherichia coli

source_name: E. coli O157:H7 and B. longum invitro coculture

tag: strain(s)

value: Escherichia coli o157:H7 and Bifidobacterium longum

tag: culture condition

value: invitro coculture


title: Baseline2 vs. Exp2_Macrophage_Regression-1


title: PMT_sample5

description:
Sample name: RJ324
Raw data file: july3_251486819145_S01_GE2-v5_95_Feb07_1_1.txt

tag: initial tumour onset (days)

tag: tumor regression (days)

tag: tumor recurrence (days)


title: BreastTumorTissue-HEL_096

tag: 10years vital status

value: 0 (alive or censored)

tag: bddm followup time (months)


title: RST_sample3

description:
Sample name: RJ427
Raw data file: july3_251486819144_S01_GE2-v5_95_Feb07_1_3.txt

tag: age at tissue collection (days)


title: PMT_sample6

description:
Sample name: RJ281
Raw data file: july3_251486819145_S01_GE2-v5_95_Feb07_1_2.txt


title: MDCKII, 2D, biological rep3

description: Gene expression data from polarized cells grown in 2D monolayer

source_name: MDCKII cells, monolayer, 36h

tag: cell line

tag: culture type

value: Monolayer (culture dish)


title: MDCKII, 3D, biological rep2

tag: time after plating


title: BreastTumorTissue-HEL_093

tag: bddm status

value: 0 (no event or censored)


title: Baseline2 vs. Exp2_Macrophage_Control-2

tag: genotype

tag: cell type

tag: sample id


title: BreastTumorTissue-HEL_094


title: MDCKII, 2D, biological rep2


title: E.coli O157:H7 and B. longum_rep1


title: Baseline1 vs. Exp1_Macrophage_Control-2

tag: disease state


title: bone marrow cells, 48h stimulated with Flt3-L rep2

source_name: Flt3_L stimulation for 48h

tag: strain

tag: age

value: 8-12 weeks

tag: tissue

value: bone marrow cells


title: PMT_sample4

description:
Sample name: RJ309
Raw data file: july3_251486819144_S01_GE2-v5_95_Feb07_1_2.txt

tag: initial tumour onset (days)

tag: sample type


title: Baseline1 vs. Exp1_Macrophage_Progression-1

description: human atherosclerotic aortic arch transplanted into a normolipidemic mouse

value: macrophages from aortic arch

value: baseline


title: WT_sample4

description:
Sample name: RJ288
Raw data file: july3_251486819144_S01_GE2-v5_95_Feb07_1_1.txt

tag: tumor regression (days)

tag: tumor recurrence (days)


title: BreastTumorTissue-HEL_090

tag: 10years followup time (months)

tag: 10years vital status

tag: bddm followup time (months)


title: BreastTumorTissue-HEL_091


title: E.coli O157:H7_rep2

source_name: E. coli O157 invitro culture

tag: strain(s)

value: Escherichia coli o157:H7

tag: culture condition

value: invitro monoculture


title: E. coli O157:H7_rep1


title: BreastTumorTissue-HEL_092

tag: bddm status


title: Baseline1 vs. Exp1_Macrophage_Control-4

tag: genotype

value: control


title: RST_sample2

description:
Sample name: RJ323
Raw data file: july3_251486819143_S01_GE2-v5_95_Feb07_1_2.txt

tag: age at tissue collection (days)


title: Baseline1 vs. Exp1_Macrophage_Progression-2

tag: cell type

tag: sample id

value: atherosclerotic progression


title: BreastTumorTissue-HEL_088


title: Study-10-Near Pool-2 vs. 128-022_Peripheral_R_SFA(entire)_denovo_FF_PCP-_Pool4-Extra tube-1

description: Gene expression profiling of peripheral plaque. 101 subjects from FoxHollow study, plus 8 carotid plaques used as a reference poolProfiled in the Merck/Agilent 44k v1.1

