title: VIN_96hr_femaleOvary_5

status: Public on Aug 22 2012

city: Cincinnati

first: Rong-Lin

last: Wang

address: 26 W MLK Dr

institute: US EPA

description:
Ave10290_1_4rProcessedSignal
Ave10290_1_4gProcessedSignal
for gene classifier discovery

hyb_protocol: Equal amounts of Cy3- and Cy5-labeled cRNA (750 ng each) were hybridized to a zebrafish oligo microarray for 17 h at 65C. The hybridized microarrays were then washed according to the manufacturer's protocol.

scan_protocol: Scanned by a 16-bit Agilent G2565BA scanner at 10-um resolution with the red and green photomultiplier tubes set to 100% and a scan area of 61 by 21.6 mm

data_processing:
Text output of individual samples (rProcessedSignal, gProcessedSignal) from Agilent Feature Extraction software were filtered according to Agilent recommendations (feature saturation, uniformity, pixel population consistency, signal strength relative to background; Agilent Technologies Training Manual, version 4.5).  Samples were then organized either by tissue types or combined. Missing data were imputed by KNNimputer (Troyanskaya et al., 2001, Bioinformatics). This was followed by thresholding, log2 transformation, per chip normalization to 75th percentile, and per gene normation to the median of all samples [available as Series supplementary files].

The biological samples for controls were duplicated between TRI_96hr_femaleOvary and TRI_96hr_femaleOvaryLowDose as well as between TRI_96hr_maleTestis and TRI_96hr_maleTestisLowDose. These redundant controls were therefore included only once in their respective matrix files (classifier_discovery_ovary.txt, classifier_discovery_testis.txt), giving rise to their odd number of columns. In total, there are five processed/normalized matrix files either for classifier discovery or validation:

The numeric identifiers in the data matrix column headers (Sample Description field above) correspond to the unique microarray identifiers in the file names of raw text files. For example, rProcessedSignal'612' for US23502387_251322310'612'_S01_22k.txt, and Ave'10237_1_2'rProcessedSignal for US23502303_2515064'10237'_S01_GE2-v5_95_Feb07_'1_2'.txt

classifier_discovery_brain.txt: 80 treated + 80 control
classifier_discovery_ovary.txt: 105 treated + 100 control
classifier_discovery_testis.txt: 84 treated + 79 control
classifier_discovery_allTissue.txt: all three tissues combined plus 21 liver samples, 290 treated + 290 control
classifier_validation.txt: 24 treated + 28 control.

The processed/normalized data files contain rProcessedSignal and gProcessedSignal (log2 transformed, per chip and per gene normalized) from the indicated samples.

organism: Danio rerio

source_name: ovary_female_VIN_96 hr

label_protocol: Purified total RNA samples were shipped overnight on dryice to an Agilent-certified contract laboratory (Cogenics, Morrisville, NC 27560, USA), where all microarray gene expression profiling was performed. The quantity and quality of the RNA samples were assessed with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies,Wilmington, DE, USA) and an Agilent 2100 bioanalyzer. One microgram of total RNA from each sample was amplified and labeled with a fluorescent dye (either Cy3 or Cy5) with the use of a low-RNA input linear amplification labeling kit following the manufacturer's protocol). The quantity and purity of the resulting fluorescently labeled cRNA was evaluated with the Nanodrop ND-1000 spectrophotometer, and the size distribution was determined with an Agilent bioanalyzer.

growth_protocol: Reproductively mature fish were obtained from an onsite culture unit at the US EPA National Health and Human Effects Research laboratory. Three days before the initiation of exposure, fish were randomly loaded into tanks receiving a continuous flow of Lake Superior water (USA) pumped from 200 m offshore at a depth of 20 m (mesh size 1 um, flow rate 45 ml/min).  Each tank held 10 males and 10 females.

extract_protocol: Tissues were removed from RNAlater and placed on ice in 1.5-ml RNase-free microcentrifuge tubes (Ambion) containing 1 ml of TriReagent (Molecular Research Center,Cincinnati, OH)and then placed on ice for a short duration.  They were homogenized by physical disruption at 30 Hz for 5 min in a Retsch MM300 mixer mill (Retsch Laboratory Equipment, Newtown, PA, USA). Individual homogenates were immediately processed or stored at 80C in TriReagent. Total RNA was extracted following the manufacturer's protocol. Briefly, 100 ul of 1-bromo-3-chloropropane (BCP, Molecular Research Center) were added to each homogenized tissue in 1 ml of TriReagent, vortexed, and incubated at room temperature for 10 min. The BCP/TriReagent mixture was then centrifuged at 12,000 g for 15 min at 4C. The aqueous phase was transferred to a new RNase-free microcentrifuge tube containing 500 ul of 100% isopropanol and then gently agitated. Precipitated samples were centrifuged at 12,000 g for 10 min at 4C, and supernatants were decanted. One milliliter of 75% ethanol was added to the precipitant, and samples were spot vortexed and centrifuged for 10 min at 12,000 g at 4C. Supernatant was decanted, and the remaining volume was aspirated. The RNA pellets were resuspended in nuclease-free water (Ambion) by incubation at 4C for several hours. To remove any trace organic contaminants, RNA samples were reprecipitated using a 0.1 volume of 3 M sodium acetate (Ambion) and two volumes of 100% ethanol and then incubating at 80C for at least 20 min. Precipitated RNA was centrifuged at 12,000 g at 4C for 20 min, and the supernatant was removed. The RNA was resuspended in RNase-free water at 4C for several hours. The RNA was then quantified spectrophotometrically, and light absorbance at 260 and 280 nm was used as a measure of relative purity and quantity. The RNA samples were analyzed for structural integrity using either agarose gel electrophoresis or the Bioanalyzer NanoRNA kit (Agilent Technologies, Palo Alto, CA, USA). All RNA displayed 260:280-nm ratios of 1.7 or greater and had 28S:18S ratios of approximately two. Extracted total RNA was stored at 80C until subsequent use.

treatment_protocol: Reproductively mature male and female zebrafish were exposed to a continuous flow of test chemical (an analytically-confirmed concentration and a control), delivered in water (with no solvent), for 24, 48, or 96 hrs

value: AB

tag: genotype/variation

value: wild-type

tag: age

value: 5 months

value: female

value: ovary

tag: treated with

value: VIN (vinclozolin) at 1000 ug/L for 96hr

source_name: ovary_female_water control_96 hr

tag: treatment

value: in water control for 96 hr


title: VIN_96hr_femaleOvary_2

type: RNA

country: USA

description:
Ave10213_1_2rProcessedSignal
Ave10213_1_2gProcessedSignal
for gene classifier discovery

molecule: total RNA

tag: strain

tag: gender

tag: tissue


title: VIN_96hr_femaleOvary_4

description:
Ave10248_1_4rProcessedSignal
Ave10248_1_4gProcessedSignal
for gene classifier discovery


title: Duke_DnaseSeq_HSMM_FSHD

status: Public on Sep 25 2012

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

library_source: genomic

data_processing:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeOpenChromDnase

Raw data witheld due to privacy concerns.

molecule: genomic DNA

organism: Homo sapiens

extract_protocol: Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeOpenChromDnase

tag: datatype

value: DnaseSeq

tag: datatype description

value: DNaseI HS Sequencing

tag: labversion

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_male,p-value cutoff:0.05

tag: cell

tag: cell organism

value: human

tag: cell description

value: primary myoblast from Facioscapulohumeral Muscular Dystrophy (FSHD) patients, muscle needle biopsies

tag: cell sex

value: U

value: baseAlignCounts.pl v 1


title: VIN_96hr_femaleOvary_3

description:
Ave10247_1_3rProcessedSignal
Ave10247_1_3gProcessedSignal
for gene classifier discovery


title: Duke_DnaseSeq_HSMM_emb

value: embryonic myoblast


title: Lung cancer ADK4

status: Public on May 24 2013

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

country: France

institute: INSERM-UGA

hyb_protocol: 20 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 array.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray scanner

data_processing: The data was normalized by Robust Multi-Array average (RMA) algorithm (Genespring software; Agilent)

label: Biotin

source_name: Lung Tumour

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

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

value: lung tumour

tag: age at surgery

value: M

tag: histology

value: ADC

tag: pt stage

tag: pn stage

tag: pm stage

tag: follow-up time (months)

tag: status

value: DEAD

tag: disease free survival in months

tag: relapse (event=1; no event=0)


title: Non tumoral lung3

source_name: Non Tumoral Lung

tag: tissue

value: NTL

tag: gender


title: VIN_96hr_femaleOvary_1

description:
Ave10201_1_3rProcessedSignal
Ave10201_1_3gProcessedSignal
for gene classifier discovery

tag: strain

value: AB

tag: genotype/variation

value: wild-type

tag: age

value: 5 months

value: female

tag: treated with

tag: treatment


title: Lung cancer ADK7

value: ALIVE


title: UNC_FaireSeq_Endometrium_OC

status: Public on Sep 28 2012

data_processing:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeOpenChromFaire

Raw data witheld due to privacy concerns.

extract_protocol: Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeOpenChromFaire

tag: datatype

value: FaireSeq

tag: datatype description

value: FAIRE-seq Open Chromatin

tag: controlid

tag: labversion

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_female,p-value cutoff:0.1

tag: cell

tag: cell organism

tag: cell description

value: Endometrium isolated from uterine lining

tag: cell karyotype

value: normal

tag: cell sex

value: F


title: VIN_48hr_femaleOvary_4

description:
Ave10351_1_2rProcessedSignal
Ave10351_1_2gProcessedSignal
for gene classifier discovery

source_name: ovary_female_VIN_48 hr

value: ovary

value: VIN (vinclozolin) at 1000 ug/L for 48hr

source_name: ovary_female_water control_48 hr

value: in water control for 48 hr


title: Lung cancer ADK33

value: lung tumour

tag: age at surgery

value: M

tag: histology

value: ADC

tag: pt stage

tag: pn stage

tag: pm stage

tag: follow-up time (months)

tag: status

tag: disease free survival in months

tag: relapse (event=1; no event=0)


title: VIN_48hr_femaleOvary_3

description:
Ave10290_1_2rProcessedSignal
Ave10290_1_2gProcessedSignal
for gene classifier discovery

tag: strain

value: AB

tag: genotype/variation

tag: age

tag: gender

tag: tissue

tag: treated with

tag: treatment


title: Lung Squamous Cell Carcinoma2

value: SQC

value: DEAD


title: VIN_48hr_femaleOvary_2

description:
Ave10247_1_2rProcessedSignal
Ave10247_1_2gProcessedSignal
for gene classifier discovery

value: wild-type

value: 5 months

value: female


title: TRI_96hr_femaleOvaryLowDose_5

description:
Ave10334_1_4rProcessedSignal
Ave10334_1_4gProcessedSignal
for gene classifier discovery

source_name: ovary_female_TRI_96 hr at low dose

value: TRI (trilostane) at 500 µg/liter for 96hr

value: in water control for 96 hr


title: TRI_96hr_femaleOvaryLowDose_3

description:
Ave10332_1_4rProcessedSignal
Ave10332_1_4gProcessedSignal
for gene classifier discovery


title: TRI_96hr_femaleOvary_2

description:
Ave10331_1_4rProcessedSignal
Ave10331_1_4gProcessedSignal
for gene classifier discovery
control sample identical to that of US23502303_251506410331_S01_GE2-v5_95_Feb07_1_3.txt

source_name: ovary_female_TRI_96 hr

value: TRI (trilostane) at 2500 µg/liter for 96hr


title: Lung Squamous Cell Carcinoma4

value: ALIVE


title: TRI_96hr_femaleOvary_4

description:
Ave10333_1_4rProcessedSignal
Ave10333_1_4gProcessedSignal
for gene classifier discovery
control sample identical to that of US23502303_251506410333_S01_GE2-v5_95_Feb07_1_2.txt


title: TRI_96hr_femaleOvary_1

description:
Ave10330_1_3rProcessedSignal
Ave10330_1_3gProcessedSignal
for gene classifier discovery
control sample identical to that of US23502303_251506410330_S01_GE2-v5_95_Feb07_1_2.txt


title: VIN_48hr_femaleOvary_5

description:
Ave10351_1_4rProcessedSignal
Ave10351_1_4gProcessedSignal
for gene classifier discovery


title: TRB_48hr_femaleOvary_2

description:
Ave10150_1_4rProcessedSignal
Ave10150_1_4gProcessedSignal
for gene classifier discovery

