title: classIIhiMECs B6aireWT rep3

description: MHC class II high thymic medullary epithelial cells, B6aireWT jos3483


title: Bmp15-/- cumulus cells #3

status: Public on Oct 22 2007

type: RNA

city: Bar Harbor

first: You-Qiang

last: Su

state: ME

address: 600 Main Street

country: USA

institute: The Jackson Laboratory

description:
References cited
Cui, X. and Churchill, G. A. (2003). Statistical tests for differential expression in cDNA microarray experiments. Genome Biol, Epub 2003 Mar 17.
Cui, X., Hwang, J. T., Qiu, J., Blades, N. J. and Churchill, G. A. (2005). Improved statistical tests for differential gene expression by shrinking variance components estimates. Biostatistics 6, 59-75.
Gautier, L., Cope, L., Bolstad, B. M. and Irizarry, R. A. (2004). affy--analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 20, 307-15.
Irizarry, R. A., Bolstad, B. M., Collin, F., Cope, L. M., Hobbs, B. and Speed, T. P. (2003). Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31.
Storey, J. D. and Tibshirani, R. (2003). Statistical significance for genomewide studies. Proc Natl Acad Sci U S A, Epub 2003 Jul 25.
Wu H, K. M., Cui X, Churchill GA. (2003). MAANOVA: A Software Package for the Analysis of Spotted cDNA Microarray Experiments. In The Analysis of Gene Expression Data: An Overview of Methods and Software,  (ed. G. E. Parmigiani G, Irizarry RA, Zeger SL), pp. 313-431. New York: Springer.

hyb_protocol: Equal amounts, 15 µg, of fragmented and biotin-labeled cRNA from each sample were then hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 Arrays for 16 h at 45°C.  Post-hybridization staining and washing were performed according to manufacturer's protocols using the Fluidics Station 450 instrument (Affymetrix).

scan_protocol: After the post-hybridization staining and washing, the arrays were scanned with a GeneChip™3000 laser confocal slide scanner (Affymetrix) and the images were quantified using Gene Chip Operating Software version 1.2 (GCOS, Affymetrix).

data_processing: Probe level data were imported into the R software environment and expression values were summarized using the RMA (Robust MultiChip Average) function (Irizarry et al., 2003) in the R/affy package (Gautier et al., 2004). Using the R/maanova package (Wu H, 2003), an analysis of variance (ANOVA) model was applied to the data, and F1, F2, F3 and Fs test statistics were constructed along with their permutation p-values(Cui and Churchill, 2003; Cui et al., 2005). False discovery rate (FDR) (Storey and Tibshirani, 2003) was then assessed using the R/qvalue package to estimate q-values from calculated Fs test statistics.  Three pair-wise comparison analyses: DM vs. WT, Bmp15-/- vs. WT, and DM vs. Bmp15-/-, were generated, and the significantly changed transcripts were identified using the criteria of FC (fold change) p < 0.01. Results were annotated using information provided by Affymetrix (12/20/2005 release).

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: Cumulus cells from PMSG (48h) primed adult Bmp15-/- ovarian follicles

label_protocol: Ten nanograms of total RNA from each sample was employed in the two-round cDNA synthesis and subsequent in vitro-transcription according to the Two-Cycle Eukaryotic Target Labeling Assay (Affymetrix Expression Analysis Technical Manual: “ Section 2: Eukaryotic Sample and Array Processing” (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).

extract_protocol: Female WT, Bmp15-/-, and DM mice were primed with eCG (5IU/mouse, EMD Biosciences, Inc., Calbiochem, La Jolla, CA) for 48 hours to stimulate follicle development.  Cumulus-oocyte complexes (COCs) were released by puncturing large antral follicles on ovarian surface with a pair of 26 gauge needles.  Released COCs were collected and washed for three times by passing through 3 dishes of medium.  Cumulus cells were then stripped from the oocyte by passing COCs several times through a hand-drawn small fine glass pipette with an inner diameter slightly narrower than the oocyte.  After removing all of the denuded oocytes, cumulus cells were gathered together by gently swirling the dish, and were transferred into a 1.5 ml eppendorf centrifuge tube.  The cells were finally spun down by gentle centrifugation, and the pellet was re-suspended in 350 µl of RLT buffer (Qiagen, Valencia, CA) after removing the supernatant.  After brief vortexing, the cumulus cell lysate was snap frozen in liquid nitrogen and temporarily stored at -80°C until RNA isolation.  Three sets of WT, Bmp15-/- and DM cumulus cell samples were collected and employed in microarray study.  For each sample, about 75-100 COCs, obtained from 3-4 mice, were used for cumulus cell collection.  Medium used for cumulus cells isolation was MEM-α (Invitrogen Corporation, Grand Island, NY) supplemented with 3 mg/ml of crystallized lyophilized bovine serum albumin (Sigma, St. Louis, MO), 75 mg/liter of penicillin G (Sigma) and 50 mg/liter streptomycin sulfate (Sigma).  Milrinone (Sigma), a selective inhibitor of oocyte-specific phosphodiesterase (PDE3), was added into the medium at the concentration of 5 µM to prevent the GV-stage oocytes from undergoing maturation during the process of COC and cumulus cell isolation.  Total RNA was extracted from cumulus cells using the RNeasy Micro Kit (Qiagen, Valencia, CA) according to the manufacturer’s instruction.  The RNA quality and yield of each sample were determined using the Bioanalyzer 2100 and RNA 6000 Pico LabChip assay (Agilent Technologies Inc, Palo Alto, CA) in combination with Quant-iTTM RiboGreen Reagent according to supplied protocols (Invitrogen, Carlsbad, CA).

tag: Strain

value: Bmp15-/- on B6/129 background; Gender:females; Age:4-5 months old; Follicle stage:large antral follicles


title: DM cumulus cells #2

source_name: Cumulus cells from PMSG (48h) primed adult DM ovarian follicles

value: DM on B6/129 background; Gender:females; Age:4-5 months old; Follicle stage:large antral follicles


title: wildtype cumulus cells #1

source_name: Cumulus cells from PMSG (48h) primed adult wildtype ovarian follicles

value: wildtype on B6/129 background; Gender:females; Age:4-5 months old; Follicle stage:large antral follicles


title: Bmp15-/- cumulus cells #2


title: wildtype cumulus cells #2


title: Muscle PCOS 24

status: Public on Oct 20 2007

city: Roskilde

first: Vibe

last: Skov

address: Koegevej 7-13

department: Hematology

country: Denmark

institute: Roskilde Hospital

description: Vastus lateralis muscle

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: The R statistical software was applied for data analysis. The RMA method was used for global background correction and qspline was used for normalization. Gene expression index calculation was done using model based index calculation (MBEI). Only perfect match probes were included in data analysis. Welch two sample t-test was used to calculate p-values.

organism: Homo sapiens

source_name: Vastus lateralis muscle

label_protocol: One µg purified total RNA was converted to biotin-labeled aRNA using the MessageAmpTM II-Biotin single round aRNA amplification kit.

extract_protocol: Frozen muscle tissue was homogenized in Trizol with a Polytron Homogenizer and total RNA was purified using TRIzol Reagent including an extra step after phase separation with chloroform. Briefly, 1 volume of phenol-chloroform-isoamylalcohol (25-24-1) was added to the aqueous phase and spun at 10.000 x g for 10 minutes at 4˚C. Then, 1 volume of chloroform was added to the aqueous phase and spun at 12.000 x g for 20 minutes at 4˚C before RNA precipitation.

tag: Vastus lateralis muscle


title: DM cumulus cells #1


title: classIIhiMECs B6aireKO rep2

status: Public on Oct 23 2007

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: MHC class II high thymic medullary epithelial cells, B6aireKO jos3482

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA

label_protocol: BioArray High Yield RNA Transcript Labeling T7 Kit (Enzo Life Sciences)

extract_protocol: RNA isolated with Trizol reagent and amplified twice with the MessageAmp aRNA Kit (Ambion)

tag: Gender

value: male Age:3-4.5 weeks Isolation:FACS of CD45-G8.8+Ly51intclassIIhi TECs


title: Muscle PCOS 14

description: Vastus lateralis muscle


title: Muscle PCOS 19

description: Vastus lateralis muscle


title: Muscle PCOS 11

description: Vastus lateralis muscle


title: Muscle PCOS 22

description: Vastus lateralis muscle


title: Muscle PCOS 13

description: Vastus lateralis muscle


title: Muscle PCOS 9

description: Vastus lateralis muscle


title: ERaKO mouse aorta with estrogen, biological rep2

status: Public on Oct 19 2007

first: Ulla

last: Hansen

address: 5 Cummington St

department: Biology

institute: Boston University

description: Gene expression data from ovarioectomized mouse aortae treated with estrogen or placebo.

hyb_protocol: Unamplified, labeled cRNA (15 ug) was hybridized to whole mouse genome 430 2.0 microarrays(Affymetrix) according to the manufacturer's instructions.  Affymetrix GeneChip® Operating Software (GCOS) was used for the control of GeneChip® Fluidics Stations for automated washing, staining, and scanning.

scan_protocol: Affymetrix GeneChip® Operating Software (GCOS) was used for the control of GeneChip® Scanners were used for scanning and data acquisition, according to the manufacturer's instructions.

data_processing: The gene expression values for each probe set were first estimated from the hybridization intensities using the corrected for GC content Robust Multichip Analysis (GCRMA) method as implemented in Bioconductor (61–63).  Gene expression values for each sample were estimated using the linear model of the data as implemented by the LIMMA package in BioConductor (63).  The differences in log (base 2) expression levels were evaluated by the t test as implemented by the LIMMA package in BioConductor by comparing distribution of expression values between different sample categories.

label: biotin

source_name: 2.5-4.5 month old ovarioectomized female mouse

label_protocol: Total RNA (5 ug; a separate aortic sample per microarray) was used for labeling (One-Cycle Eukaryotic Target Labeling Assay (Affymetrix P/N900493, Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions.  Total RNA was reverse transcribed using a T7-Oligo(dT) Promoter Primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and served as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.

extract_protocol: Total aortic RNA was isolated by homogenization in RNA STAT-60 (Tel-Test, Inc., Friendswood, TX) and purification by chloroform extraction, with a yield of approximately 6 ug total RNA per aorta. Quantity and quality of each samples was measured at the spectrophotometer (OD 260, 280, 260/280) and RNA integrity checked with the use of a Bioanalyzer (18s and 28s peaks) confirming good quality of the samples (Agilent 2100 Bioanalyzer, Agilent Technologies, Palo Alto, CA).


