title: Hirsute patients versus healthy women

city: Rome

first: Daniela

last: Minella

state: Italy

address: Via Montpellier 1

department: Dept. of Biopathology

institute: Tor Vergata University

hyb_protocol: The reactions were purified with a Purification Module (Invitrogen Corporation) to remove the unincorporated/quenched dyes. After the purification, samples were combined for hybridization. The labelled cDNAs were co-hybridized to microarrays in duplicate, with one dye swap.Slides placed in water bath for 16 h at 42 °C. Arrays then washed in 2x SSC (+0.1 % SDS), 1x SSC, 0.2x SSC and 0.1x SSC, drying and scanning.

scan_protocol: The slides were scanned on the GenePix 4000 B Microarray Scanner (Axon Instruments, Sunnyvale, USA) at the optimal wavelength for the Alexa555 (F532) and Alexa647 (F635) (Invitrogen Corporation) using lasers.

data_processing: The acquired images were analyzed with Genepix Pro 5.0 software (Axon instruments, Union City). Oligonucleotide spots were automatically segmented, total intensities (F635 and F532) and local backgrounds (B635 and B532) were calculated for each spot. The spots were flagged when they exhibited poor hybridization signals or when they were saturated (F635 or F532 median = 65,535). We removed systematic bias in the data by applying the dye-swap normalization [15] that makes use of the reverse labelling in the two microarray replicates. This normalization procedure is well suited to treat low density microarray data, where the majority of the spotted genes are expected to change their expression level. We did not subtract the local spot background signal from the foreground signal, since the correlation between M vs Mb was very low (below 0.3), as recently suggested by Scharpf et al. [16]. Genes with signal to background ratio below two were filtered, together with genes strongly disagreeing by fold change: if two out of three replicates were over expressed, while the third had a fold change below the cut off-2, the gene was filtered; and similarly for under expressed genes. To establish the significance of observed regulation for each gene, we used t-test with Welsh’s correction, and then controlled for the multiplicity of testing. Finally, only genes with a satisfactory effect (absolute value of the fold change at least 1.5) were considered.

label: AlexaFluor 555; AlexaFluor 647

source_name: Fibroblast of hirsute patients

label_protocol: Synthesis of the labelled first strand cDNA was conducted using the Superscript Indirect cDNA labelling system (Invitrogen Corporation) with starting material of 10 μg of total RNA. The amino-allyl labelled dNTP mix was added to the reaction to generate amino-allyl labelled second strand cDNA. Following the hydrolysis reaction, single-stranded cDNA probes were purified using a Purification Module (Invitrogen Corporation). Probe mixtures where then evaporated in a vacuum centrifuge, and the cDNA pellet resuspended in 3 μl of water. The dye coupling reactions were performed by mixing the cDNA samples with AlexaFluor Dyes 555 or 647 and were incubated for overnight in the dark. The reactions were purified with a Purification Module (Invitrogen Corporation) to remove the unincorporated/quenched dyes.

growth_protocol: Human fibroblasts were isolated from skin biopsies of pelvic region obtained from 8 patients and from 4 control subjects. All biopsies were obtained under institutionally approved protocols (Tor Vergata University, Rome, Italy; FatebeneFratelli Hospital, Rome, Italy). Fibroblast cultures were established by mechanical and enzymatic methods and cultured in Dulbecco’s modified Eagle’s-F12 medium (EuroClone) supplemented with 10% fetal bovine serum (EuroClone), 1% L-glutamine and 1% antibiotics. Cells were harvested at passage 4 and RNA was prepared.

extract_protocol: Total RNA was isolated from primary cells coltures of fibroblasts, obtained from genital skin bioopsies of 8 hirsute patients and 4 controls (no hirsute women), by TRIZOL standard protocol (Invitrogen Corporation, Carlsbad, USA). Small aliquot of RNA was then used for quantification and quality control using respectively a spectrophotometer (Nanodrop, Wilmingon, USA) and an agarose gel electrophoresis.

treatment_protocol: no treatment

tag: phenotype

value: hirsute

tag: gender

value: female

value: fibroblast

source_name: fibroblast of healty women (controls; no hirsute women)

value: non-hirsute


title: Donor 7 Control

status: Public on Apr 15 2010

type: RNA

city: San Francisco

first: Jun

middle: S

last: Song

state: CA

address: 513 Parnassus Avenue, Box 0794

department: Institute for Human Genetics

country: USA

institute: UCSF

description: Donor 7 Control

data_processing: Each sample had eight RNU44 and eight RNU48 technical replicate measurements for quality control and reference normalization.  For each sample, we removed any RNU48 outliers by using the Weisberg t-test at a p-value cutoff of 0.05, a method for detecting outliers in small data sets; microRNA CT values were then normalized by subtracting the mean RNU48 CT value of the resulting trimmed set. Some miRNA expression values could not be determined by PCR, and we considered only the miRNAs whose expression could be assayed in at least 3 out of 7 paired samples.  Fold-changes in miRNA expression levels after forskolin treatment in the seven samples were pooled together and ranked.  Highly ranked miRNAs were then found; more precisely, p-values for the rank distribution of  miRNA differential expression were computed using the hypergeometric test, as in the Redundant siRNA Activity (RSA) analysis.  For each miRNA, we also performed a robust paired t-test on a trimmed set obtained by removing at most one outlier sample found by the Weisberg t-test at the 5% significance level. We obtained a final list of miRNAs differentially expressed at the 5% significance level of both hypergeometric test and t-test.

label: FAM

molecule: total RNA

organism: Homo sapiens

source_name: primary melanocyte

label_protocol: Standard Applied Biosystem's Taqman Protocol

growth_protocol: Primary human melanocytes were isolated from neonatal foreskin as described (McGill et al., 2002). Primary melanocytes between passages 2 and 5 were stimulated with 20 uM forskolin (Sigma Aldrich) or with DMSO (as a vehicle control), for indicated times after an overnight starvation in F10 media supplemented with penicillin/streptomycin/glutamine (PSQ).  Serum starvation conditions did not affect cell viability.

extract_protocol: Total RNA was purified using Trizol reagent (Invitrogen) according to the manufacturer’s instructions, followed by treatment with RNase-free DNase (Qiagen). Dried RNA pellets were resuspended in DEPC/ddH2O. RNA was quantified by measuring OD260/280.

treatment_protocol: Primary human melanocytes were serum depleted for 12 hours, followed by treatment with 20uM forskolin (or DMSO control) for 16 hours.

tag: cell type

value: primary melanocyte


title: exp 2, control, rep 2

city: Boston

first: Adán

last: Colón-Carmona

state: MA

address: 100 Morrissey Blvd

department: Biology

institute: University of Massachusetts Boston

description:
Global gene expression.
21d whole plants, >=20 individuals pooled, long-day light, 23C.
batch_2_control_2

hyb_protocol: Chips were hybridized and processed on a Affymetrix Fluidics Station Model 450 per the manufacturer's instructions.

scan_protocol: Hybridized chips were read on a model M10 scanner.

data_processing:
.CEL files were produced by the Affymetrix MAS, and normalization was performed in R/Bioconductor using the just.gcrma function with default parameters.

Values are unmodified outputs from Bioconductor/just.gcrma and represent the log2 transformation of the signal level.

label: biotin

organism: Arabidopsis thaliana

source_name: whole plants, 0 mM phenanthrene

label_protocol: Labeling was performed with the Affymetrix Enzo kit per the manufacturer's instructions.

growth_protocol: 21d whole plants grown from sterilized seeds on 0.5MS + phytoagar, long-day light, 23C +/- 1C.

extract_protocol: RNA was isolated using TRIzol (Molecular Research Center) per the manufacturer's instructions, DNAse treated (Invitrogen), and purified with RNeasy Mini Cleanup (Qiagen) per the manufacturers' instructions.

treatment_protocol: Phenanthrene was thoroughly mixed into sterile media prior to pouring plates.

tag: ecotype

value: Columbia

tag: tissue

value: whole plants

tag: age

value: 21 days

tag: treatment


title: exp 1, treated, rep 1

description:
Global gene expression.
21d whole plants, >=20 individuals pooled, long-day light, 23C.
batch_1_treated_1

source_name: whole plants, 0.25 mM phenanthrene

value: phenanthrene


title: exp 1, control, rep 1

description:
Global gene expression.
21d whole plants, >=20 individuals pooled, long-day light, 23C.
batch_1_control_1


title: 292FW26

city: Bethesda

first: Jennifer

last: Barb

state: MD

address: 12 South Drive Bldg 12A Room 2001

department: DCB

institute: NIH

hyb_protocol: Biotin-labeled cRNA was then fragmented at 94oC for 35 min with 5X fragmentation buffer  (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) and then hybridized (10 ug) to Affymetrix (Santa Clara, CA) mouse 430_2 oligonucleotide probe arrays for 16 h at 45oC

scan_protocol: Hybridization fluid was removed and the arrays were washed and stained with streptavidin-phycoerythrin (SAPE), and the signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400.  Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix).

data_processing: Affymetrix Microarray Suite version 5.0

source_name: ARPE-19 cell line

label_protocol: Ten micrograms of total RNA was reverse transcribed with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using T7-(dT) 24  primer (Geneset Oligos, La Jolla, CA, USA) containing T7 RNA polymerase promoter. After synthesis of the second cDNA strand, this product was used in an in vitro transcription reaction to generate biotinylated cRNA using a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). The biotinylated cRNA was cleaned with the RNAeasy Mini Kit (Qiagen, Valencia, CA).

growth_protocol: Fetal RPE were cultured on Primaria® flasks for 6 weeks using MEM-α modified medium with additional supplements. Passages 1-2 were used for all studies. The confluent monolayers used in these experiments have the morphology, pigmentation, polarity, and physiology of native RPE.ARPE-19 spontaneously transformed cell line was cultured using MEM-α modified medium with additional supplements on flasks and inserts to match fetal RPE culturing conditions.

extract_protocol: Fetal and adult RPE cells were collected, homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and RNA was subsequently purified using an RNeasy Mini kit (Qiagen Inc, Valencia, CA).  Double-stranded cDNA was synthesized from 6µg of total RNA using the SuperScript Choice system (Invitrogen, Carlsbad, CA) and the T7-Oligo (dT) promoter primer kit (Affymetrix, Santa Clara, CA).  cDNA was purified using Phase Lock Gels (Eppendorf, Westbury, NY).  Concentration and quality of RNA samples was determined on the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA). The integrity of RNA is assessed by looking at 18 & 28s rRNA peaks and though the RIN (RNA integrity number). RNA concentrations were measured using the Nano drop spectrophotometer (Wilmington, DE) and all samples used for the study had 260/280 ratios above 2.0 and 260/230 ratios above 1.7.

tag: cell line


title: Donor 1 Forskolin Treated

description: Donor 1 Forskolin Treated


title: Donor 2 Forskolin Treated

description: Donor 2 Forskolin Treated


title: Plausible Breast metastasis in the ovary_OC01_ARN0209 [HG-U133_Plus_2]

status: Public on Apr 14 2010

city: PARIS

first: Jean-Philippe

last: MEYNIEL

address: 26, rue d'Ulm

department: Translational Research Dept

country: France

institute: Institut Curie

description: Gene expression data from breast metastasis in the ovary

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133 plus 2,0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 7G Scanner GCS3000

data_processing: The data were processed/analyzed with gc-RMA (Partek Genomic Suite 6.09.1008).

label: Biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)_mRNA.