source_name: ovary_female_TRB_48 hr

value: TRB (17 -trenbolone) 3 ug/L for 48hr


title: TRB_24hr_femaleOvary_4

description:
Ave10356_1_2rProcessedSignal
Ave10356_1_2gProcessedSignal
for gene classifier discovery

source_name: ovary_female_TRB_24 hr

value: ovary

value: TRB (17 -trenbolone) 3 ug/L for 24hr

source_name: ovary_female_water control_24 hr

value: in water control for 24 hr


title: TRB_48hr_femaleOvary_4

description:
Ave10355_1_2rProcessedSignal
Ave10355_1_2gProcessedSignal
for gene classifier discovery

value: in water control for 48 hr


title: PRO_96hr_femaleOvary_3

description:
Ave10084_1_2rProcessedSignal
Ave10084_1_2gProcessedSignal
for gene classifier discovery

source_name: ovary_female_PRO_96 hr

value: PRO (prochloraz) 500 ug/L for 96hr


title: TRB_24hr_femaleOvary_3

description:
Ave10355_1_4rProcessedSignal
Ave10355_1_4gProcessedSignal
for gene classifier discovery


title: TRB_48hr_femaleOvary_3

description:
Ave10345_1_4rProcessedSignal
Ave10345_1_4gProcessedSignal
for gene classifier discovery


title: TRB_24hr_femaleOvary_5

description:
Ave10357_1_4rProcessedSignal
Ave10357_1_4gProcessedSignal
for gene classifier discovery


title: TRB_48hr_femaleOvary_5

description:
Ave10356_1_4rProcessedSignal
Ave10356_1_4gProcessedSignal
for gene classifier discovery


title: TRB_48hr_femaleOvary_1

description:
Ave10149_1_3rProcessedSignal
Ave10149_1_3gProcessedSignal
for gene classifier discovery


title: VIN_48hr_femaleOvary_1

description:
Ave10213_1_4rProcessedSignal
Ave10213_1_4gProcessedSignal
for gene classifier discovery

value: VIN (vinclozolin) at 1000 ug/L for 48hr


title: PRO_96hr_femaleBrain_1

description:
Ave10072_1_3rProcessedSignal
Ave10072_1_3gProcessedSignal
for gene classifier discovery

source_name: brain_female_PRO_96 hr

value: AB

value: brain

source_name: brain_female_water control_96 hr


title: TRB_24hr_femaleOvary_2

description:
Ave10150_1_3rProcessedSignal
Ave10150_1_3gProcessedSignal
for gene classifier discovery


title: PRO_96hr_femaleOvary_2

description:
Ave10083_1_3rProcessedSignal
Ave10083_1_3gProcessedSignal
for gene classifier discovery


title: PRO_48hr_femaleOvary_5

description:
Ave10095_1_3rProcessedSignal
Ave10095_1_3gProcessedSignal
for gene classifier discovery

source_name: ovary_female_PRO_48 hr

value: PRO (prochloraz) 500 ug/L for 48hr


title: PRO_96hr_femaleOvary_5

description:
Ave10095_1_4rProcessedSignal
Ave10095_1_4gProcessedSignal
for gene classifier discovery

value: wild-type


title: PRO_48hr_femaleOvary_3

description:
Ave10084_1_4rProcessedSignal
Ave10084_1_4gProcessedSignal
for gene classifier discovery

value: 5 months


title: PRO_48hr_femaleOvary_4

description:
Ave10094_1_3rProcessedSignal
Ave10094_1_3gProcessedSignal
for gene classifier discovery

value: female


title: MUS_96hr_femaleOvary_5

description:
Ave10290_1_3rProcessedSignal
Ave10290_1_3gProcessedSignal
for gene classifier discovery

source_name: ovary_female_MUS_96 hr

value: MUS (muscimol) 500 ug/L for 96hr


title: MUS_96hr_femaleOvary_4

description:
Ave10248_1_2rProcessedSignal
Ave10248_1_2gProcessedSignal
for gene classifier discovery

value: in water control for 96 hr


title: PRO_48hr_femaleOvary_2

description:
Ave10083_1_1rProcessedSignal
Ave10083_1_1gProcessedSignal
for gene classifier discovery


title: PRO_96hr_femaleOvary_4

description:
Ave10094_1_4rProcessedSignal
Ave10094_1_4gProcessedSignal
for gene classifier discovery


title: PRO_48hr_femaleOvary_1

description:
Ave10072_1_2rProcessedSignal
Ave10072_1_2gProcessedSignal
for gene classifier discovery


title: MUS_96hr_femaleOvary_3

description:
Ave10247_1_4rProcessedSignal
Ave10247_1_4gProcessedSignal
for gene classifier discovery


title: MUS_96hr_femaleOvary_2

description:
Ave10213_1_3rProcessedSignal
Ave10213_1_3gProcessedSignal
for gene classifier discovery


title: MUS_96hr_femaleOvary_1

description:
Ave10201_1_2rProcessedSignal
Ave10201_1_2gProcessedSignal
for gene classifier discovery


title: KET_96hr_femaleOvary_5

description:
Ave10351_1_3rProcessedSignal
Ave10351_1_3gProcessedSignal
for gene classifier discovery

source_name: ovary_female_KET_96 hr

value: KET (ketoconazole) 370 ug/L for 96hr


title: KET_96hr_femaleOvary_3

description:
Ave10204_1_3rProcessedSignal
Ave10204_1_3gProcessedSignal
for gene classifier discovery


title: KET_96hr_femaleOvary_4

description:
Ave10206_1_2rProcessedSignal
Ave10206_1_2gProcessedSignal
for gene classifier discovery


title: KET_96hr_femaleOvary_2

description:
Ave10203_1_2rProcessedSignal
Ave10203_1_2gProcessedSignal
for gene classifier discovery


title: KET_96hr_femaleOvary_1

description:
Ave10202_1_4rProcessedSignal
Ave10202_1_4gProcessedSignal
for gene classifier discovery


title: FLU_96hr_femaleOvary_5

description:
Ave10079_1_4rProcessedSignal
Ave10079_1_4gProcessedSignal
for gene classifier discovery

source_name: ovary_female_FLU_96 hr

value: FLU (flutamide) 1700 ug/L for 96hr


title: KET_48hr_femaleOvary_3

description:
Ave10204_1_2rProcessedSignal
Ave10204_1_2gProcessedSignal
for gene classifier discovery

source_name: ovary_female_KET_48 hr

value: KET (ketoconazole) 370 ug/L for 48hr


title: KET_48hr_femaleOvary_5

description:
Ave10206_1_3rProcessedSignal
Ave10206_1_3gProcessedSignal
for gene classifier discovery

value: ovary


title: KET_24hr_femaleOvary_4

description:
Ave10205_1_2rProcessedSignal
Ave10205_1_2gProcessedSignal
for gene classifier discovery

source_name: ovary_female_KET_24 hr

value: KET (ketoconazole) 370 ug/L for 24hr


title: KET_24hr_femaleOvary_5

description:
Ave10206_1_4rProcessedSignal
Ave10206_1_4gProcessedSignal
for gene classifier discovery

value: in water control for 24 hr


title: KET_48hr_femaleOvary_2

description:
Ave10203_1_4rProcessedSignal
Ave10203_1_4gProcessedSignal
for gene classifier discovery

value: in water control for 48 hr


title: KET_48hr_femaleOvary_4

description:
Ave10205_1_4rProcessedSignal
Ave10205_1_4gProcessedSignal
for gene classifier discovery


title: FLU_96hr_femaleOvary_3

description:
Ave10077_1_3rProcessedSignal
Ave10077_1_3gProcessedSignal
for gene classifier discovery

source_name: ovary_female_water control_96 hr


title: KET_24hr_femaleOvary_2

description:
Ave10203_1_3rProcessedSignal
Ave10203_1_3gProcessedSignal
for gene classifier discovery


title: KET_24hr_femaleOvary_1

description:
Ave10202_1_2rProcessedSignal
Ave10202_1_2gProcessedSignal
for gene classifier discovery


title: FLU_96hr_femaleOvary_2

description:
Ave10077_1_2rProcessedSignal
Ave10077_1_2gProcessedSignal
for gene classifier discovery


title: FLU_96hr_femaleOvary_1

description:
Ave10076_1_1rProcessedSignal
Ave10076_1_1gProcessedSignal
for gene classifier discovery


title: FLU_48hr_femaleOvary_5

description:
Ave10079_1_3rProcessedSignal
Ave10079_1_3gProcessedSignal
for gene classifier discovery

source_name: ovary_female_FLU_48 hr

value: FLU (flutamide) 1700 ug/L for 48hr


title: FIP_96hr_femaleOvary_5

description:
Ave10093_1_2rProcessedSignal
Ave10093_1_2gProcessedSignal
for gene classifier discovery

source_name: ovary_female_FIP_96 hr

value: FIP (fipronil) 5 ug/L for 96hr


title: FIP_96hr_femaleOvary_4

description:
Ave10092_1_4rProcessedSignal
Ave10092_1_4gProcessedSignal
for gene classifier discovery

value: AB


title: FLU_48hr_femaleOvary_1

description:
Ave10075_1_3rProcessedSignal
Ave10075_1_3gProcessedSignal
for gene classifier discovery

source_name: ovary_female_water control_48 hr


title: FLU_48hr_femaleOvary_4

description:
Ave10079_1_2rProcessedSignal
Ave10079_1_2gProcessedSignal
for gene classifier discovery


title: FIP_96hr_femaleOvary_2

description:
Ave10090_1_2rProcessedSignal
Ave10090_1_2gProcessedSignal
for gene classifier discovery


title: FLU_48hr_femaleOvary_3

description:
Ave10077_1_4rProcessedSignal
Ave10077_1_4gProcessedSignal
for gene classifier discovery


title: FIP_96hr_femaleOvary_3

description:
Ave10090_1_3rProcessedSignal
Ave10090_1_3gProcessedSignal
for gene classifier discovery


title: FIP_96hr_femaleOvary_1

description:
Ave10089_1_4rProcessedSignal
Ave10089_1_4gProcessedSignal
for gene classifier discovery


title: FLU_96hr_femaleOvary_4

description:
Ave10078_1_4rProcessedSignal
Ave10078_1_4gProcessedSignal
for gene classifier discovery


title: FIP_48hr_femaleOvary_5

description:
Ave10086_1_3rProcessedSignal
Ave10086_1_3gProcessedSignal
for gene classifier discovery

source_name: ovary_female_FIP_48 hr

value: FIP (fipronil) 5 ug/L for 48hr


title: KET_24hr_femaleOvary_3

description:
Ave10204_1_4rProcessedSignal
Ave10204_1_4gProcessedSignal
for gene classifier discovery


title: FIP_48hr_femaleOvary_3

description:
Ave10082_1_2rProcessedSignal
Ave10082_1_2gProcessedSignal
for gene classifier discovery


title: FIP_48hr_femaleOvary_4

description:
Ave10085_1_3rProcessedSignal
Ave10085_1_3gProcessedSignal
for gene classifier discovery


title: FIP_48hr_femaleOvary_2

description:
Ave10082_1_1rProcessedSignal
Ave10082_1_1gProcessedSignal
for gene classifier discovery


title: FLU_48hr_femaleOvary_2

description:
Ave10077_1_1rProcessedSignal
Ave10077_1_1gProcessedSignal
for gene classifier discovery


title: FIP_48hr_femaleOvary_1

description:
Ave10080_1_4rProcessedSignal
Ave10080_1_4gProcessedSignal
for gene classifier discovery


title: FAD_24hr_femaleOvary_1

description:
Ave10149_1_4rProcessedSignal
Ave10149_1_4gProcessedSignal
for gene classifier discovery

source_name: ovary_female_FAD_24 hr

value: FAD (fadrozole) 25 ug/L for 24hr


title: FAD_24hr_femaleOvary_4

description:
Ave10355_1_3rProcessedSignal
Ave10355_1_3gProcessedSignal
for gene classifier discovery

value: wild-type


title: FAD_24hr_femaleOvary_3

description:
Ave10344_1_4rProcessedSignal
Ave10344_1_4gProcessedSignal
for gene classifier discovery

value: 5 months


title: FAD_24hr_femaleOvary_2

description:
Ave10150_1_2rProcessedSignal
Ave10150_1_2gProcessedSignal
for gene classifier discovery

value: female


title: FAD_24hr_femaleOvary_5

description:
Ave10356_1_3rProcessedSignal
Ave10356_1_3gProcessedSignal
for gene classifier discovery


title: GMP_rep2 (20_116_GMP)

status: Public on Jul 18 2012

first: Jun

last: Seita

address: Lokey Stem Cell Building #G3101, 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

description:
p20_s116.cel
Sample name: 20_116_GMP
Re-analysis of GSM507376

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

scan_protocol: GeneChips were scanned using the GeneChip 3000 7G with GCOS version 1.4.0.036.