title: ERaKO mouse aorta with placebo, biological rep2


title: ERaKO mouse aorta with estrogen, biological rep1


title: ERaKO mouse aorta with estrogen, biological rep3


title: Muscle PCOS 1

description: Vastus lateralis muscle


title: Wild type mouse aorta with estrogen, biological rep2


title: Muscle PCOS 5

description: Vastus lateralis muscle


title: Wild type mouse aorta with placebo, biological rep5


title: Wild type mouse aorta with estrogen, biological rep1


title: ERbKO mouse aorta with estrogen, biological rep1


title: ERbKO mouse aorta with placebo, biological rep3


title: ERbKO mouse aorta with estrogen, biological rep3


title: ERaKO mouse aorta with placebo, biological rep1


title: Wild type mouse aorta with estrogen, biological rep4


title: ERbKO mouse aorta with estrogen, biological rep2


title: Wild type mouse aorta with estrogen, biological rep3


title: ERaKO mouse aorta with placebo, biological rep3


title: Wild type mouse aorta with estrogen, biological rep5


title: ERbKO mouse aorta with placebo, biological rep2


title: Wild type mouse aorta with placebo, biological rep3


title: ERbKO mouse aorta with placebo, biological rep1


title: Wild type mouse aorta with placebo, biological rep2


title: Wild type mouse aorta with placebo, biological rep4


title: SKG_3

status: Public on Oct 17 2007

city: Kyoto

first: Shimon

last: Sakaguchi

address: 53 Shogoin Kawahara-cho,

country: Japan

institute: Institute for Frontier Medical Sciences Kyoto University

hyb_protocol: 16 hours; standard Affymetrix protocol

scan_protocol: GeneChip®Scanner

data_processing: GeneSpring GX

source_name: FR4- CD4+ T lymphocyte stimulated with PMA and ionomycine

label_protocol: in vitro transcription; standard Affymetrix protocol

extract_protocol: QIAGEN RNeasy

value: SKG mice (BALB/c background)

tag: Age

value: 40 weeks

value: Female

tag: Tissue

value: LN


title: Wild type mouse aorta with placebo, biological rep1

description: Gene expression data from ovarioectomized mouse aortae 7-8 days after implantation with estrogen (E2) or placebo pellets.


title: BALB_1

source_name: CD4+ T lymphocyte stimulated with PMA and ionomycine

value: BALB/c

value: Spleen and LN


title: BALB_2


title: SKG_2


title: SKG_1


title: IFNg_2

source_name: CD4+ T lymphocyte

value: RAG2 KO BALB/c with CD4 T lymphocyte of IFNg KO BALB/c

value: 7 weeks. 7 days after transfer of T cells

value: Spleen


title: IL-6_3

value: IL-6 KO RAG2 KO BALB/c with CD4 T lymphocyte of IL-6 KO BALB/c


title: IFNg_1


title: BALB_3


title: IFNg_3


title: IL-6_1


title: NeuroD1 knockout mouse, P0 Pineal Tissue, Sample 1, 05-16-06

status: Public on Oct 13 2007

city: Bethesda

first: Michael

last: Bailey

state: MD

address: 9000 Rockville Pike, Bldg 49, Rm 6A71

department: NICHD

institute: National Institutes of Health

description:
This is the homozygous sample number one of three.
Experiment compares 129 Wt pineal gland gene expression at P0 versus P0 pineal gland gene expression in NeuroD1 knockout mice.

hyb_protocol: GeneChip® One-Cycle Target Labeling from Affymetrix. Fluidics script EukGE_Ws2v5 was used with GeneChip® Fluidics Station 450.

scan_protocol: Affymetrix GCOS default settings and Genechip Scanner 3000.

data_processing: Data indicated are the signal calls from GCOS

source_name: Neurod1 KO, 129 mouse pineal glands from postnatal day zero.

label_protocol: 3' In Vitro Transcription, GeneChip® One-Cycle Target Labeling from Affymetrix.

growth_protocol: Mice housed in LD 12:12 light cycles.

extract_protocol:
Initially, total RNA was subjected to a single round of RNA amplification using Ambion Message Amp II kit.
Amplified RNA was used as starting material for the Affymetrix hybridization protocol.

treatment_protocol:
Pineal gland tissues were collected during the daytime period.
3 pineal glands were pooled per sample and total RNA extracted.

tag: NeuoD1 transgenic animals die very shortly after birth.


title: NeuroD1 knockout mouse, P0 Pineal Tissue, Sample 3, 05-31-06

description:
This is the homozygous sample number three of three.
Experiment compares 129 Wt mouse pineal gland gene expression at P0 versus P0 pineal gland gene expression in NeuroD1 knockout mice.

tag: NeuroD1 transgenic animals die very shortly after birth.


title: classIIhiMECs LTaKO rep1

description: MHC class II high thymic medullary epithelial cells, LTaKO jos3512

value: male Age:3-4.5 weeks Isolation:FACS of CD45-G8.8+Ly51intclassIIhi TECs Strain:C57BL/6


title: 129 Mouse P0 Pineal Tissue, Sample 3, 05-31-06

description:
This is WT sample number three of three.
Experiment compares 129 Wt pineal gland gene expression at P0 versus P0 pineal gland gene expression in NeuroD1 knockout mice.

source_name: Wildtype, 129 mouse pineal glands from postnatal day zero.

treatment_protocol:
Pineal tissues collected during the daytime period.
3 pineal glands were pooled per sample and total RNA extracted.

tag: 129 mouse pineal gland tissues taken at postnatal day zero.


title: 129 Mouse P0 Pineal Tissue, Sample 1, 05-16-06

description:
This is WT sample number one of three.
Experiment examines 129 Wt mouse pineal gland gene expression at P0 versus P0 pineal gland gene expression in NeuroD1 transgenic knockout mouse.

hyb_protocol: GeneChip® One-Cycle Target Labeling and hybridization. Washing and staining was performed on GeneChip® Fluidics Station 450. EukGE_Ws2v5 washing script was used.

scan_protocol: GeneChip® Scanner 3000

label_protocol:
3' In Vitro Transcription.
GeneChip® One-Cycle Target Labeling.

extract_protocol:
Initially, total RNA was subjected to a single round of RNA amplification.
Amplified RNA was used as starting material for the Affymetrix hybridization.

treatment_protocol: Pineal tissues collected during the daytime period.

tag: wildype 129 mice, pineal glands disected at postnatal day zero.


title: ESC C Affy

status: Public on Oct 11 2007

city: Leuven

first: Fernando

last: Ulloa Montoya

address: Herestraat 49 bus 804

department: Medicine

country: Belgium

institute: Katholieke Universiteit Leuven

description: mouse embryonic stem cells, biological replicate C, Affymetrix

hyb_protocol: Sample was hybridized to Affymetrix mouse 430 2.0 chips, washed, and scanned at the University of Minnesota Affymetrix Microarray Core Facility as described in the Affymetrix GeneChip Expression Analysis Technical Manual. Protocol EukGE-WS2v5_450 .

scan_protocol: Array was scanned at the University of Minnesota Affymetrix Microarray Core Facility as described in the Affymetrix GeneChip Expression Analysis Technical Manual. Pixel Size 1.56. Filter 570. Scanner ID 50209060. Number of Scans 1. Scanner Type M10

data_processing: CEL files were loaded into GeneData Expressionist Refiner (GeneData, San Francisco, CA) to assess overall quality and obtain condensed single intensity values per probeset using the Microarray Analysis Suite Statistical algorithm (MAS 5.0). The mean of mean intensity values for all chips (192) was used to normalize the mean intensity of each chip. Normalization Target: 192, Tau: 0.015, Alpha1: 0.05, Alpha2: 0.065

label_protocol: 100 ng of total cellular RNA was double amplified and labeled with the Two-Cycle Target Labeling and Control Reagents kit P/N 900494 (Affymetrix Inc., Santa Clara, CA) following the manufacturers' protocol.

growth_protocol: ES cells were grown in standard ES media (15 0.000000CS, LIF, P/S, glutamine, non-essential amino acids, BME, DMEM high glucose) on irradiated MEFs. Cells were plated feeder free before RNA sample collection

extract_protocol: Total RNA  was extracted using the RNAeasy microkit (Qiagen, Valencia, CA), DNAse treatment was performed on column

value: C57BL/6, Age:Embryo (E3), Tissue:Inner cell mass, Cell type:Embryonic stem cells


title: NeuroD1 knockout mouse, P0 Pineal Tissue, Sample 2, 05-23-06

description:
This is the homozygous sample number two of three.
Experiment compares 129 Wt pineal gland gene expression at P0 versus P0 pineal gland gene expression in NeuroD1 knockout mice.


title: mClone-3 A Affy

description: mouse clone 3, bone marrow 1, biological replicate A, Affymetrix

growth_protocol: BM was plated in 600w glucose DMEM, 40% MCDB-201 containing 10ng/mL mEGF, hPDGF-BB and 1000 units/ml mouse leukemia inhibitory factor (LIF), 2creened fetal calf serum (FCS), 1x selenium-insulin-transferrin-ethanolamine (SITE), 0.2 mg/mL linoleic acid-bovine serum albumin (LA-BSA), 0.8 mg/mL bovine serum albumin, 1x chemically defined lipid concentrate and 1x 2-mercaptoethanol, 100 units of penicillin, 1,000 units of streptomycin in a humidified, 502 and 6% CO2, 37oC incubator. After 4 weeks, CD45+ and Ter119+ cells were depleted using a MACS separation CS column, and cells replated at 10 cells/well. Expansion was done by trypsinizing (0.05% trypsin) the cells and replating them every two days at a density of 100-200 cells/cm2. Cells at population doubling >80 were used for gene arrays.

value: C57BL/6, Sex:Male, Age:Adult, Tissue:Bone marrow (cultured cells), Cell type:clone isolated using Multipotent Adult Progenitor Cells culture conditions


title: 129 Mouse P0 Pineal Tissue, Sample 2, 05-23-06

description:
This is WT sample number two of three.
Experiment compares 129 Wt pineal gland gene expression at P0 versus P0 pineal gland gene expression in NeuroD1 transgenic knockout mice.

hyb_protocol: Standard Eukaryotic Affymetrix protocols as of 05-06. Fluidics script EukGE_Ws2v5 was used with GeneChip® Fluidics Station 450.

scan_protocol: Standard Eukaryotic Affymetrix default settings and Genechip Scanner 3000.

label_protocol:
One-cycle cDNA and IVT kit from Affymetrix.
3' IVT.

extract_protocol:
Initially, total RNA was subjected to a single round of RNA amplification.
Amplified RNA was used as starting material for the Affymetrix hybridization protocol.