source_name: Peripheral plaque

tag: sample name

value: Study-10-Near Pool-2

value: carotid plaque, pool of 7 plaques

value: peripheral plaque


title: WT_sample3

description:
Sample name: RJ282
Raw data file: july3_251486819143_S01_GE2-v5_95_Feb07_1_3.txt

tag: strain

value: FVB

value: universal mouse reference RNA


title: Baseline1 vs. Exp1_Macrophage_Progression-4

tag: disease state


title: Baseline1 vs. Exp1_Macrophage_Control-1


title: BreastTumorTissue-HEL_087


title: PMT_sample2

description:
Sample name: RJ337
Raw data file: july3_251486819129_S01_GE2-v5_95_Feb07_1_4.txt

tag: initial tumour onset (days)


title: Baseline1 vs. Exp1_Macrophage_Regression-1

value: atherosclerotic regression


title: Baseline1 vs. Exp1_Macrophage_Control-3


title: Study-10-Near Pool-2 vs. 121-056_Peripheral_R_PRO(prox)_denovo_FF_19Aug05

tag: tissue


title: WT_sample2

description:
Sample name: RJ11
Raw data file: july3_251486819143_S01_GE2-v5_95_Feb07_1_1.txt

tag: tumor regression (days)

tag: sample type


title: PMT_sample3

description:
Sample name: RJ329
Raw data file: july3_251486819143_S01_GE2-v5_95_Feb07_1_4.txt

tag: tumor recurrence (days)


title: WT_sample1

description:
Sample name: RJ289
Raw data file: july3_251486819129_S01_GE2-v5_95_Feb07_1_3.txt


title: Study-10-Near Pool-2 vs. 121-056_Peripheral_R_CFA(prox)_restenotic_19Aug05


title: BreastTumorTissue-HEL_089

tag: 10years followup time (months)

tag: 10years vital status

value: 0 (alive or censored)


title: Study-10-Near Pool-2 vs. 114-077_Peripheral_L_SFA(distal)_restenotic_FF_31Oct05


title: BreastTumorTissue-HEL_086

tag: bddm followup time (months)

value: 1 (breast cancer death or distant metastasis)


title: Baseline1 vs. Exp1_Macrophage_Regression-2


title: Study-10-Near Pool-2 vs. 114-077_Peripheral_L_POP(prox)_denovo_FF_31Oct05


title: BreastTumorTissue-HEL_085

value: 0 (no event or censored)


title: Baseline1 vs. Exp1_Macrophage_Regression-4


title: RST_sample1

description:
Sample name: RJ433
Raw data file: july3_251486819129_S01_GE2-v5_95_Feb07_1_2.txt


title: BreastTumorTissue-HEL_084


title: BreastTumorTissue-HEL_083

value: 2 (breast cancer death)


title: PMT_sample1

description:
Sample name: RJ301
Raw data file: july3_251486819129_S01_GE2-v5_95_Feb07_1_1.txt


title: Baseline1 vs. Exp1_Macrophage_Regression-3


title: Study-10-Near Pool-2 vs. 101-037_Peripheral_L_PT(entire)_denovo_RL_29Jul05


title: Study-10-Near Pool-2 vs. 126-056_Peripheral_R_POP(prox)_denovo_FF_26Jul05-pool1


title: Study-10-Near Pool-2 vs. 101-037_Peripheral_L_SFA(distal)_restenotic_RL_29Jul05


title: carotid_artery-pair2b_CL46

city: Leiden

first: Peter

last: 't Hoen

address: PO Box 9600

department: Center for Human and Clinical Genetics

institute: Leiden University Medical Center

description: Gene expression profiles from young and old mice were compared

hyb_protocol: Oligonucleotide micro array slides were hybridized overnight at 55C in a GeneTAC hybridization station (Genomic Solutions, Ann Arbor, MI).