data_processing: The data were normalized using GC-RMA method on Gene Expression Commons system (http://gexc.stanford.edu/)

label: biotin

organism: Mus musculus

source_name: bone marrow

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

tag: hematopoiesis population

value: GMP

value: 3 months

value: male


title: GMP_rep1 (20_115_GMP)

description:
p20_s115.cel
Sample name: 20_115_GMP
Re-analysis of GSM507375


title: pGMPb_rep1

description:
p16_s103.cel
Sample name: 16_103_pGMPb

value: pGMPb


title: BLP_rep1

description:
p24_s125.cel
Sample name: 24_125_BLP

value: BLP

value: 2-3 months


title: MEP_rep3

description:
p17_s108.cel
Sample name: 17_108_MEP

value: MEP


title: BLP_rep2

description:
p24_s126.cel
Sample name: 24_126_BLP


title: GMP_rep3 (20_117_GMP)

description:
p20_s117.cel
Sample name: 20_117_GMP
Re-analysis of GSM507377


title: GMLPb_rep1

description:
p11_s88.cel
Sample name: 11_88_GMLPb

value: GMLPb


title: pGMP1_rep1

description:
p15_s100.cel
Sample name: 15_100_pGMPa

value: pGMPa


title: pGMPb_rep3

description:
p16_s105.cel
Sample name: 16_105_pGMPb


title: pGMPb_rep2

description:
p16_s104.cel
Sample name: 16_104_pGMPb


title: GMLPb_rep3

description:
p11_s90.cel
Sample name: 11_90_GMLPb


title: sCMP_rep3

description:
p14_s99.cel
Sample name: 14_99_sCMP

value: sCMP


title: MEP_rep1

description:
p17_s106.cel
Sample name: 17_106_MEP


title: GMLPb_rep2

description:
p11_s89.cel
Sample name: 11_89_GMLPb


title: BLP_rep3

description:
p24_s127.cel
Sample name: 24_127_BLP


title: MEP_rep2

description:
p17_s107.cel
Sample name: 17_107_MEP


title: pMEP_rep3

description:
p12_s93.cel
Sample name: 12_93_pMEP

value: pMEP


title: GMLPa_rep2

description:
p10_s86.cel
Sample name: 10_86_GMLPa

value: GMLPa


title: pGMP1_rep3

description:
p15_s102.cel
Sample name: 15_102_pGMPa


title: pGMP1_rep2

description:
p15_s101.cel
Sample name: 15_101_pGMPa


title: MPPb_rep3

description:
p9_s84.cel
Sample name: 9_84_MPPb

value: MPPb


title: sCMP_rep2

description:
p14_s98.cel
Sample name: 14_98_sCMP


title: KET_48hr_femaleOvary_1

description:
Ave10202_1_3rProcessedSignal
Ave10202_1_3gProcessedSignal
for gene classifier discovery

value: AB

value: ovary

value: KET (ketoconazole) 370 ug/L for 48hr

value: in water control for 48 hr


title: pMEP_rep1

description:
p12_s91.cel
Sample name: 12_91_pMEP


title: TRB_24hr_femaleOvary_1

description:
Ave10149_1_2rProcessedSignal
Ave10149_1_2gProcessedSignal
for gene classifier discovery

source_name: ovary_female_TRB_24 hr

value: wild-type

value: 5 months

value: female

value: TRB (17 -trenbolone) 3 ug/L for 24hr

source_name: ovary_female_water control_24 hr

value: in water control for 24 hr


title: GMLPa_rep1

description:
p10_s85.cel
Sample name: 10_85_GMLPa

value: 3 months

value: male


title: pMEP_rep2

description:
p12_s92.cel
Sample name: 12_92_pMEP


title: sCMP_rep1

description:
p14_s97.cel
Sample name: 14_97_sCMP


title: GMLPa_rep3

description:
p10_s87.cel
Sample name: 10_87_GMLPa


title: HSC_rep3

description:
p7_s77.cel
Sample name: 7_77_HSC

value: HSC


title: MPPa_rep2

description:
p8_s80.cel
Sample name: 8_80_MPPa

value: MPPa


title: MPPa_rep3

description:
p8_s81.cel
Sample name: 8_81_MPPa


title: MPPa_rep1

description:
p8_s79.cel
Sample name: 8_79_MPPa


title: HSC_rep2

description:
p7_s76.cel
Sample name: 7_76_HSC


title: MPPb_rep1

description:
p9_s82.cel
Sample name: 9_82_MPPb


title: HSC_rep4

description:
p7_s78.cel
Sample name: 7_78_HSC


title: P1CF_rep1

status: Public on Jul 06 2012

city: Tokyo

first: Mayumi

last: Oda

address: 35 Shinanomachi, Shinjuku

department: School of Medicine

country: Japan

institute: Keio University

description: Gene expression data from isolated primary neonatal cardiomyocytes.

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

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

data_processing: All CEL files were normalized by RMA using R.

source_name: neonatal cardiomyocytes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cardiomyocytes and cardiac fibroblasts freshly obtained from postnatal day 1 and 8-week-old C57BL/6J mice.

treatment_protocol: The cells were all dissociated by trypsin and collagenase. To separate the cardiomyocytes from cardiac fibroblasts, dissociated cells were expanded on a culture dish and checked the absence of cardiomyocytes by TMRM (Nat Methods 2009 Hattori).

tag: Sex

value: male/female

tag: developmental stage

value: day 1, neonatal

tag: cell type

value: cardiomyocytes

tag: isolation

value: dissociation and Percoll separation


title: P1CM_rep1

description: Gene expression data from isolated primary neonatal cardiac fibroblasts.

source_name: neonatal cardiac fibroblasts

value: cardiac fibroblasts


title: MPPb_rep2

description:
p9_s83.cel
Sample name: 9_83_MPPb

value: MPPb


title: W8CM_rep1

description: Gene expression data from isolated primary adult cardiomyocytes.

source_name: adult cardiomyocytes

value: 8 weeks, adult

value: dissociation by Langendorf perfusion


title: MDA-MB-231_Estradiol

status: Public on Jan 01 2012

city: Heraklion

first: George

last: Notas

address: PO BOX 2208

department: Medicine

country: Greece

institute: University of Crete

description: estradiol treated cells 3h

hyb_protocol: RNA was hybridized according to the Affymetrix protocol (Affymetrix Gene-Chip Expression Analysis Technical Manual), on HGU133A plus 2 chips.

scan_protocol: Signals were detected by an Affymetrix microarray chip reader.

data_processing: Normalization and analysis was performed with the raw data using Genespring GX V11.0 (Agilent, Foster City, CA)

source_name: treated for 3 hours with 10-6M estradiol

label_protocol: RNA was labeled according to the Affymetrix protocol (Affymetrix Gene-Chip Expression Analysis Technical Manual).

growth_protocol: The human breast cancer cell line MDA-MB-231 was obtained from DSMZ (Braunschweig, Germany) and cultured in RPMI 1640 supplemented with 10% fetal bovine serum, at 37 °C, 5% CO2.

extract_protocol: Total RNA was isolated using Nucleospin II columns (Macheray-Nagel, Dttren, Germany), according to the manufacturer’s instructions.

treatment_protocol: MDA-MB-231 cells were incubated with or without Estradiol, E2-BSA, ICI, G15 or combinations of E2-BSA with ICI or G15 for 3 hours after preincubation for 4 hours with medium containing 10% charcoal stripped FBS.

tag: cell line

value: breast cancer derived cells


title: MDA-MB-231_control

description: control sample (3 hours post change of medium)

source_name: untreated control (3 hours post change of medium)


title: Illumina_Drinker_188

status: Public on Dec 01 2011

type: genomic

city: Atlanta

first: Jingyu

last: Liu

state: GA

address: 55 Park Pl

institute: Georgia State University

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

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: genomic DNA from saliva sample

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from saliva samples according to standard instructions

value: saliva

value: M

tag: race

value: Native American


title: Illumina_Drinker_184

value: Caucasian


title: Illumina_Drinker_187


title: T47D_Estradiol

description: estradiol treated cells 3h

growth_protocol: The human breast cancer cell line T47D was obtained from DSMZ (Braunschweig, Germany) and cultured in RPMI 1640 supplemented with 10% fetal bovine serum, at 37 °C, 5% CO2.

extract_protocol: Total RNA was isolated using Nucleospin II columns (Macheray-Nagel, Dttren, Germany), according to the manufacturer's instructions.

treatment_protocol: T47D cells were incubated with or without Estradiol, E2-BSA, ICI, G15 or combinations of E2-BSA with ICI or G15 for 3 hours after preincubation for 4 hours with medium containing 10% charcoal stripped FBS