tag: 129 Wildtype mice, pineal glands taken at postnatal day zero


title: ESC A Affy

description: mouse embryonic stem cells, biological replicate A, Affymetrix


title: MSC A Affy

description: mouse marrow stromal cells, biological replicate A, Affymetrix

growth_protocol: Femurs and tibiae (cleaned of all connective tissue) were centrifuged to obtain the bone marrow. The cell pellet was resuspended in complete isolation medium (CIM) consisting of RPMI-1640 supplemented with FCS, HS and PenStrep followed by filtration through a 70 µm nylon mesh filter. The cells were plated in 40 ml CIM in a 175-cm2 flask for 24 hours to obtain adherent murine stromal cells (P0). Non-adherent cells were removed by washing with PBS and fresh CIM is added. CIM was added every 3-4 days for a total of 4 weeks. Lifted cells (trpysin-EDTA) were replated (P1) in CIM and CIM replaced every 3-4 days for 1-2 weeks. Cells were lifted and expanded (P2) at (50 cells/cm2) in culture expansion medium (CEM) consisting of: IMDM (Gibco, BRL) with 2mM L-glutamine (Gibco), 100 U/ml penicillin, 100µg/ml streptomycin, 0.25 ?g/ml amphotericin B (Gibco), 10creened FBS (Atlanta biologicals, Lawrenville, GA, Lot C0105) and 10 0.000000e+00quine serum (Hyclone, Lot AQH24495) which is replaced every 3-4 days for 1-2 weeks. Cells were lifted and expanded (P3). Passage 3 cells were either frozen or further expanded as above. Passage 5 frozen cells were obtained from the Tulane University Center for Gene Therapy and thawed and cultured using culture expansion medium (CEM) and serum as recommended by the same center. Briefly, cells were cultured at a plating density of 100 cells/cm2  in CEM in a humidified, 2102, 5% CO2, 37oC incubator. As recommended, a first passage was done one day after thawing and subsequently cells were passaged every six days. RNA samples for gene arrays were taken three days after passaging with plates seeded at 300 cells/cm2 during three consecutive passages (10 population doublings).

value: C57BL/6, Sex:Female, Age:Adult, Tissue:Bone marrow (cultured cells), Cell type:Marrow Stromal Cells obtained from the Tulane University Center for Gene Therapy


title: MSC C Affy

description: mouse marrow stromal cells, biological replicate C, Affymetrix


title: MSC B Affy

description: mouse marrow stromal cells, biological replicate B, Affymetrix


title: Late Embryonic tissue, Whole brain: DMSO3_le1

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

description: embryos of flies raised on DMSO control food

organism: Drosophila melanogaster

source_name: Late Embryonic tissue, Whole brain

label_protocol: standard Affymetrix protocol

extract_protocol: not supplied


title: whole animal, Whole brain: MeHg2_le1

description: Embryos from MeHg fed adults

source_name: whole animal, Whole brain


title: Late Embryonic tissue, Whole brain: DMSO 1_le1


title: whole animal, Whole brain: MeHg3_le1

description: Embryos from MeHg fed adults


title: IL-6_2


title: whole animal, Whole brain: MeHg 1_le1

description: Embryos from MeHg fed adults


title: Late Embryonic tissue, Whole brain: DMSO2_le1


title: mClone-3 C Affy

description: mouse clone 3, bone marrow 1, biological replicate C, Affymetrix


title: ESC B Affy

description: mouse embryonic stem cells, biological replicate B, Affymetrix


title: mClone-3 B Affy

description: mouse clone 3, bone marrow 1, biological replicate B, Affymetrix


title: SK-MEL-5_TPA_24hr

status: Public on Oct 10 2007

city: Brisbane

first: Glen

middle: M

last: Boyle

state: Queensland

address: 300 Herston Road Herston

department: Department of Cell and Molecular Biology, Cancer Program

country: Australia

institute: QIMR Berghofer Medical Research Insitute

description: For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2).

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

source_name: Melanoma cell line SK-MEL-5 treated with TPA 24 hr

growth_protocol: The cell line was cultured in RPMI 1640 in the presence of 10% fetal bovine serum.

extract_protocol: RNA extractions were performed using Qiagen RNeasy Midi-kits as per the manufacturer’s instructions. RNA quality and concentration were assessed using a 2100 BioAnalyser (Agilent Technologies).

treatment_protocol: Melanoma cell line SK-MEL-5 treated with 1000 ng/ml TPA (12-O-tetradecanoylphorbol-13-acetate) for 24 hr.


title: COLO-205_Mock

hyb_protocol: This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450.

scan_protocol: Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2).

label_protocol: For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA).

treatment_protocol: Colon cancer cell line COLO-205 mock treated with DMSO alone.


title: COLO-205_PEP008_72hrRecovery

source_name: Colon cancer cell line COLO-205 treated with PEP008 72 hr recovery

treatment_protocol: Colon cancer cell line COLO-205 treated with 1000 ng/ml PEP008 (20-O-acetyl-ingenol-3-angelate) for 24 hr, drug removed and allowed 72 hr recovery.


title: CBA brain ECM

first: Christian

last: Engwerda

address: 300 Herston Road, Herston

institute: Queensland Institute of Medical Research

description: Arrays were scanned using the GeneChip Scanner 3000 (Affymetrix) and GeneChip Operating Software v1.1.1 (Affymetrix). Normalisation and initial analyses were carried out in GeneSpring v7 (Agilent Technologies). Values below 0.01 were set to 0.01. Each measurement was divided by the 50th percentile of all measurements in that sample. The data was filtered for genes flagged as present, which had at least an expression level of 50. Following this, a threshold of 2.5 fold up-regulation or down-regulation of genes was set.

label: R-Phycoerythrin

source_name: Animal Resources Centre, Australia

label_protocol: Pooled RNA samples were converted to cDNA and antisense cRNA, labelled and hybridized to GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix, Surrey Hills, Australia) by the Australian Genome Research Facility (Parkville, Australia), according to Affymetrix protocols.

extract_protocol: Total RNA was extracted from brain tissue using TRIzol reagent (Invitrogen, Mount Waverley, Australia), according to manufacturer’s instructions, and contaminants were removed by passing the RNA over RNeasy mini-columns with on-column DNase treatment (Qiagen). RNA 6000 Nano Assay Kits (Agilent Technologies, Forest Hill, Australia) were used to assess RNA quality and integrity on a Bioanalyzer 2100 (Agilent Technologies). Samples were included in the study based on 260:280nm absorbance readings. Equal quantities of six samples were pooled for microarray analysis.

treatment_protocol: Mice were infected intravenously (i.v.) with 105 PbA-parasitized red blood cells (pRBCs). All mice were monitored for ECM symptoms and were allocated scores. Animals with severe ECM were sacrificed by CO2 asphyxiation, in accordance with animal ethics guidelines. Following sacrifice, mice were then perfused with 20mL PBS via the heart in order to remove blood and other non-adherent cells from the brain microvasculature. Brains were isolated, halved and preserved in either RNAlater (Qiagen, Doncaster, Australia).

value: CBA/CaH

value: 6-7 weeks

value: brain, perfused

tag: Status

value: Infected with Plasmodium berghei ANKA, tissue collected d6-7 post-infection.


title: CBA brain naive

description: Normalisation and initial analyses were carried out in GeneSpring v7 (Agilent Technologies). Values below 0.01 were set to 0.01. Each measurement was divided by the 50th percentile of all measurements in that sample. The data was filtered for genes flagged as present, which had at least an expression level of 50. Following this, a threshold of 2.5 fold up-regulation or down-regulation of genes was set.

hyb_protocol: Pooled RNA samples were converted to cDNA and antisense cRNA, labelled and hybridized to GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix, Surrey Hills, Australia) by the Australian Genome Research Facility (Parkville, Australia), according to Affymetrix protocols.

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 (Affymetrix) and GeneChip Operating Software v1.1.1 (Affymetrix).

data_processing: Transformation algorithm used was MAS5.0

source_name: CBA, brain, naive

treatment_protocol: Following sacrifice, mice were perfused with 20mL ice-cold PBS via the heart in order to remove blood and other non-adherent cells from the brain microvasculature. Brains were isolated, halved and preserved in either RNAlater (Qiagen, Doncaster, Australia).

tag: Infection Status

value: naive


title: C57BL6 brain ECM

source_name: brain, perfused, Plasmodium berghei ANKA, ECM

treatment_protocol: Following sacrifice, mice were infected intravenously (i.v.) with 10e5 PbA-parasitized red blood cells (pRBCs). All mice were monitored for ECM symptoms . Animals with severe ECM were sacrificed by CO2 asphyxiation, in accordance with animal ethics guidelines. Mice were then perfused with 20mL ice-cold PBS via the heart in order to remove blood and other non-adherent cells from the brain microvasculature. Brains were isolated, halved and preserved in either RNAlater (Qiagen, Doncaster, Australia).

value: Female

value: Plasmodium berghei ANKA infection


title: MCF7_PEP008_24hr

source_name: Breast cancer cell line MCF7 treated with PEP008 24 hr

treatment_protocol: Breast cancer cell line MCF7 treated with 1000 ng/ml PEP008 (20-O-acetyl-ingenol-3-angelate) for 24 hr.


title: C57BL6 brain naive

source_name: brain, perfused, naive

treatment_protocol: Following sacrifice, mice were perfused with 20mL PBS via the heart in order to remove blood and other non-adherent cells from the brain microvasculature. Brains were isolated, halved and preserved in either RNAlater (Qiagen, Doncaster, Australia).

value: naive.


title: SK-MEL-5_Mock

treatment_protocol: Melanoma cell line SK-MEL-5 mock treated with DMSO alone.


title: COLO-205_PEP008_24hr

source_name: Colon cancer cell line COLO-205 treated with PEP008 24 hr

treatment_protocol: Colon cancer cell line COLO-205 treated with 1000 ng/ml PEP008 (20-O-acetyl-ingenol-3-angelate) for 24 hr.


title: MCF7_Mock

treatment_protocol: Breast cancer cell line MCF7 mock treated with DMSO alone.


title: SK-MEL-5_PEP008_24hr

source_name: Melanoma cell line SK-MEL-5 treated with PEP008 24 hr

treatment_protocol: Melanoma cell line SK-MEL-5 treated with 1000 ng/ml PEP008 (20-O-acetyl-ingenol-3-angelate) for 24 hr.


title: MCF7_PEP008_72hrRecovery

source_name: Breast cancer cell line MCF7 treated with PEP008 72 hr recovery

treatment_protocol: Breast cancer cell line MCF7 treated with 1000 ng/ml PEP008 (20-O-acetyl-ingenol-3-angelate) for 24 hr, drug removed and allowed 72 hr recovery.


title: pcDNA3.1 r4

status: Public on Oct 09 2007

city: Gainesville

first: M Cecilia

last: Lopez

state: FL

address: 1376 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

description: gene expression from 293 cells with pmiRNA cluster

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG133 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix F450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 7G.

data_processing: The data were normalized and modelled with DNA-Chip Analyzer (dChip) Version 1.3 (2/23/05)

source_name: 293 cells with pcDNA3.1/V5/HisA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2003, Affymetrix).