extract_protocol: Total RNA purification was conducted using miRNeasy kit

value: Ovary

tag: histology (disease state)

tag: identifier

tag: histotype

tag: tumor/metastasis

value: M

tag: grade

tag: stade


title: Plausible Ovarian carcinoma_OC01_ARN0206 [HG-U133_Plus_2]

description: Gene expression data from ovarian carcinoma

source_name: Plausible Ovarian carcinoma

value: Plausible Ovarian carcinoma

value: Serous

value: T

value: Ic


title: Ovarian carcinoma_OC01_ARN0161 [HG-U133_Plus_2]

source_name: Ovarian carcinoma

value: Ovarian carcinoma

value: IV


title: Breast metastasis in the ovary_OC01_ARN0201 [HG-U133_Plus_2]

source_name: Breast metastasis in the ovary

value: Breast metastasis in the ovary


title: Plausible Breast metastasis in the ovary_OC01_ARN0208 [HG-U133_Plus_2]


title: Breast metastasis in the ovary_OC01_ARN0162 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0204 [HG-U133_Plus_2]

value: IIa


title: Plausible Breast metastasis in the ovary_OC01_ARN0205 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0159 [HG-U133_Plus_2]

value: Endometrioid

value: Ia


title: Ovarian carcinoma_OC01_ARN0210 [HG-U133_Plus_2]

value: Adenocarcinoma

value: IIIc


title: HOAB_146

city: Stanford

first: Rajnish

last: Gupta

address: CCSR Room 2155

institute: Stanford University

description:
Simple annotation: Absolute transcript levels, 3'endseq
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79444.gif

hyb_protocol: not provided

scan_protocol: GenePix 4000B

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: HOTAIR-shGFP infected MDA-MB-231 cells

label_protocol: not provided

extract_protocol: not provided

value: MDA-MB-231 breast cancer cells

tag: infection

value: HOTAIR-shGFP

source_name: HOTAIR-hEZH2 infected MDA-MB-231 cells


title: HOAB_120

description:
Simple annotation: Absolute transcript levels, 3'endseq
Image: http://smd.stanford.edu/MicroArray/gifs/2008-03/78872.gif

source_name: VECTOR infected MDA-MB-231 cells

value: VECTOR

source_name: HOTAIR infected MDA-MB-231 cells

value: HOTAIR


title: Ovarian carcinoma_OC01_ARN0158 [HG-U133_Plus_2]

value: Ovary


title: HOAB_142

description:
Simple annotation: Absolute transcript levels, 3'endseq
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79440.gif

source_name: HOTAIR-shSUZ12 infected MDA-MB-231 cells


title: Plausible Breast metastasis in the ovary_OC01_ARN0160 [HG-U133_Plus_2]

value: M


title: Ovarian carcinoma_OC01_ARN0157 [HG-U133_Plus_2]

value: Serous


title: Ovarian carcinoma_OC01_ARN0156 [HG-U133_Plus_2]

value: T


title: Breast metastasis in the ovary_OC01_ARN0143 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0138 [HG-U133_Plus_2]

value: IIc


title: Breast metastasis in the ovary_OC01_ARN0142 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0147 [HG-U133_Plus_2]

value: Ovarian carcinoma


title: Breast metastasis in the ovary_OC01_ARN0146 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0135 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0149 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0137 [HG-U133_Plus_2]

value: Mucinous


title: Ovarian carcinoma_OC01_ARN0154 [HG-U133_Plus_2]

value: IV


title: Breast metastasis in the ovary_OC01_ARN0126 [HG-U133_Plus_2]

value: Breast metastasis in the ovary


title: Ovarian carcinoma_OC01_ARN0134 [HG-U133_Plus_2]

value: Clear Cells


title: Ovarian carcinoma_OC01_ARN0130 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0132 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0151 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0128 [HG-U133_Plus_2]

value: Ic


title: Ovarian carcinoma_OC01_ARN0125 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0152 [HG-U133_Plus_2]


title: Breast metastasis in the ovary_OC01_ARN0153 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0148 [HG-U133_Plus_2]

value: Carcinosarcome


title: Ovarian carcinoma_OC01_ARN0155 [HG-U133_Plus_2]

value: IIIc


title: Breast metastasis in the ovary_OC01_ARN0141 [HG-U133_Plus_2]


title: Breast metastasis in the ovary_OC01_ARN0145 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0124 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0127 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0129 [HG-U133_Plus_2]

value: Endometrioid


title: Ovarian carcinoma_OC01_ARN0136 [HG-U133_Plus_2]

value: IIIa


title: Ovarian carcinoma_OC01_ARN0133 [HG-U133_Plus_2]


title: Breast metastasis in the ovary_OC01_ARN0123 [HG-U133_Plus_2]


title: Breast metastasis in the ovary_OC01_ARN0121 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0119 [HG-U133_Plus_2]


title: Breast metastasis in the ovary_OC01_ARN0112 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0115 [HG-U133_Plus_2]

value: Ia


title: Ovarian carcinoma_OC01_ARN0118 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0114 [HG-U133_Plus_2]

value: Carcinosarcoma


title: Breast metastasis in the ovary_OC01_ARN0120 [HG-U133_Plus_2]

value: Ovary


title: Ovarian carcinoma_OC01_ARN0108 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0113 [HG-U133_Plus_2]

value: IIa


title: Ovarian carcinoma_OC01_ARN0106 [HG-U133_Plus_2]

value: Serous


title: Ovarian carcinoma_OC01_ARN0116 [HG-U133_Plus_2]

value: T


title: Ovarian carcinoma_OC01_ARN0109 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0107 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0105 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0111 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0096 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0103 [HG-U133_Plus_2]


title: Breast metastasis in the ovary_OC01_ARN0092 [HG-U133_Plus_2]

value: M


title: Breast metastasis in the ovary_OC01_ARN0099 [HG-U133_Plus_2]


title: Breast metastasis in the ovary_OC01_ARN0102 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0089 [HG-U133_Plus_2]

value: Ovarian carcinoma


title: Ovarian carcinoma_OC01_ARN0095 [HG-U133_Plus_2]

value: IIIb


title: Breast metastasis in the ovary_OC01_ARN0098 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0101 [HG-U133_Plus_2]

value: IV


title: Breast metastasis in the ovary_OC01_ARN0097 [HG-U133_Plus_2]

value: Breast metastasis in the ovary


title: Ovarian carcinoma_OC01_ARN0093 [HG-U133_Plus_2]


title: Breast metastasis in the ovary_OC01_ARN0104 [HG-U133_Plus_2]


title: Plausible Breast metastasis in the ovary_OC01_ARN0090 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0100 [HG-U133_Plus_2]

value: IIb


title: Ovarian carcinoma_OC01_ARN0080 [HG-U133_Plus_2]


title: Breast metastasis in the ovary_OC01_ARN0081 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0076 [HG-U133_Plus_2]

value: Brenner Tumor


title: Ovarian carcinoma_OC01_ARN0091 [HG-U133_Plus_2]

value: Adenocarcinoma


title: Ovarian carcinoma_OC01_ARN0085 [HG-U133_Plus_2]

value: Clear Cells


title: Ovarian carcinoma_OC01_ARN0084 [HG-U133_Plus_2]

value: IIIc


title: Breast metastasis in the ovary_OC01_ARN0083 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0075 [HG-U133_Plus_2]


title: Plausible Ovarian carcinoma_OC01_ARN0078 [HG-U133_Plus_2]

value: Plausible Ovarian carcinoma


title: Breast metastasis in the ovary_OC01_ARN0079 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0070 [HG-U133_Plus_2]


title: Plausible Ovarian carcinoma_OC01_ARN0074 [HG-U133_Plus_2]

value: Ib


title: Breast metastasis in the ovary_OC01_ARN0077 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0072 [HG-U133_Plus_2]


title: Plausible Breast metastasis in the ovary_OC01_ARN0088 [HG-U133_Plus_2]


title: Breast metastasis in the ovary_OC01_ARN0073 [HG-U133_Plus_2]


title: Breast metastasis in the ovary_OC01_ARN0069 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0067 [HG-U133_Plus_2]

value: Mucinous

value: Ic


title: Breast metastasis in the ovary_OC01_ARN0053 [HG-U133_Plus_2]

value: Ovary


title: Ovarian carcinoma_OC01_ARN0061 [HG-U133_Plus_2]

value: Serous


title: Ovarian carcinoma_OC01_ARN0062 [HG-U133_Plus_2]

value: T


title: Ovarian carcinoma_OC01_ARN0064 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0057 [HG-U133_Plus_2]


title: Breast metastasis in the ovary_OC01_ARN0046 [HG-U133_Plus_2]

value: M


title: Ovarian carcinoma_OC01_ARN0049 [HG-U133_Plus_2]

value: Ovarian carcinoma


title: Plausible Ovarian carcinoma_OC01_ARN0040 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0037 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0045 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0038 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0058 [HG-U133_Plus_2]


title: Breast metastasis in the ovary_OC01_ARN0060 [HG-U133_Plus_2]


title: Breast metastasis in the ovary_OC01_ARN0055 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0066 [HG-U133_Plus_2]


title: Breast metastasis in the ovary_OC01_ARN0051 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0042 [HG-U133_Plus_2]

value: Ia


title: Ovarian carcinoma_OC01_ARN0041 [HG-U133_Plus_2]

value: IIIb


title: Plausible Breast metastasis in the ovary_OC01_ARN0056 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0025 [HG-U133_Plus_2]

value: IV


title: Ovarian carcinoma_OC01_ARN0039 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0034 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0030 [HG-U133_Plus_2]

value: Endometrioid


title: Ovarian carcinoma_OC01_ARN0032 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0036 [HG-U133_Plus_2]


title: Breast metastasis in the ovary_OC01_ARN0035 [HG-U133_Plus_2]

value: Breast metastasis in the ovary


title: Breast metastasis in the ovary_OC01_ARN0029 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0028 [HG-U133_Plus_2]


title: Breast metastasis in the ovary_OC01_ARN0020 [HG-U133_Plus_2]


title: Breast metastasis in the ovary_OC01_ARN0017 [HG-U133_Plus_2]


title: Plausible Ovarian carcinoma_OC01_ARN0019 [HG-U133_Plus_2]

value: IIb


title: Ovarian carcinoma_OC01_ARN0015 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0022 [HG-U133_Plus_2]


title: Plausible Breast metastasis in the ovary_OC01_ARN0021 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0012 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0013 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0005 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0002 [HG-U133_Plus_2]


title: Plausible Breast metastasis in the ovary_OC01_ARN0006 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0010 [HG-U133_Plus_2]


title: TAX577707 [32K]

type: genomic

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

hyb_protocol: BAC aCGH microarrays were hybridized as described (PMID: 17334996)

scan_protocol: Arrays were washed as described (PMID: 17334996) and fluorescence was recorded using an Agilent G2565AA microarray scanner (Agilent Technologies).

data_processing: TIFF images were analyzed using the Gene Pix Pro software (Axon Instruments, Foster City, CA), and the quantified data matrix was loaded into a local installation of BioArray Software Environment (BASE) (http://base.thep.lu.se). Quantified intensities for tumor sample were stored as channel 1 (ch1) whereas quantified intensities for reference sample were stored as channel 2 (ch2). Median spot pixel values were used to calculate background corrected intensities (Int1 and Int2). Spots were removed and regarded as missing values if either: (1) flagged during image-analysis, (2) background corrected intensity value >64999 signal units, (3) background corrected intensity value <0 signal units, or (4) spot diameter less than 40 um. For spots, log ratio (M) was calculated as log2(Int1/Int2) and average intensity (A) was calculated as log10(Int1*Int2)/2. Normalization was performed by applying popLowess (PMID: 17953745). Spots from dye-swap hybridization were merged using geometric mean of ratios after normalization.

molecule: genomic DNA

source_name: Breast tumor

label_protocol: Fluorescently labeled DNA targets for hybridization were prepared according to manufacturers' instructions using the Invitrogen Bioprime aCGH Genomic Labeling Module as described (PMID:17334996).

extract_protocol: Genomic DNA from fresh frozen breast tumor tissue was extracted using overnight digestion with proteinase K at 55C, followed by repeated phenol-chloroform purification steps. Genomic DNA from FFPE tissue was extracted according to protocol from http://cancer.ucsf.edu/array/protocols/index.php. DNA concentrations were measured using a Nanodrop.

tag: disease state

value: Breast cancer (HER2+)

tag: er

tag: osbin

tag: os

tag: ln

tag: primary

source_name: promega male reference

tag: reference

value: Promega male reference DNA


title: Ovarian carcinoma_OC01_ARN0001 [HG-U133_Plus_2]

tag: tissue


title: TAX577685 [32K]

tag: age


title: Ovarian carcinoma_OC01_ARN0009 [HG-U133_Plus_2]

value: IIIc


title: TAX577088 [32K]


title: TAX577036 [32K]


title: Ovarian carcinoma_OC01_ARN0007 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0004 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0008 [HG-U133_Plus_2]


title: TAX577436 [32K]


title: TAX577592 [32K]


title: TAX577490 [32K]


title: TAX577193 [32K]


title: Ovarian carcinoma_OC01_ARN0011 [HG-U133_Plus_2]

value: Ib


title: Breast metastasis in the ovary_OC01_ARN0016 [HG-U133_Plus_2]


title: Ovarian carcinoma_OC01_ARN0023 [HG-U133_Plus_2]


title: Plausible Ovarian carcinoma_OC01_ARN0014 [HG-U133_Plus_2]

value: Plausible Ovarian carcinoma


title: Ovarian carcinoma_OC01_ARN0063 [HG-U133_Plus_2]


title: TAX577053 [32K]


title: TAX577049 [32K]


title: TAX577128 [32K]


title: TAX577042 [32K]


title: TAX577724 [32K]


title: TAX577676 [32K]


title: TAX577033 [32K]


title: TAX577014 [32K]


title: TAX577052 [32K]


title: TAX577012 [32K]


title: TAX577034 [32K]


title: TAX577610 [32K]


title: TAX577001 [32K]


title: TAX577709 [32K]


title: TAX577302 [32K]


title: TAX577281 [32K]


title: TAX577015 [32K]


title: TAX577040 [32K]


title: TAX577279 [32K]


title: TAX577284 [32K]


title: Small intestine-juvenile (NF66) Replicate-3

first: Biswajit

last: Das

address: 18 Library Drive, Building 18T, Room 106

department: Laboratory of Gene Regulation and Development

institute: National Institutes of Health/National Institute of Child Health and Human Development

description: Biological replicate 3 of 3. Dissected small intestine from juvenile frog (NF66).