title: Illumina_Drinker_192


title: Illumina_Drinker_195

value: Latino


title: Illumina_Drinker_191

value: F

value: mixed


title: Illumina_Drinker_193


title: T47D_control


title: Illumina_Drinker_173


title: Illumina_Drinker_174


title: Illumina_Drinker_185


title: Illumina_Drinker_181


title: Illumina_Drinker_196


title: Illumina_Drinker_190


title: Illumina_Drinker_197


title: Illumina_Drinker_178

value: African American


title: Illumina_Drinker_177


title: Illumina_Drinker_182


title: Illumina_Drinker_183


title: Illumina_Drinker_186


title: Illumina_Drinker_176


title: Illumina_Drinker_175


title: Illumina_Drinker_179


title: Illumina_Drinker_194


title: Illumina_Drinker_189


title: Illumina_Drinker_171


title: Illumina_Drinker_168


title: Illumina_Drinker_172


title: Illumina_Drinker_169


title: HSC_rep1

description:
p7_s75.cel
Sample name: 7_75_HSC

value: HSC

value: 3 months

value: male


title: Illumina_Drinker_164


title: Illumina_Drinker_180


title: Illumina_Drinker_170


title: Illumina_Drinker_166


title: Illumina_Drinker_165


title: Illumina_Drinker_162


title: Illumina_Drinker_161


title: Illumina_Drinker_163


title: Illumina_Drinker_160


title: Illumina_Drinker_167


title: Illumina_Drinker_158


title: Illumina_Drinker_154


title: Illumina_Drinker_156


title: Illumina_Drinker_159


title: Illumina_Drinker_152


title: Illumina_Drinker_157


title: Illumina_Drinker_151


title: Illumina_Drinker_149


title: Illumina_Drinker_153


title: Illumina_Drinker_155


title: Illumina_Drinker_148


title: Illumina_Drinker_145


title: Illumina_Drinker_147


title: Illumina_Drinker_150


title: Illumina_Drinker_139


title: Illumina_Drinker_141


title: Illumina_Drinker_143


title: Illumina_Drinker_142


title: Illumina_Drinker_146


title: Illumina_Drinker_137


title: Illumina_Drinker_140


title: Illumina_Drinker_132


title: Illumina_Drinker_144


title: Illumina_Drinker_130


title: Illumina_Drinker_134


title: Illumina_Drinker_136


title: Illumina_Drinker_138


title: Illumina_Drinker_131


title: Illumina_Drinker_133


title: Illumina_Drinker_129


title: Illumina_Drinker_135


title: Illumina_Drinker_128


title: Illumina_Drinker_126


title: Illumina_Drinker_125


title: Illumina_Drinker_124


title: Illumina_Drinker_120


title: Illumina_Drinker_127


title: Illumina_Drinker_121


title: Illumina_Drinker_118


title: Illumina_Drinker_122


title: Illumina_Drinker_111


title: Illumina_Drinker_110


title: Illumina_Drinker_117


title: Illumina_Drinker_115


title: Illumina_Drinker_112


title: Illumina_Drinker_123


title: Illumina_Drinker_119


title: Illumina_Drinker_114


title: Illumina_Drinker_116


title: Illumina_Drinker_113


title: Illumina_Drinker_105


title: Illumina_Drinker_109


title: Illumina_Drinker_108


title: Illumina_Drinker_96


title: Illumina_Drinker_100


title: Illumina_Drinker_99


title: Illumina_Drinker_103


title: Illumina_Drinker_106


title: Illumina_Drinker_104


title: Illumina_Drinker_101


title: Illumina_Drinker_97


title: Illumina_Drinker_102


title: Illumina_Drinker_107


title: Illumina_Drinker_98


title: Illumina_Drinker_95


title: Illumina_Drinker_92


title: Illumina_Drinker_93


title: Illumina_Drinker_86


title: Illumina_Drinker_87


title: Illumina_Drinker_89


title: Illumina_Drinker_90


title: Illumina_Drinker_94


title: Illumina_Drinker_80


title: Illumina_Drinker_77


title: Illumina_Drinker_85


title: Illumina_Drinker_82


title: Illumina_Drinker_76


title: Illumina_Drinker_84


title: Illumina_Drinker_81

value: Asian


title: Illumina_Drinker_91


title: Illumina_Drinker_72


title: Illumina_Drinker_75


title: Illumina_Drinker_78


title: Illumina_Drinker_88


title: Illumina_Drinker_74


title: Illumina_Drinker_70


title: Illumina_Drinker_79


title: Illumina_Drinker_83


title: Illumina_Drinker_69


title: Illumina_Drinker_73


title: Illumina_Drinker_71


title: Illumina_Drinker_67


title: Illumina_Drinker_65


title: Illumina_Drinker_68


title: Illumina_Drinker_66


title: Illumina_Drinker_63


title: Illumina_Drinker_52


title: Illumina_Drinker_56


title: Illumina_Drinker_58


title: Illumina_Drinker_60


title: Illumina_Drinker_62


title: Illumina_Drinker_50


title: Illumina_Drinker_59


title: Illumina_Drinker_44


title: Illumina_Drinker_54


title: Illumina_Drinker_49


title: Illumina_Drinker_42


title: Illumina_Drinker_55


title: Illumina_Drinker_46


title: Illumina_Drinker_61


title: Illumina_Drinker_57


title: Illumina_Drinker_45


title: Illumina_Drinker_53


title: Illumina_Drinker_43


title: Illumina_Drinker_40


title: Illumina_Drinker_47


title: Illumina_Drinker_48


title: Illumina_Drinker_51


title: Illumina_Drinker_39


title: Illumina_Drinker_38


title: Illumina_Drinker_41


title: Illumina_Drinker_35


title: Illumina_Drinker_36


title: Illumina_Drinker_37


title: Illumina_Drinker_30


title: Illumina_Drinker_34


title: Illumina_Drinker_28


title: Illumina_Drinker_32


title: Illumina_Drinker_25


title: Illumina_Drinker_24


title: Illumina_Drinker_27


title: Illumina_Drinker_33


title: Illumina_Drinker_23


title: Illumina_Drinker_21


title: Illumina_Drinker_26


title: Illumina_Drinker_22


title: Illumina_Drinker_18


title: Illumina_Drinker_31


title: Illumina_Drinker_17


title: Illumina_Drinker_29


title: Illumina_Drinker_19


title: Illumina_Drinker_9


title: Illumina_Drinker_11


title: Illumina_Drinker_13


title: Illumina_Drinker_15


title: GIS_RnaPet_HeLa-S3_cell_longPolyA

status: Public on Nov 10 2011

library_source: transcriptomic

molecule: polyA RNA

extract_protocol: For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeGisRnaPet

tag: datatype

value: RnaPet

tag: datatype description

value: RNA Paired-End Tags

tag: rnaextract

value: longPolyA

tag: rnaextract description

value: Poly(A)+ RNA longer than 200 nt

tag: biorep

tag: labexpid

tag: labversion

value: clone-free

tag: readtype

tag: readtype description

value: Paired 36 nt reads

tag: cell sex

tag: localization

value: cell

tag: localization description

value: Whole cell

tag: replicate

tag: replicate description

value: tier 1


title: Illumina_Drinker_7

tag: tissue

value: saliva

tag: gender

value: M

tag: age

value: Caucasian


title: Illumina_Drinker_14

tag: race


title: Illumina_Drinker_10

value: Latino


title: Illumina_Drinker_8


title: Illumina_Drinker_4


title: Illumina_Drinker_12

value: F


title: Illumina_Drinker_20


title: Illumina_Drinker_16


title: Illumina_Drinker_3

value: mixed


title: Illumina_Drinker_2


title: Illumina_Drinker_64


title: Illumina_Drinker_1


title: Illumina_Drinker_5


title: Ovarian carcinoma 105

status: Public on Nov 01 2011

city: PARIS

first: Fatima

last: Mechta-Grigoriou

address: 26 rue d'Ulm

department: INSERM U830

institute: Institut Curie

description: Gene expression data from ovarian carcinoma

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 analyzed with Partek software (6.10.0915 version)

source_name: Ovarian carcinoma 105

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

extract_protocol: Total RNA purification was conducted using miRNeasy kit

tag: histological type

value: Serous

tag: grade

tag: Stage

value: Ic

value: ovarian carcinoma tumor

tag: os event

tag: os time (years)

tag: pfs event

tag: pfs time (years)

tag: signature

value: FIBROSIS


title: Ovarian carcinoma 93

source_name: Ovarian carcinoma 93

value: Carcinosarcome

value: IV


title: Ovarian carcinoma 100

source_name: Ovarian carcinoma 100


title: Illumina_Drinker_6


title: Ovarian carcinoma 106

source_name: Ovarian carcinoma 106

value: IIIc


title: Ovarian carcinoma 96

source_name: Ovarian carcinoma 96


title: Ovarian carcinoma 99

source_name: Ovarian carcinoma 99

value: STRESS


title: Ovarian carcinoma 90

source_name: Ovarian carcinoma 90

value: IIc


title: Ovarian carcinoma 102

source_name: Ovarian carcinoma 102

value: Endometrioid

value: Ia


title: Ovarian carcinoma 98

source_name: Ovarian carcinoma 98


title: Ovarian carcinoma 103

source_name: Ovarian carcinoma 103


title: Ovarian carcinoma 101

source_name: Ovarian carcinoma 101


title: Ovarian carcinoma 91

source_name: Ovarian carcinoma 91


title: Ovarian carcinoma 87

source_name: Ovarian carcinoma 87


title: Ovarian carcinoma 107

source_name: Ovarian carcinoma 107

value: Adenocarcinoma


title: Ovarian carcinoma 84

source_name: Ovarian carcinoma 84


title: Ovarian carcinoma 97

source_name: Ovarian carcinoma 97


title: Ovarian carcinoma 94

source_name: Ovarian carcinoma 94


title: Ovarian carcinoma 104

source_name: Ovarian carcinoma 104

value: IIa


title: Ovarian carcinoma 88

source_name: Ovarian carcinoma 88

value: IIIa


title: Ovarian carcinoma 92

source_name: Ovarian carcinoma 92


title: Ovarian carcinoma 95

source_name: Ovarian carcinoma 95


title: Ovarian carcinoma 86

source_name: Ovarian carcinoma 86

value: Clear Cells


title: Ovarian carcinoma 89

source_name: Ovarian carcinoma 89

value: Mucinous


title: Ovarian carcinoma 82

source_name: Ovarian carcinoma 82


title: Ovarian carcinoma 85

source_name: Ovarian carcinoma 85


title: Ovarian carcinoma 83

source_name: Ovarian carcinoma 83


title: Ovarian carcinoma 80

source_name: Ovarian carcinoma 80


title: Ovarian carcinoma 79

source_name: Ovarian carcinoma 79


title: Ovarian carcinoma 71

source_name: Ovarian carcinoma 71


title: Ovarian carcinoma 74

source_name: Ovarian carcinoma 74


title: Ovarian carcinoma 81

source_name: Ovarian carcinoma 81


title: Ovarian carcinoma 77

source_name: Ovarian carcinoma 77


title: Ovarian carcinoma 72

source_name: Ovarian carcinoma 72

value: Carcinosarcoma


title: Ovarian carcinoma 69

source_name: Ovarian carcinoma 69


title: Ovarian carcinoma 78

source_name: Ovarian carcinoma 78

value: Serous


title: Ovarian carcinoma 75

source_name: Ovarian carcinoma 75


title: Ovarian carcinoma 59

source_name: Ovarian carcinoma 59


title: Ovarian carcinoma 68

source_name: Ovarian carcinoma 68


title: Ovarian carcinoma 76

source_name: Ovarian carcinoma 76


title: Ovarian carcinoma 62

source_name: Ovarian carcinoma 62

value: IIb


title: Ovarian carcinoma 60

source_name: Ovarian carcinoma 60

value: IIIb

value: ovarian carcinoma tumor


title: Ovarian carcinoma 53

source_name: Ovarian carcinoma 53


title: Ovarian carcinoma 63

source_name: Ovarian carcinoma 63


title: Ovarian carcinoma 54

source_name: Ovarian carcinoma 54

value: FIBROSIS


title: Ovarian carcinoma 57

source_name: Ovarian carcinoma 57


title: Ovarian carcinoma 65

source_name: Ovarian carcinoma 65


title: Ovarian carcinoma 52

source_name: Ovarian carcinoma 52

value: Ib


title: Ovarian carcinoma 70

source_name: Ovarian carcinoma 70

value: IIIc


title: Ovarian carcinoma 73

source_name: Ovarian carcinoma 73


title: Ovarian carcinoma 66

source_name: Ovarian carcinoma 66


title: Ovarian carcinoma 56

source_name: Ovarian carcinoma 56

value: STRESS


title: Ovarian carcinoma 64

source_name: Ovarian carcinoma 64


title: Ovarian carcinoma 58

source_name: Ovarian carcinoma 58


title: Ovarian carcinoma 50

source_name: Ovarian carcinoma 50

value: Brenner Tumor


title: Ovarian carcinoma 51

source_name: Ovarian carcinoma 51


title: Ovarian carcinoma 67

source_name: Ovarian carcinoma 67


title: Ovarian carcinoma 61

source_name: Ovarian carcinoma 61


title: Ovarian carcinoma 55

source_name: Ovarian carcinoma 55


title: Ovarian carcinoma 47

source_name: Ovarian carcinoma 47


title: Ovarian carcinoma 42

source_name: Ovarian carcinoma 42

value: IV


title: Ovarian carcinoma 44

source_name: Ovarian carcinoma 44


title: Ovarian carcinoma 45

source_name: Ovarian carcinoma 45

value: Ic


title: Ovarian carcinoma 43

source_name: Ovarian carcinoma 43


title: Ovarian carcinoma 39

source_name: Ovarian carcinoma 39


title: Ovarian carcinoma 36

source_name: Ovarian carcinoma 36


title: Ovarian carcinoma 48

source_name: Ovarian carcinoma 48


title: Ovarian carcinoma 33

source_name: Ovarian carcinoma 33

value: Adenocarcinoma


title: Ovarian carcinoma 49

source_name: Ovarian carcinoma 49


title: Ovarian carcinoma 40

source_name: Ovarian carcinoma 40


title: Ovarian carcinoma 34

source_name: Ovarian carcinoma 34


title: Ovarian carcinoma 41

source_name: Ovarian carcinoma 41


title: Ovarian carcinoma 46

source_name: Ovarian carcinoma 46


title: Ovarian carcinoma 31

source_name: Ovarian carcinoma 31

value: Ia


title: Ovarian carcinoma 35

source_name: Ovarian carcinoma 35


title: Ovarian carcinoma 28

source_name: Ovarian carcinoma 28


title: Ovarian carcinoma 27

source_name: Ovarian carcinoma 27


title: Ovarian carcinoma 38

source_name: Ovarian carcinoma 38


title: Ovarian carcinoma 24

source_name: Ovarian carcinoma 24


title: Ovarian carcinoma 32

source_name: Ovarian carcinoma 32


title: Ovarian carcinoma 37

source_name: Ovarian carcinoma 37


title: Ovarian carcinoma 23

source_name: Ovarian carcinoma 23


title: Ovarian carcinoma 21

source_name: Ovarian carcinoma 21


title: Ovarian carcinoma 29

source_name: Ovarian carcinoma 29


title: Ovarian carcinoma 20

source_name: Ovarian carcinoma 20

value: Endometrioid


title: Ovarian carcinoma 25

source_name: Ovarian carcinoma 25


title: Ovarian carcinoma 30

source_name: Ovarian carcinoma 30

value: Clear Cells


title: Ovarian carcinoma 26

source_name: Ovarian carcinoma 26


title: Ovarian carcinoma 22

source_name: Ovarian carcinoma 22

value: Mucinous


title: Ovarian carcinoma 17

source_name: Ovarian carcinoma 17


title: Ovarian carcinoma 18

source_name: Ovarian carcinoma 18


title: Ovarian carcinoma 12

source_name: Ovarian carcinoma 12


title: Ovarian carcinoma 15

source_name: Ovarian carcinoma 15


title: Ovarian carcinoma 6

source_name: Ovarian carcinoma 6


title: Ovarian carcinoma 14

source_name: Ovarian carcinoma 14


title: Ovarian carcinoma 16

source_name: Ovarian carcinoma 16


title: Ovarian carcinoma 19

source_name: Ovarian carcinoma 19


title: Ovarian carcinoma 13

source_name: Ovarian carcinoma 13


title: Ovarian carcinoma 3

source_name: Ovarian carcinoma 3


title: Ovarian carcinoma 9

source_name: Ovarian carcinoma 9


title: Ovarian carcinoma 8

source_name: Ovarian carcinoma 8


title: Ovarian carcinoma 11

source_name: Ovarian carcinoma 11


title: Ovarian carcinoma 5

source_name: Ovarian carcinoma 5


title: Ovarian carcinoma 2

source_name: Ovarian carcinoma 2


title: Ovarian carcinoma 7

source_name: Ovarian carcinoma 7


title: G42 cells from Cerebellum, Mecp2 null, biological replicate 1

city: Ashburn

first: Ken

last: Sugino

state: VA

address: 19700 Helix Dr

institute: Janelia Research Campus

description: Gene expression data from G42 GFP labeled Purkinje neurons from the cerebellum (CB), Mecp2 null

hyb_protocol: Following fragmentation, 15 or 20 ug of cRNA were hybridized for 18 hr at 45C on GeneChip Mouse Genome 430 v2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with the Affymetrix GeneArray Scanner G3000.