growth_protocol: grow 293 cells to 80% confluence in DMEM with 10% FBS, collected 2 samples each 2 days apart for a total of 8 (4 each miR-155 or miR-K12-11) experimental and 4 control samples (pCDNA3.1)

extract_protocol: Qiagen RNeasy according to manufacturer's instructions

treatment_protocol: 293 cells were stably expressing either miR-155, mir-K12-11, or pcDNA vector control  while selected under 100 ug/mL G418

tag: human embryonic kidney cells expressing control vector pcDNA3.1/V5/HisA


title: pcDNA3.1 r3


title: pcDNA3.1 r1


title: miR-155 r4

description: gene expression from 293 cells with pcDNA3.1/V5/HisA

tag: human embryonic kidney cells expressing miR-155


title: pcDNA3.1 r2


title: miR-K12-11 r3

source_name: 293 cells with pmiRNA cluster

tag: human embryonic kidney cells expressing miR-K12-11


title: miR-155 r3


title: miR-K12-11 r2


title: miR-155 r1


title: miR-K12-11 r1


title: miR-K12-11 r4


title: miR-155 r2


title: SK-MEL-5_PEP008_72hrRecovery

source_name: Melanoma cell line SK-MEL-5 treated with PEP008 72 hr recovery

treatment_protocol: Melanoma cell line SK-MEL-5 treated with 1000 ng/ml PEP008 (20-O-acetyl-ingenol-3-angelate) for 24 hr, drug removed and allowed 72 hr recovery.


title: MT-2_Velcade_5nM_24h_dup2

city: Tokyo

first: Junko

middle: H

last: Ohyashiki

address: 6-7-1, Nishishinjuku, Shinjuku-ku

department: Intractable Immune System Diseases Research Center

institute: Tokyo Medical University

description: Effect of bortezomib

hyb_protocol: GeneChip Expression Analysis Technical Mannual, 701021 Rev.5 Hybridization Oven 640 110V (Affymetrix 800138) Wash and staining: Fluidics Station 450 (Affymetrix 00-0079)

scan_protocol: GeneChip Scanner 3000 (Affymetrix 00-0074) GeneChip Operating Software ver.1.4 (Affymetrix 690036)

source_name: Velcade

label_protocol: One-cycle Target Labeling GeneChip Expression Analysis Technical Mannual, 701021 Rev.5 Section 2 Eukaryotic Sample and Array processing Chapter 1 Eukaryotic Target Prepartion

extract_protocol: RNeasy kit

tag: ATL cell line treated with velcade


title: MT-4_Mock_dup1

description: Effect of bortezomib

data_processing: GeneChip Operating Software ver.1.4 (Affymetrix 690036)

source_name: Mock

tag: ATL cell line


title: MT-4_Vel_5nM_24h_dup1

description: Effect of bortezomib


title: MT-2_Velcade_5nM_24h_dup1

description: Effect of bortezomib


title: TaT_OK_Velcade_15nM_24h_dup2

description: Effect of bortezomib


title: TaY_E10_OK_Vel_15nM_24h_dup1

description: Effect of bortezomib


title: MT-4_Mock_dup2

description: Effect of bortezomib


title: MT-2_Mock_dup1

description: Effect of bortezomib


title: TaY_E10_OK_Mock_dup2

description: Effect of bortezomib

label_protocol:
One-cycle Target Labeling
GeneChip Expression Analysis Technical Mannual, 701021 Rev.5
Section 2 Eukaryotic Sample and Array processing
Chapter 1 Eukaryotic Target Prepartion

tag: Mock


title: TaY_E10_Velcade_5nM_24h_dup2

description: Effect of bortezomib

source_name: Velcade 5nM

tag: Velcade 5nM 24hrs


title: MT-2_Mock_dup2

description: Effect of bortezomib


title: TaY_E10_OK_Mock

description: Effect of bortezomib

tag: MOCK


title: TaY_E10_Velcade_5nM_24h

description: Effect of bortezomib

tag: Velcade 5nM, 24hrs


title: TaY_E10_MOCK_dup2

description: Effect of bortezomib

treatment_protocol: Mock


title: MT-4_Vel_5nM_24h_dup2

description: Effect of bortezomib


title: TaY_E10_MOCK_dup1

description: Effect of bortezomib


title: M10KOepi_infect_0h_rep3

status: Public on Oct 08 2007

city: Seattle

first: Sean

middle: Y

last: Kassim

state: WA

address: 815 Mercer St

department: Medicine, PCCM

institute: University of Washington

description: Gene expression data for airway epithlium exposed to Pseudomonas aeruginosa

hyb_protocol: cRNA were hybridized overnight to Mouse 430 2.0 Arrays then washed in the Affymetrix Fluidics Station.

scan_protocol: Chips were treated with phycoerythyrin-conjugated streptavidin and scnned for hybridized targets with the GeneChip Scanner 3000

data_processing: The data were inspected visually and with the Affymetrix quality control metrics in the GeneChip Operating Software. Two replicates were discarded from futher analysis (WT-24h-rep1 and M10-24h-rep2) due to high background and high scale factor. Cel files were extracted using GCOS and normalized in Bioconductor in the R environment. All samples were normalized using RMA and mean centered by genotype using the RMA function in the Affymetrix package and the scale function of the base R environment.

source_name: Mmp10-/- epithelium, uninfected, 0h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2-8 ug total RNA by the Center for Array Technologies at the University of Washington (Seattle, WA)

growth_protocol: Primary mouse airway epithelial cells were cultured at an air liquid interface

extract_protocol: Qiagen Rneasy total RNA extraction was performed according to manufacturer's specifications

treatment_protocol: Pseudomonas aeruginosa (PA51673) was exposed to cells at a MOI of 5 for 1 to 24 h

tag: Strain

value: C57BL/6, Tissue:Airway Epithlium, Culture:Organotypic Air Liquid Interface


title: M10KOepi_infect_1h_rep2

source_name: Mmp10-/- epithelium, Pseudomonas aeruginosa infected, 1h


title: M10KOepi_infect_1h_rep1


title: M7KOepi_infect_24h_rep3

source_name: Mmp7-/- epithelium, Pseudomonas aeruginosa infected, 24h


title: M10KOepi_infect_24h_rep1

source_name: Mmp10-/- epithelium, Pseudomonas aeruginosa infected, 24h


title: M7KOepi_infect_1h_rep1

source_name: Mmp7-/- epithelium, Pseudomonas aeruginosa infected, 1h


title: M7KOepi_infect_24h_rep1


title: Wtepi_infect_24h_rep3

source_name: WT epithelium, Pseudomonas aeruginosa infected, 24h


title: M10KOepi_infect_1h_rep3


title: M10KOepi_infect_0h_rep1


title: M7KOepi_infect_1h_rep3


title: M10KOepi_infect_0h_rep2


title: M7KOepi_infect_0h_rep3

source_name: Mmp7-/- epithelium, uninfected, 0h


title: M7KOepi_infect_0h_rep2


title: M7KOepi_infect_0h_rep1


title: M7KOepi_infect_24h_rep2


title: M7KOepi_infect_1h_rep2


title: M10KOepi_infect_24h_rep3


title: Wtepi_infect_1h_rep3

source_name: WT epithelium, Pseudomonas aeruginosa infected, 1h


title: Wtepi_infect_0h_rep2

source_name: WT epithelium, uninfected, 0h


title: Wtepi_infect_1h_rep2


title: Wtepi_infect_0h_rep3


title: Wtepi_infect_1h_rep1


title: Wtepi_infect_0h_rep1


title: Wtepi_infect_24h_rep2


title: TSA Treated Rep 1

status: Public on Oct 06 2007

city: Rochester

first: Jennifer

middle: J

last: Westendorf

state: MN

address: 200 First Street SW

institute: Mayo Clinic

description: Comparison of control mice and mice treated with HDAC inhibitors.

hyb_protocol: Hybridization of the biotinylated-cRNA to the Affymetrix GeneChip Mouse Genome 430 2.0 Array was performed by the BioMedical Genomics Center’s microarray facility at the University of Minnesota using Affymetrix Genechip® Hybridization Oven 640 and Fluidics Station 450.

scan_protocol: Scanning was done with the Affymetrix Genechip® Scanner 3000.

data_processing: Raw data measurements were imported into Genedata Expressionist® Refiner (EPro1.0.32) for overall chip hybridization quality assessment, correction and condensation of probe sets intensity values. Robust Multichip Average (RMA) method was applied for global background subtraction and cross array normalization.  Processed expression data were imported into Genedata Expressionist Analyst.  General assessment of the data distribution was performed with Principle Component Analysis, boxplot and log-log data plots.  Following LOESS normalization, differential expression measures were calculated by Welch test comparisons of control DMSO (vehicle) versus each HDAC inhibitor.

source_name: TSA treated MC3T3 mice

label_protocol: Biotin-labeled cRNA was prepared from each culture according to the Affymetrix protocol.  Briefly, RNA was denatured at 70oC with T7-oligo (dT) primer and reverse transcribed using Superscript II at 42oC for 1 hour.  Second strand cDNA synthesis was performed by incubating first strand cDNA with Escherichia coli DNA polymerase I, E. coli. DNA ligase, RNase H, and dNTPs for 2 hours at 16oC.  Biotin-labeled cRNA was prepared from double-stranded cDNA using the Affymetrix GeneChip IVT Labeling kit (Affymetrix, Santa Clara, CA), then purified and fragmented using the Affymetrix Sample Cleanup Module.

growth_protocol: MC3T3-E1 preosteoblasts were plated at 4x104 cells per well of a 12-well plate and differentiated in Minimal Essential Medium (Invitrogen, Carlsbad, CA) containing 10% FBS (Invitrogen and Cambrex Bioscience/Lonza, Basel. Switzerland), 100 U/ml penicillin, 100 μg/ml streptomycin, 50 µg/ml ascorbic acid, 10 mM ß-glycerol phosphate and one of the following compounds: 20 nM TSA (Sigma, St. Louis, MO), 500 nM MS-275 (Calbiochem, San Diego, CA), 500 mM VPA (Sigma), or DMSO (vehicle) for 18 hours.

extract_protocol: Total RNA was isolated from MC3T3-E1 osteoblasts with Trizol reagent (Invitrogen).

treatment_protocol: MC3T3 cells were grown in 50 µg/ml ascorbic acid, 10 mM ß-glycerol phosphate and one of the following compounds: 20 nM TSA (Sigma, St. Louis, MO), 500 nM MS-275 (Calbiochem, San Diego, CA), 500 mM VPA (Sigma), or DMSO (vehicle) for 18 hours.