hyb_protocol: Agilent 60-mer oligo microarray processing protocol (Agilent_2_color_Microarray-based Gene Exp Analysis.pdf, version 5.5). The manual can be found at Agilent support website or through a WEB search.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for data extraction from scanner generated TIFF files. Local background subtraction and LOWESS normalization settings were used.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.

organism: Xenopus laevis

source_name: Dissected intestine from ~5 juvenile frogs (NF66)

label_protocol: 2 µg of total RNA were used for each sample for cDNA synthesis and subsequent labeled Cy3-labeled cRNA synthesis using Low Input Labeling Kit (two-color) (Agilent Technologies) following manufacturer's instructions. Universal Reference cRNA (labeled with Cy5) was prepared from 200 ng of mRNA isolated from pooled mRNA for multiple stages representing all tissues and all the metamorphic stages of Xenopus laevis using the same Low Input Labeling Kit (two-color) (Agilent Technologies) following manufacturer's instructions .

growth_protocol: X. laevis tadpoles were maintained and used in accordance with the guidelines established by NICHD Animal Use and Care Committee. They were sacrificed and inteestines were collected at the indicated developmental stages according to the same established guidelines.

extract_protocol: Total RNA extracted using TRIZOL following manufacturer's instructions.

tag: developmental stage

value: Juvenile frogs (NF61)

value: Small intestine

source_name: Universal Reference mRNA made from pooled mRNA for multiple stages representing all the metamorphic stages of Xenopus laevis.

value: All stages from NF50 to NF66

value: All tissues


title: TAX577116 [32K]


title: TAX577675 [32K]


title: TAX577607 [32K]


title: Small intestine-metamorphic climax (NF61) Replicate-2

description: Biological replicate 2 of 2. Dissected small intestine from metamorphic climax tadpole (NF61).

source_name: Dissected intestine from ~5 metamorphic climax tadpoles (NF61)

value: Metamorphic climax tadpoles (NF61)


title: Small intestine-metamorphic climax (NF61) Replicate-1

description: Biological replicate 1 of 2. Dissected small intestine from metamorphic climax tadpole (NF61).


title: TAX577697 [32K]


title: Small intestine-prometamorphic (NF58) Replicate-2

description: Biological replicate 2 of 3. Dissected small intestine from prometamorphic tadpole (NF58).

source_name: Dissected intestine from ~5 prometamorphic tadpoles (NF58)

value: Prometamorphic tadpoles (NF58)


title: TAX577569 [32K]


title: TAX577461 [32K]


title: Small intestine-prometamorphic (NF58) Replicate-3

description: Biological replicate 3 of 3. Dissected small intestine from prometamorphic tadpole (NF58).


title: Small intestine-premetamorphic (NF53) Replicate-2

description: Biological replicate 2 of 3. Dissected small intestine from premetamorphic tadpole (NF53).

source_name: Dissected intestine from ~5 premetamorphic tadpoles (NF53)

value: Premetamorphic tadpoles (NF53)


title: TAX577129 [32K]


title: TAX577305 [32K]


title: TAX577595 [32K]


title: Small intestine-premetamorphic (NF53) Replicate-3

description: Biological replicate 3 of 3. Dissected small intestine from premetamorphic tadpole (NF53).


title: TAX577289 [32K]


title: Small intestine-juvenile (NF66) Replicate-1

description: Biological replicate 1 of 3. Dissected small intestine from juvenile frog (NF66).


title: TAX577720 [32K]


title: TAX577171 [32K]


title: TAX577275 [32K]


title: TAX577435 [32K]


title: TAX577331 [32K]


title: TAX577571 [32K]


title: TAX577606 [32K]


title: TAX577214 [32K]


title: Small intestine-juvenile (NF66) Replicate-2

description: Biological replicate 2 of 3. Dissected small intestine from juvenile frog (NF66).


title: TAX577446 [32K]


title: Small intestine-prometamorphic (NF58) Replicate-1

description: Biological replicate 1 of 3. Dissected small intestine from prometamorphic tadpole (NF58).


title: TAX577604 [32K]


title: Small intestine-premetamorphic (NF53) Replicate-1

description: Biological replicate 1 of 3. Dissected small intestine from premetamorphic tadpole (NF53).


title: TAX577057 [32K]


title: TAX577223 [32K]


title: TAX577598 [32K]


title: TAX577600 [32K]


title: TAX577611 [32K]


title: TAX577492 [32K]


title: TAX577522 [32K]


title: TAX577681 [32K]


title: TAX577039 [32K]


title: TAX577725 [32K]

description: This case was hybridized as dye-swap replicates.

label: Cy3, Cy5

label: Cy5, Cy3


title: TAX577723 [32K]


title: TAX577713 [32K]


title: TAX577612 [32K]


title: TAX577701 [38K]


title: TAX577601 [32K]


title: TAX577613 [32K]


title: TAX577722 [32K]


title: TAX577420 [32K]


title: TAX577485 [32K]


title: TAX577022 [32K]


title: TAX577594 [32K]


title: TAX577692 [38K]


title: TAX577710 [38K]


title: TAX577680 [32K]


title: TAX577602 [38K]


title: TAX577515 [32K]


title: TAX577714 [38K]


title: TAX577704 [38K]


title: TAX577695 [32K]


title: TAX577603 [38K]


title: TAX577593 [38K]


title: TAX577732 [33K]


title: TAX577706 [38K]


title: TAX577684 [33K]


title: TAX577596 [38K]


title: TAX577627 [33K]


title: TAX577735 [38K]


title: TAX577635 [33K]


title: TAX577677 [38K]


title: TAX577737 [38K]


title: TAX577632 [33K]


title: TAX577597 [38K]


title: TAX577699 [38K]


title: TAX577608 [38K]


title: TAX577689 [38K]


title: TAX577626 [33K]

description: This case was hybridized as replicates (non-dye-swap).


title: TAX577641 [33K]


title: TAX577702 [38K]


title: TAX577672 [33K]


title: Hepatocellular carcinoma/tumor-48

city: Chapel Hill

first: Ivan

last: Rusyn

state: NC

address: 0031 Michael Hooker Research Center

department: Gillings School of Global Public Health

institute: University of North Carolina

description:
Batch6
JT-48

hyb_protocol: Labeled samples and reference were hybridized to the microarray at 65 degree for 17 hours and washed with washing solutions.

scan_protocol: Arrays were scanned with Agilent Microarray Scanner (Agilent), and the obtained images were analyzed with Agilent Feature Extraction software (v8.5, Agilent Technologies).

data_processing: Normalization and filtering were performed with UNC Microarray Database (https://genome.unc.edu/). Inter-batch normalization was carried out using Distance Weighted Discrimination procedure.

source_name: HCC_tumor tissue

label_protocol: 1.2 ug of total RNA from each sample or human reference RNA was labeled with fluorescent dye (Cy5 and Cy3, respectively).

growth_protocol: Liver tissues were surgically resected from patients.

extract_protocol: Total RNA was isolated from tumor and nontumoral liver samples (~30 ug) with an RNeasy plus mini kit (Qiagen, Valencia, CA). Universal human reference RNA is from Stratagene (cat# 740000).

value: liver

tag: disease

value: hepatocellular carcinoma

tag: tumor tissue

value: yes

tag: hcv association

source_name: Universal human reference RNA

tag: cell line

value: multiple


title: TAX577698 [38K]

tag: grade


title: Hepatocellular carcinoma/tumor-49

description:
Batch8
JT-49


title: TAX577668 [33K]


title: TAX577621 [33K]


title: TAX577693 [33K]


title: TAX577327 [32K]


title: TAX577599 [32K]


title: TAX577671 [33K]


title: Hepatocellular carcinoma/tumor-47

description:
Batch7
JT-47


title: TAX577638 [33K]


title: Hepatocellular carcinoma/tumor-43

description:
Batch4
JT-43


title: Hepatocellular carcinoma/tumor-46

description:
Batch8
JT-46


title: TAX577618 [33K]


title: Hepatocellular carcinoma/tumor-42

description:
Batch1
JT-42


title: Hepatocellular carcinoma/tumor-38

description:
Batch2
JT-38


title: Hepatocellular carcinoma/tumor-44

description:
Batch8
JT-44


title: Hepatocellular carcinoma/tumor-40

description:
Batch5
JT-40


title: Hepatocellular carcinoma/tumor-39

description:
Batch7
JT-39


title: TAX577637 [33K]


title: TAX577617 [33K]


title: TAX577653 [33K]


title: Hepatocellular carcinoma/tumor-45

description:
Batch7
JT-45


title: Hepatocellular carcinoma/tumor-36

description:
Batch1
JT-36


title: Hepatocellular carcinoma/tumor-34

description:
Batch1
JT-34


title: Hepatocellular carcinoma/tumor-41

description:
Batch9
JT-41


title: Hepatocellular carcinoma/tumor-35

description:
Batch6
JT-35


title: Hepatocellular carcinoma/tumor-32

description:
Batch5
JT-32


title: Hepatocellular carcinoma/tumor-37

description:
Batch5
JT-37


title: TAX577694 [33K]


title: TAX577673 [33K]


title: Hepatocellular carcinoma/tumor-30

description:
Batch3
JT-30


title: Hepatocellular carcinoma/tumor-33

description:
Batch2
JT-33


title: Hepatocellular carcinoma/tumor-31

description:
Batch2
JT-31


title: TAX577661 [33K]


title: Hepatocellular carcinoma/tumor-29

description:
Batch4
JT-29


title: Hepatocellular carcinoma/tumor-27

description:
Batch1
JT-27


title: Hepatocellular carcinoma/tumor-26

description:
Batch6
JT-26


title: TAX577674 [33K]


title: Hepatocellular carcinoma/tumor-28

description:
Batch3
JT-28


title: TAX577614 [33K]


title: Hepatocellular carcinoma/tumor-25

description:
Batch8
JT-25


title: Hepatocellular carcinoma/tumor-22

description:
Batch9
JT-22


title: TAX577656 [33K]


title: TAX577615 [33K]


title: TAX577643 [33K]


title: Hepatocellular carcinoma/tumor-19

description:
Batch3
JT-19


title: TAX577640 [33K]


title: Hepatocellular carcinoma/tumor-18

description:
Batch4
JT-18


title: Hepatocellular carcinoma/tumor-20

description:
Batch5
JT-20


title: Hepatocellular carcinoma/tumor-23

description:
Batch4
JT-23


title: Hepatocellular carcinoma/tumor-14

description:
Batch3
JT-14


title: TAX577628 [33K]


title: Hepatocellular carcinoma/tumor-16

description:
Batch3
JT-16


title: Hepatocellular carcinoma/tumor-17

description:
Batch2
JT-17


title: Hepatocellular carcinoma/tumor-24

description:
Batch7
JT-24


title: Prostate basal/luminal epithelial cells

city: Wynnewood

first: Janet

last: Sawicki

address: 100 Lancaster Ave.

institute: lankenau Institute for Medical research

description: RNA has been amplified

hyb_protocol: Hybridized by Phalanx Biotech Group (http://www.phalanxbiotech.com/)

scan_protocol: Scanned by Phalanx Biotech Group (http://www.phalanxbiotech.com/)

data_processing: Data are normalized using Quantile normalization by Phalanx Biotech Group (http://www.phalanxbiotech.com/). 'T' refers to CFP+ while 'C' refers to CFP- signal. Raw data from three replicates of each cell population are available as a supplementary file.