data_processing: The data were processed with GCRMA algorithm in the Bioconductor with default settings.

source_name: brain, cerebellum, Purkinje cells, Mecp2 null

label_protocol: Biotinylated cRNA were prepared using two rounds of T7 in vitro transcription based aRNA amplification (Affymetrix Small Sample Target Labeling Assay Version II) from about 0.3 to 1 ng of total RNA.

growth_protocol: Mecp2 heterozygous null female mice were mated to male mice.  Either male or female carried one of the fluorescent alleles (G42, YFPH or TH). Male offsprings which are hemizygous to Mecp2 null allele and hemizygous to one of the fluorescent alleles were used for experiments. Littermates which are wild type for X chromosome and hemyzygous to one of the fluorescent alleles were used for controls. Mice were weaned around P30. Normal 12 hour-12 hour light dark cycle were used. Normally only up to 4 mice were put in a cage.

extract_protocol: PicoPure RNA Isolation Kit (Arcturus) was used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: Mice at around age postnatal day 40 were sacrificed, the brain extracted and sliced on a vibratome (Leica). Slices were incubated in ACSF with pronase E (1mg/mL; Sigma) for 1 hour and desired regions were microdissected. Three Pasteur pipettes with decreasing tip size were used for tritration in a 1.5 ml Eppendorf tube. Tritrated samples were diluted 20 times with ACSF with FBS (1%) and plated on a 10cm petri dish with Sylgard substriatum. Glass pipette of tip size around 50 um was used to aspirate fluorescent cells under a fluorescent stereomicroscope (Leica). Aspirated cells were transferred to a new dish with fresh ACSF and aspirated again to purify the sample. This wash was repeated twice more (total of 3 washes). After the last wash, the sample was transfered to a 200 ul PCR tube with 50 ul of XB (extraction and lysis buffer from PicoPure RNA Isolation Kit; Arcturus).

tag: strain

tag: pooled

value: No

tag: amplification batch

tag: # cells

tag: Sex

value: male

tag: region

value: CB (cerebellum)

tag: genotype

tag: cell type


title: G42 cells from Cerebellum, wild type control, biological replicate 2

description: Gene expression data from G42 GFP labeled Purkinje neurons from the cerebellum (CB), Wild type control.

source_name: brain, cerebellum, Purkinje cells, wild type


title: Ovarian carcinoma 10

source_name: Ovarian carcinoma 10

tag: tissue


title: G42 cells from Cerebellum, Mecp2 null, biological replicate 3

value: G42 GFP labeled Purkinje neurons from the cerebellum


title: Ovarian carcinoma 1

source_name: Ovarian carcinoma 1

tag: histological type

value: Serous

value: ovarian carcinoma tumor


title: G42 cells from Cerebellum, Mecp2 null, biological replicate 2


title: Ovarian carcinoma 4

source_name: Ovarian carcinoma 4

tag: grade


title: G42 cells from Cerebellum, wild type control, biological replicate 3


title: G42 cells from Cerebellum, wild type control, biological replicate 1


title: G42 cells from M1, wild type control, biological replicate 4

description: Gene expression data from G42 GFP labeled neurons from the motor cortex (M1), wild type control

source_name: brain, motor cortex, fast spiking interneurons, wild type

tag: age


title: G42 cells from M1, Mecp2 null, biological replicate 1

description: Gene expression data from G42 GFP labeled neurons from the motor cortex (M1), Mecp2 null

source_name: brain, motor cortex, fast spiking interneurons, Mecp2 null

value: Yes


title: G42 cells from M1, wild type control, biological replicate 2


title: YPFH cells from M1, Mecp2 null, biological replicate 1

description: Gene expression data from YFPH YFP labeled neurons from the motor cortex (M1), Mecp2 null

source_name: brain, motor cortex, layer 5 thick tufted pyramidal neurons, Mecp2 null


title: YPFH cells from M1, wild type control, biological replicate 2

description: Gene expression data from YFPH YFP labeled neurons from the motor cortex (M1), wild type control

source_name: brain, motor cortex, layer 5 thick tufted pyramidal neurons, wild type

value: Y/X;YFPH/-


title: TH cells from LC, wild type control, biological replicate 1

description: Gene expression data from TH GFP labeled neurons from the locus coeruleus (LC), wild type control

source_name: brain, locus coeruleus neurons, wild type

value: LC

value: Y/X;TH/-


title: G42 cells from M1, Mecp2 null, biological replicate 2


title: TH cells from LC, wild type control, biological replicate 2


title: YPFH cells from M1, wild type control, biological replicate 1


title: YPFH cells from M1, Mecp2 null, biological replicate 2


title: G42 cells from M1, wild type control, biological replicate 1


title: TH cells from LC, Mecp2 null, biological replicate 2

description: Gene expression data from TH GFP labeled neurons from the locus coeruleus (LC), Mecp2 null

source_name: brain, locus coeruleus neurons, Mecp2 null


title: UT-A_ChipSeq_Fibrobl_Input

status: Public on Oct 25 2011

source_name: Fibrobl

extract_protocol: Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeOpenChromChip

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell description

value: child fibroblast

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: controlid

tag: labversion

value: privacy-noSequence fseq v 1.84

tag: cell karyotype

value: normal

tag: cell sex

value: F

tag: antibody

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

value: Fibrobl/Input

value: align_on_cluster_bwa.pl v 1


title: YPFH cells from M1, Mecp2 null, biological replicate 3

tag: strain

tag: pooled

value: No

tag: amplification batch

tag: # cells

tag: Sex

value: male

tag: region

tag: genotype


title: G42 cells from M1, wild type control, biological replicate 3

tag: age


title: G42 cells from M1, Mecp2 null, biological replicate 4


title: UT-A_ChipSeq_ProgFib_Input

source_name: ProgFib

tag: datatype

tag: datatype description

tag: cell description

value: fibroblasts, Hutchinson-Gilford progeria syndrome (cell line HGPS, HGADFN167, progeria research foundation)

value: unknown

value: M

value: ProgFib/Input


title: UT-A_ChipSeq_ProgFib_Pol2

value: ChipSeq

tag: treatment

tag: treatment description

tag: antibody antibodydescription

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

tag: antibody targetdescription

value: RNA Polymerase II

tag: antibody vendorname

value: Covance

tag: antibody vendorid

tag: controlid

value: privacy-noSequence fseq v 1.84, iff_FB0167P,privacy-noSequence baseAlignCounts.pl v 1,privacy-noSequence p-value cutoff:0.05

value: mouse monoclonal, clone 8WG16

tag: replicate

tag: replicate description

value: tier 1


title: UT-A_ChipSeq_ProgFib_CTCF

value: Chromatin IP Sequencing

value: No special treatment or protocol applies

value: Rabbit polyclonal. Antibody Target:CTCF

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

value: Millipore

tag: labversion

value: rabbit polyclonal


title: TH cells from LC, Mecp2 null, biological replicate 3

tag: strain

tag: pooled

value: No

tag: amplification batch

tag: # cells

tag: Sex

value: male

value: LC


title: G42 cells from M1, Mecp2 null, biological replicate 3

value: Yes

tag: region

tag: age

tag: genotype


title: YPFH cells from M1, wild type control, biological replicate 3

value: Y/X;YFPH/-


title: UT-A_ChipSeq_Fibrobl_CTCF

tag: datatype

value: ChipSeq

tag: datatype description

tag: cell description

value: child fibroblast

tag: treatment

tag: treatment description

value: privacy-noSequence fseq v 1.84, iff_FB8470,privacy-noSequence baseAlignCounts.pl v 1,privacy-noSequence p-value cutoff:0.05

value: Fibrobl/Input

value: align_on_cluster_bwa.pl v 1


title: Duke_DnaseSeq_PanIsletD

status: Public on Oct 14 2011

source_name: PanIsletD

value: DnaseSeq

value: DNaseI HS Sequencing

value: dedifferentiated human pancreatic islets from the National Disease Research Interchange (NDRI), same source as PanIslets

tag: controlid

value: private-noSequence p-value cutoff:0.05,private-noSequence baseAlignCounts.pl v 1,private-noSequence fseq v 1.84, iff_generic_male

tag: cell organism

value: human

value: Dedifferentiated human pancreatic islets from one of the sources for PanIslets

tag: cell lineage

value: endoderm

tag: cell sex

value: B

value: tier 1


title: TH cells from LC, Mecp2 null, biological replicate 1

tag: strain

value: No

value: male

value: LC


title: Duke_DnaseSeq_ProgFib

value: ProgFib/Input

tag: labversion

value: private-noSequence p-value cutoff:0.05,private-noSequence baseAlignCounts.pl v 1,1% ENCODE array platform validation tests,private-noSequence fseq v 1.84, iff_FB0167P

tag: cell

value: ProgFib

value: fibroblasts, Hutchinson-Gilford progeria syndrome (cell line HGPS, HGADFN167, progeria research foundation)

tag: cell karyotype

value: unknown

value: M

value: No special treatment or protocol applies

tag: replicate

tag: replicate description


title: TH cells from LC, wild type control, biological replicate 3

tag: pooled

tag: amplification batch

tag: # cells

tag: Sex

tag: region

tag: age

value: Y/X;TH/-


title: Duke_DnaseSeq_HMEC

source_name: HMEC

tag: datatype

value: DnaseSeq

tag: datatype description

value: DNaseI HS Sequencing

tag: cell description

value: mammary epithelial cells

value: normal

value: private-noSequence p-value cutoff:0.05,private-noSequence baseAlignCounts.pl v 1,private-noSequence fseq v 1.84, iff_generic_female,1% ENCODE array platform validation tests

value: Human Mammary Epithelial Cells

value: ectoderm

value: U

value: align_on_cluster_bwa.pl v 1


title: Duke_DnaseSeq_PanIslets

source_name: PanIslets

value: pancreatic islets from 2 donors, the sources of these primary cells are cadavers from National Disease Research Interchange (NDRI) and another sample isolated as in Bucher, P. et al., Assessment of a novel two-component enzyme preparation for human islet isolation and transplantation. Transplantation 79, 917 (2005)

tag: controlid

value: private-noSequence p-value cutoff:0.05,private-noSequence baseAlignCounts.pl v 1,private-noSequence fseq v 1.84, iff_generic_male

value: human pancreatic islets

tag: cell lineage

value: endoderm

tag: treatment

tag: treatment description

value: tier 1


title: Duke_DnaseSeq_CLL

source_name: CLL

tag: labversion

value: private-noSequence p-value cutoff:0.05,private-noSequence baseAlignCounts.pl v 1,private-noSequence fseq v 1.84, iff_generic_female

tag: cell

value: CLL

tag: cell organism

value: human

value: chronic lymphocytic leukemia cell, T-cell lymphocyte

value: cancer

value: mesoderm

tag: cell sex

value: F


title: Duke_DnaseSeq_Fibrobl

value: DnaseSeq

value: DNaseI HS Sequencing

value: child fibroblast

value: Fibrobl/Input

value: private-noSequence p-value cutoff:0.05,private-noSequence baseAlignCounts.pl v 1,1% ENCODE array platform validation tests,private-noSequence fseq v 1.84, iff_FB8470