scan_protocol: Slides were scanned in an Agilent G2565BA microarray scanner at 30% PMT power

data_processing:
Feature extraction was done with GenePix 4.0. Data were processed using Rosetta's standard error model for GenePix
VALUE column represents normalized, log10-transformed (young/old) data

label_protocol: Between 130 and 500 ng of total RNA was amplified one time according to the Eberwine procedure by the Ambion MessageAmp  kit (Ambion, Austin, TX). Aminoallyl UTPs (A5660, Sigma Diagnostics) were incorporated during in vitro transcription. 3 μicrograms of aminoallyl-modified nucleotides were coupled with monoreactive Cy3 and Cy5 dyes (Amersham, Piscataway, NJ).

extract_protocol: Carotid samples were homogenized in Guanidium thiocyanate-phenol. After RNA extraction, RNA was further purified using an RNeasy mini column (Qiagen, Venlo, the Netherlands).

tag: Female C57Bl/6J LDLr -/- mice, aged 64 weeks

tag: Female C57Bl/6J LDLr -/- mice, aged 24 weeks


title: Study-10-Near Pool-2 vs. 126-056_Peripheral_R_SFA(distal)_26JUL2005-Pool4


title: BreastTumorTissue-HEL_082

data_processing:
The data were log base 2 transformed and normalised using quantile normalisation with R.
Data table below does not report controls.  For complete tables of normalized and non-normalized data, see supplementary files on Series record.

tag: bddm status


title: BreastTumorTissue-HEL_081


title: Study-10-Near Pool-2 vs. 126-074_Peripheral_R_iliac(entire)_denovo_FF


title: carotid_artery-pair4b_CL66


title: macrophage_m40_C57BL/6.MOLFc4(51Mb)-Ldlr-/-

description: Common genetic variants in a 58-kilobase (kb) region of chromosome 9p21, near the CDKN2A/B cell proliferation inhibitor genes, are strongly associated with coronary artery disease (CAD). We previously reported a congenic mouse model harboring an atherosclerosis susceptibility locus in a region of homology with the human 9p21 locus. We now report markedly decreased Cdkn2a (cyclin-dependent kinase inhibitor 2a) mRNA expression in macrophages and increased circulating levels of Ly6Chigh inflammatory monocytes in congenic mice compared to controls. A bone marrow (BM) transplantation study revealed that BM-derived cells from Cdkn2a+/- mice are capable of conferring accelerated atherosclerosis, increased inflammatory monocyte subsets and monocyte proliferation in the Ldlr-/- mouse model. These findings provide a mechanistic link between decreased expression of Cdkn2a transcripts, increased monocyte proliferation, and accelerated atherosclerosis.

source_name: macrophages

label_protocol: The reverse transcription incorporates biotin moieties that are later labeled with phycoerythrin.  After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency.  The labeled molecules are biotinylated-cDNA.

value: macrophage

tag: genetic background

tag: genotype


title: carotid_artery-pair3b_CL51


title: Study-10-Near Pool-2 vs. 128-031_PeripheralL_SFA(mid)_denovo_FF


title: macrophage_m39_C57BL/6.MOLFc4(51Mb)-Ldlr-/-

tag: cell type


title: carotid_artery-pair4a_CL52


title: carotid_artery-pair3a_CL47


title: macrophage_m37_C57BL/6.MOLFc4(51Mb)-Ldlr-/-


title: macrophage_m38_C57BL/6.MOLFc4(51Mb)-Ldlr-/-


title: BreastTumorTissue-HEL_078


title: carotid_artery-pair1b_CL44


title: Study-10-Near Pool-2 vs. 126-065_Peripheral_L_SFA(prox-dist)_02AUG2005_restenotic_FF

tag: sample name


title: BreastTumorTissue-HEL_080


title: BreastTumorTissue-HEL_077


title: macrophage_m35_C57BL/6.MOLFc4(51Mb)-Ldlr-/-


title: BreastTumorTissue-HEL_079


title: carotid_artery-pair2a_CL45


title: macrophage_m36_C57BL/6.MOLFc4(51Mb)-Ldlr-/-


title: Study-10-Near Pool-2 vs. 119-089_Peripheral_R_PT(entire)_25AUG2005_restenotic_FF_Pool3-1


title: BreastTumorTissue-HEL_076


title: DMSO6

city: OAKLAND

first: Max

last: Ruby

state: CA

address: 5700 Martin Luther King Jr. Way

institute: Children's Hospital Oakland Reserach Institue

description: replicate 6

data_processing: The data were normalised using quantile normalisation with background substraction in Beadstudio 3.2

source_name: Mouse liver

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit including DNase I treatment in accordance with the prescribed protocol provided with the kit.