organism: Mus musculus

source_name: CFP+ basal prostate epithelial cells

label_protocol: Labeled by Phalanx Biotech Group using 1 ug of total RNA after amplification (http://www.phalanxbiotech.com/)

extract_protocol: prostate epithelial cells from CK5/CFP mouse were isolated and sorted. Total RNA from sorted CFP+ and CFP- cells was prepared using a PicoPure RNA Isolation Kit (Arcturus)

value: normal prostate

tag: cell type

value: CFP+ basal epithelia cells

tag: strain

tag: genome/variation

value: CK5/CFP transgenic mouse model

value: 3 months

tag: sex

value: Male

value: adult

source_name: CFP- basal prostate epithelial cells

value: CFP- luminal epithelia cells


title: Hepatocellular carcinoma/tumor-21

description:
Batch8
JT-21


title: Hepatocellular carcinoma/tumor-15

description:
Batch6
JT-15


title: Hepatocellular carcinoma/tumor-12

description:
Batch9
JT-12


title: TAX577634 [33K]

tag: disease state

value: Breast cancer (HER2+)

tag: er

tag: osbin

value: Promega male reference DNA


title: Hepatocellular carcinoma/tumor-07

description:
Batch2
JT-07


title: Hepatocellular carcinoma/tumor-11

description:
Batch9
JT-11


title: TAX577736 [33K]

tag: os

tag: ln

tag: primary


title: TAX577648 [33K]

tag: age

tag: reference


title: TAX577642 [33K]


title: Hepatocellular carcinoma/tumor-06

description:
Batch1
JT-06

tag: tissue

tag: disease


title: Hepatocellular carcinoma/tumor-04

description:
Batch6
JT-04

tag: tumor tissue

tag: hcv association


title: fibroblast DNA sample 45 XO replicate 3

city: Pune

first: Ashwin

last: Kelkar

state: Maharashtra

address: Ganeshkhind

department: Department of Zoology

country: India

institute: University of Pune

description:
This experiment was performed to analyse the methylation in genomic DNA bound to the microarray probes. The DNA was added to the microarary unlabelled and the presence of 5 methylcytosine in the array was detected using a Cy3 labelled monoclonal antibody to 5 methylcytosine. So the florescence readout denotes the amount of antibody bound to each feature.
A detailed description is available in Kelkar A, Deobagkar D. “A novel method to assess the full genome methylation profile using monoclonal antibody combined with the high throughput based microarray approach”. Epigenetics 2009 vol 4, Issue 6, pg. 415 – 420 ( Kelkar et.al Epigenetics 2009)

hyb_protocol: The genomic DNA was sonicated to a uniform size of 1.5 – 2 kb in TE buffer ( Tris 10mM EDTA 1mM ). The hybridisation to the DNA on microarray was carried out with this sonicated DNA. The protocol described is a modification of the method reported by Proll et. al. 14 . 2 microg of DNA was used in all the experiments. The 2X hybridisation buffer, post wash buffers and the blocking reagent from GENETAC hybridisation kit ( Perkin Elmer Ltd. ) were used.  The hybridisation solution (300 microliter) contained 2X hybridisation buffer and sonicated genomic DNA . The hybridisation was carried out at 42OC for 12 – 14hr on a Quantifoil Hybridisation station. The DNA samples from 45 XO cells were used independently in three separate hybridisation experiments. After hybridisation the slides were washed, blocked with blocking reagent  for 30' at RT and incubated with anti 5mC antibody (1:1000 in TNT buffer  Tris pH 7.5, NaCl 100mM, Tween 20 0.01%) for 60' at 25OC. The slides were washed with TNT buffer  3 times for 5'  with agitation and incubated with the anti mouse Cy3 labelled IgG ( 1:1000 in TNT buffer ) for 60' at 25OC . Washing was repeated as described above and then slides were dried by centrifugation at 1500G for 30sec.  The slides were scanned using a Perkin Elmer ScanArray Express at 5m resolution at a wavelength of 543nm.

scan_protocol: The slides were scanned using a Perkin Elmer ScanArray Express at 5 micron resolution at a wavelength of 543nm. The PMT gain for the laser was 65. Proprietry software supplied by Perkin Elmer was used to scan the slides and accquire data.

data_processing:
For cDNA arrays, the labelled cDNA is hybridised to a microarray and thus the amount of label is measured using a laser, however the amount of florescent dye per molecule of cDNA is very high as the labelling reaction will result in incorporation of label along the entire length of the cDNA. When the florescent label is transferred to a protein like an IgG molecule as is the case here, the among of label per molecule is much lower than a cDNA molecule. so the amount of signal in a hybridisation reaction will be much less than a conventional microarray. As opposed to when a cDNA molecule is labelled  in the case of the antibody based microarray, each IgG molecule can have only 2 antigen binding sites, so only 2 methyl groups are detected by each IgG. Also due to stearic hindrance even if there are multiple methyl groups present in close proximity, an equivalent number of IgG molecules may not be able to bind, reducing the overall signal intensity.  The generally accepted criterion of signal to noise ratio of over and above 3.0 might be a little too stringent in this case in determining the true positives. Thus the signal to noise ratio cut off used was 1.0 and not the usual standard value of 3.0.
The microarray carried spots containing 3XSSC and Arabidopsis thaliana DNA which provided a background signal. The florescence values from these spots were considered to be representatives of non specific binding of the DNA to the slides and these values were used to determine the true positives in the data. These values were together termed as 'control' values. The control values from each individual array were used to normalise the florescence for all the genes of that array in order to provide a uniform scale for comparison of genes between arrays. Assuming an error of 10 % and 20 % in the ability to detect true positives, the florescence of the highest 10 % and 20 % of the control values were considered as errors and were removed from the analysis.  Any gene showing a signal higher than the highest value in the remaining control spots was considered a true positive.For comparison of the genes between arrays the values of florescence for each array were normalised with the respective cut off for that array.
This yielded values ranging from 1.0 and above as fold intensities for every array individually. Comparision was performed on normalised values of individual replicates.
The processed data available in this samle are the normalised fold values

source_name: Human fibroblasts from indivial with karyotpye 45 XO

label_protocol:
Anti mouse IgG (Bangalore Genei) was labelled with Cy3 using the Cy3 TM Ab labelling Kit  (GE
Healthcare Cat. No. PA33000). The efficiency of labelling was checked using A543/A280 ratio.

extract_protocol: Pure DNA used as supplied by biomatrial provider

value: skin fibroblast

tag: gender

value: female

tag: karyotype

value: 45 XO

tag: antibody


title: Hepatocellular carcinoma/tumor-01

description:
Batch7
JT-01

tag: cell line


title: Hepatocellular carcinoma/non-tumor-46

description:
Batch8
JNT-46

source_name: HCC_adjacent liver tissue

value: no


title: Hepatocellular carcinoma/non-tumor-47

description:
Batch7
JNT-47

value: liver


title: fibroblast DNA sample 47 XXX replicate 2

description:
This experiment was performed to analyse the methylation in genomic DNA bound to the microarray probes. The DNA was added to the microarary unlabelled and the presence of 5 methylcytosine in the array was detected using a Cy3 labelled monoclonal antibody to 5 methylcytosine. So the florescence readout denotes the amount of antibody bound to each feature.
A detailed description is available in: Kelkar A, Deobagkar D. “A novel method to assess the full genome methylation profile using monoclonal antibody combined with the high throughput based microarray approach”. Epigenetics 2009 vol 4, Issue 6, pg. 415 – 420 ( Kelkar et.al Epigenetics 2009)

source_name: Human fibroblasts from indivial with karyotpye 47 XXX

tag: cell type

value: 47 XXX


title: TAX577616 [33K]

tag: disease state

tag: grade


title: TAX577658 [33K]

tag: er

tag: osbin


title: fibroblast DNA sample 47 XXX replicate 1

value: Cy3 labelled monoclonal antibody to 5 methylcytosine


title: TAX577657 [33K]

tag: os

tag: ln


title: Hepatocellular carcinoma/tumor-13

description:
Batch4
JT-13

value: hepatocellular carcinoma

value: yes

value: multiple


title: Hepatocellular carcinoma/non-tumor-45

description:
Batch7
JNT-45


title: Hepatocellular carcinoma/non-tumor-44

description:
Batch8
JNT-44


title: fibroblast DNA sample 45 XO replicate 2


title: fibroblast DNA sample 45 XO replicate 1

description:
This experiment was performed to analyse the methylation in genomic DNA bound to the microarray probes. The DNA was added to the microarary unlabelled and the presence of 5 methylcytosine in the array was detected using a Cy3 labelled monoclonal antibody to 5 methylcytosine. So the florescence readout denotes the amount of antibody bound to each feature.
A detailed description is available in 1.Kelkar A, Deobagkar D. “A novel method to assess the full genome methylation profile using monoclonal antibody combined with the high throughput based microarray approach”. Epigenetics 2009 vol 4, Issue 6, pg. 415 – 420 ( Kelkar et.al Epigenetics 2009)


title: TAX577726 [33K]

tag: age

tag: primary


title: Hepatocellular carcinoma/non-tumor-43

description:
Batch4
JNT-43

tag: tissue


title: Plausible breast metastasis in the ovary_OC01_ADN0261 [50K_Xba240]

description: Hybridized to 50K_Xba

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

data_processing:
CEL files were generated with GCOS 1.4 for 50K Xba chips and with Affymetrix Genechip Command Console 3.0 for SNP6 chips. ITALICS 2.6.0 (available on http://www.bioconductor.org/packages/2.5/bioc/html/ITALICS.html) was used to generate the copy number data of 50K Xba chips and Partek Genomic Suite 6.10.0212 was used to generate copy number of SNP6 chips. CHP files were generated using apt-probeset-genotype command line tool from Affymetrix Power Tools package 1.12.0. BRLMM algorithm was used to generate genotype of 50K Xba chips, and Birdseed algorithm was used to generate genotype of SNP6 chips. Default settings were used for all the softwares and command line tools.
Samples were normalized against Hapmap reference samples BUT NOT against paired normal samples.

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA was extracted from frozen tumor samples using a standard phenol/chloroform procedure

value: Ovary

tag: pair

tag: histology (disease state)

value: Poorly differentiated Adenocarcinoma

tag: identifier

value: ND

tag: er status

tag: pr status

tag: get diagnosis

tag: time interval fromc (months)

tag: c stage

tag: oc figo stage

value: IV

tag: rca status

tag: c local treatment

tag: c systemic treatment

tag: metastatic site

tag: outcome

value: Dead of disease


title: TAX577734 [33K]

tag: disease state

value: Breast cancer (HER2+)

tag: er

tag: osbin

tag: os

tag: age

tag: ln

tag: grade

tag: reference


title: TAX577727 [33K]

tag: primary

value: Promega male reference DNA


title: Hepatocellular carcinoma/non-tumor-42

description:
Batch1
JNT-42

tag: tissue

tag: disease

tag: tumor tissue

tag: hcv association

tag: cell line


title: Plausible ovarian carcinoma_OC01_ADN0087 [50K_Xba240]

description: Hybridized to 50K_Xba

source_name: Plausible ovarian carcinoma

tag: pair

tag: histology (disease state)

tag: identifier

value: III

tag: er status

value: pos

tag: pr status

tag: get diagnosis

tag: time interval fromc (months)

tag: c stage

tag: oc figo stage

value: IIIc

tag: rca status

tag: c local treatment

tag: c systemic treatment


title: Hepatocellular carcinoma/non-tumor-41

description:
Batch9
JNT-41

tag: tissue

value: no


title: Breast carcinoma_OC01_ADN0253 [50K_Xba240]

description: Hybridized to 50K_Xba

source_name: Breast carcinoma

value: Breast

value: Undifferentiated

tag: grade

value: neg

value: II

value: Breast Conserving Surgery

value: Chemotherapy

tag: metastatic site

tag: outcome


title: Hepatocellular carcinoma/non-tumor-40

description:
Batch5
JNT-40

value: liver

tag: disease

value: hepatocellular carcinoma

tag: tumor tissue

tag: hcv association

value: yes

tag: cell line

value: multiple


title: Breast carcinoma_OC01_ADN0252 [50K_Xba240]

description: Hybridized to 50K_Xba

tag: pair

tag: histology (disease state)

value: Infiltrating Ductal Carcinoma

tag: identifier

tag: er status

value: BRCA1 wt, BRCA2 wt

value: Mastectomy

value: Pleura

value: Dead of disease


title: TAX577633 [33K]

tag: disease state

value: Breast cancer (HER2+)

tag: er

tag: osbin

tag: os

tag: age

tag: ln

tag: primary

tag: reference

value: Promega male reference DNA


title: TAX577659 [33K]

tag: grade


title: Hepatocellular carcinoma/non-tumor-39

description:
Batch7
JNT-39

tag: tissue

tag: disease

value: no


title: Ovarian carcinoma_OC01_ADN0133 [50K_Xba240]

description: Hybridized to 50K_Xba

source_name: Ovarian carcinoma

value: Ovary

value: Serous Papillary

value: III

value: ND

tag: pr status

tag: get diagnosis

tag: time interval fromc (months)

tag: c stage

tag: oc figo stage

value: Iic

tag: rca status

tag: c local treatment

tag: c systemic treatment

tag: metastatic site

tag: outcome

value: No evidence of disease


title: TAX577690 [33K]

source_name: Breast tumor

tag: disease state

tag: er

tag: osbin

tag: os

tag: age


title: Hepatocellular carcinoma/non-tumor-38

description:
Batch2
JNT-38

tag: tissue

value: liver

value: hepatocellular carcinoma

tag: tumor tissue

tag: hcv association

tag: cell line


title: TAX577047 [33K]

tag: ln

tag: primary

tag: grade

source_name: promega male reference

tag: reference


title: Hepatocellular carcinoma/non-tumor-36

description:
Batch1
JNT-36

tag: disease

value: yes

value: multiple


title: Breast metastasis in the ovary_OC01_ADN0198 [50K_Xba240]