value: Normal child fibroblast, donor sex:female

tag: cell karyotype

value: normal

value: No special treatment or protocol applies

tag: replicate

tag: replicate description


title: Duke_DnaseSeq_HSMMtube

source_name: HSMMtube

value: private-noSequence p-value cutoff:0.05,private-noSequence baseAlignCounts.pl v 1,private-noSequence fseq v 1.84, iff_generic_male

value: Normal human skeletal muscle myotubes differentiated from the HSMM cell line

value: U

value: align_on_cluster_bwa.pl v 1


title: Duke_DnaseSeq_FibroP

source_name: FibroP

value: private-noSequence p-value cutoff:0.05,private-noSequence baseAlignCounts.pl v 1,private-noSequence fseq v 1.84, iff_generic_female

value: human

value: normal fibroblasts taken from individuals with Parkinson's disease, AG20443, AG08395 and AG08396 were pooled for this sample

value: tier 1


title: Duke_DnaseSeq_Myometr

source_name: Myometr

value: myometrial cells

value: Myometrial cells

value: F


title: Duke_DnaseSeq_iPS

source_name: iPS

value: DnaseSeq

value: DNaseI HS Sequencing

value: iPS

value: induced pluripotent stem cell derived from skin fibroblast

value: Unknown

value: B


title: Duke_DnaseSeq_AoSMC_serum_free_media

source_name: AoSMC

value: Grown with growth factors, then switched to media that contains no FBS for 36 hours (Crawford)

value: private-noSequence p-value cutoff:0.05,private-noSequence baseAlignCounts.pl v 1,private-noSequence fseq v 1.84, iff_generic_male

value: aortic smooth muscle cells

value: normal

value: mesoderm

value: grown in serum free media (Crawford)


title: Duke_DnaseSeq_pHTE

source_name: pHTE

value: primary tracheal epithelial cells

value: human

value: Primary Human Tracheal Epithelial Cells

value: endoderm

value: U

value: align_on_cluster_bwa.pl v 1


title: Gingeras_prostate_cell

status: Public on Oct 08 2010

data_processing:
hg18: For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeCshlShortRnaSeq
hg19: For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq

source_name: prostate

extract_protocol:
hg18: For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeCshlShortRnaSeq
hg19: For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq

tag: lab

value: CSHL

tag: lab description

value: Gingeras - Cold Spring Harbor Laboratory

value: RnaSeq

value: Sequencing analysis of RNA expression

value: prostate

value: prostate tissue purchased for CSHL project

tag: localization

value: cell

tag: localization description

value: Whole cell

tag: protocol

value: TAP-Only

tag: protocol description

value: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.

tag: rnaextract

value: shortTotal

tag: rnaextract description

value: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation

tag: biorep

tag: labexpid

value: Produced by Hannon Lab


title: Diet study with EE2 in liver of female largemouth bass, control, replicate 3

status: Public on Mar 24 2011

city: Gainesville

first: Reyna

middle: Cristina

last: Colli-Dula

state: Florida

address: Mowry Drive 471

department: CEHT

institute: University of Florida

description:
Control_L3
Control_03
Gene expression after 60 days of control feed in LMB female liver.

hyb_protocol: Agilent protocol titled "One-color microarrays-based gene expression analysis" (document no. G4140-90040 v6.5) was used.

scan_protocol: Scanned on an Agilent G2505B microarray scanner.

data_processing: Data extraction was performed using Agilent Feature Extraction software. Background-subtracted raw expression data (gProcessedSignal) were imported into JMP Genomics v5 (SAS, Cary, NC). During import, data were log2-transformed and all control and non-uniform spots were removed prior to the final analysis. Raw intensity data for each microarray were median-centered before performing ANOVA.

organism: Micropterus salmoides

source_name: Liver, 60 d, control

growth_protocol: Adult female largemouth bass (LMB) were purchased from American Sport Fish Hatchery (Montgomery, AL). Fish were acclimated in aerated 150 gallon fiberglass tanks under constant conditions of 22.60 ± SD 1.41 °C for a minimum of 3 months prior to within the Aquatic Toxicology Laboratory at the University of Florida Center for Environmental and Human Toxicology (CEHT).

extract_protocol: Extracted total RNA from LMB samples using RNA STAT-60 (Tel-test, Friendswood, TX) according to manufacturer's protocol. RNA was reconstituted in RNAsecure (Ambion) and DNase-1 treated with DNA-free Turbo (Ambion).

treatment_protocol: Two different tanks containing female LMB (n= 6-10) were used for a dietary study, with one tank designed for control fish and the second one for EE2 exposure using feed containing 70 ng/g of EE2. All fish were fed 5 days per week for 60 days with floating pellets.

tag: tissue

value: liver

tag: gender

value: female

tag: developmental stage

value: adult

tag: treatment

tag: sample type

value: control


title: Diet study with EE2 in liver of female largemouth bass, 70 ng EE2/g feed, replicate 1

description:
70 ng EE2/g feed_L1
0.07mg/kgEE2_01
Gene expression after 60 days of a 70 ng EE2/g exposure in LMB female liver.

source_name: Liver, 60 d, 70 ng EE2/g feed

label_protocol: Agilent protocol titled "One-color microarrays-based gene expression analysis" (document no. G4140-90040 v6.5) was used.

tag: treatment dosage

value: 70 ng EE2/g feed

tag: treatment duration

value: 60 days


title: Diet study with EE2 in liver of female largemouth bass, control, replicate 2

description:
Control_L2
Control_02
Gene expression after 60 days of control feed in LMB female liver.


title: Diet study with EE2 in liver of female largemouth bass, control, replicate 1

description:
Control_L1
Control_01
Gene expression after 60 days of control feed in LMB female liver.


title: day 2 epiblast like cells  (EpiLCs), PCR amplified, biological rep2

status: Public on Aug 05 2011

city: Nara

first: Kazuki

last: Kurimoto

address: 840 Shijo-Cho, Kashihara

department: School of medicine

institute: Nara Medical University

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic Target Hybridization)

scan_protocol: The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix)

data_processing: CEL data were generated by GeneChip Operating Software and then subjected to the dCHIP software.  Data were normalized together with the default settings.  The Model-Based Expression Indices (MBEI) were calculated using the PM/MM difference mode with log-2 transformation of signal intensity and truncation of low values to zero.

source_name: EpiLCs

label_protocol: Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic One-Cycle Target Labeling Assay)

growth_protocol: ES cells were maintained with 2i+LIF, feeder free condition.  EpiLCs were induced from the ES cells.  PGCLCs were induced from day 2 EpiLCs.  EpiSCs were derived from epiblast (embryonic day 5.75).  For detail,  see Hayashi et al., Cell 2011.

extract_protocol: total RNA was extracted using Qiagen RNeasy according to manufacturer's instruction

tag: strain

tag: cell type

value: epiblast like cells (EpiLCs)

tag: amplification

value: 22-cycle PCR from 5ng total RNA (equivalent to 500 cells)


title: Gingeras_K562_polysome

molecule: cytoplasmic RNA

tag: lab

value: CSHL

tag: lab description

value: Gingeras - Cold Spring Harbor Laboratory

tag: datatype

value: RnaSeq

tag: datatype description

value: Sequencing analysis of RNA expression

tag: cell

tag: cell organism

value: human

tag: cell description

value: leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC

tag: cell lineage

value: mesoderm

tag: localization description

value: Strand of mRNA with ribosomes attached

tag: labversion


title: PGCLCs, PCR amplified, biological rep2

source_name: PGCLCs

value: primordial germ cell (PGC) like cells (PGCLCs)


title: day 2 epiblast like cells  (EpiLCs), PCR amplified, biological rep1


title: Diet study with EE2 in liver of female largemouth bass, 70 ng EE2/g feed, replicate 4

description:
70 ng EE2/g feed_L4
0.07mg/kgEE2_04
Gene expression after 60 days of a 70 ng EE2/g exposure in LMB female liver.

tag: tissue

value: liver

tag: gender

tag: developmental stage

tag: treatment


title: embryonic stem cells (ESCs), PCR amplified, biological rep2

source_name: ESCs

tag: strain

value: embryonic stem cells (ESCs)


title: Diet study with EE2 in liver of female largemouth bass, control, replicate 4

description:
Control_L4
Control_04
Gene expression after 60 days of control feed in LMB female liver.

value: female

value: adult

tag: sample type


title: Diet study with EE2 in liver of female largemouth bass, 70 ng EE2/g feed, replicate 3

description:
70 ng EE2/g feed_L3
0.07mg/kgEE2_03
Gene expression after 60 days of a 70 ng EE2/g exposure in LMB female liver.

tag: treatment dosage

value: 70 ng EE2/g feed

tag: treatment duration


title: Diet study with EE2 in liver of female largemouth bass, 70 ng EE2/g feed, replicate 2

description:
70 ng EE2/g feed_L2
0.07mg/kgEE2_02
Gene expression after 60 days of a 70 ng EE2/g exposure in LMB female liver.

value: 60 days


title: PGCLCs, PCR amplified, biological rep1

tag: cell type

tag: amplification


title: Mus_ESC_R1_rep3

status: Public on May 07 2011

city: Shanghai

first: jiayu

last: chen

address: No1239, Siping Road

country: China

institute: Tongji University

description: R1 ESC third repeat

hyb_protocol: Hybridization, Wash and Stain Kit(Affymetrix, Inc.)

scan_protocol: GeneChip® Scanner 3000 7G3000 (Affymetrix, Inc.)

data_processing: GCOS 1.4 software provided by Affymetrix

source_name: Mus ES cell line

label_protocol: WT Terminal Labeling Kit (Affymetrix, Inc.)

extract_protocol: By Trizol following manufacturer’s recommendation (Invitrogen)

tag: cell line


title: Gingeras_GM12878_cytosol_longPolyA_1

status: Public on Feb 14 2011

data_processing: For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeGisRnaSeq

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/GM12878_protocol.pdf

extract_protocol: For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeGisRnaSeq

tag: cell

value: Human

value: lymphoblastoid

tag: cell karyotype

value: relatively normal

value: International HapMap Project - CEPH/Utah - European Caucasion; Epstein-Barr Virus

tag: cell sex

value: F

tag: localization

value: cytosol

tag: rnaextract

value: longPolyA

tag: replicate


title: Mus_ESC_R1_rep1

description: R1 ESC first repeat


title: Mus_ESC_R1_rep2

description: R1 ESC second repeat


title: embryonic stem cells (ESCs), PCR amplified, biological rep1

value: 22-cycle PCR from 5ng total RNA (equivalent to 500 cells)


title: Tumor 68

status: Public on Oct 01 2010

city: Granada

first: Mª Esther

last: Farez-Vidal

address: Avda Dr. Oloriz s/n

country: Spain

institute: Hospital Universitario San Cecilio

hyb_protocol: Expression Analysis Technical Manual of Affymetrix.

data_processing: RMA.

source_name: Human Lung Tumor

extract_protocol: RNAeasy Mini Kit (Qiagen).

tag: tissue

value: lung

value: tumor


title: Tumor 66

scan_protocol: Expression Analysis Technical Manual of Affymetrix.


title: Tumor 70

label_protocol: Expression Analysis Technical Manual of Affymetrix.


title: Tumor NP_2


title: Tumor 72


title: Control 72

source_name: Human Lung Control

value: control


title: Tumor 65


title: Tumor NP_1


title: Control 70


title: Tumor 64


title: Control 66


title: Tumor 60


title: Control 61


title: Tumor 61


title: Control 53


title: Control 65


title: Tumor 55


title: Tumor 57


title: Control 68


title: Control 64


title: Control NP


title: Tumor 50


title: Control 55


title: Control 60


title: Tumor 53


title: Control 50


title: Control 57


title: Tumor 48


title: Control 48


title: Tumor 38


title: Tumor 49


title: Control 47


title: Control 33


title: Tumor 46


title: Control 41


title: Tumor 41


title: Control 16


title: Control 49


title: Control 44


title: Tumor 40


title: Tumor 43


title: Tumor 47


title: Control 42


title: Control 37


title: Control 6


title: Control 46


title: Tumor 42


title: Tumor 33


title: Tumor 31


title: Tumor 44


title: Tumor 36


title: Control 40


title: Control 36


title: Tumor 37


title: Tumor 32


title: Control 32


title: Control 31


title: Control 43


title: Tumor 26


title: Control 30


title: Tumor 30


title: Tumor 28


title: Control 24


title: Control 29


title: Control 28


title: Tumor 29


title: Control 23


title: Tumor 23


title: Tumor 22


title: Control 18


title: Control 21


title: Control 11


title: Tumor 21


title: Tumor 10


title: Tumor 16


title: Control 12


title: Tumor 18


title: Control 22


title: Tumor 24


title: Control 9


title: Control 3


title: Control 26


title: Tumor 2


title: Tumor 6


title: Control 10


title: Tumor 9


title: Tumor 12


title: Control 2


title: Tumor 3


title: CLP_rep3

status: Public on Aug 15 2010

data_processing: The data were analyzed with R/Bioconductor.