tag: strain

value: Swiss-Webster

tag: age

value: 7 weeks

tag: gender

value: Male

value: Liver

tag: treatment

value: DMSO


title: BreastTumorTissue-HEL_075


title: macrophage_m34_C57BL/6.MOLFc4(51Mb)-Ldlr-/-

tag: tissue


title: MDCKII, 2D, biological rep1

tag: cell line

value: MDCKII

tag: culture type

value: Monolayer (culture dish)

tag: time after plating


title: DMSO5

description: replicate 5


title: carotid_artery-pair1a_CL43


title: Study-10-Near Pool-2 vs. 121-049_Peripheral_L_CFA(dist)_denovo_FF_PCP-_Pool2

value: Study-10-Near Pool-2

value: carotid plaque, pool of 7 plaques


title: DMSO4

description: replicate 4


title: macrophage_m33_C57BL/6.MOLFc4(51Mb)-Ldlr-/-


title: Study-10-Near Pool-2 vs. 128-024_Peripheral_R_PER(entire)_04AUG2005_restenotic_FF_Pool3-2

value: peripheral plaque


title: Carotid-Near-Pool-VLI-v2 vs. 102-213_Peripheral_R_SFA(distal)_denovo_RL_23FEB2006


title: macrophage_m31_C57BL/6.MOLFc4(51Mb)-Ldlr-/-


title: BreastTumorTissue-HEL_073

tag: 10years followup time (months)

tag: 10years vital status


title: Study-10-Near Pool-2 vs. 126-064_Peripheral_L_SFA(dist)_02AUG2005_PCP-_Pool2


title: BreastTumorTissue-HEL_072

tag: bddm followup time (months)


title: Carotid-Near-Pool-VLI-v2 vs. 102-213_Peripheral_L_SFA(distal)_denovo_RL_23FEB2006


title: macrophage_m32_C57BL/6.MOLFc4(51Mb)-Ldlr-/-


title: macrophage_m30_C57BL/6-Ldlr-/-


title: macrophage_m29_C57BL/6-Ldlr-/-


title: DMSO3

description: replicate 3


title: BreastTumorTissue-HEL_074


title: BreastTumorTissue-HEL_071


title: DMSO2

description: replicate 2


title: Carotid-Near-Pool-VLI-v2 vs. 114-098_Peripheral_R_SFA(distal)_denovo_RL_03FEB2006


title: macrophage_m28_C57BL/6-Ldlr-/-


title: BreastTumorTissue-HEL_070


title: Carotid-Near-Pool-VLI-v2 vs. 114-096_Peripheral_R_SFA(entire)_denovo_RL_25Jan06


title: Carotid-Near-Pool-VLI-v2 vs. 114-098_Peripheral_L_SFA(distal)_denovo_RL_03FEB2006


title: DMSO1

description: replicate 1


title: Am251/IDFP5

description: replicate 5

tag: pretreatment

value: cannabinoid receptor 1 antagonist (AM251) (10 mg/kg, i.p.)

value: isopropoyl dodecyl fluorophosphonate (IDFP) (10 mg/kg, i.p.)


title: Am251/IDFP4

description: replicate 4


title: macrophage_m26_C57BL/6-Ldlr-/-


title: Carotid-Near-Pool-VLI-v2 vs. 114-090_Peripheral_R_SFA(mid)_denovo_FF_28Dec05


title: BreastTumorTissue-HEL_068

value: 0 (alive or censored)

tag: bddm status


title: macrophage_m24_C57BL/6-Ldlr-/-

tag: genetic background