description: Hybridized to 50K_Xba

source_name: Breast metastasis in the ovary

tag: pair

tag: histology (disease state)

value: Lobular Carcinoma

tag: identifier

tag: er status

value: pos

tag: pr status

tag: get diagnosis

tag: time interval fromc (months)

tag: c stage

tag: oc figo stage

value: IIIc

tag: rca status

tag: c local treatment

tag: c systemic treatment


title: TAX577048 [33K]

tag: disease state

tag: er

tag: osbin

tag: os

tag: age

tag: ln


title: TAX577711 [33K]

tag: primary

tag: grade

tag: reference


title: TAX577730 [33K]


title: Hepatocellular carcinoma/non-tumor-37

description:
Batch5
JNT-37

tag: tissue

tag: disease

tag: tumor tissue

tag: hcv association

tag: cell line


title: TAX577620 [33K]


title: Breast carcinoma_OC01_ADN0251 [50K_Xba240]

description: Hybridized to 50K_Xba

value: Breast

tag: pair

tag: histology (disease state)

value: Infiltrating Ductal Carcinoma

tag: identifier

value: II

tag: er status

tag: pr status

value: neg

tag: get diagnosis

tag: time interval fromc (months)

tag: c stage

tag: oc figo stage

tag: rca status

value: Breast Conserving Surgery

value: Tamoxifen

tag: metastatic site

tag: outcome


title: Breast carcinoma_OC01_ADN0249 [50K_Xba240]

description: Hybridized to 50K_Xba

tag: tissue

tag: grade

value: I

tag: c local treatment

tag: c systemic treatment

value: No


title: Breast carcinoma_OC01_ADN0250 [50K_Xba240]

description: Hybridized to 50K_Xba

value: Infiltrating Lobular Carcinoma

value: III

value: Familial history

value: Mastectomy

value: Chemotherapy - Tamoxifen

value: Dead of disease


title: Hepatocellular carcinoma/non-tumor-35

description:
Batch6
JNT-35

value: liver

tag: disease

value: hepatocellular carcinoma

tag: tumor tissue

value: no

tag: hcv association

value: yes

tag: cell line

value: multiple


title: Ovarian carcinoma_OC01_ADN0115 [50K_Xba240]

description: Hybridized to 50K_Xba

value: Ovary

tag: pair

tag: histology (disease state)

value: Serous Papillary

tag: identifier

tag: er status

value: IIIc

value: No evidence of disease


title: Hepatocellular carcinoma/non-tumor-34

description:
Batch1
JNT-34


title: Hepatocellular carcinoma/non-tumor-33

description:
Batch2
JNT-33


title: Breast carcinoma_OC01_ADN0248 [50K_Xba240]

description: Hybridized to 50K_Xba

value: Breast

value: Infiltrating Ductal Carcinomand Infiltrating Lobular Carcinoma (mixed)

value: pos

tag: pr status

tag: get diagnosis

tag: time interval fromc (months)

tag: c stage

value: ND

value: Tamoxifen


title: Breast carcinoma_OC01_ADN0247 [50K_Xba240]

description: Hybridized to 50K_Xba

value: Infiltrating Ductal Carcinoma

value: III

tag: oc figo stage

tag: rca status

value: Mastectomy

tag: metastatic site

value: Peritoneal carcinomatosis, supraclavicular LN,rain

tag: outcome

value: Stable disease


title: Hepatocellular carcinoma/non-tumor-32

description:
Batch5
JNT-32

tag: tissue

value: liver

value: hepatocellular carcinoma

value: no


title: Breast metastasis in the ovary_OC01_ADN0262 [50K_Xba240]

description: Hybridized to 50K_Xba

value: Ovary

value: Poorly differentiated Adenocarcinoma

tag: grade

value: IV

tag: c local treatment

tag: c systemic treatment


title: Ovarian carcinoma_OC01_ADN0220 [50K_Xba240]

description: Hybridized to 50K_Xba

value: Serous Papillary

value: II

value: neg

tag: time interval fromc (months):

value: IIa

value: Dead of disease


title: TAX577629 [33K]

tag: disease state

value: Breast cancer (HER2+)

tag: er

tag: osbin

tag: os

tag: age

tag: ln

tag: primary

tag: reference

value: Promega male reference DNA


title: Hepatocellular carcinoma/non-tumor-31

description:
Batch2
JNT-31

tag: disease

tag: tumor tissue

tag: hcv association

value: yes

tag: cell line

value: multiple


title: Hepatocellular carcinoma/non-tumor-28

description:
Batch3
JNT-28

tag: tissue


title: Hepatocellular carcinoma/non-tumor-29

description:
Batch4
JNT-29


title: Breast carcinoma_OC01_ADN0245 [50K_Xba240]

description: Hybridized to 50K_Xba

value: Breast

tag: pair

tag: histology (disease state)

value: Infiltrating Ductal Carcinoma

tag: identifier

tag: grade

value: III

tag: er status

value: pos

tag: pr status

tag: get diagnosis

tag: time interval fromc (months)

tag: c stage

tag: oc figo stage

tag: rca status

value: BRCA1 wt, BRCA2 unknown

value: Breast Conserving Surgery

value: Chemotherapy - Tamoxifen

tag: metastatic site

tag: outcome


title: Ovarian carcinoma_OC01_ADN0258 [50K_Xba240]

description: Hybridized to 50K_Xba

value: Ovary

value: ND

value: Ic

tag: c local treatment

tag: c systemic treatment

value: No evidence of disease


title: Hepatocellular carcinoma/non-tumor-30

description:
Batch3
JNT-30

value: liver

tag: disease

value: hepatocellular carcinoma

tag: tumor tissue

value: no

tag: hcv association

tag: cell line


title: TAX577636 [33K]

tag: disease state

value: Breast cancer (HER2+)

tag: er

tag: osbin

tag: os

tag: age

tag: ln

tag: primary

tag: reference

value: Promega male reference DNA


title: TAX577665 [33K]

tag: grade


title: Hepatocellular carcinoma/non-tumor-27

description:
Batch1
JNT-27

tag: tissue

value: yes

value: multiple


title: Plausible ovarian carcinoma_OC04_ADN0002 [SNP_6]

description: Hybridized to SNP6

tag: pair

tag: histology (disease state)

value: Poorly differentiated Adenocarcinoma

tag: identifier

value: II

tag: er status

tag: pr status

tag: get diagnosis

tag: time interval fromc (months)

tag: c stage

tag: oc figo stage

value: IIa

tag: rca status

tag: metastatic site

tag: outcome

value: Dead of disease


title: Plausible breast metastasis in the ovary_OC01_ADN0257 [50K_Xba240]

description: Hybridized to 50K_Xba

value: Lobular Carcinoma

value: IIIc

tag: c local treatment

tag: c systemic treatment


title: Hepatocellular carcinoma/non-tumor-26

description:
Batch6
JNT-26

tag: disease

tag: tumor tissue

tag: hcv association

tag: cell line


title: Breast carcinoma_OC01_ADN0256 [50K_Xba240]

description: Hybridized to 50K_Xba

tag: tissue

value: Breast

tag: pair

tag: histology (disease state)

value: Infiltrating Ductal Carcinoma

tag: grade

value: III

value: neg

value: I

value: BRCA2 mut

value: Breast Conserving Surgery

value: Chemotherapy


title: TAX577696 [33K]

tag: disease state

value: Breast cancer (HER2+)

tag: er

tag: osbin

tag: os

tag: age

tag: ln

tag: primary

tag: reference

value: Promega male reference DNA


title: Hepatocellular carcinoma/non-tumor-24

description:
Batch7
JNT-24

value: liver

value: hepatocellular carcinoma

value: no

value: yes

value: multiple


title: Breast carcinoma_OC01_ADN0255 [50K_Xba240]

description: Hybridized to 50K_Xba

value: Infiltrating Lobular Carcinoma

tag: identifier

value: II

tag: er status

value: pos

tag: pr status

tag: get diagnosis

tag: time interval fromc (months)

tag: c stage

tag: oc figo stage

tag: rca status

value: ND

tag: c local treatment

value: Mastectomy

tag: c systemic treatment

value: Chemotherapy - Tamoxifen

tag: metastatic site

tag: outcome

value: Dead of disease


title: Hepatocellular carcinoma/non-tumor-25

description:
Batch8
JNT-25

tag: tissue

tag: disease

tag: tumor tissue

tag: hcv association

tag: cell line


title: TAX577647 [33K]

tag: disease state

tag: er

tag: osbin

tag: os

tag: age

tag: ln

tag: primary

tag: grade

tag: reference


title: Breast carcinoma_PT01_ADN0021 [50K_Xba240]

description: Hybridized to 50K_Xba

value: Breast

tag: pair:

tag: histology (disease state)

tag: identifier

tag: er status

tag: pr status

tag: get diagnosis

tag: time interval fromc (months)

tag: c stage

value: I

tag: oc figo stage

tag: rca status

tag: c local treatment

tag: c systemic treatment

value: No

value: Peritoneal carcinomatosis,xillary LN


title: Hepatocellular carcinoma/non-tumor-21

description:
Batch8
JNT-21

tag: tissue

tag: disease

tag: tumor tissue

tag: hcv association

tag: cell line


title: Hepatocellular carcinoma/non-tumor-20

description:
Batch5
JNT-20


title: Hepatocellular carcinoma/non-tumor-23

description:
Batch4
JNT-23


title: TAX577655 [33K]

tag: disease state

value: Breast cancer (HER2+)

tag: er

tag: osbin

tag: os

tag: age

tag: ln

tag: primary

tag: grade

tag: reference

value: Promega male reference DNA


title: Hepatocellular carcinoma/non-tumor-22

description:
Batch9
JNT-22

value: liver

value: hepatocellular carcinoma


title: Breast carcinoma_OC04_ADN0001 [SNP_6]

description: Hybridized to SNP6

tag: pair

tag: histology (disease state)

value: Infiltrating Ductal Carcinoma

tag: identifier

value: III

tag: er status

value: neg

tag: pr status

tag: get diagnosis

tag: time interval fromc (months)

tag: c stage

tag: oc figo stage

tag: rca status

value: BRCA1 mut

value: Chemotherapy

tag: metastatic site

tag: outcome


title: Hepatocellular carcinoma/non-tumor-19

description:
Batch3
JNT-19

tag: tissue

tag: disease

tag: tumor tissue

value: no

tag: hcv association

value: yes

tag: cell line

value: multiple


title: TAX577290 [33K]

tag: disease state

tag: er

tag: osbin

tag: os

tag: age

tag: ln

tag: primary

tag: grade

tag: reference


title: TAX577664 [33K]


title: Breast metastasis in the ovary_PT01_ADN0027 [50K_Xba240]

description: Hybridized to 50K_Xba

value: Ovary

tag: pair:

tag: histology (disease state)

value: Lobular Carcinoma

tag: identifier

value: ND

tag: er status

value: pos

tag: pr status

tag: get diagnosis

tag: time interval fromc (months)

tag: c stage

tag: oc figo stage

value: IV

tag: rca status

tag: c local treatment

tag: c systemic treatment

value: Dead of disease


title: Breast carcinoma_PT01_ADN0017 [50K_Xba240]

description: Hybridized to 50K_Xba

tag: tissue

value: Breast

value: Infiltrating Lobular Carcinoma

value: Mastectomy

value: Tamoxifen

tag: metastatic site

tag: outcome


title: TAX577650 [33K]

tag: disease state

value: Breast cancer (HER2+)

tag: er

tag: osbin

tag: os

tag: age

tag: ln

tag: primary

tag: grade

value: Promega male reference DNA


title: Hepatocellular carcinoma/non-tumor-18

description:
Batch4
JNT-18

value: liver

tag: disease

value: hepatocellular carcinoma

tag: tumor tissue

tag: hcv association

tag: cell line


title: Breast metastasis in the ovary_PT01_ADN0029 [50K_Xba240]

description: Hybridized to 50K_Xba

tag: pair

tag: histology (disease state)

tag: identifier

tag: er status

tag: pr status

tag: get diagnosis

tag: time interval fromc (months)

tag: c stage

tag: oc figo stage

tag: rca status

tag: c local treatment


title: TAX577682 [33K]

tag: disease state

tag: er

tag: osbin

tag: os

tag: age

tag: ln

tag: primary

tag: reference


title: Breast carcinoma_PT01_ADN0022 [50K_Xba240]

description: Hybridized to 50K_Xba

tag: tissue

tag: pair

tag: histology (disease state)

tag: identifier

tag: grade

value: I

value: III

tag: c systemic treatment

value: Chemotherapy - Tamoxifen

tag: metastatic site

value: Liver

tag: outcome


title: Breast carcinoma_PT01_ADN0002 [50K_Xba240]