source_name: bone marrow

tag: progenitor population

value: ALP

tag: age

value: 2 month

tag: gender

value: male


title: control d6 393

status: Public on Jan 03 2010

city: Jerusalem

first: Reba

last: Condiotti

department: Goldyne Savad Institute of Gene Therapy

country: Israel

institute: Hadassah Medical Center

hyb_protocol: 3-prime IVT hybridization protocol

scan_protocol: MOE430A protocol for GCF3000

data_processing: Array data were normalized by the GCRMA algorithm using R and bioconductor (http://www.bioconductor.org/).Gene and Gene Ontology (GO) annotations were determined for each probe set according to the annotation files published in the Affymetrix website (www.affymetrix.com). Log 2 normalized expression values, after thresholding and filtering, were submitted to unsupervised cluster analysis using Cluster software 6. Paired t-test, and two-way ANOVA for the factors day and strain were performed using Matlab software (Mathworks Inc.).

label: biotin-pseudouridine

source_name: Liver day 6 post PHx

label_protocol: 3-prime IVT labeling protocol

treatment_protocol: Total RNA was isolated from liver samples of 9-month-old mice obtained at different time points after 30% partial hepatectomy

tag: strain:FVB129P2/FVBNJ; gender:male; Age

value: 9 months; Tissue:liver;


title: control d0 263

source_name: Liver day 0 post PHx


title: KO d6 337

tag: strain:FVB129P2; gender:male; Age


title: KO d0 337


title: control d6 392


title: KO d0 258


title: control d2 264

source_name: Liver day 2 post PHx


title: control d6 303


title: control d2 265


title: control d0 265


title: control d2 263


title: KO d2 254


title: control d0 303


title: KO d6 332


title: KO d0 254


title: KO d2 250


title: KO d0 312


title: CLP_rep2

tag: strain


title: CLP_rep1


title: NSCLC EMC TB0064tu

status: Public on May 07 2010

city: Rotterdam

first: Sjaak

last: Philipsen

address: Dr. Molewaterplein 50

department: Cell Biology

country: Netherlands

institute: Erasmus MC

description: Gene expression data from primary NSCLC

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station Fluidics 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray scanner 3000

data_processing: The data was normalized by Robust Multi-Array average (RMA) algorithm. Intensities of probe sets lower than 30 were reset to 30.The intensity values of individual probe sets in each sample were then displayed as the log 2 of the deviations to the calculated geometric means for that probe sets.

source_name: frozen tissue

tag: tissue type

value: LCC

tag: overall survival

tag: status

value: alive


title: KO d0 332


title: KO d2 258


title: KO d6 312


title: KO d0 250


title: Tg5

status: Public on Dec 25 2009

city: Brussels

first: Jean-Christophe

last: Renauld

address: Avenue Hippocrate, 74

country: Belgium

institute: Ludwig Institute for Cancer Research

description: Gene expression data from IL-9 transgenic colon

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse expression Array 430A. GeneChips were washed and stained in the Affymetrix genechip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: IL-9 transgenic mice

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

growth_protocol: IL-9 transgenic mice were  described previously (Renauld et al., 1994. Oncogene 9:1327-32)

extract_protocol: RNA was extracted using Tripure isolation reagent (Roche) according to the manufacturer’s instructions.

treatment_protocol: Mice were bred under specific pathogen free (SPF) condiitons

tag: distal colon


title: Lung Adenocarcinoma #55

status: Public on Aug 04 2009

city: Munich

first: Jens

last: Neumann

address: Thalkirchner Straße 36

department: Institute of Pathology

country: Germany

institute: Ludwig-Maximilians-Universität München

description: Gene expression data from lung adneocarcinoma

hyb_protocol: Targets were fragmented at 94°C for 35 minutes and 15µg of it was hybridized to HG-U133A chips 45°C for 16 hours. The arrays were washed and stained with 10µg/ml streptavidin-phycoerythrin. After signal amplification with biotinylated anti-streptavidin antibodies.

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000.

data_processing: Microarray Suite 5.0 software provided by Affymetrix was used for data acquisitionFollowing data acquisition, the scanned images were quantified according to the Affymetrix GeneChip Manual by using the Data Mining Tool (DMT) 2.0, and Microarray Database software.

source_name: Lung Adenocarcinoma

label_protocol: Biotinylated cRNAs were generated according to the manufacturer’s protocol (Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA was extracted from each frozen tumor specimen using the Qiashredder (Qiagen, Hilden, Germany) and the RNeasy Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

tag: cell type

value: lung adenocarcinoma

tag: grading

tag: age (years at surgery)

tag: sex (m=male; f=female)

tag: tumor stage (according to tnm classification 2002)

tag: nodal status (according to tnm classification 2002)

tag: distant metastasis (according to tnm classification 2002)

tag: resection status (according to tnm classification 2002)

tag: smoking status (n.a.=data not available)

value: yes


title: Lung Adenocarcinoma #43

tag: tissue


title: Lung Adenocarcinoma #36


title: Lung Adenocarcinoma #53


title: Lung Adenocarcinoma #57

value: M


title: Lung Adenocarcinoma #51


title: FVB

description: Gene expression data from wild type colon

source_name: FVB wild type mice


title: Lung Adenocarcinoma #45


title: Lung Adenocarcinoma #41


title: Lung Adenocarcinoma #37


title: Lung Adenocarcinoma #47


title: Lung Adenocarcinoma #52


title: Lung Adenocarcinoma #39


title: Lung Adenocarcinoma #40


title: Lung Adenocarcinoma #26


title: Lung Adenocarcinoma #54


title: Lung Adenocarcinoma #58

value: X


title: Lung Adenocarcinoma #49


title: Lung Adenocarcinoma #24


title: Lung Adenocarcinoma #38


title: Lung Adenocarcinoma #42

value: F

value: no


title: Lung Adenocarcinoma #23


title: Lung Adenocarcinoma #21


title: Lung Adenocarcinoma #25


title: Lung Adenocarcinoma #61


title: Lung Adenocarcinoma #19


title: Lung Adenocarcinoma #22


title: Lung Adenocarcinoma #20


title: Lung Tumor_GT01276

status: Public on Feb 20 2008

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

description: Gene expression data

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip H133-A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner.

data_processing: Gene expression data were processed and normalized using Bioconductor Affy package, based on the Robust Multichip Average (RMA) method5 for single-channel Affymetrix chips

source_name: Adenocarcinoma of the Lung

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 to 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

extract_protocol: Trizol extraction of total RNA and following clean-up with Qiagen Rneasy Mini Kit were performed according to the manufacturers instructions.

tag: Gender

value: Male

tag: Age at Diagnosis

tag: Cigarette Smoking Status

value: Current Smoker


title: Lung Tumor_GT01425

description: Gene expression data

value: Female

value: Never Smoked


title: Normal Lung_GT01239

description: Gene expression data

source_name: Normal Lung Tissue


title: Normal Lung_GT01232

description: Gene expression data

value: Former Smoker


title: Normal Lung_GT01417

description: Gene expression data


title: Normal Lung_GT01237

description: Gene expression data


title: Lung Tumor_GT01445

description: Gene expression data


title: Global gene expression profiling of human pleural mesotheliomas; ctrl 48

status: Public on Jul 30 2009

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

description: 9 mesothelioma mixed type tumors were compared to the normal pleura of 4 donors.

hyb_protocol: All the hybridization, washing, staining procedures were done using a Genechip Affymetrix station (Fluidics station 450), GeneChip Scanner 3000) as raccomended by manufacturer.

scan_protocol: Scanning was done using a Genechip Affymetrix station (GeneChip Scanner 3000) as raccomended by manufacturer.

data_processing: Microarray quality control and statistical validation were performed using Bioconductor The presence of hybridization/construction artifacts was evaluated with the fitPLM function. The probe (PM) intensity distribution was evaluated using hist function (Bioconductor package affy). Probe set intensities were obtained by means of GCRMA and normalization was done according to quantiles method.Bioconductor OneChannelGUI, a graphical interface to Bioconductor packages, was used to run any of the described analyses.

source_name: pleural tissue

label_protocol: Biotinylated cRNA target was produced starting from 3 µg of total RNA in according to Affymetrix (Santa Clara, CA) instructions and for each sample 15 µg were fragmented to a length of 20-200 bp

extract_protocol: Total RNA was extracted from each of the tumor and control samples using the RNeasy Mini kit (Qiagen, Valencia, CA).

tag: Pleural tissue was obtained from patients undergoing resection for lung cancer at an area distant from the tumour site.


title: Lung Tumor_GT01411

description: Gene expression data


title: Global gene expression profiling of human pleural mesotheliomas; ctrl 14

hyb_protocol: All the hybridization, washing, staining  procedures were done using a Genechip Affymetrix station (Fluidics station 450), GeneChip Scanner 3000) as raccomended by manufacturer.