tag: MC3T3 cell line


title: CLL_del13q_rep10

city: Ann Arbor

first: Sami

middle: N

last: Malek

state: MI

address: 4410 Cancer Center; 1500 E Medical Center Dr

department: Internal Medicine, Hematology-Oncology

institute: University of Michigan

description: 50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)

hyb_protocol: Affymetrix Hybridization Oven 640 for 16 hrs at 480C with rotation at 60 rpm. Washing and staining was done on an Affymetrix Fluidics Station 450.

scan_protocol: Scanning was done using an Affymetrix Scanner 3000 7G with autoloader.

data_processing: Affymetrix GeneChip data were analyzed as follows. Raw probe-level  data were converted to expression measures using the Robust Multi-array  Average (RMA) method, which is implemented in the Affymetrix package of  Bioconductor. Briefly, the raw perfect match (PM) probes were quartile  normalized to remove any non biological variability (due to differential binding,  chip effects, etc). The normalized probe data were then converted to an  expression measure for each gene on each chip using a robust modeling  strategy.  For differential expression analysis relating to 13q14 deletion status, we  first removed the bottom 25% of probe sets in terms of overall variability. After  this filtering step, 41007 probe sets remained. Two-way analysis of variance  (ANOVA) was then used to identify differentially expressed genes while  accounting for the two-batch design of the study. Main effects for the presence  of 13q14 deletion and for batch were included in the model. Standardized  ANOVA coefficient estimates for the 13q14 deletion factor were then analyzed  using false discovery rates (FDR).

source_name: chronic lymphocytic leukemia (CLL) with del13q

label_protocol: See extract protocol.

growth_protocol: Not applicable.  Material used was cryopreserved primary human peripheral blood cells, prepared as below.

extract_protocol: CLL peripheral blood mononuclear cells were stained with propidium iodide and CD19*PE, then sorted  using a high-speed  FACS Aria (Becton Dickinson) sorter to purity. RNA was extracted using the Trizol*  reagent. RNA was further purified using the RNAeasy kit (Qiagen). 50ng total  RNA was amplified using the Ovation RNA Amplification system (NuGen, Inc.),  labeled with the FL-Ovation cDNA Biotin module (NuGen, Inc.) and hybridized to  the Human 133 2.0 plus GeneChip (Affymetrix) following the manufacturer's  recommended protocols.

treatment_protocol: Not applicable.

tag: male


title: CLL_del13q_rep9

label: FL-Ovation cDNA Biotin module (NuGen, Inc.)


title: CLL_FISHnormal_rep4

source_name: chronic lymphocytic leukemia (CLL) with no del13q


title: TSA Treated Rep 2


title: CLL_del13q_rep7


title: CLL_FISHnormal_rep8

tag: female


title: CLL_FISHnormal_rep9


title: MS-275 Treated Rep4

source_name: MS-275 treated MC3T3 mice


title: VPA Treated Rep 4

source_name: VPA treated MC3T3 mice


title: VPA Treated Rep 2


title: CLL_FISHnormal_rep7


title: CLL_FISHnormal_rep5


title: VPA Treated Rep 1


title: MS-275 Treated Rep2


title: MS-275 Treated Rep1


title: TSA Treated Rep 3


title: CLL_del13q_rep8


title: CLL_FISHnormal_rep10


title: VPA Treated Rep 3


title: CLL_FISHnormal_rep6


title: MS-275 Treated Rep3


title: CLL_FISHnormal_rep2


title: CLL_del13q_rep3


title: Mouse sexually intact, uninfected,  biological rep2

city: Chapel Hill

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

institute: UNC-Chapel Hill

description: Gene expression data from intact uninfected male A/JCr mouse liver

hyb_protocol: Following fragmentation, cRNA was hybridized on GeneChip Mouse Genome 430 2.0

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

data_processing: The data were analyzed with Robust multichip analysis in RMA express

source_name: Mouse intact uninfected

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

extract_protocol: Qiagen RNeasy kit

treatment_protocol: Male A/JCR mouse, sexually intact, no infection, necropsied at 21 months

tag: Mouse A/JCR 21 mo intact uninfected

tag: Mouse intact uninfected


title: CLL_del13q_rep1


title: Mouse castrated, H. hepaticus,  biological rep1

description: Gene expression data from castrated H. hepaticus infected male A/JCr mouse liver

source_name: Mouse castrated infected H hepaticus

treatment_protocol: Male A/JCR mouse, infected with Helicobacter hepaticus at 4 weeks, castrated at 12 months, necropsied at 21 months

tag: Mouse A/JCR 21 mo castrated infected H hepaticus

tag: Mouse castrated infected H hepaticus


title: Stroma normal breast (NS9)

status: Public on Oct 05 2007

first: Andrea

last: Richardson

address: 75 Francis Street

department: Pathology

institute: Brigham and Women's Hospital

description: expression of breast tissue

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16hr at 45c on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the affymetrix fludics station 400

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

data_processing: dCHIP with default settings

source_name: stroma

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

growth_protocol: RNA extraction, cRNA sythesis and Hyb performed according to J. Clin. Invest. 110(2002), pp. 633-641 and Cancer Res. 64(2004), pp. 64-71

tag: normal


title: DMSO Treated Control 4

source_name: DMSO treated MC3T3 mice


title: Mouse castrated, uninfected,  biological rep1

description: Gene expression data from castrated uninfected male A/JCr mouse liver

source_name: Mouse castrated uninfected

treatment_protocol: Male A/JCR mouse, castrated at 12 months, no infection, necropsied at 21 months

tag: Mouse A/JCR 21 mo castrated uninfected

tag: Mouse castrated uninfected


title: Mouse sexually intact, uninfected,  biological rep1


title: Stroma tumor (TS816)

description: expression of breast tissue

extract_protocol: RNA extraction, cRNA sythesis and Hyb performed according to J. Clin. Invest. 110(2002), pp. 633-641 and Cancer Res. 64(2004), pp. 64-71

tag: tumor


title: Stroma tumor (TS795)

description: expression of breast tissue

treatment_protocol: RNA extraction, cRNA sythesis and Hyb performed according to J. Clin. Invest. 110(2002), pp. 633-641 and Cancer Res. 64(2004), pp. 64-71


title: CLL_del13q_rep6


title: CLL_FISHnormal_rep3


title: Mouse castrated, uninfected,  biological rep2


title: CLL_del13q_rep4


title: Stroma tumor (TS817)

description: expression of breast tissue


title: Stroma tumor (TS820)

description: expression of breast tissue


title: Stroma normal breast (Nstr101904)

description: expression of breast tissue


title: DMSO Treated Control 2


title: Stroma normal breast (Nstr112204)

description: expression of breast tissue


title: Stroma tumor (TS838)

description: expression of breast tissue


title: Mouse castrated, H. hepaticus,  biological rep2


title: CLL_FISHnormal_rep1


title: CLL_del13q_rep5


title: Stroma tumor (TS818)

description: expression of breast tissue


title: Stroma tumor (TS718)

description: expression of breast tissue


title: CLL_del13q_rep2


title: Stroma normal breast (NS768)

description: expression of breast tissue


title: DMSO Treated Control 3


title: Stroma normal breast (NS2)

description: expression of breast tissue


title: MEF_CDKO_2

city: Cambridge

first: Noam

last: Shomron

address: 77 Massachusetts Ave 68-217

institute: Massachusetts Institute of Technology

description: MEF with a conditional Dicer knockout gene

hyb_protocol: According to the standard Affymetrix protocol

data_processing: The raw CEL files were analyzed using gcrma package in bioconductor (R statistical language) using default settings. The VALUES are log2 expression levels.

source_name: Mouse embryonic Fibroblast Conditional Dicer Knockout No treatment 2

growth_protocol: DMEM 10% FBS +L-Glutamine +D-Glucose in standard cell culture conditions

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

treatment_protocol: MEFs were either non treated or treated with 4-Orthohydroxy Tamoxifen (1 or 5 uM) for 4 days then RNA was extracted using Trizol Reagent

tag: Mouse embryonic Fibroblast derived from a conditional Dicer knockout mouse

tag: Embryos were at developmental stage E16


title: Stroma normal breast (NS3)

description: expression of breast tissue


title: MEF_CDKO_1

scan_protocol: According to the standard Affymetrix protocol

source_name: Mouse embryonic Fibroblast Conditional Dicer Knockout No treatment 1


title: Stroma normal breast (NS7)

description: expression of breast tissue


title: Stroma normal breast (NS5)

description: expression of breast tissue


title: MEF_WT_5OHT_1

label: According to the standard Affymetrix protocol

source_name: Mouse embryonic Fibroblast 5 uM Tamoxifen 1

tag: Mouse embryonic Fibroblast derived from wild-type mouse


title: MEF_CDKO_5OHT_2

source_name: Mouse embryonic Fibroblast Conditional Dicer Knockout 5 uM Tamoxifen 2

label_protocol: According to the standard Affymetrix protocol


title: Stroma normal breast (NS4)

description: expression of breast tissue


title: MEF_WT_5OHT_2

source_name: Mouse embryonic Fibroblast 5 uM Tamoxifen 2


title: Stroma normal breast (NS817)

description: expression of breast tissue


title: Stroma normal breast (NS6)

description: expression of breast tissue


title: Stroma normal breast (NS1)

description: expression of breast tissue


title: MEF_CDKO_1OHT_1

source_name: Mouse embryonic Fibroblast Conditional Dicer Knockout 1 uM Tamoxifen 1


title: bh20061128m430v2_A_04_preDP-PKBa-2420

status: Public on Oct 03 2007

city: Basel

first: Brian

middle: A

last: Hemmings

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

description: This sample is the pair of bh20061128m430v2_A_03_preDP-PKBa-2416

hyb_protocol: 10 ug of fragmented cRNA was hybridised to Affymetrix MOE430v2 GeneChips as per manufacturer's instructions.

scan_protocol: The chips were scanned in an Affymetrix 7G scanner using an automated slide carosel.

data_processing: Transcript expression values were estimated using the GC-RMA function provided by Refiner 3.1 (Genedata, Basel) and statistical analysis was performed using Analyst 3.1 (Genedata, Basel). Genedata’s implementation of GC-RMA includes the generation of an Affymetrix detection P-value. A gene was considered to be reliably detected if it had a detection P-value ≤ 0.04 (Affymetrix default, marginal calls ignored) in at least 2/3 of the biological replicates of a condition. A power analysis of our experimental design showed we could expect to have a power of 0.8 to distinguish samples differing by 1.5-fold with a normalized standard deviation less than 0.461 and it could resolve differences of 2-fold (power of 0.8) when the normalized standard deviation was less than 0.613.

source_name: FACS sorted ISP8 thymocytes, PKBalpha+/+

label_protocol: The Affymetrix 2-cycle labelling kit was used to amplify and label the material as per manufacturer's instructions.

growth_protocol: Mice were group-housed with 12 h dark/light cycles and free access to food and water, in accordance to the Swiss Animal Protection Ordinance.