description: Hybridized to 50K_Xba

tag: er status

tag: pr status

tag: get diagnosis

tag: time interval fromc (months)

tag: c stage

tag: oc figo stage

tag: rca status

tag: c local treatment

value: Breast Conserving Surgery

value: Bone, Liver


title: Breast metastasis in the ovary_PT01_ADN0014 [50K_Xba240]

description: Hybridized to 50K_Xba

value: Ovary

tag: pair:

value: Lobular Carcinoma

value: ND

value: 8 (ILCnd ovarian tumorppeared simultaneously)


title: TAX577729 [33K]

tag: disease state

tag: er

tag: osbin

tag: os

tag: age

tag: ln

tag: primary

tag: reference


title: Breast carcinoma_PT01_ADN0012 [50K_Xba240]

description: Hybridized to 50K_Xba

tag: tissue

value: Breast

tag: histology (disease state)

value: Infiltrating Ductal Carcinoma, then Infiltrating Lobular Carcinoma

tag: identifier

tag: grade

value: III, then II

tag: er status

value: pos

tag: c systemic treatment

value: Chemotherapy

tag: metastatic site

tag: outcome

value: Dead of disease


title: Hepatocellular carcinoma/non-tumor-16

description:
Batch3
JNT-16

value: liver

tag: disease

value: hepatocellular carcinoma

tag: tumor tissue

value: no

tag: hcv association

value: yes

tag: cell line

value: multiple


title: Hepatocellular carcinoma/non-tumor-17

description:
Batch2
JNT-17


title: Breast metastasis in the ovary_PT01_ADN0025 [50K_Xba240]

description: Hybridized to 50K_Xba

tag: pair

tag: pr status

tag: get diagnosis

tag: time interval fromc (months)

tag: c stage

tag: oc figo stage

value: IV

tag: rca status

tag: c local treatment


title: TAX577728 [33K]

tag: disease state

value: Breast cancer (HER2+)

tag: er

tag: osbin

tag: os

tag: age

tag: ln

tag: primary

tag: grade

tag: reference

value: Promega male reference DNA


title: TAX577670 [33K]


title: TAX577669 [33K]


title: jos0674

first: Mary Elizabeth

last: Patti

address: 1 Joslin Place

department: Research Division

institute: Joslin Diabetes Center

description: Replicate of gene expression from skeletal muscle of one subject without diabetes

hyb_protocol: 15ug of biotinylated cRNA were hybridized for 16hr at 45C to the Affymetrix GeneChip HuGeneFL array.  Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneArray Scanner G2500.

data_processing: Data were analyzed using Affymetrix MAS 4.0, and normalized for overall intensity using linear regression.

source_name: Replicate from 1 patient

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

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

tag: tissue

value: skeletal muscle

value: replicate control

tag: family history

tag: sex

value: male

tag: age (years)

tag: bmi (kg/m2)

tag: fpg (mg/dl)


title: jos0595

description: Gene expression from skeletal muscle of subject without diabetes

source_name: Control, Family History Neg

value: control


title: TAX577631 [33K]


title: jos0672


title: Ovarian carcinoma_OC01_ADN0259 [50K_Xba240]

description: Hybridized to 50K_Xba

value: Ovary

tag: pair

tag: histology (disease state)

value: Clear Cells

tag: identifier

value: II

tag: er status

value: ND

tag: pr status

tag: get diagnosis

tag: time interval fromc (months)

tag: c stage

tag: oc figo stage

value: IIc

tag: rca status

tag: c systemic treatment

tag: metastatic site

tag: outcome

value: No evidence of disease


title: TAX577639 [33K]

tag: disease state

tag: er

tag: osbin

tag: os

tag: age

tag: ln

tag: primary

tag: grade

tag: reference


title: jos0596

tag: tissue

tag: family history

tag: sex

value: female

tag: age (years)

tag: bmi (kg/m2)

tag: fpg (mg/dl)


title: TAX577649 [33K]


title: jos0673


title: TAX577666 [33K]


title: Hepatocellular carcinoma/non-tumor-12

description:
Batch9
JNT-12

value: liver

tag: disease

value: hepatocellular carcinoma

tag: tumor tissue

value: no

tag: hcv association

tag: cell line


title: Hepatocellular carcinoma/non-tumor-13

description:
Batch4
JNT-13

value: yes

value: multiple


title: TAX577687 [33K]

tag: disease state

value: Breast cancer (HER2+)

tag: er

tag: osbin

value: Promega male reference DNA


title: Hepatocellular carcinoma/non-tumor-10

description:
Batch7
JNT-10


title: jos0593

value: skeletal muscle


title: Hepatocellular carcinoma/non-tumor-14

description:
Batch3
JNT-14


title: Breast metastasis in the ovary_PT01_ADN0020 [50K_Xba240]

description: Hybridized to 50K_Xba

tag: pair:

tag: histology (disease state)

value: Lobular Carcinoma

tag: identifier

tag: er status

tag: pr status

tag: get diagnosis

tag: time interval fromc (months)

tag: c stage

tag: oc figo stage

value: IIIc

tag: rca status

tag: c local treatment

tag: c systemic treatment

tag: metastatic site

tag: outcome

value: Dead of disease


title: Hepatocellular carcinoma/non-tumor-15

description:
Batch6
JNT-15

tag: tissue

tag: disease

tag: tumor tissue

tag: hcv association

tag: cell line


title: Hepatocellular carcinoma/non-tumor-11

description:
Batch9
JNT-11


title: jos0592

tag: disease state

value: control

tag: family history

tag: sex

value: male

tag: age (years)

tag: bmi (kg/m2)

tag: fpg (mg/dl)


title: jos0538

value: replicate control


title: TAX577651 [33K]

tag: er

tag: osbin

tag: os

tag: age

tag: ln

tag: primary

tag: grade

tag: reference


title: TAX577619 [33K]


title: Hepatocellular carcinoma/non-tumor-09

description:
Batch6
JNT-09

tag: tissue

tag: disease

tag: tumor tissue


title: Hepatocellular carcinoma/non-tumor-08

description:
Batch9
JNT-08

tag: hcv association

tag: cell line


title: TAX577625 [33K]

tag: disease state


title: jos0594

tag: family history

tag: sex

tag: age (years)


title: Hepatocellular carcinoma/non-tumor-06

description:
Batch1
JNT-06


title: Hepatocellular carcinoma/non-tumor-07

description:
Batch2
JNT-07


title: TAX577630 [33K]

tag: er


title: TAX577624 [33K]

tag: osbin


title: TAX577623 [33K]

tag: os


title: Hepatocellular carcinoma/non-tumor-04

description:
Batch6
JNT-04


title: jos0506

description: Gene expression from skeletal muscle of subject with type 2 diabetes

source_name: Type 2 DM

value: DM

tag: bmi (kg/m2)

tag: fpg (mg/dl)


title: metastatic liver tumor/non-tumor/control-10

description:
Batch6
JC-10

source_name: MLT_adjacent liver tissue

value: metastatic liver tumor


title: jos0537


title: jos0502

source_name: Control, Family History Pos

value: female


title: metastatic liver tumor/non-tumor/control-09

description:
Batch5
JC-09

value: liver

source_name: Universal human reference RNA


title: jos0507


title: jos0504


title: Hepatocellular carcinoma/non-tumor-05

description:
Batch8
JNT-05

value: hepatocellular carcinoma


title: jos0505


title: TAX577733 [33K]

tag: age

tag: ln

tag: primary


title: TAX577731 [33K]

tag: grade

tag: reference


title: metastatic liver tumor/non-tumor/control-11

description:
Batch7
JC-11

tag: tissue

tag: disease

tag: tumor tissue

value: no


title: TAX577663 [33K]

tag: disease state


title: jos0009-2

tag: family history

value: yes


title: jos0501

tag: sex


title: TAX577667 [33K]


title: TAX577686 [33K]


title: TAX577708 [33K]


title: KSU-AP-DM Rat Semi-Circular Canal Duct D4-A

city: Manhattan

first: Daniel

last: Marcus

state: KS

address: 228 Coles Hall

department: Anatomy & Physiology

institute: Kansas State University

description:
Absolute and comparison analysis are conducted using the following settings:
      Scaling - All Probe Sets: Target Signal = 500
      Normalization – User Defined: Scale Factor = 1

hyb_protocol: GENECHIP HYBRIDIZATION PROTOCOL: Hybridization cocktail composition: (for standard array format) Note: 10% DMSO is added for targets Prepared using the GeneChip Expression 3’-Amplificaton  IVT Labeling Protocol. 30ulfragmented cRNA 15ug(0.05ug/ul final conc.) 5ulcontrol Biotin labeled oligo B2 (3nM) (Affymetrix) (50pM final conc.) 15ul20x Eukaryotic Hybridization spike controls (bioB, bioC, BioD, cre) (Affymetrix)  (1.5, 5, 25 and 100pM final conc. respectively) 3ulHerring Sperm DNA (10mg/ml)(blocking reagent)   (0.1mg/ml final conc.) 3ulAcetylated BSA (50mg/ml)(blocking reagent)  (0.5mg/ml final conc.) 150ul2x Hybridization Buffer (Final 1x conc. is 100mM MES {12X stock: 70.4g MES free-acid monohydrate, 193.3g MES sodium Salt/L pH 6.6}, 1M [Na+], 20mM EDTA, 0.01% Tween 20) - DEPC H2O to 300ul. - Denatured at 99C 5min prior to applying to GeneChip Hybridization Conditions: - GeneChip is prehybridized with 200ul 1x Hybridization buffer (see above) at 45C 10min at 60rpm - 200ul denatured Hybridization cocktail is applied to GeneChip - GeneChip is hybridized 16 hr at 45C and 60rpm in GeneChip Hybridization Oven 640. Washing and Staining: Automated process using the GeneChip Fluidics Station 400 with the Standard Array Format. Enzo BioArray High Yield RNA Transcript Labeling Washing and Staining Protocol Post Hyb wash #1 - 10 cycles of 2 mixes/ cycle with wash buffer A at 25C - non-stringent (6xSSPE, 0.01% Tween 20) Post Hyb wash #2 - 4 cycles of 15 mixes/ cycle with wash buffer B at 50C - stringent   (100mM MES, 0.1M [Na+], 0.01% Tween 20) 1st Stain   - 10 min. at 25C  (SAPE Stain: 300ul 2x MES stain buffer {41.7ml 12x MES, 92.5ml 5M NaCl, 2.5ml 10% Tween 20/ 250ml total vol. in DEPC H2O}, 24ul 50mg/ml acetylated BSA, 6ul 1mg/ml Streptavidin-R-Phycoerythrin conjugate, 270ul DEPC H2O, 600ul total vol.) Post Stain Wash- 10 cycles of 4 mixes/cycle with wash buffer A at 25C 2nd Stain   - 10 min. at 25C   (Antibody Stain: 300ul 2x MES stain buffer {see above}, 24ul 50 mg/ml acetylated BSA, 6ul 10mg/ml normal goat IgG, 3.6ul 0.5mg/ml biotinylated anti-streptavidine antibody, 266.4ul DEPC H2O, 600ul total vol.) 3rd Stain- 10 min at 25C   (SAPE stain: see above, 600ul total vol.) Final Wash- 15 cycles of 4 mixes/cycle with wash buffer A at 30C. The GeneChip remains filled with wash buffer A for the scanning procedure. GeneChip Expression 3’-Amplification IVT Labeling Washing and Staining Protocol Post Hyb wash #1 - 10 cycles of  2 mixes/ cycle with wash buffer A at 30ºC - non-stringent (6xSSPE, 0.01% Tween 20) Post Hyb wash #2 - 6 cycles of 15 mixes/ cycle with wash buffer B at 50ºC - stringent   (100mM MES, 0.1M [Na+], 0.01% Tween 20) 1st Stain   - 5 min. at 30ºC  (SAPE Stain: 300ul 2x MES stain buffer {41.7ml 12x MES, 92.5ml 5M NaCl, 2.5ml 10% Tween 20/ 250ml total vol. in DEPC H2O}, 24ul 50mg/ml acetylated BSA, 6ul 1mg/ml Streptavidin-R-Phycoerythrin conjugate, 270ul DEPC H2O, 600ul total vol.) Post Stain Wash- 10 cycles of 4 mixes/cycle with wash buffer A at 30ºC 2nd Stain   - 5 min. at 35ºC   (Antibody Stain: 300ul 2x MES stain buffer {see above}, 24ul 50 mg/ml acetylated BSA, 6ul 10mg/ml normal goat IgG, 3.6ul 0.5mg/ml biotinylated anti-streptavidine antibody, 266.4ul DEPC H2O, 600ul total vol.) 3rd Stain- 5 min at 35ºC   (SAPE stain: see above, 600ul total vol.) Final Wash- 15 cycles of 4 mixes/cycle with wash buffer A at 35ºC. The GeneChip remains filled with wash buffer A for the scanning procedure.