title: Normal Lung_GT01247

description: Gene expression data


title: Lung Tumor_GT01279

description: Gene expression data


title: Normal Lung_GT01445

description: Gene expression data


title: Normal Lung_GT01246

description: Gene expression data


title: Lung Tumor_GT01243

description: Gene expression data


title: Lung Tumor_GT01246

description: Gene expression data


title: Lung Tumor_GT01247

description: Gene expression data


title: Lung Tumor_GT01232

description: Gene expression data


title: Lung Tumor_GT01233

description: Gene expression data


title: Global gene expression profiling of human pleural mesotheliomas; ctrl 8


title: Global gene expression profiling of human pleural mesotheliomas; ctrl 47


title: Normal Lung_GT01243

description: Gene expression data


title: Normal Lung_GT01479

description: Gene expression data


title: Normal Lung_GT01240

description: Gene expression data


title: Lung Tumor_GT01274

description: Gene expression data


title: Lung Tumor_GT01421

description: Gene expression data


title: Normal Lung_GT01233

description: Gene expression data


title: Normal Lung_GT01421

description: Gene expression data


title: Lung Tumor_GT01194

description: Gene expression data


title: Normal Lung_GT01283

description: Gene expression data


title: Normal Lung_GT01222

description: Gene expression data


title: Lung Tumor_GT01175

description: Gene expression data


title: Lung Tumor_GT01124

description: Gene expression data


title: Normal Lung_GT01194

description: Gene expression data


title: Lung Tumor_GT01151

description: Gene expression data


title: Normal Lung_GT01130

description: Gene expression data


title: Lung Tumor_GT01148

description: Gene expression data


title: Normal Lung_GT01121

description: Gene expression data


title: Lung Tumor_GT01129

description: Gene expression data


title: Lung Tumor_GT01222

description: Gene expression data


title: Lung Tumor_GT01126

description: Gene expression data


title: Normal Lung_GT01156

description: Gene expression data


title: Normal Lung_GT01129

description: Gene expression data


title: Lung Tumor_GT01182

description: Gene expression data


title: Normal Lung_GT01182

description: Gene expression data


title: Lung Tumor_GT01127

description: Gene expression data


title: Lung Adenocarcinoma #56

value: tumor


title: Lung Tumor_GT01130

description: Gene expression data


title: Normal Lung_GT01131

description: Gene expression data


title: Lung Tumor_GT01135

description: Gene expression data


title: Lung Tumor_GT01128

description: Gene expression data


title: Normal Lung_GT01119

description: Gene expression data


title: Normal Lung_GT01120

description: Gene expression data


title: Lung Tumor_GT01120

description: Gene expression data


title: Lung Tumor_GT01119

description: Gene expression data


title: Lung Tumor_GT01117

description: Gene expression data


title: Normal Lung_GT01128

description: Gene expression data


title: Lung Tumor_GT01121

description: Gene expression data


title: Normal Lung_GT01113

description: Gene expression data


title: Normal Lung_GT01107

description: Gene expression data


title: Normal Lung_GT01117

description: Gene expression data


title: Lung Tumor_GT01107

description: Gene expression data


title: Normal Lung_GT01099

description: Gene expression data


title: Lung Tumor_GT01103

description: Gene expression data


title: Normal Lung_GT01100

description: Gene expression data


title: Normal Lung_GT01105

description: Gene expression data


title: Normal Lung_GT01097

description: Gene expression data


title: Lung Tumor_GT01100

description: Gene expression data


title: Normal Lung_GT01095

description: Gene expression data


title: Lung Tumor_GT01105

description: Gene expression data


title: Lung Tumor_GT01099

description: Gene expression data


title: Lung Tumor_GT01097

description: Gene expression data


title: Lung Tumor_GT01089

description: Gene expression data


title: Normal Lung_GT01064

description: Gene expression data


title: Normal Lung_GT01061

description: Gene expression data


title: Lung Tumor_GT01054

description: Gene expression data


title: Lung Tumor_GT01087

description: Gene expression data


title: Lung Tumor_GT01061

description: Gene expression data


title: Lung Tumor_GT01052

description: Gene expression data


title: Lung Tumor_GT01049

description: Gene expression data


title: Normal Lung_GT01085

description: Gene expression data


title: Normal Lung_GT01047

description: Gene expression data


title: Normal Lung_GT01051

description: Gene expression data


title: Normal Lung_GT01038

description: Gene expression data


title: Lung Tumor_GT01077

description: Gene expression data


title: Lung Tumor_GT01025

description: Gene expression data


title: Normal Lung_GT01011

description: Gene expression data


title: Normal Lung_GT01033

description: Gene expression data


title: Lung Tumor_GT01040

description: Gene expression data


title: Lung Tumor_GT01017

description: Gene expression data


title: Lung Tumor_GT01034

description: Gene expression data


title: Normal Lung_GT01003

description: Gene expression data


title: Normal Lung_GT01024

description: Gene expression data


title: Normal Lung_GT01036

description: Gene expression data


title: Normal Lung_GT01025

description: Gene expression data


title: Lung Tumor_GT01011

description: Gene expression data


title: Lung Tumor_GT01001

description: Gene expression data


title: Lung Tumor_GT00146

description: Gene expression data


title: Lung Tumor_GT01019

description: Gene expression data


title: Lung Tumor_GT01036

description: Gene expression data


title: Lung Tumor_GT00042

description: Gene expression data


title: Normal Lung_GT00146

description: Gene expression data


title: Lung Tumor_GT01038

description: Gene expression data


title: Lung Tumor_GT00059

description: Gene expression data


title: Normal Lung_GT00007

description: Gene expression data


title: Lung Tumor_GT01003

description: Gene expression data


title: Lung Tumor_GT00007

description: Gene expression data


title: Normal Lung_GT00059

description: Gene expression data


title: Normal Lung_GT01001

description: Gene expression data


title: Lung Tumor_GT00022

description: Gene expression data


title: Normal Lung_GT00006

description: Gene expression data


title: 22T: Tumor part of adenocarcinoma

status: Public on Aug 30 2007

city: Taipei

first: Li-Jen

last: Su

address: No. 201, Sec. 2, Shih-Pai Road

department: Department of Surgery

country: Taiwan

institute: Taipei Veterans General Hospital

description: Gene expression data from lung cancer patient.

hyb_protocol: Protocols and reagents for hybridization, washing and staining followed the Affymetrix’s instructions (http://www.affymetrix.com/support/technical/manuals.affx).

scan_protocol: GeneChips were scanned using the Affemetrix Genechip scanner 6G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNA preparation and analysis were performed according to the Affymetrix's instructions. The quality of the total RNA for microarray analysis was determined using Spectra Max Plus (Molecular Devices) and had an OD260/OD280 ratio ranging from 1.9 to 2.1.

tag: Tumor part of adenocarcinoma

tag: sex

value: female


title: 25N: Adjacent normal part of adenocarcinoma

tag: Adjacent normal part of adenocarcinoma


title: 27T: Tumor part of adenocarcinoma


title: 24N: Adjacent normal part of adenocarcinoma


title: 54N: Adjacent normal part of adenocarcinoma


title: 20N: Adjacent normal part of adenocarcinoma


title: Lung Tumor_GT00006

description: Gene expression data


title: 54T: Tumor part of adenocarcinoma


title: 27N: Adjacent normal part of adenocarcinoma


title: 30T: Tumor part of adenocarcinoma


title: 22N: Adjacent normal part of adenocarcinoma


title: 23T: Tumor part of adenocarcinoma


title: 24T: Tumor part of adenocarcinoma


title: 23N: Adjacent normal part of adenocarcinoma


title: 26T: Tumor part of adenocarcinoma


title: 26N: Adjacent normal part of adenocarcinoma


title: 19T: Tumor part of lage cell lung cancer

tag: Tumor part of lage cell lung cancer


title: 25T: Tumor part of adenocarcinoma


title: 29N: Adjacent normal part of adenocarcinoma

value: male


title: 21N: Adjacent normal part of adenocarcinoma


title: 29T: Tumor part of adenocarcinoma


title: 20T: Tumor part of adenocarcinoma


title: 57N: Adjacent normal part of adenocarcinoma


title: 18T: Tumor part of adenocarcinoma


title: 21T: Tumor part of adenocarcinoma


title: 30N: Adjacent normal part of adenocarcinoma


title: 57T: Tumor part of adenocarcinoma


title: 16T: Tumor part of adenocarcinoma


title: 18N: Adjacent normal part of adenocarcinoma


title: 19N: Adjacent normal part of large cell lung cancer


title: 16N: Adjacent normal part of adenocarcinoma


title: 15T: Tumor part of adenocarcinoma


title: 13N: Adjacent normal part of adenocarcinoma


title: 14N: Adjacent normal part of adenocarcinoma


title: 5N: Adjacent normal part of adenocarcinoma


title: 8T: Tumor part of adenocarcinoma


title: 6N: Adjacent normal part of adenocarcinoma


title: 3T: Tumor part of adenocarcinoma


title: 2T: Tumor part of adenocarcinoma


title: 8N: Adjacent normal part of adenocarcinoma


title: 5T: Tumor part of adenocarcinoma


title: 13T: Tumor part of adenocarcinoma


title: 14T: Tumor part of adenocarcinoma


title: 3N: Adjacent normal part of adenocarcinoma


title: 12T: Tumor part of adenocarcinoma


title: 4T: Tumor part of adenocarcinoma


title: 7N: Adjacent normal part of adenocarcinoma


title: 6T: Tumor part of adenocarcinoma


title: 12N: Adjacent normal part of adenocarcinoma


title: 4N: Adjacent normal part of adenocarcinoma


title: 2N: Adjacent normal part of adenocarcinoma


title: 1N: Adjacent normal part of adenocarcinoma


title: 15N: Adjacent normal part of adenocarcinoma


title: 1T: Tumor part of adenocarcinoma


title: 7T: Tumor part of adenocarcinoma


title: Squamous cell carcinoma 48536_A

status: Public on Nov 10 2006

city: st louis

first: Yan

last: Lu

state: MO

address: 660 s. euclid ave

institute: washington univ.

description: Squamous cell carcinoma

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Robust Multichip Average

source_name: Squamous cell carcinoma

label_protocol: Approximately 1 to 5 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: standard Affymetrix procedures

value: M; age:80; stage:T2N0


title: Squamous cell carcinoma 44680_A

description: Squamous cell carcinoma

value: F; age:70; stage:T1N0


title: Squamous cell carcinoma 48556_A

description: Squamous cell carcinoma

value: M; age:78; stage:T2N0


title: Squamous cell carcinoma 86043_A

description: Squamous cell carcinoma

value: F; age:59; stage:T1N0


title: Squamous cell carcinoma 57774_A

description: Squamous cell carcinoma

value: M; age:76; stage:T1N0


title: Squamous cell carcinoma 86011_A

description: Squamous cell carcinoma

value: F; age:78; stage:T1N0


title: Squamous cell carcinoma 76981_A

description: Squamous cell carcinoma

value: M; age:76; stage:T2N0


title: Squamous cell carcinoma 48521_A

description: Squamous cell carcinoma

value: M; age:70; stage:T2N0


title: Squamous cell carcinoma 42616_A

description: Squamous cell carcinoma

value: M; age:63; stage:T1N0


title: Squamous cell carcinoma 41932_A

description: Squamous cell carcinoma

value: F; age:62; stage:T2N0


title: Squamous cell carcinoma 44661_A

description: Squamous cell carcinoma

value: M; age:64; stage:T2N0


title: Squamous cell carcinoma 42613_A

description: Squamous cell carcinoma

value: M; age:73; stage:T2N0


title: Squamous cell carcinoma 48549_A

description: Squamous cell carcinoma

value: F; age:62; stage:T1N0


title: Squamous cell carcinoma 40430_A

description: Squamous cell carcinoma

value: M; age:75; stage:T2N0


title: Squamous cell carcinoma 44656_A

description: Squamous cell carcinoma

value: F; age:76; stage:T2N0


title: Squamous cell carcinoma 44693_A

description: Squamous cell carcinoma

value: F; age:66; stage:T2N0


title: Squamous cell carcinoma 42081_A

description: Squamous cell carcinoma

value: F; age:73; stage:T2N0


title: Squamous cell carcinoma 41923_A

description: Squamous cell carcinoma

value: M; age:65; stage:T1N0


title: 03-221

status: Public on Nov 07 2005

city: Durham

first: Joseph

middle: R.

last: Nevins

state: NC

address: 2133 CIEMAS, 101 Science Dr.

department: IGSP

institute: Duke University

description: frozen tissue of primary lung tumors

data_processing: Affymetrix Microarray Suite version 5.0

source_name: frozen tissue of primary lung tumor

value: Cell type:A; Surv(months):27; STATUS(0=alive, 1=dead):0


title: 93-1334

description: frozen tissue of primary lung tumors

value: Cell type:A; Surv(months):24.5; STATUS(0=alive, 1=dead):1


title: 98-39

description: frozen tissue of primary lung tumors

value: Cell type:A; Surv(months):11; STATUS(0=alive, 1=dead):1


title: 04-566

description: frozen tissue of primary lung tumors

value: Cell type:A; Surv(months):6; STATUS(0=alive, 1=dead):0


title: 05-90

description: frozen tissue of primary lung tumors

value: Cell type:A; Surv(months):2; STATUS(0=alive, 1=dead):1


title: 05-42

description: frozen tissue of primary lung tumors

value: Cell type:A; Surv(months):3; STATUS(0=alive, 1=dead):1


title: 99-625

description: frozen tissue of primary lung tumors

value: Cell type:S; Surv(months):21; STATUS(0=alive, 1=dead):1


title: 96-470

description: frozen tissue of primary lung tumors

value: Cell type:A; Surv(months):9; STATUS(0=alive, 1=dead):1


title: 02-765

description: frozen tissue of primary lung tumors

value: Cell type:A; Surv(months):31; STATUS(0=alive, 1=dead):0


title: 98-645

description: frozen tissue of primary lung tumors

value: Cell type:A; Surv(months):10.5; STATUS(0=alive, 1=dead):1


title: 98-610

description: frozen tissue of primary lung tumors

value: Cell type:S; Surv(months):6; STATUS(0=alive, 1=dead):1


title: 98-180

description: frozen tissue of primary lung tumors

value: Cell type:S; Surv(months):>72 ; STATUS(0=alive, 1=dead):0


title: 97-646

description: frozen tissue of primary lung tumors

value: Cell type:S; Surv(months):34; STATUS(0=alive, 1=dead):1


title: 01-758

description: frozen tissue of primary lung tumors

value: Cell type:S; Surv(months):10.5; STATUS(0=alive, 1=dead):1


title: 00-37

description: frozen tissue of primary lung tumors

value: Cell type:S; Surv(months):64; STATUS(0=alive, 1=dead):0


title: 00-693

description: frozen tissue of primary lung tumors

value: Cell type:A; Surv(months):6.5; STATUS(0=alive, 1=dead):1


title: 01-399

description: frozen tissue of primary lung tumors

value: Cell type:A; Surv(months):7; STATUS(0=alive, 1=dead):1


title: 00-502

description: frozen tissue of primary lung tumors

value: Cell type:S; Surv(months):60; STATUS(0=alive, 1=dead):0


title: 01-994

description: frozen tissue of primary lung tumors

value: Cell type:A; Surv(months):48; STATUS(0=alive, 1=dead):0


title: 01-139

description: frozen tissue of primary lung tumors

value: Cell type:A; Surv(months):39.83333333; STATUS(0=alive, 1=dead):0


title: 01-189

description: frozen tissue of primary lung tumors

value: Cell type:S; Surv(months):36.16666667; STATUS(0=alive, 1=dead):0