extract_protocol: Total RNA was extracted using PicoPureTM RNA isolation kit (Arcturus, Sunnyvale, CA, USA) according to manufacturer's instructions. RNA quality was controlled using the 2100 Bioanalyser (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: The thymus was isolated and squeezed in PBS-2% FCS through a nylon membrane to extract the thymocytes. These cells were then FACS-sorted using FITC-CD3, PE-CD4, and Cy5-CD8 markers to separate the ISP8 thymocytes according to their surface antigens.

value: C57Bl/6 backcross

tag: Gender

value: Male

tag: Age

value: 2 weeks

tag: Tissue

value: ISP8 thymocytes

tag: Genotype

value: PKBalpha+/+


title: bh20061128m430v2_A_02_preDP-PKBa-2402

description: This sample is the pair of bh20061128m430v2_A_01_preDP-PKBa-2401

tag: Strain

value: 5 weeks


title: MEF_WT_2

source_name: Mouse embryonic Fibroblast No treatment 2


title: Stroma normal breast (NS8)

description: expression of breast tissue


title: MEF_CDKO_1OHT_2

source_name: Mouse embryonic Fibroblast Conditional Dicer Knockout 1 uM Tamoxifen 2


title: MEF_WT_1

source_name: Mouse embryonic Fibroblast No treatment 1


title: MEF_CDKO_5OHT_1

source_name: Mouse embryonic Fibroblast Conditional Dicer Knockout 5 uM Tamoxifen 1


title: Stroma normal breast (NS10)

description: expression of breast tissue


title: bh20061128m430v2_A_05_preDP-PKBa-2424

description: This sample is the pair of bh20061128m430v2_A_06_preDP-PKBa-2425

value: 3 weeks


title: bh20061128m430v2_A_01_preDP-PKBa-2401

description: This sample is the pair of bh20061128m430v2_A_02_preDP-PKBa-2402

source_name: FACS sorted ISP8 thymocytes, PKBalpha-/-

value: PKBalpha-/-


title: bh20061128m430v2_A_03_preDP-PKBa-2416

description: This sample is the pair of bh20061128m430v2_A_04_preDP-PKBa-2420


title: bh20061128m430v2_A_06_preDP-PKBa-2425

description: This sample is the pair of bh20061128m430v2_A_05_preDP-PKBa-2424


title: AV_HDM_2

status: Public on Oct 01 2007

city: Amsterdam

first: Aram

middle: Ben

last: Vroling

address: meibergdreef 9

department: ENT

country: Netherlands

institute: AMC

description: Gene expression data from cells after exposure to saline or HDM

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on Affymetrix GeneChip Human Genome U133A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with Rosetta Resolver Software using default analysis settings. Data was normailzed using the rosetta normalization algorithm.

source_name: epithelial cell line, house dust mite exposed 24h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were cultured in RPMI1640 containing 10% FCS and penicillin.

treatment_protocol: cells were preincubated with HBSS 24 hours prior to adding stimulus, cells were exposed to stimulus for 24 hours.

tag: mucoepidermoid pulmonary carcinoma cell line NCI-H296


title: bh20061128m430v2_A_10_pTN3-PKBa-2402

description: This sample is the pair of bh20061128m430v2_A_09_pTN3-PKBa-2401

source_name: FACS sorted DN3 thymocytes, PKBalpha+/+

treatment_protocol: The thymus was isolated and squeezed in PBS-2% FCS through a nylon membrane to extract the thymocytes. These cells were then FACS-sorted using FITC-CD25, PE-CD44, and Cy5-lineage markers to separate the DN3 thymocytes according to their surface antigens.

value: DN3 thymocytes


title: bh20061128m430v2_A_09_pTN3-PKBa-2401

description: This sample is the pair of bh20061128m430v2_A_10_pTN3-PKBa-2402

source_name: FACS sorted DN3 thymocytes, PKBalpha-/-


title: bh20061128m430v2_A_11_pTN3-PKBa-2416

description: This sample is the pair of bh20061128m430v2_A_12_pTN3-PKBa-2420


title: AV_HDM_3

tag: mucoepidermoid pulmonary carcinoma cell line NCI-H297


title: D39delta-cps_low, biological rep1

city: Nijmegen

first: Hester

last: Bootsma

address: Kapittelweg 29

department: Pediatrics

institute: Radboud University Medical Centre

description: Gene expression data from pharyngeal epithelial cells

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr on Affymetrix Human Genome U133 Plus 2.0 GeneChip s. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner.

data_processing: The data were analyzed with GeneSpring 7.3. Normalization was performed by the standard RMA-algorithm. Subsequent ratios were calculated between median folds per condition and the median fold for the appropriate control condition

source_name: Detroit 562 infec. w. low_dosage D39delta-cps

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

growth_protocol: Monolayers of Detroit 562 cells in tissue culture dishes (60 mm) were washed twice with PBS, after which bacteria were added at a multiplicity of infection of 20:1 (bacteria:cells). Uninfected control cells were incubated with RPMI 1640 medium with 1% FCS only (mock-infected).

extract_protocol: After washing, Detroit 562 cells were lysed directly in the tissue culture dish by addition of RLT buffer (Qiagen Benelux B.V.), collected with a rubber policeman, and transferred to a microcentrifuge tube. Subsequently, total RNA was isolated using the RNeasy mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: After a 2h incubation period, nonadherent bacteria were removed by three washes with PBS

tag: Pharyngeal epithelial cells


title: bh20061128m430v2_A_08_preDP-PKBa-2435

description: This sample is the pair of bh20061128m430v2_A_07_preDP-PKBa-2432


title: Type2cps, biological rep3

source_name: Detroit 562 infec. w. Type2 capsular polysaccharides


title: bh20061128m430v2_A_15_pTN3-PKBa-2432

description: This sample is the pair of bh20061128m430v2_A_16_pTN3-PKBa-2435


title: AV_blank_1

source_name: epithelial cell line, saline exposed 24h

tag: mucoepidermoid pulmonary carcinoma cell line NCI-H292


title: D39delta-cps_low, biological rep2


title: TIGR4delta-cps, biological rep3

source_name: Detroit 562 infec. w. TIGR4delta-cps


title: AV_blank_3

tag: mucoepidermoid pulmonary carcinoma cell line NCI-H294


title: D39delta-cps_low, biological rep3


title: AV_blank_2

tag: mucoepidermoid pulmonary carcinoma cell line NCI-H293


title: AV_HDM_1

tag: mucoepidermoid pulmonary carcinoma cell line NCI-H295


title: bh20061128m430v2_A_13_pTN3-PKBa-2424

description: This sample is the pair of bh20061128m430v2_A_14_pTN3-PKBa-2425


title: bh20061128m430v2_A_12_pTN3-PKBa-2420

description: This sample is the pair of bh20061128m430v2_A_11_pTN3-PKBa-2416


title: Control R3, biological rep1

source_name: Detroit 562 uninfected


title: Control R3, biological rep2


title: Control R3, biological rep3


title: Type2cps, biological rep2


title: bh20061128m430v2_A_16_pTN3-PKBa-2435

description: This sample is the pair of bh20061128m430v2_A_15_pTN3-PKBa-2432


title: Type2cps, biological rep1


title: bh20061128m430v2_A_07_preDP-PKBa-2432

description: This sample is the pair of bh20061128m430v2_A_08_preDP-PKBa-2435


title: TIGR4delta-cps, biological rep1


title: TIGR4delta-cps, biological rep2


title: Control R2, biological rep1


title: Control R2, biological rep2


title: Control R1, biological rep2


title: DMSO Treated Control 1

description: Comparison of control mice and mice treated with HDAC inhibitors.

source_name: DMSO treated MC3T3 mice

tag: MC3T3 cell line


title: Control R1, biological rep3


title: G54WT, biological rep1

source_name: Detroit 562 infec. w. G54WT


title: TIGR4WT, biological rep3

source_name: Detroit 562 infec. w. TIGR4WT


title: G54WT, biological rep2


title: G54delta-cps, biological rep3

source_name: Detroit 562 infec. w. G54delta-cps


title: Control R1, biological rep1


title: G54delta-cps, biological rep1


title: D39WT, biological rep3

source_name: Detroit 562 infec. w. D39WT


title: TIGR4WT, biological rep2


title: D39delta-cps, biological rep3

source_name: Detroit 562 infec. w. D39delta-cps


title: D39delta-cps, biological rep1


title: D39WT, biological rep2


title: D39delta-cps, biological rep2


title: G54delta-cps, biological rep2


title: bh20061128m430v2_A_14_pTN3-PKBa-2425

description: This sample is the pair of bh20061128m430v2_A_13_pTN3-PKBa-2424


title: JR-916 placenta, smoking, XY

city: Kuopio

first: Markus

last: Storvik

address: University of Eastern Finland

department: Pharmacology

country: Finland

institute: University of Eastern Finland

description: JR-916 placenta, smoking, XY

hyb_protocol: The biotinylated cRNA was hybridized to the GeneChip Human Genome U133 Plus 2.0 Arrays, which represents over 47,000 human transcripts. After hybridization GeneChips were washed and stained with streptavidin-phycoerythrin (Molecular Probes). Staining signal was amplified by biotinylated anti-streptavidin (Vector Laboratories) and second staining with streptavidin-phycoerythrin by using Affymetrix Fluidics station according the standard protocol.

scan_protocol: GeneChip Scanner 3000 with GeneChip Operating Software (GCOS) v. 1.2 (Affymetrix) was used in scanning.

data_processing: RMA-preprocessing was applied. Further normalized by dividing each measurement by the 50th percentile of all measurements in that sample.

source_name: Full-term placenta from smoker

label_protocol: The biotinylated cRNA probes were prepared and hybridized according to manufacturer’s instructions (Affymetrix, Santa Clara, CA) as previously described (Rysä et al., 2005). Briefly, cDNA was reverse-transcripted from 5 ug of total RNA with a T7-(dT)24-primer by means of the One-cycle cDNA synthesis kit (Affymetrix). The DNA was purified using GeneChip Sample Cleanup Module (Qiagen). The cRNA was prepared and biotin-labeled by in vitro transcription (Affymetrix) and fragmented before hybridization.

growth_protocol: Full-time pregnancy.

extract_protocol: Total RNA was extracted with guanidium thiocyanate followed by centrifugation in cesium chloride (Magga et al. 1997).

treatment_protocol: Placentas were collected immediately after delivery. Connective tissue and coagulated blood were removed and placental tissue was rinsed in cold 0.9 % NaCl solution. Small pieces around the placenta were cut and frozen in liquid nitrogen and stored at -80°C.

tag: Full term placenta. Smoking mother, boy-child.


title: D39WT, biological rep1


title: JR-31 placenta, non-smoking, XY

description: JR-31 placenta, non-smoking, XY

source_name: Full-term placenta  from non-smoker

tag: Full term placenta. Non-smoking mother, boy-child.


title: JR-915 placenta, non-smoking, XY

description: JR-915 placenta, non-smoking, XY


title: JR-12 placenta, smoking, XY

description: JR-12 placenta, smoking, XY


title: JR-917 placenta, non-smoking, XX

description: JR-917 placenta, non-smoking, XX

source_name: Full term placenta from non-smoker

tag: Full term placenta. Non-smoking mother, girl-child.


title: JR-27 placenta, non-smoking, XX

description: JR-27 placenta, non-smoking, XX


title: JR-13 placenta, smoking, XY

description: JR-13 placenta, smoking, XY


title: Melanoma cell line MM603

city: Herston

first: Leisl

last: Packer

state: QLD

address: 300 Herston Rd

department: Cancer and Cell Biology

description: For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.

source_name: Melanoma cell line MM603

growth_protocol: Melanoma cell lines were cultured in RPMI 1640 in the presence of 10% fetal bovine serum.

tag: Melanoma cell line established from metastatic melanoma


title: Melanoma cell line D28

data_processing: Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.

source_name: Melanoma cell line D28


title: Melanoma cell line MM96L

source_name: Melanoma cell line MM96L

tag: Melanoma cell line established from primary melanoma


title: JR-14 placenta, smoking, XY

description: JR-14 placenta, smoking, XY


title: G54WT, biological rep3


title: Melanoma cell line MM383

source_name: Melanoma cell line MM383


title: JR-918 placenta, smoking, XY

description: JR-918 placenta, smoking, XY


title: Melanoma cell line MM370

source_name: Melanoma cell line MM370

treatment_protocol: Melanoma cell lines were cultured in RPMI 1640 in the presence of 10% fetal bovine serum.

tag: Melanoma cell line MM370 established from a metastatic melanoma


title: Melanoma cell line D38

source_name: Melanoma cell line D38


title: Melanoma cell line D35

source_name: Melanoma cell line D35


title: melanoma cell line MM386

source_name: Melanoma cell line MM386


title: Melanoma cell line MM415

source_name: Melanoma cell line MM415

tag: Melanoma cell line MM415 established from metastatic melanoma


title: Melanoma cell line MM329

source_name: Melanoma cell line MM329


title: JR-26 placenta, non-smoking, XY

description: JR-26 placenta, non-smoking, XY

source_name: Full-term placenta from non-smoker


title: Melanoma cell line MM200

source_name: Melanoma cell line MM200

tag: Melanoma cell line established from primary nodular melanoma


title: Melanoma cell line D08

source_name: Melanoma cell line D08


title: melanoma cell line D11

source_name: melanoma cell line D11


title: Melanoma cell line MM649

source_name: Melanoma cell line MM649


title: Melanoma cell line D05

source_name: Melanoma cell line D05


title: melanoma cell line D17

source_name: Melanoma cell line D17


title: chl1 at T0, biological rep2

city: Taipei

first: Yi-Fang

last: Tsay

address: 128 Sec. 2, Academia Rd, Nankang

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

description: Gene expression data from chl1-5 plant before 25 mM nitrate induction, biological replicate 2.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix ATH1 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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 and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Arabidopsis thaliana

source_name: Arabidopsis chl1-5 root, no nitrate induction

growth_protocol: Approximately 100 sterilized seeds of Arabidopsis thaliana wild-type and chl1-5 plants (Columbia ecotype) were grown in different areas on the same mesh in a Magenta vessel (Sigma) in 60 mL of NO3--free liquid growth medium (10 mM K2HPO4/KH2PO4 pH 5.5, 2 mM MgSO4, 0.1 mM FeSO4-EDTA, 1 mM CaCl2, 50 μM H3BO3, 12 μM MnSO4•H2O, 1 μM ZnCl2, 1 μM CuSO4•5H2O, 0.2 μM Na2MoO4•2H2O, 1 g/L MES, 0.5% sucrose) containing 12.5 mM (NH4)2 succinate as the sole nitrogen source, pH 6.5.  For each biological replicate, 9 vessels ( ~ 900 seedlings / each replicate) of samples were pooled to use in a single independent experiment.  Plants were grown under continuous illumination at 24-26°C and rotated at 100 rpm.

extract_protocol: Total RNA was isolated using TRIzol Reagent (Invitrogen Life Technology, Grand Island, NY, U.S.A.) according to the manufacturer’s instructions, followed by chloroform extraction and isopropanol / EtOH precipitation.  The total RNA was further purified using an RNeasy Plant Mini Kit (Qiagen, Chatsworth, CA)

treatment_protocol: 10-day-old plants were shifted to 60 mL of the same 12.5 mM (NH4)2 succinate medium in which the pH had been changed to 5.5 by addition of HCl.  After 3 h treatment, the plants were washed twice with 10 mM K2HPO4/KH2PO4, pH 5.5, then 1) collected the root sample (T0), or 2) shifted for 0.5 hour (T0.5) to 60 mL of the same pH 5.5 growth medium, but with the 12.5 mM (NH4)2 succinate replaced by 25 mM KNO3, and the root sample was collected after 30 min induction.

tag: Columbia ecotype, root tissue of 10-day-old seedlings


title: chl1 at T0.5, biological rep3

description: Gene expression data from chl1-5 plant exposed to 25 mM nitrate for 30min, biological replicate 3.

source_name: Arabidopsis chl1-5 root, 25 mM nitrate induction for 30min


title: TIGR4WT, biological rep1

source_name: Detroit 562 infec. w. TIGR4WT


title: chl1 at T0, biological rep1

description: Gene expression data from chl1-5 plant before 25 mM nitrate induction, biological replicate 1.


title: chl1 at T0, biological rep3

description: Gene expression data from chl1-5 plant before 25 mM nitrate induction, biological replicate 3.


title: wild-type at T0.5, biological rep1

description: Gene expression data from wild-type plant exposed to 25 mM nitrate for 30min, biological replicate 1.

source_name: Arabidopsis wild-type root, 25 mM nitrate induction for 30min


title: chl1 at T0.5, biological rep2

description: Gene expression data from chl1-5 plant exposed to 25 mM nitrate for 30min, biological replicate 2.


title: wild-type at T0.5, biological rep3

description: Gene expression data from wild-type plant exposed to 25 mM nitrate for 30min, biological replicate 3.


title: wild-type at T0, biological rep1

description: Gene expression data from wild-type plant before 25 mM nitrate induction, biological replicate 1.

source_name: Arabidopsis wild-type root, no nitrate induction


title: wild-type at T0, biological rep3

description: Gene expression data from wild-type plant before 25 mM nitrate induction, biological replicate 3.


title: wild-type at T0.5, biological rep2

description: Gene expression data from wild-type plant exposed to 25 mM nitrate for 30min, biological replicate 2.


title: chl1 at T0.5, biological rep1

description: Gene expression data from chl1-5 plant exposed to 25 mM nitrate for 30min, biological replicate 1.


title: wild-type at T0, biological rep2

description: Gene expression data from wild-type plant before 25 mM nitrate induction, biological replicate 2.


title: Circulating CD4+ T cells stimulated with ConA AGM_stim_1_Affy

city: Paris cedex 15

first: Beatrice

last: JACQUELIN

address: 25 rue du Docteur Roux

department: Virologie

country: France

institute: Institut Pasteur

description: A pool of total RNA was prepared from enriched blood CD4+ T lymphocytes isolated from 5 AGM. The cells were previously activated with ConA for 48H. A unique sample was obtained and then divided to generate 4 aliquots used to hybridized 2 technical replicates for each of the ABI and Affymetrix platforms.

hyb_protocol: Fragmented cRNA was used for hybridization to Affymetrix Human Genome U133 Plus 2.0 Array according to the Affymetrix's instructions.

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

data_processing: The data were analyzed with Affymetrix GCOS and statistical (MAS5) algorithms.

organism: Chlorocebus sabaeus

source_name: circulating CD4+ T cells stimulated with ConA

label_protocol: Biotin labeled cRNA was generated and amplified from 4µg of total RNA using the Affymetrix One-Cycle cDNA Synthesis Kit according to the manufacturer’s protocol.

growth_protocol: For activation, 20 × 10^6 cells were plated in RPMI-1640 with 5% fetal calf serum (FCS) with ConA. The cells were harvested after 48H. The CD4+ cell subset was further isolated using the MACS magnetic labeling system (Miltenyi Biotec, Cologne, Germany) according to instructions of the manufacturer.

extract_protocol: Total RNA was extracted from 3 to 10 x 10^6 cells by using the RNeasy® Mini extraction Kit (Qiagen, Courtaboeuf, France) following the manufacturer's instructions.

treatment_protocol: PBMC were isolated by Ficoll-Hypaque (Pharmacia Biotech) density gradient centrifugation and activated with 10µg/ml of ConA.

tag: African Green Monkey cells (chlorocebus sabaeus from Senegal).

tag: Cells

value: CD4+ cells isolated from Peripheral Blood Mononuclear Cells (PBMC) consists of >95% of CD4+ T lymphocytes (CD3+ CD4+ cells).

tag: Stimulus

value: 48H with Concanavalin A (ConA)


title: Circulating CD4+ T cells stimulated with ConA AGM_stim_2_Affy


title: Melanoma cell line A2058

source_name: Melanoma cell line A2058

growth_protocol: Melanoma cell line was cultured in RPMI 1640 in the presence of 10% fetal bovine serum.


title: Uterus - 415961

status: Public on Sep 28 2007

first: Erin

last: Curley

address: 445 N. 5th Street

institute: IGC

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 46
Pathological T: 1b
Pathological N: 0
Pathological M: 0
Pathological Stage: 1B
Pathological Grade: 2
Primary Site: Endometrium
Histology: Endometrioid carcinoma

source_name: Uterus


title: Soft tissue of thigh - 417511

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: No
Pathological T: 1b
Pathological N: X
Pathological M: X
Pathological Stage: Unknown
Pathological Grade: 3
Primary Site: Soft tissue of thigh
Histology: Leiomyosarcoma

source_name: Soft tissue of thigh


title: Kidney - 415970

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 80-90
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: No
Clinical T: 1a
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 2
Clinical Multiple Tumors: Yes
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma

source_name: Kidney


title: Prostate - 416811

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
PSA: Elevated
Cancer discovered by digital exam?: No
Current status of disease: Under Therapy
Pathological T: 3a
Pathological N: 0
Pathological M: 0
Pathological Stage: 3
Pathological Grade: 3
Pathological Gleason Score: 7
Primary Site: Prostate
Histology: Adenocarcinoma, NOS

source_name: Prostate


title: Rectum - 416801

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 41-45
Type of Tobacco Use: Chewing Tobacco
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 11
Presenting Symptoms: Bright red stools
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 1
Pathological M: 0
Pathological Stage: 3B
Pathological Grade: 2
Pathological Dukes Stage: C
Primary Site: Rectum
Histology: Adenocarcinoma

source_name: Rectum


title: Kidney - 415976

description:
Quality metric = 28S to 18S: 2.0
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 32
Clinical T: 1a
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 2
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Uterus - 416804

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 76
Pathological T: 1b
Pathological N: 0
Pathological M: 0
Pathological Stage: 1B
Pathological Grade: 3
Primary Site: Endometrium
Histology: Serous adenocarcinoma (papillary serous)


title: Uterus - 415963

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 40-50
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 21
Pathological T: 1a
Pathological N: 0
Pathological M: 0
Pathological Stage: 1A
Pathological Grade: 2
Primary Site: Endometrium
Histology: Endometrioid carcinoma


title: Breast - 421723

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 20
Mammogram: Yes
Number of years in which a mammogram was obtained?: 41-45
Oral contraceptives?: No
Oophorectomy?: Yes
Fibrocystic disease?: No
Mammogram calcifications?: No
Hormonal therapy (# of Years)?: 26-30
Pathological T: 2
Pathological N: 0(i+)
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Primary Site: Breast
Histology: Lobular Carcinoma

source_name: Breast


title: Colon - 416802

description:
Quality metric = 28S to 18S: 2.0
Patient Age: 90-100
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 41-45
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Presenting Symptoms: Black tarry stools
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological Dukes Stage: B
Primary Site: Colon
Histology: Adenocarcinoma

source_name: Colon


title: Thyroid - 415971

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 46-50
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 30
Pathological T: 1
Pathological N: 0
Pathological M: 0
Pathological Stage: 1
Primary Site: Thyroid
Histology: Papillary carcinoma

source_name: Thyroid


title: Kidney - 409601

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 41-45
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 22
Clinical T: 1a
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 2
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Ovary - 415960

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 40-50
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Pathological T: 1a
Pathological N: 0
Pathological M: 0
Pathological Stage: 1A
Pathological Grade: 1
Primary Site: Ovary
Histology: Endometrioid Carcinoma

source_name: Ovary


title: Esophagus - 407830

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 19
Have you ever had esophagitis/reflux?: Yes
Pathological Question: T
Pathological Value: 2
Pathological Question: N
Pathological Value: 1
Pathological Question: M
Pathological Value: 0
Pathological Question: Stage
Pathological Value: 2B
Pathological Question: Grade
Pathological Value: 4
Primary Site: Esophagus
Pathological Question: Histology
Pathological Value: Signet ring cell adenocarcinoma

source_name: Esophagus


title: Colon - 409599

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 70-80
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 61-65
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Presenting Symptoms: Bright red stools
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 1
Pathological M: 0
Pathological Stage: 3B
Pathological Grade: 2
Primary Site: Colon
Histology: Adenocarcinoma


title: MCF7_RNA_rep1

status: Public on Sep 29 2007

first: Ming-Ta

last: Hsu

address: 155, Li-Nong St., Sec.2, Peitou, Taipei, Taiwan, R.O.C.

institute: National Yang-Ming University

description:
Array Image: Without seriously artifacts
Background: 20-100
Noise: <10
Hybridization controls: BioB: 50%A; 50%P
                               bioC, bioD, and cre: P
internal control genes: Either 3'/5' probe set of GAPDH or 3'/5' probe set of actin <3

hyb_protocol: Affymetrix microarray was performed using Human U133 2.0 (Affymetrix). Details of the methods for RNA quality, sample labeling, hybridization and expression analysis are according to the manual of Affymetrix Microarray Kit and Affymetrix website.

data_processing: Using scaling factor. The default settings are "scaling all probe sets to target signal: 500" and "normalization by user defined in value: 1

source_name: MCF7 cell line

extract_protocol: Cells were grown to 85 % confluence in 10 cm tissue culture dish. Each 10 cm dish was washed with 1x PBS for three times. Total RNA was extracted according to the RNeasy® Mini Kit Spin Protocol (QIAGEN). The integrity of the RNA extract was checked by 1.2 % (w/v) agarose gel electrophoresis and the concentration of RNA was estimated by ultraviolet spectrophotometry.

tag: Cell line

tag: Gender

tag: Age

tag: Tissue

value: Breast tumor


title: Prostate - 409628

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 40-50
Gender: Male
Ethnic Background: African-American
Tobacco Use : Yes
Years of Tobacco Use: 6-10
Type of Tobacco Use: Cigars
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 28
Presenting Symptoms: Nocturia
PSA: Elevated
# of years PSA Tested?: 0-5
Cancer discovered by digital exam?: No
Current status of disease: Under Therapy
Pathological T: 3b
Pathological N: 0
Pathological M: 0
Pathological Stage: 3
Pathological Grade: 3
Pathological Gleason Score: 7
Primary Site: Prostate
Histology: Adenocarcinoma, Acinar Type


title: Ovary - 409605

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 7
Presenting Symptoms: Abdominal pain
Presenting Symptoms: Bloating
Pathological T: 3c
Pathological N: 1
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: X
Primary Site: Ovary
Histology: Papillary Serous Adenocarcinoma


title: Breast - 409606

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Mammogram: Yes
Number of years in which a mammogram was obtained?: 11-15
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 0-5
Oophorectomy?: Yes
Pathological T: 1c
Pathological N: 1a
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological ER: Positive
Pathological PR: Positive
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Ductal Carcinoma


title: Prostate - 409625

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 40-50
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 30
PSA: Elevated
Current status of disease: Under Therapy
Pathological T: 3a
Pathological N: 0
Pathological M: 0
Pathological Stage: 3
Pathological Grade: 3
Pathological Gleason Score: 7
Primary Site: Prostate
Histology: Adenocarcinoma, NOS


title: Ovary - 405000

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 40-50
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 20
Presenting Symptoms: Abdominal pain
Presenting Symptoms: Vaginal bleeding
Pathological T: 1a
Pathological N: 1
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 2
Primary Site: Ovary
Histology: Mixed epithelial tumor


title: Kidney - 405002

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 70-80
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 42
Clinical T: 1a
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 3
Primary Site: Kidney
Histology: Chromophobe renal carcinoma


title: Kidney - 405001

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 11-15
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 72
Clinical T: 2
Clinical N: 0
Clinical M: 0
Clinical Stage: 2
Clinical Grade: 3
Primary Site: Kidney
Histology: Chromophobe renal carcinoma


title: Thyroid - 409602

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 30
Pathological T: 1
Pathological N: 0
Pathological M: X
Pathological Stage: Unknown
Pathological Multiple Tumours: Yes
Primary Site: Thyroid
Histology: Papillary carcinoma, follicular variant


title: Ovary - 409630

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 30-40
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 6-10
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Pathological T: 3c
Pathological N: 0
Pathological M: 0
Pathological Stage: 3C
Primary Site: Ovary
Histology: Papillary serous tumor of low malignant potential


title: Kidney - 405004

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 21-25
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 21
Clinical T: 3a
Clinical N: 0
Clinical M: 0
Clinical Stage: 3
Clinical Grade: 2
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Thyroid - 405003

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 21
Pathological T: 4a
Pathological N: 0
Pathological M: 0
Pathological Stage: 4A
Primary Site: Thyroid
Histology: Carcinoma, undifferentiated


title: Colon - 404999

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 11-15
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 20
Presenting Symptoms: Abdominal Pain
Diagnosis made by: Colonoscopy
Pathological T: 4
Pathological N: 1
Pathological M: 1
Pathological Metastatic Sites: Other
Pathological Stage: 4
Pathological Grade: 3
Primary Site: Colon
Histology: Mucinous Carcinoma


title: Ovary - 409603

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Pathological T: 3c
Pathological N: 1
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 3
Primary Site: Ovary
Histology: Serous Adenocarinoma


title: Kidney - 404998

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 0-5
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 90
Clinical T: 1a
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 1
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Uterus - 409608

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 46-50
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 21
Pathological T: 1b
Pathological N: 0
Pathological M: 0
Pathological Stage: 1B
Pathological Grade: 2
Primary Site: Endometrium
Histology: Endometrioid carcinoma


title: Colon - 404996

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 80-90
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 6-10
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 3
Presenting Symptoms: Bright red stools
Screening studies performed?: No
Pathological T: 3
Pathological N: 1
Pathological M: 0
Pathological Stage: 3B
Pathological Grade: 2
Pathological Dukes Stage: C
Primary Site: Colon
Histology: Adenocarcinoma


title: Kidney - 403740

description:
Quality metric = 28S to 18S: 1.9
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 6-10
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 30
Clinical T: 2
Clinical N: 0
Clinical M: X
Clinical Stage: Unknown
Clinical Grade: 2
Primary Site: Kidney
Histology: Chromophobe renal carcinoma


title: Kidney - 404997

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 46-50
Type of Tobacco Use: Cigars
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 14
Clinical T: 1a
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 2
Primary Site: Kidney
Histology: Chromophobe renal carcinoma


title: Colon - 404991

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 56-60
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 7
Presenting Symptoms: Abdominal Pain
Screening studies performed?: No
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological Multiple Tumors: Yes
Pathological Dukes Stage: B
Primary Site: Colon
Histology: Mucinous Carcinoma


title: Lung - 403732

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 70-80
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 56-60
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 22
Presenting Symptoms: SOB
Presenting Symptoms: Weight Loss
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2B
Pathological Grade: 3
Primary Site: Lung
Histology: Squamous cell carcinoma

source_name: Lung


title: Colon - 404990

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 0-5
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Days from Patient Diagnosis to Excision: 30
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 1
Pathological M: 0
Pathological Stage: 3B
Pathological Grade: 3
Pathological Dukes Stage: C
Primary Site: Colon
Histology: Signet Ring Cell Carcinoma


title: Colon - 404994

description:
Quality metric = 28S to 18S: 1.9
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 11-15
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 15
Presenting Symptoms: Abdominal Pain
Screening studies performed?: No
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 2
Pathological M: 1
Pathological Metastatic Sites: Hepatic
Pathological Stage: 4
Pathological Grade: 2
Primary Site: Colon
Histology: Adenocarcinoma


title: Colon - 404993

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 16-20
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 17
Presenting Symptoms: Bright red stools
Presenting Symptoms: Constipation
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 1
Pathological M: 0
Pathological Stage: 3B
Pathological Grade: 2
Pathological Dukes Stage: C
Primary Site: Colon
Histology: Adenocarcinoma


title: Ovary - 404995

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 40-50
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 14
Presenting Symptoms: Abdominal mass
Presenting Symptoms: Abdominal pain
Pathological T: 2b
Pathological N: 0
Pathological M: 0
Pathological Stage: 2B
Pathological Grade: 2
Primary Site: Ovary
Histology: Endometrioid adenocarcinoma