scan_protocol: Scanning: Automated process conducted using the Agilent GeneArray Scanner. - 2x scans are conducted for the Enzo protocol and 1x scans are conducted for the GeneChip Expression protocol as follows: Pixel value = 3um Wavelength = 570nm

data_processing: Data was generated and calculated using GCOS1.2

organism: Rattus norvegicus

source_name: Semi-Circular Canal Duct epithelium - Dex treated

label_protocol:
Affymetrix Small Sample Labeling Protocol vII (2xIVT)
First Cycle of Amplification
Step 1. First cycle, first strand cDNA synthesis
Note:  Use thermal cycler with a heated lid for incubations in this step. Use the 4oC hold for the addition of reagents.  70oC 6 minutes
4oC hold
42oC 60 minutes
70oC 10 minutes
4oC hold
a. Mix 1ul of total RNA (50ng/ul) with 1ul of 5uM T7(dT)24 in 0.2ul PCR tube and incubate at 70oC in thermal cycler with heated lid for 6 min.
(5’-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGTTTTTTTTTTTTTTTTTTTTTTTT-3’)
b. Cool to 4oC for 2 min.
c. Spin briefly.
d. Add 3ul of RT-Premix-1 master mix using the following components from the SuperScript Choice System (Invitrogen). It is recommended to assemble the master mix for at least four reactions to avoid pipetting small volumes.
1 rxn
DEPC treated water   0.375ul
5x first strand buffer   1ul
DTT, 0.1M    0.5ul
dNTP mix, 10mM   0.375ul
Rnase inhibitor, 40 U/ul  0.25ul
SuperScript II, 200 U/ul  0.5ul
Total Volume   3ul
e. Incubated at 42oC 60 minutes.
f. Heat sample at 70oC for 10 minutes to inactivate SuperScript II.
g. Spin briefly and cool sample to 4oC.
Step 2. First cycle, second strand cDNA synthesis
Note:  Use thermal cycler without heated lid for incubations in this step. Use 4oC hold for the addition of reagents.
16oC 120 minutes
4oC hold
16oC 10 minutes
4oC hold
a Prepare the SS-Premix-1 as follows using the components from the SuperScript Choice System (Invitrogen). It is recommended to assemble the master mix for at least four reactions to avoid pipetting small volumes.
1 rxn
DEPC treated water  22.75ul
5x second strand buffer  7.5ul
dNTP mix, 10mM  0.75ul
DNA ligase, E. coli, 10U/ul 0.25ul
DNA polymerase I, E. coli 10U/ul 1ul
Rnase H, 2U/ul   0.25ul
Total Volume   32.5ul
b. Add 32.5ul of the SS-Premix-1 to each first strand reaction making a final volume of 37.5ul.
c. Mix by pipetting and spin briefly.
d. Incubate the samples at 16oC for 2 hours.
e. Add 1ul of T4 DNA polymerase (5U/ul) to the reaction and mix by pipetting.
f. Continue incubation at 16oC for 10 minutes.
Step 3. First cycle, double-stranded cDNA cleanup by ethanol precipitation.
a. Transfer the reaction to a 1.5 ml centrifuge tube.
b. Add 80ul of DEPC treated water to dilute reaction.
c. Add 2ul of glycogen (5 mg/ml), 0.6 volumes (72ul) of 5M NH4OAc, and 2.5 volumes (480ul) of cold absolute ethanol. Mix by pipetting.
d. Precipitate the double-stranded cDNA at -20oC for 2 hours.
e. Centrifuge at 14,000rpm for 20 minutes at 4oC.
f. Wash pellet with 800ul of 70% cold ethanol.
g. Centrifuge at 14,000rpm for 5 minutes at 4oC.
h. Remove ethanol and dry pellet in speed vacuum for 10 minutes.
Step 4.  First cycle, IVT for cRNA amplification using MEGAscript T7 kit (Ambion).
a. At room temperature, add the following reagents to the dried double-stranded cDNA pellet, in the order indicated.

1rxn
DEPC treated water  4ul
Premixed NTPs, 18.75mM each 4ul
10x reaction buffer  1ul
10x enzyme mix   1ul
Total Volume   10ul
b. Mix well by pipetting. Spin briefly.
c. Incubate at 37oC for 5 hours mixing every 30 minutes.
Step 5.  First cycle, cRNA cleanup with Qiagen RNeasy columns.
a. Add 90ul of Rnase-free water to sample.
b. Follow the RNeasy Mini Protocol for RNA Cleanup as directed in the RNeasy Mini Kit handbook.
c. In the last step of the purification, elute the cRNA sample with 30ul of Rnase-free water first, and follow with an additional 20ul of water for the second elution.
d. Determine the cRNA yield by conducting a 1/10 dilution in water and measuring the absorbance at 260nm.
e. Transfer 400ng of cRNA to a new 1.5ml tube and use speed vacuum to concentrate sample to 4ul. Avoid drying the sample completely.  Note: If the yield is less that 400ng, use the entire sample for the second cycle of cDNA synthesis.
Second Cycle of Amplification and Labeling
Step 6.  Second cycle, first strand cDNA synthesis.
Note: Use heating blocks for incubation in this step.
a. Add random primers to the cRNA sample and mix well.
cRNA, 400ng   4ul
Random primers, 0.2 ug/ul  1ul
Total Volume   5ul
b. Incubate at 70oC for 10 minutes to denature cRNA.
c. Cool sample on ice for 2 minutes.
d. Prepare the RT-Premix-2 as follows using the components from the SuperScript Choice System (Invitrogen). It is recommended to assemble the master mix for at least two reactions to avoid pipetting small volumes.

1rxn
5x first strand buffer   2ul
DTT, 0.1M    1ul
dNTP mix, 10mM   0.5ul
RNase Inhibitor, 40 U/ul   0.5ul
SuperScript II, 200 U/ul   1ul
Total Volume    5ul
e. Add 5ul of the RT-Premix-2 to the denatured RNA and primer mixture, making a final volume 10ul. Mix well by pipetting. Spin briefly.
f. Incubate the sample at 42oC for 1 hour. Spin briefly.
g. To remove the RNA template, add 1ul of RNase H (2 U/ul) and incubate the sample at 37oC for 20 minutes.
h. Heat the sample at 95oC for 5 minutes to inactivate RNase H.
i. Cool sample on ice 2 minutes. Spin briefly.
Step 7.  Second cycle, second strand cDNA synthesis
Note:  Transfer sample to a 0.2 ml PCR tube and perform the incubations in a thermal cycler without a heated lid. Use the 4oC hold to add reagents.
70oC  6 minutes
4oC  hold
16oC  120 minutes
4oC  hold
16oC  10 minutes
4oC  hold
a. Add 2.0ul of the 5uM T7(dT)24 promoter primer to the chilled sample from the previous step.
b. Mix well. Spin briefly.
c. Incubate sample at 70oC for 6 minutes.
d. Cool the sample to 4oC and spin briefly.
e. Prepare the SS-Premix-2 as follows using the components from the SuperScript Choice System (Invitrogen).
1rxn
DEPC treated water   43.5ul
5x second strand buffer   15ul
dNTP mix, 10mM   1.5ul
DNA polymerase I, E. coli, 10 U/ul  2ul
Total Volume    62ul
f. Add 62ul of the SS-Premix-2 to the sample making a total volume of 75ul. Mix well by pipetting. Spin briefly.
g. Incubate at 16oC for 2 hours.
h. Add 2ul of T4 DNA polymerase (5 U/ul) to the reaction. Mix well.
i. Incubate at 16oC for 10 minutes.
Step 8.  Second cycle, double-strand cDNA cleanup by ethanol precipitation.
a. Add 2ul of 5 mg/ml glycogen, 0.6 volume 5M NH4OAc, and 2.5 volumes of cold absolute ethanol.
b. Mix well by pipetting.
c. Precipitate the double-stranded cDNA at -20oC for 30 minutes.
d. Centrifuge the sample at 14,000 rpm for 20 minutes at 4oC.
e. Carefully remove supernatant and wash the cDNA pellet by adding 800ul of 70% cold ethanol.
f. Centrifuge the tube at 14,000 rpm for 5 minutes at 4oC.
g. Carefully remove the ethanol. Dry pellet in a speed vacuum for 10 minutes.
h. Store dry pellet at –20oC or proceed to next step.
Step 9.  Second cycle, IVT for cRNA amplification and labeling with ENZO BioArray High Yield RNA Transcription
Labeling Kit  (Affymetrix)  or GeneChip Expression 3’-Amplification IVT Labeling kit (Affymetrix).
a. At room temperature, add the following reagents to the dried double-stranded cDNA pellet.
Enzo BioArray High Yield RNA Transcription Labeling kit
1rxn
DEPC treated water  22ul
10X HY reaction buffer  4ul
10X Biotin labeled ribonucleotides 4ul
10X DTT   4ul
10X RNase inhibitor mix  4ul
20X T7 RNA polymerase  2ul
Total Volume   40ul
1. Mix the components well after adding each reagent; especially after adding water, ensuring the cDNA
pellet is completely dissolved.
2. Incubate at 37oC for 5 hours mixing every 30 minutes.
GeneChip Expression 3’-Amplification IVT Labeling Kit
1rxn
DEPC treated water  20ul
10x IVT Labeling Buffer 4ul
IVT Labeling NTP Mix  12ul
IVT Labeling Enzyme Mix4ul
Total Volume   40ul
1. Mix components well after adding each reagent, especially after adding water, ensuring the cDNA pellet
is completely dissolved.
2. Incubate at 37ºC for 16 hours in a hybridization oven or thermal cycler with a heated lid to prevent
condensation.
Step

extract_protocol: Total RNA was extracted from SCCD primary culture cells using a RNeasy Micro kit following the manufacturer's protocol (no.74004, Qiagen; Valencia, CA).

treatment_protocol: SCCD primary culture cells treated with 100nM Dexamethasone

value: Semi-Circular Canal Duct (SCCD) Epithelia

tag: animal

value: Rat

tag: age:


title: metastatic liver tumor/non-tumor/control-01

description:
Batch1
JC-01

tag: hcv association

tag: cell line

value: multiple


title: metastatic liver tumor/non-tumor/control-07

description:
Batch8
JC-07


title: KSU-AP-DM Rat Semi-Circular Canal Duct D3-A

data_processing: Data was generated and calculated from GCOS1.2

label: Affymetrix Small Sample Labeling Protocol vII (2xIVT)

extract_protocol: Total RNA was extracted from SCCD primary culture cells treated with 100 nM Dexamethasone using a RNeasy Micro Kit following the manufacturer's protocol (no. 74004, Qiagen; Valencia, CA)


title: KSU-AP-DM Rat Semi-Circular Canal Duct C4-A

source_name: Semi-Circular Canal Duct epithelium untreated

extract_protocol: Total RNA was extracted from untreated SCCD primary culture cells using a RNeasy Micro Kit following the manufacturer's protocol (no. 74004, Qiagen; Valencia, CA)

treatment_protocol: Untreated SCCD primary culture cells

value: Semi-Circular Canal Duct(SCCD) Epithelia


title: TAX577622 [33K]

value: Breast cancer (HER2+)

tag: er

tag: osbin

tag: os

value: Promega male reference DNA


title: metastatic liver tumor/non-tumor/control-06

description:
Batch4
JC-06


title: KSU-AP-DM Rat Semi-Circular Canal Duct D2-A

source_name: Semi-Circular Canal Duct Epithelium - Dex treated


title: jos0008-2

value: skeletal muscle

tag: age (years)

tag: bmi (kg/m2)

tag: fpg (mg/dl)


title: KSU-AP-DM Rat Semi-Circular Canal Duct C1-A

description:
- Absolute and comparison analysis are conducted using the following settings:
      Scaling - All Probe Sets: Target Signal = 500
      Normalization – User Defined: Scale Factor = 1

extract_protocol: Total RNA was extracted from untreated SCCD primary culture cells using a RNeasy Micro kit following the manufacturer's protocol (no. 74004, Qiagen; Valencia, CA).


title: metastatic liver tumor/non-tumor/control-03

description:
Batch3
JC-03


title: PC-3

city: New Haven

first: Cheryl

middle: L.

last: Maier

state: CT

address: 10 Amistad St.

department: Immunobiology

institute: Yale University

description: Subculture 1

hyb_protocol: The standard Illumina hybridization protocol was followed. Labeled cRNA was mixed with the hybridization control and hybridized to the array for 16 hours on a rocking platform at 58C in a hybridization oven. The array chip was serially washed, stained with streptavidin-Cy3, washed again, then dried.

scan_protocol: The array was scanned using the Illumina BeadArray reader following the standard manufacturer's instructions.

data_processing:
Images were analyzed using the Illumina GenomeStudio software including quality control and data analysis recommendations according to the instructions provided by Illumina. Quality control parameters included housekeeping controls, hybridization controls, and negative controls (representing background). Data was normalized using quantile normalization. Mean signal intensities were generated by background subtraction of negative controls.

Non-normalized data values (available from the Series record) represent software-generated signal intensities without background subtraction. Normalized values represent quantile-normalized signal intensities with background subtraction.

source_name: Placental Pericyte Isolate 3

label_protocol: Biotinylated cRNA were prepared with the Ambion Amplification kit for Illumina arrays. Single-stranded cDNA, synthesized by reverse transcription using poly (A) RNA present in the starting total RNA sample, was converted to double-stranded cDNA and purified using the Illumina TotalPrep RNA Amplification Kit per the manufacturer's instructions. Biotin-labeled cRNA was then generated from the double-stranded cDNA by an in vitro transcription reaction carried out overnight in the presence of biotinylated UTP and CTP, which was then also purified using the Illumina TotalPrep RNA  Amplification Kit.

growth_protocol: Single-donor primary placental microvessel outgrowth cells were collected and plated onto 100mm tissue culture plates.

extract_protocol: Total RNA was isolated using the RNEasy minikit, including DNase treatment with the RNeasy cleanup protocol, per the manufacturer's instructions (Qiagen).

treatment_protocol: RNA was isolated from pericytes at subculture 1 that had reached 90% confluence and were confirmed to express pericyte markers in parallel cultures.

value: placenta

tag: cell type

value: pericyte

tag: subculture

tag: isolate


title: Case6 metastatic liver GIST

status: Public on Apr 13 2010

city: Hamamatsu

first: Hirotoshi

last: Kikuchi

address: 1-20-1 Handayama, Higashi-ku

department: Second Department of Surgery

country: Japan

institute: Hamamatsu University School of Medicine

description: Gene expression data from metastasic GIST

hyb_protocol: Following fragmentation, 4.95 ug of cDNA were hybridized for 17 hr at 45C on Genechip Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000 7G by Affymetrix Genechip Command Console (AGCC).

data_processing: The data were analyzed with Genespring GX10 software and RMA.

source_name: Case6 metastatic liver GIST

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 300ng total RNA (GeneChip Whole Transcript Sense Target Labeling Assay Manual, 2007, Affymetrix).

extract_protocol: Total RNA was extracted from frozen tumor samples using ISOGEN (WAKO) following the RNeasy Mini Kit (Qiagen).

tag: organ

value: Liver


title: metastatic liver tumor/non-tumor/control-02

description:
Batch2
JC-02

tag: tissue

tag: disease

tag: tumor tissue


title: jos0007-2

tag: disease state

value: control

tag: family history

tag: sex


title: jos0006-2

value: DM


title: TAX577679 [33K]

tag: age

tag: ln

tag: primary

tag: grade

tag: reference


title: KSU-AP-DM Rat Semi-Circular Canal Duct C3-A

value: Semi-Circular Canal Duct epithelium

tag: animal

tag: age:


title: KSU-AP-DM Rat Semi-Circular Canal Duct C2-A

source_name: Semi-Circular Canal duct epithelium untreated


title: Case7 metastatic liver GIST

source_name: Case7 metastatic liver GIST


title: Case8 metastatic liver GIST

source_name: Case8 metastatic liver GIST


title: PC-1

description: Subculture 1

source_name: Placental Pericyte Isolate 1

tag: cell type


title: Control_6h_rep5

first: Sajeev

last: Batra

hyb_protocol: Cy5 labeled sample was hybridized to the MEEBO array in 3x SSC at 63C overnight.

scan_protocol: MEEBO arrays were scanned with an Axon 4000B scanner (Axon Instruments, Union City, CA, USA) and gridded using SpotReader.

data_processing: Spot analysis was performed with Spotreader and stored in a relational database (Acuity). Data were ratio normalized, and control and poor-quality features (as determined by both visual examination and application of quantitative filters for saturation, feature diameter, and variance) were removed. Data were further filtered for spots that did not exhibit signal in any of the sample channels (based on the percentage of pixels in the feature above background and feature intensity) and for excessive missing data. The ratio of medians of the remaining data was transformed to log2 space, median centered by array, and median centered by gene.

source_name: Amplified RNA from bone marrow-derived macrophages

label_protocol: RNA extracted from the samples was amplified using Amino Allyl MessageAmp II aRNA kit from Ambion. The amplified material was then coupled to Cy5.

extract_protocol: Qiagen RNeasy Mini Kit

tag: strain

value: 8 w

value: bone marrow derived macrophages

source_name: pool of amplified RNA from each of the 4 timepoints of a given timecourse

label_protocol: RNA extracted from the samples was amplified using Amino Allyl MessageAmp II aRNA kit from Ambion . The amplified material was then coupled to Cy3.


title: Case3 primary GIST

description: Gene expression data from primary GIST

source_name: Case3 primary GIST

value: Stomach


title: Control_12h_rep5


title: KSU-AP-DM Rat Semi-Circular Canal Duct D1-A

value: Semi-Circular Canal Duct epithelium - Dex treated


title: Case4 metastatic liver GIST

source_name: Case4 metastatic liver GIST


title: Case5 metastatic liver GIST

source_name: Case5 metastatic liver GIST


title: T._cruzi_6h_rep2


title: T._cruzi_24h_rep2


title: PC-2

description: Subculture 1

source_name: Placental Pericyte Isolate 2

tag: subculture

tag: isolate


title: Case2 primary GIST

description: Gene expression data from primary GIST

source_name: Case2 primary GIST

tag: organ


title: Control_0h_for_T._cruzi_rep2


title: Control_24h_rep5


title: Case1 primary GIST

description: Gene expression data from primary GIST

source_name: Case1 primary GIST


title: Control_2h_rep5


title: Control_0h_for_Control_rep5


title: T._cruzi_12h_rep2


title: T._cruzi_2h_rep2


title: L._mex_6h_rep3


title: L._mex_2h_rep3


title: L._mex_12h_rep3


title: Control_6h_rep4


title: Reference DNA MaMel_L_119

city: Heidelberg

first: Andreas

last: Gast

state: BW

address: INF 580

department: Division of Molecular Genetic Epidemiology

country: Germany

institute: Gernman Cancer Research Center

description: Hybridized to 250K_StyI

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to the array according to manufacturer's instructions.

scan_protocol: The arrays were washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing: CEL files and TXT files (generated by Affymetrix GTYPE) were analyzed by CNAT (Affymetrix) and CNAG (Nannya et al., 2005). Genotype Call (SNP call): AA, AB, BB,  and NoCall; "confidence" = confidence score (rank score for genotype call used)

source_name: Peripheral blood mononuclear cells (PBMC)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from cell lines or mononuclear cell preparations obtained from peripheral blood using commercially available DNA or RNA Purification kits (Puregene) according to manufacturer's instructions. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

tag: disease status

value: metastatic melanoma patient

tag: tissue

value: peripheral blood

value: mononuclear cells


title: Control_0h_for_L._mex_rep3


title: Control_24h_rep4


title: Reference DNA MaMel_L_128a

description: Hybridized to 250K_StyI


title: Control_12h_rep4


title: L._mex_24h_rep3


title: Control_2h_rep4


title: LPS_24h


title: Control_0h_for_Control_rep4


title: LPS_12h_2nd_scan


title: LPS_12h


title: Reference DNA MaMel_L_130

description: Hybridized to 250K_StyI


title: LPS_6h


title: LPS_2h


title: Reference DNA MaMel_L_136

description: Hybridized to 250K_StyI


title: Reference DNA MaMel_L_114

description: Hybridized to 250K_StyI


title: Control_0h_for_LPS


title: L._mex_12h_rep2


title: L._mex_24h_rep2


title: Reference DNA MaMel_L_95

description: Hybridized to 250K_StyI


title: Reference DNA MaMel_L_107

description: Hybridized to 250K_StyI


title: L._mex_6h_rep2


title: Control_0h_for_L._mex_rep2


title: L._mex_2h_rep2


title: Reference DNA MaMel_L_KNUD

description: Hybridized to 250K_StyI


title: Reference DNA MaMel_L_126

description: Hybridized to 250K_StyI


title: Reference DNA MaMel_L_101

description: Hybridized to 250K_StyI


title: Reference DNA MaMel_L_113

description: Hybridized to 250K_StyI


title: IL17_24h


title: Reference DNA MaMel_L_85

description: Hybridized to 250K_StyI


title: IL17_12h


title: Reference DNA MaMel_L_94

description: Hybridized to 250K_StyI


title: Reference DNA MaMel_L_79b

description: Hybridized to 250K_StyI


title: IL17_2h


title: IL17_6h


title: Reference DNA MaMel_L_75

description: Hybridized to 250K_StyI


title: Reference DNA MaMel_L_103a

description: Hybridized to 250K_StyI


title: Control_0h_for_IL17


title: Reference DNA MaMel_L_110

description: Hybridized to 250K_StyI


title: IL10_24h


title: Reference DNA MaMel_L_76

description: Hybridized to 250K_StyI


title: Reference DNA MaMel_L_69

description: Hybridized to 250K_StyI


title: Reference DNA MaMel_L_80a

description: Hybridized to 250K_StyI


title: IL10_6h


title: IL10_12h


title: IL10_2h_2nd_scan


title: Control_0h_for_IL10


title: Reference DNA MaMel_L_71

description: Hybridized to 250K_StyI


title: Reference DNA MaMel_L_134

description: Hybridized to 250K_StyI


title: IL10_2h


title: Control_24h_rep3


title: Control_6h_rep3


title: Reference DNA MaMel_L_67

description: Hybridized to 250K_StyI


title: Reference DNA MaMel_L_66a

description: Hybridized to 250K_StyI


title: Reference DNA MaMel_L_59a

description: Hybridized to 250K_StyI


title: Reference DNA MaMel_L_61a

description: Hybridized to 250K_StyI


title: Reference DNA MaMel_L_86a

description: Hybridized to 250K_StyI


title: Reference DNA MaMel_L_63a

description: Hybridized to 250K_StyI


title: Control_0h_for_Control_rep3


title: IFNB_24h


title: Reference DNA MaMel_L_60

description: Hybridized to 250K_StyI


title: IFNB_2h


title: Control_0h_for_IFNB


title: Reference DNA MaMel_L_37a

description: Hybridized to 250K_StyI


title: IFNB_12h


title: Reference DNA MaMel_L_53

description: Hybridized to 250K_StyI


title: Control_12h_rep3


title: Control_2h_rep3


title: Reference DNA MaMel_L_30

description: Hybridized to 250K_StyI


title: IFNG_12h


title: IFNG_24h


title: Reference DNA MaMel_L_12

description: Hybridized to 250K_StyI


title: Reference DNA MaMel_L_19

description: Hybridized to 250K_StyI


title: Reference DNA MaMel_L_13

description: Hybridized to 250K_StyI


title: Reference DNA MaMel_L_17

description: Hybridized to 250K_StyI


title: Reference DNA MaMel_L_11

description: Hybridized to 250K_StyI


title: Reference DNA MaMel_L_62

description: Hybridized to 250K_StyI


title: Control_0h_for_IFNG


title: Reference DNA MaMel_L_08a

description: Hybridized to 250K_StyI


title: IFNG_2h


title: TNF_12h


title: IFNG_6h


title: Reference DNA MaMel_L_21

description: Hybridized to 250K_StyI


title: Reference DNA MaMel_L_27

description: Hybridized to 250K_StyI


title: TNF_24h


title: TNF_6h


title: Reference DNA MaMel_L_36

description: Hybridized to 250K_StyI


title: IFNB_6h


title: Reference DNA MaMel_L_35

description: Hybridized to 250K_StyI


title: Melanoma cell line MaMel134

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel134, derived from metastatic tumor

value: metastatic tumor

tag: cell line


title: Melanoma cell line MaMel128a

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel128a, derived from metastatic tumor


title: Reference DNA MaMel_L_5

description: Hybridized to 250K_StyI


title: Control_0h_for_TNF


title: Melanoma cell line MaMel150a

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel150a, derived from metastatic tumor


title: IL4_24h


title: Melanoma cell line MaMel_KNUD

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel_KNUD, derived from metastatic tumor


title: Melanoma cell line MaMel136

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel136, derived from metastatic tumor


title: IL4_12h


title: IL4_6h


title: IL4_2h


title: TNF_2h


title: Melanoma cell line MaMel119

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel119, derived from metastatic tumor


title: Control_12h_rep2


title: Control_0h_for_IL4


title: Control_6h_rep2


title: Melanoma cell line MaMel110

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel110, derived from metastatic tumor


title: Melanoma cell line MaMel130

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel130, derived from metastatic tumor


title: Control_2h_rep2

source_name: Amplified RNA from bone marrow-derived macrophages


title: Control_24h_rep2

source_name: pool of amplified RNA from each of the 4 timepoints of a given timecourse


title: Control_0h_for_Control_